Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 66 of 182
Found at i:20129581 original size:70 final size:70
Alignment explanation
Indices: 20129507--20129660 Score: 290
Period size: 70 Copynumber: 2.2 Consensus size: 70
20129497 TCCATAATAA
20129507 ACTAGCCTATACATCATTTACAAGCCAACTCACATGGCTAATTTCATATCTCAAAACGTATCCTA
1 ACTAGCCTATACATCATTTACAAGCCAACTCACATGGCTAATTTCATATCTCAAAACGTATCCTA
20129572 TTGAC
66 TTGAC
* *
20129577 ACTAGCCTATACATCATTTACAAGGCAACTCACATGGCTAATTTCATATCTCAAAATGTATCCTA
1 ACTAGCCTATACATCATTTACAAGCCAACTCACATGGCTAATTTCATATCTCAAAACGTATCCTA
20129642 TTGAC
66 TTGAC
20129647 ACTAGCCTATACAT
1 ACTAGCCTATACAT
20129661 GCCATATACC
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 82 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (70 bp):
ACTAGCCTATACATCATTTACAAGCCAACTCACATGGCTAATTTCATATCTCAAAACGTATCCTA
TTGAC
Found at i:20134126 original size:21 final size:21
Alignment explanation
Indices: 20134102--20134154 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
20134092 AAAATAAAAG
20134102 AAACTGAAATACATTAAACTA
1 AAACTGAAATACATTAAACTA
20134123 AAACTGAAATACATTAAACTA
1 AAACTGAAATACATTAAACTA
*
20134144 AATCTAGAAAT
1 AAACT-GAAAT
20134155 GTCTTACAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.57, C:0.13, G:0.06, T:0.25
Consensus pattern (21 bp):
AAACTGAAATACATTAAACTA
Found at i:20136189 original size:27 final size:27
Alignment explanation
Indices: 20136139--20136194 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
20136129 CAATAAAACA
* ** *
20136139 ACCGAAATACCCTCGTAGGGTAAAATG
1 ACCGAAATACCCCCACAGGATAAAATG
20136166 ACCGAAATACCCCCACAGGATAAAATG
1 ACCGAAATACCCCCACAGGATAAAATG
20136193 AC
1 AC
20136195 TGTTGTACCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.27, G:0.18, T:0.14
Consensus pattern (27 bp):
ACCGAAATACCCCCACAGGATAAAATG
Found at i:20136447 original size:26 final size:26
Alignment explanation
Indices: 20136376--20136435 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
20136366 TATATTGTTT
20136376 CTGGCAGCCTTACTGCGATACTATTA
1 CTGGCAGCCTTACTGCGATACTATTA
* *
20136402 CTGGTAGCCTTGCTGCGATACTATTA
1 CTGGCAGCCTTACTGCGATACTATTA
20136428 CTGGCAGC
1 CTGGCAGC
20136436 TTTATTACGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (26 bp):
CTGGCAGCCTTACTGCGATACTATTA
Found at i:20141471 original size:116 final size:117
Alignment explanation
Indices: 20141284--20141509 Score: 393
Period size: 116 Copynumber: 1.9 Consensus size: 117
20141274 GCTCTTCGAT
* *
20141284 AGTATCTATCGATACTTTCAAGCTTAGAAGAAAAAAAGGAATCACTTAATTGTATGACACAATAC
1 AGTATCTATCGATACTTTCAAGCTTAGAAGAAAAAAAGGAATCACTCAATTGGATGACACAATAC
*
20141349 AATATATATTTAATTTTTC-TTTTTTTT-TGTCGACCAGATATCAATCAAACG
66 AATATATATTTAATATTTCTTTTTTTTTCTGTCGACCAGAT-TCAATCAAACG
*
20141400 AGTATCTATCGATACTTTCAAGGTTAGAAGAAAAAAAGGAATCACTCAATTGGATGACACAATAC
1 AGTATCTATCGATACTTTCAAGCTTAGAAGAAAAAAAGGAATCACTCAATTGGATGACACAATAC
20141465 AATATATATTTAATATTTCTTTTTTTTTCTGTCGACCAGATTCAA
66 AATATATATTTAATATTTCTTTTTTTTTCTGTCGACCAGATTCAA
20141510 ACCTTTTCTA
Statistics
Matches: 104, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
116 80 0.77
117 12 0.12
118 12 0.12
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.36
Consensus pattern (117 bp):
AGTATCTATCGATACTTTCAAGCTTAGAAGAAAAAAAGGAATCACTCAATTGGATGACACAATAC
AATATATATTTAATATTTCTTTTTTTTTCTGTCGACCAGATTCAATCAAACG
Found at i:20143487 original size:40 final size:40
Alignment explanation
Indices: 20143443--20143525 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 40
20143433 AGCCTACTAA
** * *
20143443 GCATTAAGCCTTACAAATACACCGGCATGAAGCTTGCTAG
1 GCATTAAGCCCGACAAATACACCGACACGAAGCTTGCTAG
* * *
20143483 GCATTTAGCCCGATAGATACACCGACACGAAGCTTGCTAG
1 GCATTAAGCCCGACAAATACACCGACACGAAGCTTGCTAG
20143523 GCA
1 GCA
20143526 ACAAAACCTG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (40 bp):
GCATTAAGCCCGACAAATACACCGACACGAAGCTTGCTAG
Found at i:20154788 original size:103 final size:101
Alignment explanation
Indices: 20154646--20154860 Score: 270
Period size: 103 Copynumber: 2.1 Consensus size: 101
20154636 CATGGCCTTG
** * * *
20154646 CCATGGTCTTACGTTTGTA-GTGTCATAACCCAGTTATGGTCTTATCATCAAAATGCCACAGCCC
1 CCATGGTCTTACG-TTCAAGGTGCCATAACCCAATTATGGTCTTATAATCAAAATGCCACAGCCC
* * *
20154710 AGCTATGGTCTTACATATATATATACTGCCATGGTCCAA
65 AGCTATGGTCTTACAT-T-TAAACACTACCATGGTCCAA
* * * * *
20154749 CTATGGTCTTACGTTCAAGGTGCCATAACCCAATTATGGTCTTTTAATTAAAATTCCATAGCCCA
1 CCATGGTCTTACGTTCAAGGTGCCATAACCCAATTATGGTCTTATAATCAAAATGCCACAGCCCA
*
20154814 GCTATGGTCTTACATTTAAACACTACCATGGTCCCA
66 GCTATGGTCTTACATTTAAACACTACCATGGTCCAA
20154850 CCATGGTCTTA
1 CCATGGTCTTA
20154861 TCCGTCAATT
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
101 26 0.27
102 4 0.04
103 66 0.69
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (101 bp):
CCATGGTCTTACGTTCAAGGTGCCATAACCCAATTATGGTCTTATAATCAAAATGCCACAGCCCA
GCTATGGTCTTACATTTAAACACTACCATGGTCCAA
Found at i:20154833 original size:33 final size:33
Alignment explanation
Indices: 20154669--20154833 Score: 107
Period size: 33 Copynumber: 4.9 Consensus size: 33
20154659 TTTGTAGTGT
* * *
20154669 CATAACCCAGTTATGGTCTTATCA-TCAAAATGC
1 CATAGCCCAGCTATGGTCTTA-CATTTAAAATGC
* *
20154702 CACAGCCCAGCTATGGTCTTACATATATATATACTGC
1 CATAGCCCAGCTATGGTCTTACAT-T-TA-A-AATGC
* * * * * **
20154739 CATGGTCCAACTATGGTCTTACGTTCAAGGTGC
1 CATAGCCCAGCTATGGTCTTACATTTAAAATGC
* ** ** * *
20154772 CATAACCCAATTATGGTCTTTTAATTAAAATTC
1 CATAGCCCAGCTATGGTCTTACATTTAAAATGC
20154805 CATAGCCCAGCTATGGTCTTACATTTAAA
1 CATAGCCCAGCTATGGTCTTACATTTAAA
20154834 CACTACCATG
Statistics
Matches: 96, Mismatches: 31, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
32 2 0.02
33 65 0.68
34 2 0.02
35 2 0.02
36 2 0.02
37 23 0.24
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (33 bp):
CATAGCCCAGCTATGGTCTTACATTTAAAATGC
Found at i:20161235 original size:137 final size:137
Alignment explanation
Indices: 20160989--20161269 Score: 546
Period size: 137 Copynumber: 2.1 Consensus size: 137
20160979 TAGGGTTACA
*
20160989 GAGTATTACCGAACTTTACGAATTAAATATGAGACATTTCTCAACCTTTGTTATACATATTAAGA
1 GAGTATTACCGAACTTTACAAATTAAATATGAGACATTTCTCAACCTTTGTTATACATATTAAGA
20161054 ATCAATCATATAACACTCATATTGTCTCTTAGATGGACCCTCGAGGCCCAATATTCACCTTAGAA
66 ATCAATCATATAACACTCATATTGTCTCTTAGATGGACCCTCGAGGCCCAATATTCACCTTAGAA
20161119 GTGAATC
131 GTGAATC
20161126 GAGTATTACCGAACTTTACAAATTAAATATGAGACATTTCTCAACCTTTGTTATACATATTAAGA
1 GAGTATTACCGAACTTTACAAATTAAATATGAGACATTTCTCAACCTTTGTTATACATATTAAGA
20161191 ATCAATCATATAACACTCATATTGTCTCTTAGATGGACCCTCGAGGCCCAATATTCACCTTAGAA
66 ATCAATCATATAACACTCATATTGTCTCTTAGATGGACCCTCGAGGCCCAATATTCACCTTAGAA
20161256 GTGAATC
131 GTGAATC
20161263 GAG-ATTA
1 GAGTATTA
20161270 AACCGAATAC
Statistics
Matches: 143, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
136 4 0.03
137 139 0.97
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (137 bp):
GAGTATTACCGAACTTTACAAATTAAATATGAGACATTTCTCAACCTTTGTTATACATATTAAGA
ATCAATCATATAACACTCATATTGTCTCTTAGATGGACCCTCGAGGCCCAATATTCACCTTAGAA
GTGAATC
Found at i:20162315 original size:136 final size:136
Alignment explanation
Indices: 20162071--20162495 Score: 850
Period size: 136 Copynumber: 3.1 Consensus size: 136
20162061 TGTGTCATAG
20162071 TCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGTGCCATA
1 TCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGTGCCATA
20162136 AATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTG
66 AATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTG
20162201 CCATGA
131 CCATGA
20162207 TCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGTGCCATA
1 TCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGTGCCATA
20162272 AATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTG
66 AATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTG
20162337 CCATGA
131 CCATGA
20162343 TCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGTGCCATA
1 TCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGTGCCATA
20162408 AATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTG
66 AATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTG
20162473 CCATGA
131 CCATGA
20162479 TCCAACTATGGTCTTAC
1 TCCAACTATGGTCTTAC
20162496 GTTCAAGGTG
Statistics
Matches: 289, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 289 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (136 bp):
TCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGTGCCATA
AATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTG
CCATGA
Found at i:20162516 original size:70 final size:69
Alignment explanation
Indices: 20162143--20162495 Score: 282
Period size: 70 Copynumber: 5.2 Consensus size: 69
20162133 ATAAATCAGT
*
20162143 TATGGTCTTA-TCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTGCCATGA
1 TATGGTCTTACTCA--AGAATGACATAGCCCAGCTATGGTCTTACATATATATATACTGCCATGA
20162207 TCCAAC
64 TCCAAC
* * * * ** * * * *
20162213 TATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTAC--AT-T-TGTAGTGCCATAAA
1 TATGGTCTTACTCAAG-AATGACATAGCCCAGCTATGGTCTTACATATATATATACTGCCAT-GA
**
20162274 T-CAGT
64 TCCAAC
*
20162279 TATGGTCTTA-TCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTGCCATGA
1 TATGGTCTTACTCA--AGAATGACATAGCCCAGCTATGGTCTTACATATATATATACTGCCATGA
20162343 TCCAAC
64 TCCAAC
* * * * ** * * * *
20162349 TATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTAC--AT-T-TGTAGTGCCATAAA
1 TATGGTCTTACTCAAG-AATGACATAGCCCAGCTATGGTCTTACATATATATATACTGCCAT-GA
**
20162410 T-CAGT
64 TCCAAC
*
20162415 TATGGTCTTA-TCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTGCCATGA
1 TATGGTCTTACTCA--AGAATGACATAGCCCAGCTATGGTCTTACATATATATATACTGCCATGA
20162479 TCCAAC
64 TCCAAC
20162485 TATGGTCTTAC
1 TATGGTCTTAC
20162496 GTTCAAGGTG
Statistics
Matches: 210, Mismatches: 52, Indels: 41
0.69 0.17 0.14
Matches are distributed among these distances:
65 4 0.02
66 84 0.40
67 8 0.04
68 8 0.04
69 8 0.04
70 94 0.45
71 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (69 bp):
TATGGTCTTACTCAAGAATGACATAGCCCAGCTATGGTCTTACATATATATATACTGCCATGATC
CAAC
Found at i:20162557 original size:272 final size:271
Alignment explanation
Indices: 20162071--20162560 Score: 750
Period size: 272 Copynumber: 1.8 Consensus size: 271
20162061 TGTGTCATAG
20162071 TCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGTGCCATA
1 TCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGTGCCATA
20162136 AATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTG
66 AATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTG
* * ** ** * ** *
20162201 CCATGATCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGT
131 CCATGATCCAACTATGGTCTTACACAAG-AGTGACATAACCCAGCCACGGTCTTACATTTAAAAT
* *
20162266 GCCATAAATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATAT
195 GCCATAAACCAGCTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATAT
20162331 ATACTGCCATGA
260 ATACTGCCATGA
20162343 TCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGTGCCATA
1 TCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGTGCCATA
20162408 AATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTG
66 AATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTG
* * ** * *
20162473 CCATGATCCAACTATGGTCTTACGTTCAAG-GTGCCATAACCCAGTTACGGTTTTTTCA-TTAAA
131 CCATGATCCAACTATGGTCTTAC--ACAAGAGTGACATAACCCAGCCACGG-TCTTACATTTAAA
**
20162536 ATGCCATAGCCCAGCTATGGTCTTA
193 ATGCCATAAACCAGCTATGGTCTTA
20162561 CATTTAAACA
Statistics
Matches: 195, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
272 187 0.96
273 5 0.03
274 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (271 bp):
TCCAACTATGGTCTTACACATGCATTGACATGGCCTTGCCATGGTCTTACATTTGTAGTGCCATA
AATCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATATACTG
CCATGATCCAACTATGGTCTTACACAAGAGTGACATAACCCAGCCACGGTCTTACATTTAAAATG
CCATAAACCAGCTATGGTCTTATCATCAGAATGTCATAGCCCAGCTATGGTCTTACATATATATA
TACTGCCATGA
Found at i:20162568 original size:33 final size:33
Alignment explanation
Indices: 20162383--20162577 Score: 90
Period size: 33 Copynumber: 5.7 Consensus size: 33
20162373 TGGCCTTGCC
** * *** *
20162383 ATGGTCTTACATTTGTAGTGCCATAAATCAGTT
1 ATGGTCTTACATTTAAAATGCCATAGCCCAGCT
* * *
20162416 ATGGTCTTATCA-TCAGAATGTCATAGCCCAGCT
1 ATGGTCTTA-CATTTAAAATGCCATAGCCCAGCT
* * *
20162449 ATGGTCTTACATATATATATACTGCCAT-GATCCAACT
1 ATGGTCTTACAT-T-TA-A-AATGCCATAG-CCCAGCT
* * ** * *
20162486 ATGGTCTTACGTTCAAGGTGCCATAACCCAGTT
1 ATGGTCTTACATTTAAAATGCCATAGCCCAGCT
* * *
20162519 ACGGTTTTTTCA-TTAAAATGCCATAGCCCAGCT
1 ATGG-TCTTACATTTAAAATGCCATAGCCCAGCT
20162552 ATGGTCTTACATTTAAACATTGCCAT
1 ATGGTCTTACATTTAAA-A-TGCCAT
20162578 GGTTCAACCG
Statistics
Matches: 115, Mismatches: 35, Indels: 22
0.67 0.20 0.13
Matches are distributed among these distances:
32 7 0.06
33 67 0.58
34 9 0.08
35 8 0.07
36 2 0.02
37 22 0.19
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (33 bp):
ATGGTCTTACATTTAAAATGCCATAGCCCAGCT
Found at i:20164612 original size:10 final size:10
Alignment explanation
Indices: 20164597--20164623 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
20164587 CAGATACCAT
20164597 TTCAACTATG
1 TTCAACTATG
20164607 TTCAACTATG
1 TTCAACTATG
20164617 TTCAACT
1 TTCAACT
20164624 CATCTTTGGT
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:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (10 bp):
TTCAACTATG
Found at i:20169900 original size:68 final size:69
Alignment explanation
Indices: 20169788--20169917 Score: 203
Period size: 68 Copynumber: 1.9 Consensus size: 69
20169778 AAACTTAATA
*
20169788 ACTTTAATATTGAATTAAAATAATACTTATCAATATAAGTATTAAACTAAATTTAATATTAAGAT
1 ACTTTAATATTGAATTAAAATAATACTTATCAAGATAAGTATTAAACTAAATTTAATATTAAGAT
20169853 ACTT
66 ACTT
*
20169857 ACTTTAATATT-AAGTTAATAA-AATAC-TATCAAGATAAGTATTAAATTAAATTTAATATTAA
1 ACTTTAATATTGAA-TTAA-AATAATACTTATCAAGATAAGTATTAAACTAAATTTAATATTAA
20169918 ATTTATTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
68 35 0.61
69 20 0.35
70 2 0.04
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (69 bp):
ACTTTAATATTGAATTAAAATAATACTTATCAAGATAAGTATTAAACTAAATTTAATATTAAGAT
ACTT
Found at i:20169933 original size:68 final size:68
Alignment explanation
Indices: 20169792--20169936 Score: 172
Period size: 68 Copynumber: 2.1 Consensus size: 68
20169782 TTAATAACTT
*
20169792 TAATATTGAATTAAAATAATACTTATCAATATAAGTATTAAACTAAATTTAATATTAAGATACTT
1 TAATATT-AATTAAAATAATACTTATCAAGATAAGTATTAAACTAAATTTAATATTAAGATACTT
***
20169857 ACTT
65 AAAA
*
20169861 TAATATTAAGTTAATAA-AATAC-TATCAAGATAAGTATTAAATTAAATTTAATATTAA-ATTTA
1 TAATATTAA-TTAA-AATAATACTTATCAAGATAAGTATTAAACTAAATTTAATATTAAGA--TA
20169923 -TTAAAA
62 CTTAAAA
20169929 TAATATTA
1 TAATATTA
20169937 TTTTTGAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
67 1 0.01
68 46 0.69
69 18 0.27
70 2 0.03
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (68 bp):
TAATATTAATTAAAATAATACTTATCAAGATAAGTATTAAACTAAATTTAATATTAAGATACTTA
AAA
Found at i:20175808 original size:16 final size:17
Alignment explanation
Indices: 20175787--20175824 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
20175777 TTTTATATGA
*
20175787 ATTTTACT-TTTATTTT
1 ATTTTACTATGTATTTT
20175803 ATTTTACTAATGTATTTT
1 ATTTTACT-ATGTATTTT
20175821 ATTT
1 ATTT
20175825 AAATAAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTACTATGTATTTT
Found at i:20185002 original size:56 final size:55
Alignment explanation
Indices: 20184880--20185004 Score: 124
Period size: 55 Copynumber: 2.3 Consensus size: 55
20184870 GGATCACTGG
* * * *
20184880 TGCCACTTGACACACAGACGATACAAAAAAAAACATTTTTTAAATCTGACAAAGG
1 TGCCACTTGACACACAGACAACACAAAAAAAAACATTTTTTAAATCTAACAAAGA
*** * * * * **
20184935 TGTTGCCTGACACACTGACAACACAAGAAAAAATATTTTTTAAAATCTAACATCGA
1 TGCCACTTGACACACAGACAACACAAAAAAAAACATTTTTT-AAATCTAACAAAGA
20184991 TGCCACTTGACACA
1 TGCCACTTGACACA
20185005 TCAGTGGCAC
Statistics
Matches: 52, Mismatches: 17, Indels: 1
0.74 0.24 0.01
Matches are distributed among these distances:
55 32 0.62
56 20 0.38
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (55 bp):
TGCCACTTGACACACAGACAACACAAAAAAAAACATTTTTTAAATCTAACAAAGA
Found at i:20187212 original size:90 final size:88
Alignment explanation
Indices: 20187082--20187271 Score: 233
Period size: 90 Copynumber: 2.1 Consensus size: 88
20187072 AAATAATAAT
* * *
20187082 AATTAAGTCCCTTTTTTTTCTTGCACTCAATTGAGCACTTGAACTTTCAACA-TGTATCAAAAAG
1 AATTAAGCCCCTATTTTTTCTTGCACTCAATTGAGCACTTGAACTTTCAA-AGTGCATCAAAAAG
* * *
20187146 GCCCTTAAACTTCTTCAAAATAAAAAGC
65 ACCCTCAAAATTCTTCAAAAT----AGC
* *
20187174 AATTAAGCCCCTATTTTTT-TT-CACTCAATTGGGTACTTGAACTTTCAAAGTGCATCAAAAAGA
1 AATTAAGCCCCTATTTTTTCTTGCACTCAATTGAGCACTTGAACTTTCAAAGTGCATCAAAAAGA
*
20187237 CCCTCAAAATTTTTCAAAATAGC
66 CCCTCAAAATTCTTCAAAATAGC
20187260 AATTAAGCCCCT
1 AATTAAGCCCCT
20187272 GCTCTTATTA
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
86 15 0.17
89 1 0.01
90 53 0.60
91 2 0.02
92 17 0.19
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (88 bp):
AATTAAGCCCCTATTTTTTCTTGCACTCAATTGAGCACTTGAACTTTCAAAGTGCATCAAAAAGA
CCCTCAAAATTCTTCAAAATAGC
Found at i:20187331 original size:18 final size:19
Alignment explanation
Indices: 20187309--20187356 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
20187299 ATAAAAGATA
*
20187309 AAAAAATAATAAATTTTAG
1 AAAAATTAATAAATTTTAG
* *
20187328 AAAAATTATTAAATTTTAAT
1 AAAAATTAATAAATTTT-AG
20187348 AAAAATTAA
1 AAAAATTAA
20187357 AAAAATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATTAATAAATTTTAG
Found at i:20187351 original size:20 final size:19
Alignment explanation
Indices: 20187318--20187355 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
20187308 AAAAAAATAA
20187318 TAAATTTTAGAAAAATTAT
1 TAAATTTTAGAAAAATTAT
*
20187337 TAAATTTTAATAAAAATTA
1 TAAATTTT-AGAAAAATTA
20187356 AAAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAATTTTAGAAAAATTAT
Found at i:20187365 original size:20 final size:20
Alignment explanation
Indices: 20187328--20187366 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20187318 TAAATTTTAG
** *
20187328 AAAAATTATTAAATTTTAAT
1 AAAAATTAAAAAAATTTAAT
20187348 AAAAATTAAAAAAATTTAA
1 AAAAATTAAAAAAATTTAA
20187367 GATTTATTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATTAAAAAAATTTAAT
Found at i:20187546 original size:21 final size:21
Alignment explanation
Indices: 20187520--20187594 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
20187510 TTGGTACGAT
20187520 AATTTTTATAATTTTTTTACG
1 AATTTTTATAATTTTTTTACG
* *
20187541 AA-TTTTAT-ATATCTTTAC-
1 AATTTTTATAATTTTTTTACG
*
20187559 -ATTTTGTATAATTTTCTTACG
1 AATTTT-TATAATTTTTTTACG
* *
20187580 AATTTATAAAATTTT
1 AATTTTTATAATTTT
20187595 ATATTTTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
17 1 0.02
18 3 0.07
19 11 0.26
20 13 0.31
21 10 0.24
22 4 0.10
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (21 bp):
AATTTTTATAATTTTTTTACG
Found at i:20187600 original size:28 final size:28
Alignment explanation
Indices: 20187569--20187651 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 28
20187559 ATTTTGTATA
*
20187569 ATTTTCTTACGAATTTATAAAATTTTAT
1 ATTTTCTTACGTATTTATAAAATTTTAT
* * *
20187597 ATTTTTTTA--TATTTCTATATATTTTAT
1 ATTTTCTTACGTATTTATA-AAATTTTAT
* *
20187624 AATTTCTTACGGTTTTTATAAAATTTTA
1 ATTTTCTTAC-GTATTTATAAAATTTTA
20187652 CGATTTTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
26 6 0.14
27 15 0.36
28 8 0.19
29 7 0.17
30 6 0.14
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (28 bp):
ATTTTCTTACGTATTTATAAAATTTTAT
Found at i:20187601 original size:38 final size:38
Alignment explanation
Indices: 20187521--20187602 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
20187511 TGGTACGATA
* *
20187521 ATTTTTATAATTTTTTTACGAATTTTATATATCTTTAC
1 ATTTTTATAATTTTCTTACGAATTTTATAAATCTTTAC
*
20187559 ATTTTGTATAATTTTCTTACGAA-TTTATAAAAT-TTTAT
1 ATTTT-TATAATTTTCTTACGAATTTTAT-AAATCTTTAC
20187597 ATTTTT
1 ATTTTT
20187603 TTATATTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
37 1 0.03
38 19 0.49
39 19 0.49
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (38 bp):
ATTTTTATAATTTTCTTACGAATTTTATAAATCTTTAC
Found at i:20187640 original size:19 final size:18
Alignment explanation
Indices: 20187618--20187662 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
20187608 TTTCTATATA
* *
20187618 TTTTATAATTTCTTACGGT
1 TTTTATAAATT-TTACGAT
20187637 TTTTATAAAATTTTACGAT
1 TTTTAT-AAATTTTACGAT
20187656 TTTTATA
1 TTTTATA
20187663 TTTTTCTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 18 0.78
20 4 0.17
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.58
Consensus pattern (18 bp):
TTTTATAAATTTTACGAT
Found at i:20187642 original size:56 final size:55
Alignment explanation
Indices: 20187534--20187686 Score: 159
Period size: 56 Copynumber: 2.7 Consensus size: 55
20187524 TTTATAATTT
*
20187534 TTTTACGAATTTTATATATCTT-TACATTTTGTATAATTTTCTTACGAATTTATAAAA
1 TTTTACGATTTTTATATAT-TTCTA-ATTTT-TATAATTTTCTTACGAATTTATAAAA
* * **
20187591 TTTTA-TATTTTTTTATATTTCTATATATTTTATAA-TTTCTTACGGTTTTTATAAAA
1 TTTTACGATTTTTATATATTTCTA-AT-TTTTATAATTTTCTTAC-GAATTTATAAAA
*
20187647 TTTTACGATTTTTATATTTTTCTAATTTTTAATAAATTTT
1 TTTTACGATTTTTATATATTTCTAATTTTT-AT-AATTTT
20187687 TAATATTTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
55 14 0.17
56 38 0.47
57 25 0.31
58 3 0.04
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (55 bp):
TTTTACGATTTTTATATATTTCTAATTTTTATAATTTTCTTACGAATTTATAAAA
Found at i:20189387 original size:7 final size:7
Alignment explanation
Indices: 20189375--20189419 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
20189365 TTTCTAGCCA
20189375 ATTTAGT
1 ATTTAGT
20189382 ATTTAGT
1 ATTTAGT
20189389 A-TTACGT
1 ATTTA-GT
*
20189396 TTTTAGT
1 ATTTAGT
20189403 ATTTAGT
1 ATTTAGT
*
20189410 ACTTAGT
1 ATTTAGT
20189417 ATT
1 ATT
20189420 AAAAGTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 3 0.09
7 26 0.81
8 3 0.09
ACGTcount: A:0.27, C:0.04, G:0.13, T:0.56
Consensus pattern (7 bp):
ATTTAGT
Found at i:20191853 original size:25 final size:25
Alignment explanation
Indices: 20191814--20191904 Score: 82
Period size: 25 Copynumber: 3.6 Consensus size: 25
20191804 TCATGTACAC
*
20191814 GTATGCTCATACGAGCTGT-GAATCG
1 GTATGCTCATACGAGCTATAG-ATCG
20191839 GTATGCTCACT-CGAGCTATAGATCG
1 GTATGCTCA-TACGAGCTATAGATCG
* * *
20191864 GTATGCTC-TCACTAGCTATAAATTG
1 GTATGCTCAT-ACGAGCTATAGATCG
20191889 GTATGCTC-TCACGAGC
1 GTATGCTCAT-ACGAGC
20191905 GGTGGAGTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
23 1 0.02
25 54 0.95
26 2 0.04
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATAGATCG
Found at i:20198030 original size:64 final size:64
Alignment explanation
Indices: 20197950--20198080 Score: 235
Period size: 64 Copynumber: 2.0 Consensus size: 64
20197940 GTATGACATG
*
20197950 ATGTGATATATATTAACTTTTTTTAATATATAAAAAACAATGATTATTACCTTATCTATAATCA
1 ATGTAATATATATTAACTTTTTTTAATATATAAAAAACAATGATTATTACCTTATCTATAATCA
* *
20198014 ATGTAATATATATTAACTTTTTTTAGTATATAAAAAACAATGATTATTATCTTATCTATAATCA
1 ATGTAATATATATTAACTTTTTTTAATATATAAAAAACAATGATTATTACCTTATCTATAATCA
20198078 ATG
1 ATG
20198081 GAGTAAAAGA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (64 bp):
ATGTAATATATATTAACTTTTTTTAATATATAAAAAACAATGATTATTACCTTATCTATAATCA
Found at i:20199822 original size:7 final size:7
Alignment explanation
Indices: 20199810--20199843 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
20199800 TTAGAATCTT
20199810 TTTCATA
1 TTTCATA
20199817 TTTCATA
1 TTTCATA
20199824 TTTCATA
1 TTTCATA
20199831 TTTCATA
1 TTTCATA
20199838 TTTCAT
1 TTTCAT
20199844 TCAATACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTCATA
Found at i:20204457 original size:25 final size:25
Alignment explanation
Indices: 20204422--20204478 Score: 105
Period size: 25 Copynumber: 2.2 Consensus size: 25
20204412 ATGGCCTTAC
20204422 AAGTAGAATTGCTTGAATGTATGAAA
1 AAGTA-AATTGCTTGAATGTATGAAA
20204448 AAGTAAATTGCTTGAATGTATGAAA
1 AAGTAAATTGCTTGAATGTATGAAA
20204473 AAGTAA
1 AAGTAA
20204479 GGCTTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 26 0.84
26 5 0.16
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.30
Consensus pattern (25 bp):
AAGTAAATTGCTTGAATGTATGAAA
Found at i:20205221 original size:27 final size:27
Alignment explanation
Indices: 20205171--20205222 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
20205161 ACACGTTAGA
** *
20205171 AAATGGAAGTTTTTGTGGTAATCTATG
1 AAATGGAAGCCTTTGTGGCAATCTATG
*
20205198 AAATGGAAGCCTTTGTGGCGATCTA
1 AAATGGAAGCCTTTGTGGCAATCTA
20205223 AAGAAGGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.35
Consensus pattern (27 bp):
AAATGGAAGCCTTTGTGGCAATCTATG
Found at i:20205363 original size:27 final size:27
Alignment explanation
Indices: 20205333--20205399 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
20205323 GTATTATCGA
*
20205333 CAAACACTGAATGGATAGTATGTGTGG
1 CAAACACTGAAGGGATAGTATGTGTGG
* * *
20205360 CAAACATTAAAGGGATAGTATGTTTGG
1 CAAACACTGAAGGGATAGTATGTGTGG
* *
20205387 CGAACTCTGAAGG
1 CAAACACTGAAGG
20205400 AATGGTAGGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.25
Consensus pattern (27 bp):
CAAACACTGAAGGGATAGTATGTGTGG
Found at i:20206507 original size:390 final size:390
Alignment explanation
Indices: 20205788--20206570 Score: 1548
Period size: 390 Copynumber: 2.0 Consensus size: 390
20205778 AGTCTAAGGG
20205788 AAAGAGTATGAGTAATATATCAAAGATGTAGAGGTAAAGCATGAATCAAAATAAGGTATGACATC
1 AAAGAGTATGAGTAATATATCAAAGATGTAGAGGTAAAGCATGAATCAAAATAAGGTATGACATC
20205853 TAAAGTATGAAGAGTGGAATTATGGAAAGGTAATTGCCATAAACAAATTGAAGGATAAGATCTGC
66 TAAAGTATGAAGAGTGGAATTATGGAAAGGTAATTGCCATAAACAAATTGAAGGATAAGATCTGC
20205918 AAGATAGTGGTCGAAACCTTAGATGCATTATGCAAGTACAACTCAAGTAGTTGGTGTGGGCCTCA
131 AAGATAGTGGTCGAAACCTTAGATGCATTATGCAAGTACAACTCAAGTAGTTGGTGTGGGCCTCA
20205983 TTAAGTTCTCTCGAACTTATTTCTATATGTTATGTTTCAGGTGAGCTCTTAAGGATCTGCACCTA
196 TTAAGTTCTCTCGAACTTATTTCTATATGTTATGTTTCAGGTGAGCTCTTAAGGATCTGCACCTA
20206048 GAAGGACGATGCCAGGGCTACGTCAAAGGATTGGGAGGCGTATTATTATGCATACAGAGCAAGTT
261 GAAGGACGATGCCAGGGCTACGTCAAAGGATTGGGAGGCGTATTATTATGCATACAGAGCAAGTT
20206113 TGTTGGCGTGTTCAAGTCTGAATTGTTTATAGAAGTCTTTTACACGGAATAATTATAATAGGCCA
326 TGTTGGCGTGTTCAAGTCTGAATTGTTTATAGAAGTCTTTTACACGGAATAATTATAATAGGCCA
* *
20206178 AAAGAGTGTGAGTAATGTATCAAAGATGTAGAGGTAAAGCATGAATCAAAATAAGGTATGACATC
1 AAAGAGTATGAGTAATATATCAAAGATGTAGAGGTAAAGCATGAATCAAAATAAGGTATGACATC
20206243 TAAAGTATGAAGAGTGGAATTATGGAAAGGTAATTGCCATAAACAAATTGAAGGATAAGATCTGC
66 TAAAGTATGAAGAGTGGAATTATGGAAAGGTAATTGCCATAAACAAATTGAAGGATAAGATCTGC
20206308 AAGATAGTGGTCGAAACCTTAGATGCATTATGCAAGTACAACTCAAGTAGTTGGTGTGGGCCTCA
131 AAGATAGTGGTCGAAACCTTAGATGCATTATGCAAGTACAACTCAAGTAGTTGGTGTGGGCCTCA
20206373 TTAAGTTCTCTCGAACTTATTTCTATATGTTATGTTTCAGGTGAGCTCTTAAGGATCTGCACCTA
196 TTAAGTTCTCTCGAACTTATTTCTATATGTTATGTTTCAGGTGAGCTCTTAAGGATCTGCACCTA
20206438 GAAGGACGATGCCAGGGCTACGTCAAAGGATTGGGAGGCGTATTATTATGCATACAGAGCAAGTT
261 GAAGGACGATGCCAGGGCTACGTCAAAGGATTGGGAGGCGTATTATTATGCATACAGAGCAAGTT
20206503 TGTTGGCGTGTTCAAGTCTGAATTGTTTATAGAAGTCTTTTACACGGAATAATTATAATAGGCCA
326 TGTTGGCGTGTTCAAGTCTGAATTGTTTATAGAAGTCTTTTACACGGAATAATTATAATAGGCCA
20206568 AAA
1 AAA
20206571 CATCAAGTCA
Statistics
Matches: 391, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
390 391 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (390 bp):
AAAGAGTATGAGTAATATATCAAAGATGTAGAGGTAAAGCATGAATCAAAATAAGGTATGACATC
TAAAGTATGAAGAGTGGAATTATGGAAAGGTAATTGCCATAAACAAATTGAAGGATAAGATCTGC
AAGATAGTGGTCGAAACCTTAGATGCATTATGCAAGTACAACTCAAGTAGTTGGTGTGGGCCTCA
TTAAGTTCTCTCGAACTTATTTCTATATGTTATGTTTCAGGTGAGCTCTTAAGGATCTGCACCTA
GAAGGACGATGCCAGGGCTACGTCAAAGGATTGGGAGGCGTATTATTATGCATACAGAGCAAGTT
TGTTGGCGTGTTCAAGTCTGAATTGTTTATAGAAGTCTTTTACACGGAATAATTATAATAGGCCA
Found at i:20209379 original size:6 final size:6
Alignment explanation
Indices: 20209368--20209395 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20209358 CATATAAAGA
20209368 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
20209396 TTAAATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:20213771 original size:18 final size:18
Alignment explanation
Indices: 20213748--20213790 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
20213738 TGAGCAAGAC
*
20213748 CAGCATGATCTTGATTGA
1 CAGCATGATCTTGACTGA
*
20213766 CAGCATGATCTTGACTGG
1 CAGCATGATCTTGACTGA
20213784 CAGCATG
1 CAGCATG
20213791 CTGAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (18 bp):
CAGCATGATCTTGACTGA
Found at i:20215924 original size:21 final size:21
Alignment explanation
Indices: 20215900--20215943 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20215890 CATGACAGAT
20215900 GCTATGAATGTTGAATGAGCA
1 GCTATGAATGTTGAATGAGCA
20215921 GCTATGAATGTTGAATGAGCA
1 GCTATGAATGTTGAATGAGCA
20215942 GC
1 GC
20215944 GCACTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (21 bp):
GCTATGAATGTTGAATGAGCA
Found at i:20241769 original size:14 final size:14
Alignment explanation
Indices: 20241750--20241779 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20241740 TATAAATGAG
*
20241750 TATTTAGAAAGAAA
1 TATTTAAAAAGAAA
20241764 TATTTAAAAAGAAA
1 TATTTAAAAAGAAA
20241778 TA
1 TA
20241780 AGGGACTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (14 bp):
TATTTAAAAAGAAA
Found at i:20244008 original size:22 final size:22
Alignment explanation
Indices: 20243983--20244028 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
20243973 AAAGGAAGAA
20243983 CCTAAACCCTAGACCTGATAAC
1 CCTAAACCCTAGACCTGATAAC
20244005 CCTAAACCCTAGACCTGATAAC
1 CCTAAACCCTAGACCTGATAAC
20244027 CC
1 CC
20244029 AAATTTGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.39, G:0.09, T:0.17
Consensus pattern (22 bp):
CCTAAACCCTAGACCTGATAAC
Found at i:20249536 original size:20 final size:20
Alignment explanation
Indices: 20249511--20249552 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
20249501 TTTATACATA
20249511 TATATTAAGTTTATAATTTG
1 TATATTAAGTTTATAATTTG
* * *
20249531 TATATTTATTTTATATTTTG
1 TATATTAAGTTTATAATTTG
20249551 TA
1 TA
20249553 ATTTGGAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (20 bp):
TATATTAAGTTTATAATTTG
Found at i:20249726 original size:20 final size:20
Alignment explanation
Indices: 20249703--20249741 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20249693 TTTTGTAAAA
* *
20249703 TTTTAATAATTTTTTTTATC
1 TTTTAACAATTTCTTTTATC
*
20249723 TTTTTACAATTTCTTTTAT
1 TTTTAACAATTTCTTTTAT
20249742 AAACTTTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTAACAATTTCTTTTATC
Found at i:20255455 original size:24 final size:24
Alignment explanation
Indices: 20255427--20255472 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
20255417 ATCATTTTTT
* *
20255427 GCTGCTCATTCATTTTCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
*
20255451 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
20255473 GGATTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Found at i:20257815 original size:19 final size:19
Alignment explanation
Indices: 20257791--20257863 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
20257781 AATCATATAT
20257791 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
20257810 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
* *
20257829 TCTAAAATTGGATATCATA
1 TCTAAGATTGCATATCATA
*
20257848 TCTAAGAGTGCATATC
1 TCTAAGATTGCATATC
20257864 CCTGAAGATT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:20266193 original size:3 final size:3
Alignment explanation
Indices: 20266185--20266220 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
20266175 CATTTAACCC
20266185 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20266221 AAACCACAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20267790 original size:10 final size:10
Alignment explanation
Indices: 20267777--20267849 Score: 53
Period size: 10 Copynumber: 7.5 Consensus size: 10
20267767 TTTTGATGCA
20267777 TTTTATAATT
1 TTTTATAATT
**
20267787 TTTTAT-GGT
1 TTTTATAATT
*
20267796 TTTTATAAAT
1 TTTTATAATT
20267806 TTTTAT-ATT
1 TTTTATAATT
* *
20267815 CTTTTATGA-C
1 -TTTTATAATT
20267825 TTTTATAATT
1 TTTTATAATT
* *
20267835 TTTAATATTT
1 TTTTATAATT
20267845 TTTTA
1 TTTTA
20267850 ATAAATTTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
9 16 0.33
10 31 0.65
11 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:20267809 original size:29 final size:28
Alignment explanation
Indices: 20267777--20267849 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
20267767 TTTTGATGCA
**
20267777 TTTTATAATTTTTTATGGTTTTTATAAAT
1 TTTTATAATTTTTTATGACTTTTAT-AAT
20267806 TTTTAT-ATTCTTTTATGACTTTTATAAT
1 TTTTATAATT-TTTTATGACTTTTATAAT
*
20267834 TTTTAATATTTTTTTA
1 TTTT-ATAATTTTTTA
20267850 ATAAATTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 10 0.26
29 26 0.68
30 2 0.05
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (28 bp):
TTTTATAATTTTTTATGACTTTTATAAT
Found at i:20267891 original size:9 final size:9
Alignment explanation
Indices: 20267777--20267893 Score: 60
Period size: 9 Copynumber: 12.4 Consensus size: 9
20267767 TTTTGATGCA
20267777 TTTTATAATT
1 TTTTATAA-T
**
20267787 TTTTATGGT
1 TTTTATAAT
20267796 TTTTATAAAT
1 TTTTAT-AAT
*
20267806 TTTTATATT
1 TTTTATAAT
* *
20267815 CTTTTATGAC
1 -TTTTATAAT
20267825 TTTTATAAT
1 TTTTATAAT
*
20267834 TTTTAATATTT
1 TTTT-ATA-AT
*
20267845 TTTTAATAAA
1 TTTT-ATAAT
*
20267855 TTTAATAAAT
1 TTTTAT-AAT
*
20267865 TTTTATTGA-
1 TTTTA-TAAT
20267874 TTTT-T-AT
1 TTTTATAAT
20267881 TTTTATAAT
1 TTTTATAAT
20267890 TTTT
1 TTTT
20267894 TTGTCAATGG
Statistics
Matches: 81, Mismatches: 17, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
6 1 0.01
7 5 0.06
8 1 0.01
9 32 0.40
10 32 0.40
11 10 0.12
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:20268496 original size:11 final size:12
Alignment explanation
Indices: 20268459--20268501 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
20268449 TCTTAACTCC
20268459 TTTTTT-AAATA
1 TTTTTTAAAATA
* *
20268470 ATTTTAAAAATA
1 TTTTTTAAAATA
20268482 TTTTTTAAAAT-
1 TTTTTTAAAATA
20268493 TTTTTTAAA
1 TTTTTTAAA
20268502 CCGTAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 13 0.48
12 14 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTTTAAAATA
Found at i:20269618 original size:7 final size:7
Alignment explanation
Indices: 20269603--20269634 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
20269593 AGTCGATTGA
20269603 TATTTAG
1 TATTTAG
*
20269610 TACTTAG
1 TATTTAG
20269617 TATTTAG
1 TATTTAG
20269624 TATTTAG
1 TATTTAG
20269631 TATT
1 TATT
20269635 ATGTATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.56
Consensus pattern (7 bp):
TATTTAG
Found at i:20270310 original size:18 final size:18
Alignment explanation
Indices: 20270284--20270318 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20270274 AGGTGCGTTT
*
20270284 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
20270302 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
20270319 TCCTTTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:20270591 original size:25 final size:25
Alignment explanation
Indices: 20270557--20270694 Score: 173
Period size: 25 Copynumber: 5.7 Consensus size: 25
20270547 TATTTTGATA
20270557 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
20270582 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
20270607 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
** *
20270632 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
20270651 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
20270677 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
20270695 ACTCTAACCT
Statistics
Matches: 97, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
19 1 0.01
20 5 0.05
21 8 0.08
22 1 0.01
23 1 0.01
24 8 0.08
25 72 0.74
26 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.43
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:20270671 original size:45 final size:44
Alignment explanation
Indices: 20270522--20270684 Score: 184
Period size: 45 Copynumber: 3.5 Consensus size: 44
20270512 ACACCTCCGC
*
20270522 GTAAAAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGAT
1 GTAATAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGAT
* ** *
20270566 GTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGA-AGTTTATTTGAT
1 GTAATAAAATAGAAATTT-TTTGA-GT--T-ATTTTGATA--TTATTTGAT
20270616 GTAATAAAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGAT
1 GTAATAAAATAGAAATTTTTT-GAGTTATTTTGATATTATTTGAT
*
20270661 GTAATAAAATAGAAGTTTATTTGA
1 GTAATAAAATAGAAATTT-TTTGA
20270685 TGTAATAAAA
Statistics
Matches: 99, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
44 16 0.16
45 33 0.33
46 9 0.09
47 2 0.02
48 2 0.02
49 9 0.09
50 28 0.28
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (44 bp):
GTAATAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGAT
Found at i:20270689 original size:95 final size:94
Alignment explanation
Indices: 20270522--20270694 Score: 328
Period size: 95 Copynumber: 1.8 Consensus size: 94
20270512 ACACCTCCGC
20270522 GTAAAAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATT
1 GTAAAAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATT
20270587 TGATGTAATAAAATAGAAGTTTATTTGAT
66 TGATGTAATAAAATAGAAGTTTATTTGAT
*
20270616 GTAATAAAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTAT
1 GTAAAAAAATAGAAATTTTTT-GAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTAT
20270681 TTGATGTAATAAAA
65 TTGATGTAATAAAA
20270695 ACTCTAACCT
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
94 20 0.26
95 57 0.74
ACGTcount: A:0.42, C:0.01, G:0.14, T:0.43
Consensus pattern (94 bp):
GTAAAAAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATT
TGATGTAATAAAATAGAAGTTTATTTGAT
Found at i:20270758 original size:29 final size:29
Alignment explanation
Indices: 20270710--20270899 Score: 156
Period size: 29 Copynumber: 7.3 Consensus size: 29
20270700 AACCTAATTT
*
20270710 AACCCTAAACCCTAATCTAATTTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
*
20270740 AACCCTAATCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
20270769 AACCCT-A----AACC----TTAACTTAAA
1 AACCCTAACCCTAACCTAATTTAA-TTAAA
* *
20270790 AACCCTAAACCT----TAA-CT--TTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
20270812 AACCCT-A-----ACCTAATTTAATT-AA
1 AACCCTAACCCTAACCTAATTTAATTAAA
20270834 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
20270863 AACCCTAACTCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
20270892 AACCCTAA
1 AACCCTAA
20270900 ATCTTAACTT
Statistics
Matches: 133, Mismatches: 5, Indels: 45
0.73 0.03 0.25
Matches are distributed among these distances:
20 7 0.05
21 13 0.10
22 20 0.15
23 3 0.02
24 4 0.03
25 1 0.01
28 14 0.11
29 65 0.49
30 6 0.05
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:20270826 original size:66 final size:65
Alignment explanation
Indices: 20270749--20271062 Score: 239
Period size: 66 Copynumber: 4.5 Consensus size: 65
20270739 AAACCCTAAT
20270749 CCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAA
1 CCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTTAAAAACCCT-AACCTTAACTTTAAAAA
20270814 C
65 C
20270815 CCTAACCTAATTTAATT-AAAACCCTAACCCTAACCTAATTTAA-TTAAAAACCCTAACTCTAAC
1 CCTAACCTAATTTAATTAAAAACCCT-A----AACC----TTAACTTAAAAACCCTAAC-CT---
*
20270878 CTAATTTAATTAAAAAC
53 -TAA-CT--TTAAAAAC
*
20270895 CCT-A---AATCTTAACTTAAAACCCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAA-TT
1 CCTAACCTAAT-TTAA-TTAAAAACCCTAAACCTTAAC-TTAAAAACCCTAACC----TTAACTT
*
20270955 AAAACCCCTAAC
59 TAAA-----AAC
*
20270967 CCTAACCTAATTTAATTAAAAACCCTAACCCCTTAACTTAAAAACCCTAACCCTTAACTTT-AAA
1 CCTAACCTAATTTAATTAAAAACCCTAA-ACCTTAACTTAAAAACCCTAA-CCTTAACTTTAAAA
20271031 AC
64 AC
*
20271033 CCTAACCTAATTTAATTAAAACCCCTAAAC
1 CCTAACCTAATTTAATTAAAAACCCTAAAC
20271063 TAAGTTAATA
Statistics
Matches: 202, Mismatches: 8, Indels: 77
0.70 0.03 0.27
Matches are distributed among these distances:
65 9 0.04
66 48 0.24
67 4 0.02
69 1 0.00
70 8 0.04
71 10 0.05
72 25 0.12
73 14 0.07
74 33 0.16
75 14 0.07
76 6 0.03
77 7 0.03
78 4 0.02
79 8 0.04
80 11 0.05
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (65 bp):
CCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTTAAAAACCCTAACCTTAACTTTAAAAAC
Found at i:20270861 original size:123 final size:122
Alignment explanation
Indices: 20270710--20271037 Score: 517
Period size: 123 Copynumber: 2.7 Consensus size: 122
20270700 AACCTAATTT
*
20270710 AACCCTAAACCCTAATCTAATTTAATTAAAAACCCTAATCCTAACCTAATTTAATTAAAAACCCT
1 AACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAACCTAATTTAATTAAAAACCCT
20270775 AAACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATTAA
64 AAACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATTAA
20270834 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACTCTAACCTAATTTAATTAAAAACCCTA
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAC-CTAACCTAATTTAATTAAAAACCCTA
* *
20270899 AATCTTAACTTAAAACCCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATTAA
65 AACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATTAA
20270957 AACCCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC---CC----TTAACTTAAAAACCCT
1 AA-CCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAA-TTAAAAACCCT
* *
20271015 AACCCTTAACTTTAAAACCCTAA
64 AAACCTTAACTTAAAAACCCTAA
20271038 CCTAATTTAA
Statistics
Matches: 194, Mismatches: 7, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
116 4 0.02
117 30 0.15
120 2 0.01
122 1 0.01
123 115 0.59
124 42 0.22
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (122 bp):
AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAA
ACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATTAA
Found at i:20270957 original size:95 final size:95
Alignment explanation
Indices: 20270840--20271060 Score: 372
Period size: 95 Copynumber: 2.3 Consensus size: 95
20270830 TTAAAACCCT
* * *
20270840 AACCCTAACCTAATTTAATTAAAAACCCTAACTCTAACCTAATTTAATTAAAAACCCTAA-ATCT
1 AACCCTAACCTAATTTAATTAAAACCCCTAACCCTAACCTAATTTAATTAAAAACCCTAACACCT
*
20270904 TAACTTAAAACCCCTAAACCTTAACTTTAAA
66 TAACTTAAAAACCCTAAACCTTAACTTT-AA
*
20270935 AACCCTAACCTAATTTAATTAAAACCCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCCT
1 AACCCTAACCTAATTTAATTAAAACCCCTAACCCTAACCTAATTTAATTAAAAACCCTAACACCT
*
20271000 TAACTTAAAAACCCTAACCCTTAACTTTAA
66 TAACTTAAAAACCCTAAACCTTAACTTTAA
20271030 AACCCTAACCTAATTTAATTAAAACCCCTAA
1 AACCCTAACCTAATTTAATTAAAACCCCTAA
20271061 ACTAAGTTAA
Statistics
Matches: 119, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
95 91 0.76
96 28 0.24
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (95 bp):
AACCCTAACCTAATTTAATTAAAACCCCTAACCCTAACCTAATTTAATTAAAAACCCTAACACCT
TAACTTAAAAACCCTAAACCTTAACTTTAA
Found at i:20270967 original size:29 final size:29
Alignment explanation
Indices: 20270935--20270997 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
20270925 TAACTTTAAA
*
20270935 AACCCTAACCTAATTTAATTAAAACCCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
20270964 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
20270993 AACCC
1 AACCC
20270998 CTTAACTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:20271051 original size:22 final size:23
Alignment explanation
Indices: 20270716--20271071 Score: 179
Period size: 21 Copynumber: 14.9 Consensus size: 23
20270706 ATTTAACCCT
* *
20270716 AAACCCTAATCTAATTTAATTAA
1 AAACCCTAACCTAACTTAATTAA
20270739 AAACCCTAATCCTAACCTAATTTAATTAA
1 AAACCCTAA-CCTAA-C----TTAATTAA
*
20270768 AAACCCTAA---ACCTTAACTTAA
1 AAACCCTAACCTAACTTAA-TTAA
20270789 AAACCCTAAACCTTAAC-T--TTAA
1 AAACCCT-AACC-TAACTTAATTAA
*
20270811 AAACCCTAACCTAATTTAATTAAA
1 AAACCCTAACCTAACTTAATT-AA
*
20270835 ACCCTAACCCTAACCTAATTTAATTAA
1 A----AACCCTAACCTAACTTAATTAA
20270862 AAACCCTAACTCTAACCTAATTTAATTAA
1 AAACCCTAAC-CTAA-C----TTAATTAA
*
20270891 AAACCCTAA---ATCTTAACTTAA
1 AAACCCTAACCTAACTTAA-TTAA
*
20270912 AACCCCTAAACCTTAAC-T--TTAA
1 AAACCCT-AACC-TAACTTAATTAA
*
20270934 AAACCCTAACCTAATTTAATTAAA
1 AAACCCTAACCTAACTTAATT-AA
*
20270958 ACCCCTAACCCTAACCTAATTTAATTAA
1 A-----AACCCTAACCTAACTTAATTAA
*
20270986 AAACCCTAACC--CCTTAACTTAA
1 AAACCCTAACCTAACTTAA-TTAA
*
20271008 AAACCCTAACC---CTTAACTTTA
1 AAACCCTAACCTAACTTAA-TTAA
*
20271029 AAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAACTTAATTAA
* * *
20271052 AACCCCTAAACTAAGTTAAT
1 AAACCCTAACCTAACTTAAT
20271072 AATTTTACAT
Statistics
Matches: 269, Mismatches: 19, Indels: 90
0.71 0.05 0.24
Matches are distributed among these distances:
20 14 0.05
21 55 0.20
22 40 0.15
23 52 0.19
24 20 0.07
25 4 0.01
26 4 0.01
27 3 0.01
28 23 0.09
29 54 0.20
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (23 bp):
AAACCCTAACCTAACTTAATTAA
Found at i:20271269 original size:116 final size:116
Alignment explanation
Indices: 20271065--20271304 Score: 453
Period size: 116 Copynumber: 2.1 Consensus size: 116
20271055 CCCTAAACTA
20271065 AGTTAATAATTTTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAATAATT
1 AGTTAATAATTTTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAATAATT
*
20271130 AATAATTTTATATAATTTGATAATTTTACTATCCATTAATACAATTTTTAC
66 AATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTAC
20271181 AGTTAATAATTTTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAATAATT
1 AGTTAATAATTTTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAATAATT
**
20271246 AATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTG
66 AATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTAC
20271297 AGTTAATA
1 AGTTAATA
20271305 CAATTTATCA
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 121 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (116 bp):
AGTTAATAATTTTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAATAATT
AATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTAC
Found at i:20271321 original size:17 final size:18
Alignment explanation
Indices: 20271280--20271321 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
20271270 TTTACTAACC
* *
20271280 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
20271298 GTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
20271315 ATTAATA
1 ATTAATA
20271322 ATTGCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:20274756 original size:125 final size:125
Alignment explanation
Indices: 20274512--20274738 Score: 409
Period size: 125 Copynumber: 1.8 Consensus size: 125
20274502 CCCAAACATG
*
20274512 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
20274577 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAAAAAATAATTATTTCTTCCGTGAC
* * *
20274637 CTACTGTAGCAAAAGTGCATCTACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTTC
1 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
20274702 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA
20274739 CTCGAAATTA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 97 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAAAAAATAATTATTTCTTCCGTGAC
Found at i:20275774 original size:15 final size:17
Alignment explanation
Indices: 20275742--20275774 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
20275732 TTTAGAAGAA
20275742 AGGTGTGTTTATATATT
1 AGGTGTGTTTATATATT
20275759 AGGTGT-TTTATA-ATT
1 AGGTGTGTTTATATATT
20275774 A
1 A
20275775 TAGCAGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 6 0.38
17 6 0.38
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (17 bp):
AGGTGTGTTTATATATT
Found at i:20278671 original size:29 final size:29
Alignment explanation
Indices: 20278594--20278672 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 29
20278584 CAATTGAATT
* *
20278594 AAATCAGAATTATATGTACATATTTGAGTCA
1 AAATCAAAATT-TATGTATATATTTGAG-CA
20278625 AAATCAAAATTTAATGTATATATTTGCA-CA
1 AAATCAAAATTT-ATGTATATATTTG-AGCA
*
20278655 AAATCAAAGTTTATGTAT
1 AAATCAAAATTTATGTAT
20278673 CAAACTGTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
29 6 0.14
30 14 0.33
31 22 0.51
32 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (29 bp):
AAATCAAAATTTATGTATATATTTGAGCA
Found at i:20282540 original size:748 final size:744
Alignment explanation
Indices: 20281110--20282600 Score: 2398
Period size: 748 Copynumber: 2.0 Consensus size: 744
20281100 AGTTGATAAA
* * *
20281110 AGGCTTAATGAATGATTGACTAAGGATTTGCATGGAAAATAAGCCATTACAAATCATAGTGTATG
1 AGGCTTAATGAATGATTCACTAAGGATTTGCATGGAAAATAAGCCATTACAAATCATAGCGGATG
* *
20281175 GTAGGTGACCTTAAAATGGGTGAAAAATGTTTAATTTTATATTTTATTTAGTTAGAATAATAATG
66 ATAGGTGACCTTAAAATGGATGAAAAATGTTTAATTTTATATTTTATTTAGTTAGAATAATAATG
* *
20281240 AAAAAAATATTAAAACATAAAGTAAAAGAAAGAAAACAATTCATTCATCTTATTCACCCCAAAAA
131 AAAAAAATATTAAAACATAAAGTAAAACAAAGAAAACAATTCATTCATCTTAGTCACCCCAAAAA
*
20281305 TCGAGGATGAAAGAGACCTAGCTTCCGTCCAAACTTTTCTTTTCAATTGATCGAGATTTACTACA
196 TCGAGGATGAAAGAGACCTAGCTTCCGTCCAAACTTTGCTTTTCAATTGATCGAGATTTACTACA
* * *
20281370 ATCGGAAGATATACGTGGAAAAAAATTGTTGAATAGTCCCTAATGCTTTATCCATTGTTGTTTTG
261 ATCAGAAGATATACGTGAAAAAAAATTGTTGAATAGTCCCTAATGCTTTATCCATTGTTGTTTTA
* * *
20281435 CCAGGTAAGTTTATATGATATTTATGATTTTATGTTTCGGTTAAATTGTATCCAAATGCGTAAAT
326 CCAGGTAAGTTTATATGATATTTATGATTTTAAGTTGCGATTAAATTGTATCCAAATGCGTAAAT
* *
20281500 AAGTTCAATTGAAGGTTTGGATTATTTATAAATTGGAACTTAAGTTATAATTGGACTAAATTGTG
391 AAGTTCAATTGAAGGTTTGGATTATTTATAAATTGGAACTTAAGTTATAATCGGACTAAATTGTA
* *
20281565 AGAGGATATTATTGAACTTAAATGTTGAGATAGTCCCAATGAACTTAGTAAAAATTTCGTACATA
456 AGAGGATATTATTGAACTTAAATGTTGAGATAGTCCCAATGAACTTAGTAAAAATTTCATACACA
* *
20281630 TGGTTACAGGTTAATTTCCAATGATTCTGAGATCCAGCATTTGTTGCAGACTCAAAGATACATGT
521 TGGTTACAGGTTAATTTCCAATGATTCTGAGATCCAACATTTGTTGCAGACTCAAAGATACATAT
* * * *
20281695 GACACGAGTTTAGGTCGGATGAGTAACCTGATGTCGTTTTATGGGTTTAGCTCAGATGGGTGACC
586 GACACGAGTTTAGCTCGGATGAGTAACCTGATGTCGTTTTATAGGTTTAGCTCAGACGAGTGACC
*
20281760 TTACATGCATATACAACTCTAGCCAAACTATTTATTGTACCGGTAAAGGTTTAACCTAG-ATGGG
651 TTACATGCATATACAACTCTAGCCAAACTATTTATTGTACCAGTAAAGGTTTAA-CTAGAATGGG
*
20281824 TAACCTGACACTAATGTATGTGATTAGCTC
715 TAACCTGACACTAATGTATATGATTAGCTC
*
20281854 AGGCTTAATGAATGATTCACTAAGGATTTGCATGGAAAATAAGCCATTACAAATCTTAGCGGATG
1 AGGCTTAATGAATGATTCACTAAGGATTTGCATGGAAAATAAGCCATTACAAATCATAGCGGATG
* *
20281919 ATAGGTGACCTTAAAATGGATGAAAATTGTTTATTTTTATATTTTATTTAGTTAGAATAATAATG
66 ATAGGTGACCTTAAAATGGATGAAAAATGTTTAATTTTATATTTTATTTAGTTAGAATAATAATG
**
20281984 AAAAAAATATTAAAACATAAAGTAAAACAAAGAAAACAATTCATTCATCTTAGTCACTTCAAAAA
131 AAAAAAATATTAAAACATAAAGTAAAACAAAGAAAACAATTCATTCATCTTAGTCACCCCAAAAA
* *
20282049 TCGAGGATGAAGGAG-CCTAGCTTCTG-CCTAAACTTTGCTTTTCAATTGATCGAGATTTACTAC
196 TCGAGGATGAAAGAGACCTAGCTTCCGTCC-AAACTTTGCTTTTCAATTGATCGAGATTTACTAC
*
20282112 AATCAGAAGATATACGTAGAAAAAAAGAAAATTGTTGAATAGTCCCTAATGCTTTATCCGTTGTT
260 AATCAGAAGATATACGT-G---AAAA-AAAATTGTTGAATAGTCCCTAATGCTTTATCCATTGTT
*
20282177 GTTTTACCAGGTAAGTTTATATGATATTTATGATTTTAAGTTGCTATTAAATTGTATCCAAATGC
320 GTTTTACCAGGTAAGTTTATATGATATTTATGATTTTAAGTTGCGATTAAATTGTATCCAAATGC
* * *
20282242 GTAGATAAGTTCAATTGAAGGTTTGGATTATTTATAAATTGGTACTTAAGTTGTAATCGGACTAA
385 GTAAATAAGTTCAATTGAAGGTTTGGATTATTTATAAATTGGAACTTAAGTTATAATCGGACTAA
* * *
20282307 ATTGTAAGAGGATATTATTGAACTTAAATGTTGAGATTGTTCCGATGAACTCT-GTAAAAATTTC
450 ATTGTAAGAGGATATTATTGAACTTAAATGTTGAGATAGTCCCAATGAACT-TAGTAAAAATTTC
* * *
20282371 ATACACATGGTTACAGGTTAATTTCCAATGATTTTGAGATTCAACATTTGTTGCGGACTCAAAGA
514 ATACACATGGTTACAGGTTAATTTCCAATGATTCTGAGATCCAACATTTGTTGCAGACTCAAAGA
* * *
20282436 TACATATGACATGGGTTTAGCTCGGATGAGTAACCTGATGTCGTTTTATAGGTTTAGCTTAGACG
579 TACATATGACACGAGTTTAGCTCGGATGAGTAACCTGATGTCGTTTTATAGGTTTAGCTCAGACG
* * * *
20282501 AGTGACCTTACATGCATATACAAC-CATGGCCAGACTATTTATTGTATCAGTAAAGGTTTAACTT
644 AGTGACCTTACATGCATATACAACTC-TAGCCAAACTATTTATTGTACCAGTAAAGGTTTAACTA
*
20282565 GAATGGGTAACCTGACACTAATTTATATGATTAGCT
708 GAATGGGTAACCTGACACTAATGTATATGATTAGCT
20282601 TGGAAGAGCA
Statistics
Matches: 686, Mismatches: 52, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
742 2 0.00
743 59 0.09
744 198 0.29
747 7 0.01
748 419 0.61
749 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (744 bp):
AGGCTTAATGAATGATTCACTAAGGATTTGCATGGAAAATAAGCCATTACAAATCATAGCGGATG
ATAGGTGACCTTAAAATGGATGAAAAATGTTTAATTTTATATTTTATTTAGTTAGAATAATAATG
AAAAAAATATTAAAACATAAAGTAAAACAAAGAAAACAATTCATTCATCTTAGTCACCCCAAAAA
TCGAGGATGAAAGAGACCTAGCTTCCGTCCAAACTTTGCTTTTCAATTGATCGAGATTTACTACA
ATCAGAAGATATACGTGAAAAAAAATTGTTGAATAGTCCCTAATGCTTTATCCATTGTTGTTTTA
CCAGGTAAGTTTATATGATATTTATGATTTTAAGTTGCGATTAAATTGTATCCAAATGCGTAAAT
AAGTTCAATTGAAGGTTTGGATTATTTATAAATTGGAACTTAAGTTATAATCGGACTAAATTGTA
AGAGGATATTATTGAACTTAAATGTTGAGATAGTCCCAATGAACTTAGTAAAAATTTCATACACA
TGGTTACAGGTTAATTTCCAATGATTCTGAGATCCAACATTTGTTGCAGACTCAAAGATACATAT
GACACGAGTTTAGCTCGGATGAGTAACCTGATGTCGTTTTATAGGTTTAGCTCAGACGAGTGACC
TTACATGCATATACAACTCTAGCCAAACTATTTATTGTACCAGTAAAGGTTTAACTAGAATGGGT
AACCTGACACTAATGTATATGATTAGCTC
Found at i:20286036 original size:27 final size:26
Alignment explanation
Indices: 20286001--20286065 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
20285991 ATTAGAGTAC
20286001 ATAATCAGGAAGCACTCACT-CGAGCCAT
1 ATAA-CAGGAAGC-CTCA-TGCGAGCCAT
*
20286029 ATAACAGGAAG-CTCATGTGAGCCAT
1 ATAACAGGAAGCCTCATGCGAGCCAT
*
20286054 GTAACAGGAAGC
1 ATAACAGGAAGC
20286066 TTATCCGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 1 0.03
25 21 0.64
27 7 0.21
28 4 0.12
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
ATAACAGGAAGCCTCATGCGAGCCAT
Found at i:20287117 original size:42 final size:42
Alignment explanation
Indices: 20287070--20287152 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
20287060 TAATATTTGT
*
20287070 ATAACTTTGCAAATTGATCCCCAAAATAAATAGATTAGGTTG
1 ATAACTGTGCAAATTGATCCCCAAAATAAATAGATTAGGTTG
20287112 ATAACTGTGCAAATTGATCCCCAAAATAAATAGATTAGGTT
1 ATAACTGTGCAAATTGATCCCCAAAATAAATAGATTAGGTT
20287153 ATTACGATCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (42 bp):
ATAACTGTGCAAATTGATCCCCAAAATAAATAGATTAGGTTG
Found at i:20292657 original size:23 final size:26
Alignment explanation
Indices: 20292609--20292657 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
20292599 TTTATACACA
*
20292609 AATTAGTACGAGATACATTTGAATAT
1 AATTAGTACGAAATACATTTGAATAT
20292635 AATTA-TACGAAAT-CATTT-AATAT
1 AATTAGTACGAAATACATTTGAATAT
20292658 CAAGTCACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 5 0.23
25 7 0.32
26 5 0.23
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (26 bp):
AATTAGTACGAAATACATTTGAATAT
Found at i:20293015 original size:26 final size:26
Alignment explanation
Indices: 20292986--20293037 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
20292976 CAGTATACTC
20292986 AGTGTATAAACAAAAGTCAGGTATCA
1 AGTGTATAAACAAAAGTCAGGTATCA
20293012 AGTGTATAAACAAAAGTCAGGTATCA
1 AGTGTATAAACAAAAGTCAGGTATCA
20293038 TCACCTCATC
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:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (26 bp):
AGTGTATAAACAAAAGTCAGGTATCA
Found at i:20295946 original size:8 final size:8
Alignment explanation
Indices: 20295923--20295963 Score: 73
Period size: 8 Copynumber: 5.0 Consensus size: 8
20295913 AATAAATAAG
20295923 TATTATAT
1 TATTATAT
20295931 TAATTATAT
1 T-ATTATAT
20295940 TATTATAT
1 TATTATAT
20295948 TATTATAT
1 TATTATAT
20295956 TATTATAT
1 TATTATAT
20295964 ATATAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 24 0.75
9 8 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTATAT
Found at i:20297070 original size:41 final size:40
Alignment explanation
Indices: 20296993--20297091 Score: 99
Period size: 41 Copynumber: 2.4 Consensus size: 40
20296983 TTGATGGTAC
* * * * *
20296993 ATTGATTGGAAAGTGGAAAAATGTATTGGTATTGAATTGTAT
1 ATTGATTAGAAAGT-GAAAAATGAATTGGAAATGAATTGT-G
* *
20297035 ATTGATTAGAAAGTGAAAAGTGAATTTGAAATGAATTGTG
1 ATTGATTAGAAAGTGAAAAATGAATTGGAAATGAATTGTG
* *
20297075 ATTGAATCGAAAGTGAA
1 ATTGATTAGAAAGTGAA
20297092 TTTGAAATAG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
40 15 0.31
41 20 0.42
42 13 0.27
ACGTcount: A:0.40, C:0.01, G:0.25, T:0.33
Consensus pattern (40 bp):
ATTGATTAGAAAGTGAAAAATGAATTGGAAATGAATTGTG
Found at i:20297259 original size:41 final size:40
Alignment explanation
Indices: 20297202--20297311 Score: 131
Period size: 38 Copynumber: 2.8 Consensus size: 40
20297192 TGACCTCGAG
** * *
20297202 TCGATGAGACACTGGGTGTCACTATA-TTTCTTCGGATAGAT
1 TCGATGAGGTACTGGGTGT-ACCA-ACTTTCTTCGAATAGAT
20297243 TCGATGAGGTACT-GG-GTACCAACTTTCTTCGAATAGAT
1 TCGATGAGGTACTGGGTGTACCAACTTTCTTCGAATAGAT
20297281 TCGATGAGGTACT-GG-GTACCAACTTTCTTCG
1 TCGATGAGGTACTGGGTGTACCAACTTTCTTCG
20297312 GCTTTGCCGA
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
37 1 0.02
38 48 0.75
39 2 0.03
40 2 0.03
41 11 0.17
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (40 bp):
TCGATGAGGTACTGGGTGTACCAACTTTCTTCGAATAGAT
Found at i:20297279 original size:38 final size:38
Alignment explanation
Indices: 20297228--20297311 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 38
20297218 TGTCACTATA
*
20297228 TTTCTTCGGATAGATTCGATGAGGTACTGGGTACCAAC
1 TTTCTTCGAATAGATTCGATGAGGTACTGGGTACCAAC
20297266 TTTCTTCGAATAGATTCGATGAGGTACTGGGTACCAAC
1 TTTCTTCGAATAGATTCGATGAGGTACTGGGTACCAAC
20297304 TTTCTTCG
1 TTTCTTCG
20297312 GCTTTGCCGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (38 bp):
TTTCTTCGAATAGATTCGATGAGGTACTGGGTACCAAC
Found at i:20297341 original size:37 final size:39
Alignment explanation
Indices: 20297244--20297377 Score: 118
Period size: 38 Copynumber: 3.5 Consensus size: 39
20297234 CGGATAGATT
* * *
20297244 CGATGAGGTACTGGGTACCAACT-TT-CTTCGAA-TAGATT
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACT--ATC
* * * *
20297282 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
20297319 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
20297358 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
20297378 TTCTGGTGTG
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
36 1 0.01
37 19 0.24
38 33 0.41
39 24 0.30
40 3 0.04
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:20300545 original size:37 final size:37
Alignment explanation
Indices: 20300495--20300568 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
20300485 CTAGCTAGGT
20300495 TTTATTTTTTTTCTTGGTTCAAATTCGGCAATAGGAA
1 TTTATTTTTTTTCTTGGTTCAAATTCGGCAATAGGAA
*
20300532 TTTATTTTTTTTCTTGTTTCAAATTCGGCAATAGGAA
1 TTTATTTTTTTTCTTGGTTCAAATTCGGCAATAGGAA
20300569 GATGATGATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (37 bp):
TTTATTTTTTTTCTTGGTTCAAATTCGGCAATAGGAA
Found at i:20306940 original size:41 final size:41
Alignment explanation
Indices: 20306895--20306975 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
20306885 AATGTATCAC
* * *
20306895 CGGCATTAAGCCTGCTAGACTTATAGTCTGAATAATTTCAG
1 CGGCATCAAGCCTGCTAGACATAAAGTCTGAATAATTTCAG
*
20306936 CGGCATCAAGCCTGCTAGACATAAAGTCTGAATTATTTCA
1 CGGCATCAAGCCTGCTAGACATAAAGTCTGAATAATTTCA
20306976 CTGACAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (41 bp):
CGGCATCAAGCCTGCTAGACATAAAGTCTGAATAATTTCAG
Found at i:20319146 original size:18 final size:19
Alignment explanation
Indices: 20319123--20319159 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20319113 TGAACATGTC
*
20319123 GATGCATACTTTA-AAAAT
1 GATGCACACTTTATAAAAT
20319141 GATGCACACTTTATAAAAT
1 GATGCACACTTTATAAAAT
20319160 TTCCTACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (19 bp):
GATGCACACTTTATAAAAT
Found at i:20323486 original size:48 final size:48
Alignment explanation
Indices: 20323423--20323518 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
20323413 AATATTTTAT
*
20323423 TAAGCAAACCTATGAACACTTTTCTTTTTCTTCCCGTATAAAAATTGC
1 TAAGCAAACCAATGAACACTTTTCTTTTTCTTCCCGTATAAAAATTGC
* *
20323471 TAAGCAAACCAATGAACATTTTTCTTTTTCTTCCCGTGTAAAAATTGC
1 TAAGCAAACCAATGAACACTTTTCTTTTTCTTCCCGTATAAAAATTGC
20323519 ACCTTAAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (48 bp):
TAAGCAAACCAATGAACACTTTTCTTTTTCTTCCCGTATAAAAATTGC
Found at i:20328981 original size:7 final size:7
Alignment explanation
Indices: 20328969--20328994 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20328959 ACCAGCCACT
20328969 GCAATTA
1 GCAATTA
20328976 GCAATTA
1 GCAATTA
20328983 GCAATTA
1 GCAATTA
20328990 GCAAT
1 GCAAT
20328995 CAACTATCAA
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:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (7 bp):
GCAATTA
Found at i:20329003 original size:7 final size:7
Alignment explanation
Indices: 20328993--20329019 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
20328983 GCAATTAGCA
20328993 ATCAACT
1 ATCAACT
20329000 ATCAACT
1 ATCAACT
20329007 ATCAACT
1 ATCAACT
20329014 ATCAAC
1 ATCAAC
20329020 CAATTGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (7 bp):
ATCAACT
Found at i:20329530 original size:19 final size:20
Alignment explanation
Indices: 20329486--20329535 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
20329476 ATTAATTATT
*
20329486 TATAAAATTTAATTAGAATA
1 TATAAAATATAATTAGAATA
*
20329506 TATAAAATATATTTA-AATA
1 TATAAAATATAATTAGAATA
*
20329525 T-TTAAATATAA
1 TATAAAATATAA
20329536 AAATTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 8 0.31
19 5 0.19
20 13 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TATAAAATATAATTAGAATA
Found at i:20329900 original size:22 final size:22
Alignment explanation
Indices: 20329875--20329945 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
20329865 TCAATAAATG
20329875 ATTTGGTTAATACAATACTTAT
1 ATTTGGTTAATACAATACTTAT
* * **
20329897 ATTT-GATAA-GCATATGA-AAAT
1 ATTTGGTTAATACA-AT-ACTTAT
20329918 GATTTGGTTAATACAATACTTAT
1 -ATTTGGTTAATACAATACTTAT
20329941 ATTTG
1 ATTTG
20329946 ATAAGCATAC
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 2 0.06
21 8 0.23
22 15 0.43
23 8 0.23
24 2 0.06
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (22 bp):
ATTTGGTTAATACAATACTTAT
Found at i:20329920 original size:44 final size:44
Alignment explanation
Indices: 20329870--20329963 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 44
20329860 TATAGTCAAT
**
20329870 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATACAA
20329914 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATACAA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATACAA
20329958 AAATGA
1 AAATGA
20329964 AAGTCGAGAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (44 bp):
AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATACAA
Found at i:20334763 original size:27 final size:25
Alignment explanation
Indices: 20334726--20334792 Score: 98
Period size: 25 Copynumber: 2.6 Consensus size: 25
20334716 AAAAAATAAA
20334726 AATTTACCAAAATATTATCCTTTTTTT
1 AATTTACCAAAATATTAT--TTTTTTT
*
20334753 TATTTACCAAAATATTATTTTTTTT
1 AATTTACCAAAATATTATTTTTTTT
*
20334778 AAATTACCAAAATAT
1 AATTTACCAAAATAT
20334793 ACCAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 20 0.54
27 17 0.46
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTTACCAAAATATTATTTTTTTT
Found at i:20334923 original size:4 final size:4
Alignment explanation
Indices: 20334914--20334977 Score: 69
Period size: 4 Copynumber: 16.0 Consensus size: 4
20334904 GAAGGAGAGG
* *
20334914 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GGAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA GAAA
*
20334963 -AAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA
20334978 AGGAAAGGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
3 4 0.08
4 41 0.79
5 7 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:20334957 original size:18 final size:18
Alignment explanation
Indices: 20334904--20334988 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 18
20334894 CTGGGGGGAA
20334904 GAAGGAGAGGGAAAGAAAG
1 GAAGGAGA-GGAAAGAAAG
* * *
20334923 AAAGAAAGAAAGAAAGAAAG
1 GAAG-GAG-AGGAAAGAAAG
20334943 GAAGGAGAGGAAAGAAA-
1 GAAGGAGAGGAAAGAAAG
**
20334960 GAAAAAGAAGGAAAGAAAAG
1 GAAGGAG-AGGAAAG-AAAG
20334980 GAAAGGAGA
1 G-AAGGAGA
20334989 AGAGAAAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
17 5 0.10
18 16 0.32
19 8 0.16
20 16 0.32
21 5 0.10
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (18 bp):
GAAGGAGAGGAAAGAAAG
Found at i:20334995 original size:36 final size:34
Alignment explanation
Indices: 20334905--20335017 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 34
20334895 TGGGGGGAAG
* *
20334905 AAGGAGAGG-GAAAGAAAGAAAGAAAGAAAGAAAGA
1 AAGGAAAGGAGAAAGAAAG-AA-AAAGAAGGAAAGA
*
20334940 AAGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAA
1 AAGGAAAG-GA-GAAAGAAAGAAAAAGAAGGAAAG-A
* * *
20334977 AAGGAAAGGAGAAGAGAAAAAAAAAG-AGGGAAGG
1 AAGGAAAGGAGAA-AGAAAGAAAAAGAAGGAAAGA
20335011 AAGGAAA
1 AAGGAAA
20335018 AAAAGGAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
34 7 0.11
35 15 0.23
36 25 0.38
37 10 0.15
38 9 0.14
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (34 bp):
AAGGAAAGGAGAAAGAAAGAAAAAGAAGGAAAGA
Found at i:20335002 original size:18 final size:18
Alignment explanation
Indices: 20334944--20335024 Score: 53
Period size: 18 Copynumber: 4.3 Consensus size: 18
20334934 GAAAGAAAGG
20334944 AAGGAG-AGGAAAGAAAGAA
1 AAGGAGAAGG-AAGAAA-AA
20334963 AA--AGAAGGAAAGAAAAGGA
1 AAGGAGAAGG-AAGAAAA--A
20334982 AAGGAGAAGAGAA-AAAAA
1 AAGGAGAAG-GAAGAAAAA
*
20335000 AAGAGGGAAGGAAGGAAAAA
1 AAG-GAGAAGGAA-GAAAAA
20335020 AAGGA
1 AAGGA
20335025 AAAAAAGGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
17 3 0.06
18 17 0.33
19 11 0.22
20 12 0.24
21 7 0.14
22 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (18 bp):
AAGGAGAAGGAAGAAAAA
Found at i:20335025 original size:9 final size:9
Alignment explanation
Indices: 20335011--20335035 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20335001 AGAGGGAAGG
20335011 AAGGAAAAA
1 AAGGAAAAA
20335020 AAGGAAAAA
1 AAGGAAAAA
20335029 AAGGAAA
1 AAGGAAA
20335036 TTTTTTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAGGAAAAA
Found at i:20335145 original size:24 final size:25
Alignment explanation
Indices: 20335063--20335149 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 25
20335053 ATGTTAAAAA
20335063 TTTATGTTATGTACATTATACGTATT
1 TTTATGTTATGTACATTATACGTA-T
* *
20335089 TTAATATTTTATTTAGCA-TATA--TAT
1 TT--TATGTTATGTA-CATTATACGTAT
20335114 TTTGATGTTATGTACATTATACGTA-
1 TTT-ATGTTATGTACATTATACGTAT
20335139 TTTATGTTATG
1 TTTATGTTATG
20335150 ATATGTACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
23 3 0.06
24 20 0.40
25 6 0.12
26 6 0.12
28 13 0.26
29 2 0.04
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (25 bp):
TTTATGTTATGTACATTATACGTAT
Found at i:20338243 original size:11 final size:11
Alignment explanation
Indices: 20338227--20338253 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20338217 TTTATAACTT
20338227 AATTTGGATAC
1 AATTTGGATAC
20338238 AATTTGGATAC
1 AATTTGGATAC
20338249 AATTT
1 AATTT
20338254 AAGCATAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (11 bp):
AATTTGGATAC
Found at i:20340530 original size:18 final size:18
Alignment explanation
Indices: 20340507--20340551 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
20340497 ATCCCAATGA
20340507 TCGCCACCACATTCTTCT
1 TCGCCACCACATTCTTCT
* *
20340525 TCGCCAGCACCTTCTTCT
1 TCGCCACCACATTCTTCT
*
20340543 TCACCACCA
1 TCGCCACCA
20340552 ACCATATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.47, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACATTCTTCT
Found at i:20341399 original size:3 final size:3
Alignment explanation
Indices: 20341391--20341425 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
20341381 TCTTAATACT
*
20341391 AAC AAC AAC AAT AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
20341426 TAATAATACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.29, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:20341407 original size:12 final size:12
Alignment explanation
Indices: 20341390--20341428 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
20341380 ATCTTAATAC
20341390 TAACAACAACAA
1 TAACAACAACAA
20341402 TAACAACAACAA
1 TAACAACAACAA
*
20341414 CAACAACAACAA
1 TAACAACAACAA
20341426 TAA
1 TAA
20341429 TAATACTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.67, C:0.26, G:0.00, T:0.08
Consensus pattern (12 bp):
TAACAACAACAA
Found at i:20341592 original size:10 final size:11
Alignment explanation
Indices: 20341551--20341590 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
20341541 AAAAAAATAC
20341551 CTTCTTTTTCT
1 CTTCTTTTTCT
*
20341562 TTTCTTTTTCT
1 CTTCTTTTTCT
20341573 C-TCTTTTTCT
1 CTTCTTTTTCT
20341583 CTTCTTTT
1 CTTCTTTT
20341591 CTGCAGCACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:20343887 original size:8 final size:8
Alignment explanation
Indices: 20343874--20343912 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
20343864 CTCGATTGCT
20343874 TGTTTGTA
1 TGTTTGTA
20343882 TGTTTGTA
1 TGTTTGTA
*
20343890 TGGTT-T-
1 TGTTTGTA
20343896 TGTTTGTA
1 TGTTTGTA
20343904 TGTTTGTA
1 TGTTTGTA
20343912 T
1 T
20343913 TGCTCATTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 4 0.15
7 2 0.07
8 21 0.78
ACGTcount: A:0.10, C:0.00, G:0.26, T:0.64
Consensus pattern (8 bp):
TGTTTGTA
Found at i:20344882 original size:12 final size:12
Alignment explanation
Indices: 20344859--20344914 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
20344849 GCAAAACTAC
20344859 ATATACCTTTAAT
1 ATATA-CTTTAAT
*
20344872 ATATACTTTAAA
1 ATATACTTTAAT
*
20344884 ATGTA-TTTAA-
1 ATATACTTTAAT
20344894 ATAT-CATTTAAT
1 ATATAC-TTTAAT
20344906 ATATACTTT
1 ATATACTTT
20344915 TTTGGGTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
10 3 0.08
11 10 0.28
12 17 0.47
13 6 0.17
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (12 bp):
ATATACTTTAAT
Found at i:20348018 original size:91 final size:91
Alignment explanation
Indices: 20347889--20348096 Score: 317
Period size: 91 Copynumber: 2.3 Consensus size: 91
20347879 TTGATTTTAG
* *
20347889 TAAATTCATATAAGAACATTTTATTATTAAGAAATTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAAATTTATGAAATTATATATCACTATTAAATTAT
* * *
20347954 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* * *
20347981 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAAATTTATGAAATTATATATCACTATTAAATTATA
20348046 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
20348072 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
20348097 GTTATAATTA
Statistics
Matches: 106, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
91 90 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAAATTTATGAAATTATATATCACTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:20348065 original size:26 final size:28
Alignment explanation
Indices: 20348011--20348071 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
20348001 TATTATCAAG
* *
20348011 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
20348039 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
20348065 AATTATA
1 AATTATA
20348072 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:20348189 original size:59 final size:58
Alignment explanation
Indices: 20348101--20348311 Score: 143
Period size: 54 Copynumber: 3.6 Consensus size: 58
20348091 TTATTAGTTA
*
20348101 TAATTATTTTAAATT-T-TATTA-A-ATCATATATTTTAAATAAAATATATTTAATAT
1 TAATTATTTTAAATTATATTTTATATATCATATATTTTAAATAAAATATATTTAATAT
* * * **
20348155 TAATTATTTTAAATTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATA
1 TAATTATTTTAAATTATATTTTATA-TATC--ATA-TAT--TTTAAATAAAAT-ATAT-TTAATA
20348220 T
58 T
* * * * * *
20348221 TAATTA--TT-AA-GA-ATTTTATTAAATTATATATTTTAATTATAATATATTTAATAA
1 TAATTATTTTAAATTATATTTTA-TATATCATATATTTTAAATAAAATATATTTAATAT
* *
20348275 TAATTATGTTAATTTATATTTTATAGTATCATATATT
1 TAATTATTTTAAATTATATTTTATA-TATCATATATT
20348312 ATGATTTGAA
Statistics
Matches: 118, Mismatches: 20, Indels: 33
0.69 0.12 0.19
Matches are distributed among these distances:
54 25 0.21
55 5 0.04
56 14 0.12
57 2 0.02
58 6 0.05
59 21 0.18
61 11 0.09
62 6 0.05
63 2 0.02
64 11 0.09
65 4 0.03
66 11 0.09
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (58 bp):
TAATTATTTTAAATTATATTTTATATATCATATATTTTAAATAAAATATATTTAATAT
Found at i:20348236 original size:120 final size:120
Alignment explanation
Indices: 20348112--20348409 Score: 474
Period size: 120 Copynumber: 2.5 Consensus size: 120
20348102 AATTATTTTA
* *
20348112 AATTTTATTAAATCATATATTTTAAATAAAATATATTTAATATTAATTATTTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAAATATAATATATTTAATATTAATTATTTTAAATTATATTTT
*
20348177 ATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTCAATAAATTCATATAAGAATATTAATTATTAAG
* * * *
20348232 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAAATATAATATATTTAATATTAATTATTTTAAATTATATTTT
* *
20348297 ATAGTATCATATATTATGATTTGAATAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTCAATAAATTCATATAAGAATATTAATTATTAAG
20348352 AATTTTATTAAATTATATA-TTTAAATTATAATATATTTAATAATT-ATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAAA-TATAATATATTTAAT-ATTAATTAT-TTTAAAT
20348410 ATGATTAAAT
Statistics
Matches: 162, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
119 5 0.03
120 150 0.93
121 7 0.04
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAAATATAATATATTTAATATTAATTATTTTAAATTATATTTT
ATAGTATCATATATTATGATTTCAATAAATTCATATAAGAATATTAATTATTAAG
Found at i:20348272 original size:15 final size:15
Alignment explanation
Indices: 20348237--20348288 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
20348227 TTAAGAATTT
*
20348237 TATTAAATTAT-ATA
1 TATTTAATTATAATA
20348251 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
20348265 TATTTAATAATAAT-
1 TATTTAATTATAATA
20348279 TATGTTAATT
1 TAT-TTAATT
20348289 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:20348369 original size:59 final size:59
Alignment explanation
Indices: 20348185--20348372 Score: 170
Period size: 61 Copynumber: 3.1 Consensus size: 59
20348175 TTATAGTATC
* *
20348185 ATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTT-AATAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAA-T
* * * * * * * *
20348246 ATATATTTTAATTATAATATATTTA-ATAATAAT-TATG-TTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATT-TAATAAATTCATATAAGAATAT-TGATT-ATTAAGAATTTTATTA-AAT
20348304 CATATATTATGATTTGAATAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 -ATATATTATGATTT-AATAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAA-T
20348366 ATATATT
1 ATATATT
20348373 TAAATTATAA
Statistics
Matches: 97, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
58 4 0.04
59 29 0.30
60 25 0.26
61 35 0.36
62 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (59 bp):
ATATATTATGATTTAATAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
Found at i:20348642 original size:16 final size:16
Alignment explanation
Indices: 20348621--20348674 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
20348611 TTGATTTGCT
20348621 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
20348637 ATTACACCTCTATTAC
1 ATTACACCTCTATTCC
*
20348653 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
20348669 AATACA
1 ATTACA
20348675 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.02, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:20363344 original size:35 final size:35
Alignment explanation
Indices: 20363305--20363550 Score: 262
Period size: 35 Copynumber: 7.0 Consensus size: 35
20363295 TGTTATGAAA
* *
20363305 TATTGGTGTTGTGGCAAGATGTTAAATGAACGAGG
1 TATTGGTGTTGTGGCGAGATGTTAAATGAATGAGG
** *
20363340 TATTGGTGTTGTAAC-AGAATGTTAAATGAATGAAG
1 TATTGGTGTTGTGGCGAG-ATGTTAAATGAATGAGG
* ** * * *
20363375 TGTTGGAATTGTGGTGGGATGTTAAATGAATAAGG
1 TATTGGTGTTGTGGCGAGATGTTAAATGAATGAGG
* *
20363410 TATTGGTGTTGTGGCGGGATGTTAAATTAATGAGG
1 TATTGGTGTTGTGGCGAGATGTTAAATGAATGAGG
** * * * *
20363445 TATTGGCATTGTGTCGAGATGTTAAATGTACGATG
1 TATTGGTGTTGTGGCGAGATGTTAAATGAATGAGG
**
20363480 TATTGGCCTTGTGGCG-GAATGTTAAATGAATGAGG
1 TATTGGTGTTGTGGCGAG-ATGTTAAATGAATGAGG
*
20363515 TATTGGTGTTGTGGCGAGATGTTAATTGAATGAGG
1 TATTGGTGTTGTGGCGAGATGTTAAATGAATGAGG
20363550 T
1 T
20363551 GTGTGGAATG
Statistics
Matches: 172, Mismatches: 35, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
34 3 0.02
35 167 0.97
36 2 0.01
ACGTcount: A:0.27, C:0.04, G:0.33, T:0.35
Consensus pattern (35 bp):
TATTGGTGTTGTGGCGAGATGTTAAATGAATGAGG
Found at i:20363424 original size:105 final size:105
Alignment explanation
Indices: 20363305--20363550 Score: 314
Period size: 105 Copynumber: 2.3 Consensus size: 105
20363295 TGTTATGAAA
* * **
20363305 TATTGGTGTTGTGGCAAGATGTTAAATGAACGAGGTATTGGTGTTGTAAC-AGAATGTTAAATGA
1 TATTGGTGTTGTGGCGAGATGTTAAATGAATGAGGTATTGGCATTGTAACGAG-ATGTTAAATGA
* * * *
20363369 ATGAAGTGTTGGAATTGTGGTGGGATGTTAAATGAATAAGG
65 ACGAAGTATTGGAATTGTGGCGGAATGTTAAATGAATAAGG
* * ** *
20363410 TATTGGTGTTGTGGCGGGATGTTAAATTAATGAGGTATTGGCATTGTGTCGAGATGTTAAATGTA
1 TATTGGTGTTGTGGCGAGATGTTAAATGAATGAGGTATTGGCATTGTAACGAGATGTTAAATGAA
* ** *
20363475 CGATGTATTGGCCTTGTGGCGGAATGTTAAATGAATGAGG
66 CGAAGTATTGGAATTGTGGCGGAATGTTAAATGAATAAGG
*
20363515 TATTGGTGTTGTGGCGAGATGTTAATTGAATGAGGT
1 TATTGGTGTTGTGGCGAGATGTTAAATGAATGAGGT
20363551 GTGTGGAATG
Statistics
Matches: 120, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
105 118 0.98
106 2 0.02
ACGTcount: A:0.27, C:0.04, G:0.33, T:0.35
Consensus pattern (105 bp):
TATTGGTGTTGTGGCGAGATGTTAAATGAATGAGGTATTGGCATTGTAACGAGATGTTAAATGAA
CGAAGTATTGGAATTGTGGCGGAATGTTAAATGAATAAGG
Found at i:20371798 original size:19 final size:18
Alignment explanation
Indices: 20371776--20371816 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
20371766 GACTCGAATC
20371776 TTAACATTTATAAATTTTT
1 TTAACATTTAT-AATTTTT
* *
20371795 TTAACTTTTATGATTTTT
1 TTAACATTTATAATTTTT
20371813 TTAA
1 TTAA
20371817 GAAAAGGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (18 bp):
TTAACATTTATAATTTTT
Found at i:20379571 original size:25 final size:25
Alignment explanation
Indices: 20379543--20379590 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
20379533 ATACACATTA
* *
20379543 AATATTTAAAATTTATTTTAAATTT
1 AATATATAAAATTTATTTAAAATTT
**
20379568 AATATATAATTTTTATTTAAAAT
1 AATATATAAAATTTATTTAAAAT
20379591 AAATAGGATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AATATATAAAATTTATTTAAAATTT
Found at i:20395897 original size:35 final size:35
Alignment explanation
Indices: 20395842--20395924 Score: 139
Period size: 35 Copynumber: 2.4 Consensus size: 35
20395832 CTTAAAAATT
* *
20395842 CTTCTTTTTTAATCAAATTTAATATCTAAAGTACA
1 CTTCATTTCTAATCAAATTTAATATCTAAAGTACA
20395877 CTTCATTTCTAATCAAATTTAATATCTAAAGTACA
1 CTTCATTTCTAATCAAATTTAATATCTAAAGTACA
*
20395912 CTTCATTCCTAAT
1 CTTCATTTCTAAT
20395925 TTGGTACCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.43
Consensus pattern (35 bp):
CTTCATTTCTAATCAAATTTAATATCTAAAGTACA
Found at i:20396124 original size:29 final size:27
Alignment explanation
Indices: 20396056--20396124 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
20396046 TTTTTTAATC
* *
20396056 AAATGTATATAAACATTAAAAATTATA
1 AAATATATATAAACATTAAAAATTAGA
* * *
20396083 AAAAATAAAATAAATATATAAAAATTCAGA
1 AAATAT-ATATAAACAT-TAAAAATT-AGA
20396113 AAATATATATAA
1 AAATATATATAA
20396125 TCTAGGAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
27 4 0.12
28 8 0.25
29 13 0.41
30 7 0.22
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (27 bp):
AAATATATATAAACATTAAAAATTAGA
Found at i:20396157 original size:14 final size:15
Alignment explanation
Indices: 20396132--20396165 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
20396122 TAATCTAGGA
*
20396132 AAAAATATAAATTAT
1 AAAAATATAAATTAC
20396147 AAAAATA-AAATTAC
1 AAAAATATAAATTAC
20396161 AAAAA
1 AAAAA
20396166 ATACGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATATAAATTAC
Found at i:20396166 original size:15 final size:15
Alignment explanation
Indices: 20396131--20396168 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
20396121 ATAATCTAGG
20396131 AAAAAATATAAATTA
1 AAAAAATATAAATTA
*
20396146 TAAAAATA-AAATTA
1 AAAAAATATAAATTA
20396160 CAAAAAATA
1 -AAAAAATA
20396169 CGATAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAAATATAAATTA
Found at i:20399395 original size:22 final size:21
Alignment explanation
Indices: 20399364--20399404 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
20399354 TAATGCTGGT
*
20399364 AAAAAGGAAAAAAAACAAGAAG
1 AAAAAAGAAAAAAAA-AAGAAG
20399386 AAAAAAGAAAAAAAAAAGA
1 AAAAAAGAAAAAAAAAAGA
20399405 CTTATTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAAAAAAAAGAAG
Found at i:20400313 original size:16 final size:16
Alignment explanation
Indices: 20400292--20400326 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20400282 TTGAATTATT
*
20400292 ATTATAGCTCTATTCC
1 ATTATAGCCCTATTCC
20400308 ATTATAGCCCTATTCC
1 ATTATAGCCCTATTCC
20400324 ATT
1 ATT
20400327 CACCCCAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (16 bp):
ATTATAGCCCTATTCC
Found at i:20403546 original size:21 final size:21
Alignment explanation
Indices: 20403512--20403551 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20403502 TATTAAAGCT
*
20403512 AGTTACAATCAAACTAAACTA
1 AGTTACAATCAAACAAAACTA
20403533 AGTTAC-ATCAAAACAAAAC
1 AGTTACAATC-AAACAAAAC
20403552 AGCAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (21 bp):
AGTTACAATCAAACAAAACTA
Found at i:20407857 original size:21 final size:21
Alignment explanation
Indices: 20407823--20407862 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20407813 TATTAAAGCT
*
20407823 AGTTACAATCAAACTAAACTA
1 AGTTACAATCAAACAAAACTA
20407844 AGTTAC-ATCAAAACAAAAC
1 AGTTACAATC-AAACAAAAC
20407863 AGCAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (21 bp):
AGTTACAATCAAACAAAACTA
Found at i:20413455 original size:59 final size:61
Alignment explanation
Indices: 20413345--20413482 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 61
20413335 ATCCTAAATA
* * ** * *
20413345 TAAAATATTCAACAAATTTAGCATTCAATGTTTACAAAATTTGTCATTTTAGTT-TGAATT-T
1 TAAAA-ATTCAATAAATTTAGCACTCAAAATTTACAAAATTTATCAATTTAGTTCT-AATTCT
*
20413406 TAAAAATTCAATAAATTTAGC-CTCAAAATTTACAAAATTTATGAATTTAGTTCTAATTCT
1 TAAAAATTCAATAAATTTAGCACTCAAAATTTACAAAATTTATCAATTTAGTTCTAATTCT
* *
20413466 AAAAAACTCAATAAATT
1 TAAAAATTCAATAAATT
20413483 AGTTTATAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
59 29 0.44
60 32 0.48
61 5 0.08
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (61 bp):
TAAAAATTCAATAAATTTAGCACTCAAAATTTACAAAATTTATCAATTTAGTTCTAATTCT
Found at i:20422885 original size:33 final size:33
Alignment explanation
Indices: 20422848--20422913 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
20422838 GTACAACTGA
*
20422848 AAATCACAAGAAAATAGCAACTAAGCTGATACT
1 AAATCACAAGAAAATAGCAACTAAGCAGATACT
* * * *
20422881 AAATCCCTAGAAAATAGGAACTAATCAGATACT
1 AAATCACAAGAAAATAGCAACTAAGCAGATACT
20422914 CCTAAACAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.20
Consensus pattern (33 bp):
AAATCACAAGAAAATAGCAACTAAGCAGATACT
Found at i:20423091 original size:3 final size:3
Alignment explanation
Indices: 20423083--20423111 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20423073 ATCACATGTT
20423083 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20423112 TGGATGTAAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.