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Nhunt 1.5.6.2 [May-16-2011]

Length of query file: 300 bp
Length of database file: 10953209 bp

lambda = 0.204

Number Sequences producing significant alignments: Score E-value
1 AE009441 378.4 1.05698e-25
2 AE006641 355.6 1.10392e-23
3 AE000782 335.7 6.34508e-22
4 AE017261 291.5 5.27347e-18
5 AE004437 259.6 3.52182e-15
6 AE017261 122.5 0.00491219
7 AE006641 115.9 0.0187841
8 AE009441 110.1 0.0616833
9 AE017261 109.7 0.0676854
10 AE009441 106.1 0.140989
11 AE000782 100.5 0.437679
12 AE006641 97.3 0.837773
13 AE006641 96.9 0.90851



Alignment 1: NC_000913.2 from 68 to 300, AE009441 from 1090800 to 1091033
Initial score: 374.2 (113.4 bits), adjusted score: 378.37 (114.6 bits), E-value: 1.05698e-25
Identity = 150/234 (64%)
Strand: Plus/Plus

Compositional adjustment is on.
Enthropy = 0.387486.
Query frequences: A: 0.257049, T: 0.196629, G: 0.321496, C: 0.224825,
Subject frequences: A: 0.171780, T: 0.147712, G: 0.388389, C: 0.292118,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 5.618143 -10.495569 -3.803610 -7.242836
T -7.535749 7.106987 -4.842992 -11.168794
G -1.738375 -2.425498 2.767941 -2.046944
C -2.479287 -3.587058 -1.871697 4.378087

Query: 68 cccgcagaagaagcaccggctaactc-cgtgccagcagccgcggtaatacggagggtgca 126
|| | ||| |||| || || || ||| |||| ||||||||||||| ||
Sbjct: 1090800 ccgggcgaataagcggggggcaagtctggtgtcagccgccgcggtaataccagctccgcg 1090859

Query: 127 agcgttaatcggaattactgggcgtaaagcgcacgcaggcggtttgttaagtcagatgtg 186
|| | | | ||||||||| |||||||| || || ||| | ||||| ||
Sbjct: 1090860 agtggtcggggtgtttactgggcttaaagcgcccgtagccggcccggcaagtcgctcctg 1090919

Query: 187 aaatccccgggctcaacctgggaactgcatctgatactggcaagcttgagtctcgtagag 246
|||||||||||||||||| ||| | | ||||||| | ||| | | | ||||
Sbjct: 1090920 aaatccccgggctcaacccgggggcggggggcgatactgccgggctagggggcgggagag 1090979

Query: 247 gggggtagaattccaggtgtagcggtgaaatgcgtagagatctggaggaatacc 300
| | | | ||| || |||| || ||||| ||| | | |||||| |||
Sbjct: 1090980 gccgccggtactccgggggtaggggcgaaatccgttaatccccggaggaccacc 1091033


Alignment 2: NC_000913.2 from 74 to 300, AE006641 from 872124 to 872351
Initial score: 369.5 (112.0 bits), adjusted score: 355.58 (107.9 bits), E-value: 1.10392e-23
Identity = 150/231 (65%)
Strand: Plus/Plus

Compositional adjustment is on.
Enthropy = 0.390882.
Query frequences: A: 0.259295, T: 0.201460, G: 0.325393, C: 0.213853,
Subject frequences: A: 0.208865, T: 0.151275, G: 0.356952, C: 0.282908,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 5.041319 -6.372089 -2.933962 -5.667107
T -7.430030 7.026318 -4.766818 -14.323153
G -1.968325 -2.718227 2.983025 -2.512090
C -2.647169 -3.775219 -1.981488 4.699498

Query: 74 gaagaagcaccggctaactc-cgtgccagcagccgcggtaatacggagggtgcaagcgtt 132
||| |||| || || || ||| |||| ||||||||||||| || || |
Sbjct: 872124 gaataagcggggggcaagtctggtgtcagccgccgcggtaataccagccccgcgag---t 872180

Query: 133 aatcggaa---ttactgggcgtaaagcgcacgcaggcggtttgttaagtcagatgtgaaa 189
|||| | ||||||||| |||||||| || || ||| | |||||| | |||
Sbjct: 872181 ggtcgggactcttactgggcctaaagcgcccgtagccggcccgacaagtcactccttaaa 872240

Query: 190 tccccgggctcaacctgggaactgcatctgatactggcaagcttgagtctcgtagagggg 249
||| ||||||||| ||| | || |||||||| | ||| | | | |||||
Sbjct: 872241 gaccccggctcaaccgggggaatgggggtgatactgtcgggctagggggcgggagaggcc 872300

Query: 250 ggtagaattccaggtgtagcggtgaaatgcgtagagatctggaggaatacc 300
| | | ||| || |||| || ||||| | ||| || |||||| |||
Sbjct: 872301 agcggtactcccggagtaggggcgaaatcctcagatctcgggaggaccacc 872351


Alignment 3: NC_000913.2 from 69 to 300, AE000782 from 1790038 to 1789805
Initial score: 359.5 (109.0 bits), adjusted score: 335.72 (102.0 bits), E-value: 6.34508e-22
Identity = 151/235 (64%)
Strand: Plus/Minus

Compositional adjustment is on.
Enthropy = 0.399981.
Query frequences: A: 0.258090, T: 0.197418, G: 0.322806, C: 0.221686,
Subject frequences: A: 0.195848, T: 0.155735, G: 0.356299, C: 0.292118,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 5.305197 -7.950942 -3.308209 -6.147135
T -7.246084 7.044195 -4.706947 -11.224584
G -2.017666 -2.851970 3.035616 -2.445734
C -2.599291 -3.785507 -1.956093 4.536681

Query: 69 ccgcagaagaagcaccggctaactccg-tgccagcagccgcggtaatacggagggtgcaa 127
|| || | ||| |||| || ||| || |||| ||||||||||||| | || | |
Sbjct: 1790038 ccccacagcaagggccgggcaaggccggtggcagccgccgcggtaataccggcggcccga 1789979

Query: 128 gcgttaatcggaattactgggcgtaaagcgcacgcaggcggtttgttaagtcagatgtga 187
| | | ||| ||||| ||||||| || || ||| || |||||| | ||
Sbjct: 1789978 gtggcggccacttttattgggcctaaagcgtccgtagccgggctggtaagtcctccggga 1789919

Query: 188 aatccccgggctcaacctgggaactgcatc-tgatactggcaagcttgagtctcgtagag 246
|||| |||| |||| ||||| ||||||| || || | | | | ||||
Sbjct: 1789918 aatctggcggcttaaccgtcagactgccggaggatactgccagcctagggaccgggagag 1789859

Query: 247 gggggtagaattccaggtgtagcggtgaaatgc-gtagagatctggaggaatacc 300
| || | ||||| || |||| |||||||| | ||| | | |||||| |||
Sbjct: 1789858 gccgggggtattcccggagtaggggtgaaatcctgta-atcccgggaggaccacc 1789805


Alignment 4: NC_000913.2 from 74 to 279, AE017261 from 471758 to 471552
Initial score: 270.8 (82.9 bits), adjusted score: 291.48 (89.0 bits), E-value: 5.27347e-18
Identity = 129/208 (62%)
Strand: Plus/Minus

Compositional adjustment is on.
Enthropy = 0.428268.
Query frequences: A: 0.252269, T: 0.202349, G: 0.324880, C: 0.220502,
Subject frequences: A: 0.237578, T: 0.233061, G: 0.305333, C: 0.224027,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 5.026249 -5.922359 -2.814062 -5.056309
T -4.175891 5.811410 -2.888296 -5.230886
G -2.821886 -3.867020 3.590852 -3.404876
C -4.449044 -6.673008 -3.049565 5.654665

Query: 74 gaagaagcaccggctaactccg-tgccagcagccgcggtaatacggagggtgcaagcgtt 132
||| ||| | || ||| | | ||||||| |||||||||| || | |||| | |
Sbjct: 471758 gaataagggctgggtaagacgggtgccagccgccgcggtaacacccgcagctcaagtggt 471699

Query: 133 aatcggaattactgggcgtaaagcgcacgcaggcggtttgttaagtcagatgtgaaatcc 192
|| |||||| || ||||||| || || ||| || ||| || | |||| |
Sbjct: 471698 ggtcacttttactgagcctaaagcgttcgtagccggctttgtaaatctccaggtaaattc 471639

Query: 193 ccgggctcaacctgggaactgcatctgatactggcaagcttgagtc-tcgtagagggggg 251
| ||| ||| | || || | || |||| ||||||| | | || | | |
Sbjct: 471638 tagcgcttaacgttagatctcctggagagactgcaaagcttgggaccgggtggggttgaa 471579

Query: 252 tagaattccaggtgtagcggtgaaatgc 279
| || |||| |||| ||| |||| |
Sbjct: 471578 cgtactttcagg-gtaggggtaaaatcc 471552


Alignment 5: NC_000913.2 from 74 to 296, AE004437 from 1875935 to 1876158
Initial score: 264.3 (81.0 bits), adjusted score: 259.60 (79.6 bits), E-value: 3.52182e-15
Identity = 139/225 (62%)
Strand: Plus/Plus

Compositional adjustment is on.
Enthropy = 0.422163.
Query frequences: A: 0.259456, T: 0.200616, G: 0.330905, C: 0.209022,
Subject frequences: A: 0.229077, T: 0.195599, G: 0.337878, C: 0.237446,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 4.976957 -6.172455 -2.791349 -5.698824
T -5.124968 6.368234 -3.481453 -8.012299
G -2.307145 -3.257784 3.237616 -3.075197
C -3.745040 -5.754907 -2.660540 5.558546

Query: 74 gaagaagcaccggctaactcc-gtgccagcagccgcggtaatacggagggtgcaagcgtt 132
||| ||| || || || || |||||||| ||||||||||||| | || | || | |
Sbjct: 1875935 gaataaggactgggcaagaccggtgccagccgccgcggtaataccggcagtccgagtgat 1875994

Query: 133 aatcggaattactgggcgtaaagcgcacgcaggcggtttgttaagtcagatgtgaaatcc 192
|| ||| ||||| ||||||| || || || | ||||| | || ||||||
Sbjct: 1875995 ggccgatcttattgggcctaaagcgtccgtagctggctgaacaagtccgttgggaaatct 1876054

Query: 193 ccgggctcaacctgggaac-tgcatctgatactggcaagcttgagtctcgtagagggggg 251
||| ||| | | | || | || |||| |||||| | | | ||| | |
Sbjct: 1876055 gtccgcttaacgggcaggcgtccagcggaaactgttcagcttgggaccggaagacctgag 1876114

Query: 252 tagaattccaggtgtagcggtgaaatgcgtagagatctggaggaa 296
| | | || |||| ||||||| | | | ||||| | |
Sbjct: 1876115 gggtacgtctggggtaggagtgaaat-cctgtaatcctggacgga 1876158


Alignment 6: NC_000913.2 from 139 to 237, AE017261 from 267644 to 267747
Initial score: 126.0 (40.3 bits), adjusted score: 122.52 (39.3 bits), E-value: 0.00491219
Identity = 61/104 (59%)
Strand: Plus/Plus

Compositional adjustment is on.
Enthropy = 0.412684.
Query frequences: A: 0.252295, T: 0.233938, G: 0.289009, C: 0.224759,
Subject frequences: A: 0.267513, T: 0.346324, G: 0.179946, C: 0.206216,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 4.563508 -3.612406 -2.687689 -3.835508
T -2.291864 4.040811 -1.934066 -2.663572
G -6.218312 -7.315470 5.376513 -8.059298
C -4.836745 -5.530766 -3.887294 5.759649

Query: 139 aattactgggcgtaaagcgcacgcag-gcggtttgttaagtcagatgtgaaatccccggg 197
| |||||| | | || || | ||| | |||| |||| | |||||||||
Sbjct: 267644 atttactgtaacaacatcgtcaacatagttttttacaatgtcaaatgttatatccccggg 267703

Query: 198 ctcaacctgggaactg-catctgatactg--gca-agcttgagt 237
| | || || |||| | || || || |||||| ||
Sbjct: 267704 atatttcacggctatgccatcggctattgtatcagagcttgtgt 267747


Alignment 7: NC_000913.2 from 55 to 215, AE006641 from 388752 to 388593
Initial score: 93.5 (30.7 bits), adjusted score: 115.94 (37.3 bits), E-value: 0.0187841
Identity = 81/164 (49%)
Strand: Plus/Minus

Compositional adjustment is on.
Enthropy = 0.272368.
Query frequences: A: 0.254318, T: 0.190986, G: 0.294620, C: 0.260076,
Subject frequences: A: 0.336881, T: 0.342674, G: 0.128366, C: 0.192079,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 3.170423 -2.350591 -1.390180 -1.608464
T -1.618667 3.843628 -1.363087 -1.576391
G -6.809958 -39.431721 5.482493 -6.493563
C -3.414607 -5.406231 -2.782065 4.607083

Query: 55 ctcattgacgttacccgcagaagaagcaccggctaactccg-tgccagcagccgcggtaa 113
|| | | | || | || || ||| | || || | | | |||
Sbjct: 388752 cttaattttgctattcacaaaaaaagaccttacttccttagg-atttaaattagatataa 388694

Query: 114 tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggtt--t 171
| ||| || ||||||| | | ||| | | ||| || |
Sbjct: 388693 cataataggtaatagagttaatccgccaaattggtac--acgtttttccagttccttact 388636

Query: 172 gttaagtcagatgtgaaatccccgggctcaacctgggaactgca 215
||| ||| || ||||| || ||||| | |||| ||||
Sbjct: 388635 tttatgtcctat-tgaaaaaccaaatctcaatcctggaattgca 388593


Alignment 8: NC_000913.2 from 199 to 256, AE009441 from 97798 to 97855
Initial score: 112.9 (36.5 bits), adjusted score: 110.12 (35.6 bits), E-value: 0.0616833
Identity = 37/58 (64%)
Strand: Plus/Plus

Compositional adjustment is on.
Enthropy = 0.420842.
Query frequences: A: 0.257620, T: 0.227140, G: 0.318581, C: 0.196659,
Subject frequences: A: 0.318581, T: 0.211899, G: 0.227140, C: 0.242380,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 4.057661 -3.017010 -1.946266 -3.709957
T -4.606317 5.696565 -3.326435 -7.843237
G -4.118584 -5.071733 4.414667 -6.689990
C -3.728642 -4.542247 -2.761628 5.729283

Query: 199 tcaacctgggaactgcatctgatactggcaagcttgagtctcgtagaggggggtagaa 256
|| || ||| ||| | |||||| |||| | ||| |||| | || || | ||
Sbjct: 97798 tctcccgccgaagtgcttgagatactcgcaaccgtgaatctcaaaaagaggattgaaa 97855


Alignment 9: NC_000913.2 from 177 to 231, AE017261 from 879552 to 879501
Initial score: 91.7 (30.2 bits), adjusted score: 109.66 (35.5 bits), E-value: 0.0676854
Identity = 37/55 (67%)
Strand: Plus/Minus

Compositional adjustment is on.
Enthropy = 0.418373.
Query frequences: A: 0.254005, T: 0.205941, G: 0.270027, C: 0.270027,
Subject frequences: A: 0.199334, T: 0.334444, G: 0.233111, C: 0.233111,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 5.527279 -8.145494 -4.716029 -4.716029
T -2.435147 4.559821 -2.251497 -2.251497
G -4.043314 -5.785356 4.831738 -3.684082
C -4.043314 -5.785356 -3.684082 4.831738

Query: 177 gtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactggcaagc 231
|||| || || |||| |||||||| | | | ||| | || || ||||||
Sbjct: 879552 gtcaaatttgtaatcgccgggctctatgtatgttgtgc---tcatccttgcaagc 879501


Alignment 10: NC_000913.2 from 106 to 182, AE009441 from 1981674 to 1981751
Initial score: 102.9 (33.5 bits), adjusted score: 106.06 (34.4 bits), E-value: 0.140989
Identity = 51/81 (63%)
Strand: Plus/Plus

Compositional adjustment is on.
Enthropy = 0.398645.
Query frequences: A: 0.258744, T: 0.212110, G: 0.340353, C: 0.188793,
Subject frequences: A: 0.301824, T: 0.244242, G: 0.186659, C: 0.267275,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 4.073553 -3.370193 -1.817838 -4.008641
T -3.433800 5.308096 -2.366248 -5.745422
G -5.274393 -7.986633 4.670034 -11.447453
C -3.022848 -4.040556 -2.110907 5.393852

Query: 106 cgcggtaa-tacggagggtgcaagcgttaatcggaattactgggc---gtaaagcgcacg 161
|||| || | || | | ||||||||||| | | |||||| |||||||
Sbjct: 1981674 cgcgtcaattccgtattttacaagcgttaataaaatctcctgggccctcccaagcgcaaa 1981733

Query: 162 caggcggtttgttaagtcaga 182
| | ||| | |||| ||||
Sbjct: 1981734 c-gacgg--tattaatacaga 1981751


Alignment 11: NC_000913.2 from 117 to 162, AE000782 from 526968 to 526923
Initial score: 93.3 (30.7 bits), adjusted score: 100.51 (32.8 bits), E-value: 0.437679
Identity = 30/46 (65%)
Strand: Plus/Minus

Compositional adjustment is on.
Enthropy = 0.396081.
Query frequences: A: 0.259473, T: 0.183690, G: 0.354202, C: 0.202636,
Subject frequences: A: 0.221581, T: 0.164744, G: 0.278419, C: 0.335256,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 4.890025 -7.007762 -2.458871 -5.732857
T -6.314394 7.095043 -3.706615 -12.853496
G -2.742847 -4.557279 3.392686 -3.900401
C -2.156215 -3.424317 -1.480654 4.389820

Query: 117 ggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgc 162
| ||| ||||| | || || | | | |||| | ||||||| |
Sbjct: 526968 gaaggctgcaacccttcctccatagtggtaggcgcagagcgcaccc 526923


Alignment 12: NC_000913.2 from 159 to 230, AE006641 from 2040818 to 2040744
Initial score: 95.2 (31.3 bits), adjusted score: 97.33 (31.9 bits), E-value: 0.837773
Identity = 48/76 (63%)
Strand: Plus/Minus

Compositional adjustment is on.
Enthropy = 0.401696.
Query frequences: A: 0.250000, T: 0.225151, G: 0.287274, C: 0.237575,
Subject frequences: A: 0.384472, T: 0.241035, G: 0.217129, C: 0.157363,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 3.503160 -2.222073 -1.648978 -2.077212
T -3.634613 5.130662 -2.981169 -3.924774
G -4.266829 -5.081884 4.698809 -4.636219
C -7.938096 -10.841811 -5.867960 6.390454

Query: 159 acgcaggcggt--ttgttaagtcagatgtgaaatcc-ccgggctcaacctgggaactgc- 214
||||||| ||| | | | | | | |||| | || | | ||||||| || |||
Sbjct: 2040818 acgcaggaggtcataaatgaaataaaggataaatactccagatttaacctggaaattgct 2040759

Query: 215 atctgatactggcaag 230
|| | | |||| |||
Sbjct: 2040758 atatcgt-ctggaaag 2040744


Alignment 13: NC_000913.2 from 171 to 205, AE006641 from 2695655 to 2695621
Initial score: 92.3 (30.4 bits), adjusted score: 96.93 (31.8 bits), E-value: 0.90851
Identity = 26/35 (74%)
Strand: Plus/Minus

Compositional adjustment is on.
Enthropy = 0.425374.
Query frequences: A: 0.256110, T: 0.256110, G: 0.231670, C: 0.256110,
Subject frequences: A: 0.256110, T: 0.329431, G: 0.182789, C: 0.231670,
Adjusted substitution matrix (subject letters are in rows, query letters are in columns):
A T G C
A 4.737799 -3.520545 -4.096456 -3.520545
T -2.490423 4.010418 -2.845333 -2.490423
G -6.203192 -6.203192 6.172878 -6.203192
C -4.096456 -4.096456 -4.823360 5.048177

Query: 171 tgttaagtcagatgtgaaatccccgggctcaacct 205
||| || | || |||||||| | | ||||| |||
Sbjct: 2695655 tgtaaacttagctgtgaaattcttgagctcaccct 2695621