Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 97 of 310
Found at i:31128273 original size:76 final size:76
Alignment explanation
Indices: 31128176--31128353 Score: 243
Period size: 76 Copynumber: 2.3 Consensus size: 76
31128166 ATAGGTACAC
* * *
31128176 CTTTAGCGGCGCTTTTTAAAAAACGCTGCAAAAGAATTTTGCAAAAC-ACTGTCGTTTTGTATTG
1 CTTTAGCGGCGCTTTTTAAAAAACGCAGCAAAAGAATTTTGCAAAACGACAG-CGTTTTGTAATG
*
31128240 AGCTTTTAATGG
65 AGCTTTTAATGA
*
31128252 CTTTAGCGGCG-TTTTTCAAAAAACGCAGCAAAAGAATTTTGCAAAACGCCAGCGTTTTGTAATG
1 CTTTAGCGGCGCTTTTT-AAAAAACGCAGCAAAAGAATTTTGCAAAACGACAGCGTTTTGTAATG
*
31128316 AGCTTTTAGTGA
65 AGCTTTTAATGA
* * *
31128328 CTATAGCAGCGCTTTTTGAAAAACGC
1 CTTTAGCGGCGCTTTTTAAAAAACGC
31128354 CACAAAAAAT
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
75 5 0.06
76 78 0.87
77 7 0.08
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (76 bp):
CTTTAGCGGCGCTTTTTAAAAAACGCAGCAAAAGAATTTTGCAAAACGACAGCGTTTTGTAATGA
GCTTTTAATGA
Found at i:31128684 original size:21 final size:21
Alignment explanation
Indices: 31128660--31128701 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31128650 ATTATAGTTT
31128660 AGGGTTTACA-GTATATGGTTA
1 AGGGTTTA-ATGTATATGGTTA
*
31128681 AGGGTTTAATGTTTATGGTTA
1 AGGGTTTAATGTATATGGTTA
31128702 CTATTTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.26, C:0.02, G:0.29, T:0.43
Consensus pattern (21 bp):
AGGGTTTAATGTATATGGTTA
Found at i:31128731 original size:15 final size:14
Alignment explanation
Indices: 31128711--31128745 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
31128701 ACTATTTTAA
*
31128711 GGTTTATGGATTAT
1 GGTTTAGGGATTAT
31128725 GGGTTTAGGGATTAT
1 -GGTTTAGGGATTAT
31128740 GGTTTA
1 GGTTTA
31128746 ATGGTGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:31128792 original size:21 final size:22
Alignment explanation
Indices: 31128750--31128797 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
31128740 GGTTTAATGG
*
31128750 TGGTTTAAGTGTTGGGGTTTAA
1 TGGTTTAAGTGTTGAGGTTTAA
*
31128772 -GGTTTATGTGTTAGAGG-TTAA
1 TGGTTTAAGTGTT-GAGGTTTAA
31128793 TGGTT
1 TGGTT
31128798 AGGGGTCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (22 bp):
TGGTTTAAGTGTTGAGGTTTAA
Found at i:31129056 original size:7 final size:7
Alignment explanation
Indices: 31128965--31129059 Score: 50
Period size: 7 Copynumber: 13.4 Consensus size: 7
31128955 TTAATTATCA
*
31128965 TTATAGT
1 TTATGGT
*
31128972 TTAGGGT
1 TTATGGT
*
31128979 TTATGAT
1 TTATGGT
*
31128986 TTAGGGT
1 TTATGGT
*
31128993 ATATGGT
1 TTATGGT
*
31129000 TTAAGGT
1 TTATGGT
**
31129007 TTAAAGT
1 TTATGGT
*
31129014 GTATGAGTT
1 TTATG-G-T
31129023 GTTAT--T
1 -TTATGGT
*
31129029 TTAAGGT
1 TTATGGT
*
31129036 TTATGGA
1 TTATGGT
31129043 TTATGGT
1 TTATGGT
31129050 TTATGGT
1 TTATGGT
31129057 TTA
1 TTA
31129060 GGGGTTTGGG
Statistics
Matches: 64, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
5 3 0.05
6 1 0.02
7 55 0.86
8 1 0.02
9 1 0.02
10 3 0.05
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.49
Consensus pattern (7 bp):
TTATGGT
Found at i:31129259 original size:29 final size:29
Alignment explanation
Indices: 31129227--31129295 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
31129217 ATAACGTCAT
31129227 TTTATATTTATATATTGTATACATAAATA
1 TTTATATTTATATATTGTATACATAAATA
31129256 TTTATATTTATATATTGTATACATAAATA
1 TTTATATTTATATATTGTATACATAAATA
31129285 TTTATATTTAT
1 TTTATATTTAT
31129296 CCAATATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTATATTTATATATTGTATACATAAATA
Found at i:31129645 original size:9 final size:8
Alignment explanation
Indices: 31129627--31129700 Score: 55
Period size: 7 Copynumber: 8.9 Consensus size: 8
31129617 TTTATATGAT
31129627 AATTTAAA
1 AATTTAAA
31129635 AATTATAAA
1 AATT-TAAA
31129644 AATATTCAAAA
1 AAT-TT--AAA
31129655 AATTTTAAA
1 AA-TTTAAA
31129664 AA-TTAAA
1 AATTTAAA
31129671 AA-TTAAA
1 AATTTAAA
31129678 AA-TTAAA
1 AATTTAAA
**
31129685 AAACTAAA
1 AATTTAAA
31129693 ATATTTAA
1 A-ATTTAA
31129701 TATTTAATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
7 21 0.38
8 9 0.16
9 17 0.30
10 1 0.02
11 7 0.12
12 1 0.02
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (8 bp):
AATTTAAA
Found at i:31129693 original size:7 final size:7
Alignment explanation
Indices: 31129659--31129686 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
31129649 TCAAAAAATT
31129659 TTAAAAA
1 TTAAAAA
31129666 TTAAAAA
1 TTAAAAA
31129673 TTAAAAA
1 TTAAAAA
31129680 TTAAAAA
1 TTAAAAA
31129687 ACTAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:31129694 original size:14 final size:14
Alignment explanation
Indices: 31129660--31129693 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
31129650 CAAAAAATTT
*
31129660 TAAAAATTAAAAAT
1 TAAAAATTAAAAAC
31129674 TAAAAATTAAAAAAC
1 TAAAAATT-AAAAAC
31129689 TAAAA
1 TAAAA
31129694 TATTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAAATTAAAAAC
Found at i:31129904 original size:42 final size:43
Alignment explanation
Indices: 31129849--31129947 Score: 130
Period size: 42 Copynumber: 2.3 Consensus size: 43
31129839 ATTAAATAGG
* * *
31129849 AAAACGCCACAAAAAAATTAAATTATAGTGGCG-TTTTTATTA
1 AAAACGCCGCAAAAAAATTAAACTATAGTGACGCTTTTTATTA
* * *
31129891 AAAAGGCCGC-AAAAAATTAAACTATAGTGACGCTTTTTGTTG
1 AAAACGCCGCAAAAAAATTAAACTATAGTGACGCTTTTTATTA
31129933 AAAACGCCGCAAAAA
1 AAAACGCCGCAAAAA
31129948 GCCATTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 20 0.42
42 24 0.50
43 4 0.08
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (43 bp):
AAAACGCCGCAAAAAAATTAAACTATAGTGACGCTTTTTATTA
Found at i:31134429 original size:43 final size:42
Alignment explanation
Indices: 31134304--31134445 Score: 117
Period size: 43 Copynumber: 3.4 Consensus size: 42
31134294 GGTTATATTC
* * * *
31134304 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGT-TTGTT
1 TTTAGCGGCGTTTGTTAAAAAAGCGACGCTAAAAGTATGGTT
* * * * * *
31134345 CTGTAGCAGCGTTTG-TAAAAAAGTGTCGCTAGAGGTTATGGTT
1 -TTTAGCGGCGTTTGTTAAAAAAGCGACGCTAAAAG-TATGGTT
* *
31134388 TTTAGCGGTGTTTGTTAAAAAAGCGACGCTAAAAGTCATGGTC
1 TTTAGCGGCGTTTGTTAAAAAAGCGACGCTAAAAGT-ATGGTT
* *
31134431 TTTAACGGCATTTGT
1 TTTAGCGGCGTTTGT
31134446 GGGAAAGCGT
Statistics
Matches: 76, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
41 14 0.18
42 25 0.33
43 37 0.49
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.33
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTTAAAAAAGCGACGCTAAAAGTATGGTT
Found at i:31134485 original size:42 final size:42
Alignment explanation
Indices: 31134414--31134528 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
31134404 AAAAAAGCGA
* * * * * *
31134414 CGCTAAAAGTCATGGTCTTTAACGGCATTTGTGGGAAAG-CGT
1 CGCTAAAGGTCATGGTCTTTAGCGACATTTGT-GAAAAGAAGC
* *
31134456 TGCTAAAGGTCATGGTCTTTAGTGACATTTGTGAAAAGAAGC
1 CGCTAAAGGTCATGGTCTTTAGCGACATTTGTGAAAAGAAGC
* *
31134498 CGCTAAAGGTTATGGTCTTTAGCGACGTTTG
1 CGCTAAAGGTCATGGTCTTTAGCGACATTTG
31134529 CTATAGCGGT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 5 0.08
42 55 0.92
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (42 bp):
CGCTAAAGGTCATGGTCTTTAGCGACATTTGTGAAAAGAAGC
Found at i:31140127 original size:26 final size:27
Alignment explanation
Indices: 31140091--31140157 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
31140081 TGTGGGCCCC
31140091 ACCATTTGCGCCTCT-GGATAGGCACA
1 ACCATTTGCGCCTCTGGGATAGGCACA
31140117 ACCATTTGCGCCTCTGGGATAGGCACA
1 ACCATTTGCGCCTCTGGGATAGGCACA
31140144 ACCATTTGCGCCTC
1 ACCATTTGCGCCTC
31140158 AGAGAAAGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 15 0.38
27 25 0.62
ACGTcount: A:0.21, C:0.33, G:0.22, T:0.24
Consensus pattern (27 bp):
ACCATTTGCGCCTCTGGGATAGGCACA
Found at i:31144925 original size:16 final size:16
Alignment explanation
Indices: 31144904--31144944 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
31144894 TTGAATTACT
31144904 TATTACAGCTCTATTC
1 TATTACAGCTCTATTC
31144920 TATTACAGCTCTATTC
1 TATTACAGCTCTATTC
*
31144936 AATTACAGC
1 TATTACAGC
31144945 AAACCAAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.39
Consensus pattern (16 bp):
TATTACAGCTCTATTC
Found at i:31163258 original size:42 final size:44
Alignment explanation
Indices: 31163212--31163300 Score: 130
Period size: 42 Copynumber: 2.1 Consensus size: 44
31163202 ATTGATGTAA
* *
31163212 AATAGAAGTT-GTGATAGTTATAT-TTTAAAAA-AATTATAATTT
1 AATAGAAGTTACT-ATAATTATATATTTAAAAATAATTATAATTT
31163254 AATAGAAGTTACTATAATTATATATTTAAAAATAATTATAATTT
1 AATAGAAGTTACTATAATTATATATTTAAAAATAATTATAATTT
31163298 AAT
1 AAT
31163301 TTATAATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
42 19 0.45
43 9 0.21
44 14 0.33
ACGTcount: A:0.48, C:0.01, G:0.08, T:0.43
Consensus pattern (44 bp):
AATAGAAGTTACTATAATTATATATTTAAAAATAATTATAATTT
Found at i:31163306 original size:18 final size:18
Alignment explanation
Indices: 31163266--31163310 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
31163256 TAGAAGTTAC
31163266 TATAATTATATATTTAAA
1 TATAATTATATATTTAAA
* *
31163284 AATAATTATA-ATTTAATT
1 TATAATTATATATTTAA-A
31163302 TATAATTAT
1 TATAATTAT
31163311 TAGTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATAATTATATATTTAAA
Found at i:31166821 original size:19 final size:19
Alignment explanation
Indices: 31166783--31166821 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31166773 TATATTTTTC
* * *
31166783 AAAAATTATTATTATTATA
1 AAAAAATATTAGTATGATA
31166802 AAAAAATATTAGTATGATA
1 AAAAAATATTAGTATGATA
31166821 A
1 A
31166822 CAATAATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAAAATATTAGTATGATA
Found at i:31178381 original size:258 final size:258
Alignment explanation
Indices: 31177924--31178956 Score: 2066
Period size: 258 Copynumber: 4.0 Consensus size: 258
31177914 CTATATCAAG
31177924 CAGAAATACTATAAAGTTAGAACATGTTCACTGTGAATCTCAAATTTTTTTGAGGCACAAATACT
1 CAGAAATACTATAAAGTTAGAACATGTTCACTGTGAATCTCAAATTTTTTTGAGGCACAAATACT
31177989 ATAAATTAGTTTTGTTTTATAAGATGGAATTAGCAAAATTCCTATCCTACTTTCTCTTAGTTCTA
66 ATAAATTAGTTTTGTTTTATAAGATGGAATTAGCAAAATTCCTATCCTACTTTCTCTTAGTTCTA
31178054 AAGTAACTACGTATTCCCATGTTCTAGCAAAAAAAAAAAAAAAGCAAAATACATAATTTCAAGAA
131 AAGTAACTACGTATTCCCATGTTCTAGCAAAAAAAAAAAAAAAGCAAAATACATAATTTCAAGAA
31178119 TGTACAAAGTAGTTCCATTAGGTTTTACAAAATTCTCATTATTCAGCAAAAAATCCCCAAACC
196 TGTACAAAGTAGTTCCATTAGGTTTTACAAAATTCTCATTATTCAGCAAAAAATCCCCAAACC
31178182 CAGAAATACTATAAAGTTAGAACATGTTCACTGTGAATCTCAAATTTTTTTGAGGCACAAATACT
1 CAGAAATACTATAAAGTTAGAACATGTTCACTGTGAATCTCAAATTTTTTTGAGGCACAAATACT
31178247 ATAAATTAGTTTTGTTTTATAAGATGGAATTAGCAAAATTCCTATCCTACTTTCTCTTAGTTCTA
66 ATAAATTAGTTTTGTTTTATAAGATGGAATTAGCAAAATTCCTATCCTACTTTCTCTTAGTTCTA
31178312 AAGTAACTACGTATTCCCATGTTCTAGCAAAAAAAAAAAAAAAGCAAAATACATAATTTCAAGAA
131 AAGTAACTACGTATTCCCATGTTCTAGCAAAAAAAAAAAAAAAGCAAAATACATAATTTCAAGAA
31178377 TGTACAAAGTAGTTCCATTAGGTTTTACAAAATTCTCATTATTCAGCAAAAAATCCCCAAACC
196 TGTACAAAGTAGTTCCATTAGGTTTTACAAAATTCTCATTATTCAGCAAAAAATCCCCAAACC
31178440 CAGAAATACTATAAAGTTAGAACATGTTCACTGTGAATCTCAAATTTTTTTGAGGCACAAATACT
1 CAGAAATACTATAAAGTTAGAACATGTTCACTGTGAATCTCAAATTTTTTTGAGGCACAAATACT
31178505 ATAAATTAGTTTTGTTTTATAAGATGGAATTAGCAAAATTCCTATCCTACTTTCTCTTAGTTCTA
66 ATAAATTAGTTTTGTTTTATAAGATGGAATTAGCAAAATTCCTATCCTACTTTCTCTTAGTTCTA
31178570 AAGTAACTACGTATTCCCATGTTCTAGCAAAAAAAAAAAAAAAGCAAAATACATAATTTCAAGAA
131 AAGTAACTACGTATTCCCATGTTCTAGCAAAAAAAAAAAAAAAGCAAAATACATAATTTCAAGAA
31178635 TGTACAAAGTAGTTCCATTAGGTTTTACAAAATTCTCATTATTCAGCAAAAAATCCCCAAACC
196 TGTACAAAGTAGTTCCATTAGGTTTTACAAAATTCTCATTATTCAGCAAAAAATCCCCAAACC
31178698 CAGAAATACTATAAAGTTAGAACATGTTCACTGTGAATCTCAAATTTTTTTGAGGCACAAATACT
1 CAGAAATACTATAAAGTTAGAACATGTTCACTGTGAATCTCAAATTTTTTTGAGGCACAAATACT
31178763 ATAAATTAGTTTTGTTTTATAAGATGGAATTAGCAAAATTCCTATCCTACTTTCTCTTAGTTCTA
66 ATAAATTAGTTTTGTTTTATAAGATGGAATTAGCAAAATTCCTATCCTACTTTCTCTTAGTTCTA
31178828 AAGTAACTACGTATTCCCATGTTCTAGCAAAAAAAAAAAAAAAGCAAAATACATAATTTCAAGAA
131 AAGTAACTACGTATTCCCATGTTCTAGCAAAAAAAAAAAAAAAGCAAAATACATAATTTCAAGAA
31178893 TGTACAAAGTAGTTCCATTAGGTTTTACAAAATTCTCATTATTCAGCAAAAAATCCCCAAACC
196 TGTACAAAGTAGTTCCATTAGGTTTTACAAAATTCTCATTATTCAGCAAAAAATCCCCAAACC
31178956 C
1 C
31178957 TTTTATGCCA
Statistics
Matches: 775, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
258 775 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (258 bp):
CAGAAATACTATAAAGTTAGAACATGTTCACTGTGAATCTCAAATTTTTTTGAGGCACAAATACT
ATAAATTAGTTTTGTTTTATAAGATGGAATTAGCAAAATTCCTATCCTACTTTCTCTTAGTTCTA
AAGTAACTACGTATTCCCATGTTCTAGCAAAAAAAAAAAAAAAGCAAAATACATAATTTCAAGAA
TGTACAAAGTAGTTCCATTAGGTTTTACAAAATTCTCATTATTCAGCAAAAAATCCCCAAACC
Found at i:31187444 original size:18 final size:18
Alignment explanation
Indices: 31187421--31187458 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
31187411 CTTATTCTAC
31187421 AAGAATAAAAACCTATGT
1 AAGAATAAAAACCTATGT
31187439 AAGAATAAAAACCTATGT
1 AAGAATAAAAACCTATGT
31187457 AA
1 AA
31187459 CCTCTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.21
Consensus pattern (18 bp):
AAGAATAAAAACCTATGT
Found at i:31193058 original size:22 final size:22
Alignment explanation
Indices: 31193030--31193074 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
31193020 AGGGGGAGTG
31193030 TAGGAATAT-TCTGTAAATATTT
1 TAGGAATATAT-TGTAAATATTT
*
31193052 TAGGAATATATTGTAGATATTT
1 TAGGAATATATTGTAAATATTT
31193074 T
1 T
31193075 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATATTGTAAATATTT
Found at i:31198455 original size:5 final size:5
Alignment explanation
Indices: 31198445--31198475 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
31198435 AGAAGATTCC
31198445 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
31198476 TATAAACACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:31201066 original size:19 final size:19
Alignment explanation
Indices: 31201042--31201080 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
31201032 ACTAACGTAA
31201042 GTAGAGAGGACCTTTACTT
1 GTAGAGAGGACCTTTACTT
*
31201061 GTAGAGAGGATCTTTACTT
1 GTAGAGAGGACCTTTACTT
31201080 G
1 G
31201081 GCATGTATTA
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:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (19 bp):
GTAGAGAGGACCTTTACTT
Found at i:31207433 original size:16 final size:16
Alignment explanation
Indices: 31207417--31207448 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
31207407 TCAAACGCCT
31207417 CTCCACCCCTCCTCCTC
1 CTCCA-CCCTCCTCCTC
31207434 CTCCACCCTCCTCCT
1 CTCCACCCTCCTCCT
31207449 TCTTCCTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.06, C:0.69, G:0.00, T:0.25
Consensus pattern (16 bp):
CTCCACCCTCCTCCTC
Found at i:31207563 original size:24 final size:22
Alignment explanation
Indices: 31207523--31207566 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
31207513 NACTCTTTCC
31207523 TCTCTCTCCTCTACCACCACCT
1 TCTCTCTCCTCTACCACCACCT
*
31207545 TCTCTCATCCTTCTTCCACCAC
1 TCTCTC-TCC-TCTACCACCAC
31207567 ATCCACAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 3 0.16
24 10 0.53
ACGTcount: A:0.14, C:0.52, G:0.00, T:0.34
Consensus pattern (22 bp):
TCTCTCTCCTCTACCACCACCT
Found at i:31218988 original size:3 final size:3
Alignment explanation
Indices: 31218980--31219015 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
31218970 TTCTGACGTT
31218980 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
31219016 CTCCTCTACC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:31220277 original size:421 final size:418
Alignment explanation
Indices: 31219457--31220291 Score: 1510
Period size: 421 Copynumber: 2.0 Consensus size: 418
31219447 TTGACAAAAA
*
31219457 GCTGAAATTGCTTGTTGTCGACAAATAAGAGAAATAAAAAAATGATATGAAAAAAATTGTAGAGA
1 GCTGAAATTGCTTGCTGTCGACAAATAAGAGAAATAAAAAAATGATATGAAAAAAATTGTAGAGA
*
31219522 AAGGAAATAAGGGTGTTATAACCTTGAAAATCAACATTTTGCACTAAAATAGTTTTGAACAGCAA
66 AAGGAAATAAGGGTGTTATAACCTTGAAAATAAACATTTTGCACTAAAATAGTTTTGAACAGCAA
31219587 CAATAGTCTAACTTTGAAAAATCATAAAAAATAGTGAAAATTAAGTTAGGTTGAATAAAATATGA
131 CAATAGTCTAACTTTGAAAAATCATAAAAAATAGTGAAAATTAAGTTAGGTTGAATAAAATATGA
*
31219652 AATTAAAGTTTTTTGAGTCTAGTTTTTCATGGAATAAATAGTGTAAGAATGGAATTGTAAATTAT
196 AATTAAAGTTTATTGAGTCTAGTTTTTCATGGAATAAATAGTGTAAGAATGGAATTGTAAATTAT
31219717 GAGATATAATAAAGTTTGTGAGACAAGGTCAAAATGATTTCTGGTTCCTCTATTTTAAATTTGGA
261 GAGATATAATAAAGTTTGTGAGACAAGGTCAAAATGATTTCTGGTTCCTCTATTTTAAATTTGGA
* *
31219782 GAATCATCAAAAGTTGTAAAAAAATTAATTAGGGGCTTAATTTATATGTTTAAATCCTTAATGAG
326 AAATCATCAAAAATTGTAAAAAAATTAATTAGGGGCTTAATTTATATGTTTAAATCCTTAATGAG
*
31219847 TCTATTTTCAAGAGAAACAAACGAGATT
391 TCGATTTTCAAGAGAAACAAACGAGATT
* *
31219875 GCTGAAATTGCTTGCTGTCGAGAAATAAGAGAAATAAGAAAAAAATGATGTGAAAAAAATTGTAG
1 GCTGAAATTGCTTGCTGTCGACAAATAAGAGAAAT---AAAAAAATGATATGAAAAAAATTGTAG
* *
31219940 AGAAAGGAAATAAGGGTGTTATAACCTTGGAAATAAACATTTTGCACTAAAATAGTTTTGGACAG
63 AGAAAGGAAATAAGGGTGTTATAACCTTGAAAATAAACATTTTGCACTAAAATAGTTTTGAACAG
*
31220005 CAACAATAGTCTAACTTTGAAAAATCATAAAAAATAGTGAAAATTGAGTTAGGTTGAATAAAATA
128 CAACAATAGTCTAACTTTGAAAAATCATAAAAAATAGTGAAAATTAAGTTAGGTTGAATAAAATA
31220070 TGAAATTAAAGTTTATTGAGTCTAGTTTTTCATGGAATAAATAGTGTAAGAATGGAATTGTAAAT
193 TGAAATTAAAGTTTATTGAGTCTAGTTTTTCATGGAATAAATAGTGTAAGAATGGAATTGTAAAT
* *
31220135 TATGAGATATAATAAAGTTTGTGAGATAAGGTCAAAATGATTTTTGGTT-CTCCTATTTTAAATT
258 TATGAGATATAATAAAGTTTGTGAGACAAGGTCAAAATGATTTCTGGTTCCT-CTATTTTAAATT
31220199 TGGAAAATCATCAAAAATTGTAAAAAAATTAATTAGGGGCTTAATTTATATGTTTAAATCCTTAA
322 TGGAAAATCATCAAAAATTGTAAAAAAATTAATTAGGGGCTTAATTTATATGTTTAAATCCTTAA
31220264 TGAGTCGATTTTCAAGAGAAACAAACGA
387 TGAGTCGATTTTCAAGAGAAACAAACGA
31220292 AAACATCATC
Statistics
Matches: 400, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
418 33 0.08
420 2 0.00
421 365 0.91
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.32
Consensus pattern (418 bp):
GCTGAAATTGCTTGCTGTCGACAAATAAGAGAAATAAAAAAATGATATGAAAAAAATTGTAGAGA
AAGGAAATAAGGGTGTTATAACCTTGAAAATAAACATTTTGCACTAAAATAGTTTTGAACAGCAA
CAATAGTCTAACTTTGAAAAATCATAAAAAATAGTGAAAATTAAGTTAGGTTGAATAAAATATGA
AATTAAAGTTTATTGAGTCTAGTTTTTCATGGAATAAATAGTGTAAGAATGGAATTGTAAATTAT
GAGATATAATAAAGTTTGTGAGACAAGGTCAAAATGATTTCTGGTTCCTCTATTTTAAATTTGGA
AAATCATCAAAAATTGTAAAAAAATTAATTAGGGGCTTAATTTATATGTTTAAATCCTTAATGAG
TCGATTTTCAAGAGAAACAAACGAGATT
Found at i:31224859 original size:16 final size:17
Alignment explanation
Indices: 31224827--31224859 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31224817 GTTGTGGATT
*
31224827 ATGGGTTTTATAAAAAA
1 ATGGGTTTTACAAAAAA
31224844 ATGGGTTTT-CAAAAAA
1 ATGGGTTTTACAAAAAA
31224860 TTGATTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.33
Consensus pattern (17 bp):
ATGGGTTTTACAAAAAA
Found at i:31235300 original size:28 final size:28
Alignment explanation
Indices: 31235260--31235316 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
31235250 GGCTTACCTA
*
31235260 TCTGATATGCTATTCAAACCAAACTCAT
1 TCTGATATGCTATTCAAACCAAAATCAT
* * **
31235288 TCTGATTTTCTATTTGAACCAAAATCAT
1 TCTGATATGCTATTCAAACCAAAATCAT
31235316 T
1 T
31235317 TTCTAGTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (28 bp):
TCTGATATGCTATTCAAACCAAAATCAT
Found at i:31235940 original size:23 final size:23
Alignment explanation
Indices: 31235896--31235942 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
31235886 ACAAACAAAT
*
31235896 AAAAAGAAAAAGAAAGCCAAGCC
1 AAAAAGAAAAAGAAAGCAAAGCC
*
31235919 AAAACGAAAGAAGAAAG-AAAGCC
1 AAAAAGAAA-AAGAAAGCAAAGCC
31235942 A
1 A
31235943 CGGCCTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.66, C:0.15, G:0.19, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAGAAAGCAAAGCC
Found at i:31236421 original size:36 final size:38
Alignment explanation
Indices: 31236340--31236441 Score: 111
Period size: 36 Copynumber: 2.7 Consensus size: 38
31236330 CTTCGAGTCA
* *
31236340 ATGAGACACTGGGTGTCAATTTATTACTTCGGATTTATTCG
1 ATGAGACACTGGATGTCAA--T-TTACTTCGGATTTAATCG
* *
31236381 ATGAGGCACTGGGT-TCCAATTTACTTC-G-TTTAATCG
1 ATGAGACACTGGATGT-CAATTTACTTCGGATTTAATCG
31236417 ATGAGACACTGGATGTCAATTTACT
1 ATGAGACACTGGATGTCAATTTACT
31236442 ACTTCGAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
36 28 0.51
37 2 0.04
38 7 0.13
39 1 0.02
40 1 0.02
41 16 0.29
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (38 bp):
ATGAGACACTGGATGTCAATTTACTTCGGATTTAATCG
Found at i:31237209 original size:21 final size:20
Alignment explanation
Indices: 31237167--31237209 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
31237157 ATTTAAAATG
* * *
31237167 ATGATTTGAATGATGTTTTA
1 ATGATATGAATGATGATATA
31237187 ATGATATGAAATGATGATATA
1 ATGATATG-AATGATGATATA
31237208 AT
1 AT
31237210 TGTGGTACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.42
Consensus pattern (20 bp):
ATGATATGAATGATGATATA
Found at i:31238600 original size:21 final size:21
Alignment explanation
Indices: 31238575--31238614 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31238565 TCATAAAGCT
31238575 TGTTTATA-TGTTAATTAATTA
1 TGTTT-TAGTGTTAATTAATTA
*
31238596 TGTTTTAGTTTTAATTAAT
1 TGTTTTAGTGTTAATTAAT
31238615 CTTAATTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (21 bp):
TGTTTTAGTGTTAATTAATTA
Found at i:31242646 original size:6 final size:6
Alignment explanation
Indices: 31242637--31242677 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
31242627 AAAAATTTAT
31242637 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTC
1 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTC
31242678 TCAATCCTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.15, C:0.68, G:0.00, T:0.17
Consensus pattern (6 bp):
CCCTCA
Found at i:31246776 original size:22 final size:22
Alignment explanation
Indices: 31246751--31246797 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
31246741 AAGGTGTTAC
31246751 AAGACACCATAAAGATGTGTCT
1 AAGACACCATAAAGATGTGTCT
31246773 AAGACACCATAAAGATGTGTCT
1 AAGACACCATAAAGATGTGTCT
31246795 AAG
1 AAG
31246798 TCAATATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (22 bp):
AAGACACCATAAAGATGTGTCT
Found at i:31250348 original size:105 final size:105
Alignment explanation
Indices: 31250233--31250442 Score: 411
Period size: 105 Copynumber: 2.0 Consensus size: 105
31250223 TTTTGAATTT
31250233 TTCAAAATGTCTTTAACTGGCCAATATATAAATGAAGGCCAAAATTTTGATAATGAAAAACAAAT
1 TTCAAAATGTCTTTAACTGGCCAATATATAAATGAAGGCCAAAATTTTGATAATGAAAAACAAAT
31250298 TTTTCTAAGGCTTAAATTGAAAATGATTTTTAGAAAGGGG
66 TTTTCTAAGGCTTAAATTGAAAATGATTTTTAGAAAGGGG
*
31250338 TTCAAAATGTCTTTAACTGGCGAATATATAAATGAAGGCCAAAATTTTGATAATGAAAAACAAAT
1 TTCAAAATGTCTTTAACTGGCCAATATATAAATGAAGGCCAAAATTTTGATAATGAAAAACAAAT
31250403 TTTTCTAAGGCTTAAATTGAAAATGATTTTTAGAAAGGGG
66 TTTTCTAAGGCTTAAATTGAAAATGATTTTTAGAAAGGGG
31250443 GAGAAAATTT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (105 bp):
TTCAAAATGTCTTTAACTGGCCAATATATAAATGAAGGCCAAAATTTTGATAATGAAAAACAAAT
TTTTCTAAGGCTTAAATTGAAAATGATTTTTAGAAAGGGG
Found at i:31250476 original size:105 final size:104
Alignment explanation
Indices: 31250255--31250476 Score: 311
Period size: 105 Copynumber: 2.1 Consensus size: 104
31250245 TTAACTGGCC
*
31250255 AATATATAAATGAAGGCCAAAATTTTGATAATGAAAAACAAATTTTTCTAAGGCTTAAATTGAAA
1 AATATAAAAATGAAGGCCAAAATTTTGATAATGAAAAACAAATTTTTCTAAGGCTTAAATTGAAA
** * * * *
31250320 ATGATTTTTAGAAAGGGGTTCAAAATGTCTTTAACTGGCG
66 ATGATTTTTAGAAAGGGGGACAAAATGTATTAAAAT-GCA
*
31250360 AATATATAAATGAAGGCCAAAATTTTGATAATGAAAAACAAATTTTTCTAAGGCTTAAATTGAAA
1 AATATAAAAATGAAGGCCAAAATTTTGATAATGAAAAACAAATTTTTCTAAGGCTTAAATTGAAA
* *
31250425 ATGATTTTTAGAAAGGGGGAGAAAATTTATTCAAAAT-CA
66 ATGATTTTTAGAAAGGGGGACAAAATGTATT-AAAATGCA
*
31250464 AATTTACAAAATG
1 AATATA-AAAATG
31250477 TTTTGTTATA
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
104 6 0.06
105 96 0.91
106 3 0.03
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (104 bp):
AATATAAAAATGAAGGCCAAAATTTTGATAATGAAAAACAAATTTTTCTAAGGCTTAAATTGAAA
ATGATTTTTAGAAAGGGGGACAAAATGTATTAAAATGCA
Found at i:31254727 original size:41 final size:41
Alignment explanation
Indices: 31254670--31254752 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
31254660 AAGGTTGTAA
*
31254670 GGGTTTATGGGAAACATGAAGGCTTGGAAAGTAGCCTAAGT
1 GGGTTTATGGGAAACATGAAGGCTTGGAAAATAGCCTAAGT
31254711 GGGTTTATGGGAAACATGAAGGCTTGGAAAATAGCCTAAGT
1 GGGTTTATGGGAAACATGAAGGCTTGGAAAATAGCCTAAGT
31254752 G
1 G
31254753 TTAGCCATAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.33, C:0.10, G:0.34, T:0.24
Consensus pattern (41 bp):
GGGTTTATGGGAAACATGAAGGCTTGGAAAATAGCCTAAGT
Found at i:31255995 original size:383 final size:383
Alignment explanation
Indices: 31255288--31257377 Score: 4089
Period size: 383 Copynumber: 5.5 Consensus size: 383
31255278 CCAATTCACC
31255288 GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTCTTCCTTGATTAGATGTGAACATAA
1 GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTCTTCCTTGATTAGATGTGAACATAA
31255353 TATTGAGCTGAATGTTCCGGATGAAACTTGCTTAATTTATTTTTAAACTAAATGTTCAAGTAAAG
66 TATTGAGCTGAATGTTCCGGATGAAACTTGCTTAATTTATTTTTAAACTAAATGTTCAAGTAAAG
31255418 CTTGCAGAATCCATCTTTGAATAGAGATATATGAACATACTATTGAGTTCATTGCTTGGGTAAAA
131 CTTGCAGAATCCATCTTTGAATAGAGATATATGAACATACTATTGAGTTCATTGCTTGGGTAAAA
31255483 CTTGCACTTAATTTTCTATTGAATTGAATGTCCGAGTAAAGCTTGTAGAAATCACTTTTGTACTG
196 CTTGCACTTAATTTTCTATTGAATTGAATGTCCGAGTAAAGCTTGTAGAAATCACTTTTGTACTG
31255548 AAAGTTCGGGTGAAACTTGCTCCATAGTTTATTTTTGAATTACATATTTAAATGTCCGAGAAAAG
261 AAAGTTCGGGTGAAACTTGCTCCATAGTTTATTTTTGAATTACATATTTAAATGTCCGAGAAAAG
31255613 CTTGCCAAGTTCATCTTTGAATACGATATATGAATATATAGTGGAGCTAAATGTTCAG
326 CTTGCCAAGTTCATCTTTGAATACGATATATGAATATATAGTGGAGCTAAATGTTCAG
31255671 GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTCTTCCTTGATTAGATGTGAACATAA
1 GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTCTTCCTTGATTAGATGTGAACATAA
31255736 TATTGAGCTGAATGTTCCGGATGAAACTTGCTTAATTTATTTTTAAACTAAATGTTCAAGTAAAG
66 TATTGAGCTGAATGTTCCGGATGAAACTTGCTTAATTTATTTTTAAACTAAATGTTCAAGTAAAG
31255801 CTTGCAGAATCCATCTTTGAATAGAGATATATGAACATACTATTGAGTTCATTGCTTGGGTAAAA
131 CTTGCAGAATCCATCTTTGAATAGAGATATATGAACATACTATTGAGTTCATTGCTTGGGTAAAA
31255866 CTTGCACTTAATTTTCTATTGAATTGAATGTCCGAGTAAAGCTTGTAGAAATCACTTTTGTACTG
196 CTTGCACTTAATTTTCTATTGAATTGAATGTCCGAGTAAAGCTTGTAGAAATCACTTTTGTACTG
31255931 AAAGTTCGGGTGAAACTTGCTCCATAGTTTATTTTTGAATTACATATTTAAATGTCCGAGAAAAG
261 AAAGTTCGGGTGAAACTTGCTCCATAGTTTATTTTTGAATTACATATTTAAATGTCCGAGAAAAG
31255996 CTTGCCAAGTTCATCTTTGAATACGATATATGAATATATAGTGGAGCTAAATGTTCAG
326 CTTGCCAAGTTCATCTTTGAATACGATATATGAATATATAGTGGAGCTAAATGTTCAG
31256054 GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTCTTCCTTGATTAGATGTGAACATAA
1 GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTCTTCCTTGATTAGATGTGAACATAA
31256119 TATTGAGCTGAATGTTCCGGATGAAACTTGCTTAATTTATTTTTAAACTAAATGTTCAAGTAAAG
66 TATTGAGCTGAATGTTCCGGATGAAACTTGCTTAATTTATTTTTAAACTAAATGTTCAAGTAAAG
31256184 CTTGCAGAATCCATCTTTGAATAGAGATATATGAACATACTATTGAGTTCATTGCTTGGGTAAAA
131 CTTGCAGAATCCATCTTTGAATAGAGATATATGAACATACTATTGAGTTCATTGCTTGGGTAAAA
31256249 CTTGCACTTAATTTTCTATTGAATTGAATGTCCGAGTAAAGCTTGTAGAAATCACTTTTGTACTG
196 CTTGCACTTAATTTTCTATTGAATTGAATGTCCGAGTAAAGCTTGTAGAAATCACTTTTGTACTG
31256314 AAAGTTCGGGTGAAACTTGCTCCATAGTTTATTTTTGAATTACATATTTAAATGTCCGAGAAAAG
261 AAAGTTCGGGTGAAACTTGCTCCATAGTTTATTTTTGAATTACATATTTAAATGTCCGAGAAAAG
31256379 CTTGCCAAGTTCATCTTTGAATACGATATATGAATATATAGTGGAGCTAAATGTTCAG
326 CTTGCCAAGTTCATCTTTGAATACGATATATGAATATATAGTGGAGCTAAATGTTCAG
31256437 GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTCTTCCTTGATTAGATGTGAACATAA
1 GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTCTTCCTTGATTAGATGTGAACATAA
31256502 TATTGAGCTGAATGTTCCGGATGAAACTTGCTTAATTTATTTTTAAACTAAATGTTCAAGTAAAG
66 TATTGAGCTGAATGTTCCGGATGAAACTTGCTTAATTTATTTTTAAACTAAATGTTCAAGTAAAG
31256567 CTTGCAGAATCCATCTTTGAATAGAGATATATGAACATACTATTGAGTTCATTGCTTGGGTAAAA
131 CTTGCAGAATCCATCTTTGAATAGAGATATATGAACATACTATTGAGTTCATTGCTTGGGTAAAA
31256632 CTTGCACTTAATTTTCTATTGAATTGAATGTCCGAGTAAAGCTTGTAGAAATCACTTTTGTACTG
196 CTTGCACTTAATTTTCTATTGAATTGAATGTCCGAGTAAAGCTTGTAGAAATCACTTTTGTACTG
31256697 AAAGTTCGGGTGAAACTTGCTCCATAGTTTATTTTTGAATTACATATTTAAATGTCCGAGAAAAG
261 AAAGTTCGGGTGAAACTTGCTCCATAGTTTATTTTTGAATTACATATTTAAATGTCCGAGAAAAG
31256762 CTTGCCAAGTTCATCTTTGAATACGATATATGAATATATAGTGGAGCTAAATGTTCAG
326 CTTGCCAAGTTCATCTTTGAATACGATATATGAATATATAGTGGAGCTAAATGTTCAG
31256820 GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTCTTCCTTGATTAGATGTGAACATAA
1 GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTCTTCCTTGATTAGATGTGAACATAA
31256885 TATTGAGCTGAATGTTCCGGATGAAACTTGCTTAATTTATTTTTAAACTAAATGTTCAAGTAAAG
66 TATTGAGCTGAATGTTCCGGATGAAACTTGCTTAATTTATTTTTAAACTAAATGTTCAAGTAAAG
31256950 CTTGCAGAATCCATCTTTGAATAGAGATATATGAACATACTATTGAGTTCATTGCTTGGGTAAAA
131 CTTGCAGAATCCATCTTTGAATAGAGATATATGAACATACTATTGAGTTCATTGCTTGGGTAAAA
31257015 CTTGCACTTAATTTTCTATTGAATTGAATGTCCGAGTAAAGCTTGTAGAAATCACTTTTGTACTG
196 CTTGCACTTAATTTTCTATTGAATTGAATGTCCGAGTAAAGCTTGTAGAAATCACTTTTGTACTG
31257080 AAAGTTCGGGTGAAACTTGCTCCATAGTTTATTTTTGAATTACATATTTAAATGTCCGAGAAAAG
261 AAAGTTCGGGTGAAACTTGCTCCATAGTTTATTTTTGAATTACATATTTAAATGTCCGAGAAAAG
31257145 CTTGCCAAGTTCATCTTTGAATACGATATATGAATATATAGTGGAGCTAAATGTTCAG
326 CTTGCCAAGTTCATCTTTGAATACGATATATGAATATATAGTGGAGCTAAATGTTCAG
* *
31257203 GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTATTCCTTGAATAGAGGTGTGAACAT
1 GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTCTTCCTTGATTAGA--TGTGAACAT
*
31257268 ACTATTGAGCTGAATGTTCCGGATGAAA----CTTAATTTATTTTTAAACTAAATGTTCAAGTAA
64 AATATTGAGCTGAATGTTCCGGATGAAACTTGCTTAATTTATTTTTAAACTAAATGTTCAAGTAA
* *
31257329 AGCTTGCAGAATCCATCTCTGAATAGAGATATATGATCATACTATTGAG
129 AGCTTGCAGAATCCATCTTTGAATAGAGATATATGAACATACTATTGAG
31257378 CGGAATGTCC
Statistics
Matches: 1700, Mismatches: 5, Indels: 6
0.99 0.00 0.00
Matches are distributed among these distances:
381 80 0.05
383 1584 0.93
385 36 0.02
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (383 bp):
GTGAAGCTTGCTTAATATTTTATTTAAGCTTGCAGAAATTCTTCCTTGATTAGATGTGAACATAA
TATTGAGCTGAATGTTCCGGATGAAACTTGCTTAATTTATTTTTAAACTAAATGTTCAAGTAAAG
CTTGCAGAATCCATCTTTGAATAGAGATATATGAACATACTATTGAGTTCATTGCTTGGGTAAAA
CTTGCACTTAATTTTCTATTGAATTGAATGTCCGAGTAAAGCTTGTAGAAATCACTTTTGTACTG
AAAGTTCGGGTGAAACTTGCTCCATAGTTTATTTTTGAATTACATATTTAAATGTCCGAGAAAAG
CTTGCCAAGTTCATCTTTGAATACGATATATGAATATATAGTGGAGCTAAATGTTCAG
Found at i:31261247 original size:19 final size:18
Alignment explanation
Indices: 31261196--31261251 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
31261186 TGAAAATAAA
31261196 TATAATTG-TAATAATTT
1 TATAATTGTTAATAATTT
*
31261213 T-TAATCAT-TTATTAATTT
1 TATAAT--TGTTAATAATTT
31261231 TATAATTGTTAAATAATTT
1 TATAATTGTT-AATAATTT
31261250 TA
1 TA
31261252 AAAATTTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
16 4 0.13
17 2 0.06
18 12 0.39
19 13 0.42
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (18 bp):
TATAATTGTTAATAATTT
Found at i:31261391 original size:21 final size:21
Alignment explanation
Indices: 31261365--31261417 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
31261355 TGCTGTTTCT
*
31261365 AATCTCACTGCTACAATACCC
1 AATCTCACTGCTACAATAACC
* * *
31261386 AATCTCACCGCTACAGTAACT
1 AATCTCACTGCTACAATAACC
31261407 AATCTCACTGC
1 AATCTCACTGC
31261418 CACCGCTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.25
Consensus pattern (21 bp):
AATCTCACTGCTACAATAACC
Found at i:31266825 original size:25 final size:25
Alignment explanation
Indices: 31266761--31266826 Score: 89
Period size: 24 Copynumber: 2.6 Consensus size: 25
31266751 AAAACAAAAT
*
31266761 GGACAAAATAAAAACCATGAAAATGT
1 GGACAAAAT-AAAACCATGAAAATGG
* *
31266787 GGAC-AAATCAAACCATGAAATTGG
1 GGACAAAATAAAACCATGAAAATGG
31266811 GGACAAAATAAAACCA
1 GGACAAAATAAAACCA
31266827 CAAAACTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 17 0.49
25 14 0.40
26 4 0.11
ACGTcount: A:0.55, C:0.15, G:0.17, T:0.14
Consensus pattern (25 bp):
GGACAAAATAAAACCATGAAAATGG
Found at i:31267470 original size:16 final size:16
Alignment explanation
Indices: 31267439--31267469 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31267429 AGTGAAAAAA
31267439 ATAATTAAGATATTTT
1 ATAATTAAGATATTTT
31267455 ATAATTAAGAT-TTTT
1 ATAATTAAGATATTTT
31267470 TTTTATGAAA
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:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATAATTAAGATATTTT
Found at i:31268633 original size:13 final size:13
Alignment explanation
Indices: 31268615--31268680 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
31268605 TTAGATTTTC
31268615 CTAAATATTATCA
1 CTAAATATTATCA
31268628 CTAAATA--ATC-
1 CTAAATATTATCA
*
31268638 TTAAATATTATCA
1 CTAAATATTATCA
31268651 CTAAATAATT-T--
1 CTAAAT-ATTATCA
31268662 -TAAATATTATCA
1 CTAAATATTATCA
31268674 CTAAATA
1 CTAAATA
31268681 ATTTTAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
9 3 0.07
10 12 0.28
11 3 0.07
12 3 0.07
13 19 0.44
14 3 0.07
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:31268646 original size:23 final size:23
Alignment explanation
Indices: 31268616--31268689 Score: 139
Period size: 23 Copynumber: 3.2 Consensus size: 23
31268606 TAGATTTTCC
*
31268616 TAAATATTATCACTAAATAATCT
1 TAAATATTATCACTAAATAATTT
31268639 TAAATATTATCACTAAATAATTT
1 TAAATATTATCACTAAATAATTT
31268662 TAAATATTATCACTAAATAATTT
1 TAAATATTATCACTAAATAATTT
31268685 TAAAT
1 TAAAT
31268690 TTTAAAAATC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAATATTATCACTAAATAATTT
Found at i:31279892 original size:20 final size:20
Alignment explanation
Indices: 31279855--31279892 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31279845 TGATGGGGAG
*
31279855 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
31279875 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
31279893 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:31281854 original size:46 final size:46
Alignment explanation
Indices: 31281802--31282075 Score: 415
Period size: 46 Copynumber: 6.0 Consensus size: 46
31281792 AGTGTGCTCT
*
31281802 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
31281848 CTGATATGAAATGTGTAAGACCATGGTTGAAAGAGACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
31281894 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
31281940 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ***
31281986 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
31282032 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
31282076 TCATGTCAAA
Statistics
Matches: 211, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.00
46 210 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:31284907 original size:25 final size:26
Alignment explanation
Indices: 31284860--31284913 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
31284850 GTTTTATTAT
*
31284860 AATTAACCTTTAATTATTAAATACCAA
1 AATTAACCTTT-ATTATTAAATAACAA
31284887 AATTAACCTTT-TTATTAAATAACAA
1 AATTAACCTTTATTATTAAATAACAA
31284912 AA
1 AA
31284914 ATCACTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 15 0.58
27 11 0.42
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (26 bp):
AATTAACCTTTATTATTAAATAACAA
Found at i:31286172 original size:15 final size:15
Alignment explanation
Indices: 31286150--31286188 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
31286140 TTAATAAATA
31286150 ACATTTCATG-CCAT
1 ACATTTCATGTCCAT
31286164 ACGATTTCATGTCCAT
1 AC-ATTTCATGTCCAT
*
31286180 TCATTTCAT
1 ACATTTCAT
31286189 TAACTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 15 0.68
16 5 0.23
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.41
Consensus pattern (15 bp):
ACATTTCATGTCCAT
Found at i:31286436 original size:30 final size:29
Alignment explanation
Indices: 31286367--31286453 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 29
31286357 ACTGGTACAT
* *
31286367 AGTACCTGATAAATATAACATCGGCACAT
1 AGTACCTAATAAATATAACATCGGCACAA
* *
31286396 AGTGCCTAATAAATATAACA-CGGTACAA
1 AGTACCTAATAAATATAACATCGGCACAA
*
31286424 AGTATACCTAATAAATATAATCATGGGCAC
1 AG--TACCTAATAAATATAA-CATCGGCAC
31286454 TTAGTGCCTG
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 8 0.17
29 18 0.38
30 15 0.32
31 2 0.04
32 4 0.09
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (29 bp):
AGTACCTAATAAATATAACATCGGCACAA
Found at i:31286468 original size:30 final size:29
Alignment explanation
Indices: 31286363--31286468 Score: 106
Period size: 30 Copynumber: 3.6 Consensus size: 29
31286353 CACCACTGGT
*
31286363 ACATAGTACCTGATAAATATAACATCGGC
1 ACATAGTACCTAATAAATATAACATCGGC
* *
31286392 ACATAGTGCCTAATAAATATAACA-CGGT
1 ACATAGTACCTAATAAATATAACATCGGC
* *
31286420 ACAAAGTATACCTAATAAATATAATCATGGGC
1 ACATAG--TACCTAATAAATATAA-CATCGGC
* * *
31286452 ACTTAGTGCCTGATAAA
1 ACATAGTACCTAATAAA
31286469 CCCTAATGAC
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
28 8 0.13
29 22 0.35
30 24 0.39
31 2 0.03
32 6 0.10
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.25
Consensus pattern (29 bp):
ACATAGTACCTAATAAATATAACATCGGC
Found at i:31286989 original size:28 final size:28
Alignment explanation
Indices: 31286958--31287014 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
31286948 AAACTTTTAC
31286958 AGTTTATCCAATTTAGTTCCTAAAATTG
1 AGTTTATCCAATTTAGTTCCTAAAATTG
31286986 AGTTTATCCAATTTAGTTCCTAAAATTG
1 AGTTTATCCAATTTAGTTCCTAAAATTG
31287014 A
1 A
31287015 AACTTACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (28 bp):
AGTTTATCCAATTTAGTTCCTAAAATTG
Found at i:31293385 original size:43 final size:42
Alignment explanation
Indices: 31293288--31293409 Score: 167
Period size: 43 Copynumber: 2.9 Consensus size: 42
31293278 TTAGGGTTAT
* * *
31293288 TGAGATAACGTGTAAGACCATATCTGGGATATGGCTTCGATA
1 TGAGATTACATGTAAGACCATATCTGGGATATGGCATCGATA
*
31293330 TGAGAATT-CATGTAAGACCATAGCTGGGCA-ATTGGCATCGATA
1 TGAG-ATTACATGTAAGACCATATCTGGG-ATA-TGGCATCGATA
31293373 TGAGATTACATGTAAGACCATATCTGGGATATGGCAT
1 TGAGATTACATGTAAGACCATATCTGGGATATGGCAT
31293410 TGGTACAGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
42 33 0.47
43 37 0.53
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (42 bp):
TGAGATTACATGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:31296941 original size:25 final size:25
Alignment explanation
Indices: 31296907--31296958 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
31296897 AGCAGCTTAG
31296907 GCTTAGGTTTCAATTCTCTACAAGT
1 GCTTAGGTTTCAATTCTCTACAAGT
*
31296932 GCTTAGGTTTCAGTTCTCTACAAGT
1 GCTTAGGTTTCAATTCTCTACAAGT
31296957 GC
1 GC
31296959 AATGTAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (25 bp):
GCTTAGGTTTCAATTCTCTACAAGT
Found at i:31303437 original size:18 final size:18
Alignment explanation
Indices: 31303394--31303438 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
31303384 TTTCAGTTGA
* *
31303394 ACAGTAACACATTCAGTC
1 ACAGTATCACATTCACTC
* *
31303412 ACAATATCACATTCACTT
1 ACAGTATCACATTCACTC
31303430 ACAGTATCA
1 ACAGTATCA
31303439 GTAATTCTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (18 bp):
ACAGTATCACATTCACTC
Found at i:31304618 original size:21 final size:21
Alignment explanation
Indices: 31304594--31304641 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
31304584 CACACGGCCA
*
31304594 TGTGACAGAGGCACACGCTCG
1 TGTGAAAGAGGCACACGCTCG
* * *
31304615 TGTGAAATAGGGACACGGTCG
1 TGTGAAAGAGGCACACGCTCG
31304636 TGTGAA
1 TGTGAA
31304642 CAGGCCGTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.19, G:0.35, T:0.19
Consensus pattern (21 bp):
TGTGAAAGAGGCACACGCTCG
Found at i:31305286 original size:6 final size:6
Alignment explanation
Indices: 31305277--31305304 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
31305267 AAAAGAATTA
31305277 GAGAGG GAGAGG GAGAGG GAGAGG GAGA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGA
31305305 ACGTGTAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:31308372 original size:48 final size:47
Alignment explanation
Indices: 31308296--31308530 Score: 231
Period size: 48 Copynumber: 4.9 Consensus size: 47
31308286 ATACTAGGGT
*
31308296 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGAAATTTA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGAAA-TTA
* * *
31308344 TATGAGAGCCAGTGTAAGACCATGTTTGGAATATGGCATCGGTATTTA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATC-GAAATTA
* * * * ** **
31308392 TATGAGAGCTAGAGTAAGACCATATCTAGG-ACATGGCATCGGCCACGA
1 TATGAGAGCCAGTGTAAGACCATGT-TTGGAACATGGCATC-GAAATTA
* * *
31308440 CATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGTACCAA-TA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATC-G-A--AATTA
* *
31308490 TATGAGAGCCAGTGTAAGACCATGTATGGGACATGGCATCG
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCG
31308531 GAATCTTACC
Statistics
Matches: 154, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
47 3 0.02
48 108 0.70
49 6 0.04
50 36 0.23
51 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.26
Consensus pattern (47 bp):
TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGAAATTA
Found at i:31308476 original size:96 final size:97
Alignment explanation
Indices: 31308349--31308531 Score: 269
Period size: 98 Copynumber: 1.9 Consensus size: 97
31308339 ATTTATATGA
* ** *
31308349 GAGCCAGTGTAAGACCATGTTTGGAATATGGCATCGGTA-TTTATATGAGAGCTAGAGTAAGACC
1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGTACAATATATGAGAGCCAGAGTAAGACC
*
31308413 ATATCTAGGACATGGCATCGGCCACGACATGT
66 ATATATAGGACATGGCATCGGCCACGACATGT
* *
31308445 GAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGTACCAATATATGAGAGCCAGTGTAAGAC
1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGTA-CAATATATGAGAGCCAGAGTAAGAC
* *
31308510 CATGTATGGGACATGGCATCGG
65 CATATATAGGACATGGCATCGG
31308532 AATCTTACCA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
96 37 0.49
98 39 0.51
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.24
Consensus pattern (97 bp):
GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGTACAATATATGAGAGCCAGAGTAAGACC
ATATATAGGACATGGCATCGGCCACGACATGT
Found at i:31309736 original size:38 final size:38
Alignment explanation
Indices: 31309677--31309760 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
31309667 CGGCCTGGGG
31309677 ACACGGGCGTGTCCCTATATGTTCAGGCCGTGTGAGCC
1 ACACGGGCGTGTCCCTATATGTTCAGGCCGTGTGAGCC
* *
31309715 ACATGGGCGTGTCCC-ATTATGTTCAGGTCGTGTGAGCC
1 ACACGGGCGTGTCCCTA-TATGTTCAGGCCGTGTGAGCC
31309753 ACACGGGC
1 ACACGGGC
31309761 CTTCAACATG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
37 1 0.02
38 41 0.98
ACGTcount: A:0.17, C:0.27, G:0.32, T:0.24
Consensus pattern (38 bp):
ACACGGGCGTGTCCCTATATGTTCAGGCCGTGTGAGCC
Found at i:31312828 original size:43 final size:43
Alignment explanation
Indices: 31312780--31312937 Score: 169
Period size: 43 Copynumber: 3.7 Consensus size: 43
31312770 GTTACCGAGA
31312780 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* *
31312823 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTTAA
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTG-TAT
* * * * * *
31312867 T-CGATTTCAT-TAAAGACCCTGTCTGGGATAGTGGCATCG-AT
1 TGTGATTACATGT-AAGACCATGTCTGGGACATTGGCATTGTAT
* * *
31312908 ATGTGATAACATGTAATACCATATCTGGGA
1 -TGTGATTACATGTAAGACCATGTCTGGGA
31312938 TATGGTATTG
Statistics
Matches: 94, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 87 0.93
44 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:31319644 original size:46 final size:46
Alignment explanation
Indices: 31319592--31320004 Score: 648
Period size: 46 Copynumber: 9.0 Consensus size: 46
31319582 GAGTGTGCTC
31319592 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* *
31319638 CCTGATATGAAATGTGTAAGACCTTGGTTGAAAGATACCATGGCAG
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
*
31319684 CCTGATATGAAATGTGTAAGACCGTGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* *
31319730 CCTGATATGAAATGTGTAAGACCTTGGTTGAAAGATACCATGGCAG
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
*
31319776 CCTGATATGAAATGTGTAAGACCGTGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* *
31319822 CCTAATATGAAATGTGTAAGACCGTGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
31319868 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* ***
31319914 CGTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* * * * * *
31319960 CATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CCTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
31320005 TCATGCCAAA
Statistics
Matches: 344, Mismatches: 22, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 1 0.00
46 343 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (46 bp):
CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
Found at i:31324020 original size:45 final size:45
Alignment explanation
Indices: 31323956--31324099 Score: 162
Period size: 45 Copynumber: 3.2 Consensus size: 45
31323946 GATTGGAGAG
* *
31323956 TGCCATGGTGTCTTTCAACCATGGTCTTATTTATTCTCGTCTTGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCGTCGTGA
* * *
31324001 TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTTCGTCGTGT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTA-TTCTCGTCGTGA
* * * * * ** *
31324047 TGCTATAATGTTTTTCAACTATGGTCTTATTTATTTTATTTGTGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCGTCGTGA
31324092 TGCCATAG
1 TGCCATAG
31324100 CATCTTTTAG
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
45 45 0.55
46 37 0.45
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCGTCGTGA
Found at i:31324071 original size:46 final size:46
Alignment explanation
Indices: 31323964--31324083 Score: 161
Period size: 46 Copynumber: 2.6 Consensus size: 46
31323954 AGTGCCATGG
* * *
31323964 TGTCTTTCAACCATGGTCTTATTTA-TTCTCGTCTTGATGCCATAG
1 TGTCTTTCAACCATGGTCTTATTTATTTTTCGTCGTGATGCCATAA
* * *
31324009 TGTCTTTCAACCATGGTCTTATTCATTTTTCGTCGTGTTGCTATAA
1 TGTCTTTCAACCATGGTCTTATTTATTTTTCGTCGTGATGCCATAA
* *
31324055 TGTTTTTCAACTATGGTCTTATTTATTTT
1 TGTCTTTCAACCATGGTCTTATTTATTTT
31324084 ATTTGTGATG
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
45 24 0.37
46 41 0.63
ACGTcount: A:0.17, C:0.18, G:0.14, T:0.50
Consensus pattern (46 bp):
TGTCTTTCAACCATGGTCTTATTTATTTTTCGTCGTGATGCCATAA
Found at i:31324196 original size:45 final size:45
Alignment explanation
Indices: 31324147--31324264 Score: 128
Period size: 45 Copynumber: 2.6 Consensus size: 45
31324137 TGCGATAGCA
* * * *
31324147 TCTTTCAGCTATAGTTTTACTCGTTTCTGGTATGGTGCCATAGTG
1 TCTTTCAACTATAGTATTACTCATTTCTGGTATAGTGCCATAGTG
* * * *
31324192 TCTTTCAACTATGGTATTATTTATTTTTGGTATAGTGCCATAGTG
1 TCTTTCAACTATAGTATTACTCATTTCTGGTATAGTGCCATAGTG
* * * *
31324237 TCTTTTAACTATGGTCTTAATCATTTCT
1 TCTTTCAACTATAGTATTACTCATTTCT
31324265 TTTACGCCAA
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.48
Consensus pattern (45 bp):
TCTTTCAACTATAGTATTACTCATTTCTGGTATAGTGCCATAGTG
Found at i:31327395 original size:19 final size:18
Alignment explanation
Indices: 31327373--31327438 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 18
31327363 GTTTTAATGA
31327373 TTTATCAATATATCTAAAT
1 TTTATCAATAT-TCTAAAT
* *
31327392 TTTA-CTAATATTTTAAAGA
1 TTTATC-AATATTCTAAA-T
*
31327411 TTTATCAATATTTCTAAGCT
1 TTTATCAATA-TTCTAA-AT
31327431 TTTATCAA
1 TTTATCAA
31327439 AATTGATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
18 6 0.16
19 17 0.46
20 14 0.38
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (18 bp):
TTTATCAATATTCTAAAT
Found at i:31327406 original size:38 final size:38
Alignment explanation
Indices: 31327354--31327427 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
31327344 TTAAAAAGAA
* *
31327354 TTTACTAATGTTTTAATGATTTATCAATATATCTAAAT
1 TTTACTAATATTTTAAAGATTTATCAATATATCTAAAT
*
31327392 TTTACTAATATTTTAAAGATTTATCAATATTTCTAA
1 TTTACTAATATTTTAAAGATTTATCAATATATCTAA
31327428 GCTTTTATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (38 bp):
TTTACTAATATTTTAAAGATTTATCAATATATCTAAAT
Found at i:31327480 original size:20 final size:20
Alignment explanation
Indices: 31327365--31327498 Score: 79
Period size: 20 Copynumber: 7.0 Consensus size: 20
31327355 TTACTAATGT
*
31327365 TTTAATGATTTATCAATATA
1 TTTAAAGATTTATCAATATA
* *
31327385 TCTAAA-TTTTA-CTAATAT-
1 TTTAAAGATTTATC-AATATA
31327403 TTTAAAGATTTATCAATAT-
1 TTTAAAGATTTATCAATATA
*
31327422 TTCT-AAGCTTTTATCAA-A-A
1 TT-TAAAG-ATTTATCAATATA
* ** *
31327441 -TTGATCATTTA-CAAGAATA
1 TTTAAAGATTTATCAA-TATA
31327460 TTTAAAGATTTATCAATATA
1 TTTAAAGATTTATCAATATA
* *
31327480 TATAAATATTTATCAATAT
1 TTTAAAGATTTATCAATAT
31327499 TTCTAAGACT
Statistics
Matches: 87, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
16 3 0.03
17 5 0.06
18 9 0.10
19 25 0.29
20 42 0.48
21 3 0.03
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (20 bp):
TTTAAAGATTTATCAATATA
Found at i:31327497 original size:10 final size:10
Alignment explanation
Indices: 31327467--31327500 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
31327457 ATATTTAAAG
31327467 ATTTATCAAT
1 ATTTATCAAT
* *
31327477 ATATATAAAT
1 ATTTATCAAT
31327487 ATTTATCAAT
1 ATTTATCAAT
31327497 ATTT
1 ATTT
31327501 CTAAGACTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTTATCAAT
Found at i:31335891 original size:30 final size:30
Alignment explanation
Indices: 31335855--31335914 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
31335845 GGGTGCATAA
31335855 AAGGTAAGTGATTGTTTATGTAAGATCATG
1 AAGGTAAGTGATTGTTTATGTAAGATCATG
31335885 AAGGTAAGTGATTGTTTATGTAAGATCATG
1 AAGGTAAGTGATTGTTTATGTAAGATCATG
31335915 CACATAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (30 bp):
AAGGTAAGTGATTGTTTATGTAAGATCATG
Found at i:31340526 original size:18 final size:19
Alignment explanation
Indices: 31340473--31340526 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
31340463 TTAGAAAATT
* *
31340473 TTTA-AAAATATAATCAAAT
1 TTTAGAAAATATAA-AAAAA
31340492 TTTAGAAAAT-TACAAAAAA
1 TTTAGAAAATATA-AAAAAA
31340511 TTT-GAAAATATAAAAA
1 TTTAGAAAATATAAAAA
31340527 TTCAAAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 10 0.33
19 14 0.47
20 6 0.20
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (19 bp):
TTTAGAAAATATAAAAAAA
Found at i:31340855 original size:22 final size:22
Alignment explanation
Indices: 31340819--31340881 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 22
31340809 AAAATTTTAC
* *
31340819 TTTTTTTT-AAATTTAT-ATAA
1 TTTTTTTTGAAATTTTTAAGAA
**
31340839 TTTTTTTTG-AATTTTTAAGGT
1 TTTTTTTTGAAATTTTTAAGAA
31340860 TTTTTTTTGAAATTTTT-AGAA
1 TTTTTTTTGAAATTTTTAAGAA
31340881 T
1 T
31340882 AATTATATGG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 14 0.41
21 13 0.38
22 7 0.21
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (22 bp):
TTTTTTTTGAAATTTTTAAGAA
Found at i:31341545 original size:18 final size:18
Alignment explanation
Indices: 31341483--31341552 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 18
31341473 CCACCTGTCA
* *
31341483 ATTAAAGTAAAAAAGGATC
1 ATTAAATTAAAAAA-AATC
*
31341502 -TTAAATTTAAAAAAAAGTA
1 ATTAAA-TTAAAAAAAA-TC
**
31341521 AGAAAATTAAAAAAAATC
1 ATTAAATTAAAAAAAATC
31341539 ATTAAATATAAAAA
1 ATTAAAT-TAAAAA
31341553 TTGATAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
18 12 0.31
19 24 0.62
20 3 0.08
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (18 bp):
ATTAAATTAAAAAAAATC
Found at i:31341844 original size:20 final size:20
Alignment explanation
Indices: 31341821--31341879 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
31341811 TTTAGGAATT
*
31341821 TTTTGAATATTTAATGAAAA
1 TTTTGAATTTTTAATGAAAA
*
31341841 TTTT-ATATTTTTAAAG-AAA
1 TTTTGA-ATTTTTAATGAAAA
*
31341860 -TTTGAATTTTTAATAAAAA
1 TTTTGAATTTTTAATGAAAA
31341879 T
1 T
31341880 ACCATAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
18 11 0.35
19 8 0.26
20 12 0.39
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
TTTTGAATTTTTAATGAAAA
Found at i:31341868 original size:18 final size:19
Alignment explanation
Indices: 31341822--31341872 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
31341812 TTAGGAATTT
* *
31341822 TTTGAATATTTAATGAAAA
1 TTTGAATTTTTAAAGAAAA
*
31341841 TTTTATATTTTTAAAG-AAA
1 TTTGA-ATTTTTAAAGAAAA
31341860 TTTGAATTTTTAA
1 TTTGAATTTTTAA
31341873 TAAAAATACC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 8 0.30
19 11 0.41
20 8 0.30
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
TTTGAATTTTTAAAGAAAA
Found at i:31342191 original size:21 final size:21
Alignment explanation
Indices: 31342166--31342205 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31342156 ATTAAGTTAT
31342166 CTTTAACCCT-TTTTTAAACAA
1 CTTT-ACCCTATTTTTAAACAA
*
31342187 CTTTATCCTATTTTTAAAC
1 CTTTACCCTATTTTTAAAC
31342206 TAAAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (21 bp):
CTTTACCCTATTTTTAAACAA
Found at i:31343383 original size:23 final size:23
Alignment explanation
Indices: 31343356--31343401 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
31343346 TATGTTGGCA
*
31343356 TTATATATTATACTTCTTTCCCT
1 TTATATATGATACTTCTTTCCCT
31343379 TTATATATGATACTTCTTTCCCT
1 TTATATATGATACTTCTTTCCCT
31343402 AGAAGCATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.02, T:0.54
Consensus pattern (23 bp):
TTATATATGATACTTCTTTCCCT
Found at i:31361312 original size:18 final size:18
Alignment explanation
Indices: 31361289--31361326 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
31361279 TTTTGAATGT
31361289 ATGAAAATTTAGATATTC
1 ATGAAAATTTAGATATTC
31361307 ATGAAAATTTAGATATTC
1 ATGAAAATTTAGATATTC
31361325 AT
1 AT
31361327 TGCATGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (18 bp):
ATGAAAATTTAGATATTC
Found at i:31362973 original size:13 final size:13
Alignment explanation
Indices: 31362955--31362979 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31362945 AAGTCGTGTG
31362955 AGGGACACGGGCC
1 AGGGACACGGGCC
31362968 AGGGACACGGGC
1 AGGGACACGGGC
31362980 GTGTGTTTGG
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:0.28, G:0.48, T:0.00
Consensus pattern (13 bp):
AGGGACACGGGCC
Found at i:31364951 original size:19 final size:19
Alignment explanation
Indices: 31364924--31364963 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
31364914 CCCTCTAGGC
*
31364924 AAGTCGGTCTTAGTTGATA
1 AAGTCGGTCCTAGTTGATA
*
31364943 AAGTTGGTCCTAGTTGATA
1 AAGTCGGTCCTAGTTGATA
31364962 AA
1 AA
31364964 CTCCTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (19 bp):
AAGTCGGTCCTAGTTGATA
Found at i:31369853 original size:13 final size:13
Alignment explanation
Indices: 31369829--31369867 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
31369819 TAGGGGCACA
*
31369829 AGCCCGTGTGGCT
1 AGCCCATGTGGCT
*
31369842 AGCTCATGTGGCT
1 AGCCCATGTGGCT
31369855 AGCCCATGTGGCT
1 AGCCCATGTGGCT
31369868 CTCATGGCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.13, C:0.28, G:0.33, T:0.26
Consensus pattern (13 bp):
AGCCCATGTGGCT
Found at i:31375122 original size:18 final size:18
Alignment explanation
Indices: 31375101--31375140 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
31375091 TGTGTACCGA
31375101 TACTGCTATTGTTACTGT
1 TACTGCTATTGTTACTGT
* *
31375119 TACTGTTATTGTTGCTGT
1 TACTGCTATTGTTACTGT
31375137 TACT
1 TACT
31375141 ATTACTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.53
Consensus pattern (18 bp):
TACTGCTATTGTTACTGT
Found at i:31378471 original size:18 final size:20
Alignment explanation
Indices: 31378432--31378468 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
31378422 GGTAAAATTA
*
31378432 TTATTCTCAGAAAATAAAAT
1 TTATTCTCAAAAAATAAAAT
31378452 TTATTCT-AAAAAATAAA
1 TTATTCTCAAAAAATAAA
31378469 TTTCTACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (20 bp):
TTATTCTCAAAAAATAAAAT
Found at i:31378877 original size:22 final size:22
Alignment explanation
Indices: 31378852--31378894 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
31378842 AATAGACATT
31378852 ATTTATTAAT-TTAAATAATTTA
1 ATTT-TTAATATTAAATAATTTA
**
31378874 ATTTTTTCTATTAAATAATTT
1 ATTTTTAATATTAAATAATTT
31378895 TCTCAATCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTTAATATTAAATAATTTA
Found at i:31379836 original size:14 final size:14
Alignment explanation
Indices: 31379817--31379846 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
31379807 AAATTCGATG
31379817 TAATATTCAAAGGA
1 TAATATTCAAAGGA
31379831 TAATATTCAAAGGA
1 TAATATTCAAAGGA
31379845 TA
1 TA
31379847 TTAATGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (14 bp):
TAATATTCAAAGGA
Found at i:31387138 original size:3 final size:3
Alignment explanation
Indices: 31387130--31387159 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31387120 TAAAAGTATT
31387130 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31387160 TAGAAAATTT
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):
ATA
Found at i:31388379 original size:21 final size:22
Alignment explanation
Indices: 31388344--31388397 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
31388334 TTACATGTGT
*
31388344 AATATT-TAATTAG-TTTTTTA
1 AATATTATATTTAGTTTTTTTA
31388364 AATATTATATTTAGTTTTTTTA
1 AATATTATATTTAGTTTTTTTA
31388386 AATATTATATTT
1 AATATTATATTT
31388398 TTAATTACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 6 0.19
21 6 0.19
22 19 0.61
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
AATATTATATTTAGTTTTTTTA
Found at i:31397969 original size:21 final size:21
Alignment explanation
Indices: 31397903--31398258 Score: 356
Period size: 21 Copynumber: 17.0 Consensus size: 21
31397893 ACTCGAAAGC
* *
31397903 TGAACAGAAGCTCGTAAGAGC
1 TGAACAGAAGCTCATAAGAGT
* * * *
31397924 TAAATAGAAACCCATAAG-GAT
1 TGAACAGAAGCTCATAAGAG-T
*
31397945 TGAACAGAAGCT-AGTAAGAGC
1 TGAACAGAAGCTCA-TAAGAGT
* * *
31397966 TGAACGGAAACTCATATGAGT
1 TGAACAGAAGCTCATAAGAGT
*
31397987 TAAACAGAAGCTCATAAGAGT
1 TGAACAGAAGCTCATAAGAGT
*
31398008 TGAACAGAAACTCATAAGAGT
1 TGAACAGAAGCTCATAAGAGT
* * *
31398029 TGAATAGAAGCTTAAAAGAGT
1 TGAACAGAAGCTCATAAGAGT
* * *
31398050 TGAACGGAAACTCATATGAGT
1 TGAACAGAAGCTCATAAGAGT
*
31398071 TAAACAGAAGCTCATAAGAGT
1 TGAACAGAAGCTCATAAGAGT
*
31398092 TGAACAGAAACTCATAAGAGT
1 TGAACAGAAGCTCATAAGAGT
* * *
31398113 TGAATAGAAGCTTAAAAGAGT
1 TGAACAGAAGCTCATAAGAGT
* * *
31398134 TGAACGGAAACTCATATGAGT
1 TGAACAGAAGCTCATAAGAGT
*
31398155 TAAACAGAAGCTCATAAGAGT
1 TGAACAGAAGCTCATAAGAGT
*
31398176 TGAACAGAAACTCATAAGAGT
1 TGAACAGAAGCTCATAAGAGT
* * *
31398197 TGAATAGAAGCTTAAAAGAGT
1 TGAACAGAAGCTCATAAGAGT
* * *
31398218 TGAACGGAAACTCATATGAGT
1 TGAACAGAAGCTCATAAGAGT
* *
31398239 TAAACAGAAGCTCGTAAGAG
1 TGAACAGAAGCTCATAAGAG
31398259 CTAAAAGAAA
Statistics
Matches: 263, Mismatches: 68, Indels: 8
0.78 0.20 0.02
Matches are distributed among these distances:
20 2 0.01
21 259 0.98
22 2 0.01
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (21 bp):
TGAACAGAAGCTCATAAGAGT
Found at i:31398017 original size:84 final size:84
Alignment explanation
Indices: 31397905--31398258 Score: 595
Period size: 84 Copynumber: 4.2 Consensus size: 84
31397895 TCGAAAGCTG
* * * * * * * *
31397905 AACAGAAGCTCGTAAGAGCTAAATAGAAACCCATAAG-GATTGAACAGAAGC-TAGTAAGAGCTG
1 AACAGAAGCTCATAAGAGTTGAACAGAAACTCATAAGAG-TTGAATAGAAGCTTA-AAAGAGTTG
31397968 AACGGAAACTCATATGAGTTA
64 AACGGAAACTCATATGAGTTA
31397989 AACAGAAGCTCATAAGAGTTGAACAGAAACTCATAAGAGTTGAATAGAAGCTTAAAAGAGTTGAA
1 AACAGAAGCTCATAAGAGTTGAACAGAAACTCATAAGAGTTGAATAGAAGCTTAAAAGAGTTGAA
31398054 CGGAAACTCATATGAGTTA
66 CGGAAACTCATATGAGTTA
31398073 AACAGAAGCTCATAAGAGTTGAACAGAAACTCATAAGAGTTGAATAGAAGCTTAAAAGAGTTGAA
1 AACAGAAGCTCATAAGAGTTGAACAGAAACTCATAAGAGTTGAATAGAAGCTTAAAAGAGTTGAA
31398138 CGGAAACTCATATGAGTTA
66 CGGAAACTCATATGAGTTA
31398157 AACAGAAGCTCATAAGAGTTGAACAGAAACTCATAAGAGTTGAATAGAAGCTTAAAAGAGTTGAA
1 AACAGAAGCTCATAAGAGTTGAACAGAAACTCATAAGAGTTGAATAGAAGCTTAAAAGAGTTGAA
31398222 CGGAAACTCATATGAGTTA
66 CGGAAACTCATATGAGTTA
*
31398241 AACAGAAGCTCGTAAGAG
1 AACAGAAGCTCATAAGAG
31398259 CTAAAAGAAA
Statistics
Matches: 259, Mismatches: 9, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
84 256 0.99
85 3 0.01
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (84 bp):
AACAGAAGCTCATAAGAGTTGAACAGAAACTCATAAGAGTTGAATAGAAGCTTAAAAGAGTTGAA
CGGAAACTCATATGAGTTA
Found at i:31401652 original size:5 final size:5
Alignment explanation
Indices: 31401644--31401669 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31401634 TCTTTTCACG
31401644 AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA A
31401670 GATTTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:31402370 original size:24 final size:24
Alignment explanation
Indices: 31402321--31402370 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
31402311 TATAAATACT
*
31402321 AAATCCCTAAATAAAATATTTCAA
1 AAATCCCTAAATAAAATATATCAA
31402345 AAATCCCTAAATAAAATAATAT-AA
1 AAATCCCTAAATAAAAT-ATATCAA
31402369 AA
1 AA
31402371 TATCTTAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (24 bp):
AAATCCCTAAATAAAATATATCAA
Found at i:31403785 original size:15 final size:15
Alignment explanation
Indices: 31403757--31403786 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31403747 TGATTTAAAG
*
31403757 TTAATTGAATTGAAT
1 TTAATTGAAATGAAT
31403772 TTAATTGAAATGAAT
1 TTAATTGAAATGAAT
31403787 ATGTGTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (15 bp):
TTAATTGAAATGAAT
Found at i:31404852 original size:13 final size:13
Alignment explanation
Indices: 31404834--31404867 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
31404824 TGAATGATGT
31404834 TTTGATAATATAA
1 TTTGATAATATAA
*
31404847 TTTGATGATATAA
1 TTTGATAATATAA
31404860 TTGTGATA
1 TT-TGATA
31404868 CTAATTGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (13 bp):
TTTGATAATATAA
Found at i:31410657 original size:40 final size:39
Alignment explanation
Indices: 31410571--31410657 Score: 88
Period size: 42 Copynumber: 2.2 Consensus size: 39
31410561 GTAAGATATT
* * * *
31410571 TATAA-ATTTAATATATATATATTATAATAAAATTAGTT
1 TATAATATTTAATATATATATATAATAATAAAACTAATG
31410609 TACTTAATATTTAAGTATATATATTATAATAAT-AAACTAATG
1 TA--TAATATTTAA-TATATATA-TATAATAATAAAACTAATG
31410651 TATAATA
1 TATAATA
31410658 AAATAAGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
38 2 0.05
40 8 0.20
41 6 0.15
42 16 0.40
43 8 0.20
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45
Consensus pattern (39 bp):
TATAATATTTAATATATATATATAATAATAAAACTAATG
Found at i:31410746 original size:16 final size:15
Alignment explanation
Indices: 31410721--31410750 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
31410711 ACAAAAACAG
31410721 AAAGGAAAGAAAGAA
1 AAAGGAAAGAAAGAA
31410736 AAAGAGAAAGAAAGA
1 AAAG-GAAAGAAAGA
31410751 CGCAAGGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAGGAAAGAAAGAA
Found at i:31414316 original size:42 final size:42
Alignment explanation
Indices: 31414227--31414344 Score: 105
Period size: 42 Copynumber: 2.8 Consensus size: 42
31414217 AGGTTATTAA
* * * * * *
31414227 GATTCCGTATAAGACCATATCCGGGATATGGCCTCGGTATGT
1 GATTTCGTATAACACCATATCAGGGACATGGCATCGATATGT
*
31414269 GATTTCGTATAACACCATGTCAGGGACATGGCATCGATATGAT
1 GATTTCGTATAACACCATATCAGGGACATGGCATCGATATG-T
* * * *
31414312 -ATTTCATGTAAGACCATATC-GAGGATATGGCAT
1 GATTTCGTATAACACCATATCAG-GGACATGGCAT
31414345 TGAAACAATA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
41 1 0.02
42 60 0.97
43 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (42 bp):
GATTTCGTATAACACCATATCAGGGACATGGCATCGATATGT
Found at i:31416953 original size:46 final size:47
Alignment explanation
Indices: 31416878--31417346 Score: 303
Period size: 46 Copynumber: 9.9 Consensus size: 47
31416868 CATTGGGTGG
* *
31416878 TATGTGAGCCAGTGTAAGACATGTTTGGGACATGCATCGACCAC-AT
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCACGAT
*
31416924 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-AT
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCACGAT
* * * * *
31416970 TATGAGAGCCAGTATAAGACATGTCTGGGACATACACCG-GCATTGA-
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCA-CGAT
* * * * * * *
31417016 GATGAGAGCTAGTGTAAAACATGCCTGGGACATGCGTCGACCTCGAGA
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCACGA-T
* * * * * * *
31417064 TAT-ACTAGCTAGTGTAAGACCTTTCTGGGACATGCACCG-GCATTGA-
1 TATGA-GAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCA-CGAT
* * * * *
31417110 GATGAGAGCTAGTATAAGACATGTCTGGGACATGCATCGGCCTCGGGA-
1 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCAC--GAT
* * *
31417158 TAT-ACAAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGA-CACCGAT
1 TATGA-GAGCCAGTGTAAGACATGTCTGGGACAT-GCATCGACCA-CGAT
* * * * * * *
31417206 AGATGAGAGCTAGTATGAGACCTGTCTGGGATATGGCATTGA-CACTGAT
1 -TATGAGAGCCAGTGTAAGACATGTCTGGGACAT-GCATCGACCAC-GAT
* * * *
31417255 AGATGAGAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGAT
1 -TATGAGAGCCAGTGTAAGACATGTCTGGGACAT-GCATCGACCACGAT
* * * * *
31417304 ATATGAAAGTCAGTGTAAGACCTGTCTGGAACACGACATCGAC
1 -TATGAGAGCCAGTGTAAGACATGTCTGGGACATG-CATCGAC
31417347 TTTAATGTGT
Statistics
Matches: 339, Mismatches: 64, Indels: 37
0.77 0.15 0.08
Matches are distributed among these distances:
45 2 0.01
46 143 0.42
47 9 0.03
48 63 0.19
49 119 0.35
50 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (47 bp):
TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCACGAT
Found at i:31417112 original size:94 final size:94
Alignment explanation
Indices: 31416984--31417289 Score: 328
Period size: 94 Copynumber: 3.2 Consensus size: 94
31416974 AGAGCCAGTA
* * *
31416984 TAAGACATGTCTGGGACATACACCGGCATTGAGATGAGAGCTAGTGTAAAACATGCCTGGGACAT
1 TAAGACCTGTCTGGGACATGCACCGGCATTGAGATGAGAGCTAGTATAAAACATGCCTGGGACAT
* *
31417049 GCGTCGACCTCGAGATATACTAGCTAGTG
66 GCATCGACCTCGAGATATACAAGCTAGTG
* * *
31417078 TAAGACCTTTCTGGGACATGCACCGGCATTGAGATGAGAGCTAGTATAAGACATGTCTGGGACAT
1 TAAGACCTGTCTGGGACATGCACCGGCATTGAGATGAGAGCTAGTATAAAACATGCCTGGGACAT
* *
31417143 GCATCGGCCTCGGGATATACAAGCTAGTG
66 GCATCGACCTCGAGATATACAAGCTAGTG
* * ** * * * *
31417172 TAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAGAGCTAGTATGAGACCTGTCTGGGA
1 TAAGACCTGTCTGGGACAT-GCACCGGCATTG--AGATGAGAGCTAGTATAAAACATGCCTGGGA
* * * * * *
31417237 TATGGCATTGACACT-GATAGATGA-GAGCCAGTG
63 CAT-GCATCGAC-CTCGAGATAT-ACAAGCTAGTG
31417270 TAAGACCTGTCTGGGACATG
1 TAAGACCTGTCTGGGACATG
31417290 GCATCGGCCT
Statistics
Matches: 181, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
94 102 0.56
95 8 0.04
97 32 0.18
98 36 0.20
99 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (94 bp):
TAAGACCTGTCTGGGACATGCACCGGCATTGAGATGAGAGCTAGTATAAAACATGCCTGGGACAT
GCATCGACCTCGAGATATACAAGCTAGTG
Found at i:31417227 original size:49 final size:49
Alignment explanation
Indices: 31417109--31417346 Score: 227
Period size: 49 Copynumber: 4.9 Consensus size: 49
31417099 ACCGGCATTG
* *
31417109 AGATGAGAGCTAGTATAAGACATGTCTGGGACAT-GCATCGGC-CTCGGGAT
1 AGATGAGAGCTAGTATAAGACCTGTCTGGGACATGGCATCGACAC-C--GAT
* * *
31417159 ATA-CA-AGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGAT
1 AGATGAGAGCTAGTATAAGACCTGTCTGGGACATGGCATCGACACCGAT
* * * *
31417206 AGATGAGAGCTAGTATGAGACCTGTCTGGGATATGGCATTGACACTGAT
1 AGATGAGAGCTAGTATAAGACCTGTCTGGGACATGGCATCGACACCGAT
* * *
31417255 AGATGAGAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGC-CTCGAT
1 AGATGAGAGCTAGTATAAGACCTGTCTGGGACATGGCATCGACAC-CGAT
* * * * * *
31417304 ATATGAAAG-TCAGTGTAAGACCTGTCTGGAACACGACATCGAC
1 AGATGAGAGCT-AGTATAAGACCTGTCTGGGACATGGCATCGAC
31417347 TTTAATGTGT
Statistics
Matches: 156, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
47 5 0.03
48 27 0.17
49 121 0.78
50 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (49 bp):
AGATGAGAGCTAGTATAAGACCTGTCTGGGACATGGCATCGACACCGAT
Found at i:31417304 original size:98 final size:95
Alignment explanation
Indices: 31416884--31417346 Score: 315
Period size: 94 Copynumber: 4.9 Consensus size: 95
31416874 GTGGTATGTG
* * * * * * * *
31416884 AGCCAGTGTAAGACATGTTTGGGACAT-GCATCGACCAC-AT-TATGAGAGCCAGTGTAAGACAT
1 AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATAGATGAGAGCTAGTATAAGACCT
* ** *
31416946 GTCTGGGACATGCATCGGCC-ACATTATGA-G
66 GTCTGGGACATGCATCGACCTGGA-TA-GACA
* * * * * * * * *
31416976 AGCCAGTATAAGACATGTCTGGGACAT-ACACCGGCATTG--AGATGAGAGCTAGTGTAAAACAT
1 AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATAGATGAGAGCTAGTATAAGACCT
* * * *
31417038 GCCTGGGACATGCGTCGACCTCGAGATATACT
66 GTCTGGGACATGCATCGACCT-G-GATAGACA
* * * * * *
31417070 AGCTAGTGTAAGACCTTTCTGGGACAT-GCACCGGCATTG--AGATGAGAGCTAGTATAAGACAT
1 AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATAGATGAGAGCTAGTATAAGACCT
* *
31417132 GTCTGGGACATGCATCGGCCTCGGGATATACA
66 GTCTGGGACATGCATCGACCT--GGATAGACA
* * *
31417164 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAGAGCTAGTATGAGACC
1 AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGC-CTCGATAGATGAGAGCTAGTATAAGACC
* * *
31417228 TGTCTGGGATATGGCATTGACACT-GATAGATGA
65 TGTCTGGGACAT-GCATCGAC-CTGGATAGA-CA
* * *
31417261 GAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGAAAG-TCAGTGTAAGAC
1 -AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATAGATGAGAGCT-AGTATAAGAC
* *
31417325 CTGTCTGGAACACGACATCGAC
64 CTGTCTGGGACATG-CATCGAC
31417347 TTTAATGTGT
Statistics
Matches: 301, Mismatches: 52, Indels: 30
0.79 0.14 0.08
Matches are distributed among these distances:
92 66 0.22
93 1 0.00
94 108 0.36
95 9 0.03
96 5 0.02
97 35 0.12
98 75 0.25
99 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (95 bp):
AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATAGATGAGAGCTAGTATAAGACCT
GTCTGGGACATGCATCGACCTGGATAGACA
Found at i:31421569 original size:42 final size:42
Alignment explanation
Indices: 31421487--31421597 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
31421477 TAAGATTCCG
* * ** *
31421487 TATAAGACCATATCTGGGATATGGCCTCGGTATGTGATTTCT
1 TATAAGACCATATCAGGGATATGGCATCAATATGTGATTTCA
* *
31421529 TATAAGACCATGTCAGGGACATGGCATCAATATGAT-ATTTCA
1 TATAAGACCATATCAGGGATATGGCATCAATATG-TGATTTCA
* *
31421571 TGTAAGACCATATCGGGGATATGGCAT
1 TATAAGACCATATCAGGGATATGGCAT
31421598 TGAAACGATT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 56 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (42 bp):
TATAAGACCATATCAGGGATATGGCATCAATATGTGATTTCA
Found at i:31431094 original size:19 final size:19
Alignment explanation
Indices: 31431057--31431094 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
31431047 ACCTGTCAAA
*
31431057 AGAAAATAAATGAAGAATT
1 AGAAAATAAATGAAAAATT
31431076 AGAAAATAAAAT-AAAAATT
1 AGAAAAT-AAATGAAAAATT
31431095 TAAATTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATGAAAAATT
Found at i:31435523 original size:17 final size:18
Alignment explanation
Indices: 31435501--31435534 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31435491 ACAGTTATAA
31435501 TTTAAAT-TCTAATTATT
1 TTTAAATGTCTAATTATT
*
31435518 TTTAAATGTGTAATTAT
1 TTTAAATGTCTAATTAT
31435535 CACAACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAAATGTCTAATTATT
Found at i:31435586 original size:44 final size:44
Alignment explanation
Indices: 31435502--31435591 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
31435492 CAGTTATAAT
* * *
31435502 TTAAATTCTAATTATTTTTAAATGTGTAATTATCACAACTTCTA
1 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTATA
**
31435546 TTAAATTATAATTATTTTTAAATGTATAATTATCGTAACTTATA
1 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTATA
31435590 TT
1 TT
31435592 TTTTTTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (44 bp):
TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTATA
Found at i:31439161 original size:16 final size:16
Alignment explanation
Indices: 31439140--31439170 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31439130 ACAATTATGT
*
31439140 AAATAATATTAAAATC
1 AAATAATAGTAAAATC
31439156 AAATAATAGTAAAAT
1 AAATAATAGTAAAAT
31439171 TATTGAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
AAATAATAGTAAAATC
Found at i:31439467 original size:22 final size:22
Alignment explanation
Indices: 31439420--31439472 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
31439410 CAATTAAGTT
* **
31439420 ATAATTAACAATTATTACATTG
1 ATAATTAAAAATTATTACATAA
31439442 ATAATTAAAATATTATTA-ATAA
1 ATAATTAAAA-ATTATTACATAA
*
31439464 ATAAATAAA
1 ATAATTAAA
31439473 TTTATACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
ATAATTAAAAATTATTACATAA
Found at i:31439705 original size:35 final size:38
Alignment explanation
Indices: 31439630--31439706 Score: 88
Period size: 39 Copynumber: 2.1 Consensus size: 38
31439620 TATAAAAATA
* * *
31439630 TATTTATTTAATTAAATTTTTTGGATTTTTATTATTATT
1 TATTTATTTAATTAAATTTATT-GAATTTTATTATGATT
*
31439669 TATTTATTTAATTATATTTATT-AATTTTA-TA-GATT
1 TATTTATTTAATTAAATTTATTGAATTTTATTATGATT
31439704 TAT
1 TAT
31439707 AATTTTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
35 6 0.18
36 2 0.06
37 6 0.18
39 20 0.59
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (38 bp):
TATTTATTTAATTAAATTTATTGAATTTTATTATGATT
Found at i:31442834 original size:13 final size:13
Alignment explanation
Indices: 31442816--31442841 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31442806 AATTGGTTTG
31442816 GTAGTCTCCAAAA
1 GTAGTCTCCAAAA
31442829 GTAGTCTCCAAAA
1 GTAGTCTCCAAAA
31442842 CCAACTAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
GTAGTCTCCAAAA
Found at i:31445661 original size:58 final size:58
Alignment explanation
Indices: 31445566--31445681 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
31445556 AGTGGCTTTT
31445566 CCCCCCTAGTTCCAATGTAATTTTGCCATTAATTACAATATTAGAGGAGACGGAATGA
1 CCCCCCTAGTTCCAATGTAATTTTGCCATTAATTACAATATTAGAGGAGACGGAATGA
*
31445624 CCCCTCTAGTTCCAATGTAATTTTGCCATTAATTACAATATTAGAGGAGACGGAATGA
1 CCCCCCTAGTTCCAATGTAATTTTGCCATTAATTACAATATTAGAGGAGACGGAATGA
31445682 GATGGTAATA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (58 bp):
CCCCCCTAGTTCCAATGTAATTTTGCCATTAATTACAATATTAGAGGAGACGGAATGA
Found at i:31448076 original size:21 final size:21
Alignment explanation
Indices: 31448052--31448117 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
31448042 TTTTGCTCTG
31448052 CTCTG-CTGCCATCGCTGCTGC
1 CTCTGCCT-CCATCGCTGCTGC
*
31448073 CTCTGCCTCCCTCGCTGCTGC
1 CTCTGCCTCCATCGCTGCTGC
* *
31448094 CGT-TGCCTCCCTCTCTGCTGC
1 C-TCTGCCTCCATCGCTGCTGC
31448115 CTC
1 CTC
31448118 CGCTCTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.03
21 36 0.90
22 3 0.08
ACGTcount: A:0.02, C:0.48, G:0.20, T:0.30
Consensus pattern (21 bp):
CTCTGCCTCCATCGCTGCTGC
Found at i:31448557 original size:13 final size:14
Alignment explanation
Indices: 31448532--31448560 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31448522 TGATGAATTG
31448532 AATTAAACAATTAT
1 AATTAAACAATTAT
31448546 AATTAAAC-ATTAT
1 AATTAAACAATTAT
31448559 AA
1 AA
31448561 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:31454344 original size:12 final size:12
Alignment explanation
Indices: 31454329--31454353 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31454319 TCATCCTCTC
31454329 CATCAGATTCAT
1 CATCAGATTCAT
31454341 CATCAGATTCAT
1 CATCAGATTCAT
31454353 C
1 C
31454354 CATCGATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (12 bp):
CATCAGATTCAT
Found at i:31456592 original size:102 final size:103
Alignment explanation
Indices: 31456243--31456681 Score: 641
Period size: 102 Copynumber: 4.2 Consensus size: 103
31456233 GGTTATTAGA
*
31456243 TTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAAATAAAATAAAATAAAATAACA
1 TTAAAAATAAAA-AAAAGTAGACAAAATATTTTTTGTGA-T----TAAAATAAAATAAAATAACA
*
31456308 TATT-AGAAATAAAACTTTAACTACAATTTAATTTAATTAGGTAAT
60 TATTCA-AAATAAAAC-TTAAATACAATTTAATTTAATTAGGTAAT
* * * *
31456353 TTAAAAAATAAAATAAAAGTAGACAAAATATTTTTAGTGATTAAATTAAAATCAAATAAAATATT
1 TT-AAAAATAAAA-AAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAATAAAATAACATATT
*
31456418 TAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAAT
64 CAAAATAAAAC-TTAAATACAATTTAATTTAATTAGGTAAT
*
31456459 TTAAAAAATAAAATAAA-TAGACAAAATATTTTTTGTGATTAAAATAAAATAAAATAACATATTC
1 TT-AAAAATAAAAAAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAATAAAATAACATATTC
31456523 AAAATAAAA-TTAAATACAATTTAATTTAATTAGGTAAT
65 AAAATAAAACTTAAATACAATTTAATTTAATTAGGTAAT
31456561 TTAAAAATAAAAAAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAATAAAATAACATATTCA
1 TTAAAAATAAAAAAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAATAAAATAACATATTCA
*
31456626 AAATAAAACTTTAAATATAATTTAATTTAATTAGGTAAT
66 AAATAAAAC-TTAAATACAATTTAATTTAATTAGGTAAT
*
31456665 TTAAAAATTAAATAAAA
1 TTAAAAA-TAAAAAAAA
31456682 TATTTAAAAT
Statistics
Matches: 309, Mismatches: 14, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
101 13 0.04
102 87 0.28
104 86 0.28
105 11 0.04
106 72 0.23
107 1 0.00
110 3 0.01
111 36 0.12
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.34
Consensus pattern (103 bp):
TTAAAAATAAAAAAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAATAAAATAACATATTCA
AAATAAAACTTAAATACAATTTAATTTAATTAGGTAAT
Found at i:31456633 original size:206 final size:211
Alignment explanation
Indices: 31456243--31456680 Score: 683
Period size: 206 Copynumber: 2.1 Consensus size: 211
31456233 GGTTATTAGA
31456243 TTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAAATAAAATAAAATAAAATAACA
1 TTAAAAATAAAAT-AAAGTAGACAAAATATTTTTCGTGATT---ATAAAATAAAATAAAATAACA
*
31456308 TATTAGAAATAAAACTTTAACTACAATTTAATTTAATTAGGTAATTTAAAAAATAAAATAAAAGT
62 TATTAGAAATAAAAC-TTAAATACAATTTAATTTAATTAGGTAATTTAAAAAATAAAATAAAAGT
* * *
31456373 AGACAAAATATTTTTAGTGATTAAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAATAC
126 AGACAAAATATTTTTAGTGATTAAAATAAAATAAAATAAAATATTCAAAATAAAACTTTAAATAC
31456438 AATTTAATTTAATTAGGTAAT
191 AATTTAATTTAATTAGGTAAT
*
31456459 TTAAAAAATAAAATAAA-TAGACAAAATATTTTTTGTGA-T-TAAAATAAAATAAAATAACATAT
1 TT-AAAAATAAAATAAAGTAGACAAAATATTTTTCGTGATTATAAAATAAAATAAAATAACATAT
31456521 TCA-AAATAAAA-TTAAATACAATTTAATTTAATTAGGTAATTT-AAAAATAAAA-AAAAGTAGA
65 T-AGAAATAAAACTTAAATACAATTTAATTTAATTAGGTAATTTAAAAAATAAAATAAAAGTAGA
* * *
31456582 CAAAATATTTTTTGTGATTAAAATAAAATAAAATAACATATTCAAAATAAAACTTTAAATATAAT
129 CAAAATATTTTTAGTGATTAAAATAAAATAAAATAAAATATTCAAAATAAAACTTTAAATACAAT
31456647 TTAATTTAATTAGGTAAT
194 TTAATTTAATTAGGTAAT
*
31456665 TTAAAAATTAAATAAA
1 TTAAAAATAAAATAAA
31456681 ATATTTAAAA
Statistics
Matches: 211, Mismatches: 9, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
205 13 0.06
206 88 0.42
207 10 0.05
208 30 0.14
210 32 0.15
211 1 0.00
214 1 0.00
215 20 0.09
216 5 0.02
217 11 0.05
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.34
Consensus pattern (211 bp):
TTAAAAATAAAATAAAGTAGACAAAATATTTTTCGTGATTATAAAATAAAATAAAATAACATATT
AGAAATAAAACTTAAATACAATTTAATTTAATTAGGTAATTTAAAAAATAAAATAAAAGTAGACA
AAATATTTTTAGTGATTAAAATAAAATAAAATAAAATATTCAAAATAAAACTTTAAATACAATTT
AATTTAATTAGGTAAT
Found at i:31458148 original size:24 final size:26
Alignment explanation
Indices: 31458120--31458170 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
31458110 TTAAAGATTC
* *
31458120 ATATAAA-TA-ATATAACTTTATAAT
1 ATATAAAGTATATATAAATATATAAT
31458144 ATATAAAGTATATATAAATATATAAT
1 ATATAAAGTATATATAAATATATAAT
31458170 A
1 A
31458171 ATCATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 2 0.09
26 14 0.61
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (26 bp):
ATATAAAGTATATATAAATATATAAT
Found at i:31459821 original size:28 final size:29
Alignment explanation
Indices: 31459767--31459837 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
31459757 AATCAAAACT
31459767 CTAAACCTTAAAC-CATTAAAATATATCCC
1 CTAAACCTTAAACTCA-TAAAATATATCCC
*
31459796 C-ATAACCTTAAACTC-TAAACTATATCCC
1 CTA-AACCTTAAACTCATAAAATATATCCC
*
31459824 CTAAACCCTAAACT
1 CTAAACCTTAAACT
31459838 ATATCCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 24 0.65
29 12 0.32
30 1 0.03
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (29 bp):
CTAAACCTTAAACTCATAAAATATATCCC
Found at i:31459850 original size:20 final size:21
Alignment explanation
Indices: 31459804--31459844 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31459794 CCCATAACCT
*
31459804 TAAACTCTAAACTATATCCCC
1 TAAACCCTAAACTATATCCCC
31459825 TAAACCCTAAACTATATCCC
1 TAAACCCTAAACTATATCCC
31459845 TTAACCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.34, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAACCCTAAACTATATCCCC
Found at i:31459855 original size:20 final size:21
Alignment explanation
Indices: 31459811--31459856 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
31459801 CCTTAAACTC
*
31459811 TAAACTATATCCCCTAAACCC
1 TAAACTATATCCCCTAAACCA
*
31459832 TAAACTATAT-CCCTTAACCA
1 TAAACTATATCCCCTAAACCA
31459852 TAAAC
1 TAAAC
31459857 CACAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACTATATCCCCTAAACCA
Found at i:31459886 original size:34 final size:34
Alignment explanation
Indices: 31459843--31459969 Score: 101
Period size: 34 Copynumber: 3.4 Consensus size: 34
31459833 AAACTATATC
31459843 CCTTAACCATAAACCACAAAATAATAACCCCTAG
1 CCTTAACCATAAACCACAAAATAATAACCCCTAG
** * * *
31459877 CCTTAACCATAAAATGTATGAATTAATCATAACCCTAAACTATATC
1 CCTTAACCAT-AAA-CCA-CAA--AATAATAACCC----C--TA-G
31459923 CCTTAACCATAAACCACAAAATAATAACCCCTAG
1 CCTTAACCATAAACCACAAAATAATAACCCCTAG
31459957 CCTTAACCATAAA
1 CCTTAACCATAAA
31459970 ATGTATGAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 24
0.68 0.10 0.23
Matches are distributed among these distances:
34 23 0.32
35 5 0.07
36 1 0.01
37 3 0.04
39 10 0.14
41 10 0.14
43 3 0.04
44 1 0.01
45 5 0.07
46 10 0.14
ACGTcount: A:0.46, C:0.28, G:0.03, T:0.23
Consensus pattern (34 bp):
CCTTAACCATAAACCACAAAATAATAACCCCTAG
Found at i:31459918 original size:80 final size:80
Alignment explanation
Indices: 31459827--31460032 Score: 360
Period size: 80 Copynumber: 2.6 Consensus size: 80
31459817 ATATCCCCTA
31459827 AACCCTAAACTATATCCCTTAACCATAAACCACAAAATAATAACCCCTAGCCTTAACCATAAAAT
1 AACCCTAAACTATATCCCTTAACCATAAACCACAAAATAATAACCCCTAGCCTTAACCATAAAAT
31459892 GTATGAATTAATCAT
66 GTATGAATTAATCAT
31459907 AACCCTAAACTATATCCCTTAACCATAAACCACAAAATAATAACCCCTAGCCTTAACCATAAAAT
1 AACCCTAAACTATATCCCTTAACCATAAACCACAAAATAATAACCCCTAGCCTTAACCATAAAAT
31459972 GTATGAATTAATCAT
66 GTATGAATTAATCAT
* * **
31459987 AACCCTAAACTATATCCCCTGATCTTTAAACCAC-AAATAATAACCC
1 AACCCTAAACTATAT-CCCTTAACCATAAACCACAAAATAATAACCC
31460033 TAATTAATCA
Statistics
Matches: 121, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
80 107 0.88
81 14 0.12
ACGTcount: A:0.44, C:0.28, G:0.03, T:0.25
Consensus pattern (80 bp):
AACCCTAAACTATATCCCTTAACCATAAACCACAAAATAATAACCCCTAGCCTTAACCATAAAAT
GTATGAATTAATCAT
Found at i:31460112 original size:21 final size:21
Alignment explanation
Indices: 31460087--31460136 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
31460077 CTACTAAAGT
*
31460087 ACCCTAAATTATATCCCCTAA
1 ACCCTAAACTATATCCCCTAA
31460108 ACCCTAAACTATATCCCCT-A
1 ACCCTAAACTATATCCCCTAA
*
31460128 ACCATAAAC
1 ACCCTAAAC
31460137 CACAAAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (21 bp):
ACCCTAAACTATATCCCCTAA
Done.