Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 8 of 20
Found at i:1219540 original size:8 final size:9
Alignment explanation
Indices: 1219516--1219549 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1219506 ATAAAATATG
1219516 AATATTTTT
1 AATATTTTT
1219525 AATATTTTT
1 AATATTTTT
*
1219534 AATTTTTTT
1 AATATTTTT
*
1219543 TATATTT
1 AATATTT
1219550 AAAAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
AATATTTTT
Found at i:1219583 original size:14 final size:14
Alignment explanation
Indices: 1219541--1219594 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
1219531 TTTAATTTTT
*
1219541 TTTATATTTAAAAA
1 TTTATATTTAAATA
* **
1219555 ATTATATTTTTATA
1 TTTATATTTAAATA
1219569 TTTATATTTAAATA
1 TTTATATTTAAATA
1219583 --TATA-TTAAATA
1 TTTATATTTAAATA
1219594 T
1 T
1219595 AAATATAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 7 0.22
12 4 0.12
14 21 0.66
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTATATTTAAATA
Found at i:1220410 original size:25 final size:25
Alignment explanation
Indices: 1220369--1220432 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
1220359 ATCTTTCTGC
*
1220369 AATTT-ATTTTTTCATTAAAAATATA
1 AATTTAATTTATT-ATTAAAAATATA
** *
1220394 AATTTAATTTATTATTATTATTATA
1 AATTTAATTTATTATTAAAAATATA
*
1220419 TATTTAATTTATTA
1 AATTTAATTTATTA
1220433 ATTCTTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 27 0.82
26 6 0.18
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
AATTTAATTTATTATTAAAAATATA
Found at i:1220832 original size:34 final size:34
Alignment explanation
Indices: 1220777--1220993 Score: 249
Period size: 34 Copynumber: 6.4 Consensus size: 34
1220767 ATGTATCTTG
* *
1220777 TGTTGATTAAAT-GGTGATTTGGTAGTTTACTAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
1220810 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
1220844 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* **
1220878 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
1220912 TATTGATTAAATGCGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
1220946 TGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
**
1220980 TGCAGATTAAATGG
1 TGTTGATTAAATGG
1220994 TGGTTTTTAC
Statistics
Matches: 156, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
33 14 0.09
34 141 0.90
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:1220918 original size:102 final size:101
Alignment explanation
Indices: 1220777--1220993 Score: 308
Period size: 102 Copynumber: 2.1 Consensus size: 101
1220767 ATGTATCTTG
** * * * * * *
1220777 TGTTGATTAAATGGTGATTTGGTAGTTTACTATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGCGTGATTTGGTGGCTTACC
1220842 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1220878 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGCGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGCGTGATTTGGTGGCTTAC
* * *
1220943 CATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
65 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
**
1220980 TGCAGATTAAATGG
1 TGTTGATTAAATGG
1220994 TGGTTTTTAC
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 14 0.14
102 88 0.86
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGCGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1225460 original size:34 final size:34
Alignment explanation
Indices: 1225403--1225622 Score: 255
Period size: 34 Copynumber: 6.5 Consensus size: 34
1225393 AAGTGGGAGA
*
1225403 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
1225436 ATTGTTTATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1225470 ATTGTTGACTAAACTGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAA-TGGGTGATTTGGTAGCTTACC
* **
1225505 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1225539 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
1225573 ATTGTTGACTAAAT-GATAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
*
1225607 ATTGTTAATTAAATGG
1 ATTGTTGATTAAATGG
1225623 TTGTTTTTAC
Statistics
Matches: 158, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
33 15 0.09
34 113 0.72
35 30 0.19
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1225581 original size:103 final size:101
Alignment explanation
Indices: 1225403--1225622 Score: 314
Period size: 103 Copynumber: 2.2 Consensus size: 101
1225393 AAGTGGGAGA
** * * * * *
1225403 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTTATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
*
1225468 CCATTGTTGACTAAACTGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAA-TGAGAGATTTGGTAGCTTACC
1225505 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
1225570 ACCATTGTTGACTAAATGATAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGAGAGATTTGGTAGCTTACC
*
1225607 ATTGTTAATTAAATGG
1 ATTGTTGATTAAATGG
1225623 TTGTTTTTAC
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
101 1 0.01
102 46 0.44
103 58 0.55
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGAGAGATTTGGTAGCTTACC
Found at i:1226883 original size:16 final size:16
Alignment explanation
Indices: 1226862--1226893 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1226852 TATTCTATAT
*
1226862 TTTATAATTTAAATTA
1 TTTATAATTAAAATTA
1226878 TTTATAATTAAAATTA
1 TTTATAATTAAAATTA
1226894 AGTAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTATAATTAAAATTA
Found at i:1227438 original size:21 final size:21
Alignment explanation
Indices: 1227414--1227454 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1227404 ATAATATATA
1227414 TTAAAA-ATAATATAAATTTTT
1 TTAAAATATAATA-AAATTTTT
1227435 TTAAAATATAATAAAATTTT
1 TTAAAATATAATAAAATTTT
1227455 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAAAATATAATAAAATTTTT
Found at i:1227633 original size:34 final size:35
Alignment explanation
Indices: 1227595--1227668 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
1227585 TTATATCGTT
**
1227595 ATAATTAAA-T-ATATAATATTATTTTTAATTTTAA
1 ATAATTAAATTAATATAAT-TTATTTAAAATTTTAA
* *
1227629 ATAATAAAATTAATTTAATTTATTTAAAATTTTAA
1 ATAATTAAATTAATATAATTTATTTAAAATTTTAA
1227664 A-AATT
1 ATAATT
1227669 TTATAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
34 11 0.33
35 16 0.48
36 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (35 bp):
ATAATTAAATTAATATAATTTATTTAAAATTTTAA
Found at i:1227640 original size:25 final size:25
Alignment explanation
Indices: 1227599--1227649 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
1227589 ATCGTTATAA
* *
1227599 TTAAATATATAATATTATTTTTAATT
1 TTAAATATATAAAATTA-ATTTAATT
1227625 TTAAATA-ATAAAATTAATTTAATT
1 TTAAATATATAAAATTAATTTAATT
1227649 T
1 T
1227650 ATTTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 8 0.35
25 8 0.35
26 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTAAATATATAAAATTAATTTAATT
Found at i:1228066 original size:15 final size:15
Alignment explanation
Indices: 1228046--1228075 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1228036 CTTCCTCTCT
*
1228046 AAAAAAAGAAAAAAG
1 AAAAAAAAAAAAAAG
1228061 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
1228076 GAGATATTTC
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:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:1228415 original size:13 final size:11
Alignment explanation
Indices: 1228395--1228432 Score: 51
Period size: 10 Copynumber: 3.4 Consensus size: 11
1228385 TAAAAAATAA
1228395 AAAATTATATTT
1 AAAATTAT-TTT
1228407 AATAATTATTTT
1 AA-AATTATTTT
1228419 AAAA-TATTTT
1 AAAATTATTTT
1228429 AAAA
1 AAAA
1228433 ATAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.40
11 2 0.08
12 7 0.28
13 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:1228501 original size:33 final size:32
Alignment explanation
Indices: 1228428--1228502 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 32
1228418 TAAAATATTT
* *
1228428 TAAAAATAATATTTATTTTTAATATTATTAAA
1 TAAAAATAATATTTATTTTTAAAATAATTAAA
1228460 TAATAAATAATATTTATTTTTAAAATAATTAAA
1 TAA-AAATAATATTTATTTTTAAAATAATTAAA
*
1228493 TTTAAAATAA
1 -TAAAAATAA
1228503 AAAATATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 3 0.08
33 33 0.87
34 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
TAAAAATAATATTTATTTTTAAAATAATTAAA
Found at i:1228503 original size:37 final size:33
Alignment explanation
Indices: 1228431--1228493 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1228421 AATATTTTAA
* *
1228431 AAATAATATTTATTTTTAATATTATTAAATAAT
1 AAATAATATTTATTTTTAAAATAATTAAATAAT
1228464 AAATAATATTTATTTTTAAAATAATTAAAT
1 AAATAATATTTATTTTTAAAATAATTAAAT
1228494 TTAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
AAATAATATTTATTTTTAAAATAATTAAATAAT
Found at i:1228906 original size:14 final size:14
Alignment explanation
Indices: 1228887--1228913 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1228877 CATTAATTTG
1228887 AAATATATCTTAAA
1 AAATATATCTTAAA
1228901 AAATATATCTTAA
1 AAATATATCTTAA
1228914 TGATAAAAGG
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:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATATATCTTAAA
Found at i:1231289 original size:24 final size:22
Alignment explanation
Indices: 1231230--1231315 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 22
1231220 GAATAATAAA
1231230 TATAAATATATATTTAATTTTTT
1 TATAAATATAT-TTTAATTTTTT
*
1231253 TAAATAATCATATTTTAATTTTTAT
1 TATA-AAT-ATATTTTAATTTTT-T
* *
1231278 GTTTAAATATATTTAAATATTATTT
1 -TATAAATATATTTTAAT-TT-TTT
*
1231303 TAAAAATTATATT
1 TATAAA-TATATT
1231316 ACTTATATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
23 3 0.06
24 26 0.52
25 17 0.34
26 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (22 bp):
TATAAATATATTTTAATTTTTT
Found at i:1231292 original size:23 final size:21
Alignment explanation
Indices: 1231262--1231306 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1231252 TTAAATAATC
* *
1231262 ATATTTTAATTTTTATGTTTAA
1 ATATTTTAAATATTAT-TTTAA
1231284 ATATATTTAAATATTATTTTAA
1 ATAT-TTTAAATATTATTTTAA
1231306 A
1 A
1231307 AATTATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATATTTTAAATATTATTTTAA
Found at i:1231306 original size:12 final size:12
Alignment explanation
Indices: 1231263--1231312 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1231253 TAAATAATCA
* *
1231263 TATTTTAATTTT
1 TATTTTAAATAT
1231275 TATGTTTAAATA-
1 TAT-TTTAAATAT
1231287 TA-TTTAAATAT
1 TATTTTAAATAT
*
1231298 TATTTTAAAAAT
1 TATTTTAAATAT
1231310 TAT
1 TAT
1231313 ATTACTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.25
11 2 0.06
12 16 0.50
13 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TATTTTAAATAT
Found at i:1231338 original size:13 final size:13
Alignment explanation
Indices: 1231320--1231346 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1231310 TATATTACTT
1231320 ATATAAATATTAA
1 ATATAAATATTAA
1231333 ATATAAATATTAA
1 ATATAAATATTAA
1231346 A
1 A
1231347 AAAATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATAAATATTAA
Found at i:1249953 original size:20 final size:19
Alignment explanation
Indices: 1249918--1249955 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1249908 ATATTTAAAA
1249918 AAATTTAAATAAAAATATT
1 AAATTTAAATAAAAATATT
*
1249937 AAATTTAAAATATAAATAT
1 AAATTT-AAATAAAAATAT
1249956 ATATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTTAAATAAAAATATT
Found at i:1250400 original size:6 final size:6
Alignment explanation
Indices: 1250389--1250484 Score: 50
Period size: 6 Copynumber: 14.2 Consensus size: 6
1250379 TAATATATAT
*
1250389 TATTTA TATTTATA TATTTA TATTATCA TAATTA TATTTAAAA TATTATA
1 TATTTA TA-TT-TA TATTTA TATT-T-A TATTTA TATTT---A TATT-TA
**
1250439 TATTTA TATAAA T-TTTAA TATATTAA TAATTTA TATTTA TATTTA T
1 TATTTA TATTTA TATTT-A TAT-TT-A T-ATTTA TATTTA TATTTA T
1250485 TTATTAATAA
Statistics
Matches: 72, Mismatches: 6, Indels: 24
0.71 0.06 0.24
Matches are distributed among these distances:
5 1 0.01
6 34 0.47
7 14 0.19
8 15 0.21
9 7 0.10
10 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (6 bp):
TATTTA
Found at i:1250408 original size:14 final size:14
Alignment explanation
Indices: 1250384--1250489 Score: 78
Period size: 14 Copynumber: 7.6 Consensus size: 14
1250374 ATGATTAATA
1250384 TATATTATTTATATT
1 TATA-TATTTATATT
1250399 TATATATTTATA-T
1 TATATATTTATATT
*
1250412 TATCATAATTATATT
1 TAT-ATATTTATATT
*
1250427 TAAAATATTATATATT
1 T-ATATATT-TATATT
*
1250443 TATATA--AAT-TT
1 TATATATTTATATT
* *
1250454 TAATATATTAATAAT
1 T-ATATATTTATATT
1250469 T-TATATTTATATT
1 TATATATTTATATT
*
1250482 TATTTATT
1 TATATATT
1250490 AATAAAATAT
Statistics
Matches: 73, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
11 3 0.04
12 7 0.10
13 15 0.21
14 24 0.33
15 16 0.22
16 8 0.11
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATATTTATATT
Found at i:1250411 original size:27 final size:27
Alignment explanation
Indices: 1250377--1250516 Score: 92
Period size: 27 Copynumber: 5.0 Consensus size: 27
1250367 TTAGAAAATG
1250377 ATTAATATATATTATTTATATTTATAT
1 ATTAATATATATTATTTATATTTATAT
* * *
1250404 ATTTATAT-TATCATAATTATATTTAAAAT
1 ATTAATATATAT--TATTTATATTT-ATAT
* *
1250433 ATT-ATATAT-TTATATAAATTTTAATAT
1 ATTAATATATATTATTTATA-TTT-ATAT
* *
1250460 ATTAATA-ATTTATATTTATATTTATTT
1 ATTAATATATAT-TATTTATATTTATAT
*
1250487 ATTAATAAAATATTTATATTAT-TTTATAT
1 ATTAAT-ATATA-TTAT-TTATATTTATAT
1250516 A
1 A
1250517 ACTAGTTGAA
Statistics
Matches: 89, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
26 8 0.09
27 28 0.31
28 23 0.26
29 25 0.28
30 5 0.06
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTAATATATATTATTTATATTTATAT
Found at i:1250461 original size:36 final size:34
Alignment explanation
Indices: 1250398--1250480 Score: 89
Period size: 36 Copynumber: 2.4 Consensus size: 34
1250388 TTATTTATAT
*
1250398 TTATATATTTATATTATCATAATTATATTTAAAATA
1 TTATATATTTATATAATCATAATTATA-TTAAAA-A
** *
1250434 TTATATATTTATATAAATTTTAA-TATATTAATAA
1 TTATATATTTATAT-AATCATAATTATATTAAAAA
1250468 TT-TATATTTATAT
1 TTATATATTTATAT
1250481 TTATTTATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 11 0.26
34 3 0.07
35 5 0.12
36 18 0.43
37 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (34 bp):
TTATATATTTATATAATCATAATTATATTAAAAA
Found at i:1250626 original size:26 final size:27
Alignment explanation
Indices: 1250566--1250627 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
1250556 GAAGTTCAAA
1250566 ATAAAATT-TTTAATTTAAATTAAATT
1 ATAAAATTATTTAATTTAAATTAAATT
* * *
1250592 A-AATTATTATTT-ATTTAATTTTAATT
1 ATAA-AATTATTTAATTTAAATTAAATT
1250618 ATAAAATTAT
1 ATAAAATTAT
1250628 AAATAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
25 2 0.07
26 22 0.76
27 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATAAAATTATTTAATTTAAATTAAATT
Found at i:1250942 original size:3 final size:3
Alignment explanation
Indices: 1250934--1250969 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
1250924 CTATTAACCA
*
1250934 AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
1250970 AGAAGGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:1259288 original size:24 final size:24
Alignment explanation
Indices: 1259260--1259313 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1259250 AAAATAATAT
**
1259260 TAAATATTAA-ATATTATTTTTATA
1 TAAATATTAATA-ATTAAATTTATA
*
1259284 TAAATATTTATAATTAAATTTATA
1 TAAATATTAATAATTAAATTTATA
1259308 TAAATA
1 TAAATA
1259314 ATTTTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAATATTAATAATTAAATTTATA
Found at i:1259308 original size:18 final size:17
Alignment explanation
Indices: 1259287--1259364 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 17
1259277 TTTTATATAA
1259287 ATATTTATAATTAAATTT
1 ATATTTA-AATTAAATTT
*
1259305 ATA--TAAA-TAATTTTT
1 ATATTTAAATTAA-ATTT
*
1259320 ATTATTTAAATCATAA-TT
1 A-TATTTAAATTA-AATTT
1259338 ATATTTAAATTAAA--T
1 ATATTTAAATTAAATTT
*
1259353 AAATTTAAATTA
1 ATATTTAAATTA
1259365 TCAAAATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
14 3 0.06
15 18 0.37
16 6 0.12
17 10 0.20
18 10 0.20
19 1 0.02
20 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTTAAATTAAATTT
Found at i:1259400 original size:15 final size:15
Alignment explanation
Indices: 1259340--1259400 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
1259330 TCATAATTAT
*
1259340 ATTTAAATTAAATAA
1 ATTTAAATTTAATAA
*
1259355 ATTTAAATTATCA-AA
1 ATTTAAATT-TAATAA
**
1259370 ATTTTTATTT--TAA
1 ATTTAAATTTAATAA
1259383 ATTTAAATTTAATAA
1 ATTTAAATTTAATAA
1259398 ATT
1 ATT
1259401 GAATAAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
15 24 0.67
16 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTAAATTTAATAA
Found at i:1259429 original size:19 final size:19
Alignment explanation
Indices: 1259402--1259441 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1259392 TAATAAATTG
1259402 AATAAATTATTTAATTTAT
1 AATAAATTATTTAATTTAT
* *
1259421 AATATATTATTTATTTTAT
1 AATAAATTATTTAATTTAT
1259440 AA
1 AA
1259442 ACTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATAAATTATTTAATTTAT
Found at i:1259479 original size:16 final size:16
Alignment explanation
Indices: 1259445--1259495 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
1259435 TTTATAAACT
**
1259445 TATTTTTAAATATTTA
1 TATTTTTAAATATAAA
*
1259461 TATTTTTTAATATAAA
1 TATTTTTAAATATAAA
1259477 TA---TTAAATATAAA
1 TATTTTTAAATATAAA
1259490 TATTTT
1 TATTTT
1259496 AAAAAAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 12 0.43
16 16 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTTTAAATATAAA
Found at i:1259487 original size:13 final size:13
Alignment explanation
Indices: 1259469--1259493 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1259459 TATATTTTTT
1259469 AATATAAATATTA
1 AATATAAATATTA
1259482 AATATAAATATT
1 AATATAAATATT
1259494 TTAAAAAAAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATATAAATATTA
Found at i:1265874 original size:4 final size:4
Alignment explanation
Indices: 1265865--1265899 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1265855 ATTTATCTCC
* *
1265865 TTTA TTTA TTTA TTTA TATA TTTA TGTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1265900 TTGGGTACCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1267894 original size:3 final size:3
Alignment explanation
Indices: 1267888--1267924 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1267878 AATTCTCAAC
1267888 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1267925 CTAACATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1268148 original size:3 final size:3
Alignment explanation
Indices: 1268140--1268164 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1268130 GAAAGATTCT
1268140 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1268165 TAAAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1269043 original size:19 final size:20
Alignment explanation
Indices: 1268992--1269044 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1268982 GGAGAGAAGG
* *
1268992 AAAGAAAGGAGAGAGAAAAAA
1 AAAGAAA-GAAAGAAAAAAAA
*
1269013 AATGAAAGAAAGAAAAAAAA
1 AAAGAAAGAAAGAAAAAAAA
1269033 AAAGAAA-AAAGA
1 AAAGAAAGAAAGA
1269045 GAGACAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 5 0.18
20 17 0.61
21 6 0.21
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AAAGAAAGAAAGAAAAAAAA
Found at i:1269346 original size:27 final size:29
Alignment explanation
Indices: 1269316--1269371 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1269306 CATTTCTATC
1269316 ATATTCAT-ATTA-TTTTT-ATATTATATT
1 ATATT-ATAATTATTTTTTAATATTATATT
*
1269343 ATATTTTAATTATTTTTTAATATTATATT
1 ATATTATAATTATTTTTTAATATTATATT
1269372 TATGTTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 1 0.04
27 9 0.36
28 5 0.20
29 10 0.40
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (29 bp):
ATATTATAATTATTTTTTAATATTATATT
Found at i:1270701 original size:24 final size:24
Alignment explanation
Indices: 1270674--1270723 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1270664 TTTTAAAATT
*
1270674 ATTTTTAAAATATAAA-ATATTAAA
1 ATTTATAAAATA-AAATATATTAAA
* *
1270698 ATTTATATAATAAAATTTATTAAA
1 ATTTATAAAATAAAATATATTAAA
1270722 AT
1 AT
1270724 ATTAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTATAAAATAAAATATATTAAA
Found at i:1270709 original size:17 final size:17
Alignment explanation
Indices: 1270684--1270743 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 17
1270674 ATTTTTAAAA
1270684 TATAAAATATTAAAATT
1 TATAAAATATTAAAATT
*
1270701 TAT---ATAATAAAATT
1 TATAAAATATTAAAATT
*
1270715 TATTAAAATATTAAATTT
1 TA-TAAAATATTAAAATT
1270733 TATATAAATAT
1 TATA-AAATAT
1270744 ATAATATATC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 12 0.34
15 1 0.03
17 5 0.14
18 17 0.49
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATAAAATATTAAAATT
Found at i:1270735 original size:18 final size:17
Alignment explanation
Indices: 1270686--1270732 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1270676 TTTTAAAATA
1270686 TAAAATATTAAAATTTA-
1 TAAAATATT-AAATTTAT
*
1270703 TATAATA--AAATTTAT
1 TAAAATATTAAATTTAT
1270718 TAAAATATTAAATTT
1 TAAAATATTAAATTT
1270733 TATATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 7 0.28
15 6 0.24
17 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAATATTAAATTTAT
Found at i:1270741 original size:18 final size:18
Alignment explanation
Indices: 1270683--1270745 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 18
1270673 TATTTTTAAA
1270683 ATATAAAATATTAAAATTT
1 ATATAAAATATT-AAATTT
1270702 ATAT--AATA--AAATTT
1 ATATAAAATATTAAATTT
1270716 AT-TAAAATATTAAATTTT
1 ATATAAAATATTAAA-TTT
1270734 ATATAAATATAT
1 ATATAAA-ATAT
1270746 AATATATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 8 0.22
15 4 0.11
17 7 0.19
18 5 0.14
19 8 0.22
20 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAAAATATTAAATTT
Found at i:1271010 original size:19 final size:20
Alignment explanation
Indices: 1270967--1271016 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1270957 TAATGCTTAT
*
1270967 ATATAAATATTAAATTATTA
1 ATATAAATATAAAATTATTA
1270987 A-ATAAAT-TAAAATT-TTAA
1 ATATAAATATAAAATTATT-A
1271005 ATATAAATATAA
1 ATATAAATATAA
1271017 TATATATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.08
18 8 0.31
19 12 0.46
20 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATAAATATAAAATTATTA
Found at i:1271103 original size:32 final size:32
Alignment explanation
Indices: 1271031--1271106 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
1271021 TATTTAATCA
*
1271031 ATTATATT-TATTATATTTAAATACTTATATT
1 ATTATATTATATTATATTTAAATAATTATATT
* * *
1271062 AATAAATTATTTTATATTTAAATATATTAT-TT
1 ATTATATTATATTATATTTAAATA-ATTATATT
*
1271094 TTTATATTATATT
1 ATTATATTATATT
1271107 TTTTATCATA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
31 6 0.17
32 25 0.71
33 4 0.11
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (32 bp):
ATTATATTATATTATATTTAAATAATTATATT
Found at i:1272700 original size:19 final size:20
Alignment explanation
Indices: 1272663--1272702 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1272653 TCTTTTTTCT
* *
1272663 TTTTTTTAATTATTATTTTA
1 TTTTTTAAAGTATTATTTTA
1272683 TTTTTTAAAGTATT-TTTTA
1 TTTTTTAAAGTATTATTTTA
1272702 T
1 T
1272703 ATATATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTTTAAAGTATTATTTTA
Found at i:1272709 original size:13 final size:13
Alignment explanation
Indices: 1272681--1272721 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1272671 ATTATTATTT
1272681 TATTTTTTA-A-A
1 TATTTTTTATATA
1272692 GTATTTTTTATATA
1 -TATTTTTTATATA
*
1272706 TATTTTATATATA
1 TATTTTTTATATA
1272719 TAT
1 TAT
1272722 ATATACTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 9 0.35
13 16 0.62
14 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
TATTTTTTATATA
Found at i:1273814 original size:25 final size:25
Alignment explanation
Indices: 1273761--1273817 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
1273751 TCAAATTCAA
**
1273761 TTAAATTCAAATCAAATTTTAAATT
1 TTAAATTCAAATCAAATTTTAAACC
* * *
1273786 TTAAATTCGAATTAAATTTTATACC
1 TTAAATTCAAATCAAATTTTAAACC
1273811 TTAAATT
1 TTAAATT
1273818 TTTAAATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.46
Consensus pattern (25 bp):
TTAAATTCAAATCAAATTTTAAACC
Found at i:1278845 original size:22 final size:21
Alignment explanation
Indices: 1278820--1278876 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
1278810 TAATAAAAAT
1278820 AATATATTATAATAATATTTAA
1 AATATATTATAA-AATATTTAA
*
1278842 AATAATAATTA-AAAATTTTTAA
1 AAT-AT-ATTATAAAATATTTAA
1278864 AA-ATACTTATAAA
1 AATATA-TTATAAA
1278877 TATAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
19 1 0.03
20 5 0.17
21 3 0.10
22 13 0.43
23 4 0.13
24 4 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATATTATAAAATATTTAA
Found at i:1278847 original size:12 final size:12
Alignment explanation
Indices: 1278815--1278855 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1278805 AAATTTAATA
1278815 AAAATAATATATT
1 AAAATAATAT-TT
*
1278828 ATAATAATATTT
1 AAAATAATATTT
*
1278840 AAAATAATAATT
1 AAAATAATATTT
1278852 AAAA
1 AAAA
1278856 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAAATAATATTT
Found at i:1278929 original size:16 final size:15
Alignment explanation
Indices: 1278910--1278973 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 15
1278900 AATAACAAAA
1278910 AAATATTAAATTTATT
1 AAATATT-AATTTATT
1278926 AAATATTTTAA-TTATT
1 AAATA--TTAATTTATT
*
1278942 TAATATT-ATTTA-T
1 AAATATTAATTTATT
*
1278955 AAATATTAATTAATT
1 AAATATTAATTTATT
1278970 AAAT
1 AAAT
1278974 CTACGAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
13 8 0.20
14 9 0.22
15 5 0.12
16 14 0.35
17 2 0.05
18 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATATTAATTTATT
Found at i:1279127 original size:3 final size:3
Alignment explanation
Indices: 1279119--1279145 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1279109 TCATGTGCCT
1279119 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1279146 ACCTTAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1282268 original size:16 final size:18
Alignment explanation
Indices: 1282242--1282274 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1282232 TTTTTTGTGT
1282242 ATATCAATTT-ATGTTAC
1 ATATCAATTTAATGTTAC
1282259 ATAT-AATTTAATGTTA
1 ATATCAATTTAATGTTA
1282275 ATTTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (18 bp):
ATATCAATTTAATGTTAC
Found at i:1287432 original size:2 final size:2
Alignment explanation
Indices: 1287425--1287449 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1287415 TTTGCAGTCA
1287425 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
1287450 AAAAGAAAGG
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:1288092 original size:2 final size:2
Alignment explanation
Indices: 1288085--1288114 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1288075 AATGTTAATT
1288085 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1288115 ACACACACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1288446 original size:26 final size:25
Alignment explanation
Indices: 1288391--1288447 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
1288381 CTTTGAATTC
* *
1288391 AAAA-ATTTTATATTGGATCAAATT
1 AAAATATTTTATATTAGATCAAATA
* *
1288415 TAAATATTTTATATTAGATTGAAATA
1 AAAATATTTTATATTAGA-TCAAATA
1288441 AAAATAT
1 AAAATAT
1288448 AATTTTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 3 0.12
25 12 0.46
26 11 0.42
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (25 bp):
AAAATATTTTATATTAGATCAAATA
Found at i:1289681 original size:19 final size:20
Alignment explanation
Indices: 1289652--1289691 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1289642 GATATATTTA
*
1289652 AAAATATAAAAAATTTAATT
1 AAAATATAAAAAATGTAATT
*
1289672 AAAA-ATAAAATATGTAATT
1 AAAATATAAAAAATGTAATT
1289691 A
1 A
1289692 TTTTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAATATAAAAAATGTAATT
Found at i:1289710 original size:58 final size:59
Alignment explanation
Indices: 1289613--1289731 Score: 138
Period size: 58 Copynumber: 2.0 Consensus size: 59
1289603 AATTTATAAA
* *
1289613 TAAAATTAAAAAATTAATATATTTTTTAAGATATATTT-AAAAATATAAAAAATTTA-AT
1 TAAAAATAAAAAATTAATATATTTTTTAAGATATATTTAAAAAAT-TAAAAAAATTATAT
* * *
1289671 TAAAAATAAAATATGTAAT-TATTTTTTAA-TTTTATTTTAAAAAATTAAAAAAATTATAT
1 TAAAAATAAAAAAT-TAATATATTTTTTAAGATATA-TTTAAAAAATTAAAAAAATTATAT
1289730 TA
1 TA
1289732 TTAGTGTATA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
57 3 0.06
58 35 0.67
59 14 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (59 bp):
TAAAAATAAAAAATTAATATATTTTTTAAGATATATTTAAAAAATTAAAAAAATTATAT
Found at i:1290374 original size:18 final size:18
Alignment explanation
Indices: 1290353--1290418 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
1290343 TTTTAAAAAA
*
1290353 ATATTAGATGTTAATTTT
1 ATATTATATGTTAATTTT
* * *
1290371 ATATTTTATTTTTAAATTAT
1 ATATTATA-TGTT-AATTTT
*
1290391 ATAATATATGTTAATTTT
1 ATATTATATGTTAATTTT
1290409 ATATTTATAT
1 ATA-TTATAT
1290419 AAATTATATA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
18 14 0.39
19 11 0.31
20 11 0.31
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
ATATTATATGTTAATTTT
Found at i:1290407 original size:38 final size:35
Alignment explanation
Indices: 1290360--1290430 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 35
1290350 AAAATATTAG
*
1290360 ATGTTAATTTTATATTTTATTTTTAAATTATATAATAT
1 ATGTTAATTTTATA-TTTA--TATAAATTATATAATAT
1290398 ATGTTAATTTTATATTTATATAAATTATATAAT
1 ATGTTAATTTTATATTTATATAAATTATATAAT
1290431 TTTTATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 14 0.44
37 4 0.12
38 14 0.44
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (35 bp):
ATGTTAATTTTATATTTATATAAATTATATAATAT
Found at i:1290408 original size:25 final size:26
Alignment explanation
Indices: 1290370--1290420 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1290360 ATGTTAATTT
* *
1290370 TATATTTTATTTTTA-AATTATATAA
1 TATATGTTAATTTTATAATTATATAA
*
1290395 TATATGTTAATTTTATATTTATATAA
1 TATATGTTAATTTTATAATTATATAA
1290421 ATTATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
TATATGTTAATTTTATAATTATATAA
Found at i:1290416 original size:26 final size:25
Alignment explanation
Indices: 1290370--1290443 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 25
1290360 ATGTTAATTT
* *
1290370 TATATTTTATTTT-TAAATTATATAA
1 TATATTTAATTTTAT-ATTTATATAA
1290395 TATATGTTAATTTTATATTTATATAA
1 TATAT-TTAATTTTATATTTATATAA
*
1290421 -ATTATATAATTTT-TATTT-TATAA
1 TA-TATTTAATTTTATATTTATATAA
1290444 AAAATAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
23 5 0.12
24 5 0.12
25 13 0.30
26 19 0.44
27 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (25 bp):
TATATTTAATTTTATATTTATATAA
Found at i:1290439 original size:31 final size:30
Alignment explanation
Indices: 1290366--1290442 Score: 86
Period size: 35 Copynumber: 2.4 Consensus size: 30
1290356 TTAGATGTTA
1290366 ATTTTATATTT-TATTTTTAAATTATATAAT
1 ATTTTAT-TTTATATTTTTAAATTATATAAT
1290396 ATATGTTAATTTTATATTTATATAAATTATATAAT
1 AT-T-TT-ATTTTATATTT-T-TAAATTATATAAT
1290431 -TTTTATTTTATA
1 ATTTTATTTTATA
1290443 AAAAATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
30 2 0.05
31 9 0.22
32 7 0.17
33 8 0.20
34 2 0.05
35 13 0.32
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (30 bp):
ATTTTATTTTATATTTTTAAATTATATAAT
Found at i:1290493 original size:15 final size:14
Alignment explanation
Indices: 1290473--1290520 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
1290463 TATATTTTAA
1290473 ATTTAATAATAAATT
1 ATTTAATAATAAA-T
1290488 ATTTAATTAATAAAT
1 ATTTAA-TAATAAAT
*
1290503 A-TTAA-AATATAT
1 ATTTAATAATAAAT
1290515 ATTTAA
1 ATTTAA
1290521 AAAATAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 7 0.23
13 4 0.13
14 4 0.13
15 8 0.27
16 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTTAATAATAAAT
Found at i:1290500 original size:16 final size:15
Alignment explanation
Indices: 1290473--1290531 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
1290463 TATATTTTAA
1290473 ATTTAATAATAAATT
1 ATTTAATAATAAATT
1290488 ATTTAATTAATAAA-T
1 ATTTAA-TAATAAATT
*
1290503 A-TTAA-AATATA-T
1 ATTTAATAATAAATT
*
1290515 ATTTAAAAAATAAATT
1 ATTT-AATAATAAATT
1290531 A
1 A
1290532 AAAATATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
12 7 0.19
13 2 0.05
14 6 0.16
15 13 0.35
16 9 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTTAATAATAAATT
Found at i:1290508 original size:23 final size:23
Alignment explanation
Indices: 1290477--1290546 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
1290467 TTTTAAATTT
* * *
1290477 AATAATAAATTATTTAATTAATA
1 AATAATAAAATATATAATTAAAA
* *
1290500 AATATTAAAATATATATTTAAAA
1 AATAATAAAATATATAATTAAAA
1290523 AATAAATTAAAA-ATATAATATAAA
1 AAT-AA-TAAAATATATAAT-TAAA
1290547 TAAGTTTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 21 0.57
24 7 0.19
25 9 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AATAATAAAATATATAATTAAAA
Found at i:1290543 original size:27 final size:27
Alignment explanation
Indices: 1290470--1290543 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
1290460 ATTTATATTT
* **
1290470 TAAATTTAATAATA-AATTATTTAATTAA
1 TAAA-TTAAAAATATAA-TATTTAAAAAA
*
1290498 TAAATATTAAAATAT-ATATTTAAAAAA
1 TAAAT-TAAAAATATAATATTTAAAAAA
1290525 TAAATTAAAAATATAATAT
1 TAAATTAAAAATATAATAT
1290544 AAATAAGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 8 0.21
27 19 0.50
28 11 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAATTAAAAATATAATATTTAAAAAA
Found at i:1291661 original size:2 final size:2
Alignment explanation
Indices: 1291654--1291694 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1291644 GTTTATTCAG
1291654 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1291695 TCCATGATTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1293226 original size:9 final size:10
Alignment explanation
Indices: 1293206--1293390 Score: 53
Period size: 9 Copynumber: 19.0 Consensus size: 10
1293196 TATGTATATT
1293206 TTTAATAATA
1 TTTAATAATA
1293216 TTTAA-AATA
1 TTTAATAATA
1293225 -TT-AT-ATA
1 TTTAATAATA
1293232 TTTATATAA-A
1 TTTA-ATAATA
1293242 TTT-A-AATA
1 TTTAATAATA
*
1293250 TATTAAT-ATT
1 T-TTAATAATA
*
1293260 TTTATTATATAAA
1 TTTA--ATA-ATA
1293273 GTTTAAT-ATA
1 -TTTAATAATA
1293283 TTT-AT-ATA
1 TTTAATAATA
1293291 TTT-ATAATA
1 TTTAATAATA
*
1293300 TTT-ATATTA
1 TTTAATAATA
*
1293309 TTTTTATAA-A
1 -TTTAATAATA
*
1293319 -TAATATAATA
1 TTTA-ATAATA
*
1293329 TTTTATATTATA
1 -TTTA-ATAATA
*
1293341 TTTTAATTATA
1 -TTTAATAATA
*
1293352 TTT-ATATTA
1 TTTAATAATA
*
1293361 TATAATAAT-
1 TTTAATAATA
*
1293370 TTTAAAAATAA
1 TTTAATAAT-A
1293381 TTTAATAATA
1 TTTAATAATA
1293391 AAAAATTATA
Statistics
Matches: 134, Mismatches: 17, Indels: 48
0.67 0.09 0.24
Matches are distributed among these distances:
7 6 0.04
8 18 0.13
9 40 0.30
10 30 0.22
11 20 0.15
12 15 0.11
13 1 0.01
14 4 0.03
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (10 bp):
TTTAATAATA
Found at i:1293229 original size:26 final size:27
Alignment explanation
Indices: 1293200--1293303 Score: 90
Period size: 26 Copynumber: 3.8 Consensus size: 27
1293190 ATGTGGTATG
*
1293200 TATATTTTTA-ATAATATTTAAAATAT
1 TATATATTTATATAATATTTAAAATAT
1293226 TATATATTTATATAA-ATTTAAATATAT
1 TATATATTTATATAATATTTAAA-ATAT
* * *
1293253 TAATATTTTTATTATATAAAGTTTAATATAT
1 T-ATATATTTA-TATA-ATA-TTTAAAATAT
1293284 T-TATATATT-TATAATATTTA
1 TATATAT-TTATATAATATTTA
1293304 TATTATTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
26 20 0.31
27 11 0.17
28 12 0.18
29 8 0.12
30 3 0.05
31 6 0.09
32 5 0.08
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
TATATATTTATATAATATTTAAAATAT
Found at i:1293271 original size:31 final size:31
Alignment explanation
Indices: 1293233--1293300 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1293223 TATTATATAT
*
1293233 TTATATAAA-TTTAAATATATTAATATTTTTA
1 TTATATAAAGTTT-AATATATTAATATATTTA
*
1293264 TTATATAAAGTTTAATATATTTATATATTTA
1 TTATATAAAGTTTAATATATTAATATATTTA
*
1293295 TAATAT
1 TTATAT
1293301 TTATATTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 30 0.91
32 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
TTATATAAAGTTTAATATATTAATATATTTA
Found at i:1293350 original size:41 final size:43
Alignment explanation
Indices: 1293280--1293373 Score: 106
Period size: 41 Copynumber: 2.2 Consensus size: 43
1293270 AAAGTTTAAT
*
1293280 ATATTTATATATTTATAATATTTATATTATTTTTATAAATAATATA
1 ATATTT-TATATTTATAATATTTATATTATATTTAT--ATAATATA
*
1293326 ATATTTTATA-TTAT-AT-TTTA-ATTATATTTATATTATATA
1 ATATTTTATATTTATAATATTTATATTATATTTATATAATATA
1293365 ATAATTTTA
1 AT-ATTTTA
1293374 AAAATAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
39 9 0.20
40 6 0.13
41 10 0.22
42 4 0.09
43 2 0.04
44 4 0.09
45 4 0.09
46 6 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (43 bp):
ATATTTTATATTTATAATATTTATATTATATTTATATAATATA
Found at i:1293356 original size:17 final size:17
Alignment explanation
Indices: 1293228--1293359 Score: 51
Period size: 17 Copynumber: 7.7 Consensus size: 17
1293218 TAAAATATTA
*
1293228 TATATTTATATAAATTTAAA
1 TATATTTATAT---TTTAAT
* *
1293248 TATATTAATATTTTTAT
1 TATATTTATATTTTAAT
* *
1293265 TATA--TAAAGTTTAA-
1 TATATTTATATTTTAAT
1293279 TATATTTATATATTT-AT
1 TATATTTATAT-TTTAAT
* *
1293296 AATATTTATATTATT-TT
1 TATATTTATATT-TTAAT
** * *
1293313 TATAAATA-ATATAATAT
1 TATATTTATATTTTA-AT
*
1293330 TTTATATTATATTTTAAT
1 TATAT-TTATATTTTAAT
1293348 TATATTTATATT
1 TATATTTATATT
1293360 ATATAATAAT
Statistics
Matches: 80, Mismatches: 23, Indels: 21
0.65 0.19 0.17
Matches are distributed among these distances:
14 4 0.05
15 7 0.09
16 7 0.09
17 40 0.50
18 8 0.10
19 4 0.05
20 10 0.12
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (17 bp):
TATATTTATATTTTAAT
Found at i:1293362 original size:11 final size:11
Alignment explanation
Indices: 1293287--1293363 Score: 67
Period size: 11 Copynumber: 7.5 Consensus size: 11
1293277 AATATATTTA
1293287 TATATTTATA-
1 TATATTTATAT
1293297 -ATATTTATAT
1 TATATTTATAT
*
1293307 TATTTTTATA-
1 TATATTTATAT
* * *
1293317 AATA-ATATAA
1 TATATTTATAT
1293327 TAT-TTTATAT
1 TATATTTATAT
1293337 TATATTT-TAAT
1 TATATTTAT-AT
1293348 TATATTTATAT
1 TATATTTATAT
1293359 TATAT
1 TATAT
1293364 AATAATTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
9 13 0.25
10 12 0.23
11 27 0.51
12 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1293383 original size:29 final size:28
Alignment explanation
Indices: 1293297--1293384 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 28
1293287 TATATTTATA
* * *
1293297 ATATTTATATTATTTTTATAAATAATATA
1 ATATTTATATTAATTTTAAAAATAAT-TT
**
1293326 ATATTTTATATTATATTTTAATTAT-ATTT
1 ATA-TTTATATTA-ATTTTAAAAATAATTT
*
1293355 ATATTATATAATAATTTTAAAAATAATTT
1 ATATT-TATATTAATTTTAAAAATAATTT
1293384 A
1 A
1293385 ATAATAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
28 11 0.23
29 18 0.38
30 11 0.23
31 7 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATATTTATATTAATTTTAAAAATAATTT
Found at i:1293417 original size:21 final size:22
Alignment explanation
Indices: 1293393--1293441 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
1293383 TAATAATAAA
1293393 AAATTAT-AAATATTA-AAATTT
1 AAATTATAAAAT-TTATAAATTT
1293414 AAATT-TAAAATTTATAAATTT
1 AAATTATAAAATTTATAAATTT
1293435 AAATTAT
1 AAATTAT
1293442 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.16
21 20 0.80
22 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATTATAAAATTTATAAATTT
Found at i:1293424 original size:7 final size:7
Alignment explanation
Indices: 1293400--1293447 Score: 53
Period size: 7 Copynumber: 6.4 Consensus size: 7
1293390 AAAAAATTAT
1293400 AAATATTA
1 AAAT-TTA
1293408 AAATTT-
1 AAATTTA
1293414 AAATTTA
1 AAATTTA
1293421 AAATTTA
1 AAATTTA
1293428 TAAATTTA
1 -AAATTTA
1293436 AATTATTTA
1 AA--ATTTA
1293445 AAA
1 AAA
1293448 AAATAATCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
6 6 0.17
7 12 0.33
8 11 0.31
9 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:1293446 original size:15 final size:16
Alignment explanation
Indices: 1293410--1293446 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1293400 AAATATTAAA
1293410 ATTTAAATTTAAAATT
1 ATTTAAATTTAAAATT
*
1293426 -TATAAATTT-AAATT
1 ATTTAAATTTAAAATT
1293440 ATTTAAA
1 ATTTAAA
1293447 AAAATAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTAAATTTAAAATT
Found at i:1297490 original size:27 final size:27
Alignment explanation
Indices: 1297435--1297493 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
1297425 TATATTTTTT
* **
1297435 ATATT-AATATTTAAAAATATATCAAA
1 ATATTAAATATTTAAAAAAATAAAAAA
1297461 ATATTAAAT-TTTAAAAAAATAAAAATA
1 ATATTAAATATTTAAAAAAATAAAAA-A
1297488 ATATTA
1 ATATTA
1297494 TCAATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
ATATTAAATATTTAAAAAAATAAAAAA
Found at i:1299196 original size:13 final size:12
Alignment explanation
Indices: 1299179--1299212 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1299169 AATATTAATA
1299179 AAATATATATTT
1 AAATATATATTT
*
1299191 ACAATATATTTTT
1 A-AATATATATTT
1299204 AAATATATA
1 AAATATATA
1299213 AGCATACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
AAATATATATTT
Found at i:1299269 original size:15 final size:16
Alignment explanation
Indices: 1299249--1299279 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1299239 ATTTATACAT
1299249 AATTATAAAT-TTTAA
1 AATTATAAATATTTAA
1299264 AATTATAAATATTTAA
1 AATTATAAATATTTAA
1299280 TTTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTATAAATATTTAA
Found at i:1299539 original size:23 final size:24
Alignment explanation
Indices: 1299492--1299539 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1299482 AAACGATATA
*
1299492 AATTAATATACATCAATACATAAC
1 AATTAATATACATCAATACAAAAC
*
1299516 AATTAATATA-ATTAATACAAAAC
1 AATTAATATACATCAATACAAAAC
1299539 A
1 A
1299540 TTATGTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.29
Consensus pattern (24 bp):
AATTAATATACATCAATACAAAAC
Found at i:1299774 original size:18 final size:20
Alignment explanation
Indices: 1299751--1299788 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
1299741 TAATCAAATT
1299751 AATATTTAA-AT-TATTTAA
1 AATATTTAAGATATATTTAA
1299769 AATATTTAAGATATATTTAA
1 AATATTTAAGATATATTTAA
1299789 TAAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AATATTTAAGATATATTTAA
Found at i:1299890 original size:23 final size:23
Alignment explanation
Indices: 1299796--1299884 Score: 99
Period size: 23 Copynumber: 3.9 Consensus size: 23
1299786 TAATAAAATA
* * * *
1299796 TAAATTTAAACT-TAAACCCATT
1 TAAACTTAAACTAAAAACCTATC
* **
1299818 TAAACCTAAACTAAAAATTTATC
1 TAAACTTAAACTAAAAACCTATC
1299841 TAAACTTAAACTAAAAACCTATC
1 TAAACTTAAACTAAAAACCTATC
*
1299864 TAAACTTCAACTAAAAACCTA
1 TAAACTTAAACTAAAAACCTA
1299885 ATTAAAAAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
22 10 0.18
23 45 0.82
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAACTTAAACTAAAAACCTATC
Found at i:1299907 original size:21 final size:21
Alignment explanation
Indices: 1299883--1299923 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1299873 ACTAAAAACC
1299883 TAATTAAAAAATAATA-AAATT
1 TAATTAAAAAA-AATATAAATT
1299904 TAATTAAAAAAAATATAAAT
1 TAATTAAAAAAAATATAAAT
1299924 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TAATTAAAAAAAATATAAATT
Found at i:1299926 original size:15 final size:16
Alignment explanation
Indices: 1299895--1299934 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1299885 ATTAAAAAAT
* *
1299895 AATAAAATTTAATTAA
1 AATAAAATATAAATAA
1299911 AA-AAAATATAAATAA
1 AATAAAATATAAATAA
1299926 AATAAAATA
1 AATAAAATA
1299935 ACGCAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATAAAATATAAATAA
Found at i:1307424 original size:20 final size:22
Alignment explanation
Indices: 1307384--1307424 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
1307374 TAAAAATACA
*
1307384 TATATTATATATTTTTGTTATT
1 TATATTATATATTTTTATTATT
1307406 TATATTAT-T-TTTTTATTAT
1 TATATTATATATTTTTATTAT
1307425 ATTTTATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
TATATTATATATTTTTATTATT
Found at i:1307431 original size:18 final size:18
Alignment explanation
Indices: 1307388--1307427 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
1307378 AATACATATA
1307388 TTATA-TATTTTTGTTAT
1 TTATATTATTTTTGTTAT
1307405 TTATATTATTTTT-TTA-
1 TTATATTATTTTTGTTAT
1307421 TTATATT
1 TTATATT
1307428 TTATATCGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 8 0.36
18 7 0.32
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTATATTATTTTTGTTAT
Found at i:1309597 original size:17 final size:16
Alignment explanation
Indices: 1309563--1309600 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
1309553 CTTCCTACAA
1309563 AAATACGTTAATATTT
1 AAATACGTTAATATTT
1309579 AAATA-GTTACATAATTT
1 AAATACGTTA-AT-ATTT
1309596 AAATA
1 AAATA
1309601 TAAGGTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 9 0.45
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (16 bp):
AAATACGTTAATATTT
Found at i:1316984 original size:15 final size:14
Alignment explanation
Indices: 1316954--1316987 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1316944 CCATAAAAAA
*
1316954 AAATATATATATAT
1 AAATATATATAAAT
1316968 AAATATAATATAAAT
1 AAATAT-ATATAAAT
1316983 AAATA
1 AAATA
1316988 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATATATATAAAT
Found at i:1317054 original size:17 final size:18
Alignment explanation
Indices: 1317016--1317057 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1317006 TTATATATGT
*
1317016 AATATAAAAAATAAATTG
1 AATATAAAAAATAAATTA
1317034 AATA-AAAAAAT-AATTAA
1 AATATAAAAAATAAATT-A
1317051 AATATAA
1 AATATAA
1317058 TATAAGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 11 0.52
18 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AATATAAAAAATAAATTA
Found at i:1317057 original size:11 final size:12
Alignment explanation
Indices: 1317034--1317112 Score: 62
Period size: 11 Copynumber: 6.9 Consensus size: 12
1317024 AAATAAATTG
*
1317034 AATA-AAAAAAT
1 AATATAAAATAT
1317045 AAT-TAAAATAT
1 AATATAAAATAT
*
1317056 AATATAAGA-AT
1 AATATAAAATAT
*
1317067 AATATATAATAT
1 AATATAAAATAT
1317079 AAATATATAAATAT
1 -AATATA-AAATAT
1317093 -AT-TAAAAT-T
1 AATATAAAATAT
*
1317102 TATATAAAATA
1 AATATAAAATA
1317113 AATCATTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
9 1 0.02
10 6 0.11
11 29 0.53
12 8 0.15
13 6 0.11
14 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (12 bp):
AATATAAAATAT
Found at i:1317073 original size:13 final size:13
Alignment explanation
Indices: 1317016--1317115 Score: 51
Period size: 13 Copynumber: 8.2 Consensus size: 13
1317006 TTATATATGT
*
1317016 AATATAAAAAATA
1 AATATATAAAATA
1317029 AAT-TGAATAAAA-A
1 AATAT--ATAAAATA
1317042 AATA-ATTAAAATA
1 AATATA-TAAAATA
*
1317055 TAATATA-AGAAT-
1 -AATATATAAAATA
*
1317067 AATATATAATATA
1 AATATATAAAATA
1317080 AATATAT-AAAT-
1 AATATATAAAATA
1317091 -ATAT-TAAAAT-
1 AATATATAAAATA
*
1317101 -TTATATAAAATA
1 AATATATAAAATA
1317113 AAT
1 AAT
1317116 CATTAATATA
Statistics
Matches: 67, Mismatches: 7, Indels: 26
0.67 0.07 0.26
Matches are distributed among these distances:
9 1 0.01
10 11 0.16
11 13 0.19
12 12 0.18
13 20 0.30
14 9 0.13
15 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
AATATATAAAATA
Found at i:1317108 original size:33 final size:32
Alignment explanation
Indices: 1317069--1317134 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 32
1317059 ATAAGAATAA
* *
1317069 TATATAATATAAAT-ATATAAATATATTAAAATT
1 TATATAAAATAAATCAT-T-AATATATAAAAATT
1317102 TATATAAAATAAATCATTAATATATAAAAATT
1 TATATAAAATAAATCATTAATATATAAAAATT
1317134 T
1 T
1317135 TTAGTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 14 0.47
33 14 0.47
34 2 0.07
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (32 bp):
TATATAAAATAAATCATTAATATATAAAAATT
Found at i:1322296 original size:2 final size:2
Alignment explanation
Indices: 1322289--1322325 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1322279 TCTTCCTCTT
1322289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1322326 TTCTTTCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1326440 original size:41 final size:40
Alignment explanation
Indices: 1326352--1326442 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 40
1326342 AAACTCAAGC
*
1326352 TTTTATATTTTAATTTTTTTAATATTTATAAATTTTAGTTA
1 TTTTA-ATTTTAATTTTTTTAATATTTATAAATATTAGTTA
*
1326393 -TATAATTTTAATTTTTATTTAATATATTA-AAATATTA-TTA
1 TTTTAATTTTAA-TTTT-TTTAATAT-TTATAAATATTAGTTA
1326433 TTTTAATTTT
1 TTTTAATTTT
1326443 TTTTATATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
39 7 0.16
40 10 0.23
41 23 0.53
42 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (40 bp):
TTTTAATTTTAATTTTTTTAATATTTATAAATATTAGTTA
Found at i:1326460 original size:35 final size:35
Alignment explanation
Indices: 1326355--1326452 Score: 94
Period size: 35 Copynumber: 2.7 Consensus size: 35
1326345 CTCAAGCTTT
* *
1326355 TATATTTTAATTTTTTTAATATTTATAAATTTTAGTTA
1 TATATTTTAATTTTTTTTATATTTA-AAA--ATAGTTA
1326393 TATAATTTTAATTTTTATTTAATATATT-AAAATA-TTA
1 TAT-ATTTTAATTTTT-TTT-ATAT-TTAAAAATAGTTA
1326430 T-TATTTTAATTTTTTTTATATTT
1 TATATTTTAATTTTTTTTATATTT
1326453 CACAAAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
32 2 0.04
33 4 0.07
34 3 0.06
35 12 0.22
36 1 0.02
37 4 0.07
38 5 0.09
39 12 0.22
40 5 0.09
41 4 0.07
42 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (35 bp):
TATATTTTAATTTTTTTTATATTTAAAAATAGTTA
Found at i:1331403 original size:25 final size:25
Alignment explanation
Indices: 1331371--1331432 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
1331361 ATATGAATTA
1331371 AATA-ATTAAATATAATATAATATT
1 AATATATTAAATATAATATAATATT
* *
1331395 AATATATTAAATTTAATATAATTTT
1 AATATATTAAATATAATATAATATT
1331420 AAT-T-TTAAATATA
1 AATATATTAAATATA
1331433 TTAAATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.24
24 5 0.15
25 21 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATATATTAAATATAATATAATATT
Found at i:1331434 original size:32 final size:30
Alignment explanation
Indices: 1331374--1331473 Score: 98
Period size: 32 Copynumber: 3.4 Consensus size: 30
1331364 TGAATTAAAT
*
1331374 AATTAAATATAATATAATATTAATATATTA
1 AATTTAATATAATATAATATTAATATATTA
* *
1331404 AATTTAATATAATTTTAATTTTAAATATATTA
1 AATTTAATATAA-TATAATATT-AATATATTA
* *
1331436 AATTTTATATAA-AT-ATA-TAATATTTTA
1 AATTTAATATAATATAATATTAATATATTA
**
1331463 AACATAATATA
1 AATTTAATATA
1331474 TAAAAATATA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
27 16 0.28
28 1 0.02
29 2 0.03
30 12 0.21
31 7 0.12
32 20 0.34
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
AATTTAATATAATATAATATTAATATATTA
Found at i:1331439 original size:16 final size:16
Alignment explanation
Indices: 1331376--1331442 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
1331366 AATTAAATAA
* *
1331376 TTAAATATAATATAATA
1 TTAAATATATTA-AATT
1331393 TT-AATATATTAAA-T
1 TTAAATATATTAAATT
*
1331407 TT-AATATAATTTTAATT
1 TTAAATAT-A-TTAAATT
1331424 TTAAATATATTAAATT
1 TTAAATATATTAAATT
1331440 TTA
1 TTA
1331443 TATAAATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
14 7 0.17
15 3 0.07
16 21 0.50
17 6 0.14
18 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAATATATTAAATT
Found at i:1331460 original size:20 final size:19
Alignment explanation
Indices: 1331425--1331500 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 19
1331415 ATTTTAATTT
*
1331425 TAAATATATTAAATTTTATA
1 TAAATATA-TAAATTTTAAA
1331445 TAAATATATAATATTTTAAA
1 TAAATATATAA-ATTTTAAA
* * *
1331465 CATAATATATAAAAATATAATA
1 TA-AATATAT-AAATTTTAA-A
*
1331487 AAAATATATAAATT
1 TAAATATATAAATT
1331501 ATCAAATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.07
20 20 0.43
21 19 0.41
22 4 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATATATAAATTTTAAA
Found at i:1331483 original size:10 final size:10
Alignment explanation
Indices: 1331468--1331498 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
1331458 TTTTAAACAT
1331468 AATATATAAA
1 AATATATAAA
1331478 AATATAATAAA
1 AATAT-ATAAA
1331489 AATATATAAA
1 AATATATAAA
1331499 TTATCAAATA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATATATAAA
Found at i:1332432 original size:23 final size:23
Alignment explanation
Indices: 1332406--1332449 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1332396 ATGATTATTT
1332406 TTTAAAAATT-AATATTTAATAAA
1 TTTAAAAATTAAATA-TTAATAAA
*
1332429 TTTAAAATTTAAATATTAATA
1 TTTAAAAATTAAATATTAATA
1332450 CTCACAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAAATTAAATATTAATAAA
Found at i:1333159 original size:19 final size:19
Alignment explanation
Indices: 1333135--1333179 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1333125 ATTAATCATT
1333135 TATATTATATAAATTT-TAA
1 TATATT-TATAAATTTATAA
* *
1333154 TATATTTATATATTTATAT
1 TATATTTATAAATTTATAA
1333173 TATATTT
1 TATATTT
1333180 TACTTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATTTATAAATTTATAA
Found at i:1334124 original size:137 final size:137
Alignment explanation
Indices: 1333932--1334196 Score: 404
Period size: 137 Copynumber: 1.9 Consensus size: 137
1333922 TAATTAAGCA
* * * *
1333932 ATAATTGTTCAATCATAATTAAACTTGATCTAAACCCTTAAACACAATAAGATTTTGATGTTAAA
1 ATAATTATTCAATCATAATTAAACTCGATCTAAACCCTTAAACACAATAAAATTTTAATGTTAAA
** * * *
1333997 TTCTATAATTTGAAGAAAATACACTTACTATCATTTGAAGCTTTTAACACTTCCACATACACAGC
66 TTCTATAATTCAAAAAAAATACACTTACTATCATTTAAAGCTTTTAACACTACCACATACACAGC
1334062 ATATAAT
131 ATATAAT
* * * *
1334069 ATAATTATTCAATCATAATTAAACTCGATCTAAATCTTTAAATACGATAAAATTTTAATGTTAAA
1 ATAATTATTCAATCATAATTAAACTCGATCTAAACCCTTAAACACAATAAAATTTTAATGTTAAA
*
1334134 TTCTATAATTCAAAAAAAATACACTTATTATCATTTAAAGCTTTTAACACTACCACATACACA
66 TTCTATAATTCAAAAAAAATACACTTACTATCATTTAAAGCTTTTAACACTACCACATACACA
1334197 ATGATAAAAT
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
137 114 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.35
Consensus pattern (137 bp):
ATAATTATTCAATCATAATTAAACTCGATCTAAACCCTTAAACACAATAAAATTTTAATGTTAAA
TTCTATAATTCAAAAAAAATACACTTACTATCATTTAAAGCTTTTAACACTACCACATACACAGC
ATATAAT
Found at i:1339576 original size:4 final size:4
Alignment explanation
Indices: 1339557--1339591 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1339547 TAATTAAATA
*
1339557 TATT TATA TA-T TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT
1339592 AATAATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 26 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:1339618 original size:20 final size:20
Alignment explanation
Indices: 1339595--1339634 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1339585 ATTTATTAAT
1339595 AATTAAATAAATTTAATATA
1 AATTAAATAAATTTAATATA
* * *
1339615 AATTACATTAATTTTATATA
1 AATTAAATAAATTTAATATA
1339635 TTATCAAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTAAATAAATTTAATATA
Found at i:1342245 original size:2 final size:2
Alignment explanation
Indices: 1342238--1342281 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1342228 AGAAAGAGAT
* *
1342238 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1342280 TA
1 TA
1342282 GCTTAGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1347241 original size:6 final size:6
Alignment explanation
Indices: 1347233--1347263 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1347223 TAAGGGTTTG
*
1347233 GGGTTG GGGTTA GGGTTA GGGTTA GGGTTA G
1 GGGTTA GGGTTA GGGTTA GGGTTA GGGTTA G
1347264 AGCTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.55, T:0.32
Consensus pattern (6 bp):
GGGTTA
Found at i:1347708 original size:30 final size:29
Alignment explanation
Indices: 1347653--1347718 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 29
1347643 TAAATAAGTT
1347653 TTTTTATAATTTTTATTGTAATAAATAAA
1 TTTTTATAATTTTTATTGTAATAAATAAA
1347682 TTTTTAT-ATTTTTATT-TATATTTAAATAAA
1 TTTTTATAATTTTTATTGTA-A--TAAATAAA
1347712 TTTTTAT
1 TTTTTAT
1347719 TTAAAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
27 2 0.06
28 10 0.29
29 7 0.21
30 15 0.44
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTTATAATTTTTATTGTAATAAATAAA
Found at i:1347719 original size:16 final size:16
Alignment explanation
Indices: 1347695--1347729 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1347685 TTATATTTTT
*
1347695 ATTTATATTTAAATAA
1 ATTTATATTTAAAAAA
*
1347711 ATTTTTATTTAAAAAA
1 ATTTATATTTAAAAAA
1347727 ATT
1 ATT
1347730 GATTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTATATTTAAAAAA
Found at i:1347811 original size:47 final size:46
Alignment explanation
Indices: 1347723--1347828 Score: 119
Period size: 47 Copynumber: 2.3 Consensus size: 46
1347713 TTTTATTTAA
* *
1347723 AAAAATTGATTTATTTTAAAATTTATTTAGATATAAATTAAAAA-T
1 AAAAATTTATTTATATTAAAATTTATTTAGATATAAATTAAAAATT
*
1347768 AAAAATTTATTTGATATTAAGAATTTATTTA-AT-TACAGTTTAAAAATT
1 AAAAATTTATTT-ATATTAA-AATTTATTTAGATATA-A-ATTAAAAATT
*
1347816 AATAATTTATTTA
1 AAAAATTTATTTA
1347829 AATATAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
45 13 0.25
46 9 0.17
47 18 0.35
48 12 0.23
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.46
Consensus pattern (46 bp):
AAAAATTTATTTATATTAAAATTTATTTAGATATAAATTAAAAATT
Found at i:1351636 original size:17 final size:17
Alignment explanation
Indices: 1351614--1351649 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1351604 GAACTTCAGA
1351614 ATTATCTTGCACTTTGC
1 ATTATCTTGCACTTTGC
*
1351631 ATTATCTTGGACTTTGC
1 ATTATCTTGCACTTTGC
1351648 AT
1 AT
1351650 ATATTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (17 bp):
ATTATCTTGCACTTTGC
Found at i:1352733 original size:1 final size:1
Alignment explanation
Indices: 1352729--1352754 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1352719 CATTTTTTTT
1352729 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
1352755 TCAAGAATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1353269 original size:15 final size:16
Alignment explanation
Indices: 1353251--1353283 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1353241 AAAAAATTTA
1353251 AAATTA-AATTTTATT
1 AAATTATAATTTTATT
*
1353266 AAATTATAATTTTTTT
1 AAATTATAATTTTATT
1353282 AA
1 AA
1353284 TTTTTTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATTATAATTTTATT
Found at i:1353307 original size:24 final size:25
Alignment explanation
Indices: 1353257--1353307 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
1353247 TTTAAAATTA
** *
1353257 AATTTTATTAAATTATAATTTTTTT
1 AATTTTATTAAATTATAATAATATT
*
1353282 AATTTT-TTAAGTTATAATAATATT
1 AATTTTATTAAATTATAATAATATT
1353306 AA
1 AA
1353308 AATATTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
AATTTTATTAAATTATAATAATATT
Found at i:1353324 original size:34 final size:33
Alignment explanation
Indices: 1353278--1353341 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
1353268 ATTATAATTT
* *
1353278 TTTTAATTTTTTAAGT-TATAATAATATTAAAATA
1 TTTTAATATTTTAAATATATAA-AA-ATTAAAATA
1353312 TTTTAATATTTTAAATATATAAAAATTAAA
1 TTTTAATATTTTAAATATATAAAAATTAAA
1353342 TTTATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 6 0.22
34 16 0.59
35 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (33 bp):
TTTTAATATTTTAAATATATAAAAATTAAAATA
Found at i:1353432 original size:14 final size:14
Alignment explanation
Indices: 1353415--1353450 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1353405 TAGTCACTTT
1353415 AAAATATACTACTC
1 AAAATATACTACTC
* *
1353429 AAAATATATTACTT
1 AAAATATACTACTC
1353443 AAAATATA
1 AAAATATA
1353451 AAATATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATATACTACTC
Found at i:1355052 original size:30 final size:27
Alignment explanation
Indices: 1355012--1355076 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
1355002 GTAAGAGCAA
*
1355012 AAAAACATATACTTATCTTTTTAAATTTTT
1 AAAAA-ATATACTTAT-TTTTT-AATATTT
*
1355042 ATAAAAATATATTTATTTTTTAATATTT
1 A-AAAAATATACTTATTTTTTAATATTT
1355070 AAAAAAT
1 AAAAAAT
1355077 GTTTACTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 6 0.19
28 7 0.22
29 5 0.16
30 10 0.31
31 4 0.12
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (27 bp):
AAAAAATATACTTATTTTTTAATATTT
Found at i:1355958 original size:24 final size:23
Alignment explanation
Indices: 1355912--1355958 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1355902 ATTTTGTATC
* **
1355912 AAATTTTTAAAAAAATATTATTA
1 AAATTTTAAAAAAAATAAAATTA
1355935 AAATTTTAAAAATAAATAAAATTA
1 AAATTTTAAAAA-AAATAAAATTA
1355959 CTTTTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTTTAAAAAAAATAAAATTA
Found at i:1356946 original size:23 final size:24
Alignment explanation
Indices: 1356901--1356947 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1356891 TTTAACATAG
* *
1356901 ATTAATCTTTAATTTAAAATAAAA
1 ATTAATCTTGAATATAAAATAAAA
*
1356925 ATTAA-CTTGAATATAAATTAAAA
1 ATTAATCTTGAATATAAAATAAAA
1356948 GATAAAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTAATCTTGAATATAAAATAAAA
Done.