Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 88 of 93
Found at i:34440326 original size:3 final size:3
Alignment explanation
Indices: 34440318--34440346 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
34440308 AGGTAATTGC
34440318 TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
34440347 CTGCTGCTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
TGT
Found at i:34443124 original size:3 final size:3
Alignment explanation
Indices: 34443116--34443144 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
34443106 AGACGTTATA
34443116 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
34443145 TTGTTGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:34443691 original size:2 final size:2
Alignment explanation
Indices: 34443678--34443724 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
34443668 GCCCACTAAC
34443678 CT CT CAT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT C-T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
34443721 CT CT
1 CT CT
34443725 GAAATTTCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:34444610 original size:21 final size:22
Alignment explanation
Indices: 34444586--34444635 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
34444576 ATTATTTAAG
34444586 TATCATT-ATCAAAAAAATATA
1 TATCATTAATCAAAAAAATATA
* *
34444607 TATCATTAATCAAAATAATATT
1 TATCATTAATCAAAAAAATATA
34444629 TATCATT
1 TATCATT
34444636 TTATGTGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
TATCATTAATCAAAAAAATATA
Found at i:34444789 original size:8 final size:8
Alignment explanation
Indices: 34444771--34444801 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
34444761 TGATCTCGAT
34444771 TAAATATAA
1 TAAA-ATAA
34444780 TAAAATAA
1 TAAAATAA
34444788 TAAAATAA
1 TAAAATAA
34444796 TAAAAT
1 TAAAAT
34444802 TGTATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
TAAAATAA
Found at i:34445217 original size:12 final size:12
Alignment explanation
Indices: 34445200--34445230 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
34445190 TTATCTGTTC
*
34445200 ATAATTTTATTT
1 ATAATTTTATCT
34445212 ATAATTTTATCT
1 ATAATTTTATCT
34445224 ATAATTT
1 ATAATTT
34445231 CCTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (12 bp):
ATAATTTTATCT
Found at i:34445331 original size:16 final size:16
Alignment explanation
Indices: 34445303--34445337 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
34445293 CGCTCTGCCT
34445303 TTTTTCTTTCCTC-AC
1 TTTTTCTTTCCTCTAC
34445318 TTTTTCTTTCCCTCTAC
1 TTTTTCTTT-CCTCTAC
34445335 TTT
1 TTT
34445338 CATCCCTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 4 0.22
17 5 0.28
ACGTcount: A:0.06, C:0.31, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTTCTTTCCTCTAC
Found at i:34446632 original size:102 final size:106
Alignment explanation
Indices: 34446521--34446726 Score: 289
Period size: 102 Copynumber: 2.0 Consensus size: 106
34446511 TGATTAATTA
34446521 TCATTAATTAAAA-TGTAATTTGTCTTTTTTATTCT-CACACC-T-ATCATAAAAGCTATAAAAG
1 TCATTAATTAAAACT-TAATTTGTCTTTTTTATT-TACACACCTTAATCATAAAAGCTATAAAAG
34446582 CTTGATCTTGTTAATCT-T-AAGTAAAATTTAAATAGAGATTG
64 CTTGATCTTGTTAATCTATAAAGTAAAATTTAAATAGAGATTG
* ** *
34446623 TCATTAATTAAAACTTAATTTGTCTTTTTTATTTACACACCTTAATTATAAGGGCTATAAAGGCT
1 TCATTAATTAAAACTTAATTTGTCTTTTTTATTTACACACCTTAATCATAAAAGCTATAAAAGCT
* *
34446688 TGATCTTGTTTATTTATAAAAGTAAAATTTAAATAGAGA
66 TGATCTTGTTAATCTAT-AAAGTAAAATTTAAATAGAGA
34446727 CCTTGTTAAC
Statistics
Matches: 91, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
101 1 0.01
102 37 0.41
103 2 0.02
104 30 0.33
105 1 0.01
107 20 0.22
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (106 bp):
TCATTAATTAAAACTTAATTTGTCTTTTTTATTTACACACCTTAATCATAAAAGCTATAAAAGCT
TGATCTTGTTAATCTATAAAGTAAAATTTAAATAGAGATTG
Found at i:34446750 original size:107 final size:100
Alignment explanation
Indices: 34446537--34446726 Score: 229
Period size: 104 Copynumber: 1.8 Consensus size: 100
34446527 ATTAAAATGT
34446537 AATTTGTCTTTTTTATTCTCACACCTATCATAAAAGCTATAAAAGCTTGATCTTGTTAATCTTAA
1 AATTTGTCTTTTTTATTCTCACACCTATCATAAAAGCTATAAAAGCTTGATCTTGTTAATCTTAA
* *
34446602 GTAAAATTTAAATAGAGATTGTCATTAATTAAAACTT
66 GTAAAATTTAAATAGAGATTG--ATTAATCAAAACTA
* ** * * *
34446639 AATTTGTCTTTTTTATT-TACACACCTTAATTATAAGGGCTATAAAGGCTTGATCTTGTTTATTT
1 AATTTGTCTTTTTTATTCT-CACACC-T-ATCATAAAAGCTATAAAAGCTTGATCTTGTTAATCT
34446703 ATAAAAGTAAAATTTAAATAGAGA
63 -T--AAGTAAAATTTAAATAGAGA
34446727 CCTTGTTAAC
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
101 1 0.01
102 23 0.30
103 1 0.01
104 30 0.39
105 1 0.01
107 20 0.26
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (100 bp):
AATTTGTCTTTTTTATTCTCACACCTATCATAAAAGCTATAAAAGCTTGATCTTGTTAATCTTAA
GTAAAATTTAAATAGAGATTGATTAATCAAAACTA
Found at i:34456018 original size:33 final size:33
Alignment explanation
Indices: 34455981--34456047 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
34455971 AACATGATCG
* * *
34455981 TGTTATTATATCATTTCATCATTAATTATGATA
1 TGTTATTATATCACTTCATCATAAATTATAATA
*
34456014 TGTTATTATGTCACTTCATCATAAATTATAATA
1 TGTTATTATATCACTTCATCATAAATTATAATA
34456047 T
1 T
34456048 ATATTGATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.49
Consensus pattern (33 bp):
TGTTATTATATCACTTCATCATAAATTATAATA
Found at i:34456121 original size:30 final size:30
Alignment explanation
Indices: 34456081--34456153 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
34456071 CATTCGGTAT
34456081 AAAATAATAAATAATAT-TTTAATTAAAAATA
1 AAAAT-ATAAA-AATATATTTAATTAAAAATA
* * *
34456112 AAAATAT-AAAATTTATTTGATTAATAATA
1 AAAATATAAAAATATATTTAATTAAAAATA
34456141 AAAATATAAAAAT
1 AAAATATAAAAAT
34456154 TTAACTCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.11
29 21 0.57
30 7 0.19
31 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAATATAAAAATATATTTAATTAAAAATA
Found at i:34463100 original size:18 final size:20
Alignment explanation
Indices: 34463077--34463116 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
34463067 AATGTTTATA
34463077 AAATGAT-ATA-ATATAATT
1 AAATGATAATATATATAATT
34463095 AAATGATAATATATATAATT
1 AAATGATAATATATATAATT
34463115 AA
1 AA
34463117 CAATACATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 3 0.15
20 10 0.50
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
AAATGATAATATATATAATT
Found at i:34471349 original size:2 final size:2
Alignment explanation
Indices: 34471344--34471374 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
34471334 TATATGGTAG
34471344 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34471375 TTATGATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34488234 original size:30 final size:30
Alignment explanation
Indices: 34488198--34488256 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
34488188 GTTCTGTTTT
34488198 CCTCTGCTCTTTCAAGGGGCCAAGTGAACG
1 CCTCTGCTCTTTCAAGGGGCCAAGTGAACG
34488228 CCTCTGCTCTTTCAAGGGGCCAAGTGAAC
1 CCTCTGCTCTTTCAAGGGGCCAAGTGAAC
34488257 AGGCGTTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.31, G:0.25, T:0.24
Consensus pattern (30 bp):
CCTCTGCTCTTTCAAGGGGCCAAGTGAACG
Found at i:34495656 original size:17 final size:17
Alignment explanation
Indices: 34495636--34495671 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
34495626 TGATAAACAG
34495636 ATATACATACAGTATAT
1 ATATACATACAGTATAT
*
34495653 ATATACATATAGTATAT
1 ATATACATACAGTATAT
34495670 AT
1 AT
34495672 TTGTATAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (17 bp):
ATATACATACAGTATAT
Found at i:34506546 original size:15 final size:15
Alignment explanation
Indices: 34506507--34506546 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
34506497 CCAAGCAAAC
*
34506507 AAAAATAAAAAAAAG
1 AAAAATAAAGAAAAG
*
34506522 AAAAAAAAAGAAAAG
1 AAAAATAAAGAAAAG
*
34506537 AGAAATAAAG
1 AAAAATAAAG
34506547 GAGTGATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.05
Consensus pattern (15 bp):
AAAAATAAAGAAAAG
Found at i:34521647 original size:19 final size:19
Alignment explanation
Indices: 34521619--34521670 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
34521609 CATGGCAATG
* *
34521619 GGATTGAAGAAAGCAAGTT
1 GGATTAAAGAAAGAAAGTT
34521638 GGATTAAAGAAAGAAAGTT
1 GGATTAAAGAAAGAAAGTT
34521657 GGATTAAAGAAAGA
1 GGATTAAAGAAAGA
34521671 TAGCATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.50, C:0.02, G:0.29, T:0.19
Consensus pattern (19 bp):
GGATTAAAGAAAGAAAGTT
Found at i:34526868 original size:100 final size:100
Alignment explanation
Indices: 34526695--34526896 Score: 379
Period size: 100 Copynumber: 2.0 Consensus size: 100
34526685 ACATCCACCT
34526695 AACACAGAATAAACAGATGTCATTCAGTGCTAACTAAACTCGAACAGAATACAGTTTCACTCTTC
1 AACACAGAATAAACAGATGTCATTCAGTGCTAACTAAACTCGAACAGAATACAGTTTCACTCTTC
34526760 TAAGTGTGCAGTTTTATGCCACTTCCAAAACATAA
66 TAAGTGTGCAGTTTTATGCCACTTCCAAAACATAA
*
34526795 AACACAGAATAAACAGATGTCATTCAGTGCTAACTAAACTTGAA-AGGAATACAGTTTCACTCTT
1 AACACAGAATAAACAGATGTCATTCAGTGCTAACTAAACTCGAACA-GAATACAGTTTCACTCTT
34526859 CTAAGTGTGCAGTTTTATGCCACTTCCAAAACATAA
65 CTAAGTGTGCAGTTTTATGCCACTTCCAAAACATAA
34526895 AA
1 AA
34526897 TAACCTTTCA
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
99 1 0.01
100 99 0.99
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (100 bp):
AACACAGAATAAACAGATGTCATTCAGTGCTAACTAAACTCGAACAGAATACAGTTTCACTCTTC
TAAGTGTGCAGTTTTATGCCACTTCCAAAACATAA
Found at i:34531920 original size:23 final size:24
Alignment explanation
Indices: 34531884--34531929 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
34531874 TATTTTAAAA
*
34531884 ATTATTTTTATATTAAATCAAATT
1 ATTATATTTATATTAAATCAAATT
**
34531908 ATTATATTT-TATTTTATCAAAT
1 ATTATATTTATATTAAATCAAAT
34531930 AAATTTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATATTTATATTAAATCAAATT
Found at i:34536143 original size:25 final size:24
Alignment explanation
Indices: 34536090--34536143 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
34536080 TATTGTTGAA
* *
34536090 AATATTTATTTTACATGATTTTTG
1 AATATTTATTTTACATCATTTATG
34536114 AATATTTATTTTTACA-CATTTATG
1 AATATTTA-TTTTACATCATTTATG
34536138 AGATAT
1 A-ATAT
34536144 ATACATGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (24 bp):
AATATTTATTTTACATCATTTATG
Found at i:34536683 original size:24 final size:24
Alignment explanation
Indices: 34536636--34536685 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
34536626 ATTATAAAAA
* * **
34536636 AATTTAAATTTTTATTTTTTTATT
1 AATTTAAAATTTTATTATCATATT
34536660 AATTTAAAATTTTATTATCATATT
1 AATTTAAAATTTTATTATCATATT
34536684 AA
1 AA
34536686 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
AATTTAAAATTTTATTATCATATT
Found at i:34547733 original size:20 final size:20
Alignment explanation
Indices: 34547710--34547753 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
34547700 TGTATAATTA
* *
34547710 ATTTTATAATTTTATATAAT
1 ATTTTATAATATAATATAAT
*
34547730 ATTTTATGATATAATATAAT
1 ATTTTATAATATAATATAAT
34547750 ATTT
1 ATTT
34547754 AATATTAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTTATAATATAATATAAT
Found at i:34557813 original size:90 final size:91
Alignment explanation
Indices: 34557660--34557850 Score: 314
Period size: 90 Copynumber: 2.1 Consensus size: 91
34557650 AACAATATAC
*
34557660 TTTTTCTTGGTTTTTGTTGGAGTAGACTAACATCTAGGGAATCATTTTGGAGATTGGGAGAACTT
1 TTTTTCTTGGTTTTTGTTGGAGTAGACTAACATCTAGGAAATCATTTTGGAGATTGGGAGAACTT
*
34557725 -ACCATATTTCCCT-GAATGTTATTGT
66 CAACATATTTCCCTGGAA-GTTATTGT
*
34557750 TTTTTCTTGGTTTTTGTTGGAGTAGACTAACATCTAGGAAATGATTTTGGAGATTGGGAGAACTT
1 TTTTTCTTGGTTTTTGTTGGAGTAGACTAACATCTAGGAAATCATTTTGGAGATTGGGAGAACTT
34557815 CAACATATTTCCCTGGAAGTTATTGT
66 CAACATATTTCCCTGGAAGTTATTGT
* *
34557841 TATTGCTTGG
1 TTTTTCTTGG
34557851 GATTGGATTA
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
90 63 0.67
91 28 0.30
92 3 0.03
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.42
Consensus pattern (91 bp):
TTTTTCTTGGTTTTTGTTGGAGTAGACTAACATCTAGGAAATCATTTTGGAGATTGGGAGAACTT
CAACATATTTCCCTGGAAGTTATTGT
Found at i:34564409 original size:16 final size:16
Alignment explanation
Indices: 34564388--34564427 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
34564378 CCATCCCTGA
* *
34564388 ATATATATGTATATAT
1 ATATATATGTAAAAAT
*
34564404 ATATATATTTAAAAAT
1 ATATATATGTAAAAAT
34564420 ATATATAT
1 ATATATAT
34564428 CAGATTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATATATATGTAAAAAT
Found at i:34565714 original size:11 final size:11
Alignment explanation
Indices: 34565672--34565714 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
34565662 GCAAAAAACC
34565672 TGTTAAAAATG
1 TGTTAAAAATG
** **
34565683 TACTAAAAACA
1 TGTTAAAAATG
34565694 TGTTAAAAATG
1 TGTTAAAAATG
34565705 TGTTAAAAAT
1 TGTTAAAAAT
34565715 ATGCAAAAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.33
Consensus pattern (11 bp):
TGTTAAAAATG
Found at i:34590217 original size:21 final size:21
Alignment explanation
Indices: 34590193--34590238 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
34590183 ACGCGTGAAA
34590193 CCCTAACCCTCACGCGCTCAC
1 CCCTAACCCTCACGCGCTCAC
** **
34590214 CCCTCTCTGTCACGCGCTCAC
1 CCCTAACCCTCACGCGCTCAC
34590235 CCCT
1 CCCT
34590239 CCCTCGCCGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.57, G:0.11, T:0.20
Consensus pattern (21 bp):
CCCTAACCCTCACGCGCTCAC
Found at i:34604909 original size:30 final size:30
Alignment explanation
Indices: 34604849--34604917 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
34604839 TAGTCAAATT
* *
34604849 TAATTATAATTGTTATTTATACTCATGTGA
1 TAATTATATTTGTTATTTATACTCACGTGA
* * *
34604879 TAATTATATTTTTTATTTATATTTACGTGA
1 TAATTATATTTGTTATTTATACTCACGTGA
34604909 T-A-TATATTT
1 TAATTATATTT
34604918 CATGTAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 7 0.21
29 1 0.03
30 26 0.76
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.57
Consensus pattern (30 bp):
TAATTATATTTGTTATTTATACTCACGTGA
Found at i:34605346 original size:2 final size:2
Alignment explanation
Indices: 34605335--34605375 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
34605325 NNNNNNNTAT
34605335 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34605376 AGTTAAGTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:34623826 original size:17 final size:15
Alignment explanation
Indices: 34623804--34623837 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
34623794 TTATTTACAT
34623804 ATCTTTTAATACTATAA
1 ATCTTTT-ATACT-TAA
34623821 ATCTTTTATACTTAA
1 ATCTTTTATACTTAA
34623836 AT
1 AT
34623838 ATTTCATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 5 0.29
17 7 0.41
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (15 bp):
ATCTTTTATACTTAA
Found at i:34624413 original size:59 final size:59
Alignment explanation
Indices: 34624320--34624470 Score: 212
Period size: 59 Copynumber: 2.6 Consensus size: 59
34624310 TTTAACTAAA
* * * * * * *
34624320 TTTTTTACTCAACAAAATTTTCGTTTTACATTTACGTTCTAAAATCGAAAGACATTATT
1 TTTTTTACTCAATAAAATTTACCTTTTACCTTTACCTACTAAAATCGAAAGACATTAAT
* *
34624379 TTTTTTACTGAATAAAATTTACCTTTTACCTTTACCTACTAAAATCGAAGGACATTAAT
1 TTTTTTACTCAATAAAATTTACCTTTTACCTTTACCTACTAAAATCGAAAGACATTAAT
*
34624438 TTTTTTACTCAATAAAATTTACCTTTTAACTTT
1 TTTTTTACTCAATAAAATTTACCTTTTACCTTT
34624471 TAAAATTTCC
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 81 1.00
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (59 bp):
TTTTTTACTCAATAAAATTTACCTTTTACCTTTACCTACTAAAATCGAAAGACATTAAT
Found at i:34632595 original size:21 final size:22
Alignment explanation
Indices: 34632554--34632597 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
34632544 TAATAAATTT
*
34632554 TAAAAATATAAAATACCATTAA
1 TAAAAATATAAAATACAATTAA
34632576 TAAAATATATAAAA-A-AATTAA
1 TAAAA-ATATAAAATACAATTAA
34632597 T
1 T
34632598 TTTTTTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 6 0.30
23 8 0.40
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAATATAAAATACAATTAA
Found at i:34639534 original size:2 final size:2
Alignment explanation
Indices: 34639527--34639556 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34639517 AGGCAAATAA
34639527 AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
34639557 AAGATTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:34650360 original size:24 final size:25
Alignment explanation
Indices: 34650331--34650397 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
34650321 TGTCAAATTG
*
34650331 TATGCT-CAGCT-ATATTGTTGGGAA
1 TATGCTACAGCTGATA-TATTGGGAA
*
34650355 TATGCTGAGAGCTGATATATTGGGAA
1 TATGCT-ACAGCTGATATATTGGGAA
*
34650381 TATGCTGAGAGCTGATA
1 TATGCT-ACAGCTGATA
34650398 AAGTTTTAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 6 0.16
26 29 0.76
27 3 0.08
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.33
Consensus pattern (25 bp):
TATGCTACAGCTGATATATTGGGAA
Found at i:34650377 original size:26 final size:26
Alignment explanation
Indices: 34650348--34650397 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
34650338 AGCTATATTG
34650348 TTGGGAATATGCTGAGAGCTGATATA
1 TTGGGAATATGCTGAGAGCTGATATA
34650374 TTGGGAATATGCTGAGAGCTGATA
1 TTGGGAATATGCTGAGAGCTGATA
34650398 AAGTTTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (26 bp):
TTGGGAATATGCTGAGAGCTGATATA
Found at i:34654752 original size:20 final size:20
Alignment explanation
Indices: 34654707--34654762 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
34654697 ATCAATTGAA
34654707 AATAAATAT-TTTTTATTAT
1 AATAAATATATTTTTATTAT
*
34654726 ATTTAAATATATTTTTAATT-T
1 A-ATAAATATATTTTT-ATTAT
34654747 AATAAATATGATTTTT
1 AATAAATAT-ATTTTT
34654763 CTTAATTACC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 1 0.03
20 14 0.45
21 13 0.42
22 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
AATAAATATATTTTTATTAT
Found at i:34655397 original size:42 final size:42
Alignment explanation
Indices: 34655350--34655434 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
34655340 AAGTTCTTAT
*
34655350 ACTTTTATTTTAAATCAAATAAACTCTTATA-TTTTTTTTTGA
1 ACTTTTATTTTAAATC-AATAAACTCTTATACTTTTATTTTGA
* *
34655392 ACTTTTATTTTGAATCAATAAACTTTTATACTTTTATTTTGA
1 ACTTTTATTTTAAATCAATAAACTCTTATACTTTTATTTTGA
34655434 A
1 A
34655435 TTTACAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
41 13 0.33
42 26 0.67
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (42 bp):
ACTTTTATTTTAAATCAATAAACTCTTATACTTTTATTTTGA
Found at i:34655531 original size:29 final size:29
Alignment explanation
Indices: 34655499--34655559 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
34655489 AATGAGGCCC
* *
34655499 TTTTACTTTTATTT-TGAGTTAAATAAATT
1 TTTTACTTTTATTTAT-AGTCAAATAAACT
34655528 TTTTACTTTTATTTATAGTCAAATAAACT
1 TTTTACTTTTATTTATAGTCAAATAAACT
34655557 TTT
1 TTT
34655560 ATAACTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.57
Consensus pattern (29 bp):
TTTTACTTTTATTTATAGTCAAATAAACT
Found at i:34656073 original size:18 final size:18
Alignment explanation
Indices: 34656041--34656076 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
34656031 GCATTTTATG
34656041 CTTCTATTTTCTCAAAAT
1 CTTCTATTTTCTCAAAAT
34656059 CTTCATATTTT-TCAAAAT
1 CTTC-TATTTTCTCAAAAT
34656077 AAAATGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTCTATTTTCTCAAAAT
Found at i:34656357 original size:24 final size:24
Alignment explanation
Indices: 34656329--34656378 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
34656319 CAATGATAAT
34656329 GAAGAGCAA-GACG-TGACAAAGCCA
1 GAAGAGCAAGGA-GATG-CAAAGCCA
34656353 GAAGAGCAAGGAGATGCAAAGCCA
1 GAAGAGCAAGGAGATGCAAAGCCA
34656377 GA
1 GA
34656379 GGAACAGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.46, C:0.18, G:0.32, T:0.04
Consensus pattern (24 bp):
GAAGAGCAAGGAGATGCAAAGCCA
Found at i:34658839 original size:21 final size:21
Alignment explanation
Indices: 34658813--34658871 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
34658803 AATATAACAA
34658813 TATTTAAAAAAGTTT-ATAAAT
1 TATTTAAAAAA-TTTAATAAAT
34658834 TATTTAAAAAATTTAAATAAAT
1 TATTTAAAAAATTT-AATAAAT
*
34658856 TAAATTAAATAAATTT
1 T-ATTTAAA-AAATTT
34658872 TTATAATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 3 0.09
21 11 0.33
22 7 0.21
23 6 0.18
24 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TATTTAAAAAATTTAATAAAT
Found at i:34667369 original size:5 final size:5
Alignment explanation
Indices: 34667361--34667436 Score: 52
Period size: 5 Copynumber: 15.0 Consensus size: 5
34667351 ATAAATTAAA
* * *
34667361 AAAAT AAAAA ATAAAT ATAAAT ATAAAT ATAAAT TAAAT TAAAT AAAAT
1 AAAAT AAAAT A-AAAT A-AAAT A-AAAT A-AAAT AAAAT AAAAT AAAAT
34667410 -AAAT -AAAT AAAAT AATAA- AAAA- AAAAT
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT
34667437 CGGGATGGCT
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
4 14 0.22
5 26 0.41
6 23 0.37
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (5 bp):
AAAAT
Found at i:34667380 original size:6 final size:6
Alignment explanation
Indices: 34667351--34667428 Score: 64
Period size: 5 Copynumber: 13.8 Consensus size: 6
34667341 TTGTAGACAC
*
34667351 ATAAAT -TAAA- A-AAAT A-AAAA ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
34667395 -TAAAT -TAAAT A-AAAT AAATAAAT A-AAAT AATAAA
1 ATAAAT ATAAAT ATAAAT --ATAAAT ATAAAT -ATAAA
34667429 AAAAAAATCG
Statistics
Matches: 61, Mismatches: 2, Indels: 17
0.76 0.03 0.21
Matches are distributed among these distances:
4 3 0.05
5 27 0.44
6 23 0.38
7 4 0.07
8 4 0.07
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (6 bp):
ATAAAT
Found at i:34697189 original size:82 final size:83
Alignment explanation
Indices: 34697047--34697270 Score: 255
Period size: 82 Copynumber: 2.8 Consensus size: 83
34697037 GTGCACATGA
* * * *
34697047 TGTTACACGTCATGTTG--AAAAAAATATTGTTGTTACACGTCATATACAAAAACATGTTACATG
1 TGTTACACGTCATGTTGAAAAAAAAACATTATTGTTACACGTCATATACAAAAACATATTACACG
*
34697110 TTATGATTAAAAAAGA-T
66 TTATGATTAAAAAAAAGT
** * * * *
34697127 TGTTACATATCATGTTGAAAAAAAAACATTATTGTTACATGTCATGTATAAAAATATATTACACG
1 TGTTACACGTCATGTTGAAAAAAAAACATTATTGTTACACGTCATATACAAAAACATATTACACG
34697192 TTATGATTAAAAAAAAGT
66 TTATGATTAAAAAAAAGT
* * * *
34697210 TATTACACGTCATGTT--AAAAAAAA-ATTGTTGTTACACG-CTATGTACAAAAACATGTTACAC
1 TGTTACACGTCATGTTGAAAAAAAAACATTATTGTTACACGTC-ATATACAAAAACATATTACAC
34697271 ACCATGTTAA
Statistics
Matches: 121, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
79 1 0.01
80 45 0.37
81 8 0.07
82 53 0.44
83 14 0.12
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (83 bp):
TGTTACACGTCATGTTGAAAAAAAAACATTATTGTTACACGTCATATACAAAAACATATTACACG
TTATGATTAAAAAAAAGT
Found at i:34697202 original size:24 final size:24
Alignment explanation
Indices: 34697161--34697232 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 24
34697151 AACATTATTG
* *
34697161 TTACATGTCATGTATAAAAATA-TA
1 TTACACGTCATGT-TAAAAAAAGTA
*
34697185 TTACACGTTATGATTAAAAAAAAGTTA
1 TTACACGTCATG-TT-AAAAAAAG-TA
34697212 TTACACGTCATGTTAAAAAAA
1 TTACACGTCATGTTAAAAAAA
34697233 AATTGTTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 11 0.28
25 14 0.35
26 2 0.05
27 13 0.32
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (24 bp):
TTACACGTCATGTTAAAAAAAGTA
Found at i:34697227 original size:26 final size:27
Alignment explanation
Indices: 34697183--34697233 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
34697173 TATAAAAATA
*
34697183 TATTACACGTTATGATTAAAAAAAAGT
1 TATTACACGTCATGATTAAAAAAAAGT
34697210 TATTACACGTCATG-TTAAAAAAAA
1 TATTACACGTCATGATTAAAAAAAA
34697234 ATTGTTGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (27 bp):
TATTACACGTCATGATTAAAAAAAAGT
Found at i:34697269 original size:80 final size:80
Alignment explanation
Indices: 34697049--34697292 Score: 287
Period size: 80 Copynumber: 3.0 Consensus size: 80
34697039 GCACATGATG
* * *
34697049 TTACACGTCATGTTGAAAAAAATATTGTTGTTACACGTCATATACAAAAACATGTTACATGTTAT
1 TTACACGTCATGTTGAAAAAAAAATTGTTGTTACACGTCATGTACAAAAACATGTTACACGTTAT
* *
34697114 GATTAAAAAAGATTG
66 GATTAAAAAAAATTA
** * * * * *
34697129 TTACATATCATGTTGAAAAAAAAACATTATTGTTACATGTCATGTATAAAAATATATTACACGTT
1 TTACACGTCATGTTG-AAAAAAAA-ATTGTTGTTACACGTCATGTACAAAAACATGTTACACGTT
34697194 ATGATTAAAAAAAAGTTA
64 ATGATTAAAAAAAA-TTA
***
34697212 TTACACGTCATGTT-AAAAAAAAATTGTTGTTACACG-CTATGTACAAAAACATGTTACACACCA
1 TTACACGTCATGTTGAAAAAAAAATTGTTGTTACACGTC-ATGTACAAAAACATGTTACACGTTA
34697275 TG-TTAAAAAAATATTA
65 TGATTAAAAAAA-ATTA
34697291 TT
1 TT
34697293 GTTATATATC
Statistics
Matches: 137, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
79 15 0.11
80 47 0.34
81 15 0.11
82 46 0.34
83 14 0.10
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (80 bp):
TTACACGTCATGTTGAAAAAAAAATTGTTGTTACACGTCATGTACAAAAACATGTTACACGTTAT
GATTAAAAAAAATTA
Found at i:34703952 original size:4 final size:4
Alignment explanation
Indices: 34703939--34704035 Score: 103
Period size: 4 Copynumber: 24.0 Consensus size: 4
34703929 AACCATCCTA
*
34703939 ATTT -TTT ATTT ATTT ATTT ATTT ATTT ATTT AATTT ATATT -TAT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT AT-TT ATTT ATTT
*
34703987 ATTT ATTT ATTTT ATTT AATTT ATATT -TAT ATTT ATTT ATTT A-TT ATTT
1 ATTT ATTT A-TTT ATTT -ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT
34704036 TAATTTATGT
Statistics
Matches: 80, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
3 8 0.10
4 56 0.70
5 16 0.20
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:34703982 original size:6 final size:6
Alignment explanation
Indices: 34703965--34704022 Score: 70
Period size: 6 Copynumber: 10.2 Consensus size: 6
34703955 TTTATTTATT
*
34703965 TATTTA -ATTTA TATTTA TATTTA T-TTATT TATTT- TATTTA -ATTTA
1 TATTTA TATTTA TATTTA TATTTA TATT-TA TATTTA TATTTA TATTTA
34704010 TATTTA TATTTA T
1 TATTTA TATTTA T
34704023 TTATTTATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
5 17 0.37
6 27 0.59
7 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATTTA
Found at i:34704006 original size:34 final size:34
Alignment explanation
Indices: 34703949--34704043 Score: 167
Period size: 34 Copynumber: 2.9 Consensus size: 34
34703939 ATTTTTTATT
34703949 TATTTATTTATTTA-TTTATTTAATTTATATTTA
1 TATTTATTTATTTATTTTATTTAATTTATATTTA
34703982 TATTTATTTATTTATTTTATTTAATTTATATTTA
1 TATTTATTTATTTATTTTATTTAATTTATATTTA
*
34704016 TATTTATTTATTTATTAT-TTTAATTTAT
1 TATTTATTTATTTATTTTATTTAATTTAT
34704044 GTGTCTACAG
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
33 24 0.40
34 36 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (34 bp):
TATTTATTTATTTATTTTATTTAATTTATATTTA
Found at i:34720350 original size:20 final size:20
Alignment explanation
Indices: 34720325--34720376 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
34720315 TGCCTGATAA
*
34720325 AAAAGATTAAAA-GTGTATAT
1 AAAAGATTAAAATATGTAT-T
34720345 AAAAGATTAAAATATGTATT
1 AAAAGATTAAAATATGTATT
34720365 AAAAGATTAAAA
1 AAAAGATTAAAA
34720377 CCTGACTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 25 0.83
21 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (20 bp):
AAAAGATTAAAATATGTATT
Found at i:34722087 original size:2 final size:2
Alignment explanation
Indices: 34722080--34722120 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
34722070 CTGCGTTTGG
34722080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34722121 CTACACACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34726990 original size:64 final size:64
Alignment explanation
Indices: 34726889--34727020 Score: 264
Period size: 64 Copynumber: 2.1 Consensus size: 64
34726879 GGCAGCCCAC
34726889 CTGTGAAAATCACGAAGATGAAAAAGAAGGAAACTTTTCATCCTTGCGTTTGATACTAACAATT
1 CTGTGAAAATCACGAAGATGAAAAAGAAGGAAACTTTTCATCCTTGCGTTTGATACTAACAATT
34726953 CTGTGAAAATCACGAAGATGAAAAAGAAGGAAACTTTTCATCCTTGCGTTTGATACTAACAATT
1 CTGTGAAAATCACGAAGATGAAAAAGAAGGAAACTTTTCATCCTTGCGTTTGATACTAACAATT
34727017 CTGT
1 CTGT
34727021 TAATTTCCTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (64 bp):
CTGTGAAAATCACGAAGATGAAAAAGAAGGAAACTTTTCATCCTTGCGTTTGATACTAACAATT
Found at i:34729032 original size:5 final size:5
Alignment explanation
Indices: 34729018--34729046 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
34729008 CAAAACGAAA
34729018 GGGA- GGGAG GGGAG GGGAG GGGAG GGGAG
1 GGGAG GGGAG GGGAG GGGAG GGGAG GGGAG
34729047 AGTGGGGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.21, C:0.00, G:0.79, T:0.00
Consensus pattern (5 bp):
GGGAG
Found at i:34735775 original size:9 final size:9
Alignment explanation
Indices: 34735761--34735817 Score: 66
Period size: 9 Copynumber: 6.7 Consensus size: 9
34735751 GCCTGAGCCA
34735761 CTGTTGTTG
1 CTGTTGTTG
*
34735770 CTGTTGATG
1 CTGTTGTTG
*
34735779 CTGTTGATG
1 CTGTTGTTG
34735788 CTGTTGTTG
1 CTGTTGTTG
34735797 CTG--G-TG
1 CTGTTGTTG
*
34735803 ATGTTGTTG
1 CTGTTGTTG
34735812 CTGTTG
1 CTGTTG
34735818 GTGATGTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 4 0.10
7 1 0.02
8 1 0.02
9 35 0.85
ACGTcount: A:0.05, C:0.11, G:0.35, T:0.49
Consensus pattern (9 bp):
CTGTTGTTG
Found at i:34735819 original size:18 final size:18
Alignment explanation
Indices: 34735761--34735826 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
34735751 GCCTGAGCCA
* * *
34735761 CTGTTGTTGCTGTTGATG
1 CTGTTGGTGATGTTGTTG
* *
34735779 CTGTTGATGCTGTTGTTG
1 CTGTTGGTGATGTTGTTG
34735797 C---TGGTGATGTTGTTG
1 CTGTTGGTGATGTTGTTG
34735812 CTGTTGGTGATGTTG
1 CTGTTGGTGATGTTG
34735827 AAACTGCTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 13 0.32
18 28 0.68
ACGTcount: A:0.06, C:0.09, G:0.36, T:0.48
Consensus pattern (18 bp):
CTGTTGGTGATGTTGTTG
Found at i:34735837 original size:18 final size:18
Alignment explanation
Indices: 34735795--34735840 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
34735785 ATGCTGTTGT
***
34735795 TGCTGGTGATGTTGTTGC
1 TGCTGGTGATGTTGAAAC
*
34735813 TGTTGGTGATGTTGAAAC
1 TGCTGGTGATGTTGAAAC
34735831 TGCTGGTGAT
1 TGCTGGTGAT
34735841 TCTGCACCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.09, G:0.37, T:0.41
Consensus pattern (18 bp):
TGCTGGTGATGTTGAAAC
Found at i:34754188 original size:57 final size:57
Alignment explanation
Indices: 34754127--34754235 Score: 146
Period size: 57 Copynumber: 1.9 Consensus size: 57
34754117 ACTGTTAGTG
* * * *
34754127 TGTTGTGACTAAGGTAGAAATGTCATATTTATAGATTGGAGCAAAAAGTTAACAGTT
1 TGTTGTGACTAAGATAGAAATATCATATTTACAGACTGGAGCAAAAAGTTAACAGTT
* ** *
34754184 TGTTGTGACTAAGATGGAAATATTGTATTTACAGACTGGAGCAGAAAGTTAA
1 TGTTGTGACTAAGATAGAAATATCATATTTACAGACTGGAGCAAAAAGTTAA
34754236 TGTGTCATGA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 44 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (57 bp):
TGTTGTGACTAAGATAGAAATATCATATTTACAGACTGGAGCAAAAAGTTAACAGTT
Found at i:34754258 original size:27 final size:26
Alignment explanation
Indices: 34754228--34754291 Score: 60
Period size: 27 Copynumber: 2.4 Consensus size: 26
34754218 ACTGGAGCAG
*
34754228 AAAGTTAATGTGTCAT-GACTAAAATAA
1 AAAGTTAATGT-T-ATAGACTAAAACAA
*
34754255 AAAGGTTATAT-TTATAGACTGAAACAA
1 AAA-GTTA-ATGTTATAGACTAAAACAA
34754282 AAAGTTAATG
1 AAAGTTAATG
34754292 ATACGTGGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
25 2 0.06
26 6 0.19
27 16 0.52
28 5 0.16
29 2 0.06
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.30
Consensus pattern (26 bp):
AAAGTTAATGTTATAGACTAAAACAA
Found at i:34755308 original size:19 final size:19
Alignment explanation
Indices: 34755266--34755309 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
34755256 AACAAAACCA
* *
34755266 ATATTATTTTGTTCTTCAT
1 ATATTATATTGTTCTTAAT
34755285 ATATTATATTGTTCATTAAT
1 ATATTATATTGTTC-TTAAT
34755305 -TATTA
1 ATATTA
34755310 ACTAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.59
Consensus pattern (19 bp):
ATATTATATTGTTCTTAAT
Found at i:34788060 original size:41 final size:40
Alignment explanation
Indices: 34787981--34788102 Score: 156
Period size: 41 Copynumber: 3.0 Consensus size: 40
34787971 AATAATTACC
* *
34787981 TTATTAAATATAACTTTTA-AATAGTTGTATTATGAAAGG
1 TTATTAAATATAATTTTTAGAACAGTTGTATTATGAAAGG
* *
34788020 TTGTTAAATATAATTTTTATGAACAGTTGTATTATAAAAGG
1 TTATTAAATATAATTTTTA-GAACAGTTGTATTATGAAAGG
* *
34788061 TTATTAAAAATAATTGTTTAGAAACAATTGTATTATGAAAGG
1 TTATTAAATATAATT-TTTAG-AACAGTTGTATTATGAAAGG
34788103 AAATAGTTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
39 17 0.24
41 32 0.45
42 22 0.31
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (40 bp):
TTATTAAATATAATTTTTAGAACAGTTGTATTATGAAAGG
Found at i:34799455 original size:1 final size:1
Alignment explanation
Indices: 34799415--34799444 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
34799405 TGCTAACATC
*
34799415 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
34799445 GGTCCATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:34806144 original size:3 final size:3
Alignment explanation
Indices: 34806103--34806132 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
34806093 TTAAAAAAAA
34806103 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34806133 ACTAATATTA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:34854240 original size:22 final size:20
Alignment explanation
Indices: 34854200--34854263 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 20
34854190 AACATTTTGA
*
34854200 TTAATAATAATTTAAA-TTT
1 TTAAAAATAATTTAAATTTT
34854219 TTAAAAATAATTTAAGATATTTT
1 TTAAAAATAATTT-A-A-ATTTT
*
34854242 TTAAATATAATGTCTAAATTTT
1 TTAAAAATAAT-T-TAAATTTT
34854264 GAAAAAGCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 12 0.32
20 1 0.03
21 1 0.03
22 6 0.16
23 14 0.38
24 2 0.05
25 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (20 bp):
TTAAAAATAATTTAAATTTT
Found at i:34860147 original size:30 final size:29
Alignment explanation
Indices: 34860060--34860147 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
34860050 ATCTATCAAT
* * *
34860060 AACAAGAAGCACCGGTGGTCT--TGTAGT
1 AACAACAAGCACCAGTGGTCTAGTGTAGA
* *
34860087 AACAACAAGTACCAGTGGTCTAGTACTAGA
1 AACAACAAGCACCAGTGGTCTAGT-GTAGA
*
34860117 AATAACAAGCACCAGTGGTCTAGTGGTAGA
1 AACAACAAGCACCAGTGGTCTAGT-GTAGA
34860147 A
1 A
34860148 TAGTACCCTG
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
27 18 0.37
29 1 0.02
30 30 0.61
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (29 bp):
AACAACAAGCACCAGTGGTCTAGTGTAGA
Found at i:34869237 original size:19 final size:19
Alignment explanation
Indices: 34869213--34869252 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34869203 AAACCACGAA
* *
34869213 AGCCATTAAAGCATTATAG
1 AGCCATGAAAGCATTAGAG
*
34869232 AGCCATGCAAGCATTAGAG
1 AGCCATGAAAGCATTAGAG
34869251 AG
1 AG
34869253 GTAAATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (19 bp):
AGCCATGAAAGCATTAGAG
Found at i:34880737 original size:14 final size:14
Alignment explanation
Indices: 34880718--34880744 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34880708 GACGAAATCC
34880718 ATTGAATTTAATTA
1 ATTGAATTTAATTA
34880732 ATTGAATTTAATT
1 ATTGAATTTAATT
34880745 TTTTAAAAAT
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
ATTGAATTTAATTA
Found at i:34883290 original size:2 final size:2
Alignment explanation
Indices: 34883283--34883313 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34883273 ATTCACTAGT
*
34883283 CA CA CA CA CA CA CA CA CA CA CA CA CT CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
34883314 TCACTCTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.52, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:34883454 original size:15 final size:16
Alignment explanation
Indices: 34883425--34883454 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34883415 TTAAAATTAA
34883425 AAAAAAGGAAGAAGAG
1 AAAAAAGGAAGAAGAG
34883441 AAAAAAGGAA-AAGA
1 AAAAAAGGAAGAAGA
34883455 AAGGGCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (16 bp):
AAAAAAGGAAGAAGAG
Found at i:34906574 original size:17 final size:17
Alignment explanation
Indices: 34906552--34906592 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
34906542 ATTCTTCTTA
*
34906552 ATATATAAAAATATTAT
1 ATATATAAAAATATAAT
* *
34906569 ATATATCAACATATAAT
1 ATATATAAAAATATAAT
34906586 ATATATA
1 ATATATA
34906593 TATATAATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATATAAAAATATAAT
Found at i:34906597 original size:15 final size:15
Alignment explanation
Indices: 34906550--34906601 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
34906540 CAATTCTTCT
*
34906550 TAATATATAAAAATA
1 TAATATATATAAATA
*
34906565 TTATATATATCAACATA
1 TAATATATAT-AA-ATA
*
34906582 TAATATATATATATA
1 TAATATATATAAATA
34906597 TAATA
1 TAATA
34906602 GTTTGATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 16 0.52
16 3 0.10
17 12 0.39
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATATATATAAATA
Found at i:34907109 original size:30 final size:30
Alignment explanation
Indices: 34907063--34907125 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
34907053 GTTTAATTAT
* *
34907063 ATAAGAAAAGTTATTTGATTTGAAATAAAA
1 ATAAAAAAAGTTATTTGATTTAAAATAAAA
*
34907093 ATAAAAAAATTTATTTGATTTAAAATAAAA
1 ATAAAAAAAGTTATTTGATTTAAAATAAAA
34907123 ATA
1 ATA
34907126 TAAACGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (30 bp):
ATAAAAAAAGTTATTTGATTTAAAATAAAA
Found at i:34914999 original size:12 final size:12
Alignment explanation
Indices: 34914982--34915038 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
34914972 ATTTATTCCA
34914982 ATTATATTATTT
1 ATTATATTATTT
34914994 ATTATATTTATTT
1 ATTATA-TTATTT
34915007 ATT-TATT-TTT
1 ATTATATTATTT
34915017 CATT-T-TTA-TT
1 -ATTATATTATTT
34915027 ATTATCATTATT
1 ATTAT-ATTATT
34915039 ATTTTTTNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
9 3 0.08
10 8 0.21
11 6 0.16
12 11 0.29
13 10 0.26
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTATATTATTT
Found at i:34931307 original size:79 final size:76
Alignment explanation
Indices: 34931174--34931325 Score: 241
Period size: 79 Copynumber: 2.0 Consensus size: 76
34931164 CCCCCCAGCA
* * *
34931174 TGTGATATATGTACCAAAAATAATAATAATGCAAGGGATAAGCTGGTCTGTTCTTCAACAGTAAT
1 TGTGATATATGTACCAAAAAAAATAATAATGCAAGGGATAAGCTGGTCTATTCTTCAACAATAAT
34931239 ATTTCCAAGCT
66 ATTTCCAAGCT
*
34931250 TGTGATATATGTACCCAAAAAGAAAATAATAATGCAAGGGATATGCTGGTCTATTCTTCAACAAT
1 TGTGATATATGTA-CC-AAAA-AAAATAATAATGCAAGGGATAAGCTGGTCTATTCTTCAACAAT
34931315 AATATTTCCAA
63 AATATTTCCAA
34931326 ATCCTCTATA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
76 13 0.19
77 2 0.03
78 4 0.06
79 50 0.72
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (76 bp):
TGTGATATATGTACCAAAAAAAATAATAATGCAAGGGATAAGCTGGTCTATTCTTCAACAATAAT
ATTTCCAAGCT
Found at i:34932773 original size:22 final size:22
Alignment explanation
Indices: 34932745--34932813 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 22
34932735 AATATTATTG
*
34932745 ATAATTAAATTATTAATTTTAT
1 ATAATTAAATTATTAATTTTAA
*
34932767 ATAATTAAATATATAAAATTATTAA
1 ATAATTAAAT-TAT-TAATT-TTAA
34932792 ATTAATTAAAATTATTAATTTT
1 A-TAATT-AAATTATTAATTTT
34932814 TTTGACTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 10 0.26
23 3 0.08
24 6 0.15
25 8 0.21
26 8 0.21
27 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATTAAATTATTAATTTTAA
Found at i:34932793 original size:8 final size:8
Alignment explanation
Indices: 34932748--34932809 Score: 56
Period size: 8 Copynumber: 7.6 Consensus size: 8
34932738 ATTATTGATA
34932748 ATTAAATT
1 ATTAAATT
34932756 ATT-AATT
1 ATTAAATT
* *
34932763 -TTATATA
1 ATTAAATT
34932770 ATTAAATAT
1 ATTAAAT-T
*
34932779 ATAAAATT
1 ATTAAATT
34932787 ATTAAATT
1 ATTAAATT
34932795 AATTAAAATT
1 -ATT-AAATT
34932805 ATTAA
1 ATTAA
34932810 TTTTTTTGAC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
6 2 0.05
7 6 0.14
8 18 0.42
9 12 0.28
10 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
ATTAAATT
Found at i:34935574 original size:20 final size:22
Alignment explanation
Indices: 34935546--34935591 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
34935536 TATTGTTCTC
*
34935546 TAAACTTATAATAC-T-AAATA
1 TAAAATTATAATACATAAAATA
34935566 TAAAATTATAATACATAAAATA
1 TAAAATTATAATACATAAAATA
34935588 TAAA
1 TAAA
34935592 TAATTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.57
21 1 0.04
22 9 0.39
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATTATAATACATAAAATA
Found at i:34936031 original size:26 final size:25
Alignment explanation
Indices: 34935995--34936044 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
34935985 TATATAAGCA
*
34935995 AATAGTATAAAAAAATAAATAAAAAT
1 AATAATATAAAAAAA-AAATAAAAAT
**
34936021 AATAATATAAATTAAAAATAAAAA
1 AATAATATAAAAAAAAAATAAAAA
34936045 AATTTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (25 bp):
AATAATATAAAAAAAAAATAAAAAT
Found at i:34936040 original size:16 final size:15
Alignment explanation
Indices: 34936005--34936054 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
34935995 AATAGTATAA
34936005 AAAAATAAATAAA--
1 AAAAATAAATAAATT
*
34936018 AATAATAATATAAATT
1 AAAAATAA-ATAAATT
*
34936034 AAAAATAAAAAAATT
1 AAAAATAAATAAATT
*
34936049 TAAAAT
1 AAAAAT
34936055 TGAATGAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 7 0.23
14 5 0.17
15 11 0.37
16 7 0.23
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATAAATAAATT
Found at i:34943637 original size:20 final size:20
Alignment explanation
Indices: 34943612--34943651 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
34943602 TCTCAGTGTG
* *
34943612 CAGTTTGGTTGTTGTGACTT
1 CAGTTTAGTTGTTGTCACTT
*
34943632 CAGTTTAGTTTTTGTCACTT
1 CAGTTTAGTTGTTGTCACTT
34943652 GGTCCTTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.53
Consensus pattern (20 bp):
CAGTTTAGTTGTTGTCACTT
Found at i:34965976 original size:3 final size:3
Alignment explanation
Indices: 34965968--34965996 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
34965958 AAAAAATGGA
34965968 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
34965997 AATGAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34982386 original size:224 final size:220
Alignment explanation
Indices: 34981996--34982436 Score: 828
Period size: 224 Copynumber: 2.0 Consensus size: 220
34981986 ACTCAAATAC
34981996 CTTCATACCCAAGCCTGCGAAGCATTTTTGATACGATAGTAAGACAGGTTGAATCACCATCTACA
1 CTTCATACCCAAGCCTGCGAAGCATTTTTGATACGATAGTAAGACAGGTTGAATCACCATCTACA
34982061 AGCAAAACTGTAACACCTGCACATGCAGTATTTATGCTGGATTCAACTGAGATAGCCATCTCGCT
66 AGCAAAACTGTAACACCTGCACATGCAGTATTTATGCTGGATTCAACTGAGATAGCCATCTCGCT
*
34982126 ATTCATGTGGATGGGCAAGAATGATGTTATCAAGTTCAAGCTCACAAAGAGAGAGAGAGAGAGAG
131 ATTCATGTGGATGGGCAAGAATGATGTTATCAAGTTCAAGCACACAAAGAGAGAGAGAGAGAGA-
*
34982191 GAGGGGGGAGGGGGGGAGGGAGAGAGAG
195 GAGAGGGG-GGGGGGGAGGG-GAGAGAG
34982219 NCTTCATACCCAAGCCTGCGAAGCATTTTTGATACGATAGTAAGACAGGTTGAATCACCATCTAC
1 -CTTCATACCCAAGCCTGCGAAGCATTTTTGATACGATAGTAAGACAGGTTGAATCACCATCTAC
34982284 AAGCAAAACTGTAACACCTGCACATGCAGTATTTATGCTGGATTCAACTGAGATAGCCATCTCGC
65 AAGCAAAACTGTAACACCTGCACATGCAGTATTTATGCTGGATTCAACTGAGATAGCCATCTCGC
34982349 TATTCATGTGGATGGGCAAGAATGATGTTATCAAGTTCAAGCACACAAAGAGAGAGAGAGAGAGA
130 TATTCATGTGGATGGGCAAGAATGATGTTATCAAGTTCAAGCACACAAAGAGAGAGAGAGAGAGA
34982414 GAGAGGGGGGGGGGGAGGGGAGA
195 GAGAGGGGGGGGGGGAGGGGAGA
34982437 AGAGAAGCTT
Statistics
Matches: 215, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
221 4 0.02
222 11 0.05
223 7 0.03
224 193 0.90
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (220 bp):
CTTCATACCCAAGCCTGCGAAGCATTTTTGATACGATAGTAAGACAGGTTGAATCACCATCTACA
AGCAAAACTGTAACACCTGCACATGCAGTATTTATGCTGGATTCAACTGAGATAGCCATCTCGCT
ATTCATGTGGATGGGCAAGAATGATGTTATCAAGTTCAAGCACACAAAGAGAGAGAGAGAGAGAG
AGAGGGGGGGGGGGAGGGGAGAGAG
Found at i:34985676 original size:17 final size:17
Alignment explanation
Indices: 34985635--34985676 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
34985625 GCACATTATA
34985635 TATATATACATATATTT
1 TATATATACATATATTT
* *
34985652 AATTTATACATA-ATTT
1 TATATATACATATATTT
34985668 GTATATATA
1 -TATATATA
34985677 TTTTATAATG
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (17 bp):
TATATATACATATATTT
Found at i:34989167 original size:21 final size:22
Alignment explanation
Indices: 34989127--34989169 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
34989117 GTCGTTTCCG
*
34989127 ATCTGATTTCTTACATAATTTA
1 ATCTGATTTCTTACAAAATTTA
34989149 ATCTGATTT-TTACAAAATTTA
1 ATCTGATTTCTTACAAAATTTA
34989170 CAAGCATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (22 bp):
ATCTGATTTCTTACAAAATTTA
Found at i:34992566 original size:28 final size:28
Alignment explanation
Indices: 34992521--34992587 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
34992511 TAAATTGAAT
* * *
34992521 AATAAAAATATGTTAATAAATTATATCA
1 AATATAAATAAGTAAATAAATTATATCA
34992549 AATATAAATAAGTAAATAAATTATATCA
1 AATATAAATAAGTAAATAAATTATATCA
*
34992577 AACATAAATAA
1 AATATAAATAA
34992588 AATTTTAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (28 bp):
AATATAAATAAGTAAATAAATTATATCA
Found at i:34994061 original size:26 final size:26
Alignment explanation
Indices: 34994025--34994076 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
34994015 GGGCCATAAT
34994025 TTTTAAAATTTTTTATTTATTATATA
1 TTTTAAAATTTTTTATTTATTATATA
*
34994051 TTTTAACATTTTTTATTTATTATATA
1 TTTTAAAATTTTTTATTTATTATATA
34994077 CATCTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTAAAATTTTTTATTTATTATATA
Found at i:34994066 original size:19 final size:20
Alignment explanation
Indices: 34994039--34994085 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
34994029 AAAATTTTTT
* *
34994039 ATTTATTATATATTTTA-AC
1 ATTTTTTATATATTATATAC
*
34994058 ATTTTTTATTTATTATATAC
1 ATTTTTTATATATTATATAC
*
34994078 ATCTTTTA
1 ATTTTTTA
34994086 AATGATTCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTTATATATTATATAC
Found at i:34994394 original size:6 final size:7
Alignment explanation
Indices: 34994376--34994400 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34994366 AAAAAGTATA
34994376 ATTTTTT
1 ATTTTTT
34994383 ATTTTTT
1 ATTTTTT
34994390 ATTTTTT
1 ATTTTTT
34994397 ATTT
1 ATTT
34994401 ACATTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
ATTTTTT
Found at i:34994424 original size:16 final size:17
Alignment explanation
Indices: 34994395--34994433 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
34994385 TTTTTATTTT
34994395 TTATTTACATTATTTAA
1 TTATTTACATTATTTAA
*
34994412 TTATTTATA-TATTTAA
1 TTATTTACATTATTTAA
*
34994428 TCATTT
1 TTATTT
34994434 TATGAATTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTTACATTATTTAA
Found at i:34994500 original size:20 final size:23
Alignment explanation
Indices: 34994462--34994507 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
34994452 ATATTTAACT
34994462 TTTTATACTTTATGTATTGT-AG
1 TTTTATACTTTATGTATTGTAAG
34994484 TTTTATA-TTTA-GTATTGTAAG
1 TTTTATACTTTATGTATTGTAAG
34994505 TTT
1 TTT
34994508 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.30
21 9 0.39
22 7 0.30
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.61
Consensus pattern (23 bp):
TTTTATACTTTATGTATTGTAAG
Found at i:34995437 original size:18 final size:20
Alignment explanation
Indices: 34995395--34995440 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
34995385 TAGTTATAAA
*
34995395 AATTTATTTAAATAATTTAT
1 AATTTTTTTAAATAATTTAT
*
34995415 GATTTTTTTAAAT-A-TTAT
1 AATTTTTTTAAATAATTTAT
34995433 AATTTTTT
1 AATTTTTT
34995441 AATTGATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
AATTTTTTTAAATAATTTAT
Found at i:34995440 original size:17 final size:20
Alignment explanation
Indices: 34995395--34995442 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 20
34995385 TAGTTATAAA
34995395 AATTTATTTAAATAATTTATG
1 AATTT-TTTAAATAATTTATG
*
34995416 ATTTTTTTAAAT-A-TTAT-
1 AATTTTTTAAATAATTTATG
34995433 AATTTTTTAA
1 AATTTTTTAA
34995443 TTGATGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 9 0.36
18 4 0.16
19 1 0.04
20 7 0.28
21 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
AATTTTTTAAATAATTTATG
Found at i:35003766 original size:35 final size:35
Alignment explanation
Indices: 35003725--35003791 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
35003715 AGGACTGTGA
*
35003725 TTGTAAAACATTTACCACATCTTGAATGTGGAGTT
1 TTGTAAAACATATACCACATCTTGAATGTGGAGTT
* **
35003760 TTGTAAAACATATCCCATGTCTTGAATGTGGA
1 TTGTAAAACATATACCACATCTTGAATGTGGA
35003792 TAATAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (35 bp):
TTGTAAAACATATACCACATCTTGAATGTGGAGTT
Found at i:35005772 original size:16 final size:16
Alignment explanation
Indices: 35005747--35005778 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35005737 AAGCATGTGG
*
35005747 CATGCTAGCCACCAAA
1 CATGCCAGCCACCAAA
35005763 CATGCCAGCCACCAAA
1 CATGCCAGCCACCAAA
35005779 AGATCATCTA
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:0.38, C:0.41, G:0.12, T:0.09
Consensus pattern (16 bp):
CATGCCAGCCACCAAA
Found at i:35043212 original size:2 final size:2
Alignment explanation
Indices: 35043205--35043247 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
35043195 AGAAAGAATA
35043205 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35043246 AT
1 AT
35043248 GACNNNNNNN
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35043270 original size:2 final size:2
Alignment explanation
Indices: 35043263--35043303 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35043253 NNNNNNNNNN
35043263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35043304 CCCTAAATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35051483 original size:57 final size:57
Alignment explanation
Indices: 35051387--35051526 Score: 208
Period size: 57 Copynumber: 2.5 Consensus size: 57
35051377 GGAGTGTAGC
* *
35051387 TGAGAATTACTTTCAGGAGGAGGGTATCGTGCAGGTTGTTGATAAGAGGAAGATACT
1 TGAGAATTACTTTCAGGAGGAGGGTATCGTGCAGATTGTTGATAAGACGAAGATACT
* * *
35051444 TGTGAGTTACTTTCAGGAGGAGGGTATTGTGCAGATTGTTGATAAGACGAAGATACT
1 TGAGAATTACTTTCAGGAGGAGGGTATCGTGCAGATTGTTGATAAGACGAAGATACT
* * *
35051501 TGAGAATCACTCTCAGGAGGTGGGTA
1 TGAGAATTACTTTCAGGAGGAGGGTA
35051527 ATGTCCTGGT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 73 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (57 bp):
TGAGAATTACTTTCAGGAGGAGGGTATCGTGCAGATTGTTGATAAGACGAAGATACT
Found at i:35056254 original size:2 final size:2
Alignment explanation
Indices: 35056247--35056293 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
35056237 CTATGTTCAA
*
35056247 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35056288 A- AT AT A
1 AT AT AT A
35056294 AAATTAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:35084619 original size:2 final size:2
Alignment explanation
Indices: 35084612--35084636 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35084602 AGATTATTCT
35084612 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
35084637 TCAAATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35084839 original size:18 final size:21
Alignment explanation
Indices: 35084816--35084860 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 21
35084806 TTAGTAAAAA
*
35084816 AATATTT-TTAATTT-TAA-T
1 AATATTTAATAATTTATAATT
35084834 AATATTTAATAATTTATAATT
1 AATATTTAATAATTTATAATT
35084855 AATATT
1 AATATT
35084861 ACAAAATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 6 0.26
20 3 0.13
21 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATATTTAATAATTTATAATT
Found at i:35088779 original size:6 final size:6
Alignment explanation
Indices: 35088768--35088797 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
35088758 GGTGAACATA
35088768 CAGGTT CAGGTT CAGGTT CAGGTT CAGGTT
1 CAGGTT CAGGTT CAGGTT CAGGTT CAGGTT
35088798 GTTGAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
CAGGTT
Found at i:35097594 original size:2 final size:2
Alignment explanation
Indices: 35097589--35097618 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35097579 CTTAGTATGC
35097589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35097619 TTAATGGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35097840 original size:33 final size:33
Alignment explanation
Indices: 35097779--35097849 Score: 76
Period size: 34 Copynumber: 2.1 Consensus size: 33
35097769 AATTGTTAAT
35097779 TAAAAATTTATTGTAATTT-AAAATAAAAACATA
1 TAAAAATTTATTG-AATTTAAAAATAAAAACATA
*
35097812 TAAAAATTTAATTG-ATTGTAATAAA-AAAAACATT
1 TAAAAATTT-ATTGAATT-TAA-AAATAAAAACATA
35097846 TAAA
1 TAAA
35097850 TTTTTATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
32 3 0.09
33 10 0.30
34 17 0.52
35 3 0.09
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (33 bp):
TAAAAATTTATTGAATTTAAAAATAAAAACATA
Found at i:35099488 original size:24 final size:23
Alignment explanation
Indices: 35099471--35099519 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
35099461 AAAACAAGTC
35099471 GAAAAGAAAAAAGAAAAAAAAGA
1 GAAAAGAAAAAAGAAAAAAAAGA
*
35099494 GAAAAAAAAAAAGAAAAGAAAAGA
1 GAAAAGAAAAAAGAAAA-AAAAGA
35099518 GA
1 GA
35099520 CGTCAGTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
GAAAAGAAAAAAGAAAAAAAAGA
Found at i:35099499 original size:12 final size:12
Alignment explanation
Indices: 35099471--35099519 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
35099461 AAAACAAGTC
35099471 GAAAAGAAAAA-A
1 GAAAA-AAAAAGA
35099483 G-AAAAAAAAGA
1 GAAAAAAAAAGA
*
35099494 GAAAAAAAAAAA
1 GAAAAAAAAAGA
*
35099506 GAAAAGAAAAGA
1 GAAAAAAAAAGA
35099518 GA
1 GA
35099520 CGTCAGTACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 5 0.16
11 5 0.16
12 22 0.69
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAGA
Found at i:35105210 original size:19 final size:20
Alignment explanation
Indices: 35105168--35105210 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
35105158 CCATAATTAG
* *
35105168 TGTCTTTCACAACGTCCGGG
1 TGTCTTTCACAACGTCCCGA
35105188 TGTCTTT-ACAACGTCCCGA
1 TGTCTTTCACAACGTCCCGA
35105207 TGTC
1 TGTC
35105211 AAATAGAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.16, C:0.30, G:0.21, T:0.33
Consensus pattern (20 bp):
TGTCTTTCACAACGTCCCGA
Found at i:35116155 original size:45 final size:44
Alignment explanation
Indices: 35116100--35116184 Score: 143
Period size: 45 Copynumber: 1.9 Consensus size: 44
35116090 GTTCAGAATA
35116100 TTGTAATATAAAATTCAATTATTTACAAAATCATGTAATTATGT
1 TTGTAATATAAAATTCAATTATTTACAAAATCATGTAATTATGT
**
35116144 TTGTCAATATAAAATTTGATTATTTACAAAATCATGTAATT
1 TTGT-AATATAAAATTCAATTATTTACAAAATCATGTAATT
35116185 TTTTTTTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 4 0.11
45 34 0.89
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (44 bp):
TTGTAATATAAAATTCAATTATTTACAAAATCATGTAATTATGT
Found at i:35122428 original size:12 final size:12
Alignment explanation
Indices: 35122411--35122435 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35122401 GCTCCTTTGT
35122411 TCTCTCTCTTTC
1 TCTCTCTCTTTC
35122423 TCTCTCTCTTTC
1 TCTCTCTCTTTC
35122435 T
1 T
35122436 TTTTTTCTTG
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:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (12 bp):
TCTCTCTCTTTC
Found at i:35146547 original size:86 final size:86
Alignment explanation
Indices: 35146402--35146579 Score: 311
Period size: 86 Copynumber: 2.1 Consensus size: 86
35146392 TTAAAACAAG
* **
35146402 AAATTCAGTAAGTCTTCCTTGTTACTCAATGAGATCACTCATTGACTACTGGGGTAAGTAAGGGT
1 AAATTCAGTAAGTCTTCCTTGTTAATCAATGAGATCACTCATCAACTACTGGGGTAAGTAAGGGT
35146467 TTATTTGAGAAGAAAGCTTCA
66 TTATTTGAGAAGAAAGCTTCA
* *
35146488 AAATTCAGTAATTCTTCCTTGTTAATCAATGAGATCATTCATCAACTACTGGGGTAAGTAAGGGT
1 AAATTCAGTAAGTCTTCCTTGTTAATCAATGAGATCACTCATCAACTACTGGGGTAAGTAAGGGT
35146553 TTATTTGAGAAGAAAGCTTCA
66 TTATTTGAGAAGAAAGCTTCA
35146574 AAATTC
1 AAATTC
35146580 CCCACCACAA
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (86 bp):
AAATTCAGTAAGTCTTCCTTGTTAATCAATGAGATCACTCATCAACTACTGGGGTAAGTAAGGGT
TTATTTGAGAAGAAAGCTTCA
Found at i:35151731 original size:3 final size:3
Alignment explanation
Indices: 35151725--35151749 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35151715 GAGATGGTGG
35151725 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
35151750 AAATGAGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:35155132 original size:15 final size:15
Alignment explanation
Indices: 35155108--35155140 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35155098 TTCTTTACAC
*
35155108 AAAGCTAAAAGCCCT
1 AAAGCCAAAAGCCCT
35155123 AAAGCCAAAAGCCCT
1 AAAGCCAAAAGCCCT
35155138 AAA
1 AAA
35155141 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.27, G:0.12, T:0.09
Consensus pattern (15 bp):
AAAGCCAAAAGCCCT
Found at i:35159600 original size:6 final size:6
Alignment explanation
Indices: 35159586--35159616 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
35159576 ATGACGAGCG
*
35159586 GTTGTT GTTGCT GTTGCT GTTGCT GTTGCT G
1 GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT G
35159617 CGGTTGCGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.13, G:0.35, T:0.52
Consensus pattern (6 bp):
GTTGCT
Found at i:35160429 original size:30 final size:29
Alignment explanation
Indices: 35160377--35160442 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
35160367 AAATTATTCT
35160377 TTTATTATATTCAATCAAATTTTTATATA
1 TTTATTATATTCAATCAAATTTTTATATA
*
35160406 TTTATTTTATATCAAAT-AAATTTTTATA-A
1 TTTATTATAT-TC-AATCAAATTTTTATATA
*
35160435 TTAATTAT
1 TTTATTAT
35160443 CATTAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 16 0.50
30 13 0.41
31 3 0.09
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTATTATATTCAATCAAATTTTTATATA
Found at i:35164225 original size:30 final size:30
Alignment explanation
Indices: 35164132--35164232 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 30
35164122 CCCCCCACCT
35164132 AAATTTTTTATAACATATTTTTAT-TTTCTTA
1 AAATTTTTT-TAACATATTTTTATATTT-TTA
* * *
35164163 AAA-TTATATAATTCA-ATTTTTACAAAATTTTTA
1 AAATTTTTTTAA--CATATTTTT---ATATTTTTA
35164196 AAATTTTTTTAACATATTTTTATATTTTTA
1 AAATTTTTTTAACATATTTTTATATTTTTA
35164226 AAATTTT
1 AAATTTT
35164233 ATAATTTCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
29 3 0.05
30 24 0.43
31 5 0.09
32 2 0.04
33 13 0.23
34 9 0.16
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (30 bp):
AAATTTTTTTAACATATTTTTATATTTTTA
Found at i:35164249 original size:63 final size:65
Alignment explanation
Indices: 35164132--35164260 Score: 169
Period size: 63 Copynumber: 2.0 Consensus size: 65
35164122 CCCCCCACCT
*
35164132 AAATTTTTTATAACATATTTTTATTTTCTTAAAATTATATAATTCAATTTTTAC-A-AAATTTTT
1 AAATTTTTTATAACATATTTTTATTTTCTTAAAATTATATAATTCAA-TCTTACAATAAATTTTT
35164195 A
65 A
*
35164196 AAATTTTTT-TAACATATTTTTATATTT-TTAAAATTTTATAATTTCACA-CTTACAATAAATTT
1 AAATTTTTTATAACATATTTTTAT-TTTCTTAAAATTATATAA-TTCA-ATCTTACAATAAATTT
35164258 TTA
63 TTA
35164261 TTTGGTGAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
63 31 0.53
64 17 0.29
65 10 0.17
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (65 bp):
AAATTTTTTATAACATATTTTTATTTTCTTAAAATTATATAATTCAATCTTACAATAAATTTTTA
Found at i:35164570 original size:13 final size:12
Alignment explanation
Indices: 35164525--35164581 Score: 57
Period size: 13 Copynumber: 4.8 Consensus size: 12
35164515 GTTTATTGAC
35164525 TTATT-TTATTT
1 TTATTATTATTT
*
35164536 TTAATATT-TTT
1 TTATTATTATTT
35164547 TAATATT-TTATTT
1 T--TATTATTATTT
35164560 TTATTTATTATTT
1 TTA-TTATTATTT
35164573 TTATTATTA
1 TTATTATTA
35164582 AATTATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
11 10 0.26
12 12 0.32
13 16 0.42
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:35164577 original size:9 final size:9
Alignment explanation
Indices: 35164530--35164580 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
35164520 TTGACTTATT
35164530 TTATTTTTA
1 TTATTTTTA
*
35164539 ATATTTTT-
1 TTATTTTTA
*
35164547 TAATATTTTA
1 TTAT-TTTTA
*
35164557 TTTTTATTTA
1 TTATT-TTTA
35164567 TTATTTTTA
1 TTATTTTTA
35164576 TTATT
1 TTATT
35164581 AAATTATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
8 2 0.06
9 21 0.64
10 10 0.30
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTATTTTTA
Found at i:35164577 original size:24 final size:22
Alignment explanation
Indices: 35164525--35164577 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 22
35164515 GTTTATTGAC
35164525 TTATTTTATTTTTAATATTTTT
1 TTATTTTATTTTTAATATTTTT
*
35164547 TAATATTTTATTTTTATTTATTATTT
1 T--TATTTTATTTTTA-ATATT-TTT
35164573 TTATT
1 TTATT
35164578 ATTAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.04
24 17 0.65
25 4 0.15
26 4 0.15
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (22 bp):
TTATTTTATTTTTAATATTTTT
Found at i:35164587 original size:24 final size:24
Alignment explanation
Indices: 35164560--35164609 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
35164550 TATTTTATTT
* *
35164560 TTATTTATTATTTTTATT-ATTAAA
1 TTATTTA-TAATTATATTAATTAAA
35164584 TTATTTATAATTATATTAATTAAA
1 TTATTTATAATTATATTAATTAAA
35164608 TT
1 TT
35164610 TTAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTATTTATAATTATATTAATTAAA
Found at i:35164617 original size:24 final size:23
Alignment explanation
Indices: 35164574--35164644 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 23
35164564 TTATTATTTT
*
35164574 TATT-ATTAAATTATTTATAATTA
1 TATTAATTAAATT-TTAATAATTA
35164597 TATTAATTAAATTTTAAATAAATTA
1 TATTAATTAAATTTT-AAT-AATTA
* *
35164622 T-TAAAATTAATTTTTTAATAATT
1 TAT-TAATTAA-ATTTTAATAATT
35164645 TTTAGAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
23 6 0.15
24 15 0.38
25 15 0.38
26 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTAATTAAATTTTAATAATTA
Found at i:35164653 original size:24 final size:23
Alignment explanation
Indices: 35164601--35164670 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 23
35164591 TAATTATATT
* *
35164601 AATTAAATTTTAAATAAATTATTAA
1 AATT-AATTTTTAAT-AATTTTTAA
*
35164626 AATTAATTTTTTAATAATTTTTAG
1 AATTAA-TTTTTAATAATTTTTAA
* *
35164650 AATTTATTTATAA-AATTTTTA
1 AATTAATTTTTAATAATTTTTA
35164671 TATGAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 8 0.21
23 6 0.15
24 14 0.36
25 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (23 bp):
AATTAATTTTTAATAATTTTTAA
Done.