Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 24 of 45
Found at i:4338363 original size:26 final size:27
Alignment explanation
Indices: 4338320--4338371 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
4338310 ATGTAATTTT
*
4338320 AAAATTAAATAATTTTAAATATGTAAA
1 AAAATTAAATAATATTAAATATGTAAA
*
4338347 AAAATTTAA-AATATTAAATATGTAA
1 AAAATTAAATAATATTAAATATGTAA
4338372 TTTTAACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
AAAATTAAATAATATTAAATATGTAAA
Found at i:4338419 original size:17 final size:16
Alignment explanation
Indices: 4338383--4338436 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
4338373 TTTAACAATG
* *
4338383 AATAAATATTAAATAT
1 AATAAATATTTAATAA
4338399 AATAAATATTTAATAAA
1 AATAAATATTTAAT-AA
* *
4338416 AATATATATTTAATTA
1 AATAAATATTTAATAA
4338432 AATAA
1 AATAA
4338437 TATCATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 18 0.56
17 14 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAAATATTTAATAA
Found at i:4338439 original size:17 final size:16
Alignment explanation
Indices: 4338383--4338444 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
4338373 TTTAACAATG
*
4338383 AATAA-ATATTAAATA
1 AATAATATATTTAATA
4338398 TAATAA-ATATTTAATA
1 -AATAATATATTTAATA
*
4338414 AAAATATATATTTAATTA
1 AATA-ATATATTTAA-TA
4338432 AATAATATCATTT
1 AATAATAT-ATTT
4338445 TTAATATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
15 3 0.08
16 15 0.38
17 12 0.31
18 9 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATATATTTAATA
Found at i:4338702 original size:20 final size:19
Alignment explanation
Indices: 4338664--4338702 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
4338654 TTTTAACATT
*
4338664 ATATTTAACAAACATAAAA
1 ATATTTAACAAACACAAAA
*
4338683 ATATTATAATAAACACAAAA
1 ATATT-TAACAAACACAAAA
4338703 TGTTAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (19 bp):
ATATTTAACAAACACAAAA
Found at i:4339268 original size:41 final size:37
Alignment explanation
Indices: 4339222--4339306 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 37
4339212 TTTAGTTTTT
* *
4339222 TTTATAACCTTATATTCAAATATAATAATATTCAAATATTA
1 TTTATAAACTTAAATT-AAA-A-AATAATATTCAAATA-TA
* **
4339263 TTTATAAATTTAAATTAAAAAATAATATTTTAATATA
1 TTTATAAACTTAAATTAAAAAATAATATTCAAATATA
4339300 TTTATAA
1 TTTATAA
4339307 TATTATTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
37 9 0.23
38 13 0.33
39 1 0.03
40 3 0.08
41 13 0.33
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (37 bp):
TTTATAAACTTAAATTAAAAAATAATATTCAAATATA
Found at i:4339714 original size:21 final size:21
Alignment explanation
Indices: 4339655--4339714 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
4339645 ATTGAATTAA
4339655 TTAAT-TTAAATTAAAATAATTT
1 TTAATATTAAATT-AAAT-ATTT
*
4339677 TAAATATTAAA--AGAATATTT
1 TTAATATTAAATTA-AATATTT
4339697 TTAATATTAAATTAAATA
1 TTAATATTAAATTAAATA
4339715 AATAATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
20 15 0.47
21 7 0.22
22 5 0.16
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAATATTAAATTAAATATTT
Found at i:4339723 original size:16 final size:16
Alignment explanation
Indices: 4339711--4339741 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4339701 TATTAAATTA
4339711 AATAAATAATAAATAT
1 AATAAATAATAAATAT
*
4339727 AATAAATAATTAATA
1 AATAAATAATAAATA
4339742 AAAATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAATAATAAATAT
Found at i:4341867 original size:20 final size:20
Alignment explanation
Indices: 4341821--4341865 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
4341811 TTTTTAATGT
4341821 TAAAAATAAAATATAGAATA
1 TAAAAATAAAATATAGAATA
*
4341841 TAAAAAT-AAATTTAGAATA
1 TAAAAATAAAATATAGAATA
4341860 TAAAAA
1 TAAAAA
4341866 ATTTATGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (20 bp):
TAAAAATAAAATATAGAATA
Found at i:4343795 original size:2 final size:2
Alignment explanation
Indices: 4343788--4343838 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
4343778 CACTCAAAAG
4343788 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
4343830 TA TA TA TA T
1 TA TA TA TA T
4343839 TTAAGATGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4344280 original size:16 final size:16
Alignment explanation
Indices: 4344259--4344332 Score: 67
Period size: 16 Copynumber: 4.6 Consensus size: 16
4344249 GTCATGTCAA
*
4344259 TTAAAATAATTTAAAT
1 TTAAAATAATTTAAAC
** *
4344275 TTAAAATAATAAAAAAT
1 TTAAAATAAT-TTAAAC
*
4344292 TTAAAATAAATTAAAC
1 TTAAAATAATTTAAAC
* * *
4344308 ATAAATTAACTTAAAC
1 TTAAAATAATTTAAAC
4344324 TTAAAATAA
1 TTAAAATAA
4344333 CTAAGTTCAA
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
16 33 0.72
17 13 0.28
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAATAATTTAAAC
Found at i:4344334 original size:10 final size:10
Alignment explanation
Indices: 4344257--4344332 Score: 53
Period size: 11 Copynumber: 7.1 Consensus size: 10
4344247 ATGTCATGTC
4344257 AATTAAAATA
1 AATTAAAATA
* *
4344267 ATTTAAATTTA
1 AATTAAA-ATA
* *
4344278 AAATAATAAAA
1 AATTAA-AATA
4344289 AATTTAAAATA
1 AA-TTAAAATA
4344300 AATTAAACATA
1 AATTAAA-ATA
**
4344311 AATTAACTTA
1 AATTAAAATA
4344321 AACTTAAAATA
1 AA-TTAAAATA
4344332 A
1 A
4344333 CTAAGTTCAA
Statistics
Matches: 49, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
10 15 0.31
11 30 0.61
12 4 0.08
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (10 bp):
AATTAAAATA
Found at i:4345239 original size:50 final size:50
Alignment explanation
Indices: 4345180--4345417 Score: 370
Period size: 50 Copynumber: 4.8 Consensus size: 50
4345170 TATACTTAGA
* *
4345180 GTCAACAATTATGGCCACATTTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
4345230 GTCAACAATTATGGCCACCTCTCTCTATTGTC-AAGGTTTGGTAAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGG-TTGGTGAAGAATC
* *
4345280 GTCAACAATTATAGCCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
4345330 ATCAACAATTATTGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
4345380 GTCAACAATTATGACAACCTCTCTCTATTGTCAAAGGT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGT
4345418 ATTTTCCACT
Statistics
Matches: 171, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
49 4 0.02
50 163 0.95
51 4 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:4349877 original size:50 final size:50
Alignment explanation
Indices: 4349797--4350032 Score: 341
Period size: 50 Copynumber: 4.8 Consensus size: 50
4349787 TATGCTTAAA
* *
4349797 GTCAACAATTATGACCACCTTTCTCCATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
4349847 ATCAACAATTATGGCCACCTCTCTCTATTGTTAAAGTTTGGTGAAGAATC
1 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * * *
4349897 GTTAACAATTATGA-C-CCTTTCTCTATTATCAAAGGTTGGTGAAAAATT
1 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
4349945 GTCAACAATTATGATCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
4349995 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGT
1 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGT
4350033 ACTTTTCACC
Statistics
Matches: 161, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
48 40 0.25
49 2 0.01
50 119 0.74
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (50 bp):
GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:4349971 original size:98 final size:100
Alignment explanation
Indices: 4349797--4350032 Score: 350
Period size: 98 Copynumber: 2.4 Consensus size: 100
4349787 TATGCTTAAA
* * *
4349797 GTCAACAATTATGACCACCTTTCTCCATTGTCAAAGGTTGGTGAAGAATCATCAACAATTATGGC
1 GTCAACAATTATGACCACCTTTCTCTATTGTCAAAGGTTGGTGAAAAATCATCAACAATTATGAC
* * *
4349862 CACCTCTCTCTATTGTTAAAGTTTGGTGAAGAATC
66 CACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * ** *
4349897 GTTAACAATTATGA-C-CCTTTCTCTATTATCAAAGGTTGGTGAAAAATTGTCAACAATTATGAT
1 GTCAACAATTATGACCACCTTTCTCTATTGTCAAAGGTTGGTGAAAAATCATCAACAATTATGAC
4349960 CACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
66 CACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
4349995 GTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGT
1 GTCAACAATTATGACCACCTTTCTCTATTGTCAAAGGT
4350033 ACTTTTCACC
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
98 86 0.72
99 2 0.02
100 32 0.27
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (100 bp):
GTCAACAATTATGACCACCTTTCTCTATTGTCAAAGGTTGGTGAAAAATCATCAACAATTATGAC
CACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:4350873 original size:22 final size:21
Alignment explanation
Indices: 4350818--4350873 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
4350808 AACAATTAAG
* *
4350818 AATTATTTAGTTTTCATTTTA
1 AATTAATTATTTTTCATTTTA
* *
4350839 AAATGA-TATTTTTCTATTTTA
1 AATTAATTATTTTTC-ATTTTA
4350860 AATTAATTATTTTT
1 AATTAATTATTTTT
4350874 TCTAAATTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 7 0.26
21 13 0.48
22 7 0.26
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (21 bp):
AATTAATTATTTTTCATTTTA
Found at i:4352173 original size:21 final size:21
Alignment explanation
Indices: 4352119--4352177 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
4352109 AGTATCAAAG
*
4352119 GTTATTAAAATTATATTAAAAA
1 GTTATTAAAATCATA-TAAAAA
* * *
4352141 GCTATAAAAATCATATAAGAA
1 GTTATTAAAATCATATAAAAA
4352162 GTTATTAAAATCATAT
1 GTTATTAAAATCATAT
4352178 CAAGTCACTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.36
Consensus pattern (21 bp):
GTTATTAAAATCATATAAAAA
Found at i:4352966 original size:2 final size:2
Alignment explanation
Indices: 4352961--4353002 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
4352951 TGCGTGTGTG
* *
4352961 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TC TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4353002 T
1 T
4353003 TTATTAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4355637 original size:29 final size:28
Alignment explanation
Indices: 4355590--4355660 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
4355580 TTACTTAGTA
* *
4355590 ATTTGTATATTCAT-ATCATATTT-ATAT
1 ATTT-TATATTTATAATCATATTTAAAAT
4355617 ATTTTATCATGTTATAATCATATTTAAAAT
1 ATTTTAT-AT-TTATAATCATATTTAAAAT
4355647 ATTTTATATTTATA
1 ATTTTATATTTATA
4355661 TTGATTCTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 3 0.08
27 6 0.16
28 8 0.21
29 11 0.29
30 10 0.26
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.55
Consensus pattern (28 bp):
ATTTTATATTTATAATCATATTTAAAAT
Found at i:4355858 original size:19 final size:18
Alignment explanation
Indices: 4355819--4355869 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
4355809 AAGTATTAAA
*
4355819 ATATTAATAATTTATTTTT
1 ATATTAAT-ATTTATTATT
4355838 ATATTAATATTTATATATT
1 ATATTAATATTTAT-TATT
4355857 ATAATTAA-ATTTA
1 AT-ATTAATATTTA
4355870 AATAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 6 0.21
19 18 0.62
20 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTAATATTTATTATT
Found at i:4356621 original size:7 final size:7
Alignment explanation
Indices: 4356609--4356637 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
4356599 TTTAATGCTG
4356609 AAAATAA
1 AAAATAA
4356616 AAAATAA
1 AAAATAA
4356623 AAAATAA
1 AAAATAA
4356630 AAAATAA
1 AAAATAA
4356637 A
1 A
4356638 TTTAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:4358564 original size:2 final size:2
Alignment explanation
Indices: 4358557--4358594 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
4358547 AAACACTCTC
* *
4358557 AT AT AT AT AT AT AT AT AT AT AT GT AT TT 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
4358595 TTATTTAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4359045 original size:16 final size:16
Alignment explanation
Indices: 4359012--4359060 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
4359002 AAATCAATTT
4359012 TTTTGAAATAACTT-AAA
1 TTTT-AAATAA-TTAAAA
4359029 TTTTAAATAATTAAAA
1 TTTTAAATAATTAAAA
*
4359045 TATTAAAT--TTAAAA
1 TTTTAAATAATTAAAA
4359059 TT
1 TT
4359061 AATTTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 7 0.24
15 2 0.07
16 16 0.55
17 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTTAAATAATTAAAA
Found at i:4359052 original size:23 final size:24
Alignment explanation
Indices: 4359024--4359069 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
4359014 TTGAAATAAC
*
4359024 TTAAATTTTAAA-TAATTAAAATA
1 TTAAATTTAAAATTAATTAAAATA
*
4359047 TTAAATTTAAAATTAATTTAAAT
1 TTAAATTTAAAATTAATTAAAAT
4359070 TTTTTAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAAATTTAAAATTAATTAAAATA
Found at i:4359089 original size:22 final size:20
Alignment explanation
Indices: 4359052--4359091 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
4359042 AAATATTAAA
4359052 TTTAAAATTAATTTAAATTT
1 TTTAAAATTAATTTAAATTT
4359072 TTTAAAACTTAAATTTAAAT
1 TTTAAAA-TT-AATTTAAAT
4359092 CAATCAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAAATTAATTTAAATTT
Found at i:4360766 original size:24 final size:26
Alignment explanation
Indices: 4360739--4360786 Score: 82
Period size: 24 Copynumber: 1.9 Consensus size: 26
4360729 TTTCATACTC
4360739 ATAAATTT-ATTTTATT-AATATAAT
1 ATAAATTTGATTTTATTAAATATAAT
4360763 ATAAATTTGATTTTATTAAATATA
1 ATAAATTTGATTTTATTAAATATA
4360787 TCATTTGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.36
25 8 0.36
26 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
ATAAATTTGATTTTATTAAATATAAT
Found at i:4361950 original size:21 final size:21
Alignment explanation
Indices: 4361888--4361954 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
4361878 AACTGTGTAG
4361888 TATCAAAATA-TATTAAAATCA
1 TATCAAAA-AGTATTAAAATCA
* *
4361909 TAAT-AAAAGGCTATCAAAATCA
1 T-ATCAAAAAG-TATTAAAATCA
4361931 TATCAAAAAGTATTAAAATCA
1 TATCAAAAAGTATTAAAATCA
4361952 TAT
1 TAT
4361955 TAAATCACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.30
Consensus pattern (21 bp):
TATCAAAAAGTATTAAAATCA
Found at i:4361961 original size:10 final size:11
Alignment explanation
Indices: 4361892--4361958 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
4361882 GTGTAGTATC
4361892 AAAAT-ATATT
1 AAAATCATATT
*
4361902 AAAATCATAAT
1 AAAATCATATT
* *
4361913 AAAAGGC-TATC
1 AAAA-TCATATT
*
4361924 AAAATCATATC
1 AAAATCATATT
4361935 AAAA--AGTATT
1 AAAATCA-TATT
4361945 AAAATCATATT
1 AAAATCATATT
4361956 AAA
1 AAA
4361959 TCACCAAAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
9 1 0.02
10 13 0.29
11 29 0.64
12 2 0.04
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.28
Consensus pattern (11 bp):
AAAATCATATT
Found at i:4362194 original size:30 final size:28
Alignment explanation
Indices: 4362157--4362241 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 28
4362147 ACTTTTACTA
*
4362157 TATTCAAATAAACTTTTAATCTTTATAT
1 TATTCAAATAAACTTTTAATCTTTAGAT
* * * *
4362185 TACATTCAAACAAACCTTTAATTTTTAGCT
1 T--ATTCAAATAAACTTTTAATCTTTAGAT
*
4362215 TTTGTCTAAATAAACTTTTAATCTTTA
1 TAT-TC-AAATAAACTTTTAATCTTTA
4362242 ACATATACCT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
28 2 0.05
29 2 0.05
30 40 0.91
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.47
Consensus pattern (28 bp):
TATTCAAATAAACTTTTAATCTTTAGAT
Found at i:4363436 original size:84 final size:84
Alignment explanation
Indices: 4363295--4363459 Score: 267
Period size: 84 Copynumber: 2.0 Consensus size: 84
4363285 TCATTCAAGA
*
4363295 TACCTGGAAATCCCAAAGCTTGCAAGCTTCCAGAATCTTGAACCTAACACTGTAAGACATGAGAC
1 TACCTGGAAATCCCAAAGCTTGCAAGCTTCCAGAATCTTGAACCTAACACCGTAAGACATGAGAC
4363360 ATCTGCCTTTGGCCGTTGG
66 ATCTGCCTTTGGCCGTTGG
* * * * *
4363379 TACCTGGAAATCCCAAAGCTTGCAAGCTTCCGGAGTCTTGAAGCTAACGCCGTAAGACATTAGAC
1 TACCTGGAAATCCCAAAGCTTGCAAGCTTCCAGAATCTTGAACCTAACACCGTAAGACATGAGAC
*
4363444 ATCTGCCTTTTGCCGT
66 ATCTGCCTTTGGCCGT
4363460 CGGTTTTCAA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (84 bp):
TACCTGGAAATCCCAAAGCTTGCAAGCTTCCAGAATCTTGAACCTAACACCGTAAGACATGAGAC
ATCTGCCTTTGGCCGTTGG
Found at i:4367811 original size:2 final size:2
Alignment explanation
Indices: 4367804--4367837 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4367794 ACTTGGATAA
*
4367804 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4367838 CGCTAGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4369887 original size:22 final size:22
Alignment explanation
Indices: 4369852--4369894 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4369842 AATTTTTATT
4369852 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
4369874 TAAATATTAA-TATAAAAATAT
1 TAAAT-TTAATTATAAAAATAT
4369895 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:4370263 original size:13 final size:13
Alignment explanation
Indices: 4370245--4370269 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4370235 ACTAATTTTA
4370245 TATTTTTTTTAAT
1 TATTTTTTTTAAT
4370258 TATTTTTTTTAA
1 TATTTTTTTTAA
4370270 AAACTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTTTTTAAT
Found at i:4371835 original size:2 final size:2
Alignment explanation
Indices: 4371828--4371870 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4371818 TGATTAGCTT
4371828 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4371870 T
1 T
4371871 TGAGTTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4376024 original size:2 final size:2
Alignment explanation
Indices: 4376017--4376049 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4376007 TAAGTAGCTC
4376017 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
4376050 GTATCAAAAA
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:4379513 original size:2 final size:2
Alignment explanation
Indices: 4379508--4379537 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4379498 TAGGGGGGGG
4379508 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4379538 CCAAAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4383956 original size:10 final size:10
Alignment explanation
Indices: 4383925--4383958 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4383915 GTGAGCTGAG
4383925 ATATACATAT
1 ATATACATAT
*
4383935 ACATACATAT
1 ATATACATAT
*
4383945 ATATATATAT
1 ATATACATAT
4383955 ATAT
1 ATAT
4383959 GTATATATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATACATAT
Found at i:4384222 original size:2 final size:2
Alignment explanation
Indices: 4384215--4384251 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4384205 TAAGTTGGTG
4384215 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4384252 CACGGGGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4386327 original size:23 final size:21
Alignment explanation
Indices: 4386287--4386329 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
4386277 AATATTTAAT
4386287 ATATTTAAATTTTAAATTTTA
1 ATATTTAAATTTTAAATTTTA
*
4386308 ATATTTATAATCTTTTAATTTT
1 ATATTTA-AAT-TTTAAATTTT
4386330 TAAACCGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 9 0.47
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATTTAAATTTTAAATTTTA
Found at i:4386672 original size:2 final size:2
Alignment explanation
Indices: 4386665--4386689 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4386655 TTCAACAATA
4386665 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4386690 AGAAAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4389686 original size:2 final size:2
Alignment explanation
Indices: 4389679--4389714 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4389669 TTTCAAATTA
* *
4389679 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4389715 TAAAAGCTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4389694 original size:10 final size:10
Alignment explanation
Indices: 4389679--4389714 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
4389669 TTTCAAATTA
4389679 ATATATATAC
1 ATATATATAC
*
4389689 ATATATATAT
1 ATATATATAC
4389699 ATATATATAC
1 ATATATATAC
4389709 ATATAT
1 ATATAT
4389715 TAAAAGCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATATATAC
Found at i:4390000 original size:17 final size:17
Alignment explanation
Indices: 4389962--4390020 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
4389952 GATATATGAT
*
4389962 TATAATAATATTTAAAA
1 TATAAAAATATTTAAAA
*
4389979 AATAAAAATAATTT-AAA
1 TATAAAAAT-ATTTAAAA
*
4389996 TATAAAAA-A-TAAAAA
1 TATAAAAATATTTAAAA
*
4390011 TAAAAAAATA
1 TATAAAAATA
4390021 ATATAATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
14 1 0.03
15 11 0.32
16 1 0.03
17 17 0.50
18 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TATAAAAATATTTAAAA
Found at i:4391505 original size:3 final size:3
Alignment explanation
Indices: 4391499--4391527 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4391489 TTTTTTAAAG
4391499 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4391528 GCTAATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4392872 original size:28 final size:26
Alignment explanation
Indices: 4392808--4392873 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 26
4392798 TGAGGTTTTG
*
4392808 AAAAAATACTATAAAAAATTAAAATAT
1 AAAAAATA-TATAAAAAATAAAAATAT
4392835 AAAAATATATATTCAAAATAATAAAAAT-T
1 AAAAA-ATATA-T-AAAA-AATAAAAATAT
4392864 AAAAAATATA
1 AAAAAATATA
4392874 AATGTAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 7 0.21
28 9 0.26
29 10 0.29
30 8 0.24
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (26 bp):
AAAAAATATATAAAAAATAAAAATAT
Found at i:4393306 original size:17 final size:17
Alignment explanation
Indices: 4393284--4393340 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
4393274 CGTATCATAT
4393284 TTATATTATTTTTTATA
1 TTATATTATTTTTTATA
* *
4393301 TTATATCATATTTTATA
1 TTATATTATTTTTTATA
* *
4393318 TAATAAT-TTTTTTATA
1 TTATATTATTTTTTATA
*
4393334 TTGTATT
1 TTATATT
4393341 CACGTTAATA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TTATATTATTTTTTATA
Found at i:4393332 original size:28 final size:28
Alignment explanation
Indices: 4393233--4393334 Score: 68
Period size: 28 Copynumber: 3.6 Consensus size: 28
4393223 TATGACATAT
* * *
4393233 TAATAATTTATATTATATAATTTTTA-A
1 TAATATTTTATATTATATCATATTTATA
* **
4393260 T-ATATTTATGTAATCGTATCATATTTATA
1 TAATATTT-TAT-ATTATATCATATTTATA
* *
4393289 TTATTTTTTATATTATATCATATTTTATA
1 TAATATTTTATATTATATCATA-TTTATA
4393318 TAATAATTTT-T-TTATAT
1 TAAT-ATTTTATATTATAT
4393335 TGTATTCACG
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
26 5 0.09
27 3 0.05
28 26 0.46
29 14 0.25
30 9 0.16
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (28 bp):
TAATATTTTATATTATATCATATTTATA
Found at i:4395300 original size:18 final size:17
Alignment explanation
Indices: 4395277--4395327 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
4395267 AATATAGCAT
4395277 AAATATTATAATATTAAA
1 AAATATT-TAATATTAAA
*
4395295 AAATATTTATTATTAATA
1 AAATATTTAATATTAA-A
*
4395313 TTAATATTTAATATT
1 -AAATATTTAATATT
4395328 TTAATATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 8 0.29
18 8 0.29
19 12 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATATTTAATATTAAA
Found at i:4395310 original size:17 final size:18
Alignment explanation
Indices: 4395277--4395310 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4395267 AATATAGCAT
4395277 AAATATTATAATATTAAA
1 AAATATTATAATATTAAA
*
4395295 AAATATT-TATTATTAA
1 AAATATTATAATATTAA
4395311 TATTAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATATTATAATATTAAA
Found at i:4395314 original size:13 final size:13
Alignment explanation
Indices: 4395296--4395393 Score: 62
Period size: 13 Copynumber: 7.5 Consensus size: 13
4395286 AATATTAAAA
*
4395296 AATATTTATTATT
1 AATATTTAATATT
4395309 AATA-TTAATATTT
1 AATATTTAATA-TT
4395322 AATATTTTAATATT
1 AATA-TTTAATATT
**
4395336 AATATTTTAAATAAA
1 AATA-TTT-AATATT
*
4395351 AATATTT--TAAT
1 AATATTTAATATT
*
4395362 AATATTTAATACT
1 AATATTTAATATT
4395375 AA-ACTATT-ATATT
1 AATA-T-TTAATATT
4395388 AATATT
1 AATATT
4395394 GAAAATTTAA
Statistics
Matches: 70, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
11 10 0.14
12 7 0.10
13 23 0.33
14 16 0.23
15 14 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
AATATTTAATATT
Found at i:4395333 original size:21 final size:22
Alignment explanation
Indices: 4395302--4395342 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
4395292 AAAAAATATT
4395302 TATTATTAATATTAATATTTAA
1 TATTATTAATATTAATATTTAA
4395324 TATT-TTAATATTAATATTT
1 TATTATTAATATTAATATTT
4395343 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTATTAATATTAATATTTAA
Found at i:4395348 original size:15 final size:15
Alignment explanation
Indices: 4395315--4395360 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4395305 TATTAATATT
4395315 AATATTTAATATTTT-
1 AATA-TTAATATTTTA
4395330 AATATTAATATTTTA
1 AATATTAATATTTTA
**
4395345 AATAAAAATATTTTA
1 AATATTAATATTTTA
4395360 A
1 A
4395361 TAATATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTAATATTTTA
Found at i:4395363 original size:14 final size:14
Alignment explanation
Indices: 4395322--4395363 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
4395312 ATTAATATTT
**
4395322 AATATTTTAATATT
1 AATATTTTAATAAA
4395336 AATATTTTAAATAAA
1 AATATTTT-AATAAA
4395351 AATATTTTAATAA
1 AATATTTTAATAA
4395364 TATTTAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTTAATAAA
Found at i:4395696 original size:17 final size:18
Alignment explanation
Indices: 4395674--4395712 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
4395664 TGTTACAATT
*
4395674 TATTATTACACTAA-TAA
1 TATTATTAAACTAAGTAA
*
4395691 TATTATTAAATTAAGTAA
1 TATTATTAAACTAAGTAA
4395709 TATT
1 TATT
4395713 TTTATAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (18 bp):
TATTATTAAACTAAGTAA
Found at i:4395717 original size:21 final size:21
Alignment explanation
Indices: 4395697--4395736 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4395687 ATAATATTAT
*
4395697 TAAAT-TAAGTAATATTTTTA
1 TAAATATAAATAATATTTTTA
4395717 TAAATGATAAATAATATTTT
1 TAAAT-ATAAATAATATTTT
4395737 ACATTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
22 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
TAAATATAAATAATATTTTTA
Found at i:4395737 original size:21 final size:19
Alignment explanation
Indices: 4395686--4395737 Score: 52
Period size: 22 Copynumber: 2.6 Consensus size: 19
4395676 TTATTACACT
*
4395686 AATAATATTAT-TAAATTA
1 AATAATATTTTATAAATTA
*
4395704 AGTAATATTTTTATAAATGATA
1 AATAATA-TTTTATAAAT--TA
4395726 AATAATATTTTA
1 AATAATATTTTA
4395738 CATTAATAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.22
19 3 0.11
20 5 0.19
21 5 0.19
22 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (19 bp):
AATAATATTTTATAAATTA
Found at i:4395815 original size:29 final size:28
Alignment explanation
Indices: 4395758--4395827 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
4395748 TTATTAATTC
* *
4395758 TTATTAAAATAATAATATTATATTATATA
1 TTATTAAAAT-ATAAAAATATATTATATA
*
4395787 TTATTAAAATATAAAAATATATGTTTATA
1 TTATTAAAATATAAAAATATAT-TATATA
*
4395816 ATATTGAAAATA
1 TTATT-AAAATA
4395828 GAAATATTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.29
29 19 0.54
30 6 0.17
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (28 bp):
TTATTAAAATATAAAAATATATTATATA
Found at i:4395815 original size:36 final size:34
Alignment explanation
Indices: 4395784--4395871 Score: 60
Period size: 36 Copynumber: 2.6 Consensus size: 34
4395774 ATTATATTAT
*
4395784 ATATTATTAAAATATAAAAATATATGTTTATAATAT
1 ATATTATTAAAATATAAAAATA-AT-TTTATATTAT
* * **
4395820 -TGA-AAATAGAAATATTGAAATAATTTTATATTA-
1 AT-ATTATTA-AAATATAAAAATAATTTTATATTAT
4395853 ATATT-TTAAAAT-TAAAAAT
1 ATATTATTAAAATATAAAAAT
4395872 TTCTTATTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 13
0.64 0.15 0.21
Matches are distributed among these distances:
31 5 0.13
32 4 0.10
33 3 0.08
34 9 0.23
35 6 0.15
36 12 0.31
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (34 bp):
ATATTATTAAAATATAAAAATAATTTTATATTAT
Found at i:4396667 original size:20 final size:20
Alignment explanation
Indices: 4396630--4396668 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4396620 TTTATAAGCA
* *
4396630 TTTTAATTTTAGTGCCTTAC
1 TTTTAATTTCAGTACCTTAC
*
4396650 TTTTAGTTTCAGTACCTTA
1 TTTTAATTTCAGTACCTTA
4396669 GGAGATTCAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.54
Consensus pattern (20 bp):
TTTTAATTTCAGTACCTTAC
Found at i:4400187 original size:2 final size:2
Alignment explanation
Indices: 4400174--4400209 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4400164 CAGGGACAAA
*
4400174 AT AT AT AC 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
4400210 GATGGGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4407127 original size:18 final size:18
Alignment explanation
Indices: 4407063--4407128 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 18
4407053 TTTTTTTATA
4407063 TTATAATTATATTCAA-AAT
1 TTAT-ATTATATT-AATAAT
4407082 ATTATA-TAT-TTATATAAAT
1 -TTATATTATATTA-AT-AAT
*
4407101 TT-TAATATATTAATAAT
1 TTATATTATATTAATAAT
4407118 TTATATTATAT
1 TTATATTATAT
4407129 AAATTTTAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
16 1 0.03
17 10 0.26
18 17 0.44
19 7 0.18
20 4 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATATTATATTAATAAT
Found at i:4407153 original size:33 final size:31
Alignment explanation
Indices: 4407079--4407161 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 31
4407069 TTATATTCAA
*
4407079 AATATTATATATTTATATAAATTTTAATATATT
1 AATATT-TATA-TTATATAAATTTTAATACATT
4407112 AATAATTTATATTATATAAATTTTAACATACACTT
1 AAT-ATTTATATTATATAAATTTT-A-ATACA-TT
4407147 -ATATTTATATTATAT
1 AATATTTATATTATAT
4407162 TTATATTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
32 13 0.29
33 21 0.47
34 9 0.20
35 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (31 bp):
AATATTTATATTATATAAATTTTAATACATT
Found at i:4407161 original size:5 final size:5
Alignment explanation
Indices: 4407145--4407217 Score: 55
Period size: 5 Copynumber: 14.4 Consensus size: 5
4407135 TAACATACAC
*
4407145 TTATA TTTATA TTATA TTTATA TT-T- TT-TA TCT-TA TTATA TTTTAA
1 TTATA -TTATA TTATA -TTATA TTATA TTATA T-TATA TTATA TTAT-A
*
4407190 TTATT TTATA TTATA TTTATA TTATA TT
1 TTATA TTATA TTATA -TTATA TTATA TT
4407218 TAAAATTATC
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
3 3 0.05
4 3 0.05
5 32 0.56
6 19 0.33
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (5 bp):
TTATA
Found at i:4407161 original size:11 final size:11
Alignment explanation
Indices: 4407145--4407219 Score: 86
Period size: 11 Copynumber: 6.8 Consensus size: 11
4407135 TAACATACAC
4407145 TTATATTTATA
1 TTATATTTATA
4407156 TTATATTTATA
1 TTATATTTATA
4407167 TT-T-TTTATCTTA
1 TTATATTTA---TA
4407179 TTATATTT-TAA
1 TTATATTTAT-A
4407190 TTAT-TTTATA
1 TTATATTTATA
4407200 TTATATTTATA
1 TTATATTTATA
4407211 TTATATTTA
1 TTATATTTA
4407220 AAATTATCAA
Statistics
Matches: 56, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
9 4 0.07
10 10 0.18
11 34 0.61
12 4 0.07
13 1 0.02
14 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATATTTATA
Found at i:4407184 original size:23 final size:21
Alignment explanation
Indices: 4407145--4407219 Score: 82
Period size: 21 Copynumber: 3.4 Consensus size: 21
4407135 TAACATACAC
4407145 TTATATTTATATTATATTTATA
1 TTAT-TTTATATTATATTTATA
4407167 TT-TTTTATCTTATTATATTT-TAA
1 TTATTTTA---TATTATATTTAT-A
4407190 TTATTTTATATTATATTTATA
1 TTATTTTATATTATATTTATA
4407211 TTATATTTA
1 TTAT-TTTA
4407220 AAATTATCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
20 4 0.09
21 16 0.35
22 8 0.17
23 13 0.28
24 5 0.11
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATTTTATATTATATTTATA
Found at i:4409938 original size:12 final size:12
Alignment explanation
Indices: 4409917--4409951 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4409907 GATTGATTTC
*
4409917 AATAAAATTAAA
1 AATAAGATTAAA
4409929 AATAAGATTAAA
1 AATAAGATTAAA
*
4409941 AATGAGATTAA
1 AATAAGATTAA
4409952 TCATTATAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (12 bp):
AATAAGATTAAA
Found at i:4410115 original size:28 final size:28
Alignment explanation
Indices: 4410084--4410160 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 28
4410074 AGGATATTAG
*
4410084 ATTAAAATATATGT-ATA-TATAATAAAT
1 ATTAAAATATAT-TAAAATTATAATAAAT
*
4410111 AATTAAAA-ATTATTAAAATTATATTAAAT
1 -ATTAAAATA-TATTAAAATTATAATAAAT
4410140 ATTAAAATATATT-AAATTATA
1 ATTAAAATATATTAAAATTATA
4410161 TTTATGTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
27 10 0.23
28 23 0.53
29 10 0.23
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
ATTAAAATATATTAAAATTATAATAAAT
Found at i:4410142 original size:18 final size:17
Alignment explanation
Indices: 4410084--4410156 Score: 67
Period size: 18 Copynumber: 4.0 Consensus size: 17
4410074 AGGATATTAG
*
4410084 ATTAAAATATATGTATAT
1 ATTAAAATATAT-TAAAT
*
4410102 ATAATAAATA-ATTAAAAATT
1 ATTA-AAATATATT--AAA-T
4410122 ATTAAAATTATATTAAAT
1 ATTAAAA-TATATTAAAT
4410140 ATTAAAATATATTAAAT
1 ATTAAAATATATTAAAT
4410157 TATATTTATG
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
17 11 0.24
18 13 0.28
19 13 0.28
20 6 0.13
21 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (17 bp):
ATTAAAATATATTAAAT
Found at i:4410176 original size:28 final size:28
Alignment explanation
Indices: 4410087--4410162 Score: 86
Period size: 27 Copynumber: 2.7 Consensus size: 28
4410077 ATATTAGATT
* *
4410087 AAAATATATGTATA-TATAATAAATAATTA
1 AAAATATAT-TAAATTATATTAAAT-ATTA
4410116 AAAAT-TATTAAAATTATATTAAATATT-
1 AAAATATATT-AAATTATATTAAATATTA
4410143 AAAATATATTAAATTATATT
1 AAAATATATTAAATTATATT
4410163 TATGTTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 16 0.38
28 12 0.29
29 14 0.33
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
AAAATATATTAAATTATATTAAATATTA
Found at i:4410205 original size:19 final size:20
Alignment explanation
Indices: 4410167--4410219 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
4410157 TATATTTATG
* *
4410167 TTAAATAATAATTAAAAAAT
1 TTAAATAATTATTTAAAAAT
4410187 TTAAA-AATTATTTAAAAAT
1 TTAAATAATTATTTAAAAAT
4410206 TTAAATAA-TATTTA
1 TTAAATAATTATTTA
4410220 TATTATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 23 0.77
20 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAATAATTATTTAAAAAT
Found at i:4410247 original size:14 final size:14
Alignment explanation
Indices: 4410217--4410262 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
4410207 TAAATAATAT
4410217 TTATATTATTATT-A
1 TTAT-TTATTATTAA
*
4410231 TTATTTATTTTTAA
1 TTATTTATTATTAA
4410245 TTAATTTA-TATTAA
1 TT-ATTTATTATTAA
4410259 TTAT
1 TTAT
4410263 ATAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 9 0.32
14 14 0.50
15 5 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATTATTAA
Found at i:4412006 original size:13 final size:13
Alignment explanation
Indices: 4411988--4412028 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
4411978 TTAAAAAATA
4411988 TTTAATTATTATT
1 TTTAATTATTATT
*
4412001 TTTAATT-TTTTT
1 TTTAATTATTATT
4412013 ATTTAATTATTATT
1 -TTTAATTATTATT
4412027 TT
1 TT
4412029 ATTAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
13 16 0.67
14 4 0.17
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTAATTATTATT
Found at i:4438074 original size:2 final size:2
Alignment explanation
Indices: 4438069--4438098 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4438059 TGTGTGTGTG
4438069 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
4438099 AGTACGTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4439543 original size:30 final size:30
Alignment explanation
Indices: 4439509--4439569 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
4439499 TTATCCGTAC
*
4439509 TTTTAATTTTTTATA-ATATTTATATTTAAA
1 TTTT-ATTTTTTATATATATATATATTTAAA
4439539 TTTTATTTTTTATATATATATATATTTAAA
1 TTTTATTTTTTATATATATATATATTTAAA
4439569 T
1 T
4439570 ATAAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TTTTATTTTTTATATATATATATATTTAAA
Found at i:4439577 original size:14 final size:14
Alignment explanation
Indices: 4439554--4439600 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
4439544 TTTTTTATAT
*
4439554 ATATATATATTTAA
1 ATATAAATATTTAA
**
4439568 ATATAAATATAAAA
1 ATATAAATATTTAA
4439582 ATAT-AATCATTTAA
1 ATATAAAT-ATTTAA
4439596 ATATA
1 ATATA
4439601 TAACAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
13 3 0.12
14 23 0.88
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAAATATTTAA
Found at i:4439603 original size:16 final size:15
Alignment explanation
Indices: 4439547--4439603 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
4439537 AATTTTATTT
*
4439547 TTTATATATATATATA
1 TTTAAATATATA-ATA
4439563 TTTAAATATA-AATA
1 TTTAAATATATAATA
*
4439577 --TAAAAATATAATCA
1 TTTAAATATATAAT-A
4439591 TTTAAATATATAA
1 TTTAAATATATAA
4439604 CAAATTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
12 7 0.21
13 3 0.09
14 4 0.12
15 1 0.03
16 19 0.56
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTAAATATATAATA
Found at i:4439625 original size:2 final size:2
Alignment explanation
Indices: 4439620--4439662 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
4439610 TTAAAAAACC
* * *
4439620 AT AT AT AC AT AC AT AT AT -T AA 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
4439661 AT
1 AT
4439663 CCATAATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4439972 original size:13 final size:14
Alignment explanation
Indices: 4439956--4439988 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4439946 TAAAATAAAA
*
4439956 TTATATT-AAATTT
1 TTATATTAAAAGTT
4439969 TTATATTAAAAGTT
1 TTATATTAAAAGTT
4439983 TTATAT
1 TTATAT
4439989 ACATTTCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
TTATATTAAAAGTT
Found at i:4441550 original size:2 final size:2
Alignment explanation
Indices: 4441543--4441583 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4441533 ATAATTAAAA
4441543 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4441584 ATCTCACTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4442668 original size:26 final size:26
Alignment explanation
Indices: 4442623--4442681 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
4442613 TCTTTTATAT
4442623 TAAATAT-ATTTTTAAATATA-AATA
1 TAAATATAATTTTTAAATATATAATA
*
4442647 TAAATATAATTTTTTAATTATATAATA
1 TAAATATAA-TTTTTAAATATATAATA
*
4442674 -AAAAATAA
1 TAAATATAA
4442682 ATATGTTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 7 0.23
25 1 0.03
26 18 0.60
27 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAATATAATTTTTAAATATATAATA
Found at i:4443623 original size:20 final size:19
Alignment explanation
Indices: 4443594--4443638 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
4443584 TTATATTTAA
*
4443594 TATATCATTAGTATATAAATT
1 TATAT-ATTAATA-ATAAATT
4443615 TATATATTAATAATAAATT
1 TATATATTAATAATAAATT
4443634 T-TATA
1 TATATA
4443639 ACATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 8 0.35
20 6 0.26
21 5 0.22
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TATATATTAATAATAAATT
Found at i:4443659 original size:13 final size:13
Alignment explanation
Indices: 4443625--4443708 Score: 52
Period size: 13 Copynumber: 6.8 Consensus size: 13
4443615 TATATATTAA
4443625 TAATAAATTTTA-
1 TAATAAATTTTAT
*
4443637 T-A-ACATTTTAT
1 TAATAAATTTTAT
*
4443648 TAATAAATTTTAA
1 TAATAAATTTTAT
* * *
4443661 AAATAAATATTAA
1 TAATAAATTTTAT
*
4443674 TAATTATATTTT-T
1 TAA-TAAATTTTAT
**
4443687 TAATAAATAGTAT
1 TAATAAATTTTAT
4443700 T-ATAAATTT
1 TAATAAATTT
4443709 ATACATTGAA
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
10 7 0.13
11 2 0.04
12 13 0.25
13 25 0.47
14 6 0.11
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (13 bp):
TAATAAATTTTAT
Found at i:4444234 original size:14 final size:16
Alignment explanation
Indices: 4444200--4444238 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
4444190 TATCTTAATT
4444200 ATATAAATATATTAAA
1 ATATAAATATATTAAA
*
4444216 ATATAAAT-TATTTAAT
1 ATATAAATATA-TTAAA
4444232 ATATAAA
1 ATATAAA
4444239 ATGTTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAAATATATTAAA
Found at i:4444318 original size:36 final size:33
Alignment explanation
Indices: 4444278--4444360 Score: 103
Period size: 36 Copynumber: 2.4 Consensus size: 33
4444268 ATATGTTATA
4444278 TTTAAAAATATTTAAAAATAATAATAAAATATCTAT
1 TTTAAAAATATTTAAAAAT-ATAATAAAATA-C-AT
* *
4444314 TTTAATAATATATTAAAAATATAATAAATTACAT
1 TTTAAAAATAT-TTAAAAATATAATAAAATACAT
4444348 TTTAAAATATATT
1 TTTAAAA-ATATT
4444361 ATTTTCTCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 9 0.21
35 5 0.12
36 20 0.48
37 8 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.42
Consensus pattern (33 bp):
TTTAAAAATATTTAAAAATATAATAAAATACAT
Found at i:4444906 original size:23 final size:23
Alignment explanation
Indices: 4444876--4444919 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
4444866 ATTATTATTT
*
4444876 ATTATTTT-TATTAATAAAAATAA
1 ATTATTTTAAATTAA-AAAAATAA
4444899 ATTATTTTAAATTAAAAAAAT
1 ATTATTTTAAATTAAAAAAAT
4444920 TAAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTATTTTAAATTAAAAAAATAA
Found at i:4444918 original size:24 final size:23
Alignment explanation
Indices: 4444876--4444923 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
4444866 ATTATTATTT
* *
4444876 ATTATTTTTATTAATAAAAATAA
1 ATTATTTTAATTAAAAAAAATAA
*
4444899 ATTATTTTAAATTAAAAAAATTAA
1 ATTATTTT-AATTAAAAAAAATAA
4444923 A
1 A
4444924 AAGAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTATTTTAATTAAAAAAAATAA
Found at i:4448936 original size:14 final size:15
Alignment explanation
Indices: 4448917--4448947 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4448907 TTGTCTATGC
4448917 TTTCACCTTTT-CTT
1 TTTCACCTTTTCCTT
4448931 TTTCACCTTTTCCTT
1 TTTCACCTTTTCCTT
4448946 TT
1 TT
4448948 ACAAGGAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTCACCTTTTCCTT
Found at i:4452750 original size:19 final size:19
Alignment explanation
Indices: 4452714--4452772 Score: 93
Period size: 19 Copynumber: 3.2 Consensus size: 19
4452704 TAATTTAACG
*
4452714 TAATCTTTT-AATACATAA
1 TAATCTTTTAAATAAATAA
4452732 TAATCTTTTAAATAAATAA
1 TAATCTTTTAAATAAATAA
*
4452751 CAATCTTTTAAATAAATAA
1 TAATCTTTTAAATAAATAA
4452770 TAA
1 TAA
4452773 AATGTTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
18 9 0.24
19 28 0.76
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATCTTTTAAATAAATAA
Found at i:4453518 original size:30 final size:30
Alignment explanation
Indices: 4453478--4453538 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
4453468 ATTAAAAAAA
4453478 TCAAACTTAAATAA-TCTAAACTCAAATAAC
1 TCAAACTTAAATAACT-TAAACTCAAATAAC
* *
4453508 TCAAATTTAAATAACTTAAACTCGAATAAC
1 TCAAACTTAAATAACTTAAACTCAAATAAC
4453538 T
1 T
4453539 TGAATGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.30
Consensus pattern (30 bp):
TCAAACTTAAATAACTTAAACTCAAATAAC
Found at i:4453522 original size:15 final size:15
Alignment explanation
Indices: 4453478--4453529 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
4453468 ATTAAAAAAA
4453478 TCAAACTTAAATAA-
1 TCAAACTTAAATAAC
*
4453492 TCTAAACTCAAATAAC
1 TC-AAACTTAAATAAC
*
4453508 TCAAATTTAAATAAC
1 TCAAACTTAAATAAC
*
4453523 TTAAACT
1 TCAAACT
4453530 CGAATAACTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (15 bp):
TCAAACTTAAATAAC
Found at i:4453535 original size:15 final size:15
Alignment explanation
Indices: 4453480--4453539 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 15
4453470 TAAAAAAATC
*
4453480 AAACTTAAATAA-TCT
1 AAACTCAAATAACT-T
*
4453495 AAACTCAAATAACTC
1 AAACTCAAATAACTT
* *
4453510 AAATTTAAATAACTT
1 AAACTCAAATAACTT
*
4453525 AAACTCGAATAACTT
1 AAACTCAAATAACTT
4453540 GAATGTTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
15 35 0.97
16 1 0.03
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.30
Consensus pattern (15 bp):
AAACTCAAATAACTT
Found at i:4455353 original size:25 final size:25
Alignment explanation
Indices: 4455291--4455338 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
4455281 CATTTTATAT
*
4455291 ATTTTTTATTTTTAATTTTTGTTAA
1 ATTTTTTATTTTTAATTTTAGTTAA
4455316 ATTTTTTATTTTTAA-TTTAGTTA
1 ATTTTTTATTTTTAATTTTAGTTA
4455339 CTTATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (25 bp):
ATTTTTTATTTTTAATTTTAGTTAA
Found at i:4456196 original size:91 final size:91
Alignment explanation
Indices: 4456041--4456221 Score: 353
Period size: 91 Copynumber: 2.0 Consensus size: 91
4456031 CATATTACTA
4456041 GATTATGAATCTTAATTCGTAAATGCTTATTTTCCTATTCATTAGTAGTAATTTATGATTAATGA
1 GATTATGAATCTTAATTCGTAAATGCTTATTTTCCTATTCATTAGTAGTAATTTATGATTAATGA
*
4456106 TTATGGTTAAGTTTTTATTGATTATT
66 TTATGGTTAAATTTTTATTGATTATT
4456132 GATTATGAATCTTAATTCGTAAATGCTTATTTTCCTATTCATTAGTAGTAATTTATGATTAATGA
1 GATTATGAATCTTAATTCGTAAATGCTTATTTTCCTATTCATTAGTAGTAATTTATGATTAATGA
4456197 TTATGGTTAAATTTTTATTGATTAT
66 TTATGGTTAAATTTTTATTGATTAT
4456222 GAGATGGAAC
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (91 bp):
GATTATGAATCTTAATTCGTAAATGCTTATTTTCCTATTCATTAGTAGTAATTTATGATTAATGA
TTATGGTTAAATTTTTATTGATTATT
Found at i:4458917 original size:16 final size:17
Alignment explanation
Indices: 4458890--4458922 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
4458880 CCTGAATGCA
4458890 TATTATTATTAAATATT
1 TATTATTATTAAATATT
4458907 TATTA-TATTAAATATT
1 TATTATTATTAAATATT
4458923 AAAATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATTATTAAATATT
Found at i:4459926 original size:14 final size:14
Alignment explanation
Indices: 4459901--4459962 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 14
4459891 AATAATTAAA
4459901 ATTTTAATATATATT
1 ATTTTAATATAT-TT
4459916 ATTTT-ATATATTT
1 ATTTTAATATATTT
4459929 A-TTTAA-ATACTTT
1 ATTTTAATATA-TTT
* *
4459942 A-ATTAAT-TAATT
1 ATTTTAATATATTT
4459954 ATTTTAATA
1 ATTTTAATA
4459963 ATAAAGATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
12 9 0.23
13 19 0.49
14 6 0.15
15 5 0.13
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTTAATATATTT
Found at i:4459931 original size:16 final size:15
Alignment explanation
Indices: 4459901--4459937 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
4459891 AATAATTAAA
4459901 ATTTTAATATATATT
1 ATTTTAATATATATT
4459916 ATTTT-ATATAT-TT
1 ATTTTAATATATATT
*
4459929 ATTTAAATA
1 ATTTTAATA
4459938 CTTTAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 6 0.30
14 9 0.45
15 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTAATATATATT
Found at i:4460626 original size:21 final size:21
Alignment explanation
Indices: 4460602--4460643 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4460592 TCATAACTCC
*
4460602 AATATTTAATTTTATAATTAT
1 AATAATTAATTTTATAATTAT
*
4460623 AATAATTAATTTTATTATTAT
1 AATAATTAATTTTATAATTAT
4460644 TATTATTATT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AATAATTAATTTTATAATTAT
Found at i:4460640 original size:3 final size:3
Alignment explanation
Indices: 4460634--4460665 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
4460624 ATAATTAATT
4460634 TTA TTA TTA TTA TTA TTA TTA TT- TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4460666 CAAAATTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:4461970 original size:26 final size:26
Alignment explanation
Indices: 4461941--4461996 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
4461931 GAATTGGTGG
4461941 TTAACATCAAGCTTTCACATCCACCA
1 TTAACATCAAGCTTTCACATCCACCA
*
4461967 TTAACATCAAGTTTTCACATCCACCA
1 TTAACATCAAGCTTTCACATCCACCA
4461993 TTAA
1 TTAA
4461997 AAAGCACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (26 bp):
TTAACATCAAGCTTTCACATCCACCA
Found at i:4462007 original size:26 final size:26
Alignment explanation
Indices: 4461953--4462007 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
4461943 AACATCAAGC
* * *
4461953 TTTCACATCCACCATTAACATCAAGT
1 TTTCACATCCACCATTAAAAGCAACT
4461979 TTTCACATCCACCATTAAAAAGC-ACT
1 TTTCACATCCACCATT-AAAAGCAACT
4462005 TTT
1 TTT
4462008 GACAATTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.33
Consensus pattern (26 bp):
TTTCACATCCACCATTAAAAGCAACT
Found at i:4462219 original size:23 final size:22
Alignment explanation
Indices: 4462184--4462226 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4462174 CGAATGATAT
*
4462184 AATTATATTTATTTTAAAAATAA
1 AATTATATATA-TTTAAAAATAA
*
4462207 AATTTTATATATTTAAAAAT
1 AATTATATATATTTAAAAAT
4462227 TTATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTATATATATTTAAAAATAA
Found at i:4462962 original size:17 final size:17
Alignment explanation
Indices: 4462911--4462976 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 17
4462901 CTACTGAACG
4462911 TGATATAAAATATATATATA
1 TGATATAAAATA-A-A-ATA
*
4462931 T-ATATATATATTAAAATA
1 TGATATA-A-AATAAAATA
4462949 TGATATAAAATAAAATA
1 TGATATAAAATAAAATA
*
4462966 TAATATAAAAT
1 TGATATAAAAT
4462977 TAATATAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
17 18 0.45
18 5 0.12
19 11 0.28
20 3 0.08
21 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TGATATAAAATAAAATA
Found at i:4462982 original size:11 final size:12
Alignment explanation
Indices: 4462951--4463073 Score: 64
Period size: 11 Copynumber: 10.3 Consensus size: 12
4462941 TTAAAATATG
*
4462951 ATATAAAATAAA
1 ATATAATATAAA
4462963 ATATAATATAAA
1 ATATAATATAAA
4462975 AT-TAATAT-AA
1 ATATAATATAAA
* *
4462985 ATGTAATGTAAA
1 ATATAATATAAA
*
4462997 TACATAATTATTAAA
1 -ATATAA-TA-TAAA
* *
4463012 AT-TTATATAAT
1 ATATAATATAAA
4463023 ATA-AATA-AATA
1 ATATAATATAA-A
4463034 ATAT-AT-TAAA
1 ATATAATATAAA
*
4463044 AT-TTATATAAA
1 ATATAATATAAA
4463055 TATATAATAATTAAA
1 -ATATAAT-A-TAAA
4463070 ATAT
1 ATAT
4463074 GATTATGATA
Statistics
Matches: 85, Mismatches: 11, Indels: 28
0.69 0.09 0.23
Matches are distributed among these distances:
9 1 0.01
10 11 0.13
11 30 0.35
12 19 0.22
13 9 0.11
14 7 0.08
15 8 0.09
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:4463028 original size:31 final size:30
Alignment explanation
Indices: 4462988--4463067 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 30
4462978 AATATAAATG
*
4462988 TAATGTAAATACATAATTATTAAAATTTATA
1 TAATATAAATA-ATAATTATTAAAATTTATA
4463019 TAATATAAATAAATAATATATTAAAATTTATA
1 TAATATAAAT-AATAAT-TATTAAAATTTATA
*
4463051 TAA-ATATATAATAATTA
1 TAATATAAATAATAATTA
4463068 AAATATGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
29 2 0.04
30 6 0.13
31 19 0.42
32 18 0.40
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (30 bp):
TAATATAAATAATAATTATTAAAATTTATA
Found at i:4463030 original size:27 final size:29
Alignment explanation
Indices: 4462993--4463067 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 29
4462983 AAATGTAATG
*
4462993 TAAATACATAATTATTAAAATTTATATAATA
1 TAAATAAATAATTATTAAAATTTATAT-A-A
4463024 TAAATAAATAATATATTAAAATTTATATAA
1 TAAATAAATAAT-TATTAAAATTTATATAA
*
4463054 -ATATATAATAATTA
1 TAAATA-AATAATTA
4463068 AAATATGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
29 6 0.15
30 7 0.17
31 12 0.30
32 15 0.38
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAATAAATAATTATTAAAATTTATATAA
Found at i:4463060 original size:10 final size:10
Alignment explanation
Indices: 4462913--4463060 Score: 52
Period size: 10 Copynumber: 15.3 Consensus size: 10
4462903 ACTGAACGTG
4462913 ATATAAA-AT
1 ATATAAATAT
*
4462922 ATATATATAT
1 ATATAAATAT
*
4462932 ATATATATAT
1 ATATAAATAT
4462942 -TA-AAATAT
1 ATATAAATAT
4462950 GATAT-AA-A-
1 -ATATAAATAT
4462958 ATA-AAATAT
1 ATATAAATAT
4462967 AATATAAA-ATT
1 -ATATAAATA-T
*
4462978 AATATAAATGT
1 -ATATAAATAT
*
4462989 A-ATGTAA-AT
1 ATAT-AAATAT
* *
4462998 ACATAATTAT
1 ATATAAATAT
*
4463008 -TA-AAATTT
1 ATATAAATAT
4463016 ATAT-AATAT
1 ATATAAATAT
*
4463025 AAATAAATAAT
1 ATATAAAT-AT
*
4463036 ATATTAAAATTT
1 ATA-T-AAATAT
4463048 ATATAAATAT
1 ATATAAATAT
4463058 ATA
1 ATA
4463061 ATAATTAAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 39
0.66 0.09 0.25
Matches are distributed among these distances:
7 5 0.05
8 10 0.10
9 24 0.23
10 38 0.37
11 18 0.17
12 5 0.05
13 4 0.04
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (10 bp):
ATATAAATAT
Found at i:4463096 original size:24 final size:26
Alignment explanation
Indices: 4463016--4463111 Score: 83
Period size: 27 Copynumber: 3.7 Consensus size: 26
4463006 ATTAAAATTT
*
4463016 ATAT-AATATAAATAAATAATATATTAA
1 ATATGAATAT-AATATATAATA-ATTAA
**
4463043 A-ATTTATATAAATATATAATAATTAAA
1 ATATGAATAT-AATATATAATAATT-AA
* *
4463070 ATATGATTATGATATATAA-AATT-A
1 ATATGAATATAATATATAATAATTAA
4463094 ATATGAATATAATATATA
1 ATATGAATATAATATATA
4463112 TTTATATAGA
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
24 17 0.29
26 9 0.16
27 27 0.47
28 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (26 bp):
ATATGAATATAATATATAATAATTAA
Found at i:4464207 original size:16 final size:18
Alignment explanation
Indices: 4464186--4464220 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4464176 TTTTTGTTAA
4464186 ATATTTA-TT-ATATTTT
1 ATATTTATTTAATATTTT
4464202 ATATTTATTTAATATTTT
1 ATATTTATTTAATATTTT
4464220 A
1 A
4464221 ACAAATACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 2 0.12
18 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATTTATTTAATATTTT
Found at i:4464865 original size:39 final size:37
Alignment explanation
Indices: 4464821--4464916 Score: 113
Period size: 39 Copynumber: 2.5 Consensus size: 37
4464811 ATAACAAAAA
* *
4464821 TTAAAAATAAATATATAAGATATTTATTTGATAGGCTAT
1 TTAAAAATAAATATATAA-ATATTTATTTGATAGACT-C
4464860 TTAAAAA-AAATTATATATAATATTTATTTGATAGACTC
1 TTAAAAATAAA-TATATA-AATATTTATTTGATAGACTC
*
4464898 TTAAAAGATAAATGTATAA
1 TTAAAA-ATAAATATATAA
4464917 TGTAATAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
38 10 0.20
39 36 0.72
40 4 0.08
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (37 bp):
TTAAAAATAAATATATAAATATTTATTTGATAGACTC
Found at i:4470317 original size:23 final size:22
Alignment explanation
Indices: 4470287--4470330 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
4470277 TAAAAGGTAC
4470287 GATGGTTCAATTAGGAAACTTAT
1 GATGGTTCAATTAGG-AACTTAT
4470310 GATGGTTCAATTAGGAACTTA
1 GATGGTTCAATTAGGAACTTA
4470331 ACCCACTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (22 bp):
GATGGTTCAATTAGGAACTTAT
Found at i:4474993 original size:2 final size:2
Alignment explanation
Indices: 4474986--4475025 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
4474976 ACAAAGTAGA
* * *
4474986 AT AT AT AT AT AT AT AT AT AT TT AT AT AC AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4475026 CAAGAAGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4475397 original size:18 final size:17
Alignment explanation
Indices: 4475349--4475398 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
4475339 GCAAATTATA
*
4475349 TTTATATATAATATAAATT
1 TTTATATATTA-AT-AATT
*
4475368 TTTATATTTTAATAATT
1 TTTATATATTAATAATT
4475385 TTTATTATATTAAT
1 TTTA-TATATTAAT
4475399 TTTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 8 0.30
18 10 0.37
19 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATATATTAATAATT
Found at i:4475401 original size:24 final size:22
Alignment explanation
Indices: 4475373--4475417 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
4475363 AAATTTTTAT
*
4475373 ATTTTAATAATTTTTATTATATTA
1 ATTTTAA-AATATTTA-TATATTA
4475397 ATTTTAAAATATTTATATATT
1 ATTTTAAAATATTTATATATT
4475418 TATATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 7 0.35
24 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTAAAATATTTATATATTA
Found at i:4475429 original size:28 final size:29
Alignment explanation
Indices: 4475389--4475452 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
4475379 ATAATTTTTA
4475389 TTATATTAATTTTAAAATATTT-A-TATAT
1 TTATATTAATTTTAAAAT-TTTAATTATAT
* * *
4475417 TTATATTATTTTTTAAATTTTAATTATTT
1 TTATATTAATTTTAAAATTTTAATTATAT
4475446 TTATATT
1 TTATATT
4475453 CAAAATTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 3 0.10
28 17 0.55
29 11 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
TTATATTAATTTTAAAATTTTAATTATAT
Found at i:4477129 original size:22 final size:21
Alignment explanation
Indices: 4477103--4477145 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4477093 TTAATCAATA
4477103 AATTTAACAAAA-TAAATTAAAT
1 AATTTAA-AAAATTAAA-TAAAT
4477125 AATTTAAAAAATTAAATAAAT
1 AATTTAAAAAATTAAATAAAT
4477146 GAAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTAAAAAATTAAATAAAT
Found at i:4477139 original size:8 final size:9
Alignment explanation
Indices: 4477112--4477165 Score: 65
Period size: 9 Copynumber: 6.0 Consensus size: 9
4477102 AAATTTAACA
4477112 AAATAAATT
1 AAATAAATT
*
4477121 AAATAATTT
1 AAATAAATT
4477130 AAA-AAATT
1 AAATAAATT
*
4477138 AAATAAATG
1 AAATAAATT
4477147 AAATAAAATT
1 AAAT-AAATT
*
4477157 AATTAAATT
1 AAATAAATT
4477166 TATTTCCTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
8 7 0.18
9 24 0.63
10 7 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATAAATT
Found at i:4481709 original size:3 final size:3
Alignment explanation
Indices: 4481701--4481726 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4481691 AGATTTTCTT
4481701 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
4481727 TTTCTGGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4488322 original size:17 final size:19
Alignment explanation
Indices: 4488300--4488336 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
4488290 GCAGACTCTC
4488300 CTCTTTCA-TTCAC-ATCT
1 CTCTTTCACTTCACAATCT
*
4488317 CTCTTTTACTTCACAATCT
1 CTCTTTCACTTCACAATCT
4488336 C
1 C
4488337 GACAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 5 0.29
19 5 0.29
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.46
Consensus pattern (19 bp):
CTCTTTCACTTCACAATCT
Found at i:4489583 original size:214 final size:214
Alignment explanation
Indices: 4489207--4489633 Score: 800
Period size: 214 Copynumber: 2.0 Consensus size: 214
4489197 TTTTTAAGCA
*
4489207 AGTTAGTCTGGCATTGTGGAATTCACTCCATGTAATTTACGTGCAAATAAAACATCTAGCTTCTA
1 AGTTAGTCTGGCATTGTGGAATTCACTCCATGTAATTTACGTGCAAAAAAAACATCTAGCTTCTA
*
4489272 ATGGTAGATTCAGTGAAAATAAATGGAAATATACTGCACAGATAGCTGGAACATGCATTTGGAGT
66 ATGGTAGATTCAATGAAAATAAATGGAAATATACTGCACAGATAGCTGGAACATGCATTTGGAGT
*
4489337 TTGAAATGACGTAGAAGGTAATGTGACTTCTAGCTTGCCCTGGCCATTCTTCGTTGGCAAACCAA
131 TTGAAATGACGTAGAAGGTAATGTGACTTCTAGCTTGCCCTGGCCATTCGTCGTTGGCAAACCAA
4489402 GCTTTTATCGCCCATTTGG
196 GCTTTTATCGCCCATTTGG
*
4489421 AGTTAGTCTGGCATTGTGGAATTCACTCCATGTAATTTTCGTGCAAAAAAAACATCTAGCTTCTA
1 AGTTAGTCTGGCATTGTGGAATTCACTCCATGTAATTTACGTGCAAAAAAAACATCTAGCTTCTA
4489486 ATGGTAGATTCAATGAAAATAAATGGAAATATACTGCACAGATAGCTGGAACATGCATTTGGAGT
66 ATGGTAGATTCAATGAAAATAAATGGAAATATACTGCACAGATAGCTGGAACATGCATTTGGAGT
* *
4489551 TTGAAATGACGTAGAAGGTAATGTGTCTTCTAGCTTGCCCTGGCCATTCGTCGTTGGCAAACTAA
131 TTGAAATGACGTAGAAGGTAATGTGACTTCTAGCTTGCCCTGGCCATTCGTCGTTGGCAAACCAA
4489616 GCTTTTATCGCCCATTTG
196 GCTTTTATCGCCCATTTG
4489634 ACATGCTGAA
Statistics
Matches: 207, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
214 207 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (214 bp):
AGTTAGTCTGGCATTGTGGAATTCACTCCATGTAATTTACGTGCAAAAAAAACATCTAGCTTCTA
ATGGTAGATTCAATGAAAATAAATGGAAATATACTGCACAGATAGCTGGAACATGCATTTGGAGT
TTGAAATGACGTAGAAGGTAATGTGACTTCTAGCTTGCCCTGGCCATTCGTCGTTGGCAAACCAA
GCTTTTATCGCCCATTTGG
Found at i:4490233 original size:1 final size:1
Alignment explanation
Indices: 4490229--4490254 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4490219 TTCCCCCTCA
4490229 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
4490255 GAAATGCGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:4494888 original size:2 final size:2
Alignment explanation
Indices: 4494881--4494921 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4494871 TGATTTCTTT
4494881 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4494922 TTGACAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.