Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 19 of 33
Found at i:3007259 original size:5 final size:5
Alignment explanation
Indices: 3007249--3007296 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
3007239 AAATAATTAA
3007249 AATAT AATAT AATAT AA-A- AA-AT AATAT AAATAT AATAT AA-AT -ATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT
3007295 AA
1 AA
3007297 ATATCATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
3 4 0.11
4 7 0.18
5 22 0.58
6 5 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
AATAT
Found at i:3007305 original size:17 final size:17
Alignment explanation
Indices: 3007248--3007390 Score: 61
Period size: 19 Copynumber: 7.8 Consensus size: 17
3007238 AAAATAATTA
*
3007248 AAATATAATATAATATAAA
1 AAATAT-ATA-AATATAAT
3007267 AAATAATATAAATATAATAT
1 AAAT-ATATAAATAT-A-AT
*
3007287 AAATATATAAATATCAT
1 AAATATATAAATATAAT
* * *
3007304 AAATTTTTATAATGTAAT
1 AAATATATA-AATATAAT
* * * * *
3007322 TAATTTATGTATTAAAAT
1 AAATATAT-AAATATAAT
* *
3007340 TAATATAAAAATATAAACT
1 AAATATATAAATAT-AA-T
* *
3007359 AAATATATAATTATATT
1 AAATATATAAATATAAT
3007376 AAAATAATATAAATA
1 -AAAT-ATATAAATA
3007391 CGTGAATTAT
Statistics
Matches: 93, Mismatches: 22, Indels: 18
0.70 0.17 0.14
Matches are distributed among these distances:
17 13 0.14
18 35 0.38
19 38 0.41
20 7 0.08
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (17 bp):
AAATATATAAATATAAT
Found at i:3007307 original size:28 final size:28
Alignment explanation
Indices: 3007227--3007293 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
3007217 AGACTTCTCA
*
3007227 AATATAATA-CAAAAATAAT-TAAAATAT
1 AATATAATATAAAAAATAATAT-AAATAT
3007254 AATATAATATAAAAAATAATATAAATAT
1 AATATAATATAAAAAATAATATAAATAT
3007282 AATATAAATATA
1 AATAT-AATATA
3007294 TAAATATCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
27 9 0.25
28 20 0.56
29 7 0.19
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (28 bp):
AATATAATATAAAAAATAATATAAATAT
Found at i:3007958 original size:26 final size:24
Alignment explanation
Indices: 3007908--3007976 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
3007898 TTCAATTTGA
*
3007908 TTTATTTTTTAATTATATAATTTAT
1 TTTA-TTTTTATTTATATAATTTAT
3007933 TTTATTTTTATTTATATATATATTAT
1 TTTATTTTTATTTATATA-AT-TTAT
* * *
3007959 GTAATTTATATTT-TATAA
1 TTTATTTTTATTTATATAA
3007977 AGAATAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
24 14 0.37
25 10 0.26
26 14 0.37
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (24 bp):
TTTATTTTTATTTATATAATTTAT
Found at i:3008747 original size:50 final size:48
Alignment explanation
Indices: 3008629--3008756 Score: 129
Period size: 50 Copynumber: 2.6 Consensus size: 48
3008619 AAAGTAACTT
* * *
3008629 TTTAAATATGTAATTTTATTCATTTATTT-AAATTAATAAATATTTTA
1 TTTAAATAAGTAATTTTATTAATTTATTTAAAATTAATAAAAATTTTA
**
3008676 ---AAATAGAGATCATATGATATTAATTTACTTTAAAATTAATAAAAATTTTTA
1 TTTAAATA-AG-T-A-ATTTTATTAATTTA-TTTAAAATTAATAAAAA-TTTTA
3008727 TTTAAATAAGTAATTTTATTAATTTATTTA
1 TTTAAATAAGTAATTTTATTAATTTATTTA
3008757 TATGTAAATT
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
44 5 0.08
45 1 0.02
46 1 0.02
47 1 0.02
48 11 0.17
49 7 0.11
50 24 0.38
51 6 0.09
52 1 0.02
53 2 0.03
54 5 0.08
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (48 bp):
TTTAAATAAGTAATTTTATTAATTTATTTAAAATTAATAAAAATTTTA
Found at i:3015567 original size:21 final size:21
Alignment explanation
Indices: 3015527--3015573 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
3015517 ATAAATTATT
*
3015527 ATATAATTTTGACACTCTTTA
1 ATATAATTTTGAAACTCTTTA
*
3015548 ATATAATTTTGATAACCTTTTTA
1 ATATAATTTTGA-AA-CTCTTTA
3015571 ATA
1 ATA
3015574 GTTTTTGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 12 0.55
22 1 0.05
23 9 0.41
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (21 bp):
ATATAATTTTGAAACTCTTTA
Found at i:3015664 original size:105 final size:105
Alignment explanation
Indices: 3015548--3015777 Score: 433
Period size: 105 Copynumber: 2.2 Consensus size: 105
3015538 ACACTCTTTA
* *
3015548 ATATAATTTTGATAACCTTTTTAATAGTTTTTGTAACCTTTGATATTTGATGATATTTAACATAA
1 ATATATTTTTGATAACCTTTCTAATAGTTTTTGTAACCTTTGATATTTGATGATATTTAACATAA
3015613 TTTTTTGTAACTTTTGTAAGTGTTTTTGGTAAAATCTTGG
66 TTTTTTGTAACTTTTGTAAGTGTTTTTGGTAAAATCTTGG
*
3015653 ATATATTTTTGATAACCTTTCTAATAGTTTTTGTAACTTTTGATATTTGATGATATTTAACATAA
1 ATATATTTTTGATAACCTTTCTAATAGTTTTTGTAACCTTTGATATTTGATGATATTTAACATAA
3015718 TTTTTTGTAACTTTTGTAAGTGTTTTTGGTAAAATCTTGG
66 TTTTTTGTAACTTTTGTAAGTGTTTTTGGTAAAATCTTGG
3015758 ATATATTTTTGATAACCTTT
1 ATATATTTTTGATAACCTTT
3015778 GATATAATTG
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 122 1.00
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (105 bp):
ATATATTTTTGATAACCTTTCTAATAGTTTTTGTAACCTTTGATATTTGATGATATTTAACATAA
TTTTTTGTAACTTTTGTAAGTGTTTTTGGTAAAATCTTGG
Found at i:3015783 original size:21 final size:22
Alignment explanation
Indices: 3015757--3015830 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
3015747 TAAAATCTTG
*
3015757 GATAT-ATTTTTGATAACCTTT
1 GATATAATTTTTGATAACATTT
* *
3015778 GATATAA-TTGTAATAACATTT
1 GATATAATTTTTGATAACATTT
3015799 GATATAATTTTTG-TAACATTT
1 GATATAATTTTTGATAACATTT
*
3015820 GATATGATTTT
1 GATATAATTTT
3015831 GACAATCTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 41 0.91
22 4 0.09
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (22 bp):
GATATAATTTTTGATAACATTT
Found at i:3015800 original size:105 final size:105
Alignment explanation
Indices: 3015548--3015803 Score: 379
Period size: 105 Copynumber: 2.4 Consensus size: 105
3015538 ACACTCTTTA
* * * * ** *
3015548 ATATAATTTTGATAACCTTTTTAATAGTTTTTGTAACCTTTGATATTTGATGATATTTAACATAA
1 ATATATTTTTGATAACCTTTATAATAATTGTAATAACATTTGATATTTGATGATATTTAACATAA
3015613 TTTTTTGTAACTTTTGTAAGTGTTTTTGGTAAAATCTTGG
66 TTTTTTGTAACTTTTGTAAGTGTTTTTGGTAAAATCTTGG
* * * ** *
3015653 ATATATTTTTGATAACCTTTCTAATAGTTTTTGTAACTTTTGATATTTGATGATATTTAACATAA
1 ATATATTTTTGATAACCTTTATAATAATTGTAATAACATTTGATATTTGATGATATTTAACATAA
3015718 TTTTTTGTAACTTTTGTAAGTGTTTTTGGTAAAATCTTGG
66 TTTTTTGTAACTTTTGTAAGTGTTTTTGGTAAAATCTTGG
3015758 ATATATTTTTGATAACCTTTGAT-ATAATTGTAATAACATTTGATAT
1 ATATATTTTTGATAACCTTT-ATAATAATTGTAATAACATTTGATAT
3015804 AATTTTTGTA
Statistics
Matches: 141, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
105 140 0.99
106 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (105 bp):
ATATATTTTTGATAACCTTTATAATAATTGTAATAACATTTGATATTTGATGATATTTAACATAA
TTTTTTGTAACTTTTGTAAGTGTTTTTGGTAAAATCTTGG
Found at i:3016117 original size:21 final size:21
Alignment explanation
Indices: 3016093--3016151 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3016083 GCCTTAAATT
*
3016093 TAATTTTGGTAACTTTTAACA
1 TAATTTTGATAACTTTTAACA
* *
3016114 TAATTTTGATAACTTTTGATA
1 TAATTTTGATAACTTTTAACA
* *
3016135 TAATTTTAATAATTTTT
1 TAATTTTGATAACTTTT
3016152 TTATATTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (21 bp):
TAATTTTGATAACTTTTAACA
Found at i:3016237 original size:21 final size:20
Alignment explanation
Indices: 3016204--3016285 Score: 53
Period size: 21 Copynumber: 3.9 Consensus size: 20
3016194 TTGATATCGT
*
3016204 TTTTGTAATTTTTAATATAA
1 TTTTGTAACTTTTAATATAA
3016224 TTTTGTGAACTTTTGTAA-A-AA
1 TTTTGT-AAC-TTT-TAATATAA
*
3016245 TTTTATTAACTTTT-ATAATAA
1 TTTT-GTAACTTTTAAT-ATAA
3016266 TTTTGATAACATTTCTAATA
1 TTTTG-TAAC-TTT-TAATA
3016286 GCTTTGATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 19
0.69 0.04 0.27
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 10 0.21
21 21 0.44
22 8 0.17
23 5 0.10
24 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTTGTAACTTTTAATATAA
Found at i:3016460 original size:21 final size:21
Alignment explanation
Indices: 3016434--3016584 Score: 98
Period size: 21 Copynumber: 7.2 Consensus size: 21
3016424 ACTTGATTAG
*
3016434 TTTTGATTACCTTTTATATAA
1 TTTTGATTAACTTTTATATAA
*
3016455 TTTTGA-TAACTTTCGATATAA
1 TTTTGATTAACTTT-TATATAA
* * *
3016476 ATTT-AATAACATTTAATATAA
1 TTTTGATTAAC-TTTTATATAA
* *
3016497 TTTT-AGTAATTTTTGATATAA
1 TTTTGATTAACTTTT-ATATAA
* * *
3016518 TTTTGA-CAATATTTTATACAA
1 TTTTGATTAA-CTTTTATATAA
* *
3016539 TTTTAATTAACTTTTGATATGA
1 TTTTGATTAACTTTT-ATATAA
3016561 TTTTGA-TAACTTTT-TATAA
1 TTTTGATTAACTTTTATATAA
3016580 CTTTT
1 -TTTT
3016585 AATATAATTT
Statistics
Matches: 103, Mismatches: 18, Indels: 19
0.74 0.13 0.14
Matches are distributed among these distances:
19 4 0.04
20 14 0.14
21 66 0.64
22 19 0.18
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.53
Consensus pattern (21 bp):
TTTTGATTAACTTTTATATAA
Found at i:3016495 original size:42 final size:42
Alignment explanation
Indices: 3016449--3016720 Score: 138
Period size: 42 Copynumber: 6.2 Consensus size: 42
3016439 ATTACCTTTT
*
3016449 ATATAATTTTGATAACTTTCGATATAAATTTAATAACATTTA
1 ATATAATTTTGATAACTTTTGATATAAATTTAATAACATTTA
* * * * * *
3016491 ATATAATTTT-AGTAATTTTTGATATAATTTTGACAATATTTT
1 ATATAATTTTGA-TAACTTTTGATATAAATTTAATAACATTTA
* * * *
3016533 ATACAATTTTAATTAACTTTTGATATGATTTTGATAACTTTTTATAACTTTTA
1 ATATAATTTTGA-TAACTTTTG--AT-A---T-A-AA--TTTAATAACATTTA
* * * **
3016586 ATATAATTTTGATAACTATTGATAT-AATTCAAGTATC-CCTA
1 ATATAATTTTGATAACTTTTGATATAAATTTAA-TAACATTTA
** * * * * *
3016627 ATATAATTTTGGCAACTATTGATGTAAGTTTAATGACATTTG
1 ATATAATTTTGATAACTTTTGATATAAATTTAATAACATTTA
* * *
3016669 ATATAATCTTGATAACTTTTAAAAT-AATTTAATAACAATTTTA
1 ATATAATTTTGATAACTTTTGATATAAATTTAATAAC-A-TTTA
3016712 ATAGTAATT
1 ATA-TAATT
3016721 GTAATAGTTT
Statistics
Matches: 167, Mismatches: 45, Indels: 34
0.68 0.18 0.14
Matches are distributed among these distances:
41 39 0.23
42 70 0.42
43 17 0.10
44 4 0.02
45 2 0.01
46 2 0.01
49 2 0.01
50 3 0.02
51 1 0.01
52 8 0.05
53 19 0.11
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (42 bp):
ATATAATTTTGATAACTTTTGATATAAATTTAATAACATTTA
Found at i:3016600 original size:21 final size:21
Alignment explanation
Indices: 3016566--3016614 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3016556 TATGATTTTG
* *
3016566 ATAACTTTTTATAACTTTTAAT
1 ATAA-TTTTGATAACTATTAAT
*
3016588 ATAATTTTGATAACTATTGAT
1 ATAATTTTGATAACTATTAAT
3016609 ATAATT
1 ATAATT
3016615 CAAGTATCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (21 bp):
ATAATTTTGATAACTATTAAT
Found at i:3020931 original size:23 final size:23
Alignment explanation
Indices: 3020905--3020969 Score: 57
Period size: 24 Copynumber: 2.9 Consensus size: 23
3020895 TATTTAATAC
3020905 ATATTTTAAATATAAATATAAAA
1 ATATTTTAAATATAAATATAAAA
3020928 ATATTATTCATAA-A-AAATATAAAA
1 ATATT-TT-A-AATATAAATATAAAA
* *
3020952 A-AATTTAAAT-TAATTATA
1 ATATTTTAAATATAAATATA
3020970 TTTATATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
20 2 0.06
21 7 0.20
22 2 0.06
23 7 0.20
24 13 0.37
25 2 0.06
26 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATTTTAAATATAAATATAAAA
Found at i:3022399 original size:13 final size:13
Alignment explanation
Indices: 3022378--3022411 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3022368 GTTATTAATT
*
3022378 ATAATAAATATTA
1 ATAATAAATATCA
*
3022391 ATTATAAATATCA
1 ATAATAAATATCA
3022404 ATAATAAA
1 ATAATAAA
3022412 AAATATAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAATAAATATCA
Found at i:3022730 original size:13 final size:13
Alignment explanation
Indices: 3022712--3022737 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3022702 AAAGATAATT
3022712 ATTGTATTTATTG
1 ATTGTATTTATTG
3022725 ATTGTATTTATTG
1 ATTGTATTTATTG
3022738 TTATTGTGGT
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:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (13 bp):
ATTGTATTTATTG
Found at i:3025481 original size:27 final size:27
Alignment explanation
Indices: 3025451--3025508 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
3025441 CGAACAATAC
3025451 CATGGAGTAGAGTTGTTTCGAGAAACT
1 CATGGAGTAGAGTTGTTTCGAGAAACT
3025478 CATGGAGTAGAGTTGTTTCGAGAAACT
1 CATGGAGTAGAGTTGTTTCGAGAAACT
3025505 CATG
1 CATG
3025509 AGTGGTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (27 bp):
CATGGAGTAGAGTTGTTTCGAGAAACT
Found at i:3031554 original size:37 final size:37
Alignment explanation
Indices: 3031500--3031570 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
3031490 GAATTTTTTA
3031500 TTGGGTCAAAATCAAAATAT-AATTTATTGCGAGGATG
1 TTGGGTCAAAATCAAAATATAAATTT-TTGCGAGGATG
*
3031537 TTGGGTCAAAATTAAAATATAAATTTTTGCGAGG
1 TTGGGTCAAAATCAAAATATAAATTTTTGCGAGG
3031571 TAAAAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
37 27 0.84
38 5 0.16
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (37 bp):
TTGGGTCAAAATCAAAATATAAATTTTTGCGAGGATG
Found at i:3037113 original size:15 final size:16
Alignment explanation
Indices: 3037089--3037121 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3037079 ATATTATTTA
3037089 ATCATATTT-AAAATT
1 ATCATATTTAAAAATT
*
3037104 ATCATGTTTAAAAATT
1 ATCATATTTAAAAATT
3037120 AT
1 AT
3037122 TTATAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (16 bp):
ATCATATTTAAAAATT
Found at i:3037734 original size:16 final size:16
Alignment explanation
Indices: 3037715--3037750 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
3037705 CTAAAAAAAA
*
3037715 TTAAACTTAAAATAAT
1 TTAAAATTAAAATAAT
3037731 TTAAAATTAAAATAAT
1 TTAAAATTAAAATAAT
3037747 TTAA
1 TTAA
3037751 TTCAAACGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAATTAAAATAAT
Found at i:3039061 original size:2 final size:2
Alignment explanation
Indices: 3039054--3039088 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3039044 ATAATTGATC
*
3039054 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3039089 TCTCTTTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3043080 original size:12 final size:12
Alignment explanation
Indices: 3043065--3043115 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
3043055 TTTGTATGTA
3043065 TTTATATTATAT
1 TTTATATTATAT
* *
3043077 TTTATGTTGTAT
1 TTTATATTATAT
*
3043089 TTT-TAATTATTT
1 TTTAT-ATTATAT
*
3043101 TTTATGTTATAT
1 TTTATATTATAT
3043113 TTT
1 TTT
3043116 TTTCATGTGA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
11 1 0.03
12 28 0.93
13 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:3043103 original size:24 final size:23
Alignment explanation
Indices: 3043061--3043116 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
3043051 TATATTTGTA
*
3043061 TGTATTTATATTATATTTTATGT
1 TGTATTTTTATTATATTTTATGT
*
3043084 TGTATTTTTAATTATTTTTTATGT
1 TGTATTTTT-ATTATATTTTATGT
*
3043108 TATATTTTT
1 TGTATTTTT
3043117 TTCATGTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 8 0.28
24 21 0.72
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (23 bp):
TGTATTTTTATTATATTTTATGT
Found at i:3043224 original size:36 final size:36
Alignment explanation
Indices: 3043178--3043248 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
3043168 TTACACTTAT
* *
3043178 CATATATTAATATAAATA-ATATATTCAGAATTTTAC
1 CATACATTAATATAAATATAT-TATTCAAAATTTTAC
3043214 CATACATTAATATAAATATATTATTCAAAATTTTA
1 CATACATTAATATAAATATATTATTCAAAATTTTA
3043249 ATCCAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.94
37 2 0.06
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.42
Consensus pattern (36 bp):
CATACATTAATATAAATATATTATTCAAAATTTTAC
Found at i:3044753 original size:28 final size:28
Alignment explanation
Indices: 3044691--3044753 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
3044681 ATTAATATAA
*
3044691 AAATATTTTTTATTTAAAAAAAGATTAG
1 AAATATTTTTTATTTAAAAAAACATTAG
* *
3044719 AATTATTTTTT-TCTTCAAAAAACATGT-G
1 AAATATTTTTTAT-TTAAAAAAACAT-TAG
3044747 AAATATT
1 AAATATT
3044754 GTTTGGAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 27 0.93
29 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (28 bp):
AAATATTTTTTATTTAAAAAAACATTAG
Found at i:3044781 original size:147 final size:148
Alignment explanation
Indices: 3044561--3044841 Score: 442
Period size: 147 Copynumber: 1.9 Consensus size: 148
3044551 GTAGATTGGC
* *
3044561 AAAAAAGATAAGAATTTTTTTTCTTAAAAAAAAATGTGAAAATATTGTTTGGAGTTTACGAATTC
1 AAAAAAGATAAGAATTTTTTTTCTTAAAAAAAAATGTGAAAATATTGTTTGGAGTCTACAAATTC
* *
3044626 CACCGATAGATTTAATAAACAATACACATTCTTGTAAGATATAAAAAAA-A-TTAAAATTAATAT
66 CACCGATAGATTTAACAAACAATACACATTCTTGTAAAATATAAAAAAATATTTAAAATTAATAT
3044689 AAAAATATTTTTTATTTA
131 AAAAATATTTTTTATTTA
* * *
3044707 AAAAAAGATTAGAATTATTTTTTTCTTCAAAAAACATGTG-AAATATTGTTTGGAGTCTACAAAT
1 AAAAAAGATAAGAA-T-TTTTTTTCTTAAAAAAAAATGTGAAAATATTGTTTGGAGTCTACAAAT
*
3044771 TCCATCGATAGATTTAACAAACAATACACATTCTTGTAAAATATAAAAAAATATTTTAAAATTAA
64 TCCACCGATAGATTTAACAAACAATACACATTCTTGTAAAATATAAAAAAATA-TTTAAAATTAA
3044836 TATAAA
128 TATAAA
3044842 TTTTTTTTCA
Statistics
Matches: 122, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
146 13 0.11
147 71 0.58
148 22 0.18
150 16 0.13
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.36
Consensus pattern (148 bp):
AAAAAAGATAAGAATTTTTTTTCTTAAAAAAAAATGTGAAAATATTGTTTGGAGTCTACAAATTC
CACCGATAGATTTAACAAACAATACACATTCTTGTAAAATATAAAAAAATATTTAAAATTAATAT
AAAAATATTTTTTATTTA
Found at i:3045737 original size:69 final size:73
Alignment explanation
Indices: 3045653--3045793 Score: 191
Period size: 74 Copynumber: 2.0 Consensus size: 73
3045643 TTTAACAAAG
* *
3045653 TTTTTAAAATAAAAAAT-TATAATTATT-T-TT-TATGTTTTATCGTAAAAGTAATTAATTTAAT
1 TTTTTAAAATAAAAAATATATAATTATTATATTATATGTTTTATCATAAAAGTAATTAATTTAAC
3045714 ATAAAATT
66 ATAAAATT
* * * *
3045722 TTTTTAAAAGTAAAAAATATATAATTATTATATTATCTTTTTTATCATGAAAGTAATTGATTTAA
1 TTTTTAAAA-TAAAAAATATATAATTATTATATTATATGTTTTATCATAAAAGTAATTAATTTAA
3045787 CATAAAA
65 CATAAAA
3045794 AAATTTCTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
69 9 0.15
70 8 0.13
71 10 0.16
72 1 0.02
73 2 0.03
74 31 0.51
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (73 bp):
TTTTTAAAATAAAAAATATATAATTATTATATTATATGTTTTATCATAAAAGTAATTAATTTAAC
ATAAAATT
Found at i:3045962 original size:22 final size:23
Alignment explanation
Indices: 3045915--3045968 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
3045905 TTATTAATTT
* *
3045915 TAAAAATTATATTTATAAATATGA
1 TAAAAA-TATATTTAAAAATAAGA
3045939 TAAAAATATA-TTAAAAATAAGA
1 TAAAAATATATTTAAAAATAAGA
*
3045961 TAATAATA
1 TAAAAATA
3045969 AATAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 17 0.63
23 4 0.15
24 6 0.22
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
TAAAAATATATTTAAAAATAAGA
Found at i:3045998 original size:24 final size:24
Alignment explanation
Indices: 3045970--3046025 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
3045960 ATAATAATAA
*
3045970 ATAAATAAAT-ATTATTTGATATTT
1 ATAAATAAATAATTAATTGA-ATTT
*
3045994 ATAAAT-ATTAATTAATTGAATTT
1 ATAAATAAATAATTAATTGAATTT
3046017 ATAATATAA
1 ATAA-ATAA
3046026 TGGTAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 16 0.59
25 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
ATAAATAAATAATTAATTGAATTT
Found at i:3046214 original size:2 final size:2
Alignment explanation
Indices: 3046209--3046235 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3046199 AAAAGGGGGA
3046209 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
3046236 ATCTTCTTTT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3047807 original size:26 final size:26
Alignment explanation
Indices: 3047778--3047831 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
3047768 TGCTTCAATT
* *
3047778 TTTAATATTTCTA-AATTTTAATTAAA
1 TTTAA-ATTTATATAATTTAAATTAAA
3047804 TTTAAATTTATATAATTTAAATTAAA
1 TTTAAATTTATATAATTTAAATTAAA
3047830 TT
1 TT
3047832 ATATTAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTAAATTTATATAATTTAAATTAAA
Found at i:3049285 original size:30 final size:31
Alignment explanation
Indices: 3049249--3049306 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
3049239 GATAGAATCT
*
3049249 CCTCCTTATCTTTTGC-AAGCTAAGATAAAA
1 CCTCCTTATCTTTTACAAAGCTAAGATAAAA
3049279 CCTCCTTATCTTTTACAAAGCTAAGATA
1 CCTCCTTATCTTTTACAAAGCTAAGATA
3049307 GAACATTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (31 bp):
CCTCCTTATCTTTTACAAAGCTAAGATAAAA
Found at i:3050654 original size:2 final size:2
Alignment explanation
Indices: 3050647--3050677 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3050637 CATTATTCAC
3050647 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3050678 TGAATTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3051100 original size:20 final size:20
Alignment explanation
Indices: 3051074--3051116 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3051064 TTTATTAATT
*
3051074 ATTTAT-TTAATTTAATA-A
1 ATTTATATTAAATTAATATA
3051092 ATTTATATTAAATTAATATA
1 ATTTATATTAAATTAATATA
3051112 ATTTA
1 ATTTA
3051117 AAATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 10 0.45
20 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTATATTAAATTAATATA
Found at i:3051402 original size:26 final size:26
Alignment explanation
Indices: 3051349--3051410 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
3051339 TGTTTAGTTG
* * *
3051349 TTTATTTGTTTTTAAAGTATTAACAA
1 TTTATTTATTTTTAAAGTAATAAAAA
* *
3051375 TTTATTTATTTTTATATTAATAAAAA
1 TTTATTTATTTTTAAAGTAATAAAAA
3051401 TTATATTTAT
1 TT-TATTTAT
3051411 ATTATTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 23 0.77
27 7 0.23
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (26 bp):
TTTATTTATTTTTAAAGTAATAAAAA
Found at i:3051429 original size:17 final size:18
Alignment explanation
Indices: 3051401--3051439 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
3051391 TTAATAAAAA
*
3051401 TTATATTTATATTATTTT
1 TTATATTTATATTATGTT
3051419 TTATA-TTATATTATGTT
1 TTATATTTATATTATGTT
3051436 TTAT
1 TTAT
3051440 TTAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTATATTTATATTATGTT
Found at i:3051704 original size:19 final size:19
Alignment explanation
Indices: 3051671--3051727 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 19
3051661 CATGTTTATT
*
3051671 TTTATGTTATA-TTTTTAA
1 TTTATTTTATATTTTTTAA
3051689 TTTATTTTATATTTTTTATA
1 TTTATTTTATATTTTTTA-A
3051709 TAATTA-TTTAT-TTTTTTAA
1 T--TTATTTTATATTTTTTAA
3051728 AATAATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 10 0.29
19 7 0.21
20 9 0.26
21 5 0.15
22 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTATTTTATATTTTTTAA
Found at i:3051724 original size:21 final size:22
Alignment explanation
Indices: 3051694--3051740 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3051684 TTTAATTTAT
* *
3051694 TTTATATTTTTTATATAAT-TA
1 TTTATATTTTTAAAATAATATA
*
3051715 TTTATTTTTTTAAAATAATATA
1 TTTATATTTTTAAAATAATATA
3051737 TTTA
1 TTTA
3051741 AAGTTGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATATTTTTAAAATAATATA
Found at i:3051738 original size:18 final size:19
Alignment explanation
Indices: 3051696--3051739 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
3051686 TAATTTATTT
* *
3051696 TATATTTTTTATATAATTA
1 TATATTTTTTATAAAATAA
*
3051715 TTTATTTTTT-TAAAATAA
1 TATATTTTTTATAAAATAA
3051733 TATATTT
1 TATATTT
3051740 AAAGTTGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATTTTTTATAAAATAA
Found at i:3052860 original size:18 final size:20
Alignment explanation
Indices: 3052837--3052887 Score: 79
Period size: 18 Copynumber: 2.6 Consensus size: 20
3052827 ACTAAGATTC
3052837 ATGATTTAAAAAAA-AA-TT
1 ATGATTTAAAAAAATAATTT
3052855 ATGATTTAAAAAAATAATTT
1 ATGATTTAAAAAAATAATTT
*
3052875 ATTATTTAAAAAA
1 ATGATTTAAAAAA
3052888 TATTAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 14 0.47
19 2 0.07
20 14 0.47
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
ATGATTTAAAAAAATAATTT
Found at i:3052888 original size:19 final size:19
Alignment explanation
Indices: 3052837--3052889 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
3052827 ACTAAGATTC
3052837 ATGATTTAAAAAA-AAATT
1 ATGATTTAAAAAATAAATT
*
3052855 ATGATTTAAAAAAATAATTT
1 ATGATTT-AAAAAATAAATT
*
3052875 ATTATTTAAAAAATA
1 ATGATTTAAAAAATA
3052890 TTAAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 7 0.23
19 14 0.45
20 10 0.32
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
ATGATTTAAAAAATAAATT
Found at i:3052899 original size:21 final size:20
Alignment explanation
Indices: 3052840--3052887 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3052830 AAGATTCATG
*
3052840 ATTTAAAAAAA-AAT-TATG
1 ATTTAAAAAAATAATATATT
*
3052858 ATTTAAAAAAATAATTTATT
1 ATTTAAAAAAATAATATATT
3052878 ATTTAAAAAA
1 ATTTAAAAAA
3052888 TATTAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 11 0.41
19 3 0.11
20 13 0.48
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
ATTTAAAAAAATAATATATT
Found at i:3053246 original size:32 final size:31
Alignment explanation
Indices: 3053209--3053279 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
3053199 TTTGATTTTT
3053209 AATTATTTAA-TTTTAAAATAAATTTAAATTTA
1 AATTATTTAATTTTTAAAATAAA-TTAAA-TTA
*
3053241 AATTA-TTAATTTTTAAATTAAATTAAATTA
1 AATTATTTAATTTTTAAAATAAATTAAATTA
3053271 ATATTATTT
1 A-ATTATTT
3053280 TTTAATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
30 4 0.11
31 13 0.37
32 18 0.51
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AATTATTTAATTTTTAAAATAAATTAAATTA
Found at i:3053257 original size:27 final size:29
Alignment explanation
Indices: 3053227--3053293 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
3053217 AATTTTAAAA
3053227 TAAATTTAAATTTAAATT-AT-TAATTTT
1 TAAATTTAAATTTAAATTAATATAATTTT
*
3053254 TAAA-TTAAA-TTAAATTAATATTATTTT
1 TAAATTTAAATTTAAATTAATATAATTTT
* *
3053281 TTAATTAAAATTT
1 TAAATTTAAATTT
3053294 TAAGCTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 7 0.21
26 7 0.21
27 13 0.39
28 4 0.12
29 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TAAATTTAAATTTAAATTAATATAATTTT
Found at i:3054064 original size:17 final size:17
Alignment explanation
Indices: 3054016--3054064 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3054006 TTAAATTTAA
*
3054016 ATTAAAAATTATATATTT
1 ATTAAAAATT-TATTTTT
* *
3054034 ATTAAATATATATTTTT
1 ATTAAAAATTTATTTTT
3054051 ATTAAAAATTTATT
1 ATTAAAAATTTATT
3054065 ATATTTAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAAAAATTTATTTTT
Found at i:3056413 original size:3 final size:3
Alignment explanation
Indices: 3056407--3056453 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
3056397 CAACAACAGG
* *
3056407 AGC AGC AAC AAC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AG
3056454 TTACTGCACT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.38, C:0.32, G:0.30, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:3056417 original size:15 final size:15
Alignment explanation
Indices: 3056397--3056453 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
3056387 TTTGCATCAA
*
3056397 CAACAACAGGAGCAG
1 CAACAACAGCAGCAG
3056412 CAACAACAGCAGCAG
1 CAACAACAGCAGCAG
* *
3056427 CAGCAGCAGCAGCAG
1 CAACAACAGCAGCAG
* *
3056442 CAGCAGCAGCAG
1 CAACAACAGCAG
3056454 TTACTGCACT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.40, C:0.32, G:0.28, T:0.00
Consensus pattern (15 bp):
CAACAACAGCAGCAG
Found at i:3056417 original size:18 final size:18
Alignment explanation
Indices: 3056394--3056449 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
3056384 GTTTTTGCAT
*
3056394 CAACAACAACAGGAGCAG
1 CAACAACAACAGCAGCAG
*
3056412 CAACAACAGCAGCAGCAG
1 CAACAACAACAGCAGCAG
* * *
3056430 CAGCAGCAGCAGCAGCAG
1 CAACAACAACAGCAGCAG
3056448 CA
1 CA
3056450 GCAGTTACTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.43, C:0.32, G:0.25, T:0.00
Consensus pattern (18 bp):
CAACAACAACAGCAGCAG
Found at i:3074790 original size:2 final size:2
Alignment explanation
Indices: 3074778--3074821 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3074768 GTCACGCTCA
*
3074778 TC TC CC TC TC TC 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 TC TC TC TC TC TC
3074820 TC
1 TC
3074822 CCCCTCCCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:3074832 original size:12 final size:12
Alignment explanation
Indices: 3074817--3074841 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3074807 CTCTCTCTCT
3074817 CTCTCCCCCTCC
1 CTCTCCCCCTCC
3074829 CTCTCCCCCTCC
1 CTCTCCCCCTCC
3074841 C
1 C
3074842 ATGGGGTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (12 bp):
CTCTCCCCCTCC
Found at i:3075072 original size:18 final size:18
Alignment explanation
Indices: 3075028--3075074 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
3075018 TTTAATTAAA
3075028 TTTAAA-TAAAAAATTAT
1 TTTAAATTAAAAAATTAT
*
3075045 TTTATTATTAAAATAA-TAT
1 TTTA-AATTAAAA-AATTAT
3075064 TTTAAATTAAA
1 TTTAAATTAAA
3075075 TCGAATTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.16
18 7 0.28
19 12 0.48
20 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAAATTAAAAAATTAT
Found at i:3075555 original size:32 final size:31
Alignment explanation
Indices: 3075501--3075575 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 31
3075491 AGTTGATAAT
*
3075501 ATAATATATTTAAATAAATTTTAATATATTA
1 ATAATATATTTAAATAAATTTTAACATATTA
* *
3075532 ATAATTTATATTATATAAATTTTAACATATTA
1 ATAATATAT-TTAAATAAATTTTAACATATTA
* *
3075564 ATATTATTTTTA
1 ATAATATATTTA
3075576 TATTATCTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 11 0.30
32 26 0.70
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
ATAATATATTTAAATAAATTTTAACATATTA
Found at i:3075581 original size:36 final size:32
Alignment explanation
Indices: 3075501--3075566 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
3075491 AGTTGATAAT
* * *
3075501 ATAATATAT-TTAAATAAATTTTAATATATTA
1 ATAATTTATATTATATAAATTTTAACATATTA
3075532 ATAATTTATATTATATAAATTTTAACATATTA
1 ATAATTTATATTATATAAATTTTAACATATTA
3075564 ATA
1 ATA
3075567 TTATTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
ATAATTTATATTATATAAATTTTAACATATTA
Found at i:3075743 original size:19 final size:19
Alignment explanation
Indices: 3075710--3075753 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
3075700 AATGATTTTG
3075710 TTAAATCATGATTAATAAAA
1 TTAAATCATGATTAAT-AAA
*
3075730 TTAAATCA-GATTAATCAA
1 TTAAATCATGATTAATAAA
3075748 TTAAAT
1 TTAAAT
3075754 TGAGAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 7 0.30
20 8 0.35
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (19 bp):
TTAAATCATGATTAATAAA
Found at i:3075962 original size:17 final size:18
Alignment explanation
Indices: 3075920--3075972 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 18
3075910 TAATTTAATA
3075920 AATTTATATTAAATATCAT
1 AATTTA-ATTAAATATCAT
3075939 ATCATTTAATTAAATAT-AT
1 A--ATTTAATTAAATATCAT
*
3075958 AATTTTATTAAATAT
1 AATTTAATTAAATAT
3075973 GTAAAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 13 0.42
19 4 0.13
20 9 0.29
21 5 0.16
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTTAATTAAATATCAT
Found at i:3076327 original size:3 final size:3
Alignment explanation
Indices: 3076319--3076352 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3076309 ATGGAGATGA
3076319 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3076353 TGATAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3076370 original size:14 final size:15
Alignment explanation
Indices: 3076318--3076371 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 15
3076308 TATGGAGATG
3076318 AAATAATAATA--AT
1 AAATAATAATATGAT
3076331 -AATAATAATA--AT
1 AAATAATAATATGAT
3076343 -AATAATAATATGAT
1 AAATAATAATATGAT
*
3076357 AAATAA-AATTTGAT
1 AAATAATAATATGAT
3076371 A
1 A
3076372 TATTTAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
12 22 0.59
14 10 0.27
15 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (15 bp):
AAATAATAATATGAT
Found at i:3076540 original size:3 final size:3
Alignment explanation
Indices: 3076532--3076569 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3076522 GGCCCAAAGA
3076532 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3076570 GGAAGAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3077148 original size:19 final size:19
Alignment explanation
Indices: 3077120--3077158 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
3077110 CTATTTATAT
3077120 TATATTTTTTATATTTTTAAA
1 TATA-TTTTTA-ATTTTTAAA
3077141 TATATTTTTAATTTTTAA
1 TATATTTTTAATTTTTAA
3077159 TAATTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 6 0.33
21 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATTTTTAATTTTTAAA
Found at i:3079043 original size:33 final size:38
Alignment explanation
Indices: 3078976--3079045 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 38
3078966 TGTTATATAA
3078976 ATTTTAATATATTTATATATTAATATTATGTTTATTTT
1 ATTTTAATATATTTATATATTAATATTATGTTTATTTT
*
3079014 ATTTTAAT-TATTT-T-TA-TAATA-TATTTTTATTT
1 ATTTTAATATATTTATATATTAATATTATGTTTATTT
3079046 AAAATTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
33 10 0.32
34 5 0.16
35 2 0.06
36 1 0.03
37 5 0.16
38 8 0.26
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (38 bp):
ATTTTAATATATTTATATATTAATATTATGTTTATTTT
Found at i:3082011 original size:2 final size:2
Alignment explanation
Indices: 3082004--3082036 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3081994 TTTATTCTAT
3082004 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 T
3082037 CCTATTAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3083296 original size:18 final size:17
Alignment explanation
Indices: 3083273--3083307 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3083263 AAATATGACA
3083273 TAATAAAAAATTAAAATG
1 TAATAAAAAA-TAAAATG
*
3083291 TAATAAAATATAAAATG
1 TAATAAAAAATAAAATG
3083308 ATATGTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATAAAAAATAAAATG
Found at i:3085015 original size:18 final size:19
Alignment explanation
Indices: 3084968--3085018 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
3084958 TTATTTAATT
3084968 ATATATAAATATATATTTTAA
1 ATATAT-AATAT-TATTTTAA
*
3084989 ATATTTAATATTATTTTAA
1 ATATATAATATTATTTTAA
3085008 ATA-ATAATATT
1 ATATATAATATT
3085019 GAGTTTTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 7 0.25
19 11 0.39
20 5 0.18
21 5 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATAATATTATTTTAA
Found at i:3085894 original size:14 final size:14
Alignment explanation
Indices: 3085877--3085938 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
3085867 TTAATTTAAT
3085877 TATAAATTATAAAA
1 TATAAATTATAAAA
*
3085891 TATAAAATATATAAA
1 TATAAATTATA-AAA
*
3085906 TATTAA-TATAAAA
1 TATAAATTATAAAA
*
3085919 -ATAATATTTTAATAA
1 TATAA-ATTATAA-AA
3085934 TATAA
1 TATAA
3085939 TGAGTAATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 3 0.08
13 4 0.10
14 18 0.46
15 10 0.26
16 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATAAATTATAAAA
Found at i:3092903 original size:2 final size:2
Alignment explanation
Indices: 3092896--3092927 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3092886 TAGTGGGAAC
3092896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3092928 CAATATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3093823 original size:24 final size:24
Alignment explanation
Indices: 3093777--3093823 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3093767 GAGAATGTAC
* *
3093777 ATATTAAAATTTAAAATTTATTAA
1 ATATTAAAATTTAAAAATAATTAA
* *
3093801 ATATTATATTTTAAAAATAATTA
1 ATATTAAAATTTAAAAATAATTA
3093824 TATAAATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATTAAAATTTAAAAATAATTAA
Found at i:3095469 original size:31 final size:29
Alignment explanation
Indices: 3095417--3095474 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
3095407 AAAATTTTAT
3095417 TTAAATTTAATAATATAAAATATATAAATA
1 TTAAATTTAATAATATAAAATA-ATAAATA
* * *
3095447 TTAATATTTAATTATTTTAAATAATAAA
1 TTAA-ATTTAATAATATAAAATAATAAA
3095475 ACTATTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TTAAATTTAATAATATAAAATAATAAATA
Found at i:3095588 original size:26 final size:22
Alignment explanation
Indices: 3095553--3095604 Score: 59
Period size: 26 Copynumber: 2.2 Consensus size: 22
3095543 ACAAAATGAT
3095553 TTAATCTATAGATATATTTAATTTGA
1 TTAATCTATA-A-ATATTT-ATTT-A
*
3095579 TTAATGTATAAATATTTATTTA
1 TTAATCTATAAATATTTATTTA
3095601 TTAA
1 TTAA
3095605 AAATTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 5 0.20
23 4 0.16
24 6 0.24
25 1 0.04
26 9 0.36
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (22 bp):
TTAATCTATAAATATTTATTTA
Found at i:3095641 original size:28 final size:28
Alignment explanation
Indices: 3095587--3095642 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
3095577 GATTAATGTA
*
3095587 TAAATATTTATTTATTAAAAATTAAATT
1 TAAATATTTATTTATTAAAAATAAAATT
3095615 TAAATATTCT-TTTATTAAATAA-AAAATT
1 TAAATATT-TATTTATTAAA-AATAAAATT
3095643 AGAAGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
TAAATATTTATTTATTAAAAATAAAATT
Found at i:3101962 original size:2 final size:2
Alignment explanation
Indices: 3101955--3101987 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3101945 GTTGCAGAAT
3101955 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3101988 AACGACATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3103089 original size:3 final size:3
Alignment explanation
Indices: 3103081--3103106 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3103071 GCTGAAGCAA
3103081 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
3103107 AAGATTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3107018 original size:5 final size:5
Alignment explanation
Indices: 3107008--3107041 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
3106998 TCACACCCAA
*
3107008 CTTTT CTTTT CTTTT CTTTT C-TTT CCTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
3107042 TCTCTTCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
CTTTT
Found at i:3107028 original size:15 final size:14
Alignment explanation
Indices: 3107008--3107041 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3106998 TCACACCCAA
*
3107008 CTTTTCTTTTCTTTT
1 CTTTTC-TTTCCTTT
3107023 CTTTTCTTTCCTTT
1 CTTTTCTTTCCTTT
3107037 CTTTT
1 CTTTT
3107042 TCTCTTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
CTTTTCTTTCCTTT
Found at i:3110265 original size:2 final size:2
Alignment explanation
Indices: 3110260--3110310 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
3110250 TGTGACATAG
* * *
3110260 AT AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT GT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3110303 AT -T AT AT A
1 AT AT AT AT A
3110311 CACAAACCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3117347 original size:15 final size:16
Alignment explanation
Indices: 3117327--3117360 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3117317 ATGTTCACTG
*
3117327 AAATAATTATATTT-A
1 AAATAATTAAATTTGA
3117342 AAATAATTAAATTTGA
1 AAATAATTAAATTTGA
3117358 AAA
1 AAA
3117361 AGAATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAATAATTAAATTTGA
Found at i:3117870 original size:2 final size:2
Alignment explanation
Indices: 3117863--3117889 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3117853 TTCTTTTCTT
3117863 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
3117890 TGTGCTTGTT
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:3118567 original size:12 final size:12
Alignment explanation
Indices: 3118550--3118594 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
3118540 TTATATCATG
3118550 TCATATTTTATA
1 TCATATTTTATA
3118562 TCATATTTTA-A
1 TCATATTTTATA
3118573 T--TATTTT-TA
1 TCATATTTTATA
*
3118582 TCATATCTTATA
1 TCATATTTTATA
3118594 T
1 T
3118595 GTATTATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
9 8 0.29
11 7 0.25
12 13 0.46
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATATTTTATA
Found at i:3118599 original size:22 final size:21
Alignment explanation
Indices: 3118553--3118591 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3118543 TATCATGTCA
*
3118553 TATTTTATATCATATTTTAAT
1 TATTTTATATCATATCTTAAT
3118574 TATTTT-TATCATATCTTA
1 TATTTTATATCATATCTTA
3118592 TATGTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATATCATATCTTAAT
Found at i:3119500 original size:24 final size:23
Alignment explanation
Indices: 3119473--3119523 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
3119463 TTTAAACAAT
* * *
3119473 AAATATATTTATATTTTAATTATA
1 AAATATATATAAATATTAA-TATA
3119497 AAATATATATAAATATTAATATA
1 AAATATATATAAATATTAATATA
3119520 AAAT
1 AAAT
3119524 TAATTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATATATATAAATATTAATATA
Found at i:3120994 original size:24 final size:25
Alignment explanation
Indices: 3120967--3121013 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
3120957 AAATCACCTT
3120967 TTTATCAT-AATTGTTA-AGTATTGA
1 TTTA-CATGAATTGTTATAGTATTGA
*
3120991 TTTACTTGAATTGTTATAGTATT
1 TTTACATGAATTGTTATAGTATT
3121014 TGAGTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 12 0.60
25 6 0.30
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.53
Consensus pattern (25 bp):
TTTACATGAATTGTTATAGTATTGA
Found at i:3121633 original size:14 final size:14
Alignment explanation
Indices: 3121614--3121660 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3121604 TCATAATTTT
3121614 TTAAAATTAGTTGA
1 TTAAAATTAGTTGA
* *
3121628 TTAAAAATA-TTCGT
1 TTAAAATTAGTT-GA
*
3121642 TTAAAATTAGATGA
1 TTAAAATTAGTTGA
3121656 TTAAA
1 TTAAA
3121661 TGTATAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 2 0.08
14 23 0.88
15 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (14 bp):
TTAAAATTAGTTGA
Found at i:3121829 original size:2 final size:2
Alignment explanation
Indices: 3121822--3121855 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3121812 GTAATTGTTT
3121822 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
3121856 CTCAATTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3122120 original size:3 final size:3
Alignment explanation
Indices: 3122107--3122150 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
3122097 TGAGAATGAA
*
3122107 AAT ATAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3122151 TTCTTTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3122726 original size:2 final size:2
Alignment explanation
Indices: 3122719--3122758 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3122709 CAAGCTTCAC
3122719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3122759 TACAAACATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3127840 original size:37 final size:38
Alignment explanation
Indices: 3127798--3127881 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 38
3127788 TAAATTAAAA
* *
3127798 ATTATTTAT-TTAATATTTAAAAAAATTATA-ATTAATT
1 ATTATTTATATTAA-ATTTAAAAAAATAATACAATAATT
* *
3127835 ATTATTTTTATTAAATTTTAAAAAATAATACAATAATT
1 ATTATTTATATTAAATTTAAAAAAATAATACAATAATT
3127873 ATATATTTA
1 AT-TATTTA
3127882 ATAGAATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
37 22 0.56
38 12 0.31
39 5 0.13
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (38 bp):
ATTATTTATATTAAATTTAAAAAAATAATACAATAATT
Found at i:3127859 original size:39 final size:39
Alignment explanation
Indices: 3127802--3127880 Score: 92
Period size: 39 Copynumber: 2.0 Consensus size: 39
3127792 TTAAAAATTA
* *
3127802 TTTATTTAATATTTAAAAA-AATTATAATTAATTAT-TATT
1 TTTATTAAATATTTAAAAATAA-TACAA-TAATTATATATT
3127841 TTTATTAAAT-TTTAAAAAATAATACAATAATTATATATT
1 TTTATTAAATATTT-AAAAATAATACAATAATTATATATT
3127880 T
1 T
3127881 AATAGAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
38 10 0.29
39 23 0.66
40 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (39 bp):
TTTATTAAATATTTAAAAATAATACAATAATTATATATT
Found at i:3128305 original size:14 final size:13
Alignment explanation
Indices: 3128286--3128324 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
3128276 TTTTTATTTT
3128286 TTTAAATATTTATA
1 TTTAAA-ATTTATA
*
3128300 TTTAAAACTTATA
1 TTTAAAATTTATA
3128313 TTTAAAATTTAT
1 TTTAAAATTTAT
3128325 TCAAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAAAATTTATA
Found at i:3128492 original size:22 final size:22
Alignment explanation
Indices: 3128464--3128508 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3128454 ATCTTTAAGA
3128464 TAATTTAGGTTATGAAAAGATT
1 TAATTTAGGTTATGAAAAGATT
3128486 TAATTTAGGTTATGAAAAGATT
1 TAATTTAGGTTATGAAAAGATT
3128508 T
1 T
3128509 GCTGAACGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (22 bp):
TAATTTAGGTTATGAAAAGATT
Found at i:3128621 original size:2 final size:2
Alignment explanation
Indices: 3128616--3128642 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3128606 TAAAAAAAAG
3128616 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3128643 GAGGGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3131179 original size:23 final size:26
Alignment explanation
Indices: 3131122--3131185 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 26
3131112 TTTAAAAATT
*
3131122 TTAATAAGATA-ATATAATTTAATTTA
1 TTAATAA-ATATATATAATTTAATATA
3131148 TTAAT-AATATATA-AATTT-ATATA
1 TTAATAAATATATATAATTTAATATA
*
3131171 -TAATAAATATTTATA
1 TTAATAAATATATATA
3131186 TAATGCTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 4 0.12
23 11 0.33
24 9 0.27
25 4 0.12
26 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TTAATAAATATATATAATTTAATATA
Found at i:3131216 original size:2 final size:2
Alignment explanation
Indices: 3131211--3131236 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3131201 ATATAAACTC
3131211 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
3131237 TTTTAAACAC
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:3133163 original size:21 final size:20
Alignment explanation
Indices: 3133128--3133166 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3133118 ATTAAAAAAA
*
3133128 ATTTTATATATTTTTATTAT
1 ATTTTATAAATTTTTATTAT
3133148 ATTTTAATAAATTTTTATT
1 ATTTT-ATAAATTTTTATT
3133167 TAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTATAAATTTTTATTAT
Found at i:3133200 original size:34 final size:35
Alignment explanation
Indices: 3133161--3133241 Score: 119
Period size: 36 Copynumber: 2.3 Consensus size: 35
3133151 TTAATAAATT
*
3133161 TTTATTTAAATTAATTTTTTT-AAAAAATTAAGAG
1 TTTATTTAAATTAATTTTTTTAAAAAAATTAAGAA
* *
3133195 TTTATTTAAATTGATTTTTTTAAAAAAAATTGAGAA
1 TTTATTTAAATTAATTTTTTT-AAAAAAATTAAGAA
3133231 TTTATTTAAAT
1 TTTATTTAAAT
3133242 ATAAATTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
34 20 0.48
36 22 0.52
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (35 bp):
TTTATTTAAATTAATTTTTTTAAAAAAATTAAGAA
Found at i:3133257 original size:30 final size:30
Alignment explanation
Indices: 3133223--3133295 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
3133213 TTTAAAAAAA
3133223 ATTGAGAATTTATTTAAATATAAATTAAAG
1 ATTGAGAATTTATTTAAATATAAATTAAAG
*
3133253 ATTGAGAACTTATTTAAATATAAATTAAAG
1 ATTGAGAATTTATTTAAATATAAATTAAAG
* *
3133283 ATTAAAAATTTAT
1 ATTGAGAATTTAT
3133296 CTGAATACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (30 bp):
ATTGAGAATTTATTTAAATATAAATTAAAG
Found at i:3133426 original size:34 final size:34
Alignment explanation
Indices: 3133382--3133451 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
3133372 AGAAGTTAAG
* *
3133382 AATTAATTTGGATGCATATTGAAAATA-AAAAATTT
1 AATTAATTTGGATG--TAATAAAAATATAAAAATTT
3133417 AATT-ATTTGGATGTAATAAAAATATAAAAATTT
1 AATTAATTTGGATGTAATAAAAATATAAAAATTT
3133450 AA
1 AA
3133452 ATAAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 9 0.28
33 10 0.31
34 9 0.28
35 4 0.12
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.37
Consensus pattern (34 bp):
AATTAATTTGGATGTAATAAAAATATAAAAATTT
Found at i:3133866 original size:22 final size:22
Alignment explanation
Indices: 3133834--3133876 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3133824 ATTAATTTTT
3133834 ATAATTAAAATTAAAA-TAAATA
1 ATAATTAAAA-TAAAATTAAATA
*
3133856 ATAATTCAAATAAAATTAAAT
1 ATAATTAAAATAAAATTAAAT
3133877 TAATTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATTAAAATAAAATTAAATA
Found at i:3133894 original size:6 final size:5
Alignment explanation
Indices: 3133836--3133928 Score: 55
Period size: 5 Copynumber: 18.0 Consensus size: 5
3133826 TAATTTTTAT
* * * *
3133836 AATTAA AATTA AAATA AATAA TAATTCA AATAA AATTA AATTA ATTTA
1 AATT-A AATTA AATTA AATTA -AATT-A AATTA AATTA AATTA AATTA
* * * *
3133884 TATTA TAATTA AACTTG AATTA AATT- TATCA AATTA AA-TA AATTA
1 AATTA -AATTA AA-TTA AATTA AATTA AATTA AATTA AATTA AATTA
3133929 TCTAACTCTT
Statistics
Matches: 65, Mismatches: 16, Indels: 13
0.69 0.17 0.14
Matches are distributed among these distances:
4 6 0.09
5 40 0.62
6 18 0.28
7 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (5 bp):
AATTA
Found at i:3133896 original size:27 final size:28
Alignment explanation
Indices: 3133832--3133912 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 28
3133822 ATATTAATTT
* * *
3133832 TTATAATTAAAATTAAAATAAATAATAA
1 TTATAATTAAAATTAAATTAATTTATAA
3133860 TTCA-AA-TAAAATTAAATTAATTTAT-A
1 TT-ATAATTAAAATTAAATTAATTTATAA
* *
3133886 TTATAATTAAACTTGAATTAAATTTAT
1 TTATAATTAAAATTAAATT-AATTTAT
3133913 CAAATTAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
25 1 0.02
26 5 0.11
27 26 0.59
28 11 0.25
29 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (28 bp):
TTATAATTAAAATTAAATTAATTTATAA
Found at i:3135194 original size:16 final size:17
Alignment explanation
Indices: 3135169--3135201 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3135159 TATTATTTTA
3135169 TTATTAAAAAA-TATTT
1 TTATTAAAAAATTATTT
*
3135185 TTATTTAAAAATTATTT
1 TTATTAAAAAATTATTT
3135202 AAATATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTAAAAAATTATTT
Found at i:3135316 original size:20 final size:19
Alignment explanation
Indices: 3135291--3135329 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3135281 TAAATCAAAT
3135291 TATGAACGAGAACTTAAAAA
1 TATGAA-GAGAACTTAAAAA
**
3135311 TATGAATTGAACTTAAAAA
1 TATGAAGAGAACTTAAAAA
3135330 AAGTCCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.26
Consensus pattern (19 bp):
TATGAAGAGAACTTAAAAA
Found at i:3135802 original size:17 final size:18
Alignment explanation
Indices: 3135776--3135809 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3135766 ACTAAACAAG
3135776 AAAAATGAAAAAAAAAAC
1 AAAAATGAAAAAAAAAAC
3135794 AAAAA-GAAAAAAAAAA
1 AAAAATGAAAAAAAAAA
3135810 TTATTAGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.88, C:0.03, G:0.06, T:0.03
Consensus pattern (18 bp):
AAAAATGAAAAAAAAAAC
Found at i:3136259 original size:2 final size:2
Alignment explanation
Indices: 3136254--3136279 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3136244 AAAAAAAACC
3136254 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
3136280 GTGTGTGTGA
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:3137658 original size:21 final size:21
Alignment explanation
Indices: 3137634--3137691 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 21
3137624 GTTATTAAAA
3137634 ATATTATATTAAAATATTTAT
1 ATATTATATTAAAATATTTAT
*
3137655 ATA-TATAATTATTATATATTTAT
1 ATATTAT-ATTA--AAATATTTAT
3137678 ATAATTATATTAAA
1 AT-ATTATATTAAA
3137692 CGCCCCACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
20 3 0.10
21 7 0.23
22 1 0.03
23 11 0.37
24 5 0.17
25 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTATATTAAAATATTTAT
Found at i:3138350 original size:35 final size:33
Alignment explanation
Indices: 3138278--3138352 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 33
3138268 ATTTAATTTA
**
3138278 ATTTTAA-TTATTATTTAAATAATAAAAAAATT
1 ATTTTAATTTATTATAAAAATAATAAAAAAATT
*
3138310 ATTTTAATTTAATTATAAAAATATATAATAAAATT
1 ATTTTAATTT-ATTATAAAAATA-ATAAAAAAATT
3138345 ATTTTAAT
1 ATTTTAAT
3138353 ATTTAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 7 0.19
33 2 0.05
34 10 0.27
35 18 0.49
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
ATTTTAATTTATTATAAAAATAATAAAAAAATT
Found at i:3138549 original size:16 final size:15
Alignment explanation
Indices: 3138528--3138566 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3138518 TTTGAGCAAA
3138528 TTTAAAATAAAAGCAT
1 TTTAAAAT-AAAGCAT
* *
3138544 TTTAAAATACATCAT
1 TTTAAAATAAAGCAT
3138559 TTTAAAAT
1 TTTAAAAT
3138567 GTTAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (15 bp):
TTTAAAATAAAGCAT
Found at i:3139872 original size:9 final size:9
Alignment explanation
Indices: 3139850--3139883 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
3139840 CATAAATGGC
3139850 TATTAAAGTT
1 TATTAAA-TT
3139860 TATTAAATT
1 TATTAAATT
3139869 TATTAAATT
1 TATTAAATT
3139878 TATTAA
1 TATTAA
3139884 TATGGTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.71
10 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
TATTAAATT
Found at i:3141199 original size:3 final size:3
Alignment explanation
Indices: 3141191--3141216 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3141181 TTTCACGGGC
3141191 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3141217 GCAGCTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3143186 original size:13 final size:13
Alignment explanation
Indices: 3143168--3143196 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3143158 TACTGTTAAT
3143168 ATGAAATCTCTAA
1 ATGAAATCTCTAA
3143181 ATGAAATCTCTAA
1 ATGAAATCTCTAA
3143194 ATG
1 ATG
3143197 TGTACTTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (13 bp):
ATGAAATCTCTAA
Found at i:3144927 original size:64 final size:62
Alignment explanation
Indices: 3144800--3144980 Score: 283
Period size: 64 Copynumber: 2.9 Consensus size: 62
3144790 GACCCACAAT
* *
3144800 TGTTTTATTTTAATATTAAAATTT-AAGTCATGAAAATGAACAGTATCTTCTCTTTCCAATAA
1 TGTTTTATTTTAATATTAAAATTTAAAGTGATGAAAATG-ATAGTATCTTCTCTTTCCAATAA
* *
3144862 TGTTTTATTTTAATATTAAAATTTAAAAGTGATGAAAATGTATAGTGTCTTCTCTTTCCATTAA
1 TGTTTTATTTTAATATTAAAATTT-AAAGTGATGAAAATG-ATAGTATCTTCTCTTTCCAATAA
3144926 TGTTTTATTTTAATATTAAAATTTAAAGTGATGAAAATGATTAGTATCTTCTCTT
1 TGTTTTATTTTAATATTAAAATTTAAAGTGATGAAAATGA-TAGTATCTTCTCTT
3144981 CAATCACGTT
Statistics
Matches: 110, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
62 25 0.23
63 28 0.25
64 57 0.52
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46
Consensus pattern (62 bp):
TGTTTTATTTTAATATTAAAATTTAAAGTGATGAAAATGATAGTATCTTCTCTTTCCAATAA
Found at i:3148412 original size:13 final size:13
Alignment explanation
Indices: 3148394--3148432 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
3148384 AATTTTAAAT
3148394 TTAA-TTAATTTAA
1 TTAATTTAA-TTAA
*
3148407 TTAATTTGATTAA
1 TTAATTTAATTAA
3148420 TTAATTTAATTAA
1 TTAATTTAATTAA
3148433 AATTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 20 0.87
14 3 0.13
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:3148432 original size:9 final size:9
Alignment explanation
Indices: 3148391--3148430 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
3148381 TAAAATTTTA
3148391 AATTTAATT
1 AATTTAATT
3148400 AATTTAATT
1 AATTTAATT
*
3148409 AATTTGATT
1 AATTTAATT
3148418 AA-TTAATTT
1 AATTTAA-TT
3148427 AATT
1 AATT
3148431 AAAATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 3 0.11
9 23 0.85
10 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (9 bp):
AATTTAATT
Found at i:3148441 original size:22 final size:20
Alignment explanation
Indices: 3148393--3148432 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
3148383 AAATTTTAAA
3148393 TTTAATTAATTTAATTAATT
1 TTTAATTAATTTAATTAATT
3148413 TGATTAATTAATTTAATTAA
1 T--TTAATTAATTTAATTAA
3148433 AATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
22 17 0.94
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTAATTAATTTAATTAATT
Found at i:3148522 original size:23 final size:21
Alignment explanation
Indices: 3148494--3148566 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
3148484 CATAATAAAT
3148494 ATTTAATAAAAATATATTATTTA
1 ATTTAATAAAAATA-ATT-TTTA
* *
3148517 ATTTAATGATAATAATTTTTA
1 ATTTAATAAAAATAATTTTTA
* * *
3148538 ATATAA-AATAAAAAATTTTAA
1 ATTTAATAA-AAATAATTTTTA
3148559 TATTTAAT
1 -ATTTAAT
3148567 TTTTTGAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.03
21 18 0.46
22 8 0.21
23 12 0.31
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (21 bp):
ATTTAATAAAAATAATTTTTA
Found at i:3149211 original size:72 final size:74
Alignment explanation
Indices: 3149075--3149211 Score: 172
Period size: 73 Copynumber: 1.9 Consensus size: 74
3149065 ACCGCAAGAG
* * ** *
3149075 AAAGCTTTTTTTTTTTTTTTTCAACCTAAAATTTCATTTGGAAAAGTTAAAATTCTGTTTGAAAC
1 AAAGCTTTTTTTTTTTTTTTT-AACCTAAAATTTCATTTGAAAAAGGTAAAATTCTCATCGAAAC
3149140 ACTAATAGGA
65 ACTAATAGGA
* *
3149150 AAAGC-TTTTTTTTTTTTTTT-ACGTAAAAATTTCATTTGAAAAAGGTAAACTT-TCATCGAAAC
1 AAAGCTTTTTTTTTTTTTTTTAACCT-AAAATTTCATTTGAAAAAGGTAAAATTCTCATCGAAAC
3149212 TAAATTTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
72 10 0.19
73 24 0.44
74 15 0.28
75 5 0.09
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (74 bp):
AAAGCTTTTTTTTTTTTTTTTAACCTAAAATTTCATTTGAAAAAGGTAAAATTCTCATCGAAACA
CTAATAGGA
Found at i:3150023 original size:26 final size:28
Alignment explanation
Indices: 3149971--3150023 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
3149961 TAAGAATTTA
3149971 GTTAATCTTAAAATTATGTTTAATTATT
1 GTTAATCTTAAAATTATGTTTAATTATT
3149999 GTTAA-CTT-AAATTAT-TTTAAGTTAT
1 GTTAATCTTAAAATTATGTTTAA-TTAT
3150024 ATTCTAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 5 0.21
26 11 0.46
27 3 0.12
28 5 0.21
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (28 bp):
GTTAATCTTAAAATTATGTTTAATTATT
Found at i:3150122 original size:47 final size:48
Alignment explanation
Indices: 3150052--3150145 Score: 129
Period size: 47 Copynumber: 2.0 Consensus size: 48
3150042 ATTAAATACT
*
3150052 TTAAACTTATTTTTAATTCAATTAATT-ATTAATTTTGAAATAAATTTA
1 TTAAACTTATTTTTAATTAAATTAATTAATTAATTTTGAAA-AAATTTA
* * *
3150100 TTAAA-TTATTTTTATTTAAATTAATTAATTATTTTTTAAAAAATTT
1 TTAAACTTATTTTTAATTAAATTAATTAATTAATTTTGAAAAAATTT
3150146 GGTGTTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
47 25 0.61
48 16 0.39
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (48 bp):
TTAAACTTATTTTTAATTAAATTAATTAATTAATTTTGAAAAAATTTA
Found at i:3150137 original size:24 final size:23
Alignment explanation
Indices: 3150058--3150135 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
3150048 TACTTTAAAC
*
3150058 TTATTTTTAATTCAATTAATT-A
1 TTATTTTTAATTAAATTAATTAA
* * *
3150080 TTAATTTTGAAATAAATTTATTAAA
1 TT-ATTTTTAATTAAATTAATT-AA
*
3150105 TTATTTTTATTTAAATTAATTAA
1 TTATTTTTAATTAAATTAATTAA
3150128 TTATTTTT
1 TTATTTTT
3150136 TAAAAAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
22 2 0.04
23 25 0.56
24 15 0.33
25 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (23 bp):
TTATTTTTAATTAAATTAATTAA
Found at i:3150143 original size:23 final size:22
Alignment explanation
Indices: 3150071--3150144 Score: 60
Period size: 24 Copynumber: 3.2 Consensus size: 22
3150061 TTTTTAATTC
*
3150071 AATTAATT-ATTAATTTTGAAATA
1 AATTAATTAATT-ATTTTTAAA-A
* **
3150094 AATTTATTAAATTATTTTTATTTA
1 AATTAATT-AATTATTTTTA-AAA
3150118 AATTAATTAATTATTTTTTAAAA
1 AATTAATTAATTA-TTTTTAAAA
3150141 AATT
1 AATT
3150145 TGGTGTTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
23 17 0.43
24 20 0.50
25 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (22 bp):
AATTAATTAATTATTTTTAAAA
Found at i:3150831 original size:28 final size:29
Alignment explanation
Indices: 3150775--3150841 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 29
3150765 GAAAAGAAAA
3150775 TATTATTTAAATTTTAAAAAGATAAATAAAT
1 TATT-TTTAAATTTTAAAAAGATAAAT-AAT
**
3150806 TATTTTTAAA-TTTAAAAA-ATTTATAAT
1 TATTTTTAAATTTTAAAAAGATAAATAAT
3150833 T-TTTTTAAA
1 TATTTTTAAA
3150842 AAATTTTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 8 0.24
27 4 0.12
28 4 0.12
29 8 0.24
30 6 0.18
31 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TATTTTTAAATTTTAAAAAGATAAATAAT
Done.