Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 191 of 211
Found at i:59160373 original size:175 final size:170
Alignment explanation
Indices: 59159686--59160518 Score: 1319
Period size: 170 Copynumber: 4.8 Consensus size: 170
59159676 GCTAGATATA
* * *
59159686 TTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGAC-ACT-ATCCTATCTCTCTGAGATTACAG
1 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-CTAGTAATCCTATCTCCCTGAGATTACAG
* * *
59159749 TGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGGTCTTATC
65 TGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATT
* * * *
59159814 TCCCTAAGATTACAGTGGAGCAGACCGAAGAAATACAGATC
130 TCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATC
* ** *
59159855 TTATCTCCTTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCCTGAGATTACAGT
1 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
*
59159920 GGAGCGGATTAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATTT
66 GGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATTT
59159985 CCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATC
131 CCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATC
59160025 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
1 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
*
59160090 GGAGCAGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATTT
66 GGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATTT
* * *
59160155 TCTTGAGATTACAGTGGAACAGACCGAAAAATTTCAGATC
131 CCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATC
*
59160195 TTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
1 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
*
59160260 GGAGCGGATTAAAACCAAGGATCTTATCTCTCTGAATTTACAGTAGAGTAGATCGCATCAGGTCT
66 GGAGCGGATT---A--AAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCT
*
59160325 TATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAAATC
126 TATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATC
* *
59160370 TTATCTCCCTGAGATTACAGCGGAACAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAGT
1 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
*
59160435 GGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCT
66 GGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCT
*
59160500 TATCTCCCTGAGATTACAG
126 TATTTCCCTGAGATTACAG
59160519 CAGAGCAGAT
Statistics
Matches: 617, Mismatches: 35, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
169 35 0.06
170 354 0.57
173 1 0.00
175 224 0.36
176 1 0.00
177 1 0.00
180 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (170 bp):
TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
GGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATTT
CCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATC
Found at i:59160528 original size:129 final size:129
Alignment explanation
Indices: 59160368--59160647 Score: 497
Period size: 129 Copynumber: 2.2 Consensus size: 129
59160358 GAATTTCAAA
* *
59160368 TCTTATCTCCCTGAGATTACAGCGGAACAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCAGAACAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
* *
59160433 GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGG
66 GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGG
*
59160497 TCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCAGAACAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
59160562 GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGG
66 GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGG
* *
59160626 TCTTATGTCCCTGAGGTTACAG
1 TCTTATCTCCCTGAGATTACAG
59160648 TGGAGTAGAC
Statistics
Matches: 144, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 144 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (129 bp):
TCTTATCTCCCTGAGATTACAGCAGAACAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
GTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGG
Found at i:59160736 original size:44 final size:44
Alignment explanation
Indices: 59160671--59160918 Score: 197
Period size: 44 Copynumber: 5.7 Consensus size: 44
59160661 AGAATTTCAG
* *
59160671 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGAAACCGA
1 ATCTCATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGACACCGA
* * ** *
59160715 ATCTCATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACC-A
1 ATCTCATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGACACCGA
* * * **
59160758 GTC-CTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAG--ATGGTA
1 ATCTC-ATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGACACCG-A
**
59160801 GATC-CTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGACGGCGA
1 -ATCTC-ATCTCCCTAAGCAGTAGTGGAGCAGAT-GAAAGACACCGA
* * ** *
59160846 ATCTCATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACC--
1 ATCTCATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGACACCGA
* *
59160888 AGCCCTATCTCCCTAAGCAGTAGTGGAGCAG
1 ATCTC-ATCTCCCTAAGCAGTAGTGGAGCAG
59160919 GTCGAAGATT
Statistics
Matches: 163, Mismatches: 31, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
41 1 0.01
42 4 0.02
43 54 0.33
44 101 0.62
45 2 0.01
46 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (44 bp):
ATCTCATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGACACCGA
Found at i:59160823 original size:131 final size:131
Alignment explanation
Indices: 59160669--59160944 Score: 473
Period size: 131 Copynumber: 2.1 Consensus size: 131
59160659 GAAGAATTTC
59160669 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT-GAAAGAAACCGAATCTCATCTTCCTAAGCA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGAAACCGAATCTCATCTTCCTAAGCA
*
59160733 GTAGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATG
65 GTAGTGAAGCAGATTTAAGCCACCAGCCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATG
59160798 GT
130 GT
* ***
59160800 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTCATCTTCCTAAGCAG
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAAACCGAATCTCATCTTCCTAAGCAG
* *
59160865 TAGTGAAGCAGATTTAAGCCACCAGCCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATTG
66 TAGTGAAGCAGATTTAAGCCACCAGCCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGG
59160930 T
131 T
59160931 AGATCTTATCTCCC
1 AGATCTTATCTCCC
59160945 GATCACACCT
Statistics
Matches: 136, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
131 135 0.99
132 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (131 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAAACCGAATCTCATCTTCCTAAGCAG
TAGTGAAGCAGATTTAAGCCACCAGCCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGG
T
Found at i:59160943 original size:44 final size:44
Alignment explanation
Indices: 59160669--59160944 Score: 190
Period size: 44 Copynumber: 6.3 Consensus size: 44
59160659 GAAGAATTTC
* *
59160669 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT-GAAAGAAACCG-
1 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGATA--GT
* * ** ** **
59160714 A-AT-CTCATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACC
1 AGATCCT-ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGT
* * *
59160757 AG-TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGT
1 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGT
* *
59160800 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CGG
1 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGT
* * * ** ** **
59160843 CGAAT-CTCATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACC
1 AG-ATCCT-ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGT
* * *
59160888 AG-CCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATTGT
1 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGT
*
59160931 AGATCTTATCTCCC
1 AGATCCTATCTCCC
59160945 GATCACACCT
Statistics
Matches: 176, Mismatches: 44, Indels: 23
0.72 0.18 0.09
Matches are distributed among these distances:
43 65 0.37
44 109 0.62
45 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (44 bp):
AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGT
Found at i:59164234 original size:16 final size:16
Alignment explanation
Indices: 59164179--59164234 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
59164169 AAAAGTTAAC
*
59164179 AACCCATACCCAAAAT
1 AACCCAAACCCAAAAT
** *
59164195 AACCTGAACCTGAAAA-
1 AACCCAAACC-CAAAAT
*
59164211 AACACAAACCCAAAAT
1 AACCCAAACCCAAAAT
59164227 AACCCAAA
1 AACCCAAA
59164235 GAGGTAATCC
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 4 0.14
16 21 0.72
17 4 0.14
ACGTcount: A:0.55, C:0.32, G:0.04, T:0.09
Consensus pattern (16 bp):
AACCCAAACCCAAAAT
Found at i:59171653 original size:21 final size:22
Alignment explanation
Indices: 59171623--59171667 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
59171613 GAACAAATTG
59171623 TTGATTCTATTTCTTTCTTG-AT
1 TTGATTCTA-TTCTTTCTTGTAT
*
59171645 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCTTTCTTGTAT
59171666 TT
1 TT
59171668 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCTTTCTTGTAT
Found at i:59175766 original size:21 final size:22
Alignment explanation
Indices: 59175742--59175786 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
59175732 AGAAAAAGAG
59175742 AAATACAAAAAAG-AATAG-ATC
1 AAAT-CAAAAAAGAAATAGAATC
*
59175763 AAATCAAGAAAGAAATAGAATC
1 AAATCAAAAAAGAAATAGAATC
59175785 AA
1 AA
59175787 CAATTTGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (22 bp):
AAATCAAAAAAGAAATAGAATC
Found at i:59178569 original size:35 final size:34
Alignment explanation
Indices: 59178523--59178719 Score: 250
Period size: 35 Copynumber: 5.7 Consensus size: 34
59178513 AAATGATACA
59178523 TGAACAGGAGAGATTCCCTGCAACAACATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAA-ATAATGCG
*
59178558 TGAACAGGAGAGATTCCCAGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAAC-AAATAATGCG
* * * *
59178593 TGAACAGGAGAGATTCCTTGCAAGAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAACAAATAATGCG
*
59178627 TGAACAGGAGAAGATTTCCTGCAACAAAATAATGCG
1 TGAACAGGAG-AGATTCCCTGCAAC-AAATAATGCG
* * * * *
59178663 TGGACATGAGAGATTCCCTGCAAGAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAACAAATAATGCG
*
59178697 TGAATAGGAGAGATTCCCTGCAA
1 TGAACAGGAGAGATTCCCTGCAA
59178720 TGCGTGAACA
Statistics
Matches: 139, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
34 46 0.33
35 75 0.54
36 18 0.13
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (34 bp):
TGAACAGGAGAGATTCCCTGCAACAAATAATGCG
Found at i:59178642 original size:70 final size:69
Alignment explanation
Indices: 59178523--59178719 Score: 295
Period size: 70 Copynumber: 2.8 Consensus size: 69
59178513 AAATGATACA
* * * *
59178523 TGAACAGGAGAGATTCCCTGCAACAACATAATGCGTGAACAGGAGAGATTCCCAGCAACAAAATA
1 TGAACAGGAGAGATTCCCTGCAAGAA-ATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
59178588 ATGCG
65 ATGCG
* *
59178593 TGAACAGGAGAGATTCCTTGCAAGAAATGATGTGTGAACAGGAGAAGATTTCCTGCAACAAAATA
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAG-AGATTCCCTGCAACAAAATA
59178658 ATGCG
65 ATGCG
* * *
59178663 TGGACATGAGAGATTCCCTGCAAGAAATGATGTGTGAATAGGAGAGATTCCCTGCAA
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGCAA
59178720 TGCGTGAACA
Statistics
Matches: 115, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
69 28 0.24
70 87 0.76
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (69 bp):
TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAA
TGCG
Found at i:59179026 original size:13 final size:13
Alignment explanation
Indices: 59179008--59179045 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
59178998 AGTTTCCAAA
59179008 TTTTCAAATTAAG
1 TTTTCAAATTAAG
59179021 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
*
59179035 CTTTCAAATTA
1 TTTTCAAATTA
59179046 CAAATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:59182588 original size:20 final size:20
Alignment explanation
Indices: 59182556--59182603 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
59182546 CCTGCCACGG
59182556 CCGCCAACGTCACG-CCGCCA
1 CCGCC-ACGTCACGTCCGCCA
*
59182576 CCGCCACGATCACGTCGGCCA
1 CCGCCACG-TCACGTCCGCCA
*
59182597 CCCCCAC
1 CCGCCAC
59182604 TTGCGCCGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.19, C:0.56, G:0.19, T:0.06
Consensus pattern (20 bp):
CCGCCACGTCACGTCCGCCA
Found at i:59183695 original size:8 final size:7
Alignment explanation
Indices: 59183668--59183693 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
59183658 TATATTTAAA
59183668 AAAAATC
1 AAAAATC
59183675 AAAAATC
1 AAAAATC
59183682 AAAAATC
1 AAAAATC
59183689 AAAAA
1 AAAAA
59183694 ATACATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATC
Found at i:59183733 original size:29 final size:29
Alignment explanation
Indices: 59183695--59183767 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
59183685 AATCAAAAAA
*
59183695 TACATTTTGACCCCTGAACTTTTTGAAAT
1 TACATTTTGACCCCTCAACTTTTTGAAAT
59183724 TACATTTTGACCCAC-CAACTTTTTGAAAT
1 TACATTTTGACCC-CTCAACTTTTTGAAAT
*
59183753 TATATTTTGACCCCT
1 TACATTTTGACCCCT
59183768 AAAGTTTCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 1 0.03
29 38 0.95
30 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.41
Consensus pattern (29 bp):
TACATTTTGACCCCTCAACTTTTTGAAAT
Found at i:59184038 original size:10 final size:10
Alignment explanation
Indices: 59184023--59184067 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
59184013 TTTTTCGGAA
59184023 AAAAGAGAAG
1 AAAAGAGAAG
*
59184033 AAAAGAGGAG
1 AAAAGAGAAG
59184043 AAAAGAGAA-
1 AAAAGAGAAG
* *
59184052 AGAGGAGAAG
1 AAAAGAGAAG
59184062 AAAAGA
1 AAAAGA
59184068 AGGAGTACCG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (10 bp):
AAAAGAGAAG
Found at i:59184055 original size:16 final size:15
Alignment explanation
Indices: 59184030--59184072 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
59184020 GAAAAAAGAG
59184030 AAGAAAAGAGGAGAA
1 AAGAAAAGAGGAGAA
59184045 AAGAGAAAGAGGAG--
1 AAGA-AAAGAGGAGAA
59184059 AAGAAAAGAAGGAG
1 AAGAAAAG-AGGAG
59184073 TACCGGCGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.15
14 9 0.35
15 4 0.15
16 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAGGAGAA
Found at i:59184281 original size:20 final size:20
Alignment explanation
Indices: 59184252--59184302 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
59184242 CAGCCCAAAA
* *
59184252 CAAAAACAAAAAGAAAATGG
1 CAAAAACAAAAAAAAAAGGG
*
59184272 CAAAAGCAAAAAAAAAAGGG
1 CAAAAACAAAAAAAAAAGGG
59184292 CAGAAAA-AAAA
1 CA-AAAACAAAA
59184303 CATCCCATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.73, C:0.10, G:0.16, T:0.02
Consensus pattern (20 bp):
CAAAAACAAAAAAAAAAGGG
Found at i:59184465 original size:13 final size:12
Alignment explanation
Indices: 59184446--59184517 Score: 72
Period size: 13 Copynumber: 5.5 Consensus size: 12
59184436 GCAGCAGGCC
59184446 AAAAAAAAGAAGAG
1 AAAAAAAAG-A-AG
59184460 AAAAAAAGAGAAAG
1 AAAAAAA-AG-AAG
*
59184474 AAAAAAAAGAAA
1 AAAAAAAAGAAG
*
59184486 AAAAGAAAAAAAG
1 AAAA-AAAAGAAG
59184499 AAAAAAAAGGAAG
1 AAAAAAAA-GAAG
59184512 AAAAAA
1 AAAAAA
59184518 GGGGTTCAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
12 10 0.20
13 21 0.41
14 16 0.31
15 4 0.08
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:59184468 original size:10 final size:10
Alignment explanation
Indices: 59184449--59184516 Score: 61
Period size: 10 Copynumber: 6.7 Consensus size: 10
59184439 GCAGGCCAAA
59184449 AAAAAGAAGAG
1 AAAAA-AAGAG
59184460 AAAAAAAGAG
1 AAAAAAAGAG
*
59184470 AAAGAAAA-AA
1 AAA-AAAAGAG
*
59184480 AAGAAAAAAAG
1 AA-AAAAAGAG
59184491 AAAAAAAGA-
1 AAAAAAAGAG
59184500 AAAAAAAG-G
1 AAAAAAAGAG
59184509 AAGAAAAA
1 AA-AAAAA
59184517 AGGGGTTCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
9 10 0.20
10 26 0.53
11 13 0.27
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:59184478 original size:29 final size:25
Alignment explanation
Indices: 59184446--59184517 Score: 92
Period size: 25 Copynumber: 2.7 Consensus size: 25
59184436 GCAGCAGGCC
59184446 AAAAAAAAGAAGAGAAAAAAAGAGAAAG
1 AAAAAAAAGAAGA-AAAAAAA-A-AAAG
59184474 AAAAAAAAGAA-AAAAAGAAAAAAAG
1 AAAAAAAAGAAGAAAAA-AAAAAAAG
59184499 AAAAAAAAGGAAGAAAAAA
1 AAAAAAAA-GAAGAAAAAA
59184518 GGGGTTCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
25 12 0.29
26 9 0.22
27 9 0.22
28 11 0.27
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (25 bp):
AAAAAAAAGAAGAAAAAAAAAAAAG
Found at i:59184488 original size:8 final size:8
Alignment explanation
Indices: 59184458--59184505 Score: 71
Period size: 8 Copynumber: 6.1 Consensus size: 8
59184448 AAAAAAGAAG
59184458 AGAAAAAA
1 AGAAAAAA
* *
59184466 AGAGAAAG
1 AGAAAAAA
59184474 A-AAAAAA
1 AGAAAAAA
59184481 AGAAAAAA
1 AGAAAAAA
59184489 AGAAAAAA
1 AGAAAAAA
59184497 AGAAAAAA
1 AGAAAAAA
59184505 A
1 A
59184506 AGGAAGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
7 5 0.14
8 30 0.86
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:59184905 original size:20 final size:21
Alignment explanation
Indices: 59184880--59184922 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
59184870 TCGGGTTTCG
59184880 AAATTTT-TCGTGTCTTCAAA
1 AAATTTTCTCGTGTCTTCAAA
*
59184900 AAATTTTCTCGTGTTTTCAAA
1 AAATTTTCTCGTGTCTTCAAA
59184921 AA
1 AA
59184923 TAAGGTAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (21 bp):
AAATTTTCTCGTGTCTTCAAA
Found at i:59185057 original size:18 final size:18
Alignment explanation
Indices: 59185027--59185207 Score: 137
Period size: 17 Copynumber: 10.3 Consensus size: 18
59185017 AAAAAATCAA
*
59185027 AAAAAATTC-GTGTTTTC
1 AAAAATTTCTGTGTTTTC
59185044 AAAAATTTCTGTG-TTTC
1 AAAAATTTCTGTGTTTTC
*
59185061 AAAAATTT-TCATGTTTTC
1 AAAAATTTCT-GTGTTTTC
59185079 AAAAA-TTCTCGTGTTTTC
1 AAAAATTTCT-GTGTTTTC
* ***
59185097 AAAAAATTC-CAATTTTC
1 AAAAATTTCTGTGTTTTC
*
59185114 AAAAATTT-TCATGTTTTC
1 AAAAATTTCT-GTGTTTTC
* *
59185132 AGAAAATTCCCGTG-TTTC
1 A-AAAATTTCTGTGTTTTC
*
59185150 AAAAA-TCCTCGTGTTTTC
1 AAAAATTTCT-GTGTTTTC
*
59185168 AAAAATTTCGGTGTTTT-
1 AAAAATTTCTGTGTTTTC
* *
59185185 GAAAATTTTTGTGTTTTC
1 AAAAATTTCTGTGTTTTC
59185203 AAAAA
1 AAAAA
59185208 AAAATCTTGT
Statistics
Matches: 131, Mismatches: 20, Indels: 25
0.74 0.11 0.14
Matches are distributed among these distances:
16 4 0.03
17 57 0.44
18 57 0.44
19 13 0.10
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (18 bp):
AAAAATTTCTGTGTTTTC
Found at i:59185060 original size:17 final size:17
Alignment explanation
Indices: 59185027--59185207 Score: 113
Period size: 18 Copynumber: 10.3 Consensus size: 17
59185017 AAAAAATCAA
*
59185027 AAAAAATTC-GTGTTTTC
1 AAAAATTTCTGTG-TTTC
59185044 AAAAATTTCTGTGTTTC
1 AAAAATTTCTGTGTTTC
59185061 AAAAATTTTCATGT-TTTC
1 AAAAA-TTTC-TGTGTTTC
59185079 AAAAA-TTCTCGTGTTTTC
1 AAAAATTTCT-GTG-TTTC
* **
59185097 AAAAAATTCCAAT-TTTC
1 -AAAAATTTCTGTGTTTC
59185114 AAAAATTTTCATGT-TTTC
1 AAAAA-TTTC-TGTGTTTC
* *
59185132 AGAAAATTCCCGTGTTTC
1 A-AAAATTTCTGTGTTTC
*
59185150 AAAAA-TCCTCGTGTTTTC
1 AAAAATTTCT-GTG-TTTC
* *
59185168 AAAAATTTCGGTGTTTT
1 AAAAATTTCTGTGTTTC
* *
59185185 GAAAATTTTTGTGTTTTC
1 AAAAATTTCTGTG-TTTC
59185203 AAAAA
1 AAAAA
59185208 AAAATCTTGT
Statistics
Matches: 130, Mismatches: 18, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.01
16 13 0.10
17 46 0.35
18 53 0.41
19 15 0.12
20 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (17 bp):
AAAAATTTCTGTGTTTC
Found at i:59185076 original size:35 final size:36
Alignment explanation
Indices: 59185037--59185207 Score: 158
Period size: 35 Copynumber: 4.8 Consensus size: 36
59185027 AAAAAATTCG
*
59185037 TGTTTTCAAAAATTTCTGTG-TTTCAAAAATTTTCA
1 TGTTTTCAAAAATTTCTGTGTTTTCAAAAATTTCCA
*
59185072 TGTTTTCAAAAA-TTCTCGTGTTTTCAAAAAATTCCA
1 TGTTTTCAAAAATTTCT-GTGTTTTCAAAAATTTCCA
* * * *
59185108 -ATTTTCAAAAATTT-TCATGTTTTCAGAAAATTCCCG
1 TGTTTTCAAAAATTTCT-GTGTTTTCA-AAAATTTCCA
* **
59185144 TG-TTTCAAAAA-TCCTCGTGTTTTCAAAAATTTCGG
1 TGTTTTCAAAAATTTCT-GTGTTTTCAAAAATTTCCA
* *
59185179 TGTTTT-GAAAATTTTTGTGTTTTCAAAAA
1 TGTTTTCAAAAATTTCTGTGTTTTCAAAAA
59185208 AAAATCTTGT
Statistics
Matches: 113, Mismatches: 15, Indels: 16
0.78 0.10 0.11
Matches are distributed among these distances:
34 4 0.04
35 63 0.56
36 46 0.41
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (36 bp):
TGTTTTCAAAAATTTCTGTGTTTTCAAAAATTTCCA
Found at i:59185114 original size:53 final size:55
Alignment explanation
Indices: 59185034--59185208 Score: 179
Period size: 53 Copynumber: 3.3 Consensus size: 55
59185024 CAAAAAAAAT
* **
59185034 TCGTGTTTTC-AAAAATTTCTGTGTTTCAAAAATTTTCATGTTTTCA-AAAATTC
1 TCGTGTTTTCAAAAAATTCCAATGTTTCAAAAATTTTCATGTTTTCAGAAAATTC
59185087 TCGTGTTTTCAAAAAATTCCAAT-TTTCAAAAATTTTCATGTTTTCAGAAAATTC
1 TCGTGTTTTCAAAAAATTCCAATGTTTCAAAAATTTTCATGTTTTCAGAAAATTC
* ** * *
59185141 CCGTG-TTTC-AAAAA-TCCTCGTGTTTTCAAAAA-TTTCGGTGTTTT--GAAAATTT
1 TCGTGTTTTCAAAAAATTCC-AATG-TTTCAAAAATTTTC-ATGTTTTCAGAAAATTC
*
59185193 TTGTGTTTTCAAAAAA
1 TCGTGTTTTCAAAAAA
59185209 AAATCTTGTG
Statistics
Matches: 104, Mismatches: 10, Indels: 15
0.81 0.08 0.12
Matches are distributed among these distances:
51 3 0.03
52 16 0.15
53 45 0.43
54 40 0.38
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (55 bp):
TCGTGTTTTCAAAAAATTCCAATGTTTCAAAAATTTTCATGTTTTCAGAAAATTC
Found at i:59188747 original size:15 final size:15
Alignment explanation
Indices: 59188727--59188778 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
59188717 AACATTCAGT
*
59188727 ATTCATTAGTCGTTC
1 ATTCATTATTCGTTC
59188742 ATTCATTCATTCAG-T-
1 ATTCATT-ATTC-GTTC
*
59188757 ATTCATTATTCATTC
1 ATTCATTATTCGTTC
59188772 ATTCATT
1 ATTCATT
59188779 CATTGTATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 5 0.16
15 21 0.68
16 4 0.13
17 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (15 bp):
ATTCATTATTCGTTC
Found at i:59188748 original size:4 final size:4
Alignment explanation
Indices: 59188739--59188782 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
59188729 TCATTAGTCG
*
59188739 TTCA TTCA TTCA TTCA GT-A TTCA TT-A TTCA TTCA TTCA TTCA TT
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TT
59188783 GTATGTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 5 0.14
4 31 0.86
ACGTcount: A:0.25, C:0.20, G:0.02, T:0.52
Consensus pattern (4 bp):
TTCA
Found at i:59188755 original size:30 final size:30
Alignment explanation
Indices: 59188719--59188782 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
59188709 ACATAACTAA
*
59188719 CATTCAGTATTCATTAGTCGTTCATTCATT
1 CATTCAGTATTCATTAGTCATTCATTCATT
*
59188749 CATTCAGTATTCATTATTCATTCATTCATT
1 CATTCAGTATTCATTAGTCATTCATTCATT
59188779 CATT
1 CATT
59188783 GTATGTACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.48
Consensus pattern (30 bp):
CATTCAGTATTCATTAGTCATTCATTCATT
Found at i:59196209 original size:17 final size:17
Alignment explanation
Indices: 59196190--59196227 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
59196180 TTATACTTAA
* *
59196190 AAAAACAAAA-AAATAG
1 AAAAAGAAAAGAAAAAG
59196206 AAAAAGAAAAGAAAAAG
1 AAAAAGAAAAGAAAAAG
59196223 AAAAA
1 AAAAA
59196228 TCAAGATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.84, C:0.03, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAG
Found at i:59197202 original size:75 final size:75
Alignment explanation
Indices: 59197081--59197605 Score: 792
Period size: 75 Copynumber: 6.9 Consensus size: 75
59197071 AAGAATTTTT
*
59197081 TATTTTTAATTTCTGTTTTTTT--AAAATAAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
1 TATTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
59197144 CACGCTGAGG
66 CACGCTGAGG
*
59197154 TATTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCTTCGGGT
1 TATTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
59197219 CACGCTGAGG
66 CACGCTGAGG
*
59197229 TATTTTTAATTTCTGTAGTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTGT-TTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
59197294 TCACGCTGAGG
65 TCACGCTGAGG
59197305 TATTTTTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
1 TA---TTTTTAATTTCTG-TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
59197370 GGGTCACGCTGAGG
62 GGGTCACGCTGAGG
59197384 TATTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
1 TATTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
59197449 CACGCTGAGG
66 CACGCTGAGG
* * * * *
59197459 TATTTTTAATTTCTATTTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTC-A
1 TATTTTTAATTTC--TGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
* *
59197523 GACACATGCCGAGG
64 GTCAC--GCTGAGG
*
59197537 TATTTCTTTTAAATTTCT-ATTTTTT--AAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
1 TA--T-TTTT-AATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
59197599 GGGTCAC
62 GGGTCAC
59197606 ATGCCGAGCG
Statistics
Matches: 418, Mismatches: 18, Indels: 27
0.90 0.04 0.06
Matches are distributed among these distances:
73 22 0.05
75 138 0.33
76 76 0.18
77 78 0.19
78 12 0.03
79 79 0.19
80 3 0.01
81 4 0.01
82 6 0.01
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (75 bp):
TATTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
CACGCTGAGG
Found at i:59197446 original size:154 final size:149
Alignment explanation
Indices: 59197081--59197605 Score: 795
Period size: 154 Copynumber: 3.4 Consensus size: 149
59197071 AAGAATTTTT
*
59197081 TATTTTTAATTTCTGTTTTTTTAAAATAAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCA
1 TATTTTTAATTTCTGTTTTTTTAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCA
59197146 CGCTGAGGTATTTTTAATTTCTG-TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGA
66 CGCTGAGGTATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGA
*
59197210 GCTTCGGGTCACGCTGAGG
131 GCCTCGGGTCACGCTGAGG
*
59197229 TATTTTTAATTTCTGTAGTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTGT--TTTTT-TAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
59197294 TCACGCTGAGGTATTTTTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTG
63 TCACGCTGAGGTA---TTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTG
59197359 AGTTGAGCCTCGGGTCACGCTGAGG
125 AGTTGAGCCTCGGGTCACGCTGAGG
59197384 TATTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
1 TATTTTTAATTTCTGTTTTTTT--AAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
* * * *
59197449 CACGCTGAGGTATTTTTAATTTCTATTTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAAT
64 CACGCTGAGGTATTTTTAATTTCT-GTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGT
* * *
59197514 TGAGCCTC-AGACACATGCCGAGG
128 TGAGCCTCGGGTCAC--GCTGAGG
*
59197537 TATTTCTTTTAAATTTCT-ATTTTTTAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
1 TA--T-TTTT-AATTTCTGTTTTTTTAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
59197601 GTCAC
62 GTCAC
59197606 ATGCCGAGCG
Statistics
Matches: 349, Mismatches: 12, Indels: 26
0.90 0.03 0.07
Matches are distributed among these distances:
148 16 0.05
150 5 0.01
151 68 0.19
152 44 0.13
153 13 0.04
154 110 0.32
155 76 0.22
156 10 0.03
157 7 0.02
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (149 bp):
TATTTTTAATTTCTGTTTTTTTAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCA
CGCTGAGGTATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGA
GCCTCGGGTCACGCTGAGG
Found at i:59197818 original size:6 final size:7
Alignment explanation
Indices: 59197801--59197826 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
59197791 AAAAATTCAA
59197801 AAAAATC
1 AAAAATC
59197808 AAAAATC
1 AAAAATC
59197815 AAAAATC
1 AAAAATC
59197822 AAAAA
1 AAAAA
59197827 ATACATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATC
Found at i:59197866 original size:13 final size:13
Alignment explanation
Indices: 59197848--59197895 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
59197838 CCCCTGAACT
59197848 TTTTGAAATTACA
1 TTTTGAAATTACA
* *
59197861 TTTTGACCCATTAACC
1 TTTTGA--AATT-ACA
59197877 TTTTGAAATTACA
1 TTTTGAAATTACA
59197890 TTTTGA
1 TTTTGA
59197896 CCCCTAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 14 0.50
14 3 0.11
15 3 0.11
16 8 0.29
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTTGAAATTACA
Found at i:59197866 original size:29 final size:29
Alignment explanation
Indices: 59197828--59197900 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
59197818 AATCAAAAAA
*
59197828 TACATTTTGACCCCTGAACTTTTTGAAAT
1 TACATTTTGACCCCTGAACCTTTTGAAAT
* *
59197857 TACATTTTGACCCATTAACCTTTTGAAAT
1 TACATTTTGACCCCTGAACCTTTTGAAAT
59197886 TACATTTTGACCCCT
1 TACATTTTGACCCCT
59197901 AAATTTTCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.41
Consensus pattern (29 bp):
TACATTTTGACCCCTGAACCTTTTGAAAT
Found at i:59198288 original size:12 final size:12
Alignment explanation
Indices: 59198271--59198299 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
59198261 GAAGAGAAAG
59198271 GAGGAAGAAGAA
1 GAGGAAGAAGAA
59198283 GAGGAAGAAGAA
1 GAGGAAGAAGAA
59198295 -AGGAA
1 GAGGAA
59198300 AAAAAGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
GAGGAAGAAGAA
Found at i:59198337 original size:5 final size:5
Alignment explanation
Indices: 59198329--59198356 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
59198319 ACAGTCGGGT
59198329 CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC CGACC CGACC CGACC CGACC CGA
59198357 GCAGCAGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.57, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:59198415 original size:20 final size:19
Alignment explanation
Indices: 59198387--59198426 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
59198377 GCCCAAAACA
* *
59198387 AAAAGAAAAAGAAAAGGGC
1 AAAAGAAAAAAAAAAAGGC
59198406 AAAAGCAAAAAAAAAAAGGC
1 AAAAG-AAAAAAAAAAAGGC
59198426 A
1 A
59198427 GAAAAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.72, C:0.07, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAAAAAAGGC
Found at i:59198600 original size:13 final size:12
Alignment explanation
Indices: 59198581--59198660 Score: 67
Period size: 13 Copynumber: 6.5 Consensus size: 12
59198571 GCAGCAGGCC
59198581 AAAAAAAAGAAG
1 AAAAAAAAGAAG
59198593 AGAAAAAAAG-AG
1 A-AAAAAAAGAAG
*
59198605 AAAGAAAAAAAAG
1 AAA-AAAAAGAAG
*
59198618 -AAAAAACGAA-
1 AAAAAAAAGAAG
*
59198628 AAAAAGGAAAAAAG
1 AAAAA--AAAGAAG
59198642 AAAAAAAAAGAAG
1 -AAAAAAAAGAAG
59198655 AAAAAA
1 AAAAAA
59198661 GGGGTTCAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
11 12 0.22
12 17 0.31
13 20 0.37
15 5 0.09
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:59198600 original size:16 final size:15
Alignment explanation
Indices: 59198581--59198660 Score: 69
Period size: 15 Copynumber: 5.3 Consensus size: 15
59198571 GCAGCAGGCC
59198581 AAAAAAAAG-AAGAGA
1 AAAAAAAAGAAAGA-A
*
59198596 AAAAAAGAGAAAGAA
1 AAAAAAAAGAAAGAA
*
59198611 AAAAAAGAAAAAACGAA
1 AAAAAA-AAGAAA-GAA
59198628 AAAAAGGAAA-AAAG-A
1 AAAAA--AAAGAAAGAA
59198643 AAAAAAAAG-AAGAA
1 AAAAAAAAGAAAGAA
59198657 AAAA
1 AAAA
59198661 GGGGTTCAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
13 6 0.11
14 5 0.09
15 21 0.38
16 9 0.16
17 11 0.20
18 2 0.04
19 1 0.02
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAGAA
Found at i:59198603 original size:10 final size:10
Alignment explanation
Indices: 59198584--59198660 Score: 63
Period size: 11 Copynumber: 7.6 Consensus size: 10
59198574 GCAGGCCAAA
59198584 AAAAAGAAGAG
1 AAAAA-AAGAG
59198595 AAAAAAAGAG
1 AAAAAAAGAG
59198605 AAAGAAAA-A-
1 AAA-AAAAGAG
*
59198614 AAAGAAAAAACG
1 AAA-AAAAGA-G
59198626 AAAAAAAG-G
1 AAAAAAAGAG
*
59198635 -AAAAAAGAA
1 AAAAAAAGAG
59198644 AAAAAAAGAAG
1 AAAAAAAG-AG
59198655 AAAAAA
1 AAAAAA
59198661 GGGGTTCAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
8 7 0.12
9 9 0.16
10 17 0.30
11 20 0.36
12 3 0.05
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:59198623 original size:8 final size:8
Alignment explanation
Indices: 59198593--59198648 Score: 69
Period size: 8 Copynumber: 7.1 Consensus size: 8
59198583 AAAAAAGAAG
59198593 AGAAAAAA
1 AGAAAAAA
* *
59198601 AGAGAAAG
1 AGAAAAAA
59198609 A-AAAAAA
1 AGAAAAAA
59198616 AGAAAAAA
1 AGAAAAAA
*
59198624 CGAAAAAA
1 AGAAAAAA
*
59198632 AGGAAAAA
1 AGAAAAAA
59198640 AGAAAAAA
1 AGAAAAAA
59198648 A
1 A
59198649 AAGAAGAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 5 0.13
8 34 0.87
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:59198658 original size:8 final size:7
Alignment explanation
Indices: 59198583--59198661 Score: 65
Period size: 7 Copynumber: 11.0 Consensus size: 7
59198573 AGCAGGCCAA
59198583 AAAAAAG
1 AAAAAAG
59198590 AAGAGAAA-
1 AA-A-AAAG
*
59198598 AAAAGAG
1 AAAAAAG
*
59198605 AAAGAA-
1 AAAAAAG
59198611 AAAAAAG
1 AAAAAAG
59198618 AAAAAACG
1 AAAAAA-G
59198626 AAAAAAAGG
1 -AAAAAA-G
59198635 AAAAAAG
1 AAAAAAG
59198642 AAAAAA-
1 AAAAAAG
*
59198648 AAAGAAG
1 AAAAAAG
59198655 AAAAAAG
1 AAAAAAG
59198662 GGGTTCAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
6 12 0.21
7 26 0.45
8 10 0.17
9 10 0.17
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:59198661 original size:10 final size:10
Alignment explanation
Indices: 59198593--59198661 Score: 60
Period size: 10 Copynumber: 7.2 Consensus size: 10
59198583 AAAAAAGAAG
59198593 AGAA-AAAAA
1 AGAAGAAAAA
59198602 GAGAAAGAAAAA
1 -AG-AAGAAAAA
59198614 A-AAGAAAAA
1 AGAAGAAAAA
59198623 ACG-A-AAAAA
1 A-GAAGAAAAA
59198632 AG--GAAAAA
1 AGAAGAAAAA
*
59198640 AGAAAAAAAA
1 AGAAGAAAAA
59198650 AGAAGAAAAA
1 AGAAGAAAAA
59198660 AG
1 AG
59198662 GGGTTCAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
8 8 0.16
9 15 0.30
10 19 0.38
11 3 0.06
12 5 0.10
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.00
Consensus pattern (10 bp):
AGAAGAAAAA
Found at i:59199035 original size:19 final size:21
Alignment explanation
Indices: 59199013--59199055 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
59199003 CTCGGGTTTC
59199013 AAAATTT-TCGTGTCTTCAAA
1 AAAATTTCTCGTGTCTTCAAA
*
59199033 AAAATTTCTCGTGTTTTCAAA
1 AAAATTTCTCGTGTCTTCAAA
59199054 AA
1 AA
59199056 TAAGGTAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (21 bp):
AAAATTTCTCGTGTCTTCAAA
Found at i:59199056 original size:19 final size:18
Alignment explanation
Indices: 59199009--59199056 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
59198999 AATCCTCGGG
59199009 TTTC-AAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
*
59199026 CTTCAAAAAAATTTCTCGTGT
1 TTTC--AAAAATTT-TCGTGT
59199047 TTTCAAAAAT
1 TTTCAAAAAT
59199057 AAGGTAACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 3 0.12
19 6 0.24
20 7 0.28
21 9 0.36
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:59199196 original size:17 final size:18
Alignment explanation
Indices: 59199171--59199324 Score: 138
Period size: 18 Copynumber: 8.7 Consensus size: 18
59199161 AAATTTTCTG
59199171 TGTTTTCAAAAATTCCCA
1 TGTTTTCAAAAATTCCCA
**
59199189 TG-TTTCAAAAATTTTCA
1 TGTTTTCAAAAATTCCCA
* *
59199206 TGTTTTCAAAAATTCTCG
1 TGTTTTCAAAAATTCCCA
59199224 TGTTTTCAAAAAATT-CCA
1 TGTTTTC-AAAAATTCCCA
* **
59199242 -ATTTTCAAAAATTTTCA
1 TGTTTTCAAAAATTCCCA
*
59199259 TGTTTTCAGAAAATTCCCG
1 TGTTTTCA-AAAATTCCCA
*
59199278 TG-TTTCAAAAA-TCCTCG
1 TGTTTTCAAAAATTCC-CA
** *
59199295 TGTTTTCAAAAATTTTCG
1 TGTTTTCAAAAATTCCCA
59199313 TGTTTTCAAAAA
1 TGTTTTCAAAAA
59199325 AAAAATCTTG
Statistics
Matches: 114, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
16 10 0.09
17 30 0.26
18 57 0.50
19 17 0.15
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.42
Consensus pattern (18 bp):
TGTTTTCAAAAATTCCCA
Found at i:59199214 original size:35 final size:36
Alignment explanation
Indices: 59199160--59199324 Score: 167
Period size: 35 Copynumber: 4.6 Consensus size: 36
59199150 AAAAAATCAG
59199160 AAAATTTTCTGTGTTTTCAAAAATTCCCATG-TTTCA
1 AAAATTTTC-GTGTTTTCAAAAATTCCCATGTTTTCA
* * *
59199196 AAAATTTTCATGTTTTCAAAAATTCTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCAAAAATTCCCATGTTTTCA
* *** **
59199232 AAAA-ATTCCAATTTTCAAAAATTTTCATGTTTTCA
1 AAAATTTTCGTGTTTTCAAAAATTCCCATGTTTTCA
** *
59199267 GAAAATTCCCGTG-TTTCAAAAA-TCCTCGTGTTTTCA
1 -AAAATTTTCGTGTTTTCAAAAATTCC-CATGTTTTCA
59199303 AAAATTTTCGTGTTTTCAAAAA
1 AAAATTTTCGTGTTTTCAAAAA
59199325 AAAAATCTTG
Statistics
Matches: 104, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
35 54 0.52
36 49 0.47
37 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.42
Consensus pattern (36 bp):
AAAATTTTCGTGTTTTCAAAAATTCCCATGTTTTCA
Found at i:59199272 original size:54 final size:53
Alignment explanation
Indices: 59199156--59199325 Score: 209
Period size: 54 Copynumber: 3.2 Consensus size: 53
59199146 TAATAAAAAA
* *
59199156 TCAGAAAATTTTCTGTGTTTTCAAAAATTCCCATGTTTCAAAAATTTTCATGTTT
1 TCAGAAAATTCTC-GTGTTTTCAAAAATTCCAAT-TTTCAAAAATTTTCATGTTT
59199211 TCA-AAAATTCTCGTGTTTTCAAAAAATTCCAATTTTCAAAAATTTTCATGTTT
1 TCAGAAAATTCTCGTGTTTTC-AAAAATTCCAATTTTCAAAAATTTTCATGTTT
* *** *
59199264 TCAGAAAATTCCCGTG-TTTCAAAAATCCTCGTGTTTTCAAAAATTTTCGTGTTT
1 TCAGAAAATTCTCGTGTTTTCAAAAAT--TCCAATTTTCAAAAATTTTCATGTTT
*
59199318 TCAAAAAA
1 TCAGAAAA
59199326 AAAATCTTGT
Statistics
Matches: 103, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
52 6 0.06
53 35 0.34
54 59 0.57
55 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.42
Consensus pattern (53 bp):
TCAGAAAATTCTCGTGTTTTCAAAAATTCCAATTTTCAAAAATTTTCATGTTT
Found at i:59199369 original size:32 final size:33
Alignment explanation
Indices: 59199327--59199390 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
59199317 TTCAAAAAAA
* *
59199327 AAATCTTGTGTTT-CATAAATTTTCATTTTTTTT
1 AAATCTTGTGTTTCCA-AAATTCTCATGTTTTTT
59199360 AAAT-TTGTGTTTCCAAAATTCTCATGTTTTT
1 AAATCTTGTGTTTCCAAAATTCTCATGTTTTT
59199391 AAAAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 22 0.79
33 6 0.21
ACGTcount: A:0.25, C:0.11, G:0.08, T:0.56
Consensus pattern (33 bp):
AAATCTTGTGTTTCCAAAATTCTCATGTTTTTT
Found at i:59200674 original size:3 final size:3
Alignment explanation
Indices: 59200666--59200738 Score: 62
Period size: 3 Copynumber: 24.7 Consensus size: 3
59200656 CGCTACATAG
* * *
59200666 TTA TTA TTA TTA TTA TTA TTA TTA TTG TCT- TTA CTA TTA TT- TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* *
59200710 TTA -TA TTCA TTA ATA TTA TTG TTA TTA TT
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TT
59200739 GATAGGTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
2 5 0.09
3 48 0.84
4 4 0.07
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:59200802 original size:11 final size:11
Alignment explanation
Indices: 59200786--59200812 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
59200776 GATATGGGTT
59200786 TTATTATATTA
1 TTATTATATTA
59200797 TTATTATATTA
1 TTATTATATTA
59200808 TTATT
1 TTATT
59200813 TTTTATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTATATTA
Found at i:59203561 original size:38 final size:39
Alignment explanation
Indices: 59203511--59203610 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 39
59203501 TAAATACAAG
*
59203511 AATTTTAGAAACACGAAACTTTTGTTTAAAAAACACGA-A
1 AATTTT-GAAACACGAAATTTTTGTTTAAAAAACACGATA
* * ** *
59203550 AATTTTGAAACACGAGATTTTTTTTTTGAAAACACGATT
1 AATTTTGAAACACGAAATTTTTGTTTAAAAAACACGATA
**
59203589 TTTTTTGAAACACGAAATTTTT
1 AATTTTGAAACACGAAATTTTT
59203611 TGAAAAGACG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 26 0.51
39 25 0.49
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (39 bp):
AATTTTGAAACACGAAATTTTTGTTTAAAAAACACGATA
Found at i:59203588 original size:20 final size:20
Alignment explanation
Indices: 59203552--59203611 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 20
59203542 AACACGAAAA
59203552 TTTTGAAACACGAGATTTTTT
1 TTTTGAAACAC-AGATTTTTT
59203573 TTTTGAAA-ACACGA--TTTT
1 TTTTGAAACACA-GATTTTTT
*
59203591 TTTTGAAACACGAAATTTTTT
1 TTTTGAAACAC-AGATTTTTT
59203612 GAAAAGACGT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
18 12 0.36
19 4 0.12
20 5 0.15
21 12 0.36
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTTGAAACACAGATTTTTT
Found at i:59203590 original size:18 final size:18
Alignment explanation
Indices: 59203569--59203616 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
59203559 ACACGAGATT
59203569 TTTTTTTTGAAAACACGA
1 TTTTTTTTGAAAACACGA
59203587 TTTTTTTTG-AAACACGA
1 TTTTTTTTGAAAACACGA
**
59203604 AATTTTTTGAAAA
1 TTTTTTTTGAAAA
59203617 GACGTATCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46
Consensus pattern (18 bp):
TTTTTTTTGAAAACACGA
Found at i:59203978 original size:16 final size:14
Alignment explanation
Indices: 59203938--59203972 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
59203928 AATTGAAATT
59203938 AAAT-TAAATA-AA
1 AAATATAAATACAA
59203950 AAATATAAATACAA
1 AAATATAAATACAA
59203964 AAATATAAA
1 AAATATAAA
59203973 AATACATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 6 0.29
14 11 0.52
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATATAAATACAA
Found at i:59204134 original size:17 final size:16
Alignment explanation
Indices: 59204105--59204162 Score: 68
Period size: 15 Copynumber: 3.8 Consensus size: 16
59204095 CAAATTGAAC
59204105 CTTTTT-TTTTTCTCT
1 CTTTTTCTTTTTCTCT
*
59204120 CTTTTTCTATTT-TCT
1 CTTTTTCTTTTTCTCT
*
59204135 C-TTTTCTTTTTTCTTT
1 CTTTTTC-TTTTTCTCT
59204151 CTTTTTCTTTTT
1 CTTTTTCTTTTT
59204163 TTTGCTGGGC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.14
15 14 0.39
16 12 0.33
17 5 0.14
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (16 bp):
CTTTTTCTTTTTCTCT
Found at i:59204148 original size:31 final size:30
Alignment explanation
Indices: 59204105--59204163 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
59204095 CAAATTGAAC
59204105 CTTTTTTTTTTCTCTCTTTTTCTATTTTCT
1 CTTTTTTTTTTCTCTCTTTTTCTATTTTCT
* *
59204135 CTTTTCTTTTTTCTTTCTTTTTCTTTTTT
1 CTTTT-TTTTTTCTCTCTTTTTCTATTTT
59204164 TTGCTGGGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (30 bp):
CTTTTTTTTTTCTCTCTTTTTCTATTTTCT
Found at i:59204151 original size:18 final size:17
Alignment explanation
Indices: 59204106--59204163 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
59204096 AAATTGAACC
*
59204106 TTTT-TTTTTTCTCTCT
1 TTTTCTTTTTTCTTTCT
*
59204122 TTTTCTATTTTC--TC-
1 TTTTCTTTTTTCTTTCT
59204136 TTTTCTTTTTTCTTTCT
1 TTTTCTTTTTTCTTTCT
59204153 TTTTCTTTTTT
1 TTTTCTTTTTT
59204164 TTGCTGGGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 11 0.31
15 2 0.06
16 6 0.17
17 17 0.47
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTTTTTTCTTTCT
Found at i:59204157 original size:6 final size:6
Alignment explanation
Indices: 59204119--59204162 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
59204109 TTTTTTTCTC
*
59204119 TCTTTT TCTATTT TCTCTTT TCTTTT T-TCTT TCTTTT TCTTTT T
1 TCTTTT TCT-TTT TCT-TTT TCTTTT TCTTTT TCTTTT TCTTTT T
59204163 TTTGCTGGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 4 0.12
6 17 0.52
7 12 0.36
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:59204450 original size:7 final size:7
Alignment explanation
Indices: 59204438--59204496 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
59204428 TAATAATATT
59204438 TTTTTTC
1 TTTTTTC
59204445 -TTTTT-
1 TTTTTTC
*
59204450 TTTTTCC
1 TTTTTTC
59204457 TTTTTTC
1 TTTTTTC
59204464 TTTCCCTTTC
1 TTT---TTTC
59204474 TTCTTTT-
1 TT-TTTTC
59204481 TTTTTTC
1 TTTTTTC
59204488 TTTTTTC
1 TTTTTTC
59204495 TT
1 TT
59204497 CCTTCTTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
6 13 0.30
7 20 0.47
8 3 0.07
10 6 0.14
11 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:59204479 original size:32 final size:31
Alignment explanation
Indices: 59204442--59204509 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 31
59204432 AATATTTTTT
59204442 TTCTTTTTTTTTTCCTTTTTTCTTTCC-CTTTC
1 TTCTTTTTTTTTT-CTTTTTTC-TTCCTCTTTC
59204474 TTCTTTTTTTTTTCTTTTTTCTTCCTTCTTTC
1 TTCTTTTTTTTTTCTTTTTTCTTCC-TCTTTC
59204506 TTCT
1 TTCT
59204510 GTTCTTCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 4 0.12
31 8 0.24
32 22 0.65
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (31 bp):
TTCTTTTTTTTTTCTTTTTTCTTCCTCTTTC
Found at i:59204516 original size:8 final size:7
Alignment explanation
Indices: 59204456--59204523 Score: 54
Period size: 7 Copynumber: 10.1 Consensus size: 7
59204446 TTTTTTTTTC
*
59204456 CTTTTTT
1 CTTTCTT
*
59204463 CTTTC-C
1 CTTTCTT
59204469 CTTTCTT
1 CTTTCTT
59204476 CTTT-TT
1 CTTTCTT
59204482 -TTT-TT
1 CTTTCTT
*
59204487 CTTTTTT
1 CTTTCTT
*
59204494 CTTCCTT
1 CTTTCTT
59204501 CTTTCTT
1 CTTTCTT
59204508 CTGTTCTT
1 CT-TTCTT
*
59204516 CTTCCTT
1 CTTTCTT
59204523 C
1 C
59204524 CCTTGGACCT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
5 5 0.10
6 10 0.20
7 28 0.56
8 7 0.14
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (7 bp):
CTTTCTT
Found at i:59204742 original size:20 final size:20
Alignment explanation
Indices: 59204717--59204769 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
59204707 TTTGATGGTT
*
59204717 ACGGTGGTGGTGGTTGTGCG
1 ACGGTGGTGGTGGTTGCGCG
59204737 ACGGTGGTGGTGGTTGCGCG
1 ACGGTGGTGGTGGTTGCGCG
59204757 ACGGTGGTGGTGG
1 ACGGTGGTGGTGG
59204770 AGGCTTTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.06, C:0.11, G:0.57, T:0.26
Consensus pattern (20 bp):
ACGGTGGTGGTGGTTGCGCG
Found at i:59205068 original size:30 final size:30
Alignment explanation
Indices: 59205034--59205161 Score: 116
Period size: 30 Copynumber: 4.3 Consensus size: 30
59205024 GGGGCCAAGC
* *
59205034 ATAATTTTGAGAAAATTTAGGGGTCAAAAT
1 ATAATTTTAAGAAAATTGAGGGGTCAAAAT
* * ** *
59205064 ATAATTTCAAG-AAGTTGACTGGCCAAAAT
1 ATAATTTTAAGAAAATTGAGGGGTCAAAAT
* * *
59205093 GTAATTTTAAGAAAGTTTAGGGGTCAAAAT
1 ATAATTTTAAGAAAATTGAGGGGTCAAAAT
*
59205123 ATAATTTTTAA-AAAAGTTGAGGGGTTAAAAT
1 ATAA-TTTTAAGAAAA-TTGAGGGGTCAAAAT
*
59205154 GTAATTTT
1 ATAATTTT
59205162 TATTTTTGTT
Statistics
Matches: 77, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
29 22 0.29
30 33 0.43
31 22 0.29
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (30 bp):
ATAATTTTAAGAAAATTGAGGGGTCAAAAT
Found at i:59205139 original size:31 final size:31
Alignment explanation
Indices: 59205034--59205163 Score: 115
Period size: 31 Copynumber: 4.3 Consensus size: 31
59205024 GGGGCCAAGC
* * *
59205034 ATAATTTTGAGAAAA-TTTAGGGGTCAAAAT
1 ATAATTTTTAAAAAAGTTGAGGGGTCAAAAT
* * ** *
59205064 ATAA--TTTCAAGAAGTTGACTGGCCAAAAT
1 ATAATTTTTAAAAAAGTTGAGGGGTCAAAAT
* * *
59205093 GTAA-TTTTAAGAAAGTTTAGGGGTCAAAAT
1 ATAATTTTTAAAAAAGTTGAGGGGTCAAAAT
*
59205123 ATAATTTTTAAAAAAGTTGAGGGGTTAAAAT
1 ATAATTTTTAAAAAAGTTGAGGGGTCAAAAT
*
59205154 GTAATTTTTA
1 ATAATTTTTA
59205164 TTTTTGTTTT
Statistics
Matches: 76, Mismatches: 21, Indels: 5
0.75 0.21 0.05
Matches are distributed among these distances:
28 5 0.07
29 14 0.18
30 25 0.33
31 32 0.42
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.35
Consensus pattern (31 bp):
ATAATTTTTAAAAAAGTTGAGGGGTCAAAAT
Found at i:59209100 original size:89 final size:89
Alignment explanation
Indices: 59208949--59209432 Score: 637
Period size: 89 Copynumber: 5.4 Consensus size: 89
59208939 TATTTGAATT
* * *
59208949 AGATCGTGTTTTCTTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
* *
59209014 ACAGCGGAGCAAACTGAAAACAGC
66 GCAGCGGAGCAGACTGAAAACAGC
* *
59209038 AGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTACCTCCCTGAGTTT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
** **
59209103 ATAGCGGAGCAGACTGAAAGTAGC
66 GCAGCGGAGCAGACTGAAAACAGC
* * * * **
59209127 AGATCTTGTCTTCCTGTATTGACAGCAAAGTAAATCGAAGACACCAACCTTGCCTCTTTGAGTTT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
* *
59209192 GCAGCAGAGCAGACTGAAAACATC
66 GCAGCGGAGCAGACTGAAAACAGC
* *
59209216 AGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTACCTCCCTGAGTTT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
* * **
59209281 GTAGCGGA-CTTGACTGAAAGTAGC
66 GCAGCGGAGC-AGACTGAAAACAGC
* * * * *
59209305 AGATCTTGTCTTCCTGTATTGACAGCAAAATAGATCGAAGGCACCAACCTTGCCTCCCTGAGTTT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
* ** *
59209370 GCAACGGAATAGACTGAAAACAAC
66 GCAGCGGAGCAGACTGAAAACAGC
*
59209394 AGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAA
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAA
59209433 ATAACAAACC
Statistics
Matches: 338, Mismatches: 55, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
88 1 0.00
89 337 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (89 bp):
AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
GCAGCGGAGCAGACTGAAAACAGC
Found at i:59209454 original size:178 final size:178
Alignment explanation
Indices: 59208949--59209432 Score: 745
Period size: 178 Copynumber: 2.7 Consensus size: 178
59208939 TATTTGAATT
* * * * * *
59208949 AGATCGTGTTTTCTTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
1 AGATCTTGTCTTCCTGTATTGACAGCAAAGTAGATCGAAGACACCAACCTTGCCTCCCTGAGTTT
* * *
59209014 ACAGCGGAGCAAACTGAAAACAGCAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
66 GCAGCGGAGCAGACTGAAAACAACAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
59209079 CACCAGCCTTACCTCCCTGAGTTTATAGCGGAGCAGACTGAAAGTAGC
131 CACCAGCCTTACCTCCCTGAGTTTATAGCGGAGCAGACTGAAAGTAGC
* **
59209127 AGATCTTGTCTTCCTGTATTGACAGCAAAGTAAATCGAAGACACCAACCTTGCCTCTTTGAGTTT
1 AGATCTTGTCTTCCTGTATTGACAGCAAAGTAGATCGAAGACACCAACCTTGCCTCCCTGAGTTT
* *
59209192 GCAGCAGAGCAGACTGAAAACATCAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
66 GCAGCGGAGCAGACTGAAAACAACAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
* *
59209257 CACCAGCCTTACCTCCCTGAGTTTGTAGCGGA-CTTGACTGAAAGTAGC
131 CACCAGCCTTACCTCCCTGAGTTTATAGCGGAGC-AGACTGAAAGTAGC
* *
59209305 AGATCTTGTCTTCCTGTATTGACAGCAAAATAGATCGAAGGCACCAACCTTGCCTCCCTGAGTTT
1 AGATCTTGTCTTCCTGTATTGACAGCAAAGTAGATCGAAGACACCAACCTTGCCTCCCTGAGTTT
* ** * *
59209370 GCAACGGAATAGACTGAAAACAACAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAA
66 GCAGCGGAGCAGACTGAAAACAACAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAA
59209433 ATAACAAACC
Statistics
Matches: 278, Mismatches: 27, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
177 1 0.00
178 277 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (178 bp):
AGATCTTGTCTTCCTGTATTGACAGCAAAGTAGATCGAAGACACCAACCTTGCCTCCCTGAGTTT
GCAGCGGAGCAGACTGAAAACAACAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
CACCAGCCTTACCTCCCTGAGTTTATAGCGGAGCAGACTGAAAGTAGC
Found at i:59209933 original size:45 final size:45
Alignment explanation
Indices: 59209821--59210029 Score: 172
Period size: 44 Copynumber: 4.6 Consensus size: 45
59209811 GGCAGCTAAT
* * * * *
59209821 CTTATTTCTCTGAAGTTGCAGTAGAACAGATTGAAGCTATAAATTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT-AA--A-AAAC
* * *
59209872 CTTATCTCCTTAAAGTTGCAGTGGAGCAGACTGAAGATAAAAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAAAAAAC
* ** *
59209917 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGAT-ACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAAAAAAC
* * * ** *
59209961 CTTATCTCCCTGAAGTTG-TGATGGAGAAGATTGAAGCTATTAATC
1 CTTATCTCCCTGAAGTTGCAG-TGGAGCAGATTGAAGATAAAAAAC
59210006 C-TATCTCCCTGAAGTTGCAGTGGA
1 CTTATCTCCCTGAAGTTGCAGTGGA
59210030 ACGATTAAAA
Statistics
Matches: 130, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
43 1 0.01
44 55 0.42
45 40 0.31
46 1 0.01
48 2 0.02
49 2 0.02
51 29 0.22
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAAAAAAC
Found at i:59212696 original size:23 final size:25
Alignment explanation
Indices: 59212662--59212716 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
59212652 GATGTTTTTA
59212662 TATATATATTTTT-GGTGAAAATGTT
1 TATATAT-TTTTTAGGTGAAAATGTT
* * *
59212687 TATATCTTTTTTAGGTGAAATTTTT
1 TATATATTTTTTAGGTGAAAATGTT
59212712 TATAT
1 TATAT
59212717 GATGAACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.56
Consensus pattern (25 bp):
TATATATTTTTTAGGTGAAAATGTT
Found at i:59227257 original size:24 final size:24
Alignment explanation
Indices: 59227230--59227276 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
59227220 CCCCCATTAG
* *
59227230 CAAATATCGTATGACCCCTACCAA
1 CAAACATCGTATAACCCCTACCAA
*
59227254 CAAACATCGTATAATCCCTACCA
1 CAAACATCGTATAACCCCTACCA
59227277 GTAGGTGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.34, G:0.06, T:0.21
Consensus pattern (24 bp):
CAAACATCGTATAACCCCTACCAA
Found at i:59228564 original size:21 final size:21
Alignment explanation
Indices: 59228505--59228564 Score: 50
Period size: 25 Copynumber: 2.7 Consensus size: 21
59228495 AATACATCAA
59228505 AAATATTAAAAACA-TCAAAAT
1 AAATATTAAAAA-ATTCAAAAT
* *
59228526 AAATATTTCTCAACAAATTGAAAAT
1 AAATA--T-T-AAAAAATTCAAAAT
59228551 AAATATTAAAAAAT
1 AAATATTAAAAAAT
59228565 ATGTAGACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
21 11 0.35
22 1 0.03
23 2 0.06
24 2 0.06
25 15 0.48
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (21 bp):
AAATATTAAAAAATTCAAAAT
Found at i:59229402 original size:17 final size:18
Alignment explanation
Indices: 59229380--59229419 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
59229370 ACCCAAACCG
*
59229380 ATAAAACCCA-ACATAAA
1 ATAAAACCCAGAAATAAA
59229397 ATAAAACCCAGAAATAAA
1 ATAAAACCCAGAAATAAA
59229415 A-AAAA
1 ATAAAA
59229420 TGGACCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.70, C:0.17, G:0.03, T:0.10
Consensus pattern (18 bp):
ATAAAACCCAGAAATAAA
Found at i:59232647 original size:7 final size:7
Alignment explanation
Indices: 59232637--59232672 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
59232627 TAATATTTAT
59232637 TCTTAAA
1 TCTTAAA
59232644 TCTTAAA
1 TCTTAAA
*
59232651 TCTTAAT
1 TCTTAAA
*
59232658 TCTTAAT
1 TCTTAAA
59232665 TCTTAAA
1 TCTTAAA
59232672 T
1 T
59232673 TTCTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (7 bp):
TCTTAAA
Found at i:59235244 original size:42 final size:42
Alignment explanation
Indices: 59234891--59235242 Score: 498
Period size: 42 Copynumber: 8.4 Consensus size: 42
59234881 ATGTCACTAA
* * *
59234891 CTTTTGCGGCGCTTACATAAAAAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCGCTAAAGATCATGTT
* *
59234935 CTTTAGCGGCGCTTAGAAAAAAACGCTGCTAAAGATCATGCT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
59234977 CTTTAGCGGCGCTT--AAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
59235017 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
59235059 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
59235101 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * * *
59235143 CTTTAGCGGCGCTTTGGAAGAAAACGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCATGTT
* ***
59235186 CTATAGCGGCGCTTATTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGA-TCA-TGTT
59235228 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
59235243 TTTCACAAAC
Statistics
Matches: 284, Mismatches: 19, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
40 38 0.13
41 1 0.00
42 197 0.69
43 35 0.12
44 13 0.05
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:59235743 original size:21 final size:20
Alignment explanation
Indices: 59235674--59235742 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 20
59235664 GCTTCTATTA
59235674 CTGCTTCACTCGCTGCGACCT
1 CTGCTTCACTCGCTGCG-CCT
* * *
59235695 CTGCTTCTCTCGTTGTAGCCT
1 CTGCTTCACTCGCTG-CGCCT
59235716 CTGCTTTC-CTCGCTGCCGCCT
1 CTGC-TTCACTCGCTG-CGCCT
59235737 CTGCTT
1 CTGCTT
59235743 TAAGTTGCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 2 0.05
21 34 0.85
22 4 0.10
ACGTcount: A:0.04, C:0.41, G:0.19, T:0.36
Consensus pattern (20 bp):
CTGCTTCACTCGCTGCGCCT
Found at i:59241225 original size:9 final size:9
Alignment explanation
Indices: 59241211--59241347 Score: 88
Period size: 9 Copynumber: 15.9 Consensus size: 9
59241201 AAGATATACA
59241211 TTATGTAAG
1 TTATGTAAG
59241220 TTATGTAAG
1 TTATGTAAG
*
59241229 TTGTGTAAG
1 TTATGTAAG
**
59241238 TTGCGTAAG
1 TTATGTAAG
* *
59241247 ATGTGT-A-
1 TTATGTAAG
* *
59241254 TTATGAAAC
1 TTATGTAAG
59241263 TTATGTAAG
1 TTATGTAAG
59241272 TTATGTAAG
1 TTATGTAAG
*
59241281 TTGTGTAAG
1 TTATGTAAG
**
59241290 TTGCGTAAG
1 TTATGTAAG
* *
59241299 ATGTGT-A-
1 TTATGTAAG
* *
59241306 TTATGAAAC
1 TTATGTAAG
59241315 TTATGTAAG
1 TTATGTAAG
*
59241324 TTATGT--C
1 TTATGTAAG
*
59241331 TTATGTTAG
1 TTATGTAAG
59241340 TTATGTAA
1 TTATGTAA
59241348 TTTTTGTATT
Statistics
Matches: 101, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
7 12 0.12
8 4 0.04
9 85 0.84
ACGTcount: A:0.30, C:0.04, G:0.23, T:0.43
Consensus pattern (9 bp):
TTATGTAAG
Found at i:59241289 original size:52 final size:52
Alignment explanation
Indices: 59241211--59241329 Score: 238
Period size: 52 Copynumber: 2.3 Consensus size: 52
59241201 AAGATATACA
59241211 TTATGTAAGTTATGTAAGTTGTGTAAGTTGCGTAAGATGTGTATTATGAAAC
1 TTATGTAAGTTATGTAAGTTGTGTAAGTTGCGTAAGATGTGTATTATGAAAC
59241263 TTATGTAAGTTATGTAAGTTGTGTAAGTTGCGTAAGATGTGTATTATGAAAC
1 TTATGTAAGTTATGTAAGTTGTGTAAGTTGCGTAAGATGTGTATTATGAAAC
59241315 TTATGTAAGTTATGT
1 TTATGTAAGTTATGT
59241330 CTTATGTTAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.30, C:0.03, G:0.24, T:0.42
Consensus pattern (52 bp):
TTATGTAAGTTATGTAAGTTGTGTAAGTTGCGTAAGATGTGTATTATGAAAC
Found at i:59241333 original size:16 final size:16
Alignment explanation
Indices: 59241314--59241345 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
59241304 TATTATGAAA
59241314 CTTATGTAAGTTATGT
1 CTTATGTAAGTTATGT
*
59241330 CTTATGTTAGTTATGT
1 CTTATGTAAGTTATGT
59241346 AATTTTTGTA
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:0.22, C:0.06, G:0.19, T:0.53
Consensus pattern (16 bp):
CTTATGTAAGTTATGT
Found at i:59241334 original size:25 final size:25
Alignment explanation
Indices: 59241250--59241427 Score: 94
Period size: 25 Copynumber: 7.2 Consensus size: 25
59241240 GCGTAAGATG
59241250 TGTATTATGAAACTTATGTAAGTTA
1 TGTATTATGAAACTTATGTAAGTTA
* * * ** * *
59241275 TGTAAGTTGTGTAAGTTGCGTAAGATG
1 TGT-A-TTATGAAACTTATGTAAGTTA
59241302 TGTATTATGAAACTTATGTAAGTTA
1 TGTATTATGAAACTTATGTAAGTTA
* ** * * *
59241327 TGTCTTATGTTAGTTATGTAATTTT
1 TGTATTATGAAACTTATGTAAGTTA
* *
59241352 TGTATTATTTACAC--ATGTAAGTTA
1 TGTATTA-TGAAACTTATGTAAGTTA
* * ** ** *
59241376 TGTCTTATGTAAGATGCGTAAGTTG
1 TGTATTATGAAACTTATGTAAGTTA
*
59241401 TGTATTATGAAAGTTATGT--GTTA
1 TGTATTATGAAACTTATGTAAGTTA
59241424 TGTA
1 TGTA
59241428 AATGAATATA
Statistics
Matches: 107, Mismatches: 41, Indels: 12
0.67 0.26 0.08
Matches are distributed among these distances:
23 9 0.08
24 14 0.13
25 63 0.59
26 4 0.04
27 17 0.16
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (25 bp):
TGTATTATGAAACTTATGTAAGTTA
Found at i:59242649 original size:14 final size:14
Alignment explanation
Indices: 59242630--59242659 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
59242620 CACGAACAGC
59242630 AAGATGATTAACTA
1 AAGATGATTAACTA
59242644 AAGATGATTAACTA
1 AAGATGATTAACTA
59242658 AA
1 AA
59242660 AACCTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (14 bp):
AAGATGATTAACTA
Found at i:59242882 original size:71 final size:71
Alignment explanation
Indices: 59242795--59242995 Score: 359
Period size: 71 Copynumber: 2.8 Consensus size: 71
59242785 CCAGATCCAG
* * *
59242795 ATTTCAGAA-CCAAAGCATAATTCAGAACATAACAGCATAATCAAAAATAAATTATTTCAGACTC
1 ATTTCA-AATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTC
59242859 AGAAATT
65 AGAAATT
59242866 ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTCA
1 ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTCA
59242931 GAAATT
66 GAAATT
59242937 ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCA
1 ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCA
59242996 AATCCACTCA
Statistics
Matches: 126, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
70 2 0.02
71 124 0.98
ACGTcount: A:0.50, C:0.18, G:0.06, T:0.26
Consensus pattern (71 bp):
ATTTCAAATCCAAAGCATATTTCAGAACATAACAACATAATCAAAAACAAATTATTTCAGACTCA
GAAATT
Found at i:59242888 original size:36 final size:36
Alignment explanation
Indices: 59242847--59242962 Score: 123
Period size: 36 Copynumber: 3.2 Consensus size: 36
59242837 AAAAATAAAT
59242847 TATTTCAGACTCAGAAATTATTTCAAATCCAAAGCA
1 TATTTCAGACTCAGAAATTATTTCAAATCCAAAGCA
* * * ** *
59242883 TATTTCAGAACATAACAACA-TA-ATCAAAAACAAA--T
1 TATTTCAG-AC-TCAGAA-ATTATTTCAAATCCAAAGCA
59242918 TATTTCAGACTCAGAAATTATTTCAAATCCAAAGCA
1 TATTTCAGACTCAGAAATTATTTCAAATCCAAAGCA
59242954 TATTTCAGA
1 TATTTCAGA
59242963 ACATAACAAC
Statistics
Matches: 61, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
32 1 0.02
33 6 0.10
34 11 0.18
35 8 0.13
36 17 0.28
37 11 0.18
38 6 0.10
39 1 0.02
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (36 bp):
TATTTCAGACTCAGAAATTATTTCAAATCCAAAGCA
Found at i:59243330 original size:22 final size:22
Alignment explanation
Indices: 59243302--59243348 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
59243292 GTGGCTGTAA
*
59243302 TAACAGAAACGCCTTACCTATT
1 TAACAGAAACGCCTTACATATT
59243324 TAACAGAAACGCCTTACATATT
1 TAACAGAAACGCCTTACATATT
59243346 TAA
1 TAA
59243349 TCGGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
TAACAGAAACGCCTTACATATT
Found at i:59244360 original size:8 final size:8
Alignment explanation
Indices: 59244343--59244374 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
59244333 TTTGGGATTT
59244343 AACC-CTA
1 AACCTCTA
59244350 AACCTCTA
1 AACCTCTA
59244358 AACCTCTA
1 AACCTCTA
59244366 AACCT-TA
1 AACCTCTA
59244373 AA
1 AA
59244375 ATCTTAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 8 0.33
8 16 0.67
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (8 bp):
AACCTCTA
Found at i:59244547 original size:14 final size:15
Alignment explanation
Indices: 59244530--59244567 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
59244520 AACCCAAAAC
59244530 ACCCTAATAC-CC-TA
1 ACCCTAA-ACACCATA
59244544 ACCCTAAACACCATA
1 ACCCTAAACACCATA
59244559 ACCCTAAAC
1 ACCCTAAAC
59244568 CTACATCGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 9 0.41
15 11 0.50
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (15 bp):
ACCCTAAACACCATA
Found at i:59244586 original size:7 final size:7
Alignment explanation
Indices: 59244473--59244587 Score: 56
Period size: 7 Copynumber: 16.0 Consensus size: 7
59244463 ACTAAAGTAG
59244473 CCTAAAC
1 CCTAAAC
*
59244480 CCCAAAC
1 CCTAAAC
*
59244487 CTTAAAC
1 CCTAAAC
* *
59244494 CTTATAC
1 CCTAAAC
*
59244501 CCTAGAC
1 CCTAAAC
59244508 TCCTAAAC
1 -CCTAAAC
**
59244516 TTTAAAC
1 CCTAAAC
*
59244523 CCAAAACAC
1 CC-TAA-AC
59244532 CCTAATAC
1 CCTAA-AC
59244540 CCT-AAC
1 CCTAAAC
59244546 CCTAAAC
1 CCTAAAC
59244553 ACC-ATAAC
1 -CCTA-AAC
59244561 CCTAAA-
1 CCTAAAC
* *
59244567 CCTACAT
1 CCTAAAC
*
59244574 CGTAAAC
1 CCTAAAC
59244581 CCTAAAC
1 CCTAAAC
59244588 TTTAAACTTT
Statistics
Matches: 81, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
6 10 0.12
7 46 0.57
8 21 0.26
9 4 0.05
ACGTcount: A:0.41, C:0.38, G:0.02, T:0.19
Consensus pattern (7 bp):
CCTAAAC
Found at i:59245047 original size:113 final size:114
Alignment explanation
Indices: 59244752--59245494 Score: 565
Period size: 113 Copynumber: 6.5 Consensus size: 114
59244742 GCTTTCAACA
* * * * * * * *
59244752 AAGCGCCACTAATTTTAGTATAAATTAAGACCAAAAC-ATTGCGTTTTGTTTATGGTATGTCGCG
1 AAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGA-TGCGTTTTGGTTAAGATATTTTGCG
* * * * * **
59244816 GCGCTATCAACAAATCGCCGCTAATACTATGCTTTAGCGGCGTTTTATCAA
65 GCGCTTTC-ACAAAGCGCCGCTAATACTATGCTTTAACGGCGTTTCACCGT
* * * * * * * *
59244867 AATCGCCACTAAATCAAGGATACATCAAGACCAAAACGATGCGTTTTGGTTCAGATACTTGGTGG
1 AAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
* *
59244932 CGCTTTTATCCAAGCGCCGCTAATACTATGCTTTAACGGCGTTTCA-C-T
66 CGCTTTCA-CAAAGCGCCGCTAATACTATGCTTTAACGGCGTTTCACCGT
* * * **
59244980 AAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTTAAGATATTTTGCGG
1 AAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
* * * * * *
59245045 CGCTTCTCAAAAAGTGCCGCTATTAATATTCTTTAGCGGCGGTTT-ACCGT
66 CGCTT-TCACAAAGCGCCGCTAATACTATGCTTTAACGGC-GTTTCACCGT
* * * * * *
59245095 AAGTGCCACTAATTTTA-TATACATTAAGATCAAAACGCTGCGTTTTTGTTAAGATATTTTGCGG
1 AAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
** * * * *
59245159 CGCTAGCTACAAATCGCCGCTAATACTATTCTTTAGCGGCGTTTGACCGT
66 CGCTTTC-ACAAAGCGCCGCTAATACTATGCTTTAACGGCGTTTCACCGT
* * * ** * * * *
59245209 ATGCGCCACTAGTTCTAGTATAAATCAAGACCAAAACGATATGTTTCGCTTCAGATAGTTTGCGG
1 AAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
* ** * * * * **
59245274 CGCTTCCGTAAAGCGCCGCTATTACTGTACTTCAACGGCGTTTTC-CTAT
66 CGCTTTCACAAAGCGCCGCTAATACTATGCTTTAACGGCG-TTTCACCGT
* ** *
59245323 AAGCGCCACTAATTCTAAG-ATACCTCAAGACC-AAACTCTGCGTTTTGGTTAAGCTATTTTGCG
1 AAGCGCCACTAATTCT-AGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCG
* * * * * *
59245386 GCG-TTTCCAGAAAGCGCCACTATTACTGTCCTTTAACGGCGTTTC-GCGT
65 GCGCTTT-CACAAAGCGCCGCTAATACTATGCTTTAACGGCGTTTCACCGT
* * * * * *
59245435 AAACGCCACTATTTTTAAG-ATACATCAAGACGAAAAC-ACAGCGTTTTGGTTAAGAGATTT
1 AAGCGCCACTAATTCT-AGTATACATCAAGACCAAAACGA-TGCGTTTTGGTTAAGATATTT
59245495 CGTGGCGCAT
Statistics
Matches: 495, Mismatches: 119, Indels: 30
0.77 0.18 0.05
Matches are distributed among these distances:
112 34 0.07
113 163 0.33
114 149 0.30
115 148 0.30
116 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (114 bp):
AAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGATGCGTTTTGGTTAAGATATTTTGCGG
CGCTTTCACAAAGCGCCGCTAATACTATGCTTTAACGGCGTTTCACCGT
Found at i:59245367 original size:228 final size:227
Alignment explanation
Indices: 59244738--59245388 Score: 533
Period size: 228 Copynumber: 2.9 Consensus size: 227
59244728 AGATATTTTG
* * * * * * *
59244738 CGGCGCTTTCAACAAAGCGCCACTAATTTTAGTATAAATTAAGACCAAAAC-ATTGCGTTTTGTT
1 CGGCG-TTTC-ACTAAGCGCCACTAATTCTACTATAAATCAAGACCAAAACGA-TACGTTTCGCT
* * * * * * * * * * * *
59244802 TATGGTA-TGTCGCGGCGC-TATCAACAAATCGCCGCTAATACTATGCTTTAGCGGCGTTTTATC
63 TAAGATAGT-TTGCGGCGCTTCTCAA-AAAGCGCCGCTATTAATATACTTCAACGGCGGTTTACC
* * * * * * * * * *
59244865 AAAATCGCCACTAAATCAAGGATACATCAAGACCAAAACGATGCGTTTTGGTTCAGATACTTGGT
126 ATAAGCGCCACTAATTTAA-GATACATCAAGATCAAAACGCTGCGTTTTGGTTAAGATATTTTGC
** * *
59244930 GGCGCT-TTTATCCAAGCGCCGCTAATACTATGCTTTAA
190 GGCGCTAGCTA-CAAATCGCCGCTAATACTATGCTTTAA
* * * ** * * *
59244968 CGGCGTTTCACTAAGCGCCACTAATTCTACTATACATCGAGGCCAAAATTATGCGTTTTGGTTAA
1 CGGCGTTTCACTAAGCGCCACTAATTCTACTATAAATCAAGACCAAAACGATACGTTTCGCTTAA
* * * * * *
59245033 GATATTTTGCGGCGCTTCTCAAAAAGTGCCGCTATTAATATTCTTTAGCGGCGGTTTACCGTAAG
66 GATAGTTTGCGGCGCTTCTCAAAAAGCGCCGCTATTAATATACTTCAACGGCGGTTTACCATAAG
* * * * *
59245098 TGCCACTAATTTTATATACATTAAGATCAAAACGCTGCGTTTTTGTTAAGATATTTTGCGGCGCT
131 CGCCACTAATTTAAGATACATCAAGATCAAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCT
* *
59245163 AGCTACAAATCGCCGCTAATACTATTCTTTAG
196 AGCTACAAATCGCCGCTAATACTATGCTTTAA
* * * * *
59245195 CGGCGTTTGACCGTATGCGCCACTAGTTCTAGTATAAATCAAGACCAAAACGATATGTTTCGCTT
1 CGGCGTTTCA-C-TAAGCGCCACTAATTCTACTATAAATCAAGACCAAAACGATACGTTTCGCTT
* ** * * *
59245260 CAGATAGTTTGCGGCGCTTC-CGTAAAGCGCCGCTATTACTGTACTTCAACGGC-GTTTTCCTAT
64 AAGATAGTTTGCGGCGCTTCTCAAAAAGCGCCGCTATTAATATACTTCAACGGCGGTTTACC-AT
* * * *
59245323 AAGCGCCACTAATTCTAAGATACCTCAAGA-CCAAACTCTGCGTTTTGGTTAAGCTATTTTGCGG
128 AAGCGCCACTAATT-TAAGATACATCAAGATCAAAACGCTGCGTTTTGGTTAAGATATTTTGCGG
59245387 CG
192 CG
59245389 TTTCCAGAAA
Statistics
Matches: 337, Mismatches: 76, Indels: 18
0.78 0.18 0.04
Matches are distributed among these distances:
227 80 0.24
228 172 0.51
229 80 0.24
230 5 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (227 bp):
CGGCGTTTCACTAAGCGCCACTAATTCTACTATAAATCAAGACCAAAACGATACGTTTCGCTTAA
GATAGTTTGCGGCGCTTCTCAAAAAGCGCCGCTATTAATATACTTCAACGGCGGTTTACCATAAG
CGCCACTAATTTAAGATACATCAAGATCAAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCT
AGCTACAAATCGCCGCTAATACTATGCTTTAA
Found at i:59247627 original size:29 final size:30
Alignment explanation
Indices: 59247586--59247662 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
59247576 ACAATAATAA
**
59247586 AAAATTACATTTTGACCCCTT-ACTTTTTT
1 AAAATTACATTTTGACCCCTTAACTTTCCT
** *
59247615 AAAATTATGTTTTGACCTCTTAACTTTCCT
1 AAAATTACATTTTGACCCCTTAACTTTCCT
59247645 AAAATTACATTTTGACCC
1 AAAATTACATTTTGACCC
59247663 ATAAACTTCT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 18 0.46
30 21 0.54
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTTAACTTTCCT
Found at i:59247670 original size:30 final size:31
Alignment explanation
Indices: 59247586--59247722 Score: 99
Period size: 30 Copynumber: 4.6 Consensus size: 31
59247576 ACAATAATAA
* * *
59247586 AAAATTACATTTTGACCCCT-TACTTTT-TT
1 AAAATTACATTTTGACCCATAAACTTTTCTC
** * *
59247615 AAAATTATGTTTTGACCTC-TTAACTTTCCT-
1 AAAATTACATTTTGACC-CATAAACTTTTCTC
59247645 AAAATTACATTTTGACCCATAAAC--TTCTC
1 AAAATTACATTTTGACCCATAAACTTTTCTC
* * * *
59247674 GAAGTTATATTTTGACCCCTAAA-TTTTCTC
1 AAAATTACATTTTGACCCATAAACTTTTCTC
* *
59247704 AAAATTACACTTGGACCCA
1 AAAATTACATTTTGACCCA
59247723 GAGTTTTGCT
Statistics
Matches: 83, Mismatches: 18, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
28 3 0.04
29 36 0.43
30 43 0.52
31 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (31 bp):
AAAATTACATTTTGACCCATAAACTTTTCTC
Found at i:59248259 original size:7 final size:7
Alignment explanation
Indices: 59248249--59248302 Score: 78
Period size: 7 Copynumber: 8.1 Consensus size: 7
59248239 GAGAAGGAGG
59248249 AAGAAGA
1 AAGAAGA
59248256 AAGAAGA
1 AAGAAGA
*
59248263 AAAAAGA
1 AAGAAGA
59248270 AAGAAGA
1 AAGAAGA
59248277 AA-AAGA
1 AAGAAGA
59248283 AA-AAGA
1 AAGAAGA
59248289 AAGAA-A
1 AAGAAGA
59248295 AAGAAGA
1 AAGAAGA
59248302 A
1 A
59248303 CAAAAAGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 18 0.42
7 25 0.58
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:59248261 original size:10 final size:9
Alignment explanation
Indices: 59248248--59248324 Score: 68
Period size: 10 Copynumber: 8.0 Consensus size: 9
59248238 AGAGAAGGAG
59248248 GAAGAAGAAA
1 GAAGAA-AAA
59248258 GAAGAAAAAA
1 GAAG-AAAAA
59248268 GAAAGAAGAAA
1 G-AAGAA-AAA
59248279 -AAGAAAAA
1 GAAGAAAAA
59248287 GAAAGAAAAA
1 G-AAGAAAAA
59248297 GAAGAACAAA
1 GAAGAA-AAA
59248307 -AAGAAAAA
1 GAAGAAAAA
*
59248315 AAAGAGAAAA
1 GAAGA-AAAA
59248325 AAATAAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.10
9 19 0.32
10 26 0.44
11 8 0.14
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:59248310 original size:37 final size:39
Alignment explanation
Indices: 59248249--59248333 Score: 104
Period size: 37 Copynumber: 2.2 Consensus size: 39
59248239 GAGAAGGAGG
*
59248249 AAGAAGAAAGAAGAAAAAAGAAAGAAGAAAAAGA-AAAAGA
1 AAGAA-AAAGAAGAAAAAAGAAAGAAAAAAAAGAGAAAA-A
*
59248289 AAGAAAAAGAAG-AACAA-AAAGAAAAAAAAGAGAAAAA
1 AAGAAAAAGAAGAAAAAAGAAAGAAAAAAAAGAGAAAAA
*
59248326 AATAAAAA
1 AAGAAAAA
59248334 ATAACAGACG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 21 0.51
38 8 0.20
39 7 0.17
40 5 0.12
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.01
Consensus pattern (39 bp):
AAGAAAAAGAAGAAAAAAGAAAGAAAAAAAAGAGAAAAA
Found at i:59248332 original size:18 final size:16
Alignment explanation
Indices: 59248262--59248334 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 16
59248252 AAGAAAGAAG
59248262 AAAAAAGAAAGAAGAAAA
1 AAAAAAGAAA-AA-AAAA
*
59248280 AGAAAAAGAAAGAAAAA
1 A-AAAAAGAAAAAAAAA
* * *
59248297 GAAGAACAAAAAGAAAA
1 AAAAAAGAAAAA-AAAA
*
59248314 AAAAGAGAAAAAAATAA
1 AAAAAAGAAAAAAA-AA
59248331 AAAA
1 AAAA
59248335 TAACAGACGG
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
16 10 0.23
17 22 0.51
18 2 0.05
19 9 0.21
ACGTcount: A:0.82, C:0.01, G:0.15, T:0.01
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAA
Found at i:59248333 original size:9 final size:9
Alignment explanation
Indices: 59248249--59248334 Score: 82
Period size: 9 Copynumber: 9.0 Consensus size: 9
59248239 GAGAAGGAGG
*
59248249 AAGAAGAAAG
1 AAGAA-AAAA
59248259 AAGAAAAAAGA
1 AAG-AAAAA-A
*
59248270 AAGAAGAAA
1 AAGAAAAAA
59248279 AAGAAAAAGA
1 AAGAAAAA-A
*
59248289 AAGAAAAAG
1 AAGAAAAAA
*
59248298 AAGAACAAA
1 AAGAAAAAA
59248307 AAGAAAAAA
1 AAGAAAAAA
59248316 AAGAGAAAAA
1 AAGA-AAAAA
*
59248326 AATAAAAAA
1 AAGAAAAAA
59248335 TAACAGACGG
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
9 32 0.50
10 27 0.42
11 5 0.08
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:59248597 original size:11 final size:11
Alignment explanation
Indices: 59248581--59248621 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
59248571 GCCCAGCAGA
59248581 AAAAGAAAAAG
1 AAAAGAAAAAG
*
59248592 AAAAG-AGAAG
1 AAAAGAAAAAG
*
59248602 AAAAAAAAAAG
1 AAAAGAAAAAG
59248613 -AAAGAAAAA
1 AAAAGAAAAA
59248622 AGGGGGGCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:59248610 original size:15 final size:15
Alignment explanation
Indices: 59248582--59248622 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
59248572 CCCAGCAGAA
*
59248582 AAAGAAAAAGAAAAG
1 AAAGAAAAAAAAAAG
59248597 AGAAGAAAAAAAAAAG
1 A-AAGAAAAAAAAAAG
59248613 AAAGAAAAAA
1 AAAGAAAAAA
59248623 GGGGGGCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAAAG
Found at i:59249123 original size:18 final size:18
Alignment explanation
Indices: 59249100--59249162 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
59249090 TTTTTTTAAA
59249100 AAAAATTAATCGTGTTTC
1 AAAAATTAATCGTGTTTC
* *
59249118 AAAAATT-TTCATGTTTTC
1 AAAAATTAATCGTG-TTTC
**
59249136 -AAAATTTCTCGTGTTTC
1 AAAAATTAATCGTGTTTC
*
59249153 AAAAAATAAT
1 AAAAATTAAT
59249163 AATAAAATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
17 14 0.40
18 21 0.60
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (18 bp):
AAAAATTAATCGTGTTTC
Found at i:59249132 original size:17 final size:18
Alignment explanation
Indices: 59249112--59249157 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
59249102 AAATTAATCG
59249112 TGTTTCAAAAATTT-TCA
1 TGTTTCAAAAATTTCTCA
*
59249129 TGTTTTC-AAAATTTCTCG
1 TG-TTTCAAAAATTTCTCA
59249147 TGTTTCAAAAA
1 TGTTTCAAAAA
59249158 ATAATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (18 bp):
TGTTTCAAAAATTTCTCA
Found at i:59249237 original size:18 final size:18
Alignment explanation
Indices: 59249216--59249363 Score: 115
Period size: 18 Copynumber: 8.3 Consensus size: 18
59249206 CTTCGTTCTT
*
59249216 CAAAAATTTTCGTATTTC
1 CAAAAATTTTCGTGTTTC
59249234 CAAAAATTTTCGTGTTTC
1 CAAAAATTTTCGTGTTTC
* * * *
59249252 AAAAAAAATCTCGTGTTTT
1 -CAAAAATTTTCGTGTTTC
59249271 CAAAAATTTTCGTGTTT-
1 CAAAAATTTTCGTGTTTC
* *
59249288 TAGAAATTTTCGTGTTT-
1 CAAAAATTTTCGTGTTTC
** * * *
59249305 TTAAAATTCTCGT-ATTG
1 CAAAAATTTTCGTGTTTC
*
59249322 CAAAAATTTCCGTGTTTTC
1 CAAAAATTTTCGTG-TTTC
*
59249341 AAAAAATTTTCCGTGTTT-
1 CAAAAATTTT-CGTGTTTC
59249359 CAAAA
1 CAAAA
59249364 TTCTCATTTT
Statistics
Matches: 102, Mismatches: 23, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
16 2 0.02
17 34 0.33
18 35 0.34
19 27 0.26
20 4 0.04
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
CAAAAATTTTCGTGTTTC
Found at i:59249365 original size:17 final size:17
Alignment explanation
Indices: 59249214--59249363 Score: 138
Period size: 17 Copynumber: 8.4 Consensus size: 17
59249204 AACTTCGTTC
*
59249214 TTCAAAAATTTTCGTAT
1 TTCAAAAATTTTCGTGT
59249231 TTCCAAAAATTTTCGTGT
1 TT-CAAAAATTTTCGTGT
* *
59249249 TTCAAAAAAAATCTCGTGTT
1 TTC--AAAAATTTTCGTG-T
59249269 TTCAAAAATTTTCGTGT
1 TTCAAAAATTTTCGTGT
* *
59249286 TTTAGAAATTTTCGTGT
1 TTCAAAAATTTTCGTGT
** * *
59249303 TTTTAAAATTCTCGTAT
1 TTCAAAAATTTTCGTGT
* *
59249320 TGCAAAAATTTCCGTGTT
1 TTCAAAAATTTTCGTG-T
59249338 TTCAAAAAATTTTCCGTGT
1 TTC-AAAAATTTT-CGTGT
59249357 TTCAAAA
1 TTCAAAA
59249364 TTCTCATTTT
Statistics
Matches: 107, Mismatches: 19, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
17 42 0.39
18 34 0.32
19 23 0.21
20 8 0.07
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (17 bp):
TTCAAAAATTTTCGTGT
Found at i:59254950 original size:18 final size:18
Alignment explanation
Indices: 59254927--59254965 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
59254917 GTAGAAAAAC
59254927 ATCTCAAAATTAAGGCAT
1 ATCTCAAAATTAAGGCAT
59254945 ATCTCAAAATTAAGGCAT
1 ATCTCAAAATTAAGGCAT
59254963 ATC
1 ATC
59254966 AATGACAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (18 bp):
ATCTCAAAATTAAGGCAT
Found at i:59257694 original size:15 final size:16
Alignment explanation
Indices: 59257664--59257697 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
59257654 TTTTTTAGAA
59257664 AAAACATTAACAAAAC
1 AAAACATTAACAAAAC
*
59257680 AAAACA-TAACTAAAC
1 AAAACATTAACAAAAC
59257695 AAA
1 AAA
59257698 GAAGACGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.71, C:0.18, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAACATTAACAAAAC
Found at i:59257822 original size:12 final size:12
Alignment explanation
Indices: 59257807--59257849 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
59257797 CCTGCTCCTG
59257807 CTCCACCTCCAA
1 CTCCACCTCCAA
*
59257819 CTCCACCGCCAA
1 CTCCACCTCCAA
** *
59257831 CAGCACCTCCTA
1 CTCCACCTCCAA
59257843 CTCCACC
1 CTCCACC
59257850 CCCTACACCA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.23, C:0.58, G:0.05, T:0.14
Consensus pattern (12 bp):
CTCCACCTCCAA
Found at i:59257861 original size:24 final size:24
Alignment explanation
Indices: 59257809--59257861 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
59257799 TGCTCCTGCT
*
59257809 CCACCTCCAACTCCACCGCCAACA
1 CCACCTCCAACTCCACCCCCAACA
* * *
59257833 GCACCTCCTACTCCACCCCCTACA
1 CCACCTCCAACTCCACCCCCAACA
59257857 CCACC
1 CCACC
59257862 ACCAGCACCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.60, G:0.04, T:0.11
Consensus pattern (24 bp):
CCACCTCCAACTCCACCCCCAACA
Found at i:59257890 original size:27 final size:27
Alignment explanation
Indices: 59257872--59258017 Score: 193
Period size: 27 Copynumber: 5.4 Consensus size: 27
59257862 ACCAGCACCA
*
59257872 CCAAATCCACCGACTCCACCGGTTCCT
1 CCAAATCCACCGACTCCACCGGTACCT
* * *
59257899 CCAAGTCCATCGGCTCCACCGGTACCT
1 CCAAATCCACCGACTCCACCGGTACCT
59257926 CCAAATCCACCGACTCCACCGGTACCT
1 CCAAATCCACCGACTCCACCGGTACCT
* *
59257953 CCAAGTCCACCGACTCCACCGGTTCCT
1 CCAAATCCACCGACTCCACCGGTACCT
* * * *
59257980 CCAAGTCCACCGAATCCTCCGGTTCCT
1 CCAAATCCACCGACTCCACCGGTACCT
*
59258007 CCAAGTCCACC
1 CCAAATCCACC
59258018 CAAACCACCA
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 108 1.00
ACGTcount: A:0.21, C:0.47, G:0.14, T:0.18
Consensus pattern (27 bp):
CCAAATCCACCGACTCCACCGGTACCT
Found at i:59257945 original size:81 final size:81
Alignment explanation
Indices: 59257860--59258017 Score: 226
Period size: 81 Copynumber: 2.0 Consensus size: 81
59257850 CCCTACACCA
* **
59257860 CCACCAGCACCACCAAATCCACCGACTCCACCGGTTCCTCCAAGTCCATCGGCTCCACCGGTACC
1 CCACCAGCACCACCAAATCCACCGACTCCACCGGTTCCTCCAAGTCCACCGAATCCACCGGTACC
59257925 TCCAAATCCACCGACT
66 TCCAAATCCACCGACT
* * * * * *
59257941 CCACCGGTACCTCCAAGTCCACCGACTCCACCGGTTCCTCCAAGTCCACCGAATCCTCCGGTTCC
1 CCACCAGCACCACCAAATCCACCGACTCCACCGGTTCCTCCAAGTCCACCGAATCCACCGGTACC
*
59258006 TCCAAGTCCACC
66 TCCAAATCCACC
59258018 CAAACCACCA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 67 1.00
ACGTcount: A:0.22, C:0.48, G:0.13, T:0.16
Consensus pattern (81 bp):
CCACCAGCACCACCAAATCCACCGACTCCACCGGTTCCTCCAAGTCCACCGAATCCACCGGTACC
TCCAAATCCACCGACT
Found at i:59258026 original size:54 final size:54
Alignment explanation
Indices: 59257872--59258017 Score: 229
Period size: 54 Copynumber: 2.7 Consensus size: 54
59257862 ACCAGCACCA
* *
59257872 CCAAATCCACCGACTCCACCGGTTCCTCCAAGTCCATCGGCTCCACCGGTACCT
1 CCAAATCCACCGACTCCACCGGTTCCTCCAAGTCCACCGACTCCACCGGTACCT
* *
59257926 CCAAATCCACCGACTCCACCGGTACCTCCAAGTCCACCGACTCCACCGGTTCCT
1 CCAAATCCACCGACTCCACCGGTTCCTCCAAGTCCACCGACTCCACCGGTACCT
* * *
59257980 CCAAGTCCACCGAATCCTCCGGTTCCTCCAAGTCCACC
1 CCAAATCCACCGACTCCACCGGTTCCTCCAAGTCCACC
59258018 CAAACCACCA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.21, C:0.47, G:0.14, T:0.18
Consensus pattern (54 bp):
CCAAATCCACCGACTCCACCGGTTCCTCCAAGTCCACCGACTCCACCGGTACCT
Found at i:59259055 original size:15 final size:15
Alignment explanation
Indices: 59259006--59259063 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
59258996 TCCACTTATA
*
59259006 TTATTATTTTAAT-T
1 TTATTAATTTAATAT
* *
59259020 TTTTTAATTGTATTA-
1 TTATTAATT-TAATAT
59259035 TT-TTAATTTAATAT
1 TTATTAATTTAATAT
*
59259049 TTATTAATTTTATAT
1 TTATTAATTTAATAT
59259064 GTTTTCTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.11
14 15 0.43
15 16 0.46
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTAATTTAATAT
Found at i:59261673 original size:30 final size:30
Alignment explanation
Indices: 59261625--59261709 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
59261615 GATACTCGGG
*
59261625 AATA-AGTTACTCACACAAGTTGACAGTAT
1 AATAGAGTTGCTCACACAAGTTGACAGTAT
* * * *
59261654 -ATCAGGGTTGCTTACACAAGTTGGCATTAT
1 AAT-AGAGTTGCTCACACAAGTTGACAGTAT
*
59261684 AATAGAGTTGCTCACACAAGCTGACA
1 AATAGAGTTGCTCACACAAGTTGACA
59261710 TCATATCGAG
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
28 2 0.05
29 1 0.02
30 39 0.89
31 2 0.05
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (30 bp):
AATAGAGTTGCTCACACAAGTTGACAGTAT
Found at i:59262098 original size:35 final size:35
Alignment explanation
Indices: 59262059--59262129 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
59262049 ATTCTACTCA
*
59262059 ATTGTAATATATATATATATTCAAGTATATGTCAT
1 ATTGTAATATATATATAAATTCAAGTATATGTCAT
59262094 ATTGTAATATATATATAAATTCAAGTATATGTCAT
1 ATTGTAATATATATATAAATTCAAGTATATGTCAT
59262129 A
1 A
59262130 CATAAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (35 bp):
ATTGTAATATATATATAAATTCAAGTATATGTCAT
Found at i:59265062 original size:15 final size:15
Alignment explanation
Indices: 59265042--59265072 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
59265032 CATTAATTGC
*
59265042 TTTTCTTCTTCTTCT
1 TTTTCTTATTCTTCT
59265057 TTTTCTTATTCTTCT
1 TTTTCTTATTCTTCT
59265072 T
1 T
59265073 CTCCTTTAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCTTATTCTTCT
Found at i:59265153 original size:27 final size:27
Alignment explanation
Indices: 59265111--59265208 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 27
59265101 ATAATACAAG
* ** *
59265111 TGGTGCCGCCTGTGGCAGTGGCGCCTT
1 TGGTGCCGCCTCTGGCACAGGCACCTT
59265138 TGGTGCCGCCTCTGGCACAGGCACCTT
1 TGGTGCCGCCTCTGGCACAGGCACCTT
* ** *
59265165 TGATGCCGCCTCTACCACAAGCACCTT
1 TGGTGCCGCCTCTGGCACAGGCACCTT
*
59265192 TGGTGCCGCCTGTGGCA
1 TGGTGCCGCCTCTGGCA
59265209 TCCAGGTTTC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.11, C:0.35, G:0.31, T:0.23
Consensus pattern (27 bp):
TGGTGCCGCCTCTGGCACAGGCACCTT
Found at i:59265232 original size:5 final size:5
Alignment explanation
Indices: 59265222--59265251 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
59265212 AGGTTTCTAC
59265222 TGTTT TGTTT TGTTT TGTTT TGTTT T-TTT T
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT T
59265252 AGTATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TGTTT
Found at i:59265315 original size:18 final size:19
Alignment explanation
Indices: 59265280--59265317 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
59265270 TAAAAAATAA
*
59265280 TATTATTTTGATATTATTT
1 TATTATTTTGATAATATTT
*
59265299 TATTTTTTTG-TAATATTT
1 TATTATTTTGATAATATTT
59265317 T
1 T
59265318 GGTAAAAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TATTATTTTGATAATATTT
Found at i:59270470 original size:74 final size:76
Alignment explanation
Indices: 59270338--59270477 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 76
59270328 CCTAACTACA
* * * *
59270338 AACCCCTAAACCTTATTTAATATATAACTTAAAAAATATTGATTAATCTAAACCCTAAACCTTAA
1 AACCCCTAAACCTTATTTAATACATAACTTAAAAAATACTAATTAATCTAAACCCTAAACCCTAA
59270403 CTCAAATCTCT
66 CTCAAATCTCT
* * *
59270414 AACCCTTAAACCTTATTTAATACA-AA-TTAAAACATACTAATTAATCTAAACTCTAAACCCTAA
1 AACCCCTAAACCTTATTTAATACATAACTTAAAAAATACTAATTAATCTAAACCCTAAACCCTAA
59270477 C
66 C
59270478 CTAACACCGA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 33 0.58
75 2 0.04
76 22 0.39
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31
Consensus pattern (76 bp):
AACCCCTAAACCTTATTTAATACATAACTTAAAAAATACTAATTAATCTAAACCCTAAACCCTAA
CTCAAATCTCT
Found at i:59270672 original size:14 final size:14
Alignment explanation
Indices: 59270653--59270683 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
59270643 ATCCTAAATT
59270653 AACCATATACCCTA
1 AACCATATACCCTA
59270667 AACCATATACCCTA
1 AACCATATACCCTA
59270681 AAC
1 AAC
59270684 TATAATGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.19
Consensus pattern (14 bp):
AACCATATACCCTA
Found at i:59270991 original size:20 final size:19
Alignment explanation
Indices: 59270950--59270993 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
59270940 AATTTTAATT
*
59270950 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
* *
59270969 AATAGTAAATAGACAGATAA
1 AATA-TAAATAAACAAATAA
59270989 AATAT
1 AATAT
59270994 TTTTGCGGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:59271107 original size:41 final size:41
Alignment explanation
Indices: 59270998--59271233 Score: 323
Period size: 41 Copynumber: 5.8 Consensus size: 41
59270988 AAATATTTTT
** **
59270998 GCGGCGCTTCCCCAAAAACGCCGCTAAAGCCCCAAG--TTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
59271037 GCGGCGCTTCTCTAAAAAACGCCACTAAATCCCTGAGCATTA
1 GCGGCGCTTCT-TCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
59271079 ACGGCGCTTCTTCAAAAACGCCGCTAAATCCTTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
59271120 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
*
59271161 GCGGCGCTTCTTCAAAAACGCCACTAAAGCCCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
59271202 GCGACGCTTTTTTAAAAACGCCGCTAAAGCCC
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCC
59271234 CAAAAGTTCA
Statistics
Matches: 175, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 10 0.06
40 19 0.11
41 133 0.76
42 13 0.07
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Done.