Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold364
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: 2089110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1352066 original size:17 final size:18
Alignment explanation
Indices: 1352046--1352082 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1352036 ATTACATAAC
1352046 ATAAAAAT-AATATAAAA
1 ATAAAAATAAATATAAAA
*
1352063 AT-AAAATAAATATATAA
1 ATAAAAATAAATATAAAA
1352080 ATA
1 ATA
1352083 TATTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 3
0.81 0.05 0.14
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
ATAAAAATAAATATAAAA
Found at i:1352089 original size:17 final size:17
Alignment explanation
Indices: 1352054--1352168 Score: 68
Period size: 15 Copynumber: 7.1 Consensus size: 17
1352044 ACATAAAAAT
* * *
1352054 AATATAAAAATAAAATA
1 AATATATAAATATATTA
1352071 AATATATAAATATATTAA
1 AATATATAAATATATT-A
*
1352089 AATTTATAAA-ATATT-
1 AATATATAAATATATTA
1352104 AAT-TACT-AATATATTAA
1 AATATA-TAAATATATT-A
*
1352121 AATTTATATAA-ATA-TA
1 AATATATA-AATATATTA
*
1352137 AA-ATATAAATATAATA
1 AATATATAAATATATTA
*
1352153 AA-ATA-AAATATGTTA
1 AATATATAAATATATTA
1352168 A
1 A
1352169 CTGCTCATCA
Statistics
Matches: 81, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
14 6 0.07
15 25 0.31
16 10 0.12
17 23 0.28
18 15 0.19
19 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.37
Consensus pattern (17 bp):
AATATATAAATATATTA
Found at i:1352144 original size:13 final size:13
Alignment explanation
Indices: 1352126--1352150 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1352116 ATTAAAATTT
1352126 ATATAAATATAAA
1 ATATAAATATAAA
1352139 ATATAAATATAA
1 ATATAAATATAA
1352151 TAAAATAAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATAAATATAAA
Found at i:1352148 original size:33 final size:33
Alignment explanation
Indices: 1352063--1352156 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
1352053 TAATATAAAA
1352063 ATAAA-ATAAATATATAAATATATTAAAATTTAT
1 ATAAATATAAA-ATATAAATATATTAAAATTTAT
* *
1352096 A-AAATATTAATTACT-AATATATTAAAATTTAT
1 ATAAATATAAAATA-TAAATATATTAAAATTTAT
*
1352128 ATAAATATAAAATATAAATATAATAAAAT
1 ATAAATATAAAATATAAATATATTAAAAT
1352157 AAAATATGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
32 24 0.46
33 28 0.54
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
ATAAATATAAAATATAAATATATTAAAATTTAT
Found at i:1352389 original size:41 final size:38
Alignment explanation
Indices: 1352312--1352403 Score: 96
Period size: 41 Copynumber: 2.3 Consensus size: 38
1352302 TAAATATTTA
* * *
1352312 ATAAATATATTATATTTATTTTACTTATATTTAAAAAC
1 ATAAATATATAATATTTATTTTACTTAAATTAAAAAAC
*
1352350 ATAACATATATAATAATTTATATTTA-TTAAATTAAAAAAAT
1 ATAA-ATATATAAT-ATTTAT-TTTACTTAAATT-AAAAAAC
1352391 ATAAAATATATAA
1 AT-AAATATATAA
1352404 ATTATCAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
38 4 0.09
39 8 0.18
40 12 0.27
41 19 0.42
42 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (38 bp):
ATAAATATATAATATTTATTTTACTTAAATTAAAAAAC
Found at i:1352400 original size:39 final size:40
Alignment explanation
Indices: 1352314--1352408 Score: 90
Period size: 39 Copynumber: 2.4 Consensus size: 40
1352304 AATATTTAAT
* * *
1352314 AAATATATTATATTTATTTTACTTATATTTAAAAACATAAC
1 AAATATAATA-ATTTATTTTACTTATAATTAAAAAAATAAC
*
1352355 ATATATAATAATTTATATTTA-TTA-AATTAAAAAAATATA-
1 AAATATAATAATTTAT-TTTACTTATAATTAAAAAAATA-AC
*
1352394 AAATAT-ATAAATTAT
1 AAATATAATAATTTAT
1352409 CAAATCTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
38 8 0.17
39 16 0.35
40 10 0.22
41 12 0.26
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (40 bp):
AAATATAATAATTTATTTTACTTATAATTAAAAAAATAAC
Found at i:1356949 original size:21 final size:21
Alignment explanation
Indices: 1356908--1356949 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1356898 TTACATTGTG
*
1356908 TTAATTATATATTATTATTTA
1 TTAATTATATATTAATATTTA
*
1356929 TTAATTTTAATATTAAT-TTTA
1 TTAATTAT-ATATTAATATTTA
1356950 GAATCCTGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTAATTATATATTAATATTTA
Found at i:1357031 original size:23 final size:23
Alignment explanation
Indices: 1357003--1357072 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 23
1356993 CTTTTAAAAA
1357003 TTATTATATTTAATATATTAATT
1 TTATTATATTTAATATATTAATT
*
1357026 TTATTAAATTTAAAAATATATTAATT
1 TTATTATATTT---AATATATTAATT
*
1357052 ATATT-T-TTTAATA-ATT-ATT
1 TTATTATATTTAATATATTAATT
1357071 TT
1 TT
1357073 CTTAACAAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
19 4 0.10
20 3 0.08
21 4 0.10
23 10 0.25
24 3 0.08
26 16 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTATTATATTTAATATATTAATT
Found at i:1370677 original size:2 final size:2
Alignment explanation
Indices: 1370670--1370695 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1370660 ATACAAATCG
1370670 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
1370696 TTACCAAACA
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:1372874 original size:18 final size:17
Alignment explanation
Indices: 1372853--1372894 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
1372843 AATTTAAAAT
1372853 TATATAACATATTATTTA
1 TATATAACA-ATTATTTA
1372871 TATAT---AATTATTTA
1 TATATAACAATTATTTA
1372885 TATATAACAA
1 TATATAACAA
1372895 CATAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
14 13 0.62
15 1 0.05
17 2 0.10
18 5 0.24
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATAACAATTATTTA
Found at i:1372880 original size:14 final size:14
Alignment explanation
Indices: 1372863--1372891 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1372853 TATATAACAT
1372863 ATTATTTATATATA
1 ATTATTTATATATA
1372877 ATTATTTATATATA
1 ATTATTTATATATA
1372891 A
1 A
1372892 CAACATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTATTTATATATA
Found at i:1380991 original size:2 final size:2
Alignment explanation
Indices: 1380984--1381015 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1380974 AGTAGTGTAT
1380984 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1381016 ATTATGTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1382385 original size:30 final size:31
Alignment explanation
Indices: 1382350--1382421 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
1382340 TTTAAAAATT
* *
1382350 ATTAATAAAAAAT-TATTAAAAGTATATTTA
1 ATTAATAAAAAATAAATTAAAAATATATTTA
*
1382380 ATTAATAAAAAATAAATTAAAAATATGTTTA
1 ATTAATAAAAAATAAATTAAAAATATATTTA
*
1382411 A-AAATAAAAAA
1 ATTAATAAAAAA
1382422 AATATAAACG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 22 0.59
31 15 0.41
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (31 bp):
ATTAATAAAAAATAAATTAAAAATATATTTA
Found at i:1382971 original size:18 final size:18
Alignment explanation
Indices: 1382950--1382988 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1382940 ATTTTTTAAA
1382950 TTTAAAATA-TTATAAATT
1 TTTAAAATATTTAT-AATT
*
1382968 TTTATAATATTTATAATT
1 TTTAAAATATTTATAATT
1382986 TTT
1 TTT
1382989 TTTATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTAAAATATTTATAATT
Found at i:1382997 original size:20 final size:20
Alignment explanation
Indices: 1382965--1383041 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
1382955 AATATTATAA
1382965 ATTTTTATAATATTTATAATTT
1 ATTTTTAT-ATATTTAT-ATTT
1382987 -TTTTTATATATTTATATTT
1 ATTTTTATATATTTATATTT
*
1383006 ATATTTATAT-TTTA-A-TT
1 ATTTTTATATATTTATATTT
* *
1383023 AATTTTAAATA-TTATATTT
1 ATTTTTATATATTTATATTT
1383042 GTGTTATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
17 12 0.26
18 2 0.04
19 10 0.21
20 16 0.34
21 7 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTTATATATTTATATTT
Found at i:1383004 original size:6 final size:6
Alignment explanation
Indices: 1382974--1383017 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
1382964 AATTTTTATA
* *
1382974 ATATTT ATAATTT TTTTTAT ATATTT ATATTT ATATTT ATATTT
1 ATATTT AT-ATTT ATATT-T ATATTT ATATTT ATATTT ATATTT
1383018 TAATTAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 23 0.72
7 9 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATATTT
Found at i:1384013 original size:26 final size:27
Alignment explanation
Indices: 1383956--1384015 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
1383946 ATAATTATTT
*
1383956 AATA-TAATTTAATTTAAATTTATGTA
1 AATATTAATTTAATTTAAATTTATATA
*
1383982 ATTATTAATTTAA-TTAAATATT-TATA
1 AATATTAATTTAATTTAAAT-TTATATA
1384008 AATATTAA
1 AATATTAA
1384016 AATTCTCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
AATATTAATTTAATTTAAATTTATATA
Found at i:1384418 original size:3 final size:3
Alignment explanation
Indices: 1384410--1384449 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1384400 AAATAAACCC
*
1384410 ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1384450 ATGATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:1385408 original size:19 final size:18
Alignment explanation
Indices: 1385398--1385433 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1385388 ATTATTTTTA
1385398 AAAATTTTAATTTTATTT
1 AAAATTTTAATTTTATTT
* *
1385416 ATAATTTTAATTTAATTT
1 AAAATTTTAATTTTATTT
1385434 TTTATATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AAAATTTTAATTTTATTT
Found at i:1385422 original size:12 final size:11
Alignment explanation
Indices: 1385401--1385434 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1385391 ATTTTTAAAA
1385401 ATTTTAATTTT
1 ATTTTAATTTT
1385412 ATTTATAATTTT
1 ATTT-TAATTTT
*
1385424 AATTTAATTTT
1 ATTTTAATTTT
1385435 TTATATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTTAATTTT
Found at i:1385436 original size:13 final size:13
Alignment explanation
Indices: 1385420--1385457 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1385410 TTATTTATAA
*
1385420 TTTTAATTTAATT
1 TTTTAATATAATT
1385433 TTTT-ATATAATT
1 TTTTAATATAATT
*
1385445 TTTTAATAAAATT
1 TTTTAATATAATT
1385458 AATATCACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTAATATAATT
Found at i:1385451 original size:25 final size:23
Alignment explanation
Indices: 1385403--1385446 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1385393 TTTTAAAAAT
1385403 TTTAATTTTATTTATAATTTTAA
1 TTTAATTTTATTTATAATTTTAA
1385426 TTTAATTTT-TTATATAATTTT
1 TTTAATTTTATT-TATAATTTT
1385447 TTAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTAATTTTATTTATAATTTTAA
Found at i:1385453 original size:11 final size:12
Alignment explanation
Indices: 1385405--1385453 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1385395 TTAAAAATTT
1385405 TAATTTTATT-TA
1 TAATTTT-TTATA
* *
1385417 TAA-TTTTAATT
1 TAATTTTTTATA
1385428 TAATTTTTTATA
1 TAATTTTTTATA
1385440 TAATTTTTTA-A
1 TAATTTTTTATA
1385451 TAA
1 TAA
1385454 AATTAATATC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 1 0.03
11 11 0.35
12 19 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TAATTTTTTATA
Found at i:1386334 original size:14 final size:14
Alignment explanation
Indices: 1386315--1386396 Score: 51
Period size: 14 Copynumber: 5.9 Consensus size: 14
1386305 AATATAGTAA
1386315 ATAATTTAAAAAAT
1 ATAATTTAAAAAAT
** *
1386329 ATAATTTTTAATAT
1 ATAATTTAAAAAAT
*
1386343 A-AATTTAAAAAGTT
1 ATAATTTAAAAA-AT
* *
1386357 AAAAATTTAAATAAT
1 -ATAATTTAAAAAAT
* *
1386372 ATTACTTAAAAAAT
1 ATAATTTAAAAAAT
*
1386386 A-ATTTTAAAAA
1 ATAATTTAAAAA
1386397 TATTTTTTTA
Statistics
Matches: 49, Mismatches: 16, Indels: 7
0.68 0.22 0.10
Matches are distributed among these distances:
13 14 0.29
14 24 0.49
15 2 0.04
16 9 0.18
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (14 bp):
ATAATTTAAAAAAT
Found at i:1389795 original size:2 final size:2
Alignment explanation
Indices: 1389788--1389817 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1389778 AAATCAAAAC
1389788 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1389818 TTTCTTTTAA
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):
CT
Found at i:1393793 original size:2 final size:2
Alignment explanation
Indices: 1393786--1393819 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1393776 TCAAGTGAAT
*
1393786 GA GA GA GA GA GA GA GA GA GA GA GA GA CA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1393820 CAGAAAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1393820 original size:8 final size:8
Alignment explanation
Indices: 1393789--1393823 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1393779 AGTGAATGAG
*
1393789 AGAGAGAG
1 AGAGAGAC
*
1393797 AGAGAGAG
1 AGAGAGAC
1393805 AGAGAGAC
1 AGAGAGAC
1393813 AGAGAGAC
1 AGAGAGAC
1393821 AGA
1 AGA
1393824 AAAAAGATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.43, T:0.00
Consensus pattern (8 bp):
AGAGAGAC
Found at i:1394516 original size:22 final size:20
Alignment explanation
Indices: 1394458--1394558 Score: 64
Period size: 22 Copynumber: 4.8 Consensus size: 20
1394448 TTTATATAAA
* *
1394458 TATATAATATTTTAATAAAAT
1 TATATAATA-TTAAATAATAT
* *
1394479 TATAATAAAAAATAAATAATAT
1 TAT-AT-AATATTAAATAATAT
1394501 GTGATATAATATTAAA-AATTAT
1 -T-ATATAATATTAAATAA-TAT
*
1394523 T-TATAATATAAAAGTAATAT
1 TATATAATATTAAA-TAATAT
1394543 TAATATAATA-TAAATA
1 T-ATATAATATTAAATA
1394559 TATAAATATA
Statistics
Matches: 63, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
19 11 0.17
20 6 0.10
21 11 0.17
22 27 0.43
23 6 0.10
24 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
TATATAATATTAAATAATAT
Found at i:1394566 original size:19 final size:19
Alignment explanation
Indices: 1394451--1394568 Score: 55
Period size: 19 Copynumber: 6.0 Consensus size: 19
1394441 AAAAAAATTT
*
1394451 ATATAAATATATAATATTTTA
1 ATATAAATATATAA-A-TATA
*
1394472 ATA-AAAT-TAT-AATAAA
1 ATATAAATATATAAATATA
* **
1394488 AAATAAATAATATGTGATATA
1 ATATAAAT-ATAT-AAATATA
* **
1394509 ATATTAAAAAT-TATTTATA
1 ATA-TAAATATATAAATATA
*
1394528 ATATAAAAGTAATATTAATATA
1 ATAT-AAA-T-ATATAAATATA
1394550 ATATAAATATATAAATATA
1 ATATAAATATATAAATATA
1394569 TTAAAAATTT
Statistics
Matches: 72, Mismatches: 15, Indels: 22
0.66 0.14 0.20
Matches are distributed among these distances:
16 4 0.06
17 5 0.07
18 2 0.03
19 26 0.36
20 6 0.08
21 16 0.22
22 13 0.18
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
ATATAAATATATAAATATA
Found at i:1394576 original size:19 final size:19
Alignment explanation
Indices: 1394509--1394576 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
1394499 ATGTGATATA
*
1394509 ATATTAAAAAT-TATTTAT
1 ATATTAAAAATATATTAAT
*
1394527 A-ATATAAAAGTAATATTAAT
1 ATAT-TAAAAAT-ATATTAAT
* * *
1394547 ATAATATAAATATATAAAT
1 ATATTAAAAATATATTAAT
1394566 ATATTAAAAAT
1 ATATTAAAAAT
1394577 TTTAAAATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
17 2 0.05
18 7 0.18
19 16 0.42
20 12 0.32
21 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (19 bp):
ATATTAAAAATATATTAAT
Found at i:1394604 original size:27 final size:28
Alignment explanation
Indices: 1394539--1394606 Score: 68
Period size: 30 Copynumber: 2.4 Consensus size: 28
1394529 TATAAAAGTA
* *
1394539 ATATTAA-TATAATATAAATATATAAAT
1 ATATTAATTTTAAAATAAATATATAAAT
*
1394566 ATATTAAAAATTTTAAAATAAAT-TATTAAT
1 ATATT---AATTTTAAAATAAATATATAAAT
1394596 ATATTAATTTT
1 ATATTAATTTT
1394607 TTTTAATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
27 11 0.32
30 13 0.38
31 10 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
ATATTAATTTTAAAATAAATATATAAAT
Found at i:1394822 original size:12 final size:12
Alignment explanation
Indices: 1394805--1394833 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1394795 GCTACTATAT
1394805 TAGTAGTAGTTG
1 TAGTAGTAGTTG
1394817 TAGTAGTAGTTG
1 TAGTAGTAGTTG
1394829 TAGTA
1 TAGTA
1394834 CCATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (12 bp):
TAGTAGTAGTTG
Found at i:1394990 original size:6 final size:6
Alignment explanation
Indices: 1394979--1395003 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1394969 TAAAACACAG
1394979 AATACA AATACA AATACA AATACA A
1 AATACA AATACA AATACA AATACA A
1395004 TCAATCAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AATACA
Found at i:1395990 original size:2 final size:2
Alignment explanation
Indices: 1395983--1396010 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1395973 GCATACATCA
1395983 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
1396011 GTCTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1399512 original size:17 final size:18
Alignment explanation
Indices: 1399490--1399566 Score: 66
Period size: 18 Copynumber: 4.3 Consensus size: 18
1399480 ACAAAAAAAT
*
1399490 ATATATATTTATA-TTTA
1 ATATATATTTAAATTTTA
1399507 ATATATATTTAAATTTTA
1 ATATATATTTAAATTTTA
* ** *
1399525 ATATTAAACATAATTTTTA
1 ATA-TATATTTAAATTTTA
* **
1399544 AAATATATAAAAATTTTA
1 ATATATATTTAAATTTTA
1399562 ATATA
1 ATATA
1399567 ATACATTTGG
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
17 12 0.26
18 22 0.47
19 13 0.28
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATATATTTAAATTTTA
Found at i:1399526 original size:18 final size:18
Alignment explanation
Indices: 1399487--1399566 Score: 70
Period size: 19 Copynumber: 4.3 Consensus size: 18
1399477 TTTACAAAAA
**
1399487 AATATATATATTTATATTT
1 AATATATATATAAAT-TTT
*
1399506 AATATATATTTAAATTTT
1 AATATATATATAAATTTT
* * *
1399524 AATATTAAACATAATTTTT
1 AATA-TATATATAAATTTT
* *
1399543 AAAATATATAAAAATTTT
1 AATATATATATAAATTTT
1399561 AATATA
1 AATATA
1399567 ATACATTTGG
Statistics
Matches: 47, Mismatches: 13, Indels: 3
0.75 0.21 0.05
Matches are distributed among these distances:
18 22 0.47
19 25 0.53
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (18 bp):
AATATATATATAAATTTT
Found at i:1399697 original size:11 final size:11
Alignment explanation
Indices: 1399681--1399744 Score: 66
Period size: 11 Copynumber: 6.2 Consensus size: 11
1399671 GATATATTTT
1399681 ATTATATTATA
1 ATTATATTATA
1399692 ATTATATTTATA
1 ATTATA-TTATA
*
1399704 A-TATTTTATA
1 ATTATATTATA
*
1399714 TTTATATTAT-
1 ATTATATTATA
1399724 ATT-T-TTATA
1 ATTATATTATA
1399733 ATTATA-TATA
1 ATTATATTATA
1399743 AT
1 AT
1399745 ATTAATTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
8 4 0.09
9 4 0.09
10 14 0.32
11 16 0.36
12 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTATATTATA
Found at i:1399712 original size:16 final size:18
Alignment explanation
Indices: 1399693--1399742 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
1399683 TATATTATAA
1399693 TTATATTTATA-ATA-TT
1 TTATATTTATATATATTT
1399709 TTATATTTATATTATATTT
1 TTATATTTATA-TATATTT
*
1399728 TTATAATTATATATA
1 TTATATTTATATATA
1399743 ATATTAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 11 0.37
18 7 0.23
19 12 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTTATATATATTT
Found at i:1399740 original size:21 final size:21
Alignment explanation
Indices: 1399672--1399747 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
1399662 TGATATTTTG
*
1399672 ATATATTTTATTATATTATAATT
1 ATATATTATATT-T-TTATAATT
1399695 ATAT-TTATAATATTTTAT-ATT
1 ATATATTAT-AT-TTTTATAATT
1399716 -TATATTATATTTTTATAATT
1 ATATATTATATTTTTATAATT
*
1399736 ATATATAATATT
1 ATATATTATATT
1399748 AATTGATGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
19 6 0.13
20 8 0.17
21 17 0.37
22 7 0.15
23 7 0.15
24 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATTATATTTTTATAATT
Found at i:1402483 original size:20 final size:19
Alignment explanation
Indices: 1402456--1402502 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1402446 AATATTTTTA
* *
1402456 TATTTTTTTTTTTGTTAATT
1 TATTTTTTATATT-TTAATT
1402476 TATATTTTTATATTTTAATT
1 TAT-TTTTTATATTTTAATT
1402496 TATTTTT
1 TATTTTT
1402503 ATCATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.17
20 12 0.50
21 8 0.33
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (19 bp):
TATTTTTTATATTTTAATT
Found at i:1404215 original size:14 final size:14
Alignment explanation
Indices: 1404193--1404238 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1404183 TTAAATTTAA
*
1404193 TAAAAATAATATAT
1 TAAATATAATATAT
* *
1404207 TAAATATAATTTTT
1 TAAATATAATATAT
1404221 TAAA-ATAATA-AT
1 TAAATATAATATAT
1404233 TAAATA
1 TAAATA
1404239 ATTCATAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
12 5 0.19
13 6 0.23
14 15 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATATAATATAT
Found at i:1405577 original size:27 final size:26
Alignment explanation
Indices: 1405522--1405586 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
1405512 TTTTATTAAT
* *
1405522 ATTTTATATTTTATAATTAAATTTAA
1 ATTTAATATTTTATAATTAAATGTAA
*
1405548 ATTATAATATTTTATTATTAAATAGT-A
1 ATT-TAATATTTTATAATTAAAT-GTAA
*
1405575 ATTTAAAATTTT
1 ATTTAATATTTT
1405587 GAATTAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 11 0.33
27 21 0.64
28 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTTAATATTTTATAATTAAATGTAA
Found at i:1409316 original size:2 final size:2
Alignment explanation
Indices: 1409276--1409307 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1409266 TGATGGTATG
1409276 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1409308 AGAATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1409744 original size:21 final size:21
Alignment explanation
Indices: 1409718--1409758 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1409708 AAGCCTTCAA
* * *
1409718 TATATATATATATTAAAAATT
1 TATATAAAAATATAAAAAATT
1409739 TATATAAAAATATAAAAAAT
1 TATATAAAAATATAAAAAAT
1409759 AAAATATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TATATAAAAATATAAAAAATT
Found at i:1409868 original size:30 final size:31
Alignment explanation
Indices: 1409825--1409918 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 31
1409815 TTAATTATGC
*
1409825 ATAAAATTTTTAATTTTTAATTTATATGTAA
1 ATAAAATTTTTAATTTTTAATTTATATCTAA
* * * *
1409856 ATAAAA-TTTTAATTTTTAAATTGTAACT-C
1 ATAAAATTTTTAATTTTTAATTTATATCTAA
* * *
1409885 ATAAAATTTTTAATATTTAATTTAAATTTAA
1 ATAAAATTTTTAATTTTTAATTTATATCTAA
1409916 ATA
1 ATA
1409919 TACTATGATA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
29 6 0.12
30 34 0.69
31 9 0.18
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (31 bp):
ATAAAATTTTTAATTTTTAATTTATATCTAA
Found at i:1418230 original size:5 final size:5
Alignment explanation
Indices: 1418220--1418271 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
1418210 CCGGTTAGTC
* *
1418220 AAAAG AAAAG AAAAG AGAAGG ACAA- AAAA- AAAAG AAAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG A-AAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG
1418270 AA
1 AA
1418272 CAGGGGAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 7 0.17
5 24 0.60
6 9 0.22
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1420073 original size:62 final size:62
Alignment explanation
Indices: 1419976--1420101 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
1419966 CCGTCAAATG
1419976 TTAGTGGTTCTGAATTTCTACGTTTAACTCTTTGTATCCACTTGTTCATATATTTCTGCCTT
1 TTAGTGGTTCTGAATTTCTACGTTTAACTCTTTGTATCCACTTGTTCATATATTTCTGCCTT
*
1420038 TTAGTGGTTCTGAATTTCTACGTTTAACTCTTTGTATCCGCTTGTTCATATATTTCTGCCTT
1 TTAGTGGTTCTGAATTTCTACGTTTAACTCTTTGTATCCACTTGTTCATATATTTCTGCCTT
1420100 TT
1 TT
1420102 TTTTTGGTCA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.51
Consensus pattern (62 bp):
TTAGTGGTTCTGAATTTCTACGTTTAACTCTTTGTATCCACTTGTTCATATATTTCTGCCTT
Found at i:1426872 original size:14 final size:13
Alignment explanation
Indices: 1426847--1426915 Score: 53
Period size: 13 Copynumber: 5.7 Consensus size: 13
1426837 ATTTTATTAT
1426847 TATTTT-TAAATA
1 TATTTTATAAATA
1426859 TCATTTTATAAATA
1 T-ATTTTATAAATA
*
1426873 TATATTTAT-AATT
1 TAT-TTTATAAATA
1426886 TATTTT-T-AA-A
1 TATTTTATAAATA
*
1426896 T-TTTAATAAA-A
1 TATTTTATAAATA
1426907 TATTTTATA
1 TATTTTATA
1426916 TAAATATACA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
9 3 0.06
10 2 0.04
11 7 0.15
12 10 0.21
13 13 0.28
14 12 0.26
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTTTATAAATA
Found at i:1427137 original size:16 final size:17
Alignment explanation
Indices: 1427098--1427138 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1427088 TTTTAAATAT
1427098 AATTAT-AAGAAATAAA
1 AATTATAAAGAAATAAA
*
1427114 AATGATAAAGAAA-AAA
1 AATTATAAAGAAATAAA
*
1427130 TATTATAAA
1 AATTATAAA
1427139 TTGATTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (17 bp):
AATTATAAAGAAATAAA
Found at i:1431516 original size:2 final size:2
Alignment explanation
Indices: 1431509--1431551 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1431499 TTCCCTCTTC
1431509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1431551 T
1 T
1431552 TTCTTTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1431719 original size:2 final size:2
Alignment explanation
Indices: 1431714--1431741 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1431704 TTTTTTTTAA
1431714 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
1431742 TTTGATGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1436284 original size:17 final size:18
Alignment explanation
Indices: 1436252--1436286 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1436242 AGAAATTGTA
1436252 AACTAAAAATATTTCAAC
1 AACTAAAAATATTTCAAC
1436270 AACTAAAAATA-TTCAAC
1 AACTAAAAATATTTCAAC
1436287 CAAAAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (18 bp):
AACTAAAAATATTTCAAC
Found at i:1438269 original size:2 final size:2
Alignment explanation
Indices: 1438262--1438289 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1438252 TTTTTACTTT
1438262 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1438290 ATGCTAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1438999 original size:14 final size:15
Alignment explanation
Indices: 1438982--1439015 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1438972 AAAATTTTAA
1438982 TATATTTA-ATAATT
1 TATATTTATATAATT
1438996 TATATTTATATAATT
1 TATATTTATATAATT
*
1439011 AATAT
1 TATAT
1439016 AAAATATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATTTATATAATT
Found at i:1439139 original size:2 final size:2
Alignment explanation
Indices: 1439127--1439155 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1439117 CTAAATAGAT
1439127 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1439156 ATTAGAGGCA
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):
TA
Found at i:1460492 original size:3 final size:3
Alignment explanation
Indices: 1460484--1460514 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1460474 CAATTCGGGA
1460484 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1460515 TATTTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1463619 original size:22 final size:22
Alignment explanation
Indices: 1463572--1463619 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
1463562 TGCGAGTTTA
*
1463572 AATTTTTAAAATTTATTTAATT
1 AATTTTTAAAATATATTTAATT
1463594 -ATTTTTAAAATAATATTT-ATT
1 AATTTTTAAAAT-ATATTTAATT
1463615 AATTT
1 AATTT
1463620 ATTTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTTTTAAAATATATTTAATT
Found at i:1464243 original size:23 final size:23
Alignment explanation
Indices: 1464198--1464255 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
1464188 TATTTACGAA
1464198 TAAA-CTCATTT-ATAAATTATT
1 TAAAGCTCATTTAATAAATTATT
1464219 TAAAGCTCATTTAATAAA-TAGTT
1 TAAAGCTCATTTAATAAATTA-TT
* *
1464242 TAAAGTTAATTTAA
1 TAAAGCTCATTTAA
1464256 AACTCATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 4 0.12
22 9 0.28
23 19 0.59
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (23 bp):
TAAAGCTCATTTAATAAATTATT
Found at i:1464972 original size:2 final size:2
Alignment explanation
Indices: 1464967--1464994 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1464957 TATTTTACAG
1464967 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
1464995 GTCGGTTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1467068 original size:21 final size:21
Alignment explanation
Indices: 1467035--1467079 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
1467025 ATTTAATAAA
1467035 AATATATAATAAAT-ATTTTAT
1 AATATATAATAAATAATTTT-T
1467056 AATA-ATAATTAAATAATTTTT
1 AATATATAA-TAAATAATTTTT
1467077 AAT
1 AAT
1467080 CGAGGTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATATATAATAAATAATTTTT
Found at i:1469611 original size:28 final size:27
Alignment explanation
Indices: 1469559--1469616 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
1469549 ACAATATGAA
*
1469559 AAATAATAAAAATATGATATGAATACAT
1 AAATAATAAAAATATGATA-GAATAAAT
*
1469587 AAATATATTAAAATATAGATA-AATAAAT
1 AAATA-ATAAAAATAT-GATAGAATAAAT
1469615 AA
1 AA
1469617 TTAACGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 13 0.50
29 9 0.35
30 4 0.15
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (27 bp):
AAATAATAAAAATATGATAGAATAAAT
Found at i:1469687 original size:27 final size:25
Alignment explanation
Indices: 1469657--1469719 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
1469647 TTATTTTAAA
1469657 TATAAAAAATAATATAAATATAATATT
1 TATAAAAAATAAT-TAAA-ATAATATT
* *
1469684 TATAAAAAATACTTAAAATATTATT
1 TATAAAAAATAATTAAAATAATATT
1469709 TA-AAAATAATA
1 TATAAAA-AATA
1469720 TGCACACAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 4 0.12
25 13 0.39
26 4 0.12
27 12 0.36
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
TATAAAAAATAATTAAAATAATATT
Found at i:1469690 original size:25 final size:23
Alignment explanation
Indices: 1469661--1469750 Score: 69
Period size: 25 Copynumber: 3.8 Consensus size: 23
1469651 TTTAAATATA
1469661 AAAAATAATATAAATATAATATTT
1 AAAAATAATATAAA-ATAATATTT
*
1469685 ATAAAA-AATACTTAAAATATTATTT
1 A-AAAATAATA--TAAAATAATATTT
* * *
1469710 AAAAATAATATGCACACAATA--T
1 AAAAATAATAT-AAAATAATATTT
1469732 AAAAATATATATAAAATAA
1 AAAAATA-ATATAAAATAA
1469751 AATAAATTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
22 12 0.23
23 5 0.10
24 14 0.27
25 17 0.33
26 4 0.08
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (23 bp):
AAAAATAATATAAAATAATATTT
Found at i:1469777 original size:33 final size:30
Alignment explanation
Indices: 1469740--1469803 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 30
1469730 ATAAAAATAT
1469740 ATATAAAATAAAATAAATTATTAATATATACAA
1 ATATAAAATAAAAT-AA-TATT-ATATATACAA
* * *
1469773 ATATACAATAATATAATATTTTATATACAA
1 ATATAAAATAAAATAATATTATATATACAA
1469803 A
1 A
1469804 AAATAACACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 10 0.36
31 4 0.14
32 2 0.07
33 12 0.43
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (30 bp):
ATATAAAATAAAATAATATTATATATACAA
Found at i:1470485 original size:38 final size:37
Alignment explanation
Indices: 1470403--1470486 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 37
1470393 AAATGAATCT
* * * *
1470403 TATATATAAAAAATATAATTAATATATAAAATTTTAAA
1 TATA-ATAAAAAATATAATAAACACATAAAAATTTAAA
*
1470441 TTTAATAAAAATATATAATAAACACATAAAAAATTTAAA
1 TATAATAAAAA-ATATAATAAACACAT-AAAAATTTAAA
1470480 -ATAATAA
1 TATAATAA
1470487 TTAAATAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
37 7 0.18
38 21 0.55
39 10 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (37 bp):
TATAATAAAAAATATAATAAACACATAAAAATTTAAA
Found at i:1471124 original size:27 final size:28
Alignment explanation
Indices: 1471071--1471130 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
1471061 TTAAATTTAA
*
1471071 TAAAATTAATATATTAAATATAATTTTT
1 TAAAATTAATATAATAAATATAATTTTT
*
1471099 TAAAATTAATA-AATAAATA-ATTTTTTT
1 TAAAATTAATATAATAAATATA-ATTTTT
1471126 TAAAA
1 TAAAA
1471131 ATTTATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 1 0.03
27 17 0.59
28 11 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAAATTAATATAATAAATATAATTTTT
Found at i:1471543 original size:28 final size:32
Alignment explanation
Indices: 1471484--1471547 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
1471474 AATTTTTAAA
* *
1471484 TTTTATAAATAAATGGATATAATGATGTATAT
1 TTTTAAAAATAAATAGATATAATGATGTATAT
1471516 TTTTAAAAATAAATAG-TA-AATG-TG-ATAT
1 TTTTAAAAATAAATAGATATAATGATGTATAT
1471544 TTTT
1 TTTT
1471548 TAATATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.27
29 2 0.07
30 4 0.13
31 2 0.07
32 14 0.47
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (32 bp):
TTTTAAAAATAAATAGATATAATGATGTATAT
Found at i:1471793 original size:24 final size:23
Alignment explanation
Indices: 1471758--1471816 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 23
1471748 AAAGATTCAA
1471758 TTATATTAATTTAAATTAAATTAT
1 TTATATTAATTT-AATTAAATTAT
* *
1471782 TTATATTTATTTAATTTAATTAT
1 TTATATTAATTTAATTAAATTAT
1471805 TATATATATAAT
1 T-TATAT-TAAT
1471817 AAATATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.37
24 16 0.53
25 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATATTAATTTAATTAAATTAT
Found at i:1471825 original size:24 final size:23
Alignment explanation
Indices: 1471776--1471828 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
1471766 ATTTAAATTA
* * * *
1471776 AATTATTTATATTTATTTAATTT
1 AATTATTTATATATAATAAATAT
1471799 AATTATTATATATATAATAAATAT
1 AATTATT-TATATATAATAAATAT
1471823 AATTAT
1 AATTAT
1471829 AACAACAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTATTTATATATAATAAATAT
Found at i:1473773 original size:15 final size:15
Alignment explanation
Indices: 1473753--1473859 Score: 54
Period size: 15 Copynumber: 6.7 Consensus size: 15
1473743 AGAACCAGAG
1473753 AAGAAGGAAGAGGCA
1 AAGAAGGAAGAGGCA
**
1473768 AAGAAGGAAGAACCCA
1 AAGAAGGAAG-AGGCA
* *
1473784 AGAAAGAGGAAGA-ACAA
1 A-AGA-AGGAAGAGGC-A
* * *
1473801 AAGAAAGAAGAGCCC
1 AAGAAGGAAGAGGCA
1473816 AAGAAGGAAGATGAGCA
1 AAGAAGGAAGA-G-GCA
* *
1473833 GAAGAAAGAAGAGGAA
1 -AAGAAGGAAGAGGCA
*
1473849 AAGAAAGAAGA
1 AAGAAGGAAGA
1473860 ACCCAAGAAG
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
15 37 0.52
16 11 0.15
17 7 0.10
18 16 0.23
ACGTcount: A:0.59, C:0.08, G:0.32, T:0.01
Consensus pattern (15 bp):
AAGAAGGAAGAGGCA
Found at i:1473795 original size:18 final size:18
Alignment explanation
Indices: 1473767--1473808 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1473757 AGGAAGAGGC
**
1473767 AAAGAAGGAAGAACCCAAG
1 AAAG-AGGAAGAACAAAAG
1473786 AAAGAGGAAGAACAAAAG
1 AAAGAGGAAGAACAAAAG
1473804 AAAGA
1 AAAGA
1473809 AGAGCCCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.64, C:0.10, G:0.26, T:0.00
Consensus pattern (18 bp):
AAAGAGGAAGAACAAAAG
Found at i:1473826 original size:18 final size:16
Alignment explanation
Indices: 1473792--1473859 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
1473782 CAAGAAAGAG
*
1473792 GAAGAACAA-AAGAAA
1 GAAGAGCAAGAAGAAA
*
1473807 GAAGAGCCCAAGAAGGAA
1 GAAGAG--CAAGAAGAAA
*
1473825 GATGAGC-AGAAGAAA
1 GAAGAGCAAGAAGAAA
*
1473840 GAAGAGGAA-AAGAAA
1 GAAGAGCAAGAAGAAA
1473855 GAAGA
1 GAAGA
1473860 ACCCAAGAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
15 28 0.65
16 2 0.05
17 3 0.07
18 10 0.23
ACGTcount: A:0.60, C:0.07, G:0.31, T:0.01
Consensus pattern (16 bp):
GAAGAGCAAGAAGAAA
Found at i:1473845 original size:33 final size:31
Alignment explanation
Indices: 1473753--1473845 Score: 98
Period size: 33 Copynumber: 2.9 Consensus size: 31
1473743 AGAACCAGAG
* *
1473753 AAGAAGGAAGAG-GCAAAGAAGGAAGAACCC
1 AAGAAGGAAGAGAGCAAAGAAAGAAGAGCCC
* * *
1473783 AAGAAAGAGGAAGAACAAAAGAAAGAAGAGCCC
1 AAGAAGGAAG-AGAGC-AAAGAAAGAAGAGCCC
1473816 AAGAAGGAAGATGAGCAGAAGAAAGAAGAG
1 AAGAAGGAAGA-GAGCA-AAGAAAGAAGAG
1473846 GAAAAGAAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
30 8 0.16
31 2 0.04
32 3 0.06
33 37 0.74
ACGTcount: A:0.57, C:0.10, G:0.32, T:0.01
Consensus pattern (31 bp):
AAGAAGGAAGAGAGCAAAGAAAGAAGAGCCC
Found at i:1473899 original size:48 final size:47
Alignment explanation
Indices: 1473799--1473899 Score: 145
Period size: 48 Copynumber: 2.2 Consensus size: 47
1473789 GAGGAAGAAC
* *
1473799 AAAAGAAAGAAGAGCCCAAGAAGGAAGATGAGCAGAAGAAAGAAGAGG
1 AAAAGAAAGAAGAACCCAAGAAGGAAGA-GAGCAGAAAAAAGAAGAGG
*
1473847 AAAAGAAAGAAGAACCCAAGAAGGAGGA-AG-AGAAAAAAGAAGAGG
1 AAAAGAAAGAAGAACCCAAGAAGGAAGAGAGCAGAAAAAAGAAGAGG
1473892 AAAA-AAAG
1 AAAAGAAAG
1473900 CCACAGCCTC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 4 0.08
45 18 0.36
46 2 0.04
48 26 0.52
ACGTcount: A:0.61, C:0.07, G:0.31, T:0.01
Consensus pattern (47 bp):
AAAAGAAAGAAGAACCCAAGAAGGAAGAGAGCAGAAAAAAGAAGAGG
Found at i:1474995 original size:3 final size:3
Alignment explanation
Indices: 1474989--1475013 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1474979 TTTATTTTTT
1474989 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1475014 TAAAAAAACC
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:1479283 original size:2 final size:2
Alignment explanation
Indices: 1479276--1479308 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1479266 TAAAATTCTT
*
1479276 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1479309 TTCAAAATTC
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:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1483133 original size:22 final size:22
Alignment explanation
Indices: 1483104--1483147 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1483094 AATAAATATA
* *
1483104 TAAATCAATTAAGTTA-AATTT
1 TAAATCAAATAAATTATAATTT
1483125 TAAATTCAAATAAATTATAATTT
1 TAAA-TCAAATAAATTATAATTT
1483148 ATAAGATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATCAAATAAATTATAATTT
Found at i:1483620 original size:22 final size:22
Alignment explanation
Indices: 1483595--1483703 Score: 61
Period size: 20 Copynumber: 5.0 Consensus size: 22
1483585 TTTATATATG
1483595 TATATAATTATATTTAAATTAT
1 TATATAATTATATTTAAATTAT
* *
1483617 TATAT-ATT-TATATAAATTTTAA
1 TATATAATTATATTTAAA--TTAT
* *
1483639 TATATAAATA-ATTTATATT-T
1 TATATAATTATATTTAAATTAT
*
1483659 TATA-AATTTTATTATATTAATATAT
1 TATATAATTATATT-TA--AAT-TAT
*
1483684 T-TAT-ATTATTTTTAAATTAT
1 TATATAATTATATTTAAATTAT
1483704 ATCATATTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 24
0.65 0.11 0.24
Matches are distributed among these distances:
19 3 0.05
20 17 0.26
21 10 0.15
22 13 0.20
23 11 0.17
24 9 0.14
25 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATAATTATATTTAAATTAT
Found at i:1483675 original size:19 final size:20
Alignment explanation
Indices: 1483651--1483697 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1483641 TATAAATAAT
1483651 TTATATTTTATAAATTT-TA
1 TTATATTTTATAAATTTATA
* *
1483670 TTATA-TTAATATATTTATA
1 TTATATTTTATAAATTTATA
1483689 TTAT-TTTTA
1 TTATATTTTA
1483698 AATTATATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATATTTTATAAATTTATA
Found at i:1483686 original size:33 final size:34
Alignment explanation
Indices: 1483578--1483690 Score: 116
Period size: 32 Copynumber: 3.5 Consensus size: 34
1483568 ATTTAATAAT
*
1483578 TTAATA-ATTTATATATGTATAT-AATTATATT-TA
1 TTAATATATTTATAT-T-TATATAAATTTTATTATA
*
1483611 --AAT-TATTATATATTTATATAAATTTTAATATA
1 TTAATATATT-TATATTTATATAAATTTTATTATA
*
1483643 TAAATA-ATTTATATTT-TATAAATTTTATTATA
1 TTAATATATTTATATTTATATAAATTTTATTATA
1483675 TTAATATATTTATATT
1 TTAATATATTTATATT
1483691 ATTTTTAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
30 5 0.07
31 14 0.21
32 27 0.40
33 16 0.24
34 6 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (34 bp):
TTAATATATTTATATTTATATAAATTTTATTATA
Found at i:1485567 original size:26 final size:26
Alignment explanation
Indices: 1485538--1485603 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
1485528 TGAAAGATTT
*
1485538 TTAATATT-TATAAATATTTAATTAAA
1 TTAATATTATATAAAT-TTAAATTAAA
1485564 TTAATAATTATATAAATTTAAATTAAA
1 TTAAT-ATTATATAAATTTAAATTAAA
*
1485591 TT-ATATTAAATAA
1 TTAATATTATATAA
1485604 TTATTATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 8 0.22
26 7 0.19
27 14 0.39
28 7 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAATATTATATAAATTTAAATTAAA
Found at i:1485576 original size:22 final size:21
Alignment explanation
Indices: 1485551--1485601 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
1485541 ATATTTATAA
*
1485551 ATATTTAA-TTAAATTAATAATT
1 ATATTAAATTTAAATT-A-AATT
1485573 ATA-TAAATTTAAATTAAATT
1 ATATTAAATTTAAATTAAATT
1485593 ATATTAAAT
1 ATATTAAAT
1485602 AATTATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.27
21 9 0.35
22 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTAAATTTAAATTAAATT
Found at i:1485632 original size:18 final size:18
Alignment explanation
Indices: 1485590--1485642 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
1485580 TTTAAATTAA
* *
1485590 ATTATATTAAATAATTATT
1 ATTAT-TTAAATATTTTTT
1485609 ATTTATTTAAATATTTTTT
1 A-TTATTTAAATATTTTTT
1485628 ATTATTTAAA-ATTTT
1 ATTATTTAAATATTTT
1485643 ATATAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 5 0.16
18 9 0.29
19 13 0.42
20 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTATTTAAATATTTTTT
Found at i:1485716 original size:35 final size:34
Alignment explanation
Indices: 1485676--1485751 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 34
1485666 ATTAAATCAT
* *
1485676 TATAATA-AATTATAAAAATATAAAATGAATTAAAA
1 TATAATACAAATAT-AAAATAAAAAAT-AATTAAAA
*
1485711 TATAATACAAATATAATATAAAAAATAATT-AAA
1 TATAATACAAATATAAAATAAAAAATAATTAAAA
*
1485744 CATAATAC
1 TATAATAC
1485752 GATACAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 10 0.28
34 4 0.11
35 17 0.47
36 5 0.14
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (34 bp):
TATAATACAAATATAAAATAAAAAATAATTAAAA
Found at i:1486793 original size:18 final size:18
Alignment explanation
Indices: 1486770--1486809 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1486760 TAAACAGTAA
1486770 TTTTTC-TCCTTTCTTTTC
1 TTTTTCTTCCTTT-TTTTC
*
1486788 TTTTTCTTTCTTTTTTTC
1 TTTTTCTTCCTTTTTTTC
1486806 TTTT
1 TTTT
1486810 CCAACTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTCTTCCTTTTTTTC
Found at i:1494173 original size:50 final size:50
Alignment explanation
Indices: 1494047--1494304 Score: 414
Period size: 50 Copynumber: 5.2 Consensus size: 50
1494037 TATACTTAGA
*
1494047 GTCAACAATAATGGCCACCTTTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1494097 G-CAACAATAATGGCCACCTCTTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1494146 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1494196 GTCAACAATTATGGCCACCTC-CTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATAATGGCCACCTCTC-TCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
1494246 GTCAACAATTATGGCTACCT-TCCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATAATGGCCACCTCT-CTCTATTGTCAAAGGTTGGTGAAGAATC
1494296 GTCAACAAT
1 GTCAACAAT
1494305 GGCAACAACT
Statistics
Matches: 197, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
49 48 0.24
50 148 0.75
51 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (50 bp):
GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:1498782 original size:50 final size:50
Alignment explanation
Indices: 1498696--1498952 Score: 374
Period size: 50 Copynumber: 5.2 Consensus size: 50
1498686 TATACTTAGA
* * *
1498696 GTCAATAATAATGG-CACCT-TTTTTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1498744 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTAAAGAATC
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1498794 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTGGGTGAAGAATC
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
1498844 GTCAACAATTATGGCAACCTCTTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* ** * * *
1498894 GTCAACAATTATGATCACCTCCCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1498944 GTCAACAAT
1 GTCAACAAT
1498953 GACAATAACT
Statistics
Matches: 190, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
48 13 0.07
49 5 0.03
50 172 0.91
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (50 bp):
GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:1499804 original size:15 final size:15
Alignment explanation
Indices: 1499762--1499812 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1499752 ATATTTTAAA
1499762 AATATAATTATAATA-
1 AATATAA-TATAATAT
*
1499777 AAAATAATAATAATAT
1 AATATAAT-ATAATAT
1499793 AATATAATATAA-AT
1 AATATAATATAATAT
1499807 -ATATAA
1 AATATAA
1499813 AAAATTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 6 0.19
14 3 0.09
15 16 0.50
16 7 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATAATATAATAT
Found at i:1512684 original size:34 final size:34
Alignment explanation
Indices: 1512643--1512710 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
1512633 CTGTTATGAA
1512643 GAACTTCAAACTTAACCAAGATAAATATAAAAAT
1 GAACTTCAAACTTAACCAAGATAAATATAAAAAT
*
1512677 GAACTTCAAACTTCACCAAGATAAATATAAAAAT
1 GAACTTCAAACTTAACCAAGATAAATATAAAAAT
1512711 TAAGGCAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.54, C:0.16, G:0.06, T:0.24
Consensus pattern (34 bp):
GAACTTCAAACTTAACCAAGATAAATATAAAAAT
Found at i:1513403 original size:2 final size:2
Alignment explanation
Indices: 1513390--1513419 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1513380 AGGGCAAACA
*
1513390 AT AT AA 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
1513420 TTGAATGACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1518365 original size:32 final size:32
Alignment explanation
Indices: 1518324--1518387 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1518314 AGGATTTATA
1518324 ATCCCAAACTCAGCTCAAGCAAAATTTGGAGC
1 ATCCCAAACTCAGCTCAAGCAAAATTTGGAGC
1518356 ATCCCAAACTCAGCTCAAGCAAAATTTGGAGC
1 ATCCCAAACTCAGCTCAAGCAAAATTTGGAGC
1518388 TAGCGCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.19
Consensus pattern (32 bp):
ATCCCAAACTCAGCTCAAGCAAAATTTGGAGC
Found at i:1521296 original size:13 final size:13
Alignment explanation
Indices: 1521278--1521303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1521268 TATATTATTT
1521278 ATATTTATCATAA
1 ATATTTATCATAA
1521291 ATATTTATCATAA
1 ATATTTATCATAA
1521304 TCAATTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTTATCATAA
Found at i:1521812 original size:10 final size:10
Alignment explanation
Indices: 1521799--1521898 Score: 57
Period size: 10 Copynumber: 9.5 Consensus size: 10
1521789 GAGTTTATTT
1521799 TAAAATTATA
1 TAAAATTATA
1521809 TAAAA-TATTA
1 TAAAATTA-TA
1521819 TTAAAATTATAA
1 -TAAAATTAT-A
1521831 TTAAAA--ATCA
1 -TAAAATTAT-A
*
1521841 TCAAAATCATATT
1 T-AAAAT--TATA
1521854 TAAAATTAT-
1 TAAAATTATA
1521863 TAAAATTATA
1 TAAAATTATA
1521873 TAAAAATTAT-
1 T-AAAATTATA
*
1521883 TCAATATTATA
1 T-AAAATTATA
1521894 TAAAA
1 TAAAA
1521899 AATTATGTAT
Statistics
Matches: 73, Mismatches: 5, Indels: 24
0.72 0.05 0.24
Matches are distributed among these distances:
9 12 0.16
10 29 0.40
11 15 0.21
12 14 0.19
13 1 0.01
14 2 0.03
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (10 bp):
TAAAATTATA
Found at i:1521824 original size:21 final size:20
Alignment explanation
Indices: 1521798--1521904 Score: 115
Period size: 21 Copynumber: 5.0 Consensus size: 20
1521788 AGAGTTTATT
1521798 TTAAAATTATATAAAATATTA
1 TTAAAATTATATAAAA-ATTA
*
1521819 TTAAAATTATAATTAAAAATCA
1 TTAAAATTAT-A-TAAAAATTA
* * *
1521841 TCAAAATCATATTTAAAATTA
1 TTAAAATTATA-TAAAAATTA
1521862 TTAAAATTATATAAAAATTA
1 TTAAAATTATATAAAAATTA
*
1521882 TTCAATATTATATAAAAAATTA
1 TT-AAAATTATAT-AAAAATTA
1521904 T
1 T
1521905 GTATTTATGA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
20 10 0.14
21 37 0.51
22 21 0.29
23 5 0.07
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAAATTATATAAAAATTA
Found at i:1522641 original size:14 final size:15
Alignment explanation
Indices: 1522624--1522660 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1522614 TAATTTATTT
1522624 TTTATATA-ATAAAA
1 TTTATATATATAAAA
1522638 TTTATA-ATATAAAA
1 TTTATATATATAAAA
*
1522652 TTAATATAT
1 TTTATATAT
1522661 TATATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 17 0.85
15 2 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTATATATATAAAA
Found at i:1522664 original size:16 final size:16
Alignment explanation
Indices: 1522626--1522671 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
1522616 ATTTATTTTT
*
1522626 TATATAATAAAATT--
1 TATATTATAAAATTAA
*
1522640 TATAATATAAAATTAA
1 TATATTATAAAATTAA
*
1522656 TATATTATATAATTAA
1 TATATTATAAAATTAA
1522672 AAAATAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
16 14 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATATTATAAAATTAA
Found at i:1522769 original size:19 final size:17
Alignment explanation
Indices: 1522730--1522763 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1522720 CGACTAATTT
1522730 TTAAATATTTTTTTTAA
1 TTAAATATTTTTTTTAA
1522747 TTAAAT-TTATTTTTTAA
1 TTAAATATT-TTTTTTAA
1522764 AGTTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAAATATTTTTTTTAA
Found at i:1523359 original size:28 final size:26
Alignment explanation
Indices: 1523305--1523366 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
1523295 TTTTAATATT
* **
1523305 AAAAAAATTTAAATTTAAAAATTTAA
1 AAAAAAATCTAAATTTAAAAAAATAA
1523331 AAAAAAATCTAGAAGTTTAAAAAAATAA
1 AAAAAAATCTA-AA-TTTAAAAAAATAA
*
1523359 AAATAAAT
1 AAAAAAAT
1523367 AAATTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 10 0.33
27 2 0.07
28 18 0.60
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (26 bp):
AAAAAAATCTAAATTTAAAAAAATAA
Found at i:1525613 original size:2 final size:2
Alignment explanation
Indices: 1525606--1525632 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1525596 GTCTGAAATC
1525606 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
1525633 GTGTGTGTGT
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:1526035 original size:19 final size:20
Alignment explanation
Indices: 1526010--1526063 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1526000 AAATAACAAA
1526010 AATTATAAAAATAATATTTT
1 AATTATAAAAATAATATTTT
**
1526030 -ATTATATTAAT-ATATTTT
1 AATTATAAAAATAATATTTT
1526048 AAATTATAAAAATAAT
1 -AATTATAAAAATAAT
1526064 TATTAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 7 0.26
19 9 0.33
20 9 0.33
21 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTATAAAAATAATATTTT
Found at i:1526061 original size:20 final size:20
Alignment explanation
Indices: 1526009--1526072 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
1525999 AAAATAACAA
1526009 AAATTATAAAAATAATATTTT
1 AAATTATAAAAAT-ATATTTT
**
1526030 --ATTATATTAATATATTTT
1 AAATTATAAAAATATATTTT
1526048 AAATTATAAAAATA-ATTATT
1 AAATTATAAAAATATATT-TT
1526068 AAATT
1 AAATT
1526073 TAATAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 7 0.19
19 12 0.33
20 17 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTATAAAAATATATTTT
Found at i:1527715 original size:28 final size:29
Alignment explanation
Indices: 1527684--1527747 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
1527674 ATGTCCATTG
* * *
1527684 ATATTATTTGT-TTTAATTTTTTAAAAAT
1 ATATTATTTGTATTTAATCTTTAAAAAAA
*
1527712 ATATTATTTTTATTTAATCTTTAAAAAAA
1 ATATTATTTGTATTTAATCTTTAAAAAAA
1527741 AT-TTATT
1 ATATTATT
1527748 CTTTTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
ATATTATTTGTATTTAATCTTTAAAAAAA
Found at i:1530803 original size:23 final size:23
Alignment explanation
Indices: 1530756--1530804 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
1530746 TAAAAATAAA
*
1530756 AAATTATATAAATATTAAAATTT
1 AAATTATATAAATATTAAAAATT
1530779 AAATT-TATAAA-ATTAATTAAATT
1 AAATTATATAAATATTAA--AAATT
1530802 AAA
1 AAA
1530805 ATTAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 5 0.22
22 6 0.26
23 12 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATTATATAAATATTAAAAATT
Found at i:1530805 original size:30 final size:32
Alignment explanation
Indices: 1530755--1530814 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
1530745 TTAAAAATAA
*
1530755 AAAATTATATAAATATTAAAATTTAAATTTAT
1 AAAATTATATAAATATTAAAATTAAAATTTAT
*
1530787 AAAATTA-ATTAA-ATTAAAATTAAAATTT
1 AAAATTATATAAATATTAAAATTAAAATTT
1530815 TATAGATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 15 0.58
31 4 0.15
32 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
AAAATTATATAAATATTAAAATTAAAATTTAT
Found at i:1530829 original size:30 final size:29
Alignment explanation
Indices: 1530755--1530831 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 29
1530745 TTAAAAATAA
*
1530755 AAAATTATATAAATATTAAAATTTAAATTTAT
1 AAAATTAT-T-AA-ATTAAAATTAAAATTTAT
1530787 AAAATTAATTAAATTAAAATTAAAATTTTAT
1 AAAATT-ATTAAATTAAAATTAAAA-TTTAT
*
1530818 AGATATT-TTAAATT
1 A-AAATTATTAAATT
1530832 TTTAATATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 19 0.47
31 8 0.20
32 11 0.28
33 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (29 bp):
AAAATTATTAAATTAAAATTAAAATTTAT
Found at i:1531072 original size:10 final size:11
Alignment explanation
Indices: 1531046--1531071 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1531036 AAATACCGTG
1531046 AAAAAGAAAAA
1 AAAAAGAAAAA
1531057 AAAAAGAAAAA
1 AAAAAGAAAAA
1531068 AAAA
1 AAAA
1531072 GGGGGTTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:1532396 original size:38 final size:38
Alignment explanation
Indices: 1532345--1532421 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
1532335 TCGTGTTGCT
1532345 CTAAGGTAAAGCTCCATATTTATTTTATATGCAATATC
1 CTAAGGTAAAGCTCCATATTTATTTTATATGCAATATC
1532383 CTAAGGTAAAGCTCCATATTTATTTTATATGCAATATC
1 CTAAGGTAAAGCTCCATATTTATTTTATATGCAATATC
1532421 C
1 C
1532422 ATTTGCAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (38 bp):
CTAAGGTAAAGCTCCATATTTATTTTATATGCAATATC
Found at i:1533541 original size:26 final size:26
Alignment explanation
Indices: 1533512--1533590 Score: 158
Period size: 26 Copynumber: 3.0 Consensus size: 26
1533502 AGAGAAGGGT
1533512 TCGTAAGGTATGATTAGTTACTGGAG
1 TCGTAAGGTATGATTAGTTACTGGAG
1533538 TCGTAAGGTATGATTAGTTACTGGAG
1 TCGTAAGGTATGATTAGTTACTGGAG
1533564 TCGTAAGGTATGATTAGTTACTGGAG
1 TCGTAAGGTATGATTAGTTACTGGAG
1533590 T
1 T
1533591 TCACACTGCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.27, C:0.08, G:0.30, T:0.35
Consensus pattern (26 bp):
TCGTAAGGTATGATTAGTTACTGGAG
Found at i:1538593 original size:22 final size:21
Alignment explanation
Indices: 1538544--1538594 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
1538534 GATAATATTT
1538544 TTATAAATTAAATAAATTTAAA
1 TTATAAATTAAAT-AATTTAAA
*
1538566 TGATAAATTCAAAT-ATTTAATA
1 TTATAAATT-AAATAATTTAA-A
1538588 TTATAAA
1 TTATAAA
1538595 AAAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 6 0.24
22 15 0.60
23 4 0.16
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TTATAAATTAAATAATTTAAA
Found at i:1538757 original size:29 final size:30
Alignment explanation
Indices: 1538724--1538780 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1538714 AGATATCTTA
* *
1538724 TTTTTACTTTTCATAATCATTTT-TAAACT
1 TTTTTACCTTTCAAAATCATTTTGTAAACT
*
1538753 TTTTTACCTTTCAAAATTATTTTGTAAA
1 TTTTTACCTTTCAAAATCATTTTGTAAA
1538781 TTCAAAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTTTACCTTTCAAAATCATTTTGTAAACT
Found at i:1538860 original size:17 final size:18
Alignment explanation
Indices: 1538838--1538871 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1538828 ATAGAATAAA
1538838 ATTATAATAA-AAAATAT
1 ATTATAATAATAAAATAT
1538855 ATTATAATAATAAAATA
1 ATTATAATAATAAAATA
1538872 AAATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTATAATAATAAAATAT
Found at i:1538891 original size:22 final size:22
Alignment explanation
Indices: 1538858--1538925 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
1538848 AAAATATATT
1538858 ATAATAATAAAATAAAATTTAA
1 ATAATAATAAAATAAAATTTAA
* *
1538880 ATAA-AATAAAAATAATATTTTA
1 ATAATAAT-AAAATAAAATTTAA
* *
1538902 AT-TTAATTAAATAAATATTATAA
1 ATAATAATAAAATAAA-ATT-TAA
1538925 A
1 A
1538926 ATTTGAATGC
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
21 9 0.25
22 24 0.67
23 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAATAATAAAATAAAATTTAA
Found at i:1549430 original size:30 final size:30
Alignment explanation
Indices: 1549395--1549454 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1549385 CATATCATCA
1549395 ATGAAAAGATCTCCCAACACCTCAATCAAC
1 ATGAAAAGATCTCCCAACACCTCAATCAAC
*
1549425 ATGAAAAGATCTCCCAACAGCTCAATCAAC
1 ATGAAAAGATCTCCCAACACCTCAATCAAC
1549455 TTATTCTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.32, G:0.08, T:0.17
Consensus pattern (30 bp):
ATGAAAAGATCTCCCAACACCTCAATCAAC
Found at i:1551214 original size:22 final size:22
Alignment explanation
Indices: 1551137--1551214 Score: 52
Period size: 22 Copynumber: 3.4 Consensus size: 22
1551127 TTTGAATTAT
1551137 TTTTTATTAAT-TAAAAATAATTTTA
1 TTTTTATTAATATAAAAATAA----A
*
1551162 TTTTGGATTAATAATAAAAA-AAA
1 TTTT-TATTAAT-ATAAAAATAAA
***
1551185 TAAATATTAATATAAAAATAAA
1 TTTTTATTAATATAAAAATAAA
1551207 TTTTTATT
1 TTTTTATT
1551215 TTTATTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 11
0.68 0.13 0.18
Matches are distributed among these distances:
21 7 0.17
22 14 0.34
23 2 0.05
25 4 0.10
26 6 0.15
27 2 0.05
28 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (22 bp):
TTTTTATTAATATAAAAATAAA
Found at i:1553382 original size:11 final size:11
Alignment explanation
Indices: 1553345--1553396 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1553335 GATTTAGATA
1553345 TATATTTATAT
1 TATATTTATAT
* *
1553356 ATATTTTTTTAAT
1 -TATATTTAT-AT
* *
1553369 TATTTTTATGT
1 TATATTTATAT
1553380 TATATTTATAT
1 TATATTTATAT
1553391 TATATT
1 TATATT
1553397 ATGTAATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 16 0.48
12 15 0.45
13 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1557601 original size:38 final size:37
Alignment explanation
Indices: 1557557--1557655 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 37
1557547 AAATTTTATT
*
1557557 TTATTTTATTTTACTAAATTAAATTATTATTATTATA-G
1 TTATTTTATTTTAATAAA-TAAATTATT-TTATTATATG
* * *
1557595 TTATTTTATTATAGTATAAT-AATTATTTTATTATATTT
1 TTATTTTATTTTAATA-AATAAATTATTTTATTATA-TG
*
1557633 TTATTTCATTTTAATAAATAAAT
1 TTATTTTATTTTAATAAATAAAT
1557656 GTACTGTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
36 8 0.16
37 10 0.20
38 31 0.61
39 2 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (37 bp):
TTATTTTATTTTAATAAATAAATTATTTTATTATATG
Found at i:1557603 original size:14 final size:15
Alignment explanation
Indices: 1557580--1557609 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1557570 CTAAATTAAA
1557580 TTATTATTATTATAG
1 TTATTATTATTATAG
1557595 TTATT-TTATTATAG
1 TTATTATTATTATAG
1557609 T
1 T
1557610 ATAATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
TTATTATTATTATAG
Found at i:1558457 original size:27 final size:27
Alignment explanation
Indices: 1558414--1558465 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
1558404 TATTATTTAT
*
1558414 ATATTTTTATAATTAAAATTAAATAAAA
1 ATATTATTATAATTAAAA-TAAATAAAA
1558442 ATATTATT-TAATTAAAATAAATAA
1 ATATTATTATAATTAAAATAAATAA
1558466 TAATTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 9 0.39
28 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATTATTATAATTAAAATAAATAAAA
Found at i:1558485 original size:16 final size:16
Alignment explanation
Indices: 1558424--1558492 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
1558414 ATATTTTTAT
*
1558424 AATTAAAATTAAATAA
1 AATTAAAATTAATTAA
* * *
1558440 AAATATTATTTAATTAA
1 AATTA-AAATTAATTAA
*
1558457 AA-TAAATAATAATTAA
1 AATTAAA-ATTAATTAA
*
1558473 AATTAAAATTAATTTA
1 AATTAAAATTAATTAA
1558489 AATT
1 AATT
1558493 TTAAAATATT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
15 1 0.02
16 26 0.63
17 14 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTAAAATTAATTAA
Found at i:1558862 original size:13 final size:11
Alignment explanation
Indices: 1558824--1558850 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1558814 TACAACAACC
1558824 AAAAACAAAAA
1 AAAAACAAAAA
1558835 AAAAACAAAAA
1 AAAAACAAAAA
1558846 AAAAA
1 AAAAA
1558851 AACAGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Done.