Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 9 of 190
Found at i:1193584 original size:2 final size:2
Alignment explanation
Indices: 1193577--1193604 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1193567 TCCAGACGTG
1193577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1193605 GTTGCATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1194363 original size:17 final size:17
Alignment explanation
Indices: 1194341--1194375 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1194331 CCATGTGACC
1194341 TCTAAAATTCATGCATG
1 TCTAAAATTCATGCATG
*
1194358 TCTAAAGTTCATGCATG
1 TCTAAAATTCATGCATG
1194375 T
1 T
1194376 TACAACACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (17 bp):
TCTAAAATTCATGCATG
Found at i:1198204 original size:11 final size:12
Alignment explanation
Indices: 1198184--1198210 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1198174 AGTCTGAAGC
1198184 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1198196 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1198208 TTT
1 TTT
1198211 GCCACAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:1198585 original size:19 final size:19
Alignment explanation
Indices: 1198545--1198589 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1198535 AATACTTTAT
1198545 TATATAAAAATTTAAAATA
1 TATATAAAAATTTAAAATA
1198564 TATA-AAAAATTAATAAAA-A
1 TATATAAAAATT--TAAAATA
1198583 TATATAA
1 TATATAA
1198590 TTCGATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 7 0.30
19 9 0.39
20 7 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TATATAAAAATTTAAAATA
Found at i:1198618 original size:12 final size:13
Alignment explanation
Indices: 1198595--1198634 Score: 55
Period size: 12 Copynumber: 3.0 Consensus size: 13
1198585 TATAATTCGA
1198595 TTTAATTTAATTT
1 TTTAATTTAATTT
1198608 TTTAA-TTAATTT
1 TTTAATTTAATTT
1198620 TTTATATTTTAATTT
1 TTTA-A-TTTAATTT
1198635 AAAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.46
13 6 0.25
15 7 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTAATTTAATTT
Found at i:1199105 original size:12 final size:12
Alignment explanation
Indices: 1199079--1199123 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
1199069 TTGGACTCCG
1199079 AAAAAC-AAA-C
1 AAAAACAAAACC
1199089 AAAAAGCAAAACC
1 AAAAA-CAAAACC
*
1199102 AAAAACAAAAAC
1 AAAAACAAAACC
1199114 AAAAACAAAA
1 AAAAACAAAA
1199124 TGCAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 5 0.16
11 1 0.03
12 19 0.61
13 6 0.19
ACGTcount: A:0.80, C:0.18, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAACAAAACC
Found at i:1199106 original size:7 final size:6
Alignment explanation
Indices: 1199085--1199123 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
1199075 TCCGAAAAAC
*
1199085 AAACAA AAAGCAA AACCAA AAACAA AAACAA AAACAA AA
1 AAACAA AAA-CAA AAACAA AAACAA AAACAA AAACAA AA
1199124 TGCAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (6 bp):
AAACAA
Found at i:1199356 original size:3 final size:3
Alignment explanation
Indices: 1199348--1199382 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1199338 AGTCCCTCGC
1199348 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1199383 AACAAACAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1205710 original size:24 final size:24
Alignment explanation
Indices: 1205669--1205718 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1205659 TGTCCTATTT
* *
1205669 TTATTAGAATTTATATTTGATATA
1 TTATTAGAATATAAATTTGATATA
* *
1205693 TTATTAGTATATAAATTTTATATA
1 TTATTAGAATATAAATTTGATATA
1205717 TT
1 TT
1205719 CTCAGTGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (24 bp):
TTATTAGAATATAAATTTGATATA
Found at i:1207783 original size:16 final size:15
Alignment explanation
Indices: 1207756--1207802 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
1207746 TCAAAATTCG
1207756 ATTTAAATTTAATAT
1 ATTTAAATTTAATAT
1207771 ATTTAATATTTAATATT
1 ATTTAA-ATTTAATA-T
*
1207788 AATTTAAATTAAATA
1 -ATTTAAATTTAATA
1207803 AAAAATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 6 0.21
16 8 0.29
17 8 0.29
18 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTAAATTTAATAT
Found at i:1207799 original size:5 final size:5
Alignment explanation
Indices: 1207780--1207833 Score: 60
Period size: 5 Copynumber: 11.2 Consensus size: 5
1207770 TATTTAATAT
* *
1207780 TTAATA TTAAT TTAAA TTAAA -TAAA --AAA TTAAT TTAAA TTAAA TTAAA
1 TTAA-A TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
1207828 TTAAA T
1 TTAAA T
1207834 ATTATGATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
3 3 0.07
4 4 0.10
5 31 0.74
6 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:1210080 original size:19 final size:20
Alignment explanation
Indices: 1210056--1210094 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1210046 TTGACTAGAA
*
1210056 TTTAA-TTAAATTTTATTTT
1 TTTAATTTAAATTTAATTTT
1210075 TTTAATTTAAATTTAATTTT
1 TTTAATTTAAATTTAATTTT
1210095 AGATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTAATTTAAATTTAATTTT
Found at i:1211395 original size:608 final size:600
Alignment explanation
Indices: 1210211--1211809 Score: 1859
Period size: 608 Copynumber: 2.6 Consensus size: 600
1210201 AAATTCAAGT
* * *
1210211 TCAAGTTCGAGATATTTTATTAATTAAATTAATAAAAATATATTTAAATATAAAAGTTTGATTAA
1 TCAAGTTCGAGATATTTTATTAATTAAAATAATAAAAATATATTTAAATATAAAAGCTCGATTAA
* ** * *
1210276 GTTCGCGAGCTACTCGAGTTAAGTATAAAAATACTCGAATTCAGCTTGATTGATGAGTTAAGTTA
66 GTTCGCGAGCTACTCGAGTTAA-TATAAAAAT-GTTTAATTCAGCTTAATTGATGAG-T--G-GA
* * * *
1210341 CTCGAGCTCGAGCTCGACTCGATAATAATCAAACCGAATTCG-AGTTTTATTTTAATCAAATCCG
125 -AC-AACTCGAGCTCGACTCGATAATAATCGAA-CGAATT-GAAGTTTTATTTTAAT-AAACCCG
* * *
1210405 AGTAGCTTACGAGTACTAATGTATTATTTACACCTTTATTGATAATATTAAAAGATCAAGAGAAA
185 AGTAGCTTACGAATATTAATGTATCATTTACACCTTTA-TGAT-ATATTAAAAGATC-AGAGAAA
* ** * *
1210470 AATATTTTTTCTGTCATTGTTCGAACAGTGAGGGGGACCCACCTTTGATGTGAGTTTCTAATGCC
247 AAT-CTTTTTCTGTCGCTGTTCGGACAGTGA-GGGGACCCA-CTTTGATGTGAGTTTCTGATGCC
*
1210535 TATGCATTGTTTACCATCATTTGATCAAATCAAATAATGATGATGGATGATGGATGCCATATCGT
309 TATGCATTGTTTACCATCCTTTGATCAAATCAAATAATGATGATGGATGATGGATGCCATATCG-
* * * *
1210600 CATGGGATATGAGTGATGATTAGAAGTGTAATCGATCGAGTTCGAGCTCGATTCGAAATTCGAGG
373 CATGGGATAAGAATGATGATTAGAAGTGTAATCGATCAAGTTCGAGCTCAATTCGAAATTCGAGG
** * * *
1210665 TTCGATACTTGGTTCGAATTCGATCGAGTTTCATTTTTTTAGTTCAAGTTCGACTCGAGATAAAA
438 TTCGATACCCGATTCGAATTCGATCGAGTTTCATTTTTTTAGCTCAAGTTCAACTCGAGATAAAA
* * * * * * *
1210730 ATCGAGCTACTTGAACTCGCTTGATTAGGCTCGATTAACATGTAAAATAAGTTTGATTTTTATAT
503 ATCGAACAACTTGAACTCGCTTGATTAAGCTCAATTAACATATAAAAAAAATTTGATTTTTATAT
*
1210795 TTCATAAAAGTTCGATTATTTATGCTC-A-AAC
568 TTCATAAAAGCTCGATTATTTATGCTCGAGAAC
* * *
1210826 TCAAATTCAAGATATTTAATTAATTAAAATAATAAAAATATATTTAAATATAAAAGCTCGATTAA
1 TCAAGTTCGAGATATTTTATTAATTAAAATAATAAAAATATATTTAAATATAAAAGCTCGATTAA
* * * *
1210891 GTTCACGAGCTACTTGAGTTGAATATAAAAATGTTATAATTCGGCTTAATTGATGAGTGGAGCAA
66 GTTCGCGAGCTACTCGAGTT-AATATAAAAATGTT-TAATTCAGCTTAATTGATGAGTGGAACAA
* * *
1210956 CTCGAGCTCGACTCGATAATAATCGAGTCGAATTGAAGTTTTATTTTAATATAACCCAAGTAACT
129 CTCGAGCTCGACTCGATAATAATCGA-ACGAATTGAAGTTTTATTTTAATA-AACCCGAGTAGCT
*
1211021 TATGAATATTAATGTATCATTTACACCTTTAATGATGATATTAAAAGATCAGGAGAAAAATCTTT
192 TACGAATATTAATGTATCATTTACACCTTT-ATGAT-ATATTAAAAGATCA-GAGAAAAATCTTT
* *
1211086 TTCTGTCGCTGTTCGGACAATGAGGAGGACCCACATTTGATATGAGTTTCTGATGCCTATGCATT
254 TTCTGTCGCTGTTCGGACAGTGAGG-GGACCCAC-TTTGATGTGAGTTTCTGATGCCTATGCATT
* *
1211151 GTTTACCATCCTTTGATTAAATCAAATAATGATGATGGATGATAGATGCCATATCAGCATGGGAT
317 GTTTACCATCCTTTGATCAAATCAAATAATGATGATGGATGATGGATGCCATATC-GCATGGGAT
* ** *
1211216 AAGAATGATGATTAGAGGTGTAATTTATCAAGTTCGAGCTCAATTTGAAATTCGAGGTTCGATAC
381 AAGAATGATGATTAGAAGTGTAATCGATCAAGTTCGAGCTCAATTCGAAATTCGAGGTTCGATAC
* * * *
1211281 CCGATTCGAATTTGATCGAGTTTTATTTTTTTAGCTCGAGTTCAATTCGAGATAAAAATCGAACA
446 CCGATTCGAATTCGATCGAGTTTCATTTTTTTAGCTCAAGTTCAACTCGAGATAAAAATCGAACA
* *
1211346 ACTT-AAGTTCG-TTCGATTAAGCTCAATTAACATATAAAAAAAATTTGATTTTTATATTTGATA
511 ACTTGAA-CTCGCTT-GATTAAGCTCAATTAACATATAAAAAAAATTTGATTTTTATATTTCATA
*
1211409 AAAGCTCGATTATTTATGCTCGAGTTCGAGC
574 AAAGCTCGATTATTTATGCTCGA----GAAC
*
1211440 TCAAGTTCGAGATATTTTATTAATTAAAATAATAAAAATATATTTAAATACAAAAGCTCGATTAA
1 TCAAGTTCGAGATATTTTATTAATTAAAATAATAAAAATATATTTAAATATAAAAGCTCGATTAA
* * * * * * * *
1211505 GTTCGTGAGTTACTCGAATTATATATAAAAATGTTTGAATTCAACTTAATCGATGAATCGAACTA
66 GTTCGCGAGCTACTCGAGTTA-ATATAAAAATGTTT-AATTCAGCTTAATTGATGAGTGGAACAA
* * * * *
1211570 CTCGAACTCGAACTCGATTCTATAATAATCGAACTAAATTCAAATTTTATTTTAATAGAACTCGA
129 CTCGAGCTCG-ACTCG-----ATAATAATCGAAC-GAATTGAAGTTTTATTTTAATA-AACCCGA
* *
1211635 GTAGGTTACAAATATTAATGTATCA--T----C---------------AAGA--AGAGAAAAATC
186 GTAGCTTACGAATATTAATGTATCATTTACACCTTTATGATATATTAAAAGATCAGAGAAAAATC
1211677 TTTTTCTGTCGCTGTTCGGACAGTGAGGGAGACCCACTTTGATGTGAGTTTCTGATGCCTATGCA
251 TTTTTCTGTCGCTGTTCGGACAGTGAGGG-GACCCACTTTGATGTGAGTTTCTGATGCCTATGCA
*
1211742 TTGTTTACCATCCTTTGATCAAATCAAATAATGATGATGGATGATGGATGCCATATTGGCATGGG
315 TTGTTTACCATCCTTTGATCAAATCAAATAATGATGATGGATGATGGATGCCATA-TCGCATGGG
1211807 ATA
379 ATA
1211810 GGTGCGATGA
Statistics
Matches: 858, Mismatches: 97, Indels: 80
0.83 0.09 0.08
Matches are distributed among these distances:
593 91 0.11
594 45 0.05
595 1 0.00
597 4 0.00
607 7 0.01
608 301 0.35
609 110 0.13
610 2 0.00
611 1 0.00
612 1 0.00
613 2 0.00
614 124 0.14
615 109 0.13
616 2 0.00
618 1 0.00
619 1 0.00
620 56 0.07
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (600 bp):
TCAAGTTCGAGATATTTTATTAATTAAAATAATAAAAATATATTTAAATATAAAAGCTCGATTAA
GTTCGCGAGCTACTCGAGTTAATATAAAAATGTTTAATTCAGCTTAATTGATGAGTGGAACAACT
CGAGCTCGACTCGATAATAATCGAACGAATTGAAGTTTTATTTTAATAAACCCGAGTAGCTTACG
AATATTAATGTATCATTTACACCTTTATGATATATTAAAAGATCAGAGAAAAATCTTTTTCTGTC
GCTGTTCGGACAGTGAGGGGACCCACTTTGATGTGAGTTTCTGATGCCTATGCATTGTTTACCAT
CCTTTGATCAAATCAAATAATGATGATGGATGATGGATGCCATATCGCATGGGATAAGAATGATG
ATTAGAAGTGTAATCGATCAAGTTCGAGCTCAATTCGAAATTCGAGGTTCGATACCCGATTCGAA
TTCGATCGAGTTTCATTTTTTTAGCTCAAGTTCAACTCGAGATAAAAATCGAACAACTTGAACTC
GCTTGATTAAGCTCAATTAACATATAAAAAAAATTTGATTTTTATATTTCATAAAAGCTCGATTA
TTTATGCTCGAGAAC
Found at i:1212904 original size:14 final size:14
Alignment explanation
Indices: 1212885--1212936 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1212875 TAAAAAATTT
*
1212885 AATAATATGATAAA
1 AATAATATAATAAA
1212899 AATAATATAATAAA
1 AATAATATAATAAA
*
1212913 AATTTAATAAAATAAA
1 AA--TAATATAATAAA
*
1212929 AAAAATAT
1 AATAATAT
1212937 TATCTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 19 0.59
16 13 0.41
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
AATAATATAATAAA
Found at i:1212927 original size:19 final size:19
Alignment explanation
Indices: 1212866--1212934 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
1212856 AGTTGTGGCT
1212866 TAAAATAAATAAAAAATTTAA
1 TAAAAT-AAT-AAAAATTTAA
* *
1212887 TAATATGATAAAAA--TAA
1 TAAAATAATAAAAATTTAA
1212904 T---ATAATAAAAATTTAA
1 TAAAATAATAAAAATTTAA
*
1212920 TAAAATAAAAAAAAT
1 TAAAATAATAAAAAT
1212935 ATTATCTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
14 9 0.23
16 4 0.10
17 4 0.10
19 15 0.38
20 2 0.05
21 5 0.13
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (19 bp):
TAAAATAATAAAAATTTAA
Found at i:1212928 original size:30 final size:33
Alignment explanation
Indices: 1212867--1212936 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
1212857 GTTGTGGCTT
1212867 AAAATA-AATAAAAAATTTAATAATATGATAAAA
1 AAAATATAATAAAAAATTTAATAATA-GATAAAA
*
1212900 ATAATATAAT-AAAAATTTAATAA-A-ATAAAA
1 AAAATATAATAAAAAATTTAATAATAGATAAAA
1212930 AAAATAT
1 AAAATAT
1212937 TATCTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 12 0.35
32 1 0.03
33 18 0.53
34 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (33 bp):
AAAATATAATAAAAAATTTAATAATAGATAAAA
Found at i:1215726 original size:26 final size:24
Alignment explanation
Indices: 1215697--1215744 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
1215687 TTTTAATTAA
*
1215697 TTATTTAATTTTATGTATTTATATAT
1 TTATTTAATGTTA--TATTTATATAT
1215723 TTATTTAATGTTATATTTATAT
1 TTATTTAATGTTATATTTATAT
1215745 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
26 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TTATTTAATGTTATATTTATATAT
Found at i:1215760 original size:20 final size:20
Alignment explanation
Indices: 1215735--1215786 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1215725 ATTTAATGTT
1215735 ATATTTATATTAAAAAAATA
1 ATATTTATATTAAAAAAATA
* *
1215755 ATATTTTATATT-TATAAATA
1 ATA-TTTATATTAAAAAAATA
1215775 ATATTT-TATTAA
1 ATATTTATATTAA
1215787 TTTTTGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.15
19 3 0.11
20 12 0.44
21 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTTATATTAAAAAAATA
Found at i:1215764 original size:21 final size:20
Alignment explanation
Indices: 1215738--1215783 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1215728 TAATGTTATA
1215738 TTTATATTAAAAAAATAATAT
1 TTTATATT-AAAAAATAATAT
* *
1215759 TTTATATTTATAAATAATAT
1 TTTATATTAAAAAATAATAT
1215779 TTTAT
1 TTTAT
1215784 TAATTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTATATTAAAAAATAATAT
Found at i:1226602 original size:2 final size:2
Alignment explanation
Indices: 1226595--1226620 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1226585 TTCTAAAAGC
1226595 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1226621 CAAAAACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1228906 original size:2 final size:2
Alignment explanation
Indices: 1228899--1228937 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1228889 AGGGACATTA
*
1228899 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1228938 AACCAACCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1232016 original size:16 final size:18
Alignment explanation
Indices: 1231994--1232038 Score: 67
Period size: 16 Copynumber: 2.6 Consensus size: 18
1231984 CCGATTTATC
1231994 ATTTTTTAATTTTTA-AT
1 ATTTTTTAATTTTTATAT
1232011 -TTTTTTAATTTTTATAT
1 ATTTTTTAATTTTTATAT
1232028 ATTATTTTAAT
1 ATT-TTTTAAT
1232039 ATAAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 14 0.56
17 2 0.08
18 2 0.08
19 7 0.28
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTTTAATTTTTATAT
Found at i:1232040 original size:13 final size:13
Alignment explanation
Indices: 1232018--1232056 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1232008 AATTTTTTTA
*
1232018 ATTTTTATATATT
1 ATTTTAATATATT
**
1232031 ATTTTAATATAAA
1 ATTTTAATATATT
1232044 ATTTTAATATATT
1 ATTTTAATATATT
1232057 TAAGTAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTAATATATT
Found at i:1235195 original size:2 final size:2
Alignment explanation
Indices: 1235188--1235220 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1235178 TCAGGGCACG
1235188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1235221 GGTGGGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1236084 original size:2 final size:2
Alignment explanation
Indices: 1236077--1236105 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1236067 GTTCCATGAA
1236077 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1236106 GTGTGTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1238510 original size:25 final size:25
Alignment explanation
Indices: 1238476--1238525 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1238466 ACATATATAA
* *
1238476 ACTAAGAGTACGCAGAGAGCAATAT
1 ACTAAAAGTACACAGAGAGCAATAT
1238501 ACTAAAAGTACACAGAGAGCAATAT
1 ACTAAAAGTACACAGAGAGCAATAT
1238526 GACATGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (25 bp):
ACTAAAAGTACACAGAGAGCAATAT
Found at i:1248662 original size:20 final size:20
Alignment explanation
Indices: 1248637--1248674 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1248627 ATTAAATGTG
1248637 TAAAATTTAATAAATTTTAA
1 TAAAATTTAATAAATTTTAA
* *
1248657 TAAAATTTGATATATTTT
1 TAAAATTTAATAAATTTT
1248675 TAAATAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TAAAATTTAATAAATTTTAA
Found at i:1248687 original size:14 final size:15
Alignment explanation
Indices: 1248668--1248701 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1248658 AAAATTTGAT
*
1248668 ATATTTTTAA-ATAA
1 ATATTTTTAATAAAA
1248682 ATATTTTTAATAAAA
1 ATATTTTTAATAAAA
1248697 ATATT
1 ATATT
1248702 AACATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTTTTAATAAAA
Found at i:1251407 original size:14 final size:14
Alignment explanation
Indices: 1251382--1251424 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1251372 GTGGTGCTTT
1251382 TATATA-ATATATA
1 TATATACATATATA
1251395 TATATACATATATA
1 TATATACATATATA
*
1251409 TAT-TGACATACATA
1 TATAT-ACATATATA
1251423 TA
1 TA
1251425 CAAATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 7 0.26
14 20 0.74
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (14 bp):
TATATACATATATA
Found at i:1261800 original size:13 final size:13
Alignment explanation
Indices: 1261784--1261838 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 13
1261774 ATTTTTTTAA
1261784 TTTTATTTATAAT
1 TTTTATTTATAAT
*
1261797 TTTTA-TTAAAAT
1 TTTTATTTATAAT
* *
1261809 TTTAAATTAT-AT
1 TTTTATTTATAAT
*
1261821 TTTT-TTTATATT
1 TTTTATTTATAAT
1261833 TTTTAT
1 TTTTAT
1261839 ATAATATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
11 4 0.12
12 20 0.61
13 9 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTATTTATAAT
Found at i:1261823 original size:36 final size:38
Alignment explanation
Indices: 1261783--1261856 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 38
1261773 AATTTTTTTA
1261783 ATTTTATTTATAATTTTTAT-TAAAATT-TTAAATTAT
1 ATTTTATTTATAATTTTTATATAAAATTATTAAATTAT
* * * *
1261819 ATTTTTTTTATATTTTTTATATAATATTATTATATTAT
1 ATTTTATTTATAATTTTTATATAAAATTATTAAATTAT
1261857 GTTTAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 18 0.56
37 6 0.19
38 8 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (38 bp):
ATTTTATTTATAATTTTTATATAAAATTATTAAATTAT
Found at i:1261829 original size:11 final size:11
Alignment explanation
Indices: 1261761--1261841 Score: 58
Period size: 10 Copynumber: 7.3 Consensus size: 11
1261751 AAAATATAAA
1261761 ATATTTTTTTT
1 ATATTTTTTTT
*
1261772 -TAATTTTTTT
1 ATATTTTTTTT
*
1261782 A-ATTTTATTT
1 ATATTTTTTTT
*
1261792 ATAATTTTTATTA
1 AT-ATTTTT-TTT
* **
1261805 AAATTTTAAATT
1 ATATTTT-TTTT
1261817 ATATTTTTTTT
1 ATATTTTTTTT
*
1261828 ATATTTTTTAT
1 ATATTTTTTTT
1261839 ATA
1 ATA
1261842 ATATTATTAT
Statistics
Matches: 52, Mismatches: 13, Indels: 10
0.69 0.17 0.13
Matches are distributed among these distances:
10 17 0.33
11 15 0.29
12 17 0.33
13 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATATTTTTTTT
Found at i:1261835 original size:24 final size:22
Alignment explanation
Indices: 1261775--1261834 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
1261765 TTTTTTTTAA
*
1261775 TTTTTTTAATTTTATTTATAAT
1 TTTTTTTAATTTTAATTATAAT
*
1261797 TTTTATTAAAATTTTAAATTAT-AT
1 TTTT-TT-TAATTTT-AATTATAAT
1261821 TTTTTTTATATTTT
1 TTTTTTTA-ATTTT
1261835 TTATATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 5 0.16
23 9 0.29
24 12 0.39
25 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTTTAATTTTAATTATAAT
Found at i:1263627 original size:32 final size:31
Alignment explanation
Indices: 1263591--1263661 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 31
1263581 AAATATGATG
1263591 ATTTATATATTTATATCATATAAAATATTAAA
1 ATTTATATATTTATATCATATAAAATA-TAAA
* * * *
1263623 ATTTATGTATTTGTATCATATTATATATAAA
1 ATTTATATATTTATATCATATAAAATATAAA
*
1263654 AATTATAT
1 ATTTATAT
1263662 GCTATAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 10 0.30
32 23 0.70
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (31 bp):
ATTTATATATTTATATCATATAAAATATAAA
Found at i:1264708 original size:25 final size:24
Alignment explanation
Indices: 1264680--1264746 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 24
1264670 TAAAAAAATT
1264680 TAAATATAATTTTAAATATAAAAA
1 TAAATATAATTTTAAATATAAAAA
1264704 GT-AA-A-AATTTTAAATATTTAAAAA
1 -TAAATATAATTTTAAATA--TAAAAA
*
1264728 -AGATATAATTTTAAGATAT
1 TAAATATAATTTTAA-ATAT
1264747 CTAAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
22 11 0.31
23 2 0.06
24 10 0.29
25 9 0.26
26 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (24 bp):
TAAATATAATTTTAAATATAAAAA
Found at i:1264752 original size:25 final size:23
Alignment explanation
Indices: 1264683--1264753 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 23
1264673 AAAAATTTAA
1264683 ATATAATTTTAAATA-TAAAAAG
1 ATATAATTTTAAATATTAAAAAG
*
1264705 -TAAAAATTTTAAATATTTAAAAAAG
1 AT-ATAATTTTAAATA-TT-AAAAAG
1264730 ATATAATTTTAAGATATCTAAAAA
1 ATATAATTTTAA-ATAT-TAAAAA
1264754 AAATAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
21 1 0.03
22 12 0.30
24 1 0.03
25 21 0.52
26 5 0.12
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (23 bp):
ATATAATTTTAAATATTAAAAAG
Found at i:1265484 original size:24 final size:24
Alignment explanation
Indices: 1265457--1265515 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1265447 TGATAATTCA
*
1265457 AAATATAATAT-AATAATACGATAT
1 AAATATAATATAAAAAATA-GATAT
* *
1265481 AAATATGATATAAAAAATATATAT
1 AAATATAATATAAAAAATAGATAT
*
1265505 AAAAATAATAT
1 AAATATAATAT
1265516 GATTTAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 23 0.79
25 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (24 bp):
AAATATAATATAAAAAATAGATAT
Found at i:1265502 original size:11 final size:12
Alignment explanation
Indices: 1265456--1265515 Score: 52
Period size: 13 Copynumber: 4.9 Consensus size: 12
1265446 ATGATAATTC
1265456 AAAATATAATATA
1 AAAATAT-ATATA
* *
1265469 ATAATACGATATA
1 AAAATA-TATATA
*
1265482 AATATGATATA-A
1 AAAAT-ATATATA
1265494 AAAATATATATA
1 AAAATATATATA
1265506 AAAATA-ATAT
1 AAAATATATAT
1265516 GATTTAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
11 9 0.24
12 12 0.32
13 16 0.42
14 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (12 bp):
AAAATATATATA
Found at i:1265506 original size:13 final size:14
Alignment explanation
Indices: 1265481--1265524 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1265471 AATACGATAT
1265481 AAATATGATATAAA
1 AAATATGATATAAA
1265495 AAATAT-ATATAAAA
1 AAATATGATAT-AAA
*
1265509 ATAATATGATTTAAA
1 A-AATATGATATAAA
1265524 A
1 A
1265525 TTTTAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.15
14 10 0.38
15 9 0.35
16 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (14 bp):
AAATATGATATAAA
Found at i:1266624 original size:2 final size:2
Alignment explanation
Indices: 1266619--1266646 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1266609 AGTGTGTATG
1266619 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1266647 CACACACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1266918 original size:2 final size:2
Alignment explanation
Indices: 1266911--1266935 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1266901 TTACAGTTGA
1266911 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1266936 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1269302 original size:2 final size:2
Alignment explanation
Indices: 1269286--1269327 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
1269276 CATTCAAACA
1269286 AT AT A- AT AT AT -T AT AT AT AT -T AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1269324 AT AT
1 AT AT
1269328 GTCATAACGT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.11
2 32 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1269309 original size:14 final size:14
Alignment explanation
Indices: 1269286--1269325 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
1269276 CATTCAAACA
*
1269286 ATATAATATATTAT
1 ATATATTATATTAT
1269300 ATATATTATATTAT
1 ATATATTATATTAT
1269314 ATATATATATAT
1 ATATAT-TATAT
1269326 ATGTCATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATATTATATTAT
Found at i:1269978 original size:61 final size:59
Alignment explanation
Indices: 1269899--1270102 Score: 272
Period size: 58 Copynumber: 3.5 Consensus size: 59
1269889 TGAGAGTTTC
* *
1269899 TATTTTTAA-AAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTTTAAAAAAAAT
1 TATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATA-TTTTTTT-AAAAAAAT
* *
1269959 TATTTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTT-AAAAAAT
1 TATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAAAAAAAT
* * * *
1270017 TATTTTCAA-AGAAAATTGATACTTTCAACTTTTCCTCGAAAATA-TTTTTTAGAAAACT
1 TATTTTCAAGA-AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAAAAAAAT
*
1270075 TATTTTCAAGAAAAATTGATATTTTCAA
1 TATTTTCAAGAAAAATTGATACTTTCAA
1270103 GAAAAATTGA
Statistics
Matches: 131, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
57 6 0.05
58 76 0.58
59 1 0.01
60 16 0.12
61 32 0.24
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (59 bp):
TATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAAAAAAAT
Found at i:1270099 original size:19 final size:19
Alignment explanation
Indices: 1270075--1270121 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1270065 TTAGAAAACT
1270075 TATTTTCAAGAAAAATTGA
1 TATTTTCAAGAAAAATTGA
1270094 TATTTTCAAGAAAAATTGA
1 TATTTTCAAGAAAAATTGA
*
1270113 TACTTTCAA
1 TATTTTCAA
1270122 CTTTTCCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (19 bp):
TATTTTCAAGAAAAATTGA
Found at i:1270197 original size:17 final size:18
Alignment explanation
Indices: 1270175--1270210 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
1270165 ATCATTTTAA
1270175 AAAAATAAAATAA-AAAT
1 AAAAATAAAATAAGAAAT
1270192 AAAAATAAAATAAGAAAT
1 AAAAATAAAATAAGAAAT
1270210 A
1 A
1270211 CTAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAAATAAAATAAGAAAT
Found at i:1270244 original size:3 final size:3
Alignment explanation
Indices: 1270236--1270294 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
1270226 TTAATCAATA
* *
1270236 AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AA- AAGA AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
1270281 AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AA
1270295 ATAAATAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.92
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1271036 original size:16 final size:17
Alignment explanation
Indices: 1271015--1271046 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1271005 TTCAGAACAT
1271015 ATAAATA-AAAAAATAG
1 ATAAATATAAAAAATAG
1271031 ATAAATATAAAAAATA
1 ATAAATATAAAAAATA
1271047 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
ATAAATATAAAAAATAG
Found at i:1271057 original size:27 final size:26
Alignment explanation
Indices: 1271026--1271150 Score: 116
Period size: 27 Copynumber: 4.8 Consensus size: 26
1271016 TAAATAAAAA
1271026 AATAGATAAATATAAAAAATATACATT
1 AATAGATAAATATAAAAAATATA-ATT
1271053 AATAGATAAATAATAAAAAATAGT-ATT
1 AATAGATAAAT-ATAAAAAATA-TAATT
* *
1271080 AATGGATAACTAATAAAAAATATATATT
1 AATAGATAAAT-ATAAAAAATATA-ATT
* * *
1271108 ATTAGATAAA-A-AAAATATATAATA
1 AATAGATAAATATAAAAAATATAATT
*
1271132 AATA-ATAAA-ATTAAAAATA
1 AATAGATAAATATAAAAAATA
1271151 ATAAAACTAA
Statistics
Matches: 83, Mismatches: 10, Indels: 13
0.78 0.09 0.12
Matches are distributed among these distances:
23 6 0.07
24 11 0.13
25 9 0.11
26 2 0.02
27 34 0.41
28 20 0.24
29 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (26 bp):
AATAGATAAATATAAAAAATATAATT
Found at i:1271115 original size:28 final size:28
Alignment explanation
Indices: 1271026--1271117 Score: 125
Period size: 27 Copynumber: 3.4 Consensus size: 28
1271016 TAAATAAAAA
*
1271026 AATAGATAAAT-ATAAAAAATATACATT
1 AATAGATAAATAATAAAAAATATATATT
*
1271053 AATAGATAAATAATAAAAAATA-GTATT
1 AATAGATAAATAATAAAAAATATATATT
* *
1271080 AATGGATAACTAATAAAAAATATATATT
1 AATAGATAAATAATAAAAAATATATATT
*
1271108 ATTAGATAAA
1 AATAGATAAA
1271118 AAAAATATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 34 0.62
28 21 0.38
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (28 bp):
AATAGATAAATAATAAAAAATATATATT
Found at i:1271151 original size:15 final size:15
Alignment explanation
Indices: 1271131--1271166 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1271121 AATATATAAT
*
1271131 AAATAATAAAATTAA
1 AAATAATAAAACTAA
1271146 AAATAATAAAACTAA
1 AAATAATAAAACTAA
1271161 AAATAA
1 AAATAA
1271167 AATGGGCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (15 bp):
AAATAATAAAACTAA
Found at i:1271151 original size:22 final size:21
Alignment explanation
Indices: 1271113--1271168 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1271103 ATATTATTAG
1271113 ATAAAAA-AAATATATAATAAATA
1 ATAAAAATAAA-A-ATAATAAA-A
*
1271136 ATAAAATTAAAAATAATAAAA
1 ATAAAAATAAAAATAATAAAA
*
1271157 CTAAAAATAAAA
1 ATAAAAATAAAA
1271169 TGGGCCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 11 0.38
22 8 0.28
23 7 0.24
24 3 0.10
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
ATAAAAATAAAAATAATAAAA
Found at i:1271165 original size:27 final size:26
Alignment explanation
Indices: 1271118--1271169 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1271108 ATTAGATAAA
*
1271118 AAAAATATATAATAAATAATAAAATT
1 AAAAATATAAAATAAATAATAAAATT
1271144 AAAAATAATAAAACTAAA-AATAAAAT
1 AAAAAT-ATAAAA-TAAATAATAAAAT
1271170 GGGCCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 13 0.57
28 4 0.17
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (26 bp):
AAAAATATAAAATAAATAATAAAATT
Found at i:1271398 original size:43 final size:43
Alignment explanation
Indices: 1271351--1271587 Score: 294
Period size: 44 Copynumber: 5.4 Consensus size: 43
1271341 AATTTTGATC
* * *
1271351 AAAGCTCCTCTAAACAAAAGCTCAATGATTTTGAAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGATTTTGAAAAATAAAT
1271394 AAAGCTCCTCTAAACAGAGGCTCAACGATTTTGAAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGATTTTGAAAAATAAAT
* * * *
1271437 AAAACTTCTCTAAATAGAGGCTCAACGACTTTGAAAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGATTTTG-AAAAATAAAT
* *
1271481 AAAGCTTCTCTAAATAGAGGCTCAACGACTTTTGAAAAATAAAT
1 AAAGCTCCTCTAAACAGAGGCTCAACGA-TTTTGAAAAATAAAT
* * * * * *
1271525 AAAGCTCTTCTAAACAGAGGTTCAATGACTTTGGAAAGATAAAC
1 AAAGCTCCTCTAAACAGAGGCTCAACGA-TTTTGAAAAATAAAT
* *
1271569 AAAGTTCCTCTAAATAGAG
1 AAAGCTCCTCTAAACAGAG
1271588 TCATCACAAC
Statistics
Matches: 172, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
43 69 0.40
44 99 0.58
45 4 0.02
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (43 bp):
AAAGCTCCTCTAAACAGAGGCTCAACGATTTTGAAAAATAAAT
Found at i:1283081 original size:49 final size:48
Alignment explanation
Indices: 1282994--1283088 Score: 111
Period size: 49 Copynumber: 2.0 Consensus size: 48
1282984 AGAGTTTCTA
* ** *
1282994 TTTTAAGAAAAATTGATACTTTCAACTTTCCTTTAAAATGTTTTTTTT
1 TTTTAAGAAAAATTGATACTTCCAACTTTCCTCCAAAATATTTTTTTT
* *
1283042 TTTTAAAGGAAAATTGGTACTTCCAACTTTTCC-CCAAAATATTTTTT
1 TTTT-AAGAAAAATTGATACTTCCAAC-TTTCCTCCAAAATATTTTTT
1283089 CTGAAACTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
48 4 0.10
49 30 0.77
50 5 0.13
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (48 bp):
TTTTAAGAAAAATTGATACTTCCAACTTTCCTCCAAAATATTTTTTTT
Found at i:1283200 original size:115 final size:110
Alignment explanation
Indices: 1283041--1283398 Score: 414
Period size: 115 Copynumber: 3.1 Consensus size: 110
1283031 ATGTTTTTTT
* * * * * *
1283041 TTTTTAAAGGAAAATTGGTACTTCCAACTTTTCCCCAAAATATTTTTTCTGAAACTTTAATTTCG
1 TTTTTAAA--AAAATTGATACTTTCAATTTTTCTCAAAAATATTTTTT-TGAAAC-TTATTTTC-
*
1283106 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTTTAAAATTA
61 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAATTA
* *
1283156 TTTTTAAATAAAATTGATACTTTCAATTTTTTCTCAAAAATATTTTTTTAGAAAATTATTTTCAA
1 TTTTTAAA-AAAATTGATACTTTCAA-TTTTTCTCAAAAATATTTTTTT-GAAACTTATTTTCAG
*
1283221 AGAAAATTGATACTTTCAACTTTT-CTCAAAAATATTTTTTAAAAAACTTA
63 A-AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-TAAAA-TTA
* * *
1283271 TTTTCAAGAAAAATTGATACTTTTAACTTTTTCTCAAAAATATTTTGTTAGAAAACTTATTTTCA
1 TTTTTAA-AAAAATTGATACTTTCAA-TTTTTCTCAAAAATATTTT-TTTG-AAACTTATTTTC-
*
1283336 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAATT-
61 AGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTTAAAATTA
1283386 TTATTTAAAAAAA
1 TT-TTTAAAAAAA
1283399 ATCATTTTTA
Statistics
Matches: 211, Mismatches: 20, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
113 17 0.08
114 49 0.23
115 82 0.39
116 42 0.20
117 15 0.07
118 6 0.03
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (110 bp):
TTTTTAAAAAAATTGATACTTTCAATTTTTCTCAAAAATATTTTTTTGAAACTTATTTTCAGAAA
AATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAATTA
Found at i:1283252 original size:57 final size:57
Alignment explanation
Indices: 1283042--1283383 Score: 408
Period size: 58 Copynumber: 5.9 Consensus size: 57
1283032 TGTTTTTTTT
* * * * * * *
1283042 TTTTAAAGGAAAATTGGTACTTCCAACTTTTCCCCAAAATATTTTTTCT-GAAACTTTA
1 TTTTCAAGAAAAATTGATACTTTCAACTTTTCTCAAAAATATTTTTT-TAGAAA-ATTA
* * *
1283100 ATTTCGAGAAAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTTT--AAAATTA
1 TTTTCAAGAAAAATTGATACTTTCAACTTTT-CTCAAAAATATTTTTTTAGAAAATTA
* *
1283156 TTTTTAA-ATAAAATTGATACTTTCAATTTTTTCTCAAAAATATTTTTTTAGAAAATTA
1 TTTTCAAGA-AAAATTGATACTTTCAA-CTTTTCTCAAAAATATTTTTTTAGAAAATTA
*
1283214 TTTTCAA-AGAAAATTGATACTTTCAACTTTTCTCAAAAATA-TTTTTTAAAAAACTTA
1 TTTTCAAGA-AAAATTGATACTTTCAACTTTTCTCAAAAATATTTTTTTAGAAAA-TTA
* *
1283271 TTTTCAAGAAAAATTGATACTTTTAACTTTTTCTCAAAAATATTTTGTTAGAAAACTTA
1 TTTTCAAGAAAAATTGATACTTTCAAC-TTTTCTCAAAAATATTTTTTTAGAAAA-TTA
*
1283330 TTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAA
1 TTTTCAAGAAAAATTGATACTTTCAACTTTT-CTCAAAAATATTTTTTTAGAAA
1283384 TTTTATTTAA
Statistics
Matches: 249, Mismatches: 25, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
55 1 0.00
56 51 0.20
57 48 0.19
58 76 0.31
59 73 0.29
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (57 bp):
TTTTCAAGAAAAATTGATACTTTCAACTTTTCTCAAAAATATTTTTTTAGAAAATTA
Found at i:1283299 original size:30 final size:30
Alignment explanation
Indices: 1283264--1283358 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
1283254 ATTTTTTAAA
1283264 AAACTTATTTTCAAGAAAAATTGATACTTT
1 AAACTTATTTTCAAGAAAAATTGATACTTT
* * * **
1283294 TAACTT-TTTCTCAA-AAATATTTTGTTA--GA
1 AAACTTATTT-TCAAGAAA-A-ATTGATACTTT
1283323 AAACTTATTTTCAAGAAAAATTGATACTTT
1 AAACTTATTTTCAAGAAAAATTGATACTTT
*
1283353 CAACTT
1 AAACTT
1283359 TTCCTCAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 14
0.65 0.15 0.19
Matches are distributed among these distances:
28 5 0.11
29 16 0.34
30 21 0.45
31 5 0.11
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (30 bp):
AAACTTATTTTCAAGAAAAATTGATACTTT
Found at i:1283391 original size:59 final size:58
Alignment explanation
Indices: 1283042--1283383 Score: 421
Period size: 59 Copynumber: 5.9 Consensus size: 58
1283032 TGTTTTTTTT
* * * * * *
1283042 TTTTAAAGGAAAATTGGTACTTCCAACTTTTCC-CCAAAATATTTTTTCT-GAAACTTTA
1 TTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-TAGAAA-ATTA
* * *
1283100 ATTTCGAGAAAAATTGATACTTTCAACTTTTCCTCAAAAACATTTTTTT--AAAATTA
1 TTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAAATTA
* * *
1283156 TTTTTAA-ATAAAATTGATACTTTCAATTTTTTCTCAAAAATATTTTTTTAGAAAATTA
1 TTTTCAAGA-AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAAATTA
*
1283214 TTTTCAA-AGAAAATTGATACTTTCAACTTTT-CTCAAAAATA-TTTTTTAAAAAACTTA
1 TTTTCAAGA-AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAAA-TTA
* * *
1283271 TTTTCAAGAAAAATTGATACTTTTAACTTTTTCTCAAAAATATTTTGTTAGAAAACTTA
1 TTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAAA-TTA
*
1283330 TTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAA
1 TTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAA
1283384 TTTTATTTAA
Statistics
Matches: 250, Mismatches: 26, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
55 1 0.00
56 55 0.22
57 44 0.18
58 74 0.30
59 76 0.30
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (58 bp):
TTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAAATTA
Found at i:1283430 original size:17 final size:18
Alignment explanation
Indices: 1283410--1283445 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
1283400 TCATTTTTAA
1283410 AAAAATAAAATAA-AAAT
1 AAAAATAAAATAAGAAAT
1283427 AAAAATAAAATAAGAAAT
1 AAAAATAAAATAAGAAAT
1283445 A
1 A
1283446 CTAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAAATAAAATAAGAAAT
Found at i:1284255 original size:19 final size:17
Alignment explanation
Indices: 1284213--1284245 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1284203 TTCAAAACAA
1284213 ATAAATATAAAAAATAG
1 ATAAATATAAAAAATAG
1284230 ATAAATATAAAAAATA
1 ATAAATATAAAAAATA
1284246 TGCATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAAATATAAAAAATAG
Found at i:1284279 original size:27 final size:27
Alignment explanation
Indices: 1284225--1284330 Score: 112
Period size: 27 Copynumber: 3.9 Consensus size: 27
1284215 AAATATAAAA
1284225 AATAGATAAAT-ATAAAAAAT-ATGCATT
1 AATAGATAAATAATAAAAAATAAT--ATT
1284252 AATAGATAAATAATAAAAAATAATATT
1 AATAGATAAATAATAAAAAATAATATT
* * *
1284279 AATGGATAACTAAT-AAAAATATATATA
1 AATAGATAAATAATAAAAAATA-ATATT
*
1284306 AATA-ATAAATAATAATAAAAAAATA
1 AATAGATAAATAATAA-AAAATAATA
1284331 AAACTAAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
26 15 0.22
27 37 0.54
28 14 0.21
29 2 0.03
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (27 bp):
AATAGATAAATAATAAAAAATAATATT
Found at i:1284311 original size:19 final size:18
Alignment explanation
Indices: 1284284--1284333 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
1284274 ATATTAATGG
*
1284284 ATAACTAATAAAAATATAT
1 ATAAATAATAAAAATA-AT
1284303 ATAAATAATAAATAATAAT
1 ATAAATAATAAA-AATAAT
*
1284322 A-AAAAAATAAAA
1 ATAAATAATAAAA
1284334 CTAAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 9 0.32
19 14 0.50
20 4 0.14
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAATAATAAAAATAAT
Found at i:1284313 original size:7 final size:7
Alignment explanation
Indices: 1284252--1284344 Score: 51
Period size: 6 Copynumber: 14.3 Consensus size: 7
1284242 AATATGCATT
1284252 AATAGATA
1 AATA-ATA
1284260 AATAATA
1 AATAATA
*
1284267 AAAAAT-
1 AATAATA
*
1284273 AAT-ATT
1 AATAATA
*
1284279 AATGGATA
1 AAT-AATA
*
1284287 ACTAATA
1 AATAATA
1284294 AA-AATA
1 AATAATA
*
1284300 TAT-ATA
1 AATAATA
1284306 AATAATA
1 AATAATA
1284313 AATAAT-
1 AATAATA
1284319 AATAA-A
1 AATAATA
1284325 AA-AATA
1 AATAATA
*
1284331 AA-ACTA
1 AATAATA
1284337 AA-AATA
1 AATAATA
1284343 AA
1 AA
1284345 ATGAGCCATT
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
5 4 0.06
6 35 0.51
7 21 0.31
8 8 0.12
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (7 bp):
AATAATA
Found at i:1284323 original size:17 final size:17
Alignment explanation
Indices: 1284212--1284324 Score: 61
Period size: 17 Copynumber: 6.4 Consensus size: 17
1284202 ATTCAAAACA
1284212 AATAAAT-ATAAAAAAT
1 AATAAATAATAAAAAAT
1284228 AGATAAAT-ATAAAAAAT
1 A-ATAAATAATAAAAAAT
* *
1284245 ATGCATTAATAGATAAATAAT
1 A---ATAAATA-ATAAAAAAT
* **
1284266 AAAAAATAAT-ATTAAT
1 AATAAATAATAAAAAAT
* *
1284282 GGATAACTAATAAAAATAT
1 -AATAAATAATAAAAA-AT
*
1284301 ATATAAATAATAAATAAT
1 A-ATAAATAATAAAAAAT
1284319 AATAAA
1 AATAAA
1284325 AAAATAAAAC
Statistics
Matches: 74, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
16 6 0.08
17 30 0.41
18 10 0.14
19 19 0.26
21 9 0.12
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (17 bp):
AATAAATAATAAAAAAT
Found at i:1284344 original size:20 final size:21
Alignment explanation
Indices: 1284290--1284345 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
1284280 ATGGATAACT
*
1284290 AATAAAAATATATATAAATAATA
1 AATAAAAATA-A-AAAAATAATA
*
1284313 AATAATAATAAAAAAATAA-A
1 AATAAAAATAAAAAAATAATA
*
1284333 ACTAAAAATAAAA
1 AATAAAAATAAAA
1284346 TGAGCCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 12 0.41
21 7 0.24
22 1 0.03
23 9 0.31
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AATAAAAATAAAAAAATAATA
Found at i:1291726 original size:27 final size:27
Alignment explanation
Indices: 1291695--1291757 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
1291685 ATATAAGCTC
1291695 ATTAAAAATTGAATTTTAATTTTTAAA
1 ATTAAAAATTGAATTTTAATTTTTAAA
1291722 ATTAAAAATTGAATTTTAATTTTTAAA
1 ATTAAAAATTGAATTTTAATTTTTAAA
1291749 ATTAAAAAT
1 ATTAAAAAT
1291758 CAAACTCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (27 bp):
ATTAAAAATTGAATTTTAATTTTTAAA
Found at i:1294603 original size:33 final size:33
Alignment explanation
Indices: 1294542--1294606 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1294532 ACACATAGCA
* *
1294542 AATATATTAATAAATAGAATTCATAATGGTCCT
1 AATATATTAATAAATAGAACTCACAATGGTCCT
*
1294575 AATATATTAATAAATAGAACTGACAATGGTCC
1 AATATATTAATAAATAGAACTCACAATGGTCC
1294607 AACTTTAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (33 bp):
AATATATTAATAAATAGAACTCACAATGGTCCT
Found at i:1297241 original size:21 final size:21
Alignment explanation
Indices: 1297217--1297257 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1297207 TTTTCTTCCA
1297217 AAAATGATAAATTTTTGCATG
1 AAAATGATAAATTTTTGCATG
1297238 AAAATGATAAATTTTTGCAT
1 AAAATGATAAATTTTTGCAT
1297258 TAATAAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.39
Consensus pattern (21 bp):
AAAATGATAAATTTTTGCATG
Found at i:1298168 original size:34 final size:34
Alignment explanation
Indices: 1298104--1298168 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
1298094 TAACCTAAGA
* * *
1298104 CATTAGTAGAATTTCCTGTTTAACATTGAATTCC
1 CATTAGTAGAATTTCCAGTTCAACAATGAATTCC
*
1298138 CATTAGTAGAATTT-CAGTTCAGAGAATGAAT
1 CATTAGTAGAATTTCCAGTTCA-ACAATGAAT
1298169 AAAACTACCG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 5 0.19
34 21 0.81
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (34 bp):
CATTAGTAGAATTTCCAGTTCAACAATGAATTCC
Found at i:1300265 original size:22 final size:22
Alignment explanation
Indices: 1300224--1300276 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1300214 TTTGAATTGT
* *
1300224 TTATAAAT-ATAAAATCTTATC
1 TTATAAATAACAAAATCTTATA
*
1300245 TTATAAATAACAAAATTTTATA
1 TTATAAATAACAAAATCTTATA
*
1300267 TTATATATAA
1 TTATAAATAA
1300277 ATTAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (22 bp):
TTATAAATAACAAAATCTTATA
Found at i:1301986 original size:41 final size:41
Alignment explanation
Indices: 1301922--1302003 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
1301912 TGAACCATCT
*
1301922 ATGAATTATTGAAAAAGAGGGTAGTACAAGCTTTTTATTAG
1 ATGAATTATTGAAAAAGAAGGTAGTACAAGCTTTTTATTAG
* *
1301963 ATGAATTATTGAAAAGGAAGGTAGTTCAAGCTTTTTATTAG
1 ATGAATTATTGAAAAAGAAGGTAGTACAAGCTTTTTATTAG
1302004 TAGGATGAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (41 bp):
ATGAATTATTGAAAAAGAAGGTAGTACAAGCTTTTTATTAG
Found at i:1308553 original size:30 final size:31
Alignment explanation
Indices: 1308519--1308584 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
1308509 AAAATATTTT
* *
1308519 TATAA-TTTTATATTAATATAAATTAT-AATA
1 TATAATTTTTATA-TAAAATAAAATATAAATA
1308549 TATAATTTTTATATAAAATAAAATATAAATA
1 TATAATTTTTATATAAAATAAAATATAAATA
1308580 TATAA
1 TATAA
1308585 ATTATTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TATAATTTTTATATAAAATAAAATATAAATA
Found at i:1309495 original size:15 final size:15
Alignment explanation
Indices: 1309464--1309495 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1309454 ATTTTAATAA
*
1309464 TTTAATTTTTTAATT
1 TTTAATTTTTAAATT
1309479 TTTAATTTTTAAATT
1 TTTAATTTTTAAATT
1309494 TT
1 TT
1309496 ATATATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTAATTTTTAAATT
Found at i:1315834 original size:31 final size:31
Alignment explanation
Indices: 1315796--1315864 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1315786 TTTGTTTTTT
*
1315796 TGTACTCACATCAGACACATAAACACTGTAA
1 TGTACTCACATAAGACACATAAACACTGTAA
* *
1315827 TGTACTCATATAAGACACCTAAACACTGTAA
1 TGTACTCACATAAGACACATAAACACTGTAA
*
1315858 TATACTC
1 TGTACTC
1315865 GTTGTTCAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.26
Consensus pattern (31 bp):
TGTACTCACATAAGACACATAAACACTGTAA
Found at i:1329963 original size:13 final size:14
Alignment explanation
Indices: 1329929--1329965 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1329919 ATGATTGATG
1329929 ATAAATT-ATCATT
1 ATAAATTAATCATT
1329942 ATGAAATTAAT-ATT
1 AT-AAATTAATCATT
1329956 ATAAATTAAT
1 ATAAATTAAT
1329966 TTAATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 10 0.45
15 2 0.09
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (14 bp):
ATAAATTAATCATT
Found at i:1333295 original size:11 final size:11
Alignment explanation
Indices: 1333281--1333308 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1333271 AAAAAAAGCA
1333281 TAAAATCAATT
1 TAAAATCAATT
1333292 TAAAATCAATT
1 TAAAATCAATT
1333303 TAAAAT
1 TAAAAT
1333309 TTTTTGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAAATCAATT
Found at i:1335471 original size:23 final size:24
Alignment explanation
Indices: 1335445--1335494 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
1335435 TTCTCAAAAT
*
1335445 ATAATTCA-TACAAAG-TAAATTTC
1 ATAA-TCATTACAAAGCAAAATTTC
*
1335468 ATAATCATTCCAAAGCAAAATTTC
1 ATAATCATTACAAAGCAAAATTTC
1335492 ATA
1 ATA
1335495 TTCTGACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 10 0.43
24 10 0.43
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (24 bp):
ATAATCATTACAAAGCAAAATTTC
Found at i:1335824 original size:19 final size:19
Alignment explanation
Indices: 1335800--1335836 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1335790 AAAAAATATT
1335800 CAAAAATCA-AAATTTAACC
1 CAAAAAT-ATAAATTTAACC
1335819 CAAAAATATAAATTTAAC
1 CAAAAATATAAATTTAAC
1335837 AAGGCAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.24
Consensus pattern (19 bp):
CAAAAATATAAATTTAACC
Found at i:1336172 original size:21 final size:20
Alignment explanation
Indices: 1336131--1336168 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1336121 AAATTATCAT
1336131 AGTAAAAATTTATTAAAATA
1 AGTAAAAATTTATTAAAATA
1336151 AGTAAAAATTTATTAAAA
1 AGTAAAAATTTATTAAAA
1336169 ATAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
AGTAAAAATTTATTAAAATA
Found at i:1337353 original size:21 final size:22
Alignment explanation
Indices: 1337329--1337373 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1337319 TAAAAATATA
*
1337329 TATTTATAATA-TATTAAATTT
1 TATTTAAAATATTATTAAATTT
*
1337350 TA-TTAAAATATTTTTAAATTT
1 TATTTAAAATATTATTAAATTT
1337371 TAT
1 TAT
1337374 ATACTCAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTAAAATATTATTAAATTT
Found at i:1339549 original size:21 final size:24
Alignment explanation
Indices: 1339506--1339549 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1339496 TCTTTGCCTT
*
1339506 ACCATCATCATATGTTTTACTTCC
1 ACCATCATCATATGTATTACTTCC
1339530 ACCATCAT-ATATG-ATT-CTTC
1 ACCATCATCATATGTATTACTTC
1339550 ATATCTACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 2 0.11
23 5 0.26
24 8 0.42
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.41
Consensus pattern (24 bp):
ACCATCATCATATGTATTACTTCC
Found at i:1347191 original size:23 final size:23
Alignment explanation
Indices: 1347161--1347205 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1347151 AATGGAGACC
*
1347161 TAACTTGAATAGCTGTCAGTACA
1 TAACTTGAATAGCAGTCAGTACA
1347184 TAACTTGAATAGCAGTCAGTAC
1 TAACTTGAATAGCAGTCAGTAC
1347206 GTACTATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (23 bp):
TAACTTGAATAGCAGTCAGTACA
Found at i:1349765 original size:29 final size:30
Alignment explanation
Indices: 1349715--1349794 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
1349705 TAGGGCTTGT
* *
1349715 TTAAG-TACAAATGAAAGGTTAAGGG-CTA
1 TTAAGATACAAATTAAAGTTTAAGGGTCTA
* *
1349743 TTAAGATACAAATTAAAATTTAAGGGTTTA
1 TTAAGATACAAATTAAAGTTTAAGGGTCTA
* *
1349773 TTTAGATGCAAATTAAAGTTTA
1 TTAAGATACAAATTAAAGTTTA
1349795 GGATCTTATT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 5 0.12
29 17 0.40
30 21 0.49
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (30 bp):
TTAAGATACAAATTAAAGTTTAAGGGTCTA
Found at i:1349804 original size:30 final size:30
Alignment explanation
Indices: 1349741--1349805 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1349731 GGTTAAGGGC
* *
1349741 TATTAAGATACAAATTAAAATTTAAGGGTT
1 TATTTAGATACAAATTAAAATTTAAGGATT
* *
1349771 TATTTAGATGCAAATTAAAGTTT-AGGATCT
1 TATTTAGATACAAATTAAAATTTAAGGAT-T
1349801 TATTT
1 TATTT
1349806 GAGTATGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (30 bp):
TATTTAGATACAAATTAAAATTTAAGGATT
Found at i:1359715 original size:15 final size:15
Alignment explanation
Indices: 1359675--1359728 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
1359665 TCTAATCTAA
*
1359675 TATATATATAATTATT
1 TATATAT-TATTTATT
*
1359691 TTTA-ATTATTTATT
1 TATATATTATTTATT
1359705 TATATATTATTTATAT
1 TATATATTATTTAT-T
1359721 T-TATATTA
1 TATATATTA
1359729 AAAAATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 10 0.30
15 18 0.55
16 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATATATTATTTATT
Found at i:1359741 original size:19 final size:18
Alignment explanation
Indices: 1359717--1359766 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
1359707 TATATTATTT
1359717 ATATTTATATTAAAAAATA
1 ATATTTATATTAAAAAA-A
**
1359736 ATATTTTATATTTTAAAAA
1 ATA-TTTATATTAAAAAAA
1359755 ATATTT-TATTAA
1 ATATTTATATTAA
1359767 TTTTGAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 4 0.15
18 3 0.12
19 7 0.27
20 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTTATATTAAAAAAA
Found at i:1359745 original size:20 final size:19
Alignment explanation
Indices: 1359720--1359763 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1359710 ATTATTTATA
1359720 TTTATATTAAAAAATAATAT
1 TTTATATTAAAAAA-AATAT
**
1359740 TTTATATTTTAAAAAATAT
1 TTTATATTAAAAAAAATAT
1359759 TTTAT
1 TTTAT
1359764 TAATTTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTATATTAAAAAAAATAT
Found at i:1364029 original size:29 final size:30
Alignment explanation
Indices: 1363973--1364041 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 30
1363963 TTCAATTTAA
* * **
1363973 TATATATATATTTATTATTTATTTAATT-T
1 TATATATATATATATTATTAATAAAATTAT
*
1364002 TATATTTATATATATTATTAATAAAATTAT
1 TATATATATATATATTATTAATAAAATTAT
1364032 TATATA-ATAT
1 TATATATATAT
1364042 TTTTAATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TATATATATATATATTATTAATAAAATTAT
Found at i:1364034 original size:24 final size:24
Alignment explanation
Indices: 1364007--1364092 Score: 86
Period size: 24 Copynumber: 3.5 Consensus size: 24
1363997 AATTTTATAT
1364007 TTATATATATTATTAA-TAAAATTA
1 TTATATATATTATTAATTAAAA-TA
*
1364031 TTATATAATATTTTTAATTTAAAATA
1 TTATAT-ATATTATTAA-TTAAAATA
*
1364057 TTATATTTATGTA-TAATTAAAATA
1 TTATATATAT-TATTAATTAAAATA
* *
1364081 TAATTTATATTA
1 TTATATATATTA
1364093 AAAACAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
23 2 0.04
24 21 0.40
25 15 0.29
26 9 0.17
27 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (24 bp):
TTATATATATTATTAATTAAAATA
Found at i:1365142 original size:17 final size:18
Alignment explanation
Indices: 1365112--1365145 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1365102 TTGATTGATT
1365112 TTGTTTTTTAATTTTTAA
1 TTGTTTTTTAATTTTTAA
1365130 TTGTTTTTT-ATTTTTA
1 TTGTTTTTTAATTTTTA
1365146 CATATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (18 bp):
TTGTTTTTTAATTTTTAA
Found at i:1366397 original size:174 final size:175
Alignment explanation
Indices: 1366100--1366454 Score: 640
Period size: 174 Copynumber: 2.0 Consensus size: 175
1366090 GACTTTAAGC
*
1366100 TCATATCGCATCAAATCTTCTTAGTTGGAGAATTGAAAAAAAAAAAAATCAAATCTTCTTAAACA
1 TCATATCACATCAAATCTTCTTAGTTGGAGAATTGAAAAAAAAAAAAATCAAATCTTCTTAAACA
* *
1366165 AAATGTCTTATTCCTTCATTTTATTTCTTTGTTTGTCTTTATCTTTCTGCCTGTCTCTTCAACCC
66 AAATGTCTTATTCCTTCATTTTATTTCTTTGTTTGCCTTTATCTTTCTGCCCGTCTCTTCAACCC
* *
1366230 CATGTGGAATGTAGTTATAGTGATCATCATACATGCCTATTTATA
131 CATGTGGAATGTAGTTATAGTGATCATCATACATGCCTAATCATA
*
1366275 TCATATCACATCAACTCTTCTTAGTTGGAGAATTG-AAAAAAAAAAAATCAAATCTTCTTAAACA
1 TCATATCACATCAAATCTTCTTAGTTGGAGAATTGAAAAAAAAAAAAATCAAATCTTCTTAAACA
1366339 AAATGTCTTATTCCTTCATTTTATTTCTTTGTTTGCCTTTATCTTTCTGCCCGTCTCTTCAACCC
66 AAATGTCTTATTCCTTCATTTTATTTCTTTGTTTGCCTTTATCTTTCTGCCCGTCTCTTCAACCC
*
1366404 CATGTGGAATGTCGTTATAGTGATCATCATACATGCCTAATCATA
131 CATGTGGAATGTAGTTATAGTGATCATCATACATGCCTAATCATA
1366449 TCATAT
1 TCATAT
1366455 TATGACTCTA
Statistics
Matches: 173, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
174 140 0.81
175 33 0.19
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (175 bp):
TCATATCACATCAAATCTTCTTAGTTGGAGAATTGAAAAAAAAAAAAATCAAATCTTCTTAAACA
AAATGTCTTATTCCTTCATTTTATTTCTTTGTTTGCCTTTATCTTTCTGCCCGTCTCTTCAACCC
CATGTGGAATGTAGTTATAGTGATCATCATACATGCCTAATCATA
Found at i:1367076 original size:20 final size:19
Alignment explanation
Indices: 1367053--1367107 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 19
1367043 TAAAACATGT
1367053 TAATAATATTTAATTATATA
1 TAAT-ATATTTAATTATATA
* *
1367073 TAATATATATAA-TAAATA
1 TAATATATTTAATTATATA
1367091 T-ATCATATTTACATTAT
1 TAAT-ATATTTA-ATTAT
1367108 TTAAATGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 2 0.07
18 12 0.43
19 8 0.29
20 6 0.21
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATATATTTAATTATATA
Found at i:1367140 original size:20 final size:21
Alignment explanation
Indices: 1367115--1367156 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1367105 TATTTAAATG
1367115 TTTATATCATA-TCAAAATTA
1 TTTATATCATATTCAAAATTA
* *
1367135 TTTATATTATATTTAAAATTA
1 TTTATATCATATTCAAAATTA
1367156 T
1 T
1367157 ACCTAATACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTATATCATATTCAAAATTA
Found at i:1369056 original size:340 final size:338
Alignment explanation
Indices: 1368436--1369118 Score: 1339
Period size: 340 Copynumber: 2.0 Consensus size: 338
1368426 GCTGCTTTAA
1368436 ATTTTTTATTTTTTGTTCTGATTAGGACTTCACTTCCTTGTGTGTTTTCTGATCATGGGAAGCAT
1 ATTTTTTATTTTTTGTTCTGATTAGGACTTCACTTCCTTGTGTGTTTTCTGATCATGGGAAGCAT
1368501 TCGATATGGACCCTCCATCACATGGTTTTACTTTAGAATCATGGCCTAAATTTGAGCTTTCTTCT
66 TCGATATGGACCCTCCATCACATGGTTTTACTTTAGAATCATGGCCTAAATTTGAGCTTTCTTCT
1368566 ACTATTAATCTTTTTATTTATTTATTTATTTTGGATATGGAGGAAGCCAATTTGAATTCAAACTT
131 ACTATTAATCTTTTTATTTATTTATTTATTTTGGATATGGAGGAAGCCAATTTGAATTCAAACTT
*
1368631 CGTATTGGATATGTTATGACTTATCAGGTTCATTTGGGTATAGCCAAAAGCTGATCCTATGTTTC
196 CGTATTGGATATGTTATGACTTATCAGGTTCATTTGGGTATAGCCAAAAGCTGATCCCATGTTTC
1368696 TTCAGCCAATCTGAAGAAATTCTGCTCTTTGACTCATAAATATGCCTTTCCCGCCTTTGAAGATA
261 TTCAGCCAATCTGAAGAAATTCTGCTC--TGACTCATAAATATGCCTTTCCCGCCTTTGAAGATA
1368761 ACTAAGAACATGTTT
324 ACTAAGAACATGTTT
1368776 ATTTTTTATTTTTTGTTCTGATTAGGACTTCACTTCCTTGTGTGTTTTCTGATCATGGGAAGCAT
1 ATTTTTTATTTTTTGTTCTGATTAGGACTTCACTTCCTTGTGTGTTTTCTGATCATGGGAAGCAT
1368841 TCGATATGGACCCTCCATCACATGGTTTTACTTTAGAATCATGGCCTAAATTTGAGCTTTCTTCT
66 TCGATATGGACCCTCCATCACATGGTTTTACTTTAGAATCATGGCCTAAATTTGAGCTTTCTTCT
1368906 ACTATTAATCTTTTTATTTATTTATTTATTTTGGATATGGAGGAAGCCAATTTGAATTCAAACTT
131 ACTATTAATCTTTTTATTTATTTATTTATTTTGGATATGGAGGAAGCCAATTTGAATTCAAACTT
1368971 CGTATTGGATATGTTATGACTTATCAGGTTCATTTGGGTATAGCCAAAAGCTGATCCCATGTTTC
196 CGTATTGGATATGTTATGACTTATCAGGTTCATTTGGGTATAGCCAAAAGCTGATCCCATGTTTC
1369036 TTCAGCCAATCTGAAGAAATTCTGCTCTGACTCATAAATATGCCTTTCCCGCCTTTGAAGATAAC
261 TTCAGCCAATCTGAAGAAATTCTGCTCTGACTCATAAATATGCCTTTCCCGCCTTTGAAGATAAC
1369101 TAAGAACATGTTT
326 TAAGAACATGTTT
1369114 ATTTT
1 ATTTT
1369119 GGAGCTACCC
Statistics
Matches: 342, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
338 56 0.16
340 286 0.84
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.41
Consensus pattern (338 bp):
ATTTTTTATTTTTTGTTCTGATTAGGACTTCACTTCCTTGTGTGTTTTCTGATCATGGGAAGCAT
TCGATATGGACCCTCCATCACATGGTTTTACTTTAGAATCATGGCCTAAATTTGAGCTTTCTTCT
ACTATTAATCTTTTTATTTATTTATTTATTTTGGATATGGAGGAAGCCAATTTGAATTCAAACTT
CGTATTGGATATGTTATGACTTATCAGGTTCATTTGGGTATAGCCAAAAGCTGATCCCATGTTTC
TTCAGCCAATCTGAAGAAATTCTGCTCTGACTCATAAATATGCCTTTCCCGCCTTTGAAGATAAC
TAAGAACATGTTT
Found at i:1377975 original size:13 final size:13
Alignment explanation
Indices: 1377959--1377983 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1377949 AAAAGTTTAA
1377959 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
1377972 AAAAAAAAAAAG
1 AAAAAAAAAAAG
1377984 AAGATTCCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGG
Found at i:1378826 original size:15 final size:15
Alignment explanation
Indices: 1378806--1378842 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1378796 AGGAAAAAGG
1378806 GATGGGCGGTGGCCT
1 GATGGGCGGTGGCCT
*
1378821 GATGGGTGGTGGCCT
1 GATGGGCGGTGGCCT
*
1378836 GGTGGGC
1 GATGGGC
1378843 TGCTTTCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.05, C:0.16, G:0.57, T:0.22
Consensus pattern (15 bp):
GATGGGCGGTGGCCT
Found at i:1384975 original size:18 final size:17
Alignment explanation
Indices: 1384933--1384975 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1384923 TAAAAATAAT
*
1384933 TTTGATATTTATATCGA
1 TTTGATATTTAAATCGA
* *
1384950 TATAATATGTTAAATCGA
1 TTTGATAT-TTAAATCGA
1384968 TTTGATAT
1 TTTGATAT
1384976 ATTTAATGTT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.49
Consensus pattern (17 bp):
TTTGATATTTAAATCGA
Found at i:1387083 original size:29 final size:30
Alignment explanation
Indices: 1387014--1387086 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
1387004 GTATTAATAA
*
1387014 ATTAATAAATATTAAATTTTAAAATATATTT
1 ATTAATAAAT-TTAAATTTAAAAATATATTT
*
1387045 -TTAATAAATTTAAA-TTAAAAATATTTTTT
1 ATTAATAAATTTAAATTTAAAAATA-TATTT
1387074 ATTAAT-AATTTAA
1 ATTAATAAATTTAA
1387087 TATCTAGGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 8 0.21
29 16 0.42
30 14 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTAATAAATTTAAATTTAAAAATATATTT
Found at i:1387960 original size:159 final size:160
Alignment explanation
Indices: 1387634--1387942 Score: 426
Period size: 159 Copynumber: 1.9 Consensus size: 160
1387624 TTATCTTTTC
* *
1387634 CATTTTGGGTTTTAATTATTTTTTAATTTATTTATCCGATTTTCATTAAAAAGAATCTGGGTTTC
1 CATTTTGGGTTTTAA-TATTTTTTAATTTATTTAACCGATTTTCATTAAAAACAATCTGGGTTTC
**
1387699 TGGCTTCAGCACTTATATTTAAAAAAACGAAATAAAGATTGATTTTTTCTTGTTTGATTGACATT
65 TGGCTTCAGCACTTATATTTAAAAAAACGAAATAAAGATTGAAATTTTCTTGTTTGATTGACATT
* ** **
1387764 GTTTTGTATGTTGTTTTCTCCATTATCTTTT
130 GTTTTGTATGTTGATTAATCCATTATAATTT
* * * *
1387795 CCATTTTGGGTTTT-A-ATTTTTTAATTTATTTAACCGATTTTCATTAAAATCTATTTGGGTTTT
1 -CATTTTGGGTTTTAATATTTTTTAATTTATTTAACCGATTTTCATTAAAAACAATCTGGGTTTC
* *
1387858 TGGTTTCAGCTCTTATATTTCAAAAAAA-GAAATAAAGATTGAAAATTTTCTTGTTTGATTGACA
65 TGGCTTCAGCACTTATATTT-AAAAAAACGAAATAAAGATTG-AAATTTTCTTGTTTGATTGACA
1387922 TTGTTTTGTATGTTGATTAAT
128 TTGTTTTGTATGTTGATTAAT
1387943 GCAGGTTTAA
Statistics
Matches: 132, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
159 73 0.55
160 45 0.34
161 1 0.01
162 13 0.10
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.50
Consensus pattern (160 bp):
CATTTTGGGTTTTAATATTTTTTAATTTATTTAACCGATTTTCATTAAAAACAATCTGGGTTTCT
GGCTTCAGCACTTATATTTAAAAAAACGAAATAAAGATTGAAATTTTCTTGTTTGATTGACATTG
TTTTGTATGTTGATTAATCCATTATAATTT
Found at i:1395645 original size:18 final size:17
Alignment explanation
Indices: 1395614--1395648 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1395604 TGATGTCAAG
*
1395614 GGGGGAAAATCAAAAGA
1 GGGGGAAAACCAAAAGA
1395631 GGGGGAAAAGCCAAAAGA
1 GGGGGAAAA-CCAAAAGA
1395649 TGAGAAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.51, C:0.09, G:0.37, T:0.03
Consensus pattern (17 bp):
GGGGGAAAACCAAAAGA
Found at i:1404095 original size:22 final size:23
Alignment explanation
Indices: 1404063--1404116 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1404053 ATATTTTTTA
*
1404063 TTAAA-TAAAAT-TATAAAATTT
1 TTAAATTAAAATGAATAAAATTT
*
1404084 TTAAATTAAAATGAATAATATTT
1 TTAAATTAAAATGAATAAAATTT
1404107 TGTAAATTAA
1 T-TAAATTAA
1404117 GTATAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 5 0.18
22 6 0.21
23 9 0.32
24 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAAATTAAAATGAATAAAATTT
Found at i:1409557 original size:24 final size:25
Alignment explanation
Indices: 1409516--1409564 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1409506 TTATCCTATT
1409516 TCTTTTTCTACTTAAAAA-AAAAAC
1 TCTTTTTCTACTTAAAAACAAAAAC
*
1409540 TCTTTATTCT-CTTTAAAACAAAAAC
1 TCTTT-TTCTACTTAAAAACAAAAAC
1409565 CCAAAGGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (25 bp):
TCTTTTTCTACTTAAAAACAAAAAC
Found at i:1411213 original size:22 final size:22
Alignment explanation
Indices: 1411179--1411232 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1411169 TGTTTTTAAC
** *
1411179 ATTTTTTCATTTTTTCTCTTTT
1 ATTTTTTTTTTTTTTCTCATTT
* *
1411201 GTTTTTTTTTTTTTTGTCATTT
1 ATTTTTTTTTTTTTTCTCATTT
1411223 ATTTTTTTTT
1 ATTTTTTTTT
1411233 AAAGGCATGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.07, C:0.07, G:0.04, T:0.81
Consensus pattern (22 bp):
ATTTTTTTTTTTTTTCTCATTT
Found at i:1411351 original size:35 final size:35
Alignment explanation
Indices: 1411312--1411875 Score: 310
Period size: 35 Copynumber: 15.9 Consensus size: 35
1411302 TGAGTTTGAC
1411312 AATAAAGATGACTGAGATTGAATCGCAAGTCAAAG
1 AATAAAGATGACTGAGATTGAATCGCAAGTCAAAG
*
1411347 AATAAAGATGACTGAGATTGAATCGCAAGTTAGGAA-
1 AATAAAGATGACTGAGATTGAATCGCAAGTCA--AAG
* ** *
1411383 ATTAAA-ATGA-TCGAGATTGAATTACGAGTCAAAG
1 AATAAAGATGACT-GAGATTGAATCGCAAGTCAAAG
* * * * *
1411417 AATAAATATAACTGGGATTGAGTCACAAGTCAAAG
1 AATAAAGATGACTGAGATTGAATCGCAAGTCAAAG
* * * *
1411452 AATAAAGATGATTGAGATTGAACCACAAGTCAGAG
1 AATAAAGATGACTGAGATTGAATCGCAAGTCAAAG
* * * * *
1411487 AATAAAAATGACTGAGATTAAACCATAAGTAGTAAGTCAGAG
1 AATAAAGATGACTGAGATT------GAA-TCGCAAGTCAAAG
* * * *
1411529 AATAAAGATGACTGAAACTG-AGCTGTAAGTCAGAA-
1 AATAAAGATGACTGAGATTGAATC-GCAAGTCA-AAG
* * **
1411564 AAAAAAGATGACT-AGGATTGAATCGTAAGTTGAAG
1 AATAAAGATGACTGA-GATTGAATCGCAAGTCAAAG
* * * *
1411599 GATAAAGATGATTGAGACTG-AGC-CATGAGTCAAAG
1 AATAAAGATGACTGAGATTGAATCGCA--AGTCAAAG
*
1411634 AATAAAGATGACTGAGATTGAATTGCAAGTCATAAG
1 AATAAAGATGACTGAGATTGAATCGCAAGTCA-AAG
* * * * *
1411670 -ATAAAGATGATTGGGATTGAATTGTAAGTCAAAAA
1 AATAAAGATGACTGAGATTGAATCGCAAGTC-AAAG
* * * *
1411705 AATAAGGATGACT-AGGATTGAATCGTAAGTTAGAG
1 AATAAAGATGACTGA-GATTGAATCGCAAGTCAAAG
*
1411740 AATAAAGATAACTGAGATTGAA-CTGCAAGTCGAAAG
1 AATAAAGATGACTGAGATTGAATC-GCAAGTC-AAAG
* * * * *
1411776 -ATAAAGATGATTG-GAACTGAGTCGCAAGTCGAGG
1 AATAAAGATGACTGAG-ATTGAATCGCAAGTCAAAG
* * * * * * * *
1411810 AAT-AAGTGTGATTGGGACTAAACCACAAGTCAATG
1 AATAAAG-ATGACTGAGATTGAATCGCAAGTCAAAG
* * *
1411845 AATAAATATGACTGAGATTGAGTCGTAAGTC
1 AATAAAGATGACTGAGATTGAATCGCAAGTC
1411876 GAGAAATGAA
Statistics
Matches: 402, Mismatches: 91, Indels: 72
0.71 0.16 0.13
Matches are distributed among these distances:
33 3 0.01
34 18 0.04
35 303 0.75
36 47 0.12
37 4 0.01
41 2 0.00
42 25 0.06
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.23
Consensus pattern (35 bp):
AATAAAGATGACTGAGATTGAATCGCAAGTCAAAG
Found at i:1411676 original size:105 final size:103
Alignment explanation
Indices: 1411312--1411968 Score: 340
Period size: 105 Copynumber: 6.2 Consensus size: 103
1411302 TGAGTTTGAC
1411312 AATAAAGATGACTGAGATTGAATCGCAAGTCAAAGAATAAAGATGACT-GAGATTGAATCGCAAG
1 AATAAAGATGACTGAGATTGAATCGCAAGTCAAAG-ATAAAGATGA-TAG-GATTGAATCGCAAG
* * ** *
1411376 TT-AGGAAATTAAA-ATGATCGAGATTGAATTACGAGTCAAAG
63 TTCAAG-AA-TAAAGATGATTGAGATTGAACCATGAGTCAAAG
* * * * * * * *
1411417 AATAAATATAACTGGGATTGAGTCACAAGTCAAAGAATAAAGATGATTGAGATTGAACCACAAG-
1 AATAAAGATGACTGAGATTGAATCGCAAGTCAAAG-ATAAAGATGATAG-GATTGAATCGCAAGT
* * * *
1411481 TCAGAGAATAAAAATGACTGAGATTAAACCATAAGTAGTAAGTCAGAG
64 TCA-AGAATAAAGATGATTGAGATTGAACC---A-T-G--AGTCAAAG
* * * * * * *
1411529 AATAAAGATGACTGAAACTG-AGCTGTAAGTCAGAAAAAAAAGATGACTAGGATTGAATCGTAAG
1 AATAAAGATGACTGAGATTGAATC-GCAAGTCA-AAGATAAAGATGA-TAGGATTGAATCGCAAG
* * * *
1411593 TTGAAGGATAAAGATGATTGAGACTGAGCCATGAGTCAAAG
63 TTCAAGAATAAAGATGATTGAGATTGAACCATGAGTCAAAG
* * * *
1411634 AATAAAGATGACTGAGATTGAATTGCAAGTCATAAGATAAAGATGATTGGGATTGAATTGTAAG-
1 AATAAAGATGACTGAGATTGAATCGCAAGTCA-AAGATAAAGATGA-TAGGATTGAATCGCAAGT
* * * * * * * *
1411698 TCAAAAAAATAAGGATGACT-AGGATTGAATCGTAAGTTAGAG
64 TC--AAGAATAAAGATGATTGA-GATTGAACCATGAGTCAAAG
* * * *
1411740 AATAAAGATAACTGAGATTGAA-CTGCAAGTCGAAAGATAAAGATGATTGGAACTGAGTCGCAAG
1 AATAAAGATGACTGAGATTGAATC-GCAAGTC-AAAGATAAAGATGATAGG-ATTGAATCGCAAG
* * * * * ** *
1411804 -TCGAGGAAT-AAGTGTGATTGGGACTAAACCACAAGTCAATG
63 TTC-AAGAATAAAG-ATGATTGAGATTGAACCATGAGTCAAAG
* * *
1411845 AATAAATATGACTGAGATTGAGTCGTAAGTCGAGAA-ATGAAA-ATGATTAGGATTGAA-C-CAT
1 AATAAAGATGACTGAGATTGAATCGCAAGTC-A-AAGAT-AAAGATGA-TAGGATTGAATCGCA-
* *
1411906 GAG-TCAGAGAATAAAGATGATT-AGGATTGAGCCATGAGTTAAAG
61 -AGTTCA-AGAATAAAGATGATTGA-GATTGAACCATGAGTCAAAG
*
1411950 AATAAATG-TGACTGGGATT
1 AATAAA-GATGACTGAGATT
1411969 AAGTTATAAG
Statistics
Matches: 416, Mismatches: 102, Indels: 68
0.71 0.17 0.12
Matches are distributed among these distances:
103 2 0.00
104 11 0.03
105 231 0.56
106 91 0.22
107 2 0.00
108 2 0.00
109 1 0.00
110 1 0.00
111 1 0.00
112 68 0.16
113 6 0.01
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (103 bp):
AATAAAGATGACTGAGATTGAATCGCAAGTCAAAGATAAAGATGATAGGATTGAATCGCAAGTTC
AAGAATAAAGATGATTGAGATTGAACCATGAGTCAAAG
Found at i:1411826 original size:141 final size:139
Alignment explanation
Indices: 1411312--1411805 Score: 326
Period size: 147 Copynumber: 3.5 Consensus size: 139
1411302 TGAGTTTGAC
* * *
1411312 AATAAAGATGACTGAGATTGAATCGCA-AGTCAAAGAATAAAGATGACTGAGATTGAATCGCAAG
1 AATAAAGATAACTGAGACTGAA-C-CAGAGTCAAAGAATAAAGATGACTGAGACTGAATCGCAAG
* * * *** * * * *
1411376 TTAGGAA-ATTAAA-ATGATCGAGATTGAATTACGAGTCA-AAGAATAAATATAACTGGGATTGA
64 TCA-GAAGA-TAAAGATGATTGGGATTGAATTGTAAGTCAGAA-AAAAAAGATGACTAGGATTGA
* ** **
1411438 GTCACAAGTCAAAG
126 ATCGTAAGTTGAAG
* * * * * *
1411452 AATAAAGATGATTGAGATTGAACCACAAGTCAGAGAATAAAAATGACTGAGATTAAACCAT-AAG
1 AATAAAGATAACTGAGACTGAACCA-GAGTCAAAGAATAAAGATGACTGAG-----A-C-TGAA-
* * * ** * **
1411516 TAGTAAGTCAG-AGAATAAAGATGACTGAAACTGAGCTGTAAGTCAGAAAAAAAAGATGACTAGG
57 TCGCAAGTCAGAAG-ATAAAGATGATTGGGATTGAATTGTAAGTCAGAAAAAAAAGATGACTAGG
1411580 ATTGAATCGTAAGTTGAAG
121 ATTGAATCGTAAGTTGAAG
* * * * * *
1411599 GATAAAGATGATTGAGACTGAGCCATGAGTCAAAGAATAAAGATGACTGAGATTGAATTGCAAGT
1 AATAAAGATAACTGAGACTGAACCA-GAGTCAAAGAATAAAGATGACTGAGACTGAATCGCAAGT
*
1411664 CATAAGATAAAGATGATTGGGATTGAATTGTAAGTCA-AAAAAATAAGGATGACTAGGATTGAAT
65 CAGAAGATAAAGATGATTGGGATTGAATTGTAAGTCAGAAAAAA-AA-GATGACTAGGATTGAAT
1411728 CGTAAGTT-AGAG
128 CGTAAGTTGA-AG
* * *
1411740 AATAAAGATAACTGAGATTGAACTGCA-AGTCGAAAG-ATAAAGATGATTG-GAACTGAGTCGCA
1 AATAAAGATAACTGAGACTGAAC--CAGAGTC-AAAGAATAAAGATGACTGAG-ACTGAATCGCA
1411802 AGTC
62 AGTC
1411806 GAGGAATAAG
Statistics
Matches: 280, Mismatches: 51, Indels: 45
0.74 0.14 0.12
Matches are distributed among these distances:
138 2 0.01
139 7 0.03
140 81 0.29
141 77 0.28
142 5 0.02
143 2 0.01
145 2 0.01
146 7 0.03
147 95 0.34
148 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (139 bp):
AATAAAGATAACTGAGACTGAACCAGAGTCAAAGAATAAAGATGACTGAGACTGAATCGCAAGTC
AGAAGATAAAGATGATTGGGATTGAATTGTAAGTCAGAAAAAAAAGATGACTAGGATTGAATCGT
AAGTTGAAG
Found at i:1411899 original size:35 final size:35
Alignment explanation
Indices: 1411860--1411955 Score: 97
Period size: 35 Copynumber: 2.7 Consensus size: 35
1411850 ATATGACTGA
* *
1411860 GATTGAGTCGTAAGTC-GAGAAATGAAA-ATGATTAG
1 GATTGAGCCATAAGTCAGAG-AAT-AAAGATGATTAG
* *
1411895 GATTGAACCATGAGTCAGAGAATAAAGATGATTAG
1 GATTGAGCCATAAGTCAGAGAATAAAGATGATTAG
* * *
1411930 GATTGAGCCATGAGTTAAAGAATAAA
1 GATTGAGCCATAAGTCAGAGAATAAA
1411956 TGTGACTGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 3 0.06
35 46 0.88
36 3 0.06
ACGTcount: A:0.43, C:0.07, G:0.26, T:0.24
Consensus pattern (35 bp):
GATTGAGCCATAAGTCAGAGAATAAAGATGATTAG
Found at i:1411968 original size:35 final size:35
Alignment explanation
Indices: 1411887--1411968 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
1411877 AGAAATGAAA
* *
1411887 ATGATTAGGATTGAACCATGAGTCAGAGAATAAAG
1 ATGACTAGGATTGAACCATGAGTCAAAGAATAAAG
* * *
1411922 ATGATTAGGATTGAGCCATGAGTTAAAGAATAAATG
1 ATGACTAGGATTGAACCATGAGTCAAAGAATAAA-G
*
1411958 -TGACTGGGATT
1 ATGACTAGGATT
1411969 AAGTTATAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
35 40 0.98
36 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (35 bp):
ATGACTAGGATTGAACCATGAGTCAAAGAATAAAG
Found at i:1422730 original size:4 final size:4
Alignment explanation
Indices: 1422721--1422745 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1422711 TAATGTTAAT
1422721 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
1422746 TCAAGCATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:1424480 original size:15 final size:15
Alignment explanation
Indices: 1424462--1424591 Score: 81
Period size: 15 Copynumber: 8.7 Consensus size: 15
1424452 GGGGGTATAT
*
1424462 GGTTTTGGGGTTTAA
1 GGTTTTGGAGTTTAA
* *
1424477 GGTTTT-GAATTTAG
1 GGTTTTGGAGTTTAA
*
1424491 GGTTTTGGAGTTT-T
1 GGTTTTGGAGTTTAA
*
1424505 GGATTTT-TAGTTTAA
1 GG-TTTTGGAGTTTAA
* *
1424520 GGGTTTTGAATTTTAA
1 -GGTTTTGGAGTTTAA
*
1424536 GGTTTTGAAGTTTAA
1 GGTTTTGGAGTTTAA
*
1424551 GG-TTTGGAGGTTTAG
1 GGTTTTGGA-GTTTAA
* *
1424566 GGGTTTGAAGGGTTTAA
1 GGTTTTG--GAGTTTAA
1424583 GG-TTTGGAG
1 GGTTTTGGAG
1424592 GGTTTTAGGA
Statistics
Matches: 91, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
14 25 0.27
15 42 0.46
16 16 0.18
17 7 0.08
18 1 0.01
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (15 bp):
GGTTTTGGAGTTTAA
Found at i:1424517 original size:22 final size:23
Alignment explanation
Indices: 1424478--1424548 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 23
1424468 GGGGTTTAAG
*
1424478 GTTTTGAA-TTTAGGGTTTTGGA
1 GTTTTGAATTTTAAGGTTTTGGA
* * *
1424500 GTTTTGGATTTTTA-GTTTAAGG-
1 GTTTTGAATTTTAAGGTTT-TGGA
*
1424522 GTTTTGAATTTTAAGGTTTTGAA
1 GTTTTGAATTTTAAGGTTTTGGA
1424545 GTTT
1 GTTT
1424549 AAGGTTTGGA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
22 24 0.65
23 13 0.35
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.54
Consensus pattern (23 bp):
GTTTTGAATTTTAAGGTTTTGGA
Found at i:1424536 original size:16 final size:16
Alignment explanation
Indices: 1424471--1424575 Score: 82
Period size: 15 Copynumber: 7.1 Consensus size: 16
1424461 TGGTTTTGGG
1424471 GTTTAA-GGTTTTGAA
1 GTTTAAGGGTTTTGAA
*
1424486 -TTT-AGGGTTTTGGA
1 GTTTAAGGGTTTTGAA
* * *
1424500 GTTT-TGGATTTT-TA
1 GTTTAAGGGTTTTGAA
1424514 GTTTAAGGGTTTTGAA
1 GTTTAAGGGTTTTGAA
*
1424530 TTTTAA-GGTTTTGAA
1 GTTTAAGGGTTTTGAA
* *
1424545 GTTTAA-GGTTTGGAG
1 GTTTAAGGGTTTTGAA
*
1424560 GTTT-AGGGGTTTGAA
1 GTTTAAGGGTTTTGAA
1424575 G
1 G
1424576 GGTTTAAGGT
Statistics
Matches: 71, Mismatches: 14, Indels: 10
0.75 0.15 0.11
Matches are distributed among these distances:
13 1 0.01
14 17 0.24
15 47 0.66
16 6 0.08
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (16 bp):
GTTTAAGGGTTTTGAA
Found at i:1424555 original size:30 final size:30
Alignment explanation
Indices: 1424462--1424587 Score: 98
Period size: 30 Copynumber: 4.2 Consensus size: 30
1424452 GGGGGTATAT
* * *
1424462 GGTTTTGGGGTTTAAGGTTTTGAA-TTTAG
1 GGTTTTGAGTTTTAAGGTTTTGAAGTTTAA
*
1424491 GGTTTTGGAGTTTT--GGATTTT-TAGTTTAA
1 GGTTTT-GAGTTTTAAGG-TTTTGAAGTTTAA
*
1424520 GGGTTTTGAATTTTAAGGTTTTGAAGTTTAA
1 -GGTTTTGAGTTTTAAGGTTTTGAAGTTTAA
* * * *
1424551 GGTTTGGAGGTTTAGGGGTTTGAAGGGTTTAA
1 GGTTTTGAGTTTTAAGGTTTTGAA--GTTTAA
1424583 GGTTT
1 GGTTT
1424588 GGAGGGTTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
28 3 0.04
29 20 0.26
30 34 0.44
31 9 0.12
32 11 0.14
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (30 bp):
GGTTTTGAGTTTTAAGGTTTTGAAGTTTAA
Found at i:1424581 original size:17 final size:16
Alignment explanation
Indices: 1424531--1424596 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
1424521 GGTTTTGAAT
1424531 TTTAAGGTTTTGAA--G
1 TTTAAGG-TTTGAAGGG
*
1424546 TTTAAGGTTTGGA-GG
1 TTTAAGGTTTGAAGGG
*
1424561 TTTAGGGGTTTGAAGGG
1 TTTA-AGGTTTGAAGGG
*
1424578 TTTAAGGTTTGGAGGG
1 TTTAAGGTTTGAAGGG
1424594 TTT
1 TTT
1424597 TAGGATTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
14 5 0.12
15 12 0.28
16 20 0.47
17 6 0.14
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (16 bp):
TTTAAGGTTTGAAGGG
Found at i:1424889 original size:3 final size:3
Alignment explanation
Indices: 1424881--1424921 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1424871 GCAAAACTAT
1424881 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1424922 CTCCAACATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1425958 original size:17 final size:17
Alignment explanation
Indices: 1425914--1425962 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1425904 TGATTGATTT
1425914 TTTTTGTTTTTTTTTAGG
1 TTTTT-TTTTTTTTTAGG
***
1425932 TTTGAGTTTTTTTTAGG
1 TTTTTTTTTTTTTTAGG
1425949 TTTTTTTTTTTTTT
1 TTTTTTTTTTTTTT
1425963 TGTTCCTTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 22 0.88
18 3 0.12
ACGTcount: A:0.06, C:0.00, G:0.14, T:0.80
Consensus pattern (17 bp):
TTTTTTTTTTTTTTAGG
Found at i:1427303 original size:57 final size:56
Alignment explanation
Indices: 1427211--1427324 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 56
1427201 AAATGAGCAG
* *
1427211 AAAGGAGAGAAGGGGTGAGATACAGAAAAATGTGGCAAGT-AAGTACATAGCCAAAA
1 AAAGAAGAGAAGGGGTGAGAAACAGAAAAATGTGGCAAGTCAA-TACATAGCCAAAA
*
1427267 AAAGAAGAGAAAGGGGTGAGAAACAGAAAAATGTGGCGAGTCAATACATAGCCAAAA
1 AAAGAAGAG-AAGGGGTGAGAAACAGAAAAATGTGGCAAGTCAATACATAGCCAAAA
1427324 A
1 A
1427325 GACATGTAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
56 8 0.15
57 43 0.81
58 2 0.04
ACGTcount: A:0.50, C:0.10, G:0.29, T:0.11
Consensus pattern (56 bp):
AAAGAAGAGAAGGGGTGAGAAACAGAAAAATGTGGCAAGTCAATACATAGCCAAAA
Found at i:1431104 original size:3 final size:3
Alignment explanation
Indices: 1431098--1431130 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1431088 ATTAAATTTG
1431098 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1431131 TATATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1434570 original size:29 final size:27
Alignment explanation
Indices: 1434514--1434579 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
1434504 TAAAAGAAGC
1434514 TCTTATATTTTTATTGTATGAAAATAAT
1 TCTTAT-TTTTTATTGTATGAAAATAAT
** *
1434542 ATCTTATTTTTTATTTGTATTTAAGTAAT
1 -TCTTATTTTTTA-TTGTATGAAAATAAT
1434571 TCATTATTT
1 TC-TTATTT
1434580 CAAACAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 8 0.25
29 24 0.75
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (27 bp):
TCTTATTTTTTATTGTATGAAAATAAT
Done.