Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold316
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: 597962
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
File 3 of 5
Found at i:341982 original size:13 final size:14
Alignment explanation
Indices: 341964--341996 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
341954 TTTATTACAA
341964 TTTAAATTAAA-AT
1 TTTAAATTAAATAT
341977 TTTAAATTAAATAT
1 TTTAAATTAAATAT
341991 TTTAAA
1 TTTAAA
341997 ATAATTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAAATTAAATAT
Found at i:342385 original size:29 final size:29
Alignment explanation
Indices: 342352--342416 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
342342 TTTTCACAAG
*
342352 TTAAAATAGTAATATTCTAATAATTTATT
1 TTAAAATAATAATATTCTAATAATTTATT
* * * *
342381 TTAAATTAATATTATTTTGATAATTTATT
1 TTAAAATAATAATATTCTAATAATTTATT
*
342410 TAAAAAT
1 TTAAAAT
342417 TAAAAACAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (29 bp):
TTAAAATAATAATATTCTAATAATTTATT
Found at i:343146 original size:2 final size:2
Alignment explanation
Indices: 343136--343176 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
343126 TTATTGAGCC
*
343136 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
343177 TATGTTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:343478 original size:27 final size:29
Alignment explanation
Indices: 343448--343503 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
343438 TTCATTAAAA
*
343448 TATTTTAATAATA-AATA-TAAATAATTT
1 TATTTTAATAAAATAATATTAAATAATTT
*
343475 TATTTTAATAAAATAATATTATATAATTT
1 TATTTTAATAAAATAATATTAAATAATTT
343504 ACTAACAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.48
28 4 0.16
29 9 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TATTTTAATAAAATAATATTAAATAATTT
Found at i:343940 original size:14 final size:13
Alignment explanation
Indices: 343918--343960 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
343908 TTTTATTTTT
343918 TATATATTTAAAA
1 TATATATTTAAAA
* *
343931 TATCATATTTTATA
1 TAT-ATATTTAAAA
343945 TATATATTT-AAA
1 TATATATTTAAAA
343957 TATA
1 TATA
343961 AATCGAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 6 0.23
13 9 0.35
14 11 0.42
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
TATATATTTAAAA
Found at i:345681 original size:22 final size:23
Alignment explanation
Indices: 345653--345697 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
345643 ACTGGTGTTG
345653 GATATTTATTTAAATAT-TAAAT
1 GATATTTATTTAAATATATAAAT
*
345675 GATATTTTTTTAAATATATAAAT
1 GATATTTATTTAAATATATAAAT
345698 AAATTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
GATATTTATTTAAATATATAAAT
Found at i:346685 original size:29 final size:28
Alignment explanation
Indices: 346633--346735 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 28
346623 ATACTTAACC
*
346633 TATAATATAAAA-AAAAATCTATTAAAA
1 TATAATATAAAATAAAAATATATTAAAA
346660 TATAATATAAATATAAAAATATATTAAAA
1 TATAATATAAA-ATAAAAATATATTAAAA
* * * *
346689 TTTTATATAAAATATATAATAT-TTTAAA
1 TATAATATAAAATA-AAAATATATTAAAA
346717 TATAATTATAAAATAAAAA
1 TATAA-TATAAAATAAAAA
346736 AATTACTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
27 11 0.17
28 15 0.23
29 38 0.59
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (28 bp):
TATAATATAAAATAAAAATATATTAAAA
Found at i:346706 original size:11 final size:11
Alignment explanation
Indices: 346646--346706 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 11
346636 AATATAAAAA
*
346646 AAAATCTAT-T
1 AAAATATATAT
346656 AAAATATA-AT
1 AAAATATATAT
*
346666 ATAA-ATATA-
1 AAAATATATAT
346675 AAAATATAT-T
1 AAAATATATAT
*
346685 AAAATTTTATAT
1 AAAA-TATATAT
346697 AAAATATATA
1 AAAATATATA
346707 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
9 6 0.15
10 20 0.50
11 9 0.22
12 5 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATATATAT
Found at i:346712 original size:21 final size:21
Alignment explanation
Indices: 346670--346730 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
346660 TATAATATAA
346670 ATATAAAAATATATTAAAATTTT
1 ATAT-AAAATATA-TAAAATTTT
*
346693 ATATAAAATATATAATATTTT
1 ATATAAAATATATAAAATTTT
* *
346714 AAATATAAT-TATAAAAT
1 ATATAAAATATATAAAAT
346731 AAAAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.21
21 15 0.44
22 8 0.24
23 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATAAAATATATAAAATTTT
Found at i:347223 original size:24 final size:24
Alignment explanation
Indices: 347196--347242 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
347186 TAATTTAATT
347196 TAAAAAA-TTATAAATAAATATAAA
1 TAAAAAATTTAT-AATAAATATAAA
**
347220 TAAAATCTTTATAATAAATATAA
1 TAAAAAATTTATAATAAATATAA
347243 GATTAAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
TAAAAAATTTATAATAAATATAAA
Found at i:349330 original size:16 final size:16
Alignment explanation
Indices: 349293--349346 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
349283 ATATTAAATT
*
349293 AATTTAAATAATTTTTA
1 AATTTAAATTA-TTTTA
* *
349310 TATTTGAATTATTTTA
1 AATTTAAATTATTTTA
349326 AATTTAAATTATTTTA
1 AATTTAAATTATTTTA
349342 AATTT
1 AATTT
349347 TAACCACCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 24 0.75
17 8 0.25
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
AATTTAAATTATTTTA
Found at i:350372 original size:61 final size:61
Alignment explanation
Indices: 350265--350380 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 61
350255 AAGGGACTGA
*
350265 TTATATTAAATTCAAATCAATTTAAATTTAGATTATTTCAAAATTTGATCATATGGATTAG
1 TTATATTAAATTCAAATCAATCTAAATTTAGATTATTTCAAAATTTGATCATATGGATTAG
* * * * * *
350326 TTATATTAAATTTAAATCAATCTGAATTTAGATTGTTTTAAGATTTGATCGTATG
1 TTATATTAAATTCAAATCAATCTAAATTTAGATTATTTCAAAATTTGATCATATG
350381 AATATATTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (61 bp):
TTATATTAAATTCAAATCAATCTAAATTTAGATTATTTCAAAATTTGATCATATGGATTAG
Found at i:352289 original size:25 final size:28
Alignment explanation
Indices: 352228--352296 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 28
352218 TTTATTAGAT
*
352228 TATTATATAA-AAATAAATTTTATATAC
1 TATTATTTAATAAATAAATTTTATATAC
*
352255 TTATTGTTTAATAAATAAATTTTATA-A-
1 -TATTATTTAATAAATAAATTTTATATAC
*
352282 TA-TATTTAATTAATA
1 TATTATTTAATAAATA
352297 TGTAATAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 11 0.31
26 2 0.06
28 9 0.25
29 14 0.39
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
TATTATTTAATAAATAAATTTTATATAC
Found at i:352630 original size:28 final size:28
Alignment explanation
Indices: 352530--352650 Score: 93
Period size: 28 Copynumber: 4.2 Consensus size: 28
352520 TTCACTTATA
*
352530 ATTCATAACATTTTATTAAAATTTTATTTTT
1 ATTCATAAC--TTT-TTAAAATTTTATTTTC
*
352561 ATTCATAA-TTTTTAAAAGTTATATTTATC
1 ATTCATAACTTTTTAAAA-TTTTATTT-TC
* * ** *
352590 ATTTAGATTTTTTTAATATTTTATTTTC
1 ATTCATAACTTTTTAAAATTTTATTTTC
* **
352618 ATTCATAACTTTTAAAAATTACATTTT-
1 ATTCATAACTTTTTAAAATTTTATTTTC
352645 ATTCAT
1 ATTCAT
352651 CTATAACTTT
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
27 12 0.17
28 31 0.43
29 13 0.18
30 8 0.11
31 8 0.11
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (28 bp):
ATTCATAACTTTTTAAAATTTTATTTTC
Found at i:352657 original size:31 final size:31
Alignment explanation
Indices: 352622--352741 Score: 147
Period size: 31 Copynumber: 3.9 Consensus size: 31
352612 ATTTTCATTC
352622 ATAACTTTTAAAAATTACATTTTATTCATCT
1 ATAACTTTTAAAAATTACATTTTATTCATCT
352653 ATAACTTTTAAAAATTACATTTTATTCATCT
1 ATAACTTTTAAAAATTACATTTTATTCATCT
* * * *
352684 ATAATTTTTAAATATTATA-TTTA-TCATCC
1 ATAACTTTTAAAAATTACATTTTATTCATCT
* * *
352713 ATAATCTTTCAAAAA-AAAATTTTATTCAT
1 ATAA-CTTTTAAAAATTACATTTTATTCAT
352742 TCATTTTTAG
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
29 11 0.14
30 15 0.19
31 51 0.66
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (31 bp):
ATAACTTTTAAAAATTACATTTTATTCATCT
Found at i:352711 original size:29 final size:29
Alignment explanation
Indices: 352565--352727 Score: 132
Period size: 31 Copynumber: 5.5 Consensus size: 29
352555 ATTTTTATTC
* *
352565 ATAATTTTTAAAAGTTATATTTATCATTT
1 ATAATTTTTAAAAATTATATTTATCATCT
* * * * *
352594 AGATTTTTTTAATATTTTATTT-TCAT-T
1 ATAATTTTTAAAAATTATATTTATCATCT
* *
352621 CATAACTTTTAAAAATTACATTTTATTCATCT
1 -ATAATTTTTAAAAATTATA-TTTA-TCATCT
* *
352653 ATAACTTTTAAAAATTACATTTTATTCATCT
1 ATAATTTTTAAAAATTATA-TTTA-TCATCT
* *
352684 ATAATTTTTAAATATTATATTTATCATCC
1 ATAATTTTTAAAAATTATATTTATCATCT
*
352713 ATAATCTTTCAAAAA
1 ATAAT-TTTTAAAAA
352728 AAAATTTTAT
Statistics
Matches: 109, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
27 1 0.01
28 16 0.15
29 29 0.27
30 11 0.10
31 51 0.47
32 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (29 bp):
ATAATTTTTAAAAATTATATTTATCATCT
Found at i:353059 original size:19 final size:19
Alignment explanation
Indices: 353035--353072 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
353025 AAATCTCTTT
* *
353035 ATTTTTTCAAATAAATATG
1 ATTTTTTAAAAAAAATATG
353054 ATTTTTTAAAAAAAATATG
1 ATTTTTTAAAAAAAATATG
353073 TTATATATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTTTTAAAAAAAATATG
Found at i:354001 original size:23 final size:24
Alignment explanation
Indices: 353939--354001 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 24
353929 AATATTTTTA
353939 TTTAA-ATTTTATTATAAAAAAATAT
1 TTTAATATTTT-TTA-AAAAAAATAT
* ** *
353964 ATTAATATTAATTAAAAATAAT-T
1 TTTAATATTTTTTAAAAAAAATAT
353987 TTTAATATTTTTTAA
1 TTTAATATTTTTTAA
354002 TTTTTATATA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
23 13 0.43
24 7 0.23
25 7 0.23
26 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTAATATTTTTTAAAAAAAATAT
Found at i:354263 original size:19 final size:18
Alignment explanation
Indices: 354236--354374 Score: 62
Period size: 19 Copynumber: 7.7 Consensus size: 18
354226 CTCATATCTT
*
354236 TTATTTAAATATAAAACAA
1 TTATATAAATATAAAA-AA
354255 TTATATAAA-ATAAAAATAA
1 TTATATAAATAT-AAAA-AA
* *
354274 TTA-AAAAATTATATAAAAT
1 TTATATAAA-TATA-AAAAA
*
354293 TTATATAAATAT--AATA
1 TTATATAAATATAAAAAA
* *
354309 TGAATATAAATATATTAAAA
1 T-TATATAAATATA-AAAAA
354329 TT-TATTAAATAT---AAA
1 TTATA-TAAATATAAAAAA
* *
354344 TTAT-TAATATATTAAAAT
1 TTATATAA-ATATAAAAAA
354362 TTATATAAATATA
1 TTATATAAATATA
354375 TAGTATTTTA
Statistics
Matches: 92, Mismatches: 12, Indels: 33
0.67 0.09 0.24
Matches are distributed among these distances:
14 3 0.03
15 9 0.10
16 4 0.04
17 10 0.11
18 18 0.20
19 35 0.38
20 13 0.14
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (18 bp):
TTATATAAATATAAAAAA
Found at i:354306 original size:17 final size:17
Alignment explanation
Indices: 354284--354374 Score: 82
Period size: 17 Copynumber: 5.3 Consensus size: 17
354274 TTAAAAAATT
354284 ATATAAAATTTATATAA
1 ATATAAAATTTATATAA
* **
354301 ATATAATATGAATATAAA
1 ATATAAAATTTATAT-AA
354319 TATATTAAAATTTAT-TAA
1 -ATA-TAAAATTTATATAA
354337 ATAT-AAA-TTAT-TAA
1 ATATAAAATTTATATAA
354351 TATATTAAAATTTATATAA
1 -ATA-TAAAATTTATATAA
354370 ATATA
1 ATATA
354375 TAGTATTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
14 7 0.12
15 6 0.10
16 2 0.03
17 20 0.33
18 11 0.18
19 7 0.12
20 7 0.12
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (17 bp):
ATATAAAATTTATATAA
Found at i:354334 original size:10 final size:10
Alignment explanation
Indices: 354316--354375 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
354306 ATATGAATAT
354316 AAATATATTA
1 AAATATATTA
*
354326 AAATTTATTA
1 AAATATATTA
*
354336 AATATAAATTA
1 AA-ATATATTA
*
354347 TTAATATATTA
1 -AAATATATTA
*
354358 AAATTTA-TA
1 AAATATATTA
354367 TAAATATAT
1 -AAATATAT
354376 AGTATTTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
9 2 0.05
10 22 0.58
11 13 0.34
12 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AAATATATTA
Found at i:354400 original size:2 final size:2
Alignment explanation
Indices: 354393--354419 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
354383 TAAGTAAAAT
354393 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
354420 TAATACACAA
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:355172 original size:13 final size:13
Alignment explanation
Indices: 355151--355182 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
355141 AGTTATGAAA
*
355151 AGAAGAAAAAGAG
1 AGAAAAAAAAGAG
355164 AGAAAAAAAAGAG
1 AGAAAAAAAAGAG
355177 AGAAAA
1 AGAAAA
355183 GCATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAGAG
Found at i:355944 original size:2 final size:2
Alignment explanation
Indices: 355925--355961 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
355915 GCTTATTATT
* *
355925 TA TA TG TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
355962 TGAAAATCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:359593 original size:30 final size:30
Alignment explanation
Indices: 359557--359626 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
359547 TTTATTTAAG
*
359557 TCAATTTGACCTACAAGCTATTAATTTTGA
1 TCAATTTAACCTACAAGCTATTAATTTTGA
* * * *
359587 TCAATTTAACTTTCAAGCTTTTATTTTTGA
1 TCAATTTAACCTACAAGCTATTAATTTTGA
359617 TCAATTTAAC
1 TCAATTTAAC
359627 TTAAATTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (30 bp):
TCAATTTAACCTACAAGCTATTAATTTTGA
Found at i:359627 original size:30 final size:30
Alignment explanation
Indices: 359570--359628 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
359560 ATTTGACCTA
359570 CAAGCTATTAATTTTGATCAATTTAACTTT
1 CAAGCTATTAATTTTGATCAATTTAACTTT
* *
359600 CAAGCTTTTATTTTTGATCAATTTAACTT
1 CAAGCTATTAATTTTGATCAATTTAACTT
359629 AAATTTGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.49
Consensus pattern (30 bp):
CAAGCTATTAATTTTGATCAATTTAACTTT
Found at i:366252 original size:2 final size:2
Alignment explanation
Indices: 366245--366287 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
366235 ACAGATGAAT
*
366245 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
366287 A
1 A
366288 ATCAACAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:366862 original size:3 final size:3
Alignment explanation
Indices: 366856--366887 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
366846 AAAAAAAAAG
366856 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
366888 CGATAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:369654 original size:9 final size:9
Alignment explanation
Indices: 369640--369669 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
369630 AAATTTGCAG
369640 TTTTTTTTA
1 TTTTTTTTA
369649 TTTTTTTTA
1 TTTTTTTTA
369658 TTTTTATTTA
1 TTTTT-TTTA
369668 TT
1 TT
369670 ATTATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:369850 original size:17 final size:17
Alignment explanation
Indices: 369820--369860 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
369810 AAAAATTTTA
369820 AATAAAAATATTAAATT
1 AATAAAAATATTAAATT
369837 AATAATAAAT-TTAAA-T
1 AATAA-AAATATTAAATT
369853 AA-AAAAAT
1 AATAAAAAT
369861 TCATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.17
15 2 0.09
16 3 0.13
17 10 0.43
18 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAAAAATATTAAATT
Found at i:369860 original size:14 final size:14
Alignment explanation
Indices: 369808--369861 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
369798 ATTTAATATT
*
369808 TAAAAAATTTTAAA
1 TAAAAAAATTTAAA
*
369822 TAAAAATA-TTAAA
1 TAAAAAAATTTAAA
369835 TTAATAATAAATTTAAA
1 -TAA-AA-AAATTTAAA
369852 TAAAAAAATT
1 TAAAAAAATT
369862 CATTTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 5 0.15
14 14 0.42
15 4 0.12
16 5 0.15
17 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAAAAATTTAAA
Found at i:369948 original size:26 final size:28
Alignment explanation
Indices: 369888--369960 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 28
369878 TTTATTTTTT
* *
369888 TAAT-TATATATATATACATCAAGTTTA
1 TAATATATATATATATAAATCAAATTTA
369915 TAATATATATATATATAAAT-AATATTTA
1 TAATATATATATATATAAATCAA-ATTTA
369943 TAATAT-TATAT-TATAAAT
1 TAATATATATATATATAAAT
369961 TTTAAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 7 0.17
27 11 0.26
28 24 0.57
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (28 bp):
TAATATATATATATATAAATCAAATTTA
Found at i:370025 original size:3 final size:3
Alignment explanation
Indices: 370017--370049 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
370007 TTGTAATTAA
370017 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
370050 TTTCTGTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:370298 original size:14 final size:14
Alignment explanation
Indices: 370279--370323 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
370269 TAAAACATAC
370279 ATATATATATATAA
1 ATATATATATATAA
*
370293 ATATATATTTAT-A
1 ATATATATATATAA
370306 ATAT-TATATTATAA
1 ATATATATA-TATAA
370320 ATAT
1 ATAT
370324 TTAAAAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 8 0.30
14 16 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATATATATAA
Found at i:370445 original size:345 final size:344
Alignment explanation
Indices: 369663--370729 Score: 1263
Period size: 345 Copynumber: 3.0 Consensus size: 344
369653 TTTTATTTTT
* *
369663 ATTT-ATTATTATTATTATTATTTGTCTGTTATACTTTCCTTTGTGGACTGATTTTGAGTGTCCA
1 ATTTAATTTTTATTATTATTATTTTTCTGTTATACTTTCCTTTGTGGACTGATTTTGAGTGTCCA
*** * *
369727 AGTAAAAATAAAATCCACAAAAGTTAGCAATTAGAT-CTTTGACCACATTTATTAATTCAAATTC
66 AGTAAAAATAAAATCCACAAAAGTTAGCAATTAGATCCTTTGACTTGATTTATTAATTTAAATTT
369791 AAA-TTTTATTTAATATTTAAAAAATTTTAAATAAAAATATTAAATTAATAATAAATTTAAATAA
131 AAATTTTTATTT-ATATTTAAAAAATTTT--AT--AAATA-TAAATTAATAATAAATTTAAAT-A
* ** * * *
369855 AAAAATTCATTTTAATAATTTTATTTATTTTTTTAATTATATATAT-ATACATCAAGTTT-ATAA
189 AAAAATT--TTATAATAA-TTT-TTTATTTTTTTAATTATATATATCAT-GTTTATGTTTAAAAA
369918 T--ATATATATATATAAATAATATTTATAATATTATATTATAAAT-TTTAAAAATTATGTAAAAT
249 TACATATATATATATAAATAATATTTATAATATTATATTATAAATATTT-AAAATTATGTAAAAT
*
369980 AATTGATATATTATATTATTTTATAATTTGTAATTAAA
313 AATTAATATATTATATTATTTTATAA-TT-T-A-T--A
*
370018 TTATTATTATTATTATTATTATTATTATTATTTTTCTGTTATACTTTCCTTTGTGGACTGATTTC
1 --A-T-TTA--A-T-TT-TTATTATTATTATTTTTCTGTTATACTTTCCTTTGTGGACTGATTTT
370083 GAGTGTCCAAGTAAAAATAAAATCCACAAAAGTTAGCAATTAGATCCTTTGACTTGATTTATTAA
57 GAGTGTCCAAGTAAAAATAAAATCCACAAAAGTTAGCAATTAGATCCTTTGACTTGATTTATTAA
370148 TTTAAATTTAAATTTTTATTT-TATTT-AAAAATTTTATAAATA-AAATTAATAATAAATTTGAA
122 TTTAAATTTAAATTTTTATTTATATTTAAAAAATTTTATAAATATAAATTAATAATAAATTT-AA
370210 A-AAAAATATTTTATAATAATTTTTTATTTTTTTAATTATATATATCATGTTTATGTTCATAAAA
186 ATAAAAA-ATTTTATAATAATTTTTTATTTTTTTAATTATATATATCATGTTTATGTT--TAAAA
*
370274 CATACATATATATATATAAATATATATTTATAATATTATATTATAAATATTTAAAAGTTATG-CA
248 -ATACATATATATATATAAATA-ATATTTATAATATTATATTATAAATATTTAAAA-TTATGTAA
370338 AATAATTAATATATTATATTATTTTATAATTTATA
310 AATAATTAATATATTATATTATTTTATAATTTATA
* * *
370373 ATTTAATTTTTATTATTATTATTTTTCTG-TATACTTTCCTTTTTGGACTGATTTTGATTGCCCA
1 ATTTAATTTTTATTATTATTATTTTTCTGTTATACTTTCCTTTGTGGACTGATTTTGAGTGTCCA
* * * *
370437 AGTAAAAATAAAATCTACAAAAGTTTGCAATTAGATCCTTTGGCTTGATTTATTAATTTGAATTT
66 AGTAAAAATAAAATCCACAAAAGTTAGCAATTAGATCCTTTGACTTGATTTATTAATTTAAATTT
* * *
370502 AAATTTTTATTTAATATTTTAAAAAATTAAATAAAAATATTATATTAATAATAAATTTAAATAAA
131 AAATTTTTATTT-ATA-TTTAAAAAATT--TTATAAATA-TAAATTAATAATAAATTTAAATAAA
* * * * *
370567 AAATTTTATTATAGTAATTTTATTTTTTTAAGTATATATATCATGTTTATGTTTATAAA-ACATA
191 AAATTTTATAATAAT-TTTTTATTTTTTTAATTATATATATCATGTTTATGTTTAAAAATACATA
* * * * * *
370631 TATATA-A-AAA-AGTATTCATAATATTATATTCTGAATATTTCAAAATTATGTGAAGTAATTAA
255 TATATATATAAATAATATTTATAATATTATATTATAAATATTT-AAAATTATGTAAAATAATTAA
* * *
370693 TATGTTATAGT-TTTCATAATTTATA
319 TATATTATATTATTTTATAATTTATA
370718 ATTTAATTTTTA
1 ATTTAATTTTTA
370730 ATTAATTTTG
Statistics
Matches: 635, Mismatches: 41, Indels: 80
0.84 0.05 0.11
Matches are distributed among these distances:
345 159 0.25
346 43 0.07
347 7 0.01
348 5 0.01
349 19 0.03
350 1 0.00
351 14 0.02
352 15 0.02
353 57 0.09
354 28 0.04
355 6 0.01
356 9 0.01
357 9 0.01
358 24 0.04
359 6 0.01
360 24 0.04
361 58 0.09
362 11 0.02
363 1 0.00
364 10 0.02
365 95 0.15
366 26 0.04
367 8 0.01
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (344 bp):
ATTTAATTTTTATTATTATTATTTTTCTGTTATACTTTCCTTTGTGGACTGATTTTGAGTGTCCA
AGTAAAAATAAAATCCACAAAAGTTAGCAATTAGATCCTTTGACTTGATTTATTAATTTAAATTT
AAATTTTTATTTATATTTAAAAAATTTTATAAATATAAATTAATAATAAATTTAAATAAAAAATT
TTATAATAATTTTTTATTTTTTTAATTATATATATCATGTTTATGTTTAAAAATACATATATATA
TATAAATAATATTTATAATATTATATTATAAATATTTAAAATTATGTAAAATAATTAATATATTA
TATTATTTTATAATTTATA
Found at i:370570 original size:13 final size:13
Alignment explanation
Indices: 370521--370572 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
370511 TTTAATATTT
370521 TAAAAAA-TTAAA
1 TAAAAAATTTAAA
370533 TAAAAATATTATATTAA
1 TAAAAA-ATT-TA--AA
*
370550 TAATAAATTTAAA
1 TAAAAAATTTAAA
370563 TAAAAAATTT
1 TAAAAAATTT
370573 TATTATAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
12 6 0.18
13 12 0.36
14 1 0.03
15 4 0.12
16 3 0.09
17 7 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAAAAATTTAAA
Found at i:371162 original size:21 final size:21
Alignment explanation
Indices: 371137--371175 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
371127 TTTTTAAGTT
371137 TTTTTTA-AATTTATTTTACC
1 TTTTTTATAATTTATTTTACC
371157 TTTTTTATAATTTATTTTA
1 TTTTTTATAATTTATTTTA
371176 TATTATTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTTATAATTTATTTTACC
Found at i:371322 original size:10 final size:10
Alignment explanation
Indices: 371289--371336 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
371279 TAGTTGAAAA
371289 AAAGTAAAGAG
1 AAAG-AAAGAG
* *
371300 AAAGGAAGGG
1 AAAGAAAGAG
*
371310 AAATAAAGAG
1 AAAGAAAGAG
*
371320 AAAGAAAAAG
1 AAAGAAAGAG
371330 AAAGAAA
1 AAAGAAA
371337 TAAGGAAAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 26 0.87
11 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (10 bp):
AAAGAAAGAG
Found at i:371332 original size:20 final size:20
Alignment explanation
Indices: 371284--371332 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
371274 TTTTTTAGTT
*
371284 GAAAAA-AAGTAAAGAGAAA
1 GAAAAAGAAATAAAGAGAAA
* **
371303 GGAAGGGAAATAAAGAGAAA
1 GAAAAAGAAATAAAGAGAAA
371323 GAAAAAGAAA
1 GAAAAAGAAA
371333 GAAATAAGGA
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (20 bp):
GAAAAAGAAATAAAGAGAAA
Found at i:374343 original size:20 final size:19
Alignment explanation
Indices: 374319--374363 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
374309 TGAAAAAATA
374319 TAAAAAATGGAAATTTTTG
1 TAAAAAATGGAAATTTTTG
374338 -AAAAAATGGAAATTTTTG
1 TAAAAAATGGAAATTTTTG
374356 TGAAAAAA
1 T-AAAAAA
374364 ATATTTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 18 0.75
20 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (19 bp):
TAAAAAATGGAAATTTTTG
Found at i:375742 original size:2 final size:2
Alignment explanation
Indices: 375737--375771 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
375727 TGCATACATG
375737 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
375772 CTGATTTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:381757 original size:19 final size:19
Alignment explanation
Indices: 381733--381769 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
381723 TTAATTTGAA
* *
381733 TATTTTTTATTTTTAAAAT
1 TATTTTATATATTTAAAAT
381752 TATTTTATATATTTAAAA
1 TATTTTATATATTTAAAA
381770 AATTAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTATATATTTAAAAT
Found at i:382091 original size:12 final size:12
Alignment explanation
Indices: 382074--382109 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
382064 AAAAAATGAT
*
382074 ATATAAGATAAA
1 ATATAATATAAA
382086 ATATAATATAAA
1 ATATAATATAAA
*
382098 AAATAATATAAA
1 ATATAATATAAA
382110 TTTAATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:382145 original size:20 final size:18
Alignment explanation
Indices: 382120--382199 Score: 66
Period size: 20 Copynumber: 4.6 Consensus size: 18
382110 TTTAATTGAA
382120 TATATAAATATATTATGATT
1 TATAT-AATATATTAT-ATT
382140 TATATAATATA--A-A-T
1 TATATAATATATTATATT
*
382154 TAT-TAATATATTAAAATT
1 TATATAATATATT-ATATT
382172 TATATAAATATATTATATT
1 TATAT-AATATATTATATT
382191 T-TA-AATATA
1 TATATAATATA
382200 ATTAAAATAT
Statistics
Matches: 52, Mismatches: 1, Indels: 18
0.73 0.01 0.25
Matches are distributed among these distances:
13 7 0.13
14 4 0.08
15 1 0.02
16 7 0.13
17 2 0.04
18 6 0.12
19 12 0.23
20 13 0.25
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (18 bp):
TATATAATATATTATATT
Found at i:382163 original size:32 final size:31
Alignment explanation
Indices: 382126--382187 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
382116 TGAATATATA
**
382126 AATATATTATGATTTATATAATATAAATTATT
1 AATATATTAAAATTTATATAA-ATAAATTATT
*
382158 AATATATTAAAATTTATATAAATATATTAT
1 AATATATTAAAATTTATATAAATAAATTAT
382188 ATTTTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
AATATATTAAAATTTATATAAATAAATTATT
Found at i:382187 original size:52 final size:47
Alignment explanation
Indices: 382120--382217 Score: 133
Period size: 52 Copynumber: 2.0 Consensus size: 47
382110 TTTAATTGAA
* *
382120 TATATAAATATATTATGATTTATATAATATAAATTATTAATATATTAAAATT
1 TATATAAATATATTAT-ATTT-TA-AATAT-AATTA-AAATATATAAAAATT
382172 TATATAAATATATTATATTTTAAATATAATTAAAATATATAAAAAT
1 TATATAAATATATTATATTTTAAATATAATTAAAATATATAAAAAT
382218 AGATATCTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
47 12 0.27
48 5 0.11
49 5 0.11
50 2 0.05
51 4 0.09
52 16 0.36
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (47 bp):
TATATAAATATATTATATTTTAAATATAATTAAAATATATAAAAATT
Found at i:382188 original size:25 final size:24
Alignment explanation
Indices: 382120--382190 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
382110 TTTAATTGAA
* *
382120 TATATAAATATATTATGATTTATAT
1 TATATAAATATATTAT-ATTAAAAT
* *
382145 AATATAAATTATTAATATATTAAAATT
1 TATATAAA-TA-TATTATATTAAAA-T
382172 TATATAAATATATTATATT
1 TATATAAATATATTATATT
382191 TTAAATATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 15 0.41
26 9 0.24
27 13 0.35
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
TATATAAATATATTATATTAAAAT
Found at i:391255 original size:2 final size:2
Alignment explanation
Indices: 391248--391293 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
391238 CATACTTAAA
*
391248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
391290 AT AT
1 AT AT
391294 GAATATTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:392852 original size:35 final size:34
Alignment explanation
Indices: 392804--392901 Score: 112
Period size: 33 Copynumber: 2.9 Consensus size: 34
392794 ATTCAGTTAA
*
392804 ATTTAAA-TT-ATTATTTAAATAATTAAAAATTTT
1 ATTTAAATTTAATTATTTAAATAA-TAAAAATATT
*
392837 ATTTAAATTTAATTATTAAAAT-ATAAAAATATT
1 ATTTAAATTTAATTATTTAAATAATAAAAATATT
*
392870 ATTAATAATTTAATTTATTTTAAATAATAAAA
1 ATTTA-AATTTAA-TTA-TTTAAATAATAAAA
392902 TACGATTATC
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
33 20 0.36
34 10 0.18
35 13 0.24
36 6 0.11
37 6 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
ATTTAAATTTAATTATTTAAATAATAAAAATATT
Found at i:396465 original size:3 final size:3
Alignment explanation
Indices: 396457--396494 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
396447 AAAACACAAA
*
396457 TAT TAT TAT TAT TAT TAT TAT TAAT TA- TAT TAT AAT TA
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TA
396495 AATAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:396941 original size:2 final size:2
Alignment explanation
Indices: 396934--396965 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
396924 ACATGTTCGC
396934 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
396966 CATGCAGCTA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:397117 original size:17 final size:17
Alignment explanation
Indices: 397069--397133 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
397059 GTATTTTAAT
*
397069 ATTTATAT-AATA-CAA
1 ATTTATATAAATATAAA
397084 A-TTA-ATAACATATTAAA
1 ATTTATATAA-ATA-TAAA
397101 ATTTATATAAATATAAA
1 ATTTATATAAATATAAA
397118 ATATT-TATAAATATAA
1 AT-TTATATAAATATAA
397134 TTTTAATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 2 0.05
14 4 0.10
15 4 0.10
17 20 0.48
18 8 0.19
19 4 0.10
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTATATAAATATAAA
Found at i:397123 original size:19 final size:19
Alignment explanation
Indices: 397088--397126 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
397078 ATACAAATTA
*
397088 ATAACATATTAAAATTTAT
1 ATAACATATAAAAATTTAT
397107 ATAA-ATATAAAATATTTAT
1 ATAACATATAAAA-ATTTAT
397126 A
1 A
397127 AATATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAACATATAAAAATTTAT
Found at i:397373 original size:2 final size:2
Alignment explanation
Indices: 397366--397414 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
397356 TTCAGGCTGA
*
397366 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
397408 AT AT AT A
1 AT AT AT A
397415 CACACACATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:399065 original size:13 final size:12
Alignment explanation
Indices: 399038--399077 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
399028 TCATATATAA
399038 TTATATCAT-TT
1 TTATATCATATT
*
399049 TTATATTATTATT
1 TTATATCA-TATT
399062 TTATATCATATT
1 TTATATCATATT
399074 TTAT
1 TTAT
399078 GTAATGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 7 0.28
12 9 0.36
13 9 0.36
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATATCATATT
Found at i:399087 original size:24 final size:24
Alignment explanation
Indices: 399038--399097 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
399028 TCATATATAA
* *
399038 TTATATCATTTTTATATTATTATT
1 TTATATCATTTTTATAGTAATATT
*
399062 TTATATCATATTTTAT-GTAATGTT
1 TTATATCAT-TTTTATAGTAATATT
*
399086 TTA-ATTATTTTT
1 TTATATCATTTTT
399098 TAATTGTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 4 0.13
23 4 0.13
24 17 0.55
25 6 0.19
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (24 bp):
TTATATCATTTTTATAGTAATATT
Found at i:399549 original size:27 final size:27
Alignment explanation
Indices: 399518--399597 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 27
399508 ATATCTACAA
399518 TCTTTTTTCTTTCTACTTATTATC-CC
1 TCTTTTTTCTTTCTACTTATTATCACC
399544 -C-----TCTTTCTACTTATTATCACC
1 TCTTTTTTCTTTCTACTTATTATCACC
*
399565 TCTTTTTTCTTTTTACTTATTATCACC
1 TCTTTTTTCTTTCTACTTATTATCACC
399592 TCTTTT
1 TCTTTT
399598 ATGATATATA
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
20 17 0.37
21 2 0.04
22 1 0.02
25 1 0.02
27 25 0.54
ACGTcount: A:0.14, C:0.26, G:0.00, T:0.60
Consensus pattern (27 bp):
TCTTTTTTCTTTCTACTTATTATCACC
Found at i:399550 original size:20 final size:20
Alignment explanation
Indices: 399525--399569 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
399515 CAATCTTTTT
*
399525 TCTTTCTACTTATTATCCCC
1 TCTTTCTACTTATTATCACC
399545 TCTTTCTACTTATTATCACC
1 TCTTTCTACTTATTATCACC
399565 TCTTT
1 TCTTT
399570 TTTCTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.31, G:0.00, T:0.53
Consensus pattern (20 bp):
TCTTTCTACTTATTATCACC
Found at i:399587 original size:47 final size:49
Alignment explanation
Indices: 399506--399634 Score: 176
Period size: 47 Copynumber: 2.7 Consensus size: 49
399496 TTAAATTTTA
* *
399506 ATATATCTACAATCTTTTTTCTTTCTACTTATTATCCCCTCTTTCTACT-T
1 ATATATCTACAATCTTTTTTCTTTTTACTTATTATCACCTCTTT-TA-TAT
*
399556 AT-TATC-AC-CTCTTTTTTCTTTTTACTTATTATCACCTCTTTTATGAT
1 ATATATCTACAATCTTTTTTCTTTTTACTTATTATCACCTCTTTTAT-AT
399603 ATATATCTACAATCTTTTTTCTTTTTACTTAT
1 ATATATCTACAATCTTTTTTCTTTTTACTTAT
399635 AAAAATTAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
45 1 0.01
46 2 0.03
47 33 0.47
48 6 0.09
49 6 0.09
50 22 0.31
ACGTcount: A:0.21, C:0.22, G:0.01, T:0.57
Consensus pattern (49 bp):
ATATATCTACAATCTTTTTTCTTTTTACTTATTATCACCTCTTTTATAT
Found at i:399925 original size:24 final size:26
Alignment explanation
Indices: 399890--399952 Score: 87
Period size: 24 Copynumber: 2.5 Consensus size: 26
399880 GAATTAACCT
399890 AATA-AAAAATAAATTTAA-TA-AAA
1 AATATAAAAATAAATTTAATTATAAA
399913 AATATAAAAATAAATTTAATTATAAA
1 AATATAAAAATAAATTTAATTATAAA
*
399939 ATATATAATAATAA
1 A-ATATAAAAATAA
399953 TATAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
23 4 0.11
24 14 0.40
25 2 0.06
26 4 0.11
27 11 0.31
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (26 bp):
AATATAAAAATAAATTTAATTATAAA
Found at i:399936 original size:18 final size:17
Alignment explanation
Indices: 399913--399967 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 17
399903 TTTAATAAAA
399913 AATATAAAAATAAATTT
1 AATATAAAAATAAATTT
*
399930 AATTATAAAATATATAATAAT
1 AA-TATAAAA-ATA-AAT-TT
399951 AATATAAAAATAAATTT
1 AATATAAAAATAAATTT
399968 TAAAACTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 3 0.09
18 10 0.31
19 6 0.19
20 10 0.31
21 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATATAAAAATAAATTT
Found at i:401938 original size:28 final size:30
Alignment explanation
Indices: 401905--401963 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
401895 ATAAATTTTG
401905 ATATATTTATATTATTTTTTA-TAT-CTTATC
1 ATAT-TTTA-ATTATTTTTTATTATACTTATC
401935 ATATTTTAATTATTTTTTATTATACTTAT
1 ATATTTTAATTATTTTTTATTATACTTAT
401964 ATCTTATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 11 0.41
29 7 0.26
30 9 0.33
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (30 bp):
ATATTTTAATTATTTTTTATTATACTTATC
Found at i:402996 original size:22 final size:21
Alignment explanation
Indices: 402971--403015 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
402961 ACTAAACACT
*
402971 ATAAAATAAAAAAAATTTAAAA
1 ATAAAAT-AAAAAAATTAAAAA
*
402993 ATAAAATTAAAAAATTAAAAA
1 ATAAAATAAAAAAATTAAAAA
403014 AT
1 AT
403016 TATTCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
ATAAAATAAAAAAATTAAAAA
Found at i:403576 original size:15 final size:16
Alignment explanation
Indices: 403550--403590 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
403540 TCTGACACCT
403550 ATAATAATTAATTATA
1 ATAATAATTAATTATA
403566 ATAAT-ATTAATTATA
1 ATAATAATTAATTATA
* *
403581 TTTATAATTA
1 ATAATAATTA
403591 TGATAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAATAATTAATTATA
Found at i:403833 original size:2 final size:2
Alignment explanation
Indices: 403828--403876 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
403818 GCATATATGA
403828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
403870 AT AT AT A
1 AT AT AT A
403877 ACTTCAGCCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:412742 original size:2 final size:2
Alignment explanation
Indices: 412737--412767 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
412727 TATTGAAAGC
412737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
412768 ATAAAGACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:413266 original size:20 final size:21
Alignment explanation
Indices: 413227--413267 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
413217 TTTAATTATA
413227 AAAATATATAAATATTAAAAT
1 AAAATATATAAATATTAAAAT
* *
413248 AAAATA-ATATATTTTAAAAT
1 AAAATATATAAATATTAAAAT
413268 TATTTACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATATATAAATATTAAAAT
Found at i:415089 original size:32 final size:33
Alignment explanation
Indices: 415048--415113 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
415038 CCATTAAATT
* *
415048 AAATATATATTTTTATTAATTAATTTATTATTA
1 AAATATATATATTTAATAATTAATTTATTATTA
* *
415081 AAAT-TATATATTTAATATTTAATTTATTTTTA
1 AAATATATATATTTAATAATTAATTTATTATTA
415113 A
1 A
415114 TTGAATAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
AAATATATATATTTAATAATTAATTTATTATTA
Found at i:415542 original size:20 final size:20
Alignment explanation
Indices: 415513--415573 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
415503 TAAAATCAAT
* * *
415513 AATTAATTGAATTGATATAA
1 AATTAGTTGAATTAATAAAA
415533 AATTAGTTGAATTAATAAAA
1 AATTAGTTGAATTAATAAAA
415553 AATTAGATTGAAATT-ATAAAA
1 AATTAG-TTG-AATTAATAAAA
415574 TTTTAGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.64
21 9 0.25
22 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (20 bp):
AATTAGTTGAATTAATAAAA
Found at i:417221 original size:3 final size:3
Alignment explanation
Indices: 417213--417240 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
417203 CAAATATTTA
417213 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
417241 GTGGATTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:417574 original size:20 final size:20
Alignment explanation
Indices: 417529--417576 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
417519 AAATAGATAT
*
417529 ATATATTATATTTATAATAA
1 ATATATTAAATTTATAATAA
*
417549 AGATATTAAATTT-TAATAAA
1 ATATATTAAATTTATAAT-AA
417569 ATATATTA
1 ATATATTA
417577 TTAAGCAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATATATTAAATTTATAATAA
Found at i:418273 original size:14 final size:14
Alignment explanation
Indices: 418254--418292 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 14
418244 CATTTTAATT
418254 TTTTTAATTATTTA
1 TTTTTAATTATTTA
418268 TTTTTAA-TA-TT-
1 TTTTTAATTATTTA
418279 TTTTT-ATTATTTA
1 TTTTTAATTATTTA
418292 T
1 T
418293 GATATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
10 1 0.05
11 7 0.32
12 4 0.18
13 3 0.14
14 7 0.32
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTAATTATTTA
Found at i:418280 original size:24 final size:23
Alignment explanation
Indices: 418246--418292 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
418236 ATCTCTTCCA
418246 TTTTAATTTTTTTAATTATTTAT
1 TTTTAATTTTTTTAATTATTTAT
*
418269 TTTTAATATTTTTTTATTATTTAT
1 TTTTAAT-TTTTTTAATTATTTAT
418293 GATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTAATTTTTTTAATTATTTAT
Found at i:418300 original size:25 final size:25
Alignment explanation
Indices: 418251--418345 Score: 68
Period size: 25 Copynumber: 3.6 Consensus size: 25
418241 TTCCATTTTA
* *
418251 ATTTTTTTAATTATTTATTTTTAAT
1 ATTTTTTTAATTATTTATATATAAT
418276 ATTTTTTT-ATTATTTATGATATAAT
1 ATTTTTTTAATTATTTAT-ATATAAT
* *
418301 TTTAATATATTTTATTATTTA-ATATAAAT
1 ATT--T-T-TTTAATTATTTATATAT-AAT
**
418330 ATAATTTTAATTATTT
1 ATTTTTTTAATTATTT
418346 TTAATAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
24 9 0.16
25 25 0.45
26 1 0.02
27 1 0.02
28 5 0.09
29 7 0.12
30 8 0.14
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (25 bp):
ATTTTTTTAATTATTTATATATAAT
Found at i:418314 original size:23 final size:24
Alignment explanation
Indices: 418288--418338 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
418278 TTTTTTATTA
* *
418288 TTTATGATATAATTTTAATAT-AT
1 TTTATGATATAATATAAATATAAT
* *
418311 TTTATTATTTAATATAAATATAAT
1 TTTATGATATAATATAAATATAAT
418335 TTTA
1 TTTA
418339 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTATGATATAATATAAATATAAT
Found at i:418319 original size:33 final size:33
Alignment explanation
Indices: 418269--418347 Score: 94
Period size: 34 Copynumber: 2.5 Consensus size: 33
418259 AATTATTTAT
* *
418269 TTTTAATAT-TTTTTTA-TT-ATTTATGATATAA
1 TTTTAATATATTTTTTATTTAATATA-AATATAA
418300 TTTTAATATATTTTATTATTTAATATAAATATAA
1 TTTTAATATATTTT-TTATTTAATATAAATATAA
418334 TTTTAAT-TATTTTT
1 TTTTAATATATTTTT
418348 AATAAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
31 9 0.21
32 5 0.12
33 9 0.21
34 15 0.36
35 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (33 bp):
TTTTAATATATTTTTTATTTAATATAAATATAA
Found at i:418356 original size:27 final size:27
Alignment explanation
Indices: 418318--418400 Score: 123
Period size: 27 Copynumber: 3.1 Consensus size: 27
418308 TATTTTATTA
* *
418318 TTTAATATAAATATAATTTTAATTATT
1 TTTAATAAAAATATAATTTTAATAATT
* *
418345 TTTAATAAAAATATACTTGTAATAATT
1 TTTAATAAAAATATAATTTTAATAATT
418372 TTTAATAAAAA-ATAATTTTAATAATT
1 TTTAATAAAAATATAATTTTAATAATT
418398 TTT
1 TTT
418401 TATTTTTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
26 16 0.32
27 34 0.68
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
TTTAATAAAAATATAATTTTAATAATT
Found at i:419214 original size:32 final size:30
Alignment explanation
Indices: 419178--419238 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 30
419168 TAGTTGGTCC
419178 AAAAGTTTA-TTTTACTATTAATTATATTTATT
1 AAAAGTTTATTTTTA-TATTAA-TAT-TTTATT
419210 AAAAGTTTATTTTTATATTAATATTTTAT
1 AAAAGTTTATTTTTATATTAATATTTTAT
419239 AATTAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 5 0.18
31 3 0.11
32 15 0.54
33 5 0.18
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (30 bp):
AAAAGTTTATTTTTATATTAATATTTTATT
Found at i:419814 original size:4 final size:4
Alignment explanation
Indices: 419807--419833 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
419797 AATATATTTA
419807 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
419834 ATTGTTCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:421230 original size:17 final size:19
Alignment explanation
Indices: 421208--421245 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
421198 ATAAAATTGT
421208 TATTTATTAA-A-TAAATA
1 TATTTATTAATATTAAATA
421225 TATTTATTAATATTAAATA
1 TATTTATTAATATTAAATA
421244 TA
1 TA
421246 ATAAATATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 1 0.05
19 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTATTAATATTAAATA
Found at i:423947 original size:2 final size:2
Alignment explanation
Indices: 423942--423977 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
423932 AAAAGAAACA
423942 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
423978 TTTACATGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:425087 original size:4 final size:4
Alignment explanation
Indices: 425073--425147 Score: 68
Period size: 4 Copynumber: 19.8 Consensus size: 4
425063 AGGCTTAAAT
* * * * *
425073 ATAC CTAC ATAC ATAC ATAC AT-- ATAT ATAT ATAC ATAC ATAT ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
425119 ATAT ATAC --AC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
425148 TATATATATA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
2 4 0.06
4 58 0.94
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (4 bp):
ATAC
Found at i:425100 original size:2 final size:2
Alignment explanation
Indices: 425093--425171 Score: 86
Period size: 2 Copynumber: 39.5 Consensus size: 2
425083 ACATACATAC
* * * * *
425093 AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AC AC AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
425135 AC AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
425172 AAGCCCTTGA
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (2 bp):
AT
Found at i:425108 original size:18 final size:18
Alignment explanation
Indices: 425085--425171 Score: 115
Period size: 18 Copynumber: 4.9 Consensus size: 18
425075 ACCTACATAC
425085 ATACATACATATATATAT
1 ATACATACATATATATAT
425103 ATACATACATATATATAT
1 ATACATACATATATATAT
* * *
425121 AT--ATACACATACATAC
1 ATACATACATATATATAT
425137 ATACATACATATATATAT
1 ATACATACATATATATAT
* *
425155 ATATATATATATATATA
1 ATACATACATATATATA
425172 AAGCCCTTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
16 13 0.22
18 46 0.78
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (18 bp):
ATACATACATATATATAT
Found at i:425141 original size:34 final size:34
Alignment explanation
Indices: 425089--425159 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
425079 ACATACATAC
* * *
425089 ATACATATATATATATACATACATATATATATAT
1 ATACACATACATACATACATACATATATATATAT
425123 ATACACATACATACATACATACATATATATATAT
1 ATACACATACATACATACATACATATATATATAT
425157 ATA
1 ATA
425160 TATATATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.37
Consensus pattern (34 bp):
ATACACATACATACATACATACATATATATATAT
Found at i:426355 original size:6 final size:5
Alignment explanation
Indices: 426345--426505 Score: 51
Period size: 5 Copynumber: 32.8 Consensus size: 5
426335 TATTTTATCG
* *
426345 TATTA TAATTA TGATTA TATTA TTTTA TATTTA TATAAA TATTGA TATGT-
1 TATTA T-ATTA T-ATTA TATTA TATTA TA-TTA TAT-TA TATT-A TAT-TA
* * **
426395 TAATA -ATT- TA-TA TATATA AATTA TAAAA TATT- TA-TA TATTTA TATTA
1 TATTA TATTA TATTA TAT-TA TATTA TATTA TATTA TATTA TA-TTA TATTA
* * * *
426442 TGTT- TATT- TATT- T-TTA TATTA TTTTA T-TTT TAATTA TATTT TAATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA T-ATTA TATTA T-ATTA
426489 T-TTA T-TTA TATTA TATT
1 TATTA TATTA TATTA TATT
426506 TAATATTATT
Statistics
Matches: 117, Mismatches: 20, Indels: 38
0.67 0.11 0.22
Matches are distributed among these distances:
3 4 0.03
4 30 0.26
5 44 0.38
6 38 0.32
7 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:426447 original size:19 final size:18
Alignment explanation
Indices: 426425--426515 Score: 61
Period size: 21 Copynumber: 5.1 Consensus size: 18
426415 TTATAAAATA
426425 TTTATATATTTATATTAT
1 TTTATATATTTATATTAT
*
426443 GTTTATTTATTTTTATATTAT
1 -TTTA--TATATTTATATTAT
426464 TTTAT-T-TTTA-ATTAT
1 TTTATATATTTATATTAT
426479 ATTT-TA-A-TTAT-TTAT
1 -TTTATATATTTATATTAT
426494 TTATATTATATTTAATATTAT
1 TT-TA-TATATTT-ATATTAT
426515 T
1 T
426516 AAGTTTAATA
Statistics
Matches: 58, Mismatches: 1, Indels: 24
0.70 0.01 0.29
Matches are distributed among these distances:
14 2 0.03
15 14 0.24
16 7 0.12
17 3 0.05
18 2 0.03
19 6 0.10
20 6 0.10
21 18 0.31
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTATATATTTATATTAT
Found at i:426459 original size:21 final size:22
Alignment explanation
Indices: 426423--426505 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 22
426413 AATTATAAAA
426423 TATTTATATATTTATATTATGTT
1 TATTTATATATTTATATTAT-TT
426446 TATTTAT-T-TTTATATTATTT
1 TATTTATATATTTATATTATTT
*
426466 TATTT-T-TAATTATATT-TTAAT
1 TATTTATATATTTATATTATT--T
*
426487 TATTTATTTATATTATATT
1 TATTTATATAT-TTATATT
426506 TAATATTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.08
20 14 0.27
21 16 0.31
22 2 0.04
23 9 0.17
24 7 0.13
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (22 bp):
TATTTATATATTTATATTATTT
Found at i:426463 original size:15 final size:14
Alignment explanation
Indices: 426445--426495 Score: 63
Period size: 16 Copynumber: 3.7 Consensus size: 14
426435 TATATTATGT
426445 TTATTTATTTTTATA
1 TTATTTATTTTTA-A
426460 TTATTTTATTTTTAA
1 TTA-TTTATTTTTAA
426475 TTA--TA-TTTTAA
1 TTATTTATTTTTAA
426486 TTATTTATTT
1 TTATTTATTT
426496 ATATTATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
11 9 0.28
12 2 0.06
13 2 0.06
14 2 0.06
15 7 0.22
16 10 0.31
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTTATTTTTAA
Found at i:426483 original size:11 final size:11
Alignment explanation
Indices: 426465--426506 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
426455 TTATATTATT
426465 TTAT-TTTTAA
1 TTATATTTTAA
426475 TTATATTTTAA
1 TTATATTTTAA
*
426486 TTATTTATTTATA
1 TTATAT-TTTA-A
426499 TTATATTT
1 TTATATTT
426507 AATATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 4 0.15
11 11 0.41
12 6 0.22
13 6 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATATTTTAA
Found at i:426505 original size:15 final size:14
Alignment explanation
Indices: 426422--426507 Score: 66
Period size: 15 Copynumber: 5.8 Consensus size: 14
426412 AAATTATAAA
*
426422 ATATTTATATATTT
1 ATATTTATTTATTT
*
426436 ATATTATGTTTATTT
1 ATATT-TATTTATTT
*
426451 ATTTTTATATTATTTT
1 ATATTTAT-TTA-TTT
*
426467 ATTTTTAATTATATTT
1 ATATTT-ATT-TATTT
*
426483 -TAATTATTTATTT
1 ATATTTATTTATTT
426496 ATATTATATTTA
1 ATATT-TATTTA
426508 ATATTATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
13 5 0.09
14 13 0.22
15 23 0.40
16 13 0.22
17 4 0.07
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (14 bp):
ATATTTATTTATTT
Found at i:426527 original size:24 final size:23
Alignment explanation
Indices: 426470--426524 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
426460 TTATTTTATT
* *
426470 TTTAATTATATTTTAATTATTTA
1 TTTAATTATATTTAAATTATTAA
426493 TTTATATTATATTTAATATTATTAA
1 TTTA-ATTATATTTAA-ATTATTAA
426518 GTTTAAT
1 -TTTAAT
426525 ATAAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 4 0.15
24 10 0.37
25 9 0.33
26 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTAATTATATTTAAATTATTAA
Found at i:427485 original size:2 final size:2
Alignment explanation
Indices: 427478--427521 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
427468 TAATTATTTT
* * *
427478 TA TA TA TA T- TT TA CA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
427519 TA T
1 TA T
427522 TTTACCCACA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:434721 original size:9 final size:9
Alignment explanation
Indices: 434707--434738 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
434697 TAATATTCTG
434707 AAAAAAAGA
1 AAAAAAAGA
434716 AAAAAAAGA
1 AAAAAAAGA
434725 AAAGAAAAGA
1 AAA-AAAAGA
434735 AAAA
1 AAAA
434739 GAGCCATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:435723 original size:27 final size:28
Alignment explanation
Indices: 435680--435733 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
435670 ATAAAATTTA
* * *
435680 AAATATAAGTTTAAAATATATAATAAAT
1 AAATATAAATTTAAAATAAAAAATAAAT
435708 AAAT-TAAATTTAAAATAAAAAATAAA
1 AAATATAAATTTAAAATAAAAAATAAA
435734 CTCTACTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (28 bp):
AAATATAAATTTAAAATAAAAAATAAAT
Found at i:435810 original size:12 final size:11
Alignment explanation
Indices: 435789--435819 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
435779 TTATTTTTAT
435789 TTTAAATTAAA
1 TTTAAATTAAA
435800 TTTAAACTTAAA
1 TTTAAA-TTAAA
435812 TTTAAATT
1 TTTAAATT
435820 TTTTGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:436469 original size:17 final size:16
Alignment explanation
Indices: 436449--436491 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
436439 TCAAAAGATT
436449 ATAAAAAATAAAAAATA
1 ATAAAAAA-AAAAAATA
*
436466 ATAATAAAAATAAAATA
1 ATAA-AAAAAAAAAATA
436483 ATAAAAAAA
1 ATAAAAAAA
436492 GTTTGTCAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 15 0.62
18 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
ATAAAAAAAAAAAATA
Found at i:436475 original size:14 final size:13
Alignment explanation
Indices: 436451--436491 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 13
436441 AAAAGATTAT
436451 AAAA-AATAAAAA
1 AAAATAATAAAAA
*
436463 ATAATAATAAAAA
1 AAAATAATAAAAA
436476 TAAAATAATAAAAA
1 -AAAATAATAAAAA
436490 AA
1 AA
436492 GTTTGTCAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 3 0.12
13 10 0.40
14 12 0.48
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAATAATAAAAA
Found at i:437535 original size:20 final size:20
Alignment explanation
Indices: 437512--437567 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
437502 GATTCAAGAC
437512 TTTGATGTAATTTTATAAAT
1 TTTGATGTAATTTTATAAAT
* * **
437532 TTTGATGTCA-TCTAGGAAT
1 TTTGATGTAATTTTATAAAT
437551 TTTGATGTAATTTTATA
1 TTTGATGTAATTTTATA
437568 TATGTTGAAG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (20 bp):
TTTGATGTAATTTTATAAAT
Found at i:437566 original size:39 final size:39
Alignment explanation
Indices: 437512--437586 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
437502 GATTCAAGAC
* *
437512 TTTGATGTAATTTTATAAATTTTGATGTCATCTAGGAAT
1 TTTGATGTAATTTTATAAATGTTGAAGTCATCTAGGAAT
* *
437551 TTTGATGTAATTTTATATATGTTGAAGTCATTTAGG
1 TTTGATGTAATTTTATAAATGTTGAAGTCATCTAGG
437587 TTATTTTCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.29, C:0.04, G:0.17, T:0.49
Consensus pattern (39 bp):
TTTGATGTAATTTTATAAATGTTGAAGTCATCTAGGAAT
Found at i:437631 original size:58 final size:58
Alignment explanation
Indices: 437545--437681 Score: 168
Period size: 58 Copynumber: 2.3 Consensus size: 58
437535 GATGTCATCT
* * *
437545 AGGAATTTTGATGTAATTTTATATATGTTGAAGTCATTTAGGTTA-TTTTCTATTATTTA
1 AGGAATTTT-ATGTAATTTTAAAAATGTTGAAGTCATTTAGATTATTTTTC-ATTATTTA
* *
437604 AGGACTTTTATGTAATTTTAAAAATGTTGGAGTCATTTAGATTATTTTTCATTATTTA
1 AGGAATTTTATGTAATTTTAAAAATGTTGAAGTCATTTAGATTATTTTTCATTATTTA
* * **
437662 AAGATTTTTATACAATTTTA
1 AGGAATTTTATGTAATTTTA
437682 TACATCGTAG
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
58 55 0.81
59 13 0.19
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.51
Consensus pattern (58 bp):
AGGAATTTTATGTAATTTTAAAAATGTTGAAGTCATTTAGATTATTTTTCATTATTTA
Found at i:440128 original size:2 final size:2
Alignment explanation
Indices: 440121--440167 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
440111 GGCTTCCATG
440121 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
440163 TA TA T
1 TA TA T
440168 GCCTTTATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:441397 original size:64 final size:64
Alignment explanation
Indices: 441321--441449 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
441311 GTTATGTTTG
*
441321 ACCTTTTGTGTTGAAAATTAATTATTTGTCACATATGGAAGTCCATTCCCATTGATATTGAGTT
1 ACCTTTTATGTTGAAAATTAATTATTTGTCACATATGGAAGTCCATTCCCATTGATATTGAGTT
* * *
441385 ACCTTTTATGTTGAGAATTAATTATTTGTCACATATGGAAGTCCATTCCCCTTGTTATTGAGTT
1 ACCTTTTATGTTGAAAATTAATTATTTGTCACATATGGAAGTCCATTCCCATTGATATTGAGTT
441449 A
1 A
441450 TTTAAAACAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.43
Consensus pattern (64 bp):
ACCTTTTATGTTGAAAATTAATTATTTGTCACATATGGAAGTCCATTCCCATTGATATTGAGTT
Found at i:448186 original size:20 final size:20
Alignment explanation
Indices: 448139--448213 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
448129 AAAAAGACAT
*
448139 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
448158 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
448179 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
448199 AATGTATCGATACAT
1 AATGTATCGATACAT
448214 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:448207 original size:40 final size:39
Alignment explanation
Indices: 448136--448213 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
448126 GGTAAAAAGA
* *
448136 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
448175 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
448214 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:450903 original size:20 final size:20
Alignment explanation
Indices: 450878--450918 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
450868 ATTTTATCAA
*
450878 AATTTATAT-AAATATATAAT
1 AATTTAAATAAAAT-TATAAT
450898 AATTTAAATAAAATTATAAT
1 AATTTAAATAAAATTATAAT
450918 A
1 A
450919 TAAAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTAAATAAAATTATAAT
Found at i:451685 original size:2 final size:2
Alignment explanation
Indices: 451678--451723 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
451668 ACACAATCTC
* *
451678 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
451720 -T AT A
1 AT AT A
451724 AGAGAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:454731 original size:21 final size:21
Alignment explanation
Indices: 454702--454768 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
454692 ATTATATAAT
454702 AAAAA-ATTGATTTTTCTTAA
1 AAAAAGATTGATTTTTCTTAA
***
454722 AAAAAGATTGATCCCTCTTAA
1 AAAAAGATTGATTTTTCTTAA
454743 AAAAATGATT-ATTTCTT-TTAA
1 AAAAA-GATTGATTT-TTCTTAA
454764 AAAAA
1 AAAAA
454769 AGAGCAATCT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 5 0.13
21 28 0.74
22 5 0.13
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (21 bp):
AAAAAGATTGATTTTTCTTAA
Found at i:456719 original size:29 final size:28
Alignment explanation
Indices: 456657--456719 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
456647 AATTAATTCG
* *
456657 TATTGAAATTTAATAATTAAAAAATATA
1 TATTAAAATTTAATAATTAAAAAATAAA
* *
456685 TTTTAAAACTTTAATTA-TAAAATAATAAA
1 TATTAAAA-TTTAATAATTAAAA-AATAAA
456714 TATTAA
1 TATTAA
456720 TATAAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
TATTAAAATTTAATAATTAAAAAATAAA
Found at i:457026 original size:17 final size:18
Alignment explanation
Indices: 457001--457051 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
456991 TTAATATTAA
457001 ATTTAAATAAAAAT-ATT
1 ATTTAAATAAAAATAATT
*
457018 ATTTTAATAAATAAATAATT
1 ATTTAAAT-AA-AAATAATT
* *
457038 ATTTGAATTAAAAT
1 ATTTAAATAAAAAT
457052 GTATCAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 7 0.25
18 6 0.21
19 5 0.18
20 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTTAAATAAAAATAATT
Found at i:457250 original size:22 final size:21
Alignment explanation
Indices: 457218--457270 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 21
457208 TTAGTGATCC
457218 ATTAAATATAAAAT-ATTTTTAA
1 ATTAAA-ATAAAATAATTTTT-A
457240 ATTAATAATAAAATAATTTTTA
1 ATTAA-AATAAAATAATTTTTA
457262 ATTAAAATA
1 ATTAAAATA
457271 TATGTATCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.14
22 18 0.62
23 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAAAATAAAATAATTTTTA
Found at i:459301 original size:2 final size:2
Alignment explanation
Indices: 459288--459404 Score: 95
Period size: 2 Copynumber: 62.0 Consensus size: 2
459278 ACTCTTTCAG
*
459288 AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * ** *
459330 GT AT AT A- AT A- AT A- AT A- AT A- AT A- AT CT -T TT TT GC AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
459365 AT AT AC AT GT 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
459405 TTTACAGAGA
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
1 7 0.07
2 87 0.93
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:459486 original size:21 final size:21
Alignment explanation
Indices: 459462--459503 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
459452 TATTAAATAC
*
459462 TTAAAACATTACTATTTATTA
1 TTAAAACATTACTATATATTA
*
459483 TTAAAACATTATTATATATTA
1 TTAAAACATTACTATATATTA
459504 ATATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAAACATTACTATATATTA
Found at i:459508 original size:24 final size:23
Alignment explanation
Indices: 459451--459513 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 23
459441 AATTTTTTTA
*
459451 ATATTAAATACTTAAAACATTACT
1 ATATT-AATACTTAAAACATTAAT
*
459475 AT-TTATTA-TTAAAACATTATTAT
1 ATATTAATACTTAAAACATTA--AT
*
459498 ATATTAATATTTAAAA
1 ATATTAATACTTAAAA
459514 TATGATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 11 0.34
22 3 0.09
23 5 0.16
24 7 0.22
25 6 0.19
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATTAATACTTAAAACATTAAT
Found at i:460847 original size:2 final size:2
Alignment explanation
Indices: 460842--460874 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
460832 ATATATGCAA
460842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
460875 CATTAGAATA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:462750 original size:18 final size:19
Alignment explanation
Indices: 462704--462752 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
462694 ACAATTAAAA
462704 TTATTTAAA-AAATTATTT
1 TTATTTAAATAAATTATTT
*
462722 TTATATT-AATATA-TATTT
1 TTAT-TTAAATAAATTATTT
462740 TTATTTAAATAAA
1 TTATTTAAATAAA
462753 AAATATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 2 0.08
18 20 0.77
19 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTTAAATAAATTATTT
Found at i:462776 original size:23 final size:25
Alignment explanation
Indices: 462729--462776 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
462719 TTTTTATATT
* *
462729 AATATATATTTTTATTTAAATAAAA
1 AATATATATTTTAAATTAAATAAAA
462754 AATATA-ATTTTAAATTAAA-AAAA
1 AATATATATTTTAAATTAAATAAAA
462777 CTCAAACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AATATATATTTTAAATTAAATAAAA
Found at i:463278 original size:24 final size:22
Alignment explanation
Indices: 463226--463278 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
463216 AAAAATAAAA
*
463226 TATATTTATTAAACTAAGTTAT
1 TATATTTATTAAAATAAGTTAT
*
463248 TGA-ATTTAATTAATAATAATTTAT
1 T-ATATTT-ATTAA-AATAAGTTAT
463272 TATATTT
1 TATATTT
463279 TTCTAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 5 0.20
23 7 0.28
24 13 0.52
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (22 bp):
TATATTTATTAAAATAAGTTAT
Found at i:464899 original size:32 final size:32
Alignment explanation
Indices: 464863--464936 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
464853 GACTATTCAA
* * *
464863 AATAAGAATTATTTTAAATAACTA-TTGTTTTG
1 AATAACAACTATTTTAAAT-ACTAGTTGTTATG
* *
464895 AATAACAGCTATTTTAAATAGTAGTTGTTATG
1 AATAACAACTATTTTAAATACTAGTTGTTATG
*
464927 AATAATAACT
1 AATAACAACT
464937 GTTAAATAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
31 3 0.09
32 31 0.91
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (32 bp):
AATAACAACTATTTTAAATACTAGTTGTTATG
Found at i:465969 original size:20 final size:20
Alignment explanation
Indices: 465946--465997 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
465936 ATTTTTATTT
465946 TATTATAAT-TTTATTTAAAA
1 TATT-TAATATTTATTTAAAA
*
465966 TATTTTATATTTATTT-AAA
1 TATTTAATATTTATTTAAAA
465985 T-TTTAATAGTTTA
1 TATTTAATA-TTTA
465998 ATAATTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 11 0.39
20 11 0.39
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TATTTAATATTTATTTAAAA
Done.