Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 130 of 204
Found at i:39809583 original size:17 final size:17
Alignment explanation
Indices: 39809545--39809588 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
39809535 GGTCACCTTA
39809545 AAAAAATATTAATTTGT
1 AAAAAATATTAATTTGT
39809562 -AAAAATATATAATTT-T
1 AAAAAATAT-TAATTTGT
39809578 AAAAAAGTATT
1 AAAAAA-TATT
39809589 TTGTTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 9 0.38
17 12 0.50
18 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (17 bp):
AAAAAATATTAATTTGT
Found at i:39810327 original size:10 final size:10
Alignment explanation
Indices: 39810293--39810365 Score: 51
Period size: 10 Copynumber: 7.2 Consensus size: 10
39810283 TTTCTAAAAG
39810293 TTTTTTATGAA
1 TTTTTT-TGAA
*
39810304 ATTTTTTGAA
1 TTTTTTTGAA
39810314 TTTTTTTG-A
1 TTTTTTTGAA
* **
39810323 GTTTTTAAATA
1 TTTTTTTGA-A
*
39810334 TTTTTATTTAA
1 TTTTT-TTGAA
39810345 -TTTTTTGAA
1 TTTTTTTGAA
*
39810354 TTTTTCTGAA
1 TTTTTTTGAA
39810364 TT
1 TT
39810366 ATATGTGGAC
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
9 10 0.21
10 25 0.52
11 11 0.23
12 2 0.04
ACGTcount: A:0.25, C:0.01, G:0.08, T:0.66
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:39812933 original size:54 final size:54
Alignment explanation
Indices: 39812848--39813097 Score: 202
Period size: 54 Copynumber: 4.6 Consensus size: 54
39812838 CATAACAGTC
** * *
39812848 AATTTTAGCC-ATT-GGGGATATTTCAAAAATTTTACACATCGAGGGTATTCCGAT
1 AATTTTA-CCTATTAGGGG-TATTTCAGTAATTTTACCCATCGAGGGTATTTCGAT
* * * * * *
39812902 AATTTTACCCATTAGGGGTATTTCGGTAATTTTACCCATCAAGGGTCTTTTGGT
1 AATTTTACCTATTAGGGGTATTTCAGTAATTTTACCCATCGAGGGTATTTCGAT
** ** ** * * *
39812956 AATTTTACCTATCGGGGGTATTTTGGTAATTTTACTTATTGTGGGTATTTTGAT
1 AATTTTACCTATTAGGGGTATTTCAGTAATTTTACCCATCGAGGGTATTTCGAT
* * * *
39813010 AATTTTACCTATCCA-GGGTATTTCAGTAATTCTACCCAT-TAGGGGTATTTCGGT
1 AATTTTACCTAT-TAGGGGTATTTCAGTAATTTTACCCATCGA-GGGTATTTCGAT
* * *
39813064 AACTTTACCTATTAAGAGTATTTCAGTAATTTTA
1 AATTTTACCTATTAGGGGTATTTCAGTAATTTTA
39813098 ACGTCCTTTT
Statistics
Matches: 157, Mismatches: 34, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
53 3 0.02
54 149 0.95
55 5 0.03
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (54 bp):
AATTTTACCTATTAGGGGTATTTCAGTAATTTTACCCATCGAGGGTATTTCGAT
Found at i:39812988 original size:81 final size:80
Alignment explanation
Indices: 39812866--39813097 Score: 223
Period size: 81 Copynumber: 2.9 Consensus size: 80
39812856 CCATTGGGGA
** * * * *
39812866 TATTTCAAAAATTTTACACATCGAGGGTATTCCGATAATTTTACCCATTAGGGGTATTTCGGTAA
1 TATTTCAGTAATTTTAC-CATCGGGGGTATTTCGGTAATTTTACCTATTAGGGGTATTTCGGTAA
39812931 TTTTACCCATCAAGGG
65 TTTTACCCATCAAGGG
* ** * * * *
39812947 TCTTTTGGTAATTTTACCTATCGGGGGTATTTTGGTAATTTTACTTATT-GTGGGTATTTTGATA
1 TATTTCAGTAATTTTACC-ATCGGGGGTATTTCGGTAATTTTACCTATTAG-GGGTATTTCGGTA
* *
39813011 ATTTTACCTATCCAGGG
64 ATTTTACCCATCAAGGG
* ** * * * *
39813028 TATTTCAGTAATTCTACCCATTAGGGGTATTTCGGTAACTTTACCTATTAAGAGTATTTCAGTAA
1 TATTTCAGTAATTTTA-CCATCGGGGGTATTTCGGTAATTTTACCTATTAGGGGTATTTCGGTAA
39813093 TTTTA
65 TTTTA
39813098 ACGTCCTTTT
Statistics
Matches: 118, Mismatches: 29, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
80 2 0.02
81 114 0.97
82 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (80 bp):
TATTTCAGTAATTTTACCATCGGGGGTATTTCGGTAATTTTACCTATTAGGGGTATTTCGGTAAT
TTTACCCATCAAGGG
Found at i:39813077 original size:27 final size:27
Alignment explanation
Indices: 39812890--39813097 Score: 186
Period size: 27 Copynumber: 7.7 Consensus size: 27
39812880 TACACATCGA
* * *
39812890 GGGTATTCCGATAATTTTACCCATTAG
1 GGGTATTTCGGTAATTTTACCTATTAG
* * *
39812917 GGGTATTTCGGTAATTTTACCCATCAA
1 GGGTATTTCGGTAATTTTACCTATTAG
* * **
39812944 GGGTCTTTTGGTAATTTTACCTATCGG
1 GGGTATTTCGGTAATTTTACCTATTAG
* *
39812971 GGGTATTTTGGTAATTTTACTTATT-G
1 GGGTATTTCGGTAATTTTACCTATTAG
* * *
39812997 TGGGTATTTTGATAATTTTACCTATCCA-
1 -GGGTATTTCGGTAATTTTACCTAT-TAG
* * *
39813025 GGGTATTTCAGTAATTCTACCCATTAG
1 GGGTATTTCGGTAATTTTACCTATTAG
* *
39813052 GGGTATTTCGGTAACTTTACCTATTAA
1 GGGTATTTCGGTAATTTTACCTATTAG
* *
39813079 GAGTATTTCAGTAATTTTA
1 GGGTATTTCGGTAATTTTA
39813098 ACGTCCTTTT
Statistics
Matches: 148, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
26 2 0.01
27 146 0.99
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACCTATTAG
Found at i:39813348 original size:8 final size:7
Alignment explanation
Indices: 39813320--39813345 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39813310 AAAATATTTT
39813320 AAAAATA
1 AAAAATA
39813327 AAAAATA
1 AAAAATA
39813334 AAAAATA
1 AAAAATA
39813341 AAAAA
1 AAAAA
39813346 ATATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:39818176 original size:27 final size:27
Alignment explanation
Indices: 39818138--39818385 Score: 128
Period size: 27 Copynumber: 9.3 Consensus size: 27
39818128 CATAGTAGTC
*
39818138 AATTTTACCCATCGGAGGTATTTCAGT
1 AATTTTAACCATCGGAGGTATTTCAGT
*
39818165 AATTTTAACCATTAGG-GGTATTTC-GAT
1 AATTTTAACCA-TCGGAGGTATTTCAG-T
*
39818192 AATTTTACCCATCGG-GGTATTTCTA-T
1 AATTTTAACCATCGGAGGTATTTC-AGT
*
39818218 AATTTT-ACCTAT--GAGAGAATTTC-GAT
1 AATTTTAACC-ATCGGAG-GTATTTCAG-T
* * *
39818244 AATTTTAATCAT-TGAGGGTATTACAGT
1 AATTTTAACCATCGGA-GGTATTTCAGT
* *
39818271 AATTTT-ACTCATC-AACGATATTTCAGT
1 AATTTTAAC-CATCGGA-GGTATTTCAGT
* * **
39818298 AATTTTACCCATCGGGGGTATTTTGGT
1 AATTTTAACCATCGGAGGTATTTCAGT
*
39818325 AATTTTACCCATC-GAGGGTATTTC-GCT
1 AATTTTAACCATCGGA-GGTATTTCAG-T
* * *
39818352 AAATTTATCCATCGG-GAGTATTTCGGT
1 AATTTTAACCATCGGAG-GTATTTCAGT
*
39818379 AAATTTA
1 AATTTTA
39818386 CCTATTAGGA
Statistics
Matches: 175, Mismatches: 24, Indels: 44
0.72 0.10 0.18
Matches are distributed among these distances:
24 1 0.01
25 3 0.02
26 40 0.23
27 123 0.70
28 8 0.05
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (27 bp):
AATTTTAACCATCGGAGGTATTTCAGT
Found at i:39818317 original size:54 final size:53
Alignment explanation
Indices: 39818138--39818387 Score: 213
Period size: 54 Copynumber: 4.7 Consensus size: 53
39818128 CATAGTAGTC
* * * *
39818138 AATTTTACCCATCGGAGGTATTTCAGTAATTTTAACCATTAGGGGTATTTCGAT
1 AATTTTACCCATCGGGGGTATTTCAGTAATTTT-ACCATCAAGGATATTTCGAT
*
39818192 AATTTTACCCATC-GGGGTATTTCTA-TAATTTTACCTAT-GAGAGA-ATTTCGAT
1 AATTTTACCCATCGGGGGTATTTC-AGTAATTTTACC-ATCAAG-GATATTTCGAT
** * * * *
39818244 AATTTTAATCATTGAGGGTATTACAGTAATTTTACTCATCAACGATATTTC-AGT
1 AATTTTACCCATCGGGGGTATTTCAGTAATTTTAC-CATCAAGGATATTTCGA-T
** * * *
39818298 AATTTTACCCATCGGGGGTATTTTGGTAATTTTACCCATCGAGGGTATTTCGCT
1 AATTTTACCCATCGGGGGTATTTCAGTAATTTTA-CCATCAAGGATATTTCGAT
* * * * *
39818352 AAATTTATCCATCGGGAGTATTTCGGTAAATTTACC
1 AATTTTACCCATCGGGGGTATTTCAGTAATTTTACC
39818388 TATTAGGAGT
Statistics
Matches: 158, Mismatches: 27, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
52 23 0.15
53 43 0.27
54 91 0.58
55 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (53 bp):
AATTTTACCCATCGGGGGTATTTCAGTAATTTTACCATCAAGGATATTTCGAT
Found at i:39818396 original size:27 final size:26
Alignment explanation
Indices: 39818141--39818417 Score: 98
Period size: 27 Copynumber: 10.3 Consensus size: 26
39818131 AGTAGTCAAT
* *
39818141 TTTACCCATC-GGAGGTATTTCAGTAAT
1 TTTA-CCATCAGGA-GTATTTCGGTAAA
* * * *
39818168 TTTAACCATTAGGGGTATTTCGATAAT
1 TTT-ACCATCAGGAGTATTTCGGTAAA
* ** *
39818195 TTTACCCATC-GGGGTATTTCTATAAT
1 TTTA-CCATCAGGAGTATTTCGGTAAA
* * * *
39818221 TTTACCTATGA-GAGAATTTCGATAAT
1 TTTACC-ATCAGGAGTATTTCGGTAAA
* * * * *
39818247 TTTAATCATTGAGG-GTATTACAGTAAT
1 TTT-ACCA-TCAGGAGTATTTCGGTAAA
* * *
39818274 TTTACTCATCAACGA-TATTTCAGTAAT
1 TTTAC-CATC-AGGAGTATTTCGGTAAA
* * * *
39818301 TTTACCCATCGGGGGTATTTTGGTAAT
1 TTTA-CCATCAGGAGTATTTCGGTAAA
*
39818328 TTTACCCATCGAGG-GTATTTCGCTAAA
1 TTTA-CCATC-AGGAGTATTTCGGTAAA
*
39818355 TTTATCCATCGGGAGTATTTCGGTAAA
1 TTTA-CCATCAGGAGTATTTCGGTAAA
* * *
39818382 TTTACCTATTAGGAGTGTTTCGGTAAT
1 TTTACC-ATCAGGAGTATTTCGGTAAA
*
39818409 TTTAACATC
1 TTTACCATC
39818418 CTTTCGGAGG
Statistics
Matches: 197, Mismatches: 37, Indels: 33
0.74 0.14 0.12
Matches are distributed among these distances:
25 2 0.01
26 47 0.24
27 141 0.72
28 7 0.04
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (26 bp):
TTTACCATCAGGAGTATTTCGGTAAA
Found at i:39821678 original size:17 final size:16
Alignment explanation
Indices: 39821656--39821708 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
39821646 GACAATAATC
39821656 AAAATAAAGAAGAAAGA
1 AAAATAAAGAA-AAAGA
*
39821673 AAAATAATCGAAAAAGA
1 AAAATAA-AGAAAAAGA
*
39821690 AAAAAAAAGTAAAGAAGA
1 AAAATAAAG-AAA-AAGA
39821708 A
1 A
39821709 GAAGAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 1 0.03
17 21 0.70
18 8 0.27
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.08
Consensus pattern (16 bp):
AAAATAAAGAAAAAGA
Found at i:39821710 original size:21 final size:21
Alignment explanation
Indices: 39821658--39821711 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
39821648 CAATAATCAA
*
39821658 AATA-AAGAAGAAAGAAAAAT
1 AATAGAAGAAGAAAAAAAAAT
* *
39821678 AATCGAAAAAGAAAAAAAAAGT
1 AATAGAAGAAGAAAAAAAAA-T
39821700 AA-AGAAGAAGAA
1 AATAGAAGAAGAA
39821712 GAATTAACGT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 3 0.11
21 21 0.78
22 3 0.11
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (21 bp):
AATAGAAGAAGAAAAAAAAAT
Found at i:39828106 original size:11 final size:11
Alignment explanation
Indices: 39828092--39828132 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
39828082 TGTTTTCTCC
39828092 CTATTTTGCTA
1 CTATTTTGCTA
*
39828103 CTATTTTACTA
1 CTATTTTGCTA
* *
39828114 TTATGTTGCTA
1 CTATTTTGCTA
39828125 CTATTTTG
1 CTATTTTG
39828133 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:39828205 original size:30 final size:30
Alignment explanation
Indices: 39828169--39828231 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
39828159 ACTTATTTTA
39828169 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
39828199 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
39828229 TTG
1 TTG
39828232 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:39828777 original size:18 final size:17
Alignment explanation
Indices: 39828728--39828777 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
39828718 TCTTAAAAAT
39828728 AAATTA-AAATTATTAA
1 AAATTATAAATTATTAA
39828744 AAA-TATAAAATGTATTATA
1 AAATTAT-AAAT-TATTA-A
39828763 AAATTATAAATTATT
1 AAATTATAAATTATT
39828778 CTTATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.07
16 3 0.10
17 4 0.14
18 9 0.31
19 8 0.28
20 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATTATAAATTATTAA
Found at i:39828847 original size:21 final size:22
Alignment explanation
Indices: 39828806--39828850 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
39828796 AATTATCTTA
*
39828806 ATATTTATATTAATATTAAAAAT
1 ATATTTATATT-ATATAAAAAAT
39828829 ATATTTATATT-TATAAAAAAT
1 ATATTTATATTATATAAAAAAT
39828850 A
1 A
39828851 AACCCCCACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
23 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTTATATTATATAAAAAAT
Found at i:39829501 original size:31 final size:31
Alignment explanation
Indices: 39829465--39829533 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
39829455 TAACATCCTG
*
39829465 GTGACTTAAATAAAAAGTTTT-AAATAGTTT-A
1 GTGACTTAAACAAAAA-TTTTCAAATA-TTTGA
*
39829496 GTGACTTAAACGAAAATTTTCAAATATTTGA
1 GTGACTTAAACAAAAATTTTCAAATATTTGA
39829527 GTGACTT
1 GTGACTT
39829534 TTTTTATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 7 0.21
31 27 0.79
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (31 bp):
GTGACTTAAACAAAAATTTTCAAATATTTGA
Found at i:39833681 original size:24 final size:24
Alignment explanation
Indices: 39833649--39833705 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
39833639 AAAAAAAAAA
39833649 AAACATTATCTGTTTTGCTCAAAT
1 AAACATTATCTGTTTTGCTCAAAT
39833673 AAACATTATCTGTTTTGCTCAAAT
1 AAACATTATCTGTTTTGCTCAAAT
39833697 AAACATTAT
1 AAACATTAT
39833706 TTTCTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (24 bp):
AAACATTATCTGTTTTGCTCAAAT
Found at i:39849497 original size:36 final size:36
Alignment explanation
Indices: 39849450--39849542 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 36
39849440 AAGAATCTAT
* * * *
39849450 TGATATACTGAATAAATCTCATGGAATGATATCCAC
1 TGATATACTGAATAAAGCTCATCGAACGAAATCCAC
* *
39849486 TGATATACTGAA-GAAGCTCAATCGAACGAAATCTAC
1 TGATATACTGAATAAAGCTC-ATCGAACGAAATCCAC
*
39849522 TGATATACTGAGTAAAGCTCA
1 TGATATACTGAATAAAGCTCA
39849543 AACGAGCATT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
35 5 0.11
36 36 0.77
37 6 0.13
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (36 bp):
TGATATACTGAATAAAGCTCATCGAACGAAATCCAC
Found at i:39849561 original size:37 final size:36
Alignment explanation
Indices: 39849477--39849571 Score: 104
Period size: 37 Copynumber: 2.6 Consensus size: 36
39849467 CTCATGGAAT
*
39849477 GATATCCACTGATATACTGAAGAAGCTCAATCGAAC
1 GATATCCACTGATATACTGAAGAAGCTCAAACGAAC
* * *
39849513 GAAATCTACTGATATACTG-AGTAAAGCTCAAACGAGC
1 GATATCCACTGATATACTGAAG--AAGCTCAAACGAAC
39849550 -ATTATCCACTGAATATACTGAA
1 GA-TATCCACTG-ATATACTGAA
39849572 CTACTGTACT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
35 2 0.04
36 18 0.38
37 19 0.40
38 8 0.17
39 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (36 bp):
GATATCCACTGATATACTGAAGAAGCTCAAACGAAC
Found at i:39854023 original size:27 final size:27
Alignment explanation
Indices: 39853975--39854036 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
39853965 TCTTGGCATT
* * * *
39853975 AGTAAATACGAGATAGTCCACCGAGAC
1 AGTAAACACAAGAGAGTCCACCAAGAC
*
39854002 AGTAAACACAAGAGAGTTCACCAAGAC
1 AGTAAACACAAGAGAGTCCACCAAGAC
*
39854029 AATAAACA
1 AGTAAACA
39854037 TGTGGTTACC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (27 bp):
AGTAAACACAAGAGAGTCCACCAAGAC
Found at i:39856955 original size:27 final size:27
Alignment explanation
Indices: 39856913--39856965 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
39856903 TCAATATATG
*
39856913 ACCGAAATACCCCCATAGGGTAAAATA
1 ACCGAAATACCACCATAGGGTAAAATA
39856940 ACCGAAATACCACCATAGGGTAAAAT
1 ACCGAAATACCACCATAGGGTAAAAT
39856966 GACTATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15
Consensus pattern (27 bp):
ACCGAAATACCACCATAGGGTAAAATA
Found at i:39857161 original size:26 final size:26
Alignment explanation
Indices: 39857132--39857212 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 26
39857122 TGGAGGAAGC
* *
39857132 ATACTGTTACTAGCAATTTTGTTGCG
1 ATACTGTTACTAGCAACTTTGCTGCG
* *
39857158 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTGTTACTAGCAACTTTGCTGCG
* * * *
39857184 ATACTATTATTGGCAGCTTTGCTGCG
1 ATACTGTTACTAGCAACTTTGCTGCG
39857210 ATA
1 ATA
39857213 TTGGTGTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (26 bp):
ATACTGTTACTAGCAACTTTGCTGCG
Found at i:39857354 original size:27 final size:28
Alignment explanation
Indices: 39857296--39857356 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
39857286 TGTATTGGGC
* *
39857296 TAAGGCCTACACTGTTACTATATCGGGC
1 TAAGGCCCACACTGTTACTATATCGGGA
*
39857324 TAAGGCCCACACTG-TACTAT-TACTGGA
1 TAAGGCCCACACTGTTACTATAT-CGGGA
39857351 TAAGGC
1 TAAGGC
39857357 TCAAGCCCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 15 0.52
28 13 0.45
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (28 bp):
TAAGGCCCACACTGTTACTATATCGGGA
Found at i:39881414 original size:17 final size:17
Alignment explanation
Indices: 39881394--39881446 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
39881384 CTGTGGTGTT
*
39881394 AGCCAAACCCTTATGCG
1 AGCCATACCCTTATGCG
39881411 AGCC-TA-CCTTCATGCG
1 AGCCATACCCTT-ATGCG
* *
39881427 AGCCATACCCATAGGCG
1 AGCCATACCCTTATGCG
39881444 AGC
1 AGC
39881447 TACCCGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.13
16 10 0.33
17 13 0.43
18 3 0.10
ACGTcount: A:0.26, C:0.36, G:0.21, T:0.17
Consensus pattern (17 bp):
AGCCATACCCTTATGCG
Found at i:39881427 original size:16 final size:16
Alignment explanation
Indices: 39881402--39881435 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
39881392 TTAGCCAAAC
39881402 CCTTATGCGAGCC-TA
1 CCTTATGCGAGCCATA
39881417 CCTTCATGCGAGCCATA
1 CCTT-ATGCGAGCCATA
39881434 CC
1 CC
39881436 CATAGGCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 9 0.53
17 4 0.24
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.24
Consensus pattern (16 bp):
CCTTATGCGAGCCATA
Found at i:39881527 original size:17 final size:17
Alignment explanation
Indices: 39881505--39881537 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39881495 ATGTTGTGTG
39881505 CAAACCTTACCTATGTA
1 CAAACCTTACCTATGTA
*
39881522 CAAACCTTACTTATGT
1 CAAACCTTACCTATGT
39881538 GCGAACAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (17 bp):
CAAACCTTACCTATGTA
Found at i:39881645 original size:18 final size:18
Alignment explanation
Indices: 39881624--39881666 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
39881614 TGAACTGTGT
* *
39881624 TAATTTGGTGATTTGTAA
1 TAATTTGGCGAATTGTAA
* *
39881642 TAATATGGCGAATTGTAT
1 TAATTTGGCGAATTGTAA
39881660 TAATTTG
1 TAATTTG
39881667 CAAAACTACG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (18 bp):
TAATTTGGCGAATTGTAA
Found at i:39882343 original size:17 final size:17
Alignment explanation
Indices: 39882323--39882385 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
39882313 ATGAGTTATG
*
39882323 ATGTGGTATGAAATATT
1 ATGTGGTATGAAATGTT
* *
39882340 ATGTTGTATGAACTGTT
1 ATGTGGTATGAAATGTT
*
39882357 ATGTGTTATGAAATGTT
1 ATGTGGTATGAAATGTT
*
39882374 ATGTAGTATGAA
1 ATGTGGTATGAA
39882386 CAGCTATTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.43
Consensus pattern (17 bp):
ATGTGGTATGAAATGTT
Found at i:39882401 original size:34 final size:34
Alignment explanation
Indices: 39882323--39882409 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 34
39882313 ATGAGTTATG
* * *
39882323 ATGTGGTATGAAATATTATGTTGTATGAACTGTT
1 ATGTGGTATGAAATATTATGTAGTATGAACAGCT
* *
39882357 ATGTGTTATGAAATGTTATGTAGTATGAACAGCT
1 ATGTGGTATGAAATATTATGTAGTATGAACAGCT
* *
39882391 ATTTGGTATGAACTATTAT
1 ATGTGGTATGAAATATTAT
39882410 CTCATATGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.43
Consensus pattern (34 bp):
ATGTGGTATGAAATATTATGTAGTATGAACAGCT
Found at i:39882480 original size:18 final size:17
Alignment explanation
Indices: 39882441--39882503 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
39882431 TGCGAATTTA
39882441 TATTTTATGT-AATCTGT
1 TATTTTATGTGAAT-TGT
39882458 CTATTTTATGTGAATTGCT
1 -TATTTTATGTGAATTG-T
* * *
39882477 TATTATATGCGTATTGTT
1 TATTTTATGTGAATTG-T
39882495 TATTTTATG
1 TATTTTATG
39882504 AGTTCTGTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
18 34 0.89
19 4 0.11
ACGTcount: A:0.22, C:0.06, G:0.14, T:0.57
Consensus pattern (17 bp):
TATTTTATGTGAATTGT
Found at i:39888611 original size:16 final size:17
Alignment explanation
Indices: 39888590--39888636 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
39888580 AATCCTTAAA
39888590 CCCTAACCCCTAAATC-
1 CCCTAACCCCTAAATCT
*
39888606 CCCTAACCCATAAATCT
1 CCCTAACCCCTAAATCT
*
39888623 CCCTAACCTCTAAA
1 CCCTAACCCCTAAA
39888637 GCATAACACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (17 bp):
CCCTAACCCCTAAATCT
Found at i:39889147 original size:113 final size:113
Alignment explanation
Indices: 39888906--39889237 Score: 524
Period size: 113 Copynumber: 2.9 Consensus size: 113
39888896 ATCCCTGAGT
*
39888906 ATTAGCGACGCTTT-TGTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGAG
1 ATTAGCG-CGCTTTCT-TAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGG
*
39888970 TTTAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCTGCTAAAGCCCTGAGC
64 TTTAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCTGCTAAAGCCCTAAGC
* * * *
39889020 ATTAGCTGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAATCTCAGAAAACGACGTCGTTGGGT
1 ATTAGC-GCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGT
* * *
39889085 TTAG-TTTTTTTGCGGCACTTTCCCAAAAACGCCGCTAAAGCTCTAAGC
65 TTAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCTGCTAAAGCCCTAAGC
*
39889133 ATTAGCAGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGC
1 ATTAGC-GCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGT
39889198 TTAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCTGCTAAA
65 TTAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCTGCTAAA
39889238 TCCACAAAAG
Statistics
Matches: 198, Mismatches: 17, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
113 103 0.52
114 93 0.47
115 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (113 bp):
ATTAGCGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGTT
TAGTTTTTTTTGCGGCGCTTTCCCAAAAACGCTGCTAAAGCCCTAAGC
Found at i:39889228 original size:73 final size:72
Alignment explanation
Indices: 39889140--39889308 Score: 266
Period size: 73 Copynumber: 2.3 Consensus size: 72
39889130 AGCATTAGCA
** * * * *
39889140 GCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGCTTAGTTT
1 GCGCTTTCCCAAAAACGCCGCTAAATCCACAAAAGCTCAAAAAACGGCGCCGTTGAGCTTAG-TT
39889205 TTTTTGCG
65 TTTTTGCG
*
39889213 GCGCTTTCCCAAAAACGCTGCTAAATCCACAAAAGCTCAAAAAACGGCGCCGTTGAGCTTAGTTT
1 GCGCTTTCCCAAAAACGCCGCTAAATCCACAAAAGCTCAAAAAACGGCGCCGTTGAGCTTAGTTT
39889278 TTTTGCG
66 TTTTGCG
39889285 GCGCTTTCCCAAAAACGCCGCTAA
1 GCGCTTTCCCAAAAACGCCGCTAA
39889309 TGCCCTGAGC
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 33 0.38
73 55 0.62
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (72 bp):
GCGCTTTCCCAAAAACGCCGCTAAATCCACAAAAGCTCAAAAAACGGCGCCGTTGAGCTTAGTTT
TTTTGCG
Found at i:39889277 original size:186 final size:186
Alignment explanation
Indices: 39889027--39889430 Score: 560
Period size: 186 Copynumber: 2.2 Consensus size: 186
39889017 AGCATTAGCT
** * * * * * *
39889027 GCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAATCTCAGAAAACGACGTCGTTGGGTTTAGTTT
1 GCGCTTTCCCAAAAACGCCGCTAAATCCCTAAAAGCTCAAAAAACGACGCCGTTGAGCTTAGTTT
* * *
39889092 TTTTGCGGCACTTTCCCAAAAACGCCGCTAAAGCTCTAAGCATTAGCAGCGCTTTCTTAAAAACG
66 TTTTGCGGCACTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCAGCGCTTCCTAAAAAACG
* * *
39889157 CCGCTAAATCCCCGAAAGCTCAGAAAACGGCGCCGTTGGGCTTAGTTTTTTTTGCG
131 CCACTAAATCCCCGAAAGCTCAGAAAACGACGCCGTTGGGCTTAGGTTTTTTTGCG
* *
39889213 GCGCTTTCCCAAAAACGCTGCTAAATCCAC-AAAAGCTCAAAAAACGGCGCCGTTGAGCTTAGTT
1 GCGCTTTCCCAAAAACGCCGCTAAATCC-CTAAAAGCTCAAAAAACGACGCCGTTGAGCTTAGTT
* * * *
39889277 TTTTTGCGGCGCTTTCCCAAAAACGCCGCTAATGCCCTGAGCATTAGCGGCGCTTCCTAAAAAAC
65 TTTTTGCGGCACTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCAGCGCTTCCTAAAAAAC
* * *
39889342 GCCACTAAATCCCTGAAAGCTCAGAAAACGACGTCGTTTGGCTTAGGTTTTTTTGCG
130 GCCACTAAATCCCCGAAAGCTCAGAAAACGACGCCGTTGGGCTTAGGTTTTTTTGCG
*
39889399 GCGC-TTCACCAAAAACGCCGTTAAATCCCTAA
1 GCGCTTTC-CCAAAAACGCCGCTAAATCCCTAA
39889431 GCATTAGCGG
Statistics
Matches: 190, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
185 4 0.02
186 185 0.97
187 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (186 bp):
GCGCTTTCCCAAAAACGCCGCTAAATCCCTAAAAGCTCAAAAAACGACGCCGTTGAGCTTAGTTT
TTTTGCGGCACTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCAGCGCTTCCTAAAAAACG
CCACTAAATCCCCGAAAGCTCAGAAAACGACGCCGTTGGGCTTAGGTTTTTTTGCG
Found at i:39889342 original size:113 final size:113
Alignment explanation
Indices: 39889210--39889537 Score: 389
Period size: 114 Copynumber: 2.9 Consensus size: 113
39889200 AGTTTTTTTT
* * * * *
39889210 GCGGCGCTTTCC-CAAAAACGCTGCTAAATCCACAAAAGCTCAAAAAACGGCGCCG-TTGAGCTT
1 GCGGCGC-TTCCTAAAAAACGCCGCTAAATCCACGAAAGCTCAGAAAACGGCGTCGTTTG-GCTT
*
39889273 A-GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAATGCCCTGAGCATTA
64 AGGTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAT-CCCTAAGCATTA
* *
39889323 GCGGCGCTTCCTAAAAAACGCCACTAAATCC-CTGAAAGCTCAGAAAACGACGTCGTTTGGCTTA
1 GCGGCGCTTCCTAAAAAACGCCGCTAAATCCAC-GAAAGCTCAGAAAACGGCGTCGTTTGGCTTA
*
39889387 GGTTTTTTTGCGGCGC-TTCACCAAAAACGCCGTTAAATCCCTAAGCATTA
65 GGTTTTTTTGCGGCGCTTTC-CCAAAAACGCCGCT-AATCCCTAAGCATTA
* ** * *
39889437 GCGGCGTTTTTTAGAAAGCGCCGCTAAAT-CATCGAAAGCTCAGAAAACGGCGTCGTTTGGCTTA
1 GCGGCGCTTCCTAAAAAACGCCGCTAAATCCA-CGAAAGCTCAGAAAACGGCGTCGTTTGGCTTA
** *
39889501 GGTTTTTTTTGCGGCGCTTTCTTAAAAGCGCCGCTAA
65 GG-TTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAA
39889538 ATCTCTGAAA
Statistics
Matches: 185, Mismatches: 20, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
112 5 0.03
113 50 0.27
114 99 0.54
115 28 0.15
116 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (113 bp):
GCGGCGCTTCCTAAAAAACGCCGCTAAATCCACGAAAGCTCAGAAAACGGCGTCGTTTGGCTTAG
GTTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAATCCCTAAGCATTA
Found at i:39889563 original size:74 final size:72
Alignment explanation
Indices: 39889437--39889609 Score: 219
Period size: 74 Copynumber: 2.4 Consensus size: 72
39889427 CTAAGCATTA
* *
39889437 GCGGCG-TTTTTTAGAAAGCGCCGCTAAATCATCGAAAGCTCAGAAAACGGCGTCGTTTGGCTTA
1 GCGGCGCTTTCTTA-AAAGCGCCGCTAAATCATCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
39889501 GGTTTTTTTT
65 GG--TTTTTT
* *
39889511 GCGGCGCTTTCTTAAAAGCGCCGCTAAATC-TCTGAAAGCT-AGGTAAATGGCGTCGTTGGGCTT
1 GCGGCGCTTTCTTAAAAGCGCCGCTAAATCATC-GAAAGCTCA-GAAAACGGCGTCGTTGGGCTT
39889574 AGGTTTTTT
64 AGGTTTTTT
*
39889583 GCGGCGCTTTCTGGAAAA-CGCCGCTAA
1 GCGGCGCTTTCT-TAAAAGCGCCGCTAA
39889610 TTCTTATTTT
Statistics
Matches: 90, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
72 27 0.30
73 7 0.08
74 50 0.56
75 6 0.07
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (72 bp):
GCGGCGCTTTCTTAAAAGCGCCGCTAAATCATCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
GTTTTTT
Found at i:39889695 original size:12 final size:12
Alignment explanation
Indices: 39889678--39889703 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39889668 TTTTTTATCC
39889678 AAACGCCGCTAA
1 AAACGCCGCTAA
39889690 AAACGCCGCTAA
1 AAACGCCGCTAA
39889702 AA
1 AA
39889704 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:39890007 original size:6 final size:6
Alignment explanation
Indices: 39889998--39890068 Score: 97
Period size: 6 Copynumber: 11.8 Consensus size: 6
39889988 CCTTTTTCTT
* * * * *
39889998 TTATTC TTATTC TTATTC TTATTC TTATTC TTATTA TTATTA TTATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
39890046 TTATTA TTATTA TTATTA TTATT
1 TTATTA TTATTA TTATTA TTATT
39890069 TCCAGTCCAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATTA
Found at i:39892193 original size:16 final size:16
Alignment explanation
Indices: 39892172--39892222 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
39892162 GGTTCGCTGC
39892172 AATGGAATAGAGGCGT
1 AATGGAATAGAGGCGT
*
39892188 AATGGAATAGATGCGT
1 AATGGAATAGAGGCGT
*
39892204 AATGGAATAGAGGTGT
1 AATGGAATAGAGGCGT
39892220 AAT
1 AAT
39892223 AGCAATTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.39, C:0.04, G:0.33, T:0.24
Consensus pattern (16 bp):
AATGGAATAGAGGCGT
Found at i:39892253 original size:45 final size:44
Alignment explanation
Indices: 39892202--39892291 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
39892192 GAATAGATGC
*
39892202 GTAATGGAATAGAGGTGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AATTC-ATGTGTTTGGTTGAAT
* * *
39892247 GTAATGGAATAGATGCGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
39892291 G
1 G
39892292 GCATGAAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.03
44 18 0.45
45 21 0.52
ACGTcount: A:0.30, C:0.04, G:0.28, T:0.38
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
Found at i:39892476 original size:18 final size:17
Alignment explanation
Indices: 39892455--39892489 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39892445 TTATTATTAA
*
39892455 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39892473 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39892490 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39892554 original size:22 final size:24
Alignment explanation
Indices: 39892509--39892555 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
39892499 TCAATATTCT
39892509 TATATGAATTTACTAAAATCATAA
1 TATATGAATTTACTAAAATCATAA
39892533 TATATG-ATATTA-TAAAAT-ATAA
1 TATATGAAT-TTACTAAAATCATAA
39892555 T
1 T
39892556 TTGAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 8 0.36
24 9 0.41
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (24 bp):
TATATGAATTTACTAAAATCATAA
Found at i:39892609 original size:59 final size:59
Alignment explanation
Indices: 39892441--39892849 Score: 244
Period size: 59 Copynumber: 6.8 Consensus size: 59
39892431 ATATTTTAAC
* * * * *
39892441 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT-CA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTCAATAAAA-T-ATAAT-TTGAA
* * * * ** * * *
39892502 AT-ATTCTTATATGAATTTACTAAAATCATAATATATGATAT-TATAAAATATAATTTGAA
1 ATAATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TCAATAAAATATAATTTGAA
* * * *
39892561 ATAATTATTATTAAATATATTTTAATTAAAATACATAATTCAATAAAAT-T--CTTAATA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTCAATAAAATATAATTTGA-A
* * * * * *
39892618 ATCAA-TATTCTTATATGA-ATTTACTAAACTCATAATATATGATACTATAAAATATAATTTGAA
1 AT-AATTATTATTAAAT-ATATTT--T-AA-TTAAAATATATGATTCAATAAAATATAATTTGAA
* * * * *
39892681 ATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT-AA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTCAATAAAA-T-ATAAT-TTGAA
* * * * ** * * * *
39892742 AT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
1 ATAATTATTAT-TAAATATATTTTAATTAAAATATATGATTCAATAAAATATAATTTGAA
*
39892801 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTCAATAAAAT
39892850 TTAAAATAAT
Statistics
Matches: 252, Mismatches: 73, Indels: 48
0.68 0.20 0.13
Matches are distributed among these distances:
56 3 0.01
57 16 0.06
58 7 0.03
59 87 0.35
60 34 0.13
61 81 0.32
62 6 0.02
63 15 0.06
64 3 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (59 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATGATTCAATAAAATATAATTTGAA
Found at i:39892717 original size:18 final size:17
Alignment explanation
Indices: 39892695--39892729 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39892685 TAATTATTAA
*
39892695 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39892713 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39892730 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39892741 original size:15 final size:16
Alignment explanation
Indices: 39892721--39892750 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39892711 ATATATAATT
39892721 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
39892736 TAATAAATATTCTTA
1 TAATAAATATTCTTA
39892751 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:39892836 original size:18 final size:17
Alignment explanation
Indices: 39892813--39892849 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
39892803 AATTATTATT
39892813 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
39892829 AAATATATGATTTAATA
1 AAATATATGATTTAATA
39892846 AAAT
1 AAAT
39892850 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:39892859 original size:120 final size:120
Alignment explanation
Indices: 39892441--39892850 Score: 757
Period size: 120 Copynumber: 3.4 Consensus size: 120
39892431 ATATTTTAAC
39892441 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
*
39892506 TCTTATATGAATTTACTAAAATCATAATATATGATATTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* *
39892561 ATAATTATTATTAAATATATTTTAATTAAAATACATAATTCAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
*
39892626 TCTTATATGAATTTACTAAACTCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* *
39892681 ATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
39892746 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
*
39892801 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
39892851 TAAAATAATT
Statistics
Matches: 279, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 279 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:39892864 original size:54 final size:54
Alignment explanation
Indices: 39892548--39892920 Score: 199
Period size: 57 Copynumber: 6.6 Consensus size: 54
39892538 GATATTATAA
* * * *
39892548 AATATAATTTGAAATAATTATTATTAAATATATTTTAATTAAAATACATAATTC
1 AATATAATTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATGATTT
* * * * *
39892602 AATAAAATTCTTAATAATCAA-TATTCTTATATGA-ATTTACTAAACTCATAATATATGATACTA
1 AATATAA-T-TTAA-AAT-AATTATTATTAAAT-ATATTT--T-AA-TTAAAATATATGAT--T-
39892665 T
54 T
* * *
39892666 AAAATATAATTTGAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTT
1 --AATATAATTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATGATTT
* * * * * *
39892722 AATAAAATTCTTAATAATAAATATTCTTATATGA-ATTTACTAAAATCATAATATATGATACTAT
1 AATATAA-T-TTAA-AATAATTATTATTAAAT-ATATTT--T--AATTAAAATATATGAT--T-T
*
39892786 AAAATATAATTTGAAATAATTATTATTAAATATATTTTAATTAAAATATATGATTT
1 --AATATAATTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATGATTT
* * * * * *
39892842 AATAAAATTTAAAATAATTATTACT-AATAAATTTT-GTT-ACAT-GA--ATTT
1 AATATAATTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATGATTT
*
39892890 -GTATAATTTAAAATAATTATTATTAAATATA
1 AATATAATTTAAAATAATTATTATTAAATATA
39892921 ATATAATAAT
Statistics
Matches: 244, Mismatches: 44, Indels: 68
0.69 0.12 0.19
Matches are distributed among these distances:
47 21 0.09
48 9 0.04
50 1 0.00
51 3 0.01
52 2 0.01
53 9 0.04
54 34 0.14
55 2 0.01
56 8 0.03
57 35 0.14
58 4 0.02
59 27 0.11
60 4 0.02
61 25 0.10
62 4 0.02
63 35 0.14
64 7 0.03
65 2 0.01
66 12 0.05
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (54 bp):
AATATAATTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATGATTT
Found at i:39892900 original size:47 final size:45
Alignment explanation
Indices: 39892847--39892995 Score: 139
Period size: 47 Copynumber: 3.3 Consensus size: 45
39892837 GATTTAATAA
*
39892847 AATTTAAAATAATTATTACTAATAAATTTTGTTACATGAATTTGTAT
1 AATTTAAAATAATTATTA-TAATAAATTTTATTA-ATGAATTTGTAT
* * *
39892894 AATTTAAAATAATTATTAT--TAAATATAATATAAT-AA--TATAT
1 AATTTAAAATAATTATTATAATAAATTTTAT-TAATGAATTTGTAT
* * *
39892935 AATTTCATAA-AATTCTTGATAATAAATTTTCTTATATGAATTTGTAT
1 AATTT-AAAATAATTATT-ATAATAAATTTTATTA-ATGAATTTGTAT
39892982 AATTTAAAATAATT
1 AATTTAAAATAATT
39892996 TATATTAAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
41 15 0.19
42 5 0.06
43 4 0.05
44 18 0.22
45 4 0.05
46 4 0.05
47 31 0.38
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (45 bp):
AATTTAAAATAATTATTATAATAAATTTTATTAATGAATTTGTAT
Found at i:39892964 original size:88 final size:90
Alignment explanation
Indices: 39892857--39893068 Score: 313
Period size: 88 Copynumber: 2.4 Consensus size: 90
39892847 AATTTAAAAT
* * * *
39892857 AATTATTACTAATAAATTTTGTTACATGAATTTGTATAATTTAAAATAA-TTATTATTAAATATA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTTA-TATTAAATATA
39892921 A-T-ATAATAATATATAATTTCATAA
65 ATTAATAATAATATATAATTTCATAA
*
39892945 AATTCTTGATAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTTATATTAAATATAA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTTATATTAAATATAA
*
39893010 TTTAATAATGATATATAATTTCATAA
66 -TTAATAATAATATATAATTTCATAA
* *
39893036 AATTCTTAACAATAAATATTCTTATATGAATTT
1 AATTCTTAATAATAAATTTTCTTATATGAATTT
39893069 ACTAAAAGCA
Statistics
Matches: 111, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
88 56 0.50
89 3 0.03
90 1 0.01
91 51 0.46
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (90 bp):
AATTCTTAATAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTTATATTAAATATAA
TTAATAATAATATATAATTTCATAA
Found at i:39893676 original size:22 final size:22
Alignment explanation
Indices: 39893609--39893676 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
39893599 ATAACAACGT
*
39893609 TAAATGTCCAATTAAGAAACAC
1 TAAATGTCCAATTAAGACACAC
* * *
39893631 T-AATG-CTAATCATAA-CCACGC
1 TAAATGTCCAAT--TAAGACACAC
*
39893652 TAAATGTCCAATTAAGGCACAC
1 TAAATGTCCAATTAAGACACAC
39893674 TAA
1 TAA
39893677 TGGTAGTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
20 4 0.12
21 11 0.32
22 15 0.44
23 4 0.12
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (22 bp):
TAAATGTCCAATTAAGACACAC
Found at i:39897009 original size:3 final size:3
Alignment explanation
Indices: 39896995--39897121 Score: 175
Period size: 3 Copynumber: 42.3 Consensus size: 3
39896985 TTAATTGATC
* *
39896995 ATT ATT ACT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
39897043 ATT ATT ATT ATT GTT ATT GTT ATT ATT ACT ACT ACTT -CT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
39897088 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
39897122 GTAGTAGTAG
Statistics
Matches: 110, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
2 1 0.01
3 108 0.98
4 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:39897126 original size:3 final size:3
Alignment explanation
Indices: 39897120--39897148 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39897110 TTATTATTAT
39897120 TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
39897149 TTTTATCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:39901370 original size:2 final size:2
Alignment explanation
Indices: 39901363--39901398 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39901353 TATTATTTAC
39901363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39901399 TGGAGGGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39901680 original size:25 final size:25
Alignment explanation
Indices: 39901635--39901685 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
39901625 TAATACAATC
*
39901635 AATAAAAATATTAATATTTTAGTTT
1 AATAAAAATATTAATAATTTAGTTT
* *
39901660 AATAAAGAA-ATTATTAATTTATTTT
1 AATAAA-AATATTAATAATTTAGTTT
39901685 A
1 A
39901686 TCGATGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
AATAAAAATATTAATAATTTAGTTT
Found at i:39905569 original size:218 final size:222
Alignment explanation
Indices: 39905295--39905726 Score: 549
Period size: 218 Copynumber: 2.0 Consensus size: 222
39905285 ATATTATTAC
* ***
39905295 ATTATGTAATGCTATATCACATATTGTAATAATAATACATAATATATTAATTATTATATATCATT
1 ATTATGTAATACTATATCACATACCATAATAATAATACATAATATATTAATTATTATATATCATT
* *
39905360 G-CT-T-ATTATATTGGTTAAAATATGCAT-TAAGTCCCTATACTCTTTGTACATTTGAAAGTTA
66 GTCTATAATTATACTGGTTAAAATATG-ATCTAA-CCCCT-TACTCTTTGTACATTTGAAAGTTA
* * ** *
39905421 G-CT-CTACTATTAT-GTGTAATGTTATATCATGTCAAATAATATGA-AATATATT-AATAATTT
128 GCCTCCCACTA-TATCATGTAATGTTATATCAAATCAAATAATAT-ATAATAAATTAAATAATTT
*
39905481 ATATACATGCATTAATGATTAAACACTATAAT
191 ATATACATACATTAATGATTAAACACTATAAT
* * * *
39905513 ATTATGTAATACTATATCTCATACCATAATAGTAGTACATAATATATTAATTATTATATATTATT
1 ATTATGTAATACTATATCACATACCATAATAATAATACATAATATATTAATTATTATATATCATT
* * *
39905578 GTTTATAATTATACTGTTTGAAATATGATCTAACCCCTTACTCTTTGTACATTTGAAAGTTAGCC
66 GTCTATAATTATACTGGTTAAAATATGATCTAACCCCTTACTCTTTGTACATTTGAAAGTTAG-C
* *
39905643 CTCCCACTATATCATGTAATGTTATATCAAATCATATAATATATAATAAATTAAATAGTTTATAT
130 CTCCCACTATATCATGTAATGTTATATCAAATCAAATAATATATAATAAATTAAATAATTTATAT
*
39905708 ATATACATTAATGATTAAA
195 ACATACATTAATGATTAAA
39905727 TATAATCAGT
Statistics
Matches: 182, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
218 58 0.32
219 26 0.14
220 7 0.04
221 26 0.14
222 37 0.20
223 28 0.15
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (222 bp):
ATTATGTAATACTATATCACATACCATAATAATAATACATAATATATTAATTATTATATATCATT
GTCTATAATTATACTGGTTAAAATATGATCTAACCCCTTACTCTTTGTACATTTGAAAGTTAGCC
TCCCACTATATCATGTAATGTTATATCAAATCAAATAATATATAATAAATTAAATAATTTATATA
CATACATTAATGATTAAACACTATAAT
Found at i:39905837 original size:18 final size:18
Alignment explanation
Indices: 39905814--39905854 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
39905804 TTTGGTTTCA
39905814 ATTTAAAAATTGAAAACC
1 ATTTAAAAATTGAAAACC
39905832 ATTTAAAAATTGAAAACC
1 ATTTAAAAATTGAAAACC
39905850 ATTTA
1 ATTTA
39905855 GGCTAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTTAAAAATTGAAAACC
Found at i:39905991 original size:6 final size:6
Alignment explanation
Indices: 39905934--39905990 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
39905924 AATATATATT
*
39905934 TAAACC CAAACC TAATACC --AACC -AAATCC -AAACC TAAACC TAAACC
1 TAAACC TAAACC TAA-ACC TAAACC TAAA-CC TAAACC TAAACC TAAACC
*
39905980 TAAACT TAAAC
1 TAAACC TAAAC
39905991 TCAATTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.07
5 5 0.11
6 33 0.75
7 3 0.07
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (6 bp):
TAAACC
Found at i:39906492 original size:6 final size:6
Alignment explanation
Indices: 39906436--39906491 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
39906426 TAAAAGTATT
*
39906436 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAAATA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
39906484 AAA-TA AAA
1 AAATTA AAA
39906492 AATATATATT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 5 0.10
6 44 0.90
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAATTA
Found at i:39906492 original size:12 final size:12
Alignment explanation
Indices: 39906381--39906495 Score: 88
Period size: 12 Copynumber: 9.3 Consensus size: 12
39906371 GCCCATTTTT
39906381 AATAAATATTAAA
1 AATAAA-ATTAAA
* **
39906394 AATTATTTTAAA
1 AATAAAATTAAA
*
39906406 AATAAAAATAAA
1 AATAAAATTAAA
**
39906418 AA-ATATTTTAAA
1 AATA-AAATTAAA
*
39906430 AGTATTAAATTAAA
1 A--ATAAAATTAAA
*
39906444 ATTAAAATTAAA
1 AATAAAATTAAA
*
39906456 ATTAAAATTAAA
1 AATAAAATTAAA
*
39906468 ATTAAAATTAAA
1 AATAAAATTAAA
*
39906480 AATAAAATAAAA
1 AATAAAATTAAA
39906492 AATA
1 AATA
39906496 TATATTTATT
Statistics
Matches: 81, Mismatches: 17, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
11 1 0.01
12 68 0.84
13 4 0.05
14 8 0.10
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (12 bp):
AATAAAATTAAA
Found at i:39907949 original size:18 final size:18
Alignment explanation
Indices: 39907923--39907974 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
39907913 ATTTTGAAAC
39907923 TGGTCAAAATTGTGCTTA
1 TGGTCAAAATTGTGCTTA
* * *
39907941 TGGTGAAAATTATGTTTA
1 TGGTCAAAATTGTGCTTA
*
39907959 CGGTCAAAATTG-GCTT
1 TGGTCAAAATTGTGCTT
39907975 GCTGATGGGG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (18 bp):
TGGTCAAAATTGTGCTTA
Found at i:39908153 original size:18 final size:18
Alignment explanation
Indices: 39908130--39908174 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
39908120 TTGATGGCAA
39908130 TATTGGGCCGAATGG-TGG
1 TATTGGGCCGAA-GGATGG
*
39908148 TGTTGGGCCGAAGGATGG
1 TATTGGGCCGAAGGATGG
39908166 TATTGGGCC
1 TATTGGGCC
39908175 AAATAACGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.16, C:0.13, G:0.44, T:0.27
Consensus pattern (18 bp):
TATTGGGCCGAAGGATGG
Found at i:39909976 original size:75 final size:75
Alignment explanation
Indices: 39909877--39910018 Score: 239
Period size: 75 Copynumber: 1.9 Consensus size: 75
39909867 TTTGAGTGGA
* * * *
39909877 TCTTCGGTTCCTCAGAATGGAGTTGATGTTAATCCGACGAGTACTAATTCTCATAGTATTCCCTC
1 TCTTCGGTTCCTCAGAATGAAGTTGATATTAATCCAACGAGTACTAATTCTCATAGCATTCCCTC
39909942 TTTAAATGGG
66 TTTAAATGGG
*
39909952 TCTTCGGTTCCTCAGAATGAAGTTGATATTAGTCCAACGAGTACTAATTCTCATAGCATTCCCTC
1 TCTTCGGTTCCTCAGAATGAAGTTGATATTAATCCAACGAGTACTAATTCTCATAGCATTCCCTC
39910017 TT
66 TT
39910019 ATTTTGATGA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (75 bp):
TCTTCGGTTCCTCAGAATGAAGTTGATATTAATCCAACGAGTACTAATTCTCATAGCATTCCCTC
TTTAAATGGG
Found at i:39911976 original size:33 final size:33
Alignment explanation
Indices: 39911912--39911981 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
39911902 TTTCTTCATT
*
39911912 TTTAAATTAATATATTATTTTATTATCATTAAA
1 TTTAAATTAATATATTATTTTATAATCATTAAA
** * *
39911945 TTTAAATTTTTATA-TATTTTAATAATTATTAAT
1 TTTAAATTAATATATTATTTT-ATAATCATTAAA
39911978 TTTA
1 TTTA
39911982 GACATCTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (33 bp):
TTTAAATTAATATATTATTTTATAATCATTAAA
Found at i:39912053 original size:27 final size:29
Alignment explanation
Indices: 39912009--39912062 Score: 69
Period size: 27 Copynumber: 1.9 Consensus size: 29
39911999 TATAATTACA
*
39912009 GTTTTAAAAATATTTTATATTCA-ATTAAT
1 GTTTTAAAAATATATTAT-TTCACATTAAT
39912038 GTTTT-AAAATA-ATTATTTCACATTA
1 GTTTTAAAAATATATTATTTCACATTA
39912063 TAATTTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 4 0.17
27 8 0.35
28 6 0.26
29 5 0.22
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (29 bp):
GTTTTAAAAATATATTATTTCACATTAAT
Found at i:39913165 original size:18 final size:20
Alignment explanation
Indices: 39913134--39913172 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
39913124 CTCTGAAAAT
39913134 AAAACAATATTCTCAATCAA
1 AAAACAATATTCTCAATCAA
39913154 AAAAC-ATA-TCTCAATCAA
1 AAAACAATATTCTCAATCAA
39913172 A
1 A
39913173 GATGACAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.58
19 3 0.16
20 5 0.26
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAACAATATTCTCAATCAA
Found at i:39914137 original size:10 final size:10
Alignment explanation
Indices: 39914124--39914150 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
39914114 TAGCTGAGTA
39914124 TAAATATGTG
1 TAAATATGTG
39914134 TAAATATGTG
1 TAAATATGTG
39914144 TAAATAT
1 TAAATAT
39914151 TTATACTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (10 bp):
TAAATATGTG
Found at i:39914522 original size:10 final size:11
Alignment explanation
Indices: 39914501--39914529 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
39914491 TAGAATGGCA
39914501 TATTTCTATTT
1 TATTTCTATTT
39914512 TATTT-TATTT
1 TATTTCTATTT
39914522 TATTTCTA
1 TATTTCTA
39914530 AAGGAGACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTCTATTT
Found at i:39915643 original size:9 final size:11
Alignment explanation
Indices: 39915619--39915646 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
39915609 ATTTAGTATT
39915619 TATATAATAAA
1 TATATAATAAA
39915630 TATATAATAAA
1 TATATAATAAA
39915641 TATATA
1 TATATA
39915647 TTTTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TATATAATAAA
Found at i:39915946 original size:30 final size:29
Alignment explanation
Indices: 39915912--39915975 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
39915902 ATTAATAATA
* * *
39915912 ATAAAATTATATTTTCATTCTCTAAAAATG
1 ATAAAATT-TAATTTAACTCTCTAAAAATG
* *
39915942 ATAAAATTTAATTTAACTCTTTAAAAATT
1 ATAAAATTTAATTTAACTCTCTAAAAATG
39915971 ATAAA
1 ATAAA
39915976 TAAACTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (29 bp):
ATAAAATTTAATTTAACTCTCTAAAAATG
Found at i:39917715 original size:540 final size:540
Alignment explanation
Indices: 39916697--39917879 Score: 2190
Period size: 540 Copynumber: 2.2 Consensus size: 540
39916687 TTTTATAGTC
* *
39916697 TATATCTTTATAATTTTTAAAGGATTAAATTGAATTTTTATAATTTTAGGGAAGCCCAAAGTACA
1 TATATCTTTATAATTTTTAAAGGATTAGATCGAATTTTTATAATTTTAGGGAAGCCCAAAGTACA
*
39916762 ATTTTACCTTTTCTAATTTAAAATTTTAAAAAAATTTAAAAGGCCTAAATGACAATTTTTCATTT
66 ATTTTACCTTTACTAATTTAAAATTTTAAAAAAATTTAAAAGGCCTAAATGACAATTTTTCATTT
* *
39916827 TAGGCAAGCCGGGTCCTTTAGCCCCCTAGAATCTCCTCTATCAACAGTTACCCTTAGACCACGTA
131 TAGGCAAGCCAGGTCCTTCAGCCCCCTAGAATCTCCTCTATCAACAGTTACCCTTAGACCACGTA
39916892 ATATAATATATATTTGATACATTATATTCGTTTAAAAAATATTTGTTAATGCACTATAAATTAAT
196 ATATAATATATATTTGATACATTATATTCGTTTAAAAAATATTTGTTAATGCACTATAAATTAAT
39916957 ACCAAATTTATTTTTTATTAATACATGTACAAATCAATTTAATATAATGAGATTAGTAGTATATT
261 ACCAAATTTATTTTTTATTAATACATGTACAAATCAATTTAATATAATGAGATTAGTAGTATATT
39917022 ATATATATGTATATTATATATTATTAAAAAGCATGAGTTGTACAAATATATGTTGAGTGTTTATT
326 ATATATATGTATATTATATATTATTAAAAAGCATGAGTTGTACAAATATATGTTGAGTGTTTATT
39917087 TTTCTGTGTACTTCTTAGAGCGATTCATCGACATATATATATGTTACGGTCCATTGTTGTGATGT
391 TTTCTGTGTACTTCTTAGAGCGATTCATCGACATATATATATGTTACGGTCCATTGTTGTGATGT
39917152 GCTAGGGGTAGGTAGGCTACATGCATGGCAACACGTTATTCTCCCTAGGGGTGGCACGTGTCCTA
456 GCTAGGGGTAGGTAGGCTACATGCATGGCAACACGTTATTCTCCCTAGGGGTGGCACGTGTCCTA
39917217 GCAAAGGGCTCGCCAAACTA
521 GCAAAGGGCTCGCCAAACTA
39917237 TATATCTTTATAATTTTTAAAGGATTAGATCGAATTTTTATAATTTTAGGGAAGCCCAAAGTACA
1 TATATCTTTATAATTTTTAAAGGATTAGATCGAATTTTTATAATTTTAGGGAAGCCCAAAGTACA
*
39917302 ATTTTACCTTTACGAATTTAAAATTTTAAAAAAATTTAAAAGGCCTAAATGACAATTTTTCATTT
66 ATTTTACCTTTACTAATTTAAAATTTTAAAAAAATTTAAAAGGCCTAAATGACAATTTTTCATTT
*
39917367 TAGGCAAGCCAGGTCCTTCAGCCCCCTAGAATCTCCTCTATCAATAGTTACCCTTAGACCACGTA
131 TAGGCAAGCCAGGTCCTTCAGCCCCCTAGAATCTCCTCTATCAACAGTTACCCTTAGACCACGTA
*
39917432 ATATAATATATATTTGATACATTATTTTCGTTTAAAAAATATTTGTTAATGCACTATAAATTAAT
196 ATATAATATATATTTGATACATTATATTCGTTTAAAAAATATTTGTTAATGCACTATAAATTAAT
*
39917497 ACCAAATTTATTTTTTATTAATACATGTACAAATCGATTTAATATAATGAGATTAGTAGTATATT
261 ACCAAATTTATTTTTTATTAATACATGTACAAATCAATTTAATATAATGAGATTAGTAGTATATT
*
39917562 ATATATATGTATATTATATATTATTAAAAAGCATGAGTTGTATAAATATATGTTGAGTGTTTATT
326 ATATATATGTATATTATATATTATTAAAAAGCATGAGTTGTACAAATATATGTTGAGTGTTTATT
39917627 TTTCTGTGTACTTCTTAGAGCGATTCATCGACATATATATATGTTACGGTCCATTGTTGTGATGT
391 TTTCTGTGTACTTCTTAGAGCGATTCATCGACATATATATATGTTACGGTCCATTGTTGTGATGT
39917692 GCTAGGGGTAGGTAGGCTACATGCATGGCAACACGTTATTCTCCCTAGGGGTGGCACGTGTCCTA
456 GCTAGGGGTAGGTAGGCTACATGCATGGCAACACGTTATTCTCCCTAGGGGTGGCACGTGTCCTA
39917757 GCAAAGGGCTCGCCAAACTA
521 GCAAAGGGCTCGCCAAACTA
* * ** * **
39917777 TATATCTTTATAATTTTTAAAGGATTAGATCGAACTTTTATTATTTTAGGG--GGTCGAAGTGTA
1 TATATCTTTATAATTTTTAAAGGATTAGATCGAATTTTTATAATTTTAGGGAAGCCCAAAGTACA
39917840 ATTTTACCTTTACTAATTTAAAAATTTTAAAAAAATTTAA
66 ATTTTACCTTTACTAATTT-AAAATTTTAAAAAAATTTAA
39917880 GGGTCTAATA
Statistics
Matches: 624, Mismatches: 18, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
538 25 0.04
539 20 0.03
540 579 0.93
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (540 bp):
TATATCTTTATAATTTTTAAAGGATTAGATCGAATTTTTATAATTTTAGGGAAGCCCAAAGTACA
ATTTTACCTTTACTAATTTAAAATTTTAAAAAAATTTAAAAGGCCTAAATGACAATTTTTCATTT
TAGGCAAGCCAGGTCCTTCAGCCCCCTAGAATCTCCTCTATCAACAGTTACCCTTAGACCACGTA
ATATAATATATATTTGATACATTATATTCGTTTAAAAAATATTTGTTAATGCACTATAAATTAAT
ACCAAATTTATTTTTTATTAATACATGTACAAATCAATTTAATATAATGAGATTAGTAGTATATT
ATATATATGTATATTATATATTATTAAAAAGCATGAGTTGTACAAATATATGTTGAGTGTTTATT
TTTCTGTGTACTTCTTAGAGCGATTCATCGACATATATATATGTTACGGTCCATTGTTGTGATGT
GCTAGGGGTAGGTAGGCTACATGCATGGCAACACGTTATTCTCCCTAGGGGTGGCACGTGTCCTA
GCAAAGGGCTCGCCAAACTA
Found at i:39920814 original size:34 final size:34
Alignment explanation
Indices: 39920716--39920824 Score: 105
Period size: 34 Copynumber: 3.1 Consensus size: 34
39920706 TCACAATTGT
*
39920716 TTCTTTTCCCTTCATTGTGCTTACCGCCCCT-TG
1 TTCTTTTCCCTTCATTGTGCTTGCCGCCCCTATG
* * * * *
39920749 -CCATATCCCTTACTATTCCATTGATTGCCGCCCCTATG
1 TTCTTTTCCCTT-C-ATT---GTGCTTGCCGCCCCTATG
39920787 TTCTTTTCCCTTCATTGTGCTTGCCGCCCCTATG
1 TTCTTTTCCCTTCATTGTGCTTGCCGCCCCTATG
39920821 TTCT
1 TTCT
39920825 ATGCTTGAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
32 8 0.14
33 1 0.02
34 23 0.40
37 15 0.26
38 3 0.05
39 8 0.14
ACGTcount: A:0.10, C:0.36, G:0.12, T:0.42
Consensus pattern (34 bp):
TTCTTTTCCCTTCATTGTGCTTGCCGCCCCTATG
Found at i:39930741 original size:22 final size:22
Alignment explanation
Indices: 39930676--39930743 Score: 109
Period size: 22 Copynumber: 3.1 Consensus size: 22
39930666 TTTATTGTTC
*
39930676 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
39930698 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
39930720 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
39930742 AA
1 AA
39930744 CTAATCTCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:39932048 original size:25 final size:25
Alignment explanation
Indices: 39932014--39932086 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 25
39932004 TCTAGTATAT
39932014 GTATGCTCACACGAGCTGTGAATCG
1 GTATGCTCACACGAGCTGTGAATCG
* * * *
39932039 GTATGCTCACACAAGTTATGAAAATGG
1 GTATGCTCACACGAGCTGTG--AATCG
**
39932066 GCCTGCTCACACGAGCTGTGA
1 GTATGCTCACACGAGCTGTGA
39932087 GTAGGAACGT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
25 18 0.49
27 19 0.51
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.23
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTGAATCG
Found at i:39939896 original size:27 final size:25
Alignment explanation
Indices: 39939832--39939896 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 25
39939822 TTGTACATGT
* *
39939832 ATGCTCACACGAGCTATGAATCGGT
1 ATGCTCACACGAGCTATGAATAGGC
39939857 ATGCTCACACGAGCTATGAAAATAGGC
1 ATGCTCACACGAGCTATG--AATAGGC
*
39939884 CTGCTCACACGAG
1 ATGCTCACACGAG
39939897 TTGTGGGTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
25 18 0.51
27 17 0.49
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (25 bp):
ATGCTCACACGAGCTATGAATAGGC
Found at i:39940914 original size:9 final size:9
Alignment explanation
Indices: 39940894--39940933 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
39940884 AACCAGCAAC
39940894 GAAAAGAAAA
1 GAAAA-AAAA
39940904 GAAAAAAAA
1 GAAAAAAAA
**
39940913 GAGCAAAAA
1 GAAAAAAAA
39940922 GAAAAAAAA
1 GAAAAAAAA
39940931 GAA
1 GAA
39940934 CAGAGAGGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 21 0.81
10 5 0.19
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:39941870 original size:12 final size:12
Alignment explanation
Indices: 39941853--39941877 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39941843 ATTTAGTTTG
39941853 TATTTCTAATAT
1 TATTTCTAATAT
39941865 TATTTCTAATAT
1 TATTTCTAATAT
39941877 T
1 T
39941878 TCAAATTAAT
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:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTCTAATAT
Found at i:39946067 original size:26 final size:25
Alignment explanation
Indices: 39946031--39946100 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
39946021 ATAAAATACA
*
39946031 TCTTTGCATTCATTTTTGAGCCAA-TAT
1 TCTTT-CATTC-TTTTTGA-ACAATTAT
*
39946058 TCTTTCATTCTTTTTGAATAATTAT
1 TCTTTCATTCTTTTTGAACAATTAT
39946083 TCTTTCATTC-TTTTGAAC
1 TCTTTCATTCTTTTTGAAC
39946101 TTTCTTCCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.23
25 20 0.51
26 5 0.13
27 5 0.13
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.54
Consensus pattern (25 bp):
TCTTTCATTCTTTTTGAACAATTAT
Found at i:39946883 original size:12 final size:12
Alignment explanation
Indices: 39946862--39946972 Score: 60
Period size: 12 Copynumber: 8.8 Consensus size: 12
39946852 TTCAATAAAA
*
39946862 AAAATCAAAATC
1 AAAATAAAAATC
39946874 AAAATAAAAATC
1 AAAATAAAAATC
* *
39946886 AAAAACAAAAAATA
1 -AAAA-TAAAAATC
* **
39946900 AGAAAAAAAAAGA
1 A-AAATAAAAATC
* *
39946913 AAAATCAAAGTC
1 AAAATAAAAATC
* * *
39946925 AAAGTCAAAAGC
1 AAAATAAAAATC
*
39946937 AAAAAGGAAAAATC
1 -AAAA-TAAAAATC
*
39946951 AAAATAAAAATG
1 AAAATAAAAATC
39946963 AAAATAAAAA
1 AAAATAAAAA
39946973 AGGAGAGGCT
Statistics
Matches: 76, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
12 42 0.55
13 20 0.26
14 14 0.18
ACGTcount: A:0.74, C:0.08, G:0.07, T:0.11
Consensus pattern (12 bp):
AAAATAAAAATC
Found at i:39946948 original size:51 final size:51
Alignment explanation
Indices: 39946861--39946966 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 51
39946851 ATTCAATAAA
*
39946861 AAAAATCAAAATCAAAATAAAAATCAAAAACAAAAAAT-AAGAAAAAAAAAG
1 AAAAATCAAAATCAAAATAAAAAGCAAAAACAAAAAATCAA-AAAAAAAAAG
* * * ** * *
39946912 AAAAATCAAAGTCAAAGTCAAAAGCAAAAAGGAAAAATCAAAATAAAAATG
1 AAAAATCAAAATCAAAATAAAAAGCAAAAACAAAAAATCAAAAAAAAAAAG
39946963 AAAA
1 AAAA
39946967 TAAAAAAGGA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 44 0.96
52 2 0.04
ACGTcount: A:0.74, C:0.08, G:0.08, T:0.10
Consensus pattern (51 bp):
AAAAATCAAAATCAAAATAAAAAGCAAAAACAAAAAATCAAAAAAAAAAAG
Found at i:39946972 original size:6 final size:6
Alignment explanation
Indices: 39946861--39946972 Score: 53
Period size: 6 Copynumber: 17.8 Consensus size: 6
39946851 ATTCAATAAA
* * * * *
39946861 AAAAAT CAAAAT CAAAAT AAAAAT CAAAAACA AAAAAT AAGAAAA AAAAAG
1 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAA-T AAAAAT AA-AAAT AAAAAT
* * * * ** * *
39946912 AAAAAT CAAAGT CAAAGT CAAAAGC AAAAAGG AAAAAT CAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT -AAAAAT AAAAA-T AAAAAT AAAAAT AAAAAT
*
39946962 GAAAAT AAAAA
1 AAAAAT AAAAA
39946973 AGGAGAGGCT
Statistics
Matches: 83, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
6 59 0.71
7 24 0.29
ACGTcount: A:0.74, C:0.08, G:0.07, T:0.11
Consensus pattern (6 bp):
AAAAAT
Found at i:39946973 original size:32 final size:30
Alignment explanation
Indices: 39946879--39946976 Score: 79
Period size: 32 Copynumber: 3.0 Consensus size: 30
39946869 AAATCAAAAT
* *
39946879 AAAAATCAAAAACAAAAAATAAGAAAAAAAAAG
1 AAAAATC-AAAA-TAAAAATAA-AAAAAAAAGG
* * * *
39946912 AAAAATCAAAGTCAAAGTCAAAAGCAAAAAGG
1 AAAAATCAAAATAAAAAT-AAAA-AAAAAAGG
39946944 AAAAATCAAAATAAAAATGAAAATAAAAAAGG
1 AAAAATCAAAATAAAAAT-AAAA-AAAAAAGG
39946976 A
1 A
39946977 GAGGCTAAGG
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
31 6 0.12
32 38 0.75
33 7 0.14
ACGTcount: A:0.73, C:0.07, G:0.10, T:0.09
Consensus pattern (30 bp):
AAAAATCAAAATAAAAATAAAAAAAAAAGG
Found at i:39949385 original size:44 final size:44
Alignment explanation
Indices: 39949337--39949521 Score: 135
Period size: 44 Copynumber: 4.2 Consensus size: 44
39949327 CTAGTAATTC
39949337 TATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTACAAATCT
1 TATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTACAAATCT
* ** * * ** * * * *
39949381 TATCTCCCTAAG-CAGTAGTAGAGCAGATCGAAGATGACAGATTT
1 TATCTCCCT-GGTTGGCAGTGGAATAGATTGAAGATTACAAATCT
* * * * * **
39949425 TACCTCCCTGTGGTT-ACAGTGGAGTACATTGAAG-CTAGTAAT-T
1 TATCTCCC--TGGTTGGCAGTGGAATAGATTGAAGATTACAAATCT
*
39949468 CTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTACAGATCT
1 -TATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTACAAATCT
39949513 TATCTCCCT
1 TATCTCCCT
39949522 AAGCAATAGT
Statistics
Matches: 100, Mismatches: 33, Indels: 16
0.67 0.22 0.11
Matches are distributed among these distances:
42 5 0.05
43 17 0.17
44 61 0.61
45 16 0.16
46 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (44 bp):
TATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTACAAATCT
Found at i:39949436 original size:132 final size:132
Alignment explanation
Indices: 39949281--39949809 Score: 646
Period size: 132 Copynumber: 4.0 Consensus size: 132
39949271 GGAGCAGGTT
* *
39949281 GATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTAAAGCTAGTAATTCTATCTCCCT
1 GATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTATCTCCCT
* *
39949346 GGTTGGCAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCG
66 GGTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
39949411 AA
131 AA
*
39949413 GATGACAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTATCTCCCT
1 GATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTATCTCCCT
*
39949478 GGTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCG
66 GGTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
39949543 AA
131 AA
* * * *
39949545 GATGGC-GAATTCTACCTCCCTGAGGTTACGGTGGAGTACATTGAAGCCAGTAATTCTATCTCCC
1 GATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTATCTCCC
** * *
39949609 TGGTCAGCAGTGGAATAGGTTGGAA-ATTACAGATCTCATCTCCCTAAGCAGTAGTGGAGCAGAT
65 TGGTTGGCAGTGGAATAGATT-GAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
39949673 CGAA
129 CGAA
* * * * * * * * *
39949677 GACGGC-GAATCTTACCTTCCCCAG-GAG-T--AG-GGAAGCAAATTTAAGCCA-CAAGTCCTAT
1 GATGGCAG-ATTTTACC-T-CCCTGTG-GTTACAGTGG-AGTACATTGAAGCTAGTAA-TTCTAT
** * * * *
39949735 CTCCCTGGTCAGCAGTGGAGTAAATTGGAA-ATTACATATCTCATCTCCCTAAGCAGTAGTGGAG
60 CTCCCTGGTTGGCAGTGGAATAGATT-GAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
39949799 CAGATCGAA
124 CAGATCGAA
39949808 GA
1 GA
39949810 CGGCGAATCT
Statistics
Matches: 360, Mismatches: 30, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
130 4 0.01
131 90 0.25
132 255 0.71
133 6 0.02
134 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (132 bp):
GATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTATCTCCCT
GGTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
AA
Found at i:39949776 original size:131 final size:131
Alignment explanation
Indices: 39949334--39949907 Score: 573
Period size: 132 Copynumber: 4.4 Consensus size: 131
39949324 AAGCTAGTAA
** * *
39949334 TTCTATCTCCCTGGTTGGCAGTGGAATAGATT-GAAGATTACAAATCTTATCTCCCTAAGCAGTA
1 TTCTATCTCCCTGGTCAGCAGTGGAATAGATTGGAA-ATTACAGATCTCATCTCCCTAAGCAGTA
* * * * * * * *
39949398 GTAGAGCAGATCGAAGATGAC-AGATTTTACC-T-CCCTGTG-GTTACAGTGG-AGTACATTGAA
65 GTGGAGCAGATCGAAGACGGCGA-ATCTTACCTTCCCCAG-GAG-T--AG-GGAAGCAAATTTAA
* *
39949458 GCTAGTAA-
124 GCCA-CAAG
** * *
39949466 TTCTATCTCCCTGGTTGGCAGTGGAATAGATT-GAAGATTACAGATCTTATCTCCCTAAGCAATA
1 TTCTATCTCCCTGGTCAGCAGTGGAATAGATTGGAA-ATTACAGATCTCATCTCCCTAAGCAGTA
* * * * * * *
39949530 GTGGAGCAGATCGAAGATGGCGAAT-TCTACC-TCCCTGAGG-TTACGGTGGAGTACATTGAAGC
65 GTGGAGCAGATCGAAGACGGCGAATCT-TACCTTCCC-CAGGAGTA-GG-GAAGCAAATTTAAGC
*
39949592 CAGTAA-
126 CA-CAAG
*
39949598 TTCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTCATCTCCCTAAGCAGTAG
1 TTCTATCTCCCTGGTCAGCAGTGGAATAGATTGGAAATTACAGATCTCATCTCCCTAAGCAGTAG
39949663 TGGAGCAGATCGAAGACGGCGAATCTTACCTTCCCCAGGAGTAGGGAAGCAAATTTAAGCCACAA
66 TGGAGCAGATCGAAGACGGCGAATCTTACCTTCCCCAGGAGTAGGGAAGCAAATTTAAGCCACAA
39949728 G
131 G
* * * *
39949729 TCCTATCTCCCTGGTCAGCAGTGGAGTAAATTGGAAATTACATATCTCATCTCCCTAAGCAGTAG
1 TTCTATCTCCCTGGTCAGCAGTGGAATAGATTGGAAATTACAGATCTCATCTCCCTAAGCAGTAG
* *
39949794 TGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACAA
66 TGGAGCAGATCGAAGACGGCGAATCTTACCTTCCCCAGGAGTAGGGAAGCAAATTTAAGCCACAA
39949859 G
131 G
* * *
39949860 TTC-ATTTCCCTGAG-CAGCAGTGGAGTAGGTTGGAAAAATTACAGATCT
1 TTCTATCTCCCTG-GTCAGCAGTGGAATAGATTGG--AAATTACAGATCT
39949908 TGTCTTCCTG
Statistics
Matches: 394, Mismatches: 33, Indels: 30
0.86 0.07 0.07
Matches are distributed among these distances:
130 29 0.07
131 143 0.36
132 207 0.53
133 14 0.04
134 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (131 bp):
TTCTATCTCCCTGGTCAGCAGTGGAATAGATTGGAAATTACAGATCTCATCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGACGGCGAATCTTACCTTCCCCAGGAGTAGGGAAGCAAATTTAAGCCACAA
G
Found at i:39950123 original size:50 final size:50
Alignment explanation
Indices: 39949981--39950150 Score: 162
Period size: 50 Copynumber: 3.4 Consensus size: 50
39949971 TGGAGTAGGT
* * * *
39949981 TGAATATTACTTTCCAGGCAGTGTAGTGGAACAGATTAAAGCCACAACGG
1 TGAATCTTACTTCCCAGACAGTGCAGTGGAACAGATTAAAGCCACAACGG
* * * ** * * *
39950031 CGAATCTTGCTTCCCCA-ACATTGCAGTTAAAAAGACTAAAGCCACAATGG
1 TGAATCTTACTT-CCCAGACAGTGCAGTGGAACAGATTAAAGCCACAACGG
* * * *
39950081 TGAGTCTTACTTCCCAGACGGTGCAGTGGAACAGATTGAAGCCACAACGA
1 TGAATCTTACTTCCCAGACAGTGCAGTGGAACAGATTAAAGCCACAACGG
* *
39950131 TGAATCTTGCTTCCCCGACA
1 TGAATCTTACTTCCCAGACA
39950151 TCATAGTAAA
Statistics
Matches: 90, Mismatches: 28, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
49 4 0.04
50 83 0.92
51 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (50 bp):
TGAATCTTACTTCCCAGACAGTGCAGTGGAACAGATTAAAGCCACAACGG
Found at i:39950411 original size:11 final size:10
Alignment explanation
Indices: 39950395--39950434 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
39950385 TGCCCGACCC
39950395 AAATAAAAAA
1 AAATAAAAAA
39950405 TAAATAAACAAA
1 -AAATAAA-AAA
*
39950417 AAATATAAAA
1 AAATAAAAAA
39950427 AAATAAAA
1 AAATAAAA
39950435 TAAACCAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 10 0.38
11 13 0.50
12 3 0.12
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (10 bp):
AAATAAAAAA
Found at i:39958873 original size:15 final size:15
Alignment explanation
Indices: 39958853--39958882 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39958843 TATTTTCCAG
39958853 AAATTTAAAAAATAT
1 AAATTTAAAAAATAT
39958868 AAATTTAAAAAATAT
1 AAATTTAAAAAATAT
39958883 TTTCTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTTAAAAAATAT
Found at i:39964490 original size:3 final size:3
Alignment explanation
Indices: 39964482--39964533 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
39964472 ATTGGCTTTT
*
39964482 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA CGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
39964530 AGA A
1 AGA A
39964534 AATCAAATTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:39966974 original size:22 final size:23
Alignment explanation
Indices: 39966949--39966991 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
39966939 GAGTTTTAAT
39966949 TTAGAAAATAT-TGAAGGACCCA
1 TTAGAAAATATGTGAAGGACCCA
* *
39966971 TTAGCAATTATGTGAAGGACC
1 TTAGAAAATATGTGAAGGACC
39966992 TCATGGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (23 bp):
TTAGAAAATATGTGAAGGACCCA
Found at i:39970284 original size:8 final size:8
Alignment explanation
Indices: 39970266--39970309 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
39970256 CATAAAATAT
39970266 AAAAT-AA
1 AAAATAAA
39970273 AAAATAAA
1 AAAATAAA
39970281 AAAATAAACA
1 AAAAT-AA-A
39970291 ATAAATAAA
1 A-AAATAAA
39970300 AAAATAAA
1 AAAATAAA
39970308 AA
1 AA
39970310 TTCGGTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
7 5 0.15
8 16 0.48
9 4 0.12
10 4 0.12
11 4 0.12
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAATAAA
Found at i:39970286 original size:15 final size:16
Alignment explanation
Indices: 39970264--39970300 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
39970254 AACATAAAAT
39970264 ATAAAATAAAAAATAA
1 ATAAAATAAAAAATAA
*
39970280 A-AAAATAAACAATAA
1 ATAAAATAAAAAATAA
39970295 ATAAAA
1 ATAAAA
39970301 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (16 bp):
ATAAAATAAAAAATAA
Found at i:39970309 original size:7 final size:7
Alignment explanation
Indices: 39970259--39970309 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
39970249 AAAAGAACAT
*
39970259 AAAATAT
1 AAAATAA
39970266 AAAATAA
1 AAAATAA
39970273 AAAATAAA
1 AAAAT-AA
39970281 AAAATAA
1 AAAATAA
*
39970288 ACAAT-A
1 AAAATAA
*
39970294 AATA-AA
1 AAAATAA
39970300 AAAATAA
1 AAAATAA
39970307 AAA
1 AAA
39970310 TTCGGTTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
6 7 0.19
7 22 0.61
8 7 0.19
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:39971291 original size:22 final size:22
Alignment explanation
Indices: 39971249--39971291 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
39971239 ACTGTTCGTT
* *
39971249 TTTATTCTTTTGTTTTTTCCTC
1 TTTATTCTTTTGTATTCTCCTC
39971271 TTTATT-TCTTTGTATTCTCCT
1 TTTATTCT-TTTGTATTCTCCT
39971292 GTTGCTTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.07, C:0.19, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTATTCTTTTGTATTCTCCTC
Found at i:39972926 original size:14 final size:14
Alignment explanation
Indices: 39972907--39972934 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39972897 CTAATTTATT
39972907 AATGAATTATTAAA
1 AATGAATTATTAAA
39972921 AATGAATTATTAAA
1 AATGAATTATTAAA
39972935 TATAACTTTA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:39976211 original size:11 final size:11
Alignment explanation
Indices: 39976195--39976260 Score: 55
Period size: 11 Copynumber: 6.1 Consensus size: 11
39976185 ACATATACTA
39976195 AATAAAATAAT
1 AATAAAATAAT
39976206 AATAAAATAAT
1 AATAAAATAAT
* *
39976217 AA-AATATTAT
1 AATAAAATAAT
* *
39976227 -TTAAAAATAAA
1 AAT-AAAATAAT
*
39976238 AATAAAATACT
1 AATAAAATAAT
*
39976249 AATAAACTAAT
1 AATAAAATAAT
39976260 A
1 A
39976261 TTTATTTAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
10 6 0.15
11 34 0.83
12 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:39976982 original size:19 final size:19
Alignment explanation
Indices: 39976958--39976995 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39976948 CTATAATATA
39976958 AGTGGATTGAAGTTTGGTC
1 AGTGGATTGAAGTTTGGTC
39976977 AGTGGATTGAAGTTTGGTC
1 AGTGGATTGAAGTTTGGTC
39976996 TAGCAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.37, T:0.37
Consensus pattern (19 bp):
AGTGGATTGAAGTTTGGTC
Found at i:39978455 original size:165 final size:165
Alignment explanation
Indices: 39978177--39978668 Score: 867
Period size: 165 Copynumber: 3.0 Consensus size: 165
39978167 GGTTTGTGAT
*
39978177 TATATCTTGAATTATGATTGGAACAGTACAAAACGTGATTAATGGTTGTATTAAATGTTTCAATA
1 TATATCTTGAATTATGATTGGAACAGTACAAAACGTGATTAATGGTTGTATTAAATGTTTCGATA
39978242 TGTTAAAAGAGGTTGAATGAATGTAGGAATAGATACAATTGGCATTCCAATAGGTTTGATTGTGT
66 TGTTAAAAGAGGTTGAATGAATGTAGGAATAGATACAATTGGCATTCCAATAGGTTTGATTGTGT
*
39978307 GTTTGTACGGGATATGTGTAAAAGATGATACGGAG
131 GTTTGTACGGGATATGTGTAAAAGATCATACGGAG
* *
39978342 TATATCTTGAATTATGATTGGAATAGTACAAAACGTGGTTAATGGTTGTATTAAATGTTTCGATA
1 TATATCTTGAATTATGATTGGAACAGTACAAAACGTGATTAATGGTTGTATTAAATGTTTCGATA
* * *
39978407 TGTTAAAAGAGGTTGAATGAATGTAGGAATAGATACAATTGACATTCCAATAGGTTTGATTGCGG
66 TGTTAAAAGAGGTTGAATGAATGTAGGAATAGATACAATTGGCATTCCAATAGGTTTGATTGTGT
* * **
39978472 GTTTGTACGGGATATGTGTAAAATATTATGTGGAG
131 GTTTGTACGGGATATGTGTAAAAGATCATACGGAG
39978507 TATATCTTGAATTATGATTGGAACAGTACAAAACGTGATTAATGGTTGTATTAAATGTTTCGATA
1 TATATCTTGAATTATGATTGGAACAGTACAAAACGTGATTAATGGTTGTATTAAATGTTTCGATA
*
39978572 TGTTAAAAGAGGTTGAATAAATGTAGGAATAGATACAATTGGCATTCCAATAGGTTTGATTGTGT
66 TGTTAAAAGAGGTTGAATGAATGTAGGAATAGATACAATTGGCATTCCAATAGGTTTGATTGTGT
*
39978637 GTTTGTACAGGATATGTGTAAAAGATCATACG
131 GTTTGTACGGGATATGTGTAAAAGATCATACG
39978669 AACTAAAAGA
Statistics
Matches: 306, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
165 306 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (165 bp):
TATATCTTGAATTATGATTGGAACAGTACAAAACGTGATTAATGGTTGTATTAAATGTTTCGATA
TGTTAAAAGAGGTTGAATGAATGTAGGAATAGATACAATTGGCATTCCAATAGGTTTGATTGTGT
GTTTGTACGGGATATGTGTAAAAGATCATACGGAG
Found at i:39981207 original size:105 final size:104
Alignment explanation
Indices: 39981026--39981228 Score: 271
Period size: 105 Copynumber: 1.9 Consensus size: 104
39981016 TGTCTAGGCT
* * * * *
39981026 GTGTAACCCACTGTTTATGATTTAGGACCATACGGTCCGAGACATAGACGTGTGCCCAGGCTATG
1 GTGTAACCCACTATTTATGATTTAGAACCACACGGTCAGAGACATAGACGTATGCCCAGGCTATG
*
39981091 TGAACCGCACGGGCAAGGACATGGGCGTGTGTCCAGGTC
66 TGAACCACACGGGCAAGGACATGGGCGTGTGTCCAGGTC
* * * * * *
39981130 GTGTAACTCACTATTTGTGATTTAGAATCACACGGTCAGAGGACATATACGTATGTCCAGGCTGT
1 GTGTAACCCACTATTTATGATTTAGAACCACACGGTCAGA-GACATAGACGTATGCCCAGGCTAT
* *
39981195 GTGAGCCACACGGGCAAGGGCATGGGCGTGTGTC
65 GTGAACCACACGGGCAAGGACATGGGCGTGTGTC
39981229 TAGGCCATGT
Statistics
Matches: 84, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
104 33 0.39
105 51 0.61
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.24
Consensus pattern (104 bp):
GTGTAACCCACTATTTATGATTTAGAACCACACGGTCAGAGACATAGACGTATGCCCAGGCTATG
TGAACCACACGGGCAAGGACATGGGCGTGTGTCCAGGTC
Found at i:39984054 original size:14 final size:15
Alignment explanation
Indices: 39984029--39984065 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
39984019 CCTATAGAAA
39984029 TTAAATTAAACTAAG
1 TTAAATTAAACTAAG
39984044 TTAAA-TAAACTAA-
1 TTAAATTAAACTAAG
*
39984057 TGAAATTAA
1 TTAAATTAA
39984066 GTAAAAGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (15 bp):
TTAAATTAAACTAAG
Found at i:39985924 original size:25 final size:24
Alignment explanation
Indices: 39985880--39985926 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
39985870 TAGCCTTAAA
*
39985880 TTAAATAATTTAGTTCGTTTATAT
1 TTAAATAATTTAGTTAGTTTATAT
39985904 TTAAATTAA-TTAGTTTAGTTTAT
1 TTAAA-TAATTTAG-TTAGTTTAT
39985927 TAGACTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAAATAATTTAGTTAGTTTATAT
Found at i:39987757 original size:18 final size:18
Alignment explanation
Indices: 39987732--39987769 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
39987722 TAAGTCCTTT
39987732 TTTATTTTTC-TTATTTA
1 TTTATTTTTCGTTATTTA
39987749 TTTATTTTTCGTTATTTA
1 TTTATTTTTCGTTATTTA
39987767 TTT
1 TTT
39987770 TTATCTCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTATTTTTCGTTATTTA
Found at i:39989235 original size:2 final size:2
Alignment explanation
Indices: 39989228--39989255 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39989218 AAAGGCTTAT
39989228 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39989256 ACTCCAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39989959 original size:21 final size:20
Alignment explanation
Indices: 39989933--39990009 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 20
39989923 TTTTTAAAAG
39989933 TATTTTTTTCTAATTTTAAAT
1 TATTTTTTT-TAATTTTAAAT
* *
39989954 TATTTTCTATTAATTCT--AT
1 TATTTT-TTTTAATTTTAAAT
**
39989973 TATTTTTAATAATTTTAAAT
1 TATTTTTTTTAATTTTAAAT
*
39989993 CTAGTTTTTTTAATTTT
1 -TATTTTTTTTAATTTT
39990010 CAAAAATCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
18 8 0.18
19 8 0.18
20 2 0.04
21 25 0.56
22 2 0.04
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (20 bp):
TATTTTTTTTAATTTTAAAT
Found at i:39997052 original size:16 final size:16
Alignment explanation
Indices: 39997031--39997063 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39997021 TTATGTCTCC
*
39997031 AATGGGTTGACCTGTG
1 AATGGGTTGACATGTG
39997047 AATGGGTTGACATGTG
1 AATGGGTTGACATGTG
39997063 A
1 A
39997064 CTCTCCATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.36, T:0.30
Consensus pattern (16 bp):
AATGGGTTGACATGTG
Found at i:39997752 original size:40 final size:40
Alignment explanation
Indices: 39997681--39997771 Score: 92
Period size: 40 Copynumber: 2.3 Consensus size: 40
39997671 ACCAGGCAAG
* * ** *
39997681 GGTATTAATAAAATAGGGAAGGTATCAATACTCTATTAAA
1 GGTATTGATACAATAGGGAAAATACCAATACTCTATTAAA
* * *
39997721 GGTATTGATACAATAGGGAAAATACCGATACTTTGTTAAA
1 GGTATTGATACAATAGGGAAAATACCAATACTCTATTAAA
* *
39997761 TGTATCGATAC
1 GGTATTGATAC
39997772 TTTTGATATT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.31
Consensus pattern (40 bp):
GGTATTGATACAATAGGGAAAATACCAATACTCTATTAAA
Found at i:39999898 original size:49 final size:48
Alignment explanation
Indices: 39999817--39999910 Score: 134
Period size: 49 Copynumber: 1.9 Consensus size: 48
39999807 TTTTAGGTCA
* *
39999817 TTCATTTTCATTTTGGAGAAAATCACATTCATTTCCAAATGATTTCATT
1 TTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATG-TTTCATT
* * *
39999866 TTCATTTTCATTTTGGAGAATACCATAATCATTTTCAAATGTTTC
1 TTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGTTTC
39999911 CCATTTCTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 4 0.10
49 36 0.90
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.46
Consensus pattern (48 bp):
TTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGTTTCATT
Found at i:40025807 original size:117 final size:119
Alignment explanation
Indices: 40025587--40025817 Score: 321
Period size: 117 Copynumber: 2.0 Consensus size: 119
40025577 ACTAAACTGC
* *
40025587 AGCTCTGATACCACTAAATGTAACACCCTTAACCCGTCTCTATCATCAGATTAGGGTTACGAAGC
1 AGCTCTGACACCACTAAATGTAACACCCTTAACCCGTCTCCATCATCAGATTAGGGTTACGAAGC
* *
40025652 ATTATCGTACAAATCATAACAATAATGTCATTTAATATTAATTACCTAACCCGT
66 ATTATCATACAAATCAAAACAATAATGTCATTTAATATTAATTACCTAACCCGT
* * *
40025706 AGCTCTGACACCAGTAAATGTAACA-CCTCTAACCCGTCTCCATCGT-GGAATTA-GG-TAC-AG
1 AGCTCTGACACCACTAAATGTAACACCCT-TAACCCGTCTCCATCATCAG-ATTAGGGTTACGA-
40025766 AGCATTA-CTATACAAATCAAAACAATAATGTCATTTAATATTAATTACCTAA
63 AGCATTATC-ATACAAATCAAAACAATAATGTCATTTAATATTAATTACCTAA
40025818 AACTCATTAC
Statistics
Matches: 101, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
116 2 0.02
117 51 0.50
118 6 0.06
119 42 0.42
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (119 bp):
AGCTCTGACACCACTAAATGTAACACCCTTAACCCGTCTCCATCATCAGATTAGGGTTACGAAGC
ATTATCATACAAATCAAAACAATAATGTCATTTAATATTAATTACCTAACCCGT
Found at i:40026141 original size:42 final size:41
Alignment explanation
Indices: 40026076--40026159 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 41
40026066 TCACACGATC
* * * * *
40026076 GTGTTACAGGCCATGTGTTAGACCTTGTAACTCTCTGACTT
1 GTGTCACAGGCCATGTGCTAGACCGTGTAACTCACTAACTT
*
40026117 GTGTCACACGGCCGTGTGCTAGACCGTGTAACTCACTAACTT
1 GTGTCACA-GGCCATGTGCTAGACCGTGTAACTCACTAACTT
40026159 G
1 G
40026160 ATATACACGA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 7 0.19
42 29 0.81
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (41 bp):
GTGTCACAGGCCATGTGCTAGACCGTGTAACTCACTAACTT
Found at i:40026168 original size:42 final size:41
Alignment explanation
Indices: 40026080--40026168 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 41
40026070 ACGATCGTGT
* * * * *
40026080 TACA-GGCCATGTGTTAGACCTTGTAACTCTCTGACTTGTG
1 TACACGGCCATGTGCTAGACCGTGTAACTCACTAACTTGTA
*
40026120 TCACACGGCCGTGTGCTAGACCGTGTAACTCACTAACTTGATA
1 T-ACACGGCCATGTGCTAGACCGTGTAACTCACTAACTTG-TA
40026163 TACACG
1 TACACG
40026169 ATCGTGTCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
40 1 0.03
41 3 0.08
42 34 0.85
43 2 0.05
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (41 bp):
TACACGGCCATGTGCTAGACCGTGTAACTCACTAACTTGTA
Found at i:40032112 original size:27 final size:28
Alignment explanation
Indices: 40032082--40032134 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
40032072 CTATAACAGT
*
40032082 ACAGTGT-GGCCTTAGCCCAATACAGAA
1 ACAGTGTGGGCCTAAGCCCAATACAGAA
* *
40032109 ACAGTTTGGGCCTAAGCCCGATACAG
1 ACAGTGTGGGCCTAAGCCCAATACAG
40032135 TATCAGTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (28 bp):
ACAGTGTGGGCCTAAGCCCAATACAGAA
Found at i:40032141 original size:28 final size:26
Alignment explanation
Indices: 40032068--40032141 Score: 67
Period size: 28 Copynumber: 2.7 Consensus size: 26
40032058 TCTAGGCCAG
* *
40032068 AGCCCTATAACAGTACAGTGTGGCCTT
1 AGCCCAAT-ACAGTACAGTGTGGCCTA
* *
40032095 AGCCCAATACAGAAACAGTTTGGGCCTA
1 AGCCCAATACAG-TACAGTGT-GGCCTA
*
40032123 AGCCCGATACAGTATCAGT
1 AGCCCAATACAGTA-CAGT
40032142 ATGGTGCAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 4 0.11
27 14 0.37
28 20 0.53
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (26 bp):
AGCCCAATACAGTACAGTGTGGCCTA
Found at i:40032302 original size:26 final size:26
Alignment explanation
Indices: 40032250--40032302 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
40032240 CACCAATATC
* *
40032250 GCAGCATAGCTACCAGTAGTAATAAT
1 GCAGCAGAGCTACCAGTAGTAAGAAT
* *
40032276 GCAGCAGAGCTGCCAGTAGTCAGAAT
1 GCAGCAGAGCTACCAGTAGTAAGAAT
40032302 G
1 G
40032303 GCTAAGAGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (26 bp):
GCAGCAGAGCTACCAGTAGTAAGAAT
Found at i:40032355 original size:22 final size:21
Alignment explanation
Indices: 40032296--40032360 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
40032286 TGCCAGTAGT
*
40032296 CAGAATGGCTAAGAGCCATAAA
1 CAGAATGACTAA-AGCCATAAA
* *
40032318 CAGGAT-AGCTATAAGCTATAAA
1 CAGAATGA-CTA-AAGCCATAAA
40032340 CAGAATGACTACAAGCCATAA
1 CAGAATGACTA-AAGCCATAA
40032361 GTACAGTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
22 32 0.94
23 2 0.06
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.17
Consensus pattern (21 bp):
CAGAATGACTAAAGCCATAAA
Found at i:40032420 original size:32 final size:32
Alignment explanation
Indices: 40032352--40032519 Score: 180
Period size: 32 Copynumber: 5.3 Consensus size: 32
40032342 GAATGACTAC
* * *
40032352 AAGCCATAAGT-ACAGTAATGTGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
40032383 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
40032415 CAGCCATTAGTAACAGTGAA-ATGATCGGTACA
1 AAGCCATCAGTAACAGT-AATATGATCGGCACA
* * **
40032447 CAGCCATC-GATAACGGTAATATGATCAACACA
1 AAGCCATCAG-TAACAGTAATATGATCGGCACA
*
40032479 AAGCCATCAGTAACAGTACTATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
40032511 AAGCCATCA
1 AAGCCATCA
40032520 ATAGCATCGC
Statistics
Matches: 112, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
31 13 0.12
32 97 0.87
33 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:40032570 original size:27 final size:26
Alignment explanation
Indices: 40032540--40032604 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
40032530 AGCAAAGCTG
40032540 CCAGTAATAGTATATGTGGCTA-AGCCA
1 CCAGTAATAGTAT-TGTGGC-AGAGCCA
40032567 CCAGTAACT-GTGATTGTGGCAGAGCCA
1 CCAGTAA-TAGT-ATTGTGGCAGAGCCA
40032594 CCAGT-ATAGTA
1 CCAGTAATAGTA
40032605 CTTCCTCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
25 2 0.06
26 4 0.12
27 25 0.74
28 3 0.09
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (26 bp):
CCAGTAATAGTATTGTGGCAGAGCCA
Found at i:40032695 original size:24 final size:23
Alignment explanation
Indices: 40032668--40032740 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 23
40032658 CCATGCCCAG
40032668 AATCAGTCATTCAAATCACAGACA
1 AATCAGTCATTCAAA-CACAGACA
* * *
40032692 AATCAGTCATACCAAACATAGATA
1 AATCAGTCAT-TCAAACACAGACA
* *
40032716 AATCAGTCATTTAACCACAGACA
1 AATCAGTCATTCAAACACAGACA
40032739 AA
1 AA
40032741 ATAATCATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
23 10 0.25
24 26 0.65
25 4 0.10
ACGTcount: A:0.48, C:0.23, G:0.08, T:0.21
Consensus pattern (23 bp):
AATCAGTCATTCAAACACAGACA
Found at i:40032825 original size:27 final size:27
Alignment explanation
Indices: 40032771--40033098 Score: 430
Period size: 27 Copynumber: 12.2 Consensus size: 27
40032761 GGCAAAAATA
40032771 GTCATT-TACCC-ACTA-GGGCATTACG
1 GTCATTCTACCCTAC-AGGGGCATTACG
* *
40032796 GTCATTTTACCCTACAGGGGCATTATG
1 GTCATTCTACCCTACAGGGGCATTACG
40032823 GTCATTCTACCCTACAGGGGCATTACG
1 GTCATTCTACCCTACAGGGGCATTACG
* *
40032850 GTCATTCTACCCTACAGGAGCATTACA
1 GTCATTCTACCCTACAGGGGCATTACG
* *
40032877 GTTATTCTACCCTACAGAGGCATTACG
1 GTCATTCTACCCTACAGGGGCATTACG
*
40032904 GTCATTCTACCCTACAGGGGCATTATG
1 GTCATTCTACCCTACAGGGGCATTACG
* *
40032931 GTCATTTTACCCTACAAGGGCATTACG
1 GTCATTCTACCCTACAGGGGCATTACG
* *
40032958 GTCATTCTACCCTACAGGGGTATTATG
1 GTCATTCTACCCTACAGGGGCATTACG
40032985 GTCATTCTACCCTACAGGGGCATTACG
1 GTCATTCTACCCTACAGGGGCATTACG
* * **
40033012 ATCATTCTACCCTATAGGGGCATTATA
1 GTCATTCTACCCTACAGGGGCATTACG
* * *
40033039 GTCATTTTACCCTATAGGGGCATTATG
1 GTCATTCTACCCTACAGGGGCATTACG
* *
40033066 GTTA-TCTTTCCCTACAGGGGCATTACG
1 GTCATTC-TACCCTACAGGGGCATTACG
40033093 GTCATT
1 GTCATT
40033099 TTACAACCTT
Statistics
Matches: 264, Mismatches: 34, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
25 6 0.02
26 7 0.03
27 250 0.95
28 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (27 bp):
GTCATTCTACCCTACAGGGGCATTACG
Found at i:40040661 original size:13 final size:13
Alignment explanation
Indices: 40040643--40040669 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40040633 TGAAATCTAC
40040643 GTCTCTATCTTCT
1 GTCTCTATCTTCT
40040656 GTCTCTATCTTCT
1 GTCTCTATCTTCT
40040669 G
1 G
40040670 GGAGTTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.30, G:0.11, T:0.52
Consensus pattern (13 bp):
GTCTCTATCTTCT
Found at i:40043871 original size:36 final size:36
Alignment explanation
Indices: 40043819--40043891 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
40043809 CCAAAACATA
*
40043819 TAACCACTAAAGCTGACAGATATTTGTGTAATATTT
1 TAACCACTAAACCTGACAGATATTTGTGTAATATTT
*
40043855 TAACCACTAAACCTGACAGATATTTGTGTCATATTT
1 TAACCACTAAACCTGACAGATATTTGTGTAATATTT
40043891 T
1 T
40043892 CATAATAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (36 bp):
TAACCACTAAACCTGACAGATATTTGTGTAATATTT
Done.