Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 89 of 210
Found at i:30828998 original size:13 final size:13
Alignment explanation
Indices: 30828973--30829010 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
30828963 TATTAAATAA
30828973 GGTTTAGGGGTTAG
1 GGTTTA-GGGTTAG
30828987 GGATTT-GGGTTAG
1 GG-TTTAGGGTTAG
30829000 GGTTTAGGGTT
1 GGTTTAGGGTT
30829011 TAGATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 14 0.64
14 2 0.09
15 3 0.14
ACGTcount: A:0.13, C:0.00, G:0.47, T:0.39
Consensus pattern (13 bp):
GGTTTAGGGTTAG
Found at i:30829008 original size:74 final size:76
Alignment explanation
Indices: 30828921--30829064 Score: 202
Period size: 74 Copynumber: 1.9 Consensus size: 76
30828911 TCGGTATCAA
* * *
30828921 GTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAA-TT-TATATTAAATAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
30828984 TAGGGATTTGG
66 TAGGGATTTGG
* * * **
30828995 GTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
30829060 TAGGG
66 TAGGG
30829065 GTTAGGGGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 31 0.52
75 2 0.03
76 27 0.45
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.44
Consensus pattern (76 bp):
GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
TAGGGATTTGG
Found at i:30829064 original size:7 final size:7
Alignment explanation
Indices: 30829052--30829076 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30829042 TAAAGAAGGT
30829052 TTAGGGG
1 TTAGGGG
30829059 TTAGGGG
1 TTAGGGG
30829066 TTAGGGG
1 TTAGGGG
30829073 TTAG
1 TTAG
30829077 AGATTAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:30829193 original size:199 final size:199
Alignment explanation
Indices: 30828853--30829797 Score: 1890
Period size: 199 Copynumber: 4.7 Consensus size: 199
30828843 CAGTAAGGCG
30828853 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
1 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
30828918 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
66 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
30828983 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
131 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
30829048 AGGT
196 AGGT
30829052 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
1 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
30829117 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
66 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
30829182 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
131 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
30829247 AGGT
196 AGGT
30829251 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
1 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
30829316 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
66 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
30829381 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
131 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
30829446 AGGT
196 AGGT
30829450 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
1 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
30829515 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
66 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
30829580 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
131 TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
30829645 AGGT
196 AGGT
30829649 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
1 TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
30829714 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
66 CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
30829779 TTAGGGATTTGGGTTAGGG
131 TTAGGGATTTGGGTTAGGG
30829798 GTAAAAAACG
Statistics
Matches: 746, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
199 746 1.00
ACGTcount: A:0.29, C:0.02, G:0.28, T:0.41
Consensus pattern (199 bp):
TTAGGGGTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATAGATTCGGTAT
CAAGTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAATTTATATTAAATAAGGTTTAGGGG
TTAGGGATTTGGGTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGA
AGGT
Found at i:30829197 original size:13 final size:13
Alignment explanation
Indices: 30829172--30829209 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
30829162 TATTAAATAA
30829172 GGTTTAGGGGTTAG
1 GGTTTA-GGGTTAG
30829186 GGATTT-GGGTTAG
1 GG-TTTAGGGTTAG
30829199 GGTTTAGGGTT
1 GGTTTAGGGTT
30829210 TAGATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 14 0.64
14 2 0.09
15 3 0.14
ACGTcount: A:0.13, C:0.00, G:0.47, T:0.39
Consensus pattern (13 bp):
GGTTTAGGGTTAG
Found at i:30829230 original size:74 final size:76
Alignment explanation
Indices: 30829120--30829263 Score: 202
Period size: 74 Copynumber: 1.9 Consensus size: 76
30829110 TCGGTATCAA
* * *
30829120 GTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAA-TT-TATATTAAATAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
30829183 TAGGGATTTGG
66 TAGGGATTTGG
* * * **
30829194 GTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
30829259 TAGGG
66 TAGGG
30829264 GTTAGGGGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 31 0.52
75 2 0.03
76 27 0.45
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.44
Consensus pattern (76 bp):
GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
TAGGGATTTGG
Found at i:30829263 original size:7 final size:7
Alignment explanation
Indices: 30829251--30829275 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30829241 TAAAGAAGGT
30829251 TTAGGGG
1 TTAGGGG
30829258 TTAGGGG
1 TTAGGGG
30829265 TTAGGGG
1 TTAGGGG
30829272 TTAG
1 TTAG
30829276 AGATTAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:30829396 original size:13 final size:13
Alignment explanation
Indices: 30829371--30829408 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
30829361 TATTAAATAA
30829371 GGTTTAGGGGTTAG
1 GGTTTA-GGGTTAG
30829385 GGATTT-GGGTTAG
1 GG-TTTAGGGTTAG
30829398 GGTTTAGGGTT
1 GGTTTAGGGTT
30829409 TAGATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 14 0.64
14 2 0.09
15 3 0.14
ACGTcount: A:0.13, C:0.00, G:0.47, T:0.39
Consensus pattern (13 bp):
GGTTTAGGGTTAG
Found at i:30829429 original size:74 final size:76
Alignment explanation
Indices: 30829319--30829462 Score: 202
Period size: 74 Copynumber: 1.9 Consensus size: 76
30829309 TCGGTATCAA
* * *
30829319 GTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAA-TT-TATATTAAATAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
30829382 TAGGGATTTGG
66 TAGGGATTTGG
* * * **
30829393 GTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
30829458 TAGGG
66 TAGGG
30829463 GTTAGGGGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 31 0.52
75 2 0.03
76 27 0.45
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.44
Consensus pattern (76 bp):
GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
TAGGGATTTGG
Found at i:30829462 original size:7 final size:7
Alignment explanation
Indices: 30829450--30829474 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30829440 TAAAGAAGGT
30829450 TTAGGGG
1 TTAGGGG
30829457 TTAGGGG
1 TTAGGGG
30829464 TTAGGGG
1 TTAGGGG
30829471 TTAG
1 TTAG
30829475 AGATTAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:30829595 original size:13 final size:13
Alignment explanation
Indices: 30829570--30829607 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
30829560 TATTAAATAA
30829570 GGTTTAGGGGTTAG
1 GGTTTA-GGGTTAG
30829584 GGATTT-GGGTTAG
1 GG-TTTAGGGTTAG
30829597 GGTTTAGGGTT
1 GGTTTAGGGTT
30829608 TAGATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 14 0.64
14 2 0.09
15 3 0.14
ACGTcount: A:0.13, C:0.00, G:0.47, T:0.39
Consensus pattern (13 bp):
GGTTTAGGGTTAG
Found at i:30829628 original size:74 final size:76
Alignment explanation
Indices: 30829518--30829661 Score: 202
Period size: 74 Copynumber: 1.9 Consensus size: 76
30829508 TCGGTATCAA
* * *
30829518 GTTAAGGTTTAGGGTTTAGATTAACTAGTGCATTTTAA-TT-TATATTAAATAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
30829581 TAGGGATTTGG
66 TAGGGATTTGG
* * * **
30829592 GTTAGGGTTTAGGGTTTAGATTTATTAATATTTTTTAATTTATATATTAAAGAAGGTTTAGGGGT
1 GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
30829657 TAGGG
66 TAGGG
30829662 GTTAGGGGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 31 0.52
75 2 0.03
76 27 0.45
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.44
Consensus pattern (76 bp):
GTTAAGGTTTAGGGTTTAGATTAACTAATACATTTTAATTTATATATTAAAGAAGGTTTAGGGGT
TAGGGATTTGG
Found at i:30829661 original size:7 final size:7
Alignment explanation
Indices: 30829649--30829673 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30829639 TAAAGAAGGT
30829649 TTAGGGG
1 TTAGGGG
30829656 TTAGGGG
1 TTAGGGG
30829663 TTAGGGG
1 TTAGGGG
30829670 TTAG
1 TTAG
30829674 AGATTAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:30833708 original size:24 final size:23
Alignment explanation
Indices: 30833680--30833727 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
30833670 AATTTAAAAA
30833680 ATAAAACATAATATAATATTT-ATT
1 ATAAAA-ATAA-ATAATATTTGATT
*
30833704 ATAAAAATAAATATTATTTGATT
1 ATAAAAATAAATAATATTTGATT
30833727 A
1 A
30833728 AAATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAAAATAAATAATATTTGATT
Found at i:30833849 original size:43 final size:43
Alignment explanation
Indices: 30833772--30833999 Score: 289
Period size: 43 Copynumber: 5.3 Consensus size: 43
30833762 TTTTTGCTAG
* *
30833772 AAGCGCCGCTAAAGGT-TTGTTCTTTAGCGGCGTTTGTGGAAA
1 AAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAA
* *
30833814 AAGCGTCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTTTGGGAAA
1 AAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGT-GGAAA
* * *
30833858 AAGCGCCGCTAAAGGTTGTGGTCTTTAGTGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAA
*
30833901 AAGCGCCGCTAAAGGTCGTGGTCTTTAGC-GCGTTTGTGTAAA
1 AAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAA
* * * * * **
30833943 AAGCGCCGCTAAAGATTGTAGTATTTAGCGGCGTTTATTTAAA
1 AAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAA
*
30833986 AAACGCCGCTAAAG
1 AAGCGCCGCTAAAG
30834000 TTAGCGACGC
Statistics
Matches: 163, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
42 51 0.31
43 73 0.45
44 39 0.24
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAA
Found at i:30833988 original size:129 final size:128
Alignment explanation
Indices: 30833752--30833999 Score: 329
Period size: 129 Copynumber: 1.9 Consensus size: 128
30833742 AGATTATATT
* * * * *
30833752 TTTAGTGGCGTTTTTGCTAGAAGCGCCGCTAAAGGTTTGTTCTTTAGCGGCGTTTGTGGAAAAAG
1 TTTAGTGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTGTGGTCTTTAGCGGCGTTTGTGGAAAAAG
* * * * *
30833817 CGTCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTTTGGGAAAAAGCGCCGCTAAAGGTTGTGGTC
66 CGCCGCTAAAGATCGTAGTATTTAGCGGCGTTTTT-GGAAAAAACGCCGCTAAAGGTTGTGGTC
* *
30833881 TTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTTTAGC-GCGTTTGTGTAAAAA
1 TTTAGTGGCGTTTGTGCGAAAAGCGCCGCTAAAGGT-GTGGTCTTTAGCGGCGTTTGTGGAAAAA
* *
30833945 GCGCCGCTAAAGATTGTAGTATTTAGCGGCGTTTATT-TAAAAAACGCCGCTAAAG
65 GCGCCGCTAAAGATCGTAGTATTTAGCGGCGTTT-TTGGAAAAAACGCCGCTAAAG
30834000 TTAGCGACGC
Statistics
Matches: 103, Mismatches: 14, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
128 16 0.16
129 75 0.73
130 12 0.12
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.31
Consensus pattern (128 bp):
TTTAGTGGCGTTTGTGCGAAAAGCGCCGCTAAAGGTGTGGTCTTTAGCGGCGTTTGTGGAAAAAG
CGCCGCTAAAGATCGTAGTATTTAGCGGCGTTTTTGGAAAAAACGCCGCTAAAGGTTGTGGTC
Found at i:30834069 original size:22 final size:22
Alignment explanation
Indices: 30834041--30834083 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
30834031 AAGCGGCGCT
*
30834041 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
30834063 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
30834084 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:30834775 original size:6 final size:6
Alignment explanation
Indices: 30834764--30834798 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
30834754 CTTCATACAT
30834764 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
30834799 TACTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:30834778 original size:18 final size:18
Alignment explanation
Indices: 30834757--30834796 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
30834747 GGTACATCTT
*
30834757 CATACATATATACATATA
1 CATACACATATACATATA
*
30834775 CATATACATATACATATA
1 CATACACATATACATATA
30834793 CATA
1 CATA
30834797 TATACTATTA
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:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (18 bp):
CATACACATATACATATA
Found at i:30835526 original size:41 final size:41
Alignment explanation
Indices: 30835480--30835585 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 41
30835470 ACCGGCATGT
* * **
30835480 AGCCTGCTAGGCTTAAAGCCTGATTTAGAACACCGACATTA
1 AGCCTGCTAGACGTAAAGCCTGAAATAGAACACCGACATTA
* ***
30835521 AGCCTGCTAGACGTAAAGTCTGAAATATTTCACCGACATTA
1 AGCCTGCTAGACGTAAAGCCTGAAATAGAACACCGACATTA
* *
30835562 AGCCTGCTAAACGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGCCTGAA
30835586 TTATTTCACT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGCCTGAAATAGAACACCGACATTA
Found at i:30835591 original size:41 final size:41
Alignment explanation
Indices: 30835510--30835612 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
30835500 TGATTTAGAA
*
30835510 CACCGACATTAAGCCTGCTAGACGTAAAGTCTGAAATATTT
1 CACCGACATTAAGCCTGCTAAACGTAAAGTCTGAAATATTT
*
30835551 CACCGACATTAAGCCTGCTAAACGTAAAGTCTGAATTATTT
1 CACCGACATTAAGCCTGCTAAACGTAAAGTCTGAAATATTT
* * *
30835592 CACTGGCATTAAGCCAGCTAA
1 CACCGACATTAAGCCTGCTAA
30835613 GCACAGAGCC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (41 bp):
CACCGACATTAAGCCTGCTAAACGTAAAGTCTGAAATATTT
Found at i:30835626 original size:41 final size:41
Alignment explanation
Indices: 30835510--30835627 Score: 110
Period size: 41 Copynumber: 2.9 Consensus size: 41
30835500 TGATTTAGAA
* * ** * *
30835510 CACCGACATTAAGCCTGCTAGACGTAAAGTCTGAAATATTT
1 CACCGACATTAAGCCAGCTAAACACAAAGCCTGAATTATTT
* ** *
30835551 CACCGACATTAAGCCTGCTAAACGTAAAGTCTGAATTATTT
1 CACCGACATTAAGCCAGCTAAACACAAAGCCTGAATTATTT
* * * *
30835592 CACTGGCATTAAGCCAGCTAAGCACAGAGCCTGAAT
1 CACCGACATTAAGCCAGCTAAACACAAAGCCTGAAT
30835628 AACTCAGATA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (41 bp):
CACCGACATTAAGCCAGCTAAACACAAAGCCTGAATTATTT
Found at i:30837542 original size:18 final size:20
Alignment explanation
Indices: 30837498--30837546 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
30837488 CCTAAACAAA
*
30837498 AAGTATCGATACTTATTAGT
1 AAGTATCGATACCTATTAGT
30837518 AAGTATCGATACCT-TTAGT
1 AAGTATCGATACCTATTAGT
30837537 -AGTATCGATA
1 AAGTATCGATA
30837547 TGTATTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 10 0.36
19 5 0.18
20 13 0.46
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (20 bp):
AAGTATCGATACCTATTAGT
Found at i:30842797 original size:21 final size:21
Alignment explanation
Indices: 30842738--30842797 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
30842728 AGAATAATGA
*
30842738 TGAATTGCACATACGTGCCCC
1 TGAATTGCACATACGTACCCC
* *
30842759 T--ATCTGTAC-TTCGGTACCCC
1 TGAAT-TGCACATAC-GTACCCC
30842779 TGAATTGCACATACGTACC
1 TGAATTGCACATACGTACC
30842798 ACTGTTTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 10
0.66 0.11 0.23
Matches are distributed among these distances:
19 4 0.14
20 11 0.38
21 10 0.34
22 4 0.14
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (21 bp):
TGAATTGCACATACGTACCCC
Found at i:30842813 original size:41 final size:41
Alignment explanation
Indices: 30842738--30842820 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
30842728 AGAATAATGA
* *
30842738 TGAATTGCACATACGTGCCCCTATCTGTACTTCGGTACCCC
1 TGAATTGCACATACGTACCACTATCTGTACTTCGGTACCCC
* *
30842779 TGAATTGCACATACGTACCACTGTTTGTTA-TTCGGTACCCC
1 TGAATTGCACATACGTACCACTATCTG-TACTTCGGTACCCC
30842820 T
1 T
30842821 AGATGTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 35 0.95
42 2 0.05
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (41 bp):
TGAATTGCACATACGTACCACTATCTGTACTTCGGTACCCC
Found at i:30849650 original size:103 final size:103
Alignment explanation
Indices: 30849465--30849664 Score: 303
Period size: 103 Copynumber: 1.9 Consensus size: 103
30849455 GTTACATTTA
* *
30849465 TATGGTAATGCTCTGTAACCCTACTCCCGCGACGGATACGAGATAAGGGTGTTACATTTGCTCCC
1 TATGGTAATGCTCCGTAACCCTACTCCAGCGACGGATACGAGATAAGGGTGTTACATTTGCTCCC
*
30849530 TTCAGTGTGCAGACTTTCCTTTTCTTTTTCCCCAAACG
66 TTCAGTGTACAGACTTTCCTTTTCTTTTTCCCCAAACG
* * * *
30849568 TATGGTAATGCTCCGTAACCCTATTCCAGTGACGTATACGAGATAAGGGTGTTACATTTTCT-CC
1 TATGGTAATGCTCCGTAACCCTACTCCAGCGACGGATACGAGATAAGGGTGTTACATTTGCTCCC
* *
30849632 TCTCCGTGTACAGCCTTTCCTTTTCTTTTTCCC
66 T-TCAGTGTACAGACTTTCCTTTTCTTTTTCCC
30849665 TATTCTTTTC
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 3 0.03
103 84 0.97
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (103 bp):
TATGGTAATGCTCCGTAACCCTACTCCAGCGACGGATACGAGATAAGGGTGTTACATTTGCTCCC
TTCAGTGTACAGACTTTCCTTTTCTTTTTCCCCAAACG
Found at i:30860111 original size:41 final size:41
Alignment explanation
Indices: 30860056--30860195 Score: 185
Period size: 41 Copynumber: 3.4 Consensus size: 41
30860046 TATATGATTG
**
30860056 GCACTAAGTGTGCGAAGTTAAATAATGATGTTGAATAACGA
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
*
30860097 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
* * *
30860138 GCACTAAGTGTGCGAAACAAAATAATAATGTT-AATAGC-A
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
* *
30860177 GGCATTAAGTGTGTGAAAC
1 -GCACTAAGTGTGCGAAAC
30860196 CGAGATCAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 21 0.24
41 67 0.75
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (41 bp):
GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
Found at i:30862514 original size:18 final size:18
Alignment explanation
Indices: 30862491--30862525 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30862481 TCTAAGAAGC
30862491 ACTTTTGAGACAAAAACT
1 ACTTTTGAGACAAAAACT
*
30862509 ACTTTTGAGATAAAAAC
1 ACTTTTGAGACAAAAAC
30862526 ATTGCTAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (18 bp):
ACTTTTGAGACAAAAACT
Found at i:30869032 original size:6 final size:6
Alignment explanation
Indices: 30869021--30869069 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
30869011 ATAATAAAAT
*
30869021 AAAACA AAAACA AAAACAAA AAAATA AAAAGCA AAAACA AAAACA AAAA
1 AAAACA AAAACA AAAAC--A AAAACA AAAA-CA AAAACA AAAACA AAAA
30869070 ATATAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 28 0.74
7 5 0.13
8 5 0.13
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.02
Consensus pattern (6 bp):
AAAACA
Found at i:30869060 original size:27 final size:26
Alignment explanation
Indices: 30869016--30869077 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 26
30869006 AGTGCATAAT
30869016 AAAAT-AAAACAAAAACAAAAACAAA
1 AAAATAAAAACAAAAACAAAAACAAA
30869041 AAAATAAAAAGCAAAAACAAAAACAAA
1 AAAATAAAAA-CAAAAACAAAAACAAA
30869068 AAATATAAAA
1 AAA-ATAAAA
30869078 TATAAAACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 5 0.15
26 4 0.12
27 19 0.56
28 6 0.18
ACGTcount: A:0.82, C:0.10, G:0.02, T:0.06
Consensus pattern (26 bp):
AAAATAAAAACAAAAACAAAAACAAA
Found at i:30869070 original size:21 final size:20
Alignment explanation
Indices: 30869021--30869063 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
30869011 ATAATAAAAT
*
30869021 AAAACAAAAACAAAAACAAA
1 AAAATAAAAACAAAAACAAA
30869041 AAAATAAAAAGCAAAAACAAA
1 AAAATAAAAA-CAAAAACAAA
30869062 AA
1 AA
30869064 CAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.02
Consensus pattern (20 bp):
AAAATAAAAACAAAAACAAA
Found at i:30871977 original size:14 final size:14
Alignment explanation
Indices: 30871955--30871984 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
30871945 CGTAAAAATT
30871955 AAATAAAAATAAAA
1 AAATAAAAATAAAA
*
30871969 AAATTAAAATAAAA
1 AAATAAAAATAAAA
30871983 AA
1 AA
30871985 TGGCTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAATAAAAATAAAA
Found at i:30873935 original size:93 final size:93
Alignment explanation
Indices: 30873773--30873958 Score: 291
Period size: 93 Copynumber: 2.0 Consensus size: 93
30873763 CAATCATAGT
*
30873773 CATACATATCATAGAGCAAATCAGTCATACATAACATAAAGCCATAACATTCATTTCATCTCCTA
1 CATACATATCATAGAGCAAATCAGTCATACATAACATAAAGCCATAACAGTCATTTCATCTCCTA
*
30873838 GGGGTATAACATCCATTTTACCCTATGG
66 GGGGTATAACAGCCATTTTACCCTATGG
* * * *
30873866 CATACATATCATAGAGCAAATCAGTCATACATAATATAAGGCCATAACAGTCATTTCATCTCTTG
1 CATACATATCATAGAGCAAATCAGTCATACATAACATAAAGCCATAACAGTCATTTCATCTCCTA
** *
30873931 GGGGTATTCCGGCCATTTTACCCTATGG
66 GGGGTATAACAGCCATTTTACCCTATGG
30873959 GGGTAATTCA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (93 bp):
CATACATATCATAGAGCAAATCAGTCATACATAACATAAAGCCATAACAGTCATTTCATCTCCTA
GGGGTATAACAGCCATTTTACCCTATGG
Found at i:30873959 original size:27 final size:27
Alignment explanation
Indices: 30873929--30874550 Score: 679
Period size: 27 Copynumber: 23.0 Consensus size: 27
30873919 TTTCATCTCT
* *
30873929 TGGGGGTATTCCGGCCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * * *
30873956 TGGGGGTAATTCAGTCAATTTACCTTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
30873983 TGGGGGTATTTCGATCATTTTCCCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
30874010 TCGGGCTATTTCGGTCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
** *
30874037 TAAGGGTATTTCGATCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
*
30874064 TGGGGGTATTTCGGTCATTTTACTCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * * *
30874091 TGAGGATGTTTCGATCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
30874118 TAGGGGTATTTCGGTCAATTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * *
30874145 TGGGAGTATTTCGATCAATTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
30874172 TGGGGGTATTTCGAAT-AATTTACCCTA
1 TGGGGGTATTTCG-GTCATTTTACCCTA
** *
30874199 TAAGGGTATTTCGGTCAATTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * ** *
30874226 TAGGGCTATTTCAATCATTTTACTCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
*
30874253 TGGGGGTATTTCGATCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * *
30874280 TGGGGGTATTCCAGTCATTTTACCCTG
1 TGGGGGTATTTCGGTCATTTTACCCTA
** *
30874307 TAAGGGTATTTCGATCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * * *
30874334 TAGGGGTATTTTGGTCATTTTACCTTG
1 TGGGGGTATTTCGGTCATTTTACCCTA
* ** *
30874361 TGGGCGTATTTTAGTCATTTTATCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
30874388 TGGGGCTATTTCGATCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
30874415 TGGGGGTATTTTGGTCATTTTATCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * * *
30874442 TAGGGGTATTTCGATTATTTTATCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
30874469 TGGGGGTATTTCGGTCATTTTACCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* *
30874496 TAGGGGTATTTCGGTCATTTTATCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
* * *
30874523 TAGGGTTATTTCGGTCATTTTATCCTA
1 TGGGGGTATTTCGGTCATTTTACCCTA
30874550 T
1 T
30874551 AGGGTTTTAA
Statistics
Matches: 499, Mismatches: 94, Indels: 4
0.84 0.16 0.01
Matches are distributed among these distances:
26 1 0.00
27 496 0.99
28 2 0.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
TGGGGGTATTTCGGTCATTTTACCCTA
Found at i:30879664 original size:68 final size:69
Alignment explanation
Indices: 30879530--30879664 Score: 173
Period size: 68 Copynumber: 2.0 Consensus size: 69
30879520 TTATTAAACT
* * * * * *
30879530 TAATCACTTTCATATTAAATTAATACAATATTTATCAAGAGAAATATTAGATTAAATTTAATATT
1 TAATCACTATAATATTAAATTAATAAAATATCTATCAAGAGAAATATTAAATTAAATTTAAAATT
30879595 AAGA
66 AAGA
* * * *
30879599 TAATCACTATAATATTGAATTAATAAAATA-CTATTAAGATAAGTATTAAATTAAATTTAAAATT
1 TAATCACTATAATATTAAATTAATAAAATATCTATCAAGAGAAATATTAAATTAAATTTAAAATT
30879663 AA
66 AA
30879665 ACTATTAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
68 30 0.54
69 26 0.46
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (69 bp):
TAATCACTATAATATTAAATTAATAAAATATCTATCAAGAGAAATATTAAATTAAATTTAAAATT
AAGA
Found at i:30881299 original size:15 final size:15
Alignment explanation
Indices: 30881275--30881306 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30881265 TATGCATGCA
*
30881275 AAATATAAAAGACAT
1 AAATACAAAAGACAT
30881290 AAATACAAAAGACAT
1 AAATACAAAAGACAT
30881305 AA
1 AA
30881307 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:30887909 original size:15 final size:15
Alignment explanation
Indices: 30887889--30887919 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30887879 AAAATTCATA
30887889 TTAATTTTAATTAAT
1 TTAATTTTAATTAAT
*
30887904 TTAATTTTACTTAAT
1 TTAATTTTAATTAAT
30887919 T
1 T
30887920 AAAATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAATTTTAATTAAT
Found at i:30890321 original size:25 final size:25
Alignment explanation
Indices: 30890238--30890312 Score: 114
Period size: 25 Copynumber: 3.0 Consensus size: 25
30890228 CCATAGATTT
*
30890238 TATGAGTTTCCCGTTATTCAGCTCA
1 TATGAGCTTCCCGTTATTCAGCTCA
* *
30890263 TATGAGCTTCCCCTTATTCAGCTCG
1 TATGAGCTTCCCGTTATTCAGCTCA
*
30890288 TATGAGCTTCCCGTTATTCAACTCA
1 TATGAGCTTCCCGTTATTCAGCTCA
30890313 AAAAAGCTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (25 bp):
TATGAGCTTCCCGTTATTCAGCTCA
Found at i:30890321 original size:50 final size:49
Alignment explanation
Indices: 30890238--30890343 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 49
30890228 CCATAGATTT
* * * ** * * *
30890238 TATGAGTTTCCCGTTATTCAGCTCATATGAGCTTCCCCTTATTCAGCTCG
1 TATGAGCTTCCCGTTATTCAACTCAAAAAAGCTTACCATT-TACAGCTCG
*
30890288 TATGAGCTTCCCGTTATTCAACTCAAAAAAGCTTACTATTTACAGCTCG
1 TATGAGCTTCCCGTTATTCAACTCAAAAAAGCTTACCATTTACAGCTCG
30890337 TATGAGC
1 TATGAGC
30890344 ATACATAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
49 15 0.32
50 32 0.68
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (49 bp):
TATGAGCTTCCCGTTATTCAACTCAAAAAAGCTTACCATTTACAGCTCG
Found at i:30897522 original size:25 final size:25
Alignment explanation
Indices: 30897487--30897580 Score: 91
Period size: 25 Copynumber: 3.7 Consensus size: 25
30897477 CTCTTATGAG
*
30897487 TTTCCTGTTATTCAACTCGTATAAGC
1 TTTCC-GTTATTCAACTCATATAAGC
* *
30897513 TTTCCGTTATTCAGCTCATATGAGC
1 TTTCCGTTATTCAACTCATATAAGC
* ** *
30897538 TTCCCGTTATTCAACTCCCATGAGC
1 TTTCCGTTATTCAACTCATATAAGC
*
30897563 -TTCCTGTTATTCAGCTCA
1 TTTCC-GTTATTCAACTCA
30897581 GAAAAGATTA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
24 3 0.05
25 49 0.86
26 5 0.09
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.39
Consensus pattern (25 bp):
TTTCCGTTATTCAACTCATATAAGC
Found at i:30897549 original size:50 final size:50
Alignment explanation
Indices: 30897474--30897580 Score: 144
Period size: 50 Copynumber: 2.1 Consensus size: 50
30897464 GGATACATCA
* * * **
30897474 CAGCTCTTATGAGTTTCCTGTTATTCAACTCGTATAAGCTTTCC-GTTATT
1 CAGCTCATATGAGCTTCCCGTTATTCAACTCCCATAAGC-TTCCTGTTATT
*
30897524 CAGCTCATATGAGCTTCCCGTTATTCAACTCCCATGAGCTTCCTGTTATT
1 CAGCTCATATGAGCTTCCCGTTATTCAACTCCCATAAGCTTCCTGTTATT
30897574 CAGCTCA
1 CAGCTCA
30897581 GAAAAGATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
49 4 0.08
50 46 0.92
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (50 bp):
CAGCTCATATGAGCTTCCCGTTATTCAACTCCCATAAGCTTCCTGTTATT
Found at i:30906115 original size:40 final size:40
Alignment explanation
Indices: 30906002--30906106 Score: 183
Period size: 40 Copynumber: 2.6 Consensus size: 40
30905992 TATCTGCATT
30906002 CTGTATCTGATATGGGCCAAGGCCCTTATTTATTTTTGAGA
1 CTGTATCTGA-ATGGGCCAAGGCCCTTATTTATTTTTGAGA
*
30906043 CTGTATCTGAATGGGCCGAGGCCCTTATTTATTTTTGAGA
1 CTGTATCTGAATGGGCCAAGGCCCTTATTTATTTTTGAGA
*
30906083 CTGTATCTGAATGGGCTAAGGCCC
1 CTGTATCTGAATGGGCCAAGGCCC
30906107 AAACTTATTC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
40 51 0.84
41 10 0.16
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (40 bp):
CTGTATCTGAATGGGCCAAGGCCCTTATTTATTTTTGAGA
Found at i:30909129 original size:18 final size:18
Alignment explanation
Indices: 30909106--30909144 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
30909096 GTGACCCATG
30909106 TTTCCC-AAATTTTTATGT
1 TTTCCCAAAATTTTT-TGT
30909124 TTTCCCAAAATTTTTTGT
1 TTTCCCAAAATTTTTTGT
30909142 TTT
1 TTT
30909145 GTTCAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.21, C:0.15, G:0.05, T:0.59
Consensus pattern (18 bp):
TTTCCCAAAATTTTTTGT
Found at i:30910040 original size:130 final size:130
Alignment explanation
Indices: 30909818--30910440 Score: 747
Period size: 130 Copynumber: 4.8 Consensus size: 130
30909808 AATAACTCAT
* **
30909818 TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACAATCACAATTTAAGTTCATTG
1 TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
* * *
30909883 ATTTACTATCATAAACAATTTTCTATGACTTAGTTGATTTACTATCT-CTACTCCAAATAGCTCG
66 ATTTACTATCATGAACAATCTTCTATGAGTTAGTTGATTTACTAT-TGCTACTCCAAATAGCTCG
*
30909947 T
130 C
* * ** * *
30909948 TGAATTAAGATCACAGTTGATATTATTAAGGCTCGCTGATTTACGATCACAACCTAAGTTCATTT
1 TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
* * *
30910013 ATTTACTATTATGAACAATCTTCTATGAGTTAGTTGATTTACTATCAG-TACTCCAAACAGCTCG
66 ATTTACTATCATGAACAATCTTCTATGAGTTAGTTGATTTACTAT-TGCTACTCCAAATAGCTCG
30910077 C
130 C
** ** * * *
30910078 TGATTTAATATCACAGTTGATATTATTGGGGCTCATTGATTTACGATCGCAACCTAAGTTCGTTG
1 TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
* * ** * * *
30910143 ATTTACTATCATGAAAAATCTTCTATGATTTAGTTGATTTACTATTGCTACTTTAAACATCTCAC
66 ATTTACTATCATGAACAATCTTCTATGAGTTAGTTGATTTACTATTGCTACTCCAAATAGCTCGC
* * * *
30910208 TGATTTAATATCACAAATGATATTATTAAGGCTCGTTGATTTACGATCGCAGCCTAAGTTTATTG
1 TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
* *
30910273 A-TTACTATCATGAACAATCTTCTATAAGTTAGTTGATTTACAATTGCTACTCCAAATAGCTCGC
66 ATTTACTATCATGAACAATCTTCTATGAGTTAGTTGATTTACTATTGCTACTCCAAATAGCTCGC
* * * * *
30910337 T-AGTTTAAGATCACAACTGATATTATTAAGGCT-GACTGGTTTAGGATCACAGCCTAAGTTCAT
1 TGA-TTTAATATCACAACTGATATTATTAAGGCTCG-TTGATTTACGATCACAACCTAAGTTCAT
* * *
30910400 TAATTTACAATCATGAATAATCCTTCCTA--AGTTAGTTGATT
64 TGATTTACTATCATGAACAAT-CTT-CTATGAGTTAGTTGATT
30910441 CATAGTCATA
Statistics
Matches: 426, Mismatches: 60, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
128 2 0.00
129 109 0.26
130 309 0.73
131 3 0.01
132 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (130 bp):
TGATTTAATATCACAACTGATATTATTAAGGCTCGTTGATTTACGATCACAACCTAAGTTCATTG
ATTTACTATCATGAACAATCTTCTATGAGTTAGTTGATTTACTATTGCTACTCCAAATAGCTCGC
Found at i:30916724 original size:19 final size:19
Alignment explanation
Indices: 30916700--30916736 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
30916690 GAAAAAAACA
30916700 ATCATTTTTTAAATTTTTT
1 ATCATTTTTTAAATTTTTT
*
30916719 ATCATTTTTTTAATTTTT
1 ATCATTTTTTAAATTTTT
30916737 GGAACTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
ATCATTTTTTAAATTTTTT
Found at i:30923314 original size:38 final size:38
Alignment explanation
Indices: 30923272--30923345 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
30923262 AATGCTAGAC
* *
30923272 AAGATATTTCCAATAAACAAATTTTTCTGATCAAAATT
1 AAGATATTGCCAATAAACAAATTTCTCTGATCAAAATT
*
30923310 AAGATATTGCCAATAAACAAATTTCTCTTATCAAAA
1 AAGATATTGCCAATAAACAAATTTCTCTGATCAAAA
30923346 CGATTGACTT
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:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (38 bp):
AAGATATTGCCAATAAACAAATTTCTCTGATCAAAATT
Found at i:30925387 original size:17 final size:17
Alignment explanation
Indices: 30925365--30925399 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
30925355 TGAATGGTAC
30925365 ATATGAACATTGTAGAT
1 ATATGAACATTGTAGAT
30925382 ATATGAACATTGTAGAT
1 ATATGAACATTGTAGAT
30925399 A
1 A
30925400 AATCAATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (17 bp):
ATATGAACATTGTAGAT
Found at i:30926459 original size:13 final size:12
Alignment explanation
Indices: 30926439--30926465 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
30926429 CCAAACAACA
30926439 TCAAAAAAAATT
1 TCAAAAAAAATT
30926451 TCAAAAAAAATT
1 TCAAAAAAAATT
30926463 TCA
1 TCA
30926466 CTTTAATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (12 bp):
TCAAAAAAAATT
Found at i:30928753 original size:21 final size:21
Alignment explanation
Indices: 30928724--30928883 Score: 128
Period size: 21 Copynumber: 7.6 Consensus size: 21
30928714 GAAGCTTGTA
*
30928724 AGCTGAACAGAAGCTCATAAG
1 AGCTGAACAGAAACTCATAAG
* *
30928745 AGCTAAACAGAAACCCATAA-
1 AGCTGAACAGAAACTCATAAG
* * *
30928765 AGGTTGAACAGAATCTCGTAAG
1 A-GCTGAACAGAAACTCATAAG
** *
30928787 ATTTGAACAGAAACTCTTAAG
1 AGCTGAACAGAAACTCATAAG
* *
30928808 AGTTGAACAGAAGCTCGA-AAG
1 AGCTGAACAGAAACTC-ATAAG
*
30928829 AGCTGAAC-GAAAACTTATAAG
1 AGCTGAACAG-AAACTCATAAG
* * * *
30928850 AGTTAAACAGAAGCTCGTAAG
1 AGCTGAACAGAAACTCATAAG
30928871 AGCTGAACAGAAA
1 AGCTGAACAGAAA
30928884 GTAAAACACG
Statistics
Matches: 108, Mismatches: 25, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
20 3 0.03
21 103 0.95
22 2 0.02
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.17
Consensus pattern (21 bp):
AGCTGAACAGAAACTCATAAG
Found at i:30928775 original size:42 final size:42
Alignment explanation
Indices: 30928727--30928883 Score: 160
Period size: 42 Copynumber: 3.7 Consensus size: 42
30928717 GCTTGTAAGC
* *
30928727 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAAG-GT
1 TGAACAGAAGCTCATAAGAGCTGAACAGAAACAC-TAAAGAGT
* * ** * *
30928769 TGAACAGAATCTCGTAAGATTTGAACAGAAACTCTTAAGAGT
1 TGAACAGAAGCTCATAAGAGCTGAACAGAAACACTAAAGAGT
30928811 TGAACAGAAGCTCGA-AAGAGCTGAAC-GAAA-ACTTATAAGAGT
1 TGAACAGAAGCTC-ATAAGAGCTGAACAGAAACAC-TA-AAGAGT
* *
30928853 TAAACAGAAGCTCGTAAGAGCTGAACAGAAA
1 TGAACAGAAGCTCATAAGAGCTGAACAGAAA
30928884 GTAAAACACG
Statistics
Matches: 94, Mismatches: 15, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
40 1 0.01
41 9 0.10
42 80 0.85
43 4 0.04
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTGAACAGAAACACTAAAGAGT
Found at i:30933687 original size:18 final size:17
Alignment explanation
Indices: 30933655--30933689 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30933645 GTGTTTTGAA
30933655 TTGTTTTAATTTAATTT
1 TTGTTTTAATTTAATTT
*
30933672 TTGTTATTATTTTAATTT
1 TTGTT-TTAATTTAATTT
30933690 ATACGCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTGTTTTAATTTAATTT
Found at i:30936193 original size:22 final size:24
Alignment explanation
Indices: 30936165--30936208 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
30936155 TATGGCAAGA
30936165 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
30936187 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
30936209 AACTTAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:30937657 original size:19 final size:18
Alignment explanation
Indices: 30937627--30937678 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
30937617 GTGTGACCCC
30937627 TATTTTTT-AAATTTTTT
1 TATTTTTTAAAATTTTTT
*
30937644 TAATTTTTTAAAATTAATTT
1 T-ATTTTTTAAAATT-TTTT
*
30937664 TATTTTTAAAAATTT
1 TATTTTTTAAAATTT
30937679 AAAAACAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 1 0.03
18 7 0.24
19 17 0.59
20 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTTTTAAAATTTTTT
Found at i:30941462 original size:18 final size:18
Alignment explanation
Indices: 30941425--30941462 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
30941415 AAAAAATCAC
*
30941425 ATTTTTTATATTTAATAT
1 ATTTTTTATATTTAAAAT
30941443 ATTTTTTA-ATTTCAAAAT
1 ATTTTTTATATTT-AAAAT
30941461 AT
1 AT
30941463 ATAGTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTTATATTTAAAAT
Found at i:30947335 original size:26 final size:26
Alignment explanation
Indices: 30947306--30947366 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
30947296 ATAAGGTTAA
* *
30947306 TTATTTTAAGTT-CTTTATATATTATT
1 TTATTTTAAGTTACTTTACATATTA-C
* *
30947332 TTATTTAAAGTTATTTTACATATTAC
1 TTATTTTAAGTTACTTTACATATTAC
30947358 TTATTTTAA
1 TTATTTTAA
30947367 ATATCCACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (26 bp):
TTATTTTAAGTTACTTTACATATTAC
Found at i:30947365 original size:27 final size:25
Alignment explanation
Indices: 30947305--30947367 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
30947295 TATAAGGTTA
*
30947305 ATTATTTT-AAGTTCTTTATATATT
1 ATTATTTTAAAGTTCTTTACATATT
* *
30947329 ATTTTATTTAAAGTTATTTTACATATT
1 ATTAT-TTTAAAGTT-CTTTACATATT
30947356 ACTTATTTTAAA
1 A-TTATTTTAAA
30947368 TATCCACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 4 0.13
25 3 0.10
26 5 0.16
27 16 0.52
28 3 0.10
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (25 bp):
ATTATTTTAAAGTTCTTTACATATT
Found at i:30947512 original size:96 final size:96
Alignment explanation
Indices: 30947348--30947656 Score: 618
Period size: 96 Copynumber: 3.2 Consensus size: 96
30947338 AAAGTTATTT
30947348 TACATATTACTTATTTTAAATATCCACATATATTTAGTGTATTTCACCTTTAGCATATTAGTATA
1 TACATATTACTTATTTTAAATATCCACATATATTTAGTGTATTTCACCTTTAGCATATTAGTATA
30947413 TATTATCACTTACATGATTTTTTTCACTCCC
66 TATTATCACTTACATGATTTTTTTCACTCCC
30947444 TACATATTACTTATTTTAAATATCCACATATATTTAGTGTATTTCACCTTTAGCATATTAGTATA
1 TACATATTACTTATTTTAAATATCCACATATATTTAGTGTATTTCACCTTTAGCATATTAGTATA
30947509 TATTATCACTTACATGATTTTTTTCACTCCC
66 TATTATCACTTACATGATTTTTTTCACTCCC
30947540 TACATATTACTTATTTTAAATATCCACATATATTTAGTGTATTTCACCTTTAGCATATTAGTATA
1 TACATATTACTTATTTTAAATATCCACATATATTTAGTGTATTTCACCTTTAGCATATTAGTATA
30947605 TATTATCACTTACATGATTTTTTTCACTCCC
66 TATTATCACTTACATGATTTTTTTCACTCCC
30947636 TACATATTACTTATTTTAAAT
1 TACATATTACTTATTTTAAAT
30947657 TAGTATATGT
Statistics
Matches: 213, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 213 1.00
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.47
Consensus pattern (96 bp):
TACATATTACTTATTTTAAATATCCACATATATTTAGTGTATTTCACCTTTAGCATATTAGTATA
TATTATCACTTACATGATTTTTTTCACTCCC
Found at i:30949398 original size:18 final size:17
Alignment explanation
Indices: 30949372--30949423 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
30949362 AAAAATTACA
30949372 AAAAAAATTTCAAAAATC
1 AAAAAAATTT-AAAAATC
*
30949390 AAAATAATTTAAAAAT-
1 AAAAAAATTTAAAAATC
30949406 AATAAAATATTTATAAAA
1 AA-AAAA-ATTTA-AAAA
30949424 AATTCAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 2 0.07
17 9 0.31
18 14 0.48
19 4 0.14
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAAATTTAAAAATC
Found at i:30950521 original size:18 final size:18
Alignment explanation
Indices: 30950460--30950521 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 18
30950450 AAGCTATAAA
30950460 ATTAATATAGATTGATATTTT
1 ATTAATATA-ATT-ATA-TTT
* *
30950481 AATAATCTAATTATTGAATTT
1 ATTAATATAATTA-T--ATTT
30950502 ATTAATATAATTATATTT
1 ATTAATATAATTATATTT
30950520 AT
1 AT
30950522 CATACATCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
18 6 0.18
19 1 0.03
20 5 0.15
21 21 0.62
22 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
ATTAATATAATTATATTT
Found at i:30950531 original size:42 final size:41
Alignment explanation
Indices: 30950460--30950561 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 41
30950450 AAGCTATAAA
30950460 ATTAATATAGATTGATATTT-TAATAATCT-AATTATTGAATTT
1 ATTAATATA-ATT-ATATTTATAATAATCTAAATT-TTGAATTT
*
30950502 ATTAATATAATTATATTTATCATACATCTAAAATTTTGAATTT
1 ATTAATATAATTATATTTATAATA-ATCT-AAATTTTGAATTT
30950545 A-T-AT-TAATATATATTTA
1 ATTAATATAAT-TATATTTA
30950562 ACTGTTGAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
40 10 0.19
41 17 0.31
42 14 0.26
43 9 0.17
44 4 0.07
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (41 bp):
ATTAATATAATTATATTTATAATAATCTAAATTTTGAATTT
Found at i:30950705 original size:134 final size:135
Alignment explanation
Indices: 30950542--30950811 Score: 533
Period size: 134 Copynumber: 2.0 Consensus size: 135
30950532 AAATTTTGAA
30950542 TTTATATTAATATATATTTAACTGTTGAAGTTTCTTTTTATAAAATAAAAAGTTACAGTTATTTT
1 TTTATATTAATATATATTTAACTGTTGAAGTTTCTTTTTATAAAATAAAAAGTTACAGTTATTTT
30950607 TTTAAATTTCTGGCATGCATTATCTACAGTAAAGTACCACAAAACCCCGTAGTATACTTTAGATC
66 TTTAAATTTCTGGCATGCATTATCTACAGTAAAGTACCACAAAACCCCGTAGTATACTTTAGATC
30950672 GCATT
131 GCATT
30950677 TTTATATTAAT-TATATTTAACTGTTGAAGTTTCTTTTTATAAAATAAAAAGTTACAGTTATTTT
1 TTTATATTAATATATATTTAACTGTTGAAGTTTCTTTTTATAAAATAAAAAGTTACAGTTATTTT
30950741 TTTAAATTTCTGGCATGCATTATCTACAGTAAAGTACCACAAAACCCCGTAGTATACTTTAGATC
66 TTTAAATTTCTGGCATGCATTATCTACAGTAAAGTACCACAAAACCCCGTAGTATACTTTAGATC
30950806 GCATT
131 GCATT
30950811 T
1 T
30950812 GACCATCTAT
Statistics
Matches: 135, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
134 124 0.92
135 11 0.08
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (135 bp):
TTTATATTAATATATATTTAACTGTTGAAGTTTCTTTTTATAAAATAAAAAGTTACAGTTATTTT
TTTAAATTTCTGGCATGCATTATCTACAGTAAAGTACCACAAAACCCCGTAGTATACTTTAGATC
GCATT
Found at i:30951771 original size:20 final size:20
Alignment explanation
Indices: 30951739--30951783 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
30951729 AAAAAAAATC
*
30951739 ATTTTGTTTATAATTTTTAT
1 ATTTTGTTTATAATTTTTAA
30951759 ATTTT-TTTAATAATTTTTAA
1 ATTTTGTTT-ATAATTTTTAA
30951779 ATTTT
1 ATTTT
30951784 AAAAGGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
ATTTTGTTTATAATTTTTAA
Found at i:30952233 original size:5 final size:5
Alignment explanation
Indices: 30952225--30952252 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
30952215 AAATAAAAAT
30952225 AACGA AACGA AACGA AACGA AACGA AAC
1 AACGA AACGA AACGA AACGA AACGA AAC
30952253 AGTACAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.21, G:0.18, T:0.00
Consensus pattern (5 bp):
AACGA
Found at i:30952714 original size:17 final size:17
Alignment explanation
Indices: 30952692--30952724 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30952682 GTTTGGTTGT
30952692 TAACTTTCAAGACTTAG
1 TAACTTTCAAGACTTAG
30952709 TAACTTTCAAGACTTA
1 TAACTTTCAAGACTTA
30952725 TGTAGAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (17 bp):
TAACTTTCAAGACTTAG
Found at i:30953709 original size:18 final size:17
Alignment explanation
Indices: 30953686--30953720 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
30953676 ATCTTTTTAG
30953686 ATTAAAACAAAAATAATT
1 ATTAAAA-AAAAATAATT
*
30953704 ATTAAAATAAAATAATT
1 ATTAAAAAAAAATAATT
30953721 CTAAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTAAAAAAAAATAATT
Found at i:30953727 original size:16 final size:17
Alignment explanation
Indices: 30953695--30953727 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30953685 GATTAAAACA
*
30953695 AAAATAATTATTAAAAT
1 AAAATAATTACTAAAAT
30953712 AAAATAATT-CTAAAAT
1 AAAATAATTACTAAAAT
30953728 TTAAAATCTT
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:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAATTACTAAAAT
Found at i:30954492 original size:125 final size:125
Alignment explanation
Indices: 30954240--30954615 Score: 533
Period size: 124 Copynumber: 3.0 Consensus size: 125
30954230 TTAGGGTTTT
* *** * **
30954240 TAGGTCCTGGAAGAAATAATTTCGAGTTGAAGTTTCTGATAAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCATGGAAGAAATAATTT-TTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * *
30954305 AGGATGCTATTTGAGAATAATTTGTG-AAATCGCGCCCTAGTGGACGCGCTTTTGCTATAG
65 AGGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* *
30954365 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAACCGCTTCTAGTA
1 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
* *
30954430 GGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACACACTTTTGCTACAG
66 GGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * * * *
30954490 TAGGTCATGGAAGAAATAA-ATTTTTTGACGTTTCTGAGCAAACAGTATAAAATCGCTCCAAGGA
1 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
* *
30954554 GGAT-CTATTTGAGAAGAATTTGTAAAAATCGCGCCCTCGTGGATGCGCTTTTGCTACAG
66 GGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
30954613 TAG
1 TAG
30954616 CATGTTTGGA
Statistics
Matches: 226, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
123 54 0.24
124 102 0.45
125 70 0.31
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (125 bp):
TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
GGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:30956331 original size:21 final size:22
Alignment explanation
Indices: 30956302--30956507 Score: 226
Period size: 21 Copynumber: 9.4 Consensus size: 22
30956292 GCAAGCCCGT
*
30956302 TTAGTGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAAGTTAATGGG
*
30956323 TTAGGGTTTTTAAGTTAAGGGGG
1 TTAGGGTTTTTAAGTTAA-TGGG
30956346 TTAGGGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAAGTTAATGGG
* *
30956367 TTAGAGTTTTTAAG-TAACGGG
1 TTAGGGTTTTTAAGTTAATGGG
*
30956388 TTAGGGTTTTTAAGTTTA-GGG
1 TTAGGGTTTTTAAGTTAATGGG
*
30956409 TTTAGGGTTTTTAA-TTAAATTAGG
1 -TTAGGGTTTTTAAGTT-AA-TGGG
*
30956433 TTAGAGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAAGTTAATGGG
* *
30956454 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAA-TGGG
*
30956477 TTAGGGTTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAAGTTAA-TGGG
30956500 TTAGGGTT
1 TTAGGGTT
30956508 AGGTTAGGGT
Statistics
Matches: 162, Mismatches: 12, Indels: 20
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.02
21 72 0.44
22 16 0.10
23 67 0.41
24 4 0.02
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (22 bp):
TTAGGGTTTTTAAGTTAATGGG
Found at i:30956370 original size:44 final size:43
Alignment explanation
Indices: 30956302--30956643 Score: 296
Period size: 44 Copynumber: 8.0 Consensus size: 43
30956292 GCAAGCCCGT
*
30956302 TTAGTGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGGG
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA-GGGG
* *
30956346 TTAGGGTTTTTAAGTTAAGGGTTAGAGTTTTTAAG-TAACGGG
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGG
* **
30956388 TTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAA-TTAAATTAGG
1 TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTT-AA-GGGG
* * **
30956433 TTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA-GGGG
*
30956477 TTAGGGTTTTTAAGTTAA---TTA-GG---TTAGGGTT-A--GG
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTA-AGTTAAGGGG
* **
30956511 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA-GGGG
* * * *
30956555 TTAGAGTTTTTATGTTAATTAGGTTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAGTTAAGGGG
* * *
30956600 TTAAGGTTTTTAA-TTAAATTAGGTTAGGATTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTT-AA--GGGTTAGGGTTTTTAAGTTAAGGG
30956644 TATTAATGGT
Statistics
Matches: 253, Mismatches: 25, Indels: 39
0.80 0.08 0.12
Matches are distributed among these distances:
34 20 0.08
37 7 0.03
38 4 0.02
40 4 0.02
41 7 0.03
42 23 0.09
43 16 0.06
44 92 0.36
45 61 0.24
46 19 0.08
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (43 bp):
TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGG
Found at i:30956495 original size:23 final size:23
Alignment explanation
Indices: 30956302--30956640 Score: 240
Period size: 23 Copynumber: 14.8 Consensus size: 23
30956292 GCAAGCCCGT
* *
30956302 TTAGTGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
***
30956323 TTAGGGTTTTTAAGTTAAGGGGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
30956346 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
* **
30956367 TTAGAGTTTTTAAG-TAA-CGGG
1 TTAGGGTTTTTAAGTTAATTAGG
30956388 TTAGGGTTTTTAAG-T--TTAGGG
1 TTAGGGTTTTTAAGTTAATTA-GG
30956409 TTTAGGGTTTTTAA-TTAAATTAGG
1 -TTAGGGTTTTTAAGTT-AATTAGG
* *
30956433 TTAGAGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
30956454 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
30956477 TTAGGGTTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
* * *
30956500 TTAGGGTTAGGTTAGGGTTTTTAAGTTAAG
1 TTAGGGTT--TTTA-AG---TTAA-TTAGG
** *
30956530 GGTTAGGGTTTTTAATTTAATTAGG
1 TT--AGGGTTTTTAAGTTAATTAGG
* *
30956555 TTAGAGTTTTTATGTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
30956578 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
30956599 TTTAAGGTTTTTAA-TTAAATTAGG
1 -TTAGGGTTTTTAAGTT-AATTAGG
*
30956623 TTAGGATTTTTAAGTTAA
1 TTAGGGTTTTTAAGTTAA
30956641 GGGTATTAAT
Statistics
Matches: 259, Mismatches: 32, Indels: 52
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.01
21 74 0.29
22 28 0.11
23 114 0.44
24 8 0.03
25 10 0.04
26 5 0.02
29 4 0.02
30 7 0.03
32 6 0.02
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.46
Consensus pattern (23 bp):
TTAGGGTTTTTAAGTTAATTAGG
Found at i:30956523 original size:78 final size:78
Alignment explanation
Indices: 30956428--30956585 Score: 289
Period size: 78 Copynumber: 2.0 Consensus size: 78
30956418 TTTAATTAAA
*
30956428 TTAGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTT
1 TTAGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTAAGTT
30956493 AATTAGGTTAGGG
66 AATTAGGTTAGGG
* *
30956506 TTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTATGTT
1 TTAGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTAAGTT
30956571 AATTAGGTTAGGG
66 AATTAGGTTAGGG
30956584 TT
1 TT
30956586 TTTAAGTTAA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (78 bp):
TTAGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTAAGTT
AATTAGGTTAGGG
Found at i:30956689 original size:9 final size:9
Alignment explanation
Indices: 30956671--30956707 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
30956661 ATTCTCAAAT
30956671 AATA-TCAA
1 AATATTCAA
30956679 AATATTCAA
1 AATATTCAA
30956688 AATATTCAA
1 AATATTCAA
30956697 AATATTCAA
1 AATATTCAA
30956706 AA
1 AA
30956708 ATTTCTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 4 0.14
9 24 0.86
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (9 bp):
AATATTCAA
Found at i:30956739 original size:25 final size:25
Alignment explanation
Indices: 30956710--30956967 Score: 201
Period size: 25 Copynumber: 10.9 Consensus size: 25
30956700 ATTCAAAAAT
30956710 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
30956735 TTCTATTTTATTACATCAAAT-AA-
1 TTCTATTTTATTACATCAAATAAAC
** * * * *
30956758 TATC-A--AAATAAC-TAAAAAAAAT
1 T-TCTATTTTATTACATCAAATAAAC
30956780 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
30956805 TTCTATTTTATTACATCAAAT-AA-
1 TTCTATTTTATTACATCAAATAAAC
** * * * *
30956828 TATC-A--AAATAAC-TAAAAAAAAT
1 T-TCTATTTTATTACATCAAATAAAC
30956850 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
30956875 TTCTATTTTATTACATCAAAT-AA-
1 TTCTATTTTATTACATCAAATAAAC
** * * * *
30956898 TATC-A--AAATAAC-TAAAAAAAAT
1 T-TCTATTTTATTACATCAAATAAAC
30956920 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
30956945 TTCTATTTTATTACATCAAATAA
1 TTCTATTTTATTACATCAAATAA
30956968 TATCAAAATA
Statistics
Matches: 179, Mismatches: 33, Indels: 42
0.70 0.13 0.17
Matches are distributed among these distances:
20 12 0.07
21 24 0.13
22 6 0.03
23 6 0.03
24 24 0.13
25 107 0.60
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:30956786 original size:70 final size:70
Alignment explanation
Indices: 30956704--30956977 Score: 548
Period size: 70 Copynumber: 3.9 Consensus size: 70
30956694 CAAAATATTC
30956704 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
1 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
30956769 CTAAA
66 CTAAA
30956774 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
1 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
30956839 CTAAA
66 CTAAA
30956844 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
1 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
30956909 CTAAA
66 CTAAA
30956914 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
1 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
30956978 TTCAAAATAT
Statistics
Matches: 204, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 204 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (70 bp):
AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
CTAAA
Found at i:30957420 original size:18 final size:18
Alignment explanation
Indices: 30957397--30957436 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
30957387 GACTCGAAAA
*
30957397 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
30957415 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
30957433 AGGA
1 AGGA
30957437 AACGCACTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:30958969 original size:12 final size:12
Alignment explanation
Indices: 30958952--30958993 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
30958942 TTTACGGTTT
30958952 AAAAAGATTTTA
1 AAAAAGATTTTA
30958964 AAAAAGATTTTA
1 AAAAAGATTTTA
** *
30958976 AAAATTATTTAA
1 AAAAAGATTTTA
30958988 AAAAAG
1 AAAAAG
30958994 GGAGTTAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (12 bp):
AAAAAGATTTTA
Found at i:30959104 original size:14 final size:11
Alignment explanation
Indices: 30959061--30959100 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
30959051 AAGAGAATTT
30959061 TTGA-AGGAAA
1 TTGAGAGGAAA
30959071 TTGAGAGGAAA
1 TTGAGAGGAAA
30959082 TTGAGAGGAAA
1 TTGAGAGGAAA
30959093 TTTGAGAG
1 -TTGAGAG
30959101 AGGATTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.14
11 17 0.61
12 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:30967423 original size:17 final size:18
Alignment explanation
Indices: 30967401--30967434 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
30967391 CTAAACACTT
30967401 CTAAAATAACC-TAAACC
1 CTAAAATAACCATAAACC
30967418 CTAAAATAACCATAAAC
1 CTAAAATAACCATAAAC
30967435 TATATCCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (18 bp):
CTAAAATAACCATAAACC
Found at i:30970081 original size:19 final size:19
Alignment explanation
Indices: 30970057--30970094 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
30970047 AATTTATAAC
*
30970057 TAATTAACCTTAATTACTT
1 TAATTAAACTTAATTACTT
30970076 TAATTAAACTTAATTACTT
1 TAATTAAACTTAATTACTT
30970095 AACCTTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATTAAACTTAATTACTT
Found at i:30974283 original size:30 final size:29
Alignment explanation
Indices: 30974243--30974302 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 29
30974233 GATACATGGG
30974243 AATAAGTTGCTCACACAAGCTGACATTAT
1 AATAAGTTGCTCACACAAGCTGACATTAT
*
30974272 AATAGAGTTGCTCACACAAGTTGACATTAT
1 AATA-AGTTGCTCACACAAGCTGACATTAT
30974302 A
1 A
30974303 TCGAGGTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (29 bp):
AATAAGTTGCTCACACAAGCTGACATTAT
Found at i:30988386 original size:27 final size:26
Alignment explanation
Indices: 30988342--30988392 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
30988332 ATATTACAAA
* *
30988342 TTTTCTTTTTATTTTCTTTAATTTCT
1 TTTTCATTTGATTTTCTTTAATTTCT
30988368 TTTTCATTTGATTGTTCTTTAATTT
1 TTTTCATTTGATT-TTCTTTAATTT
30988393 TTATCAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTTCATTTGATTTTCTTTAATTTCT
Found at i:30992368 original size:2 final size:2
Alignment explanation
Indices: 30992361--30992385 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30992351 CTTATGTTTT
30992361 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30992386 CTTGAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30997741 original size:17 final size:17
Alignment explanation
Indices: 30997721--30997788 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
30997711 ATAAATTGAT
30997721 ATAAATATATAAAAATC
1 ATAAATATATAAAAATC
* *
30997738 ATAAATATTTATAAATATT
1 ATAAATA--TATAAAAATC
*
30997757 ATAAA-AAATAAAAATC
1 ATAAATATATAAAAATC
30997773 GAATAAAT-TATAAAAA
1 --ATAAATATATAAAAA
30997789 ATTATAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.17
17 7 0.17
18 13 0.32
19 13 0.32
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (17 bp):
ATAAATATATAAAAATC
Found at i:30997758 original size:9 final size:9
Alignment explanation
Indices: 30997720--30997761 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
30997710 TATAAATTGA
30997720 TATAAATA-
1 TATAAATAT
*
30997728 TATAAAAAT
1 TATAAATAT
*
30997737 CATAAATATT
1 TATAAATA-T
30997747 TATAAATAT
1 TATAAATAT
30997756 TATAAA
1 TATAAA
30997762 AAATAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 7 0.25
9 13 0.46
10 8 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (9 bp):
TATAAATAT
Found at i:30997760 original size:19 final size:17
Alignment explanation
Indices: 30997720--30997796 Score: 59
Period size: 19 Copynumber: 4.4 Consensus size: 17
30997710 TATAAATTGA
30997720 TATAAATATATAAAAAT
1 TATAAATATATAAAAAT
* *
30997737 CATAAATATTTATAAATAT
1 TATAAATA--TATAAAAAT
*
30997756 TATAAA-AAATAAAAAT
1 TATAAATATATAAAAAT
*
30997772 CGAATAAAT-TATAAAAAAT
1 --TATAAATATAT-AAAAAT
30997791 TATAAA
1 TATAAA
30997797 ATTAATAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
16 7 0.15
17 12 0.26
18 8 0.17
19 19 0.41
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (17 bp):
TATAAATATATAAAAAT
Found at i:30997797 original size:27 final size:26
Alignment explanation
Indices: 30997703--30997805 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 26
30997693 TTAAAAATAA
*
30997703 AAAAAATTATAAATTGATATAAA-TAT
1 AAAAAATTATAAAATGA-ATAAATTAT
* **
30997729 ATAAAAATCATAAATATTTATAAATATTAT
1 A-AAAAATTATAAA-ATGAAT-AA-ATTAT
30997759 AAAAAA-TA-AAAATCGAATAAATTAT
1 AAAAAATTATAAAAT-GAATAAATTAT
*
30997784 AAAAAATTATAAAATTAATAAA
1 AAAAAATTATAAAATGAATAAA
30997806 ACATATTTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
25 11 0.18
26 13 0.21
27 23 0.38
28 4 0.07
29 6 0.10
30 4 0.07
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAAAATTATAAAATGAATAAATTAT
Found at i:30999475 original size:50 final size:51
Alignment explanation
Indices: 30999372--30999613 Score: 181
Period size: 50 Copynumber: 4.7 Consensus size: 51
30999362 GGGAATGAGA
* * * *
30999372 TCCCATGTAAGACCATGTCTGGGACATGTCATTGGTATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG---CACT-ACA-GATGAGAGG
*
30999428 TCCCATGTAAGACCATGTCTGGGACAAGGCATTGGCACTA-AGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTACAGATGAGAGG
* ** * * * **
30999478 GCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCAC--CGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTAC-AGATGAGAGG
* * * * **
30999528 TCCCATGTAAGACCA-GATATGGGATATGGCATTGGCAGTACAGA--AAACA
1 TCCCATGTAAGACCATG-TCTGGGACATGGCATTGGCACTACAGATGAGAGG
* * *
30999577 TCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
30999614 TGTATTATCA
Statistics
Matches: 151, Mismatches: 29, Indels: 19
0.76 0.15 0.10
Matches are distributed among these distances:
49 33 0.22
50 77 0.51
51 3 0.02
52 2 0.01
53 3 0.02
56 33 0.22
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (51 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTACAGATGAGAGG
Found at i:31012896 original size:16 final size:16
Alignment explanation
Indices: 31012875--31012905 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31012865 GAGAAAAATA
*
31012875 AAAAGTTTTAGGGAAT
1 AAAAGTTTGAGGGAAT
31012891 AAAAGTTTGAGGGAA
1 AAAAGTTTGAGGGAA
31012906 AGTAAATAGA
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:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (16 bp):
AAAAGTTTGAGGGAAT
Found at i:31013247 original size:9 final size:9
Alignment explanation
Indices: 31013233--31013287 Score: 74
Period size: 9 Copynumber: 6.1 Consensus size: 9
31013223 TATAGTTTGA
31013233 TATTCGAAT
1 TATTCGAAT
31013242 TATTCGAAT
1 TATTCGAAT
*
31013251 TATTCGAGT
1 TATTCGAAT
31013260 TATTCGAAT
1 TATTCGAAT
* *
31013269 TATTTGAGT
1 TATTCGAAT
*
31013278 TATTCAAAT
1 TATTCGAAT
31013287 T
1 T
31013288 CGAAAACTCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31013256 original size:18 final size:18
Alignment explanation
Indices: 31013233--31013287 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
31013223 TATAGTTTGA
*
31013233 TATTCGAATTATTCGAAT
1 TATTCGAGTTATTCGAAT
31013251 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
* *
31013269 TATTTGAGTTATTCAAAT
1 TATTCGAGTTATTCGAAT
31013287 T
1 T
31013288 CGAAAACTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (18 bp):
TATTCGAGTTATTCGAAT
Found at i:31013468 original size:24 final size:24
Alignment explanation
Indices: 31013439--31013501 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
31013429 AGTGTTGCGG
* *
31013439 ACAAATCGCCAGAACAGTATTCAA
1 ACAAATCGCCAGAACAATATGCAA
* * *
31013463 ACAAATTGCCAAAATAATATGCAA
1 ACAAATCGCCAGAACAATATGCAA
*
31013487 ACAAATCGCTAGAAC
1 ACAAATCGCCAGAAC
31013502 TCCAAACAGA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.17
Consensus pattern (24 bp):
ACAAATCGCCAGAACAATATGCAA
Found at i:31013554 original size:30 final size:29
Alignment explanation
Indices: 31013508--31013580 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
31013498 GAACTCCAAA
* * *
31013508 CAGAACTCC-AAAATTGCGGATTTACTGC
1 CAGAACTCCAAAAATTGCAGATATACCGC
*
31013536 TAGAACTCCAATAAATTGCAGATATACCGC
1 CAGAACTCCAA-AAATTGCAGATATACCGC
*
31013566 CAGAACTCCACAAAT
1 CAGAACTCCAAAAAT
31013581 CTCCTGTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 8 0.22
29 5 0.14
30 24 0.65
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (29 bp):
CAGAACTCCAAAAATTGCAGATATACCGC
Found at i:31016259 original size:9 final size:9
Alignment explanation
Indices: 31016242--31016308 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
31016232 GTAGTGATTC
*
31016242 AATTCGGTT
1 AATTCGGGT
* *
31016251 AATTTGGTT
1 AATTCGGGT
31016260 AATTCGGGT
1 AATTCGGGT
*
31016269 AATTTGGGT
1 AATTCGGGT
*
31016278 AATTCAGGT
1 AATTCGGGT
31016287 AATTCGGGT
1 AATTCGGGT
*
31016296 AATTCGGTT
1 AATTCGGGT
31016305 AATT
1 AATT
31016309 TTTAACCAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (9 bp):
AATTCGGGT
Found at i:31016265 original size:18 final size:18
Alignment explanation
Indices: 31016242--31016309 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
31016232 GTAGTGATTC
*
31016242 AATTCGGTTAATTTGGTT
1 AATTCGGTTAATTTGGGT
*
31016260 AATTCGGGTAATTTGGGT
1 AATTCGGTTAATTTGGGT
*
31016278 AATTCAGG-TAATTCGGGT
1 AATTC-GGTTAATTTGGGT
31016296 AATTCGGTTAATTT
1 AATTCGGTTAATTT
31016310 TTAACCAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.05
18 40 0.91
19 2 0.05
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (18 bp):
AATTCGGTTAATTTGGGT
Found at i:31021904 original size:25 final size:25
Alignment explanation
Indices: 31021875--31021922 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
31021865 TGACGTAAAT
*
31021875 TGAATGTGAATAATGTTTAATCGCA
1 TGAATGTGAATAATGGTTAATCGCA
*
31021900 TGAATGTGAATGATGGTTAATCG
1 TGAATGTGAATAATGGTTAATCG
31021923 ATTCTAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (25 bp):
TGAATGTGAATAATGGTTAATCGCA
Found at i:31027155 original size:2 final size:2
Alignment explanation
Indices: 31027148--31027172 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31027138 AATGATACAA
31027148 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
31027173 TATTCATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:31028445 original size:20 final size:19
Alignment explanation
Indices: 31028420--31028513 Score: 61
Period size: 20 Copynumber: 4.9 Consensus size: 19
31028410 GATCGTTACA
31028420 TTATAAAAATTAATAAAAAC
1 TTATAAAAATT-ATAAAAAC
*
31028440 TTATAAATAA-TATTAAAAAA
1 TTATAAA-AATTA-TAAAAAC
* *
31028460 TCATAAAAAATTAT-TAAAC
1 TTAT-AAAAATTATAAAAAC
* *
31028479 --ATTAAAATTGATATAAAC
1 TTATAAAAATT-ATAAAAAC
*
31028497 TTATAAATATTATAAAA
1 TTATAAAAATTATAAAA
31028514 CTCTAACAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
16 6 0.10
17 4 0.07
18 5 0.09
19 9 0.16
20 27 0.47
21 7 0.12
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (19 bp):
TTATAAAAATTATAAAAAC
Found at i:31029254 original size:10 final size:10
Alignment explanation
Indices: 31029230--31029277 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
31029220 TTATAATTCC
*
31029230 TAATTT-TTC
1 TAATTTATTA
31029239 TAATTTATTA
1 TAATTTATTA
31029249 TAATTTATTA
1 TAATTTATTA
*
31029259 AAATTATATTA
1 TAATT-TATTA
*
31029270 TTATTTAT
1 TAATTTAT
31029278 AAGTTTTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 6 0.18
10 19 0.58
11 8 0.24
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TAATTTATTA
Found at i:31030326 original size:19 final size:19
Alignment explanation
Indices: 31030284--31030341 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
31030274 AAAACACCCA
*
31030284 AAATAATTCAAAATAATTTTT
1 AAAT-ATTCAAAAT-ATTTAT
31030305 AAATATTCAAAATATTTAT
1 AAATATTCAAAATATTTAT
*
31030324 AAAAATTCCAAAAT-TTTA
1 AAATATT-CAAAATATTTA
31030342 AAAAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.44
20 15 0.44
21 4 0.12
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATTCAAAATATTTAT
Found at i:31038224 original size:7 final size:7
Alignment explanation
Indices: 31038212--31038258 Score: 94
Period size: 7 Copynumber: 6.7 Consensus size: 7
31038202 TTTTTACCAT
31038212 GAACCTC
1 GAACCTC
31038219 GAACCTC
1 GAACCTC
31038226 GAACCTC
1 GAACCTC
31038233 GAACCTC
1 GAACCTC
31038240 GAACCTC
1 GAACCTC
31038247 GAACCTC
1 GAACCTC
31038254 GAACC
1 GAACC
31038259 CAAACCTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.30, C:0.43, G:0.15, T:0.13
Consensus pattern (7 bp):
GAACCTC
Found at i:31038293 original size:18 final size:19
Alignment explanation
Indices: 31038255--31038310 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 19
31038245 TCGAACCTCG
* *
31038255 AACCCAAACCTTAACCTTA
1 AACCCAAACCCTAAACTTA
* *
31038274 AACTCAAACTC-AAACTTA
1 AACCCAAACCCTAAACTTA
31038292 AACCCAAACCCTAAACTTA
1 AACCCAAACCCTAAACTTA
31038311 GACCTAAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (19 bp):
AACCCAAACCCTAAACTTA
Found at i:31038411 original size:78 final size:78
Alignment explanation
Indices: 31038282--31038437 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
31038272 TAAACTCAAA
31038282 CTCAAACTTAAACCCAAACCCTAAACTTAGACCTAAATCTTAAATCTTAAATCTTGAATCTCGAA
1 CTCAAACTTAAACCCAAACCCTAAACTTAGACCTAAATCTTAAATCTTAAATCTTGAATCTCGAA
31038347 CCCATTCAAGATT
66 CCCATTCAAGATT
31038360 CTCAAACTTAAACCCAAACCCTAAACTTAGACCTAAATCTTAAATCTTAAATCTTGAATCTCGAA
1 CTCAAACTTAAACCCAAACCCTAAACTTAGACCTAAATCTTAAATCTTAAATCTTGAATCTCGAA
31038425 CCCATTCAAGATT
66 CCCATTCAAGATT
31038438 TAAAATTTAG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.40, C:0.27, G:0.05, T:0.28
Consensus pattern (78 bp):
CTCAAACTTAAACCCAAACCCTAAACTTAGACCTAAATCTTAAATCTTAAATCTTGAATCTCGAA
CCCATTCAAGATT
Found at i:31043010 original size:16 final size:16
Alignment explanation
Indices: 31042977--31043010 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31042967 ACTCATTTAA
*
31042977 TTTTCTTTTTGAATTT
1 TTTTCTTTTTGAACTT
*
31042993 TTTTCTTTTTGCACTT
1 TTTTCTTTTTGAACTT
31043009 TT
1 TT
31043011 AAGCTAACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTCTTTTTGAACTT
Found at i:31043356 original size:22 final size:22
Alignment explanation
Indices: 31043330--31043380 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
31043320 CAACCAAATA
*
31043330 ATCACAGCTTCAACAATTTACC
1 ATCACAACTTCAACAATTTACC
*
31043352 ATCACAACTTCAACAATTTATC
1 ATCACAACTTCAACAATTTACC
31043374 ATTCACA
1 A-TCACA
31043381 CTAGCGTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.29
Consensus pattern (22 bp):
ATCACAACTTCAACAATTTACC
Found at i:31049507 original size:12 final size:12
Alignment explanation
Indices: 31049486--31049595 Score: 55
Period size: 12 Copynumber: 8.9 Consensus size: 12
31049476 AAAAACTTAA
*
31049486 TGATTAAAAACT
1 TGATGAAAAACT
*
31049498 TGATGGAAAACT
1 TGATGAAAAACT
*
31049510 TTATGAAAAGACT
1 TGATGAAAA-ACT
* *
31049523 TGATGAGAAGCT
1 TGATGAAAAACT
*
31049535 T-A-AAAAGAACT
1 TGATGAAA-AACT
*
31049546 TGATG-CAAACT
1 TGATGAAAAACT
* *
31049557 TAATAAAAAAAAACT
1 TGAT---GAAAAACT
*
31049572 TGATAAAAGAACT
1 TGATGAAA-AACT
31049585 TGATGAAAAAC
1 TGATGAAAAAC
31049596 ACTTGAAGAA
Statistics
Matches: 72, Mismatches: 17, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
10 2 0.03
11 12 0.17
12 29 0.40
13 21 0.29
15 8 0.11
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:31049584 original size:13 final size:14
Alignment explanation
Indices: 31049563--31049612 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
31049553 AACTTAATAA
31049563 AAAAAAACTTGAT-
1 AAAAAAACTTGATG
*
31049576 AAAAGAACTTGATG
1 AAAAAAACTTGATG
* *
31049590 AAAAACACTTGAAG
1 AAAAAAACTTGATG
31049604 AAAGAAAAC
1 AAA-AAAAC
31049613 ACTTAATGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 12 0.40
14 14 0.47
15 4 0.13
ACGTcount: A:0.60, C:0.10, G:0.14, T:0.16
Consensus pattern (14 bp):
AAAAAAACTTGATG
Found at i:31049593 original size:14 final size:13
Alignment explanation
Indices: 31049476--31049606 Score: 53
Period size: 12 Copynumber: 10.2 Consensus size: 13
31049466 AGCTTAATTG
*
31049476 AAAAACTTAATGA
1 AAAAACTTGATGA
31049489 TTAAAAACTTGATG-
1 --AAAAACTTGATGA
* *
31049503 GAAAACTTTATGA
1 AAAAACTTGATGA
*
31049516 AAAGACTTGATG-
1 AAAAACTTGATGA
* *
31049528 AGAAGCTT-A--A
1 AAAAACTTGATGA
31049538 AAAGAACTTGATG-
1 AAA-AACTTGATGA
* * *
31049551 -CAAACTTAATAAAA
1 AAAAACTTGAT--GA
31049565 AAAAACTTGAT-A
1 AAAAACTTGATGA
31049577 AAAGAACTTGATGA
1 AAA-AACTTGATGA
*
31049591 AAAACACTTGAAGA
1 AAAA-ACTTGATGA
31049605 AA
1 AA
31049607 GAAAACACTT
Statistics
Matches: 86, Mismatches: 17, Indels: 27
0.66 0.13 0.21
Matches are distributed among these distances:
10 2 0.02
11 12 0.14
12 21 0.24
13 18 0.21
14 14 0.16
15 19 0.22
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.24
Consensus pattern (13 bp):
AAAAACTTGATGA
Found at i:31057839 original size:14 final size:14
Alignment explanation
Indices: 31057804--31057853 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
31057794 AGAAAGAAAA
31057804 GATTAAAAACTTAATT
1 GATT-AAAACTTAA-T
31057820 GA--AAAACTTAAT
1 GATTAAAACTTAAT
31057832 GATTAAAACTTAAT
1 GATTAAAACTTAAT
31057846 GATTAAAA
1 GATTAAAA
31057854 ACTTGATGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.09
13 9 0.28
14 18 0.56
16 2 0.06
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (14 bp):
GATTAAAACTTAAT
Found at i:31057889 original size:13 final size:12
Alignment explanation
Indices: 31057808--31057953 Score: 66
Period size: 13 Copynumber: 11.5 Consensus size: 12
31057798 AGAAAAGATT
*
31057808 AAAAACTTAATTG
1 AAAAACTTGA-TG
*
31057821 AAAAACTTAATG
1 AAAAACTTGATG
*
31057833 ATTAAAACTTAATGATT
1 A--AAAAC-T--TGATG
31057850 AAAAACTTGATGG
1 AAAAACTTGAT-G
*
31057863 AAAAA-TTTATG
1 AAAAACTTGATG
31057874 AAAAGACTTGATG
1 AAAA-ACTTGATG
* *
31057887 AAAAGCTT-A-A
1 AAAAACTTGATG
31057897 AAATAACTTGATG
1 AAA-AACTTGATG
* * *
31057910 -CAAACTTAATAAA
1 AAAAACTTGAT--G
*
31057923 AAAAACTTGATA
1 AAAAACTTGATG
31057935 AAAGAACTTGATG
1 AAA-AACTTGATG
31057948 AAAAAC
1 AAAAAC
31057954 ACTTGAAGAA
Statistics
Matches: 103, Mismatches: 15, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
10 3 0.03
11 17 0.17
12 24 0.23
13 35 0.34
14 14 0.14
15 6 0.06
17 4 0.04
ACGTcount: A:0.53, C:0.08, G:0.12, T:0.27
Consensus pattern (12 bp):
AAAAACTTGATG
Found at i:31057942 original size:27 final size:27
Alignment explanation
Indices: 31057912--31057967 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
31057902 ACTTGATGCA
31057912 AACTTAATAAAAAAAACTTGATA-AAAG
1 AACTTAATAAAAAAAACTTGA-AGAAAG
* * *
31057939 AACTTGATGAAAAACACTTGAAGAAAG
1 AACTTAATAAAAAAAACTTGAAGAAAG
31057966 AA
1 AA
31057968 AACACTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.20
Consensus pattern (27 bp):
AACTTAATAAAAAAAACTTGAAGAAAG
Found at i:31060390 original size:18 final size:18
Alignment explanation
Indices: 31060367--31060401 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31060357 CTCATGGATC
31060367 TGATAAACAAAATAAACT
1 TGATAAACAAAATAAACT
* *
31060385 TGATAAAGATAATAAAC
1 TGATAAACAAAATAAAC
31060402 ATAAAGAGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (18 bp):
TGATAAACAAAATAAACT
Found at i:31066601 original size:25 final size:26
Alignment explanation
Indices: 31066573--31066631 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
31066563 TTTCTCATCC
**
31066573 CAATTTTA-CCCTAATAATTTTTTGA
1 CAATTTTACCCCTAATAAAATTTTGA
*
31066598 CAATTTTACCCCTGATAAAATTTTGA
1 CAATTTTACCCCTAATAAAATTTTGA
*
31066624 CGATTTTA
1 CAATTTTA
31066632 ATCTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 8 0.28
26 21 0.72
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (26 bp):
CAATTTTACCCCTAATAAAATTTTGA
Found at i:31066806 original size:6 final size:6
Alignment explanation
Indices: 31066795--31066830 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
31066785 TGCAAGTGTC
*
31066795 CATTTT CATTTT CATTTT CATTTT CATTTC CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT
31066831 TTGGAAACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (6 bp):
CATTTT
Found at i:31070899 original size:14 final size:14
Alignment explanation
Indices: 31070880--31070907 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31070870 TTCGTCATCC
31070880 ACTCAGGATTTAAG
1 ACTCAGGATTTAAG
31070894 ACTCAGGATTTAAG
1 ACTCAGGATTTAAG
31070908 TATGCCACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
ACTCAGGATTTAAG
Found at i:31075449 original size:15 final size:15
Alignment explanation
Indices: 31075429--31075461 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
31075419 ATATATATTT
31075429 TTTATA-AAAAATTAA
1 TTTATATAAAAA-TAA
31075444 TTTATATAAAAATAA
1 TTTATATAAAAATAA
31075459 TTT
1 TTT
31075462 GATCTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTATATAAAAATAA
Found at i:31076390 original size:14 final size:15
Alignment explanation
Indices: 31076368--31076444 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
31076358 CAATCAAACA
31076368 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
31076382 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
31076397 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
31076417 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
31076431 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
31076445 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:31076409 original size:20 final size:20
Alignment explanation
Indices: 31076384--31076423 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31076374 AATATTTTCC
*
31076384 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
31076404 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
31076424 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:31076429 original size:34 final size:35
Alignment explanation
Indices: 31076372--31076438 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
31076362 CAAACACCAG
*
31076372 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
31076407 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
31076439 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:31077982 original size:19 final size:18
Alignment explanation
Indices: 31077942--31077989 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
31077932 TTAGAGTTTT
* * *
31077942 TTTTTGTATTTTTATGAT
1 TTTTTATATTTTTAGGAA
31077960 TTTTTATATTTTTAAGGAA
1 TTTTTATATTTTT-AGGAA
31077979 TTTTTAT-TTTT
1 TTTTTATATTTT
31077990 AAAGTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (18 bp):
TTTTTATATTTTTAGGAA
Found at i:31079155 original size:13 final size:14
Alignment explanation
Indices: 31079137--31079165 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
31079127 TTAATTTGTC
31079137 TAAATTTAT-TTTT
1 TAAATTTATATTTT
31079150 TAAATTTATATTTT
1 TAAATTTATATTTT
31079164 TA
1 TA
31079166 TCTAAATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TAAATTTATATTTT
Done.