Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012939.1 Kokia drynarioides strain JFW-HI SEQ_127957, whole genome shotgun sequence
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: 280555
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 114 characters in sequence are not A, C, G, or T
Found at i:1402 original size:20 final size:21
Alignment explanation
Indices: 1360--1402 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1350 AACGTGTCAA
*
1360 GTTAACTGGCCACGTCAACTT
1 GTTAACTAGCCACGTCAACTT
*
1381 GTTAACTAGCCGCGTC-ACTT
1 GTTAACTAGCCACGTCAACTT
1401 GT
1 GT
1403 CTCATTAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (21 bp):
GTTAACTAGCCACGTCAACTT
Found at i:5362 original size:26 final size:23
Alignment explanation
Indices: 5308--5364 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
5298 AATATAAAAC
5308 TATATTATTTTATATTTTAAATT
1 TATATTATTTTATATTTTAAATT
5331 TATATTATTATTCAT-TTTTACAATT
1 TATATTATT-TT-ATATTTTA-AATT
5356 T-T-TTATTTT
1 TATATTATTTT
5365 TTTTATTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 2 0.06
23 14 0.45
24 8 0.26
25 7 0.23
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
TATATTATTTTATATTTTAAATT
Found at i:8926 original size:2 final size:2
Alignment explanation
Indices: 8919--8962 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
8909 AATATAAGAA
8919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8961 AT
1 AT
8963 TTAAAATTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9361 original size:29 final size:29
Alignment explanation
Indices: 9300--9361 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
9290 AGTTTGCATT
* * * *
9300 AAATTTTGAGGTTTAATTATAATTCTTAC
1 AAATTTTAAGGTTTAATTAAAATTCTCAA
9329 AAATTTTAAGGATTTAATTAAAATT-TCAA
1 AAATTTTAAGG-TTTAATTAAAATTCTCAA
9358 AAAT
1 AAAT
9362 ATTGAGGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (29 bp):
AAATTTTAAGGTTTAATTAAAATTCTCAA
Found at i:18946 original size:37 final size:36
Alignment explanation
Indices: 18823--19014 Score: 127
Period size: 37 Copynumber: 5.3 Consensus size: 36
18813 TTTTCTATAT
** *
18823 TTTTTATA-ATTGTTTTCACTTTTCAATATTTTTAAAATA
1 TTTTTATATATT-TTTTCA-TTTTTTATA-TTTTAATA-A
* *
18862 TTTTTA-AT-TTTTTTCATGTTTCTAT-TTTTCATAA
1 TTTTTATATATTTTTTCAT-TTTTTATATTTTAATAA
18896 --TTTATATGA-TTTTTCATTTTTTATTATTTTAATAA
1 TTTTTATAT-ATTTTTTCATTTTTTA-TATTTTAATAA
* *
18931 TTTTTATATATTTTTTTCATTTGTAATAAATTTT-ATAA
1 TTTTTATATA-TTTTTTCATTT-T-TTATATTTTAATAA
* *
18969 -TTTTATATATTTTTTCA-CTTTTATATTTTTA-AA
1 TTTTTATATATTTTTTCATTTTTTATATTTTAATAA
19002 TTTTTATGATATT
1 TTTTTAT-ATATT
19015 CTATATTCTG
Statistics
Matches: 127, Mismatches: 10, Indels: 36
0.73 0.06 0.21
Matches are distributed among these distances:
32 4 0.03
33 16 0.13
34 18 0.14
35 20 0.16
36 10 0.08
37 28 0.22
38 17 0.13
39 12 0.09
40 2 0.02
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (36 bp):
TTTTTATATATTTTTTCATTTTTTATATTTTAATAA
Found at i:18957 original size:29 final size:28
Alignment explanation
Indices: 18911--18981 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
18901 ATGATTTTTC
* *
18911 ATTTTTTATTATTTTAATAATTTTTATA
1 ATTTTTTATCATTTTAATAAATTTTATA
18939 TATTTTTT-TCATTTGTAATAAATTTTATA
1 -ATTTTTTATCATTT-TAATAAATTTTATA
*
18968 ATTTTATAT-ATTTT
1 ATTTTTTATCATTTT
18982 TTCACTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 1 0.03
28 15 0.41
29 21 0.57
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (28 bp):
ATTTTTTATCATTTTAATAAATTTTATA
Found at i:18998 original size:8 final size:8
Alignment explanation
Indices: 18859--19008 Score: 54
Period size: 9 Copynumber: 17.2 Consensus size: 8
18849 TATTTTTAAA
18859 ATATTTTT
1 ATATTTTT
18867 A-ATTTTT
1 ATATTTTT
* *
18874 TTCATGTTT
1 AT-ATTTTT
*
18883 CTATTTTT
1 ATATTTTT
*
18891 CATAATTTAT
1 -AT-ATTTTT
18901 ATGATTTTT
1 AT-ATTTTT
18910 CAT-TTTTT
1 -ATATTTTT
*
18918 ATTATTTTA
1 A-TATTTTT
18927 ATAATTTTTAT
1 AT-A-TTTT-T
18938 ATATTTTT
1 ATATTTTT
* *
18946 TTCATTTGTA
1 AT-ATTT-TT
*
18956 ATAAATTTT
1 AT-ATTTTT
18965 ATAATTTTAT
1 AT-ATTTT-T
18975 ATATTTTT
1 ATATTTTT
*
18983 -TCACTTTT
1 AT-ATTTTT
18991 ATATTTTT
1 ATATTTTT
*
18999 AAATTTTT
1 ATATTTTT
19007 AT
1 AT
19009 GATATTCTAT
Statistics
Matches: 106, Mismatches: 21, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
7 8 0.08
8 34 0.32
9 42 0.40
10 20 0.19
11 2 0.02
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (8 bp):
ATATTTTT
Found at i:19006 original size:16 final size:16
Alignment explanation
Indices: 18961--19008 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
18951 TTGTAATAAA
18961 TTTTATAATTTTATATAT
1 TTTTA-AATTTT-TATAT
** *
18979 TTTTTCACTTTTATAT
1 TTTTAAATTTTTATAT
18995 TTTTAAATTTTTAT
1 TTTTAAATTTTTAT
19009 GATATTCTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 16 0.67
17 4 0.17
18 4 0.17
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTAAATTTTTATAT
Found at i:24225 original size:2 final size:2
Alignment explanation
Indices: 24218--24249 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
24208 ATGCATACAA
*
24218 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24250 CATTCCTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25367 original size:4 final size:4
Alignment explanation
Indices: 25358--25384 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
25348 AACAGCACTT
25358 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
25385 TATATACCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:25683 original size:60 final size:60
Alignment explanation
Indices: 25611--25733 Score: 246
Period size: 60 Copynumber: 2.0 Consensus size: 60
25601 TATCAGTTGA
25611 AATATGGGTTTTGCATGAATTGCAGCCATTGGTGATTTTAAGCTGTTTTTGAGGTCTATC
1 AATATGGGTTTTGCATGAATTGCAGCCATTGGTGATTTTAAGCTGTTTTTGAGGTCTATC
25671 AATATGGGTTTTGCATGAATTGCAGCCATTGGTGATTTTAAGCTGTTTTTGAGGTCTATC
1 AATATGGGTTTTGCATGAATTGCAGCCATTGGTGATTTTAAGCTGTTTTTGAGGTCTATC
25731 AAT
1 AAT
25734 GGTGGCAGGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.41
Consensus pattern (60 bp):
AATATGGGTTTTGCATGAATTGCAGCCATTGGTGATTTTAAGCTGTTTTTGAGGTCTATC
Found at i:29626 original size:23 final size:22
Alignment explanation
Indices: 29598--29762 Score: 147
Period size: 23 Copynumber: 7.2 Consensus size: 22
29588 ACGCTAGTGC
29598 GCTTACTG-TTCAGCACTGTGTGT
1 GCTTACTGATTC-GCACT-TGTGT
*
29621 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGATTCGCACTT-GTGT
*
29644 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGATTCGCACTT-GTGT
* *
29667 GCTTACTGTTTCGCACCTCGTGT
1 GCTTACTGATTCGCA-CTTGTGT
* * *
29690 GCCTACTGATTTGCTCTATGTGT
1 GCTTACTGATTCGCACT-TGTGT
*
29713 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGATTCGCACT-TGTGT
*
29735 GCCTACTGGATT-GCACTGTGTGT
1 GCTTACT-GATTCGCACT-TGTGT
29758 GCTTA
1 GCTTA
29763 TTGTTCCTCC
Statistics
Matches: 128, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
22 19 0.15
23 104 0.81
24 5 0.04
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (22 bp):
GCTTACTGATTCGCACTTGTGT
Found at i:29713 original size:46 final size:45
Alignment explanation
Indices: 29610--29767 Score: 162
Period size: 46 Copynumber: 3.4 Consensus size: 45
29600 TTACTGTTCA
* *
29610 GCACTGTGTGTGCTTACTGTTTCGCACTTCGTGTGCTTACTG-TTT
1 GCACT-TGTGTGCTTACTGTTTCGCACCTCGTGTGCCTACTGATTT
29655 CGCACTTCGTGTGCTTACTGTTTCGCACCTCGTGTGCCTACTGATTT
1 -GCACTT-GTGTGCTTACTGTTTCGCACCTCGTGTGCCTACTGATTT
* * * *
29702 GCTCTATGTGTGCCTACTGATT-GCA-CTGTGTGTGCCTACTGGA-TT
1 GCACT-TGTGTGCTTACTGTTTCGCACCT-CGTGTGCCTACT-GATTT
*
29747 GCACTGTGTGTGCTTATTGTT
1 GCACT-TGTGTGCTTACTGTT
29768 CCTCCAGCCC
Statistics
Matches: 96, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
44 2 0.02
45 33 0.34
46 57 0.59
47 4 0.04
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.41
Consensus pattern (45 bp):
GCACTTGTGTGCTTACTGTTTCGCACCTCGTGTGCCTACTGATTT
Found at i:43312 original size:111 final size:111
Alignment explanation
Indices: 43118--43341 Score: 421
Period size: 111 Copynumber: 2.0 Consensus size: 111
43108 TTACCCAGGT
43118 ATACATATAATAGCTAGAAAATTTGTCTGCTAAATGGCAGAGTTGTTGAGTAGCTTTGATTTTAG
1 ATACATATAATAGCTAGAAAATTTGTCTGCTAAATGGCAGAGTTGTTGAGTAGCTTTGATTTTAG
43183 CTGAAGTAAGATTAGACTAAGGACGATAGCTGATTAAATATCTATA
66 CTGAAGTAAGATTAGACTAAGGACGATAGCTGATTAAATATCTATA
*
43229 ATACATATAATAGCTAGAAAATTTGTCTGCTAAATGGCATAGTTGTTGAGTAGCTTTGATTTTAG
1 ATACATATAATAGCTAGAAAATTTGTCTGCTAAATGGCAGAGTTGTTGAGTAGCTTTGATTTTAG
* *
43294 CTGAAGTAAGATTAGACTAAGGATGATAGCTGATTGAATATCTATA
66 CTGAAGTAAGATTAGACTAAGGACGATAGCTGATTAAATATCTATA
43340 AT
1 AT
43342 TTTTTTAAAT
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (111 bp):
ATACATATAATAGCTAGAAAATTTGTCTGCTAAATGGCAGAGTTGTTGAGTAGCTTTGATTTTAG
CTGAAGTAAGATTAGACTAAGGACGATAGCTGATTAAATATCTATA
Found at i:46569 original size:67 final size:65
Alignment explanation
Indices: 46451--46581 Score: 147
Period size: 67 Copynumber: 2.0 Consensus size: 65
46441 TAAATCAAGA
* * * * * *
46451 TGATAATATTTTTTTTATGTACTTTTATGTTACTTGCATCGTAAATAGCTTCGATAATATGAATC
1 TGATAATATTTTTTTTACGTACCTTTATGTTACCTGCATCCTAAATAGCTTCAATAACATGAATC
* * *
46516 TGATCATATTTTCTTTTCACGTACCTTTATGTTACCTGCGA-CCTTAATGGCTTCAATAACATGA
1 TGATAATATTTT-TTTT-ACGTACCTTTATGTTACCTGC-ATCCTAAATAGCTTCAATAACATGA
46580 AT
63 AT
46582 TTGGTCAGGT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
65 11 0.20
66 4 0.07
67 38 0.70
68 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.44
Consensus pattern (65 bp):
TGATAATATTTTTTTTACGTACCTTTATGTTACCTGCATCCTAAATAGCTTCAATAACATGAATC
Found at i:47159 original size:55 final size:55
Alignment explanation
Indices: 47094--47209 Score: 182
Period size: 55 Copynumber: 2.1 Consensus size: 55
47084 ATTAAAAAAT
*
47094 ATTT-AAAATGTGATATAAAATGTCAAATCATTATATT-AAATTATTCAAAAGTAA
1 ATTTGAAAATGTGATACAAAATGTCAAATCATTATATTAAAATT-TTCAAAAGTAA
* *
47148 ATTTGAAAATGTGATACAAAATGTCGAATCATTATATTAAAATTTTTAAAAGTAA
1 ATTTGAAAATGTGATACAAAATGTCAAATCATTATATTAAAATTTTCAAAAGTAA
47203 ATTTGAA
1 ATTTGAA
47210 TGAACAGTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
54 4 0.07
55 48 0.84
56 5 0.09
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.37
Consensus pattern (55 bp):
ATTTGAAAATGTGATACAAAATGTCAAATCATTATATTAAAATTTTCAAAAGTAA
Found at i:47395 original size:2 final size:2
Alignment explanation
Indices: 47383--47415 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
47373 TTAGATAAAA
*
47383 AT AT GT 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
47416 ATAAATAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54777 original size:42 final size:42
Alignment explanation
Indices: 54718--54802 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
54708 ATACTCCATG
54718 TCCTTTACTTAATCTTTTGTGAGAGTTATTTTTGTTTTATAA
1 TCCTTTACTTAATCTTTTGTGAGAGTTATTTTTGTTTTATAA
54760 TCCTTTACTTAATCTTTTGTGAGAGTTATTTTTGTTTTATAA
1 TCCTTTACTTAATCTTTTGTGAGAGTTATTTTTGTTTTATAA
54802 T
1 T
54803 ATATATAGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (42 bp):
TCCTTTACTTAATCTTTTGTGAGAGTTATTTTTGTTTTATAA
Found at i:55731 original size:29 final size:29
Alignment explanation
Indices: 55689--55744 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
55679 AGGAGTTAGA
55689 TTGCGTTATACCCCTCTACTCAAAAAAGG
1 TTGCGTTATACCCCTCTACTCAAAAAAGG
55718 TTGCGTTATACCCCTCTACTCAAAAAA
1 TTGCGTTATACCCCTCTACTCAAAAAA
55745 TAGTCAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.29
Consensus pattern (29 bp):
TTGCGTTATACCCCTCTACTCAAAAAAGG
Found at i:62539 original size:32 final size:33
Alignment explanation
Indices: 62501--62566 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
62491 AGTAACAAAA
62501 TGGTCACCCAACTATTTAAATTTTTTCTT-TTT
1 TGGTCACCCAACTATTTAAATTTTTTCTTGTTT
** *
62533 TGGTCACTTAACTATTTGAATTTTTTCTTGTTT
1 TGGTCACCCAACTATTTAAATTTTTTCTTGTTT
62566 T
1 T
62567 TTCATCTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.56
Consensus pattern (33 bp):
TGGTCACCCAACTATTTAAATTTTTTCTTGTTT
Found at i:67165 original size:80 final size:80
Alignment explanation
Indices: 67032--67190 Score: 300
Period size: 80 Copynumber: 2.0 Consensus size: 80
67022 ACTGAAGAAT
* *
67032 TAGGACTTTATGGAATCCAATGGAATTTAGATAGAACTGTTGACTTGAACCCTCTTGAGTTAATA
1 TAGGACTTCATGGAATCCAATGGAATTTAGATAGAACTGTTGACTTGAACCCTCTTAAGTTAATA
67097 TTTGTAGAATCACCG
66 TTTGTAGAATCACCG
67112 TAGGACTTCATGGAATCCAATGGAATTTAGATAGAACTGTTGACTTGAACCCTCTTAAGTTAATA
1 TAGGACTTCATGGAATCCAATGGAATTTAGATAGAACTGTTGACTTGAACCCTCTTAAGTTAATA
67177 TTTGTAGAATCACC
66 TTTGTAGAATCACC
67191 AAAGGATTTT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (80 bp):
TAGGACTTCATGGAATCCAATGGAATTTAGATAGAACTGTTGACTTGAACCCTCTTAAGTTAATA
TTTGTAGAATCACCG
Found at i:76705 original size:2 final size:2
Alignment explanation
Indices: 76698--76736 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
76688 CAAATTATGT
76698 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76737 CAGTAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77196 original size:24 final size:24
Alignment explanation
Indices: 77169--77214 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
77159 CCTATACATT
* **
77169 TATATATACATATTTACATACCAA
1 TATACATACATACATACATACCAA
*
77193 TATACATGCATACATACATACC
1 TATACATACATACATACATACC
77215 TGGCCGCTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (24 bp):
TATACATACATACATACATACCAA
Found at i:86352 original size:3 final size:3
Alignment explanation
Indices: 86346--86387 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
86336 ATGATTAGGG
86346 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
86388 ATCTTATTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:101869 original size:24 final size:24
Alignment explanation
Indices: 101835--101882 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
101825 TGATGTGGAA
101835 CCAGTAAAAAATGAAGATCCAACT
1 CCAGTAAAAAATGAAGATCCAACT
*
101859 CCAGTAGAAAATGAAGATCCAACT
1 CCAGTAAAAAATGAAGATCCAACT
101883 TCGTGTATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.17
Consensus pattern (24 bp):
CCAGTAAAAAATGAAGATCCAACT
Found at i:102595 original size:11 final size:12
Alignment explanation
Indices: 102573--102616 Score: 54
Period size: 11 Copynumber: 3.6 Consensus size: 12
102563 TTTACGCTAC
102573 TAAATAAAAAAT
1 TAAATAAAAAAT
102585 TAAAT-AAAAAT
1 TAAATAAAAAAT
*
102596 TAAATTAAACAAAA
1 TAAA-TAAA-AAAT
102610 TAAATAA
1 TAAATAA
102617 TTTAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 10 0.36
12 6 0.21
13 5 0.18
14 7 0.25
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAATAAAAAAT
Found at i:102636 original size:33 final size:32
Alignment explanation
Indices: 102574--102644 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
102564 TTACGCTACT
102574 AAATAAAAAATTAAATAAAAATTAAATTAAACA
1 AAATAAAAAATTAAATAAAAATT-AATTAAACA
* *
102607 AAATAAATAATTTAAAATAATAATT-ATTAAACA
1 AAATAAA-AAATT-AAATAAAAATTAATTAAACA
*
102640 GAATA
1 AAATA
102645 TAACTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 19 0.58
34 4 0.12
35 10 0.30
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (32 bp):
AAATAAAAAATTAAATAAAAATTAATTAAACA
Found at i:107871 original size:19 final size:19
Alignment explanation
Indices: 107847--107885 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
107837 GTAAAAAAAA
107847 TAATTGCAATTAATTAAAT
1 TAATTGCAATTAATTAAAT
*
107866 TAATTGCATTTAATTAAAT
1 TAATTGCAATTAATTAAAT
107885 T
1 T
107886 CAATATTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (19 bp):
TAATTGCAATTAATTAAAT
Found at i:108753 original size:16 final size:17
Alignment explanation
Indices: 108727--108759 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
108717 TAATTTAATT
*
108727 TTTTTATAATTTATAAA
1 TTTTTATAATTAATAAA
108744 TTTTTA-AATTAATAAA
1 TTTTTATAATTAATAAA
108760 AATAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTATAATTAATAAA
Found at i:115718 original size:23 final size:22
Alignment explanation
Indices: 115678--115732 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
115668 TAAGATGATT
*
115678 ATATAAAAAATTTTAATA-AAA
1 ATATATAAAATTTTAATATAAA
115699 ATATATAAAATTATTAAATATTAAA
1 ATATATAAAATT-TT-AATA-TAAA
115724 ATAATATAA
1 AT-ATATAA
115733 TATAAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 11 0.39
22 2 0.07
23 4 0.14
25 5 0.18
26 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATATAAAATTTTAATATAAA
Found at i:120652 original size:22 final size:22
Alignment explanation
Indices: 120597--120653 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
120587 AAAACCTTAA
*
120597 AAATATTAACTTTTTAAAATAAT
1 AAATATTAA-TTTTTAAAACAAT
* *
120620 AAATAAT-ATTTTTTAAACAAT
1 AAATATTAATTTTTAAAACAAT
120641 AAATATTAATTTT
1 AAATATTAATTTT
120654 ATTTCAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 17 0.59
22 6 0.21
23 6 0.21
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATATTAATTTTTAAAACAAT
Found at i:123944 original size:22 final size:23
Alignment explanation
Indices: 123919--123965 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
123909 GGGTTCGAAA
123919 TTAGGGATTTTAGTAG-GATTTG
1 TTAGGGATTTTAGTAGTGATTTG
* * *
123941 TTAGGGGTTTTGGTAGTGGTTTG
1 TTAGGGATTTTAGTAGTGATTTG
123964 TT
1 TT
123966 GATTAACTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (23 bp):
TTAGGGATTTTAGTAGTGATTTG
Found at i:130201 original size:11 final size:11
Alignment explanation
Indices: 130161--130205 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
130151 CAAAAATTAC
*
130161 AAAATAA-TTC
1 AAAATAATTTT
130171 AAAATAATTTT
1 AAAATAATTTT
*
130182 --AAGAATTTT
1 AAAATAATTTT
130191 AAAATAATTTT
1 AAAATAATTTT
130202 AAAA
1 AAAA
130206 ATTCAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
9 8 0.28
10 7 0.24
11 14 0.48
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:130226 original size:20 final size:20
Alignment explanation
Indices: 130161--130235 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
130151 CAAAAATTAC
130161 AAAATAATTCAAAATAATTTT
1 AAAA-AATTCAAAATAATTTT
* * *
130182 AAGAATTTTAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
130202 -AAAAATTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
130221 AAAAAAGTTCAAAAT
1 AAAAAA-TTCAAAAT
130236 TTATATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
18 4 0.09
19 11 0.24
20 19 0.42
21 11 0.24
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:130470 original size:20 final size:21
Alignment explanation
Indices: 130432--130469 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
130422 TAACCTAAAA
130432 TTAATTATATTGTAATTTTAT
1 TTAATTATATTGTAATTTTAT
130453 TTAA-TATATT-TAATTTT
1 TTAATTATATTGTAATTTT
130470 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (21 bp):
TTAATTATATTGTAATTTTAT
Found at i:138719 original size:38 final size:37
Alignment explanation
Indices: 138653--138745 Score: 93
Period size: 38 Copynumber: 2.5 Consensus size: 37
138643 GCAAACATTA
* * **
138653 AAAAAATTAAA-ATAATTATATATAAAATTTTAATAAAT
1 AAAAAA-TAAATATTATTAAATATAAAATTGAAAT-AAT
*
138691 AAAAAATAAATATTATTAAATATTAAATTGAAATAAT
1 AAAAAATAAATATTATTAAATATAAAATTGAAATAAT
*
138728 -ATAAATAAATATT-TTAAA
1 AAAAAATAAATATTATTAAA
138746 ATTTTTTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
35 5 0.10
36 12 0.25
37 7 0.15
38 24 0.50
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (37 bp):
AAAAAATAAATATTATTAAATATAAAATTGAAATAAT
Found at i:146718 original size:51 final size:51
Alignment explanation
Indices: 146589--146728 Score: 140
Period size: 51 Copynumber: 2.7 Consensus size: 51
146579 TGCGTAAAAG
* * * * * *
146589 TTGACAGAATATGTAAATGTTGA-GAGCAAAATTTATTAAATCAAGACCACA
1 TTGACAAAATGTGCAAATGTTGAGGA-CTAAATTTGTTAAATCAAGACCAAA
* * * * * *
146640 TTGATAGAGTGTGTAAATGTTGTGGACTAAGTTTGTTAAATCAAGACCAAA
1 TTGACAAAATGTGCAAATGTTGAGGACTAAATTTGTTAAATCAAGACCAAA
146691 TTGACAAAATGTGCAAACT-TTGAGGACTAAATTTGTTA
1 TTGACAAAATGTGCAAA-TGTTGAGGACTAAATTTGTTA
146729 TTATAATAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
51 70 0.96
52 3 0.04
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.31
Consensus pattern (51 bp):
TTGACAAAATGTGCAAATGTTGAGGACTAAATTTGTTAAATCAAGACCAAA
Found at i:150127 original size:12 final size:13
Alignment explanation
Indices: 150101--150132 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
150091 TCGGAGAAAT
150101 TTGTAAAAAAGAA
1 TTGTAAAAAAGAA
150114 TTGTAAAAAA-AA
1 TTGTAAAAAAGAA
150126 TT-TAAAA
1 TTGTAAAA
150133 GGGGATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 5 0.26
12 4 0.21
13 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28
Consensus pattern (13 bp):
TTGTAAAAAAGAA
Found at i:154789 original size:54 final size:54
Alignment explanation
Indices: 154725--154832 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
154715 AGCATATGGT
*
154725 TAACCATATTATCTCATTTACTGAAACATACAAACTATGGTCGACATTGATAAC
1 TAACCATATTATCTCATTTACTGAAACATACAAACTATGGTCGACATCGATAAC
* *
154779 TAACCATATTATCTCATTTTCTGAAACATACAAACTATGGTTGACATCGATAAC
1 TAACCATATTATCTCATTTACTGAAACATACAAACTATGGTCGACATCGATAAC
154833 AATTCGAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.32
Consensus pattern (54 bp):
TAACCATATTATCTCATTTACTGAAACATACAAACTATGGTCGACATCGATAAC
Found at i:157121 original size:15 final size:17
Alignment explanation
Indices: 157090--157126 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
157080 CACCCATTTA
*
157090 TAATTTTTTATACAA-T
1 TAATATTTTATACAATT
157106 TAATATTTTA-ACAATT
1 TAATATTTTATACAATT
157122 TAATA
1 TAATA
157127 GTTAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATATTTTATACAATT
Found at i:164606 original size:19 final size:18
Alignment explanation
Indices: 164582--164631 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
164572 GAATTCGAAT
*
164582 AAAATATAAATACAATATA
1 AAAATATAAATAAAAT-TA
164601 AAAATA-AAATAAAATTA
1 AAAATATAAATAAAATTA
*
164618 TAAATATAAA-AAAA
1 AAAATATAAATAAAA
164632 GAGTCTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 11 0.39
18 11 0.39
19 6 0.21
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATATAAATAAAATTA
Found at i:164631 original size:17 final size:17
Alignment explanation
Indices: 164579--164631 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
164569 TTTGAATTCG
*
164579 AATA-AAATATAAATAC
1 AATATAAATATAAATAA
*
164595 AATATAAAAATAAAATAA
1 AATATAAATAT-AAATAA
164613 AATTATAAATATAAA-AA
1 AA-TATAAATATAAATAA
164630 AA
1 AA
164632 GAGTCTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 4 0.13
17 9 0.29
18 10 0.32
19 8 0.26
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AATATAAATATAAATAA
Found at i:165048 original size:14 final size:14
Alignment explanation
Indices: 165028--165065 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
165018 TCACAATTTG
165028 ATTCTCAATTTCTT
1 ATTCTCAATTTCTT
* *
165042 GTTCTCAATTTGTT
1 ATTCTCAATTTCTT
165056 ATTCTCAATT
1 ATTCTCAATT
165066 CTCAATTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.55
Consensus pattern (14 bp):
ATTCTCAATTTCTT
Found at i:165084 original size:27 final size:28
Alignment explanation
Indices: 165043--165099 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
165033 CAATTTCTTG
* *
165043 TTCTCAATTTGTTATTCTCAATTCTCAA
1 TTCTCAATTTGTTATTATAAATTCTCAA
*
165071 TTCTCGATTT-TTATTATAAATTCTCAA
1 TTCTCAATTTGTTATTATAAATTCTCAA
165098 TT
1 TT
165100 ACACTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.53
Consensus pattern (28 bp):
TTCTCAATTTGTTATTATAAATTCTCAA
Found at i:167643 original size:63 final size:63
Alignment explanation
Indices: 167562--167706 Score: 263
Period size: 63 Copynumber: 2.3 Consensus size: 63
167552 CAAAGAAATT
*
167562 GAGTTTTTACTATATGAGTATTTACACTTTAATGAATAAATTAATGAATAAACCAATAAGCTA
1 GAGTTTTTACTGTATGAGTATTTACACTTTAATGAATAAATTAATGAATAAACCAATAAGCTA
* *
167625 GTGTTTTTACTGTATGAGTATTTACACTTTAATGAATAAATTAATGTATAAACCAATAAGCTA
1 GAGTTTTTACTGTATGAGTATTTACACTTTAATGAATAAATTAATGAATAAACCAATAAGCTA
167688 GAGTTTTTACTGTATGAGT
1 GAGTTTTTACTGTATGAGT
167707 TAATCTTTTA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 78 1.00
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (63 bp):
GAGTTTTTACTGTATGAGTATTTACACTTTAATGAATAAATTAATGAATAAACCAATAAGCTA
Found at i:167984 original size:24 final size:23
Alignment explanation
Indices: 167957--168001 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
167947 CTGATAATGC
167957 TTAAATATGACATACTTTTAGATA
1 TTAAATAT-ACATACTTTTAGATA
* *
167981 TTAAATATATATATTTTTAGA
1 TTAAATATACATACTTTTAGA
168002 GTATGATCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (23 bp):
TTAAATATACATACTTTTAGATA
Found at i:168210 original size:19 final size:19
Alignment explanation
Indices: 168188--168232 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
168178 TTATATTAGG
168188 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
168207 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
168226 ATTTAAT
1 ATTTAAT
168233 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:169142 original size:21 final size:20
Alignment explanation
Indices: 169095--169148 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
169085 TTTTTTTCAA
* *
169095 ATTTAATATTTTTATTTATC
1 ATTTAAAATTTTTATATATC
*
169115 A-TTAAAATTTTTAATATATT
1 ATTTAAAATTTTT-ATATATC
169135 ATTTAAAATCTTTT
1 ATTTAAAAT-TTTT
169149 CAACTTTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 10 0.36
20 7 0.25
21 7 0.25
22 4 0.14
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTAAAATTTTTATATATC
Found at i:171195 original size:23 final size:22
Alignment explanation
Indices: 171165--171217 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
171155 CTTGTCCTTC
171165 AAAATTTTTGAAATTTTTTTATT-
1 AAAATTTTT--AATTTTTTTATTG
*
171188 AAAATTTTTAATTTTTTTTTTG
1 AAAATTTTTAATTTTTTTATTG
171210 AAAATTTT
1 AAAATTTT
171218 GATTAGCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 11 0.39
22 8 0.29
23 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
AAAATTTTTAATTTTTTTATTG
Found at i:171203 original size:22 final size:23
Alignment explanation
Indices: 171165--171217 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
171155 CTTGTCCTTC
171165 AAAATTTTTGAAATTTTTTTATT-
1 AAAATTTTTGAAATTTTTTT-TTG
*
171188 AAAATTTTT-AATTTTTTTTTTG
1 AAAATTTTTGAAATTTTTTTTTG
171210 AAAATTTT
1 AAAATTTT
171218 GATTAGCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 2 0.07
22 17 0.61
23 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
AAAATTTTTGAAATTTTTTTTTG
Found at i:171331 original size:31 final size:30
Alignment explanation
Indices: 171238--171350 Score: 100
Period size: 31 Copynumber: 3.6 Consensus size: 30
171228 TAATTTTTTT
* *
171238 TTTTTGGAAATTTTAATTAATCCTTTTAAAA
1 TTTTTGAAAATTTTAATTAA-CCTTTCAAAA
* * * *
171269 GTTTTTAAAAACTTTTAATTAATCATCCAAAA
1 -TTTTTGAAAA-TTTTAATTAACCTTTCAAAA
*
171301 TTTTTGAAAATTTTTATTAAGCCTTTCAAAA
1 TTTTTGAAAATTTTAATTAA-CCTTTCAAAA
* **
171332 TTTTAGAAAAAATTAATTA
1 TTTTTGAAAATTTTAATTA
171351 GGTCTTCCAA
Statistics
Matches: 64, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
30 9 0.14
31 31 0.48
32 14 0.22
33 10 0.16
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (30 bp):
TTTTTGAAAATTTTAATTAACCTTTCAAAA
Found at i:171362 original size:31 final size:31
Alignment explanation
Indices: 171294--171362 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
171284 TAATTAATCA
* ** *
171294 TCCAAAATTTTTGAAAATTTTTATTAAGCCT
1 TCCAAAATTTTAGAAAAAATTAATTAAGCCT
* * *
171325 TTCAAAATTTTAGAAAAAATTAATTAGGTCT
1 TCCAAAATTTTAGAAAAAATTAATTAAGCCT
171356 TCCAAAA
1 TCCAAAA
171363 CCTTTAATCC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (31 bp):
TCCAAAATTTTAGAAAAAATTAATTAAGCCT
Found at i:175669 original size:19 final size:18
Alignment explanation
Indices: 175645--175690 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
175635 TGATCCCAAT
*
175645 AAAATATAAATACAATATA
1 AAAATATAAATAAAAT-TA
175664 AAAATA-AAATAAAATTA
1 AAAATATAAATAAAATTA
*
175681 TAAATATAAA
1 AAAATATAAA
175691 ATAGGAGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.29
18 11 0.46
19 6 0.25
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATATAAATAAAATTA
Found at i:175691 original size:19 final size:18
Alignment explanation
Indices: 175642--175693 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
175632 ATTTGATCCC
*
175642 AATA-AAATAT-AAATAC
1 AATATAAATATAAAATAA
*
175658 AATATAAAAATAAAATAA
1 AATATAAATATAAAATAA
175676 AATTATAAATATAAAATA
1 AA-TATAAATATAAAATA
175694 GGAGTCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 4 0.13
17 5 0.17
18 7 0.23
19 14 0.47
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
AATATAAATATAAAATAA
Found at i:175693 original size:24 final size:24
Alignment explanation
Indices: 175642--175691 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
175632 ATTTGATCCC
*
175642 AATAAAATATAAATACAATATAAA
1 AATAAAATATAAATAAAATATAAA
175666 AATAAAATA-AAATTATAAATATAAA
1 AATAAAATATAAA-TA-AAATATAAA
175691 A
1 A
175692 TAGGAGTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.13
24 11 0.48
25 9 0.39
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (24 bp):
AATAAAATATAAATAAAATATAAA
Found at i:176323 original size:55 final size:51
Alignment explanation
Indices: 176262--176368 Score: 142
Period size: 51 Copynumber: 2.0 Consensus size: 51
176252 TTACAAATGG
* **
176262 TAAGAAAATATTATTATTTAATTATTTAATTTTAATTCTTTAATTATTATGATGT
1 TAAGAAAATATTATTA---AATTATTT-ATTTTAAATAATTAATTATTATGATGT
*
176317 TAAGAAAATATTATTAAATTATTTATTTTAAATAATTAATTATTATGTTGT
1 TAAGAAAATATTATTAAATTATTTATTTTAAATAATTAATTATTATGATGT
176368 T
1 T
176369 CATATTATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
51 24 0.50
52 8 0.17
55 16 0.33
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (51 bp):
TAAGAAAATATTATTAAATTATTTATTTTAAATAATTAATTATTATGATGT
Found at i:179978 original size:2 final size:2
Alignment explanation
Indices: 179971--180002 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
179961 CGTTTAGAGA
179971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
180003 GAATATCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:181145 original size:17 final size:18
Alignment explanation
Indices: 181118--181152 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
181108 ATTTTGGAAT
*
181118 TTTTTTATTAAATTTTTA
1 TTTTTTATTAAAATTTTA
181136 TTTTTT-TTAAAATTTTA
1 TTTTTTATTAAAATTTTA
181153 ATTAGCTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTATTAAAATTTTA
Found at i:190827 original size:13 final size:13
Alignment explanation
Indices: 190793--190833 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
190783 CAACTATCCT
*
190793 TAAAATAAATTAC
1 TAAAATAAAATAC
*
190806 --AAATTAAATAC
1 TAAAATAAAATAC
190817 TAAAATAAAATAC
1 TAAAATAAAATAC
190830 TAAA
1 TAAA
190834 TTTTTTTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 9 0.39
13 14 0.61
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (13 bp):
TAAAATAAAATAC
Found at i:201385 original size:22 final size:23
Alignment explanation
Indices: 201354--201396 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
201344 GAAATTAAAT
*
201354 TGTAATTTTTACAATAATAAAAG
1 TGTAATTTTTAAAATAATAAAAG
*
201377 TGTAA-TTTTAAAATATTAAA
1 TGTAATTTTTAAAATAATAAA
201397 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (23 bp):
TGTAATTTTTAAAATAATAAAAG
Found at i:217103 original size:29 final size:29
Alignment explanation
Indices: 217070--217128 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
217060 CAAATCTAGG
* *
217070 AAAATTTTCATTATG-CCCTTCAAAATATT
1 AAAATTTTAATT-TGACCCTCCAAAATATT
*
217099 AAAATTTTAATTTGACCCTCCCAAATATT
1 AAAATTTTAATTTGACCCTCCAAAATATT
217128 A
1 A
217129 TTGGCTCGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATTTTAATTTGACCCTCCAAAATATT
Found at i:217879 original size:6 final size:6
Alignment explanation
Indices: 217868--217892 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
217858 ATTTTGTCTT
217868 TCACCA TCACCA TCACCA TCACCA T
1 TCACCA TCACCA TCACCA TCACCA T
217893 GAGCTTGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.20
Consensus pattern (6 bp):
TCACCA
Found at i:220704 original size:31 final size:30
Alignment explanation
Indices: 220642--220704 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
220632 TATCAAAATC
* *
220642 ATATATGAACTTTGGTTTAATGTGCAATTAT
1 ATATATGAACTTTGATTT-ATGTGAAATTAT
*
220673 ATATATGAACTTTGATTT-TGTGAAATTTT
1 ATATATGAACTTTGATTTATGTGAAATTAT
220702 ATA
1 ATA
220705 CATGTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (30 bp):
ATATATGAACTTTGATTTATGTGAAATTAT
Found at i:227726 original size:195 final size:195
Alignment explanation
Indices: 227394--227777 Score: 678
Period size: 195 Copynumber: 2.0 Consensus size: 195
227384 ATAGATGTGC
*
227394 TAAATGAGTAATGCATATATACAAAGAACAACCATAGGTAGATAATCAGCCGTATACAACCCGAC
1 TAAATGAGTAATGCATATATACAAAGAACAACCATAGGTAGATAATCAGCCATATACAACCCGAC
* * *
227459 GATGAAGCAGAAGTACGACACATATTAGACTAGGCTGATTCTCTGATAACCATAGGTAGACAATC
66 GATGAAGCAGAAGTACGACACATACTAGACTACGCTGATTCTCCGATAACCATAGGTAGACAATC
227524 AGCCATATACAACCAGATCATATAGGCTAGGCCAATTCTCCGACGTTTATTTGTGCCTACAGCAT
131 AGCCATATACAACCAGATCATATAGGCTAGGCCAATTCTCCGACGTTTATTTGTGCCTACAGCAT
* *
227589 TAAATGAGTAATGCATATATACAAAGAACAACCATAGGTAGATAATCAGCCATATACAACCTGAT
1 TAAATGAGTAATGCATATATACAAAGAACAACCATAGGTAGATAATCAGCCATATACAACCCGAC
* *
227654 GATGAAGCATAAGTACGACACGTACTAGACTACGCTGATTCTCCGATAACCATAGGTAGACAATC
66 GATGAAGCAGAAGTACGACACATACTAGACTACGCTGATTCTCCGATAACCATAGGTAGACAATC
* *
227719 AGCCATATACAACCCGATCATATAGGCTAGGCCGATTCTCCGACGTTTATTTGTGCCTA
131 AGCCATATACAACCAGATCATATAGGCTAGGCCAATTCTCCGACGTTTATTTGTGCCTA
227778 TATAATTCAC
Statistics
Matches: 179, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
195 179 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (195 bp):
TAAATGAGTAATGCATATATACAAAGAACAACCATAGGTAGATAATCAGCCATATACAACCCGAC
GATGAAGCAGAAGTACGACACATACTAGACTACGCTGATTCTCCGATAACCATAGGTAGACAATC
AGCCATATACAACCAGATCATATAGGCTAGGCCAATTCTCCGACGTTTATTTGTGCCTACAGCAT
Found at i:229692 original size:12 final size:12
Alignment explanation
Indices: 229675--229705 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
229665 GGAGAGCGAA
229675 GCGGTTGCGGCT
1 GCGGTTGCGGCT
229687 GCGGTTGCGGCT
1 GCGGTTGCGGCT
229699 GCGGTTG
1 GCGGTTG
229706 GGGGAAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.52, T:0.26
Consensus pattern (12 bp):
GCGGTTGCGGCT
Found at i:230684 original size:32 final size:31
Alignment explanation
Indices: 230647--230713 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
230637 TTACAATTTG
* **
230647 GTCACTAAATTATTTGAAAGTTTTTATTTTAA
1 GTCACTAAACTATTCAAAAGTTTTTA-TTTAA
*
230679 GTCACTGAACTATTCAAAAGTTTTTATTTAA
1 GTCACTAAACTATTCAAAAGTTTTTATTTAA
230710 GTCA
1 GTCA
230714 ATAGGCTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 9 0.29
32 22 0.71
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (31 bp):
GTCACTAAACTATTCAAAAGTTTTTATTTAA
Found at i:234223 original size:19 final size:17
Alignment explanation
Indices: 234191--234225 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
234181 TGACATAAAA
234191 TAAAAAAATTAAAAGAT
1 TAAAAAAATTAAAAGAT
234208 TAAAAAGAATTTAAAAGA
1 TAAAAA-AA-TTAAAAGA
234226 ACCAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (17 bp):
TAAAAAAATTAAAAGAT
Found at i:235393 original size:13 final size:13
Alignment explanation
Indices: 235376--235407 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
235366 ATTGATATTT
235376 ATTATTAATGCTA
1 ATTATTAATGCTA
*
235389 TTTATTAATGCTA
1 ATTATTAATGCTA
235402 ATTATT
1 ATTATT
235408 TTTACTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (13 bp):
ATTATTAATGCTA
Found at i:236197 original size:17 final size:17
Alignment explanation
Indices: 236127--236197 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 17
236117 ACATTAATTT
* * *
236127 ATTTTAATTTTAAATAT
1 ATTTAAATTTAAAATAA
*
236144 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
* * * * *
236161 ATTCAAACTCAAAGTGA
1 ATTTAAATTTAAAATAA
*
236178 ATTTGAATTTAAAATAA
1 ATTTAAATTTAAAATAA
236195 ATT
1 ATT
236198 CAAACTTATT
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:237510 original size:22 final size:23
Alignment explanation
Indices: 237485--237530 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
237475 AGTGCAACTG
*
237485 ACAAAC-AATTTAAACTTCAAAT
1 ACAAACAAATTTAAACTTAAAAT
*
237507 ACAATCAAATTTAAACTTAAAAT
1 ACAAACAAATTTAAACTTAAAAT
237530 A
1 A
237531 TTATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (23 bp):
ACAAACAAATTTAAACTTAAAAT
Found at i:243219 original size:101 final size:101
Alignment explanation
Indices: 243038--243219 Score: 258
Period size: 101 Copynumber: 1.8 Consensus size: 101
243028 ACTTCGCTGT
* * * * *
243038 AACTTCAGGAAGATAGGATTTGAAGTTGAAGCTTCATTTTGCTCTTACTACAACTTCGGAGAGAT
1 AACTTCAAGAAGATAGGAATTGAAGTTAAAGCTTCATTTTGCTCCTACTACAACTTCAGAGAGAT
*
243103 AAAGACTTACTATTGTTTTTAATCCGACTTTACTTC
66 AAAGACTTACCATTGTTTTTAATCCGACTTTACTTC
* * *
243139 AACTTCAAGAGGATAGGAATTGACGTTAAAGCTTCATTTTGCTCCTAC-AGCAACTTTAGAGAGA
1 AACTTCAAGAAGATAGGAATTGAAGTTAAAGCTTCATTTTGCTCCTACTA-CAACTTCAGAGAGA
*
243203 TAAAGACTTGCCATTGT
65 TAAAGACTTACCATTGT
243220 AGTTTTGATC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
100 1 0.01
101 69 0.99
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (101 bp):
AACTTCAAGAAGATAGGAATTGAAGTTAAAGCTTCATTTTGCTCCTACTACAACTTCAGAGAGAT
AAAGACTTACCATTGTTTTTAATCCGACTTTACTTC
Found at i:243402 original size:50 final size:50
Alignment explanation
Indices: 243320--243653 Score: 200
Period size: 50 Copynumber: 6.7 Consensus size: 50
243310 GTCATTGCAA
* ** * * *
243320 CTTAAACCTTTCCCCTTCAAATCTTC-GTGGTACTAGATTCGTCATTGCGG
1 CTTAAATCTTT-CCCTTCATGTCTTCTGAGGTACTAGATTCGCCGTTGCGG
* * * *
243370 CTTAAATCTTTCCCTTCTTGTCTTCTGAGGTAC-ACGGTCCGCCGTTGCGA
1 CTTAAATCTTTCCCTTCATGTCTTCTGAGGTACTA-GATTCGCCGTTGCGG
* * * * * * *
243420 CTTAAACCTTTCCCTT-TTGTATTTTTGTGGTACTGGATCCGCCGTTGCGG
1 CTTAAATCTTTCCCTTCATGT-CTTCTGAGGTACTAGATTCGCCGTTGCGG
* *
243470 TCTTAGATCTTTCCCTTCATGTCTTC--ATGGTACTAGATTCGCCGTTTCGG
1 -CTTAAATCTTTCCCTTCATGTCTTCTGA-GGTACTAGATTCGCCGTTGCGG
* * * * **
243520 CTTAAATCTTTCCCTTCGTGTCTTCTAAGGTACATAG-TCTTGCCGTTACAA
1 CTTAAATCTTTCCCTTCATGTCTTCTGAGGTAC-TAGAT-TCGCCGTTGCGG
* * * *
243571 CTTAGACCTTTCCCTT-TTGTACCTT-T-ATGGTACTAGATTCGCCGTTGCAG
1 CTTAAATCTTTCCCTTCATGT--CTTCTGA-GGTACTAGATTCGCCGTTGCGG
* * * * * *
243621 ATTAAGTATTTCCATTCGTGTCTTTTGAGGTAC
1 CTTAAATCTTTCCCTTCATGTCTTCTGAGGTAC
243654 ACGGTCCTAC
Statistics
Matches: 221, Mismatches: 45, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
49 42 0.19
50 120 0.54
51 53 0.24
52 6 0.03
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (50 bp):
CTTAAATCTTTCCCTTCATGTCTTCTGAGGTACTAGATTCGCCGTTGCGG
Found at i:243450 original size:100 final size:101
Alignment explanation
Indices: 243314--243495 Score: 240
Period size: 100 Copynumber: 1.8 Consensus size: 101
243304 GGGTTCGTCA
* *
243314 TTGCAACTTAAACCTTTCCCCTTCAAATCTTCGTGGTACTAGATTCGTCATTGCGG-CTTAAATC
1 TTGCAACTTAAACCTTTCCCCTTCAAATCTTCGTGGTACTAGATCCGCCATTGCGGTCTTAAATC
*
243378 TTTCCCTTCTTGTCTTCTGAGGTACACGGTCCGCCG
66 TTTCCCTTCATGTCTTCTGAGGTACACGGTCCGCCG
* * *** * * * * *
243414 TTGCGACTTAAACCTTTCCCTTTTGTATTTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATC
1 TTGCAACTTAAACCTTTCCCCTTCAAATCTTCGTGGTACTAGATCCGCCATTGCGGTCTTAAATC
243479 TTTCCCTTCATGTCTTC
66 TTTCCCTTCATGTCTTC
243496 ATGGTACTAG
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
100 45 0.66
101 23 0.34
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.40
Consensus pattern (101 bp):
TTGCAACTTAAACCTTTCCCCTTCAAATCTTCGTGGTACTAGATCCGCCATTGCGGTCTTAAATC
TTTCCCTTCATGTCTTCTGAGGTACACGGTCCGCCG
Found at i:243502 original size:100 final size:99
Alignment explanation
Indices: 243314--243535 Score: 232
Period size: 100 Copynumber: 2.2 Consensus size: 99
243304 GGGTTCGTCA
* * * *
243314 TTGCAACTTAAACCTTTCCCCTTCAAATCTTCGTGGTACTAGATTCGTCATTGCGGCTTAAATCT
1 TTGCGACTTAAACCTTTCCCTTTCAAATCTTCGTGGTACTAGATCCGCCATTGCGGCTTAAATCT
* *
243379 TTCCCTTCTTGTCTTCTGAGGTAC-ACGGTCCGCCG
66 TTCCCTTCATGTCTTCT-AGGTACTA-GATCCGCCG
*** * * * * *
243414 TTGCGACTTAAACCTTTCCCTTTTGTATTTTTGTGGTACTGGATCCGCCGTTGCGGTCTTAGATC
1 TTGCGACTTAAACCTTTCCCTTTCAAATCTTCGTGGTACTAGATCCGCCATTGCGG-CTTAAATC
*
243479 TTTCCCTTCATGTCTTC-ATGGTACTAGATTCGCCG
65 TTTCCCTTCATGTCTTCTA-GGTACTAGATCCGCCG
* * *
243514 TTTCGGCTTAAATCTTTCCCTT
1 TTGCGACTTAAACCTTTCCCTT
243536 CGTGTCTTCT
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
99 1 0.01
100 76 0.75
101 24 0.24
ACGTcount: A:0.16, C:0.27, G:0.18, T:0.40
Consensus pattern (99 bp):
TTGCGACTTAAACCTTTCCCTTTCAAATCTTCGTGGTACTAGATCCGCCATTGCGGCTTAAATCT
TTCCCTTCATGTCTTCTAGGTACTAGATCCGCCG
Found at i:243585 original size:51 final size:49
Alignment explanation
Indices: 243471--243616 Score: 134
Period size: 51 Copynumber: 2.9 Consensus size: 49
243461 CCGTTGCGGT
* * **
243471 CTTAGATCTTTCCCTTCATGTCTTCATGGTACTAGATTCGCCGTTTCGG
1 CTTAGATCTTTCCCTTCATGTCTTCAAGGTACTAGATTCGCCGTTACAA
* * *
243520 CTTAAATCTTTCCCTTCGTGTCTTCTAAGGTACATAG-TCTTGCCGTTACAA
1 CTTAGATCTTTCCCTTCATGTCTTC-AAGGTAC-TAGAT-TCGCCGTTACAA
* * * *
243571 CTTAGACCTTTCCCTT-TTGTACCTTTATGGTACTAGATTCGCCGTT
1 CTTAGATCTTTCCCTTCATGT--CTTCAAGGTACTAGATTCGCCGTT
243617 GCAGATTAAG
Statistics
Matches: 78, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
49 23 0.29
50 20 0.26
51 32 0.41
52 3 0.04
ACGTcount: A:0.17, C:0.26, G:0.16, T:0.41
Consensus pattern (49 bp):
CTTAGATCTTTCCCTTCATGTCTTCAAGGTACTAGATTCGCCGTTACAA
Found at i:243633 original size:101 final size:100
Alignment explanation
Indices: 243471--243702 Score: 277
Period size: 101 Copynumber: 2.3 Consensus size: 100
243461 CCGTTGCGGT
* * * * * *
243471 CTTAGATCTTTCCCTTCATGTCTTCATGGTACTAGATTCGCCGTTTCGGCTTAAATCTTTCCCTT
1 CTTAGACCTTTCCCTTCATGTCTTCATGGTACTAGATTCGCCGTTGCAGATTAAATATTTCCATT
* * *
243536 CGTGTCTTCTAAGGTACATAGTCTTGCCGTTACAA
66 CGTGTCTTCTAAGGTACACAGTCCTACCGTTACAA
* * *
243571 CTTAGACCTTTCCCTT-TTGTACCTTTATGGTACTAGATTCGCCGTTGCAGATTAAGTATTTCCA
1 CTTAGACCTTTCCCTTCATGT--CTTCATGGTACTAGATTCGCCGTTGCAGATTAAATATTTCCA
* * * ***
243635 TTCGTGTCTTTTGAGGTACACGGTCCTACCGTTGTGA
64 TTCGTGTCTTCTAAGGTACACAGTCCTACCGTTACAA
243672 CTTAGACCTTTCCCTTCATGTCTTCATGGTA
1 CTTAGACCTTTCCCTTCATGTCTTCATGGTA
243703 TCGAAACCTA
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
99 3 0.03
100 24 0.22
101 79 0.72
102 3 0.03
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (100 bp):
CTTAGACCTTTCCCTTCATGTCTTCATGGTACTAGATTCGCCGTTGCAGATTAAATATTTCCATT
CGTGTCTTCTAAGGTACACAGTCCTACCGTTACAA
Found at i:243633 original size:150 final size:150
Alignment explanation
Indices: 243332--243644 Score: 378
Period size: 150 Copynumber: 2.1 Consensus size: 150
243322 TAAACCTTTC
** * * * *
243332 CCCTTCAAATCTTCGTGGTACTAGATTCGTCATTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTG
1 CCCTTCATGTCTTCATGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCGTGTCTTCTA
* * * ** * *
243397 AGGTACACGGTCCGCCGTTGCGACTTAAACCTTTCCCTTTTGTATTTTTGTGGTACTGGATCCGC
66 AGGTACACAGTCCGCCGTTACAACTTAAACCTTTCCCTTTTGTACCTTTATGGTACTAGATCCGC
* * *
243462 CGTTGCGGTCTTAGATCTTT
131 CGTTGCGATCTAAGATATTT
* *
243482 CCCTTCATGTCTTCATGGTACTAGATTCGCCGTTTCGGCTTAAATCTTTCCCTTCGTGTCTTCTA
1 CCCTTCATGTCTTCATGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCGTGTCTTCTA
* * * *
243547 AGGTACATAGTCTTGCCGTTACAACTTAGACCTTTCCCTTTTGTACCTTTATGGTACTAGATTCG
66 AGGTACACAGTC-CGCCGTTACAACTTAAACCTTTCCCTTTTGTACCTTTATGGTACTAGATCCG
243612 CCGTTGCAGAT-TAAG-TATTT
130 CCGTTGC-GATCTAAGATATTT
* *
243632 CCATTCGTGTCTT
1 CCCTTCATGTCTT
243645 TTGAGGTACA
Statistics
Matches: 137, Mismatches: 24, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
150 82 0.60
151 53 0.39
152 2 0.01
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (150 bp):
CCCTTCATGTCTTCATGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCGTGTCTTCTA
AGGTACACAGTCCGCCGTTACAACTTAAACCTTTCCCTTTTGTACCTTTATGGTACTAGATCCGC
CGTTGCGATCTAAGATATTT
Found at i:244903 original size:6 final size:6
Alignment explanation
Indices: 244894--244979 Score: 66
Period size: 6 Copynumber: 13.5 Consensus size: 6
244884 CGACCTCTCA
* * * *
244894 TTTTCT TTTTCT TTTTCT CTTCTTTT TTATTAT TATTTTT TTTTCT TTTTGTT
1 TTTTCT TTTTCT TTTTCT -TT-TTCT TT-TTCT T-TTTCT TTTTCT TTTT-CT
*
244947 TTTTCT TTTTCT TCTTCT TTTT-T CTTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT -TTTTCT TTT
244980 ATTCATTGAA
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
5 1 0.02
6 42 0.65
7 18 0.28
8 4 0.06
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:244948 original size:13 final size:12
Alignment explanation
Indices: 244894--244979 Score: 82
Period size: 13 Copynumber: 6.8 Consensus size: 12
244884 CGACCTCTCA
244894 TTTTCTTTTTCTT
1 TTTTCTTTTT-TT
244907 TTTCTCTTCTTTTT
1 TTT-TCTT-TTTTT
* *
244921 TATTATTATTTTT
1 TTTTCTT-TTTTT
244934 TTTTCTTTTTGTT
1 TTTTCTTTTT-TT
*
244947 TTTTCTTTTTCT
1 TTTTCTTTTTTT
* *
244959 TCTTCTTTTTTC
1 TTTTCTTTTTTT
244971 TTTTCTTTT
1 TTTTCTTTT
244980 ATTCATTGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
12 21 0.35
13 28 0.47
14 8 0.13
15 3 0.05
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.81
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:251084 original size:31 final size:31
Alignment explanation
Indices: 251049--251127 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
251039 TTTTCAACAA
*
251049 ATTTATATAAATTTTTACA-ATTTAATAATTC
1 ATTTATATAAATTTTGACACA-TTAATAATTC
* * *
251080 ATTTATGTAAATTTTGACACATTAATATTTT
1 ATTTATATAAATTTTGACACATTAATAATTC
*
251111 ATTTATATAGATTTTGA
1 ATTTATATAAATTTTGA
251128 TATATTGATG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (31 bp):
ATTTATATAAATTTTGACACATTAATAATTC
Found at i:252096 original size:16 final size:16
Alignment explanation
Indices: 252063--252093 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
252053 TTGGGTTGAA
252063 ATTAATTTATATATTT
1 ATTAATTTATATATTT
252079 ATTAATTTATA-ATTT
1 ATTAATTTATATATTT
252094 TATAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTAATTTATATATTT
Found at i:264514 original size:24 final size:25
Alignment explanation
Indices: 264482--264540 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
264472 AAATTTAGTT
*
264482 ATTAATTTTTTAA-AAAAGAT-TTAA
1 ATTATTTTTTTAATAAAA-ATGTTAA
**
264506 ATTATTTTTTTAATGGAAATGTTAA
1 ATTATTTTTTTAATAAAAATGTTAA
264531 ATTATTTTTT
1 ATTATTTTTT
264541 GGTAACTCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (25 bp):
ATTATTTTTTTAATAAAAATGTTAA
Found at i:264826 original size:8 final size:8
Alignment explanation
Indices: 264813--264837 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
264803 TACTTAAAAT
264813 TGTTGTAA
1 TGTTGTAA
264821 TGTTGTAA
1 TGTTGTAA
264829 TGTTGTAA
1 TGTTGTAA
264837 T
1 T
264838 AAAGTTATCA
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:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (8 bp):
TGTTGTAA
Found at i:268221 original size:17 final size:17
Alignment explanation
Indices: 268199--268231 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
268189 AAATTACCCG
*
268199 AATTAACTGAATTAAAA
1 AATTAACCGAATTAAAA
268216 AATTAACCGAATTAAA
1 AATTAACCGAATTAAA
268232 GTATTGAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.27
Consensus pattern (17 bp):
AATTAACCGAATTAAAA
Done.