Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 64 of 378
Found at i:16631072 original size:21 final size:22
Alignment explanation
Indices: 16631039--16631080 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
16631029 TTTTGAAGAC
* *
16631039 TTTTATTTATTATTTTTATTTT
1 TTTTACTTATTATCTTTATTTT
16631061 TTTTACTT-TTATCTTTATTT
1 TTTTACTTATTATCTTTATTT
16631081 ATCTTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTACTTATTATCTTTATTTT
Found at i:16636417 original size:25 final size:25
Alignment explanation
Indices: 16636389--16636440 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
16636379 TTTGGAGCCA
16636389 TTTATATTGGTTAAAATGCTTCGTT
1 TTTATATTGGTTAAAATGCTTCGTT
*
16636414 TTTATATTGGTTAAAATGGTTCGTT
1 TTTATATTGGTTAAAATGCTTCGTT
16636439 TT
1 TT
16636441 AGCAGTAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (25 bp):
TTTATATTGGTTAAAATGCTTCGTT
Found at i:16636565 original size:14 final size:12
Alignment explanation
Indices: 16636538--16636589 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
16636528 GTTGGTACAG
16636538 AAAATTAATTTT
1 AAAATTAATTTT
16636550 AAAATATAATTTTT
1 AAAAT-TAA-TTTT
* *
16636564 AAATTTAAATTT
1 AAAATTAATTTT
*
16636576 AAATTTAAATTTT
1 AAAATT-AATTTT
16636589 A
1 A
16636590 TATTATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 14 0.41
13 12 0.35
14 8 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AAAATTAATTTT
Found at i:16636570 original size:6 final size:6
Alignment explanation
Indices: 16636561--16636587 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16636551 AAATATAATT
16636561 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
16636588 TATATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:16638627 original size:41 final size:41
Alignment explanation
Indices: 16638567--16638817 Score: 279
Period size: 41 Copynumber: 6.1 Consensus size: 41
16638557 GGAGATAGTG
* * * *
16638567 TATCAGGCCTTGAGTCTAGCAGGCTTCGTGTCAGTGTGTTA
1 TATCAGGCTTTGTGCCTAGCAGGCTTCGTGTCAGTGTATTA
* *
16638608 TATCAGGCTTTGTGCCTAGCAAGCTTCGTGCCAGTGTATTA
1 TATCAGGCTTTGTGCCTAGCAGGCTTCGTGTCAGTGTATTA
* * *
16638649 TATCAGGCTTTATGCCTAGCAAGCTTCGTGTC-GATATATTA
1 TATCAGGCTTTGTGCCTAGCAGGCTTCGTGTCAG-TGTATTA
* * ** * *
16638690 TATCAGGCTTTATGCCTAGTAGGCTTTATTTCGGTGTATTA
1 TATCAGGCTTTGTGCCTAGCAGGCTTCGTGTCAGTGTATTA
** * *
16638731 TATCAGGCTTTGTGCCTAGCAGGCTTTATGTCAATGTGTTA
1 TATCAGGCTTTGTGCCTAGCAGGCTTCGTGTCAGTGTATTA
* * * *
16638772 TATCAGGCTTTGAGCCTAGCAGGCTTCGTGCCAGTGTCTTG
1 TATCAGGCTTTGTGCCTAGCAGGCTTCGTGTCAGTGTATTA
16638813 TATCA
1 TATCA
16638818 AGTAAGTTGT
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
40 1 0.01
41 178 0.99
42 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (41 bp):
TATCAGGCTTTGTGCCTAGCAGGCTTCGTGTCAGTGTATTA
Found at i:16643483 original size:26 final size:26
Alignment explanation
Indices: 16643448--16643501 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
16643438 CATACCATAA
16643448 TTACCTTTTTACTTAACAATTTTTTT
1 TTACCTTTTTACTTAACAATTTTTTT
16643474 TTACCTTTTTACTTAACAATTTTTTT
1 TTACCTTTTTACTTAACAATTTTTTT
16643500 TT
1 TT
16643502 CTTCAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (26 bp):
TTACCTTTTTACTTAACAATTTTTTT
Found at i:16659210 original size:14 final size:13
Alignment explanation
Indices: 16659190--16659221 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
16659180 AATATTTGAC
16659190 TTGTTCTTAATTA
1 TTGTTCTTAATTA
16659203 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
16659217 TTGTT
1 TTGTT
16659222 TTGATGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:16659659 original size:26 final size:26
Alignment explanation
Indices: 16659630--16659681 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
16659620 TTTCTTTCTG
16659630 TGCATTCTTAGTTAGTAATTAGTTTA
1 TGCATTCTTAGTTAGTAATTAGTTTA
16659656 TGCATTCTTAGTTAGTAATTAGTTTA
1 TGCATTCTTAGTTAGTAATTAGTTTA
16659682 GACAACCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (26 bp):
TGCATTCTTAGTTAGTAATTAGTTTA
Found at i:16660904 original size:50 final size:49
Alignment explanation
Indices: 16660847--16660995 Score: 155
Period size: 50 Copynumber: 3.1 Consensus size: 49
16660837 ACGGTTCGAT
*
16660847 TATATATTGGCACTTAGTGTGCAAGATTGAAATAGCTTCGACTACATAAA
1 TATATATTGGCACTTAGTGTGC-AGATTGAAATAGCTTCGACTATATAAA
* *** *
16660897 TATATATTGGCACTTATTGTGCGAGACCAAAATAGCTTCGGCTATATAAA
1 TATATATTGGCACTTAGTGTGC-AGATTGAAATAGCTTCGACTATATAAA
* *
16660947 TAT-TA---GCACTTAGTGTG-AGTAATTGAGATAGCTTCGACTATATATA
1 TATATATTGGCACTTAGTGTGCAG--ATTGAAATAGCTTCGACTATATAAA
16660993 TAT
1 TAT
16660996 TGTAACACCC
Statistics
Matches: 83, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
44 2 0.02
46 33 0.40
49 2 0.02
50 46 0.55
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (49 bp):
TATATATTGGCACTTAGTGTGCAGATTGAAATAGCTTCGACTATATAAA
Found at i:16664284 original size:27 final size:28
Alignment explanation
Indices: 16664228--16664297 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
16664218 AAACTTGTAC
16664228 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
16664256 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
16664283 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
16664298 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:16664308 original size:27 final size:27
Alignment explanation
Indices: 16664228--16664309 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
16664218 AAACTTGTAC
* *
16664228 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
16664256 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
16664283 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
16664310 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.61
28 18 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:16667427 original size:26 final size:26
Alignment explanation
Indices: 16667396--16667492 Score: 158
Period size: 26 Copynumber: 3.7 Consensus size: 26
16667386 TGAAATGCCC
16667396 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
16667422 ATCATGGAACATTTACCTAACCCGTT
1 ATCATGGAACATTTACCTAAACCATT
* *
16667448 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
16667474 ATCATGGAACATTTACCTA
1 ATCATGGAACATTTACCTA
16667493 GCTCATTATC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 65 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:16667499 original size:26 final size:26
Alignment explanation
Indices: 16667396--16667503 Score: 148
Period size: 26 Copynumber: 4.2 Consensus size: 26
16667386 TGAAATGCCC
16667396 ATCATGGAACATTTACCTAAAC-CATT
1 ATCATGGAACATTTACCT-AACTCATT
* *
16667422 ATCATGGAACATTTACCTAACCCGTT
1 ATCATGGAACATTTACCTAACTCATT
*
16667448 ATCATGGAATATTTACCTAA-TCCATT
1 ATCATGGAACATTTACCTAACT-CATT
*
16667474 ATCATGGAACATTTACCTAGCTCATT
1 ATCATGGAACATTTACCTAACTCATT
16667500 ATCA
1 ATCA
16667504 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.04
26 69 0.95
27 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACTCATT
Found at i:16667502 original size:52 final size:52
Alignment explanation
Indices: 16667396--16667503 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
16667386 TGAAATGCCC
*
16667396 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCGTT
1 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
* * * *
16667448 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAGCTCATT
1 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
16667500 ATCA
1 ATCA
16667504 ATTTGTACCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.33
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
Found at i:16676155 original size:26 final size:26
Alignment explanation
Indices: 16676124--16676231 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
16676114 TGAAATGCCC
*
16676124 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
16676150 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
16676176 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
16676202 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
16676228 ATCA
1 ATCA
16676232 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:16677755 original size:41 final size:41
Alignment explanation
Indices: 16677696--16677859 Score: 238
Period size: 41 Copynumber: 4.0 Consensus size: 41
16677686 AATTTTCTAT
* * *** *
16677696 GCCTAGTACAATACACCGGCACGGAGCCTGCTAGGCAATAG
1 GCCTAATATAATACACCGGCATAAAGCCTGCTAGGCAATAA
*
16677737 GCCTAATATAATATACCGGCATAAAGCCTGCTAGGCAATAA
1 GCCTAATATAATACACCGGCATAAAGCCTGCTAGGCAATAA
*
16677778 GCCTGATATAATACACCGGCATAAAGCCTGCTAGGCAATAA
1 GCCTAATATAATACACCGGCATAAAGCCTGCTAGGCAATAA
* *
16677819 GCCTGATATAATACACTGGCATAAAGCCTGCTAGGCAATAA
1 GCCTAATATAATACACCGGCATAAAGCCTGCTAGGCAATAA
16677860 AACCTGAATA
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 113 1.00
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (41 bp):
GCCTAATATAATACACCGGCATAAAGCCTGCTAGGCAATAA
Found at i:16688836 original size:13 final size:13
Alignment explanation
Indices: 16688818--16688842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16688808 TGTGGGTGCA
16688818 CATGGCCGTGTCG
1 CATGGCCGTGTCG
16688831 CATGGCCGTGTC
1 CATGGCCGTGTC
16688843 TTGCTTTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.36, T:0.24
Consensus pattern (13 bp):
CATGGCCGTGTCG
Found at i:16690963 original size:13 final size:13
Alignment explanation
Indices: 16690945--16690973 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16690935 TTTAGTTTAA
16690945 TTAGTTAATTAGT
1 TTAGTTAATTAGT
16690958 TTAGTTAATTAGT
1 TTAGTTAATTAGT
16690971 TTA
1 TTA
16690974 ATAAACAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:16693045 original size:27 final size:25
Alignment explanation
Indices: 16693008--16693118 Score: 114
Period size: 27 Copynumber: 4.1 Consensus size: 25
16692998 AGCATGGCTT
*
16693008 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTG-CAGAGCCA
16693034 CCAGATACAGATAATAGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GT-GCAGAGCCA
*
16693062 CCAGAACAGAAATATGTTGCAGAGCCA
1 CCAGAACAGATA-ATG-TGCAGAGCCA
* *
16693089 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGT-GCAGAGCCA
16693116 CCA
1 CCA
16693119 AGACGCTTCC
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
26 7 0.10
27 48 0.66
28 17 0.23
29 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (25 bp):
CCAGAACAGATAATGTGCAGAGCCA
Found at i:16693099 original size:54 final size:54
Alignment explanation
Indices: 16693008--16693118 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
16692998 AGCATGGCTT
* *
16693008 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATAGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATAGTGGCAGAGCCA
* *
16693062 CCAGAACAGAAATATGTTG-CAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATG-TGACAGAGCCACCAGATACAGATAATAGTGGCAGAGCCA
16693116 CCA
1 CCA
16693119 AGACGCTTCC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
54 33 0.65
55 16 0.31
56 2 0.04
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATAGTGGCAGAGCCA
Found at i:16694404 original size:22 final size:22
Alignment explanation
Indices: 16694361--16694406 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
16694351 ATAGAAGAAG
* *
16694361 AAAAGAATAACAAATGGAGAGA
1 AAAAGAAAAACAAAAGGAGAGA
* *
16694383 AAAAGAAAAATAAAAGGGGAGA
1 AAAAGAAAAACAAAAGGAGAGA
16694405 AA
1 AA
16694407 GAGTGATCAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAAGAAAAACAAAAGGAGAGA
Found at i:16698929 original size:16 final size:17
Alignment explanation
Indices: 16698908--16698940 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16698898 CAACCACAAC
16698908 CAATATATA-TCAACCA
1 CAATATATACTCAACCA
*
16698924 CAATATTTACTCAACCA
1 CAATATATACTCAACCA
16698941 TATAAACATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (17 bp):
CAATATATACTCAACCA
Found at i:16699756 original size:40 final size:40
Alignment explanation
Indices: 16699665--16699799 Score: 157
Period size: 41 Copynumber: 3.3 Consensus size: 40
16699655 ACAAAAAATT
*
16699665 TGCTAGGC-ATAAAGCCT-AGTATAATACACCGGCACAGAGCC
1 TGCTAGGCAAT-AAGCCTGA-TATAATACACCGGCATA-AGCC
* * * *
16699706 TACTAGGCAATAGGTCTGATATAATATACCGGCATAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCATAAGCC
*
16699746 TGCTAGGCAATAAGCCTGATATAATACAGCGGCATAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCAT-AAGCC
*
16699787 TGCTAGCCAATAA
1 TGCTAGGCAATAA
16699800 AGCCCGAATA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 34 0.43
41 43 0.54
42 3 0.04
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (40 bp):
TGCTAGGCAATAAGCCTGATATAATACACCGGCATAAGCC
Found at i:16704532 original size:16 final size:16
Alignment explanation
Indices: 16704513--16704543 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16704503 CTTCTTCACT
16704513 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
16704529 TACTTACTTACTTAA
1 TACTCACTTACTTAA
16704544 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:16704549 original size:20 final size:20
Alignment explanation
Indices: 16704510--16704549 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16704500 AAACTTCTTC
* *
16704510 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
16704530 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
16704550 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:16704843 original size:53 final size:54
Alignment explanation
Indices: 16704731--16704964 Score: 241
Period size: 55 Copynumber: 4.4 Consensus size: 54
16704721 TTAATTTTGT
* * * * * *
16704731 CATGGTCTTACGTGGTATCC-T---TT-TGAAACTTACCATTGACATGTCTCGA
1 CATGGTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGCCATGCCTTGG
*
16704780 CATGGTCTTACATGGTATCCTTGCCTTATG-AACTCACCAATGCCATGCCTTGG
1 CATGGTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGCCATGCCTTGG
* * * * *
16704833 TATGGTCTTACATGGGA-CCTTTGCCTTATAGAAACTTATCAATGCCATGTCTTGA
1 CATGGTCTTACATGGTATCC-TTGCCTTAT-GAAACTTACCAATGCCATGCCTTGG
* * *
16704888 CATAGTCTTACATGATATCCTTGCCTTA-GAAACCTTACCAATTTCCATGCCTTGG
1 CATGGTCTTACATGGTATCCTTGCCTTATGAAA-CTTACCAA-TGCCATGCCTTGG
16704943 CATGGTCTTACATGGTATCCTT
1 CATGGTCTTACATGGTATCCTT
16704965 AAACCCCAAT
Statistics
Matches: 151, Mismatches: 23, Indels: 16
0.79 0.12 0.08
Matches are distributed among these distances:
49 19 0.13
50 1 0.01
52 2 0.01
53 47 0.31
54 10 0.07
55 70 0.46
56 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.35
Consensus pattern (54 bp):
CATGGTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGCCATGCCTTGG
Found at i:16712390 original size:55 final size:54
Alignment explanation
Indices: 16712249--16712457 Score: 230
Period size: 55 Copynumber: 3.9 Consensus size: 54
16712239 GTATCCTTTT
* * *
16712249 GAAACTTACCATTG-CATGCCTCGACATGGTCTTACATGGTATCCTAGCCTTAT-
1 GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG-CTTATA
* * *
16712302 G-AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGACTTATA
1 GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTG-CTTATA
* * * *
16712356 GAAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCT-TA
1 GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCTTATA
* *
16712409 GAAACCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 GAAA-CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
16712458 AAACCCCAAT
Statistics
Matches: 130, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
52 12 0.09
53 38 0.29
54 10 0.08
55 68 0.52
56 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (54 bp):
GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCTTATA
Found at i:16719143 original size:46 final size:45
Alignment explanation
Indices: 16719036--16719200 Score: 179
Period size: 48 Copynumber: 3.5 Consensus size: 45
16719026 TTTAGTTATG
* *
16719036 TATTGGCACTTTGTGTGCGAGATTGAAATAGCTTCGACTACATATATA
1 TATTGGCACTTAGTGTGCGAGATTGAAATAGCTTCG-CT--ATATAAA
* *
16719084 TATTGGCACTTAGTGTGCGAGACTAAAATAGCTTCAGCTATATAAA
1 TATTGGCACTTAGTGTGCGAGATTGAAATAGCTTC-GCTATATAAA
*
16719130 TATTGGCACTTAGTGTGCGTA-ATTGAGATAGCTTCTGCTATATATACA
1 TATTGGCACTTAGTGTGCG-AGATTGAAATAGCTTC-GCTATATA-A-A
* * *
16719178 CATTGGCACTTAGCGTACGAGAT
1 TATTGGCACTTAGTGTGCGAGAT
16719201 CAATAGAGTT
Statistics
Matches: 101, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
46 44 0.44
47 3 0.03
48 53 0.52
49 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (45 bp):
TATTGGCACTTAGTGTGCGAGATTGAAATAGCTTCGCTATATAAA
Found at i:16722989 original size:55 final size:55
Alignment explanation
Indices: 16722844--16723053 Score: 241
Period size: 55 Copynumber: 3.9 Consensus size: 55
16722834 GTATCCTTTT
* * * *
16722844 GAAACTTACCATTGACATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTAT-
1 GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* ** *
16722898 G-AACTCACCAATGCCATGCCTTGGTATGGTCTTACATGGGA-CCTTTGCCTTATA
1 GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATA
* * *
16722952 GAAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCC-T-TA
1 GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* *
16723005 GAAACCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 GAAA-CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
16723054 AAACCCCAAT
Statistics
Matches: 130, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
52 2 0.02
53 47 0.36
54 10 0.08
55 69 0.53
56 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (55 bp):
GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
Found at i:16725729 original size:26 final size:27
Alignment explanation
Indices: 16725679--16725732 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 27
16725669 TTGCCTCAAG
16725679 TTCAAATCTTTTTGAGTCATCAAATAT
1 TTCAAATCTTTTTGAGTCATCAAATAT
16725706 TTCAAA-CTTTTGTGA-TCAGT-AAATAT
1 TTCAAATCTTTT-TGAGTCA-TCAAATAT
16725732 T
1 T
16725733 CGGCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (27 bp):
TTCAAATCTTTTTGAGTCATCAAATAT
Found at i:16737794 original size:26 final size:26
Alignment explanation
Indices: 16737758--16737808 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
16737748 TCGCAACCCG
16737758 ACTGGCACTAGCATTTCTAGGATATA
1 ACTGGCACTAGCATTTCTAGGATATA
16737784 ACTGGCACTAGCATTTCTAGGATAT
1 ACTGGCACTAGCATTTCTAGGATAT
16737809 CTCGGAGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (26 bp):
ACTGGCACTAGCATTTCTAGGATATA
Found at i:16739495 original size:41 final size:43
Alignment explanation
Indices: 16739437--16739519 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 43
16739427 TTTTTTATTT
* *
16739437 TGTCTGGGACATCGGCATCG-TATTTGATTTCGTGTAAGACCC
1 TGTCTGGGACATCGGCATCGATATTTGATTACATGTAAGACCC
16739479 TGTCT-GGACAGT-GGCATCGATATTTGATTACATGTAAGACC
1 TGTCTGGGACA-TCGGCATCGATATTTGATTACATGTAAGACC
16739520 ATGTTTAGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 12 0.32
42 25 0.68
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (43 bp):
TGTCTGGGACATCGGCATCGATATTTGATTACATGTAAGACCC
Found at i:16748228 original size:22 final size:22
Alignment explanation
Indices: 16748170--16748230 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
16748160 GACACACCCA
**
16748170 TGTGAG-GGA-ACACACGCCCG
1 TGTGAGAGGAGACACACGGTCG
*
16748190 TGTGAGAGGAGGCACACGGTCG
1 TGTGAGAGGAGACACACGGTCG
* *
16748212 TGTGGGAGGAGATACACGG
1 TGTGAGAGGAGACACACGG
16748231 CCGAAGGCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 6 0.18
21 3 0.09
22 24 0.73
ACGTcount: A:0.25, C:0.20, G:0.43, T:0.13
Consensus pattern (22 bp):
TGTGAGAGGAGACACACGGTCG
Found at i:16751319 original size:1 final size:1
Alignment explanation
Indices: 16751315--16751339 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
16751305 ATATCAATCC
16751315 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
16751340 GAATGCCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16753464 original size:25 final size:25
Alignment explanation
Indices: 16753428--16753483 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
16753418 GTGTTCTTGG
*
16753428 TTCTTTTTTATTTT-TATTTAGTTT-T
1 TTCTTTTGTATTTTCT-TTTA-TTTCT
16753453 TTCTTTTGTATTTTCTTTTATTTCT
1 TTCTTTTGTATTTTCTTTTATTTCT
16753478 TTCTTT
1 TTCTTT
16753484 CTCTTCGCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 3 0.11
25 24 0.86
26 1 0.04
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.79
Consensus pattern (25 bp):
TTCTTTTGTATTTTCTTTTATTTCT
Found at i:16754472 original size:3 final size:3
Alignment explanation
Indices: 16754466--16754569 Score: 95
Period size: 3 Copynumber: 34.7 Consensus size: 3
16754456 CATCATCATC
*
16754466 ATT ATT ATT GA-T ATT AAT 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
* * * * * * *
16754511 ATT ATT ATT GTT ACTT TTT GTC ACT ATT GTC ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
16754556 ACT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
16754570 ACTTATATTC
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.04
3 74 0.93
4 3 0.04
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:16756366 original size:20 final size:21
Alignment explanation
Indices: 16756341--16756380 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16756331 GTTTTCACAA
*
16756341 ATTTTA-TAGACCAAAATGTC
1 ATTTTAGTAAACCAAAATGTC
*
16756361 ATTTTAGTAAACTAAAATGT
1 ATTTTAGTAAACCAAAATGT
16756381 TCTATTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
ATTTTAGTAAACCAAAATGTC
Found at i:16757373 original size:2 final size:2
Alignment explanation
Indices: 16757366--16757392 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16757356 AAAACACATT
16757366 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
16757393 TTTATAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16757832 original size:13 final size:13
Alignment explanation
Indices: 16757816--16757840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16757806 CCATTACCAG
16757816 AAATAATAATAAC
1 AAATAATAATAAC
16757829 AAATAATAATAA
1 AAATAATAATAA
16757841 ATATCTAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAATAATAAC
Found at i:16758159 original size:2 final size:2
Alignment explanation
Indices: 16758152--16758191 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
16758142 TCTCCATGCA
*
16758152 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CG CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
16758192 TTTCTGGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:16760398 original size:2 final size:2
Alignment explanation
Indices: 16760391--16760415 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16760381 TGTATATGTG
16760391 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16760416 TCTTTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16763390 original size:18 final size:19
Alignment explanation
Indices: 16763359--16763396 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
16763349 AAATAGTTCG
*
16763359 AGTTATTTGAATTAA-TCA
1 AGTTATTCGAATTAACTCA
*
16763377 AGTTATTCGGATTAACTCA
1 AGTTATTCGAATTAACTCA
16763396 A
1 A
16763397 ATAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (19 bp):
AGTTATTCGAATTAACTCA
Found at i:16769939 original size:19 final size:18
Alignment explanation
Indices: 16769915--16769962 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
16769905 ATTTTTATAT
16769915 ATTTTAATACTACGTACA
1 ATTTTAATACTACGTACA
* * *
16769933 CATTTTATTATTACGTATA
1 -ATTTTAATACTACGTACA
16769952 AGTTTTAATAC
1 A-TTTTAATAC
16769963 ATACATTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (18 bp):
ATTTTAATACTACGTACA
Found at i:16773992 original size:9 final size:9
Alignment explanation
Indices: 16773978--16774007 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16773968 GCTTTTTTTT
16773978 GCATTCATC
1 GCATTCATC
16773987 GCATTCATC
1 GCATTCATC
16773996 GCATTCAT-
1 GCATTCATC
16774004 GCAT
1 GCAT
16774008 CAGCATTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.33
Consensus pattern (9 bp):
GCATTCATC
Found at i:16782770 original size:9 final size:9
Alignment explanation
Indices: 16782756--16782785 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16782746 CGCTTTTTTT
16782756 GCATTCATC
1 GCATTCATC
16782765 GCATTCATC
1 GCATTCATC
16782774 GCATTCAT-
1 GCATTCATC
16782782 GCAT
1 GCAT
16782786 CAGCATTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.33
Consensus pattern (9 bp):
GCATTCATC
Found at i:16791110 original size:89 final size:89
Alignment explanation
Indices: 16791006--16791175 Score: 229
Period size: 89 Copynumber: 1.9 Consensus size: 89
16790996 TTCAAACCAC
* * * * *
16791006 CAAGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCTGAGGATTTAC-AGATCTTATTA-CC-CTA
1 CAAGCCTTAAACCCCTAAACAGTAGGGTAACAAGCTGAAGATTGACGA-ATCTTA--ACCCTCTA
16791068 AGCAGTAGGGAAACAGATCAAAGGTGA
63 AGCAGTAGGGAAACAGATCAAAGGTGA
*
16791095 CAAGCCTTAAACCCCTAAACAGTAGGGTAACAAGCTGAAGATTGACGAATCTTAACCCTCTAAGT
1 CAAGCCTTAAACCCCTAAACAGTAGGGTAACAAGCTGAAGATTGACGAATCTTAACCCTCTAAGC
*
16791160 AGTAGGGAAATAGATC
66 AGTAGGGAAACAGATC
16791176 GAAAATGAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
87 1 0.01
88 2 0.03
89 67 0.94
90 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (89 bp):
CAAGCCTTAAACCCCTAAACAGTAGGGTAACAAGCTGAAGATTGACGAATCTTAACCCTCTAAGC
AGTAGGGAAACAGATCAAAGGTGA
Found at i:16791152 original size:44 final size:43
Alignment explanation
Indices: 16791012--16791166 Score: 127
Period size: 45 Copynumber: 3.5 Consensus size: 43
16791002 CCACCAAGCT
* *
16791012 TTAACCCCCTAAGCAGTAGGGTAACAAGCTGAGGATTTACAGATC
1 TTAA-CCCCTAAGCAGTAGGGTAACAAGCTGAAGATTGACA-ATC
* * * * *
16791057 TTATTA-CCCTAAGCAGTAGGGAAAC-AGATCAA-AGGTGACAAGCC
1 TTA--ACCCCTAAGCAGTAGGGTAACAAGCTGAAGA-TTGACAA-TC
*
16791101 TTAAACCCCTAAACAGTAGGGTAACAAGCTGAAGATTGACGAATC
1 TT-AACCCCTAAGCAGTAGGGTAACAAGCTGAAGATTGAC-AATC
*
16791146 TTAACCCTCTAAGTAGTAGGG
1 TTAACCC-CTAAGCAGTAGGG
16791167 AAATAGATCG
Statistics
Matches: 85, Mismatches: 15, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
43 3 0.04
44 33 0.39
45 45 0.53
46 3 0.04
47 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (43 bp):
TTAACCCCTAAGCAGTAGGGTAACAAGCTGAAGATTGACAATC
Found at i:16793609 original size:19 final size:18
Alignment explanation
Indices: 16793585--16793632 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
16793575 ATTTTTATAT
16793585 ATTTTAATACTACGTACA
1 ATTTTAATACTACGTACA
* * *
16793603 CATTTTATTATTACGTATA
1 -ATTTTAATACTACGTACA
16793622 AGTTTTAATAC
1 A-TTTTAATAC
16793633 ATACATTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (18 bp):
ATTTTAATACTACGTACA
Found at i:16795734 original size:24 final size:24
Alignment explanation
Indices: 16795703--16795818 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
16795693 GCTTTATCAT
* *
16795703 ATAACTGGGGCCT-AGCCTCTTTTA
1 ATAACTGGGGCATAAGCC-CTTTTG
*
16795727 ATAACTGGGG-AAAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTG
16795749 ATAACTGGGGCATAAGCCC-TTTG
1 ATAACTGGGGCATAAGCCCTTTTG
16795772 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
16795796 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
16795819 TCACTTCCTC
Statistics
Matches: 85, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
22 13 0.15
23 31 0.36
24 41 0.48
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:16795765 original size:23 final size:23
Alignment explanation
Indices: 16795702--16795818 Score: 166
Period size: 23 Copynumber: 5.0 Consensus size: 23
16795692 TGCTTTATCA
*
16795702 TATAACTGGGGCCT-AGCCTCTTT
1 TATAACTGGGGCATAAGCC-CTTT
*
16795725 TAATAACTGGGG-AAAAGCCCTTT
1 T-ATAACTGGGGCATAAGCCCTTT
16795748 TATAACTGGGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTT
*
16795771 GATAACTGGGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTT
16795794 TGATAACTGGGGCATAAGCCCTTT
1 T-ATAACTGGGGCATAAGCCCTTT
16795818 T
1 T
16795819 TCACTTCCTC
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
22 10 0.12
23 38 0.45
24 37 0.44
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (23 bp):
TATAACTGGGGCATAAGCCCTTT
Found at i:16795805 original size:47 final size:45
Alignment explanation
Indices: 16795702--16795817 Score: 162
Period size: 47 Copynumber: 2.5 Consensus size: 45
16795692 TGCTTTATCA
*
16795702 TATAACTGGGGCCT-AGCCTCTTTTAATAACTGGGGAAAAGCCCTTT
1 TATAACTGGGGCATAAGCC-C-TTTAATAACTGGGGAAAAGCCCTTT
* *
16795748 TATAACTGGGGCATAAGCCCTTTGATAACTGGGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTTAATAACTGGGG-AAAAGCCCTTT
16795794 TGATAACTGGGGCATAAGCCCTTT
1 T-ATAACTGGGGCATAAGCCCTTT
16795818 TTCACTTCCT
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
45 13 0.20
46 25 0.39
47 26 0.41
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (45 bp):
TATAACTGGGGCATAAGCCCTTTAATAACTGGGGAAAAGCCCTTT
Found at i:16795893 original size:20 final size:20
Alignment explanation
Indices: 16795865--16795948 Score: 150
Period size: 20 Copynumber: 4.2 Consensus size: 20
16795855 GCATTTATGA
*
16795865 ACATCTCATGTGCATATCAT
1 ACATGTCATGTGCATATCAT
16795885 ACATGTCATGTGCATATCAT
1 ACATGTCATGTGCATATCAT
*
16795905 ACATATCATGTGCATATCAT
1 ACATGTCATGTGCATATCAT
16795925 ACATGTCATGTGCATATCAT
1 ACATGTCATGTGCATATCAT
16795945 ACAT
1 ACAT
16795949 ACCATGTTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (20 bp):
ACATGTCATGTGCATATCAT
Found at i:16795920 original size:11 final size:11
Alignment explanation
Indices: 16795870--16795944 Score: 63
Period size: 11 Copynumber: 7.4 Consensus size: 11
16795860 TATGAACATC
16795870 TCATGTGCATA
1 TCATGTGCATA
* *
16795881 TCA--TACATG
1 TCATGTGCATA
16795890 TCATGTGCATA
1 TCATGTGCATA
*
16795901 TCA--TACATA
1 TCATGTGCATA
16795910 TCATGTGCATA
1 TCATGTGCATA
* *
16795921 TCA--TACATG
1 TCATGTGCATA
16795930 TCATGTGCATA
1 TCATGTGCATA
16795941 TCAT
1 TCAT
16795945 ACATACCATG
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 22 0.46
11 26 0.54
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:16796031 original size:25 final size:25
Alignment explanation
Indices: 16795992--16796039 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
16795982 ATGTATAAAC
* * *
16795992 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
16796017 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
16796040 AATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:16797299 original size:27 final size:27
Alignment explanation
Indices: 16797279--16797807 Score: 653
Period size: 27 Copynumber: 19.6 Consensus size: 27
16797269 AGGGTATTTT
*
16797279 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
16797306 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
16797333 AGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
16797360 -GATAATTATGTAAATCGGGGGTAAAA-
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * *
16797386 TGATAATTATGTAAAT-TAGGGTAAAAC
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * *
16797413 GGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
16797440 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
16797467 -GATAATTCTGTAAATCGAGGGTAAAAT
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
16797494 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
* *
16797521 GGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
16797548 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
16797575 GGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
16797602 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
16797629 AATAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
* *
16797656 AGTAATTTTGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
16797683 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
16797710 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
16797737 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
16797764 AGTAATTCTATAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
16797791 GGTAATTCTGTAAATCG
1 AGTAATTCTGTAAATCG
16797808 GGAGTACTTT
Statistics
Matches: 444, Mismatches: 42, Indels: 32
0.86 0.08 0.06
Matches are distributed among these distances:
26 26 0.06
27 412 0.93
28 6 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:16802421 original size:275 final size:275
Alignment explanation
Indices: 16801930--16802478 Score: 1017
Period size: 275 Copynumber: 2.0 Consensus size: 275
16801920 TGGAACTTCT
* *
16801930 AAAGAAGTTTGCACATTTTGTTGTCAAACCAGTGAGTATTCCTTATAATGATAGCACTCAATTGA
1 AAAGAAGTTTGCACACTTTGTTGTCAAACCAGTAAGTATTCCTTATAATGATAGCACTCAATTGA
*
16801995 AGAAAAATAGAGGTGAGTCCATTACTTAGTTAGAGTATGCATAGTTTATTGAGAGACTAATACAT
66 AGAAAAATAGAGGTGAGTCCATTACTTAGTTAGAGTATGCATAGTTTATTAAGAGACTAATACAT
*
16802060 TTAATGAATTTTAAATAACCAGATATAACGTATGTTATATGTCTACTAAGAAGGTACATTCATAA
131 TTAATGAATTTTAAATAACCAGATATAACATATGTTATATGTCTACTAAGAAGGTACATTCATAA
*
16802125 CCCAAGTCATGAACATTGGGTTGCAATAATCAGATTTATGAAATATTTGAAAGGGATCATTAATT
196 CCCAAGTCATGAACATTGGGTTGCAATAATCAAATTTATGAAATATTTGAAAGGGATCATTAATT
16802190 ATGATATTTTATTTG
261 ATGATATTTTATTTG
*
16802205 AAAGAAGTTTGCTCACTTTGTTGTCAAACCAGTAAGTATTCCTTATAATGATAGCACTCAATTGA
1 AAAGAAGTTTGCACACTTTGTTGTCAAACCAGTAAGTATTCCTTATAATGATAGCACTCAATTGA
* *
16802270 AGAAAAATAGAGGTGAGTCCATTGCTTAGTTAGAGTATGCGTAGTTTATTAAGAGACTAATACAT
66 AGAAAAATAGAGGTGAGTCCATTACTTAGTTAGAGTATGCATAGTTTATTAAGAGACTAATACAT
16802335 TTAATGAATTTTAAATAACCAGATATAACATATGTTATATGTCTACTAAGAAGGTACATTCATAA
131 TTAATGAATTTTAAATAACCAGATATAACATATGTTATATGTCTACTAAGAAGGTACATTCATAA
*
16802400 CCCAAGTCATGAACATTGGGTTGCAATAATCAAATTTATGAAATATTTGAAAGGTATCATTAATT
196 CCCAAGTCATGAACATTGGGTTGCAATAATCAAATTTATGAAATATTTGAAAGGGATCATTAATT
16802465 ATGATATTTTATTT
261 ATGATATTTTATTT
16802479 AATAGATTTC
Statistics
Matches: 265, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
275 265 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (275 bp):
AAAGAAGTTTGCACACTTTGTTGTCAAACCAGTAAGTATTCCTTATAATGATAGCACTCAATTGA
AGAAAAATAGAGGTGAGTCCATTACTTAGTTAGAGTATGCATAGTTTATTAAGAGACTAATACAT
TTAATGAATTTTAAATAACCAGATATAACATATGTTATATGTCTACTAAGAAGGTACATTCATAA
CCCAAGTCATGAACATTGGGTTGCAATAATCAAATTTATGAAATATTTGAAAGGGATCATTAATT
ATGATATTTTATTTG
Found at i:16803071 original size:23 final size:23
Alignment explanation
Indices: 16803045--16803095 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
16803035 TGATTTTTAA
16803045 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
16803068 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
16803091 ATTTA
1 ATTTA
16803096 AAAAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:16803072 original size:13 final size:13
Alignment explanation
Indices: 16803054--16803095 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
16803044 AATTTAGAAT
16803054 TATTTAGTGATAA
1 TATTTAGTGATAA
*
16803067 TATTTA--GA-AT
1 TATTTAGTGATAA
16803077 TATTTAGTGATAA
1 TATTTAGTGATAA
16803090 TATTTA
1 TATTTA
16803096 AAAAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 2 0.08
13 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:16816535 original size:15 final size:15
Alignment explanation
Indices: 16816515--16816544 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16816505 TTTGAATCCC
16816515 TTTTATTTTTATTTT
1 TTTTATTTTTATTTT
16816530 TTTTATTTTTATTTT
1 TTTTATTTTTATTTT
16816545 CCTTTATTTA
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:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTATTTTTATTTT
Found at i:16816544 original size:20 final size:21
Alignment explanation
Indices: 16816515--16816559 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
16816505 TTTGAATCCC
* *
16816515 TTTTATTTTTATTTTTTTTAT
1 TTTTATTTTTACTTTATTTAT
*
16816536 TTTTA-TTTTCCTTTATTTAT
1 TTTTATTTTTACTTTATTTAT
16816556 TTTT
1 TTTT
16816560 GAAGACTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTATTTTTACTTTATTTAT
Found at i:16825685 original size:12 final size:13
Alignment explanation
Indices: 16825659--16825685 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16825649 TTTTTGCTAG
16825659 TTAGACAATTTTT
1 TTAGACAATTTTT
16825672 TTAGACAATTTTT
1 TTAGACAATTTTT
16825685 T
1 T
16825686 CAATTCGATC
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:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (13 bp):
TTAGACAATTTTT
Found at i:16830227 original size:46 final size:46
Alignment explanation
Indices: 16830151--16830410 Score: 163
Period size: 46 Copynumber: 5.6 Consensus size: 46
16830141 AACCTGCCCG
* *
16830151 TAAGCGAAATCGGACTCAACTCAACGAGCTCGGGCATTTGCATCCA
1 TAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCATTTGCATCCA
* * * *
16830197 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT-C-
1 TAAGCGAACTCAGACTCAACTCAACGAGCTCGG--G-C-ATTTGCATCCA
** * * * *
16830245 T-CCCGAACTCAGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
1 TAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCATTTGCATCCA
* * * * * *
16830290 TAAGTGAACTCGGACTCAACTTAACTAGCTCGGATGCCTAGTTACAT-C-
1 TAAGCGAACTCAGACTCAACTCAACGAGCTCGG--G-C-ATTTGCATCCA
* * * * * * *
16830338 TTA-CGAACTCAGACTCAACTCAACAAGTTCAGACGTTCGCATCCA
1 TAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCATTTGCATCCA
* *
16830383 TAAGTGAACTTAGACTCAACTCAACGAG
1 TAAGCGAACTCAGACTCAACTCAACGAG
16830411 TTCGAATGCC
Statistics
Matches: 158, Mismatches: 42, Indels: 28
0.69 0.18 0.12
Matches are distributed among these distances:
43 8 0.05
44 4 0.03
45 3 0.02
46 76 0.48
47 49 0.31
48 4 0.03
49 4 0.03
50 10 0.06
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.22
Consensus pattern (46 bp):
TAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCATTTGCATCCA
Found at i:16830271 original size:47 final size:47
Alignment explanation
Indices: 16830202--16830361 Score: 159
Period size: 47 Copynumber: 3.4 Consensus size: 47
16830192 ATCCATAAGT
* **
16830202 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCCC
1 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTAAC
* * *
16830249 GAACTCAGACTCAACTCAACGAGTTCGGA---C--GTTCGCATCCATAAGT
1 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT-C-TAA-C
* * * *
16830295 GAACTCGGACTCAACTTAACTAGCTCGGATGCCTAGTTACATCTTAC
1 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTAAC
16830342 GAACTCAGACTCAACTCAAC
1 GAACTCAGACTCAACTCAAC
16830362 AAGTTCAGAC
Statistics
Matches: 89, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 1 0.01
46 25 0.28
47 45 0.51
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (47 bp):
GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTAAC
Found at i:16830322 original size:93 final size:93
Alignment explanation
Indices: 16830163--16830420 Score: 390
Period size: 93 Copynumber: 2.8 Consensus size: 93
16830153 AGCGAAATCG
* * * *
16830163 GACTCAACTCAACGAGCTCGGGCATTTGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTC
1 GACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTC
*
16830228 GGATGCCTAGTTACATCTCCCGAACTCA
66 GGATGCCTAGTTACATCTCACGAACTCA
* *
16830256 GACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTTAACTAGCTC
1 GACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTC
*
16830321 GGATGCCTAGTTACATCTTACGAACTCA
66 GGATGCCTAGTTACATCTCACGAACTCA
* * ** *
16830349 GACTCAACTCAACAAGTTCAGACGTTCGCATCCATAAGTGAACTTAGACTCAACTCAACGAGTTC
1 GACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTC
*
16830414 GAATGCC
66 GGATGCC
16830421 CAAATATCCT
Statistics
Matches: 149, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 149 1.00
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (93 bp):
GACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTC
GGATGCCTAGTTACATCTCACGAACTCA
Found at i:16841207 original size:45 final size:45
Alignment explanation
Indices: 16841143--16841313 Score: 270
Period size: 45 Copynumber: 3.8 Consensus size: 45
16841133 TATCGTACAG
* *
16841143 TACTATTCGGGCCTTTGAGCCTAGTAGGCTATAATGTCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGACGGTGAGA
*
16841188 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGACGGTGAGA
* ** * *
16841233 TACTATTCAGGCCTTCAAGCCTAGCAGGCTATAATAACAGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGACGGTGAGA
16841278 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATG
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATG
16841314 CCGATGAAAT
Statistics
Matches: 114, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 114 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGACGGTGAGA
Found at i:16841373 original size:41 final size:40
Alignment explanation
Indices: 16841282--16841403 Score: 120
Period size: 41 Copynumber: 2.9 Consensus size: 40
16841272 GTGAGATACT
* * * *
16841282 ATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAAATG
1 ATTCGGG-CTTCGAACCTAGCAGGCCA-AATGCCGGTG-AATG
*
16841325 ATATCGGGCTTCGAACCTAGCAGGCGAAATGCCGGTGAATG
1 AT-TCGGGCTTCGAACCTAGCAGGCCAAATGCCGGTGAATG
* *
16841366 AATTCGGGTTTAC-AACCTAGCAGGCCCAATGCCGGTGA
1 -ATTCGGGCTT-CGAACCTAGCAGGCCAAATGCCGGTGA
16841404 TTTGATAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
41 34 0.49
42 12 0.17
43 18 0.26
44 5 0.07
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (40 bp):
ATTCGGGCTTCGAACCTAGCAGGCCAAATGCCGGTGAATG
Found at i:16844239 original size:37 final size:37
Alignment explanation
Indices: 16844180--16844288 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
16844170 AGCTCAGATG
* *
16844180 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
16844217 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
16844254 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
16844289 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:16844487 original size:48 final size:48
Alignment explanation
Indices: 16844429--16845009 Score: 929
Period size: 48 Copynumber: 12.0 Consensus size: 48
16844419 ATATACACAC
* * *
16844429 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCTCATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
16844477 ATCTCATACATATTTCACACTAGCCATTCGACTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
16844525 ATCTCATATATATATTTCACATTAACCATTCGGCTTTACCACATATACAT
1 ATCTC--ATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
16844575 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
16844623 ATCTCATATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTC--ATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
16844673 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACTTATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
16844721 ATCTCATATATATTTCACATT-----TTCGGCTTTACCACATAAACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
16844764 ATCTCATATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTC--ATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
16844814 ATCTCATACATATTTCACATTATCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
16844862 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
16844910 ATCTCATATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTC--ATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
16844960 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
16845008 AT
1 AT
16845010 ATTTATCTTG
Statistics
Matches: 499, Mismatches: 21, Indels: 26
0.91 0.04 0.05
Matches are distributed among these distances:
43 25 0.05
45 16 0.03
48 294 0.59
50 164 0.33
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:16844540 original size:98 final size:98
Alignment explanation
Indices: 16844438--16845009 Score: 973
Period size: 98 Copynumber: 5.9 Consensus size: 98
16844428 CATCTCCTAC
* * *
16844438 ATATTTCACACTAGCCATTCGGCTTTACCTCATATACATATCTCATACATATTTCACACTAGCCA
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
*
16844503 TTCGACTTTACCACATATACATATCTCATATAT
66 TTCGGCTTTACCACATATACATATCTCATATAT
*
16844536 ATATTTCACATTAACCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
16844601 TTCGGCTTTACCACATATACATATCTCATATAT
66 TTCGGCTTTACCACATATACATATCTCATATAT
16844634 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
*
16844699 TTCGGCTTTACCACTTATACATATCTC--ATAT
66 TTCGGCTTTACCACATATACATATCTCATATAT
* *
16844730 ATATTTCACATT-----TTCGGCTTTACCACATAAACATATCTCATATATATATTTCACATTAGC
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--ATACATATTTCACATTAGC
*
16844790 CATTCGGCTTTACCACATATACATATCTC--ATAC
64 CATTCGGCTTTACCACATATACATATCTCATATAT
*
16844823 ATATTTCACATTATCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
16844888 TTCGGCTTTACCACATATACATATCTCATATAT
66 TTCGGCTTTACCACATATACATATCTCATATAT
16844921 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
1 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
16844986 TTCGGCTTTACCACATATACATAT
66 TTCGGCTTTACCACATATACATAT
16845010 ATTTATCTTG
Statistics
Matches: 450, Mismatches: 15, Indels: 18
0.93 0.03 0.04
Matches are distributed among these distances:
91 26 0.06
93 61 0.14
96 63 0.14
98 300 0.67
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.37
Consensus pattern (98 bp):
ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
TTCGGCTTTACCACATATACATATCTCATATAT
Found at i:16844971 original size:287 final size:286
Alignment explanation
Indices: 16844455--16845009 Score: 1004
Period size: 287 Copynumber: 1.9 Consensus size: 286
16844445 ACACTAGCCA
* *
16844455 TTCGGCTTTACCTCATATACATATCTCATACATATTTCACACTAGCCATTCGACTTTACCACATA
1 TTCGGCTTTACCACATAAACATATCTCATACATATTTCACACTAGCCATTCGACTTTACCACATA
*
16844520 TACATATCTCATATATATATTTCACATTAACCATTCGGCTTTACCACATATACATATCTCATACA
66 TACATATCTCA-ATACATATTTCACATTAACCATTCGGCTTTACCACATATACATATCTCATACA
16844585 TATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATTAGCC
130 TATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATTAGCC
*
16844650 ATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACTT
195 ATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACAT
16844715 ATACATATCTCATATATATTTCACATT
260 ATACATATCTCATATATATTTCACATT
* * *
16844742 TTCGGCTTTACCACATAAACATATCTCATATATATATTTCACATTAGCCATTCGGCTTTACCACA
1 TTCGGCTTTACCACATAAACATATCTC--ATACATATTTCACACTAGCCATTCGACTTTACCACA
*
16844807 TATACATATCTC-ATACATATTTCACATTATCCATTCGGCTTTACCACATATACATATCTCATAC
64 TATACATATCTCAATACATATTTCACATTAACCATTCGGCTTTACCACATATACATATCTCATAC
16844871 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATTAGC
129 ATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATTAGC
16844936 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
194 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
16845001 TATACATAT
259 TATACATAT
16845010 ATTTATCTTG
Statistics
Matches: 258, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
287 213 0.83
289 45 0.17
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.37
Consensus pattern (286 bp):
TTCGGCTTTACCACATAAACATATCTCATACATATTTCACACTAGCCATTCGACTTTACCACATA
TACATATCTCAATACATATTTCACATTAACCATTCGGCTTTACCACATATACATATCTCATACAT
ATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATTAGCCA
TTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
TACATATCTCATATATATTTCACATT
Found at i:16851717 original size:27 final size:27
Alignment explanation
Indices: 16851684--16851995 Score: 391
Period size: 27 Copynumber: 11.6 Consensus size: 27
16851674 AAAGTACTCC
16851684 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
16851711 C-AGTTTATAGAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
16851738 CGATTTACAAAATTA-C-TATTTACCCT
1 CGATTTACAGAATTACCGT-TTTACCCT
**
16851764 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
16851791 CGATTTATAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* * * *
16851817 CTAATTTACATAATTACCATTTTACCCC
1 C-GATTTACAGAATTACCGTTTTACCCT
* *
16851845 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
16851872 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
16851899 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
16851926 CGATTTATAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
16851953 CGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
16851980 CGATTTACAAAATTAC
1 CGATTTACAGAATTAC
16851996 TAAAATACCC
Statistics
Matches: 250, Mismatches: 26, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
25 2 0.01
26 22 0.09
27 222 0.89
28 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:16852032 original size:81 final size:81
Alignment explanation
Indices: 16851665--16852039 Score: 258
Period size: 81 Copynumber: 4.6 Consensus size: 81
16851655 CTCGACTTGT
* * **** * *
16851665 AAAATTACCAAAGTACTCC-CGATTTACAGAATTACCGTTTTACCCTC-AGTTTATAGAATTACT
1 AAAATTACCAAAATAC-CCTCGATTTATAGAATTACCACAATACCCTCGA-TTTACAGAATTACC
16851728 GTTTTACCCTCGATTTAC
64 GTTTTACCCTCGATTTAC
* ** * * *** *
16851746 AAAATTA-CTATTTACCCTC-AGTTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACCG
1 AAAATTACCAAAATACCCTCGA-TTTATAGAATTACCACAATACCCTCGATTTACAGAATTACCG
*
16851809 TTTTACCC-CTAATTTAC
65 TTTTACCCTC-GATTTAC
* *** * * * * ****
16851826 ATAATTACCATTTTACCCCCGATTTACATAATTATCGTTTTACCCTCGATTTACAGAATTACCGT
1 AAAATTACCAAAATACCCTCGATTTATAGAATTACCACAATACCCTCGATTTACAGAATTACCGT
16851891 TTTACCCTCGATTTAC
66 TTTACCCTCGATTTAC
* *** * *** *
16851907 AGAATTACCATTTTACCCTCGATTTATAGAATTACTATTTTACCCTCGATTTACAGAATTACTGT
1 AAAATTACCAAAATACCCTCGATTTATAGAATTACCACAATACCCTCGATTTACAGAATTACCGT
16851972 TTTACCCTCGATTTAC
66 TTTACCCTCGATTTAC
* * * * * *
16851988 AAAATTACTAAAATACCCTTGGTTTGT-GAAATTACCGCAATACCCTCAATTT
1 AAAATTACCAAAATACCCTCGATTTATAG-AATTACCACAATACCCTCGATTT
16852040 GTAAAACTAC
Statistics
Matches: 247, Mismatches: 39, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
79 4 0.02
80 64 0.26
81 177 0.72
82 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTCGATTTATAGAATTACCACAATACCCTCGATTTACAGAATTACCGT
TTTACCCTCGATTTAC
Found at i:16853334 original size:9 final size:9
Alignment explanation
Indices: 16853322--16853378 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
16853312 TTTGATAAAC
16853322 ATGATATGT
1 ATGATATGT
*
16853331 ATGATATGCAC
1 ATGATATG--T
*
16853342 ATGACATGT
1 ATGATATGT
*
16853351 ATGATATGCAC
1 ATGATATG--T
16853362 ATGATATGT
1 ATGATATGT
16853371 ATGATATG
1 ATGATATG
16853379 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:16853345 original size:20 final size:20
Alignment explanation
Indices: 16853320--16853390 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
16853310 ATTTTGATAA
16853320 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
16853340 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
16853360 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
16853380 ACATGAGATGT
1 ACATGATATGT
16853391 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:16853367 original size:11 final size:11
Alignment explanation
Indices: 16853331--16853385 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
16853321 CATGATATGT
16853331 ATGATATGCAC
1 ATGATATGCAC
* *
16853342 ATGACATG--T
1 ATGATATGCAC
16853351 ATGATATGCAC
1 ATGATATGCAC
*
16853362 ATGATATG--T
1 ATGATATGCAC
16853371 ATGATATGCAC
1 ATGATATGCAC
16853382 ATGA
1 ATGA
16853386 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:16853467 original size:23 final size:23
Alignment explanation
Indices: 16853437--16853579 Score: 250
Period size: 23 Copynumber: 6.1 Consensus size: 23
16853427 AGGAAGTGCA
16853437 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
16853460 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
16853483 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
16853507 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
16853530 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
16853553 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
16853577 AAA
1 AAA
16853580 AGAGGCTAGG
Statistics
Matches: 115, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
23 71 0.62
24 44 0.38
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:16853515 original size:24 final size:23
Alignment explanation
Indices: 16853436--16853601 Score: 235
Period size: 23 Copynumber: 7.0 Consensus size: 23
16853426 GAGGAAGTGC
16853436 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
16853459 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
16853482 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
16853505 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
16853529 TAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
16853553 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
16853577 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
16853601 A
1 A
16853602 TGATAAAGCA
Statistics
Matches: 132, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
23 66 0.50
24 56 0.42
25 10 0.08
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:16853528 original size:47 final size:46
Alignment explanation
Indices: 16853437--16853601 Score: 251
Period size: 47 Copynumber: 3.5 Consensus size: 46
16853427 AGGAAGTGCA
*
16853437 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
16853483 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATT
*
16853530 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTA-TAAAAGGGCTTATGCCCCAGTTATT
*
16853577 AAAAGAGGC-TAGGCCTCCAGTTATA
1 -AAAG-GGCTTATGCC-CCAGTTATA
16853602 TGATAAAGCA
Statistics
Matches: 111, Mismatches: 3, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
46 22 0.20
47 67 0.60
48 12 0.11
49 10 0.09
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
Found at i:16862087 original size:5 final size:5
Alignment explanation
Indices: 16862077--16862104 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
16862067 GCAACTCACA
16862077 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
16862105 GAATTCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:16867948 original size:11 final size:11
Alignment explanation
Indices: 16867932--16867956 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16867922 AAAGTTTCCT
16867932 TTAGATAAGCA
1 TTAGATAAGCA
16867943 TTAGATAAGCA
1 TTAGATAAGCA
16867954 TTA
1 TTA
16867957 AGAAAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (11 bp):
TTAGATAAGCA
Found at i:16869352 original size:22 final size:23
Alignment explanation
Indices: 16869317--16869361 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
16869307 TTTTCTATTC
16869317 TCTCTCTTTTTTTACATTATAAG
1 TCTCTCTTTTTTTACATTATAAG
16869340 TCTCTC-TTTTTTACATTATAAG
1 TCTCTCTTTTTTTACATTATAAG
16869362 ATAATTGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (23 bp):
TCTCTCTTTTTTTACATTATAAG
Found at i:16875565 original size:7 final size:7
Alignment explanation
Indices: 16875553--16875597 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
16875543 AGGAAAAAAA
16875553 TTATATT
1 TTATATT
16875560 TTATATT
1 TTATATT
16875567 TTATATT
1 TTATATT
16875574 TTATATT
1 TTATATT
16875581 TTATATT
1 TTATATT
16875588 TTA-ATT
1 TTATATT
16875594 TTAT
1 TTAT
16875598 TTGATTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.16
7 31 0.84
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATATT
Found at i:16876941 original size:2 final size:2
Alignment explanation
Indices: 16876936--16876967 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16876926 AAACTAGTAT
16876936 TA TA 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 TA TA
16876968 GTAAAGAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16882193 original size:44 final size:44
Alignment explanation
Indices: 16882130--16882217 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
16882120 CCCAAACGAG
* *
16882130 AGTCTTACAAACATTCACAAATTTTAGCTTCCCGAGTGAGCCAT
1 AGTCTTACAAACATTCACAAATCTTAGCTTCCCAAGTGAGCCAT
16882174 AGTCTTACAAACATTCACAAATCTTAGCTTCCCAAGTGAGCCAT
1 AGTCTTACAAACATTCACAAATCTTAGCTTCCCAAGTGAGCCAT
16882218 TTTGGCAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.28
Consensus pattern (44 bp):
AGTCTTACAAACATTCACAAATCTTAGCTTCCCAAGTGAGCCAT
Found at i:16889962 original size:24 final size:23
Alignment explanation
Indices: 16889905--16889962 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
16889895 ACCATTAAAT
*
16889905 ATTTGTAATTAGTATTTTAAAAA
1 ATTTGTAATTAATATTTTAAAAA
* * *
16889928 AATT-TAATTAATAATTTTAACAC
1 ATTTGTAATTAAT-ATTTTAAAAA
16889951 ATTTGTAATTAA
1 ATTTGTAATTAA
16889963 GCACCAAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 7 0.25
23 14 0.50
24 7 0.25
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (23 bp):
ATTTGTAATTAATATTTTAAAAA
Found at i:16890749 original size:32 final size:32
Alignment explanation
Indices: 16890713--16890778 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
16890703 GCAAGGTTTG
16890713 GAGAAAGGCTGCCACATTAACAATGACTACCT
1 GAGAAAGGCTGCCACATTAACAATGACTACCT
16890745 GAGAAAGGCTGCCACATTAACAATGACTACCT
1 GAGAAAGGCTGCCACATTAACAATGACTACCT
16890777 GA
1 GA
16890779 TAAATATACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (32 bp):
GAGAAAGGCTGCCACATTAACAATGACTACCT
Found at i:16891180 original size:14 final size:14
Alignment explanation
Indices: 16891161--16891187 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16891151 GATCGTACGA
16891161 TACATAGACATAAT
1 TACATAGACATAAT
16891175 TACATAGACATAA
1 TACATAGACATAA
16891188 ACATACTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (14 bp):
TACATAGACATAAT
Found at i:16891443 original size:12 final size:12
Alignment explanation
Indices: 16891426--16891450 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16891416 AATGAATGAT
16891426 TAAAGAAGAAAA
1 TAAAGAAGAAAA
16891438 TAAAGAAGAAAA
1 TAAAGAAGAAAA
16891450 T
1 T
16891451 CGAAGCAGTA
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:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (12 bp):
TAAAGAAGAAAA
Found at i:16897295 original size:9 final size:9
Alignment explanation
Indices: 16897272--16897305 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
16897262 AAATTATATG
*
16897272 AAAAGAAGA
1 AAAAAAAGA
*
16897281 AGAAAAAGA
1 AAAAAAAGA
16897290 AAAAAAAGA
1 AAAAAAAGA
16897299 AAAAAAA
1 AAAAAAA
16897306 AGAGAGCCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:16898297 original size:14 final size:14
Alignment explanation
Indices: 16898252--16898299 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
16898242 TTTAAATTAA
16898252 ATAAATATTTAAAC
1 ATAAATATTTAAAC
* **
16898266 ATAAGT-TTTTTA-
1 ATAAATATTTAAAC
16898278 ATAAATATTTAAAC
1 ATAAATATTTAAAC
16898292 ATAAATAT
1 ATAAATAT
16898300 AAATGATTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 5 0.19
13 8 0.31
14 13 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAATATTTAAAC
Found at i:16900361 original size:42 final size:40
Alignment explanation
Indices: 16900275--16900362 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 40
16900265 ATGATTGTTG
* *
16900275 AATTGAATATATATATATTGAGAAAATGTGTTTATTGTCA
1 AATTGAATATATATATATTGAGAAAATATGTATATTGTCA
* * * * *
16900315 AATTGAATATATGTTTATATGTGATAATATGTATATATGTGA
1 AATTGAATATATATATAT-TGAGAAAATATGTATAT-TGTCA
16900357 AATTGA
1 AATTGA
16900363 GACATTGGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 16 0.41
41 13 0.33
42 10 0.26
ACGTcount: A:0.40, C:0.01, G:0.16, T:0.43
Consensus pattern (40 bp):
AATTGAATATATATATATTGAGAAAATATGTATATTGTCA
Found at i:16900737 original size:5 final size:5
Alignment explanation
Indices: 16900736--16900770 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
16900726 AATATGAAAT
16900736 GATGA GATGA GATGA GATGA GATGA GATGA GATGA
1 GATGA GATGA GATGA GATGA GATGA GATGA GATGA
16900771 AATGTGAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (5 bp):
GATGA
Found at i:16902644 original size:25 final size:26
Alignment explanation
Indices: 16902616--16902673 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
16902606 GGACACACCA
*
16902616 CAGCTCA-CATGAGTTTTCCGTTATT
1 CAGCTCAGCATGAGCTTTCCGTTATT
16902641 CAGCT-AGCATGAGCTTTCCGTTATT
1 CAGCTCAGCATGAGCTTTCCGTTATT
16902666 CAGCTCAG
1 CAGCTCAG
16902674 AAGAACTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 1 0.03
25 27 0.90
26 2 0.07
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (26 bp):
CAGCTCAGCATGAGCTTTCCGTTATT
Found at i:16916167 original size:69 final size:69
Alignment explanation
Indices: 16916085--16916244 Score: 209
Period size: 69 Copynumber: 2.3 Consensus size: 69
16916075 CTTTTTAAGT
* * *
16916085 ATTAAAATT--ATTTTTAATGAAATTAGTAAAGAATTGAGCTATAAGAGTATTCTTT-GCTCAAT
1 ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTTTAG-TCAAT
16916147 GAAGG
65 GAAGG
**
16916152 ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATGTGAGTATTCTTTAGTCAATG
1 ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTTTAGTCAATG
**
16916217 TGGG
66 AAGG
* *
16916221 ATTAAAATTAACTTTTTTATGAAA
1 ATTAAAATTAAATTTTTAATGAAA
16916245 GTAGGGAAGA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
67 9 0.11
69 71 0.88
70 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (69 bp):
ATTAAAATTAAATTTTTAATGAAAATAGTAAAGAAGTGAACTATAAGAGTATTCTTTAGTCAATG
AAGG
Found at i:16918201 original size:20 final size:20
Alignment explanation
Indices: 16918176--16918215 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16918166 TAAATTTTGG
*
16918176 ATTTATTTTTAATTATCTTT
1 ATTTATTTGTAATTATCTTT
*
16918196 ATTTATTTGTATTTATCTTT
1 ATTTATTTGTAATTATCTTT
16918216 TAAAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (20 bp):
ATTTATTTGTAATTATCTTT
Found at i:16924597 original size:5 final size:5
Alignment explanation
Indices: 16924578--16924611 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
16924568 GCAACTCAAT
16924578 TTTTA TTTT- TATTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTT
16924612 TGGATGTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 25 0.93
6 1 0.04
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:16927427 original size:96 final size:96
Alignment explanation
Indices: 16927249--16927431 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 96
16927239 TTTTTAAGAA
* ** *
16927249 TATGTTGGGCTGAGTAACCAGGGTGAGGTACTTGGCTGTCATCTCTCTTCATGTCAAAAGGTTCG
1 TATGTTGGGCTGAGTAACCAGGGTGAGGTACTTGACTGTCATCTCTCTTCACATCAAAAGGTTCA
*
16927314 ATATGTTCTTAAGAAAAATAAAAATTAGGAG
66 ATATGTTCTTAACAAAAATAAAAATTAGGAG
*** * * * *
16927345 TATGTTGGGCTGAGTAATTGGGGTGAGGTGCTTGACTGTCATCTCTTTTCGCATCAAAAGGTTTA
1 TATGTTGGGCTGAGTAACCAGGGTGAGGTACTTGACTGTCATCTCTCTTCACATCAAAAGGTTCA
*
16927410 ATATATT-TCTAACAAAAATAAA
66 ATATGTTCT-TAACAAAAATAAA
16927432 TAAATTAAAT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
95 1 0.01
96 72 0.99
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (96 bp):
TATGTTGGGCTGAGTAACCAGGGTGAGGTACTTGACTGTCATCTCTCTTCACATCAAAAGGTTCA
ATATGTTCTTAACAAAAATAAAAATTAGGAG
Found at i:16927469 original size:16 final size:16
Alignment explanation
Indices: 16927448--16927483 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
16927438 AAATCAAATT
16927448 AAAAAA-AAGAGAAAGA
1 AAAAAATAAGA-AAAGA
16927464 AAAAAATAAGAAAAGA
1 AAAAAATAAGAAAAGA
16927480 AAAA
1 AAAA
16927484 TTAATAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAAAATAAGAAAAGA
Found at i:16928066 original size:14 final size:13
Alignment explanation
Indices: 16928047--16928084 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
16928037 ATTTAATGTT
16928047 TAATTATATTAGGA
1 TAATTAT-TTAGGA
*
16928061 TAATTATTAAGGA
1 TAATTATTTAGGA
16928074 TAATTATTTAG
1 TAATTATTTAG
16928085 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (13 bp):
TAATTATTTAGGA
Found at i:16928123 original size:20 final size:20
Alignment explanation
Indices: 16928098--16928137 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16928088 TAAATTTTAG
*
16928098 ATTTATTTTTAGTTATCTTT
1 ATTTATTTGTAGTTATCTTT
*
16928118 ATTTATTTGTATTTATCTTT
1 ATTTATTTGTAGTTATCTTT
16928138 TAGAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (20 bp):
ATTTATTTGTAGTTATCTTT
Found at i:16940278 original size:20 final size:20
Alignment explanation
Indices: 16940253--16940295 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
16940243 AATTAGATTA
16940253 AAATTAGATACTGATAAATG
1 AAATTAGATACTGATAAATG
16940273 AAATTAGATACTGATAAATG
1 AAATTAGATACTGATAAATG
16940293 AAA
1 AAA
16940296 AATTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (20 bp):
AAATTAGATACTGATAAATG
Found at i:16941163 original size:16 final size:16
Alignment explanation
Indices: 16941142--16941173 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16941132 ACTAAGCACC
*
16941142 ATGTGCTTACCTCGTT
1 ATGTGCTTACCCCGTT
16941158 ATGTGCTTACCCCGTT
1 ATGTGCTTACCCCGTT
16941174 CTCTTTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.28, G:0.19, T:0.41
Consensus pattern (16 bp):
ATGTGCTTACCCCGTT
Found at i:16945539 original size:19 final size:19
Alignment explanation
Indices: 16945503--16945539 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16945493 TAATTAGGCT
* *
16945503 TTAATTAAGTGAATTTAGC
1 TTAATTAAGAGAAATTAGC
16945522 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
16945540 GAAAAAAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGC
Found at i:16947456 original size:23 final size:23
Alignment explanation
Indices: 16947412--16947456 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16947402 TTATAATTGA
* *
16947412 AAAGTGATTTTAAATTCGAAATG
1 AAAGTGATTTGAAATTCAAAATG
16947435 AAAGTGATTTGAGAATT-AAAAT
1 AAAGTGATTTGA-AATTCAAAAT
16947457 ACCCTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (23 bp):
AAAGTGATTTGAAATTCAAAATG
Found at i:16958195 original size:17 final size:16
Alignment explanation
Indices: 16958169--16958200 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
16958159 GTTATACCAA
16958169 TATGGGCCCACACGCC
1 TATGGGCCCACACGCC
16958185 TATGTGGCCCACACGC
1 TATG-GGCCCACACGC
16958201 TCAGATTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.19, C:0.41, G:0.25, T:0.16
Consensus pattern (16 bp):
TATGGGCCCACACGCC
Found at i:16961731 original size:46 final size:46
Alignment explanation
Indices: 16961664--16961845 Score: 235
Period size: 46 Copynumber: 4.0 Consensus size: 46
16961654 AGTGTGCTCT
*
16961664 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAAC
16961710 CTGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
16961756 GTGATATGAAATGA-ACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAAT-ATGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
16961802 ATGACA-GAAA-ATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATGAAATAT--GTAAGACCATGGTTGAAAGATACCATGGCA
16961846 TCATGTCAAA
Statistics
Matches: 121, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.01
45 4 0.03
46 115 0.95
47 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:16963247 original size:30 final size:30
Alignment explanation
Indices: 16963211--16963303 Score: 168
Period size: 30 Copynumber: 3.1 Consensus size: 30
16963201 ATAATCATGT
16963211 TATCTGTTTCCGTTATATTCTTTTTATAAG
1 TATCTGTTTCCGTTATATTCTTTTTATAAG
16963241 TATCTGTTTCCGTTATATTCTTTTTATAAG
1 TATCTGTTTCCGTTATATTCTTTTTATAAG
* *
16963271 TATCTATTTCCGTTATATCCTTTTTATAAG
1 TATCTGTTTCCGTTATATTCTTTTTATAAG
16963301 TAT
1 TAT
16963304 GTCATATTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.22, C:0.14, G:0.09, T:0.56
Consensus pattern (30 bp):
TATCTGTTTCCGTTATATTCTTTTTATAAG
Found at i:16969378 original size:7 final size:7
Alignment explanation
Indices: 16969366--16969390 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16969356 TATTCATGTC
16969366 CCTTCCA
1 CCTTCCA
16969373 CCTTCCA
1 CCTTCCA
16969380 CCTTCCA
1 CCTTCCA
16969387 CCTT
1 CCTT
16969391 TTAGCCGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.56, G:0.00, T:0.32
Consensus pattern (7 bp):
CCTTCCA
Found at i:16974993 original size:233 final size:233
Alignment explanation
Indices: 16974586--16975051 Score: 932
Period size: 233 Copynumber: 2.0 Consensus size: 233
16974576 ACATCCAATA
16974586 TCTCTTAAATTGGTATATTTACCACTCAAGTCCTTTAGTTTAAGATTTCAAAGCGATTGAATCCT
1 TCTCTTAAATTGGTATATTTACCACTCAAGTCCTTTAGTTTAAGATTTCAAAGCGATTGAATCCT
16974651 TTTAACTAGTAGAACTCAACTTTTACCCTTTTTACGATTTAGTCTTTTTTACTTAATTATTTATG
66 TTTAACTAGTAGAACTCAACTTTTACCCTTTTTACGATTTAGTCTTTTTTACTTAATTATTTATG
16974716 CAAACATCAAAATTTCTTAACGGATTTTTAATGCGACCTTAATATAATCCCGAAGATATTAAAAT
131 CAAACATCAAAATTTCTTAACGGATTTTTAATGCGACCTTAATATAATCCCGAAGATATTAAAAT
16974781 AATAAAAAAATAATAACTTGTACATTGAAATTGTGGTC
196 AATAAAAAAATAATAACTTGTACATTGAAATTGTGGTC
16974819 TCTCTTAAATTGGTATATTTACCACTCAAGTCCTTTAGTTTAAGATTTCAAAGCGATTGAATCCT
1 TCTCTTAAATTGGTATATTTACCACTCAAGTCCTTTAGTTTAAGATTTCAAAGCGATTGAATCCT
16974884 TTTAACTAGTAGAACTCAACTTTTACCCTTTTTACGATTTAGTCTTTTTTACTTAATTATTTATG
66 TTTAACTAGTAGAACTCAACTTTTACCCTTTTTACGATTTAGTCTTTTTTACTTAATTATTTATG
16974949 CAAACATCAAAATTTCTTAACGGATTTTTAATGCGACCTTAATATAATCCCGAAGATATTAAAAT
131 CAAACATCAAAATTTCTTAACGGATTTTTAATGCGACCTTAATATAATCCCGAAGATATTAAAAT
16975014 AATAAAAAAATAATAACTTGTACATTGAAATTGTGGTC
196 AATAAAAAAATAATAACTTGTACATTGAAATTGTGGTC
16975052 CCAAAATTAC
Statistics
Matches: 233, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
233 233 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (233 bp):
TCTCTTAAATTGGTATATTTACCACTCAAGTCCTTTAGTTTAAGATTTCAAAGCGATTGAATCCT
TTTAACTAGTAGAACTCAACTTTTACCCTTTTTACGATTTAGTCTTTTTTACTTAATTATTTATG
CAAACATCAAAATTTCTTAACGGATTTTTAATGCGACCTTAATATAATCCCGAAGATATTAAAAT
AATAAAAAAATAATAACTTGTACATTGAAATTGTGGTC
Found at i:16977497 original size:25 final size:25
Alignment explanation
Indices: 16977468--16977518 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
16977458 GAAAATAATG
*
16977468 AAGAAATATCTAGATTTCTCATGAT
1 AAGAAATATATAGATTTCTCATGAT
16977493 AAGAAATATATAGATTTCTCATGAT
1 AAGAAATATATAGATTTCTCATGAT
16977518 A
1 A
16977519 TTTCAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (25 bp):
AAGAAATATATAGATTTCTCATGAT
Found at i:16977803 original size:48 final size:48
Alignment explanation
Indices: 16977732--16977828 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
16977722 AATTGACTGT
16977732 CAAAACGTTAAAATTTTCTGACGAAACTTTAATGCTAACTCAATGACA
1 CAAAACGTTAAAATTTTCTGACGAAACTTTAATGCTAACTCAATGACA
16977780 CAAAACGTTAAAATTTTCTGACGAAACTTTAATGCTAACTCAATGACA
1 CAAAACGTTAAAATTTTCTGACGAAACTTTAATGCTAACTCAATGACA
16977828 C
1 C
16977829 TCCATAAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (48 bp):
CAAAACGTTAAAATTTTCTGACGAAACTTTAATGCTAACTCAATGACA
Found at i:16978642 original size:45 final size:45
Alignment explanation
Indices: 16978566--16978683 Score: 139
Period size: 45 Copynumber: 2.6 Consensus size: 45
16978556 TGACACAGTT
* * * * * *
16978566 CGCACGTATGAGTCCGCCATATCTATTAATCTTCTTTTATGAATC
1 CGCATGTATGAGTCCACTATATCTATGAATCTACTTCTATGAATC
* *
16978611 CGTATGTATGAGTCCACTATATTTATGAATCTACTTCTATGAATC
1 CGCATGTATGAGTCCACTATATCTATGAATCTACTTCTATGAATC
*
16978656 CGCATGAATGAG-CTCACTATATCTATGA
1 CGCATGTATGAGTC-CACTATATCTATGA
16978684 GTATTCTTCT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 1 0.02
45 60 0.98
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (45 bp):
CGCATGTATGAGTCCACTATATCTATGAATCTACTTCTATGAATC
Found at i:16980232 original size:14 final size:14
Alignment explanation
Indices: 16980210--16980245 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
16980200 CAAATTAATA
16980210 AAATATTAAATATC
1 AAATATTAAATATC
*
16980224 AATTATTAAATATC
1 AAATATTAAATATC
16980238 AAATATTA
1 AAATATTA
16980246 TTGTAATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATTAAATATC
Found at i:16980498 original size:39 final size:39
Alignment explanation
Indices: 16980444--16980522 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
16980434 TAACAGAAGT
16980444 TAAAAAAATTGATGGTCAATCACATAGCGCCACGTGGCA
1 TAAAAAAATTGATGGTCAATCACATAGCGCCACGTGGCA
*
16980483 TAAAAAAATTGATGGTCAATCACATAGCGTCACGTGGCA
1 TAAAAAAATTGATGGTCAATCACATAGCGCCACGTGGCA
16980522 T
1 T
16980523 CTTTTTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (39 bp):
TAAAAAAATTGATGGTCAATCACATAGCGCCACGTGGCA
Found at i:16980611 original size:10 final size:10
Alignment explanation
Indices: 16980578--16980626 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
16980568 TATAAACATT
16980578 AAAA-ATATA
1 AAAATATATA
*
16980587 AAAATAGA-A
1 AAAATATATA
16980596 ATAAATATATA
1 A-AAATATATA
16980607 AAAAT-TCATA
1 AAAATAT-ATA
16980617 AAAATATATA
1 AAAATATATA
16980627 TAATGTAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
9 7 0.21
10 23 0.70
11 3 0.09
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAATATATA
Found at i:16980648 original size:30 final size:29
Alignment explanation
Indices: 16980578--16980648 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 29
16980568 TATAAACATT
* *
16980578 AAAAATATAAAAATAGAAATAAATATATA
1 AAAAATATAAAAATAGAAATAAATAGAAA
* * * *
16980607 AAAATTCATAAAAATATATATAATGTAGAAA
1 AAAAAT-ATAAAAATAGAAATAA-ATAGAAA
16980638 AAAAATATAAA
1 AAAAATATAAA
16980649 TTAGAAGAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 5 0.15
30 19 0.58
31 9 0.27
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (29 bp):
AAAAATATAAAAATAGAAATAAATAGAAA
Found at i:16980653 original size:18 final size:20
Alignment explanation
Indices: 16980616--16980654 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16980606 AAAAATTCAT
*
16980616 AAAAATATATATAATGTAGA
1 AAAAAAATATATAATGTAGA
16980636 AAAAAAATATA-AAT-TAGA
1 AAAAAAATATATAATGTAGA
16980654 A
1 A
16980655 GAGAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 10 0.56
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
AAAAAAATATATAATGTAGA
Found at i:16980760 original size:20 final size:19
Alignment explanation
Indices: 16980711--16980752 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
16980701 GAAATTAGTT
16980711 AAAATTAATAATA--TTATA
1 AAAATT-ATAATATTTTATA
16980729 AAAATTATAATATTTTATA
1 AAAATTATAATATTTTATA
16980748 AAAAT
1 AAAAT
16980753 ATTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.27
18 6 0.27
19 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTATAATATTTTATA
Found at i:16980769 original size:20 final size:19
Alignment explanation
Indices: 16980715--16980770 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
16980705 TTAGTTAAAA
16980715 TTAATAATATTATAAAAATT
1 TTAATAA-ATTATAAAAATT
* **
16980735 ATAATATTTTATAAAAATAT
1 TTAATAAATTATAAAAAT-T
*
16980755 TTAATAAATTGTAAAA
1 TTAATAAATTATAAAA
16980771 TTATGAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAATAAATTATAAAAATT
Found at i:16984012 original size:12 final size:12
Alignment explanation
Indices: 16983995--16984037 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
16983985 CCTAAGATTA
16983995 TATTTTATTATG
1 TATTTTATTATG
* *
16984007 TATTTTACTATA
1 TATTTTATTATG
16984019 TATTTTATTATG
1 TATTTTATTATG
16984031 TATTTTA
1 TATTTTA
16984038 CTATCTAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (12 bp):
TATTTTATTATG
Done.