Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 10 of 20
Found at i:1499881 original size:20 final size:20
Alignment explanation
Indices: 1499837--1499874 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1499827 ATTAGCAGAT
1499837 TTAATTAAAATATATTTAAA
1 TTAATTAAAATATATTTAAA
1499857 TTAATTAACAAT-TATTTA
1 TTAATTAA-AATATATTTA
1499875 TAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATTAAAATATATTTAAA
Found at i:1500030 original size:2 final size:2
Alignment explanation
Indices: 1500023--1500049 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1500013 AGTGAAAACA
1500023 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
1500050 ACTCTCAAAC
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:1501361 original size:2 final size:2
Alignment explanation
Indices: 1501354--1501443 Score: 52
Period size: 2 Copynumber: 48.0 Consensus size: 2
1501344 CTATCAACTC
* *
1501354 AT AT AT AT AT AT AT AT AT AT GAT CAA AT AT AT A- AT -T AT AA AT
1 AT AT AT AT AT AT AT AT AT AT -AT -AT AT AT AT AT AT AT AT AT AT
* * *
1501396 AT A- AT AT AA AT -T AT -T AA AT AT AT A- AA AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1501433 TT AT AT -T AT AT
1 AT AT AT AT AT AT
1501444 TTACTTTTGA
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
1 8 0.12
2 56 0.84
3 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1501418 original size:21 final size:19
Alignment explanation
Indices: 1501379--1501429 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
1501369 TATATGATCA
1501379 AATATATAATTA-TAAATAT
1 AATATA-AATTATTAAATAT
1501398 AATATAAATTATTAAATAT
1 AATATAAATTATTAAATAT
1501417 -ATA-AAATATATTA
1 AATATAAAT-TATTA
1501430 TATTTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.13
18 13 0.43
19 13 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATAAATTATTAAATAT
Found at i:1501430 original size:21 final size:21
Alignment explanation
Indices: 1501378--1501430 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1501368 ATATATGATC
*
1501378 AAATATATAATTATAAATATA
1 AAATATATTATTATAAATATA
* *
1501399 ATATAAATTATTA-AATATATA
1 AAATATATTATTATAA-ATATA
1501420 AAATATATTAT
1 AAATATATTAT
1501431 ATTTATATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATATATTATTATAAATATA
Found at i:1507008 original size:2 final size:2
Alignment explanation
Indices: 1507003--1507027 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1506993 TGTGTGTGTG
1507003 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 T
1507028 TATTCTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1514561 original size:16 final size:17
Alignment explanation
Indices: 1514524--1514566 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1514514 AATAAAATAA
*
1514524 AATAAAATTAATTATTT
1 AATAAAATTAAATATTT
*
1514541 TATAAAA-TAAATATTT
1 AATAAAATTAAATATTT
1514557 AAT-AAATTAA
1 AATAAAATTAA
1514567 GAAAATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 3 0.14
16 13 0.59
17 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAAAATTAAATATTT
Found at i:1514622 original size:17 final size:18
Alignment explanation
Indices: 1514600--1514636 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1514590 TTAAATTAAT
1514600 TTATAATAAAATAAT-TA
1 TTATAATAAAATAATATA
*
1514617 TTATAATAAATTAATATA
1 TTATAATAAAATAATATA
1514635 TT
1 TT
1514637 TTAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATAATAAAATAATATA
Found at i:1514653 original size:14 final size:15
Alignment explanation
Indices: 1514623--1514660 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1514613 ATTATTATAA
1514623 TAAATTAATATATTT
1 TAAATTAATATATTT
*
1514638 TAAATTATTA-ATTT
1 TAAATTAATATATTT
1514652 TAAAATTAA
1 T-AAATTAA
1514661 ATTATGCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATTAATATATTT
Found at i:1514890 original size:21 final size:23
Alignment explanation
Indices: 1514866--1514908 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1514856 ATTTAAAGTA
1514866 ATTTTT-T-ATTAATAAAAAATT
1 ATTTTTATAATTAATAAAAAATT
1514887 ATTTTTAATAATTAATAAAAAA
1 ATTTTT-ATAATTAATAAAAAA
1514909 CAAATCCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
23 1 0.05
24 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTTTATAATTAATAAAAAATT
Found at i:1515298 original size:26 final size:27
Alignment explanation
Indices: 1515232--1515319 Score: 83
Period size: 26 Copynumber: 3.2 Consensus size: 27
1515222 TAAATATAAT
*
1515232 TATTTTAAAA-ATAATTAAAATATAATATAA
1 TATTTTAAAATAT-A-TATAATATAA-A-AA
* *
1515262 TTTTTTAAAATTTATATTAATAT-AAAA
1 TATTTTAAAATATATA-TAATATAAAAA
1515289 TATTTT-AAATATATATAATATAAAAA
1 TATTTTAAAATATATATAATATAAAAA
1515315 TATTT
1 TATTT
1515320 AATTATCATA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
25 6 0.12
26 17 0.34
27 7 0.14
28 1 0.02
29 3 0.06
30 15 0.30
31 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TATTTTAAAATATATATAATATAAAAA
Found at i:1516544 original size:25 final size:24
Alignment explanation
Indices: 1516507--1516555 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1516497 CCAACATTAA
* *
1516507 TAAAGTAATTTTTATCTTTTAGTTT
1 TAAACTAACTTTT-TCTTTTAGTTT
*
1516532 TAAACTAACTTTTTTTTTTAGTTT
1 TAAACTAACTTTTTCTTTTAGTTT
1516556 AATACTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (24 bp):
TAAACTAACTTTTTCTTTTAGTTT
Found at i:1517618 original size:18 final size:18
Alignment explanation
Indices: 1517587--1517639 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
1517577 TACATGCTAC
1517587 TTATATATATTAAATTTTT
1 TTATATA-ATTAAATTTTT
1517606 TTGATA-AATTAAATTTTT
1 TT-ATATAATTAAATTTTT
1517624 TTATATAATT-AATTTT
1 TTATATAATTAAATTTT
1517640 ATAACTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.28
18 17 0.53
19 3 0.09
20 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATATAATTAAATTTTT
Found at i:1517624 original size:17 final size:18
Alignment explanation
Indices: 1517589--1517639 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
1517579 CATGCTACTT
1517589 ATATATATTAAATTTTTTTG
1 ATATA-ATTAAA-TTTTTTG
*
1517609 ATA-AATTAAATTTTTTT
1 ATATAATTAAATTTTTTG
1517626 ATATAATT-AATTTT
1 ATATAATTAAATTTT
1517640 ATAACTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 15 0.52
18 10 0.34
19 1 0.03
20 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
ATATAATTAAATTTTTTG
Found at i:1518611 original size:21 final size:23
Alignment explanation
Indices: 1518578--1518624 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1518568 TTTCTTTGTT
*
1518578 TTTTTATTAATTA-TTAAAAATA
1 TTTTTATTAATTATTTAAAAAAA
*
1518600 TTTTTGTT-ATTATTTAAAAAAA
1 TTTTTATTAATTATTTAAAAAAA
1518622 TTT
1 TTT
1518625 AAATTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTTATTAATTATTTAAAAAAA
Found at i:1519011 original size:25 final size:26
Alignment explanation
Indices: 1518951--1519001 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
1518941 TGTGATTATT
1518951 AAAATGAAATATGATAGTTATTTGATA
1 AAAAT-AAATATGATAGTTATTTGATA
*
1518978 AAAATAAATATTATA-TTATTTGAT
1 AAAATAAATATGATAGTTATTTGAT
1519002 TAATTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 9 0.39
27 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATAAATATGATAGTTATTTGATA
Found at i:1519713 original size:25 final size:24
Alignment explanation
Indices: 1519664--1519714 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1519654 ATTCAAATTT
*
1519664 AAAAAATTATTTACTTTTTCTTTA
1 AAAAAATTATTTACTTTTTCGTTA
1519688 AAAAAATTATTTAACTCTTTT-GTTA
1 AAAAAATTATTT-ACT-TTTTCGTTA
1519713 AA
1 AA
1519715 TATTTTTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 12 0.50
25 8 0.33
26 4 0.17
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (24 bp):
AAAAAATTATTTACTTTTTCGTTA
Found at i:1521507 original size:47 final size:47
Alignment explanation
Indices: 1521433--1521527 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
1521423 AACTTTCTTA
*
1521433 GATATTATAATAGTAAATAGTTTTATAATTTCTGTTTCGATTGAATT
1 GATATTATAATAGTAAATAGTTGTATAATTTCTGTTTCGATTGAATT
* * *
1521480 GATATTATAATAGTTAATAGTTGTATAATTTCTGTTTTGATTTAATT
1 GATATTATAATAGTAAATAGTTGTATAATTTCTGTTTCGATTGAATT
1521527 G
1 G
1521528 CGGTGCCGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.51
Consensus pattern (47 bp):
GATATTATAATAGTAAATAGTTGTATAATTTCTGTTTCGATTGAATT
Found at i:1521979 original size:43 final size:41
Alignment explanation
Indices: 1521913--1521995 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 41
1521903 TACTCACCAG
* * * *
1521913 ACTTGGTTACTAATAGTTACTGAATATGGATATGCTGAATATT
1 ACTTAGTTACCAATAGTTACTGAACAT--AGATGCTGAATATT
1521956 ACTTAGTTACCAATAGTTACTGAACATAGATGCTGAATAT
1 ACTTAGTTACCAATAGTTACTGAACATAGATGCTGAATAT
1521996 GGAGTGATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 12 0.33
43 24 0.67
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (41 bp):
ACTTAGTTACCAATAGTTACTGAACATAGATGCTGAATATT
Found at i:1522138 original size:66 final size:66
Alignment explanation
Indices: 1522055--1522178 Score: 230
Period size: 66 Copynumber: 1.9 Consensus size: 66
1522045 TAGAGTGGTA
*
1522055 GGAACTCTGTTTGAGATTAAACAATTGAAGTTGTAGATATGTAGTTTTGTTCCAAAGCGAGGGAT
1 GGAACTCTGTTTGAGATTAAACAATTGAAGTTGTAGATATGTAGCTTTGTTCCAAAGCGAGGGAT
1522120 G
66 G
*
1522121 GGAACTTTGTTTGAGATTAAACAATTGAAGTTGTAGATATGTAGCTTTGTTCCAAAGC
1 GGAACTCTGTTTGAGATTAAACAATTGAAGTTGTAGATATGTAGCTTTGTTCCAAAGC
1522179 TTGCTCATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.35
Consensus pattern (66 bp):
GGAACTCTGTTTGAGATTAAACAATTGAAGTTGTAGATATGTAGCTTTGTTCCAAAGCGAGGGAT
G
Found at i:1531982 original size:16 final size:17
Alignment explanation
Indices: 1531963--1531995 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1531953 TATTACAGTA
1531963 ATAAAAAATT-AATTTT
1 ATAAAAAATTAAATTTT
*
1531979 ATAATAAATTAAATTTT
1 ATAAAAAATTAAATTTT
1531996 TGTATTAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAAAAAATTAAATTTT
Found at i:1532470 original size:444 final size:442
Alignment explanation
Indices: 1531817--1532616 Score: 1134
Period size: 444 Copynumber: 1.8 Consensus size: 442
1531807 TATTATTTTA
* * * *
1531817 AAAAAATAATTTTTTCAAAATACTTTTTGATTAAATTTGTTTATGTAGGAAATGGATTATTTTAG
1 AAAAAATAATTTTTTAAAAATAATTTTTGATTAAATATGTTTATGTAGGAAATGAATTATTTTAG
**
1531882 TAAATTTTTCAGTAAATAAATTTATATTTTTTAATTTATTAATATAATTTTTAATATTAGTAACA
66 TAAATTTTGAAGTAAATAAATTTATATTTTTTAATTTATTAATATAATTTTTAATATTAGTAACA
* *
1531947 AAAATATATTACAGTAATAAAAAATTAATTTTATAATAAATTAAATTTTTGTATTAGTTAAAAGA
131 AAAATATATTAAAGTAATAAAAAATTAATTTTATAAAAAATTAAATTTTTGTATTAGTTAAAAGA
* * *
1532012 ATTACTAATAAAGATTACTGAAATTACAAATATACATTATAACTTACATAAATCATTAAAGTGCA
196 ATTACTAATAAAGATTACTAAAATTACAAATAAACATTATAACTTACACAAATCATTAAAGTGCA
* * * *
1532077 AATAATATTTATATGTAATATGTGTTAT-AAGTAATATATTTATGTAAAGAATCTTTGAGTA-TA
261 AAAAATATTTATATGTAATATGTGTTATGAA-TAATATATTTATATAAAAAAT-TTTGA-AAGTA
* * * *
1532140 ATGTTTATATGTAATTATTTACATATAAATATTATAATGTTACAAACAACCATTACAGAATTATA
323 ATATTTATATGTAATAAATTACATAAAAATATTATAATGTTACAAACAACCATTACAGAATTATA
1532205 GAAAAACATGACCAAAATTGTAACGTATTTATGGAAAACATTATTTAAAGAAAAT
388 GAAAAACATGACCAAAATTGTAACGTATTTATGGAAAACATTATTTAAAGAAAAT
* *
1532260 AAAATATAATTTTTTAAAAAATAATTGTTTGATTGAATATGTTTATATGTAGGAAATGAATT-TT
1 AAAAAATAATTTTTT-AAAAATAATT-TTTGATTAAATATG-TT-TATGTAGGAAATGAATTATT
1532324 TTAAGTAAATTTTGAAGTAAA-AAATTTATATTTTTT-ATTTATT-ATATAATTTTTAATATTAG
62 TT-AGTAAATTTTGAAGTAAATAAATTTATATTTTTTAATTTATTAATATAATTTTTAATATTAG
* * * * *
1532386 T-A-ATAATTTTATTAAAGTAATAAACAATTAATTTTATAACAAAAATTAGATTTTT-TATTAGT
126 TAACAAAAATATATTAAAGTAATAAAAAATTAATTTTAT-A-AAAAATTAAATTTTTGTATTAGT
* * * *
1532448 TACAAAGAATTAC-AACTAAAGATTATTAAAATTACACATAAACATTATAATTTACACAAATTAT
189 TA-AAAGAATTACTAA-TAAAGATTACTAAAATTACAAATAAACATTATAACTTACACAAATCAT
*
1532512 TAGAGTGCAAAAAATATTTATATGTAATATGTGTTATGAATAATATATTTATATAAAAAATTTTG
252 TAAAGTGCAAAAAATATTTATATGTAATATGTGTTATGAATAATATATTTATATAAAAAATTTTG
*
1532577 AAAGTAATATTTATATGTAATAAATTATATAAAAATATTA
317 AAAGTAATATTTATATGTAATAAATTACATAAAAATATTA
1532617 CTCACGAGAT
Statistics
Matches: 314, Mismatches: 32, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
442 31 0.10
443 63 0.20
444 146 0.46
445 21 0.07
446 21 0.07
447 32 0.10
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (442 bp):
AAAAAATAATTTTTTAAAAATAATTTTTGATTAAATATGTTTATGTAGGAAATGAATTATTTTAG
TAAATTTTGAAGTAAATAAATTTATATTTTTTAATTTATTAATATAATTTTTAATATTAGTAACA
AAAATATATTAAAGTAATAAAAAATTAATTTTATAAAAAATTAAATTTTTGTATTAGTTAAAAGA
ATTACTAATAAAGATTACTAAAATTACAAATAAACATTATAACTTACACAAATCATTAAAGTGCA
AAAAATATTTATATGTAATATGTGTTATGAATAATATATTTATATAAAAAATTTTGAAAGTAATA
TTTATATGTAATAAATTACATAAAAATATTATAATGTTACAAACAACCATTACAGAATTATAGAA
AAACATGACCAAAATTGTAACGTATTTATGGAAAACATTATTTAAAGAAAAT
Found at i:1532601 original size:29 final size:28
Alignment explanation
Indices: 1532524--1532615 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
1532514 GAGTGCAAAA
**
1532524 AATATTTATATGTAATATGTGTTATGAAT
1 AATATTTATATGTAATAAAT-TTATGAAT
* *
1532553 AATATATT-TATATAAAAAATTT-TGAAAGT
1 AATAT-TTATATGTAATAAATTTATG-AA-T
*
1532582 AATATTTATATGTAATAAATTATAT-AAA
1 AATATTTATATGTAATAAATT-TATGAAT
1532610 AATATT
1 AATATT
1532616 ACTCACGAGA
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
27 2 0.04
28 12 0.24
29 32 0.64
30 3 0.06
31 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.45
Consensus pattern (28 bp):
AATATTTATATGTAATAAATTTATGAAT
Found at i:1533293 original size:2 final size:2
Alignment explanation
Indices: 1533286--1533327 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1533276 CTGTTTACGT
* *
1533286 TA TA TA TA CA TA CA 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
1533328 CACATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1534155 original size:9 final size:9
Alignment explanation
Indices: 1534132--1534163 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1534122 AAAATTTAAT
1534132 ATTAATTT-
1 ATTAATTTA
1534140 A-TAATTTA
1 ATTAATTTA
1534148 ATTAATTTA
1 ATTAATTTA
1534157 ATTAATT
1 ATTAATT
1534164 GATTAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 6 0.27
8 2 0.09
9 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTAATTTA
Found at i:1534215 original size:19 final size:19
Alignment explanation
Indices: 1534193--1534238 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1534183 TTAAATAATT
1534193 TTATAAA-AATTAATATAAA
1 TTATAAATAATTAAT-TAAA
*
1534212 TTATAAATATTTAATTAAA
1 TTATAAATAATTAATTAAA
*
1534231 TTTTAAAT
1 TTATAAAT
1534239 CTATTATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATAAATAATTAATTAAA
Found at i:1539710 original size:9 final size:9
Alignment explanation
Indices: 1539698--1539731 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1539688 GGTCAGCTTG
1539698 GTCATCATC
1 GTCATCATC
*
1539707 GTCATTATC
1 GTCATCATC
1539716 GTCATCATC
1 GTCATCATC
*
1539725 ATCATCA
1 GTCATCA
1539732 GAACTGCGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.35
Consensus pattern (9 bp):
GTCATCATC
Found at i:1543448 original size:2 final size:2
Alignment explanation
Indices: 1543441--1543467 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1543431 GGGAAACATA
1543441 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
1543468 GGGTAAAAAT
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:1544205 original size:22 final size:21
Alignment explanation
Indices: 1544167--1544208 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1544157 AATATTTATT
1544167 TAAAATTAATTATAAAATATA
1 TAAAATTAATTATAAAATATA
1544188 TAAATATTAA-TATAAAA-ATA
1 TAAA-ATTAATTATAAAATATA
1544208 T
1 T
1544209 TTTTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAATTAATTATAAAATATA
Found at i:1550272 original size:20 final size:20
Alignment explanation
Indices: 1550247--1550298 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1550237 TACCCTGATG
*
1550247 TATCGATACATTTTTCAATA
1 TATCGATACATTTATCAATA
* * *
1550267 TATCGATACATGTATGAATG
1 TATCGATACATTTATCAATA
1550287 TATCGATACATT
1 TATCGATACATT
1550299 ATGTCTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTATCAATA
Found at i:1551238 original size:22 final size:22
Alignment explanation
Indices: 1551212--1551266 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1551202 AGCCTTTGAC
1551212 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
1551234 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
1551256 CATGCATTTTT
1 CATGCATTTTT
1551267 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:1551273 original size:20 final size:21
Alignment explanation
Indices: 1551212--1551273 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
1551202 AGCCTTTGAC
**
1551212 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
1551234 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
1551256 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
1551274 CCAGCATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.26
22 28 0.74
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.58
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:1563066 original size:1 final size:1
Alignment explanation
Indices: 1563056--1563152 Score: 86
Period size: 1 Copynumber: 97.0 Consensus size: 1
1563046 TGGCAATTGG
* * * ** * * * **
1563056 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAACAAAACAAAAAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
1563121 AAAGAAAAAAAAAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1563153 GTGAAGATTT
Statistics
Matches: 76, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:1563100 original size:40 final size:36
Alignment explanation
Indices: 1563056--1563152 Score: 144
Period size: 37 Copynumber: 2.7 Consensus size: 36
1563046 TGGCAATTGG
*
1563056 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAA
1 AAAAAAAAAAAAACAAAA-AAAAAAAAGGAAAAAGAA
*
1563093 AAAAAAAACAAAAC--AAAAAAAAAAGGAAAAAGAAA
1 AAAAAAAAAAAAACAAAAAAAAAAAAGGAAAAAG-AA
1563128 AAAAAAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAACAAAAAAAAAAA
1563153 GTGAAGATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
34 16 0.30
35 17 0.31
37 21 0.39
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (36 bp):
AAAAAAAAAAAAACAAAAAAAAAAAAGGAAAAAGAA
Found at i:1563103 original size:32 final size:33
Alignment explanation
Indices: 1563057--1563149 Score: 143
Period size: 34 Copynumber: 2.8 Consensus size: 33
1563047 GGCAATTGGA
1563057 AAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAG
1 AAAA-AAAAAAACAAAACAAAAAAAAGGAAAAAG
1563091 -AAAAAAAAAACAAAACAAAAAAAAAAGGAAAAAG
1 AAAAAAAAAAACAAAAC--AAAAAAAAGGAAAAAG
*
1563125 AAAAAAAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAACAAAACAAAAAAAA
1563150 AAAGTGAAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
32 13 0.24
33 11 0.20
34 16 0.29
35 15 0.27
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (33 bp):
AAAAAAAAAAACAAAACAAAAAAAAGGAAAAAG
Found at i:1563113 original size:34 final size:35
Alignment explanation
Indices: 1563057--1563151 Score: 151
Period size: 35 Copynumber: 2.8 Consensus size: 35
1563047 GGCAATTGGA
1563057 AAAAGAAAAAAACAAAAC--AAAAAAAAGGAAAAAG
1 AAAA-AAAAAAACAAAACAAAAAAAAAAGGAAAAAG
1563091 -AAAAAAAAAACAAAACAAAAAAAAAAGGAAAAAG
1 AAAAAAAAAAACAAAACAAAAAAAAAAGGAAAAAG
*
1563125 AAAAAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAACAAAACAAAAAAAAAA
1563152 AGTGAAGATT
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
32 13 0.23
33 3 0.05
34 16 0.28
35 25 0.44
ACGTcount: A:0.87, C:0.05, G:0.07, T:0.00
Consensus pattern (35 bp):
AAAAAAAAAAACAAAACAAAAAAAAAAGGAAAAAG
Found at i:1568911 original size:27 final size:27
Alignment explanation
Indices: 1568880--1569618 Score: 1109
Period size: 27 Copynumber: 27.0 Consensus size: 27
1568870 GTGACATTTT
* *
1568880 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* * *
1568908 TTTTTAAGTCCATAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1568935 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1568963 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1568990 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1569017 CTTTTAAGTCCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1569044 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1569071 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1569099 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1569127 CTTTTAAGTCCACAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1569155 CTTTTAAGTCTACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1569182 ATTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1569209 CTTTTAAGTCCACAACTCTGTGGCATGC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1569237 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
1569264 CTTTTAAGTCCACAACTCTGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
1569291 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1569318 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1569345 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1569372 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * * *
1569400 CTTTTAAGACTACAACTCTGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1569427 CTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
1569454 CTTTTAAGTCCATAACTCTGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
1569482 TTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1569509 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1569537 CTTTTAAGTCCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1569564 CTTTTAAGTCCACAACTCCATGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1569591 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1569618 C
1 C
1569619 ATTCCAAAGC
Statistics
Matches: 651, Mismatches: 54, Indels: 13
0.91 0.08 0.02
Matches are distributed among these distances:
27 444 0.68
28 207 0.32
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1568980 original size:82 final size:81
Alignment explanation
Indices: 1568880--1569618 Score: 1111
Period size: 82 Copynumber: 9.0 Consensus size: 81
1568870 GTGACATTTT
* * * *
1568880 CTTTTAAAGTCCACAACTCTGTGGCATCTTTTTAAGTCCATAACTCTGTGGCACCCTTTTAAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
1568945 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* *
1568963 CTTTTTAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
1569028 ACAACTTCGTGGCACC
66 ACAACTCCGTGGCACC
*
1569044 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
1569109 CACAACTCCGTGGCATCC
65 CACAACTCCGTGGCA-CC
* *
1569127 CTTTTAAGTCCACAACTCCGTGGCATCTCTTTTAAGTCTACAACTCCGTGGCACCATTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCATC-CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1569192 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
1569209 CTTTTAAGTCCACAACTCTGTGGCATGCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCAT-CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* **
1569274 CACAACTCTGTGGCATT
65 CACAACTCCGTGGCACC
1569291 CTTTTAAGTCCACAACTCCGTGGCA-CCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCATCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1569355 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* * * *
1569372 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGACTACAACTCTGTAGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCAT-CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1569437 CATAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* * * *
1569454 CTTTTAAGTCCATAACTCTGTGGCATCTTTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTTAAGTCCACAACTCCGTGGCATC-CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
1569519 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* * * * *
1569537 CTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAACTCCATGGCATCCTTTTAAATCC
1 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
1569602 ACAACTCTGTGGCACC
66 ACAACTCCGTGGCACC
1569618 C
1 C
1569619 ATTCCAAAGC
Statistics
Matches: 601, Mismatches: 46, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
80 2 0.00
81 168 0.28
82 301 0.50
83 106 0.18
84 24 0.04
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:1569656 original size:32 final size:32
Alignment explanation
Indices: 1569601--1570111 Score: 862
Period size: 32 Copynumber: 16.0 Consensus size: 32
1569591 CTTTTAAATC
* *
1569601 CACAACTCTGTGGC-ACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1569632 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
1569664 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1569696 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1569728 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1569760 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1569792 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
* * *
1569824 CACAAGTCGATGGCAACCTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1569856 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1569888 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
1569920 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
1569952 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1569984 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
* * *
1570016 CATAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
* * *
1570048 CACAAGTCGGTGGCGACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
* **
1570080 CACAAGTCGGTGGTAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1570112 TGTAAATCAG
Statistics
Matches: 456, Mismatches: 23, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
31 12 0.03
32 444 0.97
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.15
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
Found at i:1570693 original size:20 final size:20
Alignment explanation
Indices: 1570668--1570719 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1570658 TACCCTGATG
*
1570668 TATCGATACATTTTTCAATA
1 TATCGATACATTTATCAATA
* * *
1570688 TATCGATACATGTATGAATG
1 TATCGATACATTTATCAATA
1570708 TATCGATACATT
1 TATCGATACATT
1570720 ATGTCTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTATCAATA
Found at i:1571659 original size:22 final size:22
Alignment explanation
Indices: 1571633--1571687 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1571623 AGCCTTTGAC
1571633 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
1571655 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
1571677 CATGCATTTTT
1 CATGCATTTTT
1571688 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:1571694 original size:20 final size:21
Alignment explanation
Indices: 1571633--1571694 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
1571623 AGCCTTTGAC
**
1571633 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
1571655 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
1571677 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
1571695 CCAGCATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.26
22 28 0.74
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.58
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:1579577 original size:14 final size:16
Alignment explanation
Indices: 1579560--1579593 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1579550 AAGTAAACAT
1579560 AAAAAAT-ATATATAA
1 AAAAAATCATATATAA
*
1579575 AAAAAATCATATCTAA
1 AAAAAATCATATATAA
1579591 AAA
1 AAA
1579594 TAATTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATCATATATAA
Found at i:1580792 original size:16 final size:16
Alignment explanation
Indices: 1580771--1580847 Score: 84
Period size: 16 Copynumber: 4.8 Consensus size: 16
1580761 GTCTCTTGAG
1580771 TTTAAATTATTTTAAT
1 TTTAAATTATTTTAAT
* *
1580787 TTTAAATCATTTTAAA
1 TTTAAATTATTTTAAT
1580803 TTTAAATTATTTTCAA-
1 TTTAAATTATTTT-AAT
** *
1580819 TTCGAATCATTTTATAT
1 TTTAAATTATTTTA-AT
1580836 TTTAAATTATTT
1 TTTAAATTATTT
1580848 GATTTCAAGT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
15 1 0.02
16 37 0.76
17 11 0.22
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.57
Consensus pattern (16 bp):
TTTAAATTATTTTAAT
Found at i:1580983 original size:14 final size:16
Alignment explanation
Indices: 1580951--1580980 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1580941 TTTATTTTAG
1580951 AATTATTACAAGTTTT
1 AATTATTACAAGTTTT
1580967 AATTATT-CAAGTTT
1 AATTATTACAAGTTT
1580981 AATACTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (16 bp):
AATTATTACAAGTTTT
Found at i:1581481 original size:74 final size:75
Alignment explanation
Indices: 1581352--1581496 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 75
1581342 TGGATTAGTT
* * * *
1581352 AAATTTTTTATTTTTGATTAAATTAGTTTAATTAATTAAATCAATAGATTTTAAAAAAGTT-TTT
1 AAATTTGTTATTTTTGATTAAATTAGTTTAATTAATCAAATCAATAGATTGTAAAAAAGTTAGTT
1581416 AAAAATATTA
66 AAAAATATTA
** *
1581426 AAATTTGTTATTTTTGATTAAATTAGTTTAATTAGA-CAGTTTAAT-GAATTGTAAAAAAGTTAG
1 AAATTTGTTATTTTTGATTAAATTAGTTTAATTA-ATCAAATCAATAG-ATTGTAAAAAAGTTAG
1581489 TTAAAAAT
64 TTAAAAAT
1581497 CACAAAGGTA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
73 1 0.02
74 51 0.84
75 9 0.15
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.46
Consensus pattern (75 bp):
AAATTTGTTATTTTTGATTAAATTAGTTTAATTAATCAAATCAATAGATTGTAAAAAAGTTAGTT
AAAAATATTA
Found at i:1581635 original size:21 final size:20
Alignment explanation
Indices: 1581609--1581661 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
1581599 TTAATTATAA
*
1581609 AATTTTGATAATATTTGATGT
1 AATTTTGATAATATTTAAT-T
** *
1581630 AATTTTTTTAATTTTTAATT
1 AATTTTGATAATATTTAATT
1581650 AATTTTGATAAT
1 AATTTTGATAAT
1581662 TTTTTTGTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
AATTTTGATAATATTTAATT
Found at i:1581672 original size:21 final size:21
Alignment explanation
Indices: 1581609--1581673 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
1581599 TTAATTATAA
**
1581609 AATTTTGATAATATTTGATG-T
1 AATTTTGATAAT-TTTTTTGTT
** **
1581630 AATTTTTTTAA-TTTTTAATT
1 AATTTTGATAATTTTTTTGTT
1581650 AATTTTGATAATTTTTTTGTT
1 AATTTTGATAATTTTTTTGTT
1581671 AAT
1 AAT
1581674 ATTTAATATA
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
19 3 0.09
20 10 0.31
21 19 0.59
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (21 bp):
AATTTTGATAATTTTTTTGTT
Found at i:1581679 original size:32 final size:32
Alignment explanation
Indices: 1581632--1581693 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
1581622 TTTGATGTAA
*
1581632 TTTTTTTAATTTTTAAT-TAATTTTGATAATT
1 TTTTTTTAATATTTAATATAATTTTGATAATT
1581663 TTTTTGTTAATATTTAATATAATTTTGATAA
1 TTTTT-TTAATATTTAATATAATTTTGATAA
1581694 CAATTAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 5 0.18
32 11 0.39
33 12 0.43
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (32 bp):
TTTTTTTAATATTTAATATAATTTTGATAATT
Found at i:1581688 original size:21 final size:21
Alignment explanation
Indices: 1581676--1581729 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1581666 TTGTTAATAT
1581676 TTAATATAATTTTGATAACAA
1 TTAATATAATTTTGATAACAA
* **
1581697 TTAATATAATATTGA-AACTC
1 TTAATATAATTTTGATAACAA
1581717 TTAATATAATTTT
1 TTAATATAATTTT
1581730 AAAAATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAATATAATTTTGATAACAA
Found at i:1581722 original size:20 final size:21
Alignment explanation
Indices: 1581676--1581726 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1581666 TTGTTAATAT
*
1581676 TTAATATAATTTTGATAACAA
1 TTAATATAATATTGATAACAA
**
1581697 TTAATATAATATTGA-AACTC
1 TTAATATAATATTGATAACAA
1581717 TTAATATAAT
1 TTAATATAAT
1581727 TTTAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (21 bp):
TTAATATAATATTGATAACAA
Found at i:1581812 original size:62 final size:60
Alignment explanation
Indices: 1581670--1581812 Score: 153
Period size: 62 Copynumber: 2.3 Consensus size: 60
1581660 ATTTTTTTGT
* *
1581670 TAATATTTAATATAATTTTGATAACAATTAATATAATATTGAAACTCTTAATATAATTTTAA
1 TAAT-TTTTATATAA-TTTGATAACAATTAATATAATATTGAAACTCTCAATATAATTTTAA
* * * * *
1581732 AAATTTTTGAAACAAATTTGATAATAATTGATATAATATTGATAA-TCCTCAATATAATTTTAA
1 TAATTTTT-ATA-TAATTTGATAACAATTAATATAATATTGA-AACT-CTCAATATAATTTTAA
1581795 TAATTTTTATTATAATTT
1 TAATTTTTA-TATAATTT
1581813 TACAAATATA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
61 3 0.05
62 36 0.55
63 27 0.41
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (60 bp):
TAATTTTTATATAATTTGATAACAATTAATATAATATTGAAACTCTCAATATAATTTTAA
Found at i:1582478 original size:13 final size:12
Alignment explanation
Indices: 1582440--1582483 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
1582430 AAATGATATT
1582440 TAAAAAAAATATA
1 TAAAAAAAATA-A
* *
1582453 TAATAATAATAA
1 TAAAAAAAATAA
1582465 TAAAAAAAATTAA
1 TAAAAAAAA-TAA
1582478 TAAAAA
1 TAAAAA
1582484 TATGATTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAAAAAAATAA
Found at i:1582478 original size:22 final size:24
Alignment explanation
Indices: 1582442--1582485 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
1582432 ATGATATTTA
*
1582442 AAAAAAATATATAATAATAATAAT
1 AAAAAAATATATAATAAAAATAAT
1582466 AAAAAAA-AT-TAATAAAAATA
1 AAAAAAATATATAATAAAAATA
1582486 TGATTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 2 0.11
24 7 0.37
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAAAATATATAATAAAAATAAT
Found at i:1582970 original size:13 final size:13
Alignment explanation
Indices: 1582928--1582977 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
1582918 CTCAGATCTA
* *
1582928 ATTTAATTTGATT
1 ATTTAATATAATT
1582941 -TTTAA-ATAATT
1 ATTTAATATAATT
1582952 AAATTTAATATAATT
1 --ATTTAATATAATT
1582967 ATTTAATATAA
1 ATTTAATATAA
1582978 ATAATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
11 4 0.13
12 5 0.16
13 11 0.35
14 5 0.16
15 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
ATTTAATATAATT
Found at i:1583520 original size:19 final size:19
Alignment explanation
Indices: 1583484--1583519 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1583474 GTATTTAATT
1583484 TTTAAATTTAATATTTTTG
1 TTTAAATTTAATATTTTTG
*
1583503 TTTAATTTTAAT-TTTTT
1 TTTAAATTTAATATTTTT
1583520 TAAAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTAAATTTAATATTTTTG
Found at i:1588826 original size:34 final size:34
Alignment explanation
Indices: 1588762--1588841 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 34
1588752 ATATCTTGCT
1588762 CACCTAACACACCTAATATGCTCACCTAACACAC
1 CACCTAACACACCTAATATGCTCACCTAACACAC
* * * * * * *
1588796 CATCTAACGCATCTAATATGTTTACGTAACATAC
1 CACCTAACACACCTAATATGCTCACCTAACACAC
1588830 CACCTAACACAC
1 CACCTAACACAC
1588842 TTAGCAAAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.38, C:0.35, G:0.05, T:0.23
Consensus pattern (34 bp):
CACCTAACACACCTAATATGCTCACCTAACACAC
Found at i:1591813 original size:255 final size:255
Alignment explanation
Indices: 1591362--1591876 Score: 1030
Period size: 255 Copynumber: 2.0 Consensus size: 255
1591352 AATACACCCA
1591362 AACATATCTTAAATAATCATCAATGAAAGTCACCATATAGTGCATACCATTGGCTGAAGACTGCT
1 AACATATCTTAAATAATCATCAATGAAAGTCACCATATAGTGCATACCATTGGCTGAAGACTGCT
1591427 TCACCTTCCCAAAGACATCTGAGTGGATCAACTCCAGTGGCTCCTTAGCTTTGAATGATGAATCC
66 TCACCTTCCCAAAGACATCTGAGTGGATCAACTCCAGTGGCTCCTTAGCTTTGAATGATGAATCC
1591492 TCAAATGGTAACTAGTGCGTTTTTCCATATTGACAACCAGCATATACTATATCAGTATGAACATC
131 TCAAATGGTAACTAGTGCGTTTTTCCATATTGACAACCAGCATATACTATATCAGTATGAACATC
1591557 AAGATTAGGAAGTCTTTTCAATGAAGACTTGCTCATCATTATCTTCAACTTGTGATAGTT
196 AAGATTAGGAAGTCTTTTCAATGAAGACTTGCTCATCATTATCTTCAACTTGTGATAGTT
1591617 AACATATCTTAAATAATCATCAATGAAAGTCACCATATAGTGCATACCATTGGCTGAAGACTGCT
1 AACATATCTTAAATAATCATCAATGAAAGTCACCATATAGTGCATACCATTGGCTGAAGACTGCT
1591682 TCACCTTCCCAAAGACATCTGAGTGGATCAACTCCAGTGGCTCCTTAGCTTTGAATGATGAATCC
66 TCACCTTCCCAAAGACATCTGAGTGGATCAACTCCAGTGGCTCCTTAGCTTTGAATGATGAATCC
1591747 TCAAATGGTAACTAGTGCGTTTTTCCATATTGACAACCAGCATATACTATATCAGTATGAACATC
131 TCAAATGGTAACTAGTGCGTTTTTCCATATTGACAACCAGCATATACTATATCAGTATGAACATC
1591812 AAGATTAGGAAGTCTTTTCAATGAAGACTTGCTCATCATTATCTTCAACTTGTGATAGTT
196 AAGATTAGGAAGTCTTTTCAATGAAGACTTGCTCATCATTATCTTCAACTTGTGATAGTT
1591872 AACAT
1 AACAT
1591877 GTCTCAACCG
Statistics
Matches: 260, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
255 260 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (255 bp):
AACATATCTTAAATAATCATCAATGAAAGTCACCATATAGTGCATACCATTGGCTGAAGACTGCT
TCACCTTCCCAAAGACATCTGAGTGGATCAACTCCAGTGGCTCCTTAGCTTTGAATGATGAATCC
TCAAATGGTAACTAGTGCGTTTTTCCATATTGACAACCAGCATATACTATATCAGTATGAACATC
AAGATTAGGAAGTCTTTTCAATGAAGACTTGCTCATCATTATCTTCAACTTGTGATAGTT
Found at i:1594021 original size:97 final size:96
Alignment explanation
Indices: 1593855--1594340 Score: 774
Period size: 97 Copynumber: 5.0 Consensus size: 96
1593845 CTAACAGACT
* * *
1593855 ACCTAACACGCTTAACAAAGATATTAATAAAGATATGTAGGTCTAGCACAAATTTAAAAAATCGA
1 ACCTAACACACTTAACAAAGATATTAATAAAGATACGTAGGTCTAACACAAATTTAAAAAATCGA
1593920 TAAAACCTGAATTAATGATGATTTTTAACACC
66 TAAAA-CTGAATTAATGATGATTTTTAACACC
* *
1593952 ACCTAACACACTTAACAAAGATATTAATAAAGATAGGTAGGTCTAACACAAATTTAAAAAATCAA
1 ACCTAACACACTTAACAAAGATATTAATAAAGATACGTAGGTCTAACACAAATTTAAAAAATCGA
*
1594017 TAAAACCCGAATTAATGATGATTTTTAACACC
66 TAAAA-CTGAATTAATGATGATTTTTAACACC
* ** *
1594049 ACCTAACACATTTAACAAAGATATTAATAAAGATACGTATATCTAACACAAATTTAAAAATTCGA
1 ACCTAACACACTTAACAAAGATATTAATAAAGATACGTAGGTCTAACACAAATTTAAAAAATCGA
*
1594114 TAAAACTCGAATTAATGATGATTTTTAACACT
66 TAAAACT-GAATTAATGATGATTTTTAACACC
* *
1594146 ACCTAACACACTTAACAAAGATATTAATAAAGATACGTAGATCTAGCACAAATTTAAAAAATCGA
1 ACCTAACACACTTAACAAAGATATTAATAAAGATACGTAGGTCTAACACAAATTTAAAAAATCGA
*
1594211 TAAAATCTGAATTAATGATGATTTTTAATACC
66 TAAAA-CTGAATTAATGATGATTTTTAACACC
* * *
1594243 ATCTAACACACTTAACAAAGATATTAATAAAGATATGTAGGTCTAACACAAATTTAAAAATTCGA
1 ACCTAACACACTTAACAAAGATATTAATAAAGATACGTAGGTCTAACACAAATTTAAAAAATCGA
1594308 TAAAACTCGAATTAATGATGATTTTTAACACC
66 TAAAACT-GAATTAATGATGATTTTTAACACC
1594340 A
1 A
1594341 ATTCACTATA
Statistics
Matches: 361, Mismatches: 25, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
96 3 0.01
97 356 0.99
98 2 0.01
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (96 bp):
ACCTAACACACTTAACAAAGATATTAATAAAGATACGTAGGTCTAACACAAATTTAAAAAATCGA
TAAAACTGAATTAATGATGATTTTTAACACC
Found at i:1595164 original size:22 final size:24
Alignment explanation
Indices: 1595116--1595180 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 24
1595106 TTAATTTAAA
1595116 TTATAATAAAATATTTAAA-ATTTT
1 TTATAAT-AAATATTTAAATATTTT
1595140 TTAT-ATAAATATTTAAATA-TTT
1 TTATAATAAATATTTAAATATTTT
*
1595162 TTATAATTAA-ATTTAAATA
1 TTATAATAAATATTTAAATA
1595181 AAAATATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
22 27 0.71
23 7 0.18
24 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTATAATAAATATTTAAATATTTT
Found at i:1595194 original size:34 final size:34
Alignment explanation
Indices: 1595146--1595212 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 34
1595136 TTTTTTATAT
1595146 AAATATTTAAATATT-TTTATAATTAAATTTAAATAA
1 AAATATTT-AATATTATTTA-AATTAAA-TTAAATAA
1595182 AAATATTT-ATATTATTTAAATTAAATTAAAT
1 AAATATTTAATATTATTTAAATTAAATTAAAT
1595213 TAATTTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 6 0.20
34 12 0.40
35 4 0.13
36 8 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
AAATATTTAATATTATTTAAATTAAATTAAATAA
Found at i:1595207 original size:58 final size:59
Alignment explanation
Indices: 1595089--1595214 Score: 138
Period size: 57 Copynumber: 2.2 Consensus size: 59
1595079 TATTATTAGT
* * *
1595089 TATTTAAATTTATTTTTTTAATTTAAATTATAATAAAATATTTAAAATTTTTTATATAAA
1 TATTTAAA-TTATTTTTATAATTTAAATTATAATAAAATATTTAAAATTATTTAAATAAA
* *
1595149 TATTTAAA-TATTTTTATAA-TTAAATT-TAAATAAAAATATTT-ATATTATTTAAATTAA
1 TATTTAAATTATTTTTATAATTTAAATTAT-AAT-AAAATATTTAAAATTATTTAAATAAA
1595206 -A-TTAAATTA
1 TATTTAAATTA
1595215 ATTTAAATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
55 5 0.09
56 4 0.07
57 22 0.38
58 19 0.33
60 8 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (59 bp):
TATTTAAATTATTTTTATAATTTAAATTATAATAAAATATTTAAAATTATTTAAATAAA
Found at i:1595218 original size:29 final size:29
Alignment explanation
Indices: 1595168--1595235 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
1595158 ATTTTTATAA
*
1595168 TTAAATTTAAATAAAAATATTTATATTAT
1 TTAAATTTAAATAAAAATATTTAAATTAT
* *
1595197 TTAAA-TTAAATTAAATTAATTTAAATTAT
1 TTAAATTTAAATAAAAAT-ATTTAAATTAT
*
1595226 TAAAAATTTA
1 T-TAAATTTA
1595236 TTTCGTATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 10 0.31
29 16 0.50
30 3 0.09
31 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TTAAATTTAAATAAAAATATTTAAATTAT
Found at i:1595802 original size:2 final size:2
Alignment explanation
Indices: 1595795--1595824 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1595785 CTAACTCTTA
*
1595795 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1595825 GTATGTATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1595829 original size:10 final size:10
Alignment explanation
Indices: 1595795--1595833 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1595785 CTAACTCTTA
*
1595795 ATATATATAT
1 ATATGTATAT
*
1595805 ATATATATAT
1 ATATGTATAT
1595815 ATATGTATAT
1 ATATGTATAT
*
1595825 GTATGTATA
1 ATATGTATA
1595834 GATTTGGATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (10 bp):
ATATGTATAT
Found at i:1596727 original size:41 final size:41
Alignment explanation
Indices: 1596666--1596748 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
1596656 CGCACATTAT
*
1596666 TTTTCTTATAAAGAAAATAGAGGTAGGAAGTTGGAAGGAAC
1 TTTTCTTATAAAGAAAATAGAGGTAAGAAGTTGGAAGGAAC
*
1596707 TTTTCTTATAAAGAAGATAGAGGTAAGAAGTTGGAAGGAAC
1 TTTTCTTATAAAGAAAATAGAGGTAAGAAGTTGGAAGGAAC
1596748 T
1 T
1596749 GATGATCTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.05, G:0.27, T:0.28
Consensus pattern (41 bp):
TTTTCTTATAAAGAAAATAGAGGTAAGAAGTTGGAAGGAAC
Found at i:1597602 original size:22 final size:21
Alignment explanation
Indices: 1597559--1597606 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1597549 TTTAATTACT
*
1597559 ATTTATAAATATGATTTTCAC
1 ATTTATAAATATGATTTGCAC
*
1597580 AATTTATAAATGTG-TTATGCAC
1 -ATTTATAAATATGATT-TGCAC
1597602 ATTTA
1 ATTTA
1597607 AATAATGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (21 bp):
ATTTATAAATATGATTTGCAC
Found at i:1598301 original size:26 final size:23
Alignment explanation
Indices: 1598272--1598327 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
1598262 AATTTGATAA
1598272 AATTTAATTTTAATTTTAATATCTAT
1 AATTTAA-TTTAATTTTAA-ATC-AT
* *
1598298 AATTTTATTTATTTTTAAATCAT
1 AATTTAATTTAATTTTAAATCAT
1598321 AATTTAA
1 AATTTAA
1598328 AAAAAAACCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 8 0.30
24 3 0.11
25 10 0.37
26 6 0.22
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTTAATTTAATTTTAAATCAT
Found at i:1599270 original size:15 final size:15
Alignment explanation
Indices: 1599235--1599266 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1599225 TTTTTTAATT
1599235 AAAT-TTAATTATAA
1 AAATATTAATTATAA
1599249 AAATATTAA-TATAA
1 AAATATTAATTATAA
1599263 AAAT
1 AAAT
1599267 TATTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATTAATTATAA
Found at i:1599834 original size:18 final size:18
Alignment explanation
Indices: 1599808--1599880 Score: 55
Period size: 18 Copynumber: 4.3 Consensus size: 18
1599798 AATTTAATAT
*
1599808 AAATATATAAAAATATTA
1 AAATTTATAAAAATATTA
*
1599826 AAATTTATATAAA-A-T-
1 AAATTTATAAAAATATTA
* **
1599841 AAA-TTATTAATTTATTA
1 AAATTTATAAAAATATTA
* *
1599858 AAATTTATATAAATATTT
1 AAATTTATAAAAATATTA
1599876 AAATT
1 AAATT
1599881 ATGAATATAT
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
14 5 0.12
15 4 0.10
16 2 0.05
17 4 0.10
18 25 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTTATAAAAATATTA
Found at i:1599852 original size:22 final size:21
Alignment explanation
Indices: 1599811--1599861 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1599801 TTAATATAAA
*
1599811 TATATAAAA-ATATTAAAATT
1 TATATAAAATAAATTAAAATT
*
1599831 TATATAAAATAAATTATTAATT
1 TATATAAAATAAATTA-AAATT
1599853 TAT-TAAAAT
1 TATATAAAAT
1599862 TTATATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 9 0.33
21 11 0.41
22 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATAAAATAAATTAAAATT
Found at i:1600321 original size:13 final size:13
Alignment explanation
Indices: 1600303--1600337 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1600293 ATTATTTTTA
1600303 ATTTTTTAAAAAT
1 ATTTTTTAAAAAT
*
1600316 ATTTTTTAAATAT
1 ATTTTTTAAAAAT
*
1600329 AATTTTTAA
1 ATTTTTTAA
1600338 TAATGTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTTTTAAAAAT
Found at i:1600428 original size:21 final size:23
Alignment explanation
Indices: 1600404--1600460 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
1600394 TTACACTATA
* *
1600404 ATATTATATATATT-TATTTT-T
1 ATATGATATAAATTATATTTTAT
1600425 ATATGATATAAATTATATTTTAT
1 ATATGATATAAATTATATTTTAT
*
1600448 ATATAAATATAAA
1 ATAT-GATATAAA
1600461 AATAATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.40
22 6 0.20
23 5 0.17
24 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATATGATATAAATTATATTTTAT
Found at i:1603952 original size:18 final size:18
Alignment explanation
Indices: 1603929--1603964 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1603919 TAAGTGGTAA
*
1603929 AAAATTTTATTTTTAAAT
1 AAAATTTTAATTTTAAAT
1603947 AAAATTTTAATTTTAAAT
1 AAAATTTTAATTTTAAAT
1603965 TTTACGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAAATTTTAATTTTAAAT
Found at i:1604634 original size:21 final size:22
Alignment explanation
Indices: 1604610--1604708 Score: 73
Period size: 21 Copynumber: 4.6 Consensus size: 22
1604600 ATTATGTGAT
*
1604610 ATTATAATAAT-ATTAAAAATA
1 ATTAAAATAATAATTAAAAATA
* *
1604631 ATTAAAAT-ATGATAAAAAATA
1 ATTAAAATAATAATTAAAAATA
1604652 A-TATAAAT-ATAATATAAAAATA
1 ATTA-AAATAATAAT-TAAAAATA
* * *
1604674 ATTATAA-AATAATTAAATATG
1 ATTAAAATAATAATTAAAAATA
*
1604695 ATAAAAATACATAA
1 ATTAAAATA-ATAA
1604709 ATATTTTAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
20 4 0.06
21 36 0.58
22 16 0.26
23 6 0.10
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (22 bp):
ATTAAAATAATAATTAAAAATA
Found at i:1604663 original size:11 final size:11
Alignment explanation
Indices: 1604616--1604703 Score: 67
Period size: 11 Copynumber: 8.1 Consensus size: 11
1604606 TGATATTATA
*
1604616 ATAATATTAAAA
1 ATAATA-TAAAT
1604628 ATAAT-TAAAAT
1 ATAATAT-AAAT
* *
1604639 ATGATA-AAAA
1 ATAATATAAAT
1604649 ATAATATAAAT
1 ATAATATAAAT
*
1604660 ATAATATAAAA
1 ATAATATAAAT
1604671 ATAATTATAAA-
1 ATAA-TATAAAT
1604682 ATAAT-TAAAT
1 ATAATATAAAT
* *
1604692 ATGATAAAAAT
1 ATAATATAAAT
1604703 A
1 A
1604704 CATAAATATT
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
9 4 0.06
10 14 0.23
11 33 0.53
12 11 0.18
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1604703 original size:43 final size:44
Alignment explanation
Indices: 1604616--1604703 Score: 108
Period size: 43 Copynumber: 2.0 Consensus size: 44
1604606 TGATATTATA
* *
1604616 ATAATATTAAAAATAATTAAAATATGATAAAAAATAATATAAAT
1 ATAATATTAAAAATAATTAAAATATAATAAAAAATAATAAAAAT
* * *
1604660 ATAATA-TAAAAATAATTATAAA-ATAATTAAATATGATAAAAAT
1 ATAATATTAAAAATAATTA-AAATATAATAAAAAATAATAAAAAT
1604703 A
1 A
1604704 CATAAATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
43 29 0.76
44 9 0.24
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (44 bp):
ATAATATTAAAAATAATTAAAATATAATAAAAAATAATAAAAAT
Found at i:1610716 original size:27 final size:27
Alignment explanation
Indices: 1610655--1610716 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
1610645 TATATATATA
*
1610655 TATATATATGTATTTAACATTATTCAT
1 TATATATATGTATATAACATTATTCAT
* **
1610682 T-TCTTATATGTATATAATGTTATTCAT
1 TAT-ATATATGTATATAACATTATTCAT
1610709 TATATATA
1 TATATATA
1610717 AAATACATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 1 0.04
27 26 0.93
28 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.53
Consensus pattern (27 bp):
TATATATATGTATATAACATTATTCAT
Found at i:1611541 original size:31 final size:31
Alignment explanation
Indices: 1611480--1611543 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
1611470 TTTTTAATAT
*
1611480 TTATATATTTTATAATTAAATTTAAATAAAA
1 TTATATATTTTATAATTAAAATTAAATAAAA
* **
1611511 TTAT-TATTTATATTATTAAAATTATTTAAAA
1 TTATATATTT-TATAATTAAAATTAAATAAAA
1611542 TT
1 TT
1611544 TAATTAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTATATATTTTATAATTAAAATTAAATAAAA
Found at i:1611997 original size:33 final size:32
Alignment explanation
Indices: 1611924--1611997 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
1611914 TTTAAAAATT
* *
1611924 TTTATACTTATATAAATTTTAATTTATTAATAA
1 TTTATA-TTATATAAAATTTAAATTATTAATAA
* *
1611957 TTAATATTATATAAAATTTAAATTATTTATATA
1 TTTATATTATATAAAATTTAAATTATTAATA-A
1611990 TTTATATT
1 TTTATATT
1611998 TTATTAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (32 bp):
TTTATATTATATAAAATTTAAATTATTAATAA
Found at i:1612047 original size:17 final size:17
Alignment explanation
Indices: 1611931--1612048 Score: 63
Period size: 17 Copynumber: 7.1 Consensus size: 17
1611921 ATTTTTATAC
1611931 TTATATAA-ATTTTAA-T
1 TTATATAATA-TTTAATT
* *
1611947 TTAT-TAATAATTAATA
1 TTATATAATATTTAATT
*
1611963 TTATATAAAATTTAAATT
1 TTATATAATATTT-AATT
1611981 ATT-TAT-ATATTTATATT
1 -TTATATAATATTTA-ATT
*
1611998 TTAT-TAATA-TTATTT
1 TTATATAATATTTAATT
** *
1612013 TTATATCTTA-TCATATT
1 TTATATAATATTTA-ATT
*
1612030 TTATATCATATTTAATT
1 TTATATAATATTTAATT
1612047 TT
1 TT
1612049 TTTATAATGT
Statistics
Matches: 78, Mismatches: 13, Indels: 21
0.70 0.12 0.19
Matches are distributed among these distances:
15 13 0.17
16 21 0.27
17 34 0.44
18 8 0.10
19 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATAATATTTAATT
Found at i:1614023 original size:16 final size:15
Alignment explanation
Indices: 1614004--1614044 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
1613994 GAGCGAATTA
1614004 ATTTTTAAATATATGT
1 ATTTTTAAATATAT-T
*
1614020 ATTTTTGAATATATT
1 ATTTTTAAATATATT
1614035 ATATTTTAAA
1 AT-TTTTAAA
1614045 ATTTAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (15 bp):
ATTTTTAAATATATT
Found at i:1614039 original size:17 final size:17
Alignment explanation
Indices: 1614000--1614046 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
1613990 ATTCGAGCGA
1614000 ATTA-ATTTTTAAATAT
1 ATTATATTTTTAAATAT
* *
1614016 A-TGTATTTTTGAATAT
1 ATTATATTTTTAAATAT
*
1614032 ATTATATTTTAAAAT
1 ATTATATTTTTAAAT
1614047 TTAATGAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
15 1 0.04
16 13 0.54
17 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
ATTATATTTTTAAATAT
Found at i:1614220 original size:6 final size:7
Alignment explanation
Indices: 1614211--1614263 Score: 57
Period size: 6 Copynumber: 8.6 Consensus size: 7
1614201 AATATAAATC
1614211 ATATCA-
1 ATATCAT
1614217 ATATCAT
1 ATATCAT
1614224 ATAT-AT
1 ATATCAT
1614230 ATAT-AT
1 ATATCAT
1614236 ATAT-AT
1 ATATCAT
1614242 ATAT-AT
1 ATATCAT
1614248 ATAT-AT
1 ATATCAT
1614254 ATAT-AT
1 ATATCAT
1614260 ATAT
1 ATAT
1614264 AAATATAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 42 0.91
7 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (7 bp):
ATATCAT
Found at i:1614229 original size:2 final size:2
Alignment explanation
Indices: 1614217--1614270 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
1614207 AATCATATCA
1614217 AT AT CAT 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
*
1614260 AT AT AA AT AT A
1 AT AT AT AT AT A
1614271 AAAGTTAGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1616061 original size:6 final size:7
Alignment explanation
Indices: 1616042--1616068 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1616032 GCCATTTCAC
1616042 TATTTTT
1 TATTTTT
1616049 TATTTTT
1 TATTTTT
1616056 TATTTTT
1 TATTTTT
1616063 TATTTT
1 TATTTT
1616069 ATCATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:1617869 original size:13 final size:13
Alignment explanation
Indices: 1617851--1617888 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1617841 TGTATGTAAA
1617851 ATAAATATATTAT
1 ATAAATATATTAT
1617864 ATAAAT-TATATAT
1 ATAAATATAT-TAT
1617877 ATATAATATATT
1 ATA-AATATATT
1617889 GCAACACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 12 0.55
14 4 0.18
15 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATAAATATATTAT
Found at i:1619887 original size:2 final size:2
Alignment explanation
Indices: 1619880--1619905 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1619870 CTATAAGTAG
1619880 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
1619906 TGAACTTATG
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:1620037 original size:15 final size:15
Alignment explanation
Indices: 1620017--1620059 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1620007 TAAATATTTA
1620017 TTAATTTTTAAAATT
1 TTAATTTTTAAAATT
* *
1620032 TTAATTATTACAATT
1 TTAATTTTTAAAATT
**
1620047 GAAATTTTTAAAA
1 TTAATTTTTAAAA
1620060 AATATTTATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TTAATTTTTAAAATT
Found at i:1621763 original size:21 final size:22
Alignment explanation
Indices: 1621739--1621785 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1621729 ATAGTATTCA
*
1621739 AAAATAAT-TT-TTATTTTTAAT
1 AAAATAATATTATT-TTATTAAT
1621760 AAAATAATATTATTTTATTAAT
1 AAAATAATATTATTTTATTAAT
1621782 AAAA
1 AAAA
1621786 ATATAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
22 13 0.57
23 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAAATAATATTATTTTATTAAT
Found at i:1621796 original size:20 final size:22
Alignment explanation
Indices: 1621751--1621797 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
1621741 AATAATTTTT
*
1621751 ATTT-TTAATAAAATAATATTA
1 ATTTATTAATAAAATAATATAA
*
1621772 TTTTATTAAT-AAA-AATATAA
1 ATTTATTAATAAAATAATATAA
1621792 ATTTAT
1 ATTTAT
1621798 ATATTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 11 0.50
21 6 0.27
22 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTATTAATAAAATAATATAA
Found at i:1624173 original size:30 final size:29
Alignment explanation
Indices: 1624128--1624222 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 29
1624118 TTATATTTTA
1624128 TTATATCAAATAAATTTTTAATTTTTAAAT
1 TTATATC-AATAAATTTTTAATTTTTAAAT
* *
1624158 TGTA-ATCAGATAAATTCTTAAGTTTT-AAT
1 T-TATATCA-ATAAATTTTTAATTTTTAAAT
* *
1624187 TTATATACTAATAAATTTTTAATATTT-AGT
1 TTATAT-C-AATAAATTTTTAATTTTTAAAT
1624217 TTATAT
1 TTATAT
1624223 TTAAATAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
28 2 0.04
29 7 0.13
30 42 0.78
31 3 0.06
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (29 bp):
TTATATCAATAAATTTTTAATTTTTAAAT
Found at i:1624230 original size:30 final size:29
Alignment explanation
Indices: 1624105--1624233 Score: 86
Period size: 30 Copynumber: 4.4 Consensus size: 29
1624095 TAAAAAAAAT
* *
1624105 TTTAGATAAATATTTATATTTT-A-TTATA
1 TTTAAATAAATTTTTA-ATTTTAATTTATA
* * *
1624133 -TCAAATAAATTTTTAATTTTTAAATTGTA
1 TTTAAATAAATTTTTAA-TTTTAATTTATA
* * * *
1624162 ATCAGATAAATTCTTAAGTTTTAATTTATA
1 TTTAAATAAATTTTTAA-TTTTAATTTATA
* *
1624192 TACT-AATAAATTTTTAATATTTAGTTTATA
1 T-TTAAATAAATTTTTAAT-TTTAATTTATA
1624222 TTTAAATAAATT
1 TTTAAATAAATT
1624234 CTCAAAATAA
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
26 1 0.01
27 16 0.21
28 1 0.01
29 6 0.08
30 54 0.69
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (29 bp):
TTTAAATAAATTTTTAATTTTAATTTATA
Found at i:1624476 original size:29 final size:28
Alignment explanation
Indices: 1624444--1624502 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1624434 TTTTGAGAGT
1624444 TTTTATATTATAATAAAA-AAATATTTTAA
1 TTTTATATTAT--TAAAATAAATATTTTAA
* *
1624473 TTTTTTATTATTAAAATTAATATTTTAA
1 TTTTATATTATTAAAATAAATATTTTAA
1624501 TT
1 TT
1624503 ATCATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 5 0.19
28 12 0.44
29 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTATATTATTAAAATAAATATTTTAA
Found at i:1624776 original size:16 final size:15
Alignment explanation
Indices: 1624726--1624783 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 15
1624716 TAATAAAATT
*
1624726 TTTAAAATATAAATA
1 TTTAAAATATAAAAA
1624741 TTTAAAAATATTAATTAAA
1 TTT-AAAATA-TAA--AAA
1624760 TTTAATAATATAAAAA
1 TTTAA-AATATAAAAA
1624776 -TTAAAATA
1 TTTAAAATA
1624784 ATTTTTTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
14 4 0.11
15 7 0.19
16 9 0.24
17 3 0.08
18 5 0.14
19 9 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTAAAATATAAAAA
Found at i:1624966 original size:2 final size:2
Alignment explanation
Indices: 1624959--1624990 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1624949 TCTGGTTGTG
1624959 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
1624991 GTTCGACGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1633161 original size:57 final size:56
Alignment explanation
Indices: 1633029--1633170 Score: 151
Period size: 56 Copynumber: 2.5 Consensus size: 56
1633019 TTGAAGATGT
* ** * * * *
1633029 TCCTGAAGCTTGGCTAGAAGACCATTTTATCGTCATCGCAGATGATGAACGAGAAC
1 TCCTGAAGCTTGCCTAGAAGAAAATTTTATCGACATCACAAATGATGAACGAGAAA
* ** * *
1633085 TTCTGAAGCTTGTTTAGAAGAAAATTTTGTTGACATCACAAATGATGAA-GCAGATAA
1 TCCTGAAGCTTGCCTAGAAGAAAATTTTATCGACATCACAAATGATGAACG-AGA-AA
1633142 TCCTGAAGCTTGCCTAGAAGAAAATTTTA
1 TCCTGAAGCTTGCCTAGAAGAAAATTTTA
1633171 CGGCTACCAC
Statistics
Matches: 69, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
55 1 0.01
56 42 0.61
57 26 0.38
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (56 bp):
TCCTGAAGCTTGCCTAGAAGAAAATTTTATCGACATCACAAATGATGAACGAGAAA
Found at i:1636478 original size:23 final size:23
Alignment explanation
Indices: 1636435--1636478 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1636425 ACTTAATAAT
* *
1636435 ATTAAATAAAATTTAATTATATA
1 ATTAAATAAAATTAAAATATATA
1636458 ATTAAA-AAATATTAAAATATA
1 ATTAAATAAA-ATTAAAATATA
1636479 ACATAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATTAAATAAAATTAAAATATATA
Found at i:1640142 original size:10 final size:10
Alignment explanation
Indices: 1640127--1640190 Score: 60
Period size: 10 Copynumber: 6.3 Consensus size: 10
1640117 TTTAATATTC
*
1640127 AAATAATATT
1 AAATAAAATT
1640137 AAATAAAA-T
1 AAATAAAATT
1640146 AAA-AATAATT
1 AAATAA-AATT
*
1640156 AGATAAAAAATT
1 A-A-ATAAAATT
1640168 AAATAAAATT
1 AAATAAAATT
*
1640178 AAAAAAAATT
1 AAATAAAATT
1640188 AAA
1 AAA
1640191 ATTTTATATC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
8 2 0.04
9 6 0.13
10 28 0.61
11 2 0.04
12 6 0.13
13 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (10 bp):
AAATAAAATT
Found at i:1640151 original size:21 final size:20
Alignment explanation
Indices: 1640127--1640192 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 20
1640117 TTTAATATTC
1640127 AAATAATATTAAATAAAATAA
1 AAATAA-ATTAAATAAAATAA
*
1640148 AAAT-AATTAGATAAAA-AA
1 AAATAAATTAAATAAAATAA
* *
1640166 TTAAATAAAATTAAAAAAAATTA
1 --AAAT-AAATTAAATAAAATAA
1640189 AAAT
1 AAAT
1640193 TTTATATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
18 2 0.06
19 10 0.28
20 5 0.14
21 8 0.22
22 10 0.28
23 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
AAATAAATTAAATAAAATAA
Found at i:1640191 original size:10 final size:10
Alignment explanation
Indices: 1640134--1640191 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
1640124 TTCAAATAAT
*
1640134 ATTAAATAAA
1 ATTAAAAAAA
*
1640144 A-TAAAAATA
1 ATTAAAAAAA
1640153 ATTAGATAAAAA
1 ATTA-A-AAAAA
*
1640165 ATTAAATAAA
1 ATTAAAAAAA
1640175 ATTAAAAAAA
1 ATTAAAAAAA
1640185 ATTAAAA
1 ATTAAAA
1640192 TTTTATATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 7 0.17
10 23 0.57
11 2 0.05
12 8 0.20
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (10 bp):
ATTAAAAAAA
Found at i:1640481 original size:129 final size:129
Alignment explanation
Indices: 1640221--1640485 Score: 433
Period size: 129 Copynumber: 2.1 Consensus size: 129
1640211 AATTTTTGTT
* * *
1640221 AAAATTAATTAATAATATTTAATATCATCGATACTAATATATTATTAATATTTAATAATTAATAA
1 AAAATTAATTAATAATATTTAATATCATCGATAATAATACATTATTAATACTTAATAATTAATAA
* * *
1640286 ATAAATTTTAATATAATATTTTTTTAATTTTTAAGAAGTGCATTAGTTTAAATTAATAAAATAA
66 ATAAATTTTAATATAATATTTTTTTAATTTTTAAGAAATGCATTAGTTAAAATTAATAAAAAAA
* *
1640350 AAAATTAATTAATAATATTTAATATCATCTATAATGATACATTATTAATACTTAATAATTAATAA
1 AAAATTAATTAATAATATTTAATATCATCGATAATAATACATTATTAATACTTAATAATTAATAA
*
1640415 ATAAATTTTGATATAATATTTTTTTAA-TTTTAAGAAATGCATTAGTTAAAATTAATAAATAAAA
66 ATAAATTTTAATATAATATTTTTTTAATTTTTAAGAAATGCATTAGTTAAAATTAATAAA-AAAA
1640479 AAAATTA
1 AAAATTA
1640486 TTCGATGTAT
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
128 30 0.24
129 96 0.76
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (129 bp):
AAAATTAATTAATAATATTTAATATCATCGATAATAATACATTATTAATACTTAATAATTAATAA
ATAAATTTTAATATAATATTTTTTTAATTTTTAAGAAATGCATTAGTTAAAATTAATAAAAAAA
Found at i:1650657 original size:19 final size:19
Alignment explanation
Indices: 1650635--1650679 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1650625 TTTTAAGGAG
* *
1650635 TTTTTAAGAAATTAATAAC
1 TTTTTAAAAAATAAATAAC
*
1650654 TTTTTAAAAAATAAATAAT
1 TTTTTAAAAAATAAATAAC
1650673 TTTTTAA
1 TTTTTAA
1650680 TTTTTTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TTTTTAAAAAATAAATAAC
Found at i:1651269 original size:29 final size:29
Alignment explanation
Indices: 1651231--1651294 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1651221 ATTTATGCTT
*
1651231 ATTTATAAAATTAA-TTATCAAAATACTATC
1 ATTT-TAAAA-TAATTTATAAAAATACTATC
*
1651261 ATTTTAAAATAATTTATAAAAATACTATT
1 ATTTTAAAATAATTTATAAAAATACTATC
1651290 ATTTT
1 ATTTT
1651295 CGATTGTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 3 0.10
29 24 0.77
30 4 0.13
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTTTAAAATAATTTATAAAAATACTATC
Found at i:1651825 original size:23 final size:23
Alignment explanation
Indices: 1651792--1651888 Score: 92
Period size: 23 Copynumber: 4.3 Consensus size: 23
1651782 ATACAAGAAT
* *
1651792 ATAATACAAATATGACACGAAAA
1 ATAATATAAATATGATACGAAAA
1651815 ATAATATAAATATGATACGAAAA
1 ATAATATAAATATGATACGAAAA
* * * *
1651838 ATAACAAAAATCA-AAAATC-AAAA
1 ATAATATAAAT-ATGATA-CGAAAA
*
1651861 ATAATATAAATATGATATGAAAA
1 ATAATATAAATATGATACGAAAA
1651884 A-AATA
1 ATAATA
1651889 ATATGAACAC
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
22 5 0.08
23 52 0.88
24 2 0.03
ACGTcount: A:0.65, C:0.07, G:0.06, T:0.22
Consensus pattern (23 bp):
ATAATATAAATATGATACGAAAA
Found at i:1651971 original size:23 final size:23
Alignment explanation
Indices: 1651792--1651971 Score: 73
Period size: 23 Copynumber: 7.7 Consensus size: 23
1651782 ATACAAGAAT
* * * *
1651792 ATAATACAAATATGACACGAAAA
1 ATAATATAAATATAATATGAAAA
* *
1651815 ATAATATAAATATGATACGAAAA
1 ATAATATAAATATAATATGAAAA
* * * *
1651838 ATAACAAAAATCA-AAAATCAAAA
1 ATAATATAAAT-ATAATATGAAAA
*
1651861 ATAATATAAATATGATATGAAAAAA
1 ATAATATAAATATAATATG--AAAA
* *
1651886 ATAATATGAACACATACTA--AAAA
1 ATAATAT-AA-ATATAATATGAAAA
* * * *
1651909 AT--TATAAGAGCACAAGACTTAAAAA
1 ATAATATAA-A-TATAATA--TGAAAA
* *
1651934 ATAATATTAACATAATATGAAAA
1 ATAATATAAATATAATATGAAAA
1651957 ATAATATAAATATAA
1 ATAATATAAATATAA
1651972 CGCTGAAAAA
Statistics
Matches: 118, Mismatches: 26, Indels: 26
0.69 0.15 0.15
Matches are distributed among these distances:
20 3 0.03
21 7 0.06
22 1 0.01
23 72 0.61
24 1 0.01
25 22 0.19
26 3 0.03
27 9 0.08
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.23
Consensus pattern (23 bp):
ATAATATAAATATAATATGAAAA
Found at i:1652049 original size:24 final size:24
Alignment explanation
Indices: 1652013--1652071 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
1652003 TTTTTCATGC
* *
1652013 TATTTTTTCATGTAGAGTTCGTGT
1 TATTTTTTAATGTAGAGTTCGTAT
* *
1652037 TATTTTTTAATGTCGTGTTCGTAT
1 TATTTTTTAATGTAGAGTTCGTAT
1652061 TATTTTTTAAT
1 TATTTTTTAAT
1652072 TTGTATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (24 bp):
TATTTTTTAATGTAGAGTTCGTAT
Found at i:1652090 original size:24 final size:23
Alignment explanation
Indices: 1652036--1652138 Score: 93
Period size: 23 Copynumber: 4.4 Consensus size: 23
1652026 AGAGTTCGTG
* **
1652036 TTATTTTTTAATGTCGTGTTCGTA
1 TTATTTTTTAAT-TCGTATTTATA
*
1652060 TTATTTTTTAATTTGTATTTATA
1 TTATTTTTTAATTCGTATTTATA
** *
1652083 TTATTTTTTCGTGTCGCATTTATA
1 TTATTTTTTAAT-TCGTATTTATA
1652107 TTATTTTTCGT-A-TCGTATTTATA
1 TTATTTTT--TAATTCGTATTTATA
1652130 TTATTTTTT
1 TTATTTTTT
1652139 TATATATTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
21 1 0.02
23 35 0.53
24 29 0.44
26 1 0.02
ACGTcount: A:0.19, C:0.07, G:0.10, T:0.64
Consensus pattern (23 bp):
TTATTTTTTAATTCGTATTTATA
Found at i:1652098 original size:47 final size:46
Alignment explanation
Indices: 1652036--1652138 Score: 109
Period size: 47 Copynumber: 2.2 Consensus size: 46
1652026 AGAGTTCGTG
** * *
1652036 TTATTTTTTAATGTCGTGTTCGTATTATTTTT-TAATTTGTATTTATA
1 TTATTTTTTAATGTCGCATTCATATTATTTTTCT-A-TCGTATTTATA
** *
1652083 TTATTTTTTCGTGTCGCATTTATATTATTTTTCGTATCGTATTTATA
1 TTATTTTTTAATGTCGCATTCATATTATTTTTC-TATCGTATTTATA
1652130 TTATTTTTT
1 TTATTTTTT
1652139 TATATATTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
47 45 0.96
48 1 0.02
49 1 0.02
ACGTcount: A:0.19, C:0.07, G:0.10, T:0.64
Consensus pattern (46 bp):
TTATTTTTTAATGTCGCATTCATATTATTTTTCTATCGTATTTATA
Found at i:1652294 original size:36 final size:39
Alignment explanation
Indices: 1652250--1652337 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 39
1652240 TACCAAATAA
*
1652250 TTTTTAAAATTATT-ATA-TTAGATAATATATTTT-TA-T
1 TTTTTAAAATTATTAATATTTACATAATA-ATTTTATATT
* *
1652286 TTTTTAAAATTTTTAATATTTACTTAATAATTTTATATT
1 TTTTTAAAATTATTAATATTTACATAATAATTTTATATT
1652325 TTTTTAATAATTA
1 TTTTTAA-AATTA
1652338 AATATATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
36 13 0.30
37 8 0.19
38 10 0.23
39 8 0.19
40 4 0.09
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (39 bp):
TTTTTAAAATTATTAATATTTACATAATAATTTTATATT
Found at i:1652323 original size:19 final size:20
Alignment explanation
Indices: 1652296--1652336 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1652286 TTTTTAAAAT
1652296 TTTTAATATTTACTTAATAA
1 TTTTAATATTTACTTAATAA
**
1652316 TTTT-ATATTTTTTTAATAA
1 TTTTAATATTTACTTAATAA
1652335 TT
1 TT
1652337 AAATATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAATATTTACTTAATAA
Found at i:1654172 original size:14 final size:16
Alignment explanation
Indices: 1654133--1654177 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
1654123 TTATTGGAGT
1654133 TTTAATAAAATATTAAG
1 TTTAATAAAATA-TAAG
1654150 TTTAA-AAAATA-AA-
1 TTTAATAAAATATAAG
*
1654163 TTTAATAAAAAATAA
1 TTTAATAAAATATAA
1654178 AATCATCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 2 0.08
16 6 0.24
17 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
TTTAATAAAATATAAG
Found at i:1654418 original size:21 final size:22
Alignment explanation
Indices: 1654394--1654446 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
1654384 ATTAAAATGT
*
1654394 TAAAATTAAATTTTAA-AAAAA
1 TAAAATTAAATTATAATAAAAA
* *
1654415 T-AAATTAAAATATAATATAAA
1 TAAAATTAAATTATAATAAAAA
*
1654436 TAAATTTAAAT
1 TAAAATTAAAT
1654447 AAACTCAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 12 0.48
21 6 0.24
22 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAATTAAATTATAATAAAAA
Found at i:1657565 original size:2 final size:2
Alignment explanation
Indices: 1657558--1657602 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1657548 AAATTAAAAC
1657558 AG AG AG AG AG 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 AG AG AG AG AG
1657600 AG A
1 AG A
1657603 ATTCAACAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1659644 original size:3 final size:3
Alignment explanation
Indices: 1659636--1659660 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1659626 CAGAACCAGG
1659636 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1659661 TAAATACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1660002 original size:15 final size:15
Alignment explanation
Indices: 1659978--1660015 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1659968 TAAATTATTT
*
1659978 TTTAAATTATATAAA
1 TTTAATTTATATAAA
1659993 TTTAATTTATATAAA
1 TTTAATTTATATAAA
*
1660008 TTAAATTT
1 TTTAATTT
1660016 TAAATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATTTATATAAA
Found at i:1660083 original size:20 final size:18
Alignment explanation
Indices: 1660044--1660111 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
1660034 ACAGTTAGAT
1660044 TAATA-TTTAATAATAAAA
1 TAATATTTTAAT-ATAAAA
*
1660062 TAATATTTTATATTTAAAAA
1 TAATATTTTA-ATAT-AAAA
* *
1660082 TATAAATATTAATATAAAA
1 TA-ATATTTTAATATAAAA
1660101 TAATATTTTAA
1 TAATATTTTAA
1660112 AATTAATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 12 0.30
19 11 0.28
20 11 0.28
21 6 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATATTTTAATATAAAA
Found at i:1660480 original size:2 final size:2
Alignment explanation
Indices: 1660473--1660517 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
1660463 TTTTATACTT
*
1660473 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TT TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1660513 CA TA T
1 TA TA T
1660518 TATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1661167 original size:31 final size:29
Alignment explanation
Indices: 1661129--1661201 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
1661119 TTTTTAATTT
1661129 ATAAATAAAT-TTTATACAATAAATATATAAA
1 ATAAATAAATATTT-TA-AA-AAATATATAAA
1661160 ATAAATAAAAATATTTTAAAAAATATATAAA
1 ATAAAT--AAATATTTTAAAAAATATATAAA
*
1661191 ATTAATAAATA
1 ATAAATAAATA
1661202 ATAATTAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 5 0.13
31 22 0.58
32 2 0.05
33 6 0.16
34 3 0.08
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
ATAAATAAATATTTTAAAAAATATATAAA
Found at i:1661199 original size:20 final size:20
Alignment explanation
Indices: 1661176--1661218 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1661166 AAAAATATTT
1661176 TAAAAAAT-ATATAAAATTAA
1 TAAAAAATAAT-TAAAATTAA
* *
1661196 TAAATAATAATTAAATTTAA
1 TAAAAAATAATTAAAATTAA
1661216 TAA
1 TAA
1661219 TATAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAAAATAATTAAAATTAA
Done.