Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold170
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: 1632119
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 57634 characters in sequence are not A, C, G, or T
File 9 of 11
Found at i:1244058 original size:19 final size:17
Alignment explanation
Indices: 1244034--1244071 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 17
1244024 AAATATGAAA
1244034 ATATTAAAAATTATTAAAT
1 ATATT-AAAATT-TTAAAT
1244053 ATATTAAAATTTTAAAT
1 ATATTAAAATTTTAAAT
1244070 AT
1 AT
1244072 GAACATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTAAAATTTTAAAT
Found at i:1246422 original size:65 final size:64
Alignment explanation
Indices: 1246297--1246424 Score: 145
Period size: 65 Copynumber: 2.0 Consensus size: 64
1246287 ATCATACGAT
* *
1246297 ATAAAATTTTAAATTTTATATAAAAAATATCTAAATTTTGATCAGTAATCTAAACTTATTTTTAA
1 ATAAAATTTAAAATTTTATATAAAAAATATCTAAATTTTGATCAATAATCTAAAC-TATTTTTAA
* * *
1246362 ATAAAATTTAAAATTTTATGTTAAAAAGATATTTCAATATTTT-ATCAAT-ATTTAAA-TATTTT
1 ATAAAATTTAAAATTTTAT-ATAAAAA-ATATCT-AA-ATTTTGATCAATAATCTAAACTATTTT
1246424 T
62 T
1246425 TAACATTCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
65 25 0.46
66 6 0.11
67 11 0.20
68 7 0.13
69 5 0.09
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (64 bp):
ATAAAATTTAAAATTTTATATAAAAAATATCTAAATTTTGATCAATAATCTAAACTATTTTTAA
Found at i:1246498 original size:29 final size:30
Alignment explanation
Indices: 1246466--1246534 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
1246456 TTTTACAAGA
1246466 ATAAAAATTAAAATATTAAATTTA-ATAGT
1 ATAAAAATTAAAATATTAAATTTATATAGT
* *
1246495 ATAAAAATTAAAATATTTATTTTATTATAGT
1 ATAAAAATTAAAATATTAAATTTA-TATAGT
1246526 ATAAAAATT
1 ATAAAAATT
1246535 CTTAATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 22 0.61
31 14 0.39
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (30 bp):
ATAAAAATTAAAATATTAAATTTATATAGT
Found at i:1246916 original size:34 final size:33
Alignment explanation
Indices: 1246850--1246966 Score: 164
Period size: 34 Copynumber: 3.5 Consensus size: 33
1246840 AAATAAATAA
*
1246850 ATTGTTGATTAAATGGTG-ATTTGGTAGTTTACC
1 ATTGTTGATTAAATGG-GAATTTGGTAGCTTACC
*
1246883 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGG-AATTTGGTAGCTTACC
* *
1246917 ATTGTTGATTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGA-ATTTGGTAGCTTACC
1246951 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1246967 TGGTTTTTAC
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.01
33 16 0.21
34 59 0.78
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.40
Consensus pattern (33 bp):
ATTGTTGATTAAATGGGAATTTGGTAGCTTACC
Found at i:1251446 original size:34 final size:34
Alignment explanation
Indices: 1251380--1251564 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
1251370 AAGTGGGAGA
* *
1251380 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1251413 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1251447 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1251481 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1251515 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1251549 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1251565 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1252274 original size:19 final size:19
Alignment explanation
Indices: 1252232--1252274 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1252222 GTTTTTAGTT
* * *
1252232 ATTTTTAAAGTTTTGTTGA
1 ATTTTTAAAATATTGTTCA
1252251 ATTTTTAAAATATTGTTCA
1 ATTTTTAAAATATTGTTCA
*
1252270 CTTTT
1 ATTTT
1252275 GAGTATGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (19 bp):
ATTTTTAAAATATTGTTCA
Found at i:1252586 original size:21 final size:21
Alignment explanation
Indices: 1252560--1252604 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1252550 ATTTTATCAA
* *
1252560 TTTAAATAAAAAATTAACTTT
1 TTTAAACAAAAAATCAACTTT
* *
1252581 TTTAAACATAAAATCAATTTT
1 TTTAAACAAAAAATCAACTTT
1252602 TTT
1 TTT
1252605 GAAAATTACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAAACAAAAAATCAACTTT
Found at i:1252926 original size:8 final size:8
Alignment explanation
Indices: 1252913--1252956 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
1252903 AACTAAAGAA
1252913 TAAAATAT
1 TAAAATAT
1252921 TAAAATAT
1 TAAAATAT
1252929 TAAAAT-T
1 TAAAATAT
1252936 T-AAAT-T
1 TAAAATAT
1252942 T-AAATAT
1 TAAAATAT
1252949 ATAAAATA
1 -TAAAATA
1252957 CTAATTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 10 0.30
7 3 0.09
8 15 0.45
9 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TAAAATAT
Found at i:1262730 original size:19 final size:18
Alignment explanation
Indices: 1262680--1262746 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 18
1262670 TACGATCAAT
1262680 AATTTATATTATTATTTAAA
1 AATTTA-ATTATT-TTTAAA
* * *
1262700 AAATAAAATATTTTTAAA
1 AATTTAATTATTTTTAAA
1262718 ATATTTAATTATTTTATAATTA
1 A-ATTTAATTATTTT-TAA--A
1262740 AATTTAA
1 AATTTAA
1262747 ATAAATAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
18 7 0.19
19 15 0.41
20 7 0.19
21 6 0.16
22 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTAATTATTTTTAAA
Found at i:1262746 original size:21 final size:21
Alignment explanation
Indices: 1262720--1262781 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
1262710 TTTTTAAAAT
*
1262720 ATTTAATTATTTTATAATTAA
1 ATTTAATTAATTTATAATTAA
* * *
1262741 ATTTAAATAAATAATAATTTAA
1 ATTTAATTAATTTATAA-TTAA
*
1262763 ATTAAATTAATTTA-AATTA
1 ATTTAATTAATTTATAATTA
1262782 TAAAAATTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 3 0.09
21 15 0.47
22 14 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTAATTAATTTATAATTAA
Found at i:1262789 original size:15 final size:15
Alignment explanation
Indices: 1262739--1262790 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
1262729 TTTTATAATT
*
1262739 AAATTTAAATAAATAA
1 AAATTTAAAT-TATAA
*
1262755 TAATTTAAATTA-AA
1 AAATTTAAATTATAA
*
1262769 TTAATTTAAATTATAA
1 -AAATTTAAATTATAA
1262785 AAATTT
1 AAATTT
1262791 TTATTCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 2 0.06
15 18 0.58
16 11 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATTTAAATTATAA
Found at i:1262962 original size:12 final size:12
Alignment explanation
Indices: 1262947--1263011 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
1262937 TATTTTTATT
1262947 TAAAT-TTAATTA
1 TAAATATTAA-TA
1262959 TAAATATTAATA
1 TAAATATTAATA
*
1262971 TAAA-AATAATTTA
1 TAAATATTAA--TA
* *
1262984 TTAATATTATTA
1 TAAATATTAATA
*
1262996 TAAATAATAATA
1 TAAATATTAATA
1263008 TAAA
1 TAAA
1263012 CTTTTAAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 4 0.10
12 26 0.62
13 9 0.21
14 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAAATATTAATA
Found at i:1262990 original size:25 final size:26
Alignment explanation
Indices: 1262956--1263006 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
1262946 TTAAATTTAA
1262956 TTATAAATATTAATATAAA-AATAAT
1 TTATAAATATTAATATAAATAATAAT
* *
1262981 TTATTAATATTATTATAAATAATAAT
1 TTATAAATATTAATATAAATAATAAT
1263007 ATAAACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TTATAAATATTAATATAAATAATAAT
Found at i:1263211 original size:14 final size:14
Alignment explanation
Indices: 1263194--1263221 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1263184 TAATTATAAA
1263194 AATATAAAAATATT
1 AATATAAAAATATT
1263208 AATATAAAAATATT
1 AATATAAAAATATT
1263222 TTTTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:1263213 original size:22 final size:22
Alignment explanation
Indices: 1263179--1263220 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1263169 ATTTTTATTT
1263179 AAATTTAATTATAAAAATATAA
1 AAATTTAATTATAAAAATATAA
1263201 AAATATTAA-TATAAAAATAT
1 AAAT-TTAATTATAAAAATAT
1263221 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATTTAATTATAAAAATATAA
Found at i:1264206 original size:2 final size:2
Alignment explanation
Indices: 1264199--1264226 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1264189 CTTGTTTAAC
1264199 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
1264227 TTTTAGTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1266261 original size:20 final size:21
Alignment explanation
Indices: 1266236--1266277 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1266226 TCCATGTATG
*
1266236 TATAAAACTTAT-TTATAAAT
1 TATAAAAATTATATTATAAAT
1266256 TATAAAAATTATACTTATAAAT
1 TATAAAAATTATA-TTATAAAT
1266278 AGTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAAAAATTATATTATAAAT
Found at i:1270787 original size:10 final size:10
Alignment explanation
Indices: 1270772--1270801 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1270762 TTTAAATATA
1270772 TAAAAAAATT
1 TAAAAAAATT
*
1270782 TAAAAAATTT
1 TAAAAAAATT
1270792 TAAAAAAATT
1 TAAAAAAATT
1270802 AAATATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:1274690 original size:2 final size:2
Alignment explanation
Indices: 1274683--1274712 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1274673 TATGAAGAGA
*
1274683 CT CT CT CT CT CT CT CT CT CT CC CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1274713 ACTGTTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:1281313 original size:13 final size:14
Alignment explanation
Indices: 1281295--1281323 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1281285 TATGAATACA
1281295 TAAATTTTTTT-TT
1 TAAATTTTTTTATT
1281308 TAAATTTTTTTATT
1 TAAATTTTTTTATT
1281322 TA
1 TA
1281324 TTTGGACGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TAAATTTTTTTATT
Found at i:1285953 original size:50 final size:50
Alignment explanation
Indices: 1285897--1286057 Score: 209
Period size: 50 Copynumber: 3.2 Consensus size: 50
1285887 AATGTATTGC
*
1285897 AATTGTTGACTATTTTTCACCAACCTTTGACAATTGAGAGAGGTGACTGT
1 AATTGTTGACTATTTTTCACCAACCTTTGACAATAGAGAGAGGTGACTGT
* * * * * **
1285947 AATTGTTGA-TAATTCTTCACCAACCTTTGACAATCGAGAAAAGTGGCCAT
1 AATTGTTGACT-ATTTTTCACCAACCTTTGACAATAGAGAGAGGTGACTGT
*
1285997 AATTGTTGACGATTTTTCACCAACCTTTGACAATAGAGAGAGGTGA-TCGT
1 AATTGTTGACTATTTTTCACCAACCTTTGACAATAGAGAGAGGTGACT-GT
1286047 AATTGTTGACT
1 AATTGTTGACT
1286058 CTAAGCAACT
Statistics
Matches: 92, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.99
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (50 bp):
AATTGTTGACTATTTTTCACCAACCTTTGACAATAGAGAGAGGTGACTGT
Found at i:1286340 original size:19 final size:19
Alignment explanation
Indices: 1286303--1286340 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1286293 TTAGTTGTCG
**
1286303 AGGCACTGTTCACTTATAC
1 AGGCACTGTTCACACATAC
1286322 AGGCACTGTTCACACATAC
1 AGGCACTGTTCACACATAC
1286341 GGTTACTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (19 bp):
AGGCACTGTTCACACATAC
Found at i:1287153 original size:18 final size:19
Alignment explanation
Indices: 1287120--1287156 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
1287110 GCACATTAAG
1287120 AAAGAGTGCTGAAAAAATAA
1 AAAGAGTGC-GAAAAAATAA
1287140 AAAGAGTG-GAAAAAATA
1 AAAGAGTGCGAAAAAATA
1287157 TAGTTGAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.62, C:0.03, G:0.22, T:0.14
Consensus pattern (19 bp):
AAAGAGTGCGAAAAAATAA
Found at i:1291427 original size:20 final size:19
Alignment explanation
Indices: 1291391--1291434 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1291381 ATTTTTTATT
1291391 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
1291410 TAAATATTAA-TATAAAA-A
1 TAAAT-TTAATTATAAAATA
1291428 TAAATTT
1 TAAATTT
1291435 TTAATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.08
18 6 0.25
19 12 0.50
20 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:1291438 original size:19 final size:19
Alignment explanation
Indices: 1291391--1291444 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1291381 ATTTTTTATT
1291391 TAAA-TTTAATTATAAAATA
1 TAAATTTTAA-TATAAAATA
*
1291410 TAAATATTAATATAAAA-A
1 TAAATTTTAATATAAAATA
*
1291428 TAAATTTTTA-ATAAAAT
1 TAAATTTTAATATAAAAT
1291445 GAATCGTGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 6 0.20
18 9 0.30
19 11 0.37
20 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATTTTAATATAAAATA
Found at i:1293516 original size:31 final size:31
Alignment explanation
Indices: 1293475--1293533 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1293465 TAAAGGTGTA
* * *
1293475 TTTTAGTTTTTTTTTATTATTAAATTAAATAT
1 TTTTAGTTTTTATATATT-TAAAATTAAATAT
1293507 TTTTA-TTTTTATATATTTAAAATTAAA
1 TTTTAGTTTTTATATATTTAAAATTAAA
1293534 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.38
31 10 0.42
32 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (31 bp):
TTTTAGTTTTTATATATTTAAAATTAAATAT
Found at i:1295074 original size:27 final size:29
Alignment explanation
Indices: 1295021--1295074 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
1295011 TTTTTATATT
**
1295021 AATATTTATATATAATTAAATTTTAATAA
1 AATATTTATATATAATTAAATAGTAATAA
*
1295050 AATATTTTTAT-TAA-TAAATAGTAAT
1 AATATTTATATATAATTAAATAGTAAT
1295075 TTAAGTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 9 0.41
28 3 0.14
29 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
AATATTTATATATAATTAAATAGTAATAA
Found at i:1295219 original size:21 final size:21
Alignment explanation
Indices: 1295181--1295233 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1295171 ATTAATTTGA
* * *
1295181 ATAATAAAAAAATTTAAATTTT
1 ATAAT-AAAATATATAAATATT
1295203 ATAATAAAATATATAAATATT
1 ATAATAAAATATATAAATATT
1295224 A-ATATAAAAT
1 ATA-ATAAAAT
1295234 TTTTTTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 21 0.78
22 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATAAAATATATAAATATT
Found at i:1295596 original size:15 final size:16
Alignment explanation
Indices: 1295578--1295612 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1295568 TTAATTTTAT
1295578 AAAAATAAAT-TTAAA
1 AAAAATAAATATTAAA
1295593 AAAAATAAATGATTAAA
1 AAAAATAAAT-ATTAAA
1295610 AAA
1 AAA
1295613 GACTTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
17 8 0.44
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAAATAAATATTAAA
Found at i:1295948 original size:16 final size:16
Alignment explanation
Indices: 1295927--1295986 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
1295917 TTTAATATAA
1295927 TAAATTTAAATTAAAT
1 TAAATTTAAATTAAAT
* *
1295943 TAAATTTAAAATAAAA
1 TAAATTTAAATTAAAT
* * *
1295959 TAATTTTAATTTGAAT
1 TAAATTTAAATTAAAT
1295975 T-AATTT-AATTAA
1 TAAATTTAAATTAA
1295987 TAAAAAAAAC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
14 4 0.12
15 4 0.12
16 26 0.76
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
TAAATTTAAATTAAAT
Found at i:1295961 original size:32 final size:32
Alignment explanation
Indices: 1295919--1295991 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
1295909 ATTATTTATT
*
1295919 TAATATAATAAATTTAAATTAAATTAAATTTAA
1 TAATAAAATAAATTTAAATTAAATT-AATTTAA
* * *
1295952 -AATAAAATAATTTTAATTTGAATTAATTTAA
1 TAATAAAATAAATTTAAATTAAATTAATTTAA
1295983 TTAATAAAA
1 -TAATAAAA
1295992 AAAACTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 7 0.21
32 20 0.59
33 7 0.21
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
TAATAAAATAAATTTAAATTAAATTAATTTAA
Found at i:1295970 original size:37 final size:37
Alignment explanation
Indices: 1295929--1296010 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 37
1295919 TAATATAATA
1295929 AATTTAAATTAAATTAAATT-TAAAATAAAA-TAATTTT
1 AATTTAAATT-AATTAAATTATAAAA-AAAACTAATTTT
* * *
1295966 AATTTGAATTAATTTAATTAATAAAAAAAACTATTTTT
1 AATTTAAATTAATTAAATT-ATAAAAAAAACTAATTTT
1296004 AATTTAA
1 AATTTAA
1296011 TTATAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
36 8 0.21
37 13 0.34
38 17 0.45
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (37 bp):
AATTTAAATTAATTAAATTATAAAAAAAACTAATTTT
Found at i:1296262 original size:12 final size:13
Alignment explanation
Indices: 1296247--1296275 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1296237 GATATTTAAA
1296247 AAAATA-TAAATT
1 AAAATATTAAATT
1296259 AAAATATTAAATT
1 AAAATATTAAATT
1296272 AAAA
1 AAAA
1296276 AAATAAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATATTAAATT
Found at i:1296296 original size:26 final size:27
Alignment explanation
Indices: 1296245--1296297 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
1296235 TCGATATTTA
*
1296245 AAAAAATATAAATTAAAATATTAAATT
1 AAAAAATATAAATTAAAATATAAAATT
*
1296272 AAAAAA-ATAAGTATAAAA-ATAAAATT
1 AAAAAATATAAAT-TAAAATATAAAATT
1296298 TATTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAAAATATAAATTAAAATATAAAATT
Found at i:1296480 original size:16 final size:18
Alignment explanation
Indices: 1296440--1296483 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
1296430 ATATTTTAAC
1296440 TTATAT-AAATATAATAT
1 TTATATAAAATATAATAT
1296457 TTATATAAAATATAAT-T
1 TTATATAAAATATAATAT
1296474 TTA-ATAAAAT
1 TTATATAAAAT
1296484 TCGATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.27
17 10 0.38
18 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTATATAAAATATAATAT
Found at i:1296870 original size:11 final size:11
Alignment explanation
Indices: 1296851--1296920 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
1296841 AGTTTGTGGC
* *
1296851 TTATATTATTT
1 TTATTTTATAT
1296862 TTATTTTATAT
1 TTATTTTATAT
**
1296873 AAATTTTA-AT
1 TTATTTTATAT
*
1296883 ATATTTATATAT
1 TTATTT-TATAT
* *
1296895 TTATATCATAT
1 TTATTTTATAT
*
1296906 TTATTTTATTT
1 TTATTTTATAT
1296917 TTAT
1 TTAT
1296921 ATCATATATT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
10 7 0.15
11 33 0.72
12 6 0.13
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATTTTATAT
Found at i:1296922 original size:22 final size:23
Alignment explanation
Indices: 1296884--1296927 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1296874 AATTTTAATA
1296884 TATTTATATATTTATATCATATT
1 TATTTATATATTTATATCATATT
*
1296907 TATTT-TATTTTTATATCATAT
1 TATTTATATATTTATATCATAT
1296928 ATTTAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTTATATATTTATATCATATT
Found at i:1296940 original size:22 final size:22
Alignment explanation
Indices: 1296881--1296945 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
1296871 ATAAATTTTA
1296881 ATATATTT-A-TATATTTATATC
1 ATATATTTAATTAT-TTTATATC
*
1296902 --ATATTTATTTTATTTTTATATC
1 ATATATTTA-ATTA-TTTTATATC
*
1296924 ATATATTTAATTATTTTTTATC
1 ATATATTTAATTATTTTATATC
1296946 TTATTCATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
19 6 0.17
22 18 0.51
23 4 0.11
24 7 0.20
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATATTTAATTATTTTATATC
Found at i:1296941 original size:24 final size:22
Alignment explanation
Indices: 1296887--1296944 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
1296877 TTTAATATAT
*
1296887 TTATATATTTATATCATATTTA
1 TTATATTTTTATATCATATTTA
*
1296909 TTTTATTTTTATATCATATATTTAA
1 TTATATTTTTATATC--ATATTT-A
1296934 TTAT-TTTTTAT
1 TTATATTTTTAT
1296945 CTTATTCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 13 0.43
24 13 0.43
25 4 0.13
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATATTTTTATATCATATTTA
Found at i:1299396 original size:22 final size:23
Alignment explanation
Indices: 1299343--1299396 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
1299333 TTATTTAAAA
1299343 AATTAAA--TAATATATTTTTAT
1 AATTAAATTTAATATATTTTTAT
1299364 -ATT-AATATTAATAT-TTTTTAT
1 AATTAAAT-TTAATATATTTTTAT
1299385 AATTAAATTTAA
1 AATTAAATTTAA
1299397 ATAAAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
19 2 0.07
20 3 0.11
21 7 0.25
22 13 0.46
23 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTAAATTTAATATATTTTTAT
Found at i:1299746 original size:26 final size:26
Alignment explanation
Indices: 1299698--1299762 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
1299688 CAATTGAATC
*
1299698 AATTTTAAACTTATTCAATAATTTTTT
1 AATTTTAAA-TTATTCAATAATTTTAT
* *
1299725 TATTTTAAATTATT-ACTAAATTTTAT
1 AATTTTAAATTATTCAAT-AATTTTAT
1299751 AATTTTATAATT
1 AATTTTA-AATT
1299763 TTTAATTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.06
26 18 0.56
27 12 0.38
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTTTAAATTATTCAATAATTTTAT
Found at i:1299756 original size:8 final size:8
Alignment explanation
Indices: 1299715--1299769 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
1299705 AACTTATTCA
1299715 ATAATTTT
1 ATAATTTT
* *
1299723 TTTATTTT
1 ATAATTTT
1299731 A-AATTATT
1 ATAATT-TT
1299739 ACTAAATTTT
1 A-T-AATTTT
1299749 ATAATTTT
1 ATAATTTT
1299757 ATAATTTT
1 ATAATTTT
1299765 -TAATT
1 ATAATT
1299770 GAATCAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
7 8 0.21
8 23 0.59
9 1 0.03
10 3 0.08
11 4 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (8 bp):
ATAATTTT
Found at i:1299975 original size:27 final size:27
Alignment explanation
Indices: 1299923--1299975 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1299913 CTTAAAAAAT
**
1299923 TATTTAATAATAAAAATATTTTATTTA
1 TATTTAATAATAAAAATATTAAATTTA
*
1299950 TATTTAATTAT-AAAATATATAAATTT
1 TATTTAATAATAAAAATAT-TAAATTT
1299976 TAATATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TATTTAATAATAAAAATATTAAATTTA
Found at i:1299996 original size:19 final size:21
Alignment explanation
Indices: 1299952--1300000 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
1299942 TTTATTTATA
1299952 TTTAATTATAAAATATATAAAT
1 TTTAA-TATAAAATATATAAAT
*
1299974 TTTAATATAAAA-ATA-ATAT
1 TTTAATATAAAATATATAAAT
1299993 TTTAATAT
1 TTTAATAT
1300001 TTTATTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.42
20 3 0.12
21 7 0.27
22 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAATATAAAATATATAAAT
Found at i:1300033 original size:30 final size:30
Alignment explanation
Indices: 1299928--1300033 Score: 78
Period size: 30 Copynumber: 3.6 Consensus size: 30
1299918 AAAATTATTT
* **
1299928 AATAAT-AAA-AATATTTTATTTATAT-TT
1 AATAATAAAATAATATTTTATTAATATAAA
* **
1299955 AATTATAAAATATATAAATT-TTAATATAAA
1 AATAATAAAATA-ATATTTTATTAATATAAA
***
1299985 AATAATATTTTAATATTTTATTAATATAATA
1 AATAATAAAATAATATTTTATTAATATAA-A
1300016 AATAATAAAATAA-ATTTT
1 AATAATAAAATAATATTTT
1300034 TAAATCAAAT
Statistics
Matches: 58, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
27 5 0.09
28 3 0.05
29 12 0.21
30 27 0.47
31 11 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AATAATAAAATAATATTTTATTAATATAAA
Found at i:1300035 original size:31 final size:30
Alignment explanation
Indices: 1299975--1300035 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
1299965 TATATAAATT
** *
1299975 TTAATATAAAAATAATATTTTAATATTTTA
1 TTAATATAAAAATAATAAATAAATATTTTA
1300005 TTAATATAATAAATAATAAAATAAAT-TTTTA
1 TTAATATAA-AAATAAT-AAATAAATATTTTA
1300036 AATCAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 9 0.35
31 12 0.46
32 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TTAATATAAAAATAATAAATAAATATTTTA
Found at i:1301567 original size:17 final size:17
Alignment explanation
Indices: 1301515--1301602 Score: 78
Period size: 16 Copynumber: 5.2 Consensus size: 17
1301505 TTGGCGATAA
1301515 ATTTTA-TA-ATTTATAT
1 ATTTTATTATATTT-TAT
1301531 ATTTATATTATATTTATAT
1 ATTT-TATTATATTT-TAT
1301550 ATTTTATTATATTTTAT
1 ATTTTATTATATTTTAT
*
1301567 A-TTTATATAAATTTTA-
1 ATTTTAT-TATATTTTAT
*
1301583 A-TTTATTAATAATTTAT
1 ATTTTATT-ATATTTTAT
1301600 ATT
1 ATT
1301603 ACATAAACTT
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
15 1 0.02
16 21 0.34
17 15 0.24
18 13 0.21
19 12 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTATTATATTTTAT
Found at i:1301609 original size:32 final size:32
Alignment explanation
Indices: 1301552--1301615 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1301542 ATTTATATAT
* * *
1301552 TTTATTATATTTTATATTTATATAAATTTTAA
1 TTTATTATAATTTATATTTACATAAACTTTAA
1301584 TTTATTAATAATTTATA-TTACATAAACTTTAA
1 TTTATT-ATAATTTATATTTACATAAACTTTAA
1301616 AAAATCTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 19 0.68
33 9 0.32
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (32 bp):
TTTATTATAATTTATATTTACATAAACTTTAA
Found at i:1301656 original size:17 final size:18
Alignment explanation
Indices: 1301636--1301701 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 18
1301626 CATATTATAT
1301636 TTATATTAT-TTTTAATG
1 TTATATTATATTTTAATG
1301653 TTATATTATATTTTAA--
1 TTATATTATATTTTAATG
* * *
1301669 TTATTTTTTATTTTATATAA
1 TTATATTATATTTTA-AT-G
1301689 TTATATTATATTT
1 TTATATTATATTT
1301702 AATATTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 13 0.32
17 10 0.25
18 6 0.15
20 11 0.28
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTATATTATATTTTAATG
Found at i:1301660 original size:28 final size:27
Alignment explanation
Indices: 1301627--1301717 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 27
1301617 AAATCTATTC
1301627 ATATTATATTTATATTATTTTTAATGTT
1 ATATTATATTTATATTATTTTTAAT-TT
*
1301655 ATATTATATTT-TAATTATTTTTTATTT
1 ATATTATATTTAT-ATTATTTTTAATTT
* * *
1301682 -TA-TATAATTATATTATATTTAATAT
1 ATATTATATTTATATTATTTTTAATTT
*
1301707 -TATTAAATTTA
1 ATATTATATTTA
1301718 GTTAGCTATA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
25 19 0.36
26 9 0.17
27 3 0.06
28 22 0.42
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (27 bp):
ATATTATATTTATATTATTTTTAATTT
Found at i:1301691 original size:20 final size:20
Alignment explanation
Indices: 1301666--1301711 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1301656 TATTATATTT
* * *
1301666 TAATTATTTTTTATTTTATA
1 TAATTATATTATATTTAATA
1301686 TAATTATATTATATTTAATA
1 TAATTATATTATATTTAATA
*
1301706 TTATTA
1 TAATTA
1301712 AATTTAGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TAATTATATTATATTTAATA
Found at i:1301893 original size:2 final size:2
Alignment explanation
Indices: 1301888--1301919 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1301878 CCATGAAGAA
*
1301888 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1301920 CTAAATTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1303544 original size:2 final size:2
Alignment explanation
Indices: 1303537--1303568 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1303527 TTTAATGGGT
1303537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1303569 AAGAGGAGTG
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):
TA
Found at i:1304817 original size:19 final size:18
Alignment explanation
Indices: 1304790--1304841 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
1304780 AGAAAAAATA
1304790 ATATAATTTTTTTAATTT
1 ATATAATTTTTTTAATTT
* *
1304808 GATTTAATTTTATTAATTT
1 -ATATAATTTTTTTAATTT
1304827 ATATAATTATTTTTA
1 ATATAATT-TTTTTA
1304842 TAAAAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATATAATTTTTTTAATTT
Found at i:1305191 original size:2 final size:2
Alignment explanation
Indices: 1305184--1305214 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1305174 TCTTGTCTTT
1305184 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 T
1305215 TTCATAAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1306386 original size:16 final size:17
Alignment explanation
Indices: 1306367--1306398 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1306357 GGCATGGCAG
1306367 ACAAAGTAATG-AAGTT
1 ACAAAGTAATGTAAGTT
1306383 ACAAAGTAATGTAAGT
1 ACAAAGTAATGTAAGT
1306399 CATGGATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (17 bp):
ACAAAGTAATGTAAGTT
Found at i:1307022 original size:50 final size:50
Alignment explanation
Indices: 1306968--1307119 Score: 173
Period size: 50 Copynumber: 3.0 Consensus size: 50
1306958 GCTTAGAGTT
* * *
1306968 AACAATTATGATCACCTTTCTCTATTATCAAAAGTTGGTAAAGAATAGTC
1 AACAATTATGATCACCTCTCTCAATTGTCAAAAGTTGGTAAAGAATAGTC
* *
1307018 AACAATTAT-AGTCACATCTCCCAATTGTCAAAAGTTGGTGAAA-AATAGTC
1 AACAATTATGA-TCACCTCTCTCAATTGTCAAAAGTTGGT-AAAGAATAGTC
* * * * * *
1307068 AACAATTACGATCACCTCTATCGATTGTCCAAGGTTAGTAAAGAATAGTC
1 AACAATTATGATCACCTCTCTCAATTGTCAAAAGTTGGTAAAGAATAGTC
1307118 AA
1 AA
1307120 ATCATTTTAC
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
49 4 0.05
50 77 0.91
51 4 0.05
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (50 bp):
AACAATTATGATCACCTCTCTCAATTGTCAAAAGTTGGTAAAGAATAGTC
Found at i:1311510 original size:50 final size:50
Alignment explanation
Indices: 1311451--1311686 Score: 328
Period size: 50 Copynumber: 4.7 Consensus size: 50
1311441 AGATGCTTAG
* * * *
1311451 AGTCAACAATTACGGTCACCTTTCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
**
1311501 AGTCAACAATTACGATCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
* * * * * *
1311551 AATCAACAATTACAGCCACCACTCTCGATTATTAAAAGTTAGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
* *
1311601 TGTCAACAATTACGGCCACCTCTTTCGATTGTCAAAGGTTAGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
* *
1311651 TGTCAACAATTACGACCACCTCTCTCGATTGTCAAA
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAA
1311687 AATTGATGAA
Statistics
Matches: 164, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 164 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (50 bp):
AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
Found at i:1313449 original size:21 final size:23
Alignment explanation
Indices: 1313411--1313452 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1313401 ATTTATAATT
*
1313411 AATATATTTTTATATAAATATAA
1 AATATAATTTTATATAAATATAA
1313434 AATATAATTTT-T-TAAATAT
1 AATATAATTTTATATAAATAT
1313453 GTAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATAATTTTATATAAATATAA
Found at i:1313895 original size:11 final size:11
Alignment explanation
Indices: 1313865--1313921 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
1313855 ATTATGAATC
* *
1313865 TTAAATTAAAA
1 TTAAATTATAT
1313876 TTAAATTATAT
1 TTAAATTATAT
1313887 TTAAATTATAT
1 TTAAATTATAT
* *
1313898 AT-AATATATTT
1 TTAAAT-TATAT
*
1313909 TTAAAATATAT
1 TTAAATTATAT
1313920 TT
1 TT
1313922 TTAAATTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
10 3 0.08
11 32 0.86
12 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAAATTATAT
Found at i:1313927 original size:12 final size:13
Alignment explanation
Indices: 1313900--1313926 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1313890 AATTATATAT
1313900 AATATATTTTTAA
1 AATATATTTTTAA
1313913 AATATATTTTTAA
1 AATATATTTTTAA
1313926 A
1 A
1313927 TTTTTTAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATATATTTTTAA
Found at i:1314021 original size:19 final size:20
Alignment explanation
Indices: 1313988--1314026 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1313978 TTAAAAAATA
*
1313988 AAATTTAAATATTAAATATT
1 AAATTAAAATATTAAATATT
*
1314008 AAATTAAAAT-TTAATTATT
1 AAATTAAAATATTAAATATT
1314027 TTTTAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATTAAAATATTAAATATT
Found at i:1314043 original size:15 final size:15
Alignment explanation
Indices: 1314019--1314049 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1314009 AATTAAAATT
1314019 TAATTATTTTTTAAA
1 TAATTATTTTTTAAA
*
1314034 TAATTTTTTTTTAAA
1 TAATTATTTTTTAAA
1314049 T
1 T
1314050 CGTAACTGCG
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TAATTATTTTTTAAA
Found at i:1317922 original size:91 final size:92
Alignment explanation
Indices: 1317767--1317950 Score: 352
Period size: 91 Copynumber: 2.0 Consensus size: 92
1317757 TGACTTCGGA
1317767 TCAGATTCCTGTGATCAAATATTTCAGGGTATAATTAGGGAACTGGAATCAAAAAGGGGG-AAAA
1 TCAGATTCCTGTGATCAAATATTTCAGGGTATAATTAGGGAACTGGAATCAAAAAGGGGGAAAAA
1317831 AAAGATAAGGCATTGGGGCATTCCGAG
66 AAAGATAAGGCATTGGGGCATTCCGAG
1317858 TCAGATTCCTGTGATCAAATATTTCAGGGTATAATTAGGGAACTGGAATCAAAAAGGGGGAAAAA
1 TCAGATTCCTGTGATCAAATATTTCAGGGTATAATTAGGGAACTGGAATCAAAAAGGGGG-AAAA
1317923 AAAAGATAAGGCATTGGGGCATTCCGAG
65 AAAAGATAAGGCATTGGGGCATTCCGAG
1317951 AATCGAACTC
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
91 60 0.66
93 31 0.34
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (92 bp):
TCAGATTCCTGTGATCAAATATTTCAGGGTATAATTAGGGAACTGGAATCAAAAAGGGGGAAAAA
AAAGATAAGGCATTGGGGCATTCCGAG
Found at i:1320864 original size:4 final size:5
Alignment explanation
Indices: 1320843--1320889 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
1320833 TTTAAGGCAG
*
1320843 ATTTT ATTTT ATTTT A-TTT ATTCTT ATTTT ATTATT AATATT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATT-TT ATTTT ATT-TT -ATTTT ATTTT
1320890 GTATAAGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
4 4 0.11
5 21 0.58
6 9 0.25
7 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:1321420 original size:2 final size:2
Alignment explanation
Indices: 1321413--1321473 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
1321403 AAATAACGCT
*
1321413 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1321455 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1321474 GCACGCACAT
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):
TA
Found at i:1323243 original size:18 final size:18
Alignment explanation
Indices: 1323190--1323244 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
1323180 AGTACAACTC
*
1323190 AATTTTCTTGGGAAAAAT
1 AATTTTCTTGGGAAAAAA
* ** *
1323208 AATTGTAAT--GAAAGAA
1 AATTTTCTTGGGAAAAAA
1323224 AATTTTCTTGGGAAAAAA
1 AATTTTCTTGGGAAAAAA
1323242 AAT
1 AAT
1323245 GAAAACTAAG
Statistics
Matches: 26, Mismatches: 9, Indels: 4
0.67 0.23 0.10
Matches are distributed among these distances:
16 11 0.42
18 15 0.58
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (18 bp):
AATTTTCTTGGGAAAAAA
Found at i:1323461 original size:59 final size:59
Alignment explanation
Indices: 1323398--1323527 Score: 152
Period size: 59 Copynumber: 2.2 Consensus size: 59
1323388 TTAAATAGTT
* *
1323398 TAAAATCAGTTCAGCACCATTTAGTACTATTTATAGAATCGGATAATATTTGAATGAAC
1 TAAAATCAGTTCAGCACCATTTAGTACTATATACAGAATCGGATAATATTTGAATGAAC
* * ** * * * * * *
1323457 TAAAATTAGTTCAGTACGGTTTGGTATTATATACAGAATTGGATGATGTTTGAATGATC
1 TAAAATCAGTTCAGCACCATTTAGTACTATATACAGAATCGGATAATATTTGAATGAAC
1323516 TAAAATCAGTTC
1 TAAAATCAGTTC
1323528 GGAAAAAATC
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (59 bp):
TAAAATCAGTTCAGCACCATTTAGTACTATATACAGAATCGGATAATATTTGAATGAAC
Found at i:1325155 original size:1 final size:1
Alignment explanation
Indices: 1325144--1325182 Score: 60
Period size: 1 Copynumber: 39.0 Consensus size: 1
1325134 AAATCCTTTC
* *
1325144 TTTTTTCTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1325183 GCAGCTTGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:1325162 original size:13 final size:13
Alignment explanation
Indices: 1325144--1325182 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1325134 AAATCCTTTC
1325144 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
1325157 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
1325170 TTTTTT-TTTTTT
1 TTTTTTCTTTTTT
1325182 T
1 T
1325183 GCAGCTTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.27
13 19 0.73
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:1325182 original size:20 final size:20
Alignment explanation
Indices: 1325140--1325181 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
1325130 CATGAAATCC
1325140 TTTCTTTTTTCTTTTTTTTT
1 TTTCTTTTTTCTTTTTTTTT
1325160 TTTCTTTTTT-TTTTTTTTT
1 TTTCTTTTTTCTTTTTTTTT
1325179 TTT
1 TTT
1325182 TGCAGCTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (20 bp):
TTTCTTTTTTCTTTTTTTTT
Found at i:1332075 original size:3 final size:3
Alignment explanation
Indices: 1332067--1332099 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1332057 ATAAAGTTAA
1332067 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1332100 TCTCCAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1332902 original size:2 final size:2
Alignment explanation
Indices: 1332895--1332924 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1332885 ATCAGAGTTC
1332895 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
1332925 GCTCTTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1335220 original size:6 final size:6
Alignment explanation
Indices: 1335202--1335245 Score: 51
Period size: 5 Copynumber: 8.0 Consensus size: 6
1335192 TATATAATCG
*
1335202 ATATTC ATA-TT ATATTT ATA-TT AT-TTT ATATTT ATATTT -TATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
1335246 TAAAAAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
5 17 0.50
6 17 0.50
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (6 bp):
ATATTT
Found at i:1335245 original size:11 final size:11
Alignment explanation
Indices: 1335202--1335244 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
1335192 TATATAATCG
*
1335202 ATATTCATATT
1 ATATTTATATT
1335213 ATATTTATATT
1 ATATTTATATT
1335224 AT-TTTATATTT
1 ATATTTATA-TT
1335235 ATATTT-TATT
1 ATATTTATATT
1335245 TTAAAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 8 0.28
11 18 0.62
12 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
ATATTTATATT
Found at i:1336311 original size:41 final size:41
Alignment explanation
Indices: 1336231--1336311 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
1336221 ATTTTAAAAA
*
1336231 AAACCCACGTTTTTTACGTACATTTATGCTTCATTTAAATG
1 AAACCCACGTTTTTTACATACATTTATGCTTCATTTAAATG
* *
1336272 AAACCCACTTTTTTTACATACGTTTATG-TTCCATTTAAAT
1 AAACCCACGTTTTTTACATACATTTATGCTT-CATTTAAAT
1336312 ACGTGATGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.06
41 34 0.94
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (41 bp):
AAACCCACGTTTTTTACATACATTTATGCTTCATTTAAATG
Found at i:1336598 original size:16 final size:17
Alignment explanation
Indices: 1336577--1336612 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1336567 AATGTAATAA
*
1336577 TTATATTTA-AAATATT
1 TTATATTTATAAAAATT
1336593 TTATATTTATAAAAATT
1 TTATATTTATAAAAATT
1336610 TTA
1 TTA
1336613 ATACAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTATAAAAATT
Found at i:1337231 original size:15 final size:15
Alignment explanation
Indices: 1337211--1337260 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1337201 GGAGCGTAAG
*
1337211 GAGGAGGGTATCCCT
1 GAGGAGGATATCCCT
* *
1337226 GAGGAGGATATGCTT
1 GAGGAGGATATCCCT
* *
1337241 GAGGAGGATAACTCT
1 GAGGAGGATATCCCT
1337256 GAGGA
1 GAGGA
1337261 TATCCTTGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.28, C:0.12, G:0.40, T:0.20
Consensus pattern (15 bp):
GAGGAGGATATCCCT
Found at i:1337276 original size:15 final size:15
Alignment explanation
Indices: 1337258--1337292 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1337248 ATAACTCTGA
**
1337258 GGATATCCTTGTGGT
1 GGATATCCCGGTGGT
1337273 GGATATCCCGGTGGT
1 GGATATCCCGGTGGT
1337288 GGATA
1 GGATA
1337293 ACCATCCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.37, T:0.31
Consensus pattern (15 bp):
GGATATCCCGGTGGT
Found at i:1337628 original size:2 final size:2
Alignment explanation
Indices: 1337621--1337653 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1337611 TTGGAAATTT
*
1337621 TA TA TA TA TA TA AA TA -A 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
1337654 GTGGAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1339620 original size:22 final size:21
Alignment explanation
Indices: 1339595--1339636 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1339585 TTATTAAAAA
1339595 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1339615 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1339636 A
1 A
1339637 AAAAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1339754 original size:190 final size:190
Alignment explanation
Indices: 1339539--1339919 Score: 762
Period size: 190 Copynumber: 2.0 Consensus size: 190
1339529 AAATTTAATT
1339539 AAGTTTAATTTATTCATTTAAATTTAAATTTAAATTATTATTTATTTTATTAAAAAATATTTTTA
1 AAGTTTAATTTATTCATTTAAATTTAAATTTAAATTATTATTTATTTTATTAAAAAATATTTTTA
1339604 TATTAATATTTATATATTTTATAATTAAATTTAAAAAATATATTATTTTAATATAAAACACTATG
66 TATTAATATTTATATATTTTATAATTAAATTTAAAAAATATATTATTTTAATATAAAACACTATG
1339669 TTGAGCCAATTCGAAATAAGAAAACGCAGGCTCCACCCATAAACAATCTACTGCACGCTA
131 TTGAGCCAATTCGAAATAAGAAAACGCAGGCTCCACCCATAAACAATCTACTGCACGCTA
1339729 AAGTTTAATTTATTCATTTAAATTTAAATTTAAATTATTATTTATTTTATTAAAAAATATTTTTA
1 AAGTTTAATTTATTCATTTAAATTTAAATTTAAATTATTATTTATTTTATTAAAAAATATTTTTA
1339794 TATTAATATTTATATATTTTATAATTAAATTTAAAAAATATATTATTTTAATATAAAACACTATG
66 TATTAATATTTATATATTTTATAATTAAATTTAAAAAATATATTATTTTAATATAAAACACTATG
1339859 TTGAGCCAATTCGAAATAAGAAAACGCAGGCTCCACCCATAAACAATCTACTGCACGCTA
131 TTGAGCCAATTCGAAATAAGAAAACGCAGGCTCCACCCATAAACAATCTACTGCACGCTA
1339919 A
1 A
1339920 CCATTTCAAC
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 191 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (190 bp):
AAGTTTAATTTATTCATTTAAATTTAAATTTAAATTATTATTTATTTTATTAAAAAATATTTTTA
TATTAATATTTATATATTTTATAATTAAATTTAAAAAATATATTATTTTAATATAAAACACTATG
TTGAGCCAATTCGAAATAAGAAAACGCAGGCTCCACCCATAAACAATCTACTGCACGCTA
Found at i:1339810 original size:22 final size:21
Alignment explanation
Indices: 1339785--1339826 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1339775 TTATTAAAAA
1339785 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1339805 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1339826 A
1 A
1339827 AAAAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1359794 original size:20 final size:20
Alignment explanation
Indices: 1359757--1359796 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1359747 GTTCAGAAAA
* *
1359757 ATTAATTAAAATTTTTTAAT
1 ATTAATTAAAAATATTTAAT
1359777 ATTAATTAAAAATATTTAAT
1 ATTAATTAAAAATATTTAAT
1359797 TAATTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTAATTAAAAATATTTAAT
Found at i:1361029 original size:20 final size:21
Alignment explanation
Indices: 1361002--1361056 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1360992 ATTTTTACTT
1361002 ATAA-ATT-AAATAAATTATA
1 ATAATATTAAAATAAATTATA
* *
1361021 TTAATATTAAAATAATTTATA
1 ATAATATTAAAATAAATTATA
1361042 ATAATAATTTAAAAT
1 ATAAT-A-TTAAAAT
1361057 TTTAGTGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 3 0.10
21 15 0.52
22 1 0.03
23 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAATATTAAAATAAATTATA
Found at i:1361035 original size:21 final size:23
Alignment explanation
Indices: 1361009--1361056 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
1360999 CTTATAAATT
*
1361009 AAATAAATTATATTAAT-A-TTA
1 AAATAAATTATAATAATAATTTA
*
1361030 AAATAATTTATAATAATAATTTA
1 AAATAAATTATAATAATAATTTA
1361053 AAAT
1 AAAT
1361057 TTTAGTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
22 1 0.04
23 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATAAATTATAATAATAATTTA
Found at i:1361889 original size:25 final size:25
Alignment explanation
Indices: 1361860--1361907 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1361850 TGATGATTGT
1361860 TTAATAATTT-TAAAATTTATTATTA
1 TTAAT-ATTTATAAAATTTATTATTA
* *
1361885 TTAATATTTATTATATTTATTAT
1 TTAATATTTATAAAATTTATTAT
1361908 AATAATAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTAATATTTATAAAATTTATTATTA
Found at i:1369595 original size:21 final size:19
Alignment explanation
Indices: 1369558--1369597 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
1369548 ATGTACTTAT
*
1369558 ATTTAATATTTATTTTAAA
1 ATTTAATATTTAATTTAAA
1369577 ATTTAAATAATTTAATTTAAA
1 ATTT-AAT-ATTTAATTTAAA
1369598 TAATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 3 0.17
21 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTAATATTTAATTTAAA
Found at i:1369609 original size:17 final size:14
Alignment explanation
Indices: 1369576--1369603 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1369566 TTTATTTTAA
1369576 AATTTAAATAATTT
1 AATTTAAATAATTT
1369590 AATTTAAATAATTT
1 AATTTAAATAATTT
1369604 TTTAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAAATAATTT
Found at i:1372045 original size:2 final size:2
Alignment explanation
Indices: 1372038--1372074 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1372028 TTATTCTTTT
1372038 TA 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 TA T
1372075 TATCGATTTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1372415 original size:28 final size:30
Alignment explanation
Indices: 1372370--1372431 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
1372360 TTTTTTTATT
*
1372370 TATTATAATTTAAAAATATAAAAATTAAAA
1 TATTATAATTTAAAAATACAAAAATTAAAA
* **
1372400 TATTA-AA-TTAATAATACCGAAATTAAAA
1 TATTATAATTTAAAAATACAAAAATTAAAA
1372428 TATT
1 TATT
1372432 TTATTCACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 21 0.75
29 2 0.07
30 5 0.18
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (30 bp):
TATTATAATTTAAAAATACAAAAATTAAAA
Found at i:1376688 original size:2 final size:2
Alignment explanation
Indices: 1376681--1376711 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1376671 TCGAAGACAA
*
1376681 AG AG AG AG AG AA 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 AG A
1376712 ACGTACTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1376862 original size:21 final size:20
Alignment explanation
Indices: 1376818--1376871 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
1376808 CTGGTTCCTG
* *
1376818 AAATACAAACAAAGAATAAC
1 AAATAAAAACAAAGAAAAAC
* *
1376838 AAATCAAAACACAAGAAAAAT
1 AAATAAAAACA-AAGAAAAAC
1376859 AAATAAAAA-AAAG
1 AAATAAAAACAAAG
1376872 TTCCCAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.11
20 10 0.36
21 15 0.54
ACGTcount: A:0.74, C:0.11, G:0.06, T:0.09
Consensus pattern (20 bp):
AAATAAAAACAAAGAAAAAC
Found at i:1376866 original size:20 final size:19
Alignment explanation
Indices: 1376818--1376871 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1376808 CTGGTTCCTG
*
1376818 AAATACAAACAAAGAATAAC
1 AAATA-AAACAAAGAAAAAC
*
1376838 AAATCAAAACACAAGAAAAAT
1 AAAT-AAAACA-AAGAAAAAC
*
1376859 AAATAAAAAAAAG
1 AAATAAAACAAAG
1376872 TTCCCAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.10
20 14 0.48
21 12 0.41
ACGTcount: A:0.74, C:0.11, G:0.06, T:0.09
Consensus pattern (19 bp):
AAATAAAACAAAGAAAAAC
Found at i:1377297 original size:24 final size:23
Alignment explanation
Indices: 1377264--1377330 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
1377254 TATATAAAAA
1377264 ATAA-TTTAATAATTAAATTAAT
1 ATAATTTTAATAATTAAATTAAT
* * *
1377286 ATAACTTTTAATTATT-ATTTTA-
1 ATAA-TTTTAATAATTAAATTAAT
*
1377308 ATAATTTTATTAATTAAATTAAT
1 ATAATTTTAATAATTAAATTAAT
1377331 GCAACCATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
21 9 0.26
22 12 0.35
23 4 0.12
24 9 0.26
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
ATAATTTTAATAATTAAATTAAT
Found at i:1377821 original size:21 final size:20
Alignment explanation
Indices: 1377797--1377860 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 20
1377787 TATTTTTATT
1377797 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATA-A
*
1377818 TAAATATTTA-TATAAAATAA
1 TAAAT-TTAATTATAAAATAA
* * *
1377838 T-ATTTTAATAATATAATAA
1 TAAATTTAATTATAAAATAA
1377857 TAAA
1 TAAA
1377861 ATAATTTTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 3 0.09
19 11 0.32
20 3 0.09
21 14 0.41
22 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATTTAATTATAAAATAA
Found at i:1389938 original size:33 final size:33
Alignment explanation
Indices: 1389899--1389961 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1389889 TCATGCAAAC
1389899 AAGATATAA-ATACATAAATATT-TTAAAAATTAT
1 AAGATATAATATA-ATAAA-ATTATTAAAAATTAT
*
1389932 AAGATATAATATATTAAAATTATTAAAAAT
1 AAGATATAATATAATAAAATTATTAAAAAT
1389962 AAATAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 3 0.11
33 21 0.78
34 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.37
Consensus pattern (33 bp):
AAGATATAATATAATAAAATTATTAAAAATTAT
Found at i:1389966 original size:24 final size:23
Alignment explanation
Indices: 1389912--1389971 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
1389902 ATATAAATAC
* *
1389912 ATAAATATTTTAAAAATTATAAG
1 ATAAATATATTAAAAATTATAAA
1389935 ATATAATATATT-AAAATTATTAAAA
1 ATA-AATATATTAAAAATTA-T-AAA
1389960 ATAAATAATATT
1 ATAAAT-ATATT
1389972 TTAAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 10 0.32
24 11 0.35
25 10 0.32
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
ATAAATATATTAAAAATTATAAA
Found at i:1389987 original size:24 final size:23
Alignment explanation
Indices: 1389955--1390014 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 23
1389945 TTAAAATTAT
* *
1389955 TAAAA-ATAAATAATATTTTAAA
1 TAAAATATAAATAAAATTTAAAA
* *
1389977 TATAATTATAATAAAAAATTTAAAA
1 TA-AAATATAA-ATAAAATTTAAAA
1390002 TAAAATATAAATA
1 TAAAATATAAATA
1390015 TCGGAATATG
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
22 2 0.07
23 4 0.14
24 11 0.38
25 12 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAAATATAAATAAAATTTAAAA
Found at i:1391515 original size:6 final size:6
Alignment explanation
Indices: 1391504--1391528 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1391494 AAGATTGAAA
1391504 GCTGAT GCTGAT GCTGAT GCTGAT G
1 GCTGAT GCTGAT GCTGAT GCTGAT G
1391529 ATGTTTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.36, T:0.32
Consensus pattern (6 bp):
GCTGAT
Found at i:1392346 original size:26 final size:29
Alignment explanation
Indices: 1392291--1392347 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
1392281 AGTAATTACG
* *
1392291 TAATTAAAAGTTTATATAATATAAATTAT
1 TAATTAAAAGTATATATAATATAAAATAT
1392320 TAATTAAAA-TATATA-AATA-AAAATAT
1 TAATTAAAAGTATATATAATATAAAATAT
1392346 TA
1 TA
1392348 TAATTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 8 0.31
27 4 0.15
28 5 0.19
29 9 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TAATTAAAAGTATATATAATATAAAATAT
Found at i:1392610 original size:10 final size:10
Alignment explanation
Indices: 1392587--1392677 Score: 50
Period size: 10 Copynumber: 8.8 Consensus size: 10
1392577 ATGAATTCAC
1392587 ATAT-TTTAT
1 ATATATTTAT
1392596 CATATATTTAT
1 -ATATATTTAT
1392607 ATATTATATTAT
1 ATA-TAT-TTAT
1392619 A-ATATTT-T
1 ATATATTTAT
*
1392627 AATAAATTTAAAAAT
1 -ATATATTT----AT
1392642 ATATATTTAT
1 ATATATTTAT
1392652 AT-TA-TTAT
1 ATATATTTAT
1392660 ATAT-TTTATT
1 ATATATTTA-T
1392670 ATATATTT
1 ATATATTT
1392678 TTTAAATAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 27
0.69 0.02 0.29
Matches are distributed among these distances:
8 7 0.11
9 9 0.14
10 24 0.37
11 12 0.18
12 5 0.08
14 7 0.11
15 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (10 bp):
ATATATTTAT
Found at i:1392662 original size:16 final size:14
Alignment explanation
Indices: 1392640--1392681 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1392630 AAATTTAAAA
1392640 ATATATATTTATATT
1 ATATATATTT-TATT
1392655 ATTATATATTTTATT
1 A-TATATATTTTATT
*
1392670 ATATATTTTTTA
1 ATATATATTTTA
1392682 AATAAATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 10 0.40
15 6 0.24
16 9 0.36
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATATATTTTATT
Found at i:1392677 original size:12 final size:12
Alignment explanation
Indices: 1392653--1392678 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1392643 TATATTTATA
1392653 TTATTATATATT
1 TTATTATATATT
1392665 TTATTATATATT
1 TTATTATATATT
1392677 TT
1 TT
1392679 TTAAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTATATATT
Found at i:1393633 original size:2 final size:2
Alignment explanation
Indices: 1393626--1393651 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1393616 TCAATTGCTC
1393626 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
1393652 TGAATTCAAC
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:1394115 original size:21 final size:20
Alignment explanation
Indices: 1394091--1394158 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
1394081 AAATTAATAA
1394091 ATTTTTAAAAACTATCTATTT
1 ATTTTTAAAAACTAT-TATTT
*
1394112 ATTTTT-AAAACTATTTGTTT
1 ATTTTTAAAAACTA-TTATTT
***
1394132 ATTAAAAAAAACTATTATTT
1 ATTTTTAAAAACTATTATTT
*
1394152 TTTTTTA
1 ATTTTTA
1394159 CCAACATGAT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
20 22 0.61
21 14 0.39
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.54
Consensus pattern (20 bp):
ATTTTTAAAAACTATTATTT
Found at i:1394127 original size:16 final size:17
Alignment explanation
Indices: 1394106--1394138 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1394096 TAAAAACTAT
1394106 CTATTTATTT-TTAAAA
1 CTATTTATTTATTAAAA
*
1394122 CTATTTGTTTATTAAAA
1 CTATTTATTTATTAAAA
1394139 AAAACTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (17 bp):
CTATTTATTTATTAAAA
Found at i:1394335 original size:17 final size:19
Alignment explanation
Indices: 1394304--1394344 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
1394294 GGTAAAGTAT
*
1394304 AAAAATATATATATTTTAA
1 AAAAATATATATATTATAA
1394323 AAAAATA-AT-TATTATAA
1 AAAAATATATATATTATAA
1394340 AAAAA
1 AAAAA
1394345 AACTTTCGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 2 0.10
19 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATATATATATTATAA
Found at i:1395013 original size:2 final size:2
Alignment explanation
Indices: 1395008--1395044 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1394998 AAGTGTGTTT
1395008 TA 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 TA T
1395045 GTATTTGTAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1397068 original size:22 final size:22
Alignment explanation
Indices: 1397043--1397084 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1397033 ATTAAAATAT
1397043 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1397065 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1397085 AGTAAAAATA
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:1402650 original size:24 final size:24
Alignment explanation
Indices: 1402604--1402650 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1402594 TATTTAATTT
* *
1402604 TTTATTTAAAATAATTATTTTTTA
1 TTTATTCAAAATAATTATATTTTA
1402628 TTTATTCAAAA-AATTATCATTTT
1 TTTATTCAAAATAATTAT-ATTTT
1402651 TAAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTATTCAAAATAATTATATTTTA
Found at i:1403808 original size:15 final size:17
Alignment explanation
Indices: 1403788--1403834 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 17
1403778 AATTTAAAAA
1403788 ATTAAATATAT-TT-AT
1 ATTAAATATATATTCAT
1403803 ATTAAATATATATTCAT
1 ATTAAATATATATTCAT
*
1403820 ATCAAATATTATATT
1 ATTAAATA-TATATT
1403835 TGAATCCGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 11 0.39
16 2 0.07
17 9 0.32
18 6 0.21
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAAATATATATTCAT
Found at i:1403815 original size:17 final size:17
Alignment explanation
Indices: 1403793--1403835 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1403783 AAAAAATTAA
*
1403793 ATATATTTATATTAAAT
1 ATATATTTATATCAAAT
*
1403810 ATATATTCATATCAAAT
1 ATATATTTATATCAAAT
1403827 ATTATATTT
1 A-TATATTT
1403836 GAATCCGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATTTATATCAAAT
Found at i:1407037 original size:19 final size:19
Alignment explanation
Indices: 1406998--1407037 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1406988 ATATTTAATT
**
1406998 TTTAAAATTTTTTTATGTA
1 TTTAAAATTTTTTTAAATA
1407017 TTTAAAATTTTTTTAAATA
1 TTTAAAATTTTTTTAAATA
1407036 TT
1 TT
1407038 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTAAAATTTTTTTAAATA
Found at i:1408297 original size:22 final size:21
Alignment explanation
Indices: 1408257--1408307 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
1408247 TAATTTTTAT
1408257 TATAAATTTAATTATAAAATA
1 TATAAATTTAATTATAAAATA
1408278 TATAAATATTAA-TATAAAA-A
1 TATAAAT-TTAATTATAAAATA
1408298 TATAATATTT
1 TATAA-ATTT
1408308 TTTAAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.29
21 16 0.57
22 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAAATTTAATTATAAAATA
Found at i:1408417 original size:142 final size:142
Alignment explanation
Indices: 1408221--1408481 Score: 495
Period size: 142 Copynumber: 1.8 Consensus size: 142
1408211 AAATTTTATC
1408221 AATTTAATATATTATTTTAATAATAATAATTTTTATTATAAATTTAATTATAAAATATATAAATA
1 AATTTAATATATTATTTTAATAATAATAATTTTTATTATAAATTTAATTATAAAATATATAAATA
* *
1408286 TTAATATAAAAATATAATATTTTTTAAATAATACCATAAATTAAATCTTAACTTGAATTATCGAT
66 TTAATATAAAAATATAATATTTTTTAAATAATAACATAAATTAAATCCTAACTTGAATTATCGAT
1408351 AATTATCAATTT
131 AATTATCAATTT
*
1408363 AATTTAATTTATTATTTTAATAATAATAATTTTTATTATAAATTTAATTATAAAATATATAAATA
1 AATTTAATATATTATTTTAATAATAATAATTTTTATTATAAATTTAATTATAAAATATATAAATA
1408428 TTAATATAAAAATATAATATTTTTTAAATAATAACATAAATTAAATCCTAACTT
66 TTAATATAAAAATATAATATTTTTTAAATAATAACATAAATTAAATCCTAACTT
1408482 AACTTATGTT
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 116 1.00
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (142 bp):
AATTTAATATATTATTTTAATAATAATAATTTTTATTATAAATTTAATTATAAAATATATAAATA
TTAATATAAAAATATAATATTTTTTAAATAATAACATAAATTAAATCCTAACTTGAATTATCGAT
AATTATCAATTT
Found at i:1408439 original size:22 final size:21
Alignment explanation
Indices: 1408399--1408449 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
1408389 TAATTTTTAT
1408399 TATAAATTTAATTATAAAATA
1 TATAAATTTAATTATAAAATA
1408420 TATAAATATTAA-TATAAAA-A
1 TATAAAT-TTAATTATAAAATA
1408440 TATAATATTT
1 TATAA-ATTT
1408450 TTTAAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.29
21 16 0.57
22 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAAATTTAATTATAAAATA
Found at i:1412939 original size:16 final size:16
Alignment explanation
Indices: 1412893--1412944 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1412883 TGCGCATACA
*
1412893 TTAAGTTAAATTATAAT
1 TTAAATTAAATTA-AAT
* *
1412910 TTAAA-GAATTTTAAAT
1 TTAAATTAA-ATTAAAT
1412926 TTAAATTAAATTAAAT
1 TTAAATTAAATTAAAT
1412942 TTA
1 TTA
1412945 TTTATCTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
TTAAATTAAATTAAAT
Found at i:1413034 original size:21 final size:21
Alignment explanation
Indices: 1412996--1413035 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1412986 TTAATAAAAT
*
1412996 TATTTTATATTATTATTTATA
1 TATTTTATATTATAATTTATA
1413017 TATTTTATAATTA-AATTTA
1 TATTTTAT-ATTATAATTTA
1413036 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATATTATAATTTATA
Found at i:1413051 original size:49 final size:51
Alignment explanation
Indices: 1412973--1413093 Score: 128
Period size: 49 Copynumber: 2.4 Consensus size: 51
1412963 ATATTTATAA
* * *
1412973 TATAATAAAATATTTAAT-AAAATTATTTTATATT-A-TTAT-TTATATATTT
1 TATAATTAAAT-TTAAATAAAAAATATTTTATATTAATTTATATTAT-TATTT
*
1413022 TATAATTAAATTTAAATAAAAAATATTTTATTTTAATTTATAATTATTATTT
1 TATAATTAAATTTAAATAAAAAATATTTTATATTAATTTAT-ATTATTATTT
*
1413074 TAT-GTT-AATTTAAATAAAAA
1 TATAATTAAATTTAAATAAAAA
1413094 TAAAAAAAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
48 5 0.08
49 24 0.39
50 15 0.24
51 6 0.10
52 8 0.13
53 4 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (51 bp):
TATAATTAAATTTAAATAAAAAATATTTTATATTAATTTATATTATTATTT
Done.