Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 8 of 28
Found at i:1266056 original size:18 final size:18
Alignment explanation
Indices: 1266033--1266081 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1266023 AAAAATTTAA
1266033 TTAATTATTAATAAAATT
1 TTAATTATTAATAAAATT
*
1266051 TTAATT-TTAAATTAAATT
1 TTAATTATT-AATAAAATT
*
1266069 TT-ATTAATAATAA
1 TTAATTATTAATAA
1266082 TTATATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATTATTAATAAAATT
Found at i:1266637 original size:21 final size:22
Alignment explanation
Indices: 1266594--1266651 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
1266584 ATACATTATT
1266594 TAAAAAT-AA-AAT-AAAAACA
1 TAAAAATAAATAATAAAAAACA
*
1266613 TAAAACTTAAAT-ATAAAAAAC-
1 TAAAA-ATAAATAATAAAAAACA
1266634 TAAAAATAAATAATAAAA
1 TAAAAATAAATAATAAAA
1266652 CATTTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 5 0.16
20 6 0.19
21 15 0.47
22 6 0.19
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (22 bp):
TAAAAATAAATAATAAAAAACA
Found at i:1267326 original size:15 final size:16
Alignment explanation
Indices: 1267295--1267327 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1267285 CTATTAAAAA
1267295 AAGGATAAAAGATATG
1 AAGGATAAAAGATATG
*
1267311 AAGGCTAAAA-ATATG
1 AAGGATAAAAGATATG
1267326 AA
1 AA
1267328 AAAATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.58, C:0.03, G:0.21, T:0.18
Consensus pattern (16 bp):
AAGGATAAAAGATATG
Found at i:1267594 original size:10 final size:11
Alignment explanation
Indices: 1267571--1267608 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
1267561 GTTAATTATA
*
1267571 TTTTTAAAATAT
1 TTTTTAGAA-AT
1267583 TTTTTAG-AAT
1 TTTTTAGAAAT
1267593 TTTTTAGAAAT
1 TTTTTAGAAAT
1267604 TTTTT
1 TTTTT
1267609 TATTTTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 9 0.38
11 9 0.38
12 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (11 bp):
TTTTTAGAAAT
Found at i:1267668 original size:27 final size:25
Alignment explanation
Indices: 1267604--1267667 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
1267594 TTTTAGAAAT
1267604 TTTTTTATTTTTCTAATATTTTTAC
1 TTTTTTATTTTTCTAATATTTTTAC
* *
1267629 TTTTTAAAATTTTCTTAATTATTTTTA-
1 TTTTT-TATTTTTC-TAA-TATTTTTAC
1267656 TTTTTTATTTTT
1 TTTTTTATTTTT
1267668 TATAATCTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 5 0.16
26 11 0.34
27 8 0.25
28 8 0.25
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTTTATTTTTCTAATATTTTTAC
Found at i:1277722 original size:2 final size:2
Alignment explanation
Indices: 1277715--1277742 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1277705 AGAAGAAATT
1277715 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
1277743 GCTGTAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1285674 original size:14 final size:14
Alignment explanation
Indices: 1285655--1285696 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
1285645 TTTGACAAAG
1285655 AAAGAAAGAAAATA
1 AAAGAAAGAAAATA
1285669 AAAGAAAGAGAAATA
1 AAAGAAAGA-AAATA
1285684 AAAGAAAAGAAAA
1 AAAG-AAAGAAAA
1285697 GGGAAGGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.35
15 12 0.46
16 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (14 bp):
AAAGAAAGAAAATA
Found at i:1285686 original size:20 final size:20
Alignment explanation
Indices: 1285657--1285695 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1285647 TGACAAAGAA
*
1285657 AGAAAGAAAATAAAAGAAAG
1 AGAAAGAAAAGAAAAGAAAG
*
1285677 AGAAATAAAAGAAAAGAAA
1 AGAAAGAAAAGAAAAGAAA
1285696 AGGGAAGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (20 bp):
AGAAAGAAAAGAAAAGAAAG
Found at i:1285713 original size:19 final size:16
Alignment explanation
Indices: 1285689--1285728 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 16
1285679 AAATAAAAGA
1285689 AAAGAAAAGGGAAGGGAAG
1 AAAGAAAA-GG-AGGG-AG
1285708 AAAGAAAAGGAGGGAG
1 AAAGAAAAGGAGGGAG
1285724 AAAGA
1 AAAGA
1285729 GAAATAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 4 0.19
18 2 0.10
19 8 0.38
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGGAGGGAG
Found at i:1286503 original size:3 final size:3
Alignment explanation
Indices: 1286497--1286546 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
1286487 CAACAACAAC
*
1286497 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1286545 AA
1 AA
1286547 AGAAGCATTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1286725 original size:2 final size:2
Alignment explanation
Indices: 1286720--1286744 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1286710 ATACACACAC
1286720 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1286745 AACATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1287066 original size:20 final size:20
Alignment explanation
Indices: 1287016--1287075 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
1287006 TTAAAAATTA
1287016 ATATAATATATATTAT-TAACAT
1 ATATAATA-AT-TTATATAA-AT
1287038 AT-TAA-AATTTATATAAAT
1 ATATAATAATTTATATAAAT
*
1287056 ATATAATAATTTAAATAAAT
1 ATATAATAATTTATATAAAT
1287076 TTTGATACGA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 8 0.24
19 8 0.24
20 13 0.38
21 3 0.09
22 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATAATAATTTATATAAAT
Found at i:1290068 original size:26 final size:25
Alignment explanation
Indices: 1290023--1290097 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 25
1290013 ATTTTAAATT
*
1290023 TTTATAAAAAA-ATTTATTTTTTTAA
1 TTTATAAAAAATATGT-TTTTTTTAA
*
1290048 TATT-TAAACAATATGTTTTTTTTAA
1 T-TTATAAAAAATATGTTTTTTTTAA
1290073 TTTAATAAAAAATATGTTTATTTTT
1 TTT-ATAAAAAATATGTTT-TTTTT
1290098 TAAAATTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
24 2 0.05
25 17 0.40
26 18 0.43
27 5 0.12
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (25 bp):
TTTATAAAAAATATGTTTTTTTTAA
Found at i:1290240 original size:17 final size:17
Alignment explanation
Indices: 1290210--1290243 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1290200 ATTATTATTA
1290210 TTAAGCTATAGTTTAAT
1 TTAAGCTATAGTTTAAT
1290227 TTAAG-TATATGTTTAAT
1 TTAAGCTATA-GTTTAAT
1290244 ACTTTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (17 bp):
TTAAGCTATAGTTTAAT
Found at i:1290368 original size:9 final size:9
Alignment explanation
Indices: 1290356--1290380 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1290346 TAAAAAAAGA
1290356 AAAAATAAT
1 AAAAATAAT
1290365 AAAAATAAT
1 AAAAATAAT
1290374 AAAAATA
1 AAAAATA
1290381 TATTTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATAAT
Found at i:1290730 original size:16 final size:15
Alignment explanation
Indices: 1290709--1290745 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
1290699 TTGAATGATG
*
1290709 ATTTAATTTAATTAT
1 ATTTAATTTAATAAT
1290724 AATTTAATTTAATAAT
1 -ATTTAATTTAATAAT
1290740 ATTTAA
1 ATTTAA
1290746 AGATAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTAATTTAATAAT
Found at i:1292226 original size:3 final size:3
Alignment explanation
Indices: 1292220--1292252 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1292210 CAAAAAAAAC
1292220 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1292253 TATTATTCGC
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):
ATA
Found at i:1295919 original size:97 final size:97
Alignment explanation
Indices: 1295753--1296043 Score: 573
Period size: 97 Copynumber: 3.0 Consensus size: 97
1295743 GCTGTATTAG
1295753 CTGAACCACCAAGATATATCTATTTTCTGACTGAAAATCATGTTCTTAATTTGTCCTTTAACCTG
1 CTGAACCACCAAGATATATCTATTTTCTGACTGAAAATCATGTTCTTAATTTGTCCTTTAACCTG
1295818 AGATATGCTTCTGGTGAGTTGCATGGCAGGAT
66 AGATATGCTTCTGGTGAGTTGCATGGCAGGAT
*
1295850 CTGAACCACCAAGATATATCTATTTTCTGACTGAAAATCAAGTTCTTAATTTGTCCTTTAACCTG
1 CTGAACCACCAAGATATATCTATTTTCTGACTGAAAATCATGTTCTTAATTTGTCCTTTAACCTG
1295915 AGATATGCTTCTGGTGAGTTGCATGGCAGGAT
66 AGATATGCTTCTGGTGAGTTGCATGGCAGGAT
1295947 CTGAACCACCAAGATATATCTATTTTCTGACTGAAAATCATGTTCTTAATTTGTCCTTTAACCTG
1 CTGAACCACCAAGATATATCTATTTTCTGACTGAAAATCATGTTCTTAATTTGTCCTTTAACCTG
1296012 AGATATGCTTCTGGTGAGTTGCATGGCAGGAT
66 AGATATGCTTCTGGTGAGTTGCATGGCAGGAT
1296044 AAGACGTGTA
Statistics
Matches: 192, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 192 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (97 bp):
CTGAACCACCAAGATATATCTATTTTCTGACTGAAAATCATGTTCTTAATTTGTCCTTTAACCTG
AGATATGCTTCTGGTGAGTTGCATGGCAGGAT
Found at i:1297588 original size:27 final size:23
Alignment explanation
Indices: 1297557--1297612 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 23
1297547 TTATTTTTAA
1297557 TTTAAAATGTATAAATATATTATTAT
1 TTTAAAAT-TAT-AATA-ATTATTAT
*
1297583 TTTTAAA-TATAATAATTATTAT
1 TTTAAAATTATAATAATTATTAT
1297605 TTTAAAAT
1 TTTAAAAT
1297613 AAAATTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 14 0.52
23 4 0.15
24 3 0.11
26 6 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTAAAATTATAATAATTATTAT
Found at i:1297601 original size:22 final size:20
Alignment explanation
Indices: 1297570--1297619 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 20
1297560 AAAATGTATA
1297570 AATATATTATTATTTTTAAATAT
1 AATA-ATTATTA-TTTTAAA-AT
1297593 AATAATTATTATTTTAAAAT
1 AATAATTATTATTTTAAAAT
1297613 AA-AATTA
1 AATAATTA
1297620 ATAAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.19
20 4 0.15
21 7 0.26
22 7 0.26
23 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATAATTATTATTTTAAAAT
Found at i:1298478 original size:26 final size:27
Alignment explanation
Indices: 1298409--1298467 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
1298399 TATTATTATT
*
1298409 ATTTAAATAATAAAAATATATTAAATTAA
1 ATTT-AATTATAAAAATATA-TAAATTAA
1298438 ATTTAATTATAAAAATATA-AATATTAA
1 ATTTAATTATAAAAATATATAA-ATTAA
1298465 ATT
1 ATT
1298468 ATTTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 8 0.29
28 14 0.50
29 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTTAATTATAAAAATATATAAATTAA
Found at i:1298478 original size:27 final size:28
Alignment explanation
Indices: 1298403--1298482 Score: 72
Period size: 32 Copynumber: 2.6 Consensus size: 28
1298393 TATTTATATT
* *
1298403 ATTATTATTTAAATAATAAAAATATATTAA
1 ATTATT-TTTAAAAAAT-ATAATATATTAA
1298433 ATTAAATTTAATTATAAAAATATAA-ATATTAA
1 ATT--ATTT--TTA-AAAAATATAATATATTAA
1298465 ATTATTTTTAAAAAATAT
1 ATTATTTTTAAAAAATAT
1298483 TTTAATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
27 8 0.19
28 3 0.07
30 7 0.16
31 1 0.02
32 13 0.30
33 6 0.14
34 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTATTTTTAAAAAATATAATATATTAA
Found at i:1299138 original size:19 final size:18
Alignment explanation
Indices: 1299111--1299150 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1299101 TTGGGTTTCC
* *
1299111 TATTGTATAATTTTGCTTG
1 TATTATATAATATTGC-TG
1299130 TATTATATAATATTGCTG
1 TATTATATAATATTGCTG
1299148 TAT
1 TAT
1299151 AATAAAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (18 bp):
TATTATATAATATTGCTG
Found at i:1299396 original size:18 final size:18
Alignment explanation
Indices: 1299373--1299410 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1299363 TAACAAATTC
1299373 TAACACTAGCTATGCATG
1 TAACACTAGCTATGCATG
*
1299391 TAACACTAGTTATGCATG
1 TAACACTAGCTATGCATG
1299409 TA
1 TA
1299411 GGTGATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (18 bp):
TAACACTAGCTATGCATG
Found at i:1301125 original size:19 final size:19
Alignment explanation
Indices: 1301101--1301214 Score: 61
Period size: 19 Copynumber: 5.8 Consensus size: 19
1301091 GAATAATCAA
1301101 AAAATTATAAAAAATATGT
1 AAAATTATAAAAAATATGT
*
1301120 AAAATT-TAAAAATTATAAGACAT
1 AAAATTATAAAAA--ATATG---T
** * *
1301143 ATAAAAAAT-AAAAATTTGG
1 A-AAATTATAAAAAATATGT
* *
1301162 AAAATTATAAAAAATTTAT
1 AAAATTATAAAAAATATGT
* * *
1301181 ATAATTATAAAAAATCTAT
1 AAAATTATAAAAAATATGT
*
1301200 ATAATTATAAAAAAT
1 AAAATTATAAAAAAT
1301215 TAAAAAATAA
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
18 11 0.15
19 47 0.63
20 4 0.05
22 3 0.04
23 2 0.03
24 7 0.09
25 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (19 bp):
AAAATTATAAAAAATATGT
Found at i:1301174 original size:9 final size:9
Alignment explanation
Indices: 1301051--1301348 Score: 107
Period size: 9 Copynumber: 33.2 Consensus size: 9
1301041 TAAAAATCCA
1301051 AAAAATTA-
1 AAAAATTAT
1301059 AAAAATTTATT
1 AAAAA-TTA-T
*
1301070 AAAAATTTT
1 AAAAATTAT
*
1301079 AAAAA-TAA
1 AAAAATTAT
*
1301087 AAATGAATAAT
1 AAA--AATTAT
1301098 CAAAAAATTAT
1 --AAAAATTAT
*
1301109 AAAAAATAT
1 AAAAATTAT
*
1301118 GTAAAATT-T
1 -AAAAATTAT
1301127 AAAAATTAT
1 AAAAATTAT
*
1301136 AAGACA-TAT
1 AA-AAATTAT
1301145 AAAAA--AT
1 AAAAATTAT
1301152 AAAAATT-T
1 AAAAATTAT
*
1301160 GGAAAATTAT
1 -AAAAATTAT
1301170 AAAAAATT-T
1 -AAAAATTAT
*
1301179 ATATAATTAT
1 A-AAAATTAT
1301189 AAAAAATCTAT
1 -AAAAAT-TAT
*
1301200 -ATAATTAT
1 AAAAATTAT
1301208 AAAAAATTA-
1 -AAAAATTAT
*
1301217 AAAAA-TAA
1 AAAAATTAT
**
1301225 AAATAAAAAT
1 AAA-AATTAT
1301235 AAAAATTCAT
1 AAAAATT-AT
**
1301245 AAATTTTA-
1 AAAAATTAT
1301253 AAAAATCTAT
1 AAAAAT-TAT
1301263 -AAAATTAT
1 AAAAATTAT
*
1301271 AAAAA-TGT
1 AAAAATTAT
1301279 -AAAA--AT
1 AAAAATTAT
1301285 AAAAATTCA-
1 AAAAATT-AT
1301294 AAAAATTAT
1 AAAAATTAT
1301303 AAAAATTAT
1 AAAAATTAT
*
1301312 AAATA-TAT
1 AAAAATTAT
*
1301320 -TAAATTCA-
1 AAAAATT-AT
*
1301328 AAACATTAT
1 AAAAATTAT
1301337 AAAAAATTAT
1 -AAAAATTAT
1301347 AA
1 AA
1301349 TTTTTTAATT
Statistics
Matches: 217, Mismatches: 35, Indels: 75
0.66 0.11 0.23
Matches are distributed among these distances:
6 1 0.00
7 19 0.09
8 45 0.21
9 85 0.39
10 49 0.23
11 15 0.07
13 3 0.01
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:1301213 original size:82 final size:80
Alignment explanation
Indices: 1301101--1301298 Score: 192
Period size: 82 Copynumber: 2.5 Consensus size: 80
1301091 GAATAATCAA
* * * * * *
1301101 AAAATTATAAAAAATATGTAAAATTTAAAAATTATAAGACATATA-AAAAATAAAAATTTGGA-A
1 AAAATTATAAAAAATATATAAAATTTAAAAATTAAAAAACAAAAATAAAAATAAAAA-TT-CATA
*
1301164 AATTATAAAAAATTTAT
64 AATTATAAAAAATCTAT
* * * *
1301181 ATAATTATAAAAAATCTATATAATTATAAAAAATTAAAAAATAAAAATAAAAATAAAAATTCATA
1 AAAATTATAAAAAATATATAAAATT-T-AAAAATTAAAAAACAAAAATAAAAATAAAAATTCATA
*
1301246 AATTTTAAAAAATCTAT
64 AATTATAAAAAATCTAT
*
1301263 AAAATTAT-AAAAATGTA-AAAA--TAAAAATTCAAAAAA
1 AAAATTATAAAAAATATATAAAATTTAAAAATT-AAAAAA
1301299 TTATAAAAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
76 7 0.07
77 7 0.07
80 24 0.24
81 10 0.10
82 39 0.40
83 11 0.11
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (80 bp):
AAAATTATAAAAAATATATAAAATTTAAAAATTAAAAAACAAAAATAAAAATAAAAATTCATAAA
TTATAAAAAATCTAT
Found at i:1301214 original size:63 final size:59
Alignment explanation
Indices: 1301100--1301305 Score: 158
Period size: 63 Copynumber: 3.4 Consensus size: 59
1301090 TGAATAATCA
* *
1301100 AAAAATTATAAAAAATATGTA-AAATTT-AAAAAT-TATAAGACATATAAAAAATAAAAATTT
1 AAAAATTATAAAAAAT-T-TATAAATTTAAAAAATCTATAA-A-TTATAAAAAATAAAAATAT
*
1301160 GGAAAATTATAAAAAATTTATATAATTATAAAAAATCTATATAATTATAAAAAATTAAAAA-AT
1 -AAAAATTATAAAAAATTTATA-AATT-TAAAAAATCTATA-AATTATAAAAAA-TAAAAATAT
* * * *
1301223 AAAAATAAAAATAAAAATTCATAAATTTTAAAAAATCTATAAAATTAT-AAAAATGTAAAA-AT
1 AAAAAT-TATA-AAAAATTTATAAA-TTTAAAAAATCTAT-AAATTATAAAAAAT-AAAAATAT
*
1301285 AAAAATT-CAAAAAA-TTATAAA
1 AAAAATTATAAAAAATTTATAAA
1301306 AATTATAAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 27
0.76 0.07 0.17
Matches are distributed among these distances:
58 6 0.05
59 7 0.06
60 3 0.02
61 20 0.16
62 23 0.19
63 38 0.31
64 24 0.20
65 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (59 bp):
AAAAATTATAAAAAATTTATAAATTTAAAAAATCTATAAATTATAAAAAATAAAAATAT
Found at i:1301224 original size:21 final size:18
Alignment explanation
Indices: 1301164--1301216 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 18
1301154 AAATTTGGAA
1301164 AATTATAAAAAATTTATAT
1 AATTATAAAAAA-TTATAT
1301183 AATTATAAAAAATCTATAT
1 AATTATAAAAAAT-TATAT
1301202 AATTATAAAAAATTA
1 AATTATAAAAAATTA
1301217 AAAAATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 3 0.09
19 30 0.91
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTATAAAAAATTATAT
Found at i:1301350 original size:25 final size:24
Alignment explanation
Indices: 1301303--1301350 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1301293 AAAAAATTAT
*
1301303 AAAAATTATAAATATATTAAATTC
1 AAAAATTATAAATAAATTAAATTC
1301327 AAAACATTATAAA-AAATTATAATT
1 AAAA-ATTATAAATAAATTA-AATT
1301351 TTTTAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAAATTATAAATAAATTAAATTC
Found at i:1301394 original size:29 final size:30
Alignment explanation
Indices: 1301351--1301408 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1301341 AATTATAATT
1301351 TTTTAATTTAATAT-ATTCTTATA-ATTTTA
1 TTTTAATTTAATATAATT-TTATATATTTTA
**
1301380 TTTTAATTTTTTATAATTTTATATATTTT
1 TTTTAATTTAATATAATTTTATATATTTT
1301409 TAATAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (30 bp):
TTTTAATTTAATATAATTTTATATATTTTA
Found at i:1301398 original size:10 final size:10
Alignment explanation
Indices: 1301369--1301417 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
1301359 TAATATATTC
1301369 TTATAATTTT
1 TTATAATTTT
*
1301379 ATTTTAATTTT
1 -TTATAATTTT
1301390 TTATAATTTT
1 TTATAATTTT
*
1301400 ATAT-ATTTT
1 TTATAATTTT
*
1301409 TAATAATTT
1 TTATAATTT
1301418 AAAAAAATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
9 7 0.22
10 16 0.50
11 9 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTATAATTTT
Found at i:1301495 original size:9 final size:9
Alignment explanation
Indices: 1301428--1301537 Score: 61
Period size: 9 Copynumber: 12.0 Consensus size: 9
1301418 AAAAAAATTC
1301428 TAATTTTTA
1 TAATTTTTA
1301437 T--TTTTTA
1 TAATTTTTA
1301444 -AATATTTTA
1 TAAT-TTTTA
*
1301453 T-AGTTTTA
1 TAATTTTTA
1301461 TGGAATTTTTA
1 T--AATTTTTA
*
1301472 TTTTATTTTT-
1 --TAATTTTTA
*
1301482 GAATTTTTA
1 TAATTTTTA
1301491 TAATTTAGTT-
1 TAATTT--TTA
* *
1301501 TTAGTTTTA
1 TAATTTTTA
1301510 TAGATTTTTA
1 TA-ATTTTTA
1301520 TAATTTTTA
1 TAATTTTTA
1301529 TAATTTTTA
1 TAATTTTTA
1301538 CCTTTTAATT
Statistics
Matches: 77, Mismatches: 10, Indels: 28
0.67 0.09 0.24
Matches are distributed among these distances:
7 6 0.08
8 15 0.19
9 29 0.38
10 12 0.16
11 14 0.18
13 1 0.01
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.65
Consensus pattern (9 bp):
TAATTTTTA
Found at i:1301502 original size:22 final size:22
Alignment explanation
Indices: 1301453--1301503 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 22
1301443 AAATATTTTA
1301453 TAGTTTTATGGAATTTTTATTT
1 TAGTTTTATGGAATTTTTATTT
1301475 TA-TTTT-T-GAATTTTTATAATT
1 TAGTTTTATGGAATTTTTAT--TT
1301496 TAGTTTTA
1 TAGTTTTA
1301504 GTTTTATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 10 0.40
20 1 0.04
21 8 0.32
22 6 0.24
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (22 bp):
TAGTTTTATGGAATTTTTATTT
Found at i:1301581 original size:33 final size:32
Alignment explanation
Indices: 1301513--1301596 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 32
1301503 AGTTTTATAG
*
1301513 ATTTTTATAATTTTTAT-AATTTTTACCTTTTA
1 ATTTTTATAATTTTT-TGAATTATTACCTTTTA
*
1301545 ATTTTTTATAATTTTTTGAATTATTA-TTTTTGA
1 A-TTTTTATAATTTTTTGAATTATTACCTTTT-A
* *
1301578 ATTTTTACATTTTTTTGAA
1 ATTTTTATAATTTTTTGAA
1301597 AAATTTACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 22 0.49
33 23 0.51
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (32 bp):
ATTTTTATAATTTTTTGAATTATTACCTTTTA
Found at i:1301935 original size:25 final size:25
Alignment explanation
Indices: 1301898--1301945 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1301888 TTATTATTTT
* * * *
1301898 AAGCTTTTTTAACCTAATTAAACTG
1 AAGCTTCTGTAACCCAACTAAACTG
1301923 AAGCTTCTGTAACCCAACTAAAC
1 AAGCTTCTGTAACCCAACTAAAC
1301946 CGGGTCTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (25 bp):
AAGCTTCTGTAACCCAACTAAACTG
Found at i:1302119 original size:17 final size:17
Alignment explanation
Indices: 1302099--1302131 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1302089 GAATATTTGA
1302099 TATTTCTTTTTA-TTTTC
1 TATTT-TTTTTAGTTTTC
1302116 TATTTTTTTTAGTTTT
1 TATTTTTTTTAGTTTT
1302132 AAGATCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (17 bp):
TATTTTTTTTAGTTTTC
Found at i:1306653 original size:60 final size:60
Alignment explanation
Indices: 1306544--1306671 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
1306534 ATCATTGTCA
* * * * * *
1306544 TAGTGACTTGGTGTCACTTAGTATCTCTTAGCGATACCATGCCTTGATGGCGAGCAGAGG
1 TAGTGACTTGGCGTCACTTAGCATCTCTTAGCGAGACAACGCCTCGATGGCGAGCAGAGG
* * * * * *
1306604 TAGTGATTTGGCGTCACTTAGCGTCTCTTAGTGAGACAACGCCTCGATGGCGAACAAAGA
1 TAGTGACTTGGCGTCACTTAGCATCTCTTAGCGAGACAACGCCTCGATGGCGAGCAGAGG
1306664 TAGTGACT
1 TAGTGACT
1306672 GGTGCCACTT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (60 bp):
TAGTGACTTGGCGTCACTTAGCATCTCTTAGCGAGACAACGCCTCGATGGCGAGCAGAGG
Found at i:1306746 original size:53 final size:54
Alignment explanation
Indices: 1306663--1306847 Score: 252
Period size: 53 Copynumber: 3.5 Consensus size: 54
1306653 GCGAACAAAG
* * * **
1306663 ATAGTGAC-TGGTGCCACTTAGTGAAGTAACACCTTGGTGGCGAAT-AAAGAGA
1 ATAGTGACTTGGTGTCACTTAGAGAAATAACACCTTGGTGGCGAATCAGGGAGA
* *
1306715 ATAGTGACTTTGTGTCACTTAGAGAAATAACACCTTGGTGGCG-ATCAGGGAAA
1 ATAGTGACTTGGTGTCACTTAGAGAAATAACACCTTGGTGGCGAATCAGGGAGA
* *
1306768 ATGGTGACTTGGTGTCACTTAGAGAAATAACGCCTTGGTGGC-AATCAGGGAGA
1 ATAGTGACTTGGTGTCACTTAGAGAAATAACACCTTGGTGGCGAATCAGGGAGA
*
1306821 ACAGTGACTTGGTGTCACTTAGAGAAA
1 ATAGTGACTTGGTGTCACTTAGAGAAA
1306848 ATAATGCCTC
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
52 10 0.09
53 107 0.91
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (54 bp):
ATAGTGACTTGGTGTCACTTAGAGAAATAACACCTTGGTGGCGAATCAGGGAGA
Found at i:1306794 original size:27 final size:27
Alignment explanation
Indices: 1306714--1306850 Score: 84
Period size: 27 Copynumber: 5.1 Consensus size: 27
1306704 GAATAAAGAG
*
1306714 AATAGTGACTTTGTGTCACTTAGAG-A
1 AATAGTGACTTGGTGTCACTTAGAGAA
** * * *
1306740 AATA-ACACCTTGGTGGCGA-TCAGGGAA
1 AATAGTGA-CTTGGTGTC-ACTTAGAGAA
*
1306767 AATGGTGACTTGGTGTCACTTAGAG-A
1 AATAGTGACTTGGTGTCACTTAGAGAA
** * * * * * *
1306793 AATAACGCCTTGGTGGCAATCAGGGAG
1 AATAGTGACTTGGTGTCACTTAGAGAA
*
1306820 AACAGTGACTTGGTGTCACTTAGAGAA
1 AATAGTGACTTGGTGTCACTTAGAGAA
1306847 AATA
1 AATA
1306851 ATGCCTCGAT
Statistics
Matches: 74, Mismatches: 31, Indels: 11
0.64 0.27 0.09
Matches are distributed among these distances:
25 1 0.01
26 34 0.46
27 38 0.51
28 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.26
Consensus pattern (27 bp):
AATAGTGACTTGGTGTCACTTAGAGAA
Found at i:1306804 original size:26 final size:26
Alignment explanation
Indices: 1306726--1306807 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
1306716 TAGTGACTTT
*
1306726 GTGTCACTTAGAGAAATAACACCTTG
1 GTGTCACTTAGAGAAATAACGCCTTG
* * * *** *
1306752 GTGGCGA-TCAGGGAAAATGGTGACTTG
1 GTGTC-ACTTAGAG-AAATAACGCCTTG
1306779 GTGTCACTTAGAGAAATAACGCCTTG
1 GTGTCACTTAGAGAAATAACGCCTTG
1306805 GTG
1 GTG
1306808 GCAATCAGGG
Statistics
Matches: 38, Mismatches: 15, Indels: 6
0.64 0.25 0.10
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (26 bp):
GTGTCACTTAGAGAAATAACGCCTTG
Found at i:1307921 original size:150 final size:150
Alignment explanation
Indices: 1307650--1307937 Score: 452
Period size: 150 Copynumber: 1.9 Consensus size: 150
1307640 TCCACAAGAA
* * *
1307650 CTTTCCATGGACCGAGTTGTGATGATGGCGACTGGTTCTGCTTCTACACATTTGGTGAAGTAGTC
1 CTTTCCATGGACCGAGCTGTGATGATGGCGACTGATTCTGCTTCTACACATTTAGTGAAGTAGTC
* * *
1307715 GCAGACAACAATGAGGAACTTCCTCTGTTCGGTAGCCAGCGAAAAAGGTTCGAGTATATCTATTC
66 ACAGACAACAATGAGGAACTTCATCTGTTCGGTAGCCAGCGAAAAAGGTCCGAGTATATCTATTC
1307780 CCCATACATAAAAAGGCTAG
131 CCCATACATAAAAAGGCTAG
* *
1307800 CTTTCCATGGACCGAGCTGTGATGGTGGCGATTGATTCTGCTTCTAC-CTATTTAGTGAAGTAGT
1 CTTTCCATGGACCGAGCTGTGATGATGGCGACTGATTCTGCTTCTACAC-ATTTAGTGAAGTAGT
* * * *
1307864 CACGGGCAACAATGAGGAACTTCATCTGTTCGGTAGCCAGTGAAAAAGGTCCGAGTATGTCTATT
65 CACAGACAACAATGAGGAACTTCATCTGTTCGGTAGCCAGCGAAAAAGGTCCGAGTATATCTATT
1307929 CCCCATACA
130 CCCCATACA
1307938 CAGAAAACTA
Statistics
Matches: 125, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
149 1 0.01
150 124 0.99
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (150 bp):
CTTTCCATGGACCGAGCTGTGATGATGGCGACTGATTCTGCTTCTACACATTTAGTGAAGTAGTC
ACAGACAACAATGAGGAACTTCATCTGTTCGGTAGCCAGCGAAAAAGGTCCGAGTATATCTATTC
CCCATACATAAAAAGGCTAG
Found at i:1312441 original size:52 final size:52
Alignment explanation
Indices: 1312293--1312421 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1312283 CGAAATATGA
* *
1312293 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATTGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
**
1312345 AAATTTGCCTATATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1312397 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1312422 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1312448 original size:13 final size:13
Alignment explanation
Indices: 1312430--1312454 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1312420 CAAAGATCAG
1312430 TGTATCGATACAA
1 TGTATCGATACAA
1312443 TGTATCGATACA
1 TGTATCGATACA
1312455 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1312531 original size:19 final size:19
Alignment explanation
Indices: 1312507--1312571 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
1312497 AGTGATACAT
1312507 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1312526 TGTATCGATAC---A-TTA
1 TGTATCGATACAAAACTTA
*
1312541 --TATCGATACAATACTTA
1 TGTATCGATACAAAACTTA
1312558 TGTATCGATACAAA
1 TGTATCGATACAAA
1312572 TCATTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 9 0.23
15 3 0.08
16 2 0.05
17 3 0.08
19 22 0.56
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1312537 original size:32 final size:32
Alignment explanation
Indices: 1312500--1312569 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
1312490 ACTTCGTAGT
*
1312500 GATACATTGTATCGATACAAAACTTATGTATC
1 GATACATTATATCGATACAAAACTTATGTATC
*
1312532 GATACATTATATCGATACAATACTTATGTATC
1 GATACATTATATCGATACAAAACTTATGTATC
1312564 GATACA
1 GATACA
1312570 AATCATTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (32 bp):
GATACATTATATCGATACAAAACTTATGTATC
Found at i:1317119 original size:18 final size:18
Alignment explanation
Indices: 1317098--1317133 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1317088 ATTTTTTTTA
*
1317098 TTTTAATGATTTTTAATT
1 TTTTAATGATCTTTAATT
*
1317116 TTTTAATTATCTTTAATT
1 TTTTAATGATCTTTAATT
1317134 CTAGTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTAATGATCTTTAATT
Found at i:1317728 original size:16 final size:16
Alignment explanation
Indices: 1317707--1317740 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1317697 TATCACTACT
1317707 ATAAAGGTATATTTGA
1 ATAAAGGTATATTTGA
1317723 ATAAAGGTATATTTGA
1 ATAAAGGTATATTTGA
1317739 AT
1 AT
1317741 GTAGTTGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (16 bp):
ATAAAGGTATATTTGA
Found at i:1320806 original size:33 final size:33
Alignment explanation
Indices: 1320764--1320827 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1320754 AAAATTTTAG
*
1320764 AGATTATATTAATTTTTAATACTATTAAATTGA
1 AGATGATATTAATTTTTAATACTATTAAATTGA
* *
1320797 AGATGATATTTATTTTTAATATTATTAAATT
1 AGATGATATTAATTTTTAATACTATTAAATT
1320828 TAAAATAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (33 bp):
AGATGATATTAATTTTTAATACTATTAAATTGA
Found at i:1321390 original size:31 final size:32
Alignment explanation
Indices: 1321347--1321423 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
1321337 TATTATTAAC
* *
1321347 TATTTTAATCTATTAAATTATT-TTTTAACT-T
1 TATTTTATTCTATTAAATAATTATTTT-ACTAT
*
1321378 TATTTTATTCTATAAAATAATTATTTTACTAT
1 TATTTTATTCTATTAAATAATTATTTTACTAT
*
1321410 TATTTTATTTTATT
1 TATTTTATTCTATT
1321424 TTAATTAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 22 0.56
32 17 0.44
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (32 bp):
TATTTTATTCTATTAAATAATTATTTTACTAT
Found at i:1321803 original size:25 final size:25
Alignment explanation
Indices: 1321767--1321826 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1321757 ATTATATATA
* *
1321767 ATATATTATTAATAATTAAATAATATT
1 ATAT-TTATTAAAAATAAAATAAT-TT
*
1321794 AT-TTTATTAAAAATAAAATTATTT
1 ATATTTATTAAAAATAAAATAATTT
1321818 ATATTTATT
1 ATATTTATT
1321827 TTAAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 4 0.14
25 22 0.76
26 1 0.03
27 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATTTATTAAAAATAAAATAATTT
Found at i:1321807 original size:20 final size:21
Alignment explanation
Indices: 1321784--1321822 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1321774 ATTAATAATT
*
1321784 AAATAATATTATTT-TATTAA
1 AAATAAAATTATTTATATTAA
1321804 AAATAAAATTATTTATATT
1 AAATAAAATTATTTATATT
1321823 TATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATAAAATTATTTATATTAA
Found at i:1321931 original size:13 final size:14
Alignment explanation
Indices: 1321897--1321949 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 14
1321887 TGATCATTGA
*
1321897 ATTAA-ATATAAAC
1 ATTAATATATAAAT
*
1321910 ATAAATATATAAAT
1 ATTAATATATAAAT
*
1321924 -TTAATATAAAAAT
1 ATTAATATATAAAT
1321937 ATT-ATAT-TAAAT
1 ATTAATATATAAAT
1321949 A
1 A
1321950 AATTTGATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
12 5 0.15
13 19 0.58
14 9 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTAATATATAAAT
Found at i:1321964 original size:18 final size:18
Alignment explanation
Indices: 1321943--1321981 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1321933 AAATATTATA
* *
1321943 TTAAATAAATTTGATATT
1 TTAAATAAATATCATATT
*
1321961 TTAAATATATATCATATT
1 TTAAATAAATATCATATT
1321979 TTA
1 TTA
1321982 TATTTTTATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
TTAAATAAATATCATATT
Found at i:1324653 original size:17 final size:18
Alignment explanation
Indices: 1324627--1324667 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
1324617 ATGAATTAGA
1324627 TAAAAA-TAATTTAGG-T
1 TAAAAATTAATTTAGGTT
1324643 TAAAAATTAATTTAGGTT
1 TAAAAATTAATTTAGGTT
1324661 TAAAAAT
1 TAAAAAT
1324668 AAAATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 6 0.26
17 9 0.39
18 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (18 bp):
TAAAAATTAATTTAGGTT
Found at i:1325460 original size:36 final size:39
Alignment explanation
Indices: 1325419--1325523 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 39
1325409 AATTATTAAT
*
1325419 TATTAAAATTATATTTAAATTAAATAATAAC-AT-ATAA
1 TATTAAAATTATATTTAAATTAAATAATAACAATCAAAA
* * ** *
1325456 -ATTAATATTATACTTAGGTTAAACAATAACAATCAAAA
1 TATTAAAATTATATTTAAATTAAATAATAACAATCAAAA
*
1325494 TTTATTAAAATTATATTTATATTAAATAAT
1 --TATTAAAATTATATTTAAATTAAATAAT
1325524 TAAATTTATA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
36 25 0.48
37 2 0.04
38 3 0.06
41 22 0.42
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (39 bp):
TATTAAAATTATATTTAAATTAAATAATAACAATCAAAA
Found at i:1325577 original size:38 final size:37
Alignment explanation
Indices: 1325480--1325600 Score: 149
Period size: 38 Copynumber: 3.2 Consensus size: 37
1325470 TAGGTTAAAC
*
1325480 AATAACAATCAAAATTTATTAAAATTATATTTATATTA
1 AATAA-AATTAAAATTTATTAAAATTATATTTATATTA
* * *
1325518 AAT--AATT-AAATTTATAGAAAATTACATTTATGTTA
1 AATAAAATTAAAATTTAT-TAAAATTATATTTATATTA
1325553 AATAAGAATTAAAATTTATTAAAATTATATTTATATTA
1 AATAA-AATTAAAATTTATTAAAATTATATTTATATTA
1325591 AATATAAATT
1 AATA-AAATT
1325601 GATAAAAATT
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
34 8 0.11
35 22 0.31
38 31 0.44
39 9 0.13
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (37 bp):
AATAAAATTAAAATTTATTAAAATTATATTTATATTA
Found at i:1325585 original size:73 final size:73
Alignment explanation
Indices: 1325418--1325611 Score: 225
Period size: 73 Copynumber: 2.6 Consensus size: 73
1325408 AAATTATTAA
* * *
1325418 TTATTAAAATTATATTTAAATTAAATAATAACATATA-AATTAATATTATACTTAGGTTAAACAA
1 TTATTAAAATTATATTTATATTAAATAATAA-ATTTATAA--AA-ATTACACTTAGGTT-AACAA
1325482 TAACAATCAAAAT
61 TAACAATCAAAAT
* *
1325495 TTATTAAAATTATATTTATATTAAATAATTAAATTTATAGAAAATTACATTTATGTT-A-AATAA
1 TTATTAAAATTATATTTATATTAAATAA-TAAATTTATA-AAAATTACACTTAGGTTAACAATAA
* *
1325558 GAATTAAAAT
64 CAATCAAAAT
*
1325568 TTATTAAAATTATATTTATATTAAAT-ATAAATTGATAAAAATTA
1 TTATTAAAATTATATTTATATTAAATAATAAATTTATAAAAATTA
1325612 AAAAATAAAT
Statistics
Matches: 106, Mismatches: 8, Indels: 13
0.83 0.06 0.10
Matches are distributed among these distances:
70 7 0.07
71 9 0.08
72 1 0.01
73 39 0.37
74 1 0.01
76 11 0.10
77 33 0.31
78 4 0.04
79 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (73 bp):
TTATTAAAATTATATTTATATTAAATAATAAATTTATAAAAATTACACTTAGGTTAACAATAACA
ATCAAAAT
Found at i:1325612 original size:38 final size:37
Alignment explanation
Indices: 1325408--1325614 Score: 110
Period size: 38 Copynumber: 5.5 Consensus size: 37
1325398 TGTAAATTAA
* *
1325408 AAATTATTAATTATTAAAATTATATTTAAATTAAATAAT
1 AAATTA-TAAATATTAAAATTATATTTATATTAAAT-AT
* * ** *
1325447 AACA-TAT-AA-ATTAATATTATACTTAGGTTAAACAAT
1 AA-ATTATAAATATTAAAATTATATTTATATTAAA-TAT
*
1325483 AACAATCA-AAATTTATTAAAATTATATTTATATTAAATAATT
1 -A-AATTATAAA--TATTAAAATTATATTTATATTAAAT-A-T
* * *
1325525 AAATT-T--ATA-GAAAATTACATTTATGTTAAATA-
1 AAATTATAAATATTAAAATTATATTTATATTAAATAT
1325557 AGAATTA-AAATTTATTAAAATTATATTTATATTAAATAT
1 A-AATTATAAA--TATTAAAATTATATTTATATTAAATAT
*
1325596 AAATTGATAAAAATTAAAA
1 AAATT-ATAAATATTAAAA
1325615 AATAAATAGA
Statistics
Matches: 126, Mismatches: 20, Indels: 45
0.66 0.10 0.24
Matches are distributed among these distances:
32 1 0.01
33 4 0.03
34 1 0.01
35 20 0.16
36 23 0.18
37 5 0.04
38 37 0.29
39 6 0.05
40 7 0.06
41 21 0.17
42 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (37 bp):
AAATTATAAATATTAAAATTATATTTATATTAAATAT
Found at i:1325868 original size:18 final size:18
Alignment explanation
Indices: 1325809--1325870 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
1325799 CATGGATCTA
*
1325809 GAATTGTATTAAAATTTT
1 GAATTGTATTTAAATTTT
*
1325827 GAATTATAGTATT-AA-TTT
1 GAATTGTA-T-TTAAATTTT
1325845 --ATTGTATTTAAATTTT
1 GAATTGTATTTAAATTTT
1325861 GAATTGTATT
1 GAATTGTATT
1325871 AAAAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
16 8 0.23
18 18 0.51
19 3 0.09
20 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
GAATTGTATTTAAATTTT
Found at i:1325883 original size:18 final size:17
Alignment explanation
Indices: 1325810--1325883 Score: 51
Period size: 18 Copynumber: 4.2 Consensus size: 17
1325800 ATGGATCTAG
*
1325810 AATTGTATTAAAATTTT
1 AATTGTATTAAAAATTT
* * **
1325827 GAATTATAGTATTAATTT
1 -AATTGTATTAAAAATTT
* *
1325845 -ATTGTATTTAAATTTT
1 AATTGTATTAAAAATTT
1325861 GAATTGTATTAAAAAATTT
1 -AATTGTATT-AAAAATTT
1325880 AATT
1 AATT
1325884 CGCCACTTCT
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
16 10 0.25
18 24 0.60
19 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (17 bp):
AATTGTATTAAAAATTT
Found at i:1326038 original size:14 final size:13
Alignment explanation
Indices: 1326012--1326037 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1326002 TTTTTTTAAA
1326012 AAAAATTATTTTT
1 AAAAATTATTTTT
1326025 AAAAATTATTTTT
1 AAAAATTATTTTT
1326038 TTAGGATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:1326039 original size:16 final size:16
Alignment explanation
Indices: 1326001--1326039 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1325991 TATTTAAGAT
1326001 TTTTTTTTAAAAAAAA
1 TTTTTTTTAAAAAAAA
* **
1326017 TTATTTTTAAAAATTA
1 TTTTTTTTAAAAAAAA
1326033 TTTTTTT
1 TTTTTTT
1326040 AGGATCATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTTTAAAAAAAA
Found at i:1330433 original size:127 final size:127
Alignment explanation
Indices: 1330207--1330454 Score: 478
Period size: 127 Copynumber: 2.0 Consensus size: 127
1330197 TAACTCATCT
*
1330207 TTCATGGTTTCTAAGCATTTGTTAGACTCATTATTTTCTATAGCTTGTGAGAAAGGAATCAGATA
1 TTCATGGTTTCTAAGCATTTGTTAGACTCATTATTTTCTATAGCTAGTGAGAAAGGAATCAGATA
*
1330272 TTTATCGATTCCAACAAAATCTGACTTTTTCAAATAAACCACATAATCATTTAGGATAATTG
66 TTTATCGATTCCAACAAAATCTAACTTTTTCAAATAAACCACATAATCATTTAGGATAATTG
1330334 TTCATGGTTTCTAAGCATTTGTTAGACTCATTATTTTCTATAGCTAGTGAGAAAGGAATCAGATA
1 TTCATGGTTTCTAAGCATTTGTTAGACTCATTATTTTCTATAGCTAGTGAGAAAGGAATCAGATA
1330399 TTTATCGATTCCAACAAAATCTAACTTTTTCAAATAAACCACATAATCATTTAGGA
66 TTTATCGATTCCAACAAAATCTAACTTTTTCAAATAAACCACATAATCATTTAGGA
1330455 CAATCGACTT
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 119 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (127 bp):
TTCATGGTTTCTAAGCATTTGTTAGACTCATTATTTTCTATAGCTAGTGAGAAAGGAATCAGATA
TTTATCGATTCCAACAAAATCTAACTTTTTCAAATAAACCACATAATCATTTAGGATAATTG
Found at i:1331707 original size:18 final size:17
Alignment explanation
Indices: 1331665--1331720 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1331655 TATCTAATTT
* * *
1331665 TATAATTATCAGATAAT
1 TATATTTATTAGATAAA
1331682 TATATTTATTAGATAAA
1 TATATTTATTAGATAAA
*
1331699 TAGTATTTATTAAAATAAA
1 TA-TATTTATT-AGATAAA
1331718 TAT
1 TAT
1331721 GGAGTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 16 0.48
18 9 0.27
19 8 0.24
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (17 bp):
TATATTTATTAGATAAA
Found at i:1331718 original size:19 final size:18
Alignment explanation
Indices: 1331684--1331719 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1331674 CAGATAATTA
*
1331684 TATTTATTAGATAAATAG
1 TATTTATTAAATAAATAG
1331702 TATTTATTAAAATAAATA
1 TATTTATT-AAATAAATA
1331720 TGGAGTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TATTTATTAAATAAATAG
Found at i:1331734 original size:26 final size:26
Alignment explanation
Indices: 1331705--1331782 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
1331695 TAAATAGTAT
1331705 TTATTAAAATAAATATGGAGTTTAAA
1 TTATTAAAATAAATATGGAGTTTAAA
* * ** *
1331731 TTA-TAGAATTAAA-CTCAAG---AAT
1 TTATTA-AAATAAATATGGAGTTTAAA
1331753 TTATTAAAATAAATATGGAGTTTAAA
1 TTATTAAAATAAATATGGAGTTTAAA
1331779 TTAT
1 TTAT
1331783 AGAATTAAAC
Statistics
Matches: 36, Mismatches: 10, Indels: 12
0.62 0.17 0.21
Matches are distributed among these distances:
22 11 0.31
23 5 0.14
25 5 0.14
26 15 0.42
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (26 bp):
TTATTAAAATAAATATGGAGTTTAAA
Found at i:1331757 original size:48 final size:48
Alignment explanation
Indices: 1331703--1331799 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
1331693 GATAAATAGT
1331703 ATTTATTAAAATAAATATGGAGTTTAAATTATAGAATTAAACTCAAGA
1 ATTTATTAAAATAAATATGGAGTTTAAATTATAGAATTAAACTCAAGA
1331751 ATTTATTAAAATAAATATGGAGTTTAAATTATAGAATTAAACTCAAGA
1 ATTTATTAAAATAAATATGGAGTTTAAATTATAGAATTAAACTCAAGA
1331799 A
1 A
1331800 AACAATACCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (48 bp):
ATTTATTAAAATAAATATGGAGTTTAAATTATAGAATTAAACTCAAGA
Found at i:1335897 original size:16 final size:16
Alignment explanation
Indices: 1335878--1335932 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
1335868 TATTTGTATT
1335878 ATTTTAAGTTCAAATC
1 ATTTTAAGTTCAAATC
* *
1335894 ATTTTTA-TTCGAATC
1 ATTTTAAGTTCAAATC
* *
1335909 ATTTTAAGTTTAAATT
1 ATTTTAAGTTCAAATC
1335925 ATTTTAAG
1 ATTTTAAG
1335933 ATGGTGTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 13 0.41
16 19 0.59
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (16 bp):
ATTTTAAGTTCAAATC
Found at i:1335902 original size:31 final size:31
Alignment explanation
Indices: 1335864--1335929 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1335854 TTTAGATTAT
* * *
1335864 TTTTTATTTGTATTATTTTAAGTTCAAATCA
1 TTTTTATTCGAATCATTTTAAGTTCAAATCA
* *
1335895 TTTTTATTCGAATCATTTTAAGTTTAAATTA
1 TTTTTATTCGAATCATTTTAAGTTCAAATCA
1335926 TTTT
1 TTTT
1335930 AAGATGGTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (31 bp):
TTTTTATTCGAATCATTTTAAGTTCAAATCA
Found at i:1337316 original size:33 final size:31
Alignment explanation
Indices: 1337251--1337336 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 31
1337241 AATAATTTAT
* *
1337251 ATATTTTAT-TTTAT-TATAATTATATATAAA
1 ATATTTTATATTTATAT-TAATTTTATAGAAA
1337281 ATATTTTATATTTATATTAATTTTGATAGATAA
1 ATATTTTATATTTATATTAATTTT-ATAGA-AA
* *
1337314 ATAATTTATA-TTATATAAATTTT
1 ATATTTTATATTTATATTAATTTT
1337337 TAAATATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.19
31 11 0.23
32 17 0.35
33 11 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
ATATTTTATATTTATATTAATTTTATAGAAA
Found at i:1337333 original size:18 final size:17
Alignment explanation
Indices: 1337266--1337333 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 17
1337256 TTATTTTATT
1337266 ATAA-TTATATATA-AA
1 ATAATTTATATATATAA
* *
1337281 ATATTTTATATTTAT-A
1 ATAATTTATATATATAA
* *
1337297 TTAATTT-TGATAGATAA
1 ATAATTTAT-ATATATAA
1337314 ATAATTTATATTATATAA
1 ATAATTTATA-TATATAA
1337332 AT
1 AT
1337334 TTTTAAATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
15 4 0.10
16 18 0.46
17 8 0.21
18 9 0.23
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATAATTTATATATATAA
Found at i:1338145 original size:192 final size:192
Alignment explanation
Indices: 1337818--1338199 Score: 714
Period size: 192 Copynumber: 2.0 Consensus size: 192
1337808 CCTGTTTGAG
1337818 TTTGATGGAACACTAGGGCATGATAGACATGTCCACAACGTAGAAGCCAGTGAGAATTGGATGAC
1 TTTGATGGAACACTAGGGCATGATAGACATGTCCACAACGTAGAAGCCAGTGAGAATTGGATGAC
1337883 ACCGATCATTGCATTTCTCAAAAACAATGTCTTTTTGGAAGATCCATTACAAAGAAGGTGATTAG
66 ACCGATCATTGCATTTCTCAAAAACAATGTCTTTTTGGAAGATCCATTACAAAGAAGGTGATTAG
1337948 AAAATAGAGTCCCAAGGGTACACAATAATCAATGACATTCTATAAAAAAAATCTTTACTCAC
131 AAAATAGAGTCCCAAGGGTACACAATAATCAATGACATTCTATAAAAAAAATCTTTACTCAC
*
1338010 TTTGTTGG-ACACTAGGGCATGATAGACATGTCCAACAACGTAGAAGCCAGTGAGGAATTGGATG
1 TTTGATGGAACACTAGGGCATGATAGACATGTCC-ACAACGTAGAAGCCAGTGA-GAATTGGATG
*
1338074 ACACCGATCATTGCATTTCTCAAAAACAATGTCTTTTTGGAAGAT-CATTACAAGGAAGGTGATT
64 ACACCGATCATTGCATTTCTCAAAAACAATGTCTTTTTGGAAGATCCATTACAAAGAAGGTGATT
1338138 AGAAAATAGAGTCCCAAGGGTACACAATAATCAATGACATTCTATAAAAAAAATCTTTACTC
129 AGAAAATAGAGTCCCAAGGGTACACAATAATCAATGACATTCTATAAAAAAAATCTTTACTC
1338200 GCCCTTTGCT
Statistics
Matches: 186, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
191 25 0.13
192 106 0.57
193 55 0.30
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (192 bp):
TTTGATGGAACACTAGGGCATGATAGACATGTCCACAACGTAGAAGCCAGTGAGAATTGGATGAC
ACCGATCATTGCATTTCTCAAAAACAATGTCTTTTTGGAAGATCCATTACAAAGAAGGTGATTAG
AAAATAGAGTCCCAAGGGTACACAATAATCAATGACATTCTATAAAAAAAATCTTTACTCAC
Found at i:1339058 original size:47 final size:47
Alignment explanation
Indices: 1338984--1339075 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 47
1338974 AGAATAACGC
** **
1338984 CTTGGTGGTGATCAGGGAAAATGGTGACTTGGTGTCACTTAGAGAGT
1 CTTGGTGGCAATCAGGGAAAACAGTGACTTGGTGTCACTTAGAGAGT
*
1339031 CTTGGTGGCAATCAGGGAGAACAGTGACTTGGTGTCACTTAGAGA
1 CTTGGTGGCAATCAGGGAAAACAGTGACTTGGTGTCACTTAGAGA
1339076 AATAATGCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.25, C:0.13, G:0.35, T:0.27
Consensus pattern (47 bp):
CTTGGTGGCAATCAGGGAAAACAGTGACTTGGTGTCACTTAGAGAGT
Found at i:1340150 original size:150 final size:150
Alignment explanation
Indices: 1339879--1340173 Score: 437
Period size: 150 Copynumber: 2.0 Consensus size: 150
1339869 TCCATAAGAA
* * * *
1339879 CTTTCCATGGACCGAGCTTTGATGATGGCGACTGGTTCTGCTTCTACACATTTGGTGAAGTAGTC
1 CTTTCCATGGACCGAGCTGTGATGATGGCAACTGATTCTGCTTCTACACATTTAGTGAAGTAGTC
* * *
1339944 GCAGACAACAATGAGGAACTTCCTCTGTTCGGTAGCCAGCGAAAAAGGTTCGAGTATATCTATTC
66 ACAGACAACAATGAGGAACTTCATCTGTTCAGTAGCCAGCGAAAAAGGTTCGAGTATATCTATTC
*
1340009 CCCATACATAGAAAGGCTAG
131 CCCATACACAGAAAGGCTAG
* * * *
1340029 CTTTCCATGGATCGAGCTGTGATGGTGGCAATTGATTCTGCTTCTACCCATTTAGTGAAGTAGTC
1 CTTTCCATGGACCGAGCTGTGATGATGGCAACTGATTCTGCTTCTACACATTTAGTGAAGTAGTC
* * * * *
1340094 ACAGGCAACCATGAGGAACTTCATCTGTTCAGTAGCCAGTGGAAAAGGTTCGAGTATGTCTATTC
66 ACAGACAACAATGAGGAACTTCATCTGTTCAGTAGCCAGCGAAAAAGGTTCGAGTATATCTATTC
1340159 CCCATACACAGAAAG
131 CCCATACACAGAAAG
1340174 CTATGGGATG
Statistics
Matches: 128, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
150 128 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (150 bp):
CTTTCCATGGACCGAGCTGTGATGATGGCAACTGATTCTGCTTCTACACATTTAGTGAAGTAGTC
ACAGACAACAATGAGGAACTTCATCTGTTCAGTAGCCAGCGAAAAAGGTTCGAGTATATCTATTC
CCCATACACAGAAAGGCTAG
Found at i:1345688 original size:19 final size:19
Alignment explanation
Indices: 1345666--1345702 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1345656 ATTTTTTTTA
*
1345666 TTTTAATGATTTTTAATTT
1 TTTTAATGATCTTTAATTT
*
1345685 TTTTAATTATCTTTAATT
1 TTTTAATGATCTTTAATT
1345703 CTAGTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTAATGATCTTTAATTT
Found at i:1347963 original size:20 final size:20
Alignment explanation
Indices: 1347938--1347993 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1347928 AGTTTACCCA
1347938 GATGTATCGATACATTTTAC
1 GATGTATCGATACATTTTAC
1347958 GATGTATCGATACATTTTAC
1 GATGTATCGATACATTTTAC
*
1347978 AATGTATCGATACATT
1 GATGTATCGATACATT
1347994 GAGGCATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (20 bp):
GATGTATCGATACATTTTAC
Found at i:1350406 original size:52 final size:51
Alignment explanation
Indices: 1350265--1350444 Score: 222
Period size: 51 Copynumber: 3.5 Consensus size: 51
1350255 TTAAGTTTCT
* *
1350265 CAATTTTTCATAATCGGGGATACTCCAACTCCGGTTTTA-TTTCTAAAACA
1 CAATTTTTCACAATCGGGGATACTCCAACTCCGGTTTTATTTTCAAAAACA
*
1350315 CTAATTTTTCACAATCGGGGATTCTCCAAC-CCTGGTTTTATTTTC-AAAACA
1 C-AATTTTTCACAATCGGGGATACTCCAACTCC-GGTTTTATTTTCAAAAACA
* ** * *
1350366 TCAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACA
1 -CAATTTTTC-ACAATCGGGGATACTCCAACTCCGGTTTTATTTTCAAAAACA
1350419 CCAATTTTTCACAATCGGGGATACTC
1 -CAATTTTTCACAATCGGGGATACTC
1350445 AAACCCCGTT
Statistics
Matches: 111, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
50 3 0.03
51 46 0.41
52 46 0.41
53 16 0.14
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (51 bp):
CAATTTTTCACAATCGGGGATACTCCAACTCCGGTTTTATTTTCAAAAACA
Found at i:1350504 original size:28 final size:28
Alignment explanation
Indices: 1350438--1350527 Score: 85
Period size: 28 Copynumber: 3.2 Consensus size: 28
1350428 CACAATCGGG
* * *
1350438 GATACTCAAACCCCGTTAATCATCG-GG-
1 GATACTCCAACCCCATTATTC-TCGAGGA
* * * *
1350465 GATACTCTAACCCCGTTATTTTTGAGGA
1 GATACTCCAACCCCATTATTCTCGAGGA
*
1350493 GATACTCCAACCCCATTATTCTCGAGGG
1 GATACTCCAACCCCATTATTCTCGAGGA
1350521 GATACTC
1 GATACTC
1350528 GAACTCCGGT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 2 0.04
27 20 0.38
28 30 0.58
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.28
Consensus pattern (28 bp):
GATACTCCAACCCCATTATTCTCGAGGA
Found at i:1350599 original size:186 final size:187
Alignment explanation
Indices: 1350331--1350692 Score: 471
Period size: 186 Copynumber: 1.9 Consensus size: 187
1350321 TTTCACAATC
* * * ** *
1350331 GGGGATTCTCCAACCCTGGTTTTATTTTCAAAACATCAATTTTCCTTTAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCTGGTTTTATTTTCAAAACACCAATTCTCCTACAATCGGGAATACTCCAA
* *
1350396 CTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCAAACCCCGTTA-ATCA
66 CTCCGATTTGATTTCC-AAAACACCAATTTTTCACAATCGAGGATACTCAAACCCCGTTATATCA
* * * * **
1350460 TCGGGGATACTCTAACCCCGTTATTTTTGAGGAGATACTCCAACCCCATTATTCTCGA
130 TCAGGGATACTCCAACCCCATTACTTCCGAGGAGATACTCCAACCCCATTATTCTCGA
* *
1350518 GGGGATACTCGAACTCC-GGTTTTA-TTTCTAAAACACCAATTCTCC-ACAATCGGGAATATTCC
1 GGGGATACTCCAAC-CCTGGTTTTATTTTC-AAAACACCAATTCTCCTACAATCGGGAATACTCC
* * * * *
1350580 AACTCCGATTTGATTTCCAAAACACTAGTTTTTCACAATCGAGGATACTCCAACCTCGTTATTTC
64 AACTCCGATTTGATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCAAACCCCGTTATATC
*
1350645 ATCAGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCCC
129 ATCAGGGATACTCCAACCCCATTACTTCCGAGGAGATACTCCAACCCC
1350693 GGCTTTATTT
Statistics
Matches: 150, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
185 38 0.25
186 77 0.51
187 33 0.22
188 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (187 bp):
GGGGATACTCCAACCCTGGTTTTATTTTCAAAACACCAATTCTCCTACAATCGGGAATACTCCAA
CTCCGATTTGATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCAAACCCCGTTATATCAT
CAGGGATACTCCAACCCCATTACTTCCGAGGAGATACTCCAACCCCATTATTCTCGA
Found at i:1350617 original size:51 final size:51
Alignment explanation
Indices: 1350520--1350633 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 51
1350510 ATTCTCGAGG
* * * *
1350520 GGATACTCGAACTCCGGTTTTATTTCTAAAACACCAATTCTCCACAATCG-
1 GGATACTCCAACTCCGATTTGATTTCCAAAACACCAATTCTCCACAATCGA
* * * * *
1350570 GGAATATTCCAACTCCGATTTGATTTCCAAAACACTAGTTTTTCACAATCGA
1 GG-ATACTCCAACTCCGATTTGATTTCCAAAACACCAATTCTCCACAATCGA
1350622 GGATACTCCAAC
1 GGATACTCCAAC
1350634 CTCGTTATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
50 2 0.04
51 48 0.92
52 2 0.04
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (51 bp):
GGATACTCCAACTCCGATTTGATTTCCAAAACACCAATTCTCCACAATCGA
Found at i:1350804 original size:79 final size:79
Alignment explanation
Indices: 1350650--1350822 Score: 188
Period size: 79 Copynumber: 2.2 Consensus size: 79
1350640 ATTTCATCAG
* ** *
1350650 GGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGA
1 GGATACTCCAACCCTATTACTTCCGAGGGGATACTCCAACCCCGAATTTATTTCTAAAACATTGA
*
1350715 TTTCTCATAATTGA
66 TTTCTCATAATCGA
* * * * *
1350729 GGATACTCCAACCCTATTATTTTC-ACGGGGATACTCCAATCCCGAATTTATTTTTGAAACATCT
1 GGATACTCCAACCCTATTACTTCCGA-GGGGATACTCCAACCCCGAATTTATTTCTAAAACAT-T
* *
1350793 GTTTTCT-ATAATCGG
64 GATTTCTCATAATCGA
* *
1350808 GGACACTTCAACCCT
1 GGATACTCCAACCCT
1350823 TATCTTATTT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
78 1 0.01
79 70 0.90
80 7 0.09
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (79 bp):
GGATACTCCAACCCTATTACTTCCGAGGGGATACTCCAACCCCGAATTTATTTCTAAAACATTGA
TTTCTCATAATCGA
Found at i:1354298 original size:31 final size:32
Alignment explanation
Indices: 1354255--1354331 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
1354245 TATTATTAAC
* *
1354255 TATTTTAATCTATTAAATTATT-TTTTAACT-T
1 TATTTTATTCTATTAAATAATTATTTT-ACTAT
*
1354286 TATTTTATTCTATAAAATAATTATTTTACTAT
1 TATTTTATTCTATTAAATAATTATTTTACTAT
*
1354318 TATTTTATTTTATT
1 TATTTTATTCTATT
1354332 TTAATTAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 22 0.56
32 17 0.44
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (32 bp):
TATTTTATTCTATTAAATAATTATTTTACTAT
Found at i:1354711 original size:25 final size:25
Alignment explanation
Indices: 1354675--1354734 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1354665 ATTATATATA
* *
1354675 ATATATTATTAATAATTAAATAATATT
1 ATAT-TTATTAAAAATAAAATAAT-TT
*
1354702 AT-TTTATTAAAAATAAAATTATTT
1 ATATTTATTAAAAATAAAATAATTT
1354726 ATATTTATT
1 ATATTTATT
1354735 TTAAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 4 0.14
25 22 0.76
26 1 0.03
27 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATTTATTAAAAATAAAATAATTT
Found at i:1354715 original size:20 final size:21
Alignment explanation
Indices: 1354692--1354730 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1354682 ATTAATAATT
*
1354692 AAATAATATTATTT-TATTAA
1 AAATAAAATTATTTATATTAA
1354712 AAATAAAATTATTTATATT
1 AAATAAAATTATTTATATT
1354731 TATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATAAAATTATTTATATTAA
Found at i:1354839 original size:13 final size:14
Alignment explanation
Indices: 1354805--1354857 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 14
1354795 TGATCATTGA
*
1354805 ATTAA-ATATAAAC
1 ATTAATATATAAAT
*
1354818 ATAAATATATAAAT
1 ATTAATATATAAAT
*
1354832 -TTAATATAAAAAT
1 ATTAATATATAAAT
1354845 ATT-ATAT-TAAAT
1 ATTAATATATAAAT
1354857 A
1 A
1354858 AATTTGATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
12 5 0.15
13 19 0.58
14 9 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTAATATATAAAT
Found at i:1354872 original size:18 final size:18
Alignment explanation
Indices: 1354851--1354889 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1354841 AAATATTATA
* *
1354851 TTAAATAAATTTGATATT
1 TTAAATAAATATCATATT
*
1354869 TTAAATATATATCATATT
1 TTAAATAAATATCATATT
1354887 TTA
1 TTA
1354890 TATTTTTATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
TTAAATAAATATCATATT
Found at i:1357563 original size:17 final size:18
Alignment explanation
Indices: 1357537--1357577 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
1357527 ATGAATTAGA
1357537 TAAAAA-TAATTTAGG-T
1 TAAAAATTAATTTAGGTT
1357553 TAAAAATTAATTTAGGTT
1 TAAAAATTAATTTAGGTT
1357571 TAAAAAT
1 TAAAAAT
1357578 AAAATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 6 0.26
17 9 0.39
18 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (18 bp):
TAAAAATTAATTTAGGTT
Found at i:1358361 original size:41 final size:40
Alignment explanation
Indices: 1358316--1358509 Score: 117
Period size: 36 Copynumber: 5.1 Consensus size: 40
1358306 AATTGTAAAT
1358316 TAAAAATTATTAATTATTAAAATTATATTTAAATTAAATAA
1 TAAAAATTA-TAATTATTAAAATTATATTTAAATTAAATAA
* * ** *
1358357 T-AAAA-TATAA--ATTAATATTATACTTAGGTTAAACAA
1 TAAAAATTATAATTATTAAAATTATATTTAAATTAAATAA
* * * *
1358393 TAACAATCAAAATTTATTAAAATTATATTTATATTAAATAA
1 TAAAAATTATAA-TTATTAAAATTATATTTAAATTAAATAA
* * * **
1358434 T-TAAATT-T-A-TA-GAAAATTACATTTATGTT--A-AA
1 TAAAAATTATAATTATTAAAATTATATTTAAATTAAATAA
* * *
1358466 TAAGAATTAAAATTTATTAAAATTATATTTATATTAAAT-A
1 TAAAAATTATAA-TTATTAAAATTATATTTAAATTAAATAA
1358506 TAAA
1 TAAA
1358510 TTGATAAAAA
Statistics
Matches: 112, Mismatches: 27, Indels: 29
0.67 0.16 0.17
Matches are distributed among these distances:
32 3 0.03
33 5 0.04
35 16 0.14
36 24 0.21
37 5 0.04
38 22 0.20
39 2 0.02
40 12 0.11
41 23 0.21
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (40 bp):
TAAAAATTATAATTATTAAAATTATATTTAAATTAAATAA
Found at i:1358488 original size:38 final size:37
Alignment explanation
Indices: 1358329--1358511 Score: 153
Period size: 38 Copynumber: 4.9 Consensus size: 37
1358319 AAATTATTAA
*
1358329 TTATTAAAATTATATTTAAATTAAAT--AA-TAAAAT
1 TTATTAAAATTATATTTATATTAAATAAAATTAAAAT
* * * ** *
1358363 ATAAATTAATATTATACTTAGGTTAAACAATAACAATCAAAAT
1 -T-TATTAAAATTATATTTATATT--A-AATAA-AATTAAAAT
1358406 TTATTAAAATTATATTTATATTAAAT--AATT-AAAT
1 TTATTAAAATTATATTTATATTAAATAAAATTAAAAT
* * *
1358440 TTATAGAAAATTACATTTATGTTAAATAAGAATTAAAAT
1 TTAT-TAAAATTATATTTATATTAAATAA-AATTAAAAT
1358479 TTATTAAAATTATATTTATATTAAATATAAATT
1 TTATTAAAATTATATTTATATTAAATA-AAATT
1358512 GATAAAAATT
Statistics
Matches: 116, Mismatches: 18, Indels: 25
0.73 0.11 0.16
Matches are distributed among these distances:
34 8 0.07
35 23 0.20
36 16 0.14
38 32 0.28
39 13 0.11
41 16 0.14
42 3 0.03
43 5 0.04
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (37 bp):
TTATTAAAATTATATTTATATTAAATAAAATTAAAAT
Found at i:1358496 original size:73 final size:74
Alignment explanation
Indices: 1358329--1358522 Score: 227
Period size: 73 Copynumber: 2.6 Consensus size: 74
1358319 AAATTATTAA
* * * *
1358329 TTATTAAAATTATATTTAAATTAAATAATAAAATATA-AATTAATATTATACTTAGGTTAAACAA
1 TTATTAAAATTATATTTATATTAAATAATTAAATTTATAA--AA-ATTACACTTAGGTT-AACAA
1358393 TAACAATCAAAAT
62 TAACAATCAAAAT
* *
1358406 TTATTAAAATTATATTTATATTAAATAATTAAATTTATAGAAAATTACATTTATGTT-A-AATAA
1 TTATTAAAATTATATTTATATTAAATAATTAAATTTATA-AAAATTACACTTAGGTTAACAATAA
* *
1358469 GAATTAAAAT
65 CAATCAAAAT
*
1358479 TTATTAAAATTATATTTATATTAAAT-A-TAAATTGATAAAAATTA
1 TTATTAAAATTATATTTATATTAAATAATTAAATTTATAAAAATTA
1358523 AAAAATAAAT
Statistics
Matches: 106, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
70 7 0.07
71 9 0.08
72 1 0.01
73 39 0.37
74 1 0.01
76 11 0.10
77 36 0.34
78 1 0.01
79 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (74 bp):
TTATTAAAATTATATTTATATTAAATAATTAAATTTATAAAAATTACACTTAGGTTAACAATAAC
AATCAAAAT
Found at i:1358523 original size:38 final size:37
Alignment explanation
Indices: 1358319--1358525 Score: 117
Period size: 38 Copynumber: 5.5 Consensus size: 37
1358309 TGTAAATTAA
* *
1358319 AAATTATTAATTATTAAAATTATATTTAAATTAAATAAT
1 AAATTA-TAAATATTAAAATTATATTTATATTAAAT-AT
* * * ** *
1358358 AAAATAT-AA-ATTAATATTATACTTAGGTTAAACAAT
1 AAATTATAAATATTAAAATTATATTTATATTAAA-TAT
*
1358394 AACAATCA-AAATTTATTAAAATTATATTTATATTAAATAATT
1 -A-AATTATAAA--TATTAAAATTATATTTATATTAAAT-A-T
* * *
1358436 AAATT-T--ATA-GAAAATTACATTTATGTTAAATA-
1 AAATTATAAATATTAAAATTATATTTATATTAAATAT
1358468 AGAATTA-AAATTTATTAAAATTATATTTATATTAAATAT
1 A-AATTATAAA--TATTAAAATTATATTTATATTAAATAT
*
1358507 AAATTGATAAAAATTAAAA
1 AAATT-ATAAATATTAAAA
1358526 AATAAATAGA
Statistics
Matches: 126, Mismatches: 22, Indels: 41
0.67 0.12 0.22
Matches are distributed among these distances:
32 1 0.01
33 4 0.03
34 1 0.01
35 20 0.16
36 23 0.18
37 4 0.03
38 38 0.30
39 7 0.06
40 6 0.05
41 21 0.17
42 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (37 bp):
AAATTATAAATATTAAAATTATATTTATATTAAATAT
Found at i:1358780 original size:18 final size:18
Alignment explanation
Indices: 1358721--1358782 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
1358711 CATGGATCTA
*
1358721 GAATTGTATTAAAATTTT
1 GAATTGTATTTAAATTTT
*
1358739 GAATTATAGTATT-AA-TTT
1 GAATTGTA-T-TTAAATTTT
1358757 --ATTGTATTTAAATTTT
1 GAATTGTATTTAAATTTT
1358773 GAATTGTATT
1 GAATTGTATT
1358783 AAAAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
16 8 0.23
18 18 0.51
19 3 0.09
20 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
GAATTGTATTTAAATTTT
Found at i:1358795 original size:18 final size:17
Alignment explanation
Indices: 1358722--1358795 Score: 51
Period size: 18 Copynumber: 4.2 Consensus size: 17
1358712 ATGGATCTAG
*
1358722 AATTGTATTAAAATTTT
1 AATTGTATTAAAAATTT
* * **
1358739 GAATTATAGTATTAATTT
1 -AATTGTATTAAAAATTT
* *
1358757 -ATTGTATTTAAATTTT
1 AATTGTATTAAAAATTT
1358773 GAATTGTATTAAAAAATTT
1 -AATTGTATT-AAAAATTT
1358792 AATT
1 AATT
1358796 CGCCACTTCT
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
16 10 0.25
18 24 0.60
19 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (17 bp):
AATTGTATTAAAAATTT
Found at i:1358953 original size:14 final size:13
Alignment explanation
Indices: 1358927--1358952 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1358917 TTTTTTAAAA
1358927 AAAAATTATTTTT
1 AAAAATTATTTTT
1358940 AAAAATTATTTTT
1 AAAAATTATTTTT
1358953 TTAGGATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:1363345 original size:127 final size:127
Alignment explanation
Indices: 1363119--1363366 Score: 469
Period size: 127 Copynumber: 2.0 Consensus size: 127
1363109 TAACTCATCT
*
1363119 TTCATGGTTTCTAAGCATTTGTTAGACTCATTATTTTCTATAGCTTGTGAGAAAGGAATCAGATA
1 TTCATGGTTTCTAAGCATTTGTTAGACTCATTATTTTCTATAGCTAGTGAGAAAGGAATCAGATA
* *
1363184 TTTATCGATTCCAACAAAATCTGACTTTTTCAAATAAACCACATAATTATTTAGGATAATTG
66 TTTATCGATTCCAACAAAATCTAACTTTTTCAAATAAACCACATAATCATTTAGGATAATTG
1363246 TTCATGGTTTCTAAGCATTTGTTAGACTCATTATTTTCTATAGCTAGTGAGAAAGGAATCAGATA
1 TTCATGGTTTCTAAGCATTTGTTAGACTCATTATTTTCTATAGCTAGTGAGAAAGGAATCAGATA
1363311 TTTATCGATTCCAACAAAATCTAACTTTTTCAAATAAACCACATAATCATTTAGGA
66 TTTATCGATTCCAACAAAATCTAACTTTTTCAAATAAACCACATAATCATTTAGGA
1363367 CAATCGACTT
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 118 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (127 bp):
TTCATGGTTTCTAAGCATTTGTTAGACTCATTATTTTCTATAGCTAGTGAGAAAGGAATCAGATA
TTTATCGATTCCAACAAAATCTAACTTTTTCAAATAAACCACATAATCATTTAGGATAATTG
Found at i:1364617 original size:18 final size:17
Alignment explanation
Indices: 1364575--1364630 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1364565 TATCTAATTT
* * *
1364575 TATAATTATCAGATAAT
1 TATATTTATTAGATAAA
1364592 TATATTTATTAGATAAA
1 TATATTTATTAGATAAA
*
1364609 TAGTATTTATTAAAATAAA
1 TA-TATTTATT-AGATAAA
1364628 TAT
1 TAT
1364631 GGAGTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 16 0.48
18 9 0.27
19 8 0.24
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (17 bp):
TATATTTATTAGATAAA
Found at i:1364628 original size:19 final size:18
Alignment explanation
Indices: 1364594--1364629 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1364584 CAGATAATTA
*
1364594 TATTTATTAGATAAATAG
1 TATTTATTAAATAAATAG
1364612 TATTTATTAAAATAAATA
1 TATTTATT-AAATAAATA
1364630 TGGAGTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TATTTATTAAATAAATAG
Found at i:1364644 original size:26 final size:26
Alignment explanation
Indices: 1364615--1364692 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
1364605 TAAATAGTAT
1364615 TTATTAAAATAAATATGGAGTTTAAA
1 TTATTAAAATAAATATGGAGTTTAAA
* * ** *
1364641 TTA-TAGAATTAAA-CTCAAG---AAT
1 TTATTA-AAATAAATATGGAGTTTAAA
1364663 TTATTAAAATAAATATGGAGTTTAAA
1 TTATTAAAATAAATATGGAGTTTAAA
1364689 TTAT
1 TTAT
1364693 AGAATTAAAC
Statistics
Matches: 36, Mismatches: 10, Indels: 12
0.62 0.17 0.21
Matches are distributed among these distances:
22 11 0.31
23 5 0.14
25 5 0.14
26 15 0.42
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (26 bp):
TTATTAAAATAAATATGGAGTTTAAA
Found at i:1364667 original size:48 final size:48
Alignment explanation
Indices: 1364613--1364709 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
1364603 GATAAATAGT
1364613 ATTTATTAAAATAAATATGGAGTTTAAATTATAGAATTAAACTCAAGA
1 ATTTATTAAAATAAATATGGAGTTTAAATTATAGAATTAAACTCAAGA
1364661 ATTTATTAAAATAAATATGGAGTTTAAATTATAGAATTAAACTCAAGA
1 ATTTATTAAAATAAATATGGAGTTTAAATTATAGAATTAAACTCAAGA
1364709 A
1 A
1364710 AACAATACCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (48 bp):
ATTTATTAAAATAAATATGGAGTTTAAATTATAGAATTAAACTCAAGA
Found at i:1368809 original size:16 final size:16
Alignment explanation
Indices: 1368790--1368844 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
1368780 TATTTGTATT
1368790 ATTTTAAGTTCAAATC
1 ATTTTAAGTTCAAATC
* *
1368806 ATTTTTA-TTCGAATC
1 ATTTTAAGTTCAAATC
* *
1368821 ATTTTAAGTTTAAATT
1 ATTTTAAGTTCAAATC
1368837 ATTTTAAG
1 ATTTTAAG
1368845 ATGGTGTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 13 0.41
16 19 0.59
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (16 bp):
ATTTTAAGTTCAAATC
Found at i:1368814 original size:31 final size:31
Alignment explanation
Indices: 1368776--1368841 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1368766 TTTAGATTAT
* * *
1368776 TTTTTATTTGTATTATTTTAAGTTCAAATCA
1 TTTTTATTCGAATCATTTTAAGTTCAAATCA
* *
1368807 TTTTTATTCGAATCATTTTAAGTTTAAATTA
1 TTTTTATTCGAATCATTTTAAGTTCAAATCA
1368838 TTTT
1 TTTT
1368842 AAGATGGTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (31 bp):
TTTTTATTCGAATCATTTTAAGTTCAAATCA
Found at i:1370234 original size:33 final size:31
Alignment explanation
Indices: 1370169--1370254 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 31
1370159 AATAATTTAT
* *
1370169 ATATTTTAT-TTTAT-TATAATTATATATAAA
1 ATATTTTATATTTATAT-TAATTTTATAGAAA
1370199 ATATTTTATATTTATATTAATTTTGATAGATAA
1 ATATTTTATATTTATATTAATTTT-ATAGA-AA
* *
1370232 ATAATTTATA-TTATATAAATTTT
1 ATATTTTATATTTATATTAATTTT
1370255 TAAATATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.19
31 11 0.23
32 17 0.35
33 11 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
ATATTTTATATTTATATTAATTTTATAGAAA
Found at i:1370251 original size:18 final size:17
Alignment explanation
Indices: 1370184--1370251 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 17
1370174 TTATTTTATT
1370184 ATAA-TTATATATA-AA
1 ATAATTTATATATATAA
* *
1370199 ATATTTTATATTTAT-A
1 ATAATTTATATATATAA
* *
1370215 TTAATTT-TGATAGATAA
1 ATAATTTAT-ATATATAA
1370232 ATAATTTATATTATATAA
1 ATAATTTATA-TATATAA
1370250 AT
1 AT
1370252 TTTTAAATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
15 4 0.10
16 18 0.46
17 8 0.21
18 9 0.23
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATAATTTATATATATAA
Found at i:1371059 original size:192 final size:192
Alignment explanation
Indices: 1370743--1371124 Score: 746
Period size: 192 Copynumber: 2.0 Consensus size: 192
1370733 CCTGTTTGAG
1370743 TTTGATGGAACACTAGGGCATGATAGACATGTCCACAACGTAGAAGCCAGTGAGAATTGGATGAC
1 TTTGATGGAACACTAGGGCATGATAGACATGTCCACAACGTAGAAGCCAGTGAGAATTGGATGAC
1370808 ACCGATCATTGCATTTCTCAAAAACAATGTCTTTTTGGAAGATCCATTACAAAGAAGGTGATTAG
66 ACCGATCATTGCATTTCTCAAAAACAATGTCTTTTTGGAAGATCCATTACAAAGAAGGTGATTAG
1370873 AAAATAGAGTCCCAAGGGTACACAATAATCAATGACATTCTATAAAAAAAATCTTTACTCAC
131 AAAATAGAGTCCCAAGGGTACACAATAATCAATGACATTCTATAAAAAAAATCTTTACTCAC
*
1370935 TTTGTTGGAACACTAGGGCATGATAGACATGTCCACAACGTAGAAGCCAGTGAGAATTGGATGAC
1 TTTGATGGAACACTAGGGCATGATAGACATGTCCACAACGTAGAAGCCAGTGAGAATTGGATGAC
*
1371000 ACCGATCATTGCATTTCTCAAAAACAATGTCTTTTTGGAAGATCCATTACAAGGAAGGTGATTAG
66 ACCGATCATTGCATTTCTCAAAAACAATGTCTTTTTGGAAGATCCATTACAAAGAAGGTGATTAG
1371065 AAAATAGAGTCCCAAGGGTACACAATAATCAATGACATTCTATAAAAAAAATCTTTACTC
131 AAAATAGAGTCCCAAGGGTACACAATAATCAATGACATTCTATAAAAAAAATCTTTACTC
1371125 GCCCTTTGCT
Statistics
Matches: 188, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
192 188 1.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.26
Consensus pattern (192 bp):
TTTGATGGAACACTAGGGCATGATAGACATGTCCACAACGTAGAAGCCAGTGAGAATTGGATGAC
ACCGATCATTGCATTTCTCAAAAACAATGTCTTTTTGGAAGATCCATTACAAAGAAGGTGATTAG
AAAATAGAGTCCCAAGGGTACACAATAATCAATGACATTCTATAAAAAAAATCTTTACTCAC
Found at i:1376214 original size:24 final size:23
Alignment explanation
Indices: 1376187--1376232 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
1376177 AAGTAATTAT
1376187 GTTATAAGAAAAACCTAATATAAG
1 GTTATAAGAAAAACCTAA-ATAAG
*
1376211 GTTATAAGGAAAACCTAAATAA
1 GTTATAAGAAAAACCTAAATAA
1376233 TTAAAACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (23 bp):
GTTATAAGAAAAACCTAAATAAG
Found at i:1381626 original size:19 final size:16
Alignment explanation
Indices: 1381587--1381624 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1381577 TAATATTATC
1381587 AATAATCATGTGATCT
1 AATAATCATGTGATCT
1381603 AATAATCATGTGATCT
1 AATAATCATGTGATCT
1381619 AATAAT
1 AATAAT
1381625 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (16 bp):
AATAATCATGTGATCT
Found at i:1384443 original size:21 final size:21
Alignment explanation
Indices: 1384392--1384443 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
1384382 ACGTATTGAA
1384392 AAAATATTAGTATTATTAAAAT
1 AAAATATTA-TATTATTAAAAT
* *
1384414 AACATTATT-TATTATTATAACT
1 AA-AATATTATATTATTA-AAAT
1384436 AAAATATT
1 AAAATATT
1384444 CCTCGTACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 13 0.52
22 7 0.28
23 5 0.20
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
AAAATATTATATTATTAAAAT
Found at i:1385676 original size:32 final size:32
Alignment explanation
Indices: 1385640--1385727 Score: 113
Period size: 32 Copynumber: 2.8 Consensus size: 32
1385630 GGCCAAAGTA
* *
1385640 AACTTATGCCAAGATGACTATTGGCTAAGCTG
1 AACTTATGCCAAGTTGACTTTTGGCTAAGCTG
* * *
1385672 AACTTATACCAAGTTGACTTTTGACTAAGGTG
1 AACTTATGCCAAGTTGACTTTTGGCTAAGCTG
* *
1385704 AACTTACGCTAAGTTGACTTTTGG
1 AACTTATGCCAAGTTGACTTTTGG
1385728 ATGAGACAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (32 bp):
AACTTATGCCAAGTTGACTTTTGGCTAAGCTG
Found at i:1390257 original size:7 final size:7
Alignment explanation
Indices: 1390245--1390323 Score: 61
Period size: 7 Copynumber: 10.9 Consensus size: 7
1390235 TTTTCATCTA
1390245 TATTTTT
1 TATTTTT
1390252 TATTTTCT
1 TATTTT-T
1390260 TATTTTT
1 TATTTTT
**
1390267 TATTTCACA
1 TATTT--TT
*
1390276 CATTTTT
1 TATTTTT
* * *
1390283 CACTTAT
1 TATTTTT
1390290 -ATTTTT
1 TATTTTT
1390296 ATATTTTT
1 -TATTTTT
1390304 TATTTTT
1 TATTTTT
1390311 TATTTTT
1 TATTTTT
1390318 TATTTT
1 TATTTT
1390324 ACCCATTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
6 4 0.07
7 37 0.64
8 13 0.22
9 4 0.07
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTTTT
Found at i:1390263 original size:15 final size:14
Alignment explanation
Indices: 1390245--1390323 Score: 61
Period size: 15 Copynumber: 5.4 Consensus size: 14
1390235 TTTTCATCTA
1390245 TATTTTTTATTTTCT
1 TATTTTTTATTTT-T
**
1390260 TATTTTTTATTTCACA
1 TATTTTTTATTT--TT
* * * *
1390276 CATTTTTCACTTAT
1 TATTTTTTATTTTT
1390290 -ATTTTTATATTTTT
1 TATTTTT-TATTTTT
1390304 TATTTTTTATTTTT
1 TATTTTTTATTTTT
1390318 TATTTT
1 TATTTT
1390324 ACCCATTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
13 6 0.12
14 17 0.34
15 18 0.36
16 9 0.18
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTTTATTTTT
Found at i:1390445 original size:22 final size:20
Alignment explanation
Indices: 1390404--1390448 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1390394 CTGAATTTAT
*
1390404 TTTTTTAGTTTAAAAGTGTA
1 TTTTTTAGTTTAAAAATGTA
*
1390424 TTTTTTATTTTAATATAATGTA
1 TTTTTTAGTTTAA-A-AATGTA
1390446 TTT
1 TTT
1390449 AAAATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 1 0.05
22 8 0.38
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (20 bp):
TTTTTTAGTTTAAAAATGTA
Found at i:1392944 original size:19 final size:20
Alignment explanation
Indices: 1392920--1392962 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1392910 ATTTCATGAG
*
1392920 AAAAATCAA-TATTTTTTAA
1 AAAAATAAATTATTTTTTAA
1392939 AAAAATAAATTTATTTTTTAA
1 AAAAATAAA-TTATTTTTTAA
1392960 AAA
1 AAA
1392963 TCATTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
21 13 0.62
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAAATAAATTATTTTTTAA
Found at i:1399299 original size:17 final size:17
Alignment explanation
Indices: 1399271--1399313 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1399261 ATCTCGTTAA
1399271 ATTTTTTATATT-TTGTTT
1 ATTTTTT-TATTGTT-TTT
*
1399289 CTTTTTTTATTGTTTTT
1 ATTTTTTTATTGTTTTT
1399306 ATTTTTTT
1 ATTTTTTT
1399314 TAATAACTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.81
Consensus pattern (17 bp):
ATTTTTTTATTGTTTTT
Found at i:1400655 original size:3 final size:3
Alignment explanation
Indices: 1400647--1400677 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1400637 GTGCTAGCTT
1400647 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1400678 CTCAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1402249 original size:195 final size:193
Alignment explanation
Indices: 1401894--1402253 Score: 472
Period size: 195 Copynumber: 1.9 Consensus size: 193
1401884 ACCGTTAAAG
*** * **
1401894 AAAATTAAAATTTTGAAAATAAAATAAATTAATGTAAACCATAACTTTTGTTTATTATTGAATAA
1 AAAATTAAAATTTTGAAAATAAAATAAATTAACAAAAACCATAACTTTTATTTATTATAAAATAA
* *
1401959 ATTTATTTAACAAAAATCTTTTAATGAAACTAAAATTTTTCTTTATAAATTTGATAAATCTTATT
66 ATTTATTTAACAAAAATCTTTTAATGAAACTAAAATTTTACTTTATAAATTGGATAAATCTTATT
* *
1402024 AATAGTAAAAAATTTTACAATAGCAATTTAGTAAATAAATTTGCTTGTTTTTTAAATTTAATGA
131 AATAGGAAAAAATCTTACAATAGCAATTTAG-AAATAAATTTGCTTGTTTTTTAAATTTAATGA
* * * ***
1402088 AAAATTAAACTTTTGGAAATAAAATAATTTAACAAAAATTTTAACTTTTTATTTATTATAAAATA
1 AAAATTAAAATTTTGAAAATAAAATAAATTAACAAAAACCATAAC-TTTTATTTATTATAAAATA
* * *
1402153 AATTTATTTAACAAAATTTTTTTAATGAAATTAAAATTCTTAC-TTATAAATTGGATAAATCTTA
65 AATTTATTTAACAAAAATCTTTTAATGAAACTAAAATT-TTACTTTATAAATTGGATAAATCTTA
* * *
1402217 TTAATAGGAAAACATCTTAGAAT-GATAATTTAGAAAT
129 TTAATAGGAAAAAATCTTACAATAG-CAATTTAGAAAT
1402254 TAAGCCCATT
Statistics
Matches: 141, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
194 41 0.29
195 97 0.69
196 3 0.02
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (193 bp):
AAAATTAAAATTTTGAAAATAAAATAAATTAACAAAAACCATAACTTTTATTTATTATAAAATAA
ATTTATTTAACAAAAATCTTTTAATGAAACTAAAATTTTACTTTATAAATTGGATAAATCTTATT
AATAGGAAAAAATCTTACAATAGCAATTTAGAAATAAATTTGCTTGTTTTTTAAATTTAATGA
Found at i:1403131 original size:16 final size:16
Alignment explanation
Indices: 1403112--1403142 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1403102 CAAGCACAAA
1403112 AAATTTAAACTTAAAT
1 AAATTTAAACTTAAAT
*
1403128 AAATTTAAATTTAAA
1 AAATTTAAACTTAAA
1403143 ACAGTCTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTTAAACTTAAAT
Found at i:1403901 original size:20 final size:20
Alignment explanation
Indices: 1403876--1403917 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1403866 AAATAATATA
*
1403876 AATATATATATGAATTTTAT
1 AATATATAAATGAATTTTAT
*
1403896 AATATATAAATTAATTTTAT
1 AATATATAAATGAATTTTAT
1403916 AA
1 AA
1403918 ATTGAGGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AATATATAAATGAATTTTAT
Found at i:1403989 original size:9 final size:9
Alignment explanation
Indices: 1403977--1404032 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
1403967 TATATATATG
1403977 AATTTTATA
1 AATTTTATA
1403986 AATTTTAT-
1 AATTTTATA
1403994 AA-TTTATA
1 AATTTTATA
* *
1404002 CATATTATA
1 AATTTTATA
*
1404011 TATTTTATA
1 AATTTTATA
*
1404020 CATATTTATA
1 AAT-TTTATA
1404030 AAT
1 AAT
1404033 ATTTTTATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
7 5 0.13
8 3 0.08
9 22 0.58
10 8 0.21
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (9 bp):
AATTTTATA
Found at i:1404017 original size:18 final size:17
Alignment explanation
Indices: 1403978--1404029 Score: 70
Period size: 18 Copynumber: 3.1 Consensus size: 17
1403968 ATATATATGA
*
1403978 ATTTTATAAAT-TTTAT
1 ATTTTATACATATTTAT
*
1403994 AATTTATACATATTATAT
1 ATTTTATACATATT-TAT
1404012 ATTTTATACATATTTAT
1 ATTTTATACATATTTAT
1404029 A
1 A
1404030 AATATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 9 0.29
17 6 0.19
18 16 0.52
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATACATATTTAT
Done.