Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 19 of 214
Found at i:5225322 original size:35 final size:36
Alignment explanation
Indices: 5225239--5225326 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 36
5225229 TAATTTTTTA
* *
5225239 TTTTAGACTTT-AATATCCTTAGATTTAATTTATGT
1 TTTTAGATTTTAAATATCCTTAGATTTAACTTATGT
*
5225274 TTGATATAAATTTTAAATATTCCTTAGATTT-ACTTAT-T
1 TT--T-TAGATTTTAAATA-TCCTTAGATTTAACTTATGT
5225312 TTTTAGATTTTAAAT
1 TTTTAGATTTTAAAT
5225327 TTTTGGTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
35 13 0.30
36 1 0.02
37 1 0.02
38 9 0.20
39 9 0.20
40 11 0.25
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.55
Consensus pattern (36 bp):
TTTTAGATTTTAAATATCCTTAGATTTAACTTATGT
Found at i:5230947 original size:18 final size:18
Alignment explanation
Indices: 5230924--5230968 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
5230914 CTCAAGGGAT
5230924 TTACAAGAT-TTCCTAAGA
1 TTACAAGATCTT-CTAAGA
*
5230942 TTACAAAATCTTCTAAGA
1 TTACAAGATCTTCTAAGA
5230960 TTACAAGAT
1 TTACAAGAT
5230969 ATTGGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (18 bp):
TTACAAGATCTTCTAAGA
Found at i:5233449 original size:27 final size:27
Alignment explanation
Indices: 5233413--5233466 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5233403 AAGGGTTCTA
5233413 AAACAAGAGCCCCCAACAGAGTAGGCT
1 AAACAAGAGCCCCCAACAGAGTAGGCT
5233440 AAACAAGAGCCCCCAACAGAGTAGGCT
1 AAACAAGAGCCCCCAACAGAGTAGGCT
5233467 CGGTTTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.30, G:0.22, T:0.07
Consensus pattern (27 bp):
AAACAAGAGCCCCCAACAGAGTAGGCT
Found at i:5233831 original size:49 final size:48
Alignment explanation
Indices: 5233728--5233832 Score: 122
Period size: 49 Copynumber: 2.2 Consensus size: 48
5233718 TGCCACACGG
* * ** *
5233728 CCGTGTGGTAGGCTGTGTGTGGCACATGGCCGTGTGAAACTCTGTAGA
1 CCGTGTGGTAGGCTATGTGTGGCACATGACCGTGTGAAACTCTACAAA
* *
5233776 CTGTGTGGCTAGGCTATGTGTGGCACATGACTGTGTGAAACT-TCACAAA
1 CCGTGTGG-TAGGCTATGTGTGGCACATGACCGTGTGAAACTCT-ACAAA
5233825 CCGTGTGG
1 CCGTGTGG
5233833 GTAGATAGTG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
48 8 0.17
49 39 0.83
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (48 bp):
CCGTGTGGTAGGCTATGTGTGGCACATGACCGTGTGAAACTCTACAAA
Found at i:5237155 original size:49 final size:49
Alignment explanation
Indices: 5237026--5237161 Score: 148
Period size: 49 Copynumber: 2.8 Consensus size: 49
5237016 TATAATGATT
* ** * *
5237026 TAAAA-CCATCATTGTCTGGCCAATCAAGATGATAGAATATGCAAAGAG
1 TAAAAGCCATCATTGTCGGGCCACCCGAGATGGTAGAATATGCAAAGAG
* ** *
5237074 TAAAAGCCGTCATTGTCGGGCCACTTGAGATGGTAGAATATGCAAATAG
1 TAAAAGCCATCATTGTCGGGCCACCCGAGATGGTAGAATATGCAAAGAG
* * * *
5237123 TGAAAGTCATCATTGTTGGGCCACCCGGGATGGTAGAAT
1 TAAAAGCCATCATTGTCGGGCCACCCGAGATGGTAGAAT
5237162 GTACAAGTTC
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
48 5 0.07
49 68 0.93
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (49 bp):
TAAAAGCCATCATTGTCGGGCCACCCGAGATGGTAGAATATGCAAAGAG
Found at i:5238255 original size:19 final size:18
Alignment explanation
Indices: 5238208--5238261 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
5238198 ATACTAAAAA
5238208 TAAACTTTAATTAATTATAAT
1 TAAA-TTTAATTAA-T-TAAT
5238229 TAAA-TTAATTAATTAAT
1 TAAATTTAATTAATTAAT
*
5238246 TAATATTTAACTAATT
1 TAA-ATTTAATTAATT
5238262 TTAACCTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.23
18 2 0.07
19 17 0.57
21 4 0.13
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTTAATTAATTAAT
Found at i:5238260 original size:23 final size:23
Alignment explanation
Indices: 5238214--5238261 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5238204 AAAATAAACT
*
5238214 TTAATTAATTATAATTAAATTAA
1 TTAATTAATTATAATTAAACTAA
*
5238237 TTAATTAATTA-ATATTTAACTAA
1 TTAATTAATTATA-ATTAAACTAA
5238260 TT
1 TT
5238262 TTAACCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATTAATTATAATTAAACTAA
Found at i:5238586 original size:19 final size:20
Alignment explanation
Indices: 5238562--5238601 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
5238552 AGATTAAACT
5238562 TTAATTAATT-ATAATTAAC
1 TTAATTAATTAATAATTAAC
5238581 TTAATTAATTAATAATTAAC
1 TTAATTAATTAATAATTAAC
5238601 T
1 T
5238602 AATGTTAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATTAATTAATAATTAAC
Found at i:5239553 original size:49 final size:49
Alignment explanation
Indices: 5239429--5239569 Score: 149
Period size: 49 Copynumber: 2.9 Consensus size: 49
5239419 ATAATGATTC
* * ** * *
5239429 AAAA-CCATCATTGTTAGGCCACTCAAGATGATAGAATATGCAAATAGT
1 AAAAGCCATCATCGTTGGGCCACTCGGGATGGTAGAATATACAAATAGT
* *
5239477 CAAAGCCATCATCGTTGTGCCACTCGGGATGGTAGAATATACAAATAGT
1 AAAAGCCATCATCGTTGGGCCACTCGGGATGGTAGAATATACAAATAGT
* * * * * *
5239526 AAAAGTCATCATTGTTGGGTCATTCGGGATGGTTGAATGTACAA
1 AAAAGCCATCATCGTTGGGCCACTCGGGATGGTAGAATATACAA
5239570 GTTCTACATG
Statistics
Matches: 76, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
48 3 0.04
49 73 0.96
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (49 bp):
AAAAGCCATCATCGTTGGGCCACTCGGGATGGTAGAATATACAAATAGT
Found at i:5240728 original size:4 final size:4
Alignment explanation
Indices: 5240712--5240758 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
5240702 ATTTCATTTA
* *
5240712 TATG TATG CATG TATG TATG TATG TATG TATG TATA TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
5240759 ATTTGATTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:5241479 original size:20 final size:20
Alignment explanation
Indices: 5241454--5241498 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5241444 TTCAGCTCTT
5241454 ATGCAGCAGGCAAGGTGGCC
1 ATGCAGCAGGCAAGGTGGCC
* *
5241474 ATGCAGGAGTCAAGGTGGCC
1 ATGCAGCAGGCAAGGTGGCC
5241494 ATGCA
1 ATGCA
5241499 AGGAACGTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.38, T:0.13
Consensus pattern (20 bp):
ATGCAGCAGGCAAGGTGGCC
Found at i:5245561 original size:20 final size:20
Alignment explanation
Indices: 5245536--5245580 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
5245526 GTCAGCTCCT
5245536 ATGCAGCAGTCAAGGTGGCC
1 ATGCAGCAGTCAAGGTGGCC
*
5245556 ATGCAGGAGTCAAGGTGGCC
1 ATGCAGCAGTCAAGGTGGCC
5245576 ATGCA
1 ATGCA
5245581 AGGAACGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.36, T:0.16
Consensus pattern (20 bp):
ATGCAGCAGTCAAGGTGGCC
Found at i:5257484 original size:33 final size:33
Alignment explanation
Indices: 5257447--5257542 Score: 174
Period size: 33 Copynumber: 2.9 Consensus size: 33
5257437 TTTATTTTAT
5257447 TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
1 TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
*
5257480 TTTAGTTTGTTTACTTATATGTTGTAGTTTTTG
1 TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
*
5257513 TTTAGTTTGTTTACTTATGTGTTTTAGTTT
1 TTTAGTTTGTTTACTTATATGTTTTAGTTT
5257543 AGTACTATGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.15, C:0.03, G:0.17, T:0.66
Consensus pattern (33 bp):
TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
Found at i:5273567 original size:19 final size:21
Alignment explanation
Indices: 5273532--5273572 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
5273522 GTGTGCATAG
5273532 CTTTTTGCATTTAATTG-CAT
1 CTTTTTGCATTTAATTGTCAT
5273552 CTTTTTG-ATATT-ATTGTCAT
1 CTTTTTGCAT-TTAATTGTCAT
5273572 C
1 C
5273573 CCATTCACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (21 bp):
CTTTTTGCATTTAATTGTCAT
Found at i:5279143 original size:71 final size:71
Alignment explanation
Indices: 5279005--5279153 Score: 203
Period size: 71 Copynumber: 2.1 Consensus size: 71
5278995 AGAATATTGG
* * * **
5279005 TAGAAGTGCAGGGAATGTTGAACTTTGGCTACTGACTTGACTTGTTTCGTTAGAAGTCCTCAAGG
1 TAGAAGTGCAGGGAATGCTAAACTTTGGCTACTGACTTGACTTGTTTCGGTAGAAGGACTCAAGG
5279070 TATCAA
66 TATCAA
*
5279076 TAGAAGTGCA-GGAGATGCTAAACTTTGGCTACTGACTTGACTTGTTTCGGTAGAAGGGAC-CAG
1 TAGAAGTGCAGGGA-ATGCTAAACTTTGGCTACTGACTTGACTTGTTTCGGTAGAA-GGACTCAA
*
5279139 GGTATCGA
64 GGTATCAA
5279147 TAGAAGT
1 TAGAAGT
5279154 CTCAGGCCAA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
70 3 0.04
71 64 0.93
72 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (71 bp):
TAGAAGTGCAGGGAATGCTAAACTTTGGCTACTGACTTGACTTGTTTCGGTAGAAGGACTCAAGG
TATCAA
Found at i:5281175 original size:4 final size:4
Alignment explanation
Indices: 5281166--5281204 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
5281156 ATTTCATTTA
5281166 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
5281205 ATTTGATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:5284182 original size:23 final size:23
Alignment explanation
Indices: 5284155--5284228 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
5284145 TGTTATTGAT
**
5284155 CAGTGGTAGCTTCGGCTACATTT
1 CAGTGGTAGCTTCGGCTACATAA
*
5284178 TAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
*
5284201 CAGTGGTAGCTTCGGCTACATAT
1 CAGTGGTAGCTTCGGCTACATAA
5284224 CAGTG
1 CAGTG
5284229 TTGCACTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (23 bp):
CAGTGGTAGCTTCGGCTACATAA
Found at i:5307629 original size:122 final size:122
Alignment explanation
Indices: 5307465--5307772 Score: 485
Period size: 122 Copynumber: 2.5 Consensus size: 122
5307455 AATTATTCAC
* *
5307465 AATATTAACTCAAAAATCAAGGCT-TGACCACTCTTGGTTCCACTAACCCAATCCTTCTAGCCCA
1 AATATTAACTCAAAAATC-AGGGTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCC-
*
5307529 GTTTTTG-GGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
64 GGTTTTGAGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* **
5307587 AATATTAACTCAAAAATCAGGGTGTGACCACTCTTGGCTCCACTAACCCAATCCTTCTAATTCGG
1 AATATTAACTCAAAAATCAGGGTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCGG
* *
5307652 TTTTGAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
66 TTTTGAGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* * *
5307709 AATATTAACTCAAAAATCATGGTGTGACCGCTGTTGGTTCCACTAACCCAATCCTTCTAACCCG
1 AATATTAACTCAAAAATCAGGGTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCG
5307773 ATTTAGGGTT
Statistics
Matches: 170, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
121 10 0.06
122 160 0.94
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (122 bp):
AATATTAACTCAAAAATCAGGGTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCGG
TTTTGAGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
Found at i:5308070 original size:15 final size:15
Alignment explanation
Indices: 5308052--5308099 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
5308042 AAATTAAATT
5308052 AATTAACTAGATGCA
1 AATTAACTAGATGCA
*
5308067 AATTAACCTAAATGCA
1 AATTAA-CTAGATGCA
* *
5308083 AATAAAATGAGATGCA
1 AATTAACT-AGATGCA
5308099 A
1 A
5308100 GGTGATGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.23
Consensus pattern (15 bp):
AATTAACTAGATGCA
Found at i:5308837 original size:49 final size:49
Alignment explanation
Indices: 5308718--5308853 Score: 150
Period size: 49 Copynumber: 2.8 Consensus size: 49
5308708 TCAAACATGT
** * * *
5308718 TAAAA-CCATCATTGTCAGGCCACTCAGGATGATAGAATATGCAAATAT
1 TAAAAGCCATCATTGTTTGGCCACTCGGGATGGTAGAATATGCAAATAG
* *
5308766 TGAAAGCCATCATTGTTTGGCCATTCGGGATGGTAGAATATGCAAATAG
1 TAAAAGCCATCATTGTTTGGCCACTCGGGATGGTAGAATATGCAAATAG
* * * *
5308815 TAAAAGTCATC-TTTTTTGGGCCACCCGAGATGGTAGAAT
1 TAAAAGCCATCATTGTTT-GGCCACTCGGGATGGTAGAAT
5308854 GTACAAGTTC
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
48 9 0.12
49 64 0.88
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (49 bp):
TAAAAGCCATCATTGTTTGGCCACTCGGGATGGTAGAATATGCAAATAG
Found at i:5311489 original size:24 final size:23
Alignment explanation
Indices: 5311444--5311491 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
5311434 GGCGATTTAT
*
5311444 TGCATTTTTACTAGCAACTTTTC
1 TGCATTTTTACTAGCAAATTTTC
*
5311467 TGCATTTTTACTGGCATAATTTTC
1 TGCATTTTTACTAGCA-AATTTTC
5311491 T
1 T
5311492 CCATATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (23 bp):
TGCATTTTTACTAGCAAATTTTC
Found at i:5312646 original size:71 final size:71
Alignment explanation
Indices: 5312530--5312670 Score: 214
Period size: 71 Copynumber: 2.0 Consensus size: 71
5312520 AGAGTATTGG
* *
5312530 TAGAAGTGCAGGGAATGTTAAACTTTGGCTACTGACTTGACTTGTTTC-GATAGAAGTCCTTAAG
1 TAGAAGTGCAGGGAATGCTAAACTTTGGCTACTGACTTGACTTGTTTCAG-TAGAAGTCCTCAAG
5312594 GTATCGA
65 GTATCGA
* *
5312601 TAGAAGTGCA-GGAGATGCTAAATTTTGGCTACTGACTTGACTTGTTTCAGTAGAAGTCCTCCAG
1 TAGAAGTGCAGGGA-ATGCTAAACTTTGGCTACTGACTTGACTTGTTTCAGTAGAAGTCCTCAAG
5312665 GTATCG
65 GTATCG
5312671 GTAACACTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
70 3 0.05
71 60 0.94
72 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.32
Consensus pattern (71 bp):
TAGAAGTGCAGGGAATGCTAAACTTTGGCTACTGACTTGACTTGTTTCAGTAGAAGTCCTCAAGG
TATCGA
Found at i:5312796 original size:20 final size:21
Alignment explanation
Indices: 5312763--5312801 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5312753 GTTCTATAGA
* *
5312763 TAGAAGTCCGAGTT-TACCGG
1 TAGAACTCCCAGTTCTACCGG
5312783 TAGAACTCCCAGTTCTACC
1 TAGAACTCCCAGTTCTACC
5312802 AGCAGAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (21 bp):
TAGAACTCCCAGTTCTACCGG
Found at i:5316016 original size:21 final size:21
Alignment explanation
Indices: 5315984--5316024 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5315974 AGGCTCGAGG
5315984 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
5316005 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
5316025 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:5318540 original size:73 final size:73
Alignment explanation
Indices: 5318421--5318675 Score: 501
Period size: 73 Copynumber: 3.5 Consensus size: 73
5318411 ACAACTTGAC
5318421 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
5318486 CACTAACA
66 CACTAACA
5318494 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
5318559 CACTAACA
66 CACTAACA
5318567 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
5318632 CACTAACA
66 CACTAACA
*
5318640 AACTTAGTTGGAATACAACTAAGTTACATCATTACA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACA
5318676 ACCAAATAAT
Statistics
Matches: 181, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 181 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:5318688 original size:3 final size:3
Alignment explanation
Indices: 5318680--5318711 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5318670 ATTACAACCA
5318680 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5318712 AACATGTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5320645 original size:73 final size:73
Alignment explanation
Indices: 5320558--5320743 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
5320548 ACAACTTGAC
5320558 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
5320623 CACTAACA
66 CACTAACA
*
5320631 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCATTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
5320696 CACTAACA
66 CACTAACA
*
5320704 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
5320744 AATAATAATA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:5320752 original size:3 final size:3
Alignment explanation
Indices: 5320744--5320778 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5320734 ATTACATCCA
5320744 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5320779 AACATGTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5326502 original size:13 final size:13
Alignment explanation
Indices: 5326486--5326511 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5326476 CTTTGCATAT
5326486 TGTCTTCAACAGG
1 TGTCTTCAACAGG
5326499 TGTCTTCAACAGG
1 TGTCTTCAACAGG
5326512 CTCGCACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TGTCTTCAACAGG
Found at i:5345126 original size:121 final size:120
Alignment explanation
Indices: 5344859--5345224 Score: 570
Period size: 122 Copynumber: 3.0 Consensus size: 120
5344849 AAATATTCAC
* * *
5344859 AATATTAACTCAAAAATCAAGGCTTAACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
*
5344924 TTTTTGCGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTTAATTAATCAACCT
66 TTTTTG-GATGTGACAATAAGG-TTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* *
5344981 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCTCTAACCCAATCCTTCTAAACTAG
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
*
5345046 TTTTTAGGATGTGACAATAAGGTTTTAATTAGAAAGAAAGTTCAATTAATTAACCT
66 TTTTT-GGATGTGACAATAAGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* * *
5345102 AATATTAACTCAAAAATCAGGGCGTGACCGCTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
* * *
5345167 TTTTTCGGATGTGATAATAGGAGTTTTAATTAGAAAGAAAGTTGAATTAATCAACCT
66 TTTTT-GGATGTGACAATAAG-GTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
5345224 A
1 A
5345225 GAGTCTGTTG
Statistics
Matches: 225, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
121 110 0.49
122 114 0.51
123 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (120 bp):
AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
TTTTTGGATGTGACAATAAGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
Found at i:5347894 original size:18 final size:18
Alignment explanation
Indices: 5347871--5347905 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5347861 TGTCTTAGTG
5347871 GACCTGTTGCTTCAAACT
1 GACCTGTTGCTTCAAACT
5347889 GACCTGTTGCTTCAAAC
1 GACCTGTTGCTTCAAAC
5347906 CAAGGAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (18 bp):
GACCTGTTGCTTCAAACT
Found at i:5350772 original size:21 final size:21
Alignment explanation
Indices: 5350740--5350780 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5350730 GAACATTTGG
5350740 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
5350761 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
5350781 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:5357619 original size:19 final size:19
Alignment explanation
Indices: 5357595--5357632 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
5357585 AACGTAAGGG
5357595 TAAAATAGTAAA-TAAATAA
1 TAAAAT-GTAAATTAAATAA
5357614 TAAAATGTAAATTAAATAA
1 TAAAATGTAAATTAAATAA
5357633 AACTTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
TAAAATGTAAATTAAATAA
Found at i:5365211 original size:122 final size:120
Alignment explanation
Indices: 5364994--5365361 Score: 565
Period size: 122 Copynumber: 3.0 Consensus size: 120
5364984 AAAATATTCA
* * *
5364994 TAATATTAACACAAAAATCAAGGCTTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
1 TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
* **
5365059 GTTTTTGCGATGTGACAATAAGAATTTTAATTAGAAAGAAAGTTCAATTAATCAACC
66 ATTTTTG-GATGTGACAAT-AGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
*
5365116 TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCTAATCCTTCTAACCCA
1 TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
5365181 ATTTTTAGGATGTGACAATATGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
66 ATTTTT-GGATGTGACAATA-GGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
* **
5365238 TAATATTAACTCAAAATTCAGGGCGTGACTGCTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
1 TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
* * *
5365303 ATTTTTTGGATGTGATAATAGGAGTTTTAATTAGAAATAAAGTTGAATTAATCAACC
66 A-TTTTTGGATGTGACAATAGG-GTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
5365360 TA
1 TA
5365362 GAGTCAGTTG
Statistics
Matches: 228, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
121 3 0.01
122 219 0.96
123 6 0.03
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.32
Consensus pattern (120 bp):
TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
ATTTTTGGATGTGACAATAGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
Found at i:5365664 original size:34 final size:34
Alignment explanation
Indices: 5365626--5365690 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
5365616 ATAGATTTTA
* *
5365626 AAATTGAATTAATTAACTAGATGCAAATTAACCG
1 AAATTAAATTAATTAACTAGATGAAAATTAACCG
5365660 AAATTAAATTAATTAACTAGATGAAAATTAA
1 AAATTAAATTAATTAACTAGATGAAAATTAA
5365691 TCAGCTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (34 bp):
AAATTAAATTAATTAACTAGATGAAAATTAACCG
Found at i:5368655 original size:122 final size:122
Alignment explanation
Indices: 5368438--5368801 Score: 568
Period size: 122 Copynumber: 3.0 Consensus size: 122
5368428 AAATATTCAC
* * *
5368438 AATATTAACTCAAAAATCAAGGCTTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAG
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
* * *
5368503 TTTTTGGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
66 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
5368560 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
5368625 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
66 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* * * ***
5368682 AATATTAACTCAAAAATTAGGGCGTGACCGCTCTTGGATCCACTAACCCAATCCTTCTAACTTGA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
* * * *
5368747 TTTTTCA-GATGTGATAATAGGAGTTTTAATTAGAAATAAAGTTGAATTAATCAAC
66 TTTTT-AGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAAC
5368802 TTAGAGTCAG
Statistics
Matches: 225, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
122 224 1.00
123 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (122 bp):
AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
Found at i:5371415 original size:71 final size:71
Alignment explanation
Indices: 5371317--5371457 Score: 230
Period size: 71 Copynumber: 2.0 Consensus size: 71
5371307 AGAGTATTGG
*
5371317 TAGAAGTGAAAGGAATGTTGAACTTTTGCTACTGACTTGACTTGTTTCAATAGAAGTCCTCAAGG
1 TAGAAGTGAAAGGAATGCTGAACTTTTGCTACTGACTTGACTTGTTTCAATAGAAGTCCTCAAGG
5371382 TATCGA
66 TATCGA
* **
5371388 TAGAAGTGCAA-GAGATGCTGAACTTTTGCTACTGACTTGACTTGTTTCTGTAGAAGTCCTCAAG
1 TAGAAGTGAAAGGA-ATGCTGAACTTTTGCTACTGACTTGACTTGTTTCAATAGAAGTCCTCAAG
5371452 GTATCG
65 GTATCG
5371458 GTAACACTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
70 2 0.03
71 63 0.97
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (71 bp):
TAGAAGTGAAAGGAATGCTGAACTTTTGCTACTGACTTGACTTGTTTCAATAGAAGTCCTCAAGG
TATCGA
Found at i:5373613 original size:105 final size:107
Alignment explanation
Indices: 5373488--5373685 Score: 274
Period size: 108 Copynumber: 1.9 Consensus size: 107
5373478 TGAAATTCAA
* *
5373488 AAGGATATTTGACTATTTGGTTAAACGAG-AAATCGAAACACAACACATTAGGGAATG-TTCCTC
1 AAGGATATTCGACTATTTGGTTAAACGAGAAAATCGAAACACAACACATTAGGGAACGTTTCCTC
* *
5373551 GAATTTCCAAACGTAAAACATTGCCTTATTTGAAATTTTTGG
66 GAATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTGG
* * * * * *
5373593 AAGGATATTCGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCT
1 AAGGATATTCGACTATTTGGTTAAACGAG-AAAATCGAAACACAACACATTAGGGAACGTTTCCT
*
5373658 CGAATTTCCAAACGCAAAATATTACCTT
65 CGAATTTCCAAACGCAAAACATTACCTT
5373686 TATTATTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
105 26 0.33
107 24 0.30
108 29 0.37
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (107 bp):
AAGGATATTCGACTATTTGGTTAAACGAGAAAATCGAAACACAACACATTAGGGAACGTTTCCTC
GAATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTGG
Found at i:5375231 original size:13 final size:13
Alignment explanation
Indices: 5375213--5375237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5375203 AAGAAAGGGT
5375213 ATAAAACAAAATG
1 ATAAAACAAAATG
5375226 ATAAAACAAAAT
1 ATAAAACAAAAT
5375238 AAAATGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.04, T:0.16
Consensus pattern (13 bp):
ATAAAACAAAATG
Found at i:5376245 original size:44 final size:44
Alignment explanation
Indices: 5376197--5376285 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
5376187 CCACTGTAAC
* * *
5376197 CTTAGGGAGGTAAAATTCG-ACATCTTCGATCTACTCCACTACTG
1 CTTAGGGAGATAAAATCCGTA-ATCTTCAATCTACTCCACTACTG
* *
5376241 CTTAGGGAGATAAGATCCGTAATCTTCAATCTATTCCACTACTG
1 CTTAGGGAGATAAAATCCGTAATCTTCAATCTACTCCACTACTG
5376285 C
1 C
5376286 CCAAGGAGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
CTTAGGGAGATAAAATCCGTAATCTTCAATCTACTCCACTACTG
Found at i:5376797 original size:129 final size:129
Alignment explanation
Indices: 5376537--5376869 Score: 355
Period size: 129 Copynumber: 2.6 Consensus size: 129
5376527 CTTCGGTCCA
* * * * *
5376537 CTCCACTGTACCCTCAGGGAGATAAGGCTTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCACTGTAACCTCAGGGAGATAAGACTGGATACAATCTGCTCTACTGTAACTTCAGAGAGATA
* ** ** **
5376602 AGATCTGTGGTCTTAGTCCACTCCAGTGCAACCTCAAGGAAGTAGGATTGGTTTCTTCTGTCTG
66 AGATCTGTGGTCTTAGTCCACTCCACTGCAACCTCAAGGAAGTAGGATTACTAGCTTCAATCTG
* * *
5376666 CTCCACTGCAACCTCAAGGAGATAAGACTGGATACAATCTGCTCTACTGCAACTTCAGAGAGATA
1 CTCCACTGTAACCTCAGGGAGATAAGACTGGATACAATCTGCTCTACTGTAACTTCAGAGAGATA
* * * * *
5376731 AGATCTGTGGT-TTTGATCCGCTCCACTGCAACTTC-AGGGAGATAGGATTACTAGCTTCAATTT
66 AGATCTGTGGTCTTAG-TCCACTCCACTGCAACCTCAAGGAAG-TAGGATTACTAGCTTCAATCT
5376794 G
129 G
* * * * * * * *
5376795 CTCCGCTGTAATCTCAGGGAAATAAGATCCCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
1 CTCCACTGTAACCTCAGGGAGATAAGA---CTGGATACAATCTGCTCTACTGTAACTTCAGAGAG
5376860 ATAAGATCTG
63 ATAAGATCTG
5376870 AAATTCTTCA
Statistics
Matches: 168, Mismatches: 31, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
128 8 0.05
129 121 0.72
132 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (129 bp):
CTCCACTGTAACCTCAGGGAGATAAGACTGGATACAATCTGCTCTACTGTAACTTCAGAGAGATA
AGATCTGTGGTCTTAGTCCACTCCACTGCAACCTCAAGGAAGTAGGATTACTAGCTTCAATCTG
Found at i:5376798 original size:44 final size:44
Alignment explanation
Indices: 5376662--5377791 Score: 469
Period size: 44 Copynumber: 25.8 Consensus size: 44
5376652 GTTTCTTCTG
* * * * * *
5376662 TCTGCTCCACTGCAACCTCAAGGAGATAAG---ACTGGATACAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* * * ** * * **
5376703 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* * * *
5376747 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTAGCTTCAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* * * * *
5376791 TTTGCTCCGCTGTAA-TCTCAGGGAAATAAGATCCCTGGCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * *
5376835 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATC--ACTA-GCTTCAA
* * * * * *
5376881 TCTACTCCATTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* ** * * * *
5376922 TCTACTCTGCTGTAACTTCAGAGAGATAAGATC-CTTGATTTTAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCAA
** * * * *
5376966 TCCACTCCACTATAA-TCTCAGGGAGATAGGATTACTATCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * * *
5377010 TCTGCTCCGCTGTAA-TCTCACGGAGATAAGATCTCTGGCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * * **
5377054 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCGG
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATC--ACTA-GCTTCAA
* * * * * * **
5377100 TCTACTCCACTGTAACCTCAGGGAGATAAGGTTTGA-AATTCTTCGG
1 TCTGCTCCACTGTAACTTCAGGGAGATAA-G-ATCACTA-GCTTCAA
* * * * *
5377146 TCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* ** * * * *
5377187 TCTACTCTGCTGTAACTTCAGAGAGATAAGATC-CTTGATTTTAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCAA
* * * *
5377231 TCCGCTCCACTGTAA-TATCAGGGAGATAGGATTACTATCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* *
5377275 TCTGCTCCGA-TGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAA
1 TCTGCTCC-ACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * * **
5377319 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCGG
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATC--ACTA-GCTTCAA
* * * * * * *
5377365 TCTACTCCACTGTAACATCAGGGAGATAAGGTTTGA-AATTCTTCAG
1 TCTGCTCCACTGTAACTTCAGGGAGATAA-G-ATCACTA-GCTTCAA
* * * * *
5377411 TCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* ** * ** * *
5377452 TCTACTCTGCTGTAACTTCAGAGAGATAAGATCTGT-GATTTTAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCAA
* * *
5377496 T-TCGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTATCTTCAA
1 TCT-GCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * *
5377540 TCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * * * **
5377584 TCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGA-AATTCTTCGG
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATC--ACTA-GCTTCAA
* * * * * *
5377630 TCTACTCCACTGTAACCTCAGGGAGATAA-AAC-CT-GATGCGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* ** * * * *
5377671 TCTACTCTGCTGTAACTTCAGAGAGATAAGATC-CTTGATTTTAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCAA
* * * * * *
5377715 TCCGCTCCACTGTAA-TCTCAAGGAGATAGGATTATTATCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
*
5377759 TCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATC
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATC
5377792 TCTAATATTC
Statistics
Matches: 826, Mismatches: 211, Indels: 101
0.73 0.19 0.09
Matches are distributed among these distances:
41 142 0.17
42 11 0.01
43 12 0.01
44 438 0.53
45 12 0.01
46 207 0.25
47 2 0.00
48 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
Found at i:5376941 original size:219 final size:219
Alignment explanation
Indices: 5376666--5377129 Score: 700
Period size: 219 Copynumber: 2.1 Consensus size: 219
5376656 CTTCTGTCTG
* * *
5376666 CTCCACTGCAACCTCAAGGAGATAAGACTGGATACAATCTGCTCTACTGCAACTTCAGAGAGATA
1 CTCCACTGTAACCTCAGGGAGATAAGACTGGATACAATCTACTCTACTGCAACTTCAGAGAGATA
* * * * *
5376731 AGAT-CTGTGGTTTTGATCCGCTCCACTGCAA-CTTCAGGGAGATAGGATTACTAGCTTCAATTT
66 AGATCCT-TGATTTTAATCCACTCCACTACAATC-TCAGGGAGATAGGATTACTAGCTTCAATCT
*
5376794 GCTCCGCTGTAATCTCAGGGAAATAAGATCCCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGA
129 GCTCCGCTGTAATCTCACGGAAATAAGATCCCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGA
5376859 GATAAGATCTGAAATTCTTCAATCTA
194 GATAAGATCTGAAATTCTTCAATCTA
* * * * *
5376885 CTCCATTGTAACCTCAGGGAGATAAGACCT-GATGCGATCTACTCTGCTGTAACTTCAGAGAGAT
1 CTCCACTGTAACCTCAGGGAGATAAGA-CTGGATACAATCTACTCTACTGCAACTTCAGAGAGAT
* *
5376949 AAGATCCTTGATTTTAATCCACTCCACTATAATCTCAGGGAGATAGGATTACTATCTTCAATCTG
65 AAGATCCTTGATTTTAATCCACTCCACTACAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
* *
5377014 CTCCGCTGTAATCTCACGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
130 CTCCGCTGTAATCTCACGGAAATAAGATCCCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
**
5377079 ATAAGATCTGAAATTCTTCGGTCTA
195 ATAAGATCTGAAATTCTTCAATCTA
5377104 CTCCACTGTAACCTCAGGGAGATAAG
1 CTCCACTGTAACCTCAGGGAGATAAG
5377130 GTTTGAAATT
Statistics
Matches: 221, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
219 216 0.98
220 5 0.02
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (219 bp):
CTCCACTGTAACCTCAGGGAGATAAGACTGGATACAATCTACTCTACTGCAACTTCAGAGAGATA
AGATCCTTGATTTTAATCCACTCCACTACAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
TCCGCTGTAATCTCACGGAAATAAGATCCCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGA
TAAGATCTGAAATTCTTCAATCTA
Found at i:5377152 original size:265 final size:265
Alignment explanation
Indices: 5376839--5377658 Score: 1507
Period size: 265 Copynumber: 3.1 Consensus size: 265
5376829 CTTCAATCTG
* * * *
5376839 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCAATCTACTCCATTGTAACCTCAGGG
1 CTCCACTGTAACCTCAGGGAGATAAGGTTTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGG
5376904 AGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTGATTTTAATCC
66 AGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTGATTTTAATCC
* * *
5376969 ACTCCACTATAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCACGGA
131 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGA
5377034 GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
196 GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
5377099 GTCTA
261 GTCTA
*
5377104 CTCCACTGTAACCTCAGGGAGATAAGGTTTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGG
1 CTCCACTGTAACCTCAGGGAGATAAGGTTTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGG
5377169 AGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTGATTTTAATCC
66 AGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTGATTTTAATCC
* *
5377234 GCTCCACTGTAATATCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGATGTAATCTCAGGGA
131 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGA
5377299 GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
196 GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
5377364 GTCTA
261 GTCTA
*
5377369 CTCCACTGTAACATCAGGGAGATAAGGTTTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGG
1 CTCCACTGTAACCTCAGGGAGATAAGGTTTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGG
*
5377434 AGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGAT-CTGTGATTTTAATT
66 AGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCT-TGATTTTAATC
5377498 CGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGG
130 CGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGG
*
5377563 AGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGAAATTCTTC
195 AGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTC
5377628 GGTCTA
260 GGTCTA
5377634 CTCCACTGTAACCTCAGGGAGATAA
1 CTCCACTGTAACCTCAGGGAGATAA
5377659 AACCTGATGC
Statistics
Matches: 537, Mismatches: 17, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
264 2 0.00
265 535 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (265 bp):
CTCCACTGTAACCTCAGGGAGATAAGGTTTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGG
AGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTGATTTTAATCC
GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGA
GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
GTCTA
Found at i:5377594 original size:484 final size:481
Alignment explanation
Indices: 5376654--5377794 Score: 1512
Period size: 484 Copynumber: 2.4 Consensus size: 481
5376644 TAGGATTGGT
* * * * * * * * *
5376654 TTCTTCTGTCTGCTCCACTGCAACCTCAAGGAGATAAGA-CTGGATACAATCTGCTCTACTGCAA
1 TTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCT-GATGCGATCTACTCTGCTGTAA
* * *
5376718 CTTCAGAGAGATAAGAT-CTGTGGTTTTGATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAC
65 CTTCAGAGAGATAAGATCCT-TGATTTTAATCCGCTCCACTGTAA-TTCAGGGAGATAGGATTAC
* * * *
5376782 TAGCTTCAATTTGCTCCGCTGTAATCTCAGGGAAATAAGATCCCTGGCTTCAATCTGCTCCACTG
128 TATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTG
* *
5376847 TAACCTCAGGGAGATAAGATCTGAAATTCTTCAATCTACTCCATTGTAACCTCAGGGAGATAAGA
193 TAACCTCAGGGAGATAAGATCTGAAATTCTTCAATCTACTCCACTGTAACATCAGGGAGATAAGA
* ** * **
5376912 CCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTGATTTTAATCCACTCCACT
258 CCTGATGCCATCTACTCCACTGTAACCTCAGAGAGATAAGATCCTTGATTGCAATCCACTCCACT
* * *
5376977 ATAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCACGGAGATAAGAT
323 ATAATCTCAGAGAGATAAGATTACTATCTTCAATCTGCTCCACTGTAATCTCACGGAGATAAGAT
* * **
5377042 CTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTC
388 CTCTAGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT--AATGCTTCAATCTACTC
* * *
5377107 CACTGTAACCTCAGGGAGATAAGGTTTGAAA
451 CACTGTAACCTCAGAGAGATAAGATCTGAAA
5377138 TTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAAC
1 TTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAAC
5377203 TTCAGAGAGATAAGATCCTTGATTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTA
66 TTCAGAGAGATAAGATCCTTGATTTTAATCCGCTCCACTGTAAT-TCAGGGAGATAGGATTACTA
*
5377268 TCTTCAATCTGCTCCGATGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTA
130 TCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTA
** ***
5377333 ACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACATCAGGGAGATAAGGTT
195 ACCTCAGGGAGATAAGATCTGAAATTCTTCAATCTACTCCACTGTAACATCAGGGAGATAAGACC
* * * * *
5377398 TGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGA-CC-TGA-TGCGATCTACTCT
260 TG--ATGC--CA-TCTACTCCACTGTAACCTCAGAGAGATAAGATCCTTGATTGCAATCCACTCC
* * * * *
5377460 GCTGTAA-CTTCAGAGAGATAAGATCT-GTGAT-TTTAAT-TCGCTCCACTGTAATCTCAGGGAG
320 ACTATAATC-TCAGAGAGATAAGAT-TACT-ATCTTCAATCT-GCTCCACTGTAATCTCACGGAG
* * * * *
5377521 ATAGGAT-TACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAA
381 ATAAGATCT-CTAGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAT-GCTTCAA
*
5377584 TCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGAAA
444 TCTACTCCACTGTAACCTCAGAGAGATAAGATCTGAAA
*
5377622 TTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAAC
1 TTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAAC
* *
5377687 TTCAGAGAGATAAGATCCTTGATTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTATTA
66 TTCAGAGAGATAAGATCCTTGATTTTAATCCGCTCCACTGTAAT-TCAGGGAGATAGGATTACTA
5377752 TCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT
130 TCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT
5377795 AATATTCACT
Statistics
Matches: 582, Mismatches: 61, Indels: 28
0.87 0.09 0.04
Matches are distributed among these distances:
483 2 0.00
484 436 0.75
485 7 0.01
486 101 0.17
487 6 0.01
488 3 0.01
489 27 0.05
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (481 bp):
TTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAAC
TTCAGAGAGATAAGATCCTTGATTTTAATCCGCTCCACTGTAATTCAGGGAGATAGGATTACTAT
CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAA
CCTCAGGGAGATAAGATCTGAAATTCTTCAATCTACTCCACTGTAACATCAGGGAGATAAGACCT
GATGCCATCTACTCCACTGTAACCTCAGAGAGATAAGATCCTTGATTGCAATCCACTCCACTATA
ATCTCAGAGAGATAAGATTACTATCTTCAATCTGCTCCACTGTAATCTCACGGAGATAAGATCTC
TAGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAATGCTTCAATCTACTCCACTG
TAACCTCAGAGAGATAAGATCTGAAA
Found at i:5377595 original size:219 final size:218
Alignment explanation
Indices: 5377285--5377794 Score: 781
Period size: 219 Copynumber: 2.3 Consensus size: 218
5377275 TCTGCTCCGA
* ** * *
5377285 TGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAG
1 TGTAATCTCAGGGAGATAGGAT-TACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAG
* * ** * * *
5377349 ATCTGAAATTCTTCGGTCTACTCCACTGTAACATCAGGGAGATAAGGTTTGAAATTCTTCAGTCT
65 ATCT---CTGCTTCAATCTACTCCACTGTAACATCAGAGAGATAAGATCTGAAATTCTTCAGTCT
*
5377414 ACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGAT
127 ACTCCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGAT
*
5377479 AAGAT-CTGTGATTTTAATTCGCTCCAC
192 AAGATCCT-TGATTTTAATCCGCTCCAC
5377506 TGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
1 TGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
* * *
5377571 TCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGAAATTCTTCGGTCTACT
66 TCTCT-GCTTCAATCTACTCCACTGTAACATCAGAGAGATAAGATCTGAAATTCTTCAGTCTACT
5377636 CCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAG
130 CCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAG
5377701 ATCCTTGATTTTAATCCGCTCCAC
195 ATCCTTGATTTTAATCCGCTCCAC
* *
5377725 TGTAATCTCAAGGAGATAGGATTATTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
1 TGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
5377790 TCTCT
66 TCTCT
5377795 AATATTCACT
Statistics
Matches: 267, Mismatches: 19, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
218 1 0.00
219 202 0.76
220 3 0.01
221 61 0.23
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (218 bp):
TGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
TCTCTGCTTCAATCTACTCCACTGTAACATCAGAGAGATAAGATCTGAAATTCTTCAGTCTACTC
CACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGA
TCCTTGATTTTAATCCGCTCCAC
Found at i:5379050 original size:20 final size:20
Alignment explanation
Indices: 5379025--5379081 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
5379015 GCCTCTCCAT
5379025 TTTTCATTTTTCATTTTTCA
1 TTTTCATTTTTCATTTTTCA
5379045 TTTTCATTTTTCATTTTTCA
1 TTTTCATTTTTCATTTTTCA
*
5379065 TTCTCATTTTTC-TTTTT
1 TTTTCATTTTTCATTTTT
5379082 TTTGACTCAG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 5 0.14
20 31 0.86
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTCATTTTTCATTTTTCA
Found at i:5379071 original size:13 final size:14
Alignment explanation
Indices: 5379022--5379081 Score: 90
Period size: 13 Copynumber: 4.5 Consensus size: 14
5379012 TTAGCCTCTC
5379022 CATTTTTCATTTTT
1 CATTTTTCATTTTT
5379036 CATTTTTCA-TTTT
1 CATTTTTCATTTTT
5379049 CATTTTTCATTTTT
1 CATTTTTCATTTTT
*
5379063 CA-TTCTCATTTTT
1 CATTTTTCATTTTT
5379076 C-TTTTT
1 CATTTTT
5379082 TTTGACTCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
13 27 0.64
14 15 0.36
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:5379076 original size:27 final size:27
Alignment explanation
Indices: 5379022--5379074 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
5379012 TTAGCCTCTC
*
5379022 CATTTTTCATTTTTCATTTTTCATTTT
1 CATTTTTCATTTTTCATTTCTCATTTT
5379049 CATTTTTCATTTTTCA-TTCTCATTTT
1 CATTTTTCATTTTTCATTTCTCATTTT
5379075 TCTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (27 bp):
CATTTTTCATTTTTCATTTCTCATTTT
Found at i:5379082 original size:7 final size:7
Alignment explanation
Indices: 5379022--5379081 Score: 90
Period size: 7 Copynumber: 9.0 Consensus size: 7
5379012 TTAGCCTCTC
5379022 CATTTTT
1 CATTTTT
5379029 CATTTTT
1 CATTTTT
5379036 CATTTTT
1 CATTTTT
5379043 CA-TTTT
1 CATTTTT
5379049 CATTTTT
1 CATTTTT
5379056 CATTTTT
1 CATTTTT
*
5379063 CA-TTCT
1 CATTTTT
5379069 CATTTTT
1 CATTTTT
5379076 C-TTTTT
1 CATTTTT
5379082 TTTGACTCAG
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
6 16 0.33
7 33 0.67
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:5380084 original size:50 final size:50
Alignment explanation
Indices: 5379990--5380087 Score: 119
Period size: 50 Copynumber: 2.0 Consensus size: 50
5379980 AGATTTCTCT
5379990 TTTTTTATTCTTCTTTCTTTTTCTCGTTTTCATTTTGATCTTGATTTTGA
1 TTTTTTATTCTTCTTTCTTTTTCTCGTTTTCATTTTGATCTTGATTTTGA
* * * * *
5380040 TTTTTTCTTCTT-TCTTCTTTTTGT-TTTTTTATTTTGATTTTTGATTTT
1 TTTTTTATTCTTCT-TTCTTTTTCTCGTTTTCATTTTGA-TCTTGATTTT
5380088 TTTCATTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
49 12 0.29
50 29 0.71
ACGTcount: A:0.08, C:0.11, G:0.07, T:0.73
Consensus pattern (50 bp):
TTTTTTATTCTTCTTTCTTTTTCTCGTTTTCATTTTGATCTTGATTTTGA
Found at i:5383602 original size:105 final size:107
Alignment explanation
Indices: 5383477--5383674 Score: 283
Period size: 108 Copynumber: 1.9 Consensus size: 107
5383467 TGAAATTCAA
*
5383477 AAGGATATTTGACTATTTGGTTAAACGAG-AAATCGAAACACAACACATTAGGGAACG-TTCCTC
1 AAGGATATTCGACTATTTGGTTAAACGAGAAAATCGAAACACAACACATTAGGGAACGTTTCCTC
* *
5383540 GAATTTCCAAACGTAAAACATTGCCTTATTTGAAATTTTTGG
66 GAATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTGG
* * * * * *
5383582 AAGGATATTCGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCT
1 AAGGATATTCGACTATTTGGTTAAACGAG-AAAATCGAAACACAACACATTAGGGAACGTTTCCT
*
5383647 CGAATTTCCAAACGCAAAATATTACCTT
65 CGAATTTCCAAACGCAAAACATTACCTT
5383675 TATTATTTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
105 26 0.32
107 25 0.31
108 29 0.36
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (107 bp):
AAGGATATTCGACTATTTGGTTAAACGAGAAAATCGAAACACAACACATTAGGGAACGTTTCCTC
GAATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTGG
Found at i:5385204 original size:13 final size:13
Alignment explanation
Indices: 5385186--5385210 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5385176 AAGAAAGGTT
5385186 ATAAAACAAAATG
1 ATAAAACAAAATG
5385199 ATAAAACAAAAT
1 ATAAAACAAAAT
5385211 AAAATGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.04, T:0.16
Consensus pattern (13 bp):
ATAAAACAAAATG
Found at i:5387047 original size:25 final size:25
Alignment explanation
Indices: 5387018--5387065 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5387008 TTTGCTATTC
*
5387018 ATATACACGCATATTTTTATATACA
1 ATATACACGCATATTTTAATATACA
***
5387043 ATATATGTGCATATTTTAATATA
1 ATATACACGCATATTTTAATATA
5387066 TACTTTTAAG
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:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (25 bp):
ATATACACGCATATTTTAATATACA
Found at i:5387189 original size:33 final size:29
Alignment explanation
Indices: 5387152--5387222 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
5387142 TTTATACTAT
5387152 ATATATACTTACACACCTTTTTTATTTTTGTAA
1 ATATATACTTACACA---TTTTTA-TTTTGTAA
* *
5387185 ATATATACATATACATTTTTATTTTGTAA
1 ATATATACTTACACATTTTTATTTTGTAA
5387214 ATATATACT
1 ATATATACT
5387223 GGTACATGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.46
30 6 0.17
33 13 0.37
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.51
Consensus pattern (29 bp):
ATATATACTTACACATTTTTATTTTGTAA
Found at i:5387493 original size:22 final size:22
Alignment explanation
Indices: 5387463--5387505 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5387453 GCACCAAAAC
* *
5387463 AGGCTTTTACCGGCGTTTTTTT
1 AGGCCTTTACCGGCGCTTTTTT
*
5387485 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTACCGGCGCTTTTT
5387506 AGCGGCGCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.21, G:0.26, T:0.44
Consensus pattern (22 bp):
AGGCCTTTACCGGCGCTTTTTT
Found at i:5387508 original size:13 final size:13
Alignment explanation
Indices: 5387490--5387514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5387480 TTTTTAGGCC
5387490 TTTAGCGGCGCTT
1 TTTAGCGGCGCTT
5387503 TTTAGCGGCGCT
1 TTTAGCGGCGCT
5387515 AAAAGTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.24, G:0.32, T:0.36
Consensus pattern (13 bp):
TTTAGCGGCGCTT
Found at i:5387665 original size:43 final size:42
Alignment explanation
Indices: 5387616--5387827 Score: 291
Period size: 43 Copynumber: 4.9 Consensus size: 42
5387606 GCTAAAAGTA
*
5387616 ATGACCTTTAGCGGCGCTTTCTCCACAAACGCCGCTATAGACC
1 ATGACCTTTAGCGGCGCTTT-TCCACAAACGCCGCTAAAGACC
5387659 ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
1 ATGACCTTTAGCGGCGCTTTT-CCACAAACGCCGCTAAAGACC
* * *
5387702 ACGAGCTTTAGCTGCGCTTTTCCCACAAACGCCGCTAAAGACC
1 ATGACCTTTAGCGGCGCTTTT-CCACAAACGCCGCTAAAGACC
* *
5387745 ATGACCTTTAGCGGCGCTTTTTCGCACAAACGCTGCTAAATACC
1 ATGACCTTTAGCGGCGC-TTTTC-CACAAACGCCGCTAAAGACC
*
5387789 ATGACCTTTAGCGACGCTTTTCGCGA-AAACGCCGCTAAA
1 ATGACCTTTAGCGGCGCTTTTC-C-ACAAACGCCGCTAAA
5387828 AACATATCAT
Statistics
Matches: 154, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
42 1 0.01
43 114 0.74
44 39 0.25
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (42 bp):
ATGACCTTTAGCGGCGCTTTTCCACAAACGCCGCTAAAGACC
Found at i:5387749 original size:86 final size:87
Alignment explanation
Indices: 5387618--5387827 Score: 293
Period size: 87 Copynumber: 2.4 Consensus size: 87
5387608 TAAAAGTAAT
* *
5387618 GACCTTTAGCGGCGC-TTTCTCCACAAACGCCGCTATAGACCATGACCTTTAGCGGCGC-TTTTC
1 GACCTTTAGC-GCGCTTTTCGCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTC
5387681 CCACAAACGCCGCTAAAGACCAC
65 CCACAAACGCCGCTAAAGACCAC
*
5387704 GAGCTTTAGCTGCGCTTTTC-CCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTC
1 GACCTTTAGC-GCGCTTTTCGCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTC
* * * *
5387768 GCACAAACGCTGCTAAATACCAT
65 CCACAAACGCCGCTAAAGACCAC
*
5387791 GACCTTTAGCGACGCTTTTCGCGA-AAACGCCGCTAAA
1 GACCTTTAGCG-CGCTTTTCGCCACAAACGCCGCTAAA
5387828 AACATATCAT
Statistics
Matches: 111, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
86 51 0.46
87 58 0.52
88 2 0.02
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (87 bp):
GACCTTTAGCGCGCTTTTCGCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCC
CACAAACGCCGCTAAAGACCAC
Found at i:5390924 original size:19 final size:17
Alignment explanation
Indices: 5390870--5390927 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 17
5390860 TATTAATTTT
*
5390870 AAATAAATAAATTTTGAA
1 AAATTAATAAATTTT-AA
5390888 AAATTAAGTAATATTTTAA
1 AAATTAA-TAA-ATTTTAA
5390907 AGAATTAGATAAATTTTAA
1 A-AATTA-ATAAATTTTAA
5390926 AA
1 AA
5390928 TTTTTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 7 0.20
19 14 0.40
20 13 0.37
21 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (17 bp):
AAATTAATAAATTTTAA
Found at i:5391228 original size:10 final size:10
Alignment explanation
Indices: 5391181--5391240 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
5391171 AAAATAAAAG
5391181 TTTAAAATCTT
1 TTTAAAATC-T
* *
5391192 TTTTAAAT-A
1 TTTAAAATCT
**
5391201 TTTAAAAAAT
1 TTTAAAATCT
5391211 TTTAAAATCT
1 TTTAAAATCT
5391221 TTTAAAATTCAT
1 TTTAAAA-TC-T
5391233 TTTAAAAT
1 TTTAAAAT
5391241 TTTAAATCAC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
9 6 0.15
10 15 0.38
11 10 0.26
12 8 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (10 bp):
TTTAAAATCT
Found at i:5391237 original size:12 final size:12
Alignment explanation
Indices: 5391209--5391241 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5391199 TATTTAAAAA
5391209 ATTTTAAAA-TC
1 ATTTTAAAATTC
5391220 -TTTTAAAATTC
1 ATTTTAAAATTC
5391231 ATTTTAAAATT
1 ATTTTAAAATT
5391242 TTAAATCACG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 2 0.10
12 10 0.50
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTTAAAATTC
Found at i:5391240 original size:30 final size:30
Alignment explanation
Indices: 5391174--5391246 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
5391164 TATTATAAAA
* *
5391174 ATAAAAGTTTAAAATCTTTTTTAAATATTT
1 ATAAAATTTTAAAATCTTTTTAAAATATTT
*
5391204 AAAAAATTTTAAAATC-TTTTAAAATTCATTT
1 ATAAAATTTTAAAATCTTTTTAAAA-T-ATTT
5391235 -TAAAATTTTAAA
1 ATAAAATTTTAAA
5391247 TCACGAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 7 0.19
30 26 0.70
31 4 0.11
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (30 bp):
ATAAAATTTTAAAATCTTTTTAAAATATTT
Found at i:5391243 original size:20 final size:19
Alignment explanation
Indices: 5391175--5391246 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
5391165 ATTATAAAAA
* *
5391175 TAAAAGTTTAAAATCTTTT
1 TAAAATTTTAAAATCATTT
* *
5391194 TTAAATATTTAAAA-AATTT
1 TAAAAT-TTTAAAATCATTT
5391213 TAAAATCTTTTAAAATTCATTT
1 TAAAA--TTTTAAAA-TCATTT
5391235 TAAAATTTTAAA
1 TAAAATTTTAAA
5391247 TCACGAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
19 11 0.26
20 21 0.50
21 1 0.02
22 9 0.21
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (19 bp):
TAAAATTTTAAAATCATTT
Found at i:5392190 original size:29 final size:30
Alignment explanation
Indices: 5392157--5392225 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
5392147 CTCTAACCCG
5392157 ACCCTTAACCCCTAAATCC-T-AAACCCTAA
1 ACCCTTAACCCCTAAA-CCTTAAAACCCTAA
5392186 ACCCTTAA-CCCTAAACCTTAAAACCCTAA
1 ACCCTTAACCCCTAAACCTTAAAACCCTAA
*
5392215 ACCCATAACCC
1 ACCCTTAACCC
5392226 TCAGCCTCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 2 0.06
28 8 0.22
29 24 0.67
30 2 0.06
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (30 bp):
ACCCTTAACCCCTAAACCTTAAAACCCTAA
Found at i:5392212 original size:15 final size:14
Alignment explanation
Indices: 5392159--5392217 Score: 68
Period size: 14 Copynumber: 4.1 Consensus size: 14
5392149 CTAACCCGAC
*
5392159 CCTTAACCCCTAAA
1 CCTTAAACCCTAAA
5392173 TCC-TAAACCCTAAA
1 -CCTTAAACCCTAAA
5392187 CCCTT-AACCCTAAA
1 -CCTTAAACCCTAAA
5392201 CCTTAAAACCCTAAA
1 CCTT-AAACCCTAAA
5392216 CC
1 CC
5392218 CATAACCCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
13 4 0.10
14 21 0.54
15 14 0.36
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (14 bp):
CCTTAAACCCTAAA
Found at i:5392215 original size:8 final size:7
Alignment explanation
Indices: 5392166--5392218 Score: 70
Period size: 7 Copynumber: 7.4 Consensus size: 7
5392156 GACCCTTAAC
5392166 CCCTAAA
1 CCCTAAA
*
5392173 TCCTAAA
1 CCCTAAA
5392180 CCCTAAA
1 CCCTAAA
*
5392187 CCCTTAA
1 CCCTAAA
5392194 CCCTAAA
1 CCCTAAA
*
5392201 CCTTAAAA
1 CCCT-AAA
5392209 CCCTAAA
1 CCCTAAA
5392216 CCC
1 CCC
5392219 ATAACCCTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
7 33 0.85
8 6 0.15
ACGTcount: A:0.40, C:0.42, G:0.00, T:0.19
Consensus pattern (7 bp):
CCCTAAA
Found at i:5392226 original size:14 final size:14
Alignment explanation
Indices: 5392178--5392226 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
5392168 CTAAATCCTA
*
5392178 AACCCTAAACCCTT
1 AACCCTAAACCCAT
* *
5392192 AACCCTAAACCTTAA
1 AACCCTAAACC-CAT
5392207 AACCCTAAACCCAT
1 AACCCTAAACCCAT
5392221 AACCCT
1 AACCCT
5392227 CAGCCTCTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.18
Consensus pattern (14 bp):
AACCCTAAACCCAT
Found at i:5392241 original size:29 final size:29
Alignment explanation
Indices: 5392157--5392246 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
5392147 CTCTAACCCG
* *
5392157 ACCCTTAACCCCTAAATC-CTAAACCCTAA
1 ACCCATAA-CCCTAAACCTCTAAACCCTAA
*
5392186 ACCCTTAACCCTAAACCT-TAAAACCCTAA
1 ACCCATAACCCTAAACCTCT-AAACCCTAA
* * * *
5392215 ACCCATAACCCTCAGCCTCTAACCCCTGA
1 ACCCATAACCCTAAACCTCTAAACCCTAA
5392244 ACC
1 ACC
5392247 TTATTTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
28 9 0.17
29 42 0.81
30 1 0.02
ACGTcount: A:0.36, C:0.43, G:0.02, T:0.19
Consensus pattern (29 bp):
ACCCATAACCCTAAACCTCTAAACCCTAA
Found at i:5415286 original size:25 final size:25
Alignment explanation
Indices: 5415258--5415403 Score: 120
Period size: 25 Copynumber: 5.9 Consensus size: 25
5415248 CGTTATTTAT
* **
5415258 CTCTTATGAGCATCCTGTTATATGG
1 CTCTTATGAGCTTCCCATTATATGG
* * * *
5415283 CTCTCACGAGCTTCCCAATATTTGG
1 CTCTTATGAGCTTCCCATTATATGG
*
5415308 CTCTCATGAGCTTCCCAATTA-ATGG
1 CTCTTATGAGCTTCCC-ATTATATGG
*
5415333 CTCTCT-TGAGCTTCCCGTT-TATGG
1 CTCT-TATGAGCTTCCCATTATATGG
*
5415357 CTCTTATGAGCTTCCCGATAAT-TGG
1 CTCTTATGAGCTTCCC-ATTATATGG
* * *
5415382 CTCGTAAGATCTTCCCATTATA
1 CTCTTATGAGCTTCCCATTATA
5415404 CAGCTCGCAT
Statistics
Matches: 96, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.01
24 24 0.25
25 67 0.70
26 4 0.04
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (25 bp):
CTCTTATGAGCTTCCCATTATATGG
Found at i:5415409 original size:25 final size:25
Alignment explanation
Indices: 5415389--5415476 Score: 97
Period size: 25 Copynumber: 3.5 Consensus size: 25
5415379 TGGCTCGTAA
*
5415389 GATCTTCCCATTATACAGCTCGCAT
1 GATCTTCCCGTTATACAGCTCGCAT
* *
5415414 GAGT-TTCTCGTTATACAGCTCACAT
1 GA-TCTTCCCGTTATACAGCTCGCAT
* *
5415439 GAGCTTCCCGTTATACAGCTCACAT
1 GATCTTCCCGTTATACAGCTCGCAT
* *
5415464 AAGCTTCCCGTTA
1 GATCTTCCCGTTA
5415477 CATGACTCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
25 54 0.98
26 1 0.02
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.32
Consensus pattern (25 bp):
GATCTTCCCGTTATACAGCTCGCAT
Found at i:5415485 original size:25 final size:25
Alignment explanation
Indices: 5415427--5415510 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
5415417 TTTCTCGTTA
* *
5415427 TACA-GCTCACATGAGCTTCCCGTT
1 TACATGCTCACATAAGCTTCCCGAT
5415451 ATACA-GCTCACATAAGCTTCCCG-T
1 -TACATGCTCACATAAGCTTCCCGAT
*
5415475 TACATGACTCAGA-AGAGCTTCCCGAT
1 TACATG-CTCACATA-AGCTTCCCGAT
5415501 TACATGCTCA
1 TACATGCTCA
5415511 TATGGACATA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
23 4 0.08
24 3 0.06
25 39 0.74
26 7 0.13
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.26
Consensus pattern (25 bp):
TACATGCTCACATAAGCTTCCCGAT
Found at i:5415493 original size:50 final size:50
Alignment explanation
Indices: 5415387--5415498 Score: 120
Period size: 50 Copynumber: 2.2 Consensus size: 50
5415377 ATTGGCTCGT
* * * * * *
5415387 AAGATCTTCCCATTATACAGCTCGCATGAGTTTCTCGTTATACAGCTCAC
1 AAGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCGTTATACAGCTCAC
* *
5415437 ATGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCG-T-TACATGACTCAG
1 AAGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCGTTATACA-G-CTCAC
5415487 AAGAGCTTCCCG
1 AAGAGCTTCCCG
5415499 ATTACATGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
48 4 0.08
49 2 0.04
50 45 0.88
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (50 bp):
AAGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCGTTATACAGCTCAC
Found at i:5420351 original size:35 final size:35
Alignment explanation
Indices: 5420311--5420385 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
5420301 CTCTAACAAT
**
5420311 CATTTCCATGATGCTGCTACGTAGAGCCAGTACAC
1 CATTTCCATGATGCCACTACGTAGAGCCAGTACAC
* *
5420346 CATTTCCATGATGCCACTCCGTAGAGCCAGTAGAC
1 CATTTCCATGATGCCACTACGTAGAGCCAGTACAC
5420381 CATTT
1 CATTT
5420386 TCGACCAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (35 bp):
CATTTCCATGATGCCACTACGTAGAGCCAGTACAC
Found at i:5424039 original size:87 final size:86
Alignment explanation
Indices: 5423916--5424223 Score: 293
Period size: 87 Copynumber: 3.6 Consensus size: 86
5423906 TCTAAAAGTG
* ** * * * *
5423916 AATAAAATATGTTTTGGGATTTATTCTA-GCCATTCAATAGATTTTATTCCAATTTGATTTTATT
1 AATAAAATCTGTTTCAGGATTTATTC-ACGCCGTTCAAAAGATTTTATTCCATTTTAATTTTATT
5423980 TCCAAAACGAGAATTTAAATTAA
65 TCCAAAACGAGAATTTAAATT-A
* * * * *
5424003 AATAAAATCTATTTCAGGATTTATTCACGCCGTTCAACATATTTTATT-CTTTTTTATTTTATTT
1 AATAAAATCTGTTTCAGGATTTATTCACGCCGTTCAAAAGATTTTATTCCATTTTAATTTTATTT
*
5424067 CCAAAACGAGAAATTAAAATTA
66 CCAAAACGAG-AATTTAAATTA
* * * *
5424089 AATAAAATCTGTTTCAGGATTTATTCCCGCCGATT-AACAAGATTCTATTCGATTTTAATTTTGT
1 AATAAAATCTGTTTCAGGATTTATTCACGCCG-TTCAA-AAGATTTTATTCCATTTTAATTTTAT
* **
5424153 TT-CTAAATTAGAA-TTAAATTA
64 TTCCAAAACGAGAATTTAAATTA
* * * * * *
5424174 AATAAAATCTGTTACGGGATTTATTCTCGTCATTTAACAAGATTTTATTC
1 AATAAAATCTGTTTCAGGATTTATTCACGCCGTTCAA-AAGATTTTATTC
5424224 AATATCAATT
Statistics
Matches: 185, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
84 2 0.01
85 48 0.26
86 59 0.32
87 64 0.35
88 12 0.06
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.43
Consensus pattern (86 bp):
AATAAAATCTGTTTCAGGATTTATTCACGCCGTTCAAAAGATTTTATTCCATTTTAATTTTATTT
CCAAAACGAGAATTTAAATTA
Found at i:5424097 original size:86 final size:84
Alignment explanation
Indices: 5423916--5424224 Score: 300
Period size: 86 Copynumber: 3.6 Consensus size: 84
5423906 TCTAAAAGTG
* ** * * * *
5423916 AATAAAATATGTTTTGGGATTTATTCTA-GCCATTCAATAGATTTTATTCCAATTTGATTTTATT
1 AATAAAATCTGTTTCAGGATTTATTC-ACGCCGTTCAACAGATTTTATT-CATTTTAATTTTATT
5423980 TCCAAAACGAGAATTTAAATTAA
64 TCCAAAACGAGAA-TTAAATT-A
* * * *
5424003 AATAAAATCTATTTCAGGATTTATTCACGCCGTTCAACATATTTTATTCTTTTTTATTTTATTTC
1 AATAAAATCTGTTTCAGGATTTATTCACGCCGTTCAACAGATTTTATTCATTTTAATTTTATTTC
5424068 CAAAACGAGAAATTAAAATTA
66 CAAAACGAG-AATT-AAATTA
* * *
5424089 AATAAAATCTGTTTCAGGATTTATTCCCGCCGATT-AACAAGATTCTATTCGATTTTAATTTTGT
1 AATAAAATCTGTTTCAGGATTTATTCACGCCG-TTCAAC-AGATTTTATTC-ATTTTAATTTTAT
* **
5424153 TT-CTAAATTAGAATTAAATTA
63 TTCCAAAACGAGAATTAAATTA
* * * * * *
5424174 AATAAAATCTGTTACGGGATTTATTCTCGTCATTTAACAAGATTTTATTCA
1 AATAAAATCTGTTTCAGGATTTATTCACGCCGTTCAAC-AGATTTTATTCA
5424225 ATATCAATTT
Statistics
Matches: 189, Mismatches: 26, Indels: 17
0.81 0.11 0.07
Matches are distributed among these distances:
84 3 0.02
85 47 0.25
86 64 0.34
87 63 0.33
88 12 0.06
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (84 bp):
AATAAAATCTGTTTCAGGATTTATTCACGCCGTTCAACAGATTTTATTCATTTTAATTTTATTTC
CAAAACGAGAATTAAATTA
Found at i:5424234 original size:85 final size:85
Alignment explanation
Indices: 5424078--5424239 Score: 220
Period size: 85 Copynumber: 1.9 Consensus size: 85
5424068 CAAAACGAGA
* * *
5424078 AATTAAAATTAAATAAAATCTGTTTCAGGATTTATTCCCGCCGATTAACAAGATTCTATTCGATT
1 AATTAAAATTAAATAAAATCTGTTACAGGATTTATTCCCGCCGATTAACAAGATTCTATTCAATA
*
5424143 TTAATTTTGTTTCTAAATTAG
66 TCAA-TTTGTTTCTAAATTAG
* * * *
5424164 AATT-AAATTAAATAAAATCTGTTACGGGATTTATTCTCGTC-ATTTAACAAGATTTTATTCAAT
1 AATTAAAATTAAATAAAATCTGTTACAGGATTTATTCCCGCCGA-TTAACAAGATTCTATTCAAT
5424227 ATCAATTTGTTTC
65 ATCAATTTGTTTC
5424240 CAAACGAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 9 0.13
85 54 0.81
86 4 0.06
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (85 bp):
AATTAAAATTAAATAAAATCTGTTACAGGATTTATTCCCGCCGATTAACAAGATTCTATTCAATA
TCAATTTGTTTCTAAATTAG
Found at i:5429228 original size:14 final size:14
Alignment explanation
Indices: 5429209--5429238 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5429199 TTATATATAT
5429209 ATCCGGTCATGCAA
1 ATCCGGTCATGCAA
5429223 ATCCGGTCATGCAA
1 ATCCGGTCATGCAA
5429237 AT
1 AT
5429239 TAACTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (14 bp):
ATCCGGTCATGCAA
Found at i:5431129 original size:41 final size:43
Alignment explanation
Indices: 5431028--5431141 Score: 142
Period size: 41 Copynumber: 2.7 Consensus size: 43
5431018 ATATCGAACA
* * * **
5431028 ATGCCAATGTCCCAGACGTGGTCTTACATGCTATCTCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
* *
5431071 ATGCCACTGTCCCAGACAAGGTCTTACACG-AATCAAATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
*
5431112 ATGCCAATGTCCTAGACATGGTCTTACACG
1 ATGCCAATGTCCCAGACATGGTCTTACACG
5431142 TAAACACAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
41 29 0.48
42 6 0.10
43 26 0.43
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
Found at i:5449740 original size:27 final size:27
Alignment explanation
Indices: 5449707--5449856 Score: 151
Period size: 27 Copynumber: 5.6 Consensus size: 27
5449697 AGACCCTAAA
*
5449707 ATAAGGTAAAATGACCAAAATACCCCT
1 ATAAGGTAAAATGACCGAAATACCCCT
* *
5449734 AGAAGGTAAAATGACTGAAATACCCCT
1 ATAAGGTAAAATGACCGAAATACCCCT
* * * *
5449761 ATAGGGTAAAATAACCGAAATACCACA
1 ATAAGGTAAAATGACCGAAATACCCCT
* * * *
5449788 ATAGGGTAAAATAATCGAAATACCCCC
1 ATAAGGTAAAATGACCGAAATACCCCT
*
5449815 AT-AGGATAAAATGACCAAAATA-CCCT
1 ATAAGG-TAAAATGACCGAAATACCCCT
*
5449841 CATATGGTAAAATGAC
1 -ATAAGGTAAAATGAC
5449857 TGTTATACCC
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
26 5 0.05
27 95 0.93
28 2 0.02
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (27 bp):
ATAAGGTAAAATGACCGAAATACCCCT
Found at i:5449796 original size:54 final size:53
Alignment explanation
Indices: 5449711--5449869 Score: 167
Period size: 54 Copynumber: 2.9 Consensus size: 53
5449701 CCTAAAATAA
* *
5449711 GGTAAAATGACCAAAATACCCCTAGAAGGTAAAATGACTGAAATACCCCTATAG
1 GGTAAAATGACCAAAATA-CCCAATAAGGTAAAATGACTGAAATACCCCTATAG
* * * * *
5449765 GGTAAAATAACCGAAATACCACAATAGGGTAAAAT-AATCGAAATACCCCCATAG
1 GGTAAAATGACCAAAATACC-CAATAAGGTAAAATGACT-GAAATACCCCTATAG
* * * **
5449819 GATAAAATGACCAAAATACCCTCATATGGTAAAATGACTGTTATACCCCTA
1 GGTAAAATGACCAAAATACCC-AATAAGGTAAAATGACTGAAATACCCCTA
5449870 GTATATGAAA
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
53 5 0.06
54 78 0.92
55 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.20
Consensus pattern (53 bp):
GGTAAAATGACCAAAATACCCAATAAGGTAAAATGACTGAAATACCCCTATAG
Found at i:5452972 original size:39 final size:39
Alignment explanation
Indices: 5452918--5453357 Score: 637
Period size: 39 Copynumber: 11.2 Consensus size: 39
5452908 AAATCTTATA
5452918 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
*
5452957 CAGTATAATCAGTGGATAATGTTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * *
5452996 CAGCATAATCAGTGGGTAATGCTCGTTTAAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * *
5453035 CAGCATAATCAGTGGGTAATGCTCGTTTAAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
** *
5453074 CAACATAATCAGTGGATATTGCTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* **
5453113 CAGCATAATCAGTGGATAATGCTTATTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * *
5453152 CAGTATAATTAATGGATAATGCTAGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* *
5453191 CAGCATAATCAGTGGATAATGCTCATTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTC-GTTTGAGCAAGCATT
* *
5453231 CAATATAATCAGTGGATAATGCTCGTTTGAGCAAACATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
*
5453270 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAACATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * * *
5453309 CAATATAATCAGTGGATATTGCTCGTTTGAACAAATCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGC-AAGCATT
5453349 CAGTATAAT
1 CAGTATAAT
5453358 TAGTATTCTA
Statistics
Matches: 366, Mismatches: 33, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
39 316 0.86
40 50 0.14
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (39 bp):
CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
Found at i:5460899 original size:63 final size:63
Alignment explanation
Indices: 5460822--5460964 Score: 180
Period size: 63 Copynumber: 2.3 Consensus size: 63
5460812 TGGTAATCCA
* * * *
5460822 TGTAACTCACTGTTTTTGAATTGGAGGCACACGAGCTAGGGGCATGGGCATGTGTCTAAGCT-G
1 TGTAACTCACTGTTTTAGAATTAGAGGCACACGAGCTAGGGACATGGACATGTGTC-AAGCTCG
* * * * *
5460885 TGTAACTCACTGTTTTAGATTTAGAGTCACACGGGCTAGGGACATGGACATGTGTCCAGGTCG
1 TGTAACTCACTGTTTTAGAATTAGAGGCACACGAGCTAGGGACATGGACATGTGTCAAGCTCG
*
5460948 TGTAACTCACTATTTTA
1 TGTAACTCACTGTTTTA
5460965 AGCCACATGG
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
62 3 0.04
63 66 0.96
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (63 bp):
TGTAACTCACTGTTTTAGAATTAGAGGCACACGAGCTAGGGACATGGACATGTGTCAAGCTCG
Found at i:5461808 original size:22 final size:22
Alignment explanation
Indices: 5461783--5461836 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
5461773 ATAGATATCT
5461783 TATTGTTTGTTTAATTTCAAAC
1 TATTGTTTGTTTAATTTCAAAC
* ** *
5461805 TATTGTATGTTTTGTTTCAGAC
1 TATTGTTTGTTTAATTTCAAAC
*
5461827 TATGGTTTGT
1 TATTGTTTGT
5461837 AAACTCGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.56
Consensus pattern (22 bp):
TATTGTTTGTTTAATTTCAAAC
Found at i:5464141 original size:22 final size:21
Alignment explanation
Indices: 5464094--5464143 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
5464084 TTCCTAAAAT
* *
5464094 ATTATTTATTTAATCAATTAT
1 ATTATTTATTTAATCAACTAA
* *
5464115 TTTATTTAGTTTAATTAACTAA
1 ATTATTTA-TTTAATCAACTAA
5464137 ATTATTT
1 ATTATTT
5464144 TTTCAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTATTTATTTAATCAACTAA
Found at i:5464156 original size:17 final size:17
Alignment explanation
Indices: 5464134--5464166 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5464124 TTTAATTAAC
5464134 TAAATTATTTTTTCAAT
1 TAAATTATTTTTTCAAT
5464151 TAAATTATTTTTTCAA
1 TAAATTATTTTTTCAA
5464167 CCCAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TAAATTATTTTTTCAAT
Found at i:5464173 original size:17 final size:17
Alignment explanation
Indices: 5464135--5464173 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5464125 TTAATTAACT
**
5464135 AAATTATTTTTTCAATT
1 AAATTATTTTTTCAACC
5464152 AAATTATTTTTTCAACC
1 AAATTATTTTTTCAACC
*
5464169 CAATT
1 AAATT
5464174 CTAATTCTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATTATTTTTTCAACC
Found at i:5468937 original size:266 final size:266
Alignment explanation
Indices: 5468464--5469265 Score: 1588
Period size: 266 Copynumber: 3.0 Consensus size: 266
5468454 ATCAAGTCTT
5468464 CCCTGACAGTAGAGCAACCAGCCAAGTTGT-TGTTTGCAGGACCCGTCCAACCCAACACTGAGCT
1 CCCTGACAGTAGAGCAACCAGCCAAGTTGTATGTTTGCAGGACCCGTCCAACCCAACACTGAGCT
*
5468528 CCATTTCTGAGAGGACAATAGACTGCCTAAACTGATCATCAGTTCCAAGGGATGCCATAATCATT
66 CCATTTCTGAGAGGACAATAGACTGCCTAAACTGATCATCAGTTCCAAGGGATGCCATAGTCATT
5468593 TTGTTTTAGTGGGTCCTATGATACTGTCTCATGCTCTTCAGCAATCCTTTCTTTAACACGCTGCA
131 TTGTTTTAGTGGGTCCTATGATACTGTCTCATGCTCTTCAGCAATCCTTTCTTTAACACGCTGCA
5468658 AAAGTTCCTCATAGACTTTGGAGGACTCGGAACTGAAGTTTTCCATTGCCTCAAATATGCGTTGC
196 AAAGTTCCTCATAGACTTTGGAGGACTCGGAACTGAAGTTTTCCATTGCCTCAAATATGCGTTGC
5468723 AAGCCC
261 AAGCCC
5468729 CCCTGACAGTAGAGCAACCAGCCAAGTTGTATGTTTGCAGGACCCGTCCAACCCAACACTGAGCT
1 CCCTGACAGTAGAGCAACCAGCCAAGTTGTATGTTTGCAGGACCCGTCCAACCCAACACTGAGCT
5468794 CCATTTCTGAGAGGACAATAGACTGCCTAAACTGATCATCAGTTCCAAGGGATGCCATAGTCATT
66 CCATTTCTGAGAGGACAATAGACTGCCTAAACTGATCATCAGTTCCAAGGGATGCCATAGTCATT
5468859 TTGTTTTAGTGGGTCCTATGATACTGTCTCATGCTCTTCAGCAATCCTTTCTTTAACACGCTGCA
131 TTGTTTTAGTGGGTCCTATGATACTGTCTCATGCTCTTCAGCAATCCTTTCTTTAACACGCTGCA
5468924 AAAGTTCCTCATAGACTTTGGAGGACTCGGAACTGAAGTTTTCCATTGCCTCAAATATGCGTTGC
196 AAAGTTCCTCATAGACTTTGGAGGACTCGGAACTGAAGTTTTCCATTGCCTCAAATATGCGTTGC
5468989 AAGCCC
261 AAGCCC
5468995 CCCTGACAGTAGAGCAACCAGCCAAGTTGTATGTTTGCAGGACCCGTCCAACCCAACACTGAGCT
1 CCCTGACAGTAGAGCAACCAGCCAAGTTGTATGTTTGCAGGACCCGTCCAACCCAACACTGAGCT
5469060 CCATTTCTGAGAGGACAATAGACTGCCTAAACTGATCATCAGTTCCAAGGGATGCCATAGTCATT
66 CCATTTCTGAGAGGACAATAGACTGCCTAAACTGATCATCAGTTCCAAGGGATGCCATAGTCATT
5469125 TTGTTTTAGTGGGTCCTATGATACTGTCTCATGCTCTTCAGCAATCCTTTCTTTAACACGCTGCA
131 TTGTTTTAGTGGGTCCTATGATACTGTCTCATGCTCTTCAGCAATCCTTTCTTTAACACGCTGCA
5469190 AAAGTTCCTCATAGACTTTGGAGGACTCGGAACTGAAGTTTTCCATTGCCTCAAATATGCGTTGC
196 AAAGTTCCTCATAGACTTTGGAGGACTCGGAACTGAAGTTTTCCATTGCCTCAAATATGCGTTGC
5469255 AAGCCC
261 AAGCCC
5469261 CCCTG
1 CCCTG
5469266 CAAACTACTG
Statistics
Matches: 535, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
265 30 0.06
266 505 0.94
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (266 bp):
CCCTGACAGTAGAGCAACCAGCCAAGTTGTATGTTTGCAGGACCCGTCCAACCCAACACTGAGCT
CCATTTCTGAGAGGACAATAGACTGCCTAAACTGATCATCAGTTCCAAGGGATGCCATAGTCATT
TTGTTTTAGTGGGTCCTATGATACTGTCTCATGCTCTTCAGCAATCCTTTCTTTAACACGCTGCA
AAAGTTCCTCATAGACTTTGGAGGACTCGGAACTGAAGTTTTCCATTGCCTCAAATATGCGTTGC
AAGCCC
Found at i:5473865 original size:16 final size:16
Alignment explanation
Indices: 5473846--5473884 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5473836 TTTTTAAGAA
5473846 TTTAATTAGTTT-ATTT
1 TTTAATT-GTTTAATTT
*
5473862 TTTAATTTTTTAATTT
1 TTTAATTGTTTAATTT
5473878 TTTAATT
1 TTTAATT
5473885 TAAATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTAATTGTTTAATTT
Found at i:5473870 original size:7 final size:8
Alignment explanation
Indices: 5473858--5473885 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5473848 TAATTAGTTT
5473858 ATTTTTTA
1 ATTTTTTA
5473866 ATTTTTTA
1 ATTTTTTA
5473874 ATTTTTTA
1 ATTTTTTA
5473882 ATTT
1 ATTT
5473886 AAATTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTTTA
Found at i:5474088 original size:31 final size:34
Alignment explanation
Indices: 5474053--5474122 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 34
5474043 ACTAAACAAT
*
5474053 TTGATTTT-CTTTTA-AAAAC-ACATTCAAAGAA
1 TTGATTTTGCTTTAAGAAAACAACATTCAAAGAA
5474084 TTGATTTTGCTTTAAGAAAACAGACATTCAAAGAA
1 TTGATTTTGCTTTAAGAAAACA-ACATTCAAAGAA
5474119 TTGA
1 TTGA
5474123 CAAATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 8 0.24
32 5 0.15
33 5 0.15
35 16 0.47
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (34 bp):
TTGATTTTGCTTTAAGAAAACAACATTCAAAGAA
Found at i:5474657 original size:26 final size:26
Alignment explanation
Indices: 5474606--5474659 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
5474596 ACATTCAATA
*
5474606 TAATCCATTATTCTTGTTAAATAATG
1 TAATCCATTATTCTTGTTAAAGAATG
* *
5474632 TAATTCATTATTCTTGTTAAGGAATG
1 TAATCCATTATTCTTGTTAAAGAATG
5474658 TA
1 TA
5474660 CTAGTATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.46
Consensus pattern (26 bp):
TAATCCATTATTCTTGTTAAAGAATG
Found at i:5477181 original size:20 final size:20
Alignment explanation
Indices: 5477156--5477195 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5477146 TGTGGTTAAC
*
5477156 TTTGATGACGATACAGAAGT
1 TTTGATGAAGATACAGAAGT
5477176 TTTGATGAAGATACAGAAGT
1 TTTGATGAAGATACAGAAGT
5477196 GTTGGAGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (20 bp):
TTTGATGAAGATACAGAAGT
Found at i:5482048 original size:21 final size:22
Alignment explanation
Indices: 5482024--5482066 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5482014 AGGTTTTTCA
5482024 AGAA-TTTTTTTCATAAATTTT
1 AGAATTTTTTTTCATAAATTTT
*
5482045 AGAATTTTTTTTTATAAATTTT
1 AGAATTTTTTTTCATAAATTTT
5482067 TTTGGCCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (22 bp):
AGAATTTTTTTTCATAAATTTT
Found at i:5482472 original size:26 final size:25
Alignment explanation
Indices: 5482423--5482472 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
5482413 TTGGTCGCTT
* *
5482423 TATTAAAATTTTCATCTATTTTTAC
1 TATTAAAATTTTCATCCATGTTTAC
5482448 TATTAAAAATTTTCATCCATGTTTA
1 TATT-AAAATTTTCATCCATGTTTA
5482473 ATTATCTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (25 bp):
TATTAAAATTTTCATCCATGTTTAC
Found at i:5486616 original size:23 final size:23
Alignment explanation
Indices: 5486586--5486629 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5486576 GTTAATTCAC
*
5486586 ATGTTAGTTATTTTTTTTTCTAT
1 ATGTTAGTTAATTTTTTTTCTAT
5486609 ATGTTAGTTAATTTTTTTTCT
1 ATGTTAGTTAATTTTTTTTCT
5486630 TTCTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.09, T:0.68
Consensus pattern (23 bp):
ATGTTAGTTAATTTTTTTTCTAT
Found at i:5490330 original size:18 final size:20
Alignment explanation
Indices: 5490292--5490331 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
5490282 AATTTTACTA
5490292 TTGATATAATATTAAAAATT
1 TTGATATAATATTAAAAATT
*
5490312 TTGA-ATAAT-TTAAACATT
1 TTGATATAATATTAAAAATT
5490330 TT
1 TT
5490332 AGTAGATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
TTGATATAATATTAAAAATT
Found at i:5491933 original size:18 final size:18
Alignment explanation
Indices: 5491912--5491947 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5491902 AACTGATAAT
5491912 ACATATATAAATTCATTC
1 ACATATATAAATTCATTC
* *
5491930 ACATATTTATATTCATTC
1 ACATATATAAATTCATTC
5491948 CGAACACATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (18 bp):
ACATATATAAATTCATTC
Found at i:5492105 original size:28 final size:28
Alignment explanation
Indices: 5492034--5492132 Score: 128
Period size: 28 Copynumber: 3.6 Consensus size: 28
5492024 ACACGTGACC
* * * *
5492034 AATTTGCTCACACAACCTCTAATATTCG
1 AATTTGCTCACACAAGCTGTGATATTTG
*
5492062 AATTTGCTCACACAAGTTGTGATATTTG
1 AATTTGCTCACACAAGCTGTGATATTTG
5492090 AATTTGCTCACACAAGCTGTGATATTTG
1 AATTTGCTCACACAAGCTGTGATATTTG
**
5492118 -GGTTGCTCACACAAG
1 AATTTGCTCACACAAG
5492133 TGTAGGTTAG
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 13 0.21
28 50 0.79
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (28 bp):
AATTTGCTCACACAAGCTGTGATATTTG
Found at i:5493712 original size:8 final size:8
Alignment explanation
Indices: 5493699--5493743 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
5493689 AATGAAACAG
5493699 AGAAGGAA
1 AGAAGGAA
5493707 AGAAGGAA
1 AGAAGGAA
5493715 AGAAGGAA
1 AGAAGGAA
*
5493723 AGAAAGAAA
1 AG-AAGGAA
*
5493732 AGAAAGAA
1 AGAAGGAA
5493740 AGAA
1 AGAA
5493744 AAGGGAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 26 0.79
9 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (8 bp):
AGAAGGAA
Found at i:5493720 original size:16 final size:16
Alignment explanation
Indices: 5493699--5493743 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
5493689 AATGAAACAG
*
5493699 AGAAGGAAAGAAGGAA
1 AGAAGGAAAGAAGAAA
5493715 AGAAGGAAAGAAAGAAA
1 AGAAGGAAAG-AAGAAA
*
5493732 AGAAAGAAAGAA
1 AGAAGGAAAGAA
5493744 AAGGGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
AGAAGGAAAGAAGAAA
Found at i:5493729 original size:4 final size:4
Alignment explanation
Indices: 5493699--5493744 Score: 56
Period size: 4 Copynumber: 11.2 Consensus size: 4
5493689 AATGAAACAG
* * *
5493699 AGAA GGAA AGAA GGAA AGAA GGAA AGAA AGAAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG-AA AGAA AGAA AGAA A
5493745 AGGGAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
4 31 0.89
5 4 0.11
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:5493738 original size:13 final size:13
Alignment explanation
Indices: 5493705--5493746 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
5493695 ACAGAGAAGG
*
5493705 AAAGAAGGAAAG-
1 AAAGAAAGAAAGA
*
5493717 AAGGAAAGAAAGA
1 AAAGAAAGAAAGA
5493730 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
5493743 AAAG
1 AAAG
5493747 GGAAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:5494888 original size:23 final size:23
Alignment explanation
Indices: 5494861--5494926 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
5494851 TCTACCGATT
*
5494861 AGGCACTTTATGTGTCGTGTATC
1 AGGCACTTTATGTGTCGTATATC
*
5494884 AGGCACTTTATGTGTCGTATTTC
1 AGGCACTTTATGTGTCGTATATC
* **
5494907 AGGCACCTCGTGTGTCGTAT
1 AGGCACTTTATGTGTCGTAT
5494927 CAGACACCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.38
Consensus pattern (23 bp):
AGGCACTTTATGTGTCGTATATC
Found at i:5494942 original size:23 final size:22
Alignment explanation
Indices: 5494894--5494945 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
5494884 AGGCACTTTA
*
5494894 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGACACCTCG
5494917 TGTGTCGTA-TCAGACACCTCG
1 TGTGTCGTATTCAGACACCTCG
5494938 TGTGTCGT
1 TGTGTCGT
5494946 TTTATGCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 19 0.68
23 9 0.32
ACGTcount: A:0.13, C:0.25, G:0.27, T:0.35
Consensus pattern (22 bp):
TGTGTCGTATTCAGACACCTCG
Found at i:5495973 original size:19 final size:19
Alignment explanation
Indices: 5495949--5495989 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5495939 TTAACATAAA
*
5495949 TAACTAATCATAATTAACT
1 TAACTAAACATAATTAACT
* *
5495968 TAACTAAACCTTATTAACT
1 TAACTAAACATAATTAACT
5495987 TAA
1 TAA
5495990 TATAATGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (19 bp):
TAACTAAACATAATTAACT
Found at i:5504805 original size:25 final size:25
Alignment explanation
Indices: 5504751--5504811 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
5504741 GGCTCTTAAT
* **
5504751 GAGCTTCCT-A-ATATGGCTCACTT
1 GAGCTTCCTGATATATGGCTAACCG
*
5504774 GAACTTCCTGATATATGGCTAACCG
1 GAGCTTCCTGATATATGGCTAACCG
5504799 GAGCTTCCTGATA
1 GAGCTTCCTGATA
5504812 ATAGCTCTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 8 0.26
24 1 0.03
25 22 0.71
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (25 bp):
GAGCTTCCTGATATATGGCTAACCG
Found at i:5508942 original size:39 final size:39
Alignment explanation
Indices: 5508913--5509106 Score: 244
Period size: 39 Copynumber: 5.0 Consensus size: 39
5508903 ATCCTATTAC
*
5508913 ACATATAATCACCTAACATTCAAGCATATATCACAATAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
* * * * **
5508952 ATATTTAATCTCATAACATTTAAGCATATATCACAACCT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
* *
5508991 TCATATAATCACATAATATTCAAGCATATATCACAATAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
* * *
5509030 ACATATAATCTCATAAAATTTAAGCATATATCACAATAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
** * *
5509069 ACATATAATCTTATAACATTTAAACATATATCACAATA
1 ACATATAATCACATAACATTCAAGCATATATCACAATA
5509107 ATAAAAAACA
Statistics
Matches: 133, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 133 1.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (39 bp):
ACATATAATCACATAACATTCAAGCATATATCACAATAT
Found at i:5508996 original size:78 final size:78
Alignment explanation
Indices: 5508913--5509106 Score: 280
Period size: 78 Copynumber: 2.5 Consensus size: 78
5508903 ATCCTATTAC
* * * *
5508913 ACATATAATCACCTAACATTCAAGCATATATCACAATATATATTTAATCTCATAACATTTAAGCA
1 ACATATAATCACATAACATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
*
5508978 TATATCACAACCT
66 TATATCACAACAT
* *
5508991 TCATATAATCACATAATATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
1 ACATATAATCACATAACATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
*
5509056 TATATCACAATAT
66 TATATCACAACAT
** * *
5509069 ACATATAATCTTATAACATTTAAACATATATCACAATA
1 ACATATAATCACATAACATTCAAGCATATATCACAATA
5509107 ATAAAAAACA
Statistics
Matches: 102, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 102 1.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (78 bp):
ACATATAATCACATAACATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
TATATCACAACAT
Found at i:5511517 original size:244 final size:242
Alignment explanation
Indices: 5510920--5511558 Score: 926
Period size: 244 Copynumber: 2.6 Consensus size: 242
5510910 ACATTTTAAA
* * * *
5510920 AAAAACCAT-AAAAA-ATTACTAATATAACATGTCGCAAAATTTCGAACGCACTAAGGCTAAAAT
1 AAAAACCATAAAAAACATTACCAATATAACATGTCGCAAAA-TTCTAACACTCTAAGGCTAAAAT
* * * *
5510983 TCTTAAAATA-CCCTAAAATTCCTAGGCCTTATTTTAGGGTGTTACATACACATTCAAGATTGTC
65 TCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGTC
* * *
5511047 TCTTATTAAATATTTTCCCAAGAAACACTCTAAGGTTAAAATTCATAAAATATCCCTAAAACCAT
130 TCTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCATAAAATACCCCTAAAACCAT
* *
5511112 AAAAAACCATAAATATTTTCCCTAAAACAATCTAAGGCTTAAATTCCT
195 AAAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
* * * * *
5511160 AAAAAGCATAAAAAACATTATCGATATATCATATCGCAAAATTCTGAACACTCTAAGGCTAAAAT
1 AAAAACCATAAAAAACATTACCAATATAACATGTCGCAAAATTCT-AACACTCTAAGGCTAAAAT
** *
5511225 TCCTAAAATACCTTTAAAACTCCTAGGCCCTATTTTGGGGTCTTACATACACATTCAAGATTGTC
65 TCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGTC
* *
5511290 TCTTATT-AATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCCTAAAGTACCCCTAAAACCAT
130 TCTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCATAAAATACCCCTAAAACCAT
* *
5511354 GAAAAAACCATAAATATTTTCCCTAAAACACTCGAAGGCTAAAATTTCT
195 -AAAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
* * *
5511403 AAAAACCATAAAAAAACATTACCAATATACCATGTCACAAAATTCCTAATACTCTAAGGCTAAAA
1 AAAAACCAT-AAAAAACATTACCAATATAACATGTCGCAAAATT-CTAACACTCTAAGGCTAAAA
* *
5511468 TTCCTAAAATACCCCTAAAACTCTTAGGCCCTATTTTGGGGTGTTACATACACATTCAAAATTGT
64 TTCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGT
*
5511533 CTCTTATTAAATATTTTTCCAAGAAA
129 CTCTTATTAAATATTTTCCCAAGAAA
5511559 TGATATTTAA
Statistics
Matches: 353, Mismatches: 38, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
240 8 0.02
241 8 0.02
242 98 0.28
243 107 0.30
244 114 0.32
245 18 0.05
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (242 bp):
AAAAACCATAAAAAACATTACCAATATAACATGTCGCAAAATTCTAACACTCTAAGGCTAAAATT
CCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGTCT
CTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCATAAAATACCCCTAAAACCATA
AAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
Found at i:5512504 original size:21 final size:21
Alignment explanation
Indices: 5512478--5512517 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5512468 CTAAAAGACG
5512478 CATAATATGACATGTTTATGC
1 CATAATATGACATGTTTATGC
* *
5512499 CATAATTTGACTTGTTTAT
1 CATAATATGACATGTTTAT
5512518 TTGTTGTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (21 bp):
CATAATATGACATGTTTATGC
Found at i:5513053 original size:13 final size:13
Alignment explanation
Indices: 5513035--5513060 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5513025 AGTAGATGAG
5513035 GTTTTATTTTTAT
1 GTTTTATTTTTAT
5513048 GTTTTATTTTTAT
1 GTTTTATTTTTAT
5513061 TTCGTGTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
GTTTTATTTTTAT
Found at i:5524566 original size:22 final size:22
Alignment explanation
Indices: 5524524--5524566 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5524514 TTTTGTTTCC
* *
5524524 AAAATTTAAATTTTAGCAAAAA
1 AAAATTAAAATTTAAGCAAAAA
*
5524546 AAAATTAAAATTTAAGTAAAA
1 AAAATTAAAATTTAAGCAAAA
5524567 TAAGGAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (22 bp):
AAAATTAAAATTTAAGCAAAAA
Found at i:5536078 original size:6 final size:6
Alignment explanation
Indices: 5536043--5536133 Score: 64
Period size: 6 Copynumber: 14.8 Consensus size: 6
5536033 TCTTTAACAT
*
5536043 TTTTTC TTTTATC TTCTTT- TGTTCTTC TTTTTC -TTTTC TTCTTTC TTTCGTC
1 TTTTTC TTTT-TC TT-TTTC T-TT-TTC TTTTTC TTTTTC TT-TTTC TTT-TTC
** *
5536095 TTTCAC -CTTTC -TTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
5536134 GCTTGCTTCC
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
5 11 0.16
6 34 0.49
7 21 0.30
8 3 0.04
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:5536090 original size:18 final size:18
Alignment explanation
Indices: 5536056--5536132 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 18
5536046 TTCTTTTATC
*
5536056 TTCTTTTGTTC-TTCTTT
1 TTCTTTTCTTCTTTCTTT
5536073 TTCTTTTCTTCTTTCTTT
1 TTCTTTTCTTCTTTCTTT
* **
5536091 CGTC-TTTCACCTTTC-TT
1 -TTCTTTTCTTCTTTCTTT
5536108 TTCTTTTTCTT-TTTCTTT
1 TTC-TTTTCTTCTTTCTTT
5536126 TTCTTTT
1 TTCTTTT
5536133 TGCTTGCTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
16 2 0.04
17 20 0.42
18 24 0.50
19 2 0.04
ACGTcount: A:0.01, C:0.22, G:0.03, T:0.74
Consensus pattern (18 bp):
TTCTTTTCTTCTTTCTTT
Found at i:5538087 original size:25 final size:25
Alignment explanation
Indices: 5538059--5538128 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
5538049 AAAGCCATTA
5538059 ATCGGGAAGCTCATGAGAGC-AAATT
1 ATCGGGAAGCTCATGAGAGCTAAA-T
*
5538084 ATCGGGAAGCTCGTGAGAGCTAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
* *
5538109 AACGGGAAGCTCAAGAGAGC
1 ATCGGGAAGCTCATGAGAGC
5538129 CATATATGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 37 0.93
26 3 0.08
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.16
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAGAGCTAAAT
Found at i:5544711 original size:12 final size:12
Alignment explanation
Indices: 5544691--5544729 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5544681 CGATACCAAT
5544691 AAATTTATTTTA
1 AAATTTATTTTA
*
5544703 AAATGTATTTT-
1 AAATTTATTTTA
5544714 AAATTTATATTTA
1 AAATTTAT-TTTA
5544727 AAA
1 AAA
5544730 ATTTTATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 7 0.30
12 13 0.57
13 3 0.13
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
AAATTTATTTTA
Found at i:5558027 original size:31 final size:28
Alignment explanation
Indices: 5557980--5558049 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 28
5557970 GTCATCCAAC
* * *
5557980 TTTTAAATCTTACAAAATTATCACTTACA
1 TTTTAAGTGTTACAAAATAATCACTTA-A
5558009 TTATTAAGGTGTTACAAAATAATCACTTAA
1 TT-TTAA-GTGTTACAAAATAATCACTTAA
5558039 TTTTAAGTGTT
1 TTTTAAGTGTT
5558050 GTTTATAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.14
29 6 0.17
30 7 0.19
31 18 0.50
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (28 bp):
TTTTAAGTGTTACAAAATAATCACTTAA
Found at i:5560665 original size:22 final size:22
Alignment explanation
Indices: 5560626--5560668 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
5560616 TGGCAATTGA
5560626 GTAATTTTTAAAGTTAGGTAAGG
1 GTAATTTTTAAAG-TAGGTAAGG
5560649 GTAATTTTGTAAA-TAGGTAA
1 GTAATTTT-TAAAGTAGGTAA
5560669 AAAGGTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (22 bp):
GTAATTTTTAAAGTAGGTAAGG
Found at i:5561598 original size:25 final size:25
Alignment explanation
Indices: 5561553--5561618 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
5561543 GTCGTTAAGG
* *
5561553 TTACCGATTC-CAGCTCTTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
5561577 TTACCGATACTCAGCTCGTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
* * *
5561602 TTATCGTTATTCAGCTC
1 TTACCGATACTCAGCTC
5561619 AGAAGAGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 9 0.25
25 27 0.75
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (25 bp):
TTACCGATACTCAGCTCGTATGAGC
Done.