Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold180
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 544442
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 40629 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:375654 original size:13 final size:13
Alignment explanation
Indices: 375636--375661 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
375626 CCTAATCCTA
375636 AAAAAAAAAAACC
1 AAAAAAAAAAACC
375649 AAAAAAAAAAACC
1 AAAAAAAAAAACC
375662 TTTTCACCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACC
Found at i:376721 original size:27 final size:27
Alignment explanation
Indices: 376689--377336 Score: 985
Period size: 27 Copynumber: 23.7 Consensus size: 27
376679 GACCTTTTCA
*
376689 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
376716 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
376743 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
** *
376770 AAGTCCACAACTCTATGGCATTCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
376798 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
376825 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
376852 AAGTCCACAACTCTGTGGCATTCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
376880 AA-TACCACAACTCCGTGGCACCCTTTT
1 AAGT-CCACAACTCCGTGGCACCCTTTT
376907 AAGTCCACAACTCCGTGGCACCC-TTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
376933 AAGTCCACAACTCCGTGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
376960 AAGTCCATAACTCCATGGCATCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
376988 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
377015 AAGACCACAACTCCGTAGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
377042 AAGACCACAACTCCGTAGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
377069 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * **
377096 AAGTCCATAACTCTGTGGCATCTTTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
*
377124 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
377151 AAAGTCCACAACTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* *
377179 TAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
377206 AAGTCCACAACTCCGTGGCATCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
377234 AAGTCCACAACTCCGTGGCATCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
377262 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
377289 AAGTCCACAACTCCGTGGCATCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
* * * *
377317 AAATTCACAAATCGGTGGCA
1 AAGTCCACAACTCCGTGGCA
377337 ACCCATTCCA
Statistics
Matches: 574, Mismatches: 37, Indels: 19
0.91 0.06 0.03
Matches are distributed among these distances:
26 25 0.04
27 349 0.61
28 200 0.35
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:376821 original size:55 final size:54
Alignment explanation
Indices: 376689--377336 Score: 985
Period size: 55 Copynumber: 11.9 Consensus size: 54
376679 GACCTTTTCA
*
376689 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
** *
376743 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTATGGCATTCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTT
376798 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
* *
376852 AAGTCCACAACTCTGTGGCATTCCTTTTAA-TACCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTTAAGT-CCACAACTCCGTGGCACCCTTTT
*
376907 AAGTCCACAACTCCGTGGCACCC-TTTAAGTCCACAACTCCGTGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
* *
376960 AAGTCCATAACTCCATGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
* * * *
377015 AAGACCACAACTCCGTAGCACCCTTTTAAGACCACAACTCCGTAGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
* * **
377069 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCTGTGGCATCTTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTT
*
377124 AAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT
* *
377179 TAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTT
377234 AAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
* * * *
377289 AAGTCCACAACTCCGTGGCATCCCTTTTAAATTCACAAATCGGTGGCA
1 AAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCA
377337 ACCCATTCCA
Statistics
Matches: 543, Mismatches: 41, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
53 45 0.08
54 169 0.31
55 284 0.52
56 45 0.08
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (54 bp):
AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
Found at i:376825 original size:82 final size:81
Alignment explanation
Indices: 376689--377336 Score: 1003
Period size: 82 Copynumber: 7.9 Consensus size: 81
376679 GACCTTTTCA
376689 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAC
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAC
376754 TCCGTGGCACCCTTTT
66 TCCGTGGCACCCTTTT
* *
376770 AAGTCCACAACTCTATGGCATTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
1 AAGTCCACAACTCTGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
376835 CTCCGTGGCACCCTTTT
65 CTCCGTGGCACCCTTTT
*
376852 AAGTCCACAACTCTGTGGCATTCCTTTTAA-TACCACAACTCCGTGGCACCCTTTTAAGTCCACA
1 AAGTCCACAACTCTGTGGCA-CCCTTTTAAGT-CCACAACTCCGTGGCACCCTTTTAAGTCCACA
376916 ACTCCGTGGCACCC-TTT
64 ACTCCGTGGCACCCTTTT
* * * *
376933 AAGTCCACAACTCCGTGGCACTCTTTTAAGTCCATAACTCCATGGCATCCCTTTTAAGTCCACAA
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAA
376998 CTCCGTGGCACCCTTTT
65 CTCCGTGGCACCCTTTT
* * * * *
377015 AAGACCACAACTCCGTAGCACCCTTTTAAGACCACAACTCCGTAGCACCCTTTTAAGTCCACAAC
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAC
377080 TCCGTGGCACCCTTTT
66 TCCGTGGCACCCTTTT
* ** *
377096 AAGTCCATAACTCTGTGGCATCTTTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACA
1 AAGTCCACAACTCTGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACA
377161 ACTCCGTGGCACCCTTTT
64 ACTCCGTGGCACCCTTTT
*
377179 TAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAA
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAA
377244 CTCCGTGGCATCCCTTTT
65 CTCCGTGGCA-CCCTTTT
* * *
377262 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAATTCACAA
1 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAA
* *
377327 ATCGGTGGCA
65 CTCCGTGGCA
377337 ACCCATTCCA
Statistics
Matches: 523, Mismatches: 35, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
80 21 0.04
81 123 0.24
82 251 0.48
83 128 0.24
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (81 bp):
AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAC
TCCGTGGCACCCTTTT
Found at i:377364 original size:32 final size:32
Alignment explanation
Indices: 377322--377764 Score: 717
Period size: 32 Copynumber: 13.8 Consensus size: 32
377312 CTTTTAAATT
* *
377322 CACAAATCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
377354 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
377386 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
377418 CACAAGTCGGTGGTAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
377450 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
377482 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
377514 CACAAGTCGGTGGCAACCCATTTCAAAGCTCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
377546 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
377578 CACAAGTCGGTGGCAACCCA-TTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
377610 CACAAGTAGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** *
377642 CACAAGTCGGTGGCAACCTTTTTCAAAGCCCC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
377674 CAGAAGTTGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
377706 CGCAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
377738 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
377765 TCACCATTTT
Statistics
Matches: 386, Mismatches: 23, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
31 3 0.01
32 380 0.98
33 3 0.01
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:379038 original size:16 final size:17
Alignment explanation
Indices: 379007--379041 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
378997 AAGGAAGATG
*
379007 AAGAAGAAAGAAAGAAA
1 AAGAAGAAAAAAAGAAA
379024 AAGAA-AAAAAAAGAAA
1 AAGAAGAAAAAAAGAAA
379040 AA
1 AA
379042 ATATGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAAAAAGAAA
Found at i:379049 original size:10 final size:10
Alignment explanation
Indices: 379013--379042 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
379003 GATGAAGAAG
*
379013 AAAGAAAGAA
1 AAAGAAAAAA
379023 AAAGAAAAAA
1 AAAGAAAAAA
379033 AAAGAAAAAA
1 AAAGAAAAAA
379043 TATGAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:383482 original size:16 final size:16
Alignment explanation
Indices: 383434--383484 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
383424 TAAACCTGAT
383434 TAATCCGAA-TCTAAAA
1 TAATCCGAACTC-AAAA
* **
383450 TAATCTGAACTTGAAA
1 TAATCCGAACTCAAAA
383466 TAATCCGAACTCAAAA
1 TAATCCGAACTCAAAA
383482 TAA
1 TAA
383485 CTATAACCTG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 27 0.96
17 1 0.04
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.25
Consensus pattern (16 bp):
TAATCCGAACTCAAAA
Found at i:383497 original size:32 final size:32
Alignment explanation
Indices: 383426--383498 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
383416 CTGAGTGTTA
*
383426 AACCTG-ATTAATCCGAATCTAAAATAATCTG
1 AACCTGAAATAATCCGAATCTAAAATAATCTG
* *
383457 AACTTGAAATAATCCGAA-CTCAAAATAA-CTAT
1 AACCTGAAATAATCCGAATCT-AAAATAATCT-G
383489 AACCTGAAAT
1 AACCTGAAAT
383499 GACCCAACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 9 0.26
32 26 0.74
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.26
Consensus pattern (32 bp):
AACCTGAAATAATCCGAATCTAAAATAATCTG
Found at i:384299 original size:39 final size:39
Alignment explanation
Indices: 384256--384332 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
384246 CTAGCATATA
384256 ATATGCCTTCTTACTTATAAAGTAAACAACTAATCTCAT
1 ATATGCCTTCTTACTTATAAAGTAAACAACTAATCTCAT
* *
384295 ATATGCCTTCTTACTTATAAAGTAAGCAATTAATCTCA
1 ATATGCCTTCTTACTTATAAAGTAAACAACTAATCTCA
384333 CAAATTGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.36
Consensus pattern (39 bp):
ATATGCCTTCTTACTTATAAAGTAAACAACTAATCTCAT
Found at i:386082 original size:134 final size:134
Alignment explanation
Indices: 385842--386109 Score: 439
Period size: 134 Copynumber: 2.0 Consensus size: 134
385832 TATGGTATTT
* * *
385842 GATGATCAAGAATTATTCTTAAGTAATTGTGGTAAAGAGAAAAATGAAAAAACTTTGTAATTATT
1 GATGATCAAGAATTATTCTTAAATAATTGTGGTAAAGAGAAAAATGAAAAAACCTTATAATTATT
*
385907 GCATTTAATTTCTTCCCTTTTATTTACTTAAATTTTGTTAA-CTTTTTCTTAAAGAAAAGAAAAT
66 GCATTTAATTTCTTCCCTTTTATTTACTTAAATTTTGTTAACCTTTTTCTTAAAGAAAA-AAAAA
385971 AAGAA
130 AAGAA
* *
385976 GATGATCAAGAATTGTTCTTAAATAATTGTGGTAAAGAGAAAAATGAAGAAACCTTATAATTATT
1 GATGATCAAGAATTATTCTTAAATAATTGTGGTAAAGAGAAAAATGAAAAAACCTTATAATTATT
* * *
386041 GCATTTAATTTCTTCCCTTTTGTTTACTTAAATTTTGTTAACCTTTTTTTTGAAGAAAAAAAAAA
66 GCATTTAATTTCTTCCCTTTTATTTACTTAAATTTTGTTAACCTTTTTCTTAAAGAAAAAAAAAA
386106 AGAA
131 AGAA
386110 AATTGACCTT
Statistics
Matches: 124, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
134 109 0.88
135 15 0.12
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (134 bp):
GATGATCAAGAATTATTCTTAAATAATTGTGGTAAAGAGAAAAATGAAAAAACCTTATAATTATT
GCATTTAATTTCTTCCCTTTTATTTACTTAAATTTTGTTAACCTTTTTCTTAAAGAAAAAAAAAA
AGAA
Found at i:389433 original size:2 final size:2
Alignment explanation
Indices: 389428--389452 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
389418 CCTTAAAAAA
389428 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
389453 ATACATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:390288 original size:2 final size:2
Alignment explanation
Indices: 390283--390307 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
390273 CCTTAAAAAA
390283 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
390308 ACATATCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:391146 original size:2 final size:2
Alignment explanation
Indices: 391141--391165 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
391131 CCTTAAAAAA
391141 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
391166 ATACATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:391728 original size:856 final size:855
Alignment explanation
Indices: 387744--391948 Score: 7430
Period size: 856 Copynumber: 4.9 Consensus size: 855
387734 AGAATATATA
*
387744 TATATATATCAAGGAAAAGGAAACATAGCACTTATAATTATTATAGTGTAATTAATCAATTATAC
1 TATACATATCAAGGAAAAGGAAACATAGCACTTATAATTATTATAGTGTAATTAATCAATTATAC
387809 CCTTGATTTGTGAAGGCTTCATGAAAATATTGCGTGAAACTCAAGCTCTTAAGTATTGGAGCTCT
66 CCTTGATTTGTGAAGGCTTCATGAAAATATTGCGTGAAACTCAAGCTCTTAAGTATTGGAGCTCT
* *
387874 ACATAATTCAATGTTGTAAGTGGATAATTGCAGGGTTTTAACAAAAAAATTTTAGGTGAAATGCT
131 ACATAATTCAATGTTGTAAGTGGATAATTGCAGGGTTTTAATAAAAAAATTTCAGGTGAAATGCT
387939 CATCTATCAATGATTTGGAAATAAAAATTTTTAGTAAGTATTTATTTTATTAGTTGTGTTATCTG
196 CATCTATCAATGATTTGGAAATAAAAATTTTTAGTAAGTATTT-TTTTATTAGTTGTGTTATCTG
388004 TGGACAGATTCTGAAGGTGAAAATTTCAATCCCAAACGTTATATAAAGTACAATTTATTTCTAAA
260 TGGACAGATTCTGAAGGTGAAAATTTCAATCCCAAACGTTATATAAAGTACAATTTATTTCTAAA
388069 AATGGTTTAAGAGGTTCAAGTAGCAGTGAGAAAACGAGATATGAAACACTATCTAAGCAAAGCTA
325 AATGGTTTAAGAGGTTCAAGTAGCAGTGAGAAAACGAGATATGAAACACTATCTAAGCAAAGCTA
388134 TTGACATGTTTCTAACCATATAATTAAGCAAGCATGAACTATACTGCATGATACAAGCACACAGT
390 TTGACATGTTTCTAACCATATAATTAAGCAAGCATGAACTATACTGCATGATACAAGCACACAGT
388199 CACAGTTAATTGAGAAGGATATATCGGAATGAGGTTTTAAGCATGAAATTTAGCATTTGAGAAGC
455 CACAGTTAATTGAGAAGGATATATCGGAATGAGGTTTTAAGCATGAAATTTAGCATTTGAGAAGC
*
388264 TTTTTTGTTGTTGGTAACTTATAACTGATTCCCGGCCCCATCGACTGAGTGCAGGACAGATCTCA
520 TTTTTTGTTGTTGGTAACTTATAACTGATTCCCGGCCCCATCGACTGAGTGCAAGACAGATCTCA
*
388329 TCCACTCTCCAGCAAAGGCTTCATCCAGCACTAAGTCGCCATTGCAGGTGAATTAAGCTTTGCGA
585 TCCACTCTCCAGCAAAGGCTTCATCCACCACTAAGTCGCCATTGCAGGTGAATTAAGCTTTGCGA
**
388394 TAGACGACCGGTTGCTGAAGCCTTTGAAGGAGAGTGAATGGGAGTTGCCTTGCCAGATAATTTTG
650 TAGACGACCGGTTGCTGAAGCCTTTGAAGGAGAGTGAATGGGAGTTGCCTTGTTAGATAATTTTG
388459 TATGTAGTTGATCCGAGTCTGACAATGTTTGGACGCAACAGACTTCTTATATAGTCTTGCAAGTA
715 TATGTAGTTGATCCGAGTCTGACAATGTTTGGACGCAACAGACTTCTTATATAGTCTTGCAAGTA
388524 TCACTCCCCAGCCCGGTATCATTTCGAGTGAATCATAATTTTCCTTAAAAAA------TGTGTGT
780 TCACTCCCCAGCCCGGTATCATTTCGAGTGAATCATAATTTTCCTTAAAAAATGTGTGTGTGTGT
388583 GTGTGTGTGTG
845 GTGTGTGTGTG
*
388594 --TACATATCAAGGAAAAGGAAACATAGCACTTATAATTATTATAGTGTAATTAATGAATTATAC
1 TATACATATCAAGGAAAAGGAAACATAGCACTTATAATTATTATAGTGTAATTAATCAATTATAC
*
388657 CCTTGATTTGTGAAGGCTTCATGAAAATATTGCGTGAAACTGAAGCTCTTAAGTATTGGAGCTCT
66 CCTTGATTTGTGAAGGCTTCATGAAAATATTGCGTGAAACTCAAGCTCTTAAGTATTGGAGCTCT
388722 ACATAATTCAATGTTGTAAGTGGATAATTGCAGGGTTTTAATAAAAAAATTTCAGGTGAAATGCT
131 ACATAATTCAATGTTGTAAGTGGATAATTGCAGGGTTTTAATAAAAAAATTTCAGGTGAAATGCT
*
388787 CATCTATCAATGATTTGGAAATAAAAATTTTTAGTAAGTATTTTTTTTTTTAATTAGTTGTGCTA
196 CATCTATCAATGATTTGGAAATAAAAATTTTTAGTAAGTA----TTTTTTT-ATTAGTTGTGTTA
388852 TCTGTGGACAGATTCTGAAGGTGAAAATTTCAATCCCAAACGTTATATAAAGTACAATTTATTTC
256 TCTGTGGACAGATTCTGAAGGTGAAAATTTCAATCCCAAACGTTATATAAAGTACAATTTATTTC
388917 TAAAAATGGTTTAAGAGGTTCAAGTAGCAGTGAGAAAACGAGATATGAAACACTATCTAAGCAAA
321 TAAAAATGGTTTAAGAGGTTCAAGTAGCAGTGAGAAAACGAGATATGAAACACTATCTAAGCAAA
*
388982 GCTATTGACATGTTTCTAATCATATAATTAAGCAAGCATGAACTATACTGCATGATACAAGCACA
386 GCTATTGACATGTTTCTAACCATATAATTAAGCAAGCATGAACTATACTGCATGATACAAGCACA
389047 CAGTCACAGTTAATTGAGAAGGATATATCGGAATGAGGTTTTAAGCATGAAATTTAGCATTTGAG
451 CAGTCACAGTTAATTGAGAAGGATATATCGGAATGAGGTTTTAAGCATGAAATTTAGCATTTGAG
*
389112 AAGCTTTTTTGTTGTTGGTAACTTATAACTGATTCCCGGCCCCATCGACTGAGTGCAGGACAGAT
516 AAGCTTTTTTGTTGTTGGTAACTTATAACTGATTCCCGGCCCCATCGACTGAGTGCAAGACAGAT
*
389177 CTCATCCACTCTCCAGCAAAGGCTTCATCCAGCACTAAGTCGCCATTGCAGGTGAATTAAGCTTT
581 CTCATCCACTCTCCAGCAAAGGCTTCATCCACCACTAAGTCGCCATTGCAGGTGAATTAAGCTTT
389242 GCGATAGACGACCGGTTGCTGAAGCCTTTGAAGGAGAGTGAATGGGAGTTGCCTTGTTAGATAAT
646 GCGATAGACGACCGGTTGCTGAAGCCTTTGAAGGAGAGTGAATGGGAGTTGCCTTGTTAGATAAT
389307 TTTGTATGTAGTTGATCCGAGTCTGACAATGTTTGGACGCAACAGACTTCTTATATAGTCTTGCA
711 TTTGTATGTAGTTGATCCGAGTCTGACAATGTTTGGACGCAACAGACTTCTTATATAGTCTTGCA
389372 AGTATCACTCCCCAGCCCGGTATCATTTCGAGTGAATCATAATTTTCCTTAAAAAATGTGTGTGT
776 AGTATCACTCCCCAGCCCGGTATCATTTCGAGTGAATCATAATTTTCCTTAAAAAATGTGTGTGT
389437 GTGTGTGTGTGTGTG
841 GTGTGTGTGTGTGTG
389452 TATACATATCAAGGAAAAGGAAACATAGCACTTATAATTATTATAGTGT-ATCTAATCAATTATA
1 TATACATATCAAGGAAAAGGAAACATAGCACTTATAATTATTATAGTGTAAT-TAATCAATTATA
* ** * *
389516 CTCTTGATTTGTGAAGGCTTCATGAAAATATTGTTTGAAACCCATGCTCTTAAGTATTGGAGCTC
65 CCCTTGATTTGTGAAGGCTTCATGAAAATATTGCGTGAAACTCAAGCTCTTAAGTATTGGAGCTC
* * * * *
389581 TACATGATTCTATGTTGTAAGTGGATAACTGCGGGGTTTTAATAAAAAAAATTTCCGGTGAAATG
130 TACATAATTCAATGTTGTAAGTGGATAATTGCAGGGTTTTAAT-AAAAAAATTTCAGGTGAAATG
* * * *
389646 CTCATCTATCAATGATTTGGAAATAAAACAATTATAGTAAGTA-TTTTTTATTGGTTGTATTATC
194 CTCATCTATCAATGATTTGGAAATAAAA-ATTTTTAGTAAGTATTTTTTTATTAGTTGTGTTATC
* * * *
389710 TGTAGAGAGAATCTGAAGGTGAAAATCTCAATCCCAAACGTTATATAAAGTACAATTTATTTCTA
258 TGTGGACAGATTCTGAAGGTGAAAATTTCAATCCCAAACGTTATATAAAGTACAATTTATTTCTA
389775 AAAATGGTTTAAGAGGTTCAAGTAGCAGTGAGAAAACGAGATATGAAACACTATCTAAGCAAAGC
323 AAAATGGTTTAAGAGGTTCAAGTAGCAGTGAGAAAACGAGATATGAAACACTATCTAAGCAAAGC
389840 TATTGACATGTTTCTAACCATATAATTAAGCAAGCATGAACTATACTGCATGATACAAGCACACA
388 TATTGACATGTTTCTAACCATATAATTAAGCAAGCATGAACTATACTGCATGATACAAGCACACA
389905 GTCACAGTTAATTGAGAAGGATATATCGGAATGAGGTTTTAAGCATGAAATTTAGCATTTGAGAA
453 GTCACAGTTAATTGAGAAGGATATATCGGAATGAGGTTTTAAGCATGAAATTTAGCATTTGAGAA
* * *
389970 GC-TTTTGGTTGTTGGTAACTTATAACTGATTCCCGGCCCCATCAACTGAGTGCAAGATAGATCT
518 GCTTTTTTGTTGTTGGTAACTTATAACTGATTCCCGGCCCCATCGACTGAGTGCAAGACAGATCT
390034 CATCCACTCTCCAGCAAAGGCTTCATCCACCACTAAGTCGCCATTGCAGGTGAATTAAGCTTTGC
583 CATCCACTCTCCAGCAAAGGCTTCATCCACCACTAAGTCGCCATTGCAGGTGAATTAAGCTTTGC
*
390099 GATAGACGACGGGTTGCTGAAGCCTTTGAAGGAGAGTGAATGGGAGTTGCCTTGTTAGATAATTT
648 GATAGACGACCGGTTGCTGAAGCCTTTGAAGGAGAGTGAATGGGAGTTGCCTTGTTAGATAATTT
* *
390164 TTTATGTAGTTGATCCGAGTCTGACAATGTTTGGACGCAACAGACTTCTTATAGAGTCTTGCAAG
713 TGTATGTAGTTGATCCGAGTCTGACAATGTTTGGACGCAACAGACTTCTTATATAGTCTTGCAAG
390229 TATCACTCCCCAGCCCGGTATCATTTCGAGTGAATCATAATTTTCCTTAAAAAATGTGTGTGTGT
778 TATCACTCCCCAGCCCGGTATCATTTCGAGTGAATCATAATTTTCCTTAAAAAATGTGTGTGTGT
390294 GTGTGTGTGTGTG
843 GTGTGTGTGTGTG
*
390307 --TACATATCAAGGAAAAGGAAACATAGCACTTATAATTATTATAGTGTAATTAATGAATTATAC
1 TATACATATCAAGGAAAAGGAAACATAGCACTTATAATTATTATAGTGTAATTAATCAATTATAC
*
390370 CCTTGATTTGTGAAGGCTTCATGAAAATATTGCGTGAAACTGAAGCTCTTAAGTATTGGAGCTCT
66 CCTTGATTTGTGAAGGCTTCATGAAAATATTGCGTGAAACTCAAGCTCTTAAGTATTGGAGCTCT
390435 ACATAATTCAATGTTGTAAGTGGATAATTGCAGGGTTTTAATAAAAAAATTTCAGGTGAAATGCT
131 ACATAATTCAATGTTGTAAGTGGATAATTGCAGGGTTTTAATAAAAAAATTTCAGGTGAAATGCT
*
390500 CATCTATCAATGATTTGGAAATAAAAATTTTTAGTAAGTATTTTTTTTTTTAATTAGTTGTGCTA
196 CATCTATCAATGATTTGGAAATAAAAATTTTTAGTAAGTA----TTTTTTT-ATTAGTTGTGTTA
390565 TCTGTGGACAGATTCTGAAGGTGAAAATTTCAATCCCAAACGTTATATAAAGTACAATTTATTTC
256 TCTGTGGACAGATTCTGAAGGTGAAAATTTCAATCCCAAACGTTATATAAAGTACAATTTATTTC
390630 TAAAAATGGTTTAAGAGGTTCAAGTAGCAGTGAGAAAACGAGATATGAAACACTATCTAAGCAAA
321 TAAAAATGGTTTAAGAGGTTCAAGTAGCAGTGAGAAAACGAGATATGAAACACTATCTAAGCAAA
*
390695 GCTATTGACATGTTTCTAATCATATAATTAAGCAAGCATGAACTATACTGCATGATACAAGCACA
386 GCTATTGACATGTTTCTAACCATATAATTAAGCAAGCATGAACTATACTGCATGATACAAGCACA
390760 CAGTCACAGTTAATTGAGAAGGATATATCGGAATGAGGTTTTAAGCATGAAATTTAGCATTTGAG
451 CAGTCACAGTTAATTGAGAAGGATATATCGGAATGAGGTTTTAAGCATGAAATTTAGCATTTGAG
390825 AAGCTTTTTTGTTGTTGGTAACTTATAACTGATTCCCGGCCCCATCGACTGAGTGCAAGACAGAT
516 AAGCTTTTTTGTTGTTGGTAACTTATAACTGATTCCCGGCCCCATCGACTGAGTGCAAGACAGAT
*
390890 CTCATCCACTCTCCAGCAAAGGCTTCATCCACCACTAAGTCGCCATTGCAGGTGAATTAAACTTT
581 CTCATCCACTCTCCAGCAAAGGCTTCATCCACCACTAAGTCGCCATTGCAGGTGAATTAAGCTTT
**
390955 GCGATAGACGATTGGTTGCTGAAGCCTTTGAAGGAGAGTGAATGGGAGTTGCCTTGTTAGATAAT
646 GCGATAGACGACCGGTTGCTGAAGCCTTTGAAGGAGAGTGAATGGGAGTTGCCTTGTTAGATAAT
*
391020 TTTGTGTGTAGTTGATCCGAGTCTGACAATGTTTGGACGCAACAGACTTCTTATATAGTCTTGCA
711 TTTGTATGTAGTTGATCCGAGTCTGACAATGTTTGGACGCAACAGACTTCTTATATAGTCTTGCA
391085 AGTATCACTCCCCAGCCCGGTATCATTTCGAGTGAATCATAATTTTCCTTAAAAAATGTGTGTGT
776 AGTATCACTCCCCAGCCCGGTATCATTTCGAGTGAATCATAATTTTCCTTAAAAAATGTGTGTGT
391150 GTGTGTGTGTGTGTG
841 GTGTGTGTGTGTGTG
* *
391165 TATACATATCAAGGAAAAGGAAACATAGCACTTATAATTATTATACTGTAACTAATCAATTATAC
1 TATACATATCAAGGAAAAGGAAACATAGCACTTATAATTATTATAGTGTAATTAATCAATTATAC
* * ** * *
391230 TCTTGATTTGTGAAGGCTTCGTGAAAATATTGTTTGAAACCCATGCTCTTAAGTATTGGAGCTCT
66 CCTTGATTTGTGAAGGCTTCATGAAAATATTGCGTGAAACTCAAGCTCTTAAGTATTGGAGCTCT
* * * * *
391295 ACATGATTCTATGTTGTAAGTGGATAACTGCGGGGTTTTAATAAAAAAAACTTCAGGTGAAATGC
131 ACATAATTCAATGTTGTAAGTGGATAATTGCAGGGTTTTAAT-AAAAAAATTTCAGGTGAAATGC
* * * *
391360 TCATCTATCAATGATTTGGAAATAAAACAATTATAGTAAGTA-TTTTTTATTGGTTGTATTATCT
195 TCATCTATCAATGATTTGGAAATAAAA-ATTTTTAGTAAGTATTTTTTTATTAGTTGTGTTATCT
* * * *
391424 GTAGAGAGAATCTGAAGGTGAAAATCTCAATCCCAAACGTTATATAAAGTACAATTTATTTCTAA
259 GTGGACAGATTCTGAAGGTGAAAATTTCAATCCCAAACGTTATATAAAGTACAATTTATTTCTAA
*
391489 AAATGGTTTAAGAGGTTCAAGTAGCAGTGAGAAAACGAGATATGAAACATTATCTAAGCAAAGCT
324 AAATGGTTTAAGAGGTTCAAGTAGCAGTGAGAAAACGAGATATGAAACACTATCTAAGCAAAGCT
* ** * *
391554 ATTGACATGTTTCCAAAAATATAATTAAGCAAGCATGAACTATGCTGCATGATAAAAGCACACAG
389 ATTGACATGTTTCTAACCATATAATTAAGCAAGCATGAACTATACTGCATGATACAAGCACACAG
* *
391619 TCACAGTTAATTGAGAAAGATAAATCGGAATGAGGTTTTAAGCATGAAATTTAGCATTTGAGAAG
454 TCACAGTTAATTGAGAAGGATATATCGGAATGAGGTTTTAAGCATGAAATTTAGCATTTGAGAAG
* *
391684 CCTTTTTGCTGTTGGTAACTTATAACTGATTCCCGGCCCCATCGACTGAGTGCAAGACAGATCTC
519 CTTTTTTGTTGTTGGTAACTTATAACTGATTCCCGGCCCCATCGACTGAGTGCAAGACAGATCTC
391749 ATCCACTCTCCAGCAAAGGCTTCATCCACCACTAAGTCGCCATTGCAGGTGAATTAAGCTTTGCG
584 ATCCACTCTCCAGCAAAGGCTTCATCCACCACTAAGTCGCCATTGCAGGTGAATTAAGCTTTGCG
*
391814 ATAGACGACGGGTTGCTGAAGCCTTTGAAGGAGAGTGAATGGGAGTTGCCTTGTTAGATAATTTT
649 ATAGACGACCGGTTGCTGAAGCCTTTGAAGGAGAGTGAATGGGAGTTGCCTTGTTAGATAATTTT
* * * * *
391879 GTATGTAGCTGATCCGACTATGAAAATGTTTGGACGCAATAGACTTCTTATATAGTCTTGCAAGT
714 GTATGTAGTTGATCCGAGTCTGACAATGTTTGGACGCAACAGACTTCTTATATAGTCTTGCAAGT
391944 ATCAC
779 ATCAC
391949 CCTCCCATCC
Statistics
Matches: 3214, Mismatches: 113, Indels: 50
0.95 0.03 0.01
Matches are distributed among these distances:
848 228 0.07
851 16 0.00
852 636 0.20
853 156 0.05
854 2 0.00
855 327 0.10
856 790 0.25
857 281 0.09
858 344 0.11
859 2 0.00
860 312 0.10
861 96 0.03
862 24 0.01
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (855 bp):
TATACATATCAAGGAAAAGGAAACATAGCACTTATAATTATTATAGTGTAATTAATCAATTATAC
CCTTGATTTGTGAAGGCTTCATGAAAATATTGCGTGAAACTCAAGCTCTTAAGTATTGGAGCTCT
ACATAATTCAATGTTGTAAGTGGATAATTGCAGGGTTTTAATAAAAAAATTTCAGGTGAAATGCT
CATCTATCAATGATTTGGAAATAAAAATTTTTAGTAAGTATTTTTTTATTAGTTGTGTTATCTGT
GGACAGATTCTGAAGGTGAAAATTTCAATCCCAAACGTTATATAAAGTACAATTTATTTCTAAAA
ATGGTTTAAGAGGTTCAAGTAGCAGTGAGAAAACGAGATATGAAACACTATCTAAGCAAAGCTAT
TGACATGTTTCTAACCATATAATTAAGCAAGCATGAACTATACTGCATGATACAAGCACACAGTC
ACAGTTAATTGAGAAGGATATATCGGAATGAGGTTTTAAGCATGAAATTTAGCATTTGAGAAGCT
TTTTTGTTGTTGGTAACTTATAACTGATTCCCGGCCCCATCGACTGAGTGCAAGACAGATCTCAT
CCACTCTCCAGCAAAGGCTTCATCCACCACTAAGTCGCCATTGCAGGTGAATTAAGCTTTGCGAT
AGACGACCGGTTGCTGAAGCCTTTGAAGGAGAGTGAATGGGAGTTGCCTTGTTAGATAATTTTGT
ATGTAGTTGATCCGAGTCTGACAATGTTTGGACGCAACAGACTTCTTATATAGTCTTGCAAGTAT
CACTCCCCAGCCCGGTATCATTTCGAGTGAATCATAATTTTCCTTAAAAAATGTGTGTGTGTGTG
TGTGTGTGTG
Found at i:393157 original size:17 final size:17
Alignment explanation
Indices: 393137--393195 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
393127 AAATAATAAA
393137 AAATAATAAATAAATTT
1 AAATAATAAATAAATTT
* *
393154 AAATATTATATAAATTT
1 AAATAATAAATAAATTT
*
393171 AAAAAATTTAAA-AAATTT
1 AAATAA--TAAATAAATTT
393189 AAA-AATA
1 AAATAATA
393196 TTGAACTCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 2 0.06
17 21 0.60
18 9 0.26
19 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATAATAAATAAATTT
Found at i:393179 original size:9 final size:9
Alignment explanation
Indices: 393165--393193 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
393155 AATATTATAT
393165 AAATTTAAA
1 AAATTTAAA
393174 AAATTTAAA
1 AAATTTAAA
393183 AAATTTAAA
1 AAATTTAAA
393192 AA
1 AA
393194 TATTGAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAATTTAAA
Found at i:393368 original size:28 final size:28
Alignment explanation
Indices: 393333--393436 Score: 72
Period size: 28 Copynumber: 3.7 Consensus size: 28
393323 TTTTTAAAGT
393333 AAAA-ATATTT-TTTTAAAATTTTTATAA
1 AAAATATATTTATTTTAAAA-TTTTATAA
** *
393360 AAAATATATTTATTTTTTAATATT-TAA
1 AAAATATATTTATTTTAAAATTTTATAA
* * *
393387 AAAATATTATTTATTATTTAAAGTTTGATTA
1 AAAATA-TATTTA-T-TTTAAAATTTTATAA
*
393418 TAAATATATATT-TTTTAAA
1 AAAATATAT-TTATTTTAAA
393437 TTATTATTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
27 13 0.22
28 21 0.35
29 8 0.13
30 9 0.15
31 9 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
AAAATATATTTATTTTAAAATTTTATAA
Found at i:393379 original size:31 final size:31
Alignment explanation
Indices: 393341--393430 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 31
393331 GTAAAAATAT
393341 TTTTTTAAAATTTTTATAAAAAATATATTTA
1 TTTTTTAAAATTTTTATAAAAAATATATTTA
*
393372 TTTTTT--AA-TATT-TAAAAAATATTATTTA
1 TTTTTTAAAATTTTTATAAAAAATA-TATTTA
* * *
393400 TTATTTAAAGTTTGATTAT-AAATATATATTT
1 TTTTTTAAAATTT--TTATAAAAAATATATTT
393431 TTTAAATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
27 9 0.19
28 14 0.30
29 2 0.04
30 1 0.02
31 7 0.15
32 5 0.11
33 8 0.17
34 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
TTTTTTAAAATTTTTATAAAAAATATATTTA
Found at i:393876 original size:22 final size:22
Alignment explanation
Indices: 393851--393906 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
393841 AAAAAAATAT
* *
393851 ATATCACTATATTATTATACAC
1 ATATCACTATAATAGTATACAC
* * *
393873 ATATCAATATAATAGTGTATAC
1 ATATCACTATAATAGTATACAC
393895 ATATCACTATAA
1 ATATCACTATAA
393907 CTACGTGTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.38
Consensus pattern (22 bp):
ATATCACTATAATAGTATACAC
Found at i:393893 original size:24 final size:25
Alignment explanation
Indices: 393866--393917 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 25
393856 ACTATATTAT
393866 TATACACATATCAATATAA-TA-GTG
1 TATA-ACATATCAATATAACTACGTG
*
393890 TAT-ACATATCACTATAACTACGTG
1 TATAACATATCAATATAACTACGTG
393914 TATA
1 TATA
393918 TTACAAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 13 0.54
23 2 0.08
24 9 0.38
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (25 bp):
TATAACATATCAATATAACTACGTG
Found at i:394029 original size:2 final size:2
Alignment explanation
Indices: 394024--394056 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
394014 TGTGTATGTC
394024 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
394057 GAAGTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:394308 original size:22 final size:22
Alignment explanation
Indices: 394222--394316 Score: 95
Period size: 22 Copynumber: 4.3 Consensus size: 22
394212 TTAAATCAAT
* *
394222 ACAATAACATAATGTATATATC
1 ACAATAATATAATGTACATATC
* *
394244 ATAATAATACT-ATGTACATATT
1 ACAATAATA-TAATGTACATATC
* *
394266 ACTATAATA-ATATGTAAATATC
1 ACAATAATATA-ATGTACATATC
*
394288 ACAATAATATAATATACATATC
1 ACAATAATATAATGTACATATC
394310 ACAATAA
1 ACAATAA
394317 CTAAGGAAAC
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
22 56 0.97
23 2 0.03
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.34
Consensus pattern (22 bp):
ACAATAATATAATGTACATATC
Found at i:394406 original size:24 final size:21
Alignment explanation
Indices: 394353--394413 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
394343 GGAACCAGCC
394353 TATACATTCTTCTAAACTATA
1 TATACATTCTTCTAAACTATA
*
394374 TATACATTCTTCTAAACAATA
1 TATACATTCTTCTAAACTATA
* * *
394395 TGTATATTATTCTAAACTA
1 TATACATTCTTCTAAACTA
394414 AATGTATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (21 bp):
TATACATTCTTCTAAACTATA
Found at i:394418 original size:21 final size:21
Alignment explanation
Indices: 394362--394422 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
394352 CTATACATTC
* * * *
394362 TTCTAAACTATATATACATTC
1 TTCTAAACTAAATGTATATTA
394383 TTCTAAAC-AATATGTATATTA
1 TTCTAAACTAA-ATGTATATTA
394404 TTCTAAACTAAATGTATAT
1 TTCTAAACTAAATGTATAT
394423 ATCATTATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 31 0.91
22 2 0.06
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.43
Consensus pattern (21 bp):
TTCTAAACTAAATGTATATTA
Found at i:394496 original size:21 final size:21
Alignment explanation
Indices: 394471--394510 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
394461 AACATATCAC
*
394471 TATAATACTATGCATATATGA
1 TATAATAATATGCATATATGA
*
394492 TATAATAATATGTATATAT
1 TATAATAATATGCATATAT
394511 CACTACAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (21 bp):
TATAATAATATGCATATATGA
Found at i:394891 original size:22 final size:22
Alignment explanation
Indices: 394830--394893 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
394820 AATAACTAAT
* * *
394830 ATACATATAAAAATAACAGTAT
1 ATACATATAACAATAACAATAC
* **
394852 ATTACATATCACTTTAACAATAC
1 A-TACATATAACAATAACAATAC
*
394875 ATACATATTACAATAACAA
1 ATACATATAACAATAACAA
394894 AATATATATA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
22 16 0.50
23 16 0.50
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.30
Consensus pattern (22 bp):
ATACATATAACAATAACAATAC
Found at i:395292 original size:14 final size:12
Alignment explanation
Indices: 395265--395289 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
395255 TGAAATATAA
395265 AAATAAGCACAT
1 AAATAAGCACAT
395277 AAATAAGCACAT
1 AAATAAGCACAT
395289 A
1 A
395290 TAAGATAGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAATAAGCACAT
Found at i:397388 original size:18 final size:18
Alignment explanation
Indices: 397334--397390 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
397324 TTATTGCAAT
*
397334 TTTAATTTA-TCTT-TTA
1 TTTACTTTATTCTTGTTA
* *
397350 CTTTACCTTATTTCATGTTA
1 -TTTACTTTA-TTCTTGTTA
397370 TTTACTTTATTCTTGTTA
1 TTTACTTTATTCTTGTTA
397388 TTT
1 TTT
397391 TAATTTATGC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 7 0.22
18 11 0.34
19 11 0.34
20 3 0.09
ACGTcount: A:0.19, C:0.12, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTACTTTATTCTTGTTA
Found at i:397392 original size:19 final size:19
Alignment explanation
Indices: 397332--397398 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
397322 TATTATTGCA
397332 ATTTTAATTTA-TCTT-TT
1 ATTTTAATTTATTCTTGTT
* ** *
397349 ACTTTACCTTATTTCATGTT
1 ATTTTAATTTA-TTCTTGTT
*
397369 A-TTTACTTTATTCTTGTT
1 ATTTTAATTTATTCTTGTT
397387 ATTTTAATTTAT
1 ATTTTAATTTAT
397399 GCAATTGTAC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
17 8 0.21
18 8 0.21
19 20 0.51
20 3 0.08
ACGTcount: A:0.22, C:0.10, G:0.03, T:0.64
Consensus pattern (19 bp):
ATTTTAATTTATTCTTGTT
Found at i:397816 original size:122 final size:124
Alignment explanation
Indices: 397676--397931 Score: 435
Period size: 124 Copynumber: 2.1 Consensus size: 124
397666 TTTCTTGTTA
* * *
397676 AAGCATACATTCCTAATGACATTTTAGGAATTGATCAAACCTTGAAGGGTATTTGTA-ATTTTTT
1 AAGCATACATTCCAAATGACATTTTAGGAATTGATCAAACCTTGAAGGATATTTGTATAATTTTT
397740 TCAAGGT-AAACATGCATTTTTAAGAGTATTTAGGTCATTTCAGTAATTATTCCATGTC
66 TCAAGGTAAAACATGCATTTTTAAGAGTATTTAGGTCATTTCAGTAATTATTCCATGTC
* *
397798 AAGCATACATTCCAAATGACATTTTAGGAATTGATCGAACCTTGAAGGATATTTTTATAATTTTT
1 AAGCATACATTCCAAATGACATTTTAGGAATTGATCAAACCTTGAAGGATATTTGTATAATTTTT
* *
397863 TCAAGGTAAAACATGCATTTTTAAGAGTATTTAGGTCCTTTTAGTAATTATTCCATGTC
66 TCAAGGTAAAACATGCATTTTTAAGAGTATTTAGGTCATTTCAGTAATTATTCCATGTC
397922 AAGCATACAT
1 AAGCATACAT
397932 CTTAGGGACA
Statistics
Matches: 125, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
122 53 0.42
123 13 0.10
124 59 0.47
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (124 bp):
AAGCATACATTCCAAATGACATTTTAGGAATTGATCAAACCTTGAAGGATATTTGTATAATTTTT
TCAAGGTAAAACATGCATTTTTAAGAGTATTTAGGTCATTTCAGTAATTATTCCATGTC
Found at i:398121 original size:39 final size:39
Alignment explanation
Indices: 398070--398215 Score: 127
Period size: 39 Copynumber: 3.7 Consensus size: 39
398060 TCACATTGTA
*
398070 ATTTTATTATCAAAACATGTCTTTTAGGGTAATTTTAGTC
1 ATTTTA-TATCAAAACATGTCTTTTAGGATAATTTTAGTC
* * * *
398110 ATTTTACATCAAAACATAGT-TCTTAAGGATCA-TGTAG-C
1 ATTTTATATCAAAACAT-GTCT-TTTAGGATAATTTTAGTC
* * * *
398148 ACTTTTATTTCAAAATATGTTTTTTAGGACAATTTTAGTC
1 A-TTTTATATCAAAACATGTCTTTTAGGATAATTTTAGTC
* *
398188 ATTTTATATCAAGACCAAGTCTTTTAGG
1 ATTTTATATCAA-AACATGTCTTTTAGG
398216 GTTATATTAG
Statistics
Matches: 82, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
38 11 0.13
39 43 0.52
40 28 0.34
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (39 bp):
ATTTTATATCAAAACATGTCTTTTAGGATAATTTTAGTC
Found at i:399549 original size:21 final size:21
Alignment explanation
Indices: 399537--399586 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
399527 AATGTTTTTG
399537 TGTAATTTTATAATATTTATA
1 TGTAATTTTATAATATTTATA
*
399558 TGTAA-TTTAGTAATATTTTTA
1 TGTAATTTTA-TAATATTTATA
*
399579 TATAATTT
1 TGTAATTT
399587 GTTACGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 19 0.76
22 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (21 bp):
TGTAATTTTATAATATTTATA
Found at i:399803 original size:21 final size:20
Alignment explanation
Indices: 399771--399824 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
399761 TTTTTTTATA
* *
399771 AATATAATATATTTATTACT
1 AATATAAAATATATATTACT
*
399791 AATATTAAAATATATATTAAT
1 AATA-TAAAATATATATTACT
* *
399812 AAAATAAACTATA
1 AATATAAAATATA
399825 AAAATTTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATAAAATATATATTACT
Found at i:400006 original size:21 final size:21
Alignment explanation
Indices: 399972--400030 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
399962 CAGTTTAATG
*
399972 TAATGTTTTATGTAATTCTAT
1 TAATGTTTTATGTAATTCCAT
*
399993 T-ATGTTTATATGTAA-CCCAT
1 TAATGTTT-TATGTAATTCCAT
400013 TAATGTTTTTATGTAATT
1 TAATG-TTTTATGTAATT
400031 TGTTATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 10 0.32
21 18 0.58
22 3 0.10
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (21 bp):
TAATGTTTTATGTAATTCCAT
Found at i:400314 original size:24 final size:23
Alignment explanation
Indices: 400269--400314 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
400259 TTAATAAAAT
*
400269 AAAAATATAAAAAATTTTACTTC
1 AAAAATATAAAAAATTTAACTTC
400292 AAAAATTATTAAAAAA-TTAACTT
1 AAAAA-TA-TAAAAAATTTAACTT
400315 TCTACGTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 8 0.40
25 7 0.35
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAAATATAAAAAATTTAACTTC
Found at i:400679 original size:17 final size:16
Alignment explanation
Indices: 400652--400685 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
400642 AAAATTTTAT
400652 TATAAATATTTATTAA
1 TATAAATATTTATTAA
400668 TATAATATATTTATTAA
1 TATAA-ATATTTATTAA
400685 T
1 T
400686 TCCTTACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATAAATATTTATTAA
Found at i:401035 original size:20 final size:21
Alignment explanation
Indices: 400980--401038 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
400970 AATACTCTTT
*
400980 TTAT-TAACTATAATGATAAAC
1 TTATGTAACTATAAT-ATAAAA
401001 TTATGTAA-TAGATAATA-AAAA
1 TTATGTAACT--ATAATATAAAA
401022 TTATGTAACTATAATAT
1 TTATGTAACTATAATAT
401039 TTTATATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 5 0.16
23 5 0.16
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (21 bp):
TTATGTAACTATAATATAAAA
Found at i:401694 original size:19 final size:19
Alignment explanation
Indices: 401664--401730 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
401654 AAATAAAAAT
401664 AAAAATTA-ATTAAATTTA
1 AAAAATTATATTAAATTTA
**
401682 AAAAATTATATTAAAAATA
1 AAAAATTATATTAAATTTA
*
401701 AAAATATTAGTTATTATATTTA
1 AAAA-ATTA--TATTAAATTTA
*
401723 ATAAATTA
1 AAAAATTA
401731 AAAAATTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 8 0.21
19 12 0.31
20 4 0.10
21 4 0.10
22 11 0.28
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (19 bp):
AAAAATTATATTAAATTTA
Found at i:401703 original size:18 final size:17
Alignment explanation
Indices: 401657--401705 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
401647 TTTAATAAAA
401657 TAAAAATAAAAATTAAT
1 TAAAAATAAAAATTAAT
**
401674 TAAATTTAAAAAATTATAT
1 TAAAAAT-AAAAATTA-AT
401693 TAAAAATAAAAAT
1 TAAAAATAAAAAT
401706 ATTAGTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 14 0.54
19 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAATAAAAATTAAT
Found at i:401744 original size:15 final size:15
Alignment explanation
Indices: 401724--401753 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
401714 TTATATTTAA
401724 TAAATTAAAAAATTT
1 TAAATTAAAAAATTT
401739 TAAATTAAAAAATTT
1 TAAATTAAAAAATTT
401754 AAAAATAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATTAAAAAATTT
Found at i:402011 original size:10 final size:10
Alignment explanation
Indices: 401996--402033 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
401986 TTCGAAACTT
401996 TAAAAAAATA
1 TAAAAAAATA
402006 TAAAAAAACTA
1 TAAAAAAA-TA
*
402017 TAAAAAACTA
1 TAAAAAAATA
402027 -AAAAAAA
1 TAAAAAAA
402034 GGCTGTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 6 0.24
10 10 0.40
11 9 0.36
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:402015 original size:21 final size:20
Alignment explanation
Indices: 401990--402033 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
401980 TCTTACTTCG
*
401990 AAACTTTAAAAAAATATAAAA
1 AAACTATAAAAAAATA-AAAA
*
402011 AAACTATAAAAAACTAAAAA
1 AAACTATAAAAAAATAAAAA
402031 AAA
1 AAA
402034 GGCTGTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (20 bp):
AAACTATAAAAAAATAAAAA
Found at i:402427 original size:14 final size:14
Alignment explanation
Indices: 402408--402454 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
402398 TTATACGTAA
402408 AAAAAATATATTTT
1 AAAAAATATATTTT
*
402422 AAAAAATATTTTTT
1 AAAAAATATATTTT
* *
402436 AAAAAATCTAATTT
1 AAAAAATATATTTT
402450 AAAAA
1 AAAAA
402455 TTTAACAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAAAATATATTTT
Found at i:402815 original size:16 final size:17
Alignment explanation
Indices: 402794--402827 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
402784 TTAATTTTTT
402794 AAAAT-ATTTTTTTAAA
1 AAAATAATTTTTTTAAA
402810 AAAATAATTTTTTTAAA
1 AAAATAATTTTTTTAAA
402827 A
1 A
402828 TTAAGATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATAATTTTTTTAAA
Found at i:405891 original size:2 final size:2
Alignment explanation
Indices: 405884--405959 Score: 102
Period size: 2 Copynumber: 38.5 Consensus size: 2
405874 AAGTAAAGAA
* *
405884 AT AT AT AT AT AT AT AT AT GT AT TT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
405925 AT A- AT AT AT AT AT AT AT AT AT AGT AG AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A
405960 ATTACGAATG
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.03
2 61 0.94
3 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:406126 original size:70 final size:75
Alignment explanation
Indices: 406052--406200 Score: 193
Period size: 73 Copynumber: 2.1 Consensus size: 75
406042 ATTTATATTT
* * *
406052 ATAAGATCTATCACA-TT-TAAAT-AAAATTTTAATTATATTGAAAGA-TTT-GATTAGAT-AAA
1 ATAAGATCTAGCACATTTGTAAATAAAAATTTTAATTATATTAAAAGATTTTGGA-TAAATAAAA
406111 TTTATTGGATA
65 TTTATTGGATA
* *
406122 ATAAGATTTAGCACATTTGTAAATAAAAATTTTAATTCTATTAAAAGATTTTGGATAAATAAAAT
1 ATAAGATCTAGCACATTTGTAAATAAAAATTTTAATTATATTAAAAGATTTTGGATAAATAAAAT
*
406187 TTATTTGATA
66 TTATTGGATA
406197 ATAA
1 ATAA
406201 ATAAAAGAGT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
70 13 0.19
71 2 0.03
72 5 0.07
73 21 0.31
74 7 0.10
75 19 0.28
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (75 bp):
ATAAGATCTAGCACATTTGTAAATAAAAATTTTAATTATATTAAAAGATTTTGGATAAATAAAAT
TTATTGGATA
Found at i:406587 original size:18 final size:17
Alignment explanation
Indices: 406554--406587 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
406544 TAATTATGAA
*
406554 TAAAACTTTTAAATAAT
1 TAAAACTTTCAAATAAT
406571 TAAAACTTATCAAATAA
1 TAAAACTT-TCAAATAA
406588 CAATTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAACTTTCAAATAAT
Found at i:407491 original size:5 final size:5
Alignment explanation
Indices: 407483--407517 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
407473 ATATAAATAT
407483 TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA
407518 AGTAGTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:415217 original size:18 final size:20
Alignment explanation
Indices: 415190--415231 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
415180 CTTTTTAAAC
415190 AATATAATTTATA-TA-TTT
1 AATATAATTTATATTATTTT
* *
415208 AATATCATTTTTATTATTTT
1 AATATAATTTATATTATTTT
415228 AATA
1 AATA
415232 ACGAATATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
19 2 0.10
20 7 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATAATTTATATTATTTT
Found at i:418063 original size:13 final size:14
Alignment explanation
Indices: 418047--418077 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
418037 TATAAAAAAT
418047 AAATAATTT-TAAA
1 AAATAATTTATAAA
418060 AAATAATTTATAAA
1 AAATAATTTATAAA
418074 AAAT
1 AAAT
418078 TTTATTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATAATTTATAAA
Found at i:418286 original size:47 final size:48
Alignment explanation
Indices: 418235--418331 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 48
418225 AGTAATATTT
* * *
418235 ATTTTTTT-AGTAAAAATGTAAATAGTTTTTTTTAAAGTAAAAAAATA
1 ATTTTTTTAAATAAAAATGTAAATAGTTTTTTTAAAAATAAAAAAATA
*** *
418282 ATTTTTTTAAATAAAAATGTGGCTAGTTTTTTTAAAAATAAATAAATA
1 ATTTTTTTAAATAAAAATGTAAATAGTTTTTTTAAAAATAAAAAAATA
418330 AT
1 AT
418332 AAATAATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 8 0.19
48 34 0.81
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.44
Consensus pattern (48 bp):
ATTTTTTTAAATAAAAATGTAAATAGTTTTTTTAAAAATAAAAAAATA
Found at i:424340 original size:2 final size:2
Alignment explanation
Indices: 424333--424371 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
424323 AGGATTTTCA
*
424333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
424372 ACAAGCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:425022 original size:146 final size:146
Alignment explanation
Indices: 424758--425056 Score: 490
Period size: 146 Copynumber: 2.0 Consensus size: 146
424748 AACGGTTAAT
* *
424758 TTTCAAATTTCACCTCTAGATACTTTTCAACTTCCTCTTTCTAAATCTAGAGTTTGATTTTTCAA
1 TTTCAAATTTCACCTCTAGACACTTTTCAACTTCCTCTTTCTAAATCTAGAGTTGGATTTTTCAA
*
424823 AGTTTTTTTAGATTTTCTTAGATATACAAGAGAAGTTCGAACCTCATACCTCAGATAGGTAATCG
66 AGTTTTTTTAGATTTTCTTAGATATACAAGAGAAGTTCAAACCTCATACCTCAGATAGGTAATCG
424888 ACTACCGTTAGATCGC
131 ACTACCGTTAGATCGC
* * *
424904 TTTCAAATTTCACCTCTAGACATTTTTCAACTTCCTCTTTCTAAATTTGGAGTTGGATTTTTCAA
1 TTTCAAATTTCACCTCTAGACACTTTTCAACTTCCTCTTTCTAAATCTAGAGTTGGATTTTTCAA
* * * *
424969 AGTTTTTTTAGATTTTCTTAGATATACAAGAGAAGTTCAAATCTTATATCTCAGATAGGTCATCG
66 AGTTTTTTTAGATTTTCTTAGATATACAAGAGAAGTTCAAACCTCATACCTCAGATAGGTAATCG
*
425034 ACTACCGTTGGATCGC
131 ACTACCGTTAGATCGC
*
425050 TCTCAAA
1 TTTCAAA
425057 ATGTAGTATG
Statistics
Matches: 141, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
146 141 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (146 bp):
TTTCAAATTTCACCTCTAGACACTTTTCAACTTCCTCTTTCTAAATCTAGAGTTGGATTTTTCAA
AGTTTTTTTAGATTTTCTTAGATATACAAGAGAAGTTCAAACCTCATACCTCAGATAGGTAATCG
ACTACCGTTAGATCGC
Found at i:425265 original size:15 final size:16
Alignment explanation
Indices: 425240--425269 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
425230 TCAAAAGTTG
425240 TTTTATTTTATTTTTC
1 TTTTATTTTATTTTTC
425256 TTTT-TTTTATTTTT
1 TTTTATTTTATTTTT
425270 TTCATTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTATTTTATTTTTC
Found at i:425315 original size:22 final size:22
Alignment explanation
Indices: 425256--425307 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
425246 TTTATTTTTC
**
425256 TTTTTTTTATTTTTTTCATTACT
1 TTTTTTTTAAATTTTTCATTA-T
425279 TTTTTTTTAAATTTTTCATT-T
1 TTTTTTTTAAATTTTTCATTAT
425300 TTTTTTTT
1 TTTTTTTT
425308 GCCATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 9 0.33
23 18 0.67
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTTTTAAATTTTTCATTAT
Found at i:426000 original size:53 final size:53
Alignment explanation
Indices: 425817--426012 Score: 175
Period size: 53 Copynumber: 3.7 Consensus size: 53
425807 TTATTCAAGG
* * * * * *
425817 TTTAAAAATGATAGAGGTGCCAATGTGCTGATTTAAAGCCAGCAACGTT-GGA
1 TTTAAAAATGATAAAAGTGTCAATGTGCTGATTCAAGGCCAGCAACATTAGGA
* * ** * * * * *
425869 CTTAAACATGATAAGGGTGTCTATATACTGATTCAAGGCCAACAACA-TAGGGC
1 TTTAAAAATGATAAAAGTGTCAATGTGCTGATTCAAGGCCAGCAACATTA-GGA
* * *
425922 TTTAAAAATGATAAAAGTG-CTAATGTGCTGATTCAAGGTCAGCGACATTAGGT
1 TTTAAAAATGATAAAAGTGTC-AATGTGCTGATTCAAGGCCAGCAACATTAGGA
425975 TTTAAAAATGATAAAAGTGTCAATGTGCT-AGTTCAAGG
1 TTTAAAAATGATAAAAGTGTCAATGTGCTGA-TTCAAGG
426013 TCAGTGACGT
Statistics
Matches: 114, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
51 1 0.01
52 37 0.32
53 73 0.64
54 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.28
Consensus pattern (53 bp):
TTTAAAAATGATAAAAGTGTCAATGTGCTGATTCAAGGCCAGCAACATTAGGA
Found at i:432416 original size:19 final size:19
Alignment explanation
Indices: 432392--432431 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
432382 AAATTATAAA
*
432392 TATTTTATAAAAT-AATAT
1 TATTTTTTAAAATAAATAT
*
432410 TATTTTTTAAATTAAATAT
1 TATTTTTTAAAATAAATAT
432429 TAT
1 TAT
432432 GATATATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTTTTAAAATAAATAT
Found at i:432448 original size:22 final size:22
Alignment explanation
Indices: 432391--432450 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
432381 AAAATTATAA
* * *
432391 ATATTTTATAAAATAATATTAT
1 ATATTATATAAAATATTATGAT
* * * *
432413 TTTTTAAATTAAATATTATGAT
1 ATATTATATAAAATATTATGAT
432435 ATATTATATAAAATAT
1 ATATTATATAAAATAT
432451 ATAAAAAATT
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATATTATATAAAATATTATGAT
Found at i:433130 original size:19 final size:18
Alignment explanation
Indices: 433088--433130 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
433078 ATTAATATGA
433088 TTTTAATATTTAATTTAT
1 TTTTAATATTTAATTTAT
433106 TATTTAATATTTTAATATT-T
1 T-TTTAATA-TTTAAT-TTAT
433126 TTTTA
1 TTTTA
433131 CAAATGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 8 0.36
21 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAATATTTAATTTAT
Found at i:433373 original size:24 final size:26
Alignment explanation
Indices: 433340--433395 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
433330 ATTTGATTTT
* *
433340 AATTTAATTAATTGA-TAA-AAATAA
1 AATTTGATTAATTGATTAACAAAAAA
433364 AATTTGATTAATTGATTAACAAAAAA
1 AATTTGATTAATTGATTAACAAAAAA
433390 AATTTG
1 AATTTG
433396 GCTTGGCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.50
25 3 0.11
26 11 0.39
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (26 bp):
AATTTGATTAATTGATTAACAAAAAA
Found at i:433483 original size:14 final size:15
Alignment explanation
Indices: 433464--433493 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
433454 ATCCTTATTA
433464 TATATTTT-AAGTTT
1 TATATTTTAAAGTTT
433478 TATATTTTAAAGTTT
1 TATATTTTAAAGTTT
433493 T
1 T
433494 TGACTTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
TATATTTTAAAGTTT
Found at i:435350 original size:2 final size:2
Alignment explanation
Indices: 435343--435378 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
435333 TTTTGTAAGG
435343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
435379 GAATATTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:435674 original size:14 final size:15
Alignment explanation
Indices: 435643--435683 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
435633 TAATTATTGA
435643 TAAAAATCT-AATTAT
1 TAAAAAT-TAAATTAT
435658 TAAAAATTAAATT-T
1 TAAAAATTAAATTAT
*
435672 TAAAAAATAAAT
1 TAAAAATTAAAT
435684 AAAAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAAATTAAATTAT
Found at i:435786 original size:40 final size:40
Alignment explanation
Indices: 435725--435815 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 40
435715 TTAAATTATC
435725 TATTTATAAATATAAATAAATTTTAAAAAAAT-TAAAAAATA
1 TATTT-TAAATATAAATAAA-TTTAAAAAAATATAAAAAATA
* *
435766 TATTTTAAAT-TAAATAAAATTTAAATATATATAAAAAATA
1 TATTTTAAATATAAAT-AAATTTAAAAAAATATAAAAAATA
435806 TCATATTTAA
1 T-AT-TTTAA
435816 GTTCAACTCG
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
39 14 0.32
40 18 0.41
41 7 0.16
42 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (40 bp):
TATTTTAAATATAAATAAATTTAAAAAAATATAAAAAATA
Found at i:435788 original size:16 final size:17
Alignment explanation
Indices: 435769--435801 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
435759 AAAAATATAT
435769 TTTAAAT-TAAATAAAA
1 TTTAAATATAAATAAAA
*
435785 TTTAAATATATATAAAA
1 TTTAAATATAAATAAAA
435802 AATATCATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTAAATATAAATAAAA
Found at i:435789 original size:39 final size:41
Alignment explanation
Indices: 435725--435815 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 41
435715 TTAAATTATC
*
435725 TATTTATAAATATAAATAAATTTTAAAAAAAT-TAAAAAATA
1 TATTT-TAAATATAAATAAAATTTAAAAAAATATAAAAAATA
* *
435766 TATTTTAAAT-TAAATAAAATTTAAATATATATAAAAAATA
1 TATTTTAAATATAAATAAAATTTAAAAAAATATAAAAAATA
435806 TCATATTTAA
1 T-AT-TTTAA
435816 GTTCAACTCG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
39 17 0.39
40 15 0.34
41 7 0.16
42 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (41 bp):
TATTTTAAATATAAATAAAATTTAAAAAAATATAAAAAATA
Found at i:436220 original size:3 final size:3
Alignment explanation
Indices: 436212--436250 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
436202 ATGCTAGTAT
436212 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
436251 TAGAAGTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:439523 original size:19 final size:20
Alignment explanation
Indices: 439499--439549 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
439489 AATATAATTC
*
439499 TTTAAAAAAATTATTTA-TT
1 TTTAAAAAAATTATCTATTT
439518 TTTAAAAAAATTATCTATTT
1 TTTAAAAAAATTATCTATTT
439538 TTTAAAAAAATT
1 TTTAAAAAAATT
439550 TACTCTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAAAAAATTATCTATTT
Found at i:439558 original size:20 final size:19
Alignment explanation
Indices: 439499--439549 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
439489 AATATAATTC
*
439499 TTTAAAAAAATTA-TTTATT
1 TTTAAAAAAATTACTAT-TT
439518 TTTAAAAAAATTATCTATTT
1 TTTAAAAAAATTA-CTATTT
439538 TTTAAAAAAATT
1 TTTAAAAAAATT
439550 TACTCTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.45
20 14 0.48
21 2 0.07
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAAAAAATTACTATTT
Found at i:441945 original size:24 final size:23
Alignment explanation
Indices: 441901--441945 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
441891 GTTAAAAGCA
* *
441901 TTTTTTAAAATATTATAATAACT
1 TTTTTTAAAAAAATATAATAACT
*
441924 TTTTTTAAAAAAAATATCATAA
1 TTTTTT-AAAAAAATATAATAA
441946 TATTGAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTTTAAAAAAATATAATAACT
Found at i:442051 original size:21 final size:20
Alignment explanation
Indices: 442027--442070 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
442017 TTATTACTGC
442027 TTATAATATAATATAAAA-TAT
1 TTATAATATAA-A-AAAATTAT
*
442048 TTATATTATAAAAAAATTAT
1 TTATAATATAAAAAAATTAT
442068 TTA
1 TTA
442071 GTTATTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTATAATATAAAAAAATTAT
Found at i:443174 original size:20 final size:21
Alignment explanation
Indices: 443137--443180 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
443127 TTTATTTATA
*
443137 AATTAAATAAATCATATTAAT
1 AATTAAATAAAACATATTAAT
*
443158 AATTAAA-AAAACATATTTAT
1 AATTAAATAAAACATATTAAT
443178 AAT
1 AAT
443181 GGTAATTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTAAATAAAACATATTAAT
Found at i:443337 original size:26 final size:27
Alignment explanation
Indices: 443284--443340 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 27
443274 TTTAATTGTT
*
443284 AATATTTTTAAATTAAATTAATAATTA
1 AATATTTTTAAATTAAATTAAAAATTA
* *
443311 AATA-TTTTAAATT-TATTAAAAATTT
1 AATATTTTTAAATTAAATTAAAAATTA
443336 AATAT
1 AATAT
443341 GCATAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 13 0.50
26 9 0.35
27 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AATATTTTTAAATTAAATTAAAAATTA
Found at i:445136 original size:16 final size:15
Alignment explanation
Indices: 445112--445182 Score: 70
Period size: 16 Copynumber: 4.5 Consensus size: 15
445102 GATTAATTCG
445112 AATTCAAAATAATCTAA
1 AATT-AAAATAA-CTAA
*
445129 AATTAAAATAACTCA
1 AATTAAAATAACTAA
*
445144 AACTAAAATAACTCAA
1 AATTAAAATAACT-AA
* *
445160 ACTTAAAATGACTTAA
1 AATTAAAATAAC-TAA
445176 AATTAAA
1 AATTAAA
445183 GTGATATGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
15 15 0.33
16 25 0.56
17 5 0.11
ACGTcount: A:0.59, C:0.13, G:0.01, T:0.27
Consensus pattern (15 bp):
AATTAAAATAACTAA
Found at i:445152 original size:15 final size:15
Alignment explanation
Indices: 445117--445168 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
445107 ATTCGAATTC
* *
445117 AAAATAATCTAAAATT
1 AAAATAA-CTCAAACT
445133 AAAATAACTCAAACT
1 AAAATAACTCAAACT
445148 AAAATAACTCAAACTT
1 AAAATAACTCAAAC-T
445164 AAAAT
1 AAAAT
445169 GACTTAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
15 20 0.61
16 13 0.39
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATAACTCAAACT
Found at i:445206 original size:32 final size:32
Alignment explanation
Indices: 445159--445244 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
445149 AAATAACTCA
* * *
445159 AACTTAAAATGACTTAAAATTAAAGTGATATG
1 AACTAAAAATAACTTAAAATTAAAATGATATG
* * *
445191 AACTCAAAATAACTTAAAATTAAAATTATTTG
1 AACTAAAAATAACTTAAAATTAAAATGATATG
*
445223 AACTTAAAAATAATTTAAAATT
1 AAC-TAAAAATAACTTAAAATT
445245 TTAAAACTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 30 0.65
33 16 0.35
ACGTcount: A:0.53, C:0.07, G:0.06, T:0.34
Consensus pattern (32 bp):
AACTAAAAATAACTTAAAATTAAAATGATATG
Found at i:446330 original size:17 final size:17
Alignment explanation
Indices: 446305--446355 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
446295 AAATTAGATA
446305 ATTTATATATTTATATT
1 ATTTATATATTTATATT
*
446322 ATTTTTATATTT-TAATT
1 ATTTATATATTTAT-ATT
*
446339 ATGTAATATATTTATAT
1 AT-TTATATATTTATAT
446356 AAAATTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.04
17 16 0.57
18 10 0.36
19 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTATATATTTATATT
Found at i:447160 original size:2 final size:2
Alignment explanation
Indices: 447153--447177 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
447143 TTGTTTAGAA
447153 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
447178 AGGAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:448200 original size:23 final size:22
Alignment explanation
Indices: 448150--448217 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 22
448140 TAACATAAAT
* * *
448150 TATTAAATATATTTAAATTTTAA
1 TATTAATTATATTTAAA-TATCA
*
448173 AATATAATATATATTTAACATATCA
1 TAT-TAAT-TATATTTAA-ATATCA
448198 TATTAATTATATTTAAATAT
1 TATTAATTATATTTAAATAT
448218 ATTATATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 4 0.11
23 11 0.30
24 7 0.19
25 14 0.38
26 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTAATTATATTTAAATATCA
Found at i:448276 original size:9 final size:10
Alignment explanation
Indices: 448234--448285 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
448224 TTATTTTTAA
*
448234 TATATTTTTT
1 TATATTATTT
**
448244 TATATTCATAA
1 TATATT-ATTT
448255 TATATTATATT
1 TATATTAT-TT
448266 TATATT-TTT
1 TATATTATTT
448275 TATATTATTT
1 TATATTATTT
448285 T
1 T
448286 TAGTACCACC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 8 0.24
10 13 0.38
11 13 0.38
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TATATTATTT
Found at i:448832 original size:16 final size:17
Alignment explanation
Indices: 448799--448841 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
448789 TTATTTAAAA
*
448799 ATATATTTGATTATATAT
1 ATATATTT-ATTAAATAT
448817 ATATATTTA-TAAATAT
1 ATATATTTATTAAATAT
*
448833 ATTTATTTA
1 ATATATTTA
448842 ATATTCACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 1 0.04
18 8 0.35
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATATATTTATTAAATAT
Found at i:449338 original size:26 final size:27
Alignment explanation
Indices: 449304--449358 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
449294 TTTTAAATAT
449304 TTAAATATT-TATAAAATACATTTAAA
1 TTAAATATTATATAAAATACATTTAAA
* **
449330 TTAATTATTAATATAAAATATTTTTAAA
1 TTAAATATT-ATATAAAATACATTTAAA
449358 T
1 T
449359 ATTTTGGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.33
28 16 0.67
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAATATTATATAAAATACATTTAAA
Found at i:449745 original size:17 final size:19
Alignment explanation
Indices: 449722--449769 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
449712 TTAAGAAATA
*
449722 ATTAAAAAATTA-TATTTT
1 ATTAAAAAATAATTATTTT
449740 -TTAAAAAATAATTATTTT
1 ATTAAAAAATAATTATTTT
*
449758 ATTAATAAATAA
1 ATTAAAAAATAA
449770 ATAATGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 10 0.38
18 6 0.23
19 10 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAAAAAATAATTATTTT
Found at i:450733 original size:15 final size:15
Alignment explanation
Indices: 450713--450744 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
450703 CATTCTCTCC
450713 TCCTCTTCTTCTTCT
1 TCCTCTTCTTCTTCT
450728 TCCTCTTCTTCTTCT
1 TCCTCTTCTTCTTCT
450743 TC
1 TC
450745 GTGTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
TCCTCTTCTTCTTCT
Found at i:454325 original size:20 final size:22
Alignment explanation
Indices: 454295--454335 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
454285 AAACGTGTTT
454295 AAAAATAATAA-TATTTTTTAA
1 AAAAATAATAATTATTTTTTAA
454316 AAAAAT-ATAATTATTTTTTA
1 AAAAATAATAATTATTTTTTA
454336 TCAGTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAAATAATAATTATTTTTTAA
Found at i:454393 original size:42 final size:41
Alignment explanation
Indices: 454301--454395 Score: 97
Period size: 42 Copynumber: 2.3 Consensus size: 41
454291 GTTTAAAAAT
*
454301 AATAATATT-TTTTAAAAAAATATAATTATTTTTTATCAGTA
1 AATAAT-TTATTTTAAAAAAATATAATTATATTTTATCAGTA
* * *
454342 ATTATTTTATTTTAAAAAAATTATAAACTTA-ATTTTAT-ATTA
1 AATAATTTATTTTAAAAAAA-TAT-AA-TTATATTTTATCAGTA
454384 AATAATTTATTT
1 AATAATTTATTT
454396 ATTTTTTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
40 2 0.05
41 15 0.34
42 16 0.36
43 8 0.18
44 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (41 bp):
AATAATTTATTTTAAAAAAATATAATTATATTTTATCAGTA
Found at i:456553 original size:3 final size:3
Alignment explanation
Indices: 456545--456578 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
456535 AAGACTTCTT
456545 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
456579 CTAATTTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:462174 original size:20 final size:21
Alignment explanation
Indices: 462132--462174 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
462122 TTTTATAGAT
* *
462132 AAATTATATTAAATTATTTTA
1 AAATTATATTAAATTAATATA
*
462153 AAATT-TATTAATTTAATATA
1 AAATTATATTAAATTAATATA
462173 AA
1 AA
462175 TAAAAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTATATTAAATTAATATA
Found at i:469985 original size:66 final size:69
Alignment explanation
Indices: 469890--470018 Score: 156
Period size: 66 Copynumber: 1.9 Consensus size: 69
469880 AGGCGAAAAG
* * * *
469890 GAGGTGCAAGAGGTATAAGTTTAATAAGTGAAGACTATA-A-AAACACCTAGTAC-AAGGGGCAA
1 GAGGTGCAAGAAGTATAAGTTCAACAAGTGAAGACTATAGATAAACACCTAATACAAAGGGGCAA
469952 GAAA
66 GAAA
* * * * *
469956 GAGGTGCAATAAGTATAGGTTCAACAAGTGACGACTGTAGATAAGCACCTAATACAAAGGGGC
1 GAGGTGCAAGAAGTATAAGTTCAACAAGTGAAGACTATAGATAAACACCTAATACAAAGGGGC
470019 TAGGAAAAGA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
66 32 0.63
67 1 0.02
68 11 0.22
69 7 0.14
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.19
Consensus pattern (69 bp):
GAGGTGCAAGAAGTATAAGTTCAACAAGTGAAGACTATAGATAAACACCTAATACAAAGGGGCAA
GAAA
Found at i:472650 original size:23 final size:23
Alignment explanation
Indices: 472637--472683 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
472627 TCATTTATTA
472637 TTAAAATATTAATTATATAATAT
1 TTAAAATATTAATTATATAATAT
*
472660 TTAAAATATTATTTATATTAATAT
1 TTAAAATATTAATTATA-TAATAT
472684 AATTATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAAATATTAATTATATAATAT
Found at i:472680 original size:32 final size:33
Alignment explanation
Indices: 472642--472711 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 33
472632 TATTATTAAA
*
472642 ATATTAATTATATAATA-T-TTAAAATATTA-TTT
1 ATATTAA-TATA-AATATTATTAAAACATTATTTT
*
472674 ATATTAATATAATTATTATTAAAACATTATTTT
1 ATATTAATATAAATATTATTAAAACATTATTTT
472707 ATATT
1 ATATT
472712 TTTTAAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 3 0.09
31 5 0.15
32 17 0.52
33 8 0.24
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (33 bp):
ATATTAATATAAATATTATTAAAACATTATTTT
Found at i:475656 original size:3 final size:3
Alignment explanation
Indices: 475648--475690 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
475638 ATCCAAACAA
475648 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
475691 GTTAACGGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:477118 original size:22 final size:23
Alignment explanation
Indices: 477086--477131 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
477076 GTATGAATAT
* *
477086 TTTATATTTATTTATTTT-TAAA
1 TTTATAATTATATATTTTATAAA
477108 TTTATAATTATATATTTTATAAA
1 TTTATAATTATATATTTTATAAA
477131 T
1 T
477132 AAATAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTATAATTATATATTTTATAAA
Found at i:477348 original size:14 final size:15
Alignment explanation
Indices: 477320--477349 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
477310 AATTTTTAAT
477320 ATTATGAATAATAAA
1 ATTATGAATAATAAA
477335 ATTATGAA-AATAAA
1 ATTATGAATAATAAA
477349 A
1 A
477350 CAATTAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
ATTATGAATAATAAA
Found at i:478112 original size:15 final size:15
Alignment explanation
Indices: 478091--478128 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
478081 TTTTATTATT
478091 TATTTAAATAATATAA
1 TATTTAAATAATA-AA
478107 -ATTTAAATAATAAA
1 TATTTAAATAATAAA
478121 TATTTAAA
1 TATTTAAA
478129 AATTTATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATTTAAATAATAAA
Found at i:478492 original size:21 final size:21
Alignment explanation
Indices: 478455--478497 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
478445 GTAAGTAATG
* *
478455 ATGTTAATTCAAAAAAATTAA
1 ATGTTAATTAAAAAAAAATAA
478476 ATGTTAA-TAAAATAAAAATAA
1 ATGTTAATTAAAA-AAAAATAA
478497 A
1 A
478498 AATAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (21 bp):
ATGTTAATTAAAAAAAAATAA
Found at i:482133 original size:12 final size:12
Alignment explanation
Indices: 482116--482141 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
482106 TTATGTATAA
482116 ATATATTATATT
1 ATATATTATATT
482128 ATATATTATATT
1 ATATATTATATT
482140 AT
1 AT
482142 TTTTATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATATTATATT
Found at i:482178 original size:28 final size:30
Alignment explanation
Indices: 482125--482196 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 30
482115 AATATATTAT
482125 ATTATATATTATATTATTTTTATTAAATAA
1 ATTATATATTATATTATTTTTATTAAATAA
482155 ATTATAT-TTATATT-TTATTT-TTAAATAA
1 ATTATATATTATATTATT-TTTATTAAATAA
482183 TATT-TAATATTATA
1 -ATTAT-ATATTATA
482197 AGTGAAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
28 11 0.29
29 15 0.39
30 12 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTATATATTATATTATTTTTATTAAATAA
Found at i:482193 original size:31 final size:29
Alignment explanation
Indices: 482125--482182 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
482115 AATATATTAT
482125 ATTATATATTATATTATTTTTATTAAATAA
1 ATTATAT-TTATATTATTTTTATTAAATAA
482155 ATTATATTTATATT-TTATTT-TTAAATAA
1 ATTATATTTATATTATT-TTTATTAAATAA
482183 TATTTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 10 0.37
29 10 0.37
30 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
ATTATATTTATATTATTTTTATTAAATAA
Found at i:482577 original size:2 final size:2
Alignment explanation
Indices: 482570--482596 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
482560 AAATACAGAC
482570 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
482597 GAACTTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:492634 original size:20 final size:20
Alignment explanation
Indices: 492611--492666 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 20
492601 TTATTTTTTT
492611 TAATTTAATTTAATTTAAAA
1 TAATTTAATTTAATTTAAAA
*
492631 TAA--TATTTTAA-TTAAAA
1 TAATTTAATTTAATTTAAAA
*
492648 TAATATT-ATTTTATTTAAA
1 TAAT-TTAATTTAATTTAAA
492667 TTTAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
17 9 0.31
18 7 0.24
19 4 0.14
20 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTTAATTTAATTTAAAA
Found at i:492645 original size:17 final size:18
Alignment explanation
Indices: 492619--492654 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
492609 TTTAATTTAA
492619 TTTAATTTAAAATAATAT
1 TTTAATTTAAAATAATAT
492637 TTTAA-TTAAAATAATAT
1 TTTAATTTAAAATAATAT
492654 T
1 T
492655 ATTTTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAATTTAAAATAATAT
Found at i:494493 original size:2 final size:2
Alignment explanation
Indices: 494488--494520 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
494478 CTTCTTTCTT
494488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
494521 TTAAGACTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:503968 original size:20 final size:20
Alignment explanation
Indices: 503940--503978 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
503930 GTAAGATGTA
503940 AAAACAATGAATGAAAATGC
1 AAAACAATGAATGAAAATGC
*
503960 AAAAGAATGAATGAAAATG
1 AAAACAATGAATGAAAATG
503979 AATTAAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.18, T:0.15
Consensus pattern (20 bp):
AAAACAATGAATGAAAATGC
Found at i:504119 original size:3 final size:3
Alignment explanation
Indices: 504113--504137 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
504103 TATTCCTATT
504113 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
504138 TAAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:504478 original size:23 final size:24
Alignment explanation
Indices: 504434--504501 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 24
504424 AATGTGATAA
*
504434 ATATAATATATAAAAAA--ATATA-
1 ATATAA-ATATAAAAAATTTTATAG
*
504456 ATATAAATTTAAAAAATTTTATATG
1 ATATAAATATAAAAAATTTTATA-G
* *
504481 ATTTAAATATAAAATATTTTA
1 ATATAAATATAAAAAATTTTA
504502 ATAAAATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
21 9 0.24
22 6 0.16
23 4 0.11
25 18 0.49
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
ATATAAATATAAAAAATTTTATAG
Found at i:504840 original size:2 final size:2
Alignment explanation
Indices: 504833--504865 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
504823 TAACTAATTA
504833 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
504866 ACATTAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:504988 original size:12 final size:12
Alignment explanation
Indices: 504967--505000 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
504957 TTTATCATGT
504967 TAAAAT-AAAAA
1 TAAAATAAAAAA
*
504978 TTAAATAAAAAA
1 TAAAATAAAAAA
504990 TAAAATAAAAA
1 TAAAATAAAAA
505001 TTTTAATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
TAAAATAAAAAA
Found at i:505008 original size:12 final size:11
Alignment explanation
Indices: 504969--505002 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
504959 TATCATGTTA
504969 AAATAAAAATT
1 AAATAAAAATT
*
504980 AAATAAAAAATA
1 AAAT-AAAAATT
504992 AAATAAAAATT
1 AAATAAAAATT
505003 TTAATATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAAAAATT
Found at i:505645 original size:1 final size:1
Alignment explanation
Indices: 505639--505673 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
505629 CTTCTCTTAG
* *
505639 TTTTTTTTTTTCTCTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
505674 GTTTGGTCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:505654 original size:23 final size:23
Alignment explanation
Indices: 505628--505672 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
505618 TTCTTTTGTT
505628 TCTTCTCTTAGTTTTTTTTTTTC
1 TCTTCTCTTAGTTTTTTTTTTTC
* * **
505651 TCTTTTTTTTTTTTTTTTTTTT
1 TCTTCTCTTAGTTTTTTTTTTT
505673 TGTTTGGTCG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.02, C:0.11, G:0.02, T:0.84
Consensus pattern (23 bp):
TCTTCTCTTAGTTTTTTTTTTTC
Found at i:509747 original size:26 final size:23
Alignment explanation
Indices: 509707--509762 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
509697 TAATAAAATG
509707 ATATTATATACTTAATAATATTTAA
1 ATATTATATACTTAAT-ATA-TTAA
509732 AT-TTATATACAATTAATATATTAA
1 ATATTATATAC--TTAATATATTAA
509756 ATATTAT
1 ATATTAT
509763 TTTTTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 14 0.50
25 9 0.32
26 5 0.18
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTATATACTTAATATATTAA
Found at i:512269 original size:5 final size:5
Alignment explanation
Indices: 512259--512379 Score: 79
Period size: 5 Copynumber: 24.4 Consensus size: 5
512249 ATTTATGTAT
* * * *
512259 TTATA TTATA TTATA TTATAA TTATA TTTAAA TTATT TTATA TTATA -AATT
1 TTATA TTATA TTATA TTAT-A TTATA -TTATA TTATA TTATA TTATA TTATA
* * * * * *
512310 TTTTA ATATA TTA-A -TATT TTATA TTATA -TAAA TTTTA ATATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* *
512357 TTTTAA TTATT TTATA TTATA TT
1 TTAT-A TTATA TTATA TTATA TT
512380 TTTAAAATTA
Statistics
Matches: 85, Mismatches: 24, Indels: 14
0.69 0.20 0.11
Matches are distributed among these distances:
3 2 0.02
4 6 0.07
5 64 0.75
6 13 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:512319 original size:14 final size:17
Alignment explanation
Indices: 512259--512377 Score: 72
Period size: 16 Copynumber: 6.9 Consensus size: 17
512249 ATTTATGTAT
*
512259 TTATATTATATTAT--A
1 TTATTTTATATTATAAA
*
512274 TTATAATTATATT-TAAA
1 TTAT-TTTATATTATAAA
512291 TTATTTTATATTATAAA
1 TTATTTTATATTATAAA
*
512308 TT-TTTTA-ATATATTAA
1 TTATTTTATAT-TATAAA
512324 -TATTTTATATTATATAAA
1 TTATTTTATA-T-TATAAA
*
512342 TTTTAATATATTATATT-TTAA
1 --TT-AT-T-TTATATTATAAA
512363 TTATTTTATATTATA
1 TTATTTTATATTATA
512378 TTTTTAAAAT
Statistics
Matches: 84, Mismatches: 5, Indels: 28
0.72 0.04 0.24
Matches are distributed among these distances:
15 8 0.10
16 37 0.44
17 14 0.17
18 9 0.11
19 2 0.02
21 4 0.05
22 3 0.04
23 2 0.02
24 5 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTTTATATTATAAA
Found at i:512328 original size:32 final size:31
Alignment explanation
Indices: 512292--512366 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 31
512282 ATATTTAAAT
*
512292 TATTTTATATTATA-AATTTTTTAATATATTAA
1 TATTTTATATTATATAA-ATTTTAATATATT-A
512324 TATTTTATATTATATAAATTTTAATATATTA
1 TATTTTATATTATATAAATTTTAATATATTA
512355 TATTTTA-ATTAT
1 TATTTTATATTAT
512367 TTTATATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 5 0.12
31 8 0.20
32 26 0.63
33 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
TATTTTATATTATATAAATTTTAATATATTA
Found at i:512368 original size:24 final size:24
Alignment explanation
Indices: 512320--512415 Score: 67
Period size: 24 Copynumber: 3.8 Consensus size: 24
512310 TTTTAATATA
*
512320 TTAATATTTTATATTATATAA--ATT
1 TTAATATATTATATT-T-TAATTATT
512344 TTAATATATTATATTTTAATTA-T
1 TTAATATATTATATTTTAATTATT
512367 TT--TATATTATATTTTTAAAATTATAT
1 TTAATATATTATA-TTTT--AATTAT-T
512393 TTAATAATATTAGATATTTTAAT
1 TTAAT-ATATT--ATATTTTAAT
512416 ATGAATGTCA
Statistics
Matches: 59, Mismatches: 1, Indels: 20
0.74 0.01 0.25
Matches are distributed among these distances:
21 9 0.15
22 7 0.12
23 4 0.07
24 20 0.34
26 3 0.05
28 4 0.07
29 5 0.08
30 4 0.07
31 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (24 bp):
TTAATATATTATATTTTAATTATT
Found at i:512415 original size:15 final size:14
Alignment explanation
Indices: 512317--512417 Score: 54
Period size: 15 Copynumber: 7.3 Consensus size: 14
512307 ATTTTTTAAT
512317 ATATTAATATTTT-
1 ATATTAATATTTTA
*
512330 ATATT-ATA--TAA
1 ATATTAATATTTTA
* *
512341 ATTTTAATATATTA
1 ATATTAATATTTTA
*
512355 TATTTTAATTATTTT-
1 -ATATTAA-TATTTTA
512370 ATATT-ATATTTTTA
1 ATATTAATA-TTTTA
*
512384 AAATT-ATATTTAATA
1 ATATTAATATTT--TA
512399 ATATTAGATATTTTA
1 ATATTA-ATATTTTA
512414 ATAT
1 ATAT
512418 GAATGTCATA
Statistics
Matches: 69, Mismatches: 7, Indels: 22
0.70 0.07 0.22
Matches are distributed among these distances:
10 1 0.01
11 4 0.06
12 8 0.12
13 13 0.19
14 13 0.19
15 19 0.28
16 5 0.07
17 6 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (14 bp):
ATATTAATATTTTA
Found at i:512853 original size:17 final size:18
Alignment explanation
Indices: 512811--512853 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
512801 TTAAAAAGTG
512811 ATTTAAAATATTTATAAAA
1 ATTT-AAATATTTATAAAA
512830 ATTTAAAT-TTTA-AAAA
1 ATTTAAATATTTATAAAA
512846 ATTATAAA
1 ATT-TAAA
512854 ATAAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.30
17 8 0.35
18 4 0.17
19 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAAATATTTATAAAA
Found at i:512858 original size:15 final size:15
Alignment explanation
Indices: 512840--512877 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
512830 ATTTAAATTT
512840 TAAAAAATTATAAAA
1 TAAAAAATTATAAAA
*
512855 TAAAATATTATAAAA
1 TAAAAAATTATAAAA
*
512870 TAATAAAT
1 TAAAAAAT
512878 ATTGTGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAAAATTATAAAA
Done.