Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 115 of 131
Found at i:38176182 original size:44 final size:44
Alignment explanation
Indices: 38176117--38176405 Score: 271
Period size: 44 Copynumber: 6.5 Consensus size: 44
38176107 GCAGATCAGT
* * *
38176117 GAAGATAGCAGATCCTATCTTCCTATATTGGTAGCGAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* *
38176162 GAAGATGCAGATCTTGTCTT-CTCATACTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCT-ATATTGGTAGCGAAGTAGATC
* * * *
38176206 GAAGAAAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* * *
38176250 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* * * * *
38176294 GAAGATGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATT
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* * * * * *
38176338 GAAGAAAGCAGATATTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* *
38176382 GAAGATAACAGATCTTGCCTTCCT
1 GAAGAT-GCAGATCTTGTCTTCCT
38176406 GCACCGACAG
Statistics
Matches: 197, Mismatches: 39, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
43 25 0.13
44 124 0.63
45 47 0.24
46 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (44 bp):
GAAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
Found at i:38176404 original size:132 final size:133
Alignment explanation
Indices: 38176117--38176405 Score: 481
Period size: 132 Copynumber: 2.2 Consensus size: 133
38176107 GCAGATCAGT
*
38176117 GAAGATAGCAGATCCTATCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
* *
38176182 CTCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAG
66 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATATTGTCTTCATATATTGGCGTGAAGTAG
38176247 ATC
131 ATC
* *
38176250 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGTAGATCTTGTCTT
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
* *
38176314 CCCATACTGGTGGCGAAGTAGATTGAAGAAAGCAGATATTGTCTTCATGTATTGGCGTGAAGTAG
66 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATATTGTCTTCATATATTGGCGTGAAGTAG
38176379 ATC
131 ATC
* * *
38176382 GAAGATAACAGATCTTGCCTTCCT
1 GAAGATAGCAGATCCTGTCTTCCT
38176406 GCACCGACAG
Statistics
Matches: 145, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
132 113 0.78
133 32 0.22
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (133 bp):
GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATATTGTCTTCATATATTGGCGTGAAGTAG
ATC
Found at i:38176627 original size:88 final size:88
Alignment explanation
Indices: 38176390--38176617 Score: 330
Period size: 88 Copynumber: 2.6 Consensus size: 88
38176380 TCGAAGATAA
* *
38176390 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAAATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
38176455 ACAGCGGAGCAGGCTAAAAATAG
66 ACAGCAGAGCAGGCTAAAAATAG
* * * *
38176478 CAGATCTTGCCTTTCTGCACCAACAGTGAAGTAGATCGAAGACACCAGACTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* * *
38176543 GCAGTAGAGCAGGCTAAAAATGG
66 ACAGCAGAGCAGGCTAAAAATAG
* * * *
38176566 TAGATCTTGCCTTCCTACACCGACAGTGAAGCAGATCGATGACCCCAGCCTT
1 CAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTT
38176618 ATCTACCTGG
Statistics
Matches: 122, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 122 1.00
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
ACAGCAGAGCAGGCTAAAAATAG
Found at i:38176671 original size:44 final size:45
Alignment explanation
Indices: 38176617--38176824 Score: 221
Period size: 44 Copynumber: 4.7 Consensus size: 45
38176607 ACCCCAGCCT
* * *
38176617 TATCTACCTGGTCAGCAGTGGAATAAGTTAAAGATTGTGAA-TCA
1 TATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATTGTGAAGTCC
* * *
38176661 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAA-TTC
1 TATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATTGTGAAGTCC
** **
38176705 TATCTCCCTGGGAATTAGTGGAAT-AGATTGAAGATTGT-AAGTCC
1 TATCTCCCTGGTCAGCAGTGGAATAAG-TTGAAGATTGTGAAGTCC
* * *
38176749 TATCTCCCTGGTGAGCAGTGGAATAGGTTGAAGATTGCG-AGTCC
1 TATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATTGTGAAGTCC
* *
38176793 TATCTCCCTGAG-CAGCAGTGGAGTAGGTTGAA
1 TATCTCCCTG-GTCAGCAGTGGAATAAGTTGAA
38176825 AATAACAGAT
Statistics
Matches: 138, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
43 3 0.02
44 133 0.96
45 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (45 bp):
TATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATTGTGAAGTCC
Found at i:38176766 original size:88 final size:88
Alignment explanation
Indices: 38176633--38176802 Score: 254
Period size: 88 Copynumber: 1.9 Consensus size: 88
38176623 CCTGGTCAGC
38176633 AGTGGAATAAGTTAAAGATTGTGAATCATATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTG
1 AGTGGAATAAGTTAAAGATTGTGAATCATATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTG
*
38176698 AGAATTCTATCTCCCTGGGAATT
66 AGAATCCTATCTCCCTGGGAATT
* * *
38176721 AGTGGAAT-AGATTGAAGATTGT-AAGTCCTATCTCCCTGGTGAGCAGTGGAATAGGTTGAAGAT
1 AGTGGAATAAG-TTAAAGATTGTGAA-TCATATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGAT
* *
38176784 TGCGAGTCCTATCTCCCTG
64 TGAGAATCCTATCTCCCTG
38176803 AGCAGCAGTG
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
87 4 0.05
88 70 0.95
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (88 bp):
AGTGGAATAAGTTAAAGATTGTGAATCATATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTG
AGAATCCTATCTCCCTGGGAATT
Found at i:38176813 original size:88 final size:88
Alignment explanation
Indices: 38176629--38176824 Score: 252
Period size: 88 Copynumber: 2.2 Consensus size: 88
38176619 TCTACCTGGT
*
38176629 CAGCAGTGGAATA-AGTTAAAGATTGTGAATCATATCTCCCTGGTCAGCAGTGGAATAGGTTGAA
1 CAGCAGTGGAATAGA-TTGAAGATTGTGAATCATATCTCCCTGGTCAGCAGTGGAATAGGTTGAA
* *
38176693 GATTGAGAATTCTATCTCCCTGGG
65 GATTGAGAATCCTATCTCCCTGAG
* ** * *
38176717 AATTAGTGGAATAGATTGAAGATTGT-AAGTCCTATCTCCCTGGTGAGCAGTGGAATAGGTTGAA
1 CAGCAGTGGAATAGATTGAAGATTGTGAA-TCATATCTCCCTGGTCAGCAGTGGAATAGGTTGAA
* *
38176781 GATTGCGAGTCCTATCTCCCTGAG
65 GATTGAGAATCCTATCTCCCTGAG
* *
38176805 CAGCAGTGGAGTAGGTTGAA
1 CAGCAGTGGAATAGATTGAA
38176825 AATAACAGAT
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
87 2 0.02
88 88 0.97
89 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (88 bp):
CAGCAGTGGAATAGATTGAAGATTGTGAATCATATCTCCCTGGTCAGCAGTGGAATAGGTTGAAG
ATTGAGAATCCTATCTCCCTGAG
Found at i:38177697 original size:22 final size:22
Alignment explanation
Indices: 38177638--38177694 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 22
38177628 TAGTTATGAT
38177638 ATATGCAATCTT---AGATATG
1 ATATGCAATCTTAGAAGATATG
38177657 ATATGCAATCTTAGAAGATATG
1 ATATGCAATCTTAGAAGATATG
* *
38177679 ATTTTGTAATCTTAGA
1 A-TATGCAATCTTAGA
38177695 GATTTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 12 0.38
22 8 0.25
23 12 0.38
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
ATATGCAATCTTAGAAGATATG
Found at i:38177704 original size:22 final size:22
Alignment explanation
Indices: 38177663--38177708 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
38177653 TATGATATGC
*
38177663 AATCTTAGAAGATATGATTTTGT
1 AATCTTAGAAGATAT-AATTTGT
*
38177686 AATCTTAG-AGATTTAATTTGT
1 AATCTTAGAAGATATAATTTGT
38177707 AA
1 AA
38177709 ATACCCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 5 0.24
23 8 0.38
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.43
Consensus pattern (22 bp):
AATCTTAGAAGATATAATTTGT
Found at i:38177707 original size:21 final size:23
Alignment explanation
Indices: 38177650--38177708 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
38177640 ATGCAATCTT
* *
38177650 AGATATG-ATATGCAATCTTAGA
1 AGATATGAATTTGTAATCTTAGA
*
38177672 AGATATGATTTTGTAATCTTAG-
1 AGATATGAATTTGTAATCTTAGA
*
38177694 AGAT-TTAATTTGTAA
1 AGATATGAATTTGTAA
38177709 ATACCCTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 9 0.29
22 11 0.35
23 11 0.35
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (23 bp):
AGATATGAATTTGTAATCTTAGA
Found at i:38179891 original size:40 final size:40
Alignment explanation
Indices: 38179846--38179979 Score: 214
Period size: 40 Copynumber: 3.4 Consensus size: 40
38179836 AAGGTAGTGG
*
38179846 CAGACAATAACCAAACACTTTAATACAACCTAGGCAATGA
1 CAGACAATAACCAAACACTTTAATACAACCTAGACAATGA
* * *
38179886 CAGACAATAGCCAAACACTTTCATACAACCTAGATAATGA
1 CAGACAATAACCAAACACTTTAATACAACCTAGACAATGA
38179926 CAGACAATAACCAAACACTTTAATACAACCTAGACAATGA
1 CAGACAATAACCAAACACTTTAATACAACCTAGACAATGA
* *
38179966 CAAACAATATCCAA
1 CAGACAATAACCAA
38179980 TACAAAAATA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.49, C:0.25, G:0.08, T:0.18
Consensus pattern (40 bp):
CAGACAATAACCAAACACTTTAATACAACCTAGACAATGA
Found at i:38181464 original size:18 final size:18
Alignment explanation
Indices: 38181441--38181476 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
38181431 TATCAATAGC
38181441 AAGTAAAGTAACAGAACA
1 AAGTAAAGTAACAGAACA
38181459 AAGTAAAGTAACAGAACA
1 AAGTAAAGTAACAGAACA
38181477 TCACAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.11, G:0.17, T:0.11
Consensus pattern (18 bp):
AAGTAAAGTAACAGAACA
Found at i:38182842 original size:24 final size:24
Alignment explanation
Indices: 38182798--38182843 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
38182788 TTTCGCTTAA
*
38182798 TTTATTTTACAGTCATGTTTTTAC
1 TTTATTTTACAGTCATATTTTTAC
*
38182822 TTTATTTTATA-TACATATTTTT
1 TTTATTTTACAGT-CATATTTTT
38182844 TTCCTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.63
Consensus pattern (24 bp):
TTTATTTTACAGTCATATTTTTAC
Found at i:38190005 original size:18 final size:18
Alignment explanation
Indices: 38189984--38190031 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
38189974 ATTTTTTATA
*
38189984 TAGTTTGAATTTAATCTC
1 TAGTTTAAATTTAATCTC
38190002 TAGTTTAAATTTAATCTC
1 TAGTTTAAATTTAATCTC
*
38190020 TGGTTTAAATTT
1 TAGTTTAAATTT
38190032 GATTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.52
Consensus pattern (18 bp):
TAGTTTAAATTTAATCTC
Found at i:38193418 original size:9 final size:9
Alignment explanation
Indices: 38193401--38193446 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
38193391 TGAGTTTTCG
38193401 AATTCGAAT
1 AATTCGAAT
*
38193410 AACTCGAAT
1 AATTCGAAT
38193419 AATTCGAAT
1 AATTCGAAT
38193428 AATTCGAAT
1 AATTCGAAT
38193437 AATTCGAAT
1 AATTCGAAT
38193446 A
1 A
38193447 TGACTCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:38194626 original size:31 final size:30
Alignment explanation
Indices: 38194591--38194657 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
38194581 AGATTTTACG
* *
38194591 CTTTTAATCTGTCACAT-AATACTTTATTTCA
1 CTTTTAAT-T-TCACATCAAAAATTTATTTCA
*
38194622 CTTTTTAATTTCATATCAAAAATTTATTTCA
1 C-TTTTAATTTCACATCAAAAATTTATTTCA
38194653 CTTTT
1 CTTTT
38194658 CTTTCTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 9 0.29
31 15 0.48
32 7 0.23
ACGTcount: A:0.30, C:0.16, G:0.01, T:0.52
Consensus pattern (30 bp):
CTTTTAATTTCACATCAAAAATTTATTTCA
Found at i:38194820 original size:17 final size:17
Alignment explanation
Indices: 38194799--38194844 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
38194789 AAAAAATTCA
38194799 AAAAAATAAAAATTATT
1 AAAAAATAAAAATTATT
* * *
38194816 TAAAATTTAAAATTATT
1 AAAAAATAAAAATTATT
38194833 AAAAAATAAAAA
1 AAAAAATAAAAA
38194845 AATTATTTTC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAAATAAAAATTATT
Found at i:38197208 original size:18 final size:19
Alignment explanation
Indices: 38197176--38197214 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
38197166 CAAGGAAATC
**
38197176 AGATCGAAATTAAACA-AA
1 AGATCGAAACAAAACATAA
38197194 AGATCGAAACAAAACATAA
1 AGATCGAAACAAAACATAA
38197213 AG
1 AG
38197215 GGACCCCTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.13
Consensus pattern (19 bp):
AGATCGAAACAAAACATAA
Found at i:38198172 original size:25 final size:24
Alignment explanation
Indices: 38198144--38198199 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
38198134 ATTACTGGAC
38198144 ATTTTATTTA-TATATATTATTATTT
1 ATTTT-TTTATTATATA-TATTATTT
*
38198169 ATTTTTTTATTATATATATTTTTT
1 ATTTTTTTATTATATATATTATTT
*
38198193 ATATTTT
1 ATTTTTT
38198200 GATTTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
ATTTTTTTATTATATATATTATTT
Found at i:38198180 original size:15 final size:16
Alignment explanation
Indices: 38198147--38198198 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 16
38198137 ACTGGACATT
* *
38198147 TTATTTATATATATTA
1 TTATTTATATTTTTTA
38198163 TTATTTAT-TTTTTTA
1 TTATTTATATTTTTTA
*
38198178 TTATATATATTTTTTA
1 TTATTTATATTTTTTA
38198194 -TATTT
1 TTATTT
38198199 TGATTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 16 0.52
16 15 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTATATTTTTTA
Found at i:38198181 original size:18 final size:18
Alignment explanation
Indices: 38198156--38198197 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
38198146 TTTATTTATA
*
38198156 TATATTATTATTTATTTTT
1 TATATTA-TATATATTTTT
38198175 T-TATTATATATATTTTT
1 TATATTATATATATTTTT
38198192 TATATT
1 TATATT
38198198 TTGATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 11 0.52
18 9 0.43
19 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TATATTATATATATTTTT
Found at i:38198205 original size:14 final size:15
Alignment explanation
Indices: 38198188--38198220 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
38198178 TTATATATAT
*
38198188 TTTTTATATTT-TGA
1 TTTTAATATTTGTGA
38198202 TTTTAATATTTGTGA
1 TTTTAATATTTGTGA
38198217 TTTT
1 TTTT
38198221 GGGCCCGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (15 bp):
TTTTAATATTTGTGA
Found at i:38198687 original size:44 final size:44
Alignment explanation
Indices: 38198639--38198727 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
38198629 ATCTTGATTC
* * *
38198639 GCTCCGCTGTAGTCTCAGGGAGATAGGATTACTAGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
* * *
38198683 GCTCCACTGTAATCTTAGGGAGATAAGATTTCTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
38198727 G
1 G
38198728 ATGCGATCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (44 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
Found at i:38199010 original size:129 final size:129
Alignment explanation
Indices: 38198812--38199123 Score: 489
Period size: 129 Copynumber: 2.4 Consensus size: 129
38198802 TATGATTATC
* * * * *
38198812 GGCTTCAATCTGCTTCCTTGCACTTGAAGATAATATTCGCCGTCTTTGATCTGTCCCACTACAAC
1 GGCTTAAATCTGCTTCCTTACAC-TGAAGATAAGATTCGCCGTCTTCGATCTGCCCCACTACAAC
*
38198877 TTCAGCCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTGCAACCTCAGGGAGAAAGGACTCGT
65 TTCAGCCAGGATAAGACCTGCTTACTTAGTCTGCTCCACTGCAACCTCAGGGAGAAAGGACTCGT
*
38198942 GGCTTAAATCTGCTTCCTTACACTGAAGATAAGATTCGCCGTCTTCGATCTGCCCCACTGCAACT
1 GGCTTAAATCTGCTTCCTTACACTGAAGATAAGATTCGCCGTCTTCGATCTGCCCCACTACAACT
** * *
38199007 TCAGTTAGGATAAGACTTGCTTACTTAGTCTGCTCCATTGCAACCTCAGGGAGAAAGGACTCGT
66 TCAGCCAGGATAAGACCTGCTTACTTAGTCTGCTCCACTGCAACCTCAGGGAGAAAGGACTCGT
* * *
38199071 GGCTTAAATATGCTTCCTTACACTAAAGATAAGATTCGTCGTCTTCGATCTGC
1 GGCTTAAATCTGCTTCCTTACACTGAAGATAAGATTCGCCGTCTTCGATCTGC
38199124 TCTGCTACTA
Statistics
Matches: 168, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
129 147 0.88
130 21 0.12
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (129 bp):
GGCTTAAATCTGCTTCCTTACACTGAAGATAAGATTCGCCGTCTTCGATCTGCCCCACTACAACT
TCAGCCAGGATAAGACCTGCTTACTTAGTCTGCTCCACTGCAACCTCAGGGAGAAAGGACTCGT
Found at i:38199251 original size:131 final size:128
Alignment explanation
Indices: 38199112--38199419 Score: 366
Period size: 131 Copynumber: 2.4 Consensus size: 128
38199102 AGATTCGTCG
* * *
38199112 TCTTCGATCTGCTCTGCTACTACTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCT
1 TCTTCGATCTGCTCTGCTACT-CTTAGGGAGACAAGATCTGTAATTT-CAACCTATTCCACTACC
* * *
38199177 GGTCAAGGACATAGGACTTGTGGCTTAAATTTGTTTCCCTACTCCTGGGGAAGATAAGGTCCGCC
64 GGTCAAGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCT-GGGAAGATAAGATCCACC
38199242 A
128 A
* * * * * * *
38199243 TCTTCGATCAG-TTTCCCTACTCATAGGGAAGATAAGATCCGTGATCTTCAACCTATTCCACTAC
1 TCTTCGATCTGCTCT-GCTACTCTTAGGG-AGACAAGATCTGTAAT-TTCAACCTATTCCACTAC
* * *
38199307 CGGTTAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGAAGATAAGATTCACC
63 CGGTCAAGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGAAGATAAGATCCACC
*
38199372 G
128 A
* * *
38199373 TCTTCGATCTACTCCGCTACTGCTTAGGGAGACCAGATCTGTAATTT
1 TCTTCGATCTGCTCTGCTACT-CTTAGGGAGACAAGATCTGTAATTT
38199420 TTAACCAGCT
Statistics
Matches: 145, Mismatches: 27, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
129 2 0.01
130 49 0.34
131 92 0.63
132 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (128 bp):
TCTTCGATCTGCTCTGCTACTCTTAGGGAGACAAGATCTGTAATTTCAACCTATTCCACTACCGG
TCAAGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGAAGATAAGATCCACCA
Found at i:38200691 original size:7 final size:7
Alignment explanation
Indices: 38200672--38200708 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
38200662 TTATTTCCAA
38200672 TTTTCA-
1 TTTTCAT
*
38200678 TTCTCAT
1 TTTTCAT
38200685 TTTTCAT
1 TTTTCAT
38200692 TTTTCA-
1 TTTTCAT
38200698 TTTTCAT
1 TTTTCAT
38200705 TTTT
1 TTTT
38200709 TTTGACTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 11 0.41
7 16 0.59
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTCAT
Found at i:38200708 original size:13 final size:13
Alignment explanation
Indices: 38200657--38200707 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
38200647 TTAGCCTCTC
*
38200657 CATTTTT-ATTTC
1 CATTTTTCATTTT
* *
38200669 CAATTTTCATTCT
1 CATTTTTCATTTT
38200682 CATTTTTCATTTTT
1 CATTTTTCA-TTTT
38200696 CA-TTTTCATTTT
1 CATTTTTCATTTT
38200708 TTTTGACTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 10 0.31
13 17 0.53
14 5 0.16
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:38201610 original size:28 final size:29
Alignment explanation
Indices: 38201579--38201633 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
38201569 CTTTTTCTCT
38201579 TTTCACATTTTG-TTTTAACTTTGATTGA
1 TTTCACATTTTGCTTTTAACTTTGATTGA
* * *
38201607 TTTCTCTTTTTGCTTTTGACTTTGATT
1 TTTCACATTTTGCTTTTAACTTTGATT
38201634 TTTTCTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.15, C:0.13, G:0.11, T:0.62
Consensus pattern (29 bp):
TTTCACATTTTGCTTTTAACTTTGATTGA
Found at i:38201629 original size:29 final size:26
Alignment explanation
Indices: 38201586--38201648 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 26
38201576 TCTTTTCACA
38201586 TTTTG-TTTTAACTTTGATTGATTTCTCT
1 TTTTGCTTTTAACTTTGATT--TTT-TCT
*
38201614 TTTTGCTTTTGACTTTGATTTTTTCT
1 TTTTGCTTTTAACTTTGATTTTTTCT
38201640 TTTT-CTTTT
1 TTTTGCTTTT
38201649 TGTTTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 5 0.15
26 7 0.21
27 3 0.09
28 5 0.15
29 13 0.39
ACGTcount: A:0.10, C:0.11, G:0.10, T:0.70
Consensus pattern (26 bp):
TTTTGCTTTTAACTTTGATTTTTTCT
Found at i:38207516 original size:16 final size:16
Alignment explanation
Indices: 38207480--38207534 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
38207470 ACTGGACATT
*
38207480 TTATTTATATATATATTA
1 TTATTTATAT-T-TTTTA
*
38207498 TTATTTATTTTTTTTA
1 TTATTTATATTTTTTA
*
38207514 TTATATATATTTTTTA
1 TTATTTATATTTTTTA
38207530 -TATTT
1 TTATTT
38207535 TGGTTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 4 0.12
16 18 0.56
17 1 0.03
18 9 0.28
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTATATTTTTTA
Found at i:38207524 original size:18 final size:19
Alignment explanation
Indices: 38207491--38207533 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
38207481 TATTTATATA
*
38207491 TATATTATTATTTATTTTT
1 TATATTATTATATATTTTT
*
38207510 TTTATTA-TATATATTTTT
1 TATATTATTATATATTTTT
38207528 TATATT
1 TATATT
38207534 TTGGTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TATATTATTATATATTTTT
Found at i:38227031 original size:19 final size:19
Alignment explanation
Indices: 38227004--38227043 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
38226994 AACATCAGCT
38227004 AAAAATAAAA-TATCTTTA
1 AAAAATAAAATTATCTTTA
*
38227022 AAAAATTAAAATTATTTTTA
1 AAAAA-TAAAATTATCTTTA
38227042 AA
1 AA
38227044 TTGTCCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 5 0.26
20 9 0.47
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATAAAATTATCTTTA
Found at i:38228916 original size:22 final size:21
Alignment explanation
Indices: 38228886--38228937 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
38228876 TCTCCAATTT
* *
38228886 CAACACCATTTGCAAAATCGA
1 CAACACCATTAGCAAAATCAA
*
38228907 CAACAACCATTAGCAAATTCAA
1 CAAC-ACCATTAGCAAAATCAA
38228929 CAAC-CCATT
1 CAACACCATT
38228938 TCTCAACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 4 0.15
22 18 0.67
ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19
Consensus pattern (21 bp):
CAACACCATTAGCAAAATCAA
Found at i:38229388 original size:17 final size:17
Alignment explanation
Indices: 38229362--38229395 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38229352 TTAAATTCTA
*
38229362 AAAATAATCAATTATAC
1 AAAATAATCAATAATAC
*
38229379 AAAATTATCAATAATAC
1 AAAATAATCAATAATAC
38229396 TTGAGAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAATCAATAATAC
Found at i:38231655 original size:51 final size:52
Alignment explanation
Indices: 38231559--38231657 Score: 130
Period size: 52 Copynumber: 1.9 Consensus size: 52
38231549 AATTTTGGTT
**
38231559 TTTTTTTAGTATTAGGACCAAATTGAGACAATATGTAAATGTTGAGGGTTAA
1 TTTTTTTAAAATTAGGACCAAATTGAGACAATATGTAAATGTTGAGGGTTAA
* * *
38231611 TTTTTTTAAAATTATGACTAAATTGATA-AATATGTGAAAT-TTGAGGG
1 TTTTTTTAAAATTAGGACCAAATTGAGACAATATGT-AAATGTTGAGGG
38231658 CTAAATTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 14 0.34
52 27 0.66
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.40
Consensus pattern (52 bp):
TTTTTTTAAAATTAGGACCAAATTGAGACAATATGTAAATGTTGAGGGTTAA
Found at i:38235989 original size:2 final size:2
Alignment explanation
Indices: 38235982--38236018 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
38235972 AACAGATAAT
38235982 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
38236019 ATTTCCTCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:38237380 original size:38 final size:38
Alignment explanation
Indices: 38237338--38237435 Score: 160
Period size: 38 Copynumber: 2.6 Consensus size: 38
38237328 CCCTATTGAG
38237338 TACATGTTAAGCATGTCTACTGCTAGTGTTGAACTGAA
1 TACATGTTAAGCATGTCTACTGCTAGTGTTGAACTGAA
* *
38237376 TACATGTTAAGCATGTCTACTGGTAGTTTTGAACTGAA
1 TACATGTTAAGCATGTCTACTGCTAGTGTTGAACTGAA
* *
38237414 TACATGTAAAGCATGTCCACTG
1 TACATGTTAAGCATGTCTACTG
38237436 TTTTTGCATT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 56 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (38 bp):
TACATGTTAAGCATGTCTACTGCTAGTGTTGAACTGAA
Found at i:38240759 original size:12 final size:12
Alignment explanation
Indices: 38240742--38240766 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38240732 TAAGTGATAC
38240742 AATTGGTACCAA
1 AATTGGTACCAA
38240754 AATTGGTACCAA
1 AATTGGTACCAA
38240766 A
1 A
38240767 TGTTAAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (12 bp):
AATTGGTACCAA
Found at i:38241880 original size:11 final size:10
Alignment explanation
Indices: 38241862--38241903 Score: 57
Period size: 11 Copynumber: 3.9 Consensus size: 10
38241852 CTCAAAAATG
38241862 AACAACATTT
1 AACAACATTT
38241872 AACCAACATTT
1 AA-CAACATTT
38241883 GAACAACATTT
1 -AACAACATTT
38241894 AAACAACATT
1 -AACAACATT
38241904 CGGACAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 2 0.07
11 25 0.86
12 2 0.07
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.26
Consensus pattern (10 bp):
AACAACATTT
Found at i:38241885 original size:22 final size:22
Alignment explanation
Indices: 38241860--38241914 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
38241850 TGCTCAAAAA
*
38241860 TGAACAACATTTAACCAACATT
1 TGAACAACATTTAAACAACATT
38241882 TGAACAACATTTAAACAACATT
1 TGAACAACATTTAAACAACATT
* *
38241904 CGGACAACATT
1 TGAACAACATT
38241915 AGTATGCTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.25
Consensus pattern (22 bp):
TGAACAACATTTAAACAACATT
Found at i:38241949 original size:11 final size:11
Alignment explanation
Indices: 38241931--38241972 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
38241921 CTCAAAAACG
38241931 AACAACATTTA
1 AACAACATTTA
*
38241942 ACCAACA-TTA
1 AACAACATTTA
*
38241952 AGACAGCATTTA
1 A-ACAACATTTA
38241964 AACAACATT
1 AACAACATT
38241973 CAGACAGCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (11 bp):
AACAACATTTA
Found at i:38241964 original size:22 final size:22
Alignment explanation
Indices: 38241936--38241983 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
38241926 AAACGAACAA
*
38241936 CATTTAACCAACATTAAGACAG
1 CATTTAAACAACATTAAGACAG
*
38241958 CATTTAAACAACATTCAGACAG
1 CATTTAAACAACATTAAGACAG
38241980 CATT
1 CATT
38241984 AGTATGCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (22 bp):
CATTTAAACAACATTAAGACAG
Found at i:38242029 original size:69 final size:69
Alignment explanation
Indices: 38241836--38242030 Score: 275
Period size: 69 Copynumber: 2.8 Consensus size: 69
38241826 GTACCAATTT
* * * *
38241836 AGACAGCATT-GATATGCTCAAAAATGAACAACATTTAACCAACATTTGAACAACATTTAAACAA
1 AGACAGCATTAG-TATGCTCAAAAACGAACAACATTTAACCAACATTAGGACAGCATTTAAACAA
38241900 CATTC
65 CATTC
* * *
38241905 GGACAACATTAGTATGCTCAAAAACGAACAACATTTAACCAACATTAAGACAGCATTTAAACAAC
1 AGACAGCATTAGTATGCTCAAAAACGAACAACATTTAACCAACATTAGGACAGCATTTAAACAAC
38241970 ATTC
66 ATTC
* * * *
38241974 AGACAGCATTAGTATGCTAAAAAACGAACAACGTTTAACCAACATTCGGATAGCATT
1 AGACAGCATTAGTATGCTCAAAAACGAACAACATTTAACCAACATTAGGACAGCATT
38242031 ATTATCAAGC
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
69 110 0.99
70 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (69 bp):
AGACAGCATTAGTATGCTCAAAAACGAACAACATTTAACCAACATTAGGACAGCATTTAAACAAC
ATTC
Found at i:38242684 original size:42 final size:42
Alignment explanation
Indices: 38242610--38242709 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
38242600 AGTACCTTAC
* ** *
38242610 ATAGCCGAAGCTATCTCAATCTTGCATGCTAAGTGTCATATAT
1 ATAGACGAAGCTATCTCAA-CTTGCACACTAAGTGCCATATAT
38242653 ATAGACGAAGCTATTCTCAA-TTGCACACTAAGTGCCATA-A-
1 ATAGACGAAGCTA-TCTCAACTTGCACACTAAGTGCCATATAT
* *
38242693 ACAGCCGAAGCTATCTC
1 ATAGACGAAGCTATCTC
38242710 GAATCGCATA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
39 4 0.08
40 11 0.22
41 1 0.02
42 16 0.32
43 12 0.24
44 6 0.12
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (42 bp):
ATAGACGAAGCTATCTCAACTTGCACACTAAGTGCCATATAT
Found at i:38243502 original size:6 final size:6
Alignment explanation
Indices: 38243491--38243517 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38243481 GCATTTTTAC
38243491 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
38243518 TTAACCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:38243516 original size:11 final size:11
Alignment explanation
Indices: 38243483--38243516 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
38243473 TTATGCATGC
*
38243483 ATTTTTACTTT
1 ATTTTTATTTT
38243494 ATTTTTATTTTT
1 ATTTTTA-TTTT
38243506 ATTTTTATTTT
1 ATTTTTATTTT
38243517 TTTAACCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:38247954 original size:15 final size:15
Alignment explanation
Indices: 38247929--38247963 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
38247919 AACTATATTT
*
38247929 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
38247943 TAATTAATATTAAGA
1 TAATTAATATTAAGA
38247958 TAATTA
1 TAATTA
38247964 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:38254699 original size:29 final size:29
Alignment explanation
Indices: 38254665--38254735 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
38254655 AAAAGAATTA
38254665 AAAATTTGAAATATTATT-T-AAATTTTGAT
1 AAAATTTGAAATATT-TTATAAAATTTT-AT
**
38254694 AAAATTACAAATATTTTATAAAATTTTAT
1 AAAATTTGAAATATTTTATAAAATTTTAT
*
38254723 AAATTATTGAAAT
1 AAAAT-TTGAAAT
38254736 TTGCTTATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
28 2 0.06
29 20 0.59
30 12 0.35
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (29 bp):
AAAATTTGAAATATTTTATAAAATTTTAT
Found at i:38254866 original size:19 final size:20
Alignment explanation
Indices: 38254834--38254873 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
38254824 TTTTTTTATA
*
38254834 TTATTTAGAATTTTTAATTT
1 TTATTTAGAATTTTCAATTT
*
38254854 TTATTTA-AGTTTTCAATTT
1 TTATTTAGAATTTTCAATTT
38254873 T
1 T
38254874 ATACAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (20 bp):
TTATTTAGAATTTTCAATTT
Found at i:38263267 original size:36 final size:36
Alignment explanation
Indices: 38263220--38263291 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
38263210 TGTCAAAGCC
38263220 TTTCCAGATAACTTCGCCACTAAGGCTTCCCAAATA
1 TTTCCAGATAACTTCGCCACTAAGGCTTCCCAAATA
38263256 TTTCCAGATAACTTCGCCACTAAGGCTTCCCAAATA
1 TTTCCAGATAACTTCGCCACTAAGGCTTCCCAAATA
38263292 ATATGCCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.28
Consensus pattern (36 bp):
TTTCCAGATAACTTCGCCACTAAGGCTTCCCAAATA
Found at i:38266683 original size:27 final size:26
Alignment explanation
Indices: 38266648--38266699 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
38266638 GACAACTAAG
*
38266648 AATAACCTTTGTGGTGAACTCTTAAAT
1 AATAACCTTTGTGGCGAACT-TTAAAT
*
38266675 AATAGCCTTTGTGGCGAACTTTAAA
1 AATAACCTTTGTGGCGAACTTTAAA
38266700 AGGAATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (26 bp):
AATAACCTTTGTGGCGAACTTTAAAT
Found at i:38266712 original size:27 final size:27
Alignment explanation
Indices: 38266655--38266747 Score: 89
Period size: 27 Copynumber: 3.4 Consensus size: 27
38266645 AAGAATAACC
* * * *
38266655 TTTGTGGTGAACTCTTAAA-TAATAGCC
1 TTTGTGGCGAACTCTAAAAGGAAT-GCA
* *
38266682 TTTGTGGCGAACTTTAAAAGGAATTCA
1 TTTGTGGCGAACTCTAAAAGGAATGCA
* *
38266709 TTTGTAGCGAACTCTAAAAGGAATGCT
1 TTTGTGGCGAACTCTAAAAGGAATGCA
*
38266736 TTTGTGGTGAAC
1 TTTGTGGCGAAC
38266748 ACTGAATGGA
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
27 50 0.94
28 3 0.06
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (27 bp):
TTTGTGGCGAACTCTAAAAGGAATGCA
Found at i:38279507 original size:37 final size:37
Alignment explanation
Indices: 38279456--38279531 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 37
38279446 AGGGCACAAG
* * *
38279456 TTTTATTTCGGTTATACTGATTAGCGCTGGATGCAAT
1 TTTTATTTCAGTTATACAGATGAGCGCTGGATGCAAT
* *
38279493 TTTTATTTCAGTTATACAGATGAGTGTTGGATGCAAT
1 TTTTATTTCAGTTATACAGATGAGCGCTGGATGCAAT
38279530 TT
1 TT
38279532 ATATACTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.45
Consensus pattern (37 bp):
TTTTATTTCAGTTATACAGATGAGCGCTGGATGCAAT
Found at i:38286546 original size:35 final size:35
Alignment explanation
Indices: 38286490--38286556 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
38286480 TGCCTAAAGT
38286490 AGATATCTCAAAGTTGAAATAGTTCAATGGGACGA
1 AGATATCTCAAAGTTGAAATAGTTCAATGGGACGA
* *
38286525 AGATGTCTCGAAGTTGAAATAGTTCAATGGGA
1 AGATATCTCAAAGTTGAAATAGTTCAATGGGA
38286557 TGATGTTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.27
Consensus pattern (35 bp):
AGATATCTCAAAGTTGAAATAGTTCAATGGGACGA
Found at i:38288375 original size:2 final size:2
Alignment explanation
Indices: 38288368--38288393 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38288358 CATGTGTTCA
38288368 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
38288394 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38293644 original size:3 final size:3
Alignment explanation
Indices: 38293636--38293668 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
38293626 GTATATTCAC
38293636 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38293669 TGAGGGACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:38299179 original size:27 final size:27
Alignment explanation
Indices: 38299149--38299206 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
38299139 GCAAAAAATC
38299149 GCCAAAAAT-GAATATTGC-AGTTAAACT
1 GCCAAAAATAG-ATATTGCGAG-TAAACT
*
38299176 GCCAAAAATAGATTTTGCGAGTAAACT
1 GCCAAAAATAGATATTGCGAGTAAACT
38299203 GCCA
1 GCCA
38299207 GAATCACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (27 bp):
GCCAAAAATAGATATTGCGAGTAAACT
Found at i:38300499 original size:16 final size:16
Alignment explanation
Indices: 38300478--38300508 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
38300468 CACAACCAGA
38300478 CACTTAACCACTGAAC
1 CACTTAACCACTGAAC
38300494 CACTTAACCACTGAA
1 CACTTAACCACTGAA
38300509 ATTGAAGTAT
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:0.39, C:0.35, G:0.06, T:0.19
Consensus pattern (16 bp):
CACTTAACCACTGAAC
Found at i:38303985 original size:18 final size:17
Alignment explanation
Indices: 38303954--38303989 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
38303944 GCCCGGCCCG
*
38303954 ATTTTAAATTTTTTTAA
1 ATTTTAAATATTTTTAA
38303971 ATTTTAAAATATTTTTAA
1 ATTTT-AAATATTTTTAA
38303989 A
1 A
38303990 ATACTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTAAATATTTTTAA
Found at i:38307552 original size:16 final size:16
Alignment explanation
Indices: 38307531--38307572 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
38307521 TTATTAAATT
*
38307531 ATATATTTTAATTATA
1 ATATATTTTAATAATA
38307547 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
38307562 AT-TATGTTTAA
1 ATATAT-TTTAA
38307573 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:38307557 original size:15 final size:15
Alignment explanation
Indices: 38307522--38307563 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38307512 NNNNGAATTT
*
38307522 TATTAAATTAT-ATA
1 TATTTAATTATAATA
38307536 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
38307550 TATTTAATAATAAT
1 TATTTAATTATAAT
38307564 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:38307773 original size:44 final size:45
Alignment explanation
Indices: 38307710--38307806 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
38307700 CTATTACACC
* * *
38307710 TCTATTCCATTCAACCAAACACA-AGA-TTGCTATTACGCCTCTAT
1 TCTATTACATTCAACCAAACA-ATACATTTGCTATTACGCCTCTAA
*
38307754 TCTATTACATTCAACCAAACAATTCATTTGCTATTACGCCTCTAA
1 TCTATTACATTCAACCAAACAATACATTTGCTATTACGCCTCTAA
38307799 TCTATTAC
1 TCTATTAC
38307807 GCCTCTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.45
45 25 0.53
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (45 bp):
TCTATTACATTCAACCAAACAATACATTTGCTATTACGCCTCTAA
Found at i:38307805 original size:16 final size:16
Alignment explanation
Indices: 38307784--38307818 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
38307774 AATTCATTTG
38307784 CTATTACGCCTCTAAT
1 CTATTACGCCTCTAAT
*
38307800 CTATTACGCCTCTATT
1 CTATTACGCCTCTAAT
38307816 CTA
1 CTA
38307819 ATACAGCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.31, G:0.06, T:0.40
Consensus pattern (16 bp):
CTATTACGCCTCTAAT
Found at i:38313663 original size:20 final size:20
Alignment explanation
Indices: 38313640--38313705 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
38313630 ATATCTAACG
38313640 ATATTGGTAAATCCTTAGAA
1 ATATTGGTAAATCCTTAGAA
*
38313660 ATATTGGTAAAGCC-----A
1 ATATTGGTAAATCCTTAGAA
*
38313675 ATATTGGTAAATCGTTAGAA
1 ATATTGGTAAATCCTTAGAA
*
38313695 ATATTAGTAAA
1 ATATTGGTAAA
38313706 AGCTTTTTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
15 13 0.35
20 24 0.65
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (20 bp):
ATATTGGTAAATCCTTAGAA
Found at i:38317512 original size:9 final size:9
Alignment explanation
Indices: 38317495--38317525 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
38317485 TATTTAATTT
*
38317495 CAAAATAAC
1 CAAATTAAC
38317504 CAAATTAAC
1 CAAATTAAC
38317513 CAAATTAAC
1 CAAATTAAC
38317522 CAAA
1 CAAA
38317526 CAATTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.61, C:0.23, G:0.00, T:0.16
Consensus pattern (9 bp):
CAAATTAAC
Found at i:38320978 original size:90 final size:90
Alignment explanation
Indices: 38320875--38321054 Score: 360
Period size: 90 Copynumber: 2.0 Consensus size: 90
38320865 GCTCATACAT
38320875 TGAGCAAACAAACGAATGCTTTCTTTGCTTTTAGAATAAAAGTTGATAAAGTAGCTGCAAAATTT
1 TGAGCAAACAAACGAATGCTTTCTTTGCTTTTAGAATAAAAGTTGATAAAGTAGCTGCAAAATTT
38320940 GATCATATTCATCCATCTCCTAGTA
66 GATCATATTCATCCATCTCCTAGTA
38320965 TGAGCAAACAAACGAATGCTTTCTTTGCTTTTAGAATAAAAGTTGATAAAGTAGCTGCAAAATTT
1 TGAGCAAACAAACGAATGCTTTCTTTGCTTTTAGAATAAAAGTTGATAAAGTAGCTGCAAAATTT
38321030 GATCATATTCATCCATCTCCTAGTA
66 GATCATATTCATCCATCTCCTAGTA
38321055 AGCAAATTTG
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (90 bp):
TGAGCAAACAAACGAATGCTTTCTTTGCTTTTAGAATAAAAGTTGATAAAGTAGCTGCAAAATTT
GATCATATTCATCCATCTCCTAGTA
Found at i:38335068 original size:24 final size:24
Alignment explanation
Indices: 38335036--38335084 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
38335026 CTTATTTTGC
**
38335036 TTTGAAAGAATTTTCTGCCATACA
1 TTTGAAAGAATTTTCAACCATACA
*
38335060 TTTGAAAGAGTTTTCAACCATACA
1 TTTGAAAGAATTTTCAACCATACA
38335084 T
1 T
38335085 GACCTCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (24 bp):
TTTGAAAGAATTTTCAACCATACA
Found at i:38336236 original size:43 final size:43
Alignment explanation
Indices: 38336119--38336345 Score: 253
Period size: 43 Copynumber: 5.3 Consensus size: 43
38336109 CCATGAACTA
* * *
38336119 TAGCGGCGC-TTTCCCAAAAACGCCGCCGCTATAGTTCGAGACCTT
1 TAGCGGCGCTTTTCCCACAAA---CGCCGCTATAGCTCAAGACCTT
* *
38336164 TAAG-GGCGCTTTT-CCACAAACGCCACTATAGCTCAAGACATT
1 T-AGCGGCGCTTTTCCCACAAACGCCGCTATAGCTCAAGACCTT
* *
38336206 TAGCGGTGCTTTTCCCACAAACGCCGCTATAGCTCAAGAGCTT
1 TAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTCAAGACCTT
* * * **
38336249 TAGCAGCGCTTTTACCACAAACGCCGCTATAGATCGCGACCTT
1 TAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTCAAGACCTT
* * *
38336292 TAGCGGCGCTTTTCCGACAAACGCCGCTATAGCTCGATACCTT
1 TAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTCAAGACCTT
*
38336335 TAACGGCGCTT
1 TAGCGGCGCTT
38336346 CTCACAAAAA
Statistics
Matches: 155, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
41 2 0.01
42 27 0.17
43 109 0.70
45 12 0.08
46 5 0.03
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (43 bp):
TAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTCAAGACCTT
Found at i:38338032 original size:28 final size:28
Alignment explanation
Indices: 38337992--38338052 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
38337982 AAAACAAGAA
*
38337992 TCAAATTAGTTCAA-CTCCAAGTCCTTAG
1 TCAAATCAGTTCAACCT-CAAGTCCTTAG
* *
38338020 TCAAATCAGTTCAACCTCAAGTTCTTTG
1 TCAAATCAGTTCAACCTCAAGTCCTTAG
38338048 TCAAA
1 TCAAA
38338053 AGAAAAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (28 bp):
TCAAATCAGTTCAACCTCAAGTCCTTAG
Found at i:38339532 original size:12 final size:12
Alignment explanation
Indices: 38339517--38339541 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38339507 ATTAATGGCC
38339517 ACCAAAATGATT
1 ACCAAAATGATT
38339529 ACCAAAATGATT
1 ACCAAAATGATT
38339541 A
1 A
38339542 TTAAAGGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (12 bp):
ACCAAAATGATT
Found at i:38341646 original size:21 final size:20
Alignment explanation
Indices: 38341622--38341662 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
38341612 CCTAACTTCT
*
38341622 AACCCTTAAACCTTAAATCCC
1 AACCCTTAAACCAT-AATCCC
38341643 AACCCTTAAACCATAATCCC
1 AACCCTTAAACCATAATCCC
38341663 TAAATCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (20 bp):
AACCCTTAAACCATAATCCC
Found at i:38341866 original size:14 final size:15
Alignment explanation
Indices: 38341837--38341884 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
38341827 ACTCGACCCA
38341837 TAAATCCCTAAACTC
1 TAAATCCCTAAACTC
*
38341852 TAAAT-CCTTAACTC
1 TAAATCCCTAAACTC
* *
38341866 TTAACCCCTAAACCTC
1 TAAATCCCTAAA-CTC
38341882 TAA
1 TAA
38341885 CCTCTAACCC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 11 0.42
15 10 0.38
16 5 0.19
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATCCCTAAACTC
Found at i:38341876 original size:29 final size:28
Alignment explanation
Indices: 38341842--38341929 Score: 106
Period size: 29 Copynumber: 3.1 Consensus size: 28
38341832 ACCCATAAAT
38341842 CCCTAAACTCTAAATCCTTAACTCTTAAC
1 CCCTAAACTCTAAA-CCTTAACTCTTAAC
*
38341871 CCCTAAACCTCT-AACCTCTAACCCTTAAC
1 CCCTAAA-CTCTAAACCT-TAACTCTTAAC
* * *
38341900 CCCTAAACCCTAAACCTTAAATCCTAAC
1 CCCTAAACTCTAAACCTTAACTCTTAAC
38341928 CC
1 CC
38341930 TTACACCATA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
28 16 0.31
29 31 0.61
30 4 0.08
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (28 bp):
CCCTAAACTCTAAACCTTAACTCTTAAC
Found at i:38341885 original size:22 final size:22
Alignment explanation
Indices: 38341851--38341928 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 22
38341841 TCCCTAAACT
38341851 CTAAATCCTTAA-CTCTTAACCC
1 CTAAATCCTTAACCTC-TAACCC
38341873 CTAAA-CCTCTAACCTCTAACCC
1 CTAAATCCT-TAACCTCTAACCC
* ** * *
38341895 TTAACCCCTAAACC-CTAAACC
1 CTAAATCCTTAACCTCTAACCC
*
38341916 TTAAATCC-TAACC
1 CTAAATCCTTAACC
38341929 CTTACACCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
20 4 0.09
21 15 0.33
22 21 0.46
23 6 0.13
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.26
Consensus pattern (22 bp):
CTAAATCCTTAACCTCTAACCC
Found at i:38341891 original size:15 final size:15
Alignment explanation
Indices: 38341867--38341912 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
38341857 CCTTAACTCT
38341867 TAACCCCTAAACCTC
1 TAACCCCTAAACCTC
* *
38341882 TAACCTCTAACCCT-
1 TAACCCCTAAACCTC
38341896 TAACCCCTAAACC-C
1 TAACCCCTAAACCTC
38341910 TAA
1 TAA
38341913 ACCTTAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (15 bp):
TAACCCCTAAACCTC
Found at i:38341915 original size:15 final size:15
Alignment explanation
Indices: 38341832--38341915 Score: 57
Period size: 15 Copynumber: 5.7 Consensus size: 15
38341822 CCCTAACTCG
*
38341832 ACCCATAAATCCCTAA
1 ACCC-TAAACCCCTAA
* * *
38341848 ACTCTAAA-TCCTTA
1 ACCCTAAACCCCTAA
* *
38341862 ACTCTTAACCCCTAA
1 ACCCTAAACCCCTAA
*
38341877 ACCTCT-AACCTCT-A
1 ACC-CTAAACCCCTAA
*
38341891 ACCCTTAACCCCTAA
1 ACCCTAAACCCCTAA
38341906 ACCCTAAACC
1 ACCCTAAACC
38341916 TTAAATCCTA
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
13 2 0.04
14 21 0.39
15 26 0.48
16 5 0.09
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (15 bp):
ACCCTAAACCCCTAA
Found at i:38341925 original size:21 final size:20
Alignment explanation
Indices: 38341874--38341930 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
38341864 TCTTAACCCC
*
38341874 TAAACCTCTAACCTCTAACCCT
1 TAAACC-CTAACC-CTAAACCT
*
38341896 TAACCCCTAAACCCTAAACCT
1 TAAACCCT-AACCCTAAACCT
*
38341917 TAAATCCTAACCCT
1 TAAACCCTAACCCT
38341931 TACACCATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.20
21 15 0.50
22 9 0.30
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (20 bp):
TAAACCCTAACCCTAAACCT
Found at i:38341931 original size:14 final size:14
Alignment explanation
Indices: 38341867--38341932 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
38341857 CCTTAACTCT
*
38341867 TAACCCCTAAACCTC
1 TAACCCTTAAACC-C
38341882 TAA-CCTCT-AACCC
1 TAACCCT-TAAACCC
*
38341895 TTAACCCCTAAACCC
1 -TAACCCTTAAACCC
* *
38341910 TAAACCTTAAATCC
1 TAACCCTTAAACCC
38341924 TAACCCTTA
1 TAACCCTTA
38341933 CACCATAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
13 1 0.02
14 29 0.71
15 11 0.27
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (14 bp):
TAACCCTTAAACCC
Found at i:38342509 original size:106 final size:106
Alignment explanation
Indices: 38342322--38342513 Score: 248
Period size: 106 Copynumber: 1.8 Consensus size: 106
38342312 TAAAATGTTT
* * **
38342322 TTAGCGGAGCTTTTTCAAAAACGCCGCTAAAGCCCACAACATTAGCGGTGCTTTTTAAGAAACGC
1 TTAGCGGAGCTTTTTCAAAAACACCGCTAAAACCCACAACATTAGCGGCACTTTTTAAGAAACGC
*
38342387 CGCTAAAACCCTGAGCATTAGTGGCGCTAAAACCCTAAGAA
66 CGCTAAAACCCAGAGCATTAGTGGCGCTAAAACCCTAAGAA
*
38342428 TTAGCGGCA-CTTTTTTAAAAACACCGCTAAAACCC-CGAGA-ATTAGCGGCACTTTTTCAA-AA
1 TTAGCGG-AGCTTTTTCAAAAACACCGCTAAAACCCAC-A-ACATTAGCGGCACTTTTT-AAGAA
* *
38342489 ATGCCGCTAAATCCCAGAGCATTAG
62 ACGCCGCTAAAACCCAGAGCATTAG
38342514 CGTCGCGGCG
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
105 1 0.01
106 69 0.93
107 4 0.05
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (106 bp):
TTAGCGGAGCTTTTTCAAAAACACCGCTAAAACCCACAACATTAGCGGCACTTTTTAAGAAACGC
CGCTAAAACCCAGAGCATTAGTGGCGCTAAAACCCTAAGAA
Found at i:38342513 original size:41 final size:41
Alignment explanation
Indices: 38342411--38342515 Score: 140
Period size: 41 Copynumber: 2.6 Consensus size: 41
38342401 GCATTAGTGG
*
38342411 CGCTAAAACCCTA-AGAATTAGCGGCACTTTTTTAAAAACAC
1 CGCTAAAACCC-AGAGAATTAGCGGCACTTTTTCAAAAACAC
* **
38342452 CGCTAAAACCCCGAGAATTAGCGGCACTTTTTCAAAAATGC
1 CGCTAAAACCCAGAGAATTAGCGGCACTTTTTCAAAAACAC
* *
38342493 CGCTAAATCCCAGAGCATTAGCG
1 CGCTAAAACCCAGAGAATTAGCG
38342516 TCGCGGCGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (41 bp):
CGCTAAAACCCAGAGAATTAGCGGCACTTTTTCAAAAACAC
Found at i:38344126 original size:16 final size:16
Alignment explanation
Indices: 38344105--38344142 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
38344095 TCCTTTTTCC
**
38344105 TTTCCATTTTCTACCA
1 TTTCCATTTTAAACCA
38344121 TTTCCA-TTTAAACCA
1 TTTCCATTTTAAACCA
38344136 TTTCCAT
1 TTTCCAT
38344143 ACACCAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTCCATTTTAAACCA
Found at i:38345210 original size:19 final size:20
Alignment explanation
Indices: 38345168--38345210 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
38345158 TCATGCTTTC
*
38345168 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
38345188 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
38345206 TATTC
1 TATTC
38345211 CACAACGACG
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:38345405 original size:38 final size:38
Alignment explanation
Indices: 38345335--38345469 Score: 121
Period size: 38 Copynumber: 3.5 Consensus size: 38
38345325 ACACACCAGA
* * * * *
38345335 TTGACACCCAGTGCCTCATCGG-ATAGTTCGAAGCAAAG
1 TTGACACCCAGTGTCTCATTGGTCTAG-CCGAAGTAAAG
38345373 TTGACACCCAGTGTCTCATTGGTCTAGCCGAAGTAAAG
1 TTGACACCCAGTGTCTCATTGGTCTAGCCGAAGTAAAG
* * * * * *
38345411 -TGATACCCAGTATCTCATTGAATCTATCGGAAGTAAAA
1 TTGACACCCAGTGTCTCATTG-GTCTAGCCGAAGTAAAG
38345449 TAGTGACACCCAGTGTCTCAT
1 T--TGACACCCAGTGTCTCAT
38345470 CGACTCGAGG
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
37 18 0.23
38 42 0.53
39 3 0.04
41 16 0.20
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.26
Consensus pattern (38 bp):
TTGACACCCAGTGTCTCATTGGTCTAGCCGAAGTAAAG
Found at i:38346142 original size:29 final size:29
Alignment explanation
Indices: 38346094--38346151 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
38346084 TTAATCAACT
38346094 CTAATCAATAATTCTATCAA-ATAAACCC
1 CTAATCAATAATTCTATCAACATAAACCC
* *
38346122 CTAATTCAATCATT-TATTCAACATGAACCC
1 CTAA-TCAATAATTCTA-TCAACATAAACCC
38346152 TACTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 6 0.24
29 12 0.48
30 7 0.28
ACGTcount: A:0.41, C:0.26, G:0.02, T:0.31
Consensus pattern (29 bp):
CTAATCAATAATTCTATCAACATAAACCC
Found at i:38346607 original size:18 final size:18
Alignment explanation
Indices: 38346546--38346616 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 18
38346536 TTCATTTATC
*
38346546 TAATAATATAATATCAATT
1 TAATAATA-AATATCTATT
*
38346565 AAATAATAATATTTAT-TATT
1 TAATAATAA-A--TATCTATT
38346585 ATAATAATAAATATCTATT
1 -TAATAATAAATATCTATT
*
38346604 TAATAACAAATAT
1 TAATAATAAATAT
38346617 AAATATTACA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
18 16 0.37
19 12 0.28
20 4 0.09
21 11 0.26
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAAATATCTATT
Found at i:38348974 original size:40 final size:39
Alignment explanation
Indices: 38348861--38348977 Score: 130
Period size: 40 Copynumber: 3.0 Consensus size: 39
38348851 CGTTTGAACA
* * *
38348861 AAAAACGCCGCAATAAATCGAGCATTCA-CGGCACTTTTT
1 AAAAACGCCGCAATAGATCAAGCATT-AGCGGCGCTTTTT
* *
38348900 AACAAACGCCGCAATAGGT-AAGCAATAGCGGCGCTTTTT
1 AA-AAACGCCGCAATAGATCAAGCATTAGCGGCGCTTTTT
* *
38348939 CTAAAACGCTGCAATAGATCAAGCATTAGCGGCGCTTTT
1 -AAAAACGCCGCAATAGATCAAGCATTAGCGGCGCTTTT
38348978 CGGAAAACGC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
38 1 0.02
39 31 0.48
40 33 0.51
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (39 bp):
AAAAACGCCGCAATAGATCAAGCATTAGCGGCGCTTTTT
Found at i:38348985 original size:40 final size:39
Alignment explanation
Indices: 38348903--38348988 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 39
38348893 ACTTTTTAAC
* *
38348903 AAACGCCGCAATAGGTAAGCAATAGCGGCGCTTTTTCTA
1 AAACGCCGCAATAGATAAGCAATAGCGGCGCTTTTTCGA
* *
38348942 AAACGCTGCAATAGATCAAGCATTAGCGGCGC-TTTTCGGA
1 AAACGCCGCAATAGAT-AAGCAATAGCGGCGCTTTTTC-GA
38348982 AAACGCC
1 AAACGCC
38348989 ACAAAAGGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 19 0.47
40 21 0.52
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.21
Consensus pattern (39 bp):
AAACGCCGCAATAGATAAGCAATAGCGGCGCTTTTTCGA
Found at i:38349129 original size:40 final size:40
Alignment explanation
Indices: 38349085--38349185 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 40
38349075 AGAATTAGCA
* * **
38349085 GCGCTTTTTGAAAAACTCTGCTAAAGATCGGGCAAT-AGTG
1 GCGCTTTTTGAAAAACGCCGCTAAAGATCAAGC-ATGAGTG
* * *
38349125 GCGCTTTTTGTAAAACGCCGCTACAGGTCAAGCATGAGTG
1 GCGCTTTTTGAAAAACGCCGCTAAAGATCAAGCATGAGTG
*
38349165 GCGCTTTTTGGAAAACGCCGC
1 GCGCTTTTTGAAAAACGCCGC
38349186 AAAAAAGTTG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.04
40 50 0.96
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
GCGCTTTTTGAAAAACGCCGCTAAAGATCAAGCATGAGTG
Found at i:38349254 original size:196 final size:195
Alignment explanation
Indices: 38348920--38349343 Score: 573
Period size: 196 Copynumber: 2.2 Consensus size: 195
38348910 GCAATAGGTA
* * * * *
38348920 AGCAATAGCGGCGCTTTTTCTAAAACGCTGCAATAGATCAAGCATTAGCGGCGCTTTTCGGAAAA
1 AGCAATAGTGGCGCTTTTTGTAAAACGCCGCAACAGATCAAGCATGAGCGGCGCTTTTCGGAAAA
* * *
38348985 CGCCACAAAAGGTTGAGCAAAACGACGTCGTTTTCTTTTTGAGCTTTAGTGGCATTAGCGGCGCT
66 CGCCACAAAAAGTTGAGCAAAACGACATCGTTTTCTTTTTGAGCTTTAGTGGCATTAGCAGCGCT
* * * * *
38349050 TTTTAACAAACACCGCAATAAATTGAGA-ATTAGC-AGCGCTTTTTGAAAAACTCTGCTAAAGAT
131 TTTTAACAAACACCGCAATAAATAGA-ACATTAGCGA-CACTTATTGAAAAACGCCGCTAAAGAT
38349113 CG
194 CG
* * * * *
38349115 GGCAATAGTGGCGCTTTTTGTAAAACGCCGCTACAGGTCAAGCATGAGTGGCGCTTTTTGGAAAA
1 AGCAATAGTGGCGCTTTTTGTAAAACGCCGCAACAGATCAAGCATGAGCGGCGCTTTTCGGAAAA
* * *
38349180 CGCCGCAAAAAAGTTGAGCAAAGCGGCATCGTTTTCTTTTTGAGCTTTAGTGGCATTAGCAGCGC
66 CGCCAC-AAAAAGTTGAGCAAAACGACATCGTTTTCTTTTTGAGCTTTAGTGGCATTAGCAGCGC
* *
38349245 TTTTTAACAAACACCGCAATAGATAGAACATTAGCGACACTTATTGAGAAACGCCGCTAAAGATC
130 TTTTTAACAAACACCGCAATAAATAGAACATTAGCGACACTTATTGAAAAACGCCGCTAAAGATC
38349310 G
195 G
* * *
38349311 AGCAATAGTGGCGCTTGTTGGAAAATGCCGCAA
1 AGCAATAGTGGCGCTTTTTGTAAAACGCCGCAA
38349344 AAAGTTGAGC
Statistics
Matches: 198, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
195 61 0.31
196 136 0.69
197 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (195 bp):
AGCAATAGTGGCGCTTTTTGTAAAACGCCGCAACAGATCAAGCATGAGCGGCGCTTTTCGGAAAA
CGCCACAAAAAGTTGAGCAAAACGACATCGTTTTCTTTTTGAGCTTTAGTGGCATTAGCAGCGCT
TTTTAACAAACACCGCAATAAATAGAACATTAGCGACACTTATTGAAAAACGCCGCTAAAGATCG
Found at i:38349413 original size:148 final size:152
Alignment explanation
Indices: 38349137--38349427 Score: 387
Period size: 148 Copynumber: 1.9 Consensus size: 152
38349127 GCTTTTTGTA
* * *
38349137 AAACGCCGCTACAGGTCAAGCATGAGTGGCGCTTTTTGGAAAACGCCGCAAAAAAGTTGAGCAAA
1 AAACGCCGCTAAAGATCAAGCATGAGTGGCGCTTGTTGGAAAACGCCGCAAAAAAGTTGAGCAAA
* **
38349202 GCGGCATCGTTTTCTTTTTGAGCTTTAGTGGCATTAGCAGCGCTTTTTAACAAACACCGCAATAG
66 ---G-ATCGTTTTCTTGTTGAGCTTTAGTGGCATTAGCAGCAATTTTTAACAAACACCGCAATAG
38349267 ATAGAACATTAGCGACACTTATTGAG
127 ATAGAACATTAGCGACACTTATTGAG
* *
38349293 AAACGCCGCTAAAGATCGAGCAAT-AGTGGCGCTTGTTGGAAAATGCCGC-AAAAAGTTGAGCAA
1 AAACGCCGCTAAAGATCAAGC-ATGAGTGGCGCTTGTTGGAAAACGCCGCAAAAAAGTTGAGCAA
*
38349356 A-AT-GTTTT-TTGTTGAGCTTTAGTGGCATTAGC-GACAATTTTTAACAAACGCCGCAATAGAT
65 AGATCGTTTTCTTGTTGAGCTTTAGTGGCATTAGCAG-CAATTTTTAACAAACACCGCAATAGAT
* *
38349417 CGAGCATTAGC
129 AGAACATTAGC
38349428 AGTGATTTTT
Statistics
Matches: 122, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
147 1 0.01
148 56 0.46
149 5 0.04
150 2 0.02
155 15 0.12
156 41 0.34
157 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (152 bp):
AAACGCCGCTAAAGATCAAGCATGAGTGGCGCTTGTTGGAAAACGCCGCAAAAAAGTTGAGCAAA
GATCGTTTTCTTGTTGAGCTTTAGTGGCATTAGCAGCAATTTTTAACAAACACCGCAATAGATAG
AACATTAGCGACACTTATTGAG
Found at i:38349436 original size:40 final size:40
Alignment explanation
Indices: 38349392--38349467 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
38349382 ATTAGCGACA
*
38349392 ATTTTTAACAAACGCCGCAATAGATCGAGCATTAGCAGTG
1 ATTTTTAACAAACGCCGCAATAGATCGAGCAATAGCAGTG
*
38349432 ATTTTTAACAAATGCCGCAATAGATCGAGCAATAGC
1 ATTTTTAACAAACGCCGCAATAGATCGAGCAATAGC
38349468 GGCGCTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (40 bp):
ATTTTTAACAAACGCCGCAATAGATCGAGCAATAGCAGTG
Found at i:38349449 original size:148 final size:152
Alignment explanation
Indices: 38349161--38349489 Score: 386
Period size: 148 Copynumber: 2.2 Consensus size: 152
38349151 GTCAAGCATG
* *
38349161 AGTGGCGCTTTTTGGAAAACGCCGCAAAAAAGTTGAGCAAAGCGGCATCGTTTTCTTTTTGAGCT
1 AGTGGCGCTTGTTGGAAAACGCCGCAAAAAAGTTGAGCAAA---G-ATCGTTTTCTTGTTGAGCT
** *
38349226 TTAGTGGCATTAGCAGCGCTTTTTAACAAACACCGCAATAGATAGAACATTAGCGACACTTATTG
62 TTAGTGGCATTAGCAGCAATTTTTAACAAACACCGCAATAGATAGAACATTAGCGACACTTATTA
*
38349291 AGAAACGCCGCTAA-AGATCGAGCAAT
127 ACAAACGCCGC-AATAGATCGAGCAAT
*
38349317 AGTGGCGCTTGTTGGAAAATGCCGC-AAAAAGTTGAGCAAA-AT-GTTTT-TTGTTGAGCTTTAG
1 AGTGGCGCTTGTTGGAAAACGCCGCAAAAAAGTTGAGCAAAGATCGTTTTCTTGTTGAGCTTTAG
* * * ** *
38349378 TGGCATTAGC-GACAATTTTTAACAAACGCCGCAATAGATCGAGCATTAGCAGTGA-TTTTTAAC
66 TGGCATTAGCAG-CAATTTTTAACAAACACCGCAATAGATAGAACATTAGC-GACACTTATTAAC
*
38349441 AAATGCCGCAATAGATCGAGCAAT
129 AAACGCCGCAATAGATCGAGCAAT
* *
38349465 AGCGGCGCTT-TCTGTAAAACGCCGC
1 AGTGGCGCTTGT-TGGAAAACGCCGC
38349490 TATAGGTCAA
Statistics
Matches: 152, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
147 4 0.03
148 101 0.66
149 7 0.05
150 2 0.01
155 15 0.10
156 23 0.15
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (152 bp):
AGTGGCGCTTGTTGGAAAACGCCGCAAAAAAGTTGAGCAAAGATCGTTTTCTTGTTGAGCTTTAG
TGGCATTAGCAGCAATTTTTAACAAACACCGCAATAGATAGAACATTAGCGACACTTATTAACAA
ACGCCGCAATAGATCGAGCAAT
Found at i:38349487 original size:188 final size:194
Alignment explanation
Indices: 38349232--38349607 Score: 446
Period size: 188 Copynumber: 2.0 Consensus size: 194
38349222 AGCTTTAGTG
* *
38349232 GCATTAGCAGCGCTTTTTAACAAACACCGCAATAGATAGAACATTAGCGACACTTATTGAGAAAC
1 GCATTAGCAGCGATTTTTAACAAACACCGCAATAGATAGAACAATAGCGACACTTATTGAGAAAC
* ** * *
38349297 GCCGCTAAAGATCGAGCAATAGTGGCGCT-TGTTGGAAAATGCCGCAAA-AAGTTGAGC-AAA-A
66 GCCGCTAAAGATCAAGCAATAGCAGCGCTGT-TTGGAAAACGCCGCAAAGAAGTTAAGCAAAACA
*
38349358 -T-GTTTT-TTGTTGAGCTTTAGTGGCATTAGCGACAATTTTTAACAAACGCCGCAATAGATCGA
130 CTCGTTTTCTTGTTGAGCTTTAGTGGCATTAGCGACAATTTTTAACAAACACCGCAATAGATCGA
* ** * * * *
38349420 GCATTAGCAGTGATTTTTAACAAATGCCGCAATAGATCGAGCAATAGCGGCGCTT-TCTGTA-AA
1 GCATTAGCAGCGATTTTTAACAAACACCGCAATAGATAGAACAATAGCGACACTTAT-TG-AGAA
* * *
38349483 ACGCCGCTATAGGTCAAGCATTAGCAGCGCTGTTTGGAAAACGCCGCAAAGAAGTTAAGCAAAAC
64 ACGCCGCTAAAGATCAAGCAATAGCAGCGCTGTTTGGAAAACGCCGCAAAGAAGTTAAGCAAAAC
* * **
38349548 GACGTCGTTTTCTTTTTGAGCTTTAGTGGCATTAGCGGCGCTTTTTAACAAACACCGCAA
129 -AC-TCGTTTTCTTGTTGAGCTTTAGTGGCATTAGCGACAATTTTTAACAAACACCGCAA
38349608 AAAATCATTT
Statistics
Matches: 155, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
187 1 0.01
188 91 0.59
189 10 0.06
190 3 0.02
192 1 0.01
194 1 0.01
195 5 0.03
196 43 0.28
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (194 bp):
GCATTAGCAGCGATTTTTAACAAACACCGCAATAGATAGAACAATAGCGACACTTATTGAGAAAC
GCCGCTAAAGATCAAGCAATAGCAGCGCTGTTTGGAAAACGCCGCAAAGAAGTTAAGCAAAACAC
TCGTTTTCTTGTTGAGCTTTAGTGGCATTAGCGACAATTTTTAACAAACACCGCAATAGATCGA
Found at i:38349489 original size:40 final size:39
Alignment explanation
Indices: 38349401--38349531 Score: 138
Period size: 40 Copynumber: 3.3 Consensus size: 39
38349391 AATTTTTAAC
* *
38349401 AAACGCCGCAATAGATCGAGCATTAGCAGTGATTTT-TAA
1 AAACGCCGCAATAGATCGAGCATTAGCAGCGCTTTTGT-A
* * *
38349440 CAAATGCCGCAATAGATCGAGCAATAGCGGCGCTTTCTGTA
1 -AAACGCCGCAATAGATCGAGCATTAGCAGCGCTTT-TGTA
* * * *
38349481 AAACGCCGCTATAGGTCAAGCATTAGCAGCGCTGTTTGGA
1 AAACGCCGCAATAGATCGAGCATTAGCAGCGCT-TTTGTA
38349521 AAACGCCGCAA
1 AAACGCCGCAA
38349532 AGAAGTTAAG
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
40 70 0.93
41 4 0.05
42 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (39 bp):
AAACGCCGCAATAGATCGAGCATTAGCAGCGCTTTTGTA
Found at i:38349645 original size:14 final size:15
Alignment explanation
Indices: 38349628--38349660 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
38349618 TATTTTAAGC
38349628 TTTACGA-TTTAGGG
1 TTTACGATTTTAGGG
*
38349642 TTTAGGATTTTAGGG
1 TTTACGATTTTAGGG
38349657 TTTA
1 TTTA
38349661 AAGGTTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.21, C:0.03, G:0.27, T:0.48
Consensus pattern (15 bp):
TTTACGATTTTAGGG
Found at i:38350174 original size:7 final size:7
Alignment explanation
Indices: 38350164--38350413 Score: 80
Period size: 7 Copynumber: 35.1 Consensus size: 7
38350154 TTAAGGACTA
38350164 AGGGTTT
1 AGGGTTT
38350171 AGGGTTT
1 AGGGTTT
* *
38350178 ATGTTTT
1 AGGGTTT
***
38350185 ATTATTT
1 AGGGTTT
38350192 AGGGTTT
1 AGGGTTT
*
38350199 AGGAG-AT
1 AGG-GTTT
38350206 AGGGGTTT
1 A-GGGTTT
*
38350214 AGGGATT
1 AGGGTTT
*
38350221 ATGGTTT
1 AGGGTTT
* *
38350228 ATGGTTCA
1 AGGGTT-T
38350236 AGGG-TT
1 AGGGTTT
38350242 AGGGTTT
1 AGGGTTT
**
38350249 AAAGTTT
1 AGGGTTT
38350256 A-GGTGTT
1 AGGGT-TT
38350263 AGGGGTTT
1 A-GGGTTT
38350271 AGGGTTT
1 AGGGTTT
**
38350278 ATAGTTT
1 AGGGTTT
* *
38350285 ATGTTTT
1 AGGGTTT
* * *
38350292 ATGATTC
1 AGGGTTT
*
38350299 AGTGTTT
1 AGGGTTT
**
38350306 AGGGGAT
1 AGGGTTT
*
38350313 AGGGGTT
1 AGGGTTT
38350320 AGGGGTTT
1 A-GGGTTT
* *
38350328 AGAGATT
1 AGGGTTT
* *
38350335 ATGATTT
1 AGGGTTT
**
38350342 ATAGTTT
1 AGGGTTT
*
38350349 ATGGTTT
1 AGGGTTT
38350356 AAGGG-TT
1 -AGGGTTT
38350363 AGGGTTT
1 AGGGTTT
*
38350370 AAGGTTT
1 AGGGTTT
38350377 A-GGTGTT
1 AGGGT-TT
*
38350384 AGGGGTTA
1 A-GGGTTT
38350392 AGGG-TT
1 AGGGTTT
38350398 AGGTGTTT
1 AGG-GTTT
38350406 AGGGTTT
1 AGGGTTT
38350413 A
1 A
38350414 TAGTTCATGT
Statistics
Matches: 181, Mismatches: 46, Indels: 32
0.70 0.18 0.12
Matches are distributed among these distances:
6 17 0.09
7 131 0.72
8 27 0.15
9 6 0.03
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.43
Consensus pattern (7 bp):
AGGGTTT
Found at i:38350227 original size:50 final size:50
Alignment explanation
Indices: 38350164--38350328 Score: 134
Period size: 50 Copynumber: 3.2 Consensus size: 50
38350154 TTAAGGACTA
* *
38350164 AGGGTTTAGGGTTTATGTTTTATTATTTAGGGTTTAGGAGATAGGGGTTT
1 AGGGTTTATGGTTTATGTTTTATTATTTAGAGTTTAGGAGATAGGGGTTT
* ** * * *
38350214 AGGGATTATGGTTTATGGTTCAAGGGTTAGGGTTTAAAGTTTAGGTGTTAGGGGTTT
1 AGGGTTTATGGTTTAT-GTTTTA---TTA---TTTAGAGTTTAGGAGATAGGGGTTT
* * * * *
38350271 AGGGTTTATAGTTTATGTTTTATGATTCAGTGTTTAGGGGATAGGGG-TT
1 AGGGTTTATGGTTTATGTTTTATTATTTAGAGTTTAGGAGATAGGGGTTT
38350320 AGGGGTTTA
1 A-GGGTTTA
38350329 GAGATTATGA
Statistics
Matches: 89, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
49 3 0.03
50 38 0.43
51 4 0.04
53 2 0.02
54 3 0.03
56 4 0.04
57 35 0.39
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.43
Consensus pattern (50 bp):
AGGGTTTATGGTTTATGTTTTATTATTTAGAGTTTAGGAGATAGGGGTTT
Found at i:38350277 original size:64 final size:63
Alignment explanation
Indices: 38350208--38350420 Score: 165
Period size: 64 Copynumber: 3.4 Consensus size: 63
38350198 TAGGAGATAG
38350208 GGGTTTAGGGATTATGGTTTATGGTTCAAGGGTTAGGGTTTAAAGTTTAGGTGTTAGGGGTTTA
1 GGGTTTAGGGATTATGGTTTATGGTTCAAGGGTTAGGGTTT-AAGTTTAGGTGTTAGGGGTTTA
** * * * * * *
38350272 GGGTTTATAGTTTATGTTTTATGATTC-AGTGTTTAGGG-----G-ATAGGGGTTAGGGGTTTA
1 GGGTTTAGGGATTATGGTTTATGGTTCAAG-GGTTAGGGTTTAAGTTTAGGTGTTAGGGGTTTA
* * * * * *
38350329 GAGATTA-TGATTTATAGTTTATGGTTTAAGGGTTAGGGTTTAAGGTTTAGGTGTTAGGGGTTAA
1 GGGTTTAGGGA-TTATGGTTTATGGTTCAAGGGTTAGGGTTTAA-GTTTAGGTGTTAGGGGTTTA
* * *
38350393 GGG-TTAGGTGTTTAGGGTTTATAGTTCA
1 GGGTTTAGG-GATTATGGTTTATGGTTCA
38350421 TGTTTTATGA
Statistics
Matches: 110, Mismatches: 27, Indels: 24
0.68 0.17 0.15
Matches are distributed among these distances:
56 1 0.01
57 40 0.36
58 3 0.03
63 6 0.05
64 59 0.54
65 1 0.01
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.42
Consensus pattern (63 bp):
GGGTTTAGGGATTATGGTTTATGGTTCAAGGGTTAGGGTTTAAGTTTAGGTGTTAGGGGTTTA
Found at i:38350306 original size:57 final size:57
Alignment explanation
Indices: 38350112--38350397 Score: 205
Period size: 57 Copynumber: 4.9 Consensus size: 57
38350102 GGATTATGGA
* * * * ** * **
38350112 TTATGGTTTAAGGGTTGGGGTTTAACGTTTAGGGGTTAGGGGTTAAGGACTAAGGGT
1 TTATGGTTTAAGGGTTAGGGTTTAAGGTTTAGGTGTTAGGGGTTTAGGGTTTATAGT
* * ** *** * * * * *
38350169 TTAGGGTTTATGTTTTATTATTTAGGGTTTAGGAGATAGGGGTTTAGGGATTATGGT
1 TTATGGTTTAAGGGTTAGGGTTTAAGGTTTAGGTGTTAGGGGTTTAGGGTTTATAGT
* *
38350226 TTATGGTTCAAGGGTTAGGGTTTAAAGTTTAGGTGTTAGGGGTTTAGGGTTTATAGT
1 TTATGGTTTAAGGGTTAGGGTTTAAGGTTTAGGTGTTAGGGGTTTAGGGTTTATAGT
* * * * * ** *
38350283 TTAT-GTTTTATGATTCAGTGTTTAGGGGATAGGGGTTAGGGGTTTAGAGATTATGATTTATAGT
1 TTATGGTTTAAGGGTT-AGGGTTTAAGGTTTAGGTGTTAGGGGTTTAG-G-----G-TTTATAGT
*
38350347 TTATGGTTTAAGGGTTAGGGTTTAAGGTTTAGGTGTTAGGGGTTAAGGGTT
1 TTATGGTTTAAGGGTTAGGGTTTAAGGTTTAGGTGTTAGGGGTTTAGGGTT
38350398 AGGTGTTTAG
Statistics
Matches: 170, Mismatches: 50, Indels: 18
0.71 0.21 0.08
Matches are distributed among these distances:
56 7 0.04
57 114 0.67
58 2 0.01
63 2 0.01
64 37 0.22
65 8 0.05
ACGTcount: A:0.21, C:0.01, G:0.36, T:0.42
Consensus pattern (57 bp):
TTATGGTTTAAGGGTTAGGGTTTAAGGTTTAGGTGTTAGGGGTTTAGGGTTTATAGT
Found at i:38350308 original size:43 final size:42
Alignment explanation
Indices: 38350256--38350445 Score: 116
Period size: 43 Copynumber: 4.3 Consensus size: 42
38350246 TTTAAAGTTT
38350256 AGGTGTTAGGGGTTTAGGGTTTATAGTTTATGTTTTATGATTC
1 AGGT-TTAGGGGTTTAGGGTTTATAGTTTATGTTTTATGATTC
* * * *
38350299 AGTGTTTAGGGGATAGGGGTTAGGGGTTTAGAGATTATGATTTAT-AGTTT
1 AG-GTTTAGGGG-T-----TTA-GGGTTTATAGTTTATGTTTTATGA-TTC
* * * * * *
38350349 ATGGTTTAAGGG-TTAGGGTTTA-AGGTTTAGGTGTTAGGGGTTA
1 A-GGTTTAGGGGTTTAGGGTTTATA-GTTTATGTTTTA-TGATTC
* * *
38350392 AGGGTTAGGTGTTTAGGGTTTATAGTTCATGTTTTATGATTC
1 AGGTTTAGGGGTTTAGGGTTTATAGTTTATGTTTTATGATTC
38350434 AAGGTTTAGGGG
1 -AGGTTTAGGGG
38350446 ATAGGAGTTA
Statistics
Matches: 108, Mismatches: 23, Indels: 32
0.66 0.14 0.20
Matches are distributed among these distances:
41 1 0.01
42 25 0.23
43 43 0.40
44 4 0.04
49 4 0.04
50 30 0.28
51 1 0.01
ACGTcount: A:0.21, C:0.02, G:0.35, T:0.43
Consensus pattern (42 bp):
AGGTTTAGGGGTTTAGGGTTTATAGTTTATGTTTTATGATTC
Found at i:38358340 original size:43 final size:42
Alignment explanation
Indices: 38358261--38358549 Score: 348
Period size: 43 Copynumber: 6.8 Consensus size: 42
38358251 CTTCATAAAT
* *
38358261 GCCGCTAAA-GTCATGTTCTTTAGTGGCTTTTGTGATAAGAGC
1 GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAT-AGAGC
*
38358303 GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTATGATAAGAGC
1 GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAT-AGAGC
** * *
38358346 GCCGCTAAAGGTCATACTCTTTAGCGGCATTTGTGATAAGAGT
1 GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAT-AGAGC
* *
38358389 TCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGT-AGTAGAAGC
1 GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGA-TAG-AGC
* *
38358432 GCCACTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGTAGAAGC
1 GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAG-AGC
** * * *
38358475 GCCGCTAAATTTCATGTTTTTTAGTGGCGTTTGTGGTAGAGGC
1 GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGA-GC
*
38358518 GCCGCTAAAGGTCATGTTCTTTAGCGGTGTTT
1 GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTT
38358550 TTTAAATAAA
Statistics
Matches: 215, Mismatches: 27, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
42 13 0.06
43 202 0.94
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (42 bp):
GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAGAGC
Found at i:38358669 original size:21 final size:21
Alignment explanation
Indices: 38358643--38358683 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
38358633 AGCGGCACAT
*
38358643 AAAAATGCCGCTAAAGGCCTA
1 AAAAATGCCGCTAAAAGCCTA
38358664 AAAAATGCCGCTAAAAGCCT
1 AAAAATGCCGCTAAAAGCCT
38358684 GTTTTGCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.15
Consensus pattern (21 bp):
AAAAATGCCGCTAAAAGCCTA
Found at i:38362148 original size:18 final size:18
Alignment explanation
Indices: 38362127--38362190 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
38362117 TTGATGATTT
38362127 CGATATTGATGATAGTGA
1 CGATATTGATGATAGTGA
*
38362145 CGATATTGATGCTAGTGA
1 CGATATTGATGATAGTGA
* *
38362163 TGTTATTGATGATAGAT-A
1 CGATATTGATGATAG-TGA
*
38362181 CGCTATTGAT
1 CGATATTGAT
38362191 CGTGACCTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 38 0.97
19 1 0.03
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.38
Consensus pattern (18 bp):
CGATATTGATGATAGTGA
Found at i:38362903 original size:75 final size:73
Alignment explanation
Indices: 38362710--38362917 Score: 213
Period size: 75 Copynumber: 2.8 Consensus size: 73
38362700 CGACGATAGA
* * *
38362710 TGTGCCCAGCACTAGTCAAACGAATCGACGAAAGTTGCGCCCAGCGCTAG-TCGAGTAAACCAAC
1 TGTG-CCAGCACTAGTCAAACAAATCGAC-AAAGTTGAGCCCAGCGCTAGTTGGA-TAAACCAAC
38362774 AAAGATAATGG
63 AAAGATAATGG
* * * * * *
38362785 TGTGCCTAGCACTAGTTAGATAAATTGACAAAGGTTGTGCCCAGCGCTAGTTGGATAAACCGAC-
1 TGTGCC-AGCACTAGTCAAACAAATCGACAAA-GTTGAGCCCAGCGCTAGTTGGATAAACCAACA
38362849 AAGTATAATGG
64 AAG-ATAATGG
* * * *
38362860 TGTGCGCAACACTAGTCAAACAAATCGACAAAGATTGAACCCAGTGGTAGTTGGATAA
1 TGTGC-CAGCACTAGTCAAACAAATCGACAAAG-TTGAGCCCAGCGCTAGTTGGATAA
38362918 TCGGCAATAG
Statistics
Matches: 110, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
74 9 0.08
75 97 0.88
76 4 0.04
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21
Consensus pattern (73 bp):
TGTGCCAGCACTAGTCAAACAAATCGACAAAGTTGAGCCCAGCGCTAGTTGGATAAACCAACAAA
GATAATGG
Found at i:38365450 original size:17 final size:17
Alignment explanation
Indices: 38365428--38365460 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38365418 GTGGCTTTAG
38365428 CTAATAAAAATCTTGAA
1 CTAATAAAAATCTTGAA
*
38365445 CTAATAAAACTCTTGA
1 CTAATAAAAATCTTGA
38365461 CATTTTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.30
Consensus pattern (17 bp):
CTAATAAAAATCTTGAA
Found at i:38366431 original size:17 final size:18
Alignment explanation
Indices: 38366409--38366442 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
38366399 ACTTAATTTG
38366409 AAAAAAGT-CAAAACAAA
1 AAAAAAGTCCAAAACAAA
38366426 AAAAAAGTCCAAAACAA
1 AAAAAAGTCCAAAACAA
38366443 TCTACAGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.74, C:0.15, G:0.06, T:0.06
Consensus pattern (18 bp):
AAAAAAGTCCAAAACAAA
Found at i:38371139 original size:45 final size:45
Alignment explanation
Indices: 38371075--38371301 Score: 420
Period size: 45 Copynumber: 5.0 Consensus size: 45
38371065 CTAAATCTGG
38371075 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAA
1 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAA
38371120 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAA
1 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAA
38371165 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAA
1 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAA
38371210 TACATTATCATCCCT-TCAGATTCCCTAAACATTCAAATTCAATTCAA
1 TACA-T-T-ATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAA
38371257 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAA
1 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAA
38371302 ACTTTACCAT
Statistics
Matches: 178, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
44 6 0.03
45 127 0.71
46 2 0.01
47 37 0.21
48 6 0.03
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.33
Consensus pattern (45 bp):
TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAA
Found at i:38371278 original size:92 final size:90
Alignment explanation
Indices: 38371075--38371301 Score: 420
Period size: 92 Copynumber: 2.5 Consensus size: 90
38371065 CTAAATCTGG
38371075 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAATACATTATCCCTATCAGATT
1 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAATACATTATCCCTATCAGATT
38371140 CCCTAAACATTCAAATTCAATTCAA
66 CCCTAAACATTCAAATTCAATTCAA
38371165 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAATACATTATCATCCCT-TCAG
1 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAATACA-T-T-ATCCCTATCAG
38371229 ATTCCCTAAACATTCAAATTCAATTCAA
63 ATTCCCTAAACATTCAAATTCAATTCAA
38371257 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAA
1 TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAA
38371302 ACTTTACCAT
Statistics
Matches: 134, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
90 49 0.37
91 1 0.01
92 78 0.58
93 6 0.04
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.33
Consensus pattern (90 bp):
TACATTATCCCTATCAGATTCCCTAAACATTCAAATTCAATTCAATACATTATCCCTATCAGATT
CCCTAAACATTCAAATTCAATTCAA
Found at i:38375200 original size:69 final size:71
Alignment explanation
Indices: 38375087--38375229 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 71
38375077 TTCTTTTCAT
* * *
38375087 CAATCATTGTTAAGTTATCGAGACTTACAAAAATAATGACCTACTTAAAAATATGAATTAATAGA
1 CAATCATTGTTAAGTTATCGAAACTTACAAAAATAAAGACCTACTTAAAAATATAAATTAATAGA
38375152 TTG-TAA
66 -TGATAA
* * *
38375158 CAATCATTGTT-A-TTATTGAAACTTATAAAAATAAA-AGTCTACTTAAAAATATAAATTAATAG
1 CAATCATTGTTAAGTTATCGAAACTTACAAAAATAAAGA-CCTACTTAAAAATATAAATTAATAG
38375220 ATGATAA
65 ATGATAA
38375227 CAA
1 CAA
38375230 GTAAAATTGT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
68 3 0.05
69 49 0.77
70 1 0.02
71 11 0.17
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (71 bp):
CAATCATTGTTAAGTTATCGAAACTTACAAAAATAAAGACCTACTTAAAAATATAAATTAATAGA
TGATAA
Found at i:38378589 original size:12 final size:12
Alignment explanation
Indices: 38378572--38378601 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
38378562 TCACTTTTTC
*
38378572 TTAATTAAAATG
1 TTAATTAAAATA
38378584 TTAATTAAAATA
1 TTAATTAAAATA
38378596 TTAATT
1 TTAATT
38378602 TTTTAATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
TTAATTAAAATA
Found at i:38380530 original size:9 final size:9
Alignment explanation
Indices: 38380516--38380552 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
38380506 NNNNNNNNNN
38380516 TATTCGAAT
1 TATTCGAAT
38380525 TATTCGAAT
1 TATTCGAAT
*
38380534 TATTCGAGT
1 TATTCGAAT
38380543 TATTCGAAT
1 TATTCGAAT
38380552 T
1 T
38380553 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:38381146 original size:30 final size:29
Alignment explanation
Indices: 38381107--38381173 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
38381097 TACCAGAAAA
38381107 GCCATTTTTTTTAAAATTTACCGAAATGG
1 GCCATTTTTTTTAAAATTTACCGAAATGG
** *
38381136 GCCGA-TTTTTTTATTATTTACCGGAATGG
1 GCC-ATTTTTTTTAAAATTTACCGAAATGG
*
38381165 TCCATTTTT
1 GCCATTTTT
38381174 CGGGAAATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 30 0.94
30 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (29 bp):
GCCATTTTTTTTAAAATTTACCGAAATGG
Found at i:38381973 original size:275 final size:275
Alignment explanation
Indices: 38381473--38382024 Score: 1034
Period size: 275 Copynumber: 2.0 Consensus size: 275
38381463 CCCTCGTGGA
38381473 CGCGATTTTGCTACAGTAGCAAGTTTGGGCTGAGGCTATAAATTAGGCAGAAAATGTTCTTAGAA
1 CGCGATTTTGCTACAGTAGCAAGTTTGGGCTGAGGCTATAAATTAGGCAGAAAATGTTCTTAGAA
38381538 TGCATAAGTCATAGCAGAAAAAATTTAAAGAGGCTAAGAAAGTTAGAATTTCAAAATGAGTGAAT
66 TGCATAAGTCATAGCAGAAAAAATTTAAAGAGGCTAAGAAAGTTAGAATTTCAAAATGAGTGAAT
*
38381603 GTATTAGTGCTGTTATTTACTACAATGGTGAGGTTTGCCACACCGAGAATGGTGTTATTTTTTTG
131 GTATTAGTGCTGTTATTTACTACAATGGTGAGGTTTGCCACACCGAGAATGGTGTTATTTTTTTA
*
38381668 TCGGAGAATACGGTGCGACTGTCATTTAACCAGAACATAGATTTGACAGAACTTCGTAAAAGAAT
196 TCGGAGAATACAGTGCGACTGTCATTTAACCAGAACATAGATTTGACAGAACTTCGTAAAAGAAT
*
38381733 TAGGTGTAAAATCTT
261 TAGGCGTAAAATCTT
38381748 CGCGATTTTGCTACAGTAGCAAGTTTGGGCTGAGGCTATAAATTAGGCAGAAAATGTTCTTAGAA
1 CGCGATTTTGCTACAGTAGCAAGTTTGGGCTGAGGCTATAAATTAGGCAGAAAATGTTCTTAGAA
38381813 TGCATAAGTCATAGCAGAAAAAATTTAAAGAGGCTAAGAAAGTTAGAATTTCAAAATGAGTGAAT
66 TGCATAAGTCATAGCAGAAAAAATTTAAAGAGGCTAAGAAAGTTAGAATTTCAAAATGAGTGAAT
38381878 GTATTAGTGCTGTTATTTACTACAATGGTGAGGTTTGCCACACCGAGAATGGTGTTATTTTTTTA
131 GTATTAGTGCTGTTATTTACTACAATGGTGAGGTTTGCCACACCGAGAATGGTGTTATTTTTTTA
* *
38381943 TCGGATAATACAGTGCGACTGGT-TTTTAACCAGAACATAGATTTGACAGAACTTCGTAAAAGAA
196 TCGGAGAATACAGTGCGACT-GTCATTTAACCAGAACATAGATTTGACAGAACTTCGTAAAAGAA
*
38382007 TTAGGCGTAAAATTTT
260 TTAGGCGTAAAATCTT
38382023 CG
1 CG
38382025 GAACGACGCC
Statistics
Matches: 270, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
275 268 0.99
276 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (275 bp):
CGCGATTTTGCTACAGTAGCAAGTTTGGGCTGAGGCTATAAATTAGGCAGAAAATGTTCTTAGAA
TGCATAAGTCATAGCAGAAAAAATTTAAAGAGGCTAAGAAAGTTAGAATTTCAAAATGAGTGAAT
GTATTAGTGCTGTTATTTACTACAATGGTGAGGTTTGCCACACCGAGAATGGTGTTATTTTTTTA
TCGGAGAATACAGTGCGACTGTCATTTAACCAGAACATAGATTTGACAGAACTTCGTAAAAGAAT
TAGGCGTAAAATCTT
Found at i:38384826 original size:110 final size:113
Alignment explanation
Indices: 38384662--38384888 Score: 388
Period size: 110 Copynumber: 2.0 Consensus size: 113
38384652 AACATTATGG
* *
38384662 AAAATTATGTAAAATTATTAAGCTAAAAAAATTGTGTTGATGGTTAGTAAAATTTATCAAATAAA
1 AAAATTATGTAAAATTATTAAGC-AAAAAAATTGTATTAATGGTTAGTAAAATTTATCAAATAAA
38384727 CTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAA-TTATC
65 CTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATC
* *
38384775 AAAA-TATGTAAAATTATTAAGC-CAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAAC
1 AAAATTATGTAAAATTATTAAGCAAAAAAATTGTATTAATGGTTAGTAAAATTTATCAAATAAAC
38384838 TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATC
66 TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATC
38384886 AAA
1 AAA
38384889 TTAAGTTANN
Statistics
Matches: 109, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
110 79 0.72
111 8 0.07
112 18 0.17
113 4 0.04
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (113 bp):
AAAATTATGTAAAATTATTAAGCAAAAAAATTGTATTAATGGTTAGTAAAATTTATCAAATAAAC
TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATC
Found at i:38384842 original size:55 final size:56
Alignment explanation
Indices: 38384671--38384889 Score: 336
Period size: 56 Copynumber: 3.9 Consensus size: 56
38384661 GAAAATTATG
** *
38384671 TAAAATTATTAAGCTAAAAAAATTGTGTTGATGGTTAGTAAAATTTATCAAATAAAC
1 TAAAATTATTAAG-TCCAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAATAAAC
**
38384728 TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAA-TTATCAAA-ATATG
1 TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAATA-AAC
* *
38384783 TAAAATTATTAAG-CCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAAC
1 TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAATAAAC
38384838 TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAAT
1 TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAAT
38384890 TAAGTTANNN
Statistics
Matches: 147, Mismatches: 11, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
54 28 0.19
55 43 0.29
56 63 0.43
57 13 0.09
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (56 bp):
TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAATAAAC
Found at i:38385317 original size:29 final size:29
Alignment explanation
Indices: 38385275--38385396 Score: 201
Period size: 29 Copynumber: 4.2 Consensus size: 29
38385265 NNNNNNNNNN
38385275 GGTTAGGGTTTTTAATTAAGTTAGGTTAG
1 GGTTAGGGTTTTTAATTAAGTTAGGTTAG
*
38385304 GGTTAGGGTTTTTAATTAATTTAGGTTAG
1 GGTTAGGGTTTTTAATTAAGTTAGGTTAG
* *
38385333 GGTTAGGGTTCTTAATTAATTTAGGTTAG
1 GGTTAGGGTTTTTAATTAAGTTAGGTTAG
*
38385362 GGTTAGGGTTTTTAATTAAGTTAGGCTA-
1 GGTTAGGGTTTTTAATTAAGTTAGGTTAG
38385390 GGTTAGG
1 GGTTAGG
38385397 TTAGGTTAGG
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
28 7 0.08
29 81 0.92
ACGTcount: A:0.24, C:0.02, G:0.30, T:0.44
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAGTTAGGTTAG
Found at i:38385396 original size:5 final size:5
Alignment explanation
Indices: 38385381--38385416 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
38385371 TTTTAATTAA
*
38385381 GTTAG GCTAG GTTAG GTTAG GTTAG GTTAG GTTAG G
1 GTTAG GTTAG GTTAG GTTAG GTTAG GTTAG GTTAG G
38385417 GTTTTCAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.19, C:0.03, G:0.42, T:0.36
Consensus pattern (5 bp):
GTTAG
Found at i:38385498 original size:15 final size:16
Alignment explanation
Indices: 38385473--38385503 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
38385463 ATAATTATCT
38385473 AAAAATACTTAAATAA
1 AAAAATACTTAAATAA
38385489 AAAAAT-CTTAAATAA
1 AAAAATACTTAAATAA
38385504 TAATTACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATACTTAAATAA
Found at i:38386930 original size:21 final size:22
Alignment explanation
Indices: 38386891--38386932 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
38386881 ATGAGAGTAC
38386891 TGTAGGAATTATAATGTGAACA
1 TGTAGGAATTATAATGTGAACA
38386913 TGTA-GAAGTTAT-ATGTGAAC
1 TGTAGGAA-TTATAATGTGAAC
38386933 CCATAGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (22 bp):
TGTAGGAATTATAATGTGAACA
Found at i:38388046 original size:30 final size:30
Alignment explanation
Indices: 38388012--38388073 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
38388002 TATTACTCTA
38388012 ATATTTGCACGTCATTCGATTTAGAAAACT
1 ATATTTGCACGTCATTCGATTTAGAAAACT
38388042 ATATTTGCACGTCATTCGATTTAGAAAACT
1 ATATTTGCACGTCATTCGATTTAGAAAACT
38388072 AT
1 AT
38388074 CTTTTGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (30 bp):
ATATTTGCACGTCATTCGATTTAGAAAACT
Found at i:38392838 original size:40 final size:40
Alignment explanation
Indices: 38392708--38392819 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
38392698 CGTTTGGACA
** * *
38392708 AAAAACGCCGCTAAAAATTAAGCGTTAGCGGCGC-TTCACG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTC-CT
* * *
38392748 CAAAACTCCGCTAAAGATCGAGCATTAGCGGCGCTTTCCT
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTCCT
38392788 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCG
38392820 TTTTTTAGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
39 14 0.23
40 44 0.72
41 3 0.05
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTCCT
Done.