Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 210 of 218
Found at i:62452708 original size:28 final size:28
Alignment explanation
Indices: 62452667--62452730 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
62452657 ATTATTTATA
** *
62452667 TAATTTTTTGTAATTTTATAA-TTTTTT
1 TAATTTTTAATAATTTTATAACTTCTTT
*
62452694 TCAATTTTTAATAATTTTGTAACTTCTTT
1 T-AATTTTTAATAATTTTATAACTTCTTT
62452723 TAATTTTT
1 TAATTTTT
62452731 GTACTTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.77
29 6 0.19
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.66
Consensus pattern (28 bp):
TAATTTTTAATAATTTTATAACTTCTTT
Found at i:62457140 original size:21 final size:21
Alignment explanation
Indices: 62457110--62457168 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
62457100 AATAAAATTT
*
62457110 AAATATTAAATAATTTATTAA
1 AAATAATAAATAATTTATTAA
*
62457131 AAATAATAAAT--TATATTAA
1 AAATAATAAATAATTTATTAA
**
62457150 TTAT-ATAAATAATTTATTA
1 AAATAATAAATAATTTATTA
62457169 TATAACTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 6 0.19
19 9 0.29
20 6 0.19
21 10 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATAATAAATAATTTATTAA
Found at i:62457168 original size:25 final size:26
Alignment explanation
Indices: 62457131--62457191 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
62457121 AATTTATTAA
* *
62457131 AAATAATAAATTATATTAA-T-TATAT
1 AAATAATTAATTATA-TAACTAAATAT
*
62457156 AAATAATTTATTATATAACTAAATAT
1 AAATAATTAATTATATAACTAAATAT
62457182 AAATAATTAA
1 AAATAATTAA
62457192 ATACGTATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 3 0.10
25 14 0.47
26 13 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATAATTAATTATATAACTAAATAT
Found at i:62460083 original size:5 final size:5
Alignment explanation
Indices: 62460073--62460097 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
62460063 CCACTACCGC
62460073 CTCGA CTCGA CTCGA CTCGA CTCGA
1 CTCGA CTCGA CTCGA CTCGA CTCGA
62460098 GTTTCAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (5 bp):
CTCGA
Found at i:62461059 original size:16 final size:16
Alignment explanation
Indices: 62461027--62461056 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
62461017 AAAATACTAA
62461027 AAATAATTTAATAAAT
1 AAATAATTTAATAAAT
62461043 AAAT-ATTTAATAAA
1 AAATAATTTAATAAA
62461057 ATACTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATAATTTAATAAAT
Found at i:62461710 original size:15 final size:14
Alignment explanation
Indices: 62461687--62461720 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
62461677 GAGCTTATGC
*
62461687 AAAAAAATTTATTA
1 AAAAAAATTTAATA
62461701 AAAAATAATTTAATA
1 AAAAA-AATTTAATA
62461716 AAAAA
1 AAAAA
62461721 CGAGATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAAAAATTTAATA
Found at i:62468229 original size:30 final size:30
Alignment explanation
Indices: 62468195--62468256 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
62468185 TTAAATTATA
*
62468195 AACCTTCTAAAAATAGAAAATTTATAATTT
1 AACCTTCTAAAAATAGAAAATTTATAAGTT
* * * *
62468225 AACCTTTTAAAACTAGTAAATTTTTAAGTT
1 AACCTTCTAAAAATAGAAAATTTATAAGTT
62468255 AA
1 AA
62468257 TACAATAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.39
Consensus pattern (30 bp):
AACCTTCTAAAAATAGAAAATTTATAAGTT
Found at i:62473864 original size:24 final size:24
Alignment explanation
Indices: 62473836--62473889 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
62473826 GCAGTTGGTG
*
62473836 GCAGGTGATAGGAGCGGCGGCAGC
1 GCAGGCGATAGGAGCGGCGGCAGC
* *
62473860 GCAGGCGCTAGGAGCGGCGGTAGC
1 GCAGGCGATAGGAGCGGCGGCAGC
*
62473884 GTAGGC
1 GCAGGC
62473890 TAGGGTGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.22, G:0.50, T:0.09
Consensus pattern (24 bp):
GCAGGCGATAGGAGCGGCGGCAGC
Found at i:62473985 original size:23 final size:23
Alignment explanation
Indices: 62473953--62474006 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
62473943 GTTGGGGTCA
*
62473953 TTGGGCCTTTAAGG-TTTTTAATT
1 TTGGGCCTTT-AGGATTTGTAATT
* *
62473976 TTGGGTCTTTTGGATTTGTAATT
1 TTGGGCCTTTAGGATTTGTAATT
62473999 TTGGGCCT
1 TTGGGCCT
62474007 GCAATTTAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.13, C:0.09, G:0.26, T:0.52
Consensus pattern (23 bp):
TTGGGCCTTTAGGATTTGTAATT
Found at i:62477655 original size:29 final size:29
Alignment explanation
Indices: 62477621--62477679 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
62477611 ATTTATTTTG
*
62477621 TTTTGTTATTTAAATAATTGTTGATATCC
1 TTTTGTTATTTAAATAATTATTGATATCC
* *
62477650 TTTTGTTATTTGAATAATTATTGTTATCC
1 TTTTGTTATTTAAATAATTATTGATATCC
62477679 T
1 T
62477680 ATTCAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.07, G:0.10, T:0.58
Consensus pattern (29 bp):
TTTTGTTATTTAAATAATTATTGATATCC
Found at i:62480550 original size:29 final size:30
Alignment explanation
Indices: 62480518--62480588 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
62480508 CAGGTACTAG
* * *
62480518 ATTAAATTAGTCTATTTATTATT-AAATGA
1 ATTAAATTAGTCTATATACTATTAAAAAGA
* * *
62480547 ATTAATTTAATCTCTATACTATTAAAAAGA
1 ATTAAATTAGTCTATATACTATTAAAAAGA
*
62480577 ATTAAATAAGTC
1 ATTAAATTAGTC
62480589 CAAATTATAA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (30 bp):
ATTAAATTAGTCTATATACTATTAAAAAGA
Found at i:62481137 original size:11 final size:11
Alignment explanation
Indices: 62481121--62481146 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
62481111 AAGTATAAAT
62481121 ATTTATTTTTA
1 ATTTATTTTTA
62481132 ATTTATTTTTA
1 ATTTATTTTTA
62481143 ATTT
1 ATTT
62481147 GTTGGGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTATTTTTA
Found at i:62488563 original size:34 final size:36
Alignment explanation
Indices: 62488497--62488567 Score: 119
Period size: 34 Copynumber: 2.0 Consensus size: 36
62488487 ACATCATTAG
62488497 TTTATCTAAATTGATAACACTACTAATTATTTTCGT
1 TTTATCTAAATTGATAACACTACTAATTATTTTCGT
*
62488533 TTTATCTAAATTGAT-A-ACTATTAATTATTTTCGT
1 TTTATCTAAATTGATAACACTACTAATTATTTTCGT
62488567 T
1 T
62488568 AAACTGATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 18 0.53
35 1 0.03
36 15 0.44
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (36 bp):
TTTATCTAAATTGATAACACTACTAATTATTTTCGT
Found at i:62494869 original size:17 final size:19
Alignment explanation
Indices: 62494849--62494893 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
62494839 TTTTCTTTCA
62494849 AAAATATTTA-TTT-AAAT
1 AAAATATTTATTTTAAAAT
*
62494866 AAAATAATTATTTTAAAAT
1 AAAATATTTATTTTAAAAT
*
62494885 AATATATTT
1 AAAATATTT
62494894 TAAGATACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 3 0.13
19 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATATTTATTTTAAAAT
Found at i:62494884 original size:14 final size:15
Alignment explanation
Indices: 62494865--62494896 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
62494855 TTTATTTAAA
62494865 TAAAATAAT-TATTT
1 TAAAATAATATATTT
62494879 TAAAATAATATATTT
1 TAAAATAATATATTT
62494894 TAA
1 TAA
62494897 GATACTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAATAATATATTT
Found at i:62496186 original size:8 final size:8
Alignment explanation
Indices: 62496173--62496197 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
62496163 GTTAAGAGGT
62496173 GGTGGTGG
1 GGTGGTGG
62496181 GGTGGTGG
1 GGTGGTGG
62496189 GGTGGTGG
1 GGTGGTGG
62496197 G
1 G
62496198 AAGACGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.76, T:0.24
Consensus pattern (8 bp):
GGTGGTGG
Found at i:62496606 original size:9 final size:8
Alignment explanation
Indices: 62496569--62496654 Score: 70
Period size: 8 Copynumber: 10.5 Consensus size: 8
62496559 TACTAATAAT
*
62496569 ATTATAAA
1 ATTAAAAA
62496577 A-TAAAAA
1 ATTAAAAA
62496584 ATT-AAAA
1 ATTAAAAA
*
62496591 TTTAAAAA
1 ATTAAAAA
62496599 TATTAAAAAA
1 -ATT-AAAAA
62496609 ATTAAAAAA
1 ATT-AAAAA
*
62496618 ATTAATAA
1 ATTAAAAA
*
62496626 ATTAATAA
1 ATTAAAAA
62496634 ATTAAATAA
1 ATTAAA-AA
62496643 A-TAAATAA
1 ATTAAA-AA
62496651 ATTA
1 ATTA
62496655 TAGTAACATA
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
7 12 0.18
8 31 0.46
9 19 0.28
10 5 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
ATTAAAAA
Found at i:62499498 original size:20 final size:19
Alignment explanation
Indices: 62499473--62499510 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
62499463 TAAGCTTTTT
62499473 TATTTTTAATATAATTAAAA
1 TATTTTT-ATATAATTAAAA
*
62499493 TATTTTTATATTATTAAA
1 TATTTTTATATAATTAAA
62499511 TTACTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTTTATATAATTAAAA
Found at i:62505872 original size:38 final size:38
Alignment explanation
Indices: 62505821--62505896 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
62505811 AACTTGACAA
62505821 ATGGTTTTAAGAATTAACTTTAATAATAAAAGAAAAAT
1 ATGGTTTTAAGAATTAACTTTAATAATAAAAGAAAAAT
62505859 ATGGTTTTAAGAATTAACTTTAATAATAAAAGAAAAAT
1 ATGGTTTTAAGAATTAACTTTAATAATAAAAGAAAAAT
62505897 TGAAGTCTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (38 bp):
ATGGTTTTAAGAATTAACTTTAATAATAAAAGAAAAAT
Found at i:62507975 original size:18 final size:19
Alignment explanation
Indices: 62507942--62507977 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
62507932 AATAAACATG
62507942 TTAAATTAACAAATTATAT
1 TTAAATTAACAAATTATAT
62507961 TTAAATTAA-AAATTATA
1 TTAAATTAACAAATTATA
62507978 AAATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAATTAACAAATTATAT
Found at i:62508404 original size:45 final size:45
Alignment explanation
Indices: 62508348--62508443 Score: 185
Period size: 45 Copynumber: 2.2 Consensus size: 45
62508338 GAAAAGGTAT
62508348 CAAAA-AGTAAATTAATCCTTTTATTAAAAGGTTAGCGTAATTAA
1 CAAAATAGTAAATTAATCCTTTTATTAAAAGGTTAGCGTAATTAA
62508392 CAAAATAGTAAATTAATCCTTTTATTAAAAGGTTAGCGTAATTAA
1 CAAAATAGTAAATTAATCCTTTTATTAAAAGGTTAGCGTAATTAA
62508437 CAAAATA
1 CAAAATA
62508444 ACCAAATAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 5 0.10
45 46 0.90
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.33
Consensus pattern (45 bp):
CAAAATAGTAAATTAATCCTTTTATTAAAAGGTTAGCGTAATTAA
Found at i:62512605 original size:12 final size:13
Alignment explanation
Indices: 62512576--62512607 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
62512566 TGTAGCTTAT
62512576 ATTGAATTAGTGG
1 ATTGAATTAGTGG
62512589 A-TGAATTAGT-G
1 ATTGAATTAGTGG
62512600 ATTGAATT
1 ATTGAATT
62512608 GATGGAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 15 0.83
13 1 0.06
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (13 bp):
ATTGAATTAGTGG
Found at i:62513136 original size:10 final size:11
Alignment explanation
Indices: 62513110--62513143 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
62513100 TAGATTTATT
62513110 TAAAAATAAAA
1 TAAAAATAAAA
*
62513121 TAAAAATAAAG
1 TAAAAATAAAA
62513132 T-AAAATAAAA
1 TAAAAATAAAA
62513142 TA
1 TA
62513144 TTATGGAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:62513486 original size:27 final size:25
Alignment explanation
Indices: 62513430--62513487 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
62513420 ACTTTAGCGC
**
62513430 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTCAGT
62513455 GCTCTCTGA-TATTTAGCACGTCAGT
1 GCTCTCTGATTA-TTAGCACGTCAGT
62513480 GCTCTCTG
1 GCTCTCTG
62513488 TTCAGCACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 28 0.93
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTCAGT
Found at i:62514642 original size:19 final size:19
Alignment explanation
Indices: 62514615--62514752 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
62514605 TCAACTCATT
*
62514615 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
62514634 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
62514652 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
62514671 TTTTAATTTAAGAA----A
1 TTTTAATTTAATAACTCTA
* *
62514686 -ATTAAGTATAATAACTCTA
1 TTTTAA-TTTAATAACTCTA
*
62514705 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
62514723 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
62514742 TTTTAATTTAA
1 TTTTAATTTAA
62514753 GAAAATTAAG
Statistics
Matches: 92, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
14 4 0.04
15 7 0.08
18 30 0.33
19 47 0.51
20 4 0.04
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:62514661 original size:37 final size:37
Alignment explanation
Indices: 62514620--62514752 Score: 202
Period size: 37 Copynumber: 3.7 Consensus size: 37
62514610 TCATTTTTTT
62514620 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
* *
62514657 ATTTAATAACTCTATTTTAATTTAAGAAA--A-T-TA
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
*
62514690 AGTATAATAACTCTATTTTAATTTAATAAACTATTCTC
1 A-TTTAATAACTCTATTTTAATTTAATAAACTATTCTC
62514728 ATTTAATAACTCTATTTTAATTTAA
1 ATTTAATAACTCTATTTTAATTTAA
62514753 GAAAATTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
33 2 0.02
34 27 0.32
35 1 0.01
36 1 0.01
37 52 0.61
38 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.47
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:62514739 original size:71 final size:71
Alignment explanation
Indices: 62514623--62514764 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
62514613 TTTTTTTATT
62514623 TAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATTTTAATTTAAGAAAAT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATTTTAATTTAAGAAAAT
62514688 TAAGTA
66 TAAGTA
62514694 TAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATTTTAATTTAAGAAAAT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATTTTAATTTAAGAAAAT
62514759 TAAGTA
66 TAAGTA
62514765 CTTAATTTTC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (71 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATTTTAATTTAAGAAAAT
TAAGTA
Found at i:62514987 original size:18 final size:18
Alignment explanation
Indices: 62514966--62515029 Score: 92
Period size: 18 Copynumber: 3.5 Consensus size: 18
62514956 CTCTATTTTA
62514966 ATTTAATAAACTATTCTC
1 ATTTAATAAACTATTCTC
* * *
62514984 ATTTAATAACTCTATTTTA
1 ATTTAATAA-ACTATTCTC
62515003 ATTTAATAAACTATTCTC
1 ATTTAATAAACTATTCTC
62515021 ATTTAATAA
1 ATTTAATAA
62515030 CTCTATTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 24 0.62
19 15 0.38
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTAATAAACTATTCTC
Found at i:62514993 original size:37 final size:37
Alignment explanation
Indices: 62514952--62515045 Score: 188
Period size: 37 Copynumber: 2.5 Consensus size: 37
62514942 CTAACTAAGT
62514952 ATAACTCTATTTTAATTTAATAAACTATTCTCATTTA
1 ATAACTCTATTTTAATTTAATAAACTATTCTCATTTA
62514989 ATAACTCTATTTTAATTTAATAAACTATTCTCATTTA
1 ATAACTCTATTTTAATTTAATAAACTATTCTCATTTA
62515026 ATAACTCTATTTTAATTTAA
1 ATAACTCTATTTTAATTTAA
62515046 ATGAGAATAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (37 bp):
ATAACTCTATTTTAATTTAATAAACTATTCTCATTTA
Found at i:62515006 original size:19 final size:19
Alignment explanation
Indices: 62514952--62515045 Score: 120
Period size: 19 Copynumber: 5.1 Consensus size: 19
62514942 CTAACTAAGT
62514952 ATAACTCTATTTTAATTTA
1 ATAACTCTATTTTAATTTA
* * *
62514971 ATAA-ACTATTCTCATTTA
1 ATAACTCTATTTTAATTTA
62514989 ATAACTCTATTTTAATTTA
1 ATAACTCTATTTTAATTTA
* * *
62515008 ATAA-ACTATTCTCATTTA
1 ATAACTCTATTTTAATTTA
62515026 ATAACTCTATTTTAATTTA
1 ATAACTCTATTTTAATTTA
62515045 A
1 A
62515046 ATGAGAATAG
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
18 30 0.49
19 31 0.51
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAACTCTATTTTAATTTA
Found at i:62515065 original size:18 final size:19
Alignment explanation
Indices: 62515042--62515088 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
62515032 CTATTTTAAT
* *
62515042 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
62515060 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
62515079 TTAAAT-AAAA
1 TTAAATGAAAA
62515089 AAATGAGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:62515096 original size:20 final size:19
Alignment explanation
Indices: 62515057--62515097 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
62515047 TGAGAATAGT
* *
62515057 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
62515076 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
62515096 TT
1 TT
62515098 GAAGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:62515334 original size:18 final size:18
Alignment explanation
Indices: 62515298--62515335 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
62515288 AGTATTACTT
62515298 AATAGTTTATTAAATTAA
1 AATAGTTTATTAAATTAA
62515316 AATAGATTTATTAAA-TAA
1 AATAG-TTTATTAAATTAA
62515334 AA
1 AA
62515336 AAATGAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (18 bp):
AATAGTTTATTAAATTAA
Found at i:62515336 original size:19 final size:18
Alignment explanation
Indices: 62515298--62515336 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
62515288 AGTATTACTT
*
62515298 AATAGTTTATTAAATTAA
1 AATAGTTTATTAAATAAA
62515316 AATAGATTTATTAAATAAA
1 AATAG-TTTATTAAATAAA
62515335 AA
1 AA
62515337 AATGAGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
AATAGTTTATTAAATAAA
Found at i:62515497 original size:27 final size:27
Alignment explanation
Indices: 62515410--62515488 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
62515400 AATTTTAGTC
*
62515410 CTTTGGCACCATTGGTGCCGCCAATCA
1 CTTTGGCACCATTGGTGCCGCCAATCT
*
62515437 CTTTGGCACCATTGGTGCCACCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
*
62515464 CTTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
62515489 GTGATTGGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.16, C:0.33, G:0.22, T:0.29
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:62515823 original size:30 final size:31
Alignment explanation
Indices: 62515789--62515848 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
62515779 CACTTTTTAA
62515789 ACAAT-TTTA-ATGATTTTCAATTTTTAAAAG
1 ACAATATTTATAT-ATTTTCAATTTTTAAAAG
* *
62515819 ACAATATTTATATTTTTTGAATTTTTAAAA
1 ACAATATTTATATATTTTCAATTTTTAAAA
62515849 ATTTAAAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 5 0.19
31 19 0.73
32 2 0.08
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (31 bp):
ACAATATTTATATATTTTCAATTTTTAAAAG
Found at i:62519945 original size:6 final size:6
Alignment explanation
Indices: 62519934--62519965 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
62519924 CACTGGATGT
*
62519934 GCCAAA GCCAAA ACCAAA GCCAAA GCCAAA GC
1 GCCAAA GCCAAA GCCAAA GCCAAA GCCAAA GC
62519966 AGAAGATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.34, G:0.16, T:0.00
Consensus pattern (6 bp):
GCCAAA
Found at i:62538336 original size:16 final size:17
Alignment explanation
Indices: 62538315--62538353 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
62538305 ATTCTATAGA
*
62538315 TATTTTACT-TTTATTT
1 TATTTTACTATGTATTT
62538331 TATTTTACTACTGTATTT
1 TATTTTACTA-TGTATTT
62538349 TATTT
1 TATTT
62538354 AAATAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (17 bp):
TATTTTACTATGTATTT
Found at i:62540003 original size:3 final size:3
Alignment explanation
Indices: 62539995--62540035 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
62539985 GTCATTATTT
62539995 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
62540036 TCCTGCAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:62542418 original size:20 final size:21
Alignment explanation
Indices: 62542393--62542441 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
62542383 GTTTATTTTT
62542393 AAATAATT-TTCTAAAAAATA
1 AAATAATTATTCTAAAAAATA
*
62542413 AAATAATTATTTTAAAAAATA
1 AAATAATTATTCTAAAAAATA
62542434 ATAATAAT
1 A-AATAAT
62542442 AAACAGGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.31
21 12 0.46
22 6 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATAATTATTCTAAAAAATA
Found at i:62550691 original size:5 final size:5
Alignment explanation
Indices: 62550655--62550707 Score: 70
Period size: 5 Copynumber: 10.6 Consensus size: 5
62550645 TCTTAGATTT
* * * *
62550655 TTATT TTATA TTATA TTATT TTATA TCATA TTGTA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
62550705 TTA
1 TTA
62550708 AATAAACTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:62550932 original size:22 final size:22
Alignment explanation
Indices: 62550894--62550940 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
62550884 ATAAAAAGAC
62550894 AAAGAAACAAGAGAAGA-ACAGA
1 AAAGAAACAAGAGAAGAGAC-GA
62550916 AAAGAAAC-AGAGAAAGAGACGA
1 AAAGAAACAAGAG-AAGAGACGA
62550938 AAA
1 AAA
62550941 CAGGGGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.17
22 17 0.74
23 2 0.09
ACGTcount: A:0.68, C:0.09, G:0.23, T:0.00
Consensus pattern (22 bp):
AAAGAAACAAGAGAAGAGACGA
Found at i:62551405 original size:9 final size:9
Alignment explanation
Indices: 62551391--62551418 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
62551381 TAGATAGAAA
62551391 TTTTATTAT
1 TTTTATTAT
62551400 TTTTATTAT
1 TTTTATTAT
62551409 TTTTATTAT
1 TTTTATTAT
62551418 T
1 T
62551419 ATAAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTATTAT
Found at i:62552037 original size:21 final size:24
Alignment explanation
Indices: 62551975--62552043 Score: 110
Period size: 23 Copynumber: 3.0 Consensus size: 24
62551965 GGCTTTGCTG
62551975 ATCAGGCACTTTATGTGTCGTA-C
1 ATCAGGCACTTTATGTGTCGTATC
62551998 ATCAGGCACTTTATGTGTCGTATC
1 ATCAGGCACTTTATGTGTCGTATC
62552022 -TCAGGCAC-TT-TGTGTCGTATC
1 ATCAGGCACTTTATGTGTCGTATC
62552043 A
1 A
62552044 GGCACCACGT
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.25
22 2 0.05
23 30 0.68
24 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (24 bp):
ATCAGGCACTTTATGTGTCGTATC
Found at i:62567557 original size:21 final size:20
Alignment explanation
Indices: 62567531--62567577 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
62567521 CATAAAAATT
* *
62567531 TTAAAAAT-TATATATAAAA
1 TTAAAAATATATAAAAAAAA
62567550 TCTAAAAATATATAAAAAAAA
1 T-TAAAAATATATAAAAAAAA
62567571 TTAAAAA
1 TTAAAAA
62567578 AAATGCTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 13 0.54
21 10 0.42
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
TTAAAAATATATAAAAAAAA
Found at i:62568438 original size:3 final size:3
Alignment explanation
Indices: 62568394--62568423 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
62568384 GGTTATTATT
62568394 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
62568424 ACTGAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:62569428 original size:20 final size:20
Alignment explanation
Indices: 62569395--62569435 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
62569385 CTAATTCAAC
62569395 TCAAGAATTATCAAATTAAAT
1 TCAAGAATTATCAAA-TAAAT
*
62569416 TCAA-AATTTTCAAATAAAT
1 TCAAGAATTATCAAATAAAT
62569435 T
1 T
62569436 TTGAATAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAAGAATTATCAAATAAAT
Found at i:62575505 original size:15 final size:15
Alignment explanation
Indices: 62575485--62575514 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
62575475 GTCGCTCGAC
62575485 TGTAATGATAACCTG
1 TGTAATGATAACCTG
62575500 TGTAATGATAACCTG
1 TGTAATGATAACCTG
62575515 AGTGCCTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
TGTAATGATAACCTG
Found at i:62577655 original size:33 final size:33
Alignment explanation
Indices: 62577613--62577679 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
62577603 GCTCTTTTAG
*
62577613 AGTTCACATCTTTTTAAGTAATTTTGAATTACT
1 AGTTCACATCTTTTTAAGTAATTTTGAATCACT
* **
62577646 AGTTTACATCTTTTTGGGTAATTTTGAATCACT
1 AGTTCACATCTTTTTAAGTAATTTTGAATCACT
62577679 A
1 A
62577680 AGTCGTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (33 bp):
AGTTCACATCTTTTTAAGTAATTTTGAATCACT
Found at i:62578398 original size:97 final size:97
Alignment explanation
Indices: 62578232--62578422 Score: 339
Period size: 97 Copynumber: 2.0 Consensus size: 97
62578222 TCAATGGTTT
* *
62578232 ACATCATTTTTCACTTTCTCAGCTGCCTTTCTTCTCTTTTTTTTTTTTTTTGCCCACATCTCCGC
1 ACATCATTTTTCACTTTCTCAGCTGCCTTTCTTCTCTTTCTTTTTTTTTTTGCCCACATCTCAGC
62578297 TGCTTTAAACTGTGGTGCTTTGGTGGGGGGGA
66 TGCTTTAAACTGTGGTGCTTTGGTGGGGGGGA
62578329 ACATCATTTTTCACTTTCTCAGCTGCCTTTCTTCT-TCTTCTTTTTTTTTTTGCCCACATCTCAG
1 ACATCATTTTTCACTTTCTCAGCTGCCTTTCTTCTCT-TTCTTTTTTTTTTTGCCCACATCTCAG
*
62578393 CTGCTTTATACTGTGGTGCTTTGGTGGGGG
65 CTGCTTTAAACTGTGGTGCTTTGGTGGGGG
62578423 ACTGTACATG
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
96 1 0.01
97 89 0.99
ACGTcount: A:0.11, C:0.24, G:0.18, T:0.47
Consensus pattern (97 bp):
ACATCATTTTTCACTTTCTCAGCTGCCTTTCTTCTCTTTCTTTTTTTTTTTGCCCACATCTCAGC
TGCTTTAAACTGTGGTGCTTTGGTGGGGGGGA
Found at i:62580213 original size:8 final size:7
Alignment explanation
Indices: 62580188--62580212 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
62580178 AATTAATTAT
62580188 TTTTCTA
1 TTTTCTA
62580195 TTTTCTA
1 TTTTCTA
62580202 TTTTCTA
1 TTTTCTA
62580209 TTTT
1 TTTT
62580213 TGCATGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCTA
Found at i:62593679 original size:22 final size:24
Alignment explanation
Indices: 62593649--62593694 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
62593639 TAATTTTAAA
*
62593649 ATTTATATTTGTAT-A-GAAATAT
1 ATTTATATTTATATAATGAAATAT
*
62593671 ATTTCTATTTATATAATGAAATAT
1 ATTTATATTTATATAATGAAATAT
62593695 CGGTATTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 1 0.05
24 7 0.35
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (24 bp):
ATTTATATTTATATAATGAAATAT
Found at i:62594427 original size:18 final size:17
Alignment explanation
Indices: 62594385--62594436 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
62594375 CGATTATGTC
62594385 AAATTTAAGTATCAAGA
1 AAATTTAAGTATCAAGA
*
62594402 AATGTTTAAGTATCAA-A
1 AA-ATTTAAGTATCAAGA
62594419 TTAAATTTAA-TATCAAGA
1 --AAATTTAAGTATCAAGA
62594437 TAAGGGGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 9 0.31
18 18 0.62
19 2 0.07
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.35
Consensus pattern (17 bp):
AAATTTAAGTATCAAGA
Found at i:62600936 original size:16 final size:16
Alignment explanation
Indices: 62600915--62600948 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
62600905 GTTTTTATGT
* *
62600915 TATAAATTATATAATA
1 TATAAATAACATAATA
62600931 TATAAATAACATAATA
1 TATAAATAACATAATA
62600947 TA
1 TA
62600949 ATGTATTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TATAAATAACATAATA
Found at i:62606575 original size:60 final size:60
Alignment explanation
Indices: 62606482--62606602 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
62606472 ATGTCGCGTG
*
62606482 AGTTAGTGGTTTGAACACAGTTAACATTAACATTTTAAAAGCTGGGTGCAGCATTGATCC
1 AGTTAGTGGTTTGAACACAGTTAACATTAACATTTTAAAAGCTGGGTGCAGCATTCATCC
62606542 AGTTAGTGGTTTGAACACAGTTAACATTAACATTTTAAAAGCTGGGTGCAGCATTCATCC
1 AGTTAGTGGTTTGAACACAGTTAACATTAACATTTTAAAAGCTGGGTGCAGCATTCATCC
62606602 A
1 A
62606603 CTCCACTTGA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (60 bp):
AGTTAGTGGTTTGAACACAGTTAACATTAACATTTTAAAAGCTGGGTGCAGCATTCATCC
Found at i:62610775 original size:21 final size:22
Alignment explanation
Indices: 62610751--62610791 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
62610741 GTCATTTCAC
62610751 ATTTAAAT-AAATTTGACTTCG
1 ATTTAAATCAAATTTGACTTCG
* *
62610772 ATTTGAATCAATTTTGACTT
1 ATTTAAATCAAATTTGACTT
62610792 TTGACAGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (22 bp):
ATTTAAATCAAATTTGACTTCG
Found at i:62612880 original size:18 final size:18
Alignment explanation
Indices: 62612837--62612896 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
62612827 GTATAAAATA
62612837 TATATAAAAAA-ATACATT
1 TATATAAAAAATATA-ATT
*
62612855 GCTAATATAAAAAATATATTT
1 --T-ATATAAAAAATATAATT
* *
62612876 TATATAATATATATAATT
1 TATATAAAAAATATAATT
62612894 TAT
1 TAT
62612897 TTTGATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 17 0.50
19 1 0.03
20 1 0.03
21 12 0.35
22 3 0.09
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (18 bp):
TATATAAAAAATATAATT
Found at i:62613559 original size:18 final size:19
Alignment explanation
Indices: 62613536--62613571 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
62613526 TCAACAACAA
*
62613536 GAAC-AATATTTTTAAATT
1 GAACAAATAATTTTAAATT
62613554 GAACAAATAATTTTAAAT
1 GAACAAATAATTTTAAAT
62613572 ACATGGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (19 bp):
GAACAAATAATTTTAAATT
Found at i:62615804 original size:73 final size:73
Alignment explanation
Indices: 62615716--62615856 Score: 180
Period size: 73 Copynumber: 1.9 Consensus size: 73
62615706 TGGCAACCTG
* *
62615716 AAAAGAAGAAAATCCACATACCGAC-AACAAAGTTTGGCAACGTGGATG-TCATCATCAAATCC-
1 AAAAGAAGAAAATCCACATACAGACAAAC-AAGTTTGGCAACGTGGAAGCT-ATCATCAAA-CCA
62615778 ATGATGGAGAC
63 ATGATGGAGAC
* * * *
62615789 AAAAGAAGACAATCCATATGCAGACAAACAAGTTTTGCAACGTGGAAGCTATCATCAAACCAATG
1 AAAAGAAGAAAATCCACATACAGACAAACAAGTTTGGCAACGTGGAAGCTATCATCAAACCAATG
62615854 ATG
66 ATG
62615857 ATGTAAGCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
72 2 0.03
73 53 0.90
74 4 0.07
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (73 bp):
AAAAGAAGAAAATCCACATACAGACAAACAAGTTTGGCAACGTGGAAGCTATCATCAAACCAATG
ATGGAGAC
Found at i:62616862 original size:9 final size:9
Alignment explanation
Indices: 62616840--62616875 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
62616830 ATCATCTATG
62616840 ATAAAAAAC
1 ATAAAAAAC
62616849 TATAAAAAAC
1 -ATAAAAAAC
62616859 ATAAAAAAC
1 ATAAAAAAC
*
62616868 GTAAAAAA
1 ATAAAAAA
62616876 GAAGATAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (9 bp):
ATAAAAAAC
Found at i:62617197 original size:27 final size:27
Alignment explanation
Indices: 62617117--62617201 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 27
62617107 AAACAATCTA
*
62617117 ATGAAGAAAAAACTTCAACAGATCAGG
1 ATGAAGAAAAAACTTAAACAGATCAGG
* * *** *
62617144 A--AATAAAAAA-TAGAAATTTATC-TG
1 ATGAAGAAAAAACT-TAAACAGATCAGG
62617168 ATGAAGAAAAAACTTAAACAGATCAGG
1 ATGAAGAAAAAACTTAAACAGATCAGG
62617195 ATGAAGA
1 ATGAAGA
62617202 TATAAAAGTC
Statistics
Matches: 40, Mismatches: 13, Indels: 10
0.63 0.21 0.16
Matches are distributed among these distances:
24 3 0.08
25 13 0.32
26 14 0.35
27 10 0.25
ACGTcount: A:0.55, C:0.09, G:0.16, T:0.19
Consensus pattern (27 bp):
ATGAAGAAAAAACTTAAACAGATCAGG
Found at i:62622873 original size:19 final size:18
Alignment explanation
Indices: 62622846--62622901 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
62622836 GTTATTATTA
62622846 TTAATTATTAATTTTTATAT
1 TTAA-TATTAA-TTTTATAT
62622866 TTAATATTAATTTTATTAT
1 TTAATATTAATTTTA-TAT
62622885 TT-ATATTTAAATTTTAT
1 TTAATA-TT-AATTTTAT
62622902 GATTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
18 8 0.24
19 14 0.42
20 11 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTAATATTAATTTTATAT
Found at i:62622912 original size:20 final size:20
Alignment explanation
Indices: 62622853--62622905 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
62622843 TTATTAATTA
*
62622853 TTAATTTTTAT-ATTTA-AT
1 TTAAATTTTATGATTTATAT
*
62622871 ATT-AATTTTATTATTTATAT
1 -TTAAATTTTATGATTTATAT
62622891 TTAAATTTTATGATT
1 TTAAATTTTATGATT
62622906 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 7 0.24
19 9 0.31
20 13 0.45
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTAAATTTTATGATTTATAT
Found at i:62628651 original size:3 final size:3
Alignment explanation
Indices: 62628643--62628667 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
62628633 TCTGCAGTTT
62628643 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
62628668 GACATTATCT
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:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:62628717 original size:4 final size:4
Alignment explanation
Indices: 62628708--62628739 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
62628698 CATAAATCTT
62628708 TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
62628740 ACATCCATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:62630625 original size:9 final size:10
Alignment explanation
Indices: 62630604--62630629 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
62630594 TTATATCTTT
62630604 AAAATTTTAA
1 AAAATTTTAA
62630614 AAAATTTTAA
1 AAAATTTTAA
62630624 AAAATT
1 AAAATT
62630630 ACAATTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:62630738 original size:19 final size:19
Alignment explanation
Indices: 62630714--62630752 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
62630704 AGCCGACGGC
62630714 CTTGCCAGCCTCCTGAATT
1 CTTGCCAGCCTCCTGAATT
62630733 CTTGCCAGCCTCCTGAATT
1 CTTGCCAGCCTCCTGAATT
62630752 C
1 C
62630753 GCCACTGCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.38, G:0.15, T:0.31
Consensus pattern (19 bp):
CTTGCCAGCCTCCTGAATT
Found at i:62634065 original size:61 final size:61
Alignment explanation
Indices: 62633990--62634115 Score: 252
Period size: 61 Copynumber: 2.1 Consensus size: 61
62633980 ACAATCTTGT
62633990 TCTATACCTTGTAAACCAGATCCTTGAAACTTATATTCAACTAGCAGTAAACTGACATTCA
1 TCTATACCTTGTAAACCAGATCCTTGAAACTTATATTCAACTAGCAGTAAACTGACATTCA
62634051 TCTATACCTTGTAAACCAGATCCTTGAAACTTATATTCAACTAGCAGTAAACTGACATTCA
1 TCTATACCTTGTAAACCAGATCCTTGAAACTTATATTCAACTAGCAGTAAACTGACATTCA
62634112 TCTA
1 TCTA
62634116 ATCCAAAAAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.32
Consensus pattern (61 bp):
TCTATACCTTGTAAACCAGATCCTTGAAACTTATATTCAACTAGCAGTAAACTGACATTCA
Found at i:62637314 original size:91 final size:93
Alignment explanation
Indices: 62637207--62637404 Score: 357
Period size: 91 Copynumber: 2.2 Consensus size: 93
62637197 AATATTAGAT
62637207 AATAT-TTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATTTTTT-ATATT
1 AATATATTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATTTTTTAATATT
62637270 TAATTGAG-AAAAATAATTATTATTTTA
66 TAATTGAGAAAAAATAATTATTATTTTA
* *
62637297 AATATATTAGTTTATAAAATAATATGTTAATTATTAATGATCGAAGCACTTAATTTTTTAATATT
1 AATATATTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATTTTTTAATATT
62637362 TAATTGAGAAAAAATAATTATTATTTTA
66 TAATTGAGAAAAAATAATTATTATTTTA
62637390 AATATATTAATTTAT
1 AATATATTAATTTAT
62637405 TTTTAATATT
Statistics
Matches: 102, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
90 5 0.05
91 51 0.50
92 13 0.13
93 33 0.32
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (93 bp):
AATATATTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATTTTTTAATATT
TAATTGAGAAAAAATAATTATTATTTTA
Found at i:62637365 original size:211 final size:214
Alignment explanation
Indices: 62637112--62637535 Score: 739
Period size: 212 Copynumber: 2.0 Consensus size: 214
62637102 TGTGTTTTAA
62637112 TTAATTATTAATGATCGAAGCACTTAATTTTTTAACATTTAATTGAGAAAAAATAATTATTATTT
1 TTAATTATTAATGATCGAAGCACTTAATTTTTTAACATTTAATTGAGAAAAAATAATTATTATTT
* *
62637177 T-AA-ATATTAATTTATAAAATAATATTAGATAATATTTAATTTATAAAATAATATATTAATTAT
66 TAAATATATTAATTTAT-AAATAATATTAGATAAGATTCAATTTATAAAATAATATATTAATTAT
*
62637240 TAATGATCGAAGCACTTAATTTTTT-ATATTTAATTGAG-AAAAATAATTATTATTTTAAATATA
130 TAATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAAATATTATTTTAAATATA
*
62637303 TTAGTTTATAAAATAATATG
195 TTAATTTATAAAATAATATG
*
62637323 TTAATTATTAATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAATTATTATTT
1 TTAATTATTAATGATCGAAGCACTTAATTTTTTAACATTTAATTGAGAAAAAATAATTATTATTT
***
62637388 TAAATATATTAATTTATTTTTAATATTAGATAAGATTCAATTTATAAAATAATATATTAATTATT
66 TAAATATATTAATTTATAAATAATATTAGATAAGATTCAATTTATAAAATAATATATTAATTATT
62637453 AATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAAATATTATTTTAAATATAT
131 AATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAAATATTATTTTAAATATAT
62637518 TAATTTATAAAATAATAT
196 TAATTTATAAAATAATAT
62637536 TAGATAATAT
Statistics
Matches: 201, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
211 65 0.32
212 69 0.34
213 25 0.12
214 42 0.21
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (214 bp):
TTAATTATTAATGATCGAAGCACTTAATTTTTTAACATTTAATTGAGAAAAAATAATTATTATTT
TAAATATATTAATTTATAAATAATATTAGATAAGATTCAATTTATAAAATAATATATTAATTATT
AATGATCGAAGCACTTAATTTTTTAATATTTAATTGAGAAAAAATAAATATTATTTTAAATATAT
TAATTTATAAAATAATATG
Found at i:62637531 original size:29 final size:29
Alignment explanation
Indices: 62637498--62637577 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
62637488 GAGAAAAAAT
*
62637498 AAATATTATTTTAAATATATTAATTTATA
1 AAATAATATTTTAAATATATTAATTTATA
**
62637527 AAATAATATTAGATAATAT-TTAATTTATA
1 AAATAATATTTTA-AATATATTAATTTATA
*
62637556 AAATAATATATT-AAT-TATTAAT
1 AAATAATATTTTAAATATATTAAT
62637578 GATCGAATCG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 8 0.19
29 29 0.67
30 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
AAATAATATTTTAAATATATTAATTTATA
Found at i:62637537 original size:18 final size:17
Alignment explanation
Indices: 62637493--62637537 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
62637483 TAATTGAGAA
62637493 AAAATAAATATT-ATTTT
1 AAAAT-AATATTAATTTT
62637510 -AAAT-ATATTAATTTAT
1 AAAATAATATTAATTT-T
62637526 AAAATAATATTA
1 AAAATAATATTA
62637538 GATAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 5 0.21
15 4 0.17
16 5 0.21
17 4 0.17
18 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATAATATTAATTTT
Found at i:62637574 original size:122 final size:122
Alignment explanation
Indices: 62637297--62637786 Score: 784
Period size: 122 Copynumber: 4.0 Consensus size: 122
62637287 TATTATTTTA
* * * *
62637297 AATATATTAGTTTATAAAATAATATGTTAATTATTAATGATCGAAGCACTTAATTTTTTAATATT
1 AATAT-TTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATCTTTTAAAATT
* ***
62637362 TAATTGAGAAAAAATAATTATTATTTTAAATATATTAATTTAT-TTTTAATATTAGAT
65 TAATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
* * * *
62637419 AAGATTCAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATTTTTTAATATTT
1 AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATCTTTTAAAATTT
62637484 AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
66 AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
* *
62637541 AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAATCGCTTAATCTTTTAAAATTT
1 AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATCTTTTAAAATTT
*
62637606 AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAACATTAGAT
66 AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
* *
62637663 AATATTTAATTTATAAAATAATACATTAATTATTAATGATCGAAGCGCTTAATCTTTTAAAATTT
1 AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATCTTTTAAAATTT
* * *
62637728 AATTGAGAAAAAATAATTATTATTTTAAACATTTTAATTTATAAAATAATATTAGAT
66 AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
62637785 AA
1 AA
62637787 GAAATTGGGG
Statistics
Matches: 346, Mismatches: 21, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
121 98 0.28
122 248 0.72
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (122 bp):
AATATTTAATTTATAAAATAATATATTAATTATTAATGATCGAAGCACTTAATCTTTTAAAATTT
AATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAATATTAGAT
Found at i:62637606 original size:58 final size:58
Alignment explanation
Indices: 62637544--62637751 Score: 153
Period size: 58 Copynumber: 3.5 Consensus size: 58
62637534 ATTAGATAAT
*
62637544 ATTTAATTTATAAAATAATATATTAATTATTAATGATCGAATCGCTTAATCTTTTAAA
1 ATTTAATTGATAAAATAATATATTAATTATTAATGATCGAATCGCTTAATCTTTTAAA
* * ** **
62637602 ATTTAATTGAGAAAAAATAAATATTATTTTAAATATATTAATTTATAAAATAACATTAGA-----
1 ATTTAATT--GATAAAAT-AATA-TA--TT-AAT-TATTAA-TGATCGAATCGC-TTA-ATCTTT
*
62637662 TAAT
55 TAAA
* * *
62637666 ATTTAATTTATAAAATAATACATTAATTATTAATGATCGAAGCGCTTAATCTTTTAAA
1 ATTTAATTGATAAAATAATATATTAATTATTAATGATCGAATCGCTTAATCTTTTAAA
*
62637724 ATTTAATTGAGAAAA-AATA-ATT-ATTATT
1 ATTTAATTGATAAAATAATATATTAATTATT
62637752 TTAAACATTT
Statistics
Matches: 114, Mismatches: 20, Indels: 35
0.67 0.12 0.21
Matches are distributed among these distances:
53 1 0.01
54 3 0.03
55 12 0.11
56 9 0.08
57 7 0.06
58 26 0.23
60 7 0.06
61 8 0.07
62 8 0.07
64 13 0.11
65 3 0.03
66 6 0.05
67 7 0.06
68 3 0.03
69 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (58 bp):
ATTTAATTGATAAAATAATATATTAATTATTAATGATCGAATCGCTTAATCTTTTAAA
Found at i:62638574 original size:23 final size:21
Alignment explanation
Indices: 62638507--62638567 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
62638497 CCTGATTAGT
*
62638507 ATACGACACATAA-GTGCCTG
1 ATACGACACACAAGGTGCCTG
* *
62638527 AAACGACACACGAGGTGCCTG
1 ATACGACACACAAGGTGCCTG
62638548 ATACGACACACAAGGTGCCT
1 ATACGACACACAAGGTGCCT
62638568 AAGATACAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 10 0.29
21 25 0.71
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.15
Consensus pattern (21 bp):
ATACGACACACAAGGTGCCTG
Found at i:62638616 original size:23 final size:23
Alignment explanation
Indices: 62638572--62638616 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
62638562 GTGCCTAAGA
* **
62638572 TACAATACATAAAGTGTTTGATG
1 TACAACACATAAAGTGCCTGATG
62638595 TACAACACATAAAGTGCCTGAT
1 TACAACACATAAAGTGCCTGAT
62638617 CGGCCAAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (23 bp):
TACAACACATAAAGTGCCTGATG
Found at i:62639673 original size:3 final size:3
Alignment explanation
Indices: 62639665--62639731 Score: 89
Period size: 3 Copynumber: 22.3 Consensus size: 3
62639655 ATGTATTAGT
* *
62639665 TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
62639713 TTA TAA TTA TAA TTA TAA T
1 TAA TAA TAA TAA TAA TAA T
62639732 TTATCAAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:62639895 original size:18 final size:19
Alignment explanation
Indices: 62639851--62639888 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
62639841 CTATTTGATT
62639851 TAATTTATAATATAATATCA
1 TAATTT-TAATATAATATCA
62639871 TAATTTTAAT-TAATATCA
1 TAATTTTAATATAATATCA
62639889 AGATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATTTTAATATAATATCA
Found at i:62639896 original size:19 final size:20
Alignment explanation
Indices: 62639851--62639897 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
62639841 CTATTTGATT
*
62639851 TAATTTATAATATAATATCA
1 TAATTTTTAATATAATATCA
62639871 TAA-TTTTAAT-TAATATCA
1 TAATTTTTAATATAATATCA
62639889 -AGATTTTTA
1 TA-ATTTTTA
62639898 TGAAGTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 9 0.38
19 11 0.46
20 3 0.12
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (20 bp):
TAATTTTTAATATAATATCA
Found at i:62640403 original size:22 final size:22
Alignment explanation
Indices: 62640375--62640421 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
62640365 ATAAAATTAT
62640375 TAAATA-TTAAAATAA-AATAAAA
1 TAAATATTTAAAA-AATAA-AAAA
62640397 TAAATATTTAAAAAATAAAAAA
1 TAAATATTTAAAAAATAAAAAA
62640419 TAA
1 TAA
62640422 TATGGGCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAATATTTAAAAAATAAAAAA
Found at i:62641358 original size:30 final size:30
Alignment explanation
Indices: 62641304--62641361 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
62641294 TTTCAATTAG
62641304 TTCAATGATCATTTTCTAACTTTTTAAAAA
1 TTCAATGATCATTTTCTAACTTTTTAAAAA
* *
62641334 TTCAATGATCATTTTGTAATTTTTTAAA
1 TTCAATGATCATTTTCTAACTTTTTAAA
62641362 GTTAAGTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.50
Consensus pattern (30 bp):
TTCAATGATCATTTTCTAACTTTTTAAAAA
Found at i:62643967 original size:11 final size:11
Alignment explanation
Indices: 62643951--62643976 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
62643941 TAGAAGAGAC
62643951 GAAACAGGGGA
1 GAAACAGGGGA
62643962 GAAACAGGGGA
1 GAAACAGGGGA
62643973 GAAA
1 GAAA
62643977 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:62644638 original size:12 final size:12
Alignment explanation
Indices: 62644621--62644669 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
62644611 ATGTGAGGTA
*
62644621 AGTATTAATGTT
1 AGTATTAATATT
62644633 AGTATTAATATT
1 AGTATTAATATT
* *
62644645 ATTATTAGTATT
1 AGTATTAATATT
* *
62644657 ATTATTATTATT
1 AGTATTAATATT
62644669 A
1 A
62644670 TGAGTGGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (12 bp):
AGTATTAATATT
Found at i:62644649 original size:3 final size:3
Alignment explanation
Indices: 62644635--62644670 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
62644625 TTAATGTTAG
* *
62644635 TAT TAA TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
62644671 GAGTGGGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:62645082 original size:37 final size:39
Alignment explanation
Indices: 62645023--62645118 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
62645013 CGGATAGATT
* * * *
62645023 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
62645060 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
62645099 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
62645119 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:62651647 original size:11 final size:11
Alignment explanation
Indices: 62651631--62651656 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
62651621 TAGAAGAGAC
62651631 GAAACAGGGGA
1 GAAACAGGGGA
62651642 GAAACAGGGGA
1 GAAACAGGGGA
62651653 GAAA
1 GAAA
62651657 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:62652318 original size:12 final size:12
Alignment explanation
Indices: 62652301--62652349 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
62652291 ATGTGAGGTA
*
62652301 AGTATTAATGTT
1 AGTATTAATATT
62652313 AGTATTAATATT
1 AGTATTAATATT
* *
62652325 ATTATTAGTATT
1 AGTATTAATATT
* *
62652337 ATTATTATTATT
1 AGTATTAATATT
62652349 A
1 A
62652350 TGAGTGGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (12 bp):
AGTATTAATATT
Found at i:62652329 original size:3 final size:3
Alignment explanation
Indices: 62652315--62652350 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
62652305 TTAATGTTAG
* *
62652315 TAT TAA TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
62652351 GAGTGGGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:62663077 original size:42 final size:43
Alignment explanation
Indices: 62663030--62663111 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 43
62663020 ATATTTGTGG
*
62663030 TGCCACCACGTTATTTGGAGGCA-CCAAAATGAAAAAAAAAAT
1 TGCCACCACATTATTTGGAGGCACCCAAAATGAAAAAAAAAAT
* *
62663072 TGCCACCACATTATTTGGAGGCACCCAAATTGAATAAAAA
1 TGCCACCACATTATTTGGAGGCACCCAAAATGAAAAAAAA
62663112 TTTTTGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 22 0.61
43 14 0.39
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.21
Consensus pattern (43 bp):
TGCCACCACATTATTTGGAGGCACCCAAAATGAAAAAAAAAAT
Found at i:62663445 original size:31 final size:30
Alignment explanation
Indices: 62663390--62663448 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
62663380 AAAATATGTC
*
62663390 GTTTTTAGGGTAGTAGTTATGCGGTTAAGA
1 GTTTTTAGGGTAGTAGTTACGCGGTTAAGA
* *
62663420 GTTTTTATTGGTAGTGGTTACGCGGTTAA
1 GTTTTTA-GGGTAGTAGTTACGCGGTTAA
62663449 TGGTCCATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.20, C:0.05, G:0.32, T:0.42
Consensus pattern (30 bp):
GTTTTTAGGGTAGTAGTTACGCGGTTAAGA
Found at i:62664034 original size:36 final size:37
Alignment explanation
Indices: 62663964--62664036 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 37
62663954 AGTGGGCGGC
*
62663964 ATGTGTATAATATATATAGTTTTTATATTAATTATAA
1 ATGTGTATAATATATATAGTTTTTATAATAATTATAA
62664001 ATGT-TATAATATATATA-TTATATTATAAT-ATTATAA
1 ATGTGTATAATATATATAGTT-T-TTATAATAATTATAA
62664037 TTAAACAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
35 2 0.06
36 21 0.64
37 10 0.30
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (37 bp):
ATGTGTATAATATATATAGTTTTTATAATAATTATAA
Found at i:62664039 original size:14 final size:14
Alignment explanation
Indices: 62663992--62664039 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
62663982 GTTTTTATAT
*
62663992 TAATTATAAATGTTA
1 TAATTAT-AATATTA
62664007 TAA-TATATATATTA
1 TAATTATA-ATATTA
62664021 T-ATTATAATATTA
1 TAATTATAATATTA
62664034 TAATTA
1 TAATTA
62664040 AACAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 9 0.31
14 17 0.59
15 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TAATTATAATATTA
Found at i:62665252 original size:41 final size:41
Alignment explanation
Indices: 62665189--62665313 Score: 151
Period size: 41 Copynumber: 3.0 Consensus size: 41
62665179 ACTAATCTGA
* * * *
62665189 TTTATTGCCAGTGAAATAATTCAGACTTTATGTCTAGTAGGC
1 TTTA-TGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
*
62665231 TTTATGCCGGTGAAATTATTCAGACTATACGTCTAGCAGGC
1 TTTATGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
* * * * *
62665272 TTAATGCCGGTGATACATTTCAGACTATAAGTCTAGCAGGC
1 TTTATGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
62665313 T
1 T
62665314 AAAAGCCGGT
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 68 0.94
42 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (41 bp):
TTTATGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
Found at i:62665526 original size:13 final size:13
Alignment explanation
Indices: 62665510--62665534 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62665500 ATATTAAATA
62665510 TATATGCATTTGG
1 TATATGCATTTGG
62665523 TATATGCATTTG
1 TATATGCATTTG
62665535 ATAAGCAATT
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:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
TATATGCATTTGG
Found at i:62666482 original size:20 final size:20
Alignment explanation
Indices: 62666453--62666490 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
62666443 AAAATGTAAA
*
62666453 AAAATGGAGTTTAATAAAAT
1 AAAATGGAGTTAAATAAAAT
*
62666473 AAAATTGAGTTAAATAAA
1 AAAATGGAGTTAAATAAA
62666491 GAAATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (20 bp):
AAAATGGAGTTAAATAAAAT
Found at i:62666774 original size:52 final size:52
Alignment explanation
Indices: 62666621--62666775 Score: 199
Period size: 51 Copynumber: 3.0 Consensus size: 52
62666611 ATGAAGAAAT
* * *
62666621 AAAAAAT-ATTTTTTATTCAATTTGGGTGCATTCAAATAATATGGCGGCACT
1 AAAAAATAATTTTTTATTCAATTTGGGTGCCTTTAAATAATATGGCGGCACC
* * *
62666672 AAAAAATAA-TTTTTATTCAATTTGGGTGCCTCTAAATAATGTGGTGGCACC
1 AAAAAATAATTTTTTATTCAATTTGGGTGCCTTTAAATAATATGGCGGCACC
* * *
62666723 AAAAAATAATTTTTTATTTC-ATTTTGGTGCCTTTAAATAACATGACGGCACC
1 AAAAAATAATTTTTTA-TTCAATTTGGGTGCCTTTAAATAATATGGCGGCACC
62666775 A
1 A
62666776 TAAATATTAA
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
51 52 0.58
52 34 0.38
53 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Consensus pattern (52 bp):
AAAAAATAATTTTTTATTCAATTTGGGTGCCTTTAAATAATATGGCGGCACC
Found at i:62691515 original size:51 final size:51
Alignment explanation
Indices: 62691434--62691536 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
62691424 TTCTGATCAG
* *
62691434 TGATAAGTGACAAGTGGAAAGTGATAAGTGATTGCTTCAGCTACACTTATC
1 TGATAAGTGACAAATGGAAAGTGATAAGTGATAGCTTCAGCTACACTTATC
* *
62691485 TGATCAGTGACAAATGGAAAGTGATAAGTGATAGCTTCAGCTATACTTATC
1 TGATAAGTGACAAATGGAAAGTGATAAGTGATAGCTTCAGCTACACTTATC
62691536 T
1 T
62691537 TCAGCTATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (51 bp):
TGATAAGTGACAAATGGAAAGTGATAAGTGATAGCTTCAGCTACACTTATC
Found at i:62691540 original size:16 final size:16
Alignment explanation
Indices: 62691519--62691552 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
62691509 TAAGTGATAG
62691519 CTTCAGCTATACTTAT
1 CTTCAGCTATACTTAT
62691535 CTTCAGCTATACTTAT
1 CTTCAGCTATACTTAT
62691551 CT
1 CT
62691553 GATCAGTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.26, G:0.06, T:0.44
Consensus pattern (16 bp):
CTTCAGCTATACTTAT
Found at i:62691549 original size:67 final size:67
Alignment explanation
Indices: 62691468--62691603 Score: 227
Period size: 67 Copynumber: 2.0 Consensus size: 67
62691458 TAAGTGATTG
*
62691468 CTTCAGCTACACTTATCTGATCAGTGACAAATGGAAAGTGATAAGTGATAGCTTCAGCTATACTT
1 CTTCAGCTACACTTATCTGATCAGTGACAAATGGAAAGTGATAAGTGATAGCTTCAGCTACACTT
62691533 AT
66 AT
* * * *
62691535 CTTCAGCTATACTTATCTGATCAGTGACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTT
1 CTTCAGCTACACTTATCTGATCAGTGACAAATGGAAAGTGATAAGTGATAGCTTCAGCTACACTT
62691600 AT
66 AT
62691602 CT
1 CT
62691604 GATCAGTGAC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (67 bp):
CTTCAGCTACACTTATCTGATCAGTGACAAATGGAAAGTGATAAGTGATAGCTTCAGCTACACTT
AT
Found at i:62695927 original size:12 final size:12
Alignment explanation
Indices: 62695899--62695931 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
62695889 CCCCCCAAAA
62695899 TTTTCC-TCCTG
1 TTTTCCTTCCTG
62695910 -TTTCCTTCCTG
1 TTTTCCTTCCTG
62695921 TTTTCCTTCCT
1 TTTTCCTTCCT
62695932 CCCAAACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 5 0.25
12 10 0.50
ACGTcount: A:0.00, C:0.36, G:0.06, T:0.58
Consensus pattern (12 bp):
TTTTCCTTCCTG
Found at i:62697540 original size:10 final size:10
Alignment explanation
Indices: 62697527--62697674 Score: 55
Period size: 10 Copynumber: 15.3 Consensus size: 10
62697517 TTTTGATGCA
62697527 TTTTATAAAT
1 TTTTATAAAT
*
62697537 TTTTAT-GAT
1 TTTTATAAAT
*
62697546 TTTTATAAAA
1 TTTTATAAAT
**
62697556 TTTTACCAAT
1 TTTTATAAAT
*
62697566 TTTTATATAT
1 TTTTATAAAT
62697576 TTTT-TACAAT
1 TTTTATA-AAT
* *
62697586 ATATAT-AA-
1 TTTTATAAAT
*
62697594 TTTTCT-AAT
1 TTTTATAAAT
*
62697603 TTTTAGT-GAT
1 TTTTA-TAAAT
62697613 TTTTA-AATAT
1 TTTTATAA-AT
*
62697623 TTTAAATATAAT
1 TTT-TATA-AAT
* *
62697635 TTAT-TAAAG
1 TTTTATAAAT
*
62697644 TTTAAT-AAT
1 TTTTATAAAT
62697653 TTTTAT-AAT
1 TTTTATAAAT
*
62697662 TTTTATAACT
1 TTTTATAAAT
62697672 TTT
1 TTT
62697675 ATTGATTTTT
Statistics
Matches: 99, Mismatches: 27, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
8 5 0.05
9 36 0.36
10 50 0.51
11 2 0.02
12 5 0.05
13 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:62697549 original size:19 final size:20
Alignment explanation
Indices: 62697527--62697579 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
62697517 TTTTGATGCA
**
62697527 TTTTATAAATTTTTA-TGAT
1 TTTTATAAATTTTTACCAAT
*
62697546 TTTTATAAAATTTTACCAAT
1 TTTTATAAATTTTTACCAAT
*
62697566 TTTTATATATTTTT
1 TTTTATAAATTTTT
62697580 TACAATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTATAAATTTTTACCAAT
Found at i:62697662 original size:9 final size:9
Alignment explanation
Indices: 62697527--62697695 Score: 81
Period size: 9 Copynumber: 17.4 Consensus size: 9
62697517 TTTTGATGCA
62697527 TTTTATAAAT
1 TTTTAT-AAT
*
62697537 TTTTATGAT
1 TTTTATAAT
*
62697546 TTTTATAAAA
1 TTTTAT-AAT
*
62697556 TTTTACCAAT
1 TTTTA-TAAT
62697566 TTTTATATATT
1 TTTTATA-A-T
*
62697577 TTTTACAAT
1 TTTTATAAT
* *
62697586 ATATATAA-
1 TTTTATAAT
*
62697594 TTTTCTAAT
1 TTTTATAAT
*
62697603 TTTTAGTGAT
1 TTTTA-TAAT
*
62697613 TTTTAAATAT
1 TTTTATA-AT
62697623 TTTAAATATAAT
1 TTT---TATAAT
*
62697635 TTATTA-AAG
1 TT-TTATAAT
*
62697644 TTTAATAAT
1 TTTTATAAT
62697653 TTTTATAAT
1 TTTTATAAT
*
62697662 TTTTATAAC
1 TTTTATAAT
*
62697671 TTTTATTGATT
1 TTTTA-T-AAT
62697682 TTTTATAACT
1 TTTTATAA-T
62697692 TTTT
1 TTTT
62697696 GCCATATGTC
Statistics
Matches: 118, Mismatches: 26, Indels: 30
0.68 0.15 0.17
Matches are distributed among these distances:
8 7 0.06
9 47 0.40
10 43 0.36
11 13 0.11
12 4 0.03
13 4 0.03
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTATAAT
Found at i:62711243 original size:31 final size:30
Alignment explanation
Indices: 62711203--62711267 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
62711193 ATTGTGTAAT
* *
62711203 GAATGAATGAAACTGTACTAAGTATTGAAA
1 GAATGAATGAAAATGTACTAAGTAATGAAA
* *
62711233 GAATAGAATGAAAATGTATTGAGTAATGAAA
1 GAAT-GAATGAAAATGTACTAAGTAATGAAA
62711264 GAAT
1 GAAT
62711268 TCTTTGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.26
Consensus pattern (30 bp):
GAATGAATGAAAATGTACTAAGTAATGAAA
Found at i:62712846 original size:85 final size:87
Alignment explanation
Indices: 62712730--62712982 Score: 237
Period size: 88 Copynumber: 2.9 Consensus size: 87
62712720 TTTTTTTCTT
** * * * * * * * * * *
62712730 TTTTTTTTACACTCAATTGAGCACTTAAACTTTTAAAATGTATCAAAAATATCTTTACA-CTTCT
1 TTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAAACCTTAAAATCTTCT
62712794 TCAAAAAAAGCAATTAAACC-C-
66 TCAAAAAAA-CAATTAAACCTCA
* * *
62712815 TTTTTTTCCCGCTCAATTGGGTACTTGAACTTTCATAATGCAT-AAAAAAACCTTAAAATTTTTT
1 TTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAAACCTTAAAA-TCTTC
* *
62712879 TTCAAAGAAACAATTAAGCCTCTA
65 TTCAAAAAAACAATTAAACCTC-A
** * * *
62712903 TTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAGGCCTT-AATTTTTTT
1 TTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAAACCTTAAAATCTTCT
*
62712967 TCAAAAAAGCAATTAA
66 TCAAAAAAACAATTAA
62712983 GCCCATACTC
Statistics
Matches: 139, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
84 11 0.08
85 43 0.31
86 12 0.09
87 20 0.14
88 44 0.32
89 9 0.06
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (87 bp):
TTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAAACCTTAAAATCTTCT
TCAAAAAAACAATTAAACCTCA
Found at i:62712921 original size:88 final size:87
Alignment explanation
Indices: 62712797--62712985 Score: 280
Period size: 88 Copynumber: 2.2 Consensus size: 87
62712787 CACTTCTTCA
* *
62712797 AAAAAAGCAATTAAACC-C--TTTTTTTCCCGCTCAATTGGGTACTTGAACTTTCATAATGCAT-
1 AAAAAAGCAATTAAGCCTCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATC
62712858 AAAAAAACCTTAAAATTTTTTTTC
66 AAAAAAACCTT--AATTTTTTTTC
62712882 AAAGAAA-CAATTAAGCCTCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
1 AAA-AAAGCAATTAAGCCTCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
**
62712946 CAAAAAGGCCTTAATTTTTTTTC
65 CAAAAAAACCTTAATTTTTTTTC
62712969 AAAAAAGCAATTAAGCC
1 AAAAAAGCAATTAAGCC
62712986 CATACTCTTA
Statistics
Matches: 94, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
85 12 0.13
86 7 0.07
87 24 0.26
88 42 0.45
89 9 0.10
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (87 bp):
AAAAAAGCAATTAAGCCTCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATC
AAAAAAACCTTAATTTTTTTTC
Found at i:62713060 original size:19 final size:20
Alignment explanation
Indices: 62713016--62713060 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
62713006 GAAAAAAATC
62713016 ATAAAAATAATAAATTTTAG
1 ATAAAAATAATAAATTTTAG
* *
62713036 AAAAAAATATTAAATTTTA-
1 ATAAAAATAATAAATTTTAG
62713055 ATAAAA
1 ATAAAA
62713061 TTTAAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAAATAATAAATTTTAG
Found at i:62713420 original size:10 final size:10
Alignment explanation
Indices: 62713407--62713477 Score: 51
Period size: 10 Copynumber: 7.5 Consensus size: 10
62713397 CTTTATAAAA
62713407 TTTTATAATT
1 TTTTATAATT
62713417 TTTTAT-A-T
1 TTTTATAATT
** *
62713425 TTCAAT-ATA
1 TTTTATAATT
62713434 TTTTATAATT
1 TTTTATAATT
*
62713444 TTTTA-AAAT
1 TTTTATAATT
*
62713453 TTTTAAAATT
1 TTTTATAATT
* *
62713463 TTTAATAAAT
1 TTTTATAATT
62713473 TTTTA
1 TTTTA
62713478 ATATTTGATT
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
8 6 0.13
9 13 0.28
10 27 0.59
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTTATAATT
Found at i:62713423 original size:20 final size:20
Alignment explanation
Indices: 62713398--62713477 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 20
62713388 TTCTTATGAC
62713398 TTTATAAAATTTTATAATTTT
1 TTTATAAAATTTTATAA-TTT
62713419 TTATATTTCAATATATTTTATAATTT
1 TT-TA--T-AA-A-ATTTTATAATTT
* *
62713445 TTTA-AAATTTTTAAAATTT
1 TTTATAAAATTTTATAATTT
* *
62713464 TTAATAAATTTTTA
1 TTTATAAAATTTTA
62713478 ATATTTGATT
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
19 13 0.27
20 10 0.20
21 4 0.08
22 2 0.04
24 1 0.02
25 4 0.08
26 6 0.12
27 9 0.18
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATAAAATTTTATAATTT
Found at i:62713455 original size:9 final size:9
Alignment explanation
Indices: 62713443--62713483 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
62713433 ATTTTATAAT
62713443 TTTTTAAAA
1 TTTTTAAAA
62713452 TTTTTAAAA
1 TTTTTAAAA
62713461 TTTTTAATAAA
1 TTTTT-A-AAA
*
62713472 TTTTTAATA
1 TTTTTAAAA
62713481 TTT
1 TTT
62713484 GATTTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 19 0.66
10 2 0.07
11 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:62713478 original size:20 final size:19
Alignment explanation
Indices: 62713434--62713483 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
62713424 TTTCAATATA
* *
62713434 TTTTATAATTTTTTAAAAT
1 TTTTAAAATTTTTAAAAAT
62713453 TTTTAAAATTTTTAATAAAT
1 TTTTAAAATTTTTAA-AAAT
*
62713473 TTTTAATATTT
1 TTTTAAAATTT
62713484 GATTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAAATTTTTAAAAAT
Found at i:62713480 original size:11 final size:10
Alignment explanation
Indices: 62713440--62713478 Score: 53
Period size: 11 Copynumber: 3.9 Consensus size: 10
62713430 TATATTTTAT
*
62713440 AATTTTTTAA
1 AATTTTTAAA
62713450 AATTTTT-AA
1 AATTTTTAAA
62713459 AATTTTTAATA
1 AATTTTTAA-A
62713470 AATTTTTAA
1 AATTTTTAA
62713479 TATTTGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.33
10 8 0.30
11 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:62713730 original size:93 final size:90
Alignment explanation
Indices: 62713554--62713723 Score: 268
Period size: 93 Copynumber: 1.9 Consensus size: 90
62713544 TTAATAAAAA
* * *
62713554 TAGGGGCTTAATTGCTTTTTTTAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTAC
1 TAGGGGCCTAATTGCTTTTTTTAAAGTTTGAGGGCCGTTTTGATGCATTTTGAAAGTTCAAGTAC
*
62713619 CCAATTGAGTGCCAAAAAAATAAAG
66 CCAAATGAGTGCCAAAAAAATAAAG
*
62713644 TAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCGTTTTGATGTATTTTGAAAGTTCAAG
1 TAGGGGCCTAATTGCTTTTTTT--AAA-GTTTGAGGGCCGTTTTGATGCATTTTGAAAGTTCAAG
62713709 TACCCAAATGAGTGC
63 TACCCAAATGAGTGC
62713724 ATAAAAAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
90 21 0.29
92 3 0.04
93 48 0.67
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (90 bp):
TAGGGGCCTAATTGCTTTTTTTAAAGTTTGAGGGCCGTTTTGATGCATTTTGAAAGTTCAAGTAC
CCAAATGAGTGCCAAAAAAATAAAG
Found at i:62719761 original size:88 final size:86
Alignment explanation
Indices: 62719648--62719842 Score: 268
Period size: 89 Copynumber: 2.2 Consensus size: 86
62719638 CACTTCTTCA
* *
62719648 AAAAAAGCAATTAAACCCCT-TTTTTTTCCCGCTCAATTAGGTACTTGAACTTTCATAATGCATA
1 AAAAAAGCAATTAAGCCCCTATTTTTTTCCCACTCAATTAGGTACTTGAACTTTCATAATGCATA
62719712 AAAAAAACCTTAAATTTTTTTTTC
66 AAAAAAACCTT-AA--TTTTTTTC
* * *
62719736 AAAGAAA-CAATTAAGCCTCTATTTTTTTCCCACTTAATTGGGTACTTGAACTTTCATAATGCAT
1 AAA-AAAGCAATTAAGCCCCTATTTTTTTCCCACTCAATTAGGTACTTGAACTTTCATAATGCAT
* **
62719800 CAAAAAGGCCTTAATTTTTTTC
65 AAAAAAAACCTTAATTTTTTTC
62719822 AAAAAAGCAATTAAGCCCCTA
1 AAAAAAGCAATTAAGCCCCTA
62719843 CTCTTATTAA
Statistics
Matches: 95, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
85 3 0.03
86 24 0.25
88 16 0.17
89 52 0.55
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (86 bp):
AAAAAAGCAATTAAGCCCCTATTTTTTTCCCACTCAATTAGGTACTTGAACTTTCATAATGCATA
AAAAAAACCTTAATTTTTTTC
Found at i:62719979 original size:27 final size:28
Alignment explanation
Indices: 62719943--62719998 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
62719933 ATTTGAATTT
*
62719943 TTTTAGAAAAAT-AGTCAAAAA-ATAAAA
1 TTTTAGAAAAATCA-TAAAAAATATAAAA
*
62719970 TTTTATAAAAATCATAAAAAATATAAAA
1 TTTTAGAAAAATCATAAAAAATATAAAA
62719998 T
1 T
62719999 CTATCAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (28 bp):
TTTTAGAAAAATCATAAAAAATATAAAA
Found at i:62720868 original size:3 final size:3
Alignment explanation
Indices: 62720860--62720902 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
62720850 TTCTTCACAT
62720860 TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
62720903 AATGTTCAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:62720885 original size:19 final size:19
Alignment explanation
Indices: 62720861--62720899 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
62720851 TCTTCACATT
62720861 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
62720880 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
62720899 A
1 A
62720900 TAAAATGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAATAATAATAATAATA
Found at i:62720888 original size:22 final size:22
Alignment explanation
Indices: 62720860--62720903 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
62720850 TTCTTCACAT
62720860 TAATAATAATAATAATAATAAA
1 TAATAATAATAATAATAATAAA
62720882 TAATAATAATAATAATAATAAA
1 TAATAATAATAATAATAATAAA
62720904 ATGTTCAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAATAATAATAATAATAATAAA
Found at i:62721508 original size:17 final size:17
Alignment explanation
Indices: 62721486--62721519 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62721476 ATCCACTAAT
*
62721486 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62721503 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62721520 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62726146 original size:17 final size:17
Alignment explanation
Indices: 62726124--62726157 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62726114 ATCCACTAAT
*
62726124 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62726141 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62726158 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Done.