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 11 of 17
Found at i:1048182 original size:16 final size:16
Alignment explanation
Indices: 1048152--1048196 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1048142 TATTTGATGT
* *
1048152 TTAAAATTTTTTAATA
1 TTAAAAATTTATAATA
* *
1048168 TTAAATATTTATAATT
1 TTAAAAATTTATAATA
1048184 TTAAAAATTTATA
1 TTAAAAATTTATA
1048197 TTTACATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAAATTTATAATA
Found at i:1048974 original size:27 final size:29
Alignment explanation
Indices: 1048943--1049007 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
1048933 TTTTTAAATA
1048943 ATATTAAAATAT-TA-AAAAAATATTTTT
1 ATATTAAAATATATATAAAAAATATTTTT
* *
1048970 ATATTTAAATTTATATAAAAAATATTTTT
1 ATATTAAAATATATATAAAAAATATTTTT
1048999 ATTATTAAA
1 A-TATTAAA
1049008 TAATAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.31
28 2 0.06
29 14 0.44
30 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATATTAAAATATATATAAAAAATATTTTT
Found at i:1050527 original size:2 final size:2
Alignment explanation
Indices: 1050522--1050553 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1050512 AAAAAATAGC
1050522 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
1050554 TACCTAAGGT
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:1050679 original size:25 final size:24
Alignment explanation
Indices: 1050639--1050703 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
1050629 ATTACTCTCT
* *
1050639 ATTTTTTAACTCAAAAAAATTACT-C
1 ATTTTTT-ACTTAAAAAAAAT-CTGC
1050664 ATTTTTTCACTTAAAAAAAATCTGC
1 ATTTTTT-ACTTAAAAAAAATCTGC
1050689 -TTTTTTACTTAAAAA
1 ATTTTTTACTTAAAAA
1050704 GAAAACTACC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 9 0.25
24 8 0.22
25 19 0.53
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTTTTTACTTAAAAAAAATCTGC
Found at i:1051213 original size:30 final size:31
Alignment explanation
Indices: 1051179--1051236 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1051169 GTATTCGATA
* *
1051179 AACTTTAAAC-TTTAATTTGTATATAAAACT
1 AACTTGAAACTTTTAATTTATATATAAAACT
1051209 AACTTGAAACTTTTAATTTATATATAAA
1 AACTTGAAACTTTTAATTTATATATAAA
1051237 TAGACATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (31 bp):
AACTTGAAACTTTTAATTTATATATAAAACT
Found at i:1051329 original size:25 final size:24
Alignment explanation
Indices: 1051296--1051347 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
1051286 GATACAAATT
* *
1051296 AAAAGATAAAGATTTATTTAAGAAA
1 AAAAGATAAAGACTTAATTAA-AAA
*
1051321 AAAATATAAAGACTTAATTAAAAA
1 AAAAGATAAAGACTTAATTAAAAA
1051345 AAA
1 AAA
1051348 TGAAATAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (24 bp):
AAAAGATAAAGACTTAATTAAAAA
Found at i:1052086 original size:28 final size:29
Alignment explanation
Indices: 1052025--1052089 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
1052015 AGGTATTTTG
*
1052025 TTTAAA-T-TTAAAAATTTAAATTATTAT
1 TTTAAATTATTAAAAATTTAAAATATTAT
1052052 TTATAAATTATTAAAAATTTAAAA-A-TAT
1 TT-TAAATTATTAAAAATTTAAAATATTAT
1052080 ATTTAAATTA
1 -TTTAAATTA
1052090 ATATTTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 2 0.06
28 14 0.42
29 4 0.12
30 13 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTAAATTATTAAAAATTTAAAATATTAT
Found at i:1052703 original size:19 final size:19
Alignment explanation
Indices: 1052666--1052768 Score: 63
Period size: 19 Copynumber: 5.4 Consensus size: 19
1052656 ACATCGCAGG
*
1052666 ATATAAATATAATATAATT
1 ATATAAATATAATAAAATT
*
1052685 ATATAAATATATTAAAATTT
1 ATATAAATATAATAAAA-TT
*
1052705 ATTTAATAAA-AAAATCAAAA-T
1 A--T-ATAAATATAAT-AAAATT
* * *
1052726 ATTTAAAT-TTATATAA--
1 ATATAAATATAATAAAATT
*
1052742 ATATAAATATAATAAAAAT
1 ATATAAATATAATAAAATT
1052761 ATATAAAT
1 ATATAAAT
1052769 TATCAAATTT
Statistics
Matches: 64, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
16 7 0.11
17 9 0.14
18 6 0.09
19 24 0.38
20 3 0.05
21 2 0.03
22 4 0.06
23 9 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAAATATAATAAAATT
Found at i:1052919 original size:6 final size:6
Alignment explanation
Indices: 1052908--1052933 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1052898 TCATTTAAAA
1052908 AAATTT AAATTT AAATTT AAATTT AA
1 AAATTT AAATTT AAATTT AAATTT AA
1052934 TTATTAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:1053451 original size:15 final size:16
Alignment explanation
Indices: 1053422--1053451 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1053412 TTCTATTCAA
1053422 TAAATTTTGTAAAAAT
1 TAAATTTTGTAAAAAT
1053438 TAAATTTT-TAAAAA
1 TAAATTTTGTAAAAA
1053452 AATTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TAAATTTTGTAAAAAT
Found at i:1053669 original size:3 final size:3
Alignment explanation
Indices: 1053661--1053700 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1053651 ATACTATCTT
1053661 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1053701 ATTTATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1054362 original size:21 final size:22
Alignment explanation
Indices: 1054308--1054368 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
1054298 GTTTATCAAT
*
1054308 TTTTTA-AAT-TTTAAAAAATA
1 TTTTTATAATATTTAAAAATTA
1054328 TTTTTATAATATTTAAAAATTA
1 TTTTTATAATATTTAAAAATTA
1054350 TTTTTACT-A-ATTTAAAAAT
1 TTTTTA-TAATATTTAAAAAT
1054369 AAAAATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 6 0.16
21 13 0.35
22 17 0.46
23 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTTATAATATTTAAAAATTA
Found at i:1054988 original size:15 final size:14
Alignment explanation
Indices: 1054968--1055016 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
1054958 GTTAAATTTA
1054968 ATAATTTAATAAATT
1 ATAATTTAATAAA-T
1054983 ATAATTGT-ATAAAT
1 ATAATT-TAATAAAT
1054997 ATAATTTATATAAA-
1 ATAATTTA-ATAAAT
1055011 ATAATT
1 ATAATT
1055017 ACGATATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.03
14 13 0.42
15 16 0.52
16 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
ATAATTTAATAAAT
Found at i:1055001 original size:14 final size:13
Alignment explanation
Indices: 1054968--1055016 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
1054958 GTTAAATTTA
1054968 ATAATTTAATAAATT
1 ATAATTT-ATAAA-T
1054983 ATAATTGTATAAAT
1 ATAATT-TATAAAT
*
1054997 ATAATTTATATAAA
1 ATAATTTATA-AAT
1055011 ATAATT
1 ATAATT
1055017 ACGATATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 11 0.35
16 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (13 bp):
ATAATTTATAAAT
Found at i:1055056 original size:32 final size:32
Alignment explanation
Indices: 1055020--1055149 Score: 93
Period size: 32 Copynumber: 4.3 Consensus size: 32
1055010 AATAATTACG
* *
1055020 ATATAATATGATTTAA-ATATATATTAAAATTT
1 ATATAATATGAATTAATA-ATATATTAAAATTA
* *
1055052 ATATAATATGAATTAGTAATATATTAATATTA
1 ATATAATATGAATTAATAATATATTAAAATTA
1055084 ATATAA-AT--A-TAA-AATATATT-AAATATA
1 ATATAATATGAATTAATAATATATTAAAAT-TA
* *
1055111 ATTATGATAT-AA-TAA-AATATATGAAAA-TA
1 A-TATAATATGAATTAATAATATATTAAAATTA
1055140 ATATGAATAT
1 ATAT-AATAT
1055150 ATATTAAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
26 3 0.04
27 11 0.13
28 9 0.11
29 10 0.12
30 11 0.13
31 5 0.06
32 32 0.39
33 1 0.01
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (32 bp):
ATATAATATGAATTAATAATATATTAAAATTA
Found at i:1055099 original size:27 final size:26
Alignment explanation
Indices: 1055069--1055150 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 26
1055059 ATGAATTAGT
1055069 AATATATTAATATTAATATAAATATAA
1 AATATATTAA-ATTAATATAAATATAA
*
1055096 AATATATTAAATATAATTATGATATAATAA
1 AATATATTAAAT-TAA-TAT-AAAT-ATAA
* * *
1055126 AATATATGAAAATAATATGAATATA
1 AATATATTAAATTAATATAAATATA
1055151 TATTAAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
26 5 0.11
27 15 0.33
28 6 0.13
29 6 0.13
30 14 0.30
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (26 bp):
AATATATTAAATTAATATAAATATAA
Found at i:1055769 original size:16 final size:16
Alignment explanation
Indices: 1055748--1055788 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
1055738 TTATATGCTG
*
1055748 AAAAAATGTATTTTAA
1 AAAAAATATATTTTAA
1055764 AAAAAATTATATTTTAA
1 AAAAAA-TATATTTTAA
*
1055781 AAGAAATA
1 AAAAAATA
1055789 ATTAGTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (16 bp):
AAAAAATATATTTTAA
Found at i:1056187 original size:2 final size:2
Alignment explanation
Indices: 1056182--1056218 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1056172 TGATATTTGA
1056182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1056219 CATGCATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1057587 original size:2 final size:2
Alignment explanation
Indices: 1057582--1057658 Score: 58
Period size: 2 Copynumber: 41.5 Consensus size: 2
1057572 GTCATAATTT
* *
1057582 TA TA TA TA TA TA TG TA TA TA TA TA TA TA T- TC T- TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1057620 TA -A TA -A TG TG TA TA TA GA TA TA TA GA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1057659 GTCGCAAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
1 6 0.10
2 55 0.90
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1057861 original size:33 final size:31
Alignment explanation
Indices: 1057824--1057892 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 31
1057814 AAATTAATTT
* *
1057824 AATTTTATTTAAATTTATTATTTATGTAATAAA
1 AATTTTATTTAAATTTA-AATTTA-ATAATAAA
**
1057857 AATTTTATTTTTATTTAAATTTAATAATAAA
1 AATTTTATTTAAATTTAAATTTAATAATAAA
1057888 AATTT
1 AATTT
1057893 ATATAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 12 0.38
32 5 0.16
33 15 0.47
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (31 bp):
AATTTTATTTAAATTTAAATTTAATAATAAA
Found at i:1058242 original size:23 final size:25
Alignment explanation
Indices: 1058211--1058257 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
1058201 GATTCAATTT
1058211 TTTTCATAAATAT-AAATTT-TTATA
1 TTTTCAT-AATATCAAATTTATTATA
1058235 TTTT-ATAATATCAAATTTATTAT
1 TTTTCATAATATCAAATTTATTAT
1058258 TCGTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.24
23 8 0.38
24 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTCATAATATCAAATTTATTATA
Found at i:1059022 original size:13 final size:13
Alignment explanation
Indices: 1059006--1059040 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1058996 TGAATGAATC
1059006 AAATTAAATAAAA
1 AAATTAAATAAAA
1059019 AAATTTAAATAAAA
1 AAA-TTAAATAAAA
*
1059033 AATTTAAA
1 AAATTAAA
1059041 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATTAAATAAAA
Found at i:1059042 original size:14 final size:14
Alignment explanation
Indices: 1059009--1059040 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1058999 ATGAATCAAA
1059009 TTAAATAAAAAAAT
1 TTAAATAAAAAAAT
1059023 TTAAAT-AAAAAAT
1 TTAAATAAAAAAAT
1059036 TTAAA
1 TTAAA
1059041 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAATAAAAAAAT
Found at i:1059322 original size:21 final size:21
Alignment explanation
Indices: 1059298--1059348 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1059288 AAAATTAATT
*
1059298 AAATATAAATTAAA-AAAGTTA
1 AAATATAAATTAAATAAA-ATA
* *
1059319 AAATTTAATTTAAATAAAATA
1 AAATATAAATTAAATAAAATA
1059340 AAATATAAA
1 AAATATAAA
1059349 ATTTTTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AAATATAAATTAAATAAAATA
Found at i:1059603 original size:2 final size:2
Alignment explanation
Indices: 1059596--1059621 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1059586 AAAATGGATG
1059596 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
1059622 TGCATGCATT
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):
GA
Found at i:1060696 original size:19 final size:20
Alignment explanation
Indices: 1060672--1060710 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1060662 ATGTATGATC
*
1060672 TTTTAAAATATA-TAAAAAT
1 TTTTAAAATAAATTAAAAAT
1060691 TTTTAAAATAAATTAAAAAT
1 TTTTAAAATAAATTAAAAAT
1060711 ACACGTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTTAAAATAAATTAAAAAT
Found at i:1062211 original size:20 final size:21
Alignment explanation
Indices: 1062174--1062212 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1062164 TGATTAAAAC
1062174 ATTTAAATTAAAAAAAATTAA
1 ATTTAAATTAAAAAAAATTAA
*
1062195 ATTTAAA-TAACAAAAATT
1 ATTTAAATTAAAAAAAATT
1062213 TACAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTTAAATTAAAAAAAATTAA
Found at i:1062841 original size:17 final size:17
Alignment explanation
Indices: 1062805--1062860 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
1062795 TAGATTTGGA
*
1062805 TCATTTTGA-ATTCTAAG
1 TCATTTTGAGATTC-AGG
1062822 TCATTTTGAGATTCAGG
1 TCATTTTGAGATTCAGG
*
1062839 TCACTTTG-GATTC-GG
1 TCATTTTGAGATTCAGG
1062854 ATCATTT
1 -TCATTT
1062861 CGGATTCGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 2 0.06
16 10 0.29
17 18 0.53
18 4 0.12
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (17 bp):
TCATTTTGAGATTCAGG
Found at i:1062865 original size:16 final size:16
Alignment explanation
Indices: 1062846--1062883 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1062836 AGGTCACTTT
1062846 GGATTCGGATCATTTC
1 GGATTCGGATCATTTC
*
1062862 GGATTCGGATTATTTC
1 GGATTCGGATCATTTC
1062878 GGATTC
1 GGATTC
1062884 AAGTTGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.39
Consensus pattern (16 bp):
GGATTCGGATCATTTC
Found at i:1063991 original size:16 final size:16
Alignment explanation
Indices: 1063958--1064016 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
1063948 TAATTTCGGA
* **
1063958 TTCGAGTCATTTTAAG
1 TTCGAATCATTTCGAG
1063974 TTCGAATCATTTCGAG
1 TTCGAATCATTTCGAG
*
1063990 TTC-AGATCATTTCGGG
1 TTCGA-ATCATTTCGAG
*
1064006 TTCGGATCATT
1 TTCGAATCATT
1064017 CTGAATTGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 1 0.03
16 35 0.97
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (16 bp):
TTCGAATCATTTCGAG
Found at i:1064204 original size:18 final size:18
Alignment explanation
Indices: 1064183--1064250 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
1064173 ATTTTAAAAT
*
1064183 TTTTTATATTTATATAAA
1 TTTTAATATTTATATAAA
1064201 TTTTAATATATTA-AT-AA
1 TTTTAATAT-TTATATAAA
1064218 -TTT-ATACTTTATA-AAA
1 TTTTAATA-TTTATATAAA
*
1064234 TTTGAAATATTTATATA
1 TTT-TAATATTTATATA
1064251 TTTCGAACCC
Statistics
Matches: 40, Mismatches: 2, Indels: 15
0.70 0.04 0.26
Matches are distributed among these distances:
15 6 0.15
16 7 0.17
17 4 0.10
18 16 0.40
19 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
TTTTAATATTTATATAAA
Found at i:1064222 original size:33 final size:33
Alignment explanation
Indices: 1064185--1064253 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
1064175 TTTAAAATTT
*
1064185 TTTATA-TTTATATAAATTTTAATATATTAATA-A
1 TTTATACTTTATA-AAATTTGAA-ATATTAATATA
*
1064218 TTTATACTTTATAAAATTTGAAATATTTATATA
1 TTTATACTTTATAAAATTTGAAATATTAATATA
1064251 TTT
1 TTT
1064254 CGAACCCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 8 0.25
33 18 0.56
34 6 0.19
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (33 bp):
TTTATACTTTATAAAATTTGAAATATTAATATA
Found at i:1064502 original size:11 final size:10
Alignment explanation
Indices: 1064486--1064621 Score: 55
Period size: 9 Copynumber: 14.4 Consensus size: 10
1064476 GGACAAAATA
1064486 AAATATATATT
1 AAATATATA-T
1064497 AAATATGATAT
1 AAATAT-ATAT
1064508 -AA-ATATAT
1 AAATATATAT
*
1064516 AAATATATAA
1 AAATATATAT
* *
1064526 AAATTTATTT
1 AAATATATAT
* *
1064536 AATTAAAATATT
1 AAAT-ATATA-T
*
1064548 ATAATTTATAT
1 A-AATATATAT
1064559 -AA-ATATAT
1 AAATATATAT
*
1064567 -AATAT-TTT
1 AAATATATAT
1064575 AAATA-A-A-
1 AAATATATAT
1064582 AAATA-ATAT
1 AAATATATAT
1064591 AAATATA-AT
1 AAATATATAT
* *
1064600 AAAAATACAT
1 AAATATATAT
1064610 AAAT-TAT-T
1 AAATATATAT
1064618 AAAT
1 AAAT
1064622 TTACTTTTTA
Statistics
Matches: 95, Mismatches: 17, Indels: 29
0.67 0.12 0.21
Matches are distributed among these distances:
7 6 0.06
8 19 0.20
9 27 0.28
10 23 0.24
11 10 0.11
12 8 0.08
13 2 0.02
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (10 bp):
AAATATATAT
Found at i:1064517 original size:8 final size:8
Alignment explanation
Indices: 1064504--1064602 Score: 53
Period size: 8 Copynumber: 11.9 Consensus size: 8
1064494 ATTAAATATG
1064504 ATATAAAT
1 ATATAAAT
1064512 ATATAAAT
1 ATATAAAT
1064520 ATATAAAAAT
1 ATAT--AAAT
* *
1064530 TTATTTAAT
1 ATA-TAAAT
1064539 -TA-AAAT
1 ATATAAAT
*
1064545 ATTATAATTT
1 A-TATAA-AT
1064555 ATATAAAT
1 ATATAAAT
1064563 ATAT-AAT
1 ATATAAAT
*
1064570 ATTTTAAAT
1 A-TATAAAT
*
1064579 A-AAAAAT
1 ATATAAAT
1064586 AATATAAAT
1 -ATATAAAT
1064595 ATAATAAA
1 AT-ATAAA
1064603 AATACATAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 23
0.69 0.09 0.23
Matches are distributed among these distances:
6 3 0.04
7 8 0.11
8 26 0.37
9 24 0.34
10 8 0.11
11 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:1064587 original size:19 final size:19
Alignment explanation
Indices: 1064533--1064590 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
1064523 TAAAAATTTA
* * *
1064533 TTTAATTAAAATATTATAA
1 TTTAAATAAAATATAATAT
*
1064552 TTTATATAAATATATAATAT
1 TTTAAATAAA-ATATAATAT
*
1064572 TTTAAATAAAAAATAATAT
1 TTTAAATAAAATATAATAT
1064591 AAATATAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTAAATAAAATATAATAT
Found at i:1064602 original size:41 final size:42
Alignment explanation
Indices: 1064504--1064602 Score: 105
Period size: 43 Copynumber: 2.4 Consensus size: 42
1064494 ATTAAATATG
**
1064504 ATATAAATAT-ATAAATATATAAAAATTTATTTAATTAAAATA
1 ATATAAATATAATAAATATATAAAAATTTAAATAA-TAAAATA
* * * *
1064546 TTAT-AATTTATATAAATATATAATATTTTAAATAA-AAAATA
1 ATATAAATATA-ATAAATATATAAAAATTTAAATAATAAAATA
1064587 ATATAAATATAATAAA
1 ATATAAATATAATAAA
1064603 AATACATAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
41 18 0.39
42 8 0.17
43 20 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (42 bp):
ATATAAATATAATAAATATATAAAAATTTAAATAATAAAATA
Found at i:1064755 original size:6 final size:6
Alignment explanation
Indices: 1064739--1064802 Score: 64
Period size: 6 Copynumber: 10.8 Consensus size: 6
1064729 TTTTAAAAAA
1064739 TTAATAT TTAAAT TTAAAT TTAAAAT TTAAAT TT-AAT TT--AT TT-AAT
1 TTAA-AT TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
1064785 TTTAAT TTAAAAT TTAAA
1 TTAAAT TT-AAAT TTAAA
1064803 ATTTTTATTT
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
4 4 0.08
5 9 0.17
6 24 0.46
7 15 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:1064764 original size:7 final size:7
Alignment explanation
Indices: 1064734--1064806 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 7
1064724 TATAATTTTA
*
1064734 AAAAATT
1 AAAATTT
*
1064741 AATATTT
1 AAAATTT
1064748 -AAATTT
1 AAAATTT
1064754 -AAATTT
1 AAAATTT
1064760 AAAATTT
1 AAAATTT
1064767 -AAATTT
1 AAAATTT
1064773 --AATTT
1 AAAATTT
*
1064778 ATTTAATTT
1 A--AAATTT
*
1064787 -TAATTT
1 AAAATTT
1064793 AAAATTT
1 AAAATTT
1064800 AAAATTT
1 AAAATTT
1064807 TTATTTAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
5 5 0.09
6 23 0.41
7 23 0.41
9 5 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (7 bp):
AAAATTT
Found at i:1064764 original size:13 final size:13
Alignment explanation
Indices: 1064734--1064817 Score: 66
Period size: 13 Copynumber: 6.4 Consensus size: 13
1064724 TATAATTTTA
*
1064734 AAAAATTAATATTT
1 AAAATTTAA-ATTT
1064748 -AAATTTAAATTT
1 AAAATTTAAATTT
1064760 AAAATTTAAATTT
1 AAAATTTAAATTT
*
1064773 AATTTATTT-AATTT
1 AA--AATTTAAATTT
*
1064787 -TAATTTAAAATTT
1 AAAATTT-AAATTT
**
1064800 AAAATTTTTATTT
1 AAAATTTAAATTT
1064813 AAAAT
1 AAAAT
1064818 ATAATAAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
11 4 0.07
12 4 0.07
13 35 0.61
14 10 0.18
15 4 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AAAATTTAAATTT
Found at i:1064955 original size:34 final size:34
Alignment explanation
Indices: 1064875--1064956 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 34
1064865 ATTAACAAAC
*
1064875 AATAATTTAAA-TTAA-ATTAATCTAAATAAATA
1 AATAATTTAAATTTAATTTTAATCTAAATAAATA
*
1064907 AATAATTTTAATTTAATTTTAATC-AAATTAAAT-
1 AATAATTTAAATTTAATTTTAATCTAAA-TAAATA
*
1064940 AATTATTTAATATTTAA
1 AATAATTTAA-ATTTAA
1064957 GCAGGTCTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
32 10 0.24
33 15 0.36
34 17 0.40
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (34 bp):
AATAATTTAAATTTAATTTTAATCTAAATAAATA
Found at i:1065568 original size:25 final size:25
Alignment explanation
Indices: 1065536--1065589 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
1065526 TCTATTATTA
1065536 TTAT-TATTATTATATGT-TAAAT-AT
1 TTATATATT-TTA-ATGTGTAAATAAT
*
1065560 TTATATATTTTAATGTGTTAATAAT
1 TTATATATTTTAATGTGTAAATAAT
1065585 TTATA
1 TTATA
1065590 AAATATGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 4 0.15
24 11 0.42
25 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (25 bp):
TTATATATTTTAATGTGTAAATAAT
Found at i:1065679 original size:25 final size:25
Alignment explanation
Indices: 1065645--1065695 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
1065635 ATTTTTTTAA
*
1065645 TTATATTATATTT-TAATTATTTATT
1 TTATATTATATTTAT-ATTATATATT
1065670 TTATATTATATTTATATTATATATT
1 TTATATTATATTTATATTATATATT
1065695 T
1 T
1065696 ACCATATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTATATTATATTTATATTATATATT
Found at i:1065688 original size:11 final size:11
Alignment explanation
Indices: 1065615--1065691 Score: 61
Period size: 11 Copynumber: 7.2 Consensus size: 11
1065605 CATTCTTAAA
1065615 ATTTATATTAT
1 ATTTATATTAT
** *
1065626 GCTTATTTTAT
1 ATTTATATTAT
* *
1065637 TTTTTTAATTAT
1 ATTTAT-ATTAT
*
1065649 A-TTATATTTT
1 ATTTATATTAT
*
1065659 AATTAT-TTAT
1 ATTTATATTAT
1065669 -TTTATATTAT
1 ATTTATATTAT
1065679 ATTTATATTAT
1 ATTTATATTAT
1065690 AT
1 AT
1065692 ATTTACCATA
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
9 4 0.08
10 12 0.24
11 30 0.60
12 4 0.08
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:1065690 original size:5 final size:5
Alignment explanation
Indices: 1065644--1065691 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
1065634 TATTTTTTTA
* *
1065644 ATTAT ATTAT ATTTT AATTAT -TTAT TTTAT ATTAT ATTTAT ATTAT AT
1 ATTAT ATTAT ATTAT -ATTAT ATTAT ATTAT ATTAT A-TTAT ATTAT AT
1065692 ATTTACCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 4 0.11
5 24 0.65
6 9 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
ATTAT
Found at i:1066261 original size:23 final size:23
Alignment explanation
Indices: 1066218--1066275 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 23
1066208 TGATTTATCA
*
1066218 ATTTTTTTAA-ATTTTAAAAAAACT
1 ATTTTTATAATATTTT--AAAAACT
*
1066242 ATTTTTATAATATTTT-AAAATT
1 ATTTTTATAATATTTTAAAAACT
1066264 ATTTTTACTAAT
1 ATTTTTA-TAAT
1066276 TTAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 12 0.40
23 4 0.13
24 9 0.30
25 5 0.17
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTTTATAATATTTTAAAAACT
Found at i:1066277 original size:21 final size:22
Alignment explanation
Indices: 1066235--1066283 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1066225 TAAATTTTAA
*
1066235 AAAAACTATTTTTATAATATTT
1 AAAAATTATTTTTATAATATTT
*
1066257 TAAAATTATTTTTACT-A-ATTT
1 AAAAATTATTTTTA-TAATATTT
1066278 AAAAAT
1 AAAAAT
1066284 AAAAAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 9 0.39
22 13 0.57
23 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
AAAAATTATTTTTATAATATTT
Found at i:1067417 original size:25 final size:23
Alignment explanation
Indices: 1067373--1067479 Score: 69
Period size: 25 Copynumber: 4.5 Consensus size: 23
1067363 TTAATAATAT
* *
1067373 TTTATATAATTATTTAAATATAA
1 TTTATATAAATAATTAAATATAA
1067396 TTTATATAAAATAATTACAATATAA
1 TTTATAT-AAATAATTA-AATATAA
* * * *
1067421 TATAATTTAAAT-ATATATATTAAAA
1 T-TTATATAAATAAT-TA-AATATAA
1067446 TTTATAT-AAT-A-TAAATTATTAA
1 TTTATATAAATAATTAAA-TA-TAA
1067468 TTTATATAAATA
1 TTTATATAAATA
1067480 TAATATATTT
Statistics
Matches: 65, Mismatches: 11, Indels: 15
0.71 0.12 0.16
Matches are distributed among these distances:
20 1 0.02
21 4 0.06
22 9 0.14
23 14 0.22
24 13 0.20
25 20 0.31
26 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTATATAAATAATTAAATATAA
Found at i:1067433 original size:16 final size:16
Alignment explanation
Indices: 1067389--1067499 Score: 83
Period size: 16 Copynumber: 7.2 Consensus size: 16
1067379 TAATTATTTA
1067389 AATATAATTT--ATAT
1 AATATAATTTAAATAT
*
1067403 AAAATAA-TTACAATAT
1 AATATAATTTA-AATAT
1067419 AATATAATTTAAATAT
1 AATATAATTTAAATAT
*
1067435 -ATAT-ATTAAAAT-T
1 AATATAATTTAAATAT
* *
1067448 TATATAATATAAATTATT
1 AATATAATTTAAA-TA-T
* *
1067466 AAT-TTATATAAATAT
1 AATATAATTTAAATAT
*
1067481 AATATATTTTAAATAT
1 AATATAATTTAAATAT
1067497 AAT
1 AAT
1067500 TATGATATAA
Statistics
Matches: 77, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
13 3 0.04
14 17 0.22
15 13 0.17
16 30 0.39
17 11 0.14
18 3 0.04
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATAATTTAAATAT
Found at i:1067537 original size:19 final size:18
Alignment explanation
Indices: 1067504--1067542 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1067494 TATAATTATG
1067504 ATATAATAAAATATATAA
1 ATATAATAAAATATATAA
*
1067522 ATATAATACGAATATATAA
1 ATATAATA-AAATATATAA
1067541 AT
1 AT
1067543 TATCAAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
ATATAATAAAATATATAA
Found at i:1067792 original size:23 final size:24
Alignment explanation
Indices: 1067750--1067794 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1067740 ATTATATAAA
*
1067750 ATTAAAATTATAAATTTTAATGAT
1 ATTAAAATTATAAATCTTAATGAT
*
1067774 ATTATAATT-TAAATCTTAATG
1 ATTAAAATTATAAATCTTAATG
1067795 TTACAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
ATTAAAATTATAAATCTTAATGAT
Found at i:1069152 original size:4 final size:4
Alignment explanation
Indices: 1069143--1069171 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1069133 TGACAAATTG
1069143 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1069172 CATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1069408 original size:2 final size:2
Alignment explanation
Indices: 1069390--1069433 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
1069380 TTCATCACAG
1069390 TA TA TA GTA TA -A T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1069431 TA T
1 TA T
1069434 GTCTCAAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1069531 original size:20 final size:20
Alignment explanation
Indices: 1069506--1069543 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1069496 GGCAGTACTC
1069506 AATTTTCCTAGTTTCTTCGT
1 AATTTTCCTAGTTTCTTCGT
1069526 AATTTTCCTAGTTTCTTC
1 AATTTTCCTAGTTTCTTC
1069544 TGTCTTGGTT
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:0.16, C:0.21, G:0.08, T:0.55
Consensus pattern (20 bp):
AATTTTCCTAGTTTCTTCGT
Found at i:1071144 original size:17 final size:17
Alignment explanation
Indices: 1071101--1071145 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
1071091 AATTTAATTT
*
1071101 AAATACATTAAAAATATA
1 AAATA-ATTTAAAATATA
*
1071119 AAA-ATTTTAAAATATA
1 AAATAATTTAAAATATA
1071135 AAATAATTTAA
1 AAATAATTTAA
1071146 TTGTTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 13 0.57
17 7 0.30
18 3 0.13
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAATTTAAAATATA
Found at i:1071576 original size:12 final size:13
Alignment explanation
Indices: 1071556--1071592 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
1071546 TTTTAATGTT
1071556 ATATAAAATAATA
1 ATATAAAATAATA
1071569 AT-TAAAAT-ATA
1 ATATAAAATAATA
1071580 ATATAAAA-AATA
1 ATATAAAATAATA
1071592 A
1 A
1071593 AATTAATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.23
12 15 0.68
13 2 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATATAAAATAATA
Found at i:1071580 original size:19 final size:19
Alignment explanation
Indices: 1071556--1071595 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1071546 TTTTAATGTT
* *
1071556 ATATAAAATAATAATTAAA
1 ATATAAAATAAAAAATAAA
*
1071575 ATATAATATAAAAAATAAA
1 ATATAAAATAAAAAATAAA
1071594 AT
1 AT
1071596 TAATGTGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATATAAAATAAAAAATAAA
Found at i:1072086 original size:32 final size:34
Alignment explanation
Indices: 1072028--1072095 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
1072018 TAAAGTTTTA
*
1072028 TTATATTTATATAAATGTTAATATATTAATA-AT
1 TTATATTTATATAAATGTTAAAATATTAATATAT
*
1072061 TTATATTT-TATAAAAT-TTAAAATATTTATATAT
1 TTATATTTATAT-AAATGTTAAAATATTAATATAT
1072094 TT
1 TT
1072096 CGTATGTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (34 bp):
TTATATTTATATAAATGTTAAAATATTAATATAT
Found at i:1072543 original size:44 final size:44
Alignment explanation
Indices: 1072466--1072549 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
1072456 AGGGGTTGGC
* * *
1072466 TGAGTTAGTTGCCAAGTGGGGAAGAATGCAAATTGATAGTCGAA
1 TGAGTTAGTTCCCAAGTGGGGAAGAATACAAATTAATAGTCGAA
*
1072510 TGAGTTAGTTCCCAAGTGGGGAAGAATATAAATTAATAGT
1 TGAGTTAGTTCCCAAGTGGGGAAGAATACAAATTAATAGT
1072550 TAAAACTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.36, C:0.08, G:0.29, T:0.27
Consensus pattern (44 bp):
TGAGTTAGTTCCCAAGTGGGGAAGAATACAAATTAATAGTCGAA
Found at i:1073217 original size:3 final size:3
Alignment explanation
Indices: 1073209--1073254 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1073199 TAAAATGCAA
1073209 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1073255 CTTATACTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1073501 original size:17 final size:18
Alignment explanation
Indices: 1073479--1073538 Score: 81
Period size: 17 Copynumber: 3.4 Consensus size: 18
1073469 GAAATATTAA
1073479 TATATT-TATAT-TATGTT
1 TATATTATATATATAT-TT
1073496 TATATTATATATATATTT
1 TATATTATATATATATTT
*
1073514 TATATTGTAT-TATATTT
1 TATATTATATATATATTT
1073531 TATATTAT
1 TATATTAT
1073539 TTTTTATGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
17 20 0.51
18 16 0.41
19 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TATATTATATATATATTT
Found at i:1073509 original size:28 final size:28
Alignment explanation
Indices: 1073478--1073547 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
1073468 TGAAATATTA
1073478 ATATATTTATATTATGT-TTATATTATAT
1 ATATATTT-TATTATGTATTATATTATAT
*
1073506 ATATATTTTA-TATTGTATTATATTTTAT
1 ATATATTTTATTA-TGTATTATATTATAT
1073534 AT-TATTTT-TTATGT
1 ATATATTTTATTATGT
1073548 CATGTTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
26 5 0.13
27 13 0.34
28 20 0.53
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (28 bp):
ATATATTTTATTATGTATTATATTATAT
Found at i:1073510 original size:11 final size:11
Alignment explanation
Indices: 1073479--1073538 Score: 66
Period size: 11 Copynumber: 5.3 Consensus size: 11
1073469 GAAATATTAA
1073479 TATATTTATAT
1 TATATTTATAT
*
1073490 TATGTTTATAT
1 TATATTTATAT
*
1073501 TATATATATAT
1 TATATTTATAT
* *
1073512 TTTATATTGTAT
1 TATAT-TTATAT
1073524 TATATTTTATAT
1 TATA-TTTATAT
1073536 TAT
1 TAT
1073539 TTTTTATGTC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
11 23 0.59
12 15 0.38
13 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1074146 original size:24 final size:22
Alignment explanation
Indices: 1074083--1074143 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
1074073 AATTTCATAA
1074083 TAAAAATATTAAAAAT-TTAAT
1 TAAAAATATTAAAAATATTAAT
**
1074104 TAATTGATATTTAAAAATATTAAT
1 TAA-AAATA-TTAAAAATATTAAT
1074128 TAAAAATAATTAAAAA
1 TAAAAAT-ATTAAAAA
1074144 ATAATTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 3 0.09
22 3 0.09
23 17 0.53
24 9 0.28
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAAAATATTAAAAATATTAAT
Found at i:1074201 original size:26 final size:25
Alignment explanation
Indices: 1074135--1074203 Score: 77
Period size: 26 Copynumber: 2.8 Consensus size: 25
1074125 AATTAAAAAT
1074135 AATTAAAAAATAATTTA-ATTATTA
1 AATTAAAAAATAATTTATATTATTA
* * ** *
1074159 AATTTAATAATTTTTTATTTTTATTA
1 AATTAAAAAATAATTTA-TATTATTA
1074185 AATTAAAAAATAATTTATA
1 AATTAAAAAATAATTTATA
1074204 AATTATATTT
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
24 13 0.39
25 1 0.03
26 19 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTAAAAAATAATTTATATTATTA
Found at i:1074468 original size:4 final size:4
Alignment explanation
Indices: 1074459--1074498 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
1074449 GAACGACCTT
* *
1074459 TTTA TTTA TTTA TTTA TTTA TTTA TTGA ATTA TCTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTT
1074499 TAAAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:1074943 original size:16 final size:16
Alignment explanation
Indices: 1074924--1074966 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
1074914 TTTATCTGAT
*
1074924 TAAAAATTTAATTAGA
1 TAAAAATTTAATTACA
*
1074940 TAAAAA--TAAATACA
1 TAAAAATTTAATTACA
1074954 TAAAAATTTAATT
1 TAAAAATTTAATT
1074967 GATTACAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 12 0.55
16 10 0.45
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
TAAAAATTTAATTACA
Found at i:1074977 original size:29 final size:30
Alignment explanation
Indices: 1074924--1074991 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
1074914 TTTATCTGAT
1074924 TAAAAATTTAATTAGATAAAAAT-AAATACA
1 TAAAAATTTAATTAGATAAAAATAAAAT-CA
* *
1074954 TAAAAATTTAATT-GATTACAATAAAATCA
1 TAAAAATTTAATTAGATAAAAATAAAATCA
*
1074983 TAAATATTT
1 TAAAAATTT
1074992 TTAAATAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.35
Consensus pattern (30 bp):
TAAAAATTTAATTAGATAAAAATAAAATCA
Found at i:1075443 original size:34 final size:30
Alignment explanation
Indices: 1075380--1075445 Score: 80
Period size: 34 Copynumber: 2.1 Consensus size: 30
1075370 TAATATGTCA
1075380 TTAATTAAAAATATAATTAATAAATTATTT
1 TTAATTAAAAATATAATTAATAAATTATTT
1075410 TTAATTTAAAAATAATATATTAAATATAA-TATTT
1 TTAA-TTAAAAAT-ATA-ATT-AATA-AATTATTT
1075444 TT
1 TT
1075446 TTATAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
30 4 0.13
31 8 0.26
32 3 0.10
33 3 0.10
34 11 0.35
35 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TTAATTAAAAATATAATTAATAAATTATTT
Found at i:1075985 original size:3 final size:3
Alignment explanation
Indices: 1075977--1076012 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1075967 TAAAGTTGGC
1075977 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1076013 GCAAAGAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1076582 original size:4 final size:5
Alignment explanation
Indices: 1076539--1076573 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
1076529 AAAATTAAAA
1076539 AATTT AATTT AATTT AATTT AA-TT AATTAT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATT-T AATTT
1076574 TTAATTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:1076609 original size:53 final size:52
Alignment explanation
Indices: 1076519--1076618 Score: 123
Period size: 53 Copynumber: 1.9 Consensus size: 52
1076509 AAAATATTTG
* * *
1076519 TTTTTATTAAAAAATTAAAAAATTTAATTTAATTTAATTTAATTAATTATAA
1 TTTTTATTAAAAAATTAAAAAATTTAATTAAACTTAATATAATTAATTATAA
*
1076571 TTTTTAATTAATAAAA-TAAAAAA-TTAAGTTAAACTTAATATATTTAAT
1 TTTTT-ATTAA-AAAATTAAAAAATTTAA-TTAAACTTAATATAATTAAT
1076619 AATTATCTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
52 9 0.22
53 28 0.68
54 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (52 bp):
TTTTTATTAAAAAATTAAAAAATTTAATTAAACTTAATATAATTAATTATAA
Found at i:1081393 original size:17 final size:18
Alignment explanation
Indices: 1081358--1081394 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1081348 TATTAAAAAA
1081358 ATAATTATTTTTAATTTT
1 ATAATTATTTTTAATTTT
1081376 ATAATT-TTGTTT-ATTTT
1 ATAATTATT-TTTAATTTT
1081393 AT
1 AT
1081395 TTTATAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATAATTATTTTTAATTTT
Found at i:1081976 original size:33 final size:35
Alignment explanation
Indices: 1081939--1082009 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
1081929 AATCATAAAA
*
1081939 TTTAAAATTTTT-ATA-CAAT-TCATAATTAAATAT
1 TTTAAAATTTTTAATATAAATATCAT-ATTAAATAT
*
1081972 TTTAATATTTTTAATATAAATATCATATTAAATAT
1 TTTAAAATTTTTAATATAAATATCATATTAAATAT
1082007 TTT
1 TTT
1082010 TCAAACACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 11 0.33
34 3 0.09
35 15 0.45
36 4 0.12
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (35 bp):
TTTAAAATTTTTAATATAAATATCATATTAAATAT
Found at i:1083279 original size:22 final size:23
Alignment explanation
Indices: 1083235--1083279 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1083225 GTCTCCTTCT
1083235 AGTTCTTCTCCCGCCAATTCGTCC
1 AGTTCTTCTCCCGCC-ATTCGTCC
1083259 AGTTCTCTCTCCC-CC-TTCGTC
1 AGTTCT-TCTCCCGCCATTCGTC
1083280 ACTTCCGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.30
24 8 0.40
25 6 0.30
ACGTcount: A:0.09, C:0.44, G:0.11, T:0.36
Consensus pattern (23 bp):
AGTTCTTCTCCCGCCATTCGTCC
Found at i:1100271 original size:25 final size:23
Alignment explanation
Indices: 1100238--1100288 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
1100228 TTTCTATTAG
*
1100238 ATAAAATATTTTAAATATAATTATA
1 ATAAAATATATTAAAT-TAA-TATA
*
1100263 ATAAAATATATTATATTAATATA
1 ATAAAATATATTAAATTAATATA
1100286 ATA
1 ATA
1100289 TAGATATACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.29
24 3 0.12
25 14 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAAAATATATTAAATTAATATA
Found at i:1101159 original size:10 final size:10
Alignment explanation
Indices: 1101144--1101168 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1101134 TTATTTATTT
1101144 TTTAATTATA
1 TTTAATTATA
1101154 TTTAATTATA
1 TTTAATTATA
1101164 TTTAA
1 TTTAA
1101169 CGAAACATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTAATTATA
Found at i:1101269 original size:18 final size:18
Alignment explanation
Indices: 1101239--1101279 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1101229 TATAATTAAC
1101239 ATATAAAATAATTATCTA
1 ATATAAAATAATTATCTA
1101257 ATATCAAAA-AATTATCTA
1 ATAT-AAAATAATTATCTA
1101275 A-ATAA
1 ATATAA
1101280 TGGTTGATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.09
17 2 0.09
18 14 0.64
19 4 0.18
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATAAAATAATTATCTA
Found at i:1104832 original size:13 final size:13
Alignment explanation
Indices: 1104816--1104842 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1104806 TTGTAATTCT
1104816 AAATATGATATAA
1 AAATATGATATAA
1104829 AAATATGATATAA
1 AAATATGATATAA
1104842 A
1 A
1104843 TATCACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (13 bp):
AAATATGATATAA
Found at i:1105203 original size:9 final size:10
Alignment explanation
Indices: 1105184--1105231 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
1105174 ATTTTTCACG
1105184 ATTATTTTTA
1 ATTATTTTTA
*
1105194 ATTATTTTAA
1 ATTATTTTTA
*
1105204 ATTTTTTTTA
1 ATTATTTTTA
1105214 ATATATATTTATA
1 AT-TAT-TTT-TA
1105227 ATTAT
1 ATTAT
1105232 AATAACATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 19 0.61
11 2 0.06
12 6 0.19
13 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTATTTTTA
Found at i:1105229 original size:23 final size:20
Alignment explanation
Indices: 1105188--1105229 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 20
1105178 TTCACGATTA
1105188 TTTTTAATTATTTTAAATTT
1 TTTTTAATTATTTTAAATTT
1105208 TTTTTAATATATATTTATAATT
1 TTTTTAAT-TAT-TTTA-AATT
1105230 ATAATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 4 0.21
23 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTAATTATTTTAAATTT
Found at i:1105879 original size:14 final size:14
Alignment explanation
Indices: 1105857--1105888 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1105847 TCATCATTTA
1105857 TTTTCATATTTATT
1 TTTTCATATTTATT
*
1105871 TTTTGATATTTATT
1 TTTTCATATTTATT
1105885 TTTT
1 TTTT
1105889 TAAATATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (14 bp):
TTTTCATATTTATT
Found at i:1106254 original size:2 final size:2
Alignment explanation
Indices: 1106249--1106283 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1106239 ATTGTGTGTG
1106249 TA TA TA 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 TA TA TA T
1106284 GATTAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1110844 original size:3 final size:3
Alignment explanation
Indices: 1110836--1110873 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1110826 AGTGATGAAG
*
1110836 GAA GAA GAA GTA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1110874 GACTAGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:1110935 original size:6 final size:6
Alignment explanation
Indices: 1110924--1110957 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1110914 CAGTGCTTCA
1110924 ACTATG ACTATG ACTATG ACTATG ACTATG ACTA
1 ACTATG ACTATG ACTATG ACTATG ACTATG ACTA
1110958 CGAGATTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (6 bp):
ACTATG
Found at i:1111834 original size:2 final size:2
Alignment explanation
Indices: 1111829--1111855 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1111819 TTGTTTAATG
1111829 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
1111856 AAAGATCACA
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:1112429 original size:21 final size:20
Alignment explanation
Indices: 1112381--1112421 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1112371 TAATTCATAC
*
1112381 AATATCAAATTTAAATTTTT
1 AATATCAAATCTAAATTTTT
*
1112401 AATCTCAACATCTAAATTTTT
1 AATATCAA-ATCTAAATTTTT
1112422 TTTATCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATCAAATCTAAATTTTT
Found at i:1115441 original size:1 final size:1
Alignment explanation
Indices: 1115435--1115469 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
1115425 AAGAGAAAGA
1115435 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1115470 AGACCTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1121758 original size:2 final size:2
Alignment explanation
Indices: 1121751--1121790 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1121741 AATTTTTACA
1121751 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
1121791 GCAATTCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1124620 original size:3 final size:3
Alignment explanation
Indices: 1124612--1124637 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1124602 ATACGAATTT
1124612 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
1124638 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1124697 original size:1 final size:1
Alignment explanation
Indices: 1124686--1124720 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
1124676 AGAGAGCTGA
* *
1124686 TTTTTTGTTTTTGTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1124721 CCTTCGAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (1 bp):
T
Found at i:1125294 original size:14 final size:14
Alignment explanation
Indices: 1125275--1125308 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1125265 TTATATTATA
1125275 TGGCACTTGACACT
1 TGGCACTTGACACT
*
1125289 TGGCACTTGACATT
1 TGGCACTTGACACT
1125303 TGGCAC
1 TGGCAC
1125309 GTGCAGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (14 bp):
TGGCACTTGACACT
Found at i:1127009 original size:7 final size:7
Alignment explanation
Indices: 1126972--1127006 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
1126962 TTATATTATA
1126972 TGGCACT
1 TGGCACT
1126979 TGGCACT
1 TGGCACT
1126986 TGGCACT
1 TGGCACT
*
1126993 TGGACACG
1 TGG-CACT
1127001 TGGCAC
1 TGGCAC
1127007 GTGCAGGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.17, C:0.29, G:0.31, T:0.23
Consensus pattern (7 bp):
TGGCACT
Found at i:1127699 original size:11 final size:11
Alignment explanation
Indices: 1127682--1127732 Score: 75
Period size: 11 Copynumber: 4.5 Consensus size: 11
1127672 TTACAATTAA
1127682 TATATTTATAT
1 TATATTTATAT
*
1127693 CATATTTATAT
1 TATATTTATAT
*
1127704 TATTTTTATAT
1 TATATTTATAT
1127715 TATATTTATTAT
1 TATATTTA-TAT
1127727 TATATT
1 TATATT
1127733 ATTATAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
11 26 0.74
12 9 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1127707 original size:20 final size:19
Alignment explanation
Indices: 1127684--1127746 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 19
1127674 ACAATTAATA
1127684 TATTTATATCATATTTATAT
1 TATTTATAT-ATATTTATAT
1127704 TATTTTTATATTATATTTATTAT
1 TA--TTTATA-TATATTTA-TAT
1127727 TATATTAT-TATAATTTATAT
1 TAT-TTATATAT-ATTTATAT
1127747 AAATTTTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
20 8 0.22
21 6 0.16
22 17 0.46
23 6 0.16
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTATATATATTTATAT
Found at i:1127711 original size:22 final size:24
Alignment explanation
Indices: 1127677--1127738 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 24
1127667 ATATATTACA
*
1127677 ATTAATATA-TTTATATCATATTT
1 ATTATTATATTTTATATCATATTT
*
1127700 A-TATTAT-TTTTATATTATATTT
1 ATTATTATATTTTATATCATATTT
1127722 ATTATTATATTATTATA
1 ATTATTATATT-TTATA
1127739 ATTTATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 19 0.58
23 7 0.21
24 2 0.06
25 5 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTATTATATTTTATATCATATTT
Found at i:1127733 original size:17 final size:17
Alignment explanation
Indices: 1127682--1127734 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
1127672 TTACAATTAA
*
1127682 TATATTTA-TATCATAT
1 TATATTTATTATTATAT
*
1127698 T-TATATTATTTTTATAT
1 TATAT-TTATTATTATAT
1127715 TATATTTATTATTATAT
1 TATATTTATTATTATAT
1127732 TAT
1 TAT
1127735 TATAATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 3 0.10
16 4 0.13
17 21 0.68
18 3 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATTTATTATTATAT
Found at i:1128251 original size:15 final size:15
Alignment explanation
Indices: 1128231--1128273 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1128221 ACATATCATT
1128231 TATAAATCTATAATC
1 TATAAATCTATAATC
*
1128246 TATAAATTTATAATC
1 TATAAATCTATAATC
1128261 TATAAA-CTATAAT
1 TATAAATCTATAAT
1128274 TAAAGCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 6 0.23
15 20 0.77
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (15 bp):
TATAAATCTATAATC
Found at i:1128257 original size:8 final size:8
Alignment explanation
Indices: 1128231--1128272 Score: 54
Period size: 7 Copynumber: 5.6 Consensus size: 8
1128221 ACATATCATT
1128231 TATAAATC
1 TATAAATC
1128239 TAT-AATC
1 TATAAATC
*
1128246 TATAAATT
1 TATAAATC
1128254 TAT-AATC
1 TATAAATC
1128261 TATAAA-C
1 TATAAATC
1128268 TATAA
1 TATAA
1128273 TTAAAGCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 19 0.63
8 11 0.37
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (8 bp):
TATAAATC
Found at i:1128260 original size:22 final size:23
Alignment explanation
Indices: 1128228--1128272 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1128218 ATAACATATC
*
1128228 ATTTATAAATCTATAATCTATAA
1 ATTTATAAATCTATAAACTATAA
1128251 ATTTAT-AATCTATAAACTATAA
1 ATTTATAAATCTATAAACTATAA
1128273 TTAAAGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTATAAATCTATAAACTATAA
Found at i:1128584 original size:31 final size:33
Alignment explanation
Indices: 1128529--1128606 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 33
1128519 ATTATTTTTA
1128529 AATTATTATATATTTATATAAATTTTAAAATATT
1 AATTATT-TATATTTATATAAATTTTAAAATATT
* * *
1128563 AATTATTTAT-TTTATGT-AATTTTGATATATT
1 AATTATTTATATTTATATAAATTTTAAAATATT
*
1128594 CATGTATTTATAT
1 AAT-TATTTATAT
1128607 GTATTAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
31 14 0.37
32 13 0.34
33 4 0.11
34 7 0.18
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (33 bp):
AATTATTTATATTTATATAAATTTTAAAATATT
Found at i:1129392 original size:21 final size:21
Alignment explanation
Indices: 1129339--1129393 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
1129329 TTGATTTTAA
* *
1129339 TAATTAAAAAATATTTAAATT
1 TAATTATAAAATATATAAATT
1129360 TAATTATAAAATATATAAATAT
1 TAATTATAAAATATATAAAT-T
1129382 TAA-TATAAAATA
1 TAATTATAAAATA
1129394 AATTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATTATAAAATATATAAATT
Found at i:1129886 original size:2 final size:2
Alignment explanation
Indices: 1129879--1129922 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1129869 CTAAACTTAG
*
1129879 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1129921 TA
1 TA
1129923 ATTTAAAGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1130985 original size:9 final size:9
Alignment explanation
Indices: 1130971--1131050 Score: 67
Period size: 9 Copynumber: 8.4 Consensus size: 9
1130961 AATATTTTTA
1130971 AATATAAAT
1 AATATAAAT
1130980 AATATAAAT
1 AATATAAAT
1130989 AATATAAAT
1 AATATAAAT
1130998 AAT-TAATAT
1 AATATAA-AT
*
1131007 ATTTATTAAAT
1 A-ATA-TAAAT
1131018 AAAATTATAATAT
1 --AA-TATAA-AT
1131031 AATA-AAAT
1 AATATAAAT
1131039 -ATATAAAT
1 AATATAAAT
1131047 AATA
1 AATA
1131051 ATACAGATAT
Statistics
Matches: 59, Mismatches: 2, Indels: 20
0.73 0.02 0.25
Matches are distributed among these distances:
7 3 0.05
8 9 0.15
9 29 0.49
10 3 0.05
11 4 0.07
12 6 0.10
13 5 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AATATAAAT
Found at i:1130999 original size:13 final size:14
Alignment explanation
Indices: 1130974--1131050 Score: 54
Period size: 13 Copynumber: 5.4 Consensus size: 14
1130964 ATTTTTAAAT
1130974 ATAA-ATAATATAA
1 ATAATATAATATAA
1130987 ATAATATAA-ATAA
1 ATAATATAATATAA
* *
1131000 TTAATATATTTATTAA
1 ATAATATA-ATA-TAA
1131016 ATAAAATTATAATAT-A
1 AT--AA-TATAATATAA
*
1131032 ATAAAAT-ATATAA
1 ATAATATAATATAA
1131045 ATAATA
1 ATAATA
1131051 ATACAGATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
12 4 0.08
13 23 0.46
14 6 0.12
15 1 0.02
16 7 0.14
17 1 0.02
18 4 0.08
19 4 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATATAATATAA
Found at i:1131036 original size:16 final size:16
Alignment explanation
Indices: 1130909--1131051 Score: 75
Period size: 16 Copynumber: 8.9 Consensus size: 16
1130899 TATGAATATG
1130909 ATAT-TAAA-AATAAA
1 ATATATAAATAATAAA
* * *
1130923 ATATAAAAAAAATAAT
1 ATATATAAATAATAAA
* *
1130939 ACATATACAA-CAT-AA
1 ATATATA-AATAATAAA
* **
1130954 ATATATAAATATTTTTA
1 ATATATAAATA-ATAAA
1130971 A-ATATAAATAATATAA
1 ATATATAAATAATA-AA
*
1130987 ATAATATAAATAAT-TA
1 AT-ATATAAATAATAAA
* *
1131003 ATATATTTATTAAATAAA
1 ATATA-TAAAT-AATAAA
1131021 AT-TATAATATAATAAA
1 ATATATAA-ATAATAAA
1131037 ATATATAAATAATAA
1 ATATATAAATAATAA
1131052 TACAGATATA
Statistics
Matches: 96, Mismatches: 19, Indels: 26
0.68 0.13 0.18
Matches are distributed among these distances:
14 6 0.06
15 14 0.15
16 47 0.49
17 15 0.16
18 14 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATATAAATAATAAA
Found at i:1131046 original size:24 final size:25
Alignment explanation
Indices: 1130969--1131063 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 25
1130959 TAAATATTTT
1130969 TAAAT-ATAA-ATAATATAAATAATA
1 TAAATAATAATATAATATAAAT-ATA
* *
1130993 TAAATAATTAATATATTTATTAA-ATA
1 TAAATAA-TAATATA-ATATAAATATA
*
1131019 -AAATTATAATATAATA-AAATATA
1 TAAATAATAATATAATATAAATATA
*
1131042 TAAATAATAATACAGATATAAA
1 TAAATAATAATATA-ATATAAA
1131064 AATTATCGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
22 2 0.04
23 5 0.09
24 23 0.41
25 9 0.16
26 9 0.16
27 3 0.05
28 5 0.09
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (25 bp):
TAAATAATAATATAATATAAATATA
Found at i:1131847 original size:19 final size:19
Alignment explanation
Indices: 1131815--1131851 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1131805 AACTTTTAAT
1131815 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
1131834 TAAATATTAA-TATAAAAT
1 TAAAT-TTAATTATAAAAT
1131852 TATTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:1132850 original size:20 final size:20
Alignment explanation
Indices: 1132822--1132892 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1132812 TTTTACCCAG
*
1132822 ATGTATCGATATATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1132842 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
1132862 ATGTGTCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1132882 ATGTATCGATA
1 ATGTATCGATA
1132893 TATTCTGTCT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1137443 original size:15 final size:13
Alignment explanation
Indices: 1137419--1137462 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
1137409 AAAAAATATG
1137419 ATTTTTTAAAAAA
1 ATTTTTTAAAAAA
1137432 ATTTTATATAAAAAA
1 ATTTT-T-TAAAAAA
*
1137447 AATTTTTAAAAAA
1 ATTTTTTAAAAAA
1137460 ATT
1 ATT
1137463 AAAATATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 14 0.52
14 2 0.07
15 11 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATTTTTTAAAAAA
Found at i:1137445 original size:16 final size:14
Alignment explanation
Indices: 1137426--1137460 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
1137416 ATGATTTTTT
1137426 AAAAAAATTTTATATA
1 AAAAAAATTTT-TA-A
1137442 AAAAAAATTTTTAA
1 AAAAAAATTTTTAA
1137456 AAAAA
1 AAAAA
1137461 TTAAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 2 0.11
16 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAAAATTTTTAA
Found at i:1138455 original size:56 final size:56
Alignment explanation
Indices: 1138389--1138568 Score: 256
Period size: 56 Copynumber: 3.2 Consensus size: 56
1138379 TTCATGTGAC
1138389 TTTTTAATTATTTTTATTAATATAAATAGAGTAATTGAGTTGAAATCAATGTCA-TT
1 TTTTTAATTATTTTTATTAATATAAA-AGAGTAATTGAGTTGAAATCAATGTCACTT
* * * *
1138445 TTTTTGATTATTTTTATTAATATAAAAAAGTAATTAAGTTGAAATCAACGTCACTT
1 TTTTTAATTATTTTTATTAATATAAAAGAGTAATTGAGTTGAAATCAATGTCACTT
* * *
1138501 TTTTTAATTATTTTTACTAATATACAAAGAGTAATTGAGTTGAAATCAAT-CCTATTT
1 TTTTTAATTATTTTTATTAATATA-AAAGAGTAATTGAGTTGAAATCAATGTC-ACTT
1138558 TTTTTAATTAT
1 TTTTTAATTAT
1138569 CTCTATTACC
Statistics
Matches: 110, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
55 24 0.22
56 50 0.45
57 36 0.33
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (56 bp):
TTTTTAATTATTTTTATTAATATAAAAGAGTAATTGAGTTGAAATCAATGTCACTT
Found at i:1138485 original size:55 final size:56
Alignment explanation
Indices: 1138389--1138598 Score: 255
Period size: 56 Copynumber: 3.8 Consensus size: 56
1138379 TTCATGTGAC
* *
1138389 TTTTTAATTATTTTTATTAATATAAATAGAGTAATTGAGTTGAAATCAATGTCA-TT
1 TTTTTAATTATTTTTATTAATATAAA-AAAGTAATTAAGTTGAAATCAATGTCACTT
* *
1138445 TTTTTGATTATTTTTATTAATATAAAAAAGTAATTAAGTTGAAATCAACGTCACTT
1 TTTTTAATTATTTTTATTAATATAAAAAAGTAATTAAGTTGAAATCAATGTCACTT
* * * * *
1138501 TTTTTAATTATTTTTACTAATATACAAAGAGTAATTGAGTTGAAATCAAT-CCTATTT
1 TTTTTAATTATTTTTATTAATATA-AAAAAGTAATTAAGTTGAAATCAATGTC-ACTT
* * **
1138558 TTTTTAATTATCTCTATTACCATAAAAAA-TAATTAAGTTGA
1 TTTTTAATTATTTTTATTAATATAAAAAAGTAATTAAGTTGA
1138599 TATTACAAGT
Statistics
Matches: 133, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
55 35 0.26
56 54 0.41
57 44 0.33
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (56 bp):
TTTTTAATTATTTTTATTAATATAAAAAAGTAATTAAGTTGAAATCAATGTCACTT
Found at i:1138511 original size:112 final size:112
Alignment explanation
Indices: 1138389--1138598 Score: 309
Period size: 112 Copynumber: 1.9 Consensus size: 112
1138379 TTCATGTGAC
* * *
1138389 TTTTTAATTATTTTTATTAATATA-AATAGAGTAATTGAGTTGAAATCAAT-GTCA-TTTTTTTG
1 TTTTTAATTATTTTTACTAATATACAA-AGAGTAATTGAGTTGAAATCAATCCT-ATTTTTTTTA
* * *
1138451 ATTATTTTTATTAATATAAAAAAGTAATTAAGTTGAAATCAACGTCACTT
64 ATTATCTCTATTAACATAAAAAA-TAATTAAGTTGAAATCAACGTCACTT
1138501 TTTTTAATTATTTTTACTAATATACAAAGAGTAATTGAGTTGAAATCAATCCTATTTTTTTTAAT
1 TTTTTAATTATTTTTACTAATATACAAAGAGTAATTGAGTTGAAATCAATCCTATTTTTTTTAAT
*
1138566 TATCTCTATTACCATAAAAAATAATTAAGTTGA
66 TATCTCTATTAACATAAAAAATAATTAAGTTGA
1138599 TATTACAAGT
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
112 59 0.67
113 29 0.33
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (112 bp):
TTTTTAATTATTTTTACTAATATACAAAGAGTAATTGAGTTGAAATCAATCCTATTTTTTTTAAT
TATCTCTATTAACATAAAAAATAATTAAGTTGAAATCAACGTCACTT
Found at i:1139269 original size:24 final size:24
Alignment explanation
Indices: 1139219--1139278 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
1139209 TTTTTATTTA
* *
1139219 AATTTAATTATAAAAATATATATT
1 AATTTAATTAAAAAAATATATAAT
*
1139243 AATTTAA-TAAAAAAATTTAATAAT
1 AATTTAATTAAAAAAATAT-ATAAT
1139267 AA-TTAGATTAAA
1 AATTTA-ATTAAA
1139279 CTAAATTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 12 0.40
24 14 0.47
25 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
AATTTAATTAAAAAAATATATAAT
Found at i:1139391 original size:2 final size:2
Alignment explanation
Indices: 1139386--1139421 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1139376 TTCACACATG
1139386 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
1139422 GGTGGCCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1141432 original size:18 final size:18
Alignment explanation
Indices: 1141409--1141444 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1141399 TTTTAATTCA
1141409 TAAATTCATTGGATGTTT
1 TAAATTCATTGGATGTTT
*
1141427 TAAATTTATTGGATGTTT
1 TAAATTCATTGGATGTTT
1141445 AGTTACTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.53
Consensus pattern (18 bp):
TAAATTCATTGGATGTTT
Found at i:1141935 original size:2 final size:2
Alignment explanation
Indices: 1141928--1141952 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1141918 AAATAAACAC
1141928 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1141953 GAGACGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1147007 original size:34 final size:34
Alignment explanation
Indices: 1146916--1147016 Score: 139
Period size: 37 Copynumber: 2.9 Consensus size: 34
1146906 TATTAAATTT
* *
1146916 GTTAGGTAAACATATTAAGTGTGTTAAGTGGTAT
1 GTTAGGTAAACATATTAAGTGTGTTAGGTGGTAC
* *
1146950 GTTAGGTGAGTAATATATTAAGTGTGTTAGGTGGTGC
1 GTTAGGT-A--AACATATTAAGTGTGTTAGGTGGTAC
1146987 GTTAGGTAAACATATTAAGTGTGTTAGGTG
1 GTTAGGTAAACATATTAAGTGTGTTAGGTG
1147017 AACATATATT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
34 28 0.47
35 1 0.02
36 1 0.02
37 29 0.49
ACGTcount: A:0.29, C:0.03, G:0.31, T:0.38
Consensus pattern (34 bp):
GTTAGGTAAACATATTAAGTGTGTTAGGTGGTAC
Found at i:1149747 original size:39 final size:39
Alignment explanation
Indices: 1149673--1149747 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
1149663 GATTATATAA
* * *
1149673 ATATAATATAAATTTAAAAATATTTTAAATATAATTATG
1 ATATAATATAAATATAAAAATATATCAAATATAATTATG
* *
1149712 ATATAATAT-AATATATAAATATAATCAAATTTAATT
1 ATATAATATAAATATAAAAATAT-ATCAAATATAATT
1149748 TTATCTTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 11 0.37
39 19 0.63
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (39 bp):
ATATAATATAAATATAAAAATATATCAAATATAATTATG
Found at i:1151555 original size:17 final size:18
Alignment explanation
Indices: 1151522--1151562 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1151512 ATGATTAATT
1151522 AAAATAAATATTAATAAA
1 AAAATAAATATTAATAAA
1151540 AAAATTAAAT-TT-ATAAA
1 AAAA-TAAATATTAATAAA
*
1151557 ATAATA
1 AAAATA
1151563 TTTTAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.10
17 8 0.38
18 6 0.29
19 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATAAATATTAATAAA
Done.