Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 2 of 205
Found at i:363778 original size:14 final size:15
Alignment explanation
Indices: 363753--363781 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
363743 CATTGCCTTC
363753 AATATATATGGTAAT
1 AATATATATGGTAAT
363768 AATAT-TATGGTAAT
1 AATATATATGGTAAT
363782 GTTCTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:363825 original size:14 final size:15
Alignment explanation
Indices: 363800--363828 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
363790 CATTGCCTTC
363800 AATATATATGGTAAT
1 AATATATATGGTAAT
363815 AATAT-TATGGTAAT
1 AATATATATGGTAAT
363829 GTTCTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:363872 original size:14 final size:15
Alignment explanation
Indices: 363847--363875 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
363837 CATTGCCTTC
363847 AATATATATGGTAAT
1 AATATATATGGTAAT
363862 AATAT-TATGGTAAT
1 AATATATATGGTAAT
363876 GTTCTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:363919 original size:14 final size:15
Alignment explanation
Indices: 363894--363922 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
363884 CATTGCCTTC
363894 AATATATATGGTAAT
1 AATATATATGGTAAT
363909 AATAT-TATGGTAAT
1 AATATATATGGTAAT
363923 GTTCTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:363966 original size:14 final size:15
Alignment explanation
Indices: 363941--363969 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
363931 CATTGCCTTC
363941 AATATATATGGTAAT
1 AATATATATGGTAAT
363956 AATAT-TATGGTAAT
1 AATATATATGGTAAT
363970 GTTCTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:364013 original size:14 final size:15
Alignment explanation
Indices: 363988--364016 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
363978 CATTGCCTTC
363988 AATATATATGGTAAT
1 AATATATATGGTAAT
364003 AATAT-TATGGTAAT
1 AATATATATGGTAAT
364017 GTTCTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:364060 original size:14 final size:15
Alignment explanation
Indices: 364035--364063 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
364025 CATTGCCTTC
364035 AATATATATGGTAAT
1 AATATATATGGTAAT
364050 AATAT-TATGGTAAT
1 AATATATATGGTAAT
364064 GTTCTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:364107 original size:14 final size:15
Alignment explanation
Indices: 364082--364110 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
364072 CATTGCCTTC
364082 AATATATATGGTAAT
1 AATATATATGGTAAT
364097 AATAT-TATGGTAAT
1 AATATATATGGTAAT
364111 GTTCTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:364154 original size:14 final size:15
Alignment explanation
Indices: 364129--364157 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
364119 CATTGCCTTC
364129 AATATATATGGTAAT
1 AATATATATGGTAAT
364144 AATAT-TATGGTAAT
1 AATATATATGGTAAT
364158 GTTCTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:364201 original size:14 final size:15
Alignment explanation
Indices: 364176--364204 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
364166 CATTGCCTTC
364176 AATATATATGGTAAT
1 AATATATATGGTAAT
364191 AATAT-TATGGTAAT
1 AATATATATGGTAAT
364205 GTTCTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:364248 original size:14 final size:15
Alignment explanation
Indices: 364223--364251 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
364213 CATTGCCTTC
364223 AATATATATGGTAAT
1 AATATATATGGTAAT
364238 AATAT-TATGGTAAT
1 AATATATATGGTAAT
364252 GTTCTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:364295 original size:14 final size:15
Alignment explanation
Indices: 364270--364298 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
364260 CATTGCCTTC
364270 AATATATATGGTAAT
1 AATATATATGGTAAT
364285 AATAT-TATGGTAAT
1 AATATATATGGTAAT
364299 GTTCTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:364342 original size:14 final size:15
Alignment explanation
Indices: 364317--364345 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
364307 CATTGCCTTC
364317 AATATATATGGTAAT
1 AATATATATGGTAAT
364332 AATAT-TATGGTAAT
1 AATATATATGGTAAT
364346 TGCTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
AATATATATGGTAAT
Found at i:364864 original size:14 final size:14
Alignment explanation
Indices: 364845--364886 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
364835 TTATATTTTA
364845 AAAAAATTTAATAT
1 AAAAAATTTAATAT
**
364859 AAAAAATAAAATTAT
1 AAAAAATTTAA-TAT
364874 AAAAAA-TTAATAT
1 AAAAAATTTAATAT
364887 GGGTCGAGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAAATTTAATAT
Found at i:386460 original size:21 final size:20
Alignment explanation
Indices: 386432--386470 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
386422 CACTTCCACC
* *
386432 TTTTATATTTTCTGAATTGA
1 TTTTATATATTCTCAATTGA
386452 TTTTGATATATTCTCAATT
1 TTTT-ATATATTCTCAATT
386471 TAATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTTATATATTCTCAATTGA
Found at i:388013 original size:16 final size:16
Alignment explanation
Indices: 387992--388022 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
387982 CGCTCTCCAA
387992 CCTCACAAGAATAAAC
1 CCTCACAAGAATAAAC
388008 CCTCACAAGAATAAA
1 CCTCACAAGAATAAA
388023 TGGTGTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.29, G:0.06, T:0.13
Consensus pattern (16 bp):
CCTCACAAGAATAAAC
Found at i:397113 original size:4 final size:4
Alignment explanation
Indices: 397104--397150 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
397094 TGACCCCTAT
397104 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
397151 TATCGTCGGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:398894 original size:80 final size:80
Alignment explanation
Indices: 398761--398922 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 80
398751 AATCTTTGGG
398761 TATGATGATGATAACCACCTTTTTTTTTTTTTGTTATTAAGACAACCAACGCGTAGAAGCTCCCT
1 TATGATGATGATAACCACCTTTTTTTTTTTTTGTTATTAAGACAACCAACGCGTAGAAGCTCCCT
398826 AGAATGGTAAACTTT
66 AGAATGGTAAACTTT
*
398841 TATGATTATGATAACCACCTTTTTTTTTTTTTGTTATTAAGACAACCAACGCGTAGAAGCTCCCT
1 TATGATGATGATAACCACCTTTTTTTTTTTTTGTTATTAAGACAACCAACGCGTAGAAGCTCCCT
398906 AGAATGGTAAACTTT
66 AGAATGGTAAACTTT
398921 TA
1 TA
398923 ATTTTAGTTC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (80 bp):
TATGATGATGATAACCACCTTTTTTTTTTTTTGTTATTAAGACAACCAACGCGTAGAAGCTCCCT
AGAATGGTAAACTTT
Found at i:402075 original size:81 final size:81
Alignment explanation
Indices: 401960--402121 Score: 306
Period size: 81 Copynumber: 2.0 Consensus size: 81
401950 CTTTTCTCTG
*
401960 CCTTACAATATTTTATTTCCGAATCTTTGACTTTTCCTTTCTTTATTACTAATTCTTAATAGTGG
1 CCTTACAATATTTTATTTCCGAAGCTTTGACTTTTCCTTTCTTTATTACTAATTCTTAATAGTGG
402025 AACTTGTTTTTCTTAT
66 AACTTGTTTTTCTTAT
*
402041 CCTTACAATATTTTATTTCCGAAGCTTTGTCTTTTCCTTTCTTTATTACTAATTCTTAATAGTGG
1 CCTTACAATATTTTATTTCCGAAGCTTTGACTTTTCCTTTCTTTATTACTAATTCTTAATAGTGG
402106 AACTTGTTTTTCTTAT
66 AACTTGTTTTTCTTAT
402122 TTCTTTCTTC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.22, C:0.17, G:0.08, T:0.53
Consensus pattern (81 bp):
CCTTACAATATTTTATTTCCGAAGCTTTGACTTTTCCTTTCTTTATTACTAATTCTTAATAGTGG
AACTTGTTTTTCTTAT
Found at i:402240 original size:51 final size:51
Alignment explanation
Indices: 402144--402240 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
402134 TTGTGTTTTC
* * * *
402144 TGCTTTCATGTTCCAATTTTGTATTTTTTATTGGAAATTATAATTACCTTT
1 TGCTTTCATGTTCCAATTTTGAATATTTTATAGGAAAATATAATTACCTTT
* *
402195 TGCTTTCATGTTCCAATTTTGAAATATTTTCTAGTAAAATA-AATTA
1 TGCTTTCATGTTCCAATTTTG-AATATTTTATAGGAAAATATAATTA
402241 AAAAAGGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 26 0.67
52 13 0.33
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (51 bp):
TGCTTTCATGTTCCAATTTTGAATATTTTATAGGAAAATATAATTACCTTT
Found at i:405843 original size:8 final size:8
Alignment explanation
Indices: 405830--405865 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
405820 TGATCACATG
405830 TTTGTTTT
1 TTTGTTTT
405838 TTTGTTTT
1 TTTGTTTT
*
405846 TTTTTTTT
1 TTTGTTTT
405854 TTTGCTTTT
1 TTTG-TTTT
405863 TTT
1 TTT
405866 TACTTGCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (8 bp):
TTTGTTTT
Found at i:413406 original size:56 final size:55
Alignment explanation
Indices: 413331--413452 Score: 138
Period size: 56 Copynumber: 2.2 Consensus size: 55
413321 TTAAAAAAAT
* * *
413331 TTGGTTGTCGTCGGTATGTCAGGCAACACCAGTAAATATTTAATAAAAAAAAT-TTTG
1 TTGG-TGTCGCCGGAATGTCAGACAACACCAGTAAA-ATTTAA-AAAAAAAATATTTG
* * * *
413388 TTGGTGTCGCCGGAATGTCAGACGACACCCGTTAAATTTAAAAAAAAAATATTTT
1 TTGGTGTCGCCGGAATGTCAGACAACACCAGTAAAATTTAAAAAAAAAATATTTG
413443 TTAGGTGTCG
1 TT-GGTGTCG
413453 TTGTCGTGTC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
54 9 0.16
55 11 0.20
56 32 0.57
57 4 0.07
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (55 bp):
TTGGTGTCGCCGGAATGTCAGACAACACCAGTAAAATTTAAAAAAAAAATATTTG
Found at i:413521 original size:11 final size:11
Alignment explanation
Indices: 413505--413531 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
413495 TTGCAGAAAG
413505 AATATTTAAAA
1 AATATTTAAAA
413516 AATATTTAAAA
1 AATATTTAAAA
413527 AATAT
1 AATAT
413532 ATATTGCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATTTAAAA
Found at i:414007 original size:47 final size:46
Alignment explanation
Indices: 413929--414037 Score: 130
Period size: 47 Copynumber: 2.3 Consensus size: 46
413919 ATTTAATATT
* * *
413929 TTATTATTTTCCACATCTGATATTTTATTTCC-TTTCTCATATTTGA
1 TTATTATTTTCCATATATGATATTCTATTTCCTTTTCT-ATATTTGA
* *
413975 TTATGTATTTTCCATATATGTTATTCTCTTTCCTTTTCTATATTTGA
1 TTAT-TATTTTCCATATATGATATTCTATTTCCTTTTCTATATTTGA
*
414022 TTCTCTATTTTCCATA
1 TTAT-TATTTTCCATA
414038 AAATATTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
46 4 0.07
47 45 0.83
48 5 0.09
ACGTcount: A:0.20, C:0.17, G:0.05, T:0.58
Consensus pattern (46 bp):
TTATTATTTTCCATATATGATATTCTATTTCCTTTTCTATATTTGA
Found at i:414084 original size:84 final size:84
Alignment explanation
Indices: 413980--414188 Score: 249
Period size: 84 Copynumber: 2.5 Consensus size: 84
413970 TTTGATTATG
* * * * * * *
413980 TATTTTCCATATATGTTATTCTCTTTCCTTTTCTATATTTGATTCTCTATTTTCCATAAAATATT
1 TATTTTCTATATTTGTTATTCTCTTTCCTTTCCTATATTAGATTCTCCATTTTCAACAAAATATT
414045 AAATT-TCCTTTCATATCTC
66 AAATTCT-CTTTCATATCTC
*
414064 TATTTTCTATATTTGTTATTCTATTTCCTTTCCTATATTAGATTCTCCATTTTCAACAAAATATT
1 TATTTTCTATATTTGTTATTCTCTTTCCTTTCCTATATTAGATTCTCCATTTTCAACAAAATATT
* *
414129 CAATTCTCTTTCATATTTC
66 AAATTCTCTTTCATATCTC
* * * * *
414148 TATTGTACATATAGTTGTTATTCTCTTGCATTTCCCATATT
1 TATT-TTC-TATATTTGTTATTCTCTTTCCTTTCCTATATT
414189 GACATTCATT
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
84 76 0.72
85 3 0.03
86 27 0.25
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.54
Consensus pattern (84 bp):
TATTTTCTATATTTGTTATTCTCTTTCCTTTCCTATATTAGATTCTCCATTTTCAACAAAATATT
AAATTCTCTTTCATATCTC
Found at i:414971 original size:17 final size:17
Alignment explanation
Indices: 414949--414982 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
414939 GATAACAACT
414949 ACTTATCACTTAATGAA
1 ACTTATCACTTAATGAA
414966 ACTTATCACTTAATGAA
1 ACTTATCACTTAATGAA
414983 GAATACTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (17 bp):
ACTTATCACTTAATGAA
Found at i:415686 original size:85 final size:85
Alignment explanation
Indices: 415538--415735 Score: 288
Period size: 85 Copynumber: 2.3 Consensus size: 85
415528 TATGGAAAAC
* * * *
415538 CGCCGCTATAGAACGTGACCTTTAGCTGCGCTTTTCCACAAACGACACTAAAGAACATGACCTTT
1 CGCCGCTATAGAACATGACCTTTAGCGGCGCTGTCCCACAAACGACACTAAAGAACATGACCTTT
*
415603 AGCGGCTCTTTCCCCACAAA
66 AGCGGCGCTTTCCCCACAAA
* * *
415623 CGCCACTATAGAACATGACCTTTAGCGGCGCTGTCCCACAAACGCCGCTAAAGAACATGACCTTT
1 CGCCGCTATAGAACATGACCTTTAGCGGCGCTGTCCCACAAACGACACTAAAGAACATGACCTTT
415688 AGCGGCGCTTTCCCCACAAA
66 AGCGGCGCTTTCCCCACAAA
* * * *
415708 CGCGGTTAAAAAACATGACCTTTAGCGG
1 CGCCGCTATAGAACATGACCTTTAGCGG
415736 TACTTTCNNN
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 100 1.00
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (85 bp):
CGCCGCTATAGAACATGACCTTTAGCGGCGCTGTCCCACAAACGACACTAAAGAACATGACCTTT
AGCGGCGCTTTCCCCACAAA
Found at i:415742 original size:43 final size:43
Alignment explanation
Indices: 415538--415735 Score: 265
Period size: 43 Copynumber: 4.7 Consensus size: 43
415528 TATGGAAAAC
* * * *
415538 CGCCGCTATAGAACGTGACCTTTAGCTGCGCTTT-TCCACAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCACAAA
* * *
415580 CGACACTAAAGAACATGACCTTTAGCGGCTCTTTCCCCACAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCACAAA
* * *
415623 CGCCACTATAGAACATGACCTTTAGCGGCGCTGT-CCCACAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCACAAA
415665 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCACAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCACAAA
* * *
415708 CGCGGTTAAAAAACATGACCTTTAGCGG
1 CGCCGCTAAAGAACATGACCTTTAGCGG
415736 TACTTTCNNN
Statistics
Matches: 137, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
42 67 0.49
43 70 0.51
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (43 bp):
CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCACAAA
Found at i:418180 original size:13 final size:13
Alignment explanation
Indices: 418162--418186 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
418152 GAATTTACTT
418162 GTGTGAAAATTTC
1 GTGTGAAAATTTC
418175 GTGTGAAAATTT
1 GTGTGAAAATTT
418187 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:419265 original size:63 final size:63
Alignment explanation
Indices: 419186--419509 Score: 179
Period size: 63 Copynumber: 5.0 Consensus size: 63
419176 ATATATATGT
* * *
419186 TTTGAATTTTATAAGTTAAAATAAAATGTATGAATTGTATATATATGTGTTAGTC-AATGTATA
1 TTTGAGTTTTATAAGTTAAAATAAAATGTATGAATTCTATATATAT-TGTTAGCCGAATGTATA
* * *
419249 TTTGAGTTTTATAAGTTAAAAT-AAAT-TACAGAAATTCTATAGATA-T-TTAGCCGAATATATA
1 TTTGAGTTTTATAAGTTAAAATAAAATGTA-TG-AATTCTATATATATTGTTAGCCG-A-ATGTA
419310 TA
62 TA
* * * * * *
419312 TGTTGGGTTTTGTAAGTT-GAATGAAATTTAATGAA-T-TACATATA-TGTTAGCCGAATGTATA
1 T-TTGAGTTTTATAAGTTAAAATAAAATGT-ATGAATTCTATATATATTGTTAGCCGAATG----
419373 TATA
60 TATA
* * *
419377 TGTTTTGAATTTTATAAGTTAAAATAAAATGTATGAATTGTATATATATATATATGTGTTAGTC-
1 ---TTTGAGTTTTATAAGTTAAAATAAAATGTATG-A----AT-TCTATATATAT-TGTTAGCCG
*
419441 AAAGTATA
56 AATGTATA
* * * * *
419449 TTTGAG-TTTATAAGATAAAATAAATTGCATAAATTCTATATATA-T-TTAGCCGAATATATA
1 TTTGAGTTTTATAAGTTAAAATAAAATGTATGAATTCTATATATATTGTTAGCCGAATGTATA
419509 T
1 T
419510 ATATGCTGAG
Statistics
Matches: 201, Mismatches: 31, Indels: 61
0.69 0.11 0.21
Matches are distributed among these distances:
59 5 0.02
60 13 0.06
61 5 0.02
62 23 0.11
63 52 0.26
64 20 0.10
65 6 0.03
66 1 0.00
67 17 0.08
68 31 0.15
69 5 0.02
72 5 0.02
74 1 0.00
75 7 0.03
76 3 0.01
77 7 0.03
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (63 bp):
TTTGAGTTTTATAAGTTAAAATAAAATGTATGAATTCTATATATATTGTTAGCCGAATGTATA
Found at i:419368 original size:194 final size:196
Alignment explanation
Indices: 419161--419569 Score: 671
Period size: 201 Copynumber: 2.1 Consensus size: 196
419151 TTGTATAAAA
419161 ATGTTAGCCGAATGTATATATATGTTTTGAATTTTATAAGTTAAAATAAAATGTATGAATTG-TA
1 ATGTTAGCCGAATGTATATATATGTTTTGAATTTTATAAGTTAAAATAAAATGTATGAATTGATA
* *
419225 TATATATGTGTTAGTCAATGTATATTTGAGTTTTATAAGTTAAAATAAATTACAGAAATTCTATA
66 TATATATGTGTTAGTCAAAGTATATTTGAG-TTTATAAGATAAAATAAATTACAGAAATTCTATA
* * *
419290 GATATTTAGCCG-A-ATATATATATGTTGGGTTTTGTAAGTTGAATGAAATTTAATGAATTACAT
130 GATATTTAGCCGAATATATATATATGCTGAGCTTTGTAAGTTGAATGAAATTTAATGAATTACAT
419353 AT
195 AT
419355 ATGTTAGCCGAATGTATATATATGTTTTGAATTTTATAAGTTAAAATAAAATGTATGAATTGTAT
1 ATGTTAGCCGAATGTATATATATGTTTTGAATTTTATAAGTTAAAATAAAATGTATGAATTG---
* *
419420 ATATATATATATGTGTTAGTCAAAGTATATTTGAGTTTATAAGATAAAATAAATTGCATAAATTC
63 --ATATATATATGTGTTAGTCAAAGTATATTTGAGTTTATAAGATAAAATAAATTACAGAAATTC
*
419485 TATATATATTTAGCCGAATATATATATATGCTGAGCTTTGTAAGTTGAATGAAATTTAATGAATT
126 TATAGATATTTAGCCGAATATATATATATGCTGAGCTTTGTAAGTTGAATGAAATTTAATGAATT
419550 ACATAT
191 ACATAT
419556 ATGTTAGCCGAATG
1 ATGTTAGCCGAATG
419570 CATGTATTGA
Statistics
Matches: 199, Mismatches: 8, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
194 62 0.31
199 42 0.21
200 32 0.16
201 63 0.32
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (196 bp):
ATGTTAGCCGAATGTATATATATGTTTTGAATTTTATAAGTTAAAATAAAATGTATGAATTGATA
TATATATGTGTTAGTCAAAGTATATTTGAGTTTATAAGATAAAATAAATTACAGAAATTCTATAG
ATATTTAGCCGAATATATATATATGCTGAGCTTTGTAAGTTGAATGAAATTTAATGAATTACATA
T
Found at i:419951 original size:41 final size:41
Alignment explanation
Indices: 419905--420078 Score: 224
Period size: 41 Copynumber: 4.2 Consensus size: 41
419895 GGCTCGATGC
* *
419905 CTAGCAGGTTTAATACCGGTGAATTATTTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
* * *
419946 TTAGCAGGATTAATGCCGGTGAATTATTTCAGACTTTATAT
1 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
*
419987 CTAGCAGGCTTAATGCCAGTGAATTATTTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
* * * * *
420028 CTAGCAGGCTTAAGGCTGGTGAAATGA-TTCGGACTTTAAGT
1 CTAGCAGGCTTAATGCCGGTG-AATTATTTCAGACTTTATGT
*
420069 CCAGCAGGCT
1 CTAGCAGGCT
420079 AAGTGCCAGT
Statistics
Matches: 117, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
41 113 0.97
42 4 0.03
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.34
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
Found at i:420116 original size:41 final size:41
Alignment explanation
Indices: 420071--420167 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 41
420061 CTTTAAGTCC
*
420071 AGCAGGCTAAGTGCCAGTGATCTGAATCAAGTTATAAACCT
1 AGCAGGCTAAGTGCCAGTGATCTGAATCAAGCTATAAACCT
* * * *
420112 AGCAGGCTAAGTACCGGTGATCTGAATCAGGCTATAAGCCT
1 AGCAGGCTAAGTGCCAGTGATCTGAATCAAGCTATAAACCT
420153 AGCAGGCTAAGTGCC
1 AGCAGGCTAAGTGCC
420168 CATGAATATG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (41 bp):
AGCAGGCTAAGTGCCAGTGATCTGAATCAAGCTATAAACCT
Found at i:423766 original size:41 final size:37
Alignment explanation
Indices: 423720--423862 Score: 147
Period size: 36 Copynumber: 3.8 Consensus size: 37
423710 TGTGATTTTC
423720 ATATATTTTGATCCAAAGTTTTATGTAAGTTATGATATGAT
1 ATATATTTTGAT---AAG-TTTATGTAAGTTATGATATGAT
423761 ATATATATTT-AT--GTATTATGTAAGTTATGATATGAT
1 ATATAT-TTTGATAAGT-TTATGTAAGTTATGATATGAT
*
423797 ATATATTTTTG-TAAG-TTACGTAAGTTATGATATGAT
1 ATATA-TTTTGATAAGTTTATGTAAGTTATGATATGAT
*
423833 ATATACTTATG-TAAG-TTATGTAAGTTATGA
1 ATATA-TTTTGATAAGTTTATGTAAGTTATGA
423863 AATTTGAACT
Statistics
Matches: 92, Mismatches: 4, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
35 1 0.01
36 78 0.85
37 1 0.01
38 1 0.01
41 8 0.09
42 3 0.03
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (37 bp):
ATATATTTTGATAAGTTTATGTAAGTTATGATATGAT
Found at i:423781 original size:36 final size:38
Alignment explanation
Indices: 423740--423862 Score: 186
Period size: 36 Copynumber: 3.4 Consensus size: 38
423730 ATCCAAAGTT
423740 TTATGTAAGTTATGATATGATATATATATTTATGT-A-
1 TTATGTAAGTTATGATATGATATATATATTTATGTAAG
423776 TTATGTAAGTTATGATATGATATATAT-TTT-TGTAAG
1 TTATGTAAGTTATGATATGATATATATATTTATGTAAG
* *
423812 TTACGTAAGTTATGATATG--ATATATACTTATGTAAG
1 TTATGTAAGTTATGATATGATATATATATTTATGTAAG
423848 TTATGTAAGTTATGA
1 TTATGTAAGTTATGA
423863 AATTTGAACT
Statistics
Matches: 80, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
34 9 0.11
35 6 0.08
36 65 0.81
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (38 bp):
TTATGTAAGTTATGATATGATATATATATTTATGTAAG
Found at i:423853 original size:9 final size:9
Alignment explanation
Indices: 423740--423861 Score: 54
Period size: 9 Copynumber: 13.6 Consensus size: 9
423730 ATCCAAAGTT
423740 TTATGTAAG
1 TTATGTAAG
*
423749 TTATGATATG
1 TTATG-TAAG
* * *
423759 ATATATATAT
1 TTATGTA-AG
423769 TTATGT-A-
1 TTATGTAAG
423776 TTATGTAAG
1 TTATGTAAG
*
423785 TTATGATATG
1 TTATG-TAAG
* * *
423795 ATATAT-AT
1 TTATGTAAG
*
423803 TTTTGTAAG
1 TTATGTAAG
*
423812 TTACGTAAG
1 TTATGTAAG
*
423821 TTATGATATG
1 TTATG-TAAG
* * *
423831 ATATAT-AC
1 TTATGTAAG
423839 TTATGTAAG
1 TTATGTAAG
423848 TTATGTAAG
1 TTATGTAAG
423857 TTATG
1 TTATG
423862 AAATTTGAAC
Statistics
Matches: 78, Mismatches: 27, Indels: 16
0.64 0.22 0.13
Matches are distributed among these distances:
7 6 0.08
8 9 0.12
9 41 0.53
10 22 0.28
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:425968 original size:23 final size:23
Alignment explanation
Indices: 425938--425982 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
425928 AGTTTGCAAG
425938 TATAGGACAATGAAGGCTTTAAA
1 TATAGGACAATGAAGGCTTTAAA
425961 TATAGGACAATGAAGGCTTTAA
1 TATAGGACAATGAAGGCTTTAA
425983 CAGTTTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (23 bp):
TATAGGACAATGAAGGCTTTAAA
Found at i:439731 original size:28 final size:27
Alignment explanation
Indices: 439686--439748 Score: 108
Period size: 28 Copynumber: 2.3 Consensus size: 27
439676 AATTTTGATT
*
439686 CAAACTTTCAAGTTTGACTTGATCAAC
1 CAAATTTTCAAGTTTGACTTGATCAAC
439713 CAGAATTTTCAAGTTTGACTTGATCAAC
1 CA-AATTTTCAAGTTTGACTTGATCAAC
439741 CAAATTTT
1 CAAATTTT
439749 AACATGAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 8 0.24
28 26 0.76
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (27 bp):
CAAATTTTCAAGTTTGACTTGATCAAC
Found at i:441767 original size:13 final size:13
Alignment explanation
Indices: 441749--441778 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
441739 AATATTTATA
*
441749 AAAGATCGAACCC
1 AAAGATCAAACCC
441762 AAAGATCAAACCC
1 AAAGATCAAACCC
441775 AAAG
1 AAAG
441779 GAAAAGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.27, G:0.13, T:0.07
Consensus pattern (13 bp):
AAAGATCAAACCC
Found at i:442149 original size:19 final size:18
Alignment explanation
Indices: 442121--442156 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
442111 AAGCAGCTAT
442121 AAAAGTAAAACTTAAGAA
1 AAAAGTAAAACTTAAGAA
*
442139 AAAATGTAAAAGTTAAGA
1 AAAA-GTAAAACTTAAGA
442157 TTTTCATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.64, C:0.03, G:0.14, T:0.19
Consensus pattern (18 bp):
AAAAGTAAAACTTAAGAA
Found at i:442485 original size:11 final size:11
Alignment explanation
Indices: 442455--442496 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
442445 ACCTAAGTGC
*
442455 AGAGAAAAACT
1 AGAGAAAACCT
*
442466 AAAGAAAACCT
1 AGAGAAAACCT
*
442477 AGAGAAAACTT
1 AGAGAAAACCT
442488 AGAGAAAAC
1 AGAGAAAAC
442497 TAAACCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.62, C:0.12, G:0.17, T:0.10
Consensus pattern (11 bp):
AGAGAAAACCT
Found at i:446041 original size:12 final size:12
Alignment explanation
Indices: 446022--446050 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
446012 TATGATTAAA
446022 AATA-TTATCTT
1 AATATTTATCTT
446033 AATATTTATCTT
1 AATATTTATCTT
446045 AATATT
1 AATATT
446051 AATTAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (12 bp):
AATATTTATCTT
Found at i:451442 original size:22 final size:21
Alignment explanation
Indices: 451417--451465 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
451407 TTTTATTTTT
*
451417 ATTTATGTTT-ATTGCCTATTTA
1 ATTT-TGTTTAATTG-CAATTTA
451439 ATTTTGTTTTAATTGCAATTTA
1 ATTTTG-TTTAATTGCAATTTA
451461 ATTTT
1 ATTTT
451466 TGTTCCTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.08
22 18 0.75
23 4 0.17
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.61
Consensus pattern (21 bp):
ATTTTGTTTAATTGCAATTTA
Found at i:461429 original size:15 final size:15
Alignment explanation
Indices: 461399--461430 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
461389 TTAGATACGC
461399 AATTAAATTTTAAAA
1 AATTAAATTTTAAAA
461414 AATTACAATTTTAAAA
1 AATTA-AATTTTAAAA
461430 A
1 A
461431 GTTGTCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTAAATTTTAAAA
Found at i:462228 original size:26 final size:27
Alignment explanation
Indices: 462190--462242 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
462180 TTTAAAATCT
* *
462190 AAAAATTAGAAGA-ATTAAATTTTTAAA
1 AAAAAGTAGAAGAGACT-AATTTTTAAA
462217 AAAAAGTA-AAGAGACTAATTTTTAAA
1 AAAAAGTAGAAGAGACTAATTTTTAAA
462243 TTTACAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (27 bp):
AAAAAGTAGAAGAGACTAATTTTTAAA
Found at i:480951 original size:14 final size:14
Alignment explanation
Indices: 480930--480963 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
480920 TGGTATGGGT
480930 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
480943 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
480957 TTATAGG
1 TTATAGG
480964 AAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:481287 original size:15 final size:15
Alignment explanation
Indices: 481267--481317 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
481257 ACAACATGAT
481267 AACGTAAATGACTAA
1 AACGTAAATGACTAA
* *
481282 AACGTAACAT--TTCA
1 AACGTAA-ATGACTAA
*
481296 AACATAAATGACTAA
1 AACGTAAATGACTAA
481311 AACGTAA
1 AACGTAA
481318 CCTAAGGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 15 0.56
16 2 0.07
ACGTcount: A:0.53, C:0.16, G:0.10, T:0.22
Consensus pattern (15 bp):
AACGTAAATGACTAA
Found at i:482385 original size:15 final size:15
Alignment explanation
Indices: 482367--482416 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
482357 GATATGGGTA
482367 TCAAATATTGGAAAG
1 TCAAATATTGGAAAG
* **
482382 TCAAAGATATGGGTA-
1 TCAAATAT-TGGAAAG
482397 TCAAATATTGGAAAG
1 TCAAATATTGGAAAG
482412 TCAAA
1 TCAAA
482417 GATATGGGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 19 0.70
16 4 0.15
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (15 bp):
TCAAATATTGGAAAG
Found at i:482389 original size:30 final size:30
Alignment explanation
Indices: 482353--482438 Score: 154
Period size: 30 Copynumber: 2.8 Consensus size: 30
482343 TCTTTGCAAG
482353 CAAAGATATGGGTATCAAATATTGGAAAGT
1 CAAAGATATGGGTATCAAATATTGGAAAGT
482383 CAAAGATATGGGTATCAAATATTGGAAAGT
1 CAAAGATATGGGTATCAAATATTGGAAAGT
*
482413 CAAAGATATGGGTATCGAGATATTGG
1 CAAAGATATGGGTATC-AAATATTGG
482439 CATAATAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 46 0.85
31 8 0.15
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.27
Consensus pattern (30 bp):
CAAAGATATGGGTATCAAATATTGGAAAGT
Found at i:487035 original size:15 final size:15
Alignment explanation
Indices: 487015--487092 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
487005 TTTATGGAAA
487015 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
487030 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
487044 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
487060 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
487074 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
487090 ATC
1 ATC
487093 GAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:487052 original size:30 final size:30
Alignment explanation
Indices: 487011--487092 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
487001 CATATTTATG
*
487011 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
487041 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
487071 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
487093 GAGATATTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:490197 original size:12 final size:12
Alignment explanation
Indices: 490169--490200 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
490159 TATTTTTTAT
490169 GAGAT-AATTAA
1 GAGATAAATTAA
490180 -AGATAAATTAA
1 GAGATAAATTAA
490191 GAGATAAATT
1 GAGATAAATT
490201 CAACTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.21
11 6 0.32
12 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (12 bp):
GAGATAAATTAA
Found at i:493970 original size:23 final size:22
Alignment explanation
Indices: 493940--493984 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
493930 TGTTAAGAGT
*
493940 TATATTTT-TAATTGATATTTAA
1 TATATTTTATAA-TGAAATTTAA
493962 TATACTTTTATAATGAAATTTAA
1 TATA-TTTTATAATGAAATTTAA
493985 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 13 0.65
24 3 0.15
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (22 bp):
TATATTTTATAATGAAATTTAA
Found at i:496092 original size:26 final size:26
Alignment explanation
Indices: 496019--496094 Score: 102
Period size: 25 Copynumber: 3.0 Consensus size: 26
496009 CAAAGTCCCG
* * *
496019 ATTCATAGCTCGTGTGAGTAATTTAT
1 ATTCACAGCTCGTGTGAGCAAATTAT
*
496045 -TTCACAGCTCGTGTTAGC-AATTAT
1 ATTCACAGCTCGTGTGAGCAAATTAT
496069 ATTCACAGCTCGTGTGAGCAAATTAT
1 ATTCACAGCTCGTGTGAGCAAATTAT
496095 GTCATGTGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
24 5 0.12
25 32 0.74
26 6 0.14
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (26 bp):
ATTCACAGCTCGTGTGAGCAAATTAT
Found at i:498329 original size:15 final size:16
Alignment explanation
Indices: 498295--498341 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
498285 CAGTTATTCG
*
498295 GAACAACCTCAATATTGA
1 GAACAA-CTC-ATGTTGA
498313 GAACAACT-ATGTTGA
1 GAACAACTCATGTTGA
498328 GAACAACTCATGTT
1 GAACAACTCATGTT
498342 TGGAACAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 14 0.52
16 5 0.19
17 2 0.07
18 6 0.22
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (16 bp):
GAACAACTCATGTTGA
Found at i:504591 original size:24 final size:24
Alignment explanation
Indices: 504536--504593 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
504526 GTTACATAAA
* * *
504536 AATTCAAAATACTAATTTAAAAAT
1 AATTTAAAATAATAATTCAAAAAT
** *
504560 AAGATAAAATAATAATTCAAAATT
1 AATTTAAAATAATAATTCAAAAAT
504584 AATTTAAAAT
1 AATTTAAAAT
504594 CAAGATAATA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (24 bp):
AATTTAAAATAATAATTCAAAAAT
Found at i:504592 original size:35 final size:37
Alignment explanation
Indices: 504531--504606 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
504521 AGATAGTTAC
504531 ATAAAAATTCAAAATACTAATTTAAAAAT-AAGATAA-A
1 ATAAAAATTCAAAATA-TAATTT-AAAATCAAGATAATA
*
504568 ATAATAATTCAAAAT-TAATTTAAAATCAAGATAATA
1 ATAAAAATTCAAAATATAATTTAAAATCAAGATAATA
504604 ATA
1 ATA
504607 GCTAATCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
34 5 0.14
35 13 0.36
36 4 0.11
37 14 0.39
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (37 bp):
ATAAAAATTCAAAATATAATTTAAAATCAAGATAATA
Found at i:506391 original size:28 final size:28
Alignment explanation
Indices: 506341--506394 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
506331 AACTTAACCT
**
506341 TTCTCTTCCCTTTTTTTTTTCTTTTCCA
1 TTCTCTTCCCTTTTTTAGTTCTTTTCCA
506369 TTCT-TTCCCTTTTATTAGTTCTTTTC
1 TTCTCTTCCCTTTT-TTAGTTCTTTTC
506395 TTCAGCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.67
Consensus pattern (28 bp):
TTCTCTTCCCTTTTTTAGTTCTTTTCCA
Found at i:516932 original size:106 final size:106
Alignment explanation
Indices: 516747--517053 Score: 596
Period size: 106 Copynumber: 2.9 Consensus size: 106
516737 AAGCTTTAAG
* *
516747 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCAAAACCCAGCACGTTAGGGCACGTTTTCTCGA
516812 TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
66 TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
516853 AGGATATTTGGCTATTTGGTCGAACGAGAAATCAAAACCCAGCACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCAAAACCCAGCACGTTAGGGCACGTTTTCTCGA
516918 TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
66 TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
516959 AGGATATTTGGCTATTTGGTCGAACGAGAAATCAAAACCCAGCACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCAAAACCCAGCACGTTAGGGCACGTTTTCTCGA
517024 TTTTCCAAACGCGAAATATTGCCTTATTTA
66 TTTTCCAAACGCGAAATATTGCCTTATTTA
517054 GAAAATTTTT
Statistics
Matches: 199, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 199 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (106 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAATCAAAACCCAGCACGTTAGGGCACGTTTTCTCGA
TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
Found at i:517574 original size:38 final size:38
Alignment explanation
Indices: 517515--517620 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
517505 TATTTTTAAG
*
517515 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
517552 AATATGTATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
517590 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
517621 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:517955 original size:22 final size:23
Alignment explanation
Indices: 517899--517955 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
517889 AGTTTAAAAT
517899 AAAATATATAAAAGAAAGTCTTA
1 AAAATATATAAAAGAAAGTCTTA
*
517922 AATAATA-A-AAAAGACAGT-TTA
1 AA-AATATATAAAAGAAAGTCTTA
517943 AAAATATATAAAA
1 AAAATATATAAAA
517956 ATAGTGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 13 0.43
23 3 0.10
24 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAATATATAAAAGAAAGTCTTA
Found at i:518684 original size:13 final size:13
Alignment explanation
Indices: 518666--518690 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
518656 AAATGCGTAG
518666 ATAAATAAATGAA
1 ATAAATAAATGAA
518679 ATAAATAAATGA
1 ATAAATAAATGA
518691 TAGATGATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
ATAAATAAATGAA
Found at i:524423 original size:16 final size:16
Alignment explanation
Indices: 524402--524435 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
524392 TTGGACTTTC
524402 TTAGGTGTAAAATAAT
1 TTAGGTGTAAAATAAT
524418 TTAGGTGTAAAATAAT
1 TTAGGTGTAAAATAAT
524434 TT
1 TT
524436 GTAGGATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (16 bp):
TTAGGTGTAAAATAAT
Found at i:527376 original size:70 final size:70
Alignment explanation
Indices: 527263--527401 Score: 251
Period size: 70 Copynumber: 2.0 Consensus size: 70
527253 AAATAAAATA
*
527263 AAATGAAATAAAACGAATAGAAAACAGTAAAGGTTTAACCTTTTTGAACTTCTATTTTTGCTATT
1 AAATGAAATAAAACGAACAGAAAACAGTAAAGGTTTAACCTTTTTGAACTTCTATTTTTGCTATT
527328 TTGAG
66 TTGAG
* *
527333 AAATGAAATAAAACGAACAGAAAACAGTAAAGGTTTAACCTTTTTGAACTTCTATTTTTGTTGTT
1 AAATGAAATAAAACGAACAGAAAACAGTAAAGGTTTAACCTTTTTGAACTTCTATTTTTGCTATT
527398 TTGA
66 TTGA
527402 TTTATAATGT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (70 bp):
AAATGAAATAAAACGAACAGAAAACAGTAAAGGTTTAACCTTTTTGAACTTCTATTTTTGCTATT
TTGAG
Found at i:528369 original size:45 final size:45
Alignment explanation
Indices: 528311--529591 Score: 1755
Period size: 45 Copynumber: 28.3 Consensus size: 45
528301 GCAGGAAAGT
*
528311 AAGATCTGTTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
528356 AAGATCTGCTATCTTCAGTCTACCTT-GCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTA-CTTCGCTGCCAATACAGGAAGAC
* * *
528401 AAGA-CTTGCTATATTC-GATCTACTTCGCTGCCAGTACAGAAAGAC
1 AAGATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
* *
528446 ATGATCTGCTATCTTCAGTCTACTTTGCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
* * *
528491 GAGA-CTTGCTATCTTC-GATCTACTTTGTTGCCAATACAGGAAGAC
1 AAGATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
528536 AAGATCTGCTATCTTCAGTCTACCTT-GCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTA-CTTCGCTGCCAATACAGGAAGAC
528581 AAGA-CTTGCTATCTTC-GATCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
528626 AAGATCTGCTATCTTCAGTCTACCTT-GCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTA-CTTCGCTGCCAATACAGGAAGAC
528671 AAGA-CTTGCTATCTTC-GATCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
528716 AAGATCTGCTATCTTCAGTCTACCTT-GCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTA-CTTCGCTGCCAATACAGGAAGAC
* * * *
528761 AAGACTTGCTATATATGTTATCTTCAGTCTATTTTGCTGCCAATACAGGAAGAT
1 AAGA--T-C------TGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
*
528815 AAGA-CTTGCTATCTT-TGATCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
528860 AAGATCTGCTATCTTCAGTCTACCTT-GCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTA-CTTCGCTGCCAATACAGGAAGAC
528905 AAGA-CTTGCTATCTTC-GATCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
528950 AAGATCTGCTATCTTCAGTCTACCTT-GCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTA-CTTCGCTGCCAATACAGGAAGAC
528995 AAGA-CTTGCTATCTTC-GATCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
529040 AAGATCTGCTATCTTCAGTCTACCTT-GCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTA-CTTCGCTGCCAATACAGGAAGAC
529085 AAGA-CTTGCTATCTTC-GATCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
529130 AAGATCTGCTATCTTCAGTCTACCTT-GCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTA-CTTCGCTGCCAATACAGGAAGAC
529175 AAGA-CTTGCTATCTTC-GATCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
529220 AAGATCTGCTATCTTCAGTCTACCTT-GCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTA-CTTCGCTGCCAATACAGGAAGAC
529265 AAGA-CTTGCTATCTTC-GATCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
*
529310 AAGATCTGCTATCTTTAGTCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
*
529355 AAGATCTGCTATCTTTAGTCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
529400 AAGATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
*
529445 AAGA-CTTGCTATCTTC-GATCTACTTCGCTACCAATACAGGAAGAC
1 AAGATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
* ** *
529490 AATATCTATTATCTTCAGTCTACTTTGCTGCCAATACAGGAAGAC
1 AAGATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
529535 AAGA-CTTGCTATCTTC-GATCTACTTCGCTGCCAATACAGGAAGAC
1 AAGATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
*
529580 AAGATCTACTAT
1 AAGATCTGCTAT
529592 AATGACTTCA
Statistics
Matches: 1126, Mismatches: 37, Indels: 146
0.86 0.03 0.11
Matches are distributed among these distances:
44 47 0.04
45 987 0.88
46 50 0.04
47 1 0.00
48 1 0.00
50 1 0.00
53 2 0.00
54 37 0.03
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (45 bp):
AAGATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
Found at i:534278 original size:31 final size:31
Alignment explanation
Indices: 534221--534280 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
534211 GGAGGTGGGA
*
534221 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
* * *
534252 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
534281 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:534509 original size:9 final size:9
Alignment explanation
Indices: 534495--534531 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
534485 TATAGTTTGA
534495 TATTCGAAT
1 TATTCGAAT
534504 TATTCGAAT
1 TATTCGAAT
*
534513 TATTCGAGT
1 TATTCGAAT
534522 TATTCGAAT
1 TATTCGAAT
534531 T
1 T
534532 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:534676 original size:16 final size:16
Alignment explanation
Indices: 534655--534685 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
534645 CACCCCTAGT
534655 GTTTAACTCGAAATTA
1 GTTTAACTCGAAATTA
534671 GTTTAACTCGAAATT
1 GTTTAACTCGAAATT
534686 CAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (16 bp):
GTTTAACTCGAAATTA
Found at i:534722 original size:83 final size:83
Alignment explanation
Indices: 534610--534906 Score: 576
Period size: 83 Copynumber: 3.6 Consensus size: 83
534600 TCGAAATTAG
* *
534610 TTTTTCGATTTTTTCGAGTCGAATCGAGTTTTTCTCACCCCTAGTGTTTAACTCGAAATTAGTTT
1 TTTTTCAATTTTTTCGTGTCGAATCGAGTTTTTCTCACCCCTAGTGTTTAACTCGAAATTAGTTT
534675 AACTCGAAATTCAAATTT
66 AACTCGAAATTCAAATTT
534693 TTTTTCAATTTTTTCGTGTCGAATCGAGTTTTTCTCACCCCTAGTGTTTAACTCGAAATTAGTTT
1 TTTTTCAATTTTTTCGTGTCGAATCGAGTTTTTCTCACCCCTAGTGTTTAACTCGAAATTAGTTT
534758 AACTCGAAATTCAAATTT
66 AACTCGAAATTCAAATTT
534776 TTTTTCAATTTTTTCGTGTCGAATCGAGTTTTTCTCACCCCTAGTGTTTAACTCGAAATTAGTTT
1 TTTTTCAATTTTTTCGTGTCGAATCGAGTTTTTCTCACCCCTAGTGTTTAACTCGAAATTAGTTT
534841 AACTCGAAATTCAAATTT
66 AACTCGAAATTCAAATTT
534859 TTTTTCAATTTTTTCGTGTCGAATCGAGTTTTTCTCACCCCTAGTGTT
1 TTTTTCAATTTTTTCGTGTCGAATCGAGTTTTTCTCACCCCTAGTGTT
534907 GTCCACTAAG
Statistics
Matches: 212, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 212 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.45
Consensus pattern (83 bp):
TTTTTCAATTTTTTCGTGTCGAATCGAGTTTTTCTCACCCCTAGTGTTTAACTCGAAATTAGTTT
AACTCGAAATTCAAATTT
Found at i:534759 original size:16 final size:16
Alignment explanation
Indices: 534738--534768 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
534728 CACCCCTAGT
534738 GTTTAACTCGAAATTA
1 GTTTAACTCGAAATTA
534754 GTTTAACTCGAAATT
1 GTTTAACTCGAAATT
534769 CAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (16 bp):
GTTTAACTCGAAATTA
Found at i:534842 original size:16 final size:16
Alignment explanation
Indices: 534821--534851 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
534811 CACCCCTAGT
534821 GTTTAACTCGAAATTA
1 GTTTAACTCGAAATTA
534837 GTTTAACTCGAAATT
1 GTTTAACTCGAAATT
534852 CAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (16 bp):
GTTTAACTCGAAATTA
Found at i:542112 original size:500 final size:500
Alignment explanation
Indices: 541156--542146 Score: 1784
Period size: 500 Copynumber: 2.0 Consensus size: 500
541146 TCGTACCAAA
* *
541156 CTCGGACGGCCGCATTATCTTCCACTTTACCAAGAAACTCCCTTTCCATGTTGAGTTCTCTATTT
1 CTCGAACGGCCGCACTATCTTCCACTTTACCAAGAAACTCCCTTTCCATGTTGAGTTCTCTATTT
541221 AAATAATGAACACGAATCAACACCTCTTTTATAATGAGAATGCCATGCAATCACAATCAAGGTAA
66 AAATAATGAACACGAATCAACACCTCTTTTATAATGAGAATGCCATGCAATCACAATCAAGGTAA
541286 AAGCAAAGCAAGTCAATATAACAATAAACTAAAATTTAAAGTATACAAGGAATAATAATTAAAGC
131 AAGCAAAGCAAGTCAATATAACAATAAACTAAAATTTAAAGTATACAAGGAATAATAATTAAAGC
*
541351 TACTATTCAGGAAACTACTAGGGTTTGAGGTGGTTCTACCTAGGGTAGGCTCCTAGGGCTCATTA
196 TACTATTCAGGAAACTACTAGGGTTCGAGGTGGTTCTACCTAGGGTAGGCTCCTAGGGCTCATTA
**
541416 AATGCGGTTCGGCTCTAAAACAAAGGTACCCGAACCAGTAAATTCCTCTATCCTCACCCATTATA
261 AATGCGGTTCGGCTCTAAAACAAAGGTACCCGAACCAACAAATTCCTCTATCCTCACCCATTATA
** *
541481 GGCTCATACGGAGTGAGTTCGGTTCAGGGGAATACATTTCCCTATGGCTGCACGGAGATGAAAAT
326 GGCTCATACGGAACGAGTTCGGTTCAGGGGAATACATTTCCCTATGGCTGCACGAAGATGAAAAT
* *
541546 CTCATGAATACATAGGTACAGATGTATCCCGAAAGCGATCCGCTATCCTGCACGAAGGTGAAAAC
391 CTCATGAAGACATAGGTACAGATGTATCCCGAAAGCGATCCGCTATCCTACACGAAGGTGAAAAC
*
541611 CTCACGAATGAGTAGCTTCTCACTCCCACTTAAAAGGGTGAAAAC
456 CTCACGAAGGAGTAGCTTCTCACTCCCACTTAAAAGGGTGAAAAC
*
541656 CTCGAACGGCTGCACTATCTTCCACTTTACCAAGAAACTCCCTTTCCATGTTGAGTTCTCTATTT
1 CTCGAACGGCCGCACTATCTTCCACTTTACCAAGAAACTCCCTTTCCATGTTGAGTTCTCTATTT
* * *
541721 AAATAATGAACGCGAATCAACACCTCTTTTATGATGAGAATGTCATGCAATCACAATCAAGGTAA
66 AAATAATGAACACGAATCAACACCTCTTTTATAATGAGAATGCCATGCAATCACAATCAAGGTAA
*
541786 AAGCAAAGCAAGTCAGTATAACAATAAACTAAAATTTAAAGTATACAAGGAATAATAATTAAAGC
131 AAGCAAAGCAAGTCAATATAACAATAAACTAAAATTTAAAGTATACAAGGAATAATAATTAAAGC
541851 TACTATTCAGGAAACTACTAGGGTTCGAGGTGGTTCTACCTAGGGTAGGCTCCTAGGGCTCATTA
196 TACTATTCAGGAAACTACTAGGGTTCGAGGTGGTTCTACCTAGGGTAGGCTCCTAGGGCTCATTA
* *
541916 CATGCGGTTCGGCTCTAAAGCAAAGGTACCCGAACCAACAAATTCCTCTATCCTCACCCATTATA
261 AATGCGGTTCGGCTCTAAAACAAAGGTACCCGAACCAACAAATTCCTCTATCCTCACCCATTATA
541981 GGCTCATACGGAACGAGTTCGGTTCAGGGGAATACATTTCCCTATGGCTGCACGAAGATGAAAAT
326 GGCTCATACGGAACGAGTTCGGTTCAGGGGAATACATTTCCCTATGGCTGCACGAAGATGAAAAT
** *
542046 CTCATGAAGACATAGGTATGGATGTATCCCGAAAGCGATCCGCTATCCTACACGGAGGTGAAAAC
391 CTCATGAAGACATAGGTACAGATGTATCCCGAAAGCGATCCGCTATCCTACACGAAGGTGAAAAC
*
542111 CTCACGAAGGAGTAGCTTCTCACTCTCACTTAAAAG
456 CTCACGAAGGAGTAGCTTCTCACTCCCACTTAAAAG
542147 AGTGTGACCA
Statistics
Matches: 469, Mismatches: 22, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
500 469 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (500 bp):
CTCGAACGGCCGCACTATCTTCCACTTTACCAAGAAACTCCCTTTCCATGTTGAGTTCTCTATTT
AAATAATGAACACGAATCAACACCTCTTTTATAATGAGAATGCCATGCAATCACAATCAAGGTAA
AAGCAAAGCAAGTCAATATAACAATAAACTAAAATTTAAAGTATACAAGGAATAATAATTAAAGC
TACTATTCAGGAAACTACTAGGGTTCGAGGTGGTTCTACCTAGGGTAGGCTCCTAGGGCTCATTA
AATGCGGTTCGGCTCTAAAACAAAGGTACCCGAACCAACAAATTCCTCTATCCTCACCCATTATA
GGCTCATACGGAACGAGTTCGGTTCAGGGGAATACATTTCCCTATGGCTGCACGAAGATGAAAAT
CTCATGAAGACATAGGTACAGATGTATCCCGAAAGCGATCCGCTATCCTACACGAAGGTGAAAAC
CTCACGAAGGAGTAGCTTCTCACTCCCACTTAAAAGGGTGAAAAC
Found at i:548719 original size:18 final size:19
Alignment explanation
Indices: 548683--548719 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
548673 TGATTGTCGG
*
548683 AGGTGAAATGAACACATAT
1 AGGTGAAATCAACACATAT
548702 AGGTGAAATCAA-ACATAT
1 AGGTGAAATCAACACATAT
548720 TTCAGGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.22
Consensus pattern (19 bp):
AGGTGAAATCAACACATAT
Found at i:548974 original size:31 final size:30
Alignment explanation
Indices: 548939--549004 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
548929 TTAATAAAAG
* * *
548939 TAAAATTGTATTTTGATTTCTTTAAAAATTA
1 TAAAATTGTAATTT-AATCCTTTAAAAATTA
*
548970 TAAAATTTTAATTTAATCCTTTAAAAATTA
1 TAAAATTGTAATTTAATCCTTTAAAAATTA
549000 TAAAA
1 TAAAA
549005 ATATAGACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (30 bp):
TAAAATTGTAATTTAATCCTTTAAAAATTA
Found at i:549583 original size:22 final size:23
Alignment explanation
Indices: 549554--549604 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
549544 AATTTATTTT
* *
549554 ATAA-TAAGATGATAT-TTTATA
1 ATAATTAAGATCATATATATATA
549575 ATAATTAAGATCATATATATATA
1 ATAATTAAGATCATATATATATA
549598 A-AATTAA
1 ATAATTAA
549605 TGATAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 16 0.62
23 6 0.23
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (23 bp):
ATAATTAAGATCATATATATATA
Found at i:549761 original size:22 final size:23
Alignment explanation
Indices: 549717--549770 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
549707 AATAATTTAA
*
549717 ATAAATACTCATATTTATATAAT
1 ATAAATATTCATATTTATATAAT
*
549740 -TAAAATATTCATATTT-TTTAAT
1 AT-AAATATTCATATTTATATAAT
549762 ATAAATATT
1 ATAAATATT
549771 TATTATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAATATTCATATTTATATAAT
Found at i:549766 original size:23 final size:23
Alignment explanation
Indices: 549711--549770 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
549701 GCAAAGAATA
*
549711 ATTTAA-ATAAATACTCATATTT
1 ATTTAATATAAATATTCATATTT
*
549733 ATATAAT-TAAAATATTCATATTT
1 ATTTAATAT-AAATATTCATATTT
549756 -TTTAATATAAATATT
1 ATTTAATATAAATATT
549771 TATTATTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAATATAAATATTCATATTT
Found at i:549859 original size:17 final size:17
Alignment explanation
Indices: 549812--549862 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
549802 ACTTTTTAAT
549812 ATTA-AATAATTTATTA
1 ATTATAATAATTTATTA
*
549828 A-AATAATAAATTTTATTA
1 ATTATAAT-AA-TTTATTA
549846 ATTATAATAATTTATTA
1 ATTATAATAATTTATTA
549863 TGTTATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 1 0.03
16 4 0.14
17 9 0.31
18 10 0.34
19 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTATAATAATTTATTA
Found at i:556911 original size:37 final size:37
Alignment explanation
Indices: 556861--556933 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
556851 CCAAATGCAT
556861 CCAATAAAGGTCTGTTGCTCAGATGAGGATCATTTGA
1 CCAATAAAGGTCTGTTGCTCAGATGAGGATCATTTGA
* *
556898 CCAATAGAGGTCTGTTGCTCAGATGGGGATCATTTG
1 CCAATAAAGGTCTGTTGCTCAGATGAGGATCATTTG
556934 GCCCACAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (37 bp):
CCAATAAAGGTCTGTTGCTCAGATGAGGATCATTTGA
Found at i:562993 original size:46 final size:46
Alignment explanation
Indices: 562940--563031 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
562930 TTGCATAGGT
*
562940 TTAACAGAGAGGAGAAGATTCTGCTGAAAAGCCTTGTTTGGGTGGC
1 TTAACAGAGAGGAGAAGATACTGCTGAAAAGCCTTGTTTGGGTGGC
*
562986 TTAACAGAGAGGAGAAGATACTGCTGAAAAGCTTTGTTTGGGTGGC
1 TTAACAGAGAGGAGAAGATACTGCTGAAAAGCCTTGTTTGGGTGGC
563032 CAGAAAGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (46 bp):
TTAACAGAGAGGAGAAGATACTGCTGAAAAGCCTTGTTTGGGTGGC
Found at i:586744 original size:17 final size:17
Alignment explanation
Indices: 586722--586755 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
586712 AAGGAGGACT
586722 ATAATAAT-ATAATCATA
1 ATAATAATCAT-ATCATA
586739 ATAATAATCATATCATA
1 ATAATAATCATATCATA
586756 GGAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATAATCATATCATA
Found at i:587684 original size:45 final size:45
Alignment explanation
Indices: 587616--587819 Score: 234
Period size: 44 Copynumber: 4.6 Consensus size: 45
587606 GTGGATCCTA
*
587616 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATAT
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCT
** * * * *
587661 TTTCTACAGCAACTTCATG-GAGATAAGATTT-ATAGCTTTAATCT
1 GCTCTACTGCAACTTCA-GAGAGATAAGATTTGCTATCTTCAATCT
* *
587705 GCTCTACTGCAATTTCAGAGAGATAAGATTTTCTATCTTCAATCT
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCT
* * *
587750 GCTCCACTGCAAATTCAGGGAGATAAGATTTG-TATCTTCAATCT
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCT
* * * *
587794 ACTCCACTGCCACTTCAGGGAGATAA
1 GCTCTACTGCAACTTCAGAGAGATAA
587820 TATTCGTAAC
Statistics
Matches: 135, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
43 1 0.01
44 69 0.51
45 64 0.47
46 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (45 bp):
GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCT
Found at i:587772 original size:89 final size:89
Alignment explanation
Indices: 587616--587819 Score: 264
Period size: 89 Copynumber: 2.3 Consensus size: 89
587606 GTGGATCCTA
** * * *
587616 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATTTTCTACAGCAACTTCATGG
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATGCTCCACAGCAAATTCAGGG
*
587681 AGATAAGATTTATAGCTTTAATCT
66 AGATAAGATTTATAGCTTCAATCT
* * * *
587705 GCTCTACTGCAATTTCAGAGAGATAAGATTTTCTATCTTCAATCTGCTCCACTGCAAATTCAGGG
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATGCTCCACAGCAAATTCAGGG
* *
587770 AGATAAGATTTGTATCTTCAATCT
66 AGATAAGATTTATAGCTTCAATCT
* * * *
587794 ACTCCACTGCCACTTCAGGGAGATAA
1 GCTCTACTGCAACTTCAGAGAGATAA
587820 TATTCGTAAC
Statistics
Matches: 98, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 98 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (89 bp):
GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATGCTCCACAGCAAATTCAGGG
AGATAAGATTTATAGCTTCAATCT
Found at i:590074 original size:51 final size:50
Alignment explanation
Indices: 589986--590265 Score: 380
Period size: 51 Copynumber: 5.4 Consensus size: 50
589976 TCGGGCTGTT
* *
589986 ACAAGTGACAAGTGATAAGTAGTAGCTTCAGCCACACTTATCTGATCAGTG
1 ACAAGTGACAAGTGATAAGT-GTAGCTTTAGCTACACTTATCTGATCAGTG
*
590037 ACAAATGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGACCAGTGACAAGTG
1 ACAAGTGACAAGTGATAAGT-GTAGCTTTAGCTACACTTATCTG---A-T--C-AGTG
590095 ACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG
1 ACAAGTGACAAGTGATAAGT-GTAGCTTTAGCTACACTTATCTGATCAGTG
* *
590146 ACAAGTAACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGGG
1 ACAAGTGACAAGTGATAAGTG-TAGCTTTAGCTACACTTATCTGATCAGTG
* * *
590197 ACAAGTGACAAGTGATAAGTGATAGATTTAGCTACACTTATCTGATTAGGG
1 ACAAGTGACAAGTGATAAGTG-TAGCTTTAGCTACACTTATCTGATCAGTG
590248 ACAAGTGACAAGTGATAA
1 ACAAGTGACAAGTGATAA
590266 ATGTGATCCG
Statistics
Matches: 211, Mismatches: 10, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
50 1 0.00
51 158 0.75
52 1 0.00
54 2 0.01
55 2 0.01
57 1 0.00
58 46 0.22
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (50 bp):
ACAAGTGACAAGTGATAAGTGTAGCTTTAGCTACACTTATCTGATCAGTG
Found at i:590094 original size:7 final size:7
Alignment explanation
Indices: 590079--590115 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
590069 TACACTTATC
*
590079 TGACCAG
1 TGACAAG
590086 TGACAAG
1 TGACAAG
590093 TGACAAG
1 TGACAAG
590100 TGACAAG
1 TGACAAG
*
590107 TGATAAG
1 TGACAAG
590114 TG
1 TG
590116 GTAGCTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.38, C:0.14, G:0.30, T:0.19
Consensus pattern (7 bp):
TGACAAG
Found at i:590172 original size:109 final size:102
Alignment explanation
Indices: 589986--590265 Score: 391
Period size: 109 Copynumber: 2.7 Consensus size: 102
589976 TCGGGCTGTT
* * * *
589986 ACAAGTGACAAGTGATAAGTAGTAGCTTCAGCCACACTTATCTGATCAGTGACAAATGACAAGTG
1 ACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTG
*
590051 ATAAGTAGTAGCTTTAGCTACACTTATCTGACCAGTGACAAGTG
66 ATAAGTAGTAGCTTTAGCTACACTTATCTG---A-T--C-AGGG
*
590095 ACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTAACAAGTG
1 ACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTG
590160 ATAAGT-GATAGCTTTAGCTACACTTATCTGATCAGGG
66 ATAAGTAG-TAGCTTTAGCTACACTTATCTGATCAGGG
* * * *
590197 ACAAGTGACAAGTGATAAGTGATAGATTTAGCTACACTTATCTGATTAGGGACAAGTGACAAGTG
1 ACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTG
590262 ATAA
66 ATAA
590266 ATGTGATCCG
Statistics
Matches: 159, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
102 67 0.42
103 1 0.01
105 1 0.01
106 1 0.01
108 1 0.01
109 88 0.55
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (102 bp):
ACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTG
ATAAGTAGTAGCTTTAGCTACACTTATCTGATCAGGG
Found at i:590999 original size:45 final size:45
Alignment explanation
Indices: 590908--591005 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
590898 GGGTAAGGGG
* **
590908 TGTTACACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAATC
1 TGTTACACTGCAACTTCAGGGAAATAAGATTAGCTATCACTAATC
* * * * *
590953 TGTTACACTGCAACTTTAGGGAGATAAGATTAGGTTTCACTGATC
1 TGTTACACTGCAACTTCAGGGAAATAAGATTAGCTATCACTAATC
590998 TGTTACAC
1 TGTTACAC
591006 CATTCTCTAG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (45 bp):
TGTTACACTGCAACTTCAGGGAAATAAGATTAGCTATCACTAATC
Found at i:604706 original size:16 final size:16
Alignment explanation
Indices: 604685--604715 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
604675 TGCCATTTCG
604685 GAATTTCCTTTTTCAT
1 GAATTTCCTTTTTCAT
604701 GAATTTCCTTTTTCA
1 GAATTTCCTTTTTCA
604716 GATAGTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (16 bp):
GAATTTCCTTTTTCAT
Found at i:608643 original size:3 final size:3
Alignment explanation
Indices: 608625--608675 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
608615 TTAAATATCC
* * * *
608625 TTA TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
608672 TTA T
1 TTA T
608676 GTACTAGTGT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:608950 original size:38 final size:37
Alignment explanation
Indices: 608866--608959 Score: 95
Period size: 38 Copynumber: 2.5 Consensus size: 37
608856 TATACATACT
608866 TATACATACTTAAATATATTTTCCATATTTCATAATTC
1 TATACATACTTAAATATATTTTCCATATTT-ATAATTC
* * *
608904 T-TATATACTTACATATATTTATGCATATTT-TACA-TC
1 TATACATACTTAAATATATTT-TCCATATTTATA-ATTC
*
608940 ATATACATACTTATATATAT
1 -TATACATACTTAAATATAT
608960 ATTCTTTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
36 4 0.09
37 19 0.40
38 24 0.51
ACGTcount: A:0.37, C:0.14, G:0.01, T:0.48
Consensus pattern (37 bp):
TATACATACTTAAATATATTTTCCATATTTATAATTC
Found at i:611209 original size:23 final size:21
Alignment explanation
Indices: 611174--611224 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
611164 TTAGCCTCTC
611174 CATTTTTACTTTTTTCCATTTT
1 CATTTTTACTTTTTTCCA-TTT
*
611196 CTATTTTT-CATTTTTTTCATTT
1 C-ATTTTTAC-TTTTTTCCATTT
611218 CATTTTT
1 CATTTTT
611225 TTTACGACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 6 0.23
22 6 0.23
23 14 0.54
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.71
Consensus pattern (21 bp):
CATTTTTACTTTTTTCCATTT
Found at i:611727 original size:13 final size:13
Alignment explanation
Indices: 611709--611757 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
611699 TTTTTGTTTC
*
611709 TTTTTGTTTTTAT
1 TTTTTGTTCTTAT
*
611722 TTTTTGTTCTTGT
1 TTTTTGTTCTTAT
611735 TTTTTGTTCTT-T
1 TTTTTGTTCTTAT
611747 TCTTTT-TTCTT
1 T-TTTTGTTCTT
611758 TTCTTTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 7 0.21
13 26 0.79
ACGTcount: A:0.02, C:0.08, G:0.08, T:0.82
Consensus pattern (13 bp):
TTTTTGTTCTTAT
Found at i:611751 original size:5 final size:5
Alignment explanation
Indices: 611741--611786 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
611731 TTGTTTTTTG
611741 TTCTT TTCTTTT TTCTT TTCTT TTCTT TTC-T TTC-T TTCTT TT-TT TT
1 TTCTT TTC--TT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
611787 GGAATTGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
4 12 0.32
5 21 0.55
7 5 0.13
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTCTT
Found at i:611754 original size:35 final size:36
Alignment explanation
Indices: 611699--611783 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 36
611689 CCGGTAGAGG
611699 TTTTTGTTTCTTTTTGTTTTTATTTT-TTGTTCTTGT
1 TTTTTGTTTCTTTTTGTTTTTATTTTCTT-TTCTTGT
*
611735 TTTTTG-TTCTTTTCT-TTTTTCTTTTCTTTTCTT-T
1 TTTTTGTTTCTTTT-TGTTTTTATTTTCTTTTCTTGT
* *
611769 TCTTTCTTTCTTTTT
1 TTTTTGTTTCTTTTT
611784 TTTGGAATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
34 6 0.14
35 28 0.65
36 9 0.21
ACGTcount: A:0.01, C:0.12, G:0.06, T:0.81
Consensus pattern (36 bp):
TTTTTGTTTCTTTTTGTTTTTATTTTCTTTTCTTGT
Found at i:611759 original size:22 final size:22
Alignment explanation
Indices: 611700--611786 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 22
611690 CGGTAGAGGT
* * *
611700 TTTTGTTTCTTT-TTGTTTTTA
1 TTTTCTTTCTTTCTTTTTTTTC
* *
611721 TTTTTTGTTCTTGT-TTTTTGTTC
1 TTTTCT-TTCTT-TCTTTTTTTTC
611744 TTTTCTTT-TTTCTTTTCTTTTC
1 TTTTCTTTCTTTCTTTT-TTTTC
611766 TTTTCTTTCTTTCTTTTTTTT
1 TTTTCTTTCTTTCTTTTTTTT
611787 GGAATTGAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
20 1 0.02
21 11 0.20
22 23 0.42
23 20 0.36
ACGTcount: A:0.01, C:0.11, G:0.06, T:0.82
Consensus pattern (22 bp):
TTTTCTTTCTTTCTTTTTTTTC
Found at i:616973 original size:41 final size:41
Alignment explanation
Indices: 616893--616975 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
616883 TAAAAAAAAT
* * *
616893 ATATTTATTATATTCGGGCAGGGTAGGGCCGGGCTCGGGCC
1 ATATTTATTATATTCGGGCAGGGCAGGGCCGGCCCCGGGCC
* *
616934 ATATTTATTATATTCGGGCCA-GGCCGGGCTGGCCCCGGGCC
1 ATATTTATTATATTCGGG-CAGGGCAGGGCCGGCCCCGGGCC
616975 A
1 A
616976 AAAAAGTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 34 0.94
42 2 0.06
ACGTcount: A:0.17, C:0.24, G:0.34, T:0.25
Consensus pattern (41 bp):
ATATTTATTATATTCGGGCAGGGCAGGGCCGGCCCCGGGCC
Found at i:617610 original size:44 final size:45
Alignment explanation
Indices: 617499--617785 Score: 129
Period size: 44 Copynumber: 6.6 Consensus size: 45
617489 ACTTGATGCG
*
617499 ATCTACTCTACTGCAACTTTAGAGAGATAAGATCTGGATGTTTTA
1 ATCTACTCTACTGCAACTTTAGGGAGATAAGATCTGGATGTTTTA
** * * * * *
617544 ATCCGCTCCACTGAAACTTTAGGGAGATAGGAT-T-GATTTCTTTT
1 ATCTACTCTACTGCAACTTTAGGGAGATAAGATCTGGATGT-TTTA
* * * **
617588 GTCTACTCTACTGCAACTTTAGGCAGATAAGA-CTGTATG---CG
1 ATCTACTCTACTGCAACTTTAGGGAGATAAGATCTGGATGTTTTA
* * * *
617629 ATCTGCTCT-CTGCAACTTCAGAGAGATAAGATAT--ATGGTTTTA
1 ATCTACTCTACTGCAACTTTAGGGAGATAAGATCTGGAT-GTTTTA
** * * * * *
617672 ATCCGCTCCACTGCAACTTCAAGAAGAT-AGAAT-TGGATG---TG
1 ATCTACTCTACTGCAACTTTAGGGAGATAAG-ATCTGGATGTTTTA
* * * *
617713 ATCTACTCTACTGTAACTTCAGAGAGATAAGAT-TTG-TGGTTTTA
1 ATCTACTCTACTGCAACTTTAGGGAGATAAGATCTGGAT-GTTTTA
* * * * *
617757 ACCTGCTCCACTACAACTTTAGAGAGATA
1 ATCTACTCTACTGCAACTTTAGGGAGATA
617786 GGATTATTGG
Statistics
Matches: 177, Mismatches: 48, Indels: 35
0.68 0.18 0.13
Matches are distributed among these distances:
39 2 0.01
40 21 0.12
41 35 0.20
42 2 0.01
43 14 0.08
44 72 0.41
45 31 0.18
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (45 bp):
ATCTACTCTACTGCAACTTTAGGGAGATAAGATCTGGATGTTTTA
Found at i:617700 original size:84 final size:85
Alignment explanation
Indices: 617597--617775 Score: 220
Period size: 85 Copynumber: 2.1 Consensus size: 85
617587 TGTCTACTCT
* * * * *
617597 ACTGCAACTTTAGGCAGATA-AGACTGTATGCGATCTGCTCT-CTGCAACTTCAGAGAGATAAGA
1 ACTGCAACTTCAAGAAGATAGA-ACTGGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGA
617660 TATATGGTTTTAATCC-GCTCC
65 TATATGGTTTTAA-CCTGCTCC
* * *
617681 ACTGCAACTTCAAGAAGATAGAATTGGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGAT
1 ACTGCAACTTCAAGAAGATAGAACTGGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGAT
* *
617746 TTGTGGTTTTAACCTGCTCC
66 ATATGGTTTTAACCTGCTCC
*
617766 ACTACAACTT
1 ACTGCAACTT
617776 TAGAGAGATA
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
84 34 0.42
85 47 0.58
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (85 bp):
ACTGCAACTTCAAGAAGATAGAACTGGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGAT
ATATGGTTTTAACCTGCTCC
Found at i:617724 original size:130 final size:129
Alignment explanation
Indices: 617414--617709 Score: 341
Period size: 130 Copynumber: 2.3 Consensus size: 129
617404 TAGTGCTTCG
* * * * * * *
617414 ATCCACTCCACTACAACATCAAGAAGATAGAATCGGTTTCTTCTGTCTACTCCATTGCACTTTCA
1 ATCCGCTCCACTGCAACTTCAAGAAGATAGAATTGGATTCATCTGTCTACTCCACTGCACTTTCA
* * *
617479 GGGAGATAAGACTTGATGCGATCTACTCTACTGCAACTTTAGAGAGATAAGATCTGGATGTTTTA
66 GGCAGATAAGACTTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATAT-GATGTTTTA
* * * * * * * *
617544 ATCCGCTCCACTGAAACTTTAGGGAGATAGGATT-GATTTCTTTTGTCTACTCTACTGCAACTTT
1 ATCCGCTCCACTGCAACTTCAAGAAGATAGAATTGGA-TTCATCTGTCTACTCCACTGC-ACTTT
*
617608 -AGGCAGATAAGAC-TGTATGCGATCTGCTCT-CTGCAACTTCAGAGAGATAAGATAT-ATGGTT
64 CAGGCAGATAAGACTTG-ATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGAT-GTT
617669 TTA
127 TTA
617672 ATCCGCTCCACTGCAACTTCAAGAAGATAGAATTGGAT
1 ATCCGCTCCACTGCAACTTCAAGAAGATAGAATTGGAT
617710 GTGATCTACT
Statistics
Matches: 139, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
127 2 0.01
128 36 0.26
129 28 0.20
130 68 0.49
131 5 0.04
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (129 bp):
ATCCGCTCCACTGCAACTTCAAGAAGATAGAATTGGATTCATCTGTCTACTCCACTGCACTTTCA
GGCAGATAAGACTTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATATGATGTTTTA
Found at i:617930 original size:50 final size:50
Alignment explanation
Indices: 617874--618549 Score: 452
Period size: 50 Copynumber: 13.5 Consensus size: 50
617864 TCGGGGAAAC
* * * *
617874 AAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCACCAGAGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* * * * * ** ** * * **
617924 AAGATTCGCTGTTGTGGCTTCAATCTATTTAACTGTAATGTCGGGGAAAC
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* * * *
617974 AAGATTCGCCATCCTAGCTTCAATCTGTTCCACTACACCACCAGGGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* * * * * ** * * **
618024 AAGATTCGTCGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAAC
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* * *
618074 AAGATTCGTCGTCGTAGCTTCAATCTGTTTCACTACACCGCTAGAGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* * * * * ** * * **
618124 AAGATTCGCCGTTGTGGCTTCAATTTATTTAACTACAATGTCGGGGAAAC
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* *
618174 AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGAGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* * * * * * ** * * **
618224 AAGATTCGTCGTTGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAAC
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* *
618274 AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGAGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* * * * * * ** * * **
618324 AAGATTCGTCGTTGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAAC
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* * *
618374 AAGATTCGCCATCGTAGCTTCAATCTGTTCCATTACACCGCCAGGGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* * * * * * ** ** * * **
618424 AAGATTCGCCATTGTGGCTTCAACCTTTTTAACTGTAATGTCGGGGAAAC
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* * * * *
618474 AAGATTCGCCGTCGTAGATTCAATCTATTCCACTACACTGCTAGGGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
* * * *
618524 AAGATTCACCGTTGTGGTTTCAATCT
1 AAGATTCGCCGTCGTAGCTTCAATCT
618550 ATTCCATTGT
Statistics
Matches: 446, Mismatches: 180, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
50 446 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (50 bp):
AAGATTCGCCGTCGTAGCTTCAATCTGTTTCACTACACCGCCAGGGAAGT
Found at i:618580 original size:100 final size:100
Alignment explanation
Indices: 617845--618552 Score: 1092
Period size: 100 Copynumber: 7.1 Consensus size: 100
617835 TGCCATCTTT
* * * *
617845 AATCTGTTTAATTGCAATATCGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC
* *
617910 ACCACCAGAGAAGTAAGATTCGCTGTTGTGGCTTC
66 ACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTC
* * *
617945 AATCTATTTAACTGTAATGTCGGGGAAACAAGATTCGCCATCCTAGCTTCAATCTGTTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC
* * * *
618010 ACCACCAGGGAAGTAAGATTCGTCGTTGTAGCTTC
66 ACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTC
* *
618045 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGTCGTCGTAGCTTCAATCTGTTTCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC
*
618110 ACCGCTAGAGAAGTAAGATTCGCCGTTGTGGCTTC
66 ACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTC
* *
618145 AATTTATTTAACTACAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC
*
618210 ACCGCCAGAGAAGTAAGATTCGTCGTTGTGGCTTC
66 ACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTC
*
618245 AATCTTTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC
*
618310 ACCGCCAGAGAAGTAAGATTCGTCGTTGTGGCTTC
66 ACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTC
* * *
618345 AATCTTTTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCATTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC
* *
618410 ACCGCCAGGGAAGTAAGATTCGCCATTGTGGCTTC
66 ACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTC
* * * * *
618445 AACCTTTTTAACTGTAATGTCGGGGAAACAAGATTCGCCGTCGTAGATTCAATCTATTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC
* * * * *
618510 ACTGCTAGGGAAGTAAGATTCACCGTTGTGGTTTC
66 ACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTC
618545 AATCTATT
1 AATCTATT
618553 CCATTGTAAT
Statistics
Matches: 560, Mismatches: 48, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 560 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (100 bp):
AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTAC
ACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTC
Found at i:618903 original size:88 final size:87
Alignment explanation
Indices: 618750--619087 Score: 447
Period size: 88 Copynumber: 3.9 Consensus size: 87
618740 TAATACTGGT
* * * *
618750 GTCTTCGATCTACTTCACTGCCAGTA-A-G--G-CAAGATCTGCCATTTTTCAACCTACTCCACT
1 GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTTCTA-TTTTCAACCTACTCCACT
618810 ACTGCTCAGGGAGACAATGCT-AG
65 ACTGCTCAGGGAGACAA-GCTAAG
* * *
618833 TATCTTCAATCTACTTCGCTGCCAATACAGGAAAACAAGATCTTCTATTTTCAACCTACTCCACT
1 -GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTTCTATTTTCAACCTACTCCACT
* *
618898 GCTGCTCAGGGAGATAAGGCTAAG
65 ACTGCTCAGGGAGACAA-GCTAAG
* *
618922 GTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
1 GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTTCTATTTTCAACCTACTCCACTA
*
618987 CTGCTCAGGGAGACAAGACTGAG
66 CTGCTCAGGGAGACAAG-CTAAG
*
619010 GTCTTCGATCTACTTCGCTGCCAATACATGAAGACAAGAT-TTGCTATTTTCAACCTACTCCACT
1 GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTT-CTATTTTCAACCTACTCCACT
*
619074 ACTGCTTAGGGAGA
65 ACTGCTCAGGGAGA
619088 TCGAATTTAT
Statistics
Matches: 224, Mismatches: 22, Indels: 12
0.87 0.09 0.05
Matches are distributed among these distances:
84 22 0.10
85 1 0.00
86 1 0.00
87 2 0.01
88 186 0.83
89 12 0.05
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (87 bp):
GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTTCTATTTTCAACCTACTCCACTA
CTGCTCAGGGAGACAAGCTAAG
Found at i:618990 original size:176 final size:172
Alignment explanation
Indices: 618750--619088 Score: 506
Period size: 176 Copynumber: 1.9 Consensus size: 172
618740 TAATACTGGT
*
618750 GTCTTCGATCTACTTCACTGCCAGTAAGGCAAGATCTGCCATTTTTCAACCTACTCCACTACTGC
1 GTCTTCGATCTACTTCACTGCCAATAAGGCAAGATCTGCCATTTTTCAACCTACTCCACTACTGC
618815 TCAGGGAGACAATG-CT-AGTATCTTCAATCTACTTCGCTGCCAATACAGGAAAACAAGATCTT-
66 TCAGGGAGACAA-GACTGAG-ATCTTCAATCTACTTCGCTGCCAATACAGGAAAACAAGAT-TTG
*
618877 CTATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAAG
128 CTATTTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTAAG
*
618922 GTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTA-TTTTCAACCTACTCCACT
1 GTCTTCGATCTACTTCACTGCCAATA-A-G--G-CAAGATCTGCCATTTTTCAACCTACTCCACT
* * * *
618986 ACTGCTCAGGGAGACAAGACTGAGGTCTTCGATCTACTTCGCTGCCAATACATGAAGACAAGATT
61 ACTGCTCAGGGAGACAAGACTGAGATCTTCAATCTACTTCGCTGCCAATACAGGAAAACAAGATT
*
619051 TGCTATTTTCAACCTACTCCACTACTGCTTAGGGAGAT
126 TGCTATTTTCAACCTACTCCACTACTGCTCAGGGAGAT
619089 CGAATTTATG
Statistics
Matches: 151, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
172 25 0.17
173 1 0.01
174 1 0.01
175 3 0.02
176 108 0.72
177 13 0.09
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (172 bp):
GTCTTCGATCTACTTCACTGCCAATAAGGCAAGATCTGCCATTTTTCAACCTACTCCACTACTGC
TCAGGGAGACAAGACTGAGATCTTCAATCTACTTCGCTGCCAATACAGGAAAACAAGATTTGCTA
TTTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTAAG
Found at i:619001 original size:44 final size:44
Alignment explanation
Indices: 618779--619087 Score: 142
Period size: 45 Copynumber: 7.0 Consensus size: 44
618769 GCCAGTAAGG
* *
618779 CAAGATCTGCCATTTTTCAACCTACTCCACTACTGCTCAGGGAGA
1 CAAGATCTGCTA-TTTTCAACCTACTCCACTGCTGCTCAGGGAGA
* * * * *** * *
618824 C-A-ATGCTAG-TATCTTCAATCTACTTCGCTGCCAATACAGGAAAA
1 CAAGAT-CT-GCTATTTTCAACCTACTCCACTGCTGCT-CAGGGAGA
*
618868 CAAGATCTTCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
1 CAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
* * **** * * * * *** *
618912 TAAG-GCTAAGGTCTTCGATCTACTTCACTGCCAATACAGGAAGA
1 CAAGATCTGCTATTTTCAACCTACTCCACTGCTGCT-CAGGGAGA
*
618956 CAAGATCTGCTATTTTCAACCTACTCCACTACTGCTCAGGGAGA
1 CAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
*** * * * * * *** * *
619000 CAAGA-CTGAGGTCTTCGATCTACTTCGCTGCCAATACATGAAGA
1 CAAGATCTGCTATTTTCAACCTACTCCACTGCTGCT-CAGGGAGA
* * *
619044 CAAGATTTGCTATTTTCAACCTACTCCACTACTGCTTAGGGAGA
1 CAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
619088 TCGAATTTAT
Statistics
Matches: 174, Mismatches: 80, Indels: 21
0.63 0.29 0.08
Matches are distributed among these distances:
43 55 0.32
44 58 0.33
45 59 0.34
46 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (44 bp):
CAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
Found at i:622142 original size:22 final size:23
Alignment explanation
Indices: 622104--622146 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
622094 AAAGAATCAT
622104 AAAAATTATAGACAAAATTTATG
1 AAAAATTATAGACAAAATTTATG
622127 AAAAAGTTATA-A-AAAATTTA
1 AAAAA-TTATAGACAAAATTTA
622147 AAATTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (23 bp):
AAAAATTATAGACAAAATTTATG
Found at i:622305 original size:11 final size:12
Alignment explanation
Indices: 622284--622320 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
622274 TAAATTTAAA
622284 TTTTTATAACTT
1 TTTTTATAACTT
622296 TTTTTA-AACTT
1 TTTTTATAACTT
*
622307 TGTTTATAA-TT
1 TTTTTATAACTT
622318 TTT
1 TTT
622321 ATGATTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTTTATAACTT
Found at i:624028 original size:44 final size:44
Alignment explanation
Indices: 623969--624053 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
623959 CCTCATAGAT
* *
623969 ACGGCACAGGATTCTGCTCAAACAGACTGCGGATGGTGTCATAC
1 ACGGCACAGGATTCTGCTCAAACAGACTGCGAATAGTGTCATAC
* *
624013 ACGGCACA-GATTTCTGTTCAAACAGGCTGCGAATAGTGTCA
1 ACGGCACAGGA-TTCTGCTCAAACAGACTGCGAATAGTGTCA
624054 GCTATCGGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (44 bp):
ACGGCACAGGATTCTGCTCAAACAGACTGCGAATAGTGTCATAC
Found at i:624613 original size:20 final size:19
Alignment explanation
Indices: 624590--624633 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
624580 TAATATAAAA
624590 TTTGAAATTTTTATAAATAT
1 TTTGAAATTTTTATAAAT-T
** *
624610 TTTGATTTTTTTTTAAATT
1 TTTGAAATTTTTATAAATT
624629 TTTGA
1 TTTGA
624634 GAGAGAGTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (19 bp):
TTTGAAATTTTTATAAATT
Found at i:635890 original size:19 final size:19
Alignment explanation
Indices: 635866--635903 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
635856 AGCCTTACCC
635866 ATATCAACAATACTATGAA
1 ATATCAACAATACTATGAA
635885 ATATCAACAATACTATGAA
1 ATATCAACAATACTATGAA
635904 TCTTGCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (19 bp):
ATATCAACAATACTATGAA
Found at i:636776 original size:37 final size:38
Alignment explanation
Indices: 636708--636787 Score: 94
Period size: 37 Copynumber: 2.1 Consensus size: 38
636698 AAATAGTCCC
* * *
636708 TAAAATTTTAATTTTATAGTTTTTACGATTTAA-TCTT
1 TAAAATTTTAATTTTATAGTTCTTACAATTTAATTCCT
636745 TAAAATTTTAATTTTTACTA-TTCTT-CAATTTAATTCCT
1 TAAAATTTTAA-TTTTA-TAGTTCTTACAATTTAATTCCT
636783 TAAAA
1 TAAAA
636788 ACAGATTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
37 18 0.49
38 17 0.46
39 2 0.05
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.54
Consensus pattern (38 bp):
TAAAATTTTAATTTTATAGTTCTTACAATTTAATTCCT
Found at i:637837 original size:21 final size:21
Alignment explanation
Indices: 637785--637838 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
637775 TCTAGTAAAA
*
637785 TAAATAAATAATTCATGAAGT
1 TAAAAAAATAATTCATGAAGT
* *
637806 TAAAAATAATAATTC-TTAATT
1 TAAAAA-AATAATTCATGAAGT
637827 TAAAGAAAATAA
1 TAAA-AAAATAA
637839 ATGTAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (21 bp):
TAAAAAAATAATTCATGAAGT
Found at i:657763 original size:11 final size:11
Alignment explanation
Indices: 657747--657810 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 11
657737 CGTGGGTAGT
657747 ATATTTTAAAA
1 ATATTTTAAAA
657758 ATATTTT--AA
1 ATATTTTAAAA
**
657767 A-ATTAAAAAA
1 ATATTTTAAAA
* **
657777 AAAAGTTAAAA
1 ATATTTTAAAA
657788 AGTATTTTAAAA
1 A-TATTTTAAAA
657800 ATATTTTAAAA
1 ATATTTTAAAA
657811 TTAAAACAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 3 0.08
11 23 0.57
12 8 0.20
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
ATATTTTAAAA
Found at i:657816 original size:17 final size:17
Alignment explanation
Indices: 657794--657841 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
657784 AAAAAGTATT
*
657794 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
*
657811 TTAAAACAAATTTAAAAA
1 TTAAAA-ATATTTAAAAA
* *
657829 ATAAATATATTTA
1 TTAAAAATATTTA
657842 TTATATCAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:658448 original size:11 final size:11
Alignment explanation
Indices: 658432--658462 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
658422 TCAATTATTT
658432 TCTCAATTTCC
1 TCTCAATTTCC
*
658443 TCTCAATTTGC
1 TCTCAATTTCC
658454 TCTCAATTT
1 TCTCAATTT
658463 TCTTCCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.29, G:0.03, T:0.48
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:658482 original size:11 final size:11
Alignment explanation
Indices: 658418--658483 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 11
658408 AAACTAATCA
658418 TCTCTCAATTATT
1 TCTCTCAA--ATT
658431 T-TCTC-AATT
1 TCTCTCAAATT
658440 TCCTCTC-AATT
1 T-CTCTCAAATT
*
658451 TGCTCTCAATTT
1 T-CTCTCAAATT
658463 TCT-TCCAAATT
1 TCTCT-CAAATT
658474 TCTCTCAAAT
1 TCTCTCAAAT
658484 CCATATTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 4 0.09
10 1 0.02
11 30 0.67
12 9 0.20
13 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.02, T:0.48
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:658519 original size:29 final size:28
Alignment explanation
Indices: 658470--658525 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
658460 TTTTCTTCCA
*
658470 AATTTCTCTCAAATCCATATTTAATTTT
1 AATTTCTCTCAAATCCATATTAAATTTT
*
658498 AATTTGCTCTCAATTTCC-TATTAAATTT
1 AATTT-CTCTCAA-ATCCATATTAAATTT
658526 CTCTTAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.21
29 16 0.67
30 3 0.12
ACGTcount: A:0.30, C:0.18, G:0.02, T:0.50
Consensus pattern (28 bp):
AATTTCTCTCAAATCCATATTAAATTTT
Found at i:660655 original size:21 final size:21
Alignment explanation
Indices: 660629--660676 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
660619 CGAACACCGA
*
660629 CAACCAG-ATGCCCTATCGGAG
1 CAACCAGAAT-CCCCATCGGAG
*
660650 CAACCAGAATCCCCGTCGGAG
1 CAACCAGAATCCCCATCGGAG
660671 CAACCA
1 CAACCA
660677 CAACCCCCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.31, C:0.38, G:0.21, T:0.10
Consensus pattern (21 bp):
CAACCAGAATCCCCATCGGAG
Found at i:660684 original size:21 final size:21
Alignment explanation
Indices: 660644--660686 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
660634 AGATGCCCTA
* *
660644 TCGGAGCAACCAGAATCCCCG
1 TCGGAGCAACCACAACCCCCG
660665 TCGGAGCAACCACAACCCCCG
1 TCGGAGCAACCACAACCCCCG
660686 T
1 T
660687 TGGAAGCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.42, G:0.21, T:0.09
Consensus pattern (21 bp):
TCGGAGCAACCACAACCCCCG
Found at i:660959 original size:27 final size:26
Alignment explanation
Indices: 660927--661007 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 26
660917 AAACCCTAAC
660927 AAAAACCCTAACCCTAACCCTTAACTT
1 AAAAA-CCTAACCCTAACCCTTAACTT
660954 --AAA---AACCCTAACCCTTAACTT
1 AAAAACCTAACCCTAACCCTTAACTT
** *
660975 AAAAACCATAACTGTAACTCTTAACTT
1 AAAAACC-TAACCCTAACCCTTAACTT
661002 AAAAAC
1 AAAAAC
661008 ACCAAAACCT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
21 18 0.40
23 3 0.07
25 3 0.07
27 21 0.47
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (26 bp):
AAAAACCTAACCCTAACCCTTAACTT
Found at i:660962 original size:21 final size:21
Alignment explanation
Indices: 660936--660986 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
660926 CAAAAACCCT
660936 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
660957 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
660978 AACCATAAC
1 AACCCTAAC
660987 TGTAACTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Done.