Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 79 of 150
Found at i:24027403 original size:27 final size:27
Alignment explanation
Indices: 24027373--24027425 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
24027363 AATTAAAAAT
*
24027373 TTTTATAAAAATT-CCAAAATATATATG
1 TTTTA-AAAAATTACAAAAATATATATG
*
24027400 TTTTAAAAAATTATAAAAATATATAT
1 TTTTAAAAAATTACAAAAATATATAT
24027426 ATAAAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (27 bp):
TTTTAAAAAATTACAAAAATATATATG
Found at i:24031525 original size:43 final size:43
Alignment explanation
Indices: 24031469--24031614 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 43
24031459 TTACTGAGAG
* * * *
24031469 GTGATAACATGTAACACCATGTCTGGGACATTGGCATTG-TATT
1 GTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTA-T
* * *
24031512 GTGATTACGTGTAAGACCATGTTTAGGACATTAGCATCGTTAT
1 GTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAT
* * * * * *
24031555 ATGATTTCGTTTAAGACCATGTCTGGGATAGTGGCATCGATAT
1 GTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAT
* *
24031598 GTGATAACATGTAAGAC
1 GTGATTACGTGTAAGAC
24031615 TATATCTAGG
Statistics
Matches: 81, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
43 79 0.98
44 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (43 bp):
GTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAT
Found at i:24033873 original size:16 final size:16
Alignment explanation
Indices: 24033852--24033883 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24033842 TGTTTTTTTA
24033852 ATATAAATGAATCTAT
1 ATATAAATGAATCTAT
*
24033868 ATATAAATGTATCTAT
1 ATATAAATGAATCTAT
24033884 GTTATGATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (16 bp):
ATATAAATGAATCTAT
Found at i:24036167 original size:14 final size:14
Alignment explanation
Indices: 24036148--24036178 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
24036138 CTAATTTATT
24036148 AATGAAATATTAAA
1 AATGAAATATTAAA
*
24036162 AATGAATTATTAAA
1 AATGAAATATTAAA
24036176 AAT
1 AAT
24036179 AACTTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (14 bp):
AATGAAATATTAAA
Found at i:24038991 original size:184 final size:184
Alignment explanation
Indices: 24038675--24039050 Score: 655
Period size: 184 Copynumber: 2.0 Consensus size: 184
24038665 AAAAATGACC
* * *
24038675 CATTAAGATGTCTACAAGCCCATCTTGAAGTTTGAAAAGTAATTTAATTAAATATCAGGCCAAAT
1 CATTAAAATGTCTACAAGCCCATCCTGAAGTTTGAAAAGCAATTTAATTAAATATCAGGCCAAAT
* *
24038740 TATCAAAGTGGCCCAAATTGTAAACTATTTAAGCTATAGGTTCAATTTTATTTTAATAGGTGGAT
66 TATCAAAATGGCCCAAATTGTAAACTATTTAAACTATAGGTTCAATTTTATTTTAATAGGTGGAT
24038805 CATCATGTAAGAATTCAGCCCAAAGAGCCCATTTAATTCCTTTGGCTAAATTCT
131 CATCATGTAAGAATTCAGCCCAAAGAGCCCATTTAATTCCTTTGGCTAAATTCT
* * *
24038859 CATTAAAATGTCTACAAGCTCATCCTGAAGTTTGGAAAGCAATTTAATTAAATATCAGGTCAAAT
1 CATTAAAATGTCTACAAGCCCATCCTGAAGTTTGAAAAGCAATTTAATTAAATATCAGGCCAAAT
24038924 TATCAAAATGGCCCAAATTGTAAGA-TATTTAAACTATAGGTTCAATTTTATTTTAATAGGTGGA
66 TATCAAAATGGCCCAAATTGTAA-ACTATTTAAACTATAGGTTCAATTTTATTTTAATAGGTGGA
*
24038988 TCATCATGTAAGAATTCAGCCCAAAGAGCCCATTTAATTCCTTTGGCTGAATTCT
130 TCATCATGTAAGAATTCAGCCCAAAGAGCCCATTTAATTCCTTTGGCTAAATTCT
24039043 CATTAAAA
1 CATTAAAA
24039051 GTTCACACTT
Statistics
Matches: 182, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
184 181 0.99
185 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (184 bp):
CATTAAAATGTCTACAAGCCCATCCTGAAGTTTGAAAAGCAATTTAATTAAATATCAGGCCAAAT
TATCAAAATGGCCCAAATTGTAAACTATTTAAACTATAGGTTCAATTTTATTTTAATAGGTGGAT
CATCATGTAAGAATTCAGCCCAAAGAGCCCATTTAATTCCTTTGGCTAAATTCT
Found at i:24049086 original size:34 final size:35
Alignment explanation
Indices: 24049042--24049108 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
24049032 CAGTAAAATA
*
24049042 TTTTCCGTAAAATGATTT-TTGGAAAATATTTTAT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAT
*
24049076 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
24049109 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAT
Found at i:24049426 original size:18 final size:19
Alignment explanation
Indices: 24049405--24049455 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 19
24049395 TTCATGAGCT
24049405 TTTTATAATTATTTTTA-A
1 TTTTATAATTATTTTTATA
24049423 TTTTA-AA--ATTTTTATA
1 TTTTATAATTATTTTTATA
*
24049439 TTTTTTAATTTATTTTT
1 TTTTATAA-TTATTTTT
24049456 TGACAGTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
15 7 0.26
16 5 0.19
17 4 0.15
18 5 0.19
20 6 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTATAATTATTTTTATA
Found at i:24052809 original size:35 final size:33
Alignment explanation
Indices: 24052746--24052811 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 33
24052736 AAAAAATAAT
*
24052746 TATTTTTATATTTAAAATATTTATAAATTATGC
1 TATTTTTATATTTAAAATATTTAAAAATTATGC
24052779 TATTTTTA-ATTTATAAAAGTATTTAAAAATTAT
1 TATTTTTATA-TT-TAAAA-TATTTAAAAATTAT
24052812 TTTTTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 1 0.03
33 10 0.34
34 5 0.17
35 13 0.45
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (33 bp):
TATTTTTATATTTAAAATATTTAAAAATTATGC
Found at i:24052827 original size:31 final size:30
Alignment explanation
Indices: 24052743--24052829 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 30
24052733 TTTAAAAAAT
* *
24052743 AATTA-TTTTTATATTTAAAA-TATTTATA
1 AATTATTTTTTAAATTTAAAAGTATTTAAA
*
24052771 AATTATGCTATTTTTAATTTATAAAAGTATTTAAA
1 AATTA---T-TTTTTAAATT-TAAAAGTATTTAAA
24052806 AATTATTTTTTAAAATTTAAAAGT
1 AATTATTTTTT-AAATTTAAAAGT
24052830 TTATAAGTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
28 5 0.11
31 12 0.26
32 5 0.11
33 8 0.17
34 5 0.11
35 12 0.26
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (30 bp):
AATTATTTTTTAAATTTAAAAGTATTTAAA
Found at i:24055487 original size:85 final size:84
Alignment explanation
Indices: 24055398--24055643 Score: 244
Period size: 84 Copynumber: 2.9 Consensus size: 84
24055388 TTGGGCAAGT
* * * *
24055398 CGAAGCAATTATAATGGCACACGAGGTGTAT-ATCGGACGAACCAAAGCAATTATACTGGCACAC
1 CGAAGTAATTATAATGGCACA-GAAGTGCATCATCAGACGAACCAAAGCAATTATACTGG--CAC
24055462 GTAA-TGCATCATCGAATAAAC
63 GTAAGTGCATCATCGAATAAAC
** * * * * *
24055483 CGAAGTAATTATGCTGGCACATAAGTGCATCATTAGATGTACCGAAGCAATTATACTGGCACGTA
1 CGAAGTAATTATAATGGCACAGAAGTGCATCATCAGACGAACCAAAGCAATTATACTGGCACGTA
*
24055548 AGTGCATCATCGGATAAAC
66 AGTGCATCATCGAATAAAC
* * * * ** * * * *
24055567 CGAAATAATTATACTGACACATAAGTGCATCATCAGATAAACCAAAACAAATATACTAGCAGGTA
1 CGAAGTAATTATAATGGCACAGAAGTGCATCATCAGACGAACCAAAGCAATTATACTGGCACGTA
*
24055632 AGTGCATTATCG
66 AGTGCATCATCG
24055644 GCTAAATCAA
Statistics
Matches: 135, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
83 7 0.05
84 87 0.64
85 41 0.30
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (84 bp):
CGAAGTAATTATAATGGCACAGAAGTGCATCATCAGACGAACCAAAGCAATTATACTGGCACGTA
AGTGCATCATCGAATAAAC
Found at i:24055527 original size:42 final size:42
Alignment explanation
Indices: 24055437--24055609 Score: 206
Period size: 42 Copynumber: 4.1 Consensus size: 42
24055427 ATATCGGACG
* *
24055437 AACCAAAGCAATTATACTGGCACACGTAA-TGCATCATC-GAATA
1 AACCGAAGTAATTATACTGGCACA--TAAGTGCATCATCAG-ATA
* * *
24055480 AACCGAAGTAATTATGCTGGCACATAAGTGCATCATTAGATG
1 AACCGAAGTAATTATACTGGCACATAAGTGCATCATCAGATA
* * * *
24055522 TACCGAAGCAATTATACTGGCACGTAAGTGCATCATCGGATA
1 AACCGAAGTAATTATACTGGCACATAAGTGCATCATCAGATA
* *
24055564 AACCGAAATAATTATACTGACACATAAGTGCATCATCAGATA
1 AACCGAAGTAATTATACTGGCACATAAGTGCATCATCAGATA
24055606 AACC
1 AACC
24055610 AAAACAAATA
Statistics
Matches: 110, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
41 3 0.03
42 85 0.77
43 22 0.20
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (42 bp):
AACCGAAGTAATTATACTGGCACATAAGTGCATCATCAGATA
Found at i:24055588 original size:84 final size:84
Alignment explanation
Indices: 24055437--24055649 Score: 275
Period size: 84 Copynumber: 2.5 Consensus size: 84
24055427 ATATCGGACG
* * * *
24055437 AACCAAAGCAATTATACTGGCACACGTAA-TGCATCATCGAATAAACCGAAGTAATTATGCTGGC
1 AACCAAAGCAATTATACTGG--CACGTAAGTGCATCATCGGATAAACCGAAATAATTATACTGAC
* *
24055501 ACATAAGTGCATCATTAGATG
64 ACATAAGTGCATCATCAGATA
* *
24055522 TACCGAAGCAATTATACTGGCACGTAAGTGCATCATCGGATAAACCGAAATAATTATACTGACAC
1 AACCAAAGCAATTATACTGGCACGTAAGTGCATCATCGGATAAACCGAAATAATTATACTGACAC
24055587 ATAAGTGCATCATCAGATA
66 ATAAGTGCATCATCAGATA
* * * * * *
24055606 AACCAAAACAAATATACTAGCAGGTAAGTGCATTATCGGCTAAA
1 AACCAAAGCAATTATACTGGCACGTAAGTGCATCATCGGATAAA
24055650 TCAAAGTATA
Statistics
Matches: 111, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
83 7 0.06
84 86 0.77
85 18 0.16
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (84 bp):
AACCAAAGCAATTATACTGGCACGTAAGTGCATCATCGGATAAACCGAAATAATTATACTGACAC
ATAAGTGCATCATCAGATA
Found at i:24055634 original size:42 final size:41
Alignment explanation
Indices: 24055437--24055638 Score: 176
Period size: 42 Copynumber: 4.8 Consensus size: 41
24055427 ATATCGGACG
24055437 AACC-AAAGCAATTATACTGGCACACGTAA-TGCATCATC-GAATA
1 AACCGAAA-CAATTATACT-G--CACGTAAGTGCATCATCAG-ATA
** * * * *
24055480 AACCGAAGTAATTATGCTGGCACATAAGTGCATCATTAGATG
1 AACCGAAACAATTATACT-GCACGTAAGTGCATCATCAGATA
* * *
24055522 TACCGAAGCAATTATACTGGCACGTAAGTGCATCATCGGATA
1 AACCGAAACAATTATACT-GCACGTAAGTGCATCATCAGATA
* *
24055564 AACCGAAATAATTATACTGACACATAAGTGCATCATCAGATA
1 AACCGAAACAATTATACTG-CACGTAAGTGCATCATCAGATA
* * *
24055606 AACCAAAACAAATATACTAGCAGGTAAGTGCAT
1 AACCGAAACAATTATACT-GCACGTAAGTGCAT
24055639 TATCGGCTAA
Statistics
Matches: 131, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
41 7 0.05
42 106 0.81
43 16 0.12
44 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.23
Consensus pattern (41 bp):
AACCGAAACAATTATACTGCACGTAAGTGCATCATCAGATA
Found at i:24060136 original size:673 final size:672
Alignment explanation
Indices: 24058851--24060198 Score: 2660
Period size: 673 Copynumber: 2.0 Consensus size: 672
24058841 CACCAAGGCC
24058851 ATTAATATTGCAACATATCATACCATTTCAAAACCCAATTTAATTCTCTTTACAAGCCATATTCA
1 ATTAATATTGCAACATATCATACCATTTCAAAACCCAATTTAATTCTCTTTACAAGCCATATTCA
*
24058916 ATTAACCAAGCTCATACATTAACCTTTAAAACCATAAGTGCATATAAACATAGTTTTATATCAAA
66 ATTAACCAAGCTCATACATTAACCTTTAAAACCATAAGTGAATATAAACATAGTTTTATATCAAA
24058981 TATGACCCAGCCTAGGTACATGCCAAAATTAGAACAAATAGAATTTGTACGAAATTCGTTGAGTT
131 TATGACCCAGCCTAGGTACATGCCAAAATTAGAACAAATAGAATTTGTACGAAATTCGTTGAGTT
24059046 AGGGATCGATTTCTAGATGCTGGATCAACTGCTCGAACAACCTAAATCTACTTTACTTGCGAGAA
196 AGGGATCGATTTCTAGATGCTGGATCAACTGCTCGAACAACCTAAATCTACTTTACTTGCGAGAA
24059111 AGAAAAACAAATCGTACACTAAGTAAGTACGTTCAGTGGTAAATTTATGATTCAAGACAACATAA
261 AGAAAAACAAATCGTACACTAAGTAAGTACGTTCAGTGGTAAATTTATGATTCAAGACAACATAA
*
24059176 TAATATTATGCAAAATGCACATATTCAATTCTTAACCCAATCATATACCATTTATGTCAACCACT
326 TAATATTATGCAAAATGCACATATTCAATTCTTAACCCAATCACATACCATTTATGTCAACCACT
24059241 TTCAATCTCAATAGTTATGTTTATACCAATATTTACATGCCAATTTACTTACCTATTCATGCCAA
391 TTCAATCTCAATAGTTATGTTTATACCAATATTTACATGCCAATTTACTTACCTATTCATGCCAA
24059306 AACTATCATTTCTACTTAACTTATACATATTCGTTTATGCAACTCAATTCAAAACATGAGTTTCT
456 AACTATCATTTCTACTTAACTTATACATATTCGTTTATGCAACTCAATTCAAAACATGAGTTTCT
24059371 AAACATACCATTCAATTCACAAGTATAAATTCATCATCTTGAATACATTTATATAGATATTTATA
521 AAACATACCATTCAATTCACAAGTATAAATTCATCATCTTGAATACATTTATATAGATATTTATA
24059436 CTCAATTACATGTTCATTTCAATCATTTCCGAGAAGCTCATTCATACTCAATCCACCCATTTGGC
586 CTCAATTACATGTTCATTTCAATCATTTCCGAGAAGCTCATTCATACTCAATCCACCCATTTGGC
24059501 TCATTGACCATTTGTTTTGCAT
651 TCATTGACCATTTGTTTTGCAT
24059523 ATTAATATTGCAACATATCATACCATTTCAAAACCCAATTTAATTCTCTTTACAAGCCATATTCA
1 ATTAATATTGCAACATATCATACCATTTCAAAACCCAATTTAATTCTCTTTACAAGCCATATTCA
24059588 ATTAACCAAGCTCATACATTAACCTTTAAAACCATAAGTGAATATAAACATAGTTTTATATCAAA
66 ATTAACCAAGCTCATACATTAACCTTTAAAACCATAAGTGAATATAAACATAGTTTTATATCAAA
24059653 TATGACCCAGCCTAGGTACATGCCAAAATTAGAACAAATAGAATTTGTACGAAATTCGTTGAGTT
131 TATGACCCAGCCTAGGTACATGCCAAAATTAGAACAAATAGAATTTGTACGAAATTCGTTGAGTT
24059718 AGGGATCGATTTCTAGATGCTGGATCAACTGCTCGAACAACCTAAATCTACTTTACTTGCGCAGA
196 AGGGATCGATTTCTAGATGCTGGATCAACTGCTCGAACAACCTAAATCTACTTTACTTGCG-AGA
24059783 AAGAAAAACAAATCGTACACTAAGTAAGTACGTTCAGTGGTAAATTTATGATTCAAGACAACATA
260 AAGAAAAACAAATCGTACACTAAGTAAGTACGTTCAGTGGTAAATTTATGATTCAAGACAACATA
24059848 ATAATATTATGCAAAATGCACATATTCAATTCTTAACCCAATCACATACCATTTATGTCAACCAC
325 ATAATATTATGCAAAATGCACATATTCAATTCTTAACCCAATCACATACCATTTATGTCAACCAC
24059913 TTTCAATCTCAATAGTTATGTTTATACCAATATTTACATGCCAATTTACTTACCTATTCATGCCA
390 TTTCAATCTCAATAGTTATGTTTATACCAATATTTACATGCCAATTTACTTACCTATTCATGCCA
24059978 AAACTATCATTTCTACTTAACTTATACATATTCGTTTATGCAACTCAATTCAAAACATGAGTTTC
455 AAACTATCATTTCTACTTAACTTATACATATTCGTTTATGCAACTCAATTCAAAACATGAGTTTC
*
24060043 TAAACATACCATTCAATTCACAAGTATAAATTCATCATTTTGAATACATTTATATAGATATTTAT
520 TAAACATACCATTCAATTCACAAGTATAAATTCATCATCTTGAATACATTTATATAGATATTTAT
24060108 ACTCAATTACATGTTCATTTCAATCATTTCCGAGAAGCTCATTCATACTCAATCCACCCATTTGG
585 ACTCAATTACATGTTCATTTCAATCATTTCCGAGAAGCTCATTCATACTCAATCCACCCATTTGG
24060173 CTCATTGACCATTTGTTTTGCAT
650 CTCATTGACCATTTGTTTTGCAT
24060196 ATT
1 ATT
24060199 GCAATTCAAA
Statistics
Matches: 672, Mismatches: 3, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
672 255 0.38
673 417 0.62
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (672 bp):
ATTAATATTGCAACATATCATACCATTTCAAAACCCAATTTAATTCTCTTTACAAGCCATATTCA
ATTAACCAAGCTCATACATTAACCTTTAAAACCATAAGTGAATATAAACATAGTTTTATATCAAA
TATGACCCAGCCTAGGTACATGCCAAAATTAGAACAAATAGAATTTGTACGAAATTCGTTGAGTT
AGGGATCGATTTCTAGATGCTGGATCAACTGCTCGAACAACCTAAATCTACTTTACTTGCGAGAA
AGAAAAACAAATCGTACACTAAGTAAGTACGTTCAGTGGTAAATTTATGATTCAAGACAACATAA
TAATATTATGCAAAATGCACATATTCAATTCTTAACCCAATCACATACCATTTATGTCAACCACT
TTCAATCTCAATAGTTATGTTTATACCAATATTTACATGCCAATTTACTTACCTATTCATGCCAA
AACTATCATTTCTACTTAACTTATACATATTCGTTTATGCAACTCAATTCAAAACATGAGTTTCT
AAACATACCATTCAATTCACAAGTATAAATTCATCATCTTGAATACATTTATATAGATATTTATA
CTCAATTACATGTTCATTTCAATCATTTCCGAGAAGCTCATTCATACTCAATCCACCCATTTGGC
TCATTGACCATTTGTTTTGCAT
Found at i:24063722 original size:17 final size:18
Alignment explanation
Indices: 24063700--24063735 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
24063690 TCCACAGAAT
24063700 ATATTTTTAT-TTTTTTC
1 ATATTTTTATATTTTTTC
*
24063717 ATATTTTTCTATTTTTTC
1 ATATTTTTATATTTTTTC
24063735 A
1 A
24063736 CTTTTTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (18 bp):
ATATTTTTATATTTTTTC
Found at i:24066633 original size:22 final size:21
Alignment explanation
Indices: 24066595--24066639 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
24066585 TTGATCATCA
*
24066595 CTTTTCTTTCTGTCACATTTT
1 CTTTTCTTTCTGTCACAATTT
24066616 CTTTTCTTTTCATG-CACAATTT
1 CTTTTC-TTTC-TGTCACAATTT
24066638 CT
1 CT
24066640 AGCAAGAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 13 0.62
23 2 0.10
ACGTcount: A:0.13, C:0.24, G:0.04, T:0.58
Consensus pattern (21 bp):
CTTTTCTTTCTGTCACAATTT
Found at i:24074679 original size:13 final size:13
Alignment explanation
Indices: 24074661--24074685 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24074651 ATGGAACCAC
24074661 ATGATCTACATGT
1 ATGATCTACATGT
24074674 ATGATCTACATG
1 ATGATCTACATG
24074686 AAAGTTGATT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
ATGATCTACATGT
Found at i:24076686 original size:18 final size:18
Alignment explanation
Indices: 24076665--24076724 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
24076655 AAAAAATATA
* *
24076665 TTAAAGTTTTTAAAGTTT
1 TTAAAATTTTTAAACTTT
*
24076683 TTAAAATTTTTATACTTT
1 TTAAAATTTTTAAACTTT
* *
24076701 TTAAATAATTTTAATAATTT
1 TTAAA-ATTTTTAA-ACTTT
24076721 TTAA
1 TTAA
24076725 TTTGAATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 20 0.59
19 6 0.18
20 8 0.24
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (18 bp):
TTAAAATTTTTAAACTTT
Found at i:24076693 original size:10 final size:9
Alignment explanation
Indices: 24076665--24076705 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
24076655 AAAAAATATA
24076665 TTAAAGTTT
1 TTAAAGTTT
24076674 TTAAAGTTT
1 TTAAAGTTT
*
24076683 TTAAAATTT
1 TTAAAGTTT
* *
24076692 TTATACTTT
1 TTAAAGTTT
24076701 TTAAA
1 TTAAA
24076706 TAATTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (9 bp):
TTAAAGTTT
Found at i:24076712 original size:20 final size:20
Alignment explanation
Indices: 24076687--24076767 Score: 60
Period size: 20 Copynumber: 4.0 Consensus size: 20
24076677 AAGTTTTTAA
* *
24076687 AATTTTTATACTTTTTAAAT
1 AATTTTAATAATTTTTAAAT
*
24076707 AATTTTAATAATTTTTAATTT
1 AATTTTAATAATTTTTAA-AT
*
24076728 GAATTTAAAATAATTTTTATAAT
1 -AATTT-TAATAATTTTTA-AAT
24076751 -ATTTT--TGAATTTTTAAA
1 AATTTTAAT-AATTTTTAAA
24076768 ATTTTAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
18 3 0.06
19 8 0.16
20 16 0.32
21 5 0.10
22 5 0.10
23 12 0.24
24 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (20 bp):
AATTTTAATAATTTTTAAAT
Found at i:24077991 original size:16 final size:16
Alignment explanation
Indices: 24077970--24078021 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
24077960 GGTTTAATCG
24077970 ATTTAGTTGTTTGTTT
1 ATTTAGTTGTTTGTTT
*
24077986 ATTTAGTTGTTTATTT
1 ATTTAGTTGTTTGTTT
*
24078002 ATTTTAGTTATTTAGTTT
1 A-TTTAGTTGTTT-GTTT
24078020 AT
1 AT
24078022 GATATTTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 16 0.52
17 11 0.35
18 4 0.13
ACGTcount: A:0.19, C:0.00, G:0.13, T:0.67
Consensus pattern (16 bp):
ATTTAGTTGTTTGTTT
Found at i:24078148 original size:33 final size:33
Alignment explanation
Indices: 24078111--24078190 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
24078101 CTTTTTATGC
*
24078111 AAGCGCCGCAAAAAGTATTTGCGGCGTTTTTGA
1 AAGCGCCGCAAAAAGTATTTCCGGCGTTTTTGA
24078144 AAGCGCCGCAAAAAGTATTTCCGGCGTTTTTGA
1 AAGCGCCGCAAAAAGTATTTCCGGCGTTTTTGA
*
24078177 AAGCACCGCAAAAA
1 AAGCGCCGCAAAAA
24078191 ATGCCGCTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.23
Consensus pattern (33 bp):
AAGCGCCGCAAAAAGTATTTCCGGCGTTTTTGA
Found at i:24078293 original size:43 final size:43
Alignment explanation
Indices: 24078226--24078451 Score: 326
Period size: 43 Copynumber: 5.3 Consensus size: 43
24078216 TTTTAGAAAT
* *
24078226 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * *
24078269 AAATGTCGCTATAGATCAGGACCTTTAGCGTCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * *
24078312 AAACGCCGCTATAGATTAGGACCTTTAGCGGCGTTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
*
24078355 AAACGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * *
24078398 AAACGCTGCTATAGCTCAAGACCTTTAGCGACGCTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
*
24078441 AAAAGCCGCTA
1 AAACGCCGCTA
24078452 AAAATACTGT
Statistics
Matches: 165, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 165 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
Found at i:24080883 original size:3 final size:3
Alignment explanation
Indices: 24080875--24080922 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
24080865 AGAAAATCAT
24080875 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
24080923 AGGAATCACC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:24082182 original size:22 final size:24
Alignment explanation
Indices: 24082145--24082188 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
24082135 AATAACTTAG
24082145 GGAAATTTAGGGGAAACGAAGTTA
1 GGAAATTTAGGGGAAACGAAGTTA
*
24082169 GGAAA-TT-GGGGAAATGAAGT
1 GGAAATTTAGGGGAAACGAAGT
24082189 CGGGAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 2 0.11
24 5 0.26
ACGTcount: A:0.41, C:0.02, G:0.36, T:0.20
Consensus pattern (24 bp):
GGAAATTTAGGGGAAACGAAGTTA
Found at i:24082194 original size:22 final size:24
Alignment explanation
Indices: 24082144--24082195 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
24082134 GAATAACTTA
*
24082144 GGGAAATTTAGGGGAAACGAAGTT
1 GGGAAATTTAGGGGAAACGAAGTC
* *
24082168 AGGAAA-TT-GGGGAAATGAAGTC
1 GGGAAATTTAGGGGAAACGAAGTC
24082190 GGGAAA
1 GGGAAA
24082196 ATCTGACATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 17 0.71
23 2 0.08
24 5 0.21
ACGTcount: A:0.40, C:0.04, G:0.38, T:0.17
Consensus pattern (24 bp):
GGGAAATTTAGGGGAAACGAAGTC
Found at i:24083380 original size:13 final size:13
Alignment explanation
Indices: 24083362--24083402 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
24083352 ACTAGTTAAT
24083362 CTAAACCTAAACC
1 CTAAACCTAAACC
24083375 CTAAACCTAAACC
1 CTAAACCTAAACC
24083388 CTAAAACCCTAAACC
1 CT-AAA-CCTAAACC
24083403 TTTAGCACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 15 0.58
14 3 0.12
15 8 0.31
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.15
Consensus pattern (13 bp):
CTAAACCTAAACC
Found at i:24083396 original size:8 final size:7
Alignment explanation
Indices: 24083362--24083402 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
24083352 ACTAGTTAAT
24083362 CTAAA-C
1 CTAAACC
24083368 CTAAACC
1 CTAAACC
24083375 CTAAA-C
1 CTAAACC
24083381 CTAAACC
1 CTAAACC
24083388 CTAAAACC
1 CT-AAACC
24083396 CTAAACC
1 CTAAACC
24083403 TTTAGCACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 11 0.34
7 14 0.44
8 7 0.22
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:24083450 original size:7 final size:7
Alignment explanation
Indices: 24083440--24083493 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
24083430 CCCCAGCCTT
24083440 TAAACCA
1 TAAACCA
24083447 TAAACCA
1 TAAACCA
*
24083454 TAAATCA
1 TAAACCA
* *
24083461 TAACCCC
1 TAAACCA
24083468 TAAACCCA
1 TAAA-CCA
*
24083476 TAATCCA
1 TAAACCA
*
24083483 TAAACCT
1 TAAACCA
24083490 TAAA
1 TAAA
24083494 ATAGTAACTC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCA
Found at i:24083968 original size:42 final size:41
Alignment explanation
Indices: 24083862--24083968 Score: 101
Period size: 42 Copynumber: 2.6 Consensus size: 41
24083852 TTTTTTGCGG
** *
24083862 CGCTTTTTCAAAAACACCGTTAAA-AATAGAGCATTAGCGG
1 CGCTTTTTCAAAAACACCGTTAAAGAATAGAGCAACAGCGA
* * * * * *
24083902 TGCTTTTCCAAAAACGCTGCTAAAGACCA-ATAGCAACAGCGA
1 CGCTTTTTCAAAAACACCGTTAAAGA--ATAGAGCAACAGCGA
24083944 CGCTTTTTCAAAAACACCGTTAAAG
1 CGCTTTTTCAAAAACACCGTTAAAG
24083969 TTGACTTTTT
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
40 19 0.38
41 1 0.02
42 29 0.58
43 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (41 bp):
CGCTTTTTCAAAAACACCGTTAAAGAATAGAGCAACAGCGA
Found at i:24084112 original size:41 final size:41
Alignment explanation
Indices: 24084044--24084123 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
24084034 AAAATCATGA
* * * * *
24084044 ACATTAGCGGCGCTTTCTCACAGACGCCGCTAAATCCCCAT
1 ACATTAGCGACGCTTTCTCAAAAACGCCACTAAAGCCCCAT
* *
24084085 ACATTAGCGACGCTTTTTGAAAAACGCCACTAAAGCCCC
1 ACATTAGCGACGCTTTCTCAAAAACGCCACTAAAGCCCC
24084124 TAAAACACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.21
Consensus pattern (41 bp):
ACATTAGCGACGCTTTCTCAAAAACGCCACTAAAGCCCCAT
Found at i:24085636 original size:27 final size:26
Alignment explanation
Indices: 24085606--24085666 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
24085596 TGCTTTTGGG
*
24085606 TTAATAAAATTCTCTTTGATTTTTATT
1 TTAATAAAATTCTC-TTGAGTTTTATT
*
24085633 TTAA-AGAAATTCTCTTGAGTTTTCTT
1 TTAATA-AAATTCTCTTGAGTTTTATT
24085659 TTAGATAA
1 TTA-ATAA
24085667 GTTTTAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 14 0.48
27 14 0.48
28 1 0.03
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.52
Consensus pattern (26 bp):
TTAATAAAATTCTCTTGAGTTTTATT
Found at i:24096059 original size:27 final size:25
Alignment explanation
Indices: 24096029--24096084 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 25
24096019 TGTTTTTCAG
24096029 TTAATGAAATTCTCTTTGAGTTTTCTT
1 TTAAT-AAATTCTC-TTGAGTTTTCTT
*
24096056 TTAAATAATTTCTCTTGAGTTTTCTT
1 TT-AATAAATTCTCTTGAGTTTTCTT
24096082 TTA
1 TTA
24096085 GAAGAGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 1 0.04
26 14 0.52
27 9 0.33
28 3 0.11
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (25 bp):
TTAATAAATTCTCTTGAGTTTTCTT
Found at i:24101904 original size:63 final size:63
Alignment explanation
Indices: 24101831--24101958 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
24101821 ATATCGGACC
24101831 ATCTATTCACTACTCACTCAATTTCATTTTGAAAACCTCTAAATTATTTCTACCTAACCCTCA
1 ATCTATTCACTACTCACTCAATTTCATTTTGAAAACCTCTAAATTATTTCTACCTAACCCTCA
* * * *
24101894 ATCTATTCACTATTCACTTAATTTCATTTTTAAAACCTCTAAATTATTTCTATCTAACCCTCA
1 ATCTATTCACTACTCACTCAATTTCATTTTGAAAACCTCTAAATTATTTCTACCTAACCCTCA
24101957 AT
1 AT
24101959 GTTCGTGCCT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.32, C:0.26, G:0.01, T:0.41
Consensus pattern (63 bp):
ATCTATTCACTACTCACTCAATTTCATTTTGAAAACCTCTAAATTATTTCTACCTAACCCTCA
Found at i:24104661 original size:24 final size:25
Alignment explanation
Indices: 24104616--24104663 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
24104606 ATTTTTGGGA
*
24104616 AAATTAATTTTAATCAAATAAAATC
1 AAATTAATTTAAATCAAATAAAATC
* *
24104641 AAATT-ATTTAAATTAATTAAAAT
1 AAATTAATTTAAATCAAATAAAAT
24104664 TAACATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
AAATTAATTTAAATCAAATAAAATC
Found at i:24106490 original size:27 final size:26
Alignment explanation
Indices: 24106431--24106600 Score: 153
Period size: 27 Copynumber: 6.3 Consensus size: 26
24106421 GTGAGGTCAA
* * *
24106431 TAAAATGACCGAAATACCCCGTAGGG
1 TAAAATAACCAAAATACCCCATAGGG
*
24106457 TAAAATAACCGAAATACCCTCATAGGG
1 TAAAATAACCAAAATACCC-CATAGGG
*
24106484 TAAAATAACCAAAATACCCCTTTAGAGG
1 TAAAATAACCAAAATACCCC-ATAG-GG
* * * * *
24106512 -AAAATGACCGAAAGACCCCTGTAAGG
1 TAAAATAACCAAAATACCCC-ATAGGG
* *
24106538 TAAAATAACCAAAACACCGCCATCGGG
1 TAAAATAACCAAAATACC-CCATAGGG
* *
24106565 TAAAATGACCAAAATACCCACATAGGT
1 TAAAATAACCAAAATACCC-CATAGGG
24106592 TAAAATAAC
1 TAAAATAAC
24106601 TATTATACCC
Statistics
Matches: 118, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
26 22 0.19
27 92 0.78
28 4 0.03
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.16
Consensus pattern (26 bp):
TAAAATAACCAAAATACCCCATAGGG
Found at i:24106567 original size:81 final size:80
Alignment explanation
Indices: 24106432--24106583 Score: 225
Period size: 81 Copynumber: 1.9 Consensus size: 80
24106422 TGAGGTCAAT
* * * *
24106432 AAAATGACCGAAATACCCCGTAGGGTAAAATAACCGAAATACCCTCATAGGGTAAAATAACCAAA
1 AAAATGACCGAAAGACCCCGTAAGGTAAAATAACCAAAACACCCTCATAGGGTAAAATAACCAAA
24106497 ATACCCCTTTAGAGG
66 ATACCCCTTTAGAGG
* *
24106512 AAAATGACCGAAAGACCCCTGTAAGGTAAAATAACCAAAACACCGC-CATCGGGTAAAATGACCA
1 AAAATGACCGAAAGACCCC-GTAAGGTAAAATAACCAAAACACC-CTCATAGGGTAAAATAACCA
24106576 AAATACCC
64 AAATACCC
24106584 ACATAGGTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 18 0.28
81 45 0.70
82 1 0.02
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (80 bp):
AAAATGACCGAAAGACCCCGTAAGGTAAAATAACCAAAACACCCTCATAGGGTAAAATAACCAAA
ATACCCCTTTAGAGG
Found at i:24114095 original size:27 final size:27
Alignment explanation
Indices: 24114043--24114184 Score: 189
Period size: 27 Copynumber: 5.3 Consensus size: 27
24114033 GTGAGGTCAA
* * *
24114043 TAAAATGACTGAAATACCTCCGTAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
* *
24114070 TAAAATGACCGGAAGACCCCCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
* *
24114097 TAAAATGATCGAAATACCCCCGTAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
*
24114124 TAAAATGACCAAAATACCCCCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
*
24114151 TAAAATGACCGAAATACCCACAT--GG
1 TAAAATGACCGAAATACCCCCATAGGG
24114176 TAAAATGAC
1 TAAAATGAC
24114185 TGTTATACCC
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
25 11 0.11
27 90 0.89
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCCCATAGGG
Found at i:24114387 original size:26 final size:26
Alignment explanation
Indices: 24114358--24114410 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
24114348 TCTGCCACAT
*
24114358 ATACTATTACTGGTAGCTTTGTTGCG
1 ATACTATTACTGGTAGCTTTGCTGCG
24114384 ATACTATTACTGGTAGCTTTGCTGCG
1 ATACTATTACTGGTAGCTTTGCTGCG
24114410 A
1 A
24114411 ATTTGGTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (26 bp):
ATACTATTACTGGTAGCTTTGCTGCG
Found at i:24122564 original size:17 final size:19
Alignment explanation
Indices: 24122516--24122565 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
24122506 AATAGTATAT
24122516 TATTAATTTTAATATTAAGA
1 TATT-ATTTTAATATTAAGA
*
24122536 TGATTATCTTAATATTAA-A
1 T-ATTATTTTAATATTAAGA
24122555 T-TTATTTTAAT
1 TATTATTTTAAT
24122566 GTTTATCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 9 0.33
19 2 0.07
20 13 0.48
21 3 0.11
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
TATTATTTTAATATTAAGA
Found at i:24125009 original size:16 final size:16
Alignment explanation
Indices: 24124988--24125019 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24124978 TTCATCACAC
*
24124988 TTAGGTTAATTTGCAT
1 TTAGGTTAACTTGCAT
24125004 TTAGGTTAACTTGCAT
1 TTAGGTTAACTTGCAT
24125020 CTAGATAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.47
Consensus pattern (16 bp):
TTAGGTTAACTTGCAT
Found at i:24125837 original size:22 final size:22
Alignment explanation
Indices: 24125803--24125847 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
24125793 AGAAAACCCT
*
24125803 AGAAAAGTGTAGAGAAAAACTAA
1 AGAAAACTGTAGAG-AAAACTAA
24125826 AGAAAACT-TAGAGAAAACTAA
1 AGAAAACTGTAGAGAAAACTAA
24125847 A
1 A
24125848 CCTAAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 5 0.24
23 7 0.33
ACGTcount: A:0.62, C:0.07, G:0.18, T:0.13
Consensus pattern (22 bp):
AGAAAACTGTAGAGAAAACTAA
Found at i:24126371 original size:19 final size:19
Alignment explanation
Indices: 24126349--24126384 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24126339 TTATTACCCA
24126349 AAAAAT-ATAAAAAAATAC
1 AAAAATAATAAAAAAATAC
*
24126367 AAAAATAATGAAAAAATA
1 AAAAATAATAAAAAAATA
24126385 GGCTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (19 bp):
AAAAATAATAAAAAAATAC
Found at i:24129871 original size:6 final size:6
Alignment explanation
Indices: 24129860--24129885 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
24129850 CATTTTGTGC
24129860 TTGCTT TTGCTT TTGCTT TTGCTT TT
1 TTGCTT TTGCTT TTGCTT TTGCTT TT
24129886 ACTGCAGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (6 bp):
TTGCTT
Found at i:24141614 original size:14 final size:15
Alignment explanation
Indices: 24141590--24141618 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
24141580 GTAAACCTTC
24141590 TATCATTTGCCATAG
1 TATCATTTGCCATAG
24141605 TATC-TTTGCCATAG
1 TATCATTTGCCATAG
24141619 CATTTTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (15 bp):
TATCATTTGCCATAG
Found at i:24142721 original size:15 final size:16
Alignment explanation
Indices: 24142698--24142742 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
24142688 TTAATTATAA
24142698 TTAACTTAATTAATCT
1 TTAACTTAATTAATCT
* *
24142714 TTAA-TTAAGTAAACT
1 TTAACTTAATTAATCT
*
24142729 TAAACTTAATTAAT
1 TTAACTTAATTAAT
24142743 ATATTTGGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (16 bp):
TTAACTTAATTAATCT
Found at i:24145958 original size:4 final size:4
Alignment explanation
Indices: 24145949--24146099 Score: 275
Period size: 4 Copynumber: 37.8 Consensus size: 4
24145939 GAGAAGTTGT
24145949 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24145997 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * *
24146045 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA CGTA TGTG TGTG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24146093 TGTA TGT
1 TGTA TGT
24146100 GTGTGTGTGT
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 143 1.00
ACGTcount: A:0.23, C:0.01, G:0.26, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:24146092 original size:2 final size:2
Alignment explanation
Indices: 24146085--24146127 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
24146075 TATGTACGTA
*
24146085 TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
24146127 T
1 T
24146128 TTCTTGTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:24149344 original size:19 final size:19
Alignment explanation
Indices: 24149320--24149459 Score: 99
Period size: 19 Copynumber: 7.5 Consensus size: 19
24149310 TAGCACATAT
*
24149320 AGTGCATATTGGCGCACAA
1 AGTGCATATTGGCACACAA
* *
24149339 AGTGCATCTTGGCCCAC-A
1 AGTGCATATTGGCACACAA
* * * *
24149357 AGCGCATACTAGCACACGA
1 AGTGCATATTGGCACACAA
* * * *
24149376 AGTGCATACTAGCGCA-TA
1 AGTGCATATTGGCACACAA
*
24149394 AGCGCAT-TCCTGGCACACAA
1 AGTGCATAT--TGGCACACAA
* * *
24149414 AGTGCATACTAGCACA-TA
1 AGTGCATATTGGCACACAA
24149432 AGTGCATATTGGCACACAA
1 AGTGCATATTGGCACACAA
24149451 AGTGCATAT
1 AGTGCATAT
24149460 ACCTGTATAG
Statistics
Matches: 93, Mismatches: 22, Indels: 12
0.73 0.17 0.09
Matches are distributed among these distances:
18 35 0.38
19 51 0.55
20 7 0.08
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (19 bp):
AGTGCATATTGGCACACAA
Found at i:24149397 original size:37 final size:37
Alignment explanation
Indices: 24149308--24149458 Score: 160
Period size: 37 Copynumber: 4.0 Consensus size: 37
24149298 AGTAAGGGAA
* * *
24149308 ACTAGCACATATAGTGCATATTGGCGCACAAAGTGCAT
1 ACTAGCACATA-AGCGCATACTGGCACACAAAGTGCAT
* * * * *
24149346 -CTTGGCCCACAAGCGCATACTAGCACACGAAGTGCAT
1 AC-TAGCACATAAGCGCATACTGGCACACAAAGTGCAT
* *
24149383 ACTAGCGCATAAGCGCATTCCTGGCACACAAAGTGCAT
1 ACTAGCACATAAGCGCA-TACTGGCACACAAAGTGCAT
* *
24149421 ACTAGCACATAAGTGCATATTGGCACACAAAGTGCAT
1 ACTAGCACATAAGCGCATACTGGCACACAAAGTGCAT
24149458 A
1 A
24149459 TACCTGTATA
Statistics
Matches: 92, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
37 53 0.58
38 39 0.42
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.20
Consensus pattern (37 bp):
ACTAGCACATAAGCGCATACTGGCACACAAAGTGCAT
Found at i:24150567 original size:45 final size:46
Alignment explanation
Indices: 24150503--24150593 Score: 166
Period size: 47 Copynumber: 2.0 Consensus size: 46
24150493 ATAATTTGAG
24150503 TTTATTATGAATA-TTTTTTTGTGTATGTATCATAACTGATAAAAA
1 TTTATTATGAATATTTTTTTTGTGTATGTATCATAACTGATAAAAA
24150548 TTTATTATGAATATTTTTTTTTGTGTATGTATCATAACTGATAAAA
1 TTTATTATGAATA-TTTTTTTTGTGTATGTATCATAACTGATAAAA
24150594 GTACCCTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 13 0.30
47 31 0.70
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (46 bp):
TTTATTATGAATATTTTTTTTGTGTATGTATCATAACTGATAAAAA
Found at i:24165623 original size:21 final size:20
Alignment explanation
Indices: 24165590--24165715 Score: 60
Period size: 21 Copynumber: 6.2 Consensus size: 20
24165580 TTTTAGAATT
*
24165590 AAAAATATAAAAAATTATTA
1 AAAAATATAAAAAATTATAA
* *
24165610 AAAAATCATTAAAATTTATAA
1 AAAAAT-ATAAAAAATTATAA
* *
24165631 AAAAATTTAGAAATAAAT-TAA
1 AAAAATATA-AAA-AATTATAA
* **
24165652 AAACA-ATAAAATTTTAT-A
1 AAAAATATAAAAAATTATAA
** *
24165670 AAATTTATAAAATAATTTATTA
1 AAAAATATAAAA-AA-TTATAA
** *
24165692 AAAACCATAAAAAATTAGAA
1 AAAAATATAAAAAATTATAA
24165712 AAAA
1 AAAA
24165716 TAATTTATAA
Statistics
Matches: 77, Mismatches: 21, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
18 5 0.06
19 10 0.13
20 17 0.22
21 33 0.43
22 12 0.16
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAATATAAAAAATTATAA
Found at i:24165636 original size:41 final size:41
Alignment explanation
Indices: 24165590--24165717 Score: 106
Period size: 41 Copynumber: 3.2 Consensus size: 41
24165580 TTTTAGAATT
*
24165590 AAAAATATAAAA-AATTATTAAAAAATCATTAAAA-TTTATAA
1 AAAAATATAAAATAATTATTAAAAAA-CAATAAAATTTTAT-A
*
24165631 AAAAATTTAGAAATAA--ATT-AAAAACAATAAAATTTTATA
1 AAAAATATA-AAATAATTATTAAAAAACAATAAAATTTTATA
** * ** *
24165670 AAATTTATAAAATAATTTATT-AAAAACCATAAAAAATTAGA
1 AAAAATATAAAATAA-TTATTAAAAAACAATAAAATTTTATA
24165711 AAAAATA
1 AAAAATA
24165718 ATTTATAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
38 6 0.09
39 14 0.20
40 10 0.14
41 35 0.50
42 3 0.04
43 2 0.03
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (41 bp):
AAAAATATAAAATAATTATTAAAAAACAATAAAATTTTATA
Found at i:24165982 original size:10 final size:10
Alignment explanation
Indices: 24165967--24166016 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
24165957 TGAGAAAAAT
24165967 AAATTTTATA
1 AAATTTTATA
24165977 AAATTTTATA
1 AAATTTTATA
24165987 AAATATTTA-A
1 AAAT-TTTATA
* *
24165997 TTATTTTTATA
1 -AAATTTTATA
24166008 AAATTTTAT
1 AAATTTTAT
24166017 GGTTTTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 26 0.79
11 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
AAATTTTATA
Found at i:24176405 original size:20 final size:19
Alignment explanation
Indices: 24176350--24176394 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
24176340 CATTTCATTG
*
24176350 AGCTCCAATTAGCTCATTTCC
1 AGCTCC-ATGAGCTCATTT-C
*
24176371 AGCTCCATGAACTCATTTC
1 AGCTCCATGAGCTCATTTC
24176390 AGCTC
1 AGCTC
24176395 ATTTGAGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.31
Consensus pattern (19 bp):
AGCTCCATGAGCTCATTTC
Found at i:24188222 original size:50 final size:50
Alignment explanation
Indices: 24188142--24188259 Score: 130
Period size: 50 Copynumber: 2.4 Consensus size: 50
24188132 CAATGCCATA
* * ** * **
24188142 TCCCAGATATGGTCTTTCATGGGAGTTCTCATATCGGTGCCCATTACATG
1 TCCCAGATATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGACATG
* * *
24188192 TCCCAGATATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGATATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGACATG
24188242 TCCCAGACT-TGGTCTTAC
1 TCCCAGA-TATGGTCTTAC
24188260 TTGGGATCTC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 56 0.98
51 1 0.02
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.30
Consensus pattern (50 bp):
TCCCAGATATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGACATG
Found at i:24195386 original size:12 final size:12
Alignment explanation
Indices: 24195360--24195398 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
24195350 CGTTTCTTCT
* *
24195360 TTACTTACTTTC
1 TTACTTGCTTAC
*
24195372 TTACTTGTTTAC
1 TTACTTGCTTAC
24195384 TTACTTGCTTAC
1 TTACTTGCTTAC
24195396 TTA
1 TTA
24195399 AATAACTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.18, C:0.21, G:0.05, T:0.56
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:24198188 original size:14 final size:15
Alignment explanation
Indices: 24198155--24198189 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
24198145 GGACAAAAGA
24198155 GAAAAGAGAAATTGG
1 GAAAAGAGAAATTGG
24198170 GAAAAGAGAAATT-G
1 GAAAAGAGAAATTGG
24198184 GAAAAG
1 GAAAAG
24198190 TGGGTAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.31, T:0.11
Consensus pattern (15 bp):
GAAAAGAGAAATTGG
Found at i:24204940 original size:64 final size:64
Alignment explanation
Indices: 24204834--24204971 Score: 267
Period size: 64 Copynumber: 2.1 Consensus size: 64
24204824 CACCTATTCA
24204834 ATTTGGTCCTAATTCATCCATTTTCCTTAGTTTCTAGATTATTCCAACCTTAAAATATTTGCACT
1 ATTT-GTCCTAATTCATCCATTTTCCTTAGTTTCTAGATTATTCCAACCTTAAAATATTTGCACT
24204899 ATTTGTCCTAATTCATCCATTTTCCTTAGTTTCTAGATTATTCCAACCTTAAAATATTTGCACT
1 ATTTGTCCTAATTCATCCATTTTCCTTAGTTTCTAGATTATTCCAACCTTAAAATATTTGCACT
24204963 ATTTGTCCT
1 ATTTGTCCT
24204972 TTAACTTTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
64 69 0.95
65 4 0.05
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.46
Consensus pattern (64 bp):
ATTTGTCCTAATTCATCCATTTTCCTTAGTTTCTAGATTATTCCAACCTTAAAATATTTGCACT
Found at i:24206557 original size:13 final size:13
Alignment explanation
Indices: 24206539--24206564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24206529 ACTCAATCCC
24206539 GCGTTCAATCCAA
1 GCGTTCAATCCAA
24206552 GCGTTCAATCCAA
1 GCGTTCAATCCAA
24206565 ACTGAGTATT
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:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (13 bp):
GCGTTCAATCCAA
Found at i:24206720 original size:19 final size:20
Alignment explanation
Indices: 24206678--24206720 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
24206668 TCATGCTTTC
*
24206678 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
24206698 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
24206716 TATTC
1 TATTC
24206721 CACTTAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:24206956 original size:51 final size:50
Alignment explanation
Indices: 24206897--24207081 Score: 167
Period size: 51 Copynumber: 3.7 Consensus size: 50
24206887 CCGGTTCACA
* * *
24206897 TAGTAGCCTGTACATAGTACTACACATGTGA-CCATTTCTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCCA--TCTATCTGATACACG
** * * *
24206948 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCTGATACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCCATCTATCTGATACACG
** * ** * *
24206999 TAGTAGCCTGCACATAGCGCTACACATGCAACCCATC-ATTCTGGTACATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCCATCTA-TCTGATACACG
* *
24207049 TAGTAGCCTGTACATAATACTACACACGTGACC
1 TAGTAGCCTGCACATAGTACTACACACGTGACC
24207082 ATCACTTTCA
Statistics
Matches: 104, Mismatches: 27, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
49 1 0.01
50 36 0.35
51 66 0.63
53 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCCATCTATCTGATACACG
Found at i:24213511 original size:413 final size:410
Alignment explanation
Indices: 24212700--24213521 Score: 1365
Period size: 413 Copynumber: 2.0 Consensus size: 410
24212690 TTACACGGCC
*
24212700 TAGCATACGGCCTAGCACACGAGTGTGTGGCTTGACCGTGTAACCCAAGTTAGAGAGTCACACAA
1 TAGCATACGGCCTAGCACACGAGTGTGTGGCTTGACCGTGTAACCCAAGTCAGAGAGTCACACAA
24212765 GCACAGACACAGGTGGGACACGGACGTGTGTCCCTATTTCAAATGTTACATGACCTGTGACACAG
66 GCACAGACACAGGTGGGACACGGACGTGTGTCCCTATTTCAAATGTTACATGACCTGTGACACAG
* * * *
24212830 ACGTGTGTCTCAGCCGTGTGAGGCACACGATCGTGTGACCCCAGTAGTGTGAATTTTTTTAACTT
131 ACGTGTGTCTCAGCCATGTGAGGCACACGACCATGTGACCCCAGCAGTGTGAATTTTTTTAACTT
**
24212895 TTTCCTTAAGGTTTTATATGTTCCCGATTTAGTCTTGAATCATTTCTAAAGTATTTCTAAGGCCT
196 TTTCCTTAAGGTTTTATACATTCCCGATTTAGTCTTGAATCATTTCTAAAGTATTTCTAAGGCCT
** *
24212960 CAAGGGCTCAAATAAGGGACGAATGCATGTATTTGAATGGATTTTTTTATGATTATGAAATGTTT
261 CAAGGGCTCAAATAAGGGACGAATGCATGTATTTGAATCAATTTTTCTATGATTATGAAATGTTT
* *
24213025 GGAAATTAATGATTTTAATTTATGTTTTTATGGTAATGCTCCATAACCCTATTCCAGCAATAGAT
326 GGAAATTAATGATATTAATTTATGTTTTTATGGTAATGCTCCATAACCCTATTCCAACAATAGAT
*
24213090 ACAGGTTAGATCCCACCATT
391 AAAGGTTAGATCCCACCATT
* * * *
24213110 TAGCATACGGCCTGGCACACGGGTGTGTGGCTTGACCGTGTGACCCAAGTCAGAGAGTCACACGA
1 TAGCATACGGCCTAGCACACGAGTGTGTGGCTTGACCGTGTAACCCAAGTCAGAGAGTCACACAA
*
24213175 GCACGGACACAGGCTGGGACACGGACGTGTGTCCCTATTTCAAATGTTACATGACCTGTGACACA
66 GCACAGACACAGG-TGGGACACGGACGTGTGTCCCTATTTCAAATGTTACATGACCTGTGACACA
* * * *
24213240 GGCGTGTGTCTCAGCCATGTGAGGCATACGGCCATGTGACCCCCGCAGTGTGAATTTTTTTCAAC
130 GACGTGTGTCTCAGCCATGTGAGGCACACGACCATGTGACCCCAGCAGTGTGAATTTTTTT-AAC
* *
24213305 TTTTTCCTTAAGGTTTTATACATTCCCGATTTAGTCTTGAATCGTTTCTAAAGTGTTTCTAAGGC
194 TTTTTCCTTAAGGTTTTATACATTCCCGATTTAGTCTTGAATCATTTCTAAAGTATTTCTAAGGC
* * *
24213370 TTCGAGGGCTCGAATAAGGGACGATATGCATGTATTTGAATCAATTTTTCTATGATTATGAAATG
259 CTCAAGGGCTCAAATAAGGGACGA-ATGCATGTATTTGAATCAATTTTTCTATGATTATGAAATG
*
24213435 TTTGGAAATTAATGATATTAATTTATGTTTTTATGGTAATGCTCCGTAACCCTATTCCAACAATA
323 TTTGGAAATTAATGATATTAATTTATGTTTTTATGGTAATGCTCCATAACCCTATTCCAACAATA
24213500 GATAAAGGTTAGATCCCACCAT
388 GATAAAGGTTAGATCCCACCAT
24213522 AGATATGCCT
Statistics
Matches: 381, Mismatches: 28, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
410 72 0.19
411 104 0.27
412 85 0.22
413 120 0.31
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (410 bp):
TAGCATACGGCCTAGCACACGAGTGTGTGGCTTGACCGTGTAACCCAAGTCAGAGAGTCACACAA
GCACAGACACAGGTGGGACACGGACGTGTGTCCCTATTTCAAATGTTACATGACCTGTGACACAG
ACGTGTGTCTCAGCCATGTGAGGCACACGACCATGTGACCCCAGCAGTGTGAATTTTTTTAACTT
TTTCCTTAAGGTTTTATACATTCCCGATTTAGTCTTGAATCATTTCTAAAGTATTTCTAAGGCCT
CAAGGGCTCAAATAAGGGACGAATGCATGTATTTGAATCAATTTTTCTATGATTATGAAATGTTT
GGAAATTAATGATATTAATTTATGTTTTTATGGTAATGCTCCATAACCCTATTCCAACAATAGAT
AAAGGTTAGATCCCACCATT
Found at i:24215615 original size:39 final size:39
Alignment explanation
Indices: 24215567--24215653 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
24215557 CATAGGTATT
24215567 GAAGTACAACAAGGGCACGTATGTGCATTCAAGGGTACC
1 GAAGTACAACAAGGGCACGTATGTGCATTCAAGGGTACC
* * *
24215606 GAAGTACAACAGGGGCACGTATGTGCATTTAGGGGTACC
1 GAAGTACAACAAGGGCACGTATGTGCATTCAAGGGTACC
24215645 GAAGTACAA
1 GAAGTACAA
24215654 TACGGTATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.33, C:0.18, G:0.30, T:0.18
Consensus pattern (39 bp):
GAAGTACAACAAGGGCACGTATGTGCATTCAAGGGTACC
Found at i:24225702 original size:33 final size:34
Alignment explanation
Indices: 24225654--24225720 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
24225644 AAAATAAATG
24225654 TAGTTCAGCTCAAATAAGTGTTAG-AATTAATTT
1 TAGTTCAGCTCAAATAAGTGTTAGTAATTAATTT
* *
24225687 TAGTTTAGCTTAAATAAGTGTTAGTAATTAATTT
1 TAGTTCAGCTCAAATAAGTGTTAGTAATTAATTT
24225721 GTTTAAATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 22 0.71
34 9 0.29
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (34 bp):
TAGTTCAGCTCAAATAAGTGTTAGTAATTAATTT
Found at i:24227596 original size:104 final size:103
Alignment explanation
Indices: 24227405--24227775 Score: 609
Period size: 104 Copynumber: 3.6 Consensus size: 103
24227395 TGTATATAAA
** * *
24227405 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
*
24227469 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
24227509 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
*
24227574 TTGAAATGAAAAGGGGGTTGCTATGTTCTGATTCCCCCG
65 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
24227613 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
*
24227678 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCTG
65 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
24227717 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
24227776 ATAACGGTTA
Statistics
Matches: 254, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
103 29 0.11
104 183 0.72
105 41 0.16
106 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:24241463 original size:31 final size:31
Alignment explanation
Indices: 24241427--24241488 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
24241417 TTAGCTGAAT
*
24241427 GTGGATTTTCATCATTAAAAAGGCCATCCGA
1 GTGGATTTTCATCATTAAAAAGGCCAGCCGA
*
24241458 GTGGATTTTCATCATTCAAAAGGCCAGCCGA
1 GTGGATTTTCATCATTAAAAAGGCCAGCCGA
24241489 ACCATCCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (31 bp):
GTGGATTTTCATCATTAAAAAGGCCAGCCGA
Found at i:24243247 original size:17 final size:17
Alignment explanation
Indices: 24243217--24243259 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
24243207 GATAAAGAAT
* *
24243217 GAAAAAGAACAAGAAAA
1 GAAAATGAAAAAGAAAA
24243234 GAAAATGAAAAAGAAAA
1 GAAAATGAAAAAGAAAA
*
24243251 -AAATTGAAA
1 GAAAATGAAA
24243260 TAAAAGAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.07
Consensus pattern (17 bp):
GAAAATGAAAAAGAAAA
Found at i:24246995 original size:19 final size:17
Alignment explanation
Indices: 24246959--24246997 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
24246949 TCAGTTGCTG
24246959 ATTAGTTAAATAAATTA
1 ATTAGTTAAATAAATTA
*
24246976 ATTAGCTTAAGATTAATTA
1 ATTAG-TTAA-ATAAATTA
24246995 ATT
1 ATT
24246998 TAATAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTAGTTAAATAAATTA
Found at i:24249169 original size:21 final size:21
Alignment explanation
Indices: 24249145--24249185 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
24249135 AAACGAAAAA
24249145 GAAGAAGAAGAAA-AAAAAAGT
1 GAAGAAGAA-AAAGAAAAAAGT
24249166 GAAGAAGAAAAAGAAAAAAG
1 GAAGAAGAAAAAGAAAAAAG
24249186 AAATTGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (21 bp):
GAAGAAGAAAAAGAAAAAAGT
Found at i:24249170 original size:24 final size:25
Alignment explanation
Indices: 24249142--24249223 Score: 87
Period size: 24 Copynumber: 3.2 Consensus size: 25
24249132 TAAAAACGAA
*
24249142 AAAGAAGAAGAAGAAAAAAAAAGTG
1 AAAGAAGAAAAAGAAAAAAAAAGTG
*
24249167 -AAGAAGAAAAAGAAAAAAGAAATTG
1 AAAGAAGAAAAAGAAAAAA-AAAGTG
* *
24249192 CAA-AAGAAAAAGAAATCGAAAAAGTG
1 AAAGAAGAAAAAGAAA--AAAAAAGTG
24249218 AAAGAA
1 AAAGAA
24249224 AAAGAAAACG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
24 17 0.36
25 17 0.36
26 9 0.19
27 4 0.09
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.06
Consensus pattern (25 bp):
AAAGAAGAAAAAGAAAAAAAAAGTG
Found at i:24249181 original size:6 final size:6
Alignment explanation
Indices: 24249133--24249257 Score: 70
Period size: 6 Copynumber: 19.5 Consensus size: 6
24249123 ACATTGTAAT
* * *
24249133 AAAAACG AAAAAG AAGAAG AAGAAAA AAAAAGTG AAGAAG AAAAAG AAAAAAG
1 AAAAA-G AAAAAG AAAAAG AA-AAAG AAAAA--G AAAAAG AAAAAG -AAAAAG
** * ** ** *
24249186 AAATTG CAAAAG AAAAAG AAATCG AAAAAG TGAAAG AAAAAG AAAACG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
*
24249234 AAGAAAAG AAAATTG AAAAAG AAA
1 -A-AAAAG AAAA-AG AAAAAG AAA
24249258 TTGAGATTGA
Statistics
Matches: 87, Mismatches: 24, Indels: 15
0.69 0.19 0.12
Matches are distributed among these distances:
6 57 0.66
7 22 0.25
8 8 0.09
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAAAG
Found at i:24249214 original size:18 final size:18
Alignment explanation
Indices: 24249172--24249306 Score: 84
Period size: 18 Copynumber: 7.6 Consensus size: 18
24249162 AAGTGAAGAA
24249172 GAAAAAGAAAAAAGAAATT
1 GAAAAAG-AAAAAGAAATT
* *
24249191 GCAAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAATT
** **
24249209 GAAAAAGTGAAAGAAAAA
1 GAAAAAGAAAAAGAAATT
*
24249227 GAAAACGAAGAAAAGAAAATT
1 GAAAAAG-A-AAAAG-AAATT
** *
24249248 GAAAAAGAAATTGAGATT
1 GAAAAAGAAAAAGAAATT
24249266 G----AG-AAAA-AAATT
1 GAAAAAGAAAAAGAAATT
**
24249278 GAAAAAGAAAAAGATGTT
1 GAAAAAGAAAAAGAAATT
24249296 GAAAAAGAAAA
1 GAAAAAGAAAA
24249307 GAGAGAAAAT
Statistics
Matches: 86, Mismatches: 21, Indels: 19
0.68 0.17 0.15
Matches are distributed among these distances:
12 5 0.06
13 2 0.02
14 2 0.02
16 2 0.02
17 4 0.05
18 48 0.56
19 9 0.10
20 5 0.06
21 9 0.10
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.11
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATT
Found at i:24249252 original size:51 final size:51
Alignment explanation
Indices: 24249159--24249258 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
24249149 AAGAAGAAAA
*
24249159 AAAAAGTGAAGAAGAAAAAGAAAAAAGAAATTGCAAAAGAAAAAGAAATCG
1 AAAAAGTGAAGAAGAAAAAGAAAAAAGAAATAGCAAAAGAAAAAGAAATCG
24249210 AAAAAGTG-A-AAGAAAAAGAAAACGAAGAAA-AG-AAAATTGAAAAAGAAAT
1 AAAAAGTGAAGAAGAAAAAGAAAA--AAGAAATAGCAAAA--GAAAAAGAAAT
24249259 TGAGATTGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
49 17 0.39
50 2 0.05
51 25 0.57
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (51 bp):
AAAAAGTGAAGAAGAAAAAGAAAAAAGAAATAGCAAAAGAAAAAGAAATCG
Found at i:24254928 original size:18 final size:18
Alignment explanation
Indices: 24254907--24254941 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24254897 TTTTTCTCTT
24254907 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
24254925 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
24254942 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:24257099 original size:27 final size:28
Alignment explanation
Indices: 24257057--24257126 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
24257047 ACTTTTAATG
24257057 CATG-TTTTAATATGTCATAGT-TAGTA
1 CATGTTTTTAATATGTCATAGTCTAGTA
* * *
24257083 CATGTTTTTAATTTGTCTTAGTCTATTA
1 CATGTTTTTAATATGTCATAGTCTAGTA
24257111 CATGTTTTTAATATGT
1 CATGTTTTTAATATGT
24257127 TCTTGTTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 4 0.11
27 15 0.39
28 19 0.50
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.53
Consensus pattern (28 bp):
CATGTTTTTAATATGTCATAGTCTAGTA
Found at i:24260036 original size:15 final size:15
Alignment explanation
Indices: 24260001--24260052 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
24259991 CTCACATGCT
*
24260001 TTTTTGCTCTCAATCTC
1 TTTTT-CTCTC-ATTTC
*
24260018 TTTTTGCTCT-TTTTC
1 TTTTT-CTCTCATTTC
24260033 TTTTTCTCTCATTTC
1 TTTTTCTCTCATTTC
24260048 TTTTT
1 TTTTT
24260053 TTCTTTTCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 4 0.13
15 17 0.55
17 10 0.32
ACGTcount: A:0.06, C:0.23, G:0.04, T:0.67
Consensus pattern (15 bp):
TTTTTCTCTCATTTC
Found at i:24260073 original size:22 final size:23
Alignment explanation
Indices: 24260027--24260073 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
24260017 CTTTTTGCTC
*
24260027 TTTTTCTTTTTCTCTCATTTCTT
1 TTTTTCTTTTTCTCTAATTTCTT
*
24260050 TTTTTC-TTTTCTC-AATTTCAT
1 TTTTTCTTTTTCTCTAATTTCTT
24260071 TTT
1 TTT
24260074 GGATTCATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 7 0.32
23 6 0.27
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTTTCTTTTTCTCTAATTTCTT
Found at i:24262518 original size:3 final size:3
Alignment explanation
Indices: 24262510--24262539 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
24262500 AAAGAATGAA
24262510 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24262540 CAAGAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:24265643 original size:24 final size:21
Alignment explanation
Indices: 24265609--24265651 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 21
24265599 GGAAAAACAA
24265609 AAAGAGATTGAAAAAGAAATTG
1 AAAGAGATTG-AAAAGAAATTG
24265631 AAAGAGAACTTGAAAAGAAAT
1 AAAGAG-A-TTGAAAAGAAAT
24265652 CGAGTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 10 0.53
24 3 0.16
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.16
Consensus pattern (21 bp):
AAAGAGATTGAAAAGAAATTG
Found at i:24274280 original size:15 final size:15
Alignment explanation
Indices: 24274260--24274290 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24274250 ACATTTCTTA
*
24274260 AGGTTTGTATACAAT
1 AGGTTTGCATACAAT
24274275 AGGTTTGCATACAAT
1 AGGTTTGCATACAAT
24274290 A
1 A
24274291 CTTCCTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (15 bp):
AGGTTTGCATACAAT
Found at i:24279683 original size:21 final size:20
Alignment explanation
Indices: 24279658--24279697 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
24279648 GAGCGAGCTT
*
24279658 ATTGAGCTTGAATTGAGCTAA
1 ATTGAGCTCG-ATTGAGCTAA
24279679 ATTGAGCTCGATTGAGCTA
1 ATTGAGCTCGATTGAGCTA
24279698 GATCAAGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (20 bp):
ATTGAGCTCGATTGAGCTAA
Found at i:24289450 original size:23 final size:21
Alignment explanation
Indices: 24289419--24289481 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
24289409 TTAGGCTCGG
*
24289419 AATGGTTTAGGATTAGGTATGAA
1 AATGATTTAGG-TTAGGTATG-A
*
24289442 AATGATTTAGGTTTAGGTTTGA
1 AATGATTTAGG-TTAGGTATGA
*
24289464 AGTGATTTAGGTTAGGTA
1 AATGATTTAGGTTAGGTA
24289482 AGATTTGGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 6 0.17
22 11 0.31
23 18 0.51
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (21 bp):
AATGATTTAGGTTAGGTATGA
Found at i:24289472 original size:22 final size:21
Alignment explanation
Indices: 24289402--24289481 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 21
24289392 TCGAAGATGG
** *
24289402 TTTAGGTTTAGGCTCGGAATGG
1 TTTAGGTTTAGG-TATGAATGA
*
24289424 TTTAGGATTAGGTATGAAAATGA
1 TTTAGGTTTAGGTATG--AATGA
*
24289447 TTTAGGTTTAGGTTTGAAGTGA
1 TTTAGGTTTAGGTATGAA-TGA
24289469 TTTAGG-TTAGGTA
1 TTTAGGTTTAGGTA
24289482 AGATTTGGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
21 10 0.21
22 20 0.42
23 18 0.38
ACGTcount: A:0.26, C:0.03, G:0.31, T:0.40
Consensus pattern (21 bp):
TTTAGGTTTAGGTATGAATGA
Found at i:24291207 original size:50 final size:52
Alignment explanation
Indices: 24291101--24291222 Score: 151
Period size: 50 Copynumber: 2.4 Consensus size: 52
24291091 TGAACAAATG
* * *
24291101 AGTTACTTAATGCAAGACTTACTTTAATGATGCAGACTTAAACTAACATGGT
1 AGTTACATAATGCATGACTTACTTTAATGATGCAGACTTAAACTAACATGGA
* * *
24291153 AGTTACATAATGCATGTCATTA-TTT-ATGATGCATACTT-AACTAGCATGGA
1 AGTTACATAATGCATGAC-TTACTTTAATGATGCAGACTTAAACTAACATGGA
*
24291203 AGTTACATAATGCATAACTT
1 AGTTACATAATGCATGACTT
24291223 TATTAAATGC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
49 2 0.03
50 26 0.43
51 12 0.20
52 18 0.30
53 3 0.05
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (52 bp):
AGTTACATAATGCATGACTTACTTTAATGATGCAGACTTAAACTAACATGGA
Found at i:24292870 original size:31 final size:30
Alignment explanation
Indices: 24292835--24292892 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
24292825 ATGCATTATC
*
24292835 TAACTCCTATGTT-AGTTTAAGTTTGCATAAG
1 TAACTCATATGTTCA-TTT-AGTTTGCATAAG
*
24292866 TAACTCATTTGTTCATTTAGTTTGCAT
1 TAACTCATATGTTCATTTAGTTTGCAT
24292893 CCTAAACCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.38
31 14 0.58
32 1 0.04
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (30 bp):
TAACTCATATGTTCATTTAGTTTGCATAAG
Found at i:24301102 original size:22 final size:21
Alignment explanation
Indices: 24301077--24301123 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
24301067 TTCTTTCATT
24301077 TTTTTAAATCTAATTTTTTTTG
1 TTTTTAAATC-AATTTTTTTTG
***
24301099 TTTTTTTTTCAATTTTTTTTG
1 TTTTTAAATCAATTTTTTTTG
24301120 TTTT
1 TTTT
24301124 GAACCACAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (21 bp):
TTTTTAAATCAATTTTTTTTG
Found at i:24301770 original size:14 final size:14
Alignment explanation
Indices: 24301751--24301777 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24301741 ATGATCTCCC
24301751 CATGCATGAATCTA
1 CATGCATGAATCTA
24301765 CATGCATGAATCT
1 CATGCATGAATCT
24301778 GTCCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:24303801 original size:16 final size:15
Alignment explanation
Indices: 24303775--24303804 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
24303765 CTTCAAACCA
24303775 TCATCCCAATCAAAG
1 TCATCCCAATCAAAG
24303790 TCATCACCAATCAAA
1 TCATC-CCAATCAAA
24303805 AATTGATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
TCATCCCAATCAAAG
Found at i:24304311 original size:5 final size:6
Alignment explanation
Indices: 24304295--24304333 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
24304285 CGCTCGCACA
**
24304295 CTTTTT CTTTTT CTTTTT CACTTT CTTTTT CTTTTT CTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTT
24304334 GTTTTTCGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (6 bp):
CTTTTT
Found at i:24306393 original size:786 final size:785
Alignment explanation
Indices: 24304877--24306531 Score: 3107
Period size: 786 Copynumber: 2.1 Consensus size: 785
24304867 ATTTGGATGG
24304877 CACTC-CACTCGTGTTTACACTCAATTTTTGGCTTTTTCTTTTGATGTAATTCACTCGTGCCTTT
1 CACTCGCACTCGTGTTTACACTCAATTTTTGGCTTTTTCTTTTGATGTAATTCACTCGTGCCTTT
** * *
24304941 TACCACTCGACCTCGTCTCACAATTTTGTAATTTATCTCGGTAGACTTAATTTGCTGCTTGAGGG
66 TACCACTCGACCTCGTCTCACAATTTCATAATTTATCTCGGTAGACTTAATTTACTACTTGAGGG
*
24305006 TCGGTTTCAAAAATGGGTAACAAAGGGAATAATGAAATGGTGTAAGGTAGGCTGAAACGAAATAA
131 TCGGTTTCAAAAATGGGTAACAAAGGGAATAATGAAATGGTGTAAGGTAGGCTGAAACAAAATAA
* * *
24305071 AATCAAGGCTAAGTGTTGCGTTGGGGAAGTAGATAAGAAGAAGAAGAACTCACTTGTTCGGAATT
196 AACCAAGGCTAAGTGTGGCGTTGGGGAAGTAGATAAGAAGAAGAAGAACTCACTTGTTCGAAATT
24305136 CAAAAGATGAATAAACCTGGAATTTTTTTTCAACACTTTACTTTTTTTGACACTCTTGAAACACG
261 CAAAAGATGAATAAACCTGGAATTTTTTTTCAACACTTTACTTTTTTTGACACTCTTGAAACACG
* *
24305201 TTCGACTCTTCGTAATCCAACATTCACAGATGAATAAATTGATGCACTTGTAGAGACATGTTTAC
326 TTCCACTCTTCGTAAGCCAACATTCACAGATGAATAAATTGATGCACTTGTAGAGACATGTTTAC
24305266 CTTTTCGTTTATCATCTCGGAAGGACTCAAATTCGGAGTTTGCTTCTCTTGGTCTCGAACGCCTT
391 CTTTTCGTTTATCATCTCGGAAGGACTCAAATTCGGAGTTTGCTTCTCTTGGTCTCGAACGCCTT
*
24305331 GTTGAATAAAAGTCTTGATAAGAGTCTCTTGTTGAATATTCGTTGGATGTTCGTCTTCTTGGCAC
456 GTTGAATAAAAGTCTTGATAAGAGTCTCTTATTGAATATTCGTTGGATGTTCGTCTTCTTGGCAC
*
24305396 TCTCAGTTCTGCCCTTTCACTTGAATTAAGTTGTCCTTGTTTCGCTCTTTTCTCCACTCGATCCA
521 TCTCAGTTCTGCCCTTTCACTTGAATTAAGTTGTCCTCGTTTCGCTCTTTTCTCCACTCGATCCA
24305461 ATCGATCATGCAATTTATCAAATTTTGATTTCACCATTCTACACATCTCTTGCATCAAATATTGA
586 ATCGATCATGCAATTTATCAAATTTTGATTTCACCATTCTACACATCTCTTGCATCAAATATTGA
24305526 AATTCTGATTCGAAAAATTCTTCTCGAGACATGATTATTCACTAAAAGAAGAAATGTTAAAAGAA
651 AATTCTGATTCGAAAAATTCTTCTCGAGACATGATTATTCACTAAAAGAAGAAATGTTAAAAGAA
24305591 TAATAACAGAAAATTAGATACCTCACCACAAAATCCTCACTAATTCTCTCGAAAAGGAAATAATG
716 TAATAACAGAAAATTAGATACCTCACCACAAAATCCTCACTAATTCTCTCGAAAAGGAAATAATG
24305656 ATTTT
781 ATTTT
24305661 CACTCGCACTCGTGTTTACACTCAATTTTTGGCTTTTTCTTTTGATGTAATTCACTCGTGCCTTT
1 CACTCGCACTCGTGTTTACACTCAATTTTTGGCTTTTTCTTTTGATGTAATTCACTCGTGCCTTT
24305726 TACCACTCGACCTCGTCTCACAATTTCATAATTTATCTCGGTAGACTTAATTTACTACTTGAGGG
66 TACCACTCGACCTCGTCTCACAATTTCATAATTTATCTCGGTAGACTTAATTTACTACTTGAGGG
*
24305791 TCGGTTTCAAAAATGGGTAACAAAGGGAATAATGAAATGGTGTAGGGTAGGCTGAAACAAAATAA
131 TCGGTTTCAAAAATGGGTAACAAAGGGAATAATGAAATGGTGTAAGGTAGGCTGAAACAAAATAA
24305856 AACCAAGGCTAAGTGTGGCGTTGGGGAAGTAGATAAGAAGAAGAAGAACTCACTTGTTCGAAATT
196 AACCAAGGCTAAGTGTGGCGTTGGGGAAGTAGATAAGAAGAAGAAGAACTCACTTGTTCGAAATT
*
24305921 CAAAAGATGAATAGACCTGGAATTTTTTTTTCAACACTTTACTTTTTTTGACACTCTTGAAACAC
261 CAAAAGATGAATAAACCTGGAA-TTTTTTTTCAACACTTTACTTTTTTTGACACTCTTGAAACAC
* * *
24305986 GTTCCCCTCTTCGTAAGCCAACCTTCACAGATGAATAAATTGATGCACTTGTAGTGACATGTTTA
325 GTTCCACTCTTCGTAAGCCAACATTCACAGATGAATAAATTGATGCACTTGTAGAGACATGTTTA
*
24306051 CCTTTTCGTTTATCATCTCGGAAGGACTCAAATTTGGAGTTTGCTTCTCTTGGTCTCGAACGCCT
390 CCTTTTCGTTTATCATCTCGGAAGGACTCAAATTCGGAGTTTGCTTCTCTTGGTCTCGAACGCCT
*
24306116 TGTTGAATAGAAGTCTTGATAAGAGTCTCTTATTGAATATTCGTTGGATGTTCGTCTTCTTGGCA
455 TGTTGAATAAAAGTCTTGATAAGAGTCTCTTATTGAATATTCGTTGGATGTTCGTCTTCTTGGCA
24306181 CTCTCAGTTCTGCCCTTTCACTTGAATTAAGTTGTCCTCGTTTCGCTCTTTTCTCCACTCGATCC
520 CTCTCAGTTCTGCCCTTTCACTTGAATTAAGTTGTCCTCGTTTCGCTCTTTTCTCCACTCGATCC
24306246 AATCGATCATGCAATTTATCAAATTTTGATTTCACCATTCTACACATCTCTTGCATCAAATATTG
585 AATCGATCATGCAATTTATCAAATTTTGATTTCACCATTCTACACATCTCTTGCATCAAATATTG
24306311 AAATTCTGATTCGAAAAATTCTTCTCGAGACATGATTATTCACTAAAAGAAGAAATGTTAAAAGA
650 AAATTCTGATTCGAAAAATTCTTCTCGAGACATGATTATTCACTAAAAGAAGAAATGTTAAAAGA
24306376 ATAATAACAGAAAATTAGATACCTCACCACAAAATCCTCACTAATTCTCTCGAAAAGGAAATAAT
715 ATAATAACAGAAAATTAGATACCTCACCACAAAATCCTCACTAATTCTCTCGAAAAGGAAATAAT
24306441 GATTTT
780 GATTTT
*
24306447 CACTCGTACTCGTGTTTACACTCAATTTTTGGCTTTTTCTTTTGATGTAATTCACTCGTGCCTTT
1 CACTCGCACTCGTGTTTACACTCAATTTTTGGCTTTTTCTTTTGATGTAATTCACTCGTGCCTTT
24306512 TACCACTCGACCTC-TCTCAC
66 TACCACTCGACCTCGTCTCAC
24306532 TTTTTCTTCC
Statistics
Matches: 849, Mismatches: 20, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
784 5 0.01
785 272 0.32
786 572 0.67
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (785 bp):
CACTCGCACTCGTGTTTACACTCAATTTTTGGCTTTTTCTTTTGATGTAATTCACTCGTGCCTTT
TACCACTCGACCTCGTCTCACAATTTCATAATTTATCTCGGTAGACTTAATTTACTACTTGAGGG
TCGGTTTCAAAAATGGGTAACAAAGGGAATAATGAAATGGTGTAAGGTAGGCTGAAACAAAATAA
AACCAAGGCTAAGTGTGGCGTTGGGGAAGTAGATAAGAAGAAGAAGAACTCACTTGTTCGAAATT
CAAAAGATGAATAAACCTGGAATTTTTTTTCAACACTTTACTTTTTTTGACACTCTTGAAACACG
TTCCACTCTTCGTAAGCCAACATTCACAGATGAATAAATTGATGCACTTGTAGAGACATGTTTAC
CTTTTCGTTTATCATCTCGGAAGGACTCAAATTCGGAGTTTGCTTCTCTTGGTCTCGAACGCCTT
GTTGAATAAAAGTCTTGATAAGAGTCTCTTATTGAATATTCGTTGGATGTTCGTCTTCTTGGCAC
TCTCAGTTCTGCCCTTTCACTTGAATTAAGTTGTCCTCGTTTCGCTCTTTTCTCCACTCGATCCA
ATCGATCATGCAATTTATCAAATTTTGATTTCACCATTCTACACATCTCTTGCATCAAATATTGA
AATTCTGATTCGAAAAATTCTTCTCGAGACATGATTATTCACTAAAAGAAGAAATGTTAAAAGAA
TAATAACAGAAAATTAGATACCTCACCACAAAATCCTCACTAATTCTCTCGAAAAGGAAATAATG
ATTTT
Found at i:24313139 original size:23 final size:23
Alignment explanation
Indices: 24313089--24313133 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
24313079 ATTCGACTGA
24313089 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
24313112 TGTAATA-CCCTGAAAATTACTA
1 TGTAATATCCC-GAAAATTACTA
24313134 TAGTAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:24315827 original size:20 final size:20
Alignment explanation
Indices: 24315799--24315840 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
24315789 TAAATGCAAA
*
24315799 CTAAATGAGCTACGAATGAG
1 CTAAATGAGCTACGAACGAG
* *
24315819 CTAAGTGAGCTAGGAACGAG
1 CTAAATGAGCTACGAACGAG
24315839 CT
1 CT
24315841 TGTTGAGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.19
Consensus pattern (20 bp):
CTAAATGAGCTACGAACGAG
Found at i:24315868 original size:29 final size:28
Alignment explanation
Indices: 24315815--24315871 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
24315805 GAGCTACGAA
24315815 TGAGCTAAGTGAGCTAGGAACGAGCTTGT
1 TGAGCTAAGTGAGCTA-GAACGAGCTTGT
*
24315844 TGAGCTAGAGTTGAGCT-GAATGAGCTTG
1 TGAGCTA-AG-TGAGCTAGAACGAGCTTG
24315872 AAGAAGGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 17 0.68
30 2 0.08
31 6 0.24
ACGTcount: A:0.26, C:0.12, G:0.35, T:0.26
Consensus pattern (28 bp):
TGAGCTAAGTGAGCTAGAACGAGCTTGT
Found at i:24316567 original size:39 final size:39
Alignment explanation
Indices: 24316513--24316591 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
24316503 TCAAAAGGAG
24316513 AATGTTTGGTGGCGGAATGCACGGATATATGATAAGCAA
1 AATGTTTGGTGGCGGAATGCACGGATATATGATAAGCAA
*
24316552 AATGTTTGGTGGCGGAATGCGCGGATATATGATAAGCAA
1 AATGTTTGGTGGCGGAATGCACGGATATATGATAAGCAA
24316591 A
1 A
24316592 CTCAACGTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.10, G:0.32, T:0.25
Consensus pattern (39 bp):
AATGTTTGGTGGCGGAATGCACGGATATATGATAAGCAA
Found at i:24326020 original size:27 final size:28
Alignment explanation
Indices: 24325990--24326049 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
24325980 ACTTTGGACA
* * *
24325990 ACATTAA-AACATGTAATAAAATTAGAC
1 ACATTAATAACATGCAATAAAATAAAAC
*
24326017 ACATTAATAACATGCATTAAAATAAAAC
1 ACATTAATAACATGCAATAAAATAAAAC
24326045 ACATT
1 ACATT
24326050 TATCACAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (28 bp):
ACATTAATAACATGCAATAAAATAAAAC
Found at i:24329273 original size:15 final size:15
Alignment explanation
Indices: 24329253--24329292 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
24329243 TGTTGTCGAT
24329253 GAAAAAGAAACAAGA
1 GAAAAAGAAACAAGA
**
24329268 GAAAAAGATGCAAGA
1 GAAAAAGAAACAAGA
*
24329283 GAACAAGAAA
1 GAAAAAGAAA
24329293 AAGTGAGGAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.68, C:0.07, G:0.23, T:0.03
Consensus pattern (15 bp):
GAAAAAGAAACAAGA
Found at i:24336592 original size:150 final size:151
Alignment explanation
Indices: 24336149--24336569 Score: 655
Period size: 151 Copynumber: 2.8 Consensus size: 151
24336139 CTACTCACTT
* * *
24336149 TCACGGGTCTGCTCACACAAGCTGTCAGTCTTTTGTTACTACTCAGTGCTGCTCACACAAGCTGT
1 TCACGGGCCTGCTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTGCTCACACAAGCTGT
*
24336214 CAGGTATCTGCAACATATGTCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAGTT
66 CAGGTATCCGCAACATATGTCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAGTT
**
24336279 CACATTAATCACAGTTTCGCA
131 CACATTAATCACAGTTTAACA
*
24336300 TCACGGGCCTGCTCACACAAGCTATCAGTCATTCGTTACTACTCAGTGCTGCTCACACAAGCTGT
1 TCACGGGCCTGCTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTGCTCACACAAGCTGT
* * * *
24336365 CAGGTATCCACAACATATGTCGGTATACCCAGCCACTGGTAGAACTCAGGACCAGCACCTGAGTT
66 CAGGTATCCGCAACATATGTCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAGTT
24336430 CACATTAATCACAGTTTAACA
131 CACATTAATCACAGTTTAACA
* * *
24336451 TCACGGG-CTGCTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTACTTACAGAAGCTGT
1 TCACGGGCCTGCTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTGCTCACACAAGCTGT
* * * * * *
24336515 CAAGTATCCGTAACATATGCCGGTATACCCAGCCACTCGTACAACTTATGACCAG
66 CAGGTATCCGCAACATATGTCGGTATACCCAGCCACTGGTAGAACTTAAGACCAG
24336570 TTCCCGAACC
Statistics
Matches: 247, Mismatches: 23, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
150 100 0.40
151 147 0.60
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (151 bp):
TCACGGGCCTGCTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTGCTCACACAAGCTGT
CAGGTATCCGCAACATATGTCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACCCGAGTT
CACATTAATCACAGTTTAACA
Found at i:24347718 original size:13 final size:13
Alignment explanation
Indices: 24347698--24347731 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
24347688 TTGTATTAGC
*
24347698 TGAAAAAAGTTCG
1 TGAAAAAAATTCG
24347711 T-AAAAAAATTCG
1 TGAAAAAAATTCG
24347723 TGAAAAAAA
1 TGAAAAAAA
24347732 AGATAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.59, C:0.06, G:0.15, T:0.21
Consensus pattern (13 bp):
TGAAAAAAATTCG
Found at i:24348948 original size:28 final size:27
Alignment explanation
Indices: 24348895--24348965 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 27
24348885 AGATTGAGAC
24348895 TGAAAAAGAATGTGATCAAGAAAAGAAAA
1 TGAAAAAGAA-GTGA-CAAGAAAAGAAAA
24348924 TTGAAAAAGAGAGTGA-AAGAAAAGAAAA
1 -TGAAAAAGA-AGTGACAAGAAAAGAAAA
*
24348952 TGAGAAAGAAGTGA
1 TGAAAAAGAAGTGA
24348966 GTGTCATCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 5 0.13
27 8 0.21
28 12 0.31
30 13 0.33
31 1 0.03
ACGTcount: A:0.61, C:0.01, G:0.25, T:0.13
Consensus pattern (27 bp):
TGAAAAAGAAGTGACAAGAAAAGAAAA
Found at i:24351552 original size:52 final size:50
Alignment explanation
Indices: 24351437--24351554 Score: 139
Period size: 50 Copynumber: 2.3 Consensus size: 50
24351427 TAATAAAGTT
* * *
24351437 ATGCATTATGTAACTTCCATGCTAGTTAAGTATGCATCATAAATAATGAC
1 ATGCATTATGTAACTCCCACGCTAGTTAAGTATACATCATAAATAATGAC
* *
24351487 ATGCATTATGTAACTCCCACGCTAGTTTAAGTCTACATCATTAAATTAA-GTC
1 ATGCATTATGTAACTCCCACGCTAG-TTAAGTATACATCA-TAAA-TAATGAC
* *
24351539 TTGCATTAAGTAACTC
1 ATGCATTATGTAACTC
24351555 ATTTGTTCAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 23 0.40
51 12 0.21
52 20 0.34
53 3 0.05
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (50 bp):
ATGCATTATGTAACTCCCACGCTAGTTAAGTATACATCATAAATAATGAC
Found at i:24353926 original size:6 final size:6
Alignment explanation
Indices: 24353915--24354010 Score: 50
Period size: 6 Copynumber: 15.0 Consensus size: 6
24353905 ATTGAAAAAT
* * ** * *
24353915 AAGAAA AAGAAA AGGGAA GTGAAA AAGAAAAA TAAGAAA AAGAGA ATGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAG--AAA -AAGAAA AAGAAA AAGAAA
**
24353966 AAGAGAA AAGAAA AAGAGAA GTGAAA GAA-AAA AATGAAA AAGAAA
1 AAGA-AA AAGAAA AAGA-AA AAGAAA -AAGAAA AA-GAAA AAGAAA
24354011 TTGAGATTGA
Statistics
Matches: 67, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
5 2 0.03
6 41 0.61
7 18 0.27
8 3 0.04
9 3 0.04
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:24353951 original size:27 final size:27
Alignment explanation
Indices: 24353907--24354008 Score: 115
Period size: 27 Copynumber: 3.9 Consensus size: 27
24353897 GTAATAAAAT
* *
24353907 TGAAAAATAAGAAAAAG-AAAAGGGAAG
1 TGAAAAAGAA-AAAAAGAAAAAGAGAAG
24353934 TGAAAAAGAAAAATAAGAAAAAGAGAA-
1 TGAAAAAGAAAAA-AAGAAAAAGAGAAG
*
24353961 TGAAAAAG-AGAAAAGAAAAAGAGAAG
1 TGAAAAAGAAAAAAAGAAAAAGAGAAG
24353987 TG--AAAGAAAAAAATGAAAAAGA
1 TGAAAAAGAAAAAAA-GAAAAAGA
24354009 AATTGAGATT
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.06
25 18 0.27
26 16 0.24
27 20 0.30
28 8 0.12
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.07
Consensus pattern (27 bp):
TGAAAAAGAAAAAAAGAAAAAGAGAAG
Found at i:24353991 original size:13 final size:13
Alignment explanation
Indices: 24353924--24354008 Score: 75
Period size: 13 Copynumber: 6.5 Consensus size: 13
24353914 TAAGAAAAAG
* *
24353924 AAAAGGGAAGTGA
1 AAAAGAGAAATGA
*
24353937 AAAAGAAAAATAAGA
1 AAAAGAGAAAT--GA
24353952 AAAAGAG-AATGA
1 AAAAGAGAAATGA
*
24353964 AAAAGAGAAAAGA
1 AAAAGAGAAATGA
*
24353977 AAAAGAGAAGTGA
1 AAAAGAGAAATGA
*
24353990 AAGAA-AAAAATGA
1 AA-AAGAGAAATGA
24354003 AAAAGA
1 AAAAGA
24354009 AATTGAGATT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
12 11 0.19
13 34 0.59
14 5 0.09
15 8 0.14
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.06
Consensus pattern (13 bp):
AAAAGAGAAATGA
Found at i:24355989 original size:52 final size:50
Alignment explanation
Indices: 24355874--24355991 Score: 130
Period size: 50 Copynumber: 2.3 Consensus size: 50
24355864 TAATAAAGTT
* *
24355874 ATGCATTATGTAACTTCCAAGCTAGTTAAGTATGCATCATAAATAATGAC
1 ATGCATTAAGTAACTCCCAAGCTAGTTAAGTATGCATCATAAATAATGAC
* * * * *
24355924 ATGCATTACGTAACTCCCATGTTAGTTTAAGTCTGCATCATTAAATTAA-GTC
1 ATGCATTAAGTAACTCCCAAGCTAG-TTAAGTATGCATCA-TAAA-TAATGAC
*
24355976 TTGCATTAAGTAACTC
1 ATGCATTAAGTAACTC
24355992 ATTTGTTCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
50 21 0.37
51 13 0.23
52 20 0.35
53 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.35
Consensus pattern (50 bp):
ATGCATTAAGTAACTCCCAAGCTAGTTAAGTATGCATCATAAATAATGAC
Found at i:24364478 original size:26 final size:27
Alignment explanation
Indices: 24364449--24364499 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
24364439 CCAATGAATC
24364449 GGGG-AATCAGCACACAGCAACCCCTT
1 GGGGAAATCAGCACACAGCAACCCCTT
**
24364475 GGGGAAATCAGCACTTAGCAACCCC
1 GGGGAAATCAGCACACAGCAACCCC
24364500 CTTCACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.31, C:0.33, G:0.24, T:0.12
Consensus pattern (27 bp):
GGGGAAATCAGCACACAGCAACCCCTT
Found at i:24364562 original size:33 final size:34
Alignment explanation
Indices: 24364520--24364675 Score: 96
Period size: 33 Copynumber: 4.6 Consensus size: 34
24364510 CAGATGCGGT
24364520 GGAATCAGCACTTAGCAACCACCAAT-GAATAGG
1 GGAATCAGCACTTAGCAACCACCAATAGAATAGG
* *
24364553 GGAATCAGCACTTAGCGACC-CC--TCG----GG
1 GGAATCAGCACTTAGCAACCACCAATAGAATAGG
* * *
24364580 GGAATCAACACTTAGCAACCCCCTTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC---CA-A--TAGAATA-GG
*
24364622 TGGAATCAGCACTTAGCAACCACCAAT-GAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATAGAATAGG
**
24364656 GGAATCAGCACACAGCAACC
1 GGAATCAGCACTTAGCAACC
24364676 CCTTGGAGGA
Statistics
Matches: 95, Mismatches: 11, Indels: 34
0.68 0.08 0.24
Matches are distributed among these distances:
27 18 0.19
28 2 0.02
29 1 0.01
30 1 0.01
31 1 0.01
32 3 0.03
33 37 0.39
34 2 0.02
35 3 0.03
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.02
42 5 0.05
43 17 0.18
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.17
Consensus pattern (34 bp):
GGAATCAGCACTTAGCAACCACCAATAGAATAGG
Found at i:24364651 original size:103 final size:102
Alignment explanation
Indices: 24364426--24364781 Score: 579
Period size: 102 Copynumber: 3.5 Consensus size: 102
24364416 GTGGATTCCA
*
24364426 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGAAATCAGCACTT
1 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACTT
24364491 AGCAACCCCCTTCACATTTCAGATGCGGTGGAATCAG
66 AGCAACCCCCTTCACATTTCAGATGCGGTGGAATCAG
* ** * * *
24364528 CACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCGACCCCTCGGGGGAATCAACACTT
1 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACTT
* * *
24364593 AGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAG
66 AGCAACCCCC-TTCACATTTCAGATGCGGTGGAATCAG
*
24364631 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGAGGAATCAGCACTT
1 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACTT
24364696 AGCAACCCCCTTCACATTTCAGATGCGGTGGAATCAG
66 AGCAACCCCCTTCACATTTCAGATGCGGTGGAATCAG
*
24364733 CAAC-TAGCAACCACCAATGAATTGGGGAATCAGCACACAGCAACCCCTT
1 C-ACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
24364782 TATATGCAAT
Statistics
Matches: 231, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
102 137 0.59
103 94 0.41
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.18
Consensus pattern (102 bp):
CACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACTT
AGCAACCCCCTTCACATTTCAGATGCGGTGGAATCAG
Found at i:24367196 original size:26 final size:26
Alignment explanation
Indices: 24367160--24367211 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
24367150 AATGAGAGTG
24367160 GTAAAATGAGCGTATTTGCGAGGGAA
1 GTAAAATGAGCGTATTTGCGAGGGAA
24367186 GTAAAATGAGCGTATTTGCGAGGGAA
1 GTAAAATGAGCGTATTTGCGAGGGAA
24367212 AAAGAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.23
Consensus pattern (26 bp):
GTAAAATGAGCGTATTTGCGAGGGAA
Found at i:24375550 original size:20 final size:20
Alignment explanation
Indices: 24375525--24375576 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
24375515 TATGAACCAC
24375525 TCCATTTACTTACTCAT-CAT
1 TCCATTTACTTACT-ATCCAT
*
24375545 TCCATTTACTTACTTTCCAT
1 TCCATTTACTTACTATCCAT
*
24375565 TTCATTTACTTA
1 TCCATTTACTTA
24375577 GCATAAGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (20 bp):
TCCATTTACTTACTATCCAT
Found at i:24379813 original size:22 final size:21
Alignment explanation
Indices: 24379788--24379829 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
24379778 TTAAATAAAT
*
24379788 TTTAGTTAATTTAGTTTAAGTA
1 TTTAATTAATTTAG-TTAAGTA
24379810 TTTAATTAATTTAGTTAAGT
1 TTTAATTAATTTAGTTAAGT
24379830 GTTAAATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTAATTAATTTAGTTAAGTA
Found at i:24379960 original size:132 final size:132
Alignment explanation
Indices: 24379819--24380088 Score: 504
Period size: 132 Copynumber: 2.0 Consensus size: 132
24379809 ATTTAATTAA
24379819 TTTAGTTAAGTGTTAAATGTGTTTTTAAGCCATTTAATTTGTCTAAGTACTTTCGACATTAATAG
1 TTTAGTTAAGTGTTAAATGTGTTTTTAAGCCATTTAATTTGTCTAAGTACTTTCGACATTAATAG
*
24379884 GTCTAAGTCATTTAATTTGTCTAAATTACGACAACAATTTTAATTGTCTTTAGCTCATTTAATTT
66 GTCTAAGTCATTTAATTTGTCTAAATTACGACAACAATTTCAATTGTCTTTAGCTCATTTAATTT
24379949 GT
131 GT
24379951 TTTAGTTAAGTGTTAAATGTGTTTTTAAGCCATTTAATTTGTCTAAGTACTTTCGACATTAATAG
1 TTTAGTTAAGTGTTAAATGTGTTTTTAAGCCATTTAATTTGTCTAAGTACTTTCGACATTAATAG
* * *
24380016 GTCTAAGTCATTTAATTTGTCTAAATTACTACAGCAATTTCAGTTGTCTTTAGCTCATTTAATTT
66 GTCTAAGTCATTTAATTTGTCTAAATTACGACAACAATTTCAATTGTCTTTAGCTCATTTAATTT
24380081 GT
131 GT
24380083 TTTAGT
1 TTTAGT
24380089 CTTAATAGCT
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 134 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (132 bp):
TTTAGTTAAGTGTTAAATGTGTTTTTAAGCCATTTAATTTGTCTAAGTACTTTCGACATTAATAG
GTCTAAGTCATTTAATTTGTCTAAATTACGACAACAATTTCAATTGTCTTTAGCTCATTTAATTT
GT
Found at i:24380937 original size:29 final size:29
Alignment explanation
Indices: 24380866--24380938 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
24380856 TTCATATACT
**
24380866 ATCG-ATTATGAAAAGGGATGATGATGACC
1 ATCGAATTATG-AAAGGGATGATGACAACC
* * *
24380895 ATC-AACTACGGAAAGGGATGGTGACAACC
1 ATCGAATTA-TGAAAGGGATGATGACAACC
24380924 ATCGAATTATGAAAG
1 ATCGAATTATGAAAG
24380939 AGATAGCTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
29 29 0.85
30 5 0.15
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.21
Consensus pattern (29 bp):
ATCGAATTATGAAAGGGATGATGACAACC
Found at i:24385688 original size:39 final size:39
Alignment explanation
Indices: 24385606--24385706 Score: 134
Period size: 39 Copynumber: 2.6 Consensus size: 39
24385596 AGTATGTCCA
** *
24385606 AAATT-TGACATAATTAAAAA-TTTTATCAATGATGTTT
1 AAATTATGACATAATTAAAAACTCATATCAATGATGTTC
* *
24385643 AGATTATGACATAATTAAAAACTCATATTAATGATGTTC
1 AAATTATGACATAATTAAAAACTCATATCAATGATGTTC
*
24385682 AAATTATGACATAATTAAAGACTCA
1 AAATTATGACATAATTAAAAACTCA
24385707 AACTAAAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
37 4 0.07
38 15 0.27
39 36 0.65
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (39 bp):
AAATTATGACATAATTAAAAACTCATATCAATGATGTTC
Found at i:24385721 original size:9 final size:9
Alignment explanation
Indices: 24385707--24385733 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
24385697 TAAAGACTCA
24385707 AACTAAAAT
1 AACTAAAAT
24385716 AACTAAAAT
1 AACTAAAAT
24385725 AACTAAAAT
1 AACTAAAAT
24385734 CAAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (9 bp):
AACTAAAAT
Found at i:24401017 original size:50 final size:52
Alignment explanation
Indices: 24400958--24401081 Score: 119
Period size: 50 Copynumber: 2.4 Consensus size: 52
24400948 GTGTGTTCTA
* * *
24400958 CATTCAATAAAGTTATGCATTATGCAACTTCCATGCTAG-TTAAGTATGCAT
1 CATTAAATAAAGTTATGCATTATGCAACTCCCATACTAGTTTAAGTATGCAT
* ** * * * *
24401009 CA-TAAATAACGACATGTATTATGTAACTCCCATATTAGTTTAAGTCTGCAT
1 CATTAAATAAAGTTATGCATTATGCAACTCCCATACTAGTTTAAGTATGCAT
*
24401060 CATTAAATTAAGTCT-TGCATTA
1 CATTAAATAAAGT-TATGCATTA
24401082 AGTAACTCAT
Statistics
Matches: 55, Mismatches: 15, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
50 27 0.49
51 15 0.27
52 13 0.24
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (52 bp):
CATTAAATAAAGTTATGCATTATGCAACTCCCATACTAGTTTAAGTATGCAT
Found at i:24401231 original size:27 final size:27
Alignment explanation
Indices: 24401180--24401231 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
24401170 CTCATCTTAG
*
24401180 TTTAATTAATAAGTGTTTTTGTTAAAC
1 TTTAATTAATAAGTGTTCTTGTTAAAC
*
24401207 TTTATTTAATAAGTGTTGCTT-TTAA
1 TTTAATTAATAAGTGTT-CTTGTTAA
24401232 TTAATCTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.54
Consensus pattern (27 bp):
TTTAATTAATAAGTGTTCTTGTTAAAC
Found at i:24402798 original size:25 final size:24
Alignment explanation
Indices: 24402752--24402798 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
24402742 TTTGAGTTAA
24402752 TAAATTCTCTTTGAGTTTTTTTTT
1 TAAATTCTCTTTGAGTTTTTTTTT
*
24402776 TAAATT-TCTCTTGAGTTTCTTTT
1 TAAATTCTCT-TTGAGTTTTTTTT
24402799 AGAAGAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.64
Consensus pattern (24 bp):
TAAATTCTCTTTGAGTTTTTTTTT
Found at i:24403636 original size:15 final size:17
Alignment explanation
Indices: 24403618--24403650 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
24403608 ATAGATGGAT
24403618 AGTTTA-ACTAA-GTTG
1 AGTTTAGACTAATGTTG
24403633 AGTTTAGACTAATGTTG
1 AGTTTAGACTAATGTTG
24403650 A
1 A
24403651 AGAACAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.39
Consensus pattern (17 bp):
AGTTTAGACTAATGTTG
Found at i:24404398 original size:13 final size:13
Alignment explanation
Indices: 24404380--24404410 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
24404370 TTAACTCCTT
24404380 TGAATATTGTTCA
1 TGAATATTGTTCA
24404393 TGAATATTGTTCA
1 TGAATATTGTTCA
24404406 TGAAT
1 TGAAT
24404411 TAATCATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.45
Consensus pattern (13 bp):
TGAATATTGTTCA
Done.