Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006125.1 Hibiscus syriacus cultivar Beakdansim tig00014526_pilon, whole genome shotgun sequence
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: 135424
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2818 original size:31 final size:31
Alignment explanation
Indices: 2774--2851 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
2764 ACCTATGTCT
* *
2774 TTCGAGACATATGGACAATTTACCTAGGCTC
1 TTCGGGACCTATGGACAATTTACCTAGGCTC
* *
2805 TTCGGGACCTATGGACAGTTTACCTAGGTTC
1 TTCGGGACCTATGGACAATTTACCTAGGCTC
* *
2836 GT-GGGAGCTATGGACA
1 TTCGGGACCTATGGACA
2852 GTTGCCGAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 13 0.32
31 28 0.68
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (31 bp):
TTCGGGACCTATGGACAATTTACCTAGGCTC
Found at i:2849 original size:30 final size:31
Alignment explanation
Indices: 2783--2854 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
2773 TTTCGAGACA
* *
2783 TATGGACAATTTACCTAGGCTCTTCGGGACC
1 TATGGACAGTTTACCTAGGCTCGTCGGGACC
* *
2814 TATGGACAGTTTACCTAGGTTCGT-GGGAGC
1 TATGGACAGTTTACCTAGGCTCGTCGGGACC
2844 TATGGACAGTT
1 TATGGACAGTT
2855 GCCGAGGTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 16 0.43
31 21 0.57
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (31 bp):
TATGGACAGTTTACCTAGGCTCGTCGGGACC
Found at i:8736 original size:2 final size:2
Alignment explanation
Indices: 8729--8757 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8719 AGTTATATGA
8729 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8758 ACAACTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8828 original size:20 final size:20
Alignment explanation
Indices: 8776--8828 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
8766 TAAACAAGGT
8776 ATAAAAAAATAATAGTAATA
1 ATAAAAAAATAATAGTAATA
8796 ATAAGTATTAAAA-AATAGTAATA
1 ATAA--A--AAAATAATAGTAATA
8819 ACTAAAAAAA
1 A-TAAAAAAA
8829 GAAATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
20 8 0.29
22 2 0.07
23 11 0.39
24 7 0.25
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
ATAAAAAAATAATAGTAATA
Found at i:9441 original size:35 final size:35
Alignment explanation
Indices: 9402--9473 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
9392 TAAAAAAAAC
*
9402 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
9437 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
9472 CT
1 CT
9474 TCTTTGTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (35 bp):
CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:10547 original size:19 final size:21
Alignment explanation
Indices: 10496--10564 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 21
10486 TAAAAAATAA
*
10496 TAAATAAATAATAATATACAAAAG
1 TAAAT-AA-AATAATA-ATAAAAG
10520 TAAATAAAATAATAATAAAAG
1 TAAATAAAATAATAATAAAAG
10541 -AAA-AAAATGAAT-ATAAAAGG
1 TAAATAAAAT-AATAATAAAA-G
10561 TAAA
1 TAAA
10565 AGGTAAAAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 11 0.27
20 7 0.17
21 9 0.22
22 7 0.17
23 2 0.05
24 5 0.12
ACGTcount: A:0.70, C:0.01, G:0.07, T:0.22
Consensus pattern (21 bp):
TAAATAAAATAATAATAAAAG
Found at i:10553 original size:28 final size:28
Alignment explanation
Indices: 10487--10553 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
10477 AAAAGTTAGT
* *
10487 AAAAAATAAT-AAATAAATAATAATATA
1 AAAAAATAATAAAATAAATAATAAAAGA
* *
10514 CAAAAGTAAATAAAAT-AATAATAAAAGA
1 AAAAAAT-AATAAAATAAATAATAAAAGA
10542 AAAAAATGAATA
1 AAAAAAT-AATA
10554 TAAAAGGTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
27 5 0.16
28 22 0.71
29 4 0.13
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (28 bp):
AAAAAATAATAAAATAAATAATAAAAGA
Found at i:12162 original size:84 final size:83
Alignment explanation
Indices: 12072--12945 Score: 722
Period size: 84 Copynumber: 10.6 Consensus size: 83
12062 GTTTGCCTCT
* * * * * * * *
12072 GAGCTGAGTGTAATCGAACTCGAAGGTATTCGATTGGCAGATAGCTCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG-TTGGCAGATAACCCTTCTAGACTTAAGTTATG
* * *
12137 CTACAGATGATGTGCCTTG
65 CTGCAAATGATATGCCTTG
** * *
12156 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTATCAGATAACCTTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* * *
12221 ATGTAAATGATATGTCGTT-
65 CTGCAAATGATATG-CCTTG
* * * * * *
12240 GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* *
12305 TGTAAATGATATGCCCTCG
66 TGCAAATGATATG-CCTTG
* * * ** * * * *
12324 AAGCTGAGTGTAATCGAACTCGGGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGATATGT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* *
12386 TGCAAATGATGTGTCGTT-
66 TGCAAATGATATG-CCTTG
* * * *
12404 GAGCTTAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* *
12469 CTACAAATGATATGCCTGG
65 CTGCAAATGATATGCCTTG
* * * * * *
12488 GAGCTGAGCGTAGTCGAACTCAAAGGTC-TTGGT-G-ACATAACCCTTCTAGCCTTGAGTTATGT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* *
12550 TGTAAATGATAT-CCTCG
66 TGCAAATGATATGCCTTG
* * * * ** * * * *
12567 AAGCTGAGTGTAATCAAACTCGGGGGTC--T-TTGGTAGATAGCCCTTTTCA-ACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT-AGACTTAAGTTATG
* *
12628 CTACAAATGATGTGCCATT-
65 CTGCAAATGATATGCC-TTG
* * * * *
12647 GAGTTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
12712 CTGCAAATGATATG-CTTGG
65 CTGCAAATGATATGCCTT-G
* * * * * *
12731 GAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATAC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
* *
12796 TGTAAATGATATGCCCTCG
66 TGCAAATGATATG-CCTTG
* * * ** * * *
12815 AAGCTGAGTGTAATCGAACTCGGGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
*
12877 TGCAAATGATGTGCCTTG
66 TGCAAATGATATGCCTTG
* * *
12895 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCT
12946 TGTCTTGACC
Statistics
Matches: 618, Mismatches: 146, Indels: 52
0.76 0.18 0.06
Matches are distributed among these distances:
77 1 0.00
78 2 0.00
79 53 0.09
80 104 0.17
81 76 0.12
82 9 0.01
83 90 0.15
84 277 0.45
85 6 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (83 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGC
TGCAAATGATATGCCTTG
Found at i:12432 original size:164 final size:164
Alignment explanation
Indices: 12071--12928 Score: 752
Period size: 164 Copynumber: 5.2 Consensus size: 164
12061 GGTTTGCCTC
* * * * * * * * * *
12071 TGAGCTGAGTGTAATCGAACTCGAAGGTATTCGATTGGCAGATAGCTCTTCTCGACTTAAGCTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG-GTGACAGATAACCCTTCTAGACTTAAGTTAT
* * * *
12136 GCTACAGATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTATCAGATAA
65 GCTACAAATGATATGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG----CAGATAA
* * *
12200 CCTTTCTCGACTTAAGTTATGATGTAAATGATATGTCGT
126 CCCTTCTCGACTTAAGTTATGTTGCAAATGATATGTCGT
* * * *
12239 TGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATG
** * * ** *
12304 CTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTT
66 CTACAAATGATATGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTT
* *
12369 CTCGACTTAAGATATGTTGCAAATGATGTGTCGT
131 CTCGACTTAAGTTATGTTGCAAATGATATGTCGT
* * * * * *
12403 TGAGCTTAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTAAGTTAT
* * * * *
12468 GCTACAAATGATATG-CCTGGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTGGTGACATAACCC
65 GCTACAAATGATATGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-CAGATAACCC
* * * * *
12531 TTCTAGCCTTGAGTTATGTTGTAAATGATATCCTCG-
129 TTCTCGACTTAAGTTATGTTGCAAATGATAT-GTCGT
* * * * ** * * *
12567 -AAGCTGAGTGTAATCAAACTCGGGGGTCTTTGGT---AGATAGCCCTTTTCA-ACTTAAGCTAT
1 TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT-AGACTTAAGTTAT
* * * * * *
12627 GCTACAAATGATGTGCCATTG-AGTTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAA
65 GCTACAAATGATATGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTC---T-TTGGCAGATAA
* * **
12691 CCCTTCTAGACTTAAGTTGTACTGCAAATGATATG-C-T
126 CCCTTCTCGACTTAAGTTATGTTGCAAATGATATGTCGT
* * *
12728 TGGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTGACAGATAACCCTTCTAGCCTTGAGTTA
1 T--GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTA
* ** * * ** *
12793 TACTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCC
64 TGCTACAAATGATATGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCC
* * * *
12858 TTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCT
129 TTCTCGACTTAAGTTATGTTGCAAATGATATGTCGT
*
12893 TGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGT
1 T-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
12929 TGGCAAATAG
Statistics
Matches: 551, Mismatches: 118, Indels: 46
0.77 0.17 0.06
Matches are distributed among these distances:
159 59 0.11
160 4 0.01
161 1 0.00
162 5 0.01
163 56 0.10
164 229 0.42
165 48 0.09
166 1 0.00
167 68 0.12
168 80 0.15
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (164 bp):
TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATG
CTACAAATGATATGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTT
CTCGACTTAAGTTATGTTGCAAATGATATGTCGT
Found at i:12945 original size:248 final size:245
Alignment explanation
Indices: 12030--12933 Score: 1228
Period size: 248 Copynumber: 3.6 Consensus size: 245
12020 TGAATAATAT
* * * * *
12030 CCCTTCTTGCCTTGAGCTATTCTGTAAATTTGGTTTGCCTCTG-AGCTGAGTGTAATCGAACTCG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAA--TGATATGCCTC-GAAGCTGAGTGTAATCGAACTCG
** * * *
12094 AAGGTATTCGATTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTACAGATGATGTGCCTTGGAG
63 --GG-GGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTT-GAG
* ** * * * *
12159 CTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTATCAGATAACCTTTCTCGACTTAAGTTATGA-T
123 CTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGT-ACT
* *
12223 GTAAATGATATGTCGTT--GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTGACAGATAA
187 GCAAATGATATG-C-TTGGGAGCTGAGCGTAGTCGAACTCAAAGGT-TTTGGTGACAGATAA
12283 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATG-CCTCGAAGCTGAGTGTAATCGAACTCGGG
* * * * *
12348 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGATATGTTGCAAATGATGTGTCGTTGAGCTTAGC
65 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTG-CCTTGAGCTGAGC
* * *
12413 GTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATG
129 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATG
* *
12478 ATATGCCTGGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGGTGAC--ATAA
194 ATATGCTTGGGAGCTGAGCGTAGTCGAACTCAAAGGTTTTGGTGACAGATAA
* *
12528 CCCTTCTAGCCTTGAGTTATGTTGTAAATGATAT-CCTCGAAGCTGAGTGTAATCAAACTCGGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTCGAAGCTGAGTGTAATCGAACTCGGGG
* * * *
12592 GTCTTTGGTAGATAGCCCTTTTCAACTTAAGCTATGCTACAAATGATGTGCCATTGAGTTGAGCG
66 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCC-TTGAGCTGAGCG
*
12657 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGA
130 TAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGA
*
12722 TATGCTTGGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTGACAGATAA
195 TATGCTTGGGAGCTGAGCGTAGTCGAACTCAAAGGT-TTTGGTGACAGATAA
*
12774 CCCTTCTAGCCTTGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATG-CCTCGAAGCTGAGTGTAATCGAACTCGGG
*
12839 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
65 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTT-GAGCTGAGC
* *
12904 GTAATCGAACTCGAAGGTCTTTGGTTGGCA
129 GTAGTCGAACTCAAAGGTCTTTGGTTGGCA
12934 AATAGCCCTT
Statistics
Matches: 582, Mismatches: 56, Indels: 31
0.87 0.08 0.05
Matches are distributed among these distances:
242 1 0.00
243 180 0.31
244 8 0.01
245 37 0.06
246 37 0.06
247 11 0.02
248 245 0.42
249 5 0.01
250 2 0.00
251 6 0.01
252 25 0.04
253 25 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (245 bp):
CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTCGAAGCTGAGTGTAATCGAACTCGGGG
GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTTGAGCTGAGCGT
AGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGAT
ATGCTTGGGAGCTGAGCGTAGTCGAACTCAAAGGTTTTGGTGACAGATAA
Found at i:18070 original size:6 final size:6
Alignment explanation
Indices: 18059--18086 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
18049 TTAGTTGCGA
18059 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
18087 GGTATTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:18272 original size:22 final size:21
Alignment explanation
Indices: 18235--18303 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
18225 TAAAAAATAA
18235 TAAATAAATAATAATATACAAAAG
1 TAAAT-AA-AATAATA-ACAAAAG
*
18259 TAAATAAAATAATAATAAAAG
1 TAAATAAAATAATAACAAAAG
* *
18280 AAAACAAAATGAATAA-AAAA-
1 TAAATAAAAT-AATAACAAAAG
18300 TAAA
1 TAAA
18304 AAAGGTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 3 0.08
21 18 0.45
22 12 0.30
23 2 0.05
24 5 0.12
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.20
Consensus pattern (21 bp):
TAAATAAAATAATAACAAAAG
Found at i:18278 original size:11 final size:11
Alignment explanation
Indices: 18228--18302 Score: 50
Period size: 11 Copynumber: 6.6 Consensus size: 11
18218 AAGTTAGTAA
18228 AAAATAATAA-
1 AAAATAATAAT
18238 ATAAATAATAAT
1 A-AAATAATAAT
18250 ATACAA-AAGTAAAT
1 A-A-AATAA-T-AAT
18264 AAAATAATAAT
1 AAAATAATAAT
* *
18275 AAAAGAA-AAC
1 AAAATAATAAT
18285 AAAATGAATAA-
1 AAAAT-AATAAT
18296 AAAATAA
1 AAAATAA
18303 AAAAGGTAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
10 9 0.17
11 25 0.46
12 10 0.19
13 6 0.11
14 4 0.07
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.20
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:18305 original size:22 final size:21
Alignment explanation
Indices: 18240--18306 Score: 53
Period size: 25 Copynumber: 2.9 Consensus size: 21
18230 AATAATAAAT
*
18240 AAATAATAATATACAAAAGTAAATA
1 AAATAATAATA-A-AAAA--AAACA
*
18265 AAATAATAATAAAAGAAAACA
1 AAATAATAATAAAAAAAAACA
*
18286 AAATGAATAAAAAATAAAAAA
1 AAAT-AATAATAAA-AAAAAA
18307 GGTAAAAGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 8 0.22
22 8 0.22
23 8 0.22
24 1 0.03
25 11 0.31
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (21 bp):
AAATAATAATAAAAAAAAACA
Found at i:19556 original size:3 final size:3
Alignment explanation
Indices: 19542--19581 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
19532 TAAAATAAGA
* *
19542 AAT AAA AAT AAT AAT AAT AA- AAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19582 ATAAATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:19565 original size:14 final size:14
Alignment explanation
Indices: 19546--19605 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 14
19536 ATAAGAAATA
19546 AAAATAATAATAAT
1 AAAATAATAATAAT
*
19560 AAAATAATGATAAT
1 AAAATAATAATAAT
19574 AATAATAAATAAATAAAT
1 AA-AAT-AAT-AAT-AAT
19592 AAAACTATATAATA
1 AAAA-TA-ATAATA
19606 TACATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 15 0.39
15 3 0.08
16 4 0.11
17 8 0.21
18 8 0.21
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:19565 original size:27 final size:32
Alignment explanation
Indices: 19529--19595 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 32
19519 GGGAAAAACA
19529 AAATAAAATAA-GA-AATAAAAAT-AAT-AAT
1 AAATAAAATAATGATAATAAAAATAAATAAAT
*
19557 -AATAAAATAATGATAATAATAATAAATAAAT
1 AAATAAAATAATGATAATAAAAATAAATAAAT
19588 AAATAAAA
1 AAATAAAA
19596 CTATATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 10 0.30
28 2 0.06
29 8 0.24
30 3 0.09
31 3 0.09
32 7 0.21
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (32 bp):
AAATAAAATAATGATAATAAAAATAAATAAAT
Found at i:19566 original size:20 final size:19
Alignment explanation
Indices: 19528--19586 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
19518 CGGGAAAAAC
*
19528 AAAATAA-AATAAGAAATA
1 AAAATAATAATAATAAATA
19546 AAAATAATAATAATAAAATA
1 AAAATAATAATAAT-AAATA
**
19566 ATGATAATAATAATAAATA
1 AAAATAATAATAATAAATA
19585 AA
1 AA
19587 TAAATAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.20
19 11 0.31
20 17 0.49
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (19 bp):
AAAATAATAATAATAAATA
Found at i:19704 original size:30 final size:30
Alignment explanation
Indices: 19647--19704 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
19637 CTATATACTA
*
19647 TATATAAATTTTCAAATTTTTTAAAAAAAC
1 TATATAAATTTTCAAATGTTTTAAAAAAAC
19677 TATAT-AATTTTCAAAAATGTTTTAAAAA
1 TATATAAATTTTC--AAATGTTTTAAAAA
19705 TTATATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 7 0.28
30 5 0.20
31 13 0.52
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (30 bp):
TATATAAATTTTCAAATGTTTTAAAAAAAC
Found at i:19721 original size:38 final size:38
Alignment explanation
Indices: 19677--19923 Score: 263
Period size: 39 Copynumber: 6.4 Consensus size: 38
19667 TTAAAAAAAC
*
19677 TATATAATTTTCAAAAATGTTTTAAAAATTATATATTA
1 TATATAATTTTCAAAAATGTTTTAAAAACTATATATTA
*
19715 TATATAAGTTTTCAAAAATGCTTTAAAAACTATATATTA
1 TATATAA-TTTTCAAAAATGTTTTAAAAACTATATATTA
* *
19754 TATA-AGTTTTCAAAAAATGATTTTAAAAACCATATATTA
1 TATATAATTTTC-AAAAATG-TTTTAAAAACTATATATTA
*
19793 TATAT-TTTTTCTAAAAATGTTTTAAAAACTATATA-T-
1 TATATAATTTTC-AAAAATGTTTTAAAAACTATATATTA
* * * * *
19829 CATATAGTTTTCATAAGTGTTTTAAAAACTATATACTA
1 TATATAATTTTCAAAAATGTTTTAAAAACTATATATTA
*
19867 TAT-TCATTTTC-AAAATGCTTTTTAAAAAAACTATATATTA
1 TATATAATTTTCAAAAATG--TTTT--AAAAACTATATATTA
*
19907 TATATGTATTTTCAAAA
1 TATAT-AATTTTCAAAA
19924 CCGTTTGCAA
Statistics
Matches: 176, Mismatches: 19, Indels: 23
0.81 0.09 0.11
Matches are distributed among these distances:
36 29 0.16
37 18 0.10
38 36 0.20
39 66 0.38
40 17 0.10
41 1 0.01
42 6 0.03
43 3 0.02
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (38 bp):
TATATAATTTTCAAAAATGTTTTAAAAACTATATATTA
Found at i:29656 original size:17 final size:19
Alignment explanation
Indices: 29616--29653 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
29606 TTGGTTCACA
29616 GAATGTAAGATTACCAGTGG
1 GAATGTAAGATTACCAG-GG
29636 GAATGTAAGATTA-CAGGG
1 GAATGTAAGATTACCAGGG
29654 AATAGGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 3 0.17
20 13 0.72
ACGTcount: A:0.37, C:0.08, G:0.32, T:0.24
Consensus pattern (19 bp):
GAATGTAAGATTACCAGGG
Found at i:36036 original size:31 final size:31
Alignment explanation
Indices: 35969--36040 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
35959 TTTTTTGGTA
*
35969 TTCGGGTCGGATTTTTTTTAAAAAAATCGAG
1 TTCGGGTCGGATTTTTTTTAAAAAAATAGAG
* *
36000 ATCGGGTCTGATTTTTTATTAAAAAAATAG-G
1 TTCGGGTCGGATTTTTT-TTAAAAAAATAGAG
36031 TTCGGGTCGG
1 TTCGGGTCGG
36041 GTCGGTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.38
Consensus pattern (31 bp):
TTCGGGTCGGATTTTTTTTAAAAAAATAGAG
Found at i:36051 original size:36 final size:37
Alignment explanation
Indices: 35999--36090 Score: 109
Period size: 36 Copynumber: 2.5 Consensus size: 37
35989 AAAAAATCGA
* * **
35999 GATCGGGTCTGATTTTTTATTAAAAAAATA-GGTTCGG
1 GATCGGGTCGGTTTTTTTATTAAAAAAA-ACAATTCGG
36036 G-TCGGGTCGGTTTTTTT-TTAAAAAAAACAATTCGG
1 GATCGGGTCGGTTTTTTTATTAAAAAAAACAATTCGG
36071 GATCGGGTCGGGTTTTTTTA
1 GATCGGGTC-GGTTTTTTTA
36091 AGTGTGATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
34 1 0.02
35 15 0.32
36 21 0.45
37 10 0.21
ACGTcount: A:0.25, C:0.10, G:0.26, T:0.39
Consensus pattern (37 bp):
GATCGGGTCGGTTTTTTTATTAAAAAAAACAATTCGG
Found at i:37549 original size:60 final size:60
Alignment explanation
Indices: 37483--37639 Score: 156
Period size: 60 Copynumber: 2.6 Consensus size: 60
37473 ATTGATCCTT
* * * * *
37483 AAACTTTTGAATATTCCAATTTTATCATTAAGCTATGAC-TATCATTCTAAATTAGTCCTC
1 AAACTTTTGAACATTCCAATTTAATCACTAAACTATGACAT-TCATTCTAAATTAGTCCCC
* ** * * *
37543 AGACTTTAAAACATTTCAATTTAATCCCTAAACTATGACATTCATTCTAAATTGGTCCCC
1 AAACTTTTGAACATTCCAATTTAATCACTAAACTATGACATTCATTCTAAATTAGTCCCC
* *
37603 AAACTTTTTTGAACATTCCAATTTCATC-CCAAACTAT
1 AAAC--TTTTGAACATTCCAATTTAATCACTAAACTAT
37640 ATTTATATAC
Statistics
Matches: 77, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
60 50 0.65
61 9 0.12
62 18 0.23
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (60 bp):
AAACTTTTGAACATTCCAATTTAATCACTAAACTATGACATTCATTCTAAATTAGTCCCC
Found at i:38944 original size:19 final size:19
Alignment explanation
Indices: 38920--38957 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38910 TATATATATA
*
38920 TATATTTCTATTTATTTTC
1 TATATTTCTATTTAATTTC
*
38939 TATATTTTTATTTAATTTC
1 TATATTTCTATTTAATTTC
38958 GTTTTAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (19 bp):
TATATTTCTATTTAATTTC
Found at i:39018 original size:3 final size:3
Alignment explanation
Indices: 39010--39049 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
39000 TCTTTTGTCT
39010 TTA TTA TTA TTA -TA TATA TTA TTA -TA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
39050 CCTATACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.18
3 24 0.73
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:39174 original size:26 final size:29
Alignment explanation
Indices: 39143--39203 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 29
39133 TGTTTAATAT
39143 TATTAT-ATTATATATATATT-TTTA-AAC
1 TATTATCA-TATATATATATTATTTATAAC
39170 -ATTATCATATATATATATTATTTATAAC
1 TATTATCATATATATATATTATTTATAAC
39198 TATTAT
1 TATTAT
39204 TTTTGTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
26 17 0.57
27 5 0.17
28 3 0.10
29 5 0.17
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (29 bp):
TATTATCATATATATATATTATTTATAAC
Found at i:39232 original size:2 final size:2
Alignment explanation
Indices: 39225--39282 Score: 77
Period size: 2 Copynumber: 30.5 Consensus size: 2
39215 TTTACTTATG
* *
39225 TA TA TA TA CA TA TT TA TA TA -A T- TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39264 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
39283 TTTTCTATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39549 original size:4 final size:4
Alignment explanation
Indices: 39534--39700 Score: 50
Period size: 4 Copynumber: 37.8 Consensus size: 4
39524 ATGTTGTTTT
* * *
39534 TTTA TCTA TTTA TTTA TTTA TTTA TTGTG TATA TGTTA TTCTTA CTATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA T-TTA -T-TTA -T-TTA
* * * *
39584 TTATC TTATA TTTAA TTTA CTTCA TTTT TTTA TTTTG TTTA TTATA TTTTA
1 TT-TA TT-TA TTT-A TTTA -TTTA TTTA TTTA -TTTA TTTA TT-TA -TTTA
* * * * *
39635 TTCA CGTTA TTTA TTTA TCT- TTT- TTTA TTTTT TTTG TTTA CTTTA TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA -TTTA TTTA
39684 TTTA TTTTA TTTTA TTT
1 TTTA -TTTA -TTTA TTT
39701 TCTATGTTTC
Statistics
Matches: 123, Mismatches: 26, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
3 5 0.04
4 64 0.52
5 44 0.36
6 10 0.08
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:39662 original size:18 final size:19
Alignment explanation
Indices: 39641--39735 Score: 78
Period size: 18 Copynumber: 5.4 Consensus size: 19
39631 TTTATTCACG
* *
39641 TTATTTATTTATCTTT-TT
1 TTATTTATTTATGTTTACT
*
39659 TTATTT-TTTTTGTTTACT
1 TTATTTATTTATGTTTACT
*
39677 TTATTTATTTAT-TTTATT
1 TTATTTATTTATGTTTACT
*
39695 TTATTT-TCTATGTTT-CT
1 TTATTTATTTATGTTTACT
* *
39712 TTATTTA--CATGTTTATT
1 TTATTTATTTATGTTTACT
39729 TTATTTA
1 TTATTTA
39736 CCTTTTATCT
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
16 6 0.10
17 26 0.41
18 27 0.43
19 4 0.06
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (19 bp):
TTATTTATTTATGTTTACT
Found at i:39697 original size:36 final size:36
Alignment explanation
Indices: 39599--39718 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
39589 TTATATTTAA
* * * * *
39599 TTTACTTCATTTTTTTAT-TTTGTTTATTATATTTTA
1 TTTACTTTATTTATTTATCTTTTTTTATT-TTTTTTG
* *
39635 TTCACGTTATTTATTTATCTTTTTTTATTTTTTTTG
1 TTTACTTTATTTATTTATCTTTTTTTATTTTTTTTG
* *
39671 TTTACTTTATTTATTTAT-TTTATTTTATTTTCTATG
1 TTTACTTTATTTATTTATCTTT-TTTTATTTTTTTTG
39707 TTT-CTTTATTTA
1 TTTACTTTATTTA
39719 CATGTTTATT
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
35 12 0.17
36 50 0.70
37 9 0.13
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (36 bp):
TTTACTTTATTTATTTATCTTTTTTTATTTTTTTTG
Found at i:39731 original size:17 final size:18
Alignment explanation
Indices: 39669--39736 Score: 70
Period size: 17 Copynumber: 3.9 Consensus size: 18
39659 TTATTTTTTT
* *
39669 TGTTTACTTTATTTATTTA
1 TGTTTATTTTATTTA-CTA
*
39688 T-TTTATTTTATTTTCTA
1 TGTTTATTTTATTTACTA
*
39705 TGTTT-CTTTATTTAC-A
1 TGTTTATTTTATTTACTA
39721 TGTTTATTTTATTTAC
1 TGTTTATTTTATTTAC
39737 CTTTTATCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
16 6 0.15
17 20 0.49
18 14 0.34
19 1 0.02
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.69
Consensus pattern (18 bp):
TGTTTATTTTATTTACTA
Found at i:39748 original size:17 final size:18
Alignment explanation
Indices: 39689--39748 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 18
39679 ATTTATTTAT
*
39689 TTTAT-TTTATTTTCTATG
1 TTTATCTTTATTTAC-ATG
39707 -TT-TCTTTATTTACATG
1 TTTATCTTTATTTACATG
*
39723 TTTAT-TTTATTTACCT-
1 TTTATCTTTATTTACATG
39739 TTTATCTTTA
1 TTTATCTTTA
39749 CTTTTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
16 9 0.25
17 26 0.72
18 1 0.03
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTATCTTTATTTACATG
Found at i:53149 original size:19 final size:19
Alignment explanation
Indices: 53127--53164 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
53117 TATATATATA
*
53127 TATATTTCTATTTATTTTC
1 TATATTTCTATTTAATTTC
*
53146 TATATTTTTATTTAATTTC
1 TATATTTCTATTTAATTTC
53165 GTTTTTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (19 bp):
TATATTTCTATTTAATTTC
Found at i:53224 original size:3 final size:3
Alignment explanation
Indices: 53216--53255 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
53206 TTTTTTGTCT
53216 TTA TTA TTA TTA -TA TATA TTA TT- TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
53256 CCTATACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.18
3 24 0.73
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:53362 original size:2 final size:2
Alignment explanation
Indices: 53355--53407 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
53345 ATATTATTAT
* * * *
53355 TA TA TA TA TA TA TA TA TA TA TA TA TT TA AA CA T- TA CCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
53397 TA TA TA TA TA T
1 TA TA TA TA TA T
53408 TATTTATAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.95
3 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:53543 original size:3 final size:3
Alignment explanation
Indices: 53529--53622 Score: 60
Period size: 3 Copynumber: 32.3 Consensus size: 3
53519 AATTTCGTTT
* * *
53529 TTA TTCA TTA TTA TTA -TA TTA -TA TTA TT- TTA TTT TTA -AA TCTT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
53572 TTA TCT- TTA TTA TTA TTA -TA TATA TTA TT- TTA TTA TTA TTA -TA
1 TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
53615 TTA CTTA T
1 TTA -TTA T
53623 ACAAACCTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
2 14 0.19
3 47 0.65
4 11 0.15
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:53555 original size:23 final size:24
Alignment explanation
Indices: 53529--53615 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 24
53519 AATTTCGTTT
53529 TTATTCATTATTATTATAT-TATA
1 TTATTCATTATTATTATATATATA
* * *
53552 TTATT--TTATT-TT-TAAATCTT
1 TTATTCATTATTATTATATATATA
*
53572 TTA-TCTTTATTATTATTATATATA
1 TTATTCATTATTATTA-TATATATA
*
53596 TTATTTTATTATTATTATAT
1 TTA-TTCATTATTATTATAT
53616 TACTTATACA
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
19 3 0.06
20 7 0.15
21 10 0.21
22 2 0.04
23 5 0.10
24 8 0.17
25 3 0.06
26 10 0.21
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (24 bp):
TTATTCATTATTATTATATATATA
Found at i:53561 original size:44 final size:42
Alignment explanation
Indices: 53511--53605 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 42
53501 TTTCTATGTT
*
53511 TTTTATTTAATTTCGTTTT-TATTCATTATTATTATATTATATTA
1 TTTTATTTAA-ATC-TTTTATATTCATTATTATTATA-TATATTA
* *
53555 TTTTATTTTTAAATCTTTTATCTTTATTATTATTATATATATTA
1 TTTTA--TTTAAATCTTTTATATTCATTATTATTATATATATTA
53599 TTTTATT
1 TTTTATT
53606 ATTATTATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
42 2 0.04
44 21 0.47
45 17 0.38
46 5 0.11
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (42 bp):
TTTTATTTAAATCTTTTATATTCATTATTATTATATATATTA
Found at i:53622 original size:23 final size:22
Alignment explanation
Indices: 53535--53622 Score: 90
Period size: 23 Copynumber: 3.9 Consensus size: 22
53525 GTTTTTATTC
53535 ATTATTATTATATTA-TATTATT
1 ATTATTATTATATTATTATT-TT
* * *
53557 -TTATTTTTAAATCTTTTATCTTT
1 ATTATTATTATAT-TATTAT-TTT
53580 ATTATTATTATATATATTATTTT
1 ATTATTATTATAT-TATTATTTT
53603 ATTATTATTATATTACTTAT
1 ATTATTATTATATTA-TTAT
53623 ACAAACCTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
21 10 0.19
22 3 0.06
23 25 0.46
24 16 0.30
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTATTATTATATTATTATTTT
Found at i:53897 original size:31 final size:31
Alignment explanation
Indices: 53859--53944 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 31
53849 ATTCACGTTA
*
53859 TTTATTTATCTTT-TTTTATTTT-TTTGTTTAC
1 TTTATTTAT-TTTATTTTATTTTCTATGTTT-C
53890 TTTATTTATTTTATTTTATTTTCTATGTTTC
1 TTTATTTATTTTATTTTATTTTCTATGTTTC
53921 TTTATTTACATGTTTATTTTATTT
1 TTTATTT--AT-TTTATTTTATTT
53945 ACCTTTTATC
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
30 3 0.06
31 26 0.53
32 6 0.12
33 2 0.04
34 12 0.24
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.74
Consensus pattern (31 bp):
TTTATTTATTTTATTTTATTTTCTATGTTTC
Found at i:53907 original size:14 final size:14
Alignment explanation
Indices: 53807--53910 Score: 61
Period size: 14 Copynumber: 7.4 Consensus size: 14
53797 TATTATCTTA
* *
53807 TATTTAATTTACTT
1 TATTTATTTTATTT
*
53821 CATTT-TTTTATTT
1 TATTTATTTTATTT
* *
53834 TGTTTATTATATTT
1 TATTTATTTTATTT
* **
53848 TATTCACGTTA-TT
1 TATTTATTTTATTT
53861 TATTTATCTTT-TTT
1 TATTTAT-TTTATTT
* *
53875 TATTTTTTTGTTTACTT
1 TA--TTTAT-TTTATTT
53892 TATTTATTTTATTT
1 TATTTATTTTATTT
53906 TATTT
1 TATTT
53911 TCTATGTTTC
Statistics
Matches: 65, Mismatches: 19, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
13 16 0.25
14 34 0.52
15 4 0.06
16 7 0.11
17 4 0.06
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (14 bp):
TATTTATTTTATTT
Found at i:53941 original size:17 final size:17
Alignment explanation
Indices: 53883--53946 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
53873 TTTATTTTTT
53883 TGTTTACTTTATTT--A
1 TGTTTACTTTATTTACA
* *
53898 T-TTTATTTTATTTTCTA
1 TGTTTACTTTATTTAC-A
53915 TGTTT-CTTTATTTACA
1 TGTTTACTTTATTTACA
*
53931 TGTTTATTTTATTTAC
1 TGTTTACTTTATTTAC
53947 CTTTTATCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 11 0.28
15 1 0.03
16 6 0.15
17 19 0.47
18 3 0.08
ACGTcount: A:0.19, C:0.08, G:0.05, T:0.69
Consensus pattern (17 bp):
TGTTTACTTTATTTACA
Found at i:53958 original size:17 final size:18
Alignment explanation
Indices: 53883--53958 Score: 62
Period size: 17 Copynumber: 4.7 Consensus size: 18
53873 TTTATTTTTT
53883 TGTTTA-CTTTATTT--A
1 TGTTTATCTTTATTTACA
*
53898 T-TTTAT-TTTATTTTCTA
1 TGTTTATCTTTATTTAC-A
53915 TG-TT-TCTTTATTTACA
1 TGTTTATCTTTATTTACA
*
53931 TGTTTAT-TTTATTTACC
1 TGTTTATCTTTATTTACA
53948 T-TTTATCTTTA
1 TGTTTATCTTTA
53959 CTTTTTCATT
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
14 11 0.22
15 1 0.02
16 9 0.18
17 28 0.56
18 1 0.02
ACGTcount: A:0.18, C:0.09, G:0.04, T:0.68
Consensus pattern (18 bp):
TGTTTATCTTTATTTACA
Found at i:56270 original size:2 final size:2
Alignment explanation
Indices: 56263--56294 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
56253 TTTTAGACTT
56263 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56295 TTAAACTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58986 original size:184 final size:183
Alignment explanation
Indices: 58669--59055 Score: 611
Period size: 184 Copynumber: 2.1 Consensus size: 183
58659 ATTAAATTTT
* *
58669 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAATCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAATCCAATTAATAA
*
58734 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
*
58799 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTT-AATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATT-AA
*
58853 AAATATTAAATATATTATATATAACATTTGGGCTAAGCCCAAACAATTTAAAA-CTCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAATC-CAATTAATA
* * *
58917 ATTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAA-T
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATT
*
58981 TTTTATTTTATAATTATATATTATTTAAATTAATTATACACTTTTTTTGAATTAA
129 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
* *
59036 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
59056 AATTAGAAAA
Statistics
Matches: 189, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
182 8 0.04
183 19 0.10
184 159 0.84
185 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAATCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAA
Found at i:59176 original size:30 final size:30
Alignment explanation
Indices: 59119--59177 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
59109 CCAAAATTAA
* **
59119 TTCGGTTCGGTTAATATGTTTGAAAAAAAG
1 TTCGGTTCGGTTAACATGTTAAAAAAAAAG
59149 TTCGGTTCGGTTAACA-GTTAAAGAAAAAA
1 TTCGGTTCGGTTAACATGTTAAA-AAAAAA
59178 AAGTTCGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.32
Consensus pattern (30 bp):
TTCGGTTCGGTTAACATGTTAAAAAAAAAG
Found at i:60403 original size:21 final size:20
Alignment explanation
Indices: 60358--60469 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
60348 ACCCAGTGTC
* *
60358 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACACGAAT-TT
60378 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
* *
60399 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
*
60419 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
60439 -AATTTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
60458 -AATTTCGCAACA
1 CAAATTCGCAACA
60470 GGTTTTAGTT
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
19 29 0.36
20 35 0.43
21 15 0.19
22 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:60410 original size:41 final size:40
Alignment explanation
Indices: 60358--60449 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 40
60348 ACCCAGTGTC
60358 CAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAATTT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACAC-GAATTT
* ** *
60399 CAAATTCGCAACTCGATTTTCGAATTCGCAACACGAATTT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAATTT
*
60439 -AATTTCGCAAC
1 CAAATTCGCAAC
60450 ACGAATTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 10 0.22
40 6 0.13
41 30 0.65
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAATTT
Found at i:60481 original size:18 final size:19
Alignment explanation
Indices: 60382--60488 Score: 110
Period size: 19 Copynumber: 5.5 Consensus size: 19
60372 GATAGTCAAA
*
60382 TTCGCAACACTGAATTTCAAA
1 TTCGCAACAC-GAATTT-AAT
* *
60403 TTCGCAACTCGATTTTCGAA-
1 TTCGCAACACGAATTT--AAT
60423 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
60442 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
60461 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
60479 TTCGCAACAC
1 TTCGCAACAC
60489 AAATGTTTTG
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
18 17 0.23
19 28 0.37
20 19 0.25
21 11 0.15
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:60644 original size:14 final size:16
Alignment explanation
Indices: 60625--60661 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
60615 TCCCCATCTC
60625 TAATTTT-TTT-TACA
1 TAATTTTATTTCTACA
*
60639 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
60655 TAATTTT
1 TAATTTT
60662 CAATGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:61277 original size:12 final size:12
Alignment explanation
Indices: 61256--61289 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
61246 ACCACATTTC
*
61256 CAATACCAAACA
1 CAATATCAAACA
61268 CAATATCAAACA
1 CAATATCAAACA
*
61280 CAATCTCAAA
1 CAATATCAAA
61290 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:61442 original size:24 final size:24
Alignment explanation
Indices: 61415--61468 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
61405 GTATTCGAAA
61415 TTTGATATTGGTCAATACTCAGAC
1 TTTGATATTGGTCAATACTCAGAC
* * *
61439 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACTCAGAC
61463 TTTGAT
1 TTTGAT
61469 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCAGAC
Found at i:63891 original size:20 final size:21
Alignment explanation
Indices: 63866--63914 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
63856 AAATCGCAAC
63866 GCGAATTTGA-CTTTCGCGTT
1 GCGAATTTGACCTTTCGCGTT
*
63886 GTGAATTT-ACCTTTCGCGTT
1 GCGAATTTGACCTTTCGCGTT
63906 GCGAATTTG
1 GCGAATTTG
63915 TATCTTCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.41
Consensus pattern (21 bp):
GCGAATTTGACCTTTCGCGTT
Found at i:64123 original size:64 final size:66
Alignment explanation
Indices: 63968--64111 Score: 240
Period size: 66 Copynumber: 2.2 Consensus size: 66
63958 AATTTAAAAC
*
63968 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAACAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATAAATTAAACAAGCAAAAAAACAATTCTTATTTACACATCAAATT
64033 A
66 A
*
64034 AACAAATCAACTTTTACAAATAAATTAAACAAGC-AAAAAATAATTCTTATTT-CATCATC-AAT
1 AACAAATCAACTTTTACAAATAAATTAAACAAGCAAAAAAACAATTCTTATTTACA-CATCAAAT
64096 TA
65 TA
64098 AACAAATCAACTTT
1 AACAAATCAACTTT
64112 CAATGTAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
64 21 0.28
65 21 0.28
66 33 0.44
ACGTcount: A:0.52, C:0.17, G:0.01, T:0.29
Consensus pattern (66 bp):
AACAAATCAACTTTTACAAATAAATTAAACAAGCAAAAAAACAATTCTTATTTACACATCAAATT
A
Found at i:65513 original size:21 final size:21
Alignment explanation
Indices: 65496--65536 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
65486 CCATTGAATG
*
65496 ATGGCAGGGGCCTCTTGAACC
1 ATGGCAGGCGCCTCTTGAACC
*
65517 ATGGGAGGCGCCTCTTGAAC
1 ATGGCAGGCGCCTCTTGAAC
65537 GATAAGAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.20
Consensus pattern (21 bp):
ATGGCAGGCGCCTCTTGAACC
Found at i:65725 original size:12 final size:12
Alignment explanation
Indices: 65706--65747 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
65696 GGGCCGCTGA
65706 AAATAAATTAAT
1 AAATAAATTAAT
* *
65718 ACATAAATTAGT
1 AAATAAATTAAT
65730 AAATAAA-TACAT
1 AAATAAATTA-AT
65742 AAATAA
1 AAATAA
65748 TGCCGAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 2 0.08
12 23 0.92
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:65870 original size:21 final size:21
Alignment explanation
Indices: 65844--65893 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
65834 TGAAACAATT
* *
65844 TCACGTAGAGCGGCTACCTCA
1 TCACGTAGAGCAGATACCTCA
* *
65865 TCACGTAAAGTAGATACCTCA
1 TCACGTAGAGCAGATACCTCA
65886 TCACGTAG
1 TCACGTAG
65894 CGCACCATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (21 bp):
TCACGTAGAGCAGATACCTCA
Found at i:70804 original size:40 final size:40
Alignment explanation
Indices: 70773--70943 Score: 160
Period size: 40 Copynumber: 4.3 Consensus size: 40
70763 CACAGTTTCT
70773 AAATTCGCAACGCGAATATGT-AAA-TCGCAACACAGAAGTC
1 AAATTCGCAACGCG-ATA-GTCAAATTCGCAACACAGAAGTC
*
70813 AAATTCGCAACGCGATAGTCAAATTCGCAACACTGAAGTC
1 AAATTCGCAACGCGATAGTCAAATTCGCAACACAGAAGTC
** * *
70853 AAATTTACAACACTGA-AGTCAAATTCGCAACGC-GAA-TC
1 AAATTCGCAACGC-GATAGTCAAATTCGCAACACAGAAGTC
*
70891 TGTAAA-TCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTC
1 ---AAATTCGCAACGCG-A-TAGTCAAATTCGCAACACAGAAGTC
70933 AAATTCGCAAC
1 AAATTCGCAAC
70944 ACTAAATTTC
Statistics
Matches: 109, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
38 4 0.04
39 13 0.12
40 77 0.71
41 11 0.10
42 4 0.04
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.20
Consensus pattern (40 bp):
AAATTCGCAACGCGATAGTCAAATTCGCAACACAGAAGTC
Found at i:70924 original size:60 final size:58
Alignment explanation
Indices: 70772--70943 Score: 206
Period size: 60 Copynumber: 2.9 Consensus size: 58
70762 ACACAGTTTC
70772 TAAATTCGCAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAG
1 TAAATTCGCAACGCGAAT-TGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAG
* ** * *
70831 TCAAATTCGCAACACTGAA--GTCAAATTTACAACACTGAAGTCAAATTCGCAACGCGAATCTG
1 T-AAATTCGCAACGC-GAATTGT-AAA-TCGCAACACAGAAGTCAAATTCGCAACGCG-AT-AG
70893 TAAA-TCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAAC
1 TAAATTCGCAACGCGAA-TTGTAAATCGCAACACAGAAGTCAAATTCGCAAC
70944 ACTAAATTTC
Statistics
Matches: 95, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
58 2 0.02
59 7 0.07
60 71 0.75
61 11 0.12
62 4 0.04
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.20
Consensus pattern (58 bp):
TAAATTCGCAACGCGAATTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAG
Found at i:70957 original size:21 final size:20
Alignment explanation
Indices: 70768--71004 Score: 127
Period size: 20 Copynumber: 11.8 Consensus size: 20
70758 TACAACACAG
*
70768 TTTCTAAATTCGCAACGCGAA
1 TTTC-AAATTCGCAACACGAA
70789 TATGT-AAA-TCGCAACACAGAA
1 T-T-TCAAATTCGCAACAC-GAA
* *
70810 -GTCAAATTCGCAACGCG-A
1 TTTCAAATTCGCAACACGAA
*
70828 TAGTCAAATTCGCAACACTGAA
1 T-TTCAAATTCGCAACAC-GAA
* **
70850 -GTCAAATTTACAACACTGAA
1 TTTCAAATTCGCAACAC-GAA
* *
70870 -GTCAAATTCGCAACGCGAA
1 TTTCAAATTCGCAACACGAA
*
70889 TCTGT-AAA-TCGCAACGCGAA
1 T-T-TCAAATTCGCAACACGAA
*
70909 TTTGTAAA-TCGCAACACAGAA
1 TTT-CAAATTCGCAACAC-GAA
* *
70930 -GTCAAATTCGCAACACTAAA
1 TTTCAAATTCGCAACAC-GAA
* * *
70950 TTTCAAATTCACAACTCGAT
1 TTTCAAATTCGCAACACGAA
*
70970 TTTCGAATTCGCAACACGAA
1 TTTCAAATTCGCAACACGAA
*
70990 TTT-AATTTCGCAACA
1 TTTCAAATTCGCAACA
71005 GGTTTTAGTT
Statistics
Matches: 173, Mismatches: 26, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.02
19 21 0.12
20 118 0.68
21 27 0.16
22 3 0.02
23 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (20 bp):
TTTCAAATTCGCAACACGAA
Found at i:71001 original size:19 final size:19
Alignment explanation
Indices: 70977--71023 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
70967 GATTTTCGAA
70977 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
70996 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
71014 TTCGCAACAC
1 TTCGCAACAC
71024 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:71001 original size:80 final size:80
Alignment explanation
Indices: 70834--71004 Score: 186
Period size: 80 Copynumber: 2.1 Consensus size: 80
70824 GCGATAGTCA
* * * *
70834 AATTCGCAACACTGAAGTCAAATTTACAACACTGAAGTCAAATTCGCAACGCGAATCTGTAAATC
1 AATTCGCAACACAGAAGTCAAATTCACAACACTAAAGTCAAATTCACAACGCGAATCTGTAAATC
*
70899 GCAACGCGAATTTGT
66 GCAACACGAATTTGT
* * * * * * *
70914 AAATCGCAACACAGAAGTCAAATTCGCAACACTAAATTTCAAATTCACAACTCGATTTTCG-AAT
1 AATTCGCAACACAGAAGTCAAATTCACAACACTAAA-GTCAAATTCACAACGCGAATCT-GTAAA
70978 TCGCAACACGAA-TT-T
64 TCGCAACACGAATTTGT
70993 AATTTCGCAACA
1 AA-TTCGCAACA
71005 GGTTTTAGTT
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
79 3 0.04
80 41 0.55
81 30 0.40
82 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (80 bp):
AATTCGCAACACAGAAGTCAAATTCACAACACTAAAGTCAAATTCACAACGCGAATCTGTAAATC
GCAACACGAATTTGT
Found at i:87086 original size:18 final size:18
Alignment explanation
Indices: 87063--87098 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
87053 AAGCAAAAGG
87063 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
87081 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
87099 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:87341 original size:14 final size:14
Alignment explanation
Indices: 87298--87341 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
87288 GTGTTTTCCT
87298 AAAATTCGCAACGCG
1 AAAA-TCGCAACGCG
87313 -AAATCGCAAAC-CG
1 AAAATCGC-AACGCG
87326 AAAATCGCAACGCG
1 AAAATCGCAACGCG
87340 AA
1 AA
87342 TTTGACTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGCG
Found at i:88970 original size:21 final size:21
Alignment explanation
Indices: 88946--89061 Score: 144
Period size: 21 Copynumber: 5.5 Consensus size: 21
88936 GAGAGACCCA
* *
88946 TTGAACGATGACAGGGGCCTC
1 TTGAACGATGAGAGGAGCCTC
* *
88967 TTGAACGGTGGGAGGAGCCTC
1 TTGAACGATGAGAGGAGCCTC
* *
88988 TTGAATGATGAGAAGAGCCTC
1 TTGAACGATGAGAGGAGCCTC
89009 TTGAACGATGAGAGGAGCCTC
1 TTGAACGATGAGAGGAGCCTC
**
89030 TTGAACGAT-AGGAGTCGCCTC
1 TTGAACGATGA-GAGGAGCCTC
89051 TTGAACGATGA
1 TTGAACGATGA
89062 CAGGTGAATC
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
20 1 0.01
21 79 0.98
22 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.22
Consensus pattern (21 bp):
TTGAACGATGAGAGGAGCCTC
Found at i:88992 original size:42 final size:42
Alignment explanation
Indices: 88922--89038 Score: 148
Period size: 42 Copynumber: 2.8 Consensus size: 42
88912 GTGAATCGGG
* *
88922 CTCTTGAACGGTGGGA-GAGACC-CATTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGAG-CCTC-TTGAACGATGACAAGAGC
* *
88964 CTCTTGAACGGTGGGAGGAGCCTCTTGAATGATGAGAAGAGC
1 CTCTTGAACGGTGGGAGGAGCCTCTTGAACGATGACAAGAGC
* *
89006 CTCTTGAACGATGAGAGGAGCCTCTTGAACGAT
1 CTCTTGAACGGTGGGAGGAGCCTCTTGAACGAT
89039 AGGAGTCGCC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGAGCCTCTTGAACGATGACAAGAGC
Found at i:89367 original size:21 final size:21
Alignment explanation
Indices: 89343--89392 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
89333 TAAAATAATC
*
89343 TCACGTAGAGCAGCTACCTCA
1 TCACGTAGAGCAGATACCTCA
* *
89364 TCACGTAAAGTAGATACCTCA
1 TCACGTAGAGCAGATACCTCA
89385 TCACGTAG
1 TCACGTAG
89393 CACACCATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
TCACGTAGAGCAGATACCTCA
Found at i:90802 original size:17 final size:17
Alignment explanation
Indices: 90780--90814 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
90770 TGGCTATGCT
90780 TAATTTATTCCTTAAGG
1 TAATTTATTCCTTAAGG
90797 TAATTTATTCCTTAAGG
1 TAATTTATTCCTTAAGG
90814 T
1 T
90815 CAACTGAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
TAATTTATTCCTTAAGG
Found at i:91248 original size:19 final size:19
Alignment explanation
Indices: 91197--91250 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
91187 AGTAGTTTCT
*
91197 GAAACTTAAATTCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
91217 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
91237 GAAACTAAAATCGC
1 GAAACTAAAATCGC
91251 GTTGCGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:91673 original size:22 final size:22
Alignment explanation
Indices: 91648--91689 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
91638 GATTTTGCCA
* *
91648 GAGATGAGGATGGATTTCGTTG
1 GAGATGAGGACGGATGTCGTTG
*
91670 GAGATGGGGACGGATGTCGT
1 GAGATGAGGACGGATGTCGT
91690 CGTAGAGAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.07, G:0.45, T:0.26
Consensus pattern (22 bp):
GAGATGAGGACGGATGTCGTTG
Found at i:91869 original size:20 final size:20
Alignment explanation
Indices: 91844--92155 Score: 231
Period size: 20 Copynumber: 15.6 Consensus size: 20
91834 TAAACGCGCT
91844 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
*
91864 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGCG
*
91884 TTGCGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GCG
* * *
91904 CTGTGAATTTGACTTAT-GTG
1 TTGCGAATTTGACTT-TCGCG
*
91924 TTGCG-ATTT-ACAAATTCGCG
1 TTGCGAATTTGAC--TTTCGCG
*
91944 TTGCGAATTTGAC-TTCAGTG
1 TTGCGAATTTGACTTTC-GCG
*
91964 TTGCGAATTTGACTTAT-GTG
1 TTGCGAATTTGACTT-TCGCG
*
91984 TTGCG-ATTT-ACAAATTCGCG
1 TTGCGAATTTGAC--TTTCGCG
*
92004 TTGCGAATTTGAC-TTCAGTG
1 TTGCGAATTTGACTTTC-GCG
*
92024 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGCG
*
92044 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGCG
*
92064 TTGCGAATTTGACTTAT-GTG
1 TTGCGAATTTGACTT-TCGCG
* *
92084 TTGTGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GCG
*
92104 TTGCG-ATTT-ACAAATTCGCG
1 TTGCGAATTTGAC--TTTCGCG
*
92124 TTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC--TTTCGCG
92144 TTGCGAATTTGA
1 TTGCGAATTTGA
92156 AAATTGGGTT
Statistics
Matches: 245, Mismatches: 21, Indels: 50
0.78 0.07 0.16
Matches are distributed among these distances:
18 7 0.03
19 23 0.09
20 188 0.77
21 20 0.08
22 7 0.03
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:91896 original size:40 final size:40
Alignment explanation
Indices: 91844--92194 Score: 264
Period size: 40 Copynumber: 8.8 Consensus size: 40
91834 TAAACGCGCT
91844 TTGCGAATTTGACTTTCGCGTTGCGAATTTGAC-TATCGCG
1 TTGCGAATTTGAC-TTCGCGTTGCGAATTTGACATATCGCG
* * * * *
91884 TTGCGAATTTGACTTCTGTGCTGTGAATTTGACTTAT-GTG
1 TTGCGAATTTGACTTC-GCGTTGCGAATTTGACATATCGCG
*
91924 TTGCG-ATTT-ACAAATTCGCGTTGCGAATTTGAC-T-TCAGTG
1 TTGCGAATTTGAC---TTCGCGTTGCGAATTTGACATATC-GCG
* * *
91964 TTGCGAATTTGACTTATGTGTTGCG-ATTT-ACAAATTCGCG
1 TTGCGAATTTGACTT-CGCGTTGCGAATTTGACATA-TCGCG
*
92004 TTGCGAATTTGACTTCAGTGTTGCGAATTTGAC-TATCGCG
1 TTGCGAATTTGACTTC-GCGTTGCGAATTTGACATATCGCG
* *
92044 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTAT-GTG
1 TTGCGAATTTGACT-TCGCGTTGCGAATTTGACATATCGCG
* * *
92084 TTGTGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCG
1 TTGCGAATTTGACTTC-GCGTTGCGAATTTGACATA-TCGCG
* * *
92124 TTGCG-ATTT-ACAGATTCGCGTTGCGAATTTGA-AAATTGGG
1 TTGCGAATTTGAC---TTCGCGTTGCGAATTTGACATATCGCG
* * *
92164 TTGCGAAATTGGAGTTCGCGTTGTGAATTTG
1 TTGCG-AATTTGACTTCGCGTTGCGAATTTG
92195 TTGGTCATTT
Statistics
Matches: 255, Mismatches: 27, Indels: 58
0.75 0.08 0.17
Matches are distributed among these distances:
38 10 0.04
39 25 0.10
40 179 0.70
41 32 0.13
42 8 0.03
43 1 0.00
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (40 bp):
TTGCGAATTTGACTTCGCGTTGCGAATTTGACATATCGCG
Found at i:92155 original size:60 final size:60
Alignment explanation
Indices: 91844--92129 Score: 379
Period size: 60 Copynumber: 4.8 Consensus size: 60
91834 TAAACGCGCT
* * *
91844 TTGCGAATTTGACTT-TCGCGTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTAT-GTGTTGCG-ATTT-ACAAATTCGCGTTGCGAATTTGACTTCAGTG
* *
91904 CTGTGAATTTGACTTATGTGTTGCGATTTACAAATTCGCGTTGCGAATTTGACTTCAGTG
1 TTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGCGTTGCGAATTTGACTTCAGTG
91964 TTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGCGTTGCGAATTTGACTTCAGTG
1 TTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGCGTTGCGAATTTGACTTCAGTG
* *
92024 TTGCGAATTTGAC-TATCGCGTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGACTT-ATGTG
1 TTGCGAATTTGACTTAT-GTGTTGCG-ATTT-ACAAATTCGCGTTGCGAATTTGACTTCA-GTG
* *
92084 TTGTGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGA
1 TTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGCGTTGCGA
92130 TTTACAGATT
Statistics
Matches: 203, Mismatches: 13, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
58 4 0.02
59 14 0.07
60 175 0.86
61 8 0.04
62 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (60 bp):
TTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGCGTTGCGAATTTGACTTCAGTG
Found at i:92604 original size:14 final size:14
Alignment explanation
Indices: 92585--92611 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
92575 AGGATTAAAA
92585 TTAAATAATAATTT
1 TTAAATAATAATTT
92599 TTAAATAATAATT
1 TTAAATAATAATT
92612 CAAATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAAATAATAATTT
Found at i:99034 original size:63 final size:62
Alignment explanation
Indices: 98947--99067 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 62
98937 TACATTTTTT
* *
98947 TCTTCTTCTAGGTAGAATTATTTAAGAAAAATTATGAATACATATTTAAAAATAGAAAAAAAA
1 TCTTCTTCTAGATAAAATTATTTAAGAAAAA-TATGAATACATATTTAAAAATAGAAAAAAAA
* * ** *
99010 TCTTCTTCTAGATAAAATTGTTTAAGAAATATATGGGTACATATTTAAAAATATAAAA
1 TCTTCTTCTAGATAAAATTATTTAAGAAAAATATGAATACATATTTAAAAATAGAAAA
99068 GGCAAGGCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
62 24 0.47
63 27 0.53
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (62 bp):
TCTTCTTCTAGATAAAATTATTTAAGAAAAATATGAATACATATTTAAAAATAGAAAAAAAA
Found at i:102930 original size:18 final size:19
Alignment explanation
Indices: 102891--102931 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
102881 AGTCATTCAA
102891 GTAGTATCGATACCTAAAGG
1 GTAGTATCGATACC-AAAGG
102911 GTAGTATCGATACC-AAGG
1 GTAGTATCGATACCAAAGG
102929 GTA
1 GTA
102932 CTGATAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (19 bp):
GTAGTATCGATACCAAAGG
Found at i:103815 original size:21 final size:21
Alignment explanation
Indices: 103687--103844 Score: 111
Period size: 21 Copynumber: 7.4 Consensus size: 21
103677 GGGTTCTATA
*
103687 TGGTCCTCCGGGACATATATG
1 TGGTCCTTCGGGACATATATG
** * *
103708 TAATCCTTTGGAACATATATG
1 TGGTCCTTCGGGACATATATG
* * * *
103729 CGGTTCTTCGGGACACATTATT
1 TGGTCCTTCGGGACATA-TATG
* * * *
103751 TGGTCCTTTGGAATATATAAG
1 TGGTCCTTCGGGACATATATG
* *
103772 TGGTCATTAAGGAGA-ATTATATG
1 TGGTCCTT-CGG-GACA-TATATG
*
103795 TGGTCCTTCGGGATATATATG
1 TGGTCCTTCGGGACATATATG
*
103816 TGGTCCTTCAGGACATATATG
1 TGGTCCTTCGGGACATATATG
*
103837 AGGTCCTT
1 TGGTCCTT
103845 AGAGACAATT
Statistics
Matches: 102, Mismatches: 30, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
21 69 0.68
22 20 0.20
23 13 0.13
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TGGTCCTTCGGGACATATATG
Found at i:103836 original size:42 final size:42
Alignment explanation
Indices: 103687--103844 Score: 136
Period size: 44 Copynumber: 3.7 Consensus size: 42
103677 GGGTTCTATA
* * ** *
103687 TGGTCCTCCGGGACATATATGTAATCCTTTGGAACATATATG
1 TGGTCCTTCAGGACATATATGTGGTCCTTTGGAATATATATG
* * * * * *
103729 CGGTTCTTCGGGACACATTATTTGGTCCTTTGGAATATATAAG
1 TGGTCCTTCAGGACATA-TATGTGGTCCTTTGGAATATATATG
* * * * *
103772 TGGTCATTAAGGAGAATTATATGTGGTCCTTCGGGATATATATG
1 TGGTCCTTCAGGA-CA-TATATGTGGTCCTTTGGAATATATATG
*
103816 TGGTCCTTCAGGACATATATGAGGTCCTT
1 TGGTCCTTCAGGACATATATGTGGTCCTT
103845 AGAGACAATT
Statistics
Matches: 89, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
42 26 0.29
43 29 0.33
44 33 0.37
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (42 bp):
TGGTCCTTCAGGACATATATGTGGTCCTTTGGAATATATATG
Found at i:105623 original size:19 final size:19
Alignment explanation
Indices: 105593--105635 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
105583 CGTATAAAAG
105593 TATTTTATATAA-TTACTT
1 TATTTTATATAATTTACTT
*
105611 TATTTTAATATAATTTATTT
1 TATTTT-ATATAATTTACTT
105631 TATTT
1 TATTT
105636 AAAATTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 6 0.27
20 10 0.45
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTATATAATTTACTT
Found at i:105636 original size:19 final size:18
Alignment explanation
Indices: 105593--105637 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
105583 CGTATAAAAG
*
105593 TATTTTATATAATTACTT
1 TATTTAATATAATTACTT
*
105611 TATTTTAATATAATTTATTT
1 TA-TTTAATATAA-TTACTT
105631 TATTTAA
1 TATTTAA
105638 AATTATTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.61
20 7 0.30
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTAATATAATTACTT
Found at i:111881 original size:25 final size:25
Alignment explanation
Indices: 111852--111901 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
111842 AATTGAATCA
* *
111852 AAATTAAAGTTTTATATATACAATT
1 AAATTAAAATTTCATATATACAATT
*
111877 AAATTAAAATTTCATATATATAATT
1 AAATTAAAATTTCATATATACAATT
111902 CCACCAAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AAATTAAAATTTCATATATACAATT
Found at i:113104 original size:3 final size:3
Alignment explanation
Indices: 113096--113124 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
113086 AGATTCTCTC
113096 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
113125 CATACAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:116378 original size:17 final size:18
Alignment explanation
Indices: 116352--116387 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
116342 TATAAATTAT
*
116352 ATAATTTTTTAA-TTAAA
1 ATAATATTTTAAGTTAAA
116369 ATAATATTTTAAGTTAAA
1 ATAATATTTTAAGTTAAA
116387 A
1 A
116388 ATCATTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATAATATTTTAAGTTAAA
Found at i:125302 original size:4 final size:4
Alignment explanation
Indices: 125260--125450 Score: 307
Period size: 4 Copynumber: 48.2 Consensus size: 4
125250 CCTTACGTAC
* * *
125260 GTAT GTAC GTAT GTAC GTAT GTAC GTAT GTACT -TAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA-T GTAT GTAT GTAT GTAT
125308 GTAT GTAT GTA- GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
125355 GTAT GTAT GTAT GTA- GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
125402 GTAC GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT ATAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
125450 G
1 G
125451 AATTTGTTGC
Statistics
Matches: 173, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
3 7 0.04
4 165 0.95
5 1 0.01
ACGTcount: A:0.26, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:130080 original size:2 final size:2
Alignment explanation
Indices: 130073--130098 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
130063 CAAATGTGTC
130073 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
130099 CTGTAATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:131750 original size:186 final size:185
Alignment explanation
Indices: 131371--131783 Score: 592
Period size: 186 Copynumber: 2.2 Consensus size: 185
131361 CTTATTTATA
* *
131371 TATTGAATAAAAAT-A-TTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGG--TCGAATACATATATTCGGGTCGGG
* * *
131434 TCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCGAATATATATATTTTACCTTATATT
64 TCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATATAAATTTTACCTTATATT
*
131499 TAGGAATAATTATAATATATCCCTCTATATATAATTTTTTCAATTAAGTCACTATTT
129 TAGGAATAATTACAATATATCCCTCTATATATAATTTTTTCAATTAAGTCACTATTT
**
131556 TATTGAATAAAAATAATTTTTTTATTATTTC-GGTCGGGT-GAA-AC-TATATT-TTGTCGGGTC
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGAATACATATATTCGGGTCGGGTC
131616 GAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAAATATAAATTTTACCTTATATAT
66 GAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCC-AAAAATATAAATTTTACC-T-TATAT
*
131681 TTAGGAATAA-TACAATA-ATACCTCTCTATATATAATTTTTTTTTCAATTAAGTCATTATTT
128 TTAGGAATAATTACAATATAT-CC-CTCTATATATAA---TTTTTTCAATTAAGTCACTATTT
131742 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCG
131784 GGTTTCTAAT
Statistics
Matches: 207, Mismatches: 9, Indels: 21
0.87 0.04 0.09
Matches are distributed among these distances:
180 46 0.22
181 23 0.11
182 10 0.05
183 29 0.14
184 1 0.00
185 14 0.07
186 61 0.29
187 22 0.11
188 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.41
Consensus pattern (185 bp):
TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGAATACATATATTCGGGTCGGGTC
GAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATATAAATTTTACCTTATATTTA
GGAATAATTACAATATATCCCTCTATATATAATTTTTTCAATTAAGTCACTATTT
Found at i:134293 original size:7 final size:6
Alignment explanation
Indices: 134247--134298 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
134237 TACAAAACAC
* * *
134247 AAATAA AAATAG AAATAG AAATAA AAATTAA AATTAAA AACATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAA-TAA AAAT-AA AA-ATAA AAATAA
134298 A
1 A
134299 TAAAGTAGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 25 0.64
7 13 0.33
8 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:134379 original size:11 final size:11
Alignment explanation
Indices: 134352--134386 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
134342 CATCAAGAAT
134352 ATAAAAAATGAA
1 ATAAAAAAT-AA
134364 ATAAAAAATAA
1 ATAAAAAATAA
*
134375 GTAAAAAATAA
1 ATAAAAAATAA
134386 A
1 A
134387 AGAGAAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (11 bp):
ATAAAAAATAA
Done.