Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold498
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: 1804022
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
File 12 of 17
Found at i:1152406 original size:2 final size:2
Alignment explanation
Indices: 1152399--1152453 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1152389 AGGAATTTGC
1152399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1152441 AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT
1152454 TTCATAGTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1152562 original size:14 final size:15
Alignment explanation
Indices: 1152538--1152570 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1152528 TTAAAATTTT
1152538 AATTTTAATTTATTA
1 AATTTTAATTTATTA
*
1152553 AATTTT-ATTTTTTA
1 AATTTTAATTTATTA
1152567 AATT
1 AATT
1152571 AATTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
AATTTTAATTTATTA
Found at i:1153386 original size:30 final size:29
Alignment explanation
Indices: 1153348--1153409 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
1153338 TTGAGACTCT
** *
1153348 TTAAAGTCAATTTCACTTAAGAATCAAGC
1 TTAAAGTCAACCTCACTTAAAAATCAAGC
*
1153377 TTAAGAGTCAACCTCACTTAAAAATCAATC
1 TTAA-AGTCAACCTCACTTAAAAATCAAGC
1153407 TTA
1 TTA
1153410 TATATATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (29 bp):
TTAAAGTCAACCTCACTTAAAAATCAAGC
Found at i:1153950 original size:17 final size:16
Alignment explanation
Indices: 1153930--1153977 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1153920 ATTATAATTA
1153930 TATTTCATAATTTTTAT
1 TATTTCA-AATTTTTAT
*
1153947 TATTTTAAATTTTTAT
1 TATTTCAAATTTTTAT
* * *
1153963 TTTTTAAAATATTTA
1 TATTTCAAATTTTTA
1153978 GATTCAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTCAAATTTTTAT
Found at i:1153972 original size:16 final size:16
Alignment explanation
Indices: 1153938--1153970 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1153928 TATATTTCAT
1153938 AATTTTTATTATTTTA
1 AATTTTTATTATTTTA
1153954 AATTTTTATT-TTTTA
1 AATTTTTATTATTTTA
1153969 AA
1 AA
1153971 ATATTTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
AATTTTTATTATTTTA
Found at i:1155092 original size:2 final size:2
Alignment explanation
Indices: 1155085--1155116 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1155075 TACTTGAGGG
1155085 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1155117 TGTATGTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1155476 original size:2 final size:2
Alignment explanation
Indices: 1155469--1155495 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1155459 ATAGAAAATA
1155469 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 A
1155496 GGAAATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1155848 original size:3 final size:3
Alignment explanation
Indices: 1155840--1155902 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
1155830 TAAATGAAGT
1155840 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1155888 ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
1155903 GCATTTAGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1156521 original size:2 final size:2
Alignment explanation
Indices: 1156509--1156569 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
1156499 GTCCAATAGC
*
1156509 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1156551 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1156570 AAATTAGTAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1157164 original size:2 final size:2
Alignment explanation
Indices: 1157157--1157197 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1157147 TTGTTGAAAA
*
1157157 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1157198 ACGAAAAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1157678 original size:15 final size:16
Alignment explanation
Indices: 1157658--1157695 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1157648 AACAGTATGG
1157658 TTTAAGAA-TATATTA
1 TTTAAGAATTATATTA
1157673 TTTAAGAACTTTATATTA
1 TTTAAGAA--TTATATTA
1157691 TTTAA
1 TTTAA
1157696 CGTAAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
18 12 0.60
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (16 bp):
TTTAAGAATTATATTA
Found at i:1157829 original size:37 final size:37
Alignment explanation
Indices: 1157786--1157862 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
1157776 ATAAAGCCAT
1157786 TTTATTAAAAATCAACTTTTGAACCACAAAATTTTTA
1 TTTATTAAAAATCAACTTTTGAACCACAAAATTTTTA
1157823 TTTATTAAAAATCAACTTTTGAACCACAAAATTTTTA
1 TTTATTAAAAATCAACTTTTGAACCACAAAATTTTTA
1157860 TTT
1 TTT
1157863 TTATTTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.43
Consensus pattern (37 bp):
TTTATTAAAAATCAACTTTTGAACCACAAAATTTTTA
Found at i:1158425 original size:20 final size:22
Alignment explanation
Indices: 1158400--1158446 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
1158390 ATATAACCGT
1158400 TATTAACAGTTAT-TTTA-TAA
1 TATTAACAGTTATCTTTATTAA
*
1158420 TATTAACTGTTATCTTTATTAA
1 TATTAACAGTTATCTTTATTAA
1158442 TATTA
1 TATTA
1158447 TTATAATCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.50
21 4 0.17
22 8 0.33
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.53
Consensus pattern (22 bp):
TATTAACAGTTATCTTTATTAA
Found at i:1158865 original size:2 final size:2
Alignment explanation
Indices: 1158848--1158889 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1158838 GTGTGAGTAG
*
1158848 AT AT AT A- AT -T AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1158888 AT
1 AT
1158890 TTCATAGTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1160549 original size:10 final size:9
Alignment explanation
Indices: 1160503--1160570 Score: 54
Period size: 9 Copynumber: 7.8 Consensus size: 9
1160493 AGTTATCAAA
1160503 ATAATT-AT
1 ATAATTAAT
*
1160511 -TAATTATT
1 ATAATTAAT
*
1160519 ATATTTAAT
1 ATAATTAAT
*
1160528 ATAA-AAAT
1 ATAATTAAT
1160536 ATAATTATAT
1 ATAATTA-AT
1160546 ATAA-TAAT
1 ATAATTAAT
*
1160554 TTAATTAAAT
1 ATAATT-AAT
1160564 ATAATTA
1 ATAATTA
1160571 GGTATTGATT
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
7 5 0.11
8 13 0.28
9 14 0.30
10 14 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATAATTAAT
Found at i:1160568 original size:18 final size:18
Alignment explanation
Indices: 1160525--1160568 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1160515 TATTATATTT
*
1160525 AATATAAAAATATAATTA
1 AATATAATAATATAATTA
* *
1160543 TATATAATAATTTAATTA
1 AATATAATAATATAATTA
1160561 AATATAAT
1 AATATAAT
1160569 TAGGTATTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATAATAATATAATTA
Found at i:1160617 original size:13 final size:13
Alignment explanation
Indices: 1160601--1160625 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1160591 TAATTACTAA
1160601 TTTTAAAGAAAAC
1 TTTTAAAGAAAAC
1160614 TTTTAAAGAAAA
1 TTTTAAAGAAAA
1160626 TCATTTAATG
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:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTTAAAGAAAAC
Found at i:1165166 original size:23 final size:23
Alignment explanation
Indices: 1165118--1165163 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
1165108 ATTTTACCGA
*
1165118 AAAAAATAAAGAAATTAATTTCT
1 AAAAAATAAAAAAATTAATTTCT
1165141 AAAAAATAAAAACTAATTAATTT
1 AAAAAATAAAAA--AATTAATTT
1165164 AAACTAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
25 9 0.45
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAAATAAAAAAATTAATTTCT
Found at i:1166016 original size:2 final size:2
Alignment explanation
Indices: 1166009--1166037 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1165999 AAAGTTAAAG
1166009 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1166038 TGGATTACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1166799 original size:23 final size:22
Alignment explanation
Indices: 1166755--1166800 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1166745 ATAATCGTTA
**
1166755 AAATTAAAATTTTAAATTTATT
1 AAATTAAAATTTTAAAAATATT
*
1166777 AAATATAATATTTTAAAAATATT
1 AAAT-TAAAATTTTAAAAATATT
1166800 A
1 A
1166801 TATAAATCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATTAAAATTTTAAAAATATT
Found at i:1166806 original size:27 final size:25
Alignment explanation
Indices: 1166768--1166820 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
1166758 TTAAAATTTT
*
1166768 AAATTTATTAAAT-ATAATATTTTAA
1 AAATTTATTAAATCA-AATAATTTAA
1166793 AAATATTATATAAATCAAATAATTTAA
1 AAAT-TTAT-TAAATCAAATAATTTAA
1166820 A
1 A
1166821 TTTTAAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 15 0.62
28 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATTTATTAAATCAAATAATTTAA
Found at i:1167157 original size:11 final size:11
Alignment explanation
Indices: 1167141--1167179 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
1167131 ATTTATATAG
1167141 TTATTTTTAAA
1 TTATTTTTAAA
1167152 TTATTTTTATAA
1 TTATTTTTA-AA
*
1167164 ATATATTTTAAA
1 TTAT-TTTTAAA
1167176 TTAT
1 TTAT
1167180 AATATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTTTAAA
Found at i:1167162 original size:23 final size:24
Alignment explanation
Indices: 1167129--1167179 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
1167119 AAATTACTAT
**
1167129 TTATTTATATAGTTAT-TTTTAAA
1 TTATTTATATAAATATATTTTAAA
*
1167152 TTATTTTTATAAATATATTTTAAA
1 TTATTTATATAAATATATTTTAAA
1167176 TTAT
1 TTAT
1167180 AATATATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TTATTTATATAAATATATTTTAAA
Found at i:1167199 original size:20 final size:18
Alignment explanation
Indices: 1167158--1167207 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
1167148 TAAATTATTT
1167158 TTATAA-ATATATTTTAAA
1 TTATAATATAT-TTTTAAA
1167176 TTATAATATATTTATTACAA
1 TTATAATATATTT-TTA-AA
1167196 TTATAATATATT
1 TTATAATATATT
1167208 ATAAATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.28
19 7 0.24
20 14 0.48
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATAATATATTTTTAAA
Found at i:1168194 original size:2 final size:2
Alignment explanation
Indices: 1168187--1168216 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1168177 TTATATTAAA
1168187 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1168217 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1168253 original size:2 final size:2
Alignment explanation
Indices: 1168216--1168242 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1168206 TCTCTCTCTC
1168216 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1168243 CTTTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1168843 original size:47 final size:45
Alignment explanation
Indices: 1168792--1168898 Score: 128
Period size: 43 Copynumber: 2.4 Consensus size: 45
1168782 AATTTGATCA
* * * *
1168792 ATTAATTTTATCTCATTCATCTTTATTTATTGTATGTAATATAATAT
1 ATTAATTTTAT-TCATT-AACCTCATTTATTGAATGTAATATAATAT
*
1168839 ATTAATTTTA-TC-TTAACCTCATTTATTGAATTTAATATAATAT
1 ATTAATTTTATTCATTAACCTCATTTATTGAATGTAATATAATAT
*
1168882 ATTAATTTCATTCATTA
1 ATTAATTTTATTCATTA
1168899 CTTTTTTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
43 33 0.63
44 4 0.08
45 5 0.10
47 10 0.19
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (45 bp):
ATTAATTTTATTCATTAACCTCATTTATTGAATGTAATATAATAT
Found at i:1169336 original size:47 final size:42
Alignment explanation
Indices: 1169264--1169381 Score: 100
Period size: 43 Copynumber: 2.7 Consensus size: 42
1169254 AATTTAACTA
* **
1169264 ATTAATTTTATCTTATTCATCTTCATTTATTGTGTGTAATATAATAT
1 ATTAATTTTATCTAATTCA-CTTCA-TTA-AAT-T-TAATATAATAT
1169311 ATTAATTTTATCTCAACTTCA-TTCATTAAATTTAATATAATAT
1 ATTAATTTTATCT-AA-TTCACTTCATTAAATTTAATATAATAT
* *
1169354 ATTAATTTCAT-TAATT-ACTT-TTTAAATT
1 ATTAATTTTATCTAATTCACTTCATTAAATT
1169382 ACATTTTAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
39 8 0.13
40 4 0.06
41 2 0.03
42 1 0.02
43 21 0.33
44 1 0.02
45 1 0.02
46 3 0.05
47 17 0.27
48 1 0.02
49 4 0.06
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (42 bp):
ATTAATTTTATCTAATTCACTTCATTAAATTTAATATAATAT
Found at i:1173677 original size:44 final size:43
Alignment explanation
Indices: 1173599--1173690 Score: 118
Period size: 46 Copynumber: 2.1 Consensus size: 43
1173589 TGCAAGGTTT
1173599 TATTTTTTTATAATAAACTAATTTAATATATATATATATATAAAAA
1 TATTTTTTTATAATAAAC-AATTTAATATATATATATAT-T-AAAA
1173645 TATTTTTTTATAAATTAAA-AA-TTAAT-TATATATATATTAAAA
1 TATTTTTTTAT-AA-TAAACAATTTAATATATATATATATTAAAA
1173687 TATT
1 TATT
1173691 AACCGTGCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
42 8 0.18
43 1 0.02
44 11 0.25
45 5 0.11
46 13 0.30
47 2 0.05
48 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (43 bp):
TATTTTTTTATAATAAACAATTTAATATATATATATATTAAAA
Found at i:1176708 original size:21 final size:21
Alignment explanation
Indices: 1176660--1176711 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1176650 TTATTCTATA
* *
1176660 AATAAAAAATTATTTAAATTT
1 AATATAAAATTATATAAATTT
1176681 AATTATAAAA-TATATAAATATT
1 AA-TATAAAATTATATAAAT-TT
1176703 AATATAAAA
1 AATATAAAA
1176712 ATAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATAAAATTATATAAATTT
Found at i:1176712 original size:22 final size:21
Alignment explanation
Indices: 1176660--1176714 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
1176650 TTATTCTATA
*
1176660 AATA-AAAAATTATTTAAATTT
1 AATATAAAAA-TATATAAATTT
1176681 AAT-TATAAAATATATAAATATT
1 AATATA-AAAATATATAAAT-TT
1176703 AATATAAAAATA
1 AATATAAAAATA
1176715 ATATTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 12 0.41
22 15 0.52
23 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATAAAAATATATAAATTT
Found at i:1177349 original size:6 final size:6
Alignment explanation
Indices: 1177340--1177408 Score: 51
Period size: 6 Copynumber: 12.5 Consensus size: 6
1177330 TAAAAATTTA
* * *
1177340 AATTAT AATTAT AATCAT -ATT-T -ATTAT GATTAT AAATAT AA-TA-
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT
* *
1177383 AA-TAT TATAAT AATTAT AATTAT AAT
1 AATTAT AATTAT AATTAT AATTAT AAT
1177409 AAATATTGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
4 8 0.16
5 6 0.12
6 37 0.73
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
AATTAT
Found at i:1177379 original size:27 final size:27
Alignment explanation
Indices: 1177340--1177415 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
1177330 TAAAAATTTA
* *
1177340 AATTATAATTATAAT-CATATTTATTAT
1 AATTATAATTATAATAAATA-TTATAAT
* *
1177367 GATTATAAATATAATAAATATTATAAT
1 AATTATAATTATAATAAATATTATAAT
1177394 AATTATAATTATAATAAATATT
1 AATTATAATTATAATAAATATT
1177416 GATGATAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 39 0.93
28 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (27 bp):
AATTATAATTATAATAAATATTATAAT
Found at i:1177393 original size:12 final size:12
Alignment explanation
Indices: 1177376--1177415 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
1177366 TGATTATAAA
1177376 TATAATAAATAT
1 TATAATAAATAT
1177388 TATAATAATTATAAT
1 TATAATAA--AT-AT
1177403 TATAATAAATAT
1 TATAATAAATAT
1177415 T
1 T
1177416 GATGATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.44
13 2 0.08
14 2 0.08
15 10 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TATAATAAATAT
Found at i:1177430 original size:27 final size:27
Alignment explanation
Indices: 1177376--1177431 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1177366 TGATTATAAA
* *
1177376 TATAATAAATATTATAATAATTATAAT
1 TATAATAAATATTATAATAATAAAAAT
*
1177403 TATAATAAATATTGATGATAA-AAAAAT
1 TATAATAAATATT-ATAATAATAAAAAT
1177430 TA
1 TA
1177432 AAATTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (27 bp):
TATAATAAATATTATAATAATAAAAAT
Found at i:1177669 original size:2 final size:2
Alignment explanation
Indices: 1177662--1177692 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1177652 TTCCAATAAA
1177662 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 A
1177693 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1177697 original size:2 final size:2
Alignment explanation
Indices: 1177692--1177720 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1177682 ATATATATAT
1177692 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1177721 CATCCTCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1177871 original size:34 final size:32
Alignment explanation
Indices: 1177828--1177933 Score: 117
Period size: 34 Copynumber: 3.2 Consensus size: 32
1177818 ATAATTATTT
*
1177828 ATATATAATATAAAAAATTATAATATAATATAAA
1 ATAT-TAATATTAAAAATTAT-ATATAATATAAA
*
1177862 TATATTAATATTTTAAAATT-TATATAATATAAA
1 -ATATTAATA-TTAAAAATTATATATAATATAAA
1177895 ATTATTAATTTATTAAAAATTATATA-AATATAAA
1 A-TATTAA--TATTAAAAATTATATATAATATAAA
1177929 ATATT
1 ATATT
1177934 TTAAACGTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
32 1 0.02
33 22 0.35
34 23 0.37
35 17 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATTAATATTAAAAATTATATATAATATAAA
Found at i:1177872 original size:19 final size:19
Alignment explanation
Indices: 1177806--1177927 Score: 68
Period size: 19 Copynumber: 6.8 Consensus size: 19
1177796 AATTAGACAT
1177806 AATATATTAAATATAAT-TA
1 AATATATT-AATATAATATA
**
1177825 TTTATATATAATATAA-A-A
1 AATATAT-TAATATAATATA
1177843 AAT-TA-TAATATAATATA
1 AATATATTAATATAATATA
*
1177860 AATATATTAATAT--TTTA
1 AATATATTAATATAATATA
1177877 AA-AT-TT-ATATAATATA
1 AATATATTAATATAATATA
* * *
1177893 AA-ATTATTAATTTATTAAA
1 AATA-TATTAATATAATATA
*
1177912 AATTATATAAATATAA
1 AA-TATATTAATATAA
1177928 AATATTTTAA
Statistics
Matches: 78, Mismatches: 12, Indels: 25
0.68 0.10 0.22
Matches are distributed among these distances:
14 4 0.05
15 10 0.13
16 9 0.12
17 12 0.15
18 6 0.08
19 27 0.35
20 9 0.12
21 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATATTAATATAATATA
Found at i:1177887 original size:33 final size:32
Alignment explanation
Indices: 1177841--1177933 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 32
1177831 TATAATATAA
1177841 AAAATTATAATATAATATAAATATATTAATATT-TT
1 AAAATT-T-ATATAATATAAA-ATATTAAT-TTATT
1177876 AAAATTTATATAATATAAAATTATTAATTTATT
1 AAAATTTATATAATATAAAA-TATTAATTTATT
*
1177909 AAAAATTATATAAATATAAAATATT
1 AAAATTTATAT-AATATAAAATATT
1177934 TTAAACGTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
32 3 0.06
33 35 0.65
34 10 0.19
35 6 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
AAAATTTATATAATATAAAATATTAATTTATT
Found at i:1178955 original size:45 final size:46
Alignment explanation
Indices: 1178860--1178957 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 46
1178850 AGGGAGAGTT
* * *
1178860 ACAGGAGGGAGATTAATTGGTGGCATCACAATTGGAGGAACTATCC
1 ACAGGAGGGAGATTAATGGGTAGCATCACAATTGGAGGAACTAGCC
* ** * *
1178906 -CAGGAGGGAGGTTAATGGGTAGTTTCACGATTGGAGGGAC-AGCC
1 ACAGGAGGGAGATTAATGGGTAGCATCACAATTGGAGGAACTAGCC
1178950 ACAGGAGG
1 ACAGGAGG
1178958 AAGAGCCGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
44 3 0.07
45 40 0.93
ACGTcount: A:0.30, C:0.14, G:0.37, T:0.19
Consensus pattern (46 bp):
ACAGGAGGGAGATTAATGGGTAGCATCACAATTGGAGGAACTAGCC
Found at i:1179060 original size:45 final size:45
Alignment explanation
Indices: 1178967--1179062 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 45
1178957 GAAGAGCCGT
* * *
1178967 AGGAGGGAGATTAATTGGTGGCTTCACAATTGGAGGAACTATCCC
1 AGGAGGGAGATTAATGGGTAGCTTCACAATTGGAGGAACTAGCCC
* * * *
1179012 AGGAGGGAGGTTAATGGGTAGTTTCACGATTGGAGGGAC-AGCCAC
1 AGGAGGGAGATTAATGGGTAGCTTCACAATTGGAGGAACTAGCC-C
1179057 AGGAGG
1 AGGAGG
1179063 AAGAGCCGTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 3 0.07
45 40 0.93
ACGTcount: A:0.28, C:0.14, G:0.38, T:0.21
Consensus pattern (45 bp):
AGGAGGGAGATTAATGGGTAGCTTCACAATTGGAGGAACTAGCCC
Found at i:1179109 original size:45 final size:46
Alignment explanation
Indices: 1179058--1179695 Score: 481
Period size: 45 Copynumber: 14.2 Consensus size: 46
1179048 GACAGCCACA
** * *
1179058 GGAGGAA-GAGCCGTAGGAGGGAGATTAATTGGTGTCTTCACAATT
1 GGAGGAACGAGCCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATT
* *
1179103 GGAGGAACGA-CCCCAGGAGGGAGGTTAATTGGTGGCTTCAGAACT
1 GGAGGAACGAGCCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATT
* * * ** * * *
1179148 GGAGGAAC-AGTCACTGGAGGGA--TTGCAACCGGTGGTTTTACTATT
1 GGAGGAACGAGCCCCAGGAGGGAGGTT--AATTGGTGGCTTCACAATT
* **
1179193 GGAGGAACGA-TCCCAGGAGGGAGGTTAATTGGTGAATTCACAATT
1 GGAGGAACGAGCCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATT
* * * * * *
1179238 GGAGGAAC-AGCCACTGGAGGGA-CTGTAATTGGTGGATTTACTATT
1 GGAGGAACGAGCCCCAGGAGGGAGGT-TAATTGGTGGCTTCACAATT
*
1179283 GGAGGAACGA-CCCCAGGAGGGAGGTTAATTGGTGGCTGCACAATT
1 GGAGGAACGAGCCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATT
* * * * * * * * *
1179328 GGAGGAAC-AGTCACTGGAGGGA-CTGCAATCGGTGGTTTTACTATT
1 GGAGGAACGAGCCCCAGGAGGGAGGT-TAATTGGTGGCTTCACAATT
*
1179373 GGAGGAACGA-CCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATA
1 GGAGGAACGAGCCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATT
* * * * ** * *
1179418 GGAGGAA-GAGTCACTGGAGGGA-CTGTAACCGGTGGATTCACTATT
1 GGAGGAACGAGCCCCAGGAGGGAGGT-TAATTGGTGGCTTCACAATT
*
1179463 GGAGGAACGA-CCCCAGGAGGGAGGCTAATTGGTGGCTTCACAATT
1 GGAGGAACGAGCCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATT
* * * * * * * * * *
1179508 GGAGGAAC-AGTCACTGGAGGGACAG-CAATCGGCGGTTTTACTATT
1 GGAGGAACGAGCCCCAGGAGGGA-GGTTAATTGGTGGCTTCACAATT
* *
1179553 GGAGGAACGA-CCCCAGGAGGGAGGTTAATTGGTGGCTTCACTATA
1 GGAGGAACGAGCCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATT
* * * * * * * *
1179598 GGAGGAAC-AGTCACTGGAGGGA-CTGTAATCGGTGGTTTAACTATT
1 GGAGGAACGAGCCCCAGGAGGGAGGT-TAATTGGTGGCTTCACAATT
* *
1179643 GGAGGAACGA-CCCCAGGAGGCAGGTTAATGGGTGGCTTCACAATT
1 GGAGGAACGAGCCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATT
1179688 GGAGGAAC
1 GGAGGAAC
1179696 AGTCACGGGA
Statistics
Matches: 453, Mismatches: 113, Indels: 54
0.73 0.18 0.09
Matches are distributed among these distances:
43 2 0.00
44 12 0.03
45 424 0.94
46 13 0.03
47 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.22
Consensus pattern (46 bp):
GGAGGAACGAGCCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATT
Found at i:1179167 original size:105 final size:105
Alignment explanation
Indices: 1178790--1179131 Score: 551
Period size: 105 Copynumber: 3.3 Consensus size: 105
1178780 CTGCCACTGA
* * * * *
1178790 AGGAACTGTCACC-GGAGGGAGGTTGATGGGTAGTTTCGCGATTGGAGGGACAGCCACTGGAGGG
1 AGGAACTATC-CCAGGAGGGAGGTTAATGGGTAGTTTCACGATTGGAGGGACAGCCACAGGAGGA
**** *
1178854 AGAGTTACAGGAGGGAGATTAATTGGTGGCATCACAATTGG
65 AGAGCCGTAGGAGGGAGATTAATTGGTGGCTTCACAATTGG
1178895 AGGAACTATCCCAGGAGGGAGGTTAATGGGTAGTTTCACGATTGGAGGGACAGCCACAGGAGGAA
1 AGGAACTATCCCAGGAGGGAGGTTAATGGGTAGTTTCACGATTGGAGGGACAGCCACAGGAGGAA
1178960 GAGCCGTAGGAGGGAGATTAATTGGTGGCTTCACAATTGG
66 GAGCCGTAGGAGGGAGATTAATTGGTGGCTTCACAATTGG
1179000 AGGAACTATCCCAGGAGGGAGGTTAATGGGTAGTTTCACGATTGGAGGGACAGCCACAGGAGGAA
1 AGGAACTATCCCAGGAGGGAGGTTAATGGGTAGTTTCACGATTGGAGGGACAGCCACAGGAGGAA
*
1179065 GAGCCGTAGGAGGGAGATTAATTGGTGTCTTCACAATTGG
66 GAGCCGTAGGAGGGAGATTAATTGGTGGCTTCACAATTGG
* *
1179105 AGGAACGACCCCAGGAGGGAGGTTAAT
1 AGGAACTATCCCAGGAGGGAGGTTAAT
1179132 TGGTGGCTTC
Statistics
Matches: 223, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
104 2 0.01
105 221 0.99
ACGTcount: A:0.28, C:0.14, G:0.38, T:0.20
Consensus pattern (105 bp):
AGGAACTATCCCAGGAGGGAGGTTAATGGGTAGTTTCACGATTGGAGGGACAGCCACAGGAGGAA
GAGCCGTAGGAGGGAGATTAATTGGTGGCTTCACAATTGG
Found at i:1179168 original size:90 final size:89
Alignment explanation
Indices: 1179100--1179715 Score: 917
Period size: 90 Copynumber: 6.9 Consensus size: 89
1179090 TGTCTTCACA
* *
1179100 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCAGAACTGGAGGAACAGTCACTGG
1 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
* * *
1179165 AGGGATTGCAACCGGTGGTTTTACT
66 AGGGACTGTAATCGGT-GTTTTACT
* ** *
1179190 ATTGGAGGAACGATCCCAGGAGGGAGGTTAATTGGTGAATTCACAATTGGAGGAACAGCCACTGG
1 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
* *
1179255 AGGGACTGTAATTGGTGGATTTACT
66 AGGGACTGTAATCGGT-GTTTTACT
*
1179280 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTGCACAATTGGAGGAACAGTCACTGG
1 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
*
1179345 AGGGACTGCAATCGGTGGTTTTACT
66 AGGGACTGTAATCGGT-GTTTTACT
* *
1179370 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATAGGAGGAAGAGTCACTGG
1 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
* * *
1179435 AGGGACTGTAACCGGTGGATTCACT
66 AGGGACTGTAATCGGT-GTTTTACT
*
1179460 ATTGGAGGAACGACCCCAGGAGGGAGGCTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
1 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
* * *
1179525 AGGGACAGCAATCGGCGGTTTTACT
66 AGGGACTGTAATCGG-TGTTTTACT
* *
1179550 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACTATAGGAGGAACAGTCACTGG
1 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
*
1179615 AGGGACTGTAATCGGTGGTTTAACT
66 AGGGACTGTAATCGGT-GTTTTACT
* * *
1179640 ATTGGAGGAACGACCCCAGGAGGCAGGTTAATGGGTGGCTTCACAATTGGAGGAACAGTCACGGG
1 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
*
1179705 AGGGACAGTAA
66 AGGGACTGTAA
1179716 CTGGCGGCAA
Statistics
Matches: 476, Mismatches: 48, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
90 476 1.00
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.21
Consensus pattern (89 bp):
ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
AGGGACTGTAATCGGTGTTTTACT
Found at i:1179299 original size:180 final size:180
Alignment explanation
Indices: 1179100--1179710 Score: 1017
Period size: 180 Copynumber: 3.4 Consensus size: 180
1179090 TGTCTTCACA
* *
1179100 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCAGAACTGGAGGAACAGTCACTGG
1 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
* * * **
1179165 AGGGATTGCAACCGGTGGTTTTACTATTGGAGGAACGATCCCAGGAGGGAGGTTAATTGGTGAAT
66 AGGGACTGCAATCGGTGGTTTTACTATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCT
* * *
1179230 TCACAATTGGAGGAACAGCCACTGGAGGGACTGTAATTGGTGGATTTACT
131 TCACAATAGGAGGAACAGTCACTGGAGGGACTGTAATCGGTGGATTTACT
*
1179280 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTGCACAATTGGAGGAACAGTCACTGG
1 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
1179345 AGGGACTGCAATCGGTGGTTTTACTATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCT
66 AGGGACTGCAATCGGTGGTTTTACTATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCT
* * *
1179410 TCACAATAGGAGGAAGAGTCACTGGAGGGACTGTAACCGGTGGATTCACT
131 TCACAATAGGAGGAACAGTCACTGGAGGGACTGTAATCGGTGGATTTACT
*
1179460 ATTGGAGGAACGACCCCAGGAGGGAGGCTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
1 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
* *
1179525 AGGGACAGCAATCGGCGGTTTTACTATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCT
66 AGGGACTGCAATCGGTGGTTTTACTATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCT
*
1179590 TCACTATAGGAGGAACAGTCACTGGAGGGACTGTAATCGGTGG-TTTAACT
131 TCACAATAGGAGGAACAGTCACTGGAGGGACTGTAATCGGTGGATTT-ACT
* * *
1179640 ATTGGAGGAACGACCCCAGGAGGCAGGTTAATGGGTGGCTTCACAATTGGAGGAACAGTCACGGG
1 ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
1179705 AGGGAC
66 AGGGAC
1179711 AGTAACTGGC
Statistics
Matches: 404, Mismatches: 26, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
179 2 0.00
180 402 1.00
ACGTcount: A:0.27, C:0.17, G:0.35, T:0.21
Consensus pattern (180 bp):
ATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCTTCACAATTGGAGGAACAGTCACTGG
AGGGACTGCAATCGGTGGTTTTACTATTGGAGGAACGACCCCAGGAGGGAGGTTAATTGGTGGCT
TCACAATAGGAGGAACAGTCACTGGAGGGACTGTAATCGGTGGATTTACT
Found at i:1183029 original size:16 final size:16
Alignment explanation
Indices: 1183010--1183086 Score: 68
Period size: 16 Copynumber: 4.8 Consensus size: 16
1183000 TACATATCTT
1183010 TATTAAATATTAATTA
1 TATTAAATATTAATTA
* *
1183026 TATTTAATATTTATTTAA
1 TATTAAATA-TTAATT-A
1183044 TATTAAA-ATTAATTA
1 TATTAAATATTAATTA
* * **
1183059 TTTTTAATATTAAAAA
1 TATTAAATATTAATTA
1183075 TATTAAA-ATTAA
1 TATTAAATATTAA
1183087 GATTCTAATA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
15 11 0.23
16 24 0.50
17 6 0.12
18 7 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTAAATATTAATTA
Found at i:1183033 original size:33 final size:32
Alignment explanation
Indices: 1182996--1183067 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
1182986 GCAAATTAAC
1182996 TTAATACATATCTT-TATTAAATATTAATTATAT
1 TTAATACATAT-TTATATTAAA-ATTAATTATAT
** *
1183029 TTAATATTTATTTAATATTAAAATTAATTATTT
1 TTAATACATATTT-ATATTAAAATTAATTATAT
1183062 TTAATA
1 TTAATA
1183068 TTAAAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 2 0.06
33 25 0.74
34 7 0.21
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (32 bp):
TTAATACATATTTATATTAAAATTAATTATAT
Found at i:1183077 original size:31 final size:33
Alignment explanation
Indices: 1183010--1183086 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
1183000 TACATATCTT
**
1183010 TATTAAATATTAATTATATTTAATATTTATTTAA
1 TATTAAA-ATTAATTATATTTAATATTTATAAAA
*
1183044 TATTAAAATTAATTATTTTTAATA-TTA-AAAA
1 TATTAAAATTAATTATATTTAATATTTATAAAA
1183075 TATTAAAATTAA
1 TATTAAAATTAA
1183087 GATTCTAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 14 0.35
32 3 0.08
33 16 0.40
34 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TATTAAAATTAATTATATTTAATATTTATAAAA
Found at i:1183424 original size:2 final size:2
Alignment explanation
Indices: 1183417--1183442 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1183407 CGTAACTTAA
1183417 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
1183443 TTTTTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1184588 original size:21 final size:21
Alignment explanation
Indices: 1184559--1184600 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1184549 TAAAAATATA
1184559 AAAATTAATTAA-ATATAATT
1 AAAATTAATTAAGATATAATT
1184579 AAAATATAATTAAGATATAATT
1 AAAAT-TAATTAAGATATAATT
1184601 TGATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAATTAATTAAGATATAATT
Found at i:1184596 original size:11 final size:10
Alignment explanation
Indices: 1184552--1184600 Score: 59
Period size: 11 Copynumber: 5.0 Consensus size: 10
1184542 AAATACATAA
1184552 AAATATAA--
1 AAATATAATT
1184560 AAAT-TAATT
1 AAATATAATT
1184569 AAATATAATT
1 AAATATAATT
1184579 AAAATATAATT
1 -AAATATAATT
1184590 AAGATATAATT
1 AA-ATATAATT
1184601 TGATATTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
7 3 0.08
8 4 0.11
9 4 0.11
10 7 0.19
11 18 0.50
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (10 bp):
AAATATAATT
Found at i:1184718 original size:20 final size:20
Alignment explanation
Indices: 1184698--1184734 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1184688 TTCATGCTTA
*
1184698 AATTTTTAAA-TTTAAAATT
1 AATTTTAAAATTTTAAAATT
1184717 AATTTTAAAATTTTAAAA
1 AATTTTAAAATTTTAAAA
1184735 ATTTACTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTTAAAATTTTAAAATT
Found at i:1185160 original size:2 final size:2
Alignment explanation
Indices: 1185153--1185181 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1185143 TTTTCAATTA
1185153 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1185182 TTTTACATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1185411 original size:15 final size:16
Alignment explanation
Indices: 1185383--1185424 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
1185373 TAATTTGTAA
*
1185383 TTAT-CTTTTTAATTT
1 TTATACTTTTAAATTT
1185398 TT-TACTTTTAAATTT
1 TTATACTTTTAAATTT
*
1185413 TTATAATTTTAA
1 TTATACTTTTAA
1185425 TATATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 1 0.04
15 14 0.61
16 8 0.35
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATACTTTTAAATTT
Found at i:1186121 original size:12 final size:12
Alignment explanation
Indices: 1186104--1186144 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1186094 ATAAAATATG
1186104 AAATAAATTAAA
1 AAATAAATTAAA
*
1186116 ATAT-AA-TAAA
1 AAATAAATTAAA
*
1186126 AAATAATTTAAA
1 AAATAAATTAAA
1186138 AAATAAA
1 AAATAAA
1186145 ACATGACATA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 7 0.30
11 3 0.13
12 13 0.57
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATAAATTAAA
Found at i:1186391 original size:18 final size:18
Alignment explanation
Indices: 1186368--1186407 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1186358 TAATAAAAAA
*
1186368 TAAATTTAAGAAATTAAT
1 TAAATTTAAAAAATTAAT
*
1186386 TAAATTTAAAAAATTTAT
1 TAAATTTAAAAAATTAAT
1186404 TAAA
1 TAAA
1186408 ATCATGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TAAATTTAAAAAATTAAT
Found at i:1186821 original size:22 final size:21
Alignment explanation
Indices: 1186796--1186852 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
1186786 TAGTTTAAAG
* *
1186796 TTATTTTATTTTAATATATGAT
1 TTATTTTATTTTAAAAT-TAAT
1186818 TTATTTTTATTTATAAAATTAAT
1 TTA-TTTTATTT-TAAAATTAAT
*
1186841 TTAATTTATTTT
1 TTATTTTATTTT
1186853 TATTAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.03
22 10 0.33
23 14 0.47
24 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTATTTTATTTTAAAATTAAT
Found at i:1186854 original size:24 final size:22
Alignment explanation
Indices: 1186827--1186873 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
1186817 TTTATTTTTA
1186827 TTTATAAAATTAATTTAATTTATT
1 TTTATAAAATTAATTT--TTTATT
* *
1186851 TTTATTAAATTTATTTTTTATT
1 TTTATAAAATTAATTTTTTATT
1186873 T
1 T
1186874 GATTATGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATAAAATTAATTTTTTATT
Found at i:1187854 original size:66 final size:64
Alignment explanation
Indices: 1187759--1187889 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 64
1187749 ACGATATATA
*
1187759 AAATGATTTTTCGTATAATCTAAGAAAAATTATTTTATTGATCATCAATAAAACTTTAAATTCT
1 AAATGATTTTTCATATAATCTAAGAAAAATTATTTTATTGATCATCAATAAAACTTTAAATTCT
*
1187823 AAATGATTTTTCATATATAATCTAAGGAAAATTATTTTATTGATCATCAATAAAACTTTAAATTC
1 AAATGATTTTTC--ATATAATCTAAGAAAAATTATTTTATTGATCATCAATAAAACTTTAAATTC
1187888 T
64 T
1187889 A
1 A
1187890 TCAACAAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 12 0.19
66 51 0.81
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (64 bp):
AAATGATTTTTCATATAATCTAAGAAAAATTATTTTATTGATCATCAATAAAACTTTAAATTCT
Found at i:1188484 original size:20 final size:19
Alignment explanation
Indices: 1188448--1188486 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1188438 AAAAAAAATC
* *
1188448 AAAATGTTTTTTCTTAAAA
1 AAAATCTTTTTACTTAAAA
1188467 AAAATCTTTTTACATTAAAA
1 AAAATCTTTTTAC-TTAAAA
1188487 TCTATTGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (19 bp):
AAAATCTTTTTACTTAAAA
Found at i:1190356 original size:24 final size:24
Alignment explanation
Indices: 1190321--1190386 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 24
1190311 CAAAAATATG
**
1190321 AAAATAATATAATTTAAATATAAA
1 AAAATAATATAAAATAAATATAAA
*
1190345 AAAAGTAA-ATAAAATAAAT-T-TA
1 AAAA-TAATATAAAATAAATATAAA
1190367 AAAATAAT-TAAAAATAAATA
1 AAAATAATAT-AAAATAAATA
1190387 AAATTTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
21 4 0.11
22 14 0.40
23 1 0.03
24 13 0.37
25 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAATAATATAAAATAAATATAAA
Found at i:1190358 original size:11 final size:10
Alignment explanation
Indices: 1190335--1190399 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 10
1190325 TAATATAATT
*
1190335 TAAATATAAA
1 TAAAAATAAA
*
1190345 -AAAAGTAAA
1 TAAAAATAAA
1190354 T-AAAATAAA
1 TAAAAATAAA
*
1190363 TTTAAAAATAAT
1 --TAAAAATAAA
1190375 TAAAAATAAA
1 TAAAAATAAA
*
1190385 TAAAATTTAAA
1 TAAAA-ATAAA
1190396 TAAA
1 TAAA
1190400 TCTTTTAAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 14 0.32
10 14 0.32
11 9 0.20
12 7 0.16
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:1190388 original size:31 final size:29
Alignment explanation
Indices: 1190322--1190390 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
1190312 AAAAATATGA
* *
1190322 AAATAATATAATTTAAATATAAAAAAAGT
1 AAATAAAATAATTTAAAAATAAAAAAAGT
1190351 AAATAAAATAAATTTAAAAATAATTAAAAA-T
1 AAATAAAAT-AATTTAAAAATAA--AAAAAGT
1190382 AAATAAAAT
1 AAATAAAAT
1190391 TTAAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 8 0.23
30 12 0.34
31 10 0.29
32 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (29 bp):
AAATAAAATAATTTAAAAATAAAAAAAGT
Found at i:1190691 original size:24 final size:22
Alignment explanation
Indices: 1190670--1190713 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1190660 TATTTATTTG
1190670 ATATTTAAAAATTTTAAATATTAA
1 ATATTT-AAAATTTT-AATATTAA
*
1190694 ATATTTATAATTTTAATATT
1 ATATTTAAAATTTTAATATT
1190714 CTTAATCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 7 0.37
24 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTTAAAATTTTAATATTAA
Found at i:1191278 original size:18 final size:18
Alignment explanation
Indices: 1191255--1191295 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1191245 TGATTTACAT
1191255 GATAATTAAATAAATTAA
1 GATAATTAAATAAATTAA
* * *
1191273 GATAATTAATTTAATTAT
1 GATAATTAAATAAATTAA
1191291 GATAA
1 GATAA
1191296 AATGATATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (18 bp):
GATAATTAAATAAATTAA
Found at i:1192526 original size:19 final size:19
Alignment explanation
Indices: 1192486--1192524 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1192476 TGTATCCATA
1192486 TTATATTCAAATTAATTTT
1 TTATATTCAAATTAATTTT
*
1192505 TTATA-TCATATTAATTTT
1 TTATATTCAAATTAATTTT
1192523 TT
1 TT
1192525 TACATGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATATTCAAATTAATTTT
Found at i:1193590 original size:18 final size:17
Alignment explanation
Indices: 1193572--1193605 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1193562 CATAAAAAAT
*
1193572 ATATAAACAA-AACATA
1 ATATAAAAAATAACATA
1193588 ATATAAAAAATAACATA
1 ATATAAAAAATAACATA
1193605 A
1 A
1193606 ATACAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (17 bp):
ATATAAAAAATAACATA
Found at i:1201892 original size:3 final size:3
Alignment explanation
Indices: 1201884--1201930 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1201874 TTACTCCATG
1201884 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1201931 CAAAAAAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1204652 original size:12 final size:12
Alignment explanation
Indices: 1204637--1204661 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1204627 TTGTTTTTGC
1204637 CTTTTTTTTTTT
1 CTTTTTTTTTTT
1204649 CTTTTTTTTTTT
1 CTTTTTTTTTTT
1204661 C
1 C
1204662 CAATTTCGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
CTTTTTTTTTTT
Found at i:1205836 original size:5 final size:5
Alignment explanation
Indices: 1205826--1205854 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1205816 CGATTTAGTA
1205826 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1205855 ATTTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1206022 original size:18 final size:16
Alignment explanation
Indices: 1205999--1206033 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1205989 TATATTATTT
1205999 ATATATTTAAATATATAA
1 ATATA-TTAAATAT-TAA
1206017 ATATATTAAATATTAA
1 ATATATTAAATATTAA
1206033 A
1 A
1206034 AAATTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATATTAAATATTAA
Found at i:1206137 original size:14 final size:14
Alignment explanation
Indices: 1206120--1206153 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1206110 ATAAAAAAAT
1206120 TTAAATTAATTTAA
1 TTAAATTAATTTAA
*
1206134 TTAAATTGATTTAA
1 TTAAATTAATTTAA
*
1206148 CTAAAT
1 TTAAAT
1206154 AACTATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (14 bp):
TTAAATTAATTTAA
Found at i:1206466 original size:18 final size:18
Alignment explanation
Indices: 1206445--1206479 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1206435 GAAAATAGAC
1206445 AAACTTATGAATTATATA
1 AAACTTATGAATTATATA
*
1206463 AAACTTATTAATTATAT
1 AAACTTATGAATTATAT
1206480 TATTGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
AAACTTATGAATTATATA
Found at i:1206986 original size:16 final size:16
Alignment explanation
Indices: 1206962--1206993 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1206952 AAATAACATG
1206962 CCACCATTTTTGACAA
1 CCACCATTTTTGACAA
*
1206978 CCACTATTTTTGACAA
1 CCACCATTTTTGACAA
1206994 ACACAAAATA
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:0.31, C:0.28, G:0.06, T:0.34
Consensus pattern (16 bp):
CCACCATTTTTGACAA
Found at i:1211545 original size:24 final size:24
Alignment explanation
Indices: 1211499--1211546 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1211489 TAACCATAAA
* * **
1211499 TTTTGACAAATAACATGTCACCAT
1 TTTTGACAAATAAAAAGAAACCAT
1211523 TTTTGACAAATAAAAAGAAACCAT
1 TTTTGACAAATAAAAAGAAACCAT
1211547 CATTTTTTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (24 bp):
TTTTGACAAATAAAAAGAAACCAT
Found at i:1214918 original size:2 final size:2
Alignment explanation
Indices: 1214911--1214941 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1214901 TAATGTACAC
1214911 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 A
1214942 CATACCAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1214998 original size:2 final size:2
Alignment explanation
Indices: 1214986--1215047 Score: 52
Period size: 2 Copynumber: 31.0 Consensus size: 2
1214976 TTCTCCCATG
* * * * * ** *
1214986 AT AT AT GT AT AT AT AT AT AT AT AC AC AT AT AT AC GT GC AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1215028 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1215048 CAAATTAAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1215700 original size:2 final size:2
Alignment explanation
Indices: 1215695--1215727 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1215685 AAAAAAATGA
1215695 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
1215728 ATGCCACGAT
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:1216709 original size:15 final size:15
Alignment explanation
Indices: 1216685--1216727 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
1216675 TTTAAATTTG
*
1216685 ATAAAAATATTAAAT
1 ATAAATATATTAAAT
*
1216700 ATAAATATATATTTAAT
1 AT-AA-ATATATTAAAT
1216717 ATAAATATATT
1 ATAAATATATT
1216728 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 9 0.38
16 4 0.17
17 11 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATATATTAAAT
Found at i:1216717 original size:17 final size:17
Alignment explanation
Indices: 1216691--1216726 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1216681 TTTGATAAAA
1216691 ATATTAAATATAAATAT
1 ATATTAAATATAAATAT
*
1216708 ATATTTAATATAAATAT
1 ATATTAAATATAAATAT
1216725 AT
1 AT
1216727 TTATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATTAAATATAAATAT
Found at i:1216728 original size:15 final size:15
Alignment explanation
Indices: 1216685--1216729 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1216675 TTTAAATTTG
* *
1216685 ATAAAAATATTAAAT
1 ATAAATATATTTAAT
1216700 ATAAATATATATTTAAT
1 AT-AA-ATATATTTAAT
1216717 ATAAATATATTTA
1 ATAAATATATTTA
1216730 TTTTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 11 0.42
16 4 0.15
17 11 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATATATTTAAT
Found at i:1216982 original size:18 final size:18
Alignment explanation
Indices: 1216955--1216991 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1216945 TAAATTTAAT
1216955 AATTTATATTATATTTATA
1 AATTTATATTATA-TTATA
1216974 AATTT-TATTATATTATA
1 AATTTATATTATATTATA
1216991 A
1 A
1216992 TTATATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTATATTATATTATA
Found at i:1216989 original size:28 final size:27
Alignment explanation
Indices: 1216945--1217052 Score: 96
Period size: 29 Copynumber: 3.9 Consensus size: 27
1216935 AAATAAAATT
* *
1216945 TAAATTTAATAATTTATATTATATTTA
1 TAAATTTTATTATTTATATTATATTTA
1216972 TAAATTTTATTATATTATAATTATATTTA
1 TAAATTTTATTAT-TTAT-ATTATATTTA
* *
1217001 -AAATATTTTTTATTTATA-TAGATTT-
1 TAAAT-TTTATTATTTATATTATATTTA
*
1217026 TAATATTTTTTTTAATTTATATTATAT
1 TAA-A-TTTTATT-ATTTATATTATAT
1217053 AAAATTTGAA
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
26 8 0.12
27 19 0.28
28 20 0.29
29 21 0.31
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
TAAATTTTATTATTTATATTATATTTA
Found at i:1220075 original size:27 final size:28
Alignment explanation
Indices: 1220019--1220093 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 28
1220009 AAATTTTAAA
* *
1220019 ATTTTTATATTAATATGAATATGAATAT
1 ATTTTTATATTAATATGAATATAAAAAT
*
1220047 ATTTTTATAATTAAT-TTAA-ATAAAAAT
1 ATTTTTAT-ATTAATATGAATATAAAAAT
1220074 ATTTTTAATATT-ATAT-AATA
1 ATTTTT-ATATTAATATGAATA
1220094 ATTTAGATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
26 4 0.10
27 17 0.43
28 13 0.32
29 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
ATTTTTATATTAATATGAATATAAAAAT
Found at i:1220797 original size:22 final size:22
Alignment explanation
Indices: 1220772--1220813 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1220762 ATTTAAATAT
1220772 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1220794 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1220814 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1225134 original size:28 final size:28
Alignment explanation
Indices: 1225097--1225154 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1225087 CAATTTTAAA
1225097 TTTAATTCAATTAATTTATATAATTATT
1 TTTAATTCAATTAATTTATATAATTATT
* *
1225125 TTTAGTTCAATTAATTTATGTAATTATT
1 TTTAATTCAATTAATTTATATAATTATT
1225153 TT
1 TT
1225155 AAAATATGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTAATTCAATTAATTTATATAATTATT
Found at i:1233213 original size:15 final size:15
Alignment explanation
Indices: 1233193--1233223 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1233183 ATTTTTTATG
*
1233193 TATTTTTTGTTTTTT
1 TATTTTTTATTTTTT
1233208 TATTTTTTATTTTTT
1 TATTTTTTATTTTTT
1233223 T
1 T
1233224 TTAATCAATT
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:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (15 bp):
TATTTTTTATTTTTT
Found at i:1233424 original size:21 final size:21
Alignment explanation
Indices: 1233385--1233424 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1233375 AATAATAACT
* *
1233385 TAATTTAATAGTAATTAAAGA
1 TAATTTAAAAGTAACTAAAGA
*
1233406 TAATTTAAAATTAACTAAA
1 TAATTTAAAAGTAACTAAA
1233425 TTATCAGACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (21 bp):
TAATTTAAAAGTAACTAAAGA
Found at i:1238312 original size:21 final size:20
Alignment explanation
Indices: 1238265--1238318 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1238255 CATTTCAGGC
1238265 ATGTATCGATACATTCATTT
1 ATGTATCGATACATTCATTT
*
1238285 ATGTATCGATACATTGC-CTT
1 ATGTATCGATACATT-CATTT
1238305 ATTGTATCGATACA
1 A-TGTATCGATACA
1238319 AATTGTTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCATTT
Found at i:1239165 original size:13 final size:13
Alignment explanation
Indices: 1239147--1239171 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1239137 TAATTTTTCA
1239147 TGTATCGATACAT
1 TGTATCGATACAT
1239160 TGTATCGATACA
1 TGTATCGATACA
1239172 AACAGTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1239224 original size:20 final size:19
Alignment explanation
Indices: 1239199--1239273 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
1239189 TATTGCCAGT
*
1239199 TTCATGTATCGATACATTTG
1 TTCATGTATCGATACA-ATG
1239219 TTCATGTATCGATACAATG
1 TTCATGTATCGATACAATG
** *
1239238 AACATGTATCGATACAAAG
1 TTCATGTATCGATACAATG
* *
1239257 CATAATGTATCGATACA
1 -TTCATGTATCGATACA
1239274 TCTAAAAGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
19 18 0.38
20 30 0.62
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (19 bp):
TTCATGTATCGATACAATG
Found at i:1240182 original size:33 final size:33
Alignment explanation
Indices: 1240137--1240211 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
1240127 TACGTCGGTT
* *
1240137 AAGTGAACTAAAGTGCTCATCTATGCGCTGCGA
1 AAGTGAAGTAAAGTGCTCATCCATGCGCTGCGA
1240170 AAGTGAAGTAAAGTGCTCATCCATGCGCTGCGA
1 AAGTGAAGTAAAGTGCTCATCCATGCGCTGCGA
1240203 AAGTGAAGT
1 AAGTGAAGT
1240212 GATCAACTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.23
Consensus pattern (33 bp):
AAGTGAAGTAAAGTGCTCATCCATGCGCTGCGA
Found at i:1241580 original size:18 final size:19
Alignment explanation
Indices: 1241556--1241597 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
1241546 CGTTTTGTTG
1241556 TGAAATTGAAAAAATTTGA
1 TGAAATTGAAAAAATTTGA
*
1241575 -GAAATTGAAGAAATTTGA
1 TGAAATTGAAAAAATTTGA
1241593 TGAAA
1 TGAAA
1241598 AAATGTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29
Consensus pattern (19 bp):
TGAAATTGAAAAAATTTGA
Found at i:1241708 original size:13 final size:13
Alignment explanation
Indices: 1241689--1241728 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1241679 ATAATAACCC
*
1241689 ATGTATCTATACA
1 ATGTATCGATACA
*
1241702 TTGTATCGATACA
1 ATGTATCGATACA
*
1241715 ATGTATTGATACA
1 ATGTATCGATACA
1241728 A
1 A
1241729 AGAACATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1241745 original size:20 final size:20
Alignment explanation
Indices: 1241716--1241767 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1241706 ATCGATACAA
*
1241716 TGTATTGATACAAAGAACAT
1 TGTATCGATACAAAGAACAT
*
1241736 TGTATCGATACAAAGAATAT
1 TGTATCGATACAAAGAACAT
1241756 TGTATCGATACA
1 TGTATCGATACA
1241768 TCTCGGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (20 bp):
TGTATCGATACAAAGAACAT
Found at i:1241807 original size:20 final size:21
Alignment explanation
Indices: 1241776--1241815 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1241766 CATCTCGGTT
1241776 TTTCAGATGTATCGATACATA
1 TTTCAGATGTATCGATACATA
*
1241797 TTTCA-ATGTATTGATACAT
1 TTTCAGATGTATCGATACAT
1241816 TCTGAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (21 bp):
TTTCAGATGTATCGATACATA
Found at i:1248044 original size:20 final size:20
Alignment explanation
Indices: 1247999--1248051 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1247989 TACATTTGTT
1247999 CATGTATCGATAC-AAGAAA
1 CATGTATCGATACAAAGAAA
*
1248018 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAAAG-AAA
1248039 -ATGTATCGATACA
1 CATGTATCGATACA
1248052 TCTGAAAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 13 0.42
20 16 0.52
21 2 0.06
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (20 bp):
CATGTATCGATACAAAGAAA
Found at i:1250260 original size:51 final size:51
Alignment explanation
Indices: 1250172--1250402 Score: 232
Period size: 51 Copynumber: 4.5 Consensus size: 51
1250162 AATTTAACCA
* * * * * * * *
1250172 AATGTATCGATGCATTGAAGAATATATCGATACATTTGGGTCAAAACCCAT
1 AATGTATCGATACAATGAAAAATGTATCAATATATTTGGATCAAAACCCAG
* * * *
1250223 AATATATCGATACAATGAATAATGTATCAATTTATTT-GAGTCAAAAACCAG
1 AATGTATCGATACAATGAAAAATGTATCAATATATTTGGA-TCAAAACCCAG
* * * * * *
1250274 AATGTATCGATACAATGAATAATGTATCGATATATTTAGATAAAAAACCTAT
1 AATGTATCGATACAATGAAAAATGTATCAATATATTTGGAT-CAAAACCCAG
* * *
1250326 AATGTATCGATATAATGAAAAATGTATCAATACATTTGGATC-AAACTCAG
1 AATGTATCGATACAATGAAAAATGTATCAATATATTTGGATCAAAACCCAG
*
1250376 AATGTATCGATACAATAAAAAATGTAT
1 AATGTATCGATACAATGAAAAATGTAT
1250403 TGATACATTT
Statistics
Matches: 148, Mismatches: 29, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
50 31 0.21
51 73 0.49
52 44 0.30
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (51 bp):
AATGTATCGATACAATGAAAAATGTATCAATATATTTGGATCAAAACCCAG
Found at i:1250645 original size:44 final size:44
Alignment explanation
Indices: 1250582--1250669 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
1250572 ATGTATCGAT
*
1250582 ACATCTAGATAAAAATATGCCAAAAGTATGGCGGCAGACGATCA
1 ACATCTAGATAAAAATATGCCAAAAGTATGGCGCCAGACGATCA
*
1250626 ACATCTAGATAAAAATATGCCAAAAGTATGGCGCCAGATGATCA
1 ACATCTAGATAAAAATATGCCAAAAGTATGGCGCCAGACGATCA
1250670 TCGCTCCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (44 bp):
ACATCTAGATAAAAATATGCCAAAAGTATGGCGCCAGACGATCA
Found at i:1251438 original size:13 final size:13
Alignment explanation
Indices: 1251416--1251450 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1251406 ATTTTTATTT
1251416 TTTAAGTATTTATA
1 TTTAA-TATTTATA
1251430 TTTAATATTTATA
1 TTTAATATTTATA
*
1251443 TTTGATAT
1 TTTAATAT
1251451 ATTTTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:1259590 original size:18 final size:19
Alignment explanation
Indices: 1259567--1259617 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
1259557 ATAATAACTG
1259567 AATCAAATTTAAAT-TTTT
1 AATCAAATTTAAATATTTT
1259585 AATCAAATTTAAATATTTT
1 AATCAAATTTAAATATTTT
*
1259604 -AT-AAATATAAATAT
1 AATCAAATTTAAATAT
1259618 CTTATTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 11 0.35
18 16 0.52
19 4 0.13
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (19 bp):
AATCAAATTTAAATATTTT
Found at i:1259614 original size:17 final size:18
Alignment explanation
Indices: 1259568--1259622 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
1259558 TAATAACTGA
1259568 ATCAAATTTAAAT-TTTT
1 ATCAAATTTAAATATTTT
1259585 AATCAAATTTAAATATTTT
1 -ATCAAATTTAAATATTTT
* *
1259604 AT-AAATATAAATATCTT
1 ATCAAATTTAAATATTTT
1259621 AT
1 AT
1259623 TTATACGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 15 0.44
18 15 0.44
19 4 0.12
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
ATCAAATTTAAATATTTT
Found at i:1260076 original size:21 final size:20
Alignment explanation
Indices: 1260036--1260074 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1260026 TTAAAAAAAT
1260036 TATTTTTAAATTAATATTTA
1 TATTTTTAAATTAATATTTA
1260056 TATTTTTATAATTAA-ATTT
1 TATTTTTA-AATTAATATTT
1260075 TAATATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTAAATTAATATTTA
Found at i:1261737 original size:2 final size:2
Alignment explanation
Indices: 1261732--1261758 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1261722 ACACACACAC
1261732 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 A
1261759 GCAAAATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1262200 original size:12 final size:12
Alignment explanation
Indices: 1262185--1262272 Score: 56
Period size: 13 Copynumber: 7.2 Consensus size: 12
1262175 TAAGAATAAC
1262185 ATAAATATAAAT
1 ATAAATATAAAT
*
1262197 ATAAAAATATAAT
1 ATAAATATA-AAT
*
1262210 -TAAAAAT-AAT
1 ATAAATATAAAT
1262220 ATAAAATATAATAT
1 AT-AAATATAA-AT
* *
1262234 AAAAAAATAATAT
1 ATAAATATAA-AT
* *
1262247 AAAAATATAAAA
1 ATAAATATAAAT
*
1262259 AT-TATATAAAT
1 ATAAATATAAAT
1262270 ATA
1 ATA
1262273 TCAAAATCTA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
10 3 0.05
11 10 0.16
12 22 0.36
13 23 0.38
14 3 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATAAATATAAAT
Found at i:1262224 original size:35 final size:35
Alignment explanation
Indices: 1262174--1262253 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
1262164 TCTAATAATT
* *
1262174 TTAAGAATAACAT-AAATATAAATATAAAAATATAA
1 TTAAAAATAACATAAAATAT-AATATAAAAAAATAA
*
1262209 TTAAAAATAATATAAAATATAATATAAAAAAATAA
1 TTAAAAATAACATAAAATATAATATAAAAAAATAA
1262244 TATAAAAATA
1 T-TAAAAATA
1262254 TAAAAATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 26 0.65
36 14 0.35
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (35 bp):
TTAAAAATAACATAAAATATAATATAAAAAAATAA
Found at i:1262243 original size:13 final size:13
Alignment explanation
Indices: 1262187--1262256 Score: 94
Period size: 13 Copynumber: 5.6 Consensus size: 13
1262177 AGAATAACAT
1262187 AAATATAAATATAA
1 AAATAT-AATATAA
1262201 AAATATAAT-T-A
1 AAATATAATATAA
1262212 AAA-ATAATAT-A
1 AAATATAATATAA
1262223 AAATATAATATAA
1 AAATATAATATAA
*
1262236 AAAAATAATATAA
1 AAATATAATATAA
1262249 AAATATAA
1 AAATATAA
1262257 AAATTATATA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
10 5 0.10
11 9 0.18
12 8 0.16
13 23 0.45
14 6 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:1262290 original size:19 final size:19
Alignment explanation
Indices: 1262225--1262287 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
1262215 ATAATATAAA
* *
1262225 ATAT-AATATAAAAAAATA
1 ATATAAATATATAAAAATT
*
1262243 ATATAAAAATATAAAAATT
1 ATATAAATATATAAAAATT
*
1262262 ATATAAATATATCAAAATCT
1 ATATAAATATATAAAAAT-T
1262282 ATATAA
1 ATATAA
1262288 TATTAATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
18 4 0.11
19 27 0.71
20 7 0.18
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATAAATATATAAAAATT
Found at i:1262316 original size:52 final size:48
Alignment explanation
Indices: 1262254--1262368 Score: 130
Period size: 52 Copynumber: 2.4 Consensus size: 48
1262244 TATAAAAATA
* *
1262254 TAAAAATTATATAAATATATCAAAATCTATATAATATTAATTATTAATATTT
1 TAAAAATTATAAAAATATAT-AAAATCT-TAAAATA-TAATTA-TAATATTT
* *
1262306 TAAAACTTATAAAAATATATAATATCTTAAAATATAATTATAATA---
1 TAAAAATTATAAAAATATATAAAATCTTAAAATATAATTATAATATTT
1262351 TAAAAA-TATAAAAATATA
1 TAAAAATTATAAAAATATA
1262369 CCACAATTGC
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
44 12 0.21
45 5 0.09
48 5 0.09
49 6 0.10
50 6 0.10
51 6 0.10
52 18 0.31
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (48 bp):
TAAAAATTATAAAAATATATAAAATCTTAAAATATAATTATAATATTT
Found at i:1262358 original size:19 final size:18
Alignment explanation
Indices: 1262191--1262368 Score: 64
Period size: 19 Copynumber: 9.4 Consensus size: 18
1262181 TAACATAAAT
1262191 ATAA-ATATAAAAATATA
1 ATAATATATAAAAATATA
*
1262208 ATTAAAAATAATATAAAATATA
1 A-T-AATAT-ATA-AAAATATA
* *
1262230 AT-ATAAAAAAATAATATA
1 ATAATATATAAA-AATATA
1262248 A-AA-ATATAAAAAT-TA
1 ATAATATATAAAAATATA
* *
1262263 TATAAATATATCAAAATCTA
1 -AT-AATATATAAAAATATA
*
1262283 TATAATAT-TAATTATTAATATT
1 -ATAATATATAA--A--AATATA
* *
1262305 TTAAAACTTATAAAAATAT-
1 ATAATA--TATAAAAATATA
* *
1262324 ATAATATCTTAAAATATA
1 ATAATATATAAAAATATA
*
1262342 ATTATAATATAAAAATATA
1 ATAAT-ATATAAAAATATA
*
1262361 AAAATATA
1 ATAATATA
1262369 CCACAATTGC
Statistics
Matches: 120, Mismatches: 20, Indels: 41
0.66 0.11 0.23
Matches are distributed among these distances:
15 2 0.02
16 4 0.03
17 17 0.14
18 22 0.18
19 36 0.30
20 13 0.11
21 8 0.07
22 14 0.12
23 1 0.01
24 3 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAATATATAAAAATATA
Found at i:1262488 original size:18 final size:19
Alignment explanation
Indices: 1262461--1262501 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1262451 TTCAGGTAAA
*
1262461 TATTTTATT-AATTTGAAT
1 TATTTGATTAAATTTGAAT
*
1262479 TATTTGATTAAATTTGATT
1 TATTTGATTAAATTTGAAT
1262498 TATT
1 TATT
1262502 ATTTAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TATTTGATTAAATTTGAAT
Found at i:1262533 original size:10 final size:10
Alignment explanation
Indices: 1262518--1262551 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1262508 TAATAAAAAA
1262518 AAATTTATTT
1 AAATTTATTT
1262528 AAATTTATTT
1 AAATTTATTT
**
1262538 AAAAATATTT
1 AAATTTATTT
1262548 AAAT
1 AAAT
1262552 ATTAATATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AAATTTATTT
Found at i:1262541 original size:22 final size:24
Alignment explanation
Indices: 1262500--1262580 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 24
1262490 ATTTGATTTA
* *
1262500 TTATTT-AATAATAA-AAAAAAAT
1 TTATTTAAATATTAATATAAAAAT
*
1262522 TTATTTAAAT-TT-ATTTAAAAA-
1 TTATTTAAATATTAATATAAAAAT
1262543 -TATTTAAATATTAATATAAAAAT
1 TTATTTAAATATTAATATAAAAAT
*
1262566 ATTTTTTAAAATATT
1 -TTATTT-AAATATT
1262581 TTATTTTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 9 0.20
21 3 0.07
22 20 0.43
23 3 0.07
25 4 0.09
26 7 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATTTAAATATTAATATAAAAAT
Found at i:1263569 original size:14 final size:14
Alignment explanation
Indices: 1263546--1263591 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
1263536 TTATGTGTGT
*
1263546 GTGTGCGCGTGGGC
1 GTGTGTGCGTGGGC
1263560 GTGTGTGCGTGGGC
1 GTGTGTGCGTGGGC
1263574 -TG-G-GCGTGGGC
1 GTGTGTGCGTGGGC
1263585 GTGTGTG
1 GTGTGTG
1263592 TGCGCAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 8 0.29
12 3 0.11
13 3 0.11
14 14 0.50
ACGTcount: A:0.00, C:0.15, G:0.59, T:0.26
Consensus pattern (14 bp):
GTGTGTGCGTGGGC
Found at i:1269224 original size:16 final size:15
Alignment explanation
Indices: 1269203--1269232 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1269193 TGAATATATA
1269203 ATTTAATATTATAAAT
1 ATTTAATATT-TAAAT
1269219 ATTTAATATTTAAA
1 ATTTAATATTTAAA
1269233 ATTATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAATATTTAAAT
Found at i:1269229 original size:23 final size:23
Alignment explanation
Indices: 1269203--1269289 Score: 68
Period size: 24 Copynumber: 3.7 Consensus size: 23
1269193 TGAATATATA
1269203 ATTTAATATTATAAATATTTAAT
1 ATTTAATATTATAAATATTTAAT
* **
1269226 ATTTAAAATTATTAAATATCAAAT
1 ATTTAATATTA-TAAATATTTAAT
** *
1269250 AAATAA-ATATAAAAATATTTAATT
1 ATTTAATAT-TATAAATATTTAA-T
*
1269274 ATTTATTATTAATAAA
1 ATTTAATATT-ATAAA
1269290 GTTCAATAAC
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
23 20 0.43
24 21 0.45
25 6 0.13
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTAATATTATAAATATTTAAT
Found at i:1269234 original size:16 final size:18
Alignment explanation
Indices: 1269203--1269244 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1269193 TGAATATATA
1269203 ATTTAATA-TTATAAA-T
1 ATTTAATATTTATAAATT
1269219 ATTTAATATTTA-AAATT
1 ATTTAATATTTATAAATT
*
1269236 ATTAAATAT
1 ATTTAATAT
1269245 CAAATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTAATATTTATAAATT
Found at i:1269383 original size:7 final size:7
Alignment explanation
Indices: 1269373--1269398 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1269363 ATTAGATATT
1269373 AATTTAA
1 AATTTAA
1269380 AATTTAA
1 AATTTAA
1269387 AATTTAA
1 AATTTAA
1269394 AATTT
1 AATTT
1269399 TGTACTAATC
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
AATTTAA
Found at i:1270106 original size:33 final size:31
Alignment explanation
Indices: 1270069--1270143 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 31
1270059 TAAAATACGA
1270069 ATAATATAAA-TATAAAAATATTTTAAAATTTAT
1 ATAATATAAATTATAAAAATA-TTT--AATTTAT
* *
1270102 ATAATATAAATTTTTAAAATATTTAATTTAT
1 ATAATATAAATTATAAAAATATTTAATTTAT
1270133 ATAAATATAAA
1 AT-AATATAAA
1270144 ATATTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
31 9 0.24
32 8 0.21
33 13 0.34
34 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAATATAAATTATAAAAATATTTAATTTAT
Done.