Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold21
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: 2821038
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 98422 characters in sequence are not A, C, G, or T
File 9 of 15
Found at i:1236090 original size:27 final size:27
Alignment explanation
Indices: 1236059--1236113 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1236049 TATATATATA
1236059 TATATATATATATATATATTGAGCTTT
1 TATATATATATATATATATTGAGCTTT
* *
1236086 TATATATATGTATATATCTTGAGCTTT
1 TATATATATATATATATATTGAGCTTT
1236113 T
1 T
1236114 GTAAATTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (27 bp):
TATATATATATATATATATTGAGCTTT
Found at i:1236094 original size:2 final size:2
Alignment explanation
Indices: 1236049--1236077 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1236039 AAGGAAGAGT
1236049 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1236078 TGAGCTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1236383 original size:20 final size:20
Alignment explanation
Indices: 1236318--1236383 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
1236308 GTTGTTTTAT
*
1236318 TATATA-TTTTATTATCAAA
1 TATATATTTTTATTATTAAA
1236337 -ATATTATTTTT-TATATTAATA
1 TATA-TATTTTTAT-TATTAA-A
1236358 TTTATATATTTTTATTATTAAA
1 --TATATATTTTTATTATTAAA
1236380 TATA
1 TATA
1236384 AATAAAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 15
0.70 0.02 0.28
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 13 0.34
21 1 0.03
22 1 0.03
23 13 0.34
24 4 0.11
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATATTTTTATTATTAAA
Found at i:1239444 original size:15 final size:16
Alignment explanation
Indices: 1239393--1239445 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
1239383 TTAAGATATT
*
1239393 TTTTAAATTATATAAA
1 TTTTATATTATATAAA
*
1239409 TTTTGATATGT-TATTAA
1 TTTT-ATAT-TATATAAA
1239426 TTTT-TATTATATAAA
1 TTTTATATTATATAAA
1239441 TTTTA
1 TTTTA
1239446 AAATAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
14 1 0.03
15 12 0.40
16 4 0.13
17 12 0.40
18 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
TTTTATATTATATAAA
Found at i:1239471 original size:11 final size:11
Alignment explanation
Indices: 1239457--1239525 Score: 61
Period size: 11 Copynumber: 6.1 Consensus size: 11
1239447 AATAATTATA
*
1239457 TATTTATATTG
1 TATTTATATTT
1239468 TATTTGTATAATTT
1 TA-TT-TAT-ATTT
*
1239482 T-TTTATATTA
1 TATTTATATTT
1239492 TA-TTATATTT
1 TATTTATATTT
1239502 TATATTATATTT
1 TAT-TTATATTT
*
1239514 TAATTATATTT
1 TATTTATATTT
1239525 T
1 T
1239526 TATATTTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
10 13 0.27
11 14 0.29
12 14 0.29
13 3 0.06
14 4 0.08
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (11 bp):
TATTTATATTT
Found at i:1239490 original size:19 final size:18
Alignment explanation
Indices: 1239468--1239537 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 18
1239458 ATTTATATTG
1239468 TATTTGTATAATTTTTTTA
1 TATTT-TATAATTTTTTTA
*
1239487 TATTATATTATATTTTATATTA
1 TATTTTA-TA-ATTTT-T-TTA
* *
1239509 TATTTTAATTATATTTTTA
1 TATTTT-ATAATTTTTTTA
1239528 TATTTTATAA
1 TATTTTATAA
1239538 ACATATCATA
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
18 5 0.12
19 15 0.37
20 6 0.15
21 5 0.12
22 9 0.22
23 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (18 bp):
TATTTTATAATTTTTTTA
Found at i:1239504 original size:17 final size:17
Alignment explanation
Indices: 1239482--1239536 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
1239472 TGTATAATTT
1239482 TTTTATATTATATTATA
1 TTTTATATTATATTATA
*
1239499 TTTTATATTATATTTTA
1 TTTTATATTATATTATA
*
1239516 -ATTATATT-T-TTATA
1 TTTTATATTATATTATA
1239530 TTTTATA
1 TTTTATA
1239537 AACATATCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 4 0.12
15 6 0.18
16 7 0.21
17 16 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATATTATATTATA
Found at i:1239504 original size:41 final size:42
Alignment explanation
Indices: 1239451--1239531 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
1239441 TTTTAAAATA
* *
1239451 ATTATATATTTATATTGTATTTGT-ATAATTTTTTTATATTAT
1 ATTATATATTTATATTATATTT-TAATAATATTTTTATATTAT
*
1239493 ATTATAT-TTTATATTATATTTTAATTATATTTTTATATT
1 ATTATATATTTATATTATATTTTAATAATATTTTTATATT
1239532 TTATAAACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 1 0.03
41 27 0.77
42 7 0.20
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.65
Consensus pattern (42 bp):
ATTATATATTTATATTATATTTTAATAATATTTTTATATTAT
Found at i:1239506 original size:12 final size:12
Alignment explanation
Indices: 1239489--1239531 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
1239479 TTTTTTTATA
1239489 TTATATTATATT
1 TTATATTATATT
1239501 TTATATTATATT
1 TTATATTATATT
1239513 TTA-ATTATATTT
1 TTATATTATA-TT
1239525 TTATATT
1 TTATATT
1239532 TTATAAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.21
12 20 0.69
13 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATTATATT
Found at i:1243141 original size:8 final size:8
Alignment explanation
Indices: 1243123--1243175 Score: 62
Period size: 8 Copynumber: 7.2 Consensus size: 8
1243113 AAAATCTATT
1243123 TTATTAT-
1 TTATTATA
1243130 TTATTATA
1 TTATTATA
*
1243138 TTATTAAA
1 TTATTATA
1243146 TTATTAT-
1 TTATTATA
1243153 TT-TTATA
1 TTATTATA
1243160 TTATTAT-
1 TTATTATA
1243167 TTA-TATA
1 TTATTATA
1243174 TT
1 TT
1243176 TTAAAAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 7 0.17
7 16 0.40
8 17 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTATTATA
Found at i:1243173 original size:14 final size:14
Alignment explanation
Indices: 1243123--1243175 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
1243113 AAAATCTATT
1243123 TTATTATTTAT-TA
1 TTATTATTTATATA
1243136 -TATTA-TTA-A-A
1 TTATTATTTATATA
*
1243146 TTATTATTTTTATA
1 TTATTATTTATATA
1243160 TTATTATTTATATA
1 TTATTATTTATATA
1243174 TT
1 TT
1243176 TTAAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 8 0.24
12 7 0.21
13 1 0.03
14 16 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATTATTTATATA
Found at i:1246654 original size:17 final size:20
Alignment explanation
Indices: 1246615--1246712 Score: 64
Period size: 20 Copynumber: 5.0 Consensus size: 20
1246605 CAAGATTAAT
*
1246615 TAATATATTATATATAATAA
1 TAATATTTTATATATAATAA
1246635 TAATATTTTAT-TA-AAT-A
1 TAATATTTTATATATAATAA
* * * *
1246652 TAATAATTTATAATTTTATTTA
1 TAATATTTTAT-A-TATAATAA
1246674 TAAT-TTTTA-ATATAATAA
1 TAATATTTTATATATAATAA
* *
1246692 -AAAAGTATTATATATAATAA
1 TAATA-TTTTATATATAATAA
1246712 T
1 T
1246713 TTAAAAATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 17
0.69 0.12 0.20
Matches are distributed among these distances:
17 13 0.22
18 8 0.14
19 7 0.12
20 20 0.34
21 6 0.10
22 5 0.08
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
TAATATTTTATATATAATAA
Found at i:1247540 original size:22 final size:20
Alignment explanation
Indices: 1247505--1247553 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
1247495 TATATATTTT
1247505 ATTAATAAATTTAAAAATAA
1 ATTAATAAATTTAAAAATAA
1247525 ATTATATATAATTTAAAAAT--
1 ATTA-ATA-AATTTAAAAATAA
1247545 ATTAATAAA
1 ATTAATAAA
1247554 CTTATATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 3 0.11
20 8 0.30
21 3 0.11
22 11 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTAATAAATTTAAAAATAA
Found at i:1250343 original size:21 final size:20
Alignment explanation
Indices: 1250317--1250355 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1250307 ATTTTAGATA
1250317 AAAAGATATATTTATTAATTG
1 AAAAGATAT-TTTATTAATTG
*
1250338 AAAAGATATTTTTTTAAT
1 AAAAGATATTTTATTAAT
1250356 AGTTATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
AAAAGATATTTTATTAATTG
Found at i:1252506 original size:15 final size:16
Alignment explanation
Indices: 1252473--1252517 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
1252463 TTTTTATTTA
*
1252473 AATTT-AATGATAA-T
1 AATTTAAATTATAATT
1252487 AATTTAAATTA-AATT
1 AATTTAAATTATAATT
1252502 AATTTAAATTATAATT
1 AATTTAAATTATAATT
1252518 TTTTTATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 7 0.26
15 16 0.59
16 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
AATTTAAATTATAATT
Found at i:1254051 original size:14 final size:14
Alignment explanation
Indices: 1254034--1254073 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1254024 GTTTTAATTT
1254034 TTTTATATTTAAAA
1 TTTTATATTTAAAA
* *
1254048 TTTTATATTT-TAT
1 TTTTATATTTAAAA
1254061 TTTTATATTTAAA
1 TTTTATATTTAAA
1254074 TATACGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTATATTTAAAA
Found at i:1255262 original size:2 final size:2
Alignment explanation
Indices: 1255255--1255284 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1255245 GAATTTTAAA
1255255 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
1255285 TGGTCACAAG
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:1265081 original size:6 final size:6
Alignment explanation
Indices: 1265070--1265189 Score: 51
Period size: 6 Copynumber: 20.7 Consensus size: 6
1265060 AAAAATTATG
*
1265070 TATTTA TATTTA TA-TT- T-TTTA TATTTA AATTATTA TAATTT- T-TTATA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TA-T-TTA T-ATTTA TATT-TA
* * * * * *
1265117 TATTAA TAATT- TATTT- TATTT- TATGTA TATTTA TATATA TATATG
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
* *
1265162 TATTCA TA-TTA TATATTA TTTTTA TATT
1 TATTTA TATTTA TAT-TTA TATTTA TATT
1265190 ATGTTTTAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
4 5 0.06
5 21 0.24
6 45 0.52
7 10 0.12
8 4 0.05
9 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (6 bp):
TATTTA
Found at i:1267189 original size:23 final size:23
Alignment explanation
Indices: 1267139--1267194 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
1267129 ATTTTAAAAA
*
1267139 ATTAAAAAATATCAATAATTATTT
1 ATTAAAAAATA-CAAAAATTATTT
1267163 -TTAAAAAATA-AAAAATTATTAT
1 ATTAAAAAATACAAAAATTATT-T
1267185 ATTAATAAAA
1 ATTAA-AAAA
1267195 ATATTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 9 0.32
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTAAAAAATACAAAAATTATTT
Found at i:1269541 original size:2 final size:2
Alignment explanation
Indices: 1269534--1269560 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1269524 CAATGTCAGT
1269534 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1269561 TGATATTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1269566 original size:6 final size:6
Alignment explanation
Indices: 1269557--1269584 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1269547 ATATATATAT
1269557 ATATTG ATATTG ATATTG ATATTG ATAT
1 ATATTG ATATTG ATATTG ATATTG ATAT
1269585 AAATGAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (6 bp):
ATATTG
Found at i:1271793 original size:2 final size:2
Alignment explanation
Indices: 1271786--1271820 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1271776 TAATTCATCC
1271786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1271821 AAGAAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1273564 original size:16 final size:17
Alignment explanation
Indices: 1273535--1273567 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1273525 TATTTTTTAT
*
1273535 TAAATTATATTTTAATA
1 TAAATAATATTTTAATA
1273552 TAAATAATA-TTTAATA
1 TAAATAATATTTTAATA
1273568 ATTATTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATAATATTTTAATA
Found at i:1273573 original size:28 final size:29
Alignment explanation
Indices: 1273540--1273604 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
1273530 TTTATTAAAT
* *
1273540 TATATTTTAATATAA-ATAATATTTAATA
1 TATATTTTAACATAATATAACATTTAATA
*
1273568 -AT-TATTTAACATAATATCACATTTAATA
1 TATAT-TTTAACATAATATAACATTTAATA
1273596 TATATTTTA
1 TATATTTTA
1273605 TTATTTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
26 1 0.03
27 11 0.37
28 11 0.37
29 6 0.20
30 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (29 bp):
TATATTTTAACATAATATAACATTTAATA
Found at i:1274136 original size:21 final size:22
Alignment explanation
Indices: 1274098--1274141 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1274088 GATGCTTCTC
*
1274098 TTAAATATAATAATTTATATAT
1 TTAAATAAAATAATTTATATAT
1274120 TTAAATAAAAT-ATTTATATAT
1 TTAAATAAAATAATTTATATAT
1274141 T
1 T
1274142 ATTTATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAATAAAATAATTTATATAT
Found at i:1274175 original size:12 final size:10
Alignment explanation
Indices: 1274129--1274215 Score: 52
Period size: 11 Copynumber: 8.0 Consensus size: 10
1274119 TTTAAATAAA
1274129 ATATTTATAT
1 ATATTTATAT
1274139 ATTATTTATGATT
1 A-TATTTAT-A-T
*
1274152 AAATTATATAT
1 ATATT-TATAT
1274163 AATATATTATAT
1 -ATAT-TTATAT
*
1274175 ATATTT-TTT
1 ATATTTATAT
1274184 AATATATT-TAT
1 -ATAT-TTATAT
1274195 ATATTTATATT
1 ATATTTATA-T
*
1274206 AAATTTATAT
1 ATATTTATAT
1274216 TTTTTTTACA
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
9 4 0.06
10 14 0.23
11 25 0.40
12 13 0.21
13 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (10 bp):
ATATTTATAT
Found at i:1274249 original size:27 final size:27
Alignment explanation
Indices: 1274135--1274249 Score: 71
Period size: 27 Copynumber: 4.3 Consensus size: 27
1274125 TAAAATATTT
* *
1274135 ATATATTAT-TTATGATTAAATTATATATA
1 ATATTTTATATTAT-ATTATATT-TA-ATA
*
1274164 ATATATTATA-TATATT-T-TTTAAT-
1 ATATTTTATATTATATTATATTTAATA
*
1274187 ATATTTATATATTTATATTAAATTT-ATA
1 ATATTT-TATA-TTATATTATATTTAATA
* * *
1274215 TTTTTTTTACATTATATTATATTTAATA
1 -ATATTTTATATTATATTATATTTAATA
1274243 ATATTTT
1 ATATTTT
1274250 TAATATCATT
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
23 5 0.07
24 6 0.09
25 2 0.03
26 8 0.12
27 19 0.28
28 12 0.18
29 16 0.24
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (27 bp):
ATATTTTATATTATATTATATTTAATA
Found at i:1274598 original size:2 final size:2
Alignment explanation
Indices: 1274591--1274615 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1274581 TATAAGAGTC
1274591 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
1274616 AAGCACTTAT
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:1280793 original size:12 final size:12
Alignment explanation
Indices: 1280778--1280802 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1280768 GTCATATGTA
1280778 TGAAATTGCTAG
1 TGAAATTGCTAG
1280790 TGAAATTGCTAG
1 TGAAATTGCTAG
1280802 T
1 T
1280803 CTAATCGGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (12 bp):
TGAAATTGCTAG
Found at i:1283582 original size:2 final size:2
Alignment explanation
Indices: 1283575--1283605 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1283565 AAGCGGAAGA
1283575 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1283606 AACCGATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1283815 original size:2 final size:2
Alignment explanation
Indices: 1283810--1283838 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1283800 TATAACTTTA
1283810 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1283839 TTTGTCTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1285313 original size:2 final size:2
Alignment explanation
Indices: 1285306--1285337 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1285296 AACCATGATA
1285306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1285338 TTGATGGCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1289226 original size:18 final size:18
Alignment explanation
Indices: 1289203--1289378 Score: 73
Period size: 18 Copynumber: 9.7 Consensus size: 18
1289193 TAAATTTGAT
1289203 AATATTAAATATAATATA
1 AATATTAAATATAATATA
* * *
1289221 AATATTATATAAAAAATTA
1 AATATTAAATATAATA-TA
* *
1289240 AATATGATATA-AATTATAA
1 AATATTAAATATAA-TAT-A
* *
1289259 AAAATTTGAATATAATATA
1 AATA-TTAAATATAATATA
*
1289278 AATA-TATAA-ATAATTTA
1 AATATTA-AATATAATATA
*
1289295 AA-ATT-TATATAATATGA
1 AATATTAAATATAATAT-A
*
1289312 ATTATT-AATATAATA-A
1 AATATTAAATATAATATA
*
1289328 AAT-TTATATA-AATATAA
1 AATATTAAATATAATAT-A
*
1289345 AATATTTTATATATAATTATA
1 AATA--TTAAATATAA-TATA
*
1289366 ATATAATAAATAT
1 A-ATATTAAATAT
1289379 GTTATTATAA
Statistics
Matches: 119, Mismatches: 20, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
15 7 0.06
16 13 0.11
17 17 0.14
18 29 0.24
19 21 0.18
20 20 0.17
21 6 0.05
22 6 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AATATTAAATATAATATA
Found at i:1289270 original size:27 final size:28
Alignment explanation
Indices: 1289207--1289296 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 28
1289197 TTTGATAATA
*
1289207 TTAAATATAATATAAATATTATATAAAAAA
1 TTAAATATAATATAAATA-TATA-AAAAAT
*
1289237 TTAAATATGATATAAAT-TATAAAAAAT
1 TTAAATATAATATAAATATATAAAAAAT
* *
1289264 TTGAATATAATATAAATATATAAATAAT
1 TTAAATATAATATAAATATATAAAAAAT
1289292 TTAAA
1 TTAAA
1289297 ATTTATATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
27 20 0.38
28 17 0.32
30 16 0.30
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
TTAAATATAATATAAATATATAAAAAAT
Found at i:1289333 original size:32 final size:32
Alignment explanation
Indices: 1289246--1289349 Score: 101
Period size: 33 Copynumber: 3.2 Consensus size: 32
1289236 ATTAAATATG
1289246 ATATA-AATTATAA-AAAATTTGAATATAATATAA
1 ATATATAA-TATAATAAAATTT--ATATAATATAA
*
1289279 ATATATAA-ATAATTTAAAATTTATATAATATGA
1 ATATATAATATAA--TAAAATTTATATAATATAA
1289312 AT-TATTAATATAATAAAATTTATATAAATATAA
1 ATATA-TAATATAATAAAATTTATAT-AATATAA
1289345 A-ATAT
1 ATATAT
1289350 TTTATATATA
Statistics
Matches: 61, Mismatches: 2, Indels: 17
0.76 0.03 0.21
Matches are distributed among these distances:
32 19 0.31
33 29 0.48
34 6 0.10
35 7 0.11
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (32 bp):
ATATATAATATAATAAAATTTATATAATATAA
Found at i:1289366 original size:28 final size:27
Alignment explanation
Indices: 1289333--1289398 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
1289323 AATAAAATTT
*
1289333 ATATAAATATA-AAATATTTTATATATA
1 ATATAAATATATAAATATGTTAT-TATA
1289360 AT-TATAATATAATAAATATGTTATTATA
1 ATATA-AATAT-ATAAATATGTTATTATA
*
1289388 ATAAAAATATA
1 ATATAAATATA
1289399 CGAATTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
26 2 0.06
27 8 0.24
28 12 0.36
29 11 0.33
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATAAATATATAAATATGTTATTATA
Found at i:1289377 original size:4 final size:5
Alignment explanation
Indices: 1289210--1289378 Score: 57
Period size: 5 Copynumber: 33.0 Consensus size: 5
1289200 GATAATATTA
* * *
1289210 AATAT AATAT AAATAT TATAT AA-AA AAT-T AAATAT GATAT AAATTAT
1 AATAT AATAT -AATAT AATAT AATAT AATAT -AATAT AATAT -AA-TAT
* * * * *
1289257 AA-AA AATTT GAATAT AATAT AA-AT -ATAT AA-AT AATTT AAAATT TATAT
1 AATAT AATAT -AATAT AATAT AATAT AATAT AATAT AATAT AATA-T AATAT
* * * * *
1289305 AATAT GAATTATT AATAT AATAA AAT-T TATAT AAATAT AAAAT ATTTT
1 AATAT -AA-TA-T AATAT AATAT AATAT AATAT -AATAT AATAT AATAT
1289353 ATATAT AATTAT AATAT AATA- AATAT
1 A-ATAT AA-TAT AATAT AATAT AATAT
1289379 GTTATTATAA
Statistics
Matches: 118, Mismatches: 26, Indels: 40
0.64 0.14 0.22
Matches are distributed among these distances:
3 1 0.01
4 20 0.17
5 57 0.48
6 32 0.27
7 7 0.06
8 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:1289378 original size:22 final size:22
Alignment explanation
Indices: 1289306--1289390 Score: 62
Period size: 22 Copynumber: 3.6 Consensus size: 22
1289296 AATTTATATA
1289306 ATATGAATTATTAATATAATAAAATTT
1 ATAT-AATTA-TAATATAAT-AAA--T
* * * **
1289333 ATATAAATATAAAATATTTTAT
1 ATATAATTATAATATAATAAAT
1289355 ATATAATTATAATATAATAAAT
1 ATATAATTATAATATAATAAAT
* *
1289377 ATGTTATTATAATA
1 ATATAATTATAATA
1289391 AAAATATACG
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
22 30 0.65
24 1 0.02
25 7 0.15
26 4 0.09
27 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATAATTATAATATAATAAAT
Found at i:1290852 original size:2 final size:2
Alignment explanation
Indices: 1290841--1290875 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1290831 ACACACACAC
* *
1290841 AT AT AC AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1290876 ATGGAATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1295768 original size:20 final size:20
Alignment explanation
Indices: 1295717--1295791 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
1295707 AAAAAGACAT
1295717 AATGTATCGATACATTGTAG
1 AATGTATCGATACATTGTAG
* *
1295737 AATATATCGATACATT-TAT
1 AATGTATCGATACATTGTAG
* * * *
1295756 ACATGTATTGATATATTGAAA
1 A-ATGTATCGATACATTGTAG
*
1295777 AATGTATCAATACAT
1 AATGTATCGATACAT
1295792 CAGGGTATGA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 3 0.07
20 38 0.88
21 2 0.05
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTGTAG
Found at i:1303097 original size:30 final size:29
Alignment explanation
Indices: 1303041--1303113 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
1303031 TATAATTATT
1303041 TTTAAAAATAATATTTAATAAATTTTAAA
1 TTTAAAAATAATATTTAATAAATTTTAAA
* **
1303070 TTTAAATATTAATATTT-AT-AATTTTTTA
1 TTTAAA-AATAATATTTAATAAATTTTAAA
*
1303098 TTTATAAATAA-ATTTA
1 TTTAAAAATAATATTTA
1303114 TTTATGAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
26 4 0.11
27 4 0.11
28 12 0.32
29 8 0.22
30 9 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTAAAAATAATATTTAATAAATTTTAAA
Found at i:1303115 original size:16 final size:16
Alignment explanation
Indices: 1303094--1303129 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1303084 TTTATAATTT
1303094 TTTATTTATAAATAAA
1 TTTATTTATAAATAAA
* *
1303110 TTTATTTATGAATCAA
1 TTTATTTATAAATAAA
1303126 TTTA
1 TTTA
1303130 AATCGTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTATTTATAAATAAA
Found at i:1303326 original size:2 final size:2
Alignment explanation
Indices: 1303319--1303349 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1303309 AACTAGACCA
1303319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1303350 ATCTGTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1305797 original size:4 final size:4
Alignment explanation
Indices: 1305782--1305828 Score: 80
Period size: 4 Copynumber: 12.2 Consensus size: 4
1305772 TTTGTTGCAA
1305782 TCTT TC-T T-TT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1305828 T
1 T
1305829 GTTTTTACGT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 4 0.10
4 37 0.90
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TCTT
Found at i:1310416 original size:47 final size:41
Alignment explanation
Indices: 1310365--1310448 Score: 96
Period size: 45 Copynumber: 1.9 Consensus size: 41
1310355 AATATTCATA
1310365 AAATATAATAAATAATTAAATATCATTTATTAAATTTTAATATATGT
1 AAATAT-AT-AATAATTAAATAT-ATTT-TT-AA-TTTAATATATGT
* *
1310412 AAATATATAATACTTATATATATTTTTAATTTAATAT
1 AAATATATAATAATTAAATATATTTTTAATTTAATAT
1310449 TTTTAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
41 8 0.23
42 2 0.06
43 2 0.06
44 4 0.11
45 11 0.31
46 2 0.06
47 6 0.17
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (41 bp):
AAATATATAATAATTAAATATATTTTTAATTTAATATATGT
Found at i:1312038 original size:17 final size:17
Alignment explanation
Indices: 1312013--1312072 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
1312003 AAAAAATATA
*
1312013 AATTTTATTATAATTTT
1 AATTATATTATAATTTT
1312030 AATTATATTAT-A-TTT
1 AATTATATTATAATTTT
1312045 -ATTATAATTATAAATTTT
1 AATTAT-ATTAT-AATTTT
*
1312063 AATTACATTA
1 AATTATATTA
1312073 AGTTTATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 5 0.14
15 8 0.22
16 1 0.03
17 11 0.31
18 7 0.19
19 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTATATTATAATTTT
Found at i:1312061 original size:33 final size:32
Alignment explanation
Indices: 1312019--1312085 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
1312009 TATAAATTTT
*
1312019 ATTATAATTTTAATTATATTATA-TTTATTATA
1 ATTATAATTTTAATTACATTA-AGTTTATTATA
1312051 ATTATAAATTTTAATTACATTAAGTTTATTATA
1 ATTAT-AATTTTAATTACATTAAGTTTATTATA
1312084 AT
1 AT
1312086 CAATATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (32 bp):
ATTATAATTTTAATTACATTAAGTTTATTATA
Found at i:1312352 original size:26 final size:29
Alignment explanation
Indices: 1312287--1312352 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 29
1312277 AAATTATTCA
1312287 TTTAATAA-AAATATAATTTTAATTTAATT
1 TTTAATAATAAATATAATTTTAA-TTAATT
*
1312316 ATTAA-ATATAAA-AT-ATTTTAA-TAATT
1 TTTAATA-ATAAATATAATTTTAATTAATT
1312342 TTTAATAATAA
1 TTTAATAATAA
1312353 TTTAACTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
26 13 0.41
27 1 0.03
28 8 0.25
29 7 0.22
30 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTAATAATAAATATAATTTTAATTAATT
Found at i:1313707 original size:16 final size:15
Alignment explanation
Indices: 1313665--1313709 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1313655 ATAAATAAAA
* *
1313665 GTTATTATTATATCT
1 GTTATTATTAAATAT
*
1313680 GTTATTAATAAATAT
1 GTTATTATTAAATAT
1313695 GTATATTATTAAATA
1 GT-TATTATTAAATA
1313710 ATTAACATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (15 bp):
GTTATTATTAAATAT
Found at i:1313967 original size:50 final size:50
Alignment explanation
Indices: 1313908--1314164 Score: 230
Period size: 50 Copynumber: 5.1 Consensus size: 50
1313898 ACAAAGTAAT
* ** * * *
1313908 TTGATTATTCTTCATTAATTTTTGACAATCGAGAGAGATGGTCATAATTA
1 TTGACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTGATCATAATTA
* * ** *
1313958 TTAACTATTCTTTATTAACTTTTGACAATCGAGAGAGGTGATCGTAATTA
1 TTGACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTGATCATAATTA
* * * * * * *
1314008 TTGATTATTTTTTACCAACTTTTGACAATCGAGAGA-GTTAGCCGTAATTG
1 TTGACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTGA-TCATAATTA
* * *
1314058 TTGATTATTCTTCACCAA-TCTTTGACAATCGAGAGGAGGTGATTATAATTG
1 TTGACTATTCTTCACCAACT-TTTGACAATCGAGA-GAGGTGATCATAATTA
* * * * * *
1314109 TTGACTATTCTTCACCAACATTTGACAATAGAGAAAGGTGACCGTAATTT
1 TTGACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTGATCATAATTA
1314159 TTGACT
1 TTGACT
1314165 CTAAGCATCT
Statistics
Matches: 173, Mismatches: 29, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
49 4 0.02
50 128 0.74
51 38 0.22
52 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTGATCATAATTA
Found at i:1314154 original size:101 final size:100
Alignment explanation
Indices: 1313978--1314162 Score: 246
Period size: 101 Copynumber: 1.8 Consensus size: 100
1313968 TTTATTAACT
* * * * * * *
1313978 TTTGACAATCGAGAGAGGTGATCGTAATTATTGATTATTTTTTACCAACTTTTGACAATCGAGAG
1 TTTGACAATCGAGAGAGGTGATCATAATTATTGACTATTCTTCACCAACATTTGACAATAGAGAA
*
1314043 AGTTAGCCGTAATTGTTGATTATTCTTCACCAATC
66 AGTGAGCCGTAATTGTTGATTATTCTTCACCAATC
* *
1314078 TTTGACAATCGAGAGGAGGTGATTATAATTGTTGACTATTCTTCACCAACATTTGACAATAGAGA
1 TTTGACAATCGAGA-GAGGTGATCATAATTATTGACTATTCTTCACCAACATTTGACAATAGAGA
*
1314143 AAGGTGA-CCGTAATTTTTGA
65 AA-GTGAGCCGTAATTGTTGA
1314163 CTCTAAGCAT
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
100 14 0.19
101 55 0.76
102 3 0.04
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (100 bp):
TTTGACAATCGAGAGAGGTGATCATAATTATTGACTATTCTTCACCAACATTTGACAATAGAGAA
AGTGAGCCGTAATTGTTGATTATTCTTCACCAATC
Found at i:1315035 original size:34 final size:35
Alignment explanation
Indices: 1314966--1315037 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
1314956 ATTAAGAAAG
*
1314966 AGTGTTGGAAAAATAAAAAGAGTAGAAGAAAATAT
1 AGTGTTAGAAAAATAAAAAGAGTAGAAGAAAATAT
*
1315001 AGTGTTAGAAAAATAAAAAGAGT-GGAGAAAATAT
1 AGTGTTAGAAAAATAAAAAGAGTAGAAGAAAATAT
1315035 AGT
1 AGT
1315038 TGAGTCGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 13 0.37
35 22 0.63
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.21
Consensus pattern (35 bp):
AGTGTTAGAAAAATAAAAAGAGTAGAAGAAAATAT
Found at i:1318355 original size:50 final size:50
Alignment explanation
Indices: 1318296--1318501 Score: 236
Period size: 50 Copynumber: 4.1 Consensus size: 50
1318286 GCAAAGTGAT
* * * *
1318296 TTGATTATTCTTCATTAATCTTTGACAATCGAGAGAGGTGATCGTAAATG
1 TTGACTATTCTTCACTAACCTTTGACAATCGAGAGAGGTGATCGTAATTG
* * * *
1318346 TTGATTATTCTTCACTAACCTTTGACAATCGAGAGAAGT-AGCCGTAATTA
1 TTGACTATTCTTCACTAACCTTTGACAATCGAGAGAGGTGA-TCGTAATTG
*
1318396 TTGACTATTC-TCTACCAACCTTTGACAATCGAGAGAGGTGATCGTAATTG
1 TTGACTATTCTTC-ACTAACCTTTGACAATCGAGAGAGGTGATCGTAATTG
* * * * * * *
1318446 TTGACTATTCTTCACCAGCATTTGACAATAGAAAAAGGTGACCGTAATTG
1 TTGACTATTCTTCACTAACCTTTGACAATCGAGAGAGGTGATCGTAATTG
1318496 TTGACT
1 TTGACT
1318502 CTAAGCATCT
Statistics
Matches: 135, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
49 3 0.02
50 129 0.96
51 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (50 bp):
TTGACTATTCTTCACTAACCTTTGACAATCGAGAGAGGTGATCGTAATTG
Found at i:1318491 original size:100 final size:100
Alignment explanation
Indices: 1318315--1318501 Score: 270
Period size: 100 Copynumber: 1.9 Consensus size: 100
1318305 CTTCATTAAT
* * * *
1318315 CTTTGACAATCGAGAGAGGTGATCGTAAATGTTGATTATTCTTCACTAACCTTTGACAATCGAGA
1 CTTTGACAATCGAGAGAGGTGATCGTAAATGTTGACTATTCTTCACCAACATTTGACAATAGAGA
*
1318380 GAAGTAGCCGTAATTATTGACTATTCTCTACCAAC
66 AAAGTAGCCGTAATTATTGACTATTCTCTACCAAC
* *
1318415 CTTTGACAATCGAGAGAGGTGATCGTAATTGTTGACTATTCTTCACCAGCATTTGACAATAGA-A
1 CTTTGACAATCGAGAGAGGTGATCGTAAATGTTGACTATTCTTCACCAACATTTGACAATAGAGA
*
1318479 AAAGGT-GACCGTAATTGTTGACT
66 AAA-GTAG-CCGTAATTATTGACT
1318502 CTAAGCATCT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
99 4 0.05
100 73 0.95
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (100 bp):
CTTTGACAATCGAGAGAGGTGATCGTAAATGTTGACTATTCTTCACCAACATTTGACAATAGAGA
AAAGTAGCCGTAATTATTGACTATTCTCTACCAAC
Found at i:1319376 original size:12 final size:12
Alignment explanation
Indices: 1319359--1319392 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1319349 ATAAAAATAT
1319359 TAAATTAAAAAA
1 TAAATTAAAAAA
*
1319371 TAAATTTAAATAA
1 TAAA-TTAAAAAA
1319384 TAAATTAAA
1 TAAATTAAA
1319393 TTTATTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAATTAAAAAA
Found at i:1319381 original size:18 final size:18
Alignment explanation
Indices: 1319353--1319396 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1319343 GTTTAGATAA
1319353 AAATATTAAATTAA-AAAAT
1 AAAT-TTAAA-TAATAAAAT
*
1319372 AAATTTAAATAATAAATT
1 AAATTTAAATAATAAAAT
1319390 AAATTTA
1 AAATTTA
1319397 TTAAGAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 16 0.70
19 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATTTAAATAATAAAAT
Found at i:1319393 original size:12 final size:12
Alignment explanation
Indices: 1319353--1319393 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1319343 GTTTAGATAA
*
1319353 AAATATTAAATT
1 AAATAATAAATT
*
1319365 AAAAAATAAATTT
1 AAATAATAAA-TT
1319378 AAATAATAAATT
1 AAATAATAAATT
1319390 AAAT
1 AAAT
1319394 TTATTAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATAATAAATT
Found at i:1319492 original size:18 final size:19
Alignment explanation
Indices: 1319463--1319510 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1319453 TAATATATTT
*
1319463 TATAATTATATAATTCATA
1 TATAATTTTATAATTCATA
**
1319482 T-TAATTTTAT-ATTTTTA
1 TATAATTTTATAATTCATA
1319499 TATAATTTTATA
1 TATAATTTTATA
1319511 TTTTTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 6 0.25
18 17 0.71
19 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TATAATTTTATAATTCATA
Found at i:1319632 original size:15 final size:15
Alignment explanation
Indices: 1319612--1319642 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1319602 ATTAAATCAC
1319612 TAAAATATATATTTT
1 TAAAATATATATTTT
1319627 TAAAATATATATTTT
1 TAAAATATATATTTT
1319642 T
1 T
1319643 TTAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAAATATATATTTT
Found at i:1319638 original size:17 final size:17
Alignment explanation
Indices: 1319616--1319648 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1319606 AATCACTAAA
1319616 ATATATATTTTTAAAAT
1 ATATATATTTTTAAAAT
*
1319633 ATATATTTTTTTAAAA
1 ATATATATTTTTAAAA
1319649 ATTATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATATTTTTAAAAT
Found at i:1319654 original size:17 final size:16
Alignment explanation
Indices: 1319612--1319656 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
1319602 ATTAAATCAC
1319612 TAAAA-TATATATTTT
1 TAAAATTATATATTTT
*
1319627 TAAAATATATATTTTTT
1 TAAAAT-TATATATTTT
1319644 TAAAAATTATATA
1 T-AAAATTATATA
1319657 AACTGATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.20
17 15 0.60
18 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAAATTATATATTTT
Found at i:1325185 original size:20 final size:22
Alignment explanation
Indices: 1325144--1325187 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
1325134 TTTAATTTTA
1325144 TTTATAATATATTTATATTATT
1 TTTATAATATATTTATATTATT
1325166 TTTAT-ATAT-TTTAT-TATATT
1 TTTATAATATATTTATAT-TATT
1325186 TT
1 TT
1325188 AATTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 1 0.05
20 11 0.52
21 4 0.19
22 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTATAATATATTTATATTATT
Found at i:1325188 original size:10 final size:10
Alignment explanation
Indices: 1325132--1325197 Score: 57
Period size: 11 Copynumber: 6.5 Consensus size: 10
1325122 TATTATACAA
*
1325132 ATTTTAATTTT
1 ATTTT-ATTAT
*
1325143 ATTTATAATAT
1 ATTT-TATTAT
1325154 ATTTATATTAT
1 ATTT-TATTAT
1325165 -TTTTA-TAT
1 ATTTTATTAT
1325173 ATTTTATTAT
1 ATTTTATTAT
1325183 ATTTTAATTA-
1 ATTTT-ATTAT
1325193 ATTTT
1 ATTTT
1325198 TTAATTGGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
8 3 0.06
9 7 0.15
10 16 0.33
11 21 0.44
12 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
ATTTTATTAT
Found at i:1325197 original size:20 final size:20
Alignment explanation
Indices: 1325132--1325190 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
1325122 TATTATACAA
*
1325132 ATTTTAATTTTATTTATAATAT
1 ATTTT-ATTATATTT-TAATAT
1325154 ATTTATATTAT-TTTT-ATAT
1 ATTT-TATTATATTTTAATAT
1325173 ATTTTATTATATTTTAAT
1 ATTTTATTATATTTTAAT
1325191 TAATTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 6 0.18
19 12 0.36
20 3 0.09
21 3 0.09
22 8 0.24
23 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTATTATATTTTAATAT
Found at i:1325724 original size:43 final size:42
Alignment explanation
Indices: 1325638--1325722 Score: 100
Period size: 44 Copynumber: 2.0 Consensus size: 42
1325628 ACCAAAATGT
* * *
1325638 TGATATTTAATTAAATATTTTATTTTTATGTATAGTTATTTTA
1 TGATATTTAATTAAATATTATATTTATATGAATAG-TATTTTA
1325681 TGATATTTAAATTAAATATTAATATTTAATATGAATA-TATTT
1 TGATATTT-AATTAAATATT-ATATTT-ATATGAATAGTATTT
1325723 ATTTTTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 8 0.22
44 16 0.44
45 5 0.14
46 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (42 bp):
TGATATTTAATTAAATATTATATTTATATGAATAGTATTTTA
Found at i:1325739 original size:16 final size:16
Alignment explanation
Indices: 1325717--1325762 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1325707 TAATATGAAT
1325717 ATATTTAT-TTTTAAA
1 ATATTTATATTTTAAA
1325732 ATTATTTATATATTTAAA
1 A-TATTTATAT-TTTAAA
1325750 A-ATTTATATTTTA
1 ATATTTATATTTTA
1325763 TATTAACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.18
16 15 0.54
17 1 0.04
18 7 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATTTATATTTTAAA
Found at i:1327723 original size:14 final size:14
Alignment explanation
Indices: 1327706--1327732 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1327696 TTAAGATTAA
1327706 ATTTTAAAAAATAT
1 ATTTTAAAAAATAT
1327720 ATTTTAAAAAATA
1 ATTTTAAAAAATA
1327733 AATTAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTTTAAAAAATAT
Found at i:1329482 original size:16 final size:15
Alignment explanation
Indices: 1329459--1329505 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 15
1329449 AGTGCACAAT
1329459 TAAATTAATT-TTATA
1 TAAATTAATTATTA-A
1329474 TATAATTAATATATTAA
1 TA-AATTAAT-TATTAA
1329491 TAAATTAATTATTAA
1 TAAATTAATTATTAA
1329506 ATTAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.28
16 14 0.48
17 4 0.14
18 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAAATTAATTATTAA
Found at i:1329515 original size:16 final size:17
Alignment explanation
Indices: 1329456--1329512 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
1329446 TGTAGTGCAC
1329456 AATTAAATTAATT-TTA
1 AATTAAATTAATTATTA
*
1329472 TA-TATAATTAATATATT-
1 AATTA-AATTAAT-TATTA
1329489 AA-TAAATTAATTATTA
1 AATTAAATTAATTATTA
1329505 AATTAAAT
1 AATTAAAT
1329513 AATATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 6 0.18
16 17 0.50
17 9 0.26
18 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATTAATTATTA
Found at i:1330517 original size:11 final size:11
Alignment explanation
Indices: 1330501--1330532 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1330491 ATAGACGCGA
1330501 AAAAAAAAAAT
1 AAAAAAAAAAT
1330512 AAAAAAAAAAT
1 AAAAAAAAAAT
1330523 AAAAGAAAAA
1 AAAA-AAAAA
1330533 CGAAAAACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.91, C:0.00, G:0.03, T:0.06
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:1331843 original size:16 final size:17
Alignment explanation
Indices: 1331818--1331851 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1331808 CTGAAGAAGA
1331818 GGAATATTGT-ATTTAT
1 GGAATATTGTGATTTAT
*
1331834 GGAATCTTGTGATTTAT
1 GGAATATTGTGATTTAT
1331851 G
1 G
1331852 TGTACAGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (17 bp):
GGAATATTGTGATTTAT
Found at i:1334894 original size:2 final size:2
Alignment explanation
Indices: 1334887--1334912 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1334877 GTTTATACAC
1334887 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
1334913 TTTACAATTG
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:1336554 original size:3 final size:3
Alignment explanation
Indices: 1336548--1336578 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1336538 TTTTTTTTTA
1336548 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1336579 GAGGATCAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1339144 original size:21 final size:22
Alignment explanation
Indices: 1339097--1339146 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1339087 ATTTTAAATG
** *
1339097 ATAAAAAATTTATTAATTTTTTT
1 ATAAAAAA-TTATTAATTTAATA
1339120 ATAAAAAA-TATTAATTTAATA
1 ATAAAAAATTATTAATTTAATA
1339141 ATAAAA
1 ATAAAA
1339147 TAAAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 16 0.67
23 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAAAAAATTATTAATTTAATA
Found at i:1339177 original size:14 final size:14
Alignment explanation
Indices: 1339143--1339205 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
1339133 ATTTAATAAT
1339143 AAAA-TAAAATTATA
1 AAAATTAAAATT-TA
*
1339157 AATATTAAAATTTA
1 AAAATTAAAATTTA
1339171 AAAATTAAAATTATTA
1 AAAATTAAAA-T-TTA
* * *
1339187 AATATTATATTTTA
1 AAAATTAAAATTTA
1339201 AAAAT
1 AAAAT
1339206 AATTATATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
14 21 0.52
15 9 0.22
16 10 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATTAAAATTTA
Found at i:1339184 original size:29 final size:28
Alignment explanation
Indices: 1339143--1339220 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 28
1339133 ATTTAATAAT
1339143 AAAATAAAATTATAAATATTAAAATTTA
1 AAAATAAAATTATAAATATTAAAATTTA
* *
1339171 AAAATTAAAATTATTAAATATTATATTTTA
1 AAAA-TAAAATTA-TAAATATTAAAATTTA
*
1339201 AAAAT--AATTATATATATTAA
1 AAAATAAAATTATAAATATTAA
1339221 TTAAATTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 8 0.18
27 5 0.11
28 4 0.09
29 9 0.20
30 18 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAATAAAATTATAAATATTAAAATTTA
Found at i:1339982 original size:28 final size:27
Alignment explanation
Indices: 1339951--1340053 Score: 77
Period size: 28 Copynumber: 3.7 Consensus size: 27
1339941 ATATATTTTT
1339951 ATTTAAATTTAATTATAAATATATATTA
1 ATTTAAATTTAATTATAAAT-TATATTA
** * *
1339979 ATTTAAAGATATTTAAAAATTAT-TTA
1 ATTTAAATTTAATTATAAATTATATTA
* * *
1340005 ATAATAAAATAAATTATTAAATTA-ATTTAA
1 AT-TTAAATTTAATTA-TAAATTATA-TT-A
1340035 ATTTAAATTTAATT-TAAAT
1 ATTTAAATTTAATTATAAAT
1340054 CTAAAAAAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
26 5 0.09
27 16 0.28
28 22 0.39
29 11 0.19
30 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (27 bp):
ATTTAAATTTAATTATAAATTATATTA
Found at i:1340048 original size:17 final size:16
Alignment explanation
Indices: 1340021--1340058 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
1340011 AAATAAATTA
1340021 TTAAATTAATTTAAAT
1 TTAAATTAATTTAAAT
1340037 TTAAATTTAATTTAAAT
1 TTAAA-TTAATTTAAAT
*
1340054 CTAAA
1 TTAAA
1340059 AAAATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTAATTTAAAT
Found at i:1343040 original size:2 final size:2
Alignment explanation
Indices: 1343033--1343064 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1343023 CCTTGCCCTT
1343033 TC TC TC TC TC TC TC TC TC TC TC TC TGC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC T
1343065 ATCAGGCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1349457 original size:2 final size:2
Alignment explanation
Indices: 1349450--1349484 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1349440 CACTCCACAG
1349450 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1349485 TCAAAGTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1350078 original size:21 final size:23
Alignment explanation
Indices: 1350036--1350078 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1350026 TTTAAAAAAA
1350036 TTAAAAATAATTAATAATTATTTT
1 TTAAAAATAA-TAATAATTATTTT
1350060 TTAAAAATAA-AAT-ATTATT
1 TTAAAAATAATAATAATTATT
1350079 CTTATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
24 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAAAAATAATAATAATTATTTT
Found at i:1353338 original size:2 final size:2
Alignment explanation
Indices: 1353333--1353361 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1353323 TCCCTAACAA
1353333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1353362 AAAAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1353772 original size:34 final size:34
Alignment explanation
Indices: 1353708--1353777 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
1353698 GTTTATTTAA
* * *
1353708 TTATTAATTTAATATATATTTAATGCATTAT-TT
1 TTATTAATTTAAAAGATATTTAATGAATTATATT
*
1353741 TTATTAAATTTAAAAGATATTTAATTAATTATATT
1 TTATT-AATTTAAAAGATATTTAATGAATTATATT
1353776 TT
1 TT
1353778 TTTGACATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 5 0.16
34 22 0.71
35 4 0.13
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (34 bp):
TTATTAATTTAAAAGATATTTAATGAATTATATT
Found at i:1353961 original size:2 final size:2
Alignment explanation
Indices: 1353954--1353998 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1353944 CACCAAAACA
1353954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1353996 AT A
1 AT A
1353999 AAGCATATAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1355044 original size:18 final size:18
Alignment explanation
Indices: 1355021--1355075 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
1355011 TTAAAATTTT
**
1355021 ATTTTATTATTTAAAATG
1 ATTTTATTATTTAAAAAA
1355039 ATTTTATTAAATTTTAAAAAA
1 ATTTTATT--A-TTTAAAAAA
1355060 ATATTTATTATTTAAA
1 AT-TTTATTATTTAAA
1355076 TAATAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 8 0.26
19 6 0.19
20 2 0.06
21 9 0.29
22 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTTATTATTTAAAAAA
Found at i:1355080 original size:18 final size:19
Alignment explanation
Indices: 1355023--1355080 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 19
1355013 AAAATTTTAT
*
1355023 TTTATTATTTAAAATGAT-
1 TTTATTATTTAAAATAATA
*
1355041 TTTATTAAATTTTAAAAAAATA
1 TTTATT--A-TTTAAAATAATA
1355063 TTTATTATTT-AAATAATA
1 TTTATTATTTAAAATAATA
1355081 ATTAATTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 13 0.39
19 3 0.09
20 2 0.06
21 9 0.27
22 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTATTATTTAAAATAATA
Found at i:1358248 original size:22 final size:22
Alignment explanation
Indices: 1358222--1358300 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 22
1358212 AAAACAAAAA
1358222 ATAGGCATTCACTTGCATAAAT
1 ATAGGCATTCACTTGCATAAAT
* *
1358244 ATAGGCATTCACTTGTATAAAA
1 ATAGGCATTCACTTGCATAAAT
* *
1358266 ATA---A-GCACTTGTATAAAT
1 ATAGGCATTCACTTGCATAAAT
1358284 ATAGGCATTCACTTGCA
1 ATAGGCATTCACTTGCA
1358301 AGTTGCATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 15 0.32
19 1 0.02
21 1 0.02
22 30 0.64
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (22 bp):
ATAGGCATTCACTTGCATAAAT
Found at i:1359869 original size:50 final size:50
Alignment explanation
Indices: 1359808--1359967 Score: 221
Period size: 50 Copynumber: 3.2 Consensus size: 50
1359798 ATATACTTAG
* * *
1359808 AGTCAACAATTATGGCCACCTCCCTCTATTGTTAAAAGTTGGTGAAGAAT
1 AGTCAACAATTATGGCCACCTCCCTATATTGTCAAAGGTTGGTGAAGAAT
* * * *
1359858 TGTCAATAATTATGACCACTTCCCTATATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGCCACCTCCCTATATTGTCAAAGGTTGGTGAAGAAT
* * * *
1359908 CGTCAACAATTATGGTCACCTCCCTTTATTGTCAAAGGTTGGTGAAGGAT
1 AGTCAACAATTATGGCCACCTCCCTATATTGTCAAAGGTTGGTGAAGAAT
1359958 AGTCAACAAT
1 AGTCAACAAT
1359968 GGCAACAACT
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 95 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTATGGCCACCTCCCTATATTGTCAAAGGTTGGTGAAGAAT
Found at i:1364466 original size:50 final size:50
Alignment explanation
Indices: 1364358--1364467 Score: 157
Period size: 50 Copynumber: 2.2 Consensus size: 50
1364348 ATATACTTAG
* * * *
1364358 AGTCAACAATTATGGCTACTTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATAATGGCCACCTCCCTCTATTGACAAAGGTTGGTGAAGAAT
* * *
1364408 CGTAAACAATAATGGCCACCTCCCTCTATTGACAAAGGTTGGTGAAGGAT
1 AGTCAACAATAATGGCCACCTCCCTCTATTGACAAAGGTTGGTGAAGAAT
1364458 AGTCAACAAT
1 AGTCAACAAT
1364468 GGCAACAACT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (50 bp):
AGTCAACAATAATGGCCACCTCCCTCTATTGACAAAGGTTGGTGAAGAAT
Found at i:1371341 original size:25 final size:24
Alignment explanation
Indices: 1371273--1371341 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 24
1371263 TTTATATTGC
* *
1371273 TATT-TATATTCATTAAATATTAA
1 TATTATATATTTATAAAATATTAA
* **
1371296 TATTATATTTTTATATTATATCTAA
1 TATTATATATTTATAAAATAT-TAA
1371321 TATTATAATATTTA-AAAATAT
1 TATTAT-ATATTTATAAAATAT
1371342 AGTTTAAAGC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
23 4 0.11
24 11 0.31
25 14 0.40
26 6 0.17
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTATATATTTATAAAATATTAA
Found at i:1371507 original size:2 final size:2
Alignment explanation
Indices: 1371500--1371564 Score: 89
Period size: 2 Copynumber: 32.5 Consensus size: 2
1371490 AGTTGGAATC
1371500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
1371542 AT AT TT AT AT AT -T AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT -AT AT A
1371565 ATTAACGACA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 2 0.04
2 52 0.91
3 3 0.05
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1376616 original size:23 final size:23
Alignment explanation
Indices: 1376565--1376616 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1376555 AATTAATATT
*
1376565 TAATATATTATTAATATATAAAA
1 TAATATATTATTAATAAATAAAA
* * * *
1376588 TTATATATTATTCATAAATCATA
1 TAATATATTATTAATAAATAAAA
1376611 TAATAT
1 TAATAT
1376617 TTTTATTATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATATATTATTAATAAATAAAA
Found at i:1382201 original size:15 final size:15
Alignment explanation
Indices: 1382181--1382210 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1382171 CTTTAAAATA
*
1382181 TAAATATATTTATAT
1 TAAATATATATATAT
1382196 TAAATATATATATAT
1 TAAATATATATATAT
1382211 GACATTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATATATATATAT
Found at i:1391018 original size:18 final size:18
Alignment explanation
Indices: 1390997--1391031 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1390987 ATTAATTTGA
1390997 TATTTATAATTT-TTTAAG
1 TATTTA-AATTTATTTAAG
1391015 TATTTAAATTTATTTAA
1 TATTTAAATTTATTTAA
1391032 TATATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TATTTAAATTTATTTAAG
Found at i:1391029 original size:28 final size:28
Alignment explanation
Indices: 1390997--1391069 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
1390987 ATTAATTTGA
1390997 TATTTATAATTTTTTAAGTATTTAAAT-T
1 TATTTATAATTTTTTAAGTA-TTAAATAT
* *
1391025 TATTTA-ATATATTTT-ATTATTAAATAT
1 TATTTATA-ATTTTTTAAGTATTAAATAT
*
1391052 TATTATTTAATTTTTTAA
1 TATT-TATAATTTTTTAA
1391070 AAATAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
26 6 0.17
27 9 0.25
28 19 0.53
29 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (28 bp):
TATTTATAATTTTTTAAGTATTAAATAT
Found at i:1391682 original size:2 final size:2
Alignment explanation
Indices: 1391675--1391716 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1391665 TTACACATAC
*
1391675 AT AT AT AT AT AT AT GT AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1391716 A
1 A
1391717 AATAGAGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1391802 original size:8 final size:8
Alignment explanation
Indices: 1391789--1391818 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1391779 AAATATTCTC
1391789 AAAAAATA
1 AAAAAATA
1391797 AAAAAATA
1 AAAAAATA
*
1391805 AAAAATTA
1 AAAAAATA
1391813 AAAAAA
1 AAAAAA
1391819 AAAGAGGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:1395258 original size:10 final size:10
Alignment explanation
Indices: 1395229--1395311 Score: 50
Period size: 10 Copynumber: 8.2 Consensus size: 10
1395219 TTAATTATTC
*
1395229 ATTTATCTAT
1 ATTTATATAT
1395239 ATTT-TGATAT
1 ATTTAT-ATAT
1395249 ATTTATATAT
1 ATTTATATAT
*
1395259 -TCGTATA-AT
1 AT-TTATATAT
1395268 ATTTATATTATT
1 ATTTATA-TA-T
*
1395280 TTTTATATTAT
1 ATTTATA-TAT
1395291 ATTT-TA-AT
1 ATTTATATAT
1395299 ATTTTATATAT
1 A-TTTATATAT
1395310 AT
1 AT
1395312 CTATTTTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
8 3 0.05
9 11 0.19
10 25 0.43
11 9 0.16
12 10 0.17
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (10 bp):
ATTTATATAT
Found at i:1395286 original size:12 final size:12
Alignment explanation
Indices: 1395269--1395309 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1395259 TCGTATAATA
1395269 TTTATATTATTT
1 TTTATATTATTT
*
1395281 TTTATATTATAT
1 TTTATATTATTT
1395293 TTTA-A-TATTT
1 TTTATATTATTT
*
1395303 TATATAT
1 TTTATAT
1395310 ATCTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 15 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:1395316 original size:15 final size:15
Alignment explanation
Indices: 1395298--1395328 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1395288 TATATTTTAA
*
1395298 TATTTTATATATATC
1 TATTTTAAATATATC
1395313 TATTTTAAATATATC
1 TATTTTAAATATATC
1395328 T
1 T
1395329 GAGTTACATT
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:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTTTAAATATATC
Found at i:1395316 original size:23 final size:22
Alignment explanation
Indices: 1395266--1395320 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
1395256 TATTCGTATA
* *
1395266 ATATTTATATTATTTTTTATATT
1 ATATTT-TAATATTTTATATATT
1395289 ATATTTTAATATTTTATATATAT
1 ATATTTTAATATTTTATATAT-T
*
1395312 CTATTTTAA
1 ATATTTTAA
1395321 ATATATCTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
ATATTTTAATATTTTATATATT
Found at i:1395559 original size:24 final size:23
Alignment explanation
Indices: 1395532--1395600 Score: 59
Period size: 26 Copynumber: 2.7 Consensus size: 23
1395522 ATGTTTGCCT
1395532 TTATAATTTTTTGTATTTAAAATA
1 TTATAATTTTTT-TATTTAAAATA
*
1395556 TTAT-ATTTTTATATATTTTTTAAATA
1 TTATAATTTTT-T-TA--TTTAAAATA
1395582 TTAATAATTTATTTTATTT
1 TT-ATAATTT-TTTTATTT
1395601 TATATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
23 6 0.16
24 7 0.19
25 3 0.08
26 10 0.27
27 4 0.11
28 5 0.14
29 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (23 bp):
TTATAATTTTTTTATTTAAAATA
Found at i:1395609 original size:18 final size:18
Alignment explanation
Indices: 1395562--1395611 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1395552 AATATTATAT
1395562 TTTTATATATTTTTTAAA
1 TTTTATATATTTTTTAAA
* *
1395580 TATTA-ATAATTTATTT-TA
1 TTTTATAT-ATTT-TTTAAA
1395598 TTTTATATATTTTT
1 TTTTATATATTTTT
1395612 ATGTATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
17 4 0.15
18 17 0.65
19 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATATATTTTTTAAA
Found at i:1396569 original size:4 final size:4
Alignment explanation
Indices: 1396560--1396612 Score: 63
Period size: 4 Copynumber: 13.2 Consensus size: 4
1396550 GTGGTGGAAG
* * *
1396560 AGAA AGAA AGAA AGAA AGAA AGAA AAAA CAAAA AGAA AGAA AAAA AG-A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA -AGAA AGAA AGAA AGAA AGAA
1396608 AGAA A
1 AGAA A
1396613 AAAAATTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 3 0.07
4 36 0.84
5 4 0.09
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1396594 original size:25 final size:24
Alignment explanation
Indices: 1396566--1396617 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
1396556 GAAGAGAAAG
*
1396566 AAAGAAAGAAAGAAAGAAAAAACAA
1 AAAGAAAGAAAAAAAGAAAAAA-AA
*
1396591 AAAGAAAGAAAAAAAGAAGAAAAA
1 AAAGAAAGAAAAAAAGAAAAAAAA
1396615 AAA
1 AAA
1396618 TTTATATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAGAAAGAAAAAAAGAAAAAAAA
Found at i:1396595 original size:21 final size:21
Alignment explanation
Indices: 1396562--1396614 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1396552 GGTGGAAGAG
*
1396562 AAAGAA-AGAAAGAAAGAAAGA
1 AAAGAACAAAAAGAAAGAAA-A
1396583 AAA-AACAAAAAGAAAGAAAA
1 AAAGAACAAAAAGAAAGAAAA
*
1396603 AAAGAAGAAAAA
1 AAAGAACAAAAA
1396615 AAATTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (21 bp):
AAAGAACAAAAAGAAAGAAAA
Found at i:1396617 original size:12 final size:12
Alignment explanation
Indices: 1396560--1396616 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
1396550 GTGGTGGAAG
*
1396560 AGAAAGAAAGAA
1 AGAAAAAAAGAA
*
1396572 AGAAAGAAAGAA
1 AGAAAAAAAGAA
*
1396584 AAAACAAAAAGAA
1 AGAA-AAAAAGAA
1396597 AGAAAAAAAG-A
1 AGAAAAAAAGAA
1396608 AGAAAAAAA
1 AGAAAAAAA
1396617 ATTTATATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
11 10 0.24
12 21 0.51
13 10 0.24
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAGAA
Found at i:1405970 original size:21 final size:21
Alignment explanation
Indices: 1405944--1406012 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 21
1405934 TATTTAATAC
1405944 TTTATATTATTTTAAAATTTA
1 TTTATATTATTTTAAAATTTA
*
1405965 TTTATA-TATTTAAATAATTATA
1 TTTATATTATTTTAA-AATT-TA
*
1405987 TTTCACATTAAATTTTAAATATTTA
1 TTT-ATATT--ATTTTAAA-ATTTA
1406012 T
1 T
1406013 CTACCATTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
20 7 0.18
21 10 0.26
22 5 0.13
23 2 0.05
24 1 0.03
25 4 0.11
26 9 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATATTATTTTAAAATTTA
Found at i:1410474 original size:11 final size:11
Alignment explanation
Indices: 1410453--1410551 Score: 52
Period size: 10 Copynumber: 9.5 Consensus size: 11
1410443 AATTTAATAA
1410453 TATATTTTATAT
1 TATA-TTTATAT
1410465 TATATTTATAT
1 TATATTTATAT
1410476 TAT-TTTATA-
1 TATATTTATAT
**
1410485 TA-AAATA-AT
1 TATATTTATAT
* *
1410494 TATATTTAAAA
1 TATATTTATAT
1410505 TAT-TTTAT-T
1 TATATTTATAT
* *
1410514 TTTATTTAAAT
1 TATATTTATAT
*
1410525 T-TA-ATATAT
1 TATATTTATAT
1410534 TAATAATTTATAT
1 T-AT-ATTTATAT
1410547 TATAT
1 TATAT
1410552 AAATTTTAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 21
0.66 0.12 0.21
Matches are distributed among these distances:
8 1 0.02
9 13 0.20
10 19 0.29
11 19 0.29
12 7 0.11
13 6 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1410479 original size:9 final size:10
Alignment explanation
Indices: 1410455--1410485 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
1410445 TTTAATAATA
1410455 TATTTTATAT
1 TATTTTATAT
1410465 TATATTTATAT
1 TAT-TTTATAT
1410476 TATTTTATAT
1 TATTTTATAT
1410486 AAAATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTTTATAT
Found at i:1410562 original size:21 final size:20
Alignment explanation
Indices: 1410537--1410591 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1410527 AATATATTAA
1410537 TAATTTATATTATATAAATTT
1 TAATTTATATTATAT-AATTT
*
1410558 TAA-TTAT-TTATATATTTT
1 TAATTTATATTATATAATTT
*
1410576 TAATATCATATTATAT
1 TAAT-TTATATTATAT
1410592 TTTAATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 7 0.24
19 6 0.21
20 7 0.24
21 9 0.31
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TAATTTATATTATATAATTT
Found at i:1410581 original size:50 final size:46
Alignment explanation
Indices: 1410456--1410581 Score: 112
Period size: 50 Copynumber: 2.6 Consensus size: 46
1410446 TTAATAATAT
*
1410456 ATTTTATATTATATT-TATATTATTTTATATAAAATAATTATATTTAAA
1 ATTTTA-ATTAT-TTATATATT-TTTAATATAAAATAATTATATTTAAA
* * ** *
1410504 ATATTTTATT-TTTATTTAAATTTAATATATTAATAATTTATATTATATAA
1 AT-TTTAATTATTTATATATTTTTAATATA-AAATAA-TTATATT-TA-AA
1410554 ATTTTAATTATTTATATATTTTTAATAT
1 ATTTTAATTATTTATATATTTTTAATAT
1410582 CATATTATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
46 10 0.16
47 9 0.15
48 12 0.20
49 11 0.18
50 19 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (46 bp):
ATTTTAATTATTTATATATTTTTAATATAAAATAATTATATTTAAA
Found at i:1414710 original size:2 final size:2
Alignment explanation
Indices: 1414658--1414690 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1414648 TCGTTACCGC
*
1414658 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1414691 CACACACACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1414908 original size:2 final size:2
Alignment explanation
Indices: 1414901--1414941 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1414891 TGAACAACGA
1414901 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1414942 TTGGTCTCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1416102 original size:23 final size:22
Alignment explanation
Indices: 1416076--1416118 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1416066 CCTTAAAGAA
*
1416076 TTTAAATACTTATTAATAAAACC
1 TTTAAATA-TTAATAATAAAACC
*
1416099 TTTATATATTAATAATAAAA
1 TTTAAATATTAATAATAAAA
1416119 ACTTAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAATATTAATAATAAAACC
Found at i:1417200 original size:28 final size:28
Alignment explanation
Indices: 1417162--1417216 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1417152 GAAAAGAAAC
1417162 AAAAATATTTACATA-AAATAGTAATTTTA
1 AAAAATATTTA-A-ACAAATAGTAATTTTA
*
1417191 AAAAAT-TTTAAACAAATATTAATTTT
1 AAAAATATTTAAACAAATAGTAATTTT
1417217 TTTAGTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.04
27 13 0.54
28 4 0.17
29 6 0.25
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (28 bp):
AAAAATATTTAAACAAATAGTAATTTTA
Found at i:1417313 original size:26 final size:26
Alignment explanation
Indices: 1417280--1417341 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
1417270 TTATATTTCG
*
1417280 TTGATTATAATTGTATATAAATATATA
1 TTGATTATAATT-TATATAAATAAATA
* * *
1417307 TT-ATTATGATTTATTTTAATAAATA
1 TTGATTATAATTTATATAAATAAATA
1417332 TTGATTATAA
1 TTGATTATAA
1417342 ATATTAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 13 0.45
26 14 0.48
27 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (26 bp):
TTGATTATAATTTATATAAATAAATA
Found at i:1417343 original size:13 final size:13
Alignment explanation
Indices: 1417325--1417383 Score: 64
Period size: 13 Copynumber: 4.3 Consensus size: 13
1417315 ATTTATTTTA
*
1417325 ATAAATATTGATT
1 ATAAATATTAATT
*
1417338 ATAAATATTAATA
1 ATAAATATTAATT
*
1417351 ATAAAATTTATAATT
1 AT-AAATAT-TAATT
1417366 ATAAAATATTAATT
1 AT-AAATATTAATT
1417380 ATAA
1 ATAA
1417384 TATCATGTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
13 15 0.38
14 12 0.31
15 12 0.31
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
ATAAATATTAATT
Found at i:1417734 original size:16 final size:16
Alignment explanation
Indices: 1417685--1417738 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
1417675 TTTTAATTCG
1417685 TTTAATTTGTTTGA-TA
1 TTTAATTTGTTT-ATTA
*
1417701 TTTGAATTTATTTATTA
1 TTT-AATTTGTTTATTA
1417718 TTTAATTTGTATT-TTA
1 TTTAATTTGT-TTATTA
1417734 TTTAA
1 TTTAA
1417739 ATAATAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 18 0.55
17 15 0.45
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (16 bp):
TTTAATTTGTTTATTA
Found at i:1418298 original size:2 final size:2
Alignment explanation
Indices: 1418291--1418321 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1418281 TTTTCAACTT
1418291 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1418322 ATTGCAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.