Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 129 of 136
Found at i:44394992 original size:18 final size:18
Alignment explanation
Indices: 44394934--44395003 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
44394924 TTCAAAATTG
*
44394934 AAATCAAAATCGAAATCA
1 AAATTAAAATCGAAATCA
* *
44394952 AAATCAAAATCAAAATCA
1 AAATTAAAATCGAAATCA
* *
44394970 AAATTAGAATCGAAATTA
1 AAATTAAAATCGAAATCA
* *
44394988 AAATTGAAATTGAAAT
1 AAATTAAAATCGAAAT
44395004 AACCCTAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATTAAAATCGAAATCA
Found at i:44394998 original size:12 final size:12
Alignment explanation
Indices: 44394925--44394997 Score: 83
Period size: 12 Copynumber: 6.1 Consensus size: 12
44394915 AGTGAGTGTT
*
44394925 TCAAAATTGAAA
1 TCAAAATCGAAA
44394937 TCAAAATCGAAA
1 TCAAAATCGAAA
*
44394949 TCAAAATCAAAA
1 TCAAAATCGAAA
*
44394961 TCAAAATCAAAA
1 TCAAAATCGAAA
* *
44394973 TTAGAATCGAAA
1 TCAAAATCGAAA
* *
44394985 TTAAAATTGAAA
1 TCAAAATCGAAA
44394997 T
1 T
44394998 TGAAATAACC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 54 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.23
Consensus pattern (12 bp):
TCAAAATCGAAA
Found at i:44395471 original size:21 final size:21
Alignment explanation
Indices: 44395447--44395486 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
44395437 AACGTGGCAA
44395447 GTTAACTTGCCACATCAGCTG
1 GTTAACTTGCCACATCAGCTG
*
44395468 GTTAACTTGCCACGTCAGC
1 GTTAACTTGCCACATCAGC
44395487 GATCCTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (21 bp):
GTTAACTTGCCACATCAGCTG
Found at i:44395760 original size:30 final size:31
Alignment explanation
Indices: 44395726--44395811 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 31
44395716 GTTTTTTTTT
* *
44395726 AAGTTATAATTT-GGTCACTAAATTATTCAA
1 AAGTTATAATTTAAGTCACTAAACTATTCAA
* *
44395756 AAGTTTTCATTTAAGTCACTAAACTATTTGC-A
1 AAGTTATAATTTAAGTCACTAAACTA-TT-CAA
* *
44395788 AA-TTTTCATTTAAGTCACTAAACT
1 AAGTTATAATTTAAGTCACTAAACT
44395812 GTTATTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 10 0.20
31 33 0.67
32 5 0.10
33 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (31 bp):
AAGTTATAATTTAAGTCACTAAACTATTCAA
Found at i:44395818 original size:26 final size:28
Alignment explanation
Indices: 44395759--44395820 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 28
44395749 TATTCAAAAG
*
44395759 TTTTCATTTAAGTCACTAAACTATTTGCAAA
1 TTTTCATTTAAGTCACTAAACTAGTT---AA
*
44395790 TTTTCATTTAAGTCACTAAACT-GTTAT
1 TTTTCATTTAAGTCACTAAACTAGTTAA
44395817 TTTT
1 TTTT
44395821 TTAAAGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
30 2 0.07
31 22 0.76
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (28 bp):
TTTTCATTTAAGTCACTAAACTAGTTAA
Found at i:44395831 original size:36 final size:31
Alignment explanation
Indices: 44395739--44395811 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
44395729 TTATAATTTG
*
44395739 GTCACTAAATTA-TT-CAAAAGTTTTCATTTAA
1 GTCACTAAACTATTTGC-AAAG-TTTCATTTAA
*
44395770 GTCACTAAACTATTTGCAAATTTTCATTTAA
1 GTCACTAAACTATTTGCAAAGTTTCATTTAA
44395801 GTCACTAAACT
1 GTCACTAAACT
44395812 GTTATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 32 0.84
32 5 0.13
33 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (31 bp):
GTCACTAAACTATTTGCAAAGTTTCATTTAA
Found at i:44425319 original size:2 final size:2
Alignment explanation
Indices: 44425312--44425352 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
44425302 TTAACACTGC
* * *
44425312 AT AT AT AT AT AT AT AT AT AT TT AT AT AT GT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44425353 GTTATGGTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44426156 original size:4 final size:4
Alignment explanation
Indices: 44426147--44426190 Score: 72
Period size: 4 Copynumber: 11.0 Consensus size: 4
44426137 AACCAAAGGT
44426147 ATAC ATAC ATAC ATAC ATAC ATAC AGT-C ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC A-TAC ATAC ATAC ATAC ATAC
44426191 TTTCTGATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 1 0.03
4 36 0.95
5 1 0.03
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:44433469 original size:19 final size:18
Alignment explanation
Indices: 44433445--44433482 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
44433435 AAAAGTTGAG
44433445 AAAAATTATAAGTAAAAAT
1 AAAAATTAT-AGTAAAAAT
*
44433464 AAAAATTATATTAAAAAT
1 AAAAATTATAGTAAAAAT
44433482 A
1 A
44433483 TATTTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAATTATAGTAAAAAT
Found at i:44448237 original size:26 final size:26
Alignment explanation
Indices: 44448208--44448257 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
44448198 AAACCGATTA
44448208 AGATTAATTACAATAAATTAAATCCT
1 AGATTAATTACAATAAATTAAATCCT
* * *
44448234 AGATTGATTATAGTAAATTAAATC
1 AGATTAATTACAATAAATTAAATC
44448258 TGGTTGTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (26 bp):
AGATTAATTACAATAAATTAAATCCT
Found at i:44449222 original size:27 final size:28
Alignment explanation
Indices: 44449170--44449222 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
44449160 TTTATAAGTG
*
44449170 AAAGAAAATACATGCACTATGATGGTGA
1 AAAGAAAATACATGCACAATGATGGTGA
44449198 AAAGAAAATACATGCACAATG-TGGT
1 AAAGAAAATACATGCACAATGATGGT
44449223 CAATGACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (28 bp):
AAAGAAAATACATGCACAATGATGGTGA
Found at i:44452993 original size:3 final size:3
Alignment explanation
Indices: 44452985--44453011 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44452975 TCACTTTAAT
44452985 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
44453012 CTGACCCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:44457095 original size:31 final size:31
Alignment explanation
Indices: 44457060--44457124 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
44457050 TGAGTACTTC
44457060 TCTACAAGTTGAAATGGATGTTCCTATATTG
1 TCTACAAGTTGAAATGGATGTTCCTATATTG
44457091 TCTACAAGTTGAAATGGATGTTCCTATATTG
1 TCTACAAGTTGAAATGGATGTTCCTATATTG
44457122 TCT
1 TCT
44457125 TGAACTGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (31 bp):
TCTACAAGTTGAAATGGATGTTCCTATATTG
Found at i:44464063 original size:21 final size:23
Alignment explanation
Indices: 44464039--44464082 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
44464029 AAATACTTTT
*
44464039 TAAATTTTT-TTATTT-TTAAAA
1 TAAATTTTTGGTATTTATTAAAA
44464060 TAAATTTTTGGTATTTATTAAAA
1 TAAATTTTTGGTATTTATTAAAA
44464083 AATGGGTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 5 0.25
23 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (23 bp):
TAAATTTTTGGTATTTATTAAAA
Found at i:44464068 original size:22 final size:22
Alignment explanation
Indices: 44464039--44464082 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
44464029 AAATACTTTT
**
44464039 TAAATTTTTTTATTT-TTAAAA
1 TAAATTTTGGTATTTATTAAAA
44464060 TAAATTTTTGGTATTTATTAAAA
1 TAAA-TTTTGGTATTTATTAAAA
44464083 AATGGGTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TAAATTTTGGTATTTATTAAAA
Found at i:44465645 original size:5 final size:5
Alignment explanation
Indices: 44465635--44465660 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
44465625 TGAGCATTCG
44465635 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
44465661 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:44469347 original size:18 final size:18
Alignment explanation
Indices: 44469320--44469355 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
44469310 ATCAAAGTTT
* *
44469320 TATTTTAATGTTTTTATA
1 TATTTCAATGTTGTTATA
44469338 TATTTCAATGTTGTTATA
1 TATTTCAATGTTGTTATA
44469356 CATATTGTTT
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:0.28, C:0.03, G:0.08, T:0.61
Consensus pattern (18 bp):
TATTTCAATGTTGTTATA
Found at i:44475993 original size:3 final size:3
Alignment explanation
Indices: 44475985--44476025 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
44475975 AAGTAGGTGC
44475985 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
44476026 GCATATTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:44476159 original size:32 final size:32
Alignment explanation
Indices: 44476099--44476161 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
44476089 ATTAATCAGT
* *
44476099 ATGAATTATAAAATTAAATTAATTAATTTATC
1 ATGAATTATAAAATTAAAGTAATCAATTTATC
* * *
44476131 ATGAGTTATTAAATTCAAGTAATCAATTTAT
1 ATGAATTATAAAATTAAAGTAATCAATTTAT
44476162 AAATTTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (32 bp):
ATGAATTATAAAATTAAAGTAATCAATTTATC
Found at i:44477026 original size:102 final size:101
Alignment explanation
Indices: 44476888--44477084 Score: 288
Period size: 102 Copynumber: 1.9 Consensus size: 101
44476878 AAAATTAATG
* *
44476888 AAAAATATTATTGAAAATAGAATCTTATTTATATTTTATATTCAAGTTTTAATAATATGGATAAT
1 AAAAATATTATTGAAAATAGAATCTTATTTATATTTTATATTCAAATTGTAATAATATGGATAAT
* *
44476953 TTATATTTCATTAGTTATTAAAATTAAATTTTAAAA
66 TGATATTTCATTAATTATTAAAATTAAATTTTAAAA
* * * *
44476989 AAAAATATTATTGAATAATAGAGTTTTATTTGA-ATTTTGTATTCAAATTGTAATAATATTGATA
1 AAAAATATTATTGAA-AATAGAATCTTATTT-ATATTTTATATTCAAATTGTAATAATATGGATA
*
44477053 ATTGATATTTCGTTAATTATTAAAATTAAATT
64 ATTGATATTTCATTAATTATTAAAATTAAATT
44477085 CATATTAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 15 0.18
102 69 0.81
103 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (101 bp):
AAAAATATTATTGAAAATAGAATCTTATTTATATTTTATATTCAAATTGTAATAATATGGATAAT
TGATATTTCATTAATTATTAAAATTAAATTTTAAAA
Found at i:44479229 original size:16 final size:16
Alignment explanation
Indices: 44479208--44479240 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
44479198 TTATATTATT
*
44479208 TTATTTAATTTTAAAA
1 TTATTTAATATTAAAA
44479224 TTATTTAATATTAAAA
1 TTATTTAATATTAAAA
44479240 T
1 T
44479241 AATATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTTAATATTAAAA
Found at i:44491475 original size:2 final size:2
Alignment explanation
Indices: 44491468--44491503 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
44491458 GGTGGGCTGC
*
44491468 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44491504 ACTAGTTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44498570 original size:20 final size:20
Alignment explanation
Indices: 44498545--44498583 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44498535 TAGTACAAAA
44498545 TTTTAATATTTTAAATTAAT
1 TTTTAATATTTTAAATTAAT
* *
44498565 TTTTAATTTTTTATATTAA
1 TTTTAATATTTTAAATTAA
44498584 AAACTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAATATTTTAAATTAAT
Found at i:44507694 original size:158 final size:156
Alignment explanation
Indices: 44507401--44507699 Score: 411
Period size: 158 Copynumber: 1.9 Consensus size: 156
44507391 CAACCGTGGC
* * *
44507401 ACTCTAGCAGAACTAGAAAAACGAGCCCGTACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCG
1 ACTCCAGCAGAACTAGAAAAACAAGCCCATACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCG
* *
44507466 CAATGGAGACCGAGTACGAGACTGCCTTGTTGACCCTCTCTGCATAAGCAAAGAATAATGTTACA
66 CAATGAAGACCGAGTACGAGACTGCCGTGTTGACCCTCTCTGCATAAGCAAAGAATAA--TTACA
44507531 GGAGGAACTTAAATTCTAAAGGAAAGGG
129 GGAGGAACTTAAATTCTAAAGGAAAGGG
* * *
44507559 ACTCCAGCAGAAGTAGGAGAACAAGCCCATACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCG
1 ACTCCAGCAGAACTAGAAAAACAAGCCCATACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCG
* * * * **
44507624 CACTGAAGACTGAGTACGGGATTGCCGTGTTGGGCCTCTCTGCATTAGAAGCAAAGAATAA-TAC
66 CAATGAAGACCGAGTACGAGACTGCCGTGTTGACCCTCTCTGCA-T--AAGCAAAGAATAATTAC
*
44507688 ATGAGGAACTTA
128 AGGAGGAACTTA
44507700 TACAAATTCA
Statistics
Matches: 123, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
158 109 0.89
159 1 0.01
161 13 0.11
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (156 bp):
ACTCCAGCAGAACTAGAAAAACAAGCCCATACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCG
CAATGAAGACCGAGTACGAGACTGCCGTGTTGACCCTCTCTGCATAAGCAAAGAATAATTACAGG
AGGAACTTAAATTCTAAAGGAAAGGG
Found at i:44512338 original size:13 final size:13
Alignment explanation
Indices: 44512320--44512345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44512310 TCACCCATGT
44512320 GACGTTTATTATA
1 GACGTTTATTATA
44512333 GACGTTTATTATA
1 GACGTTTATTATA
44512346 AACTGAATAA
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:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GACGTTTATTATA
Found at i:44540216 original size:15 final size:15
Alignment explanation
Indices: 44540196--44540229 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
44540186 CATGTTTATT
44540196 TTTTTTAA-ATATTTA
1 TTTTTTAATAT-TTTA
44540211 TTTTTTAATATTTTA
1 TTTTTTAATATTTTA
44540226 TTTT
1 TTTT
44540230 ACCCTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTAATATTTTA
Found at i:44540220 original size:14 final size:14
Alignment explanation
Indices: 44540192--44540229 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
44540182 TTGTCATGTT
44540192 TATTT-TTTTTAAA
1 TATTTATTTTTAAA
*
44540205 TATTTATTTTTTAA
1 TATTTATTTTTAAA
44540219 TATTTTATTTT
1 TA-TTTATTTT
44540230 ACCCTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.23
14 9 0.41
15 8 0.36
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTATTTTTAAA
Found at i:44541445 original size:20 final size:20
Alignment explanation
Indices: 44541399--44541438 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
44541389 TGTTTTTGAA
*
44541399 TTTTTATGAACTTTTTAATT
1 TTTTTTTGAACTTTTTAATT
44541419 TTTTTTTGAA-TTTTT-ATT
1 TTTTTTTGAACTTTTTAATT
44541437 TT
1 TT
44541439 AATTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 5 0.26
20 9 0.47
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTTTGAACTTTTTAATT
Found at i:44541446 original size:12 final size:12
Alignment explanation
Indices: 44541411--44541446 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
44541401 TTTATGAACT
44541411 TTTTAATTTTT-
1 TTTTAATTTTTA
44541422 TTTTGAATTTTTA
1 TTTT-AATTTTTA
44541435 TTTTAATTTTTA
1 TTTTAATTTTTA
44541447 AAATATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.17
12 15 0.65
13 4 0.17
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTAATTTTTA
Found at i:44546293 original size:25 final size:25
Alignment explanation
Indices: 44546244--44546293 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
44546234 TTGGCTATAA
* *
44546244 TGTCCAATTTGGTACTTGAATTTTG
1 TGTCCAATTTGGTACCTGAAGTTTG
44546269 TGTCTCAATTTGGTACCTG-AGTTTG
1 TGTC-CAATTTGGTACCTGAAGTTTG
44546294 GATTCATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.46
Consensus pattern (25 bp):
TGTCCAATTTGGTACCTGAAGTTTG
Found at i:44553996 original size:58 final size:58
Alignment explanation
Indices: 44553903--44554095 Score: 235
Period size: 58 Copynumber: 3.2 Consensus size: 58
44553893 ACTTCTGATC
* * * * *
44553903 AGTGACAAGTGATAAGTGGTAGTTTTAGTTGCACTTATCTGATCAGTGACAAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATATGATCAGTGACAAGTGACA
*
44553961 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGATCAGTGACAAGTGGCAAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATATGATCAGTG---A----CAAGTGACA
* *
44554026 AGTGATAAGTGATAAGTGGTAGC-TTAGCTACACTTATATGATCAGTGACAAGAGATA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATATGATCAGTGACAAGTGACA
*
44554083 AATGATAAGTGAT
1 AGTGATAAGTGAT
44554096 TCCATGTAAG
Statistics
Matches: 119, Mismatches: 9, Indels: 15
0.83 0.06 0.10
Matches are distributed among these distances:
57 19 0.16
58 43 0.36
61 2 0.02
64 23 0.19
65 32 0.27
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (58 bp):
AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATATGATCAGTGACAAGTGACA
Found at i:44554020 original size:7 final size:7
Alignment explanation
Indices: 44554005--44554043 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
44553995 TTATTTGATC
44554005 AGTGACA
1 AGTGACA
*
44554012 AGTGGCA
1 AGTGACA
44554019 AGTGACA
1 AGTGACA
*
44554026 AGTGATA
1 AGTGACA
*
44554033 AGTGATA
1 AGTGACA
44554040 AGTG
1 AGTG
44554044 GTAGCTTAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (7 bp):
AGTGACA
Found at i:44554028 original size:65 final size:64
Alignment explanation
Indices: 44553947--44554095 Score: 235
Period size: 64 Copynumber: 2.3 Consensus size: 64
44553937 TTATCTGATC
*
44553947 AGTGACAAGTGACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGATCAGTGACA
1 AGTGACAAGTGACAAGTGATAAGTGATAAGTGGTAGC-TTAGCTACACTTATATGATCAGTGACA
*
44554012 AGTGGCAAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATATGATCAGTGACA
1 AGTGACAAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATATGATCAGTGACA
* * * *
44554076 AGAGATAAATGATAAGTGAT
1 AGTGACAAGTGACAAGTGAT
44554096 TCCATGTAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 41 0.53
65 36 0.47
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.28
Consensus pattern (64 bp):
AGTGACAAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATATGATCAGTGACA
Found at i:44556639 original size:3 final size:3
Alignment explanation
Indices: 44556627--44556663 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
44556617 AGTCCCTCTA
44556627 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
44556664 GTTAATTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:44560181 original size:14 final size:14
Alignment explanation
Indices: 44560164--44560198 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
44560154 ATAAAATATA
*
44560164 AATTTATATTTAAT
1 AATTCATATTTAAT
*
44560178 AATTCATTTTTAAT
1 AATTCATATTTAAT
44560192 AATTCAT
1 AATTCAT
44560199 TAATTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTCATATTTAAT
Found at i:44560199 original size:14 final size:14
Alignment explanation
Indices: 44560172--44560199 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
44560162 TAAATTTATA
44560172 TTTAATAATTCATT
1 TTTAATAATTCATT
44560186 TTTAATAATTCATT
1 TTTAATAATTCATT
44560200 AATTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:44566427 original size:6 final size:6
Alignment explanation
Indices: 44566416--44566448 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
44566406 TTAAGGATAT
44566416 ATATAC ATATAC ATATAC ATATAC ATATAC ATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATA
44566449 GGTTGATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:44569589 original size:21 final size:21
Alignment explanation
Indices: 44569563--44569603 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44569553 TAGCAAGATT
44569563 GCTGATGTGGCAAGTTAACTA
1 GCTGATGTGGCAAGTTAACTA
* *
44569584 GCTGATGTTGCCAGTTAACT
1 GCTGATGTGGCAAGTTAACT
44569604 TGCCACATTG
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:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (21 bp):
GCTGATGTGGCAAGTTAACTA
Found at i:44570564 original size:49 final size:49
Alignment explanation
Indices: 44570511--44570604 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
44570501 CCTAATTGAT
*
44570511 ATTTCCTCCATAAAAACCCAAAGATTTATGAAAGGGGAAATTGAAATTG
1 ATTTCCTCCATAAAAACCCAAAGATTTATGAAAAGGGAAATTGAAATTG
*
44570560 ATTTCCTCCATGAAAACCCAAAGATTTATGAAAAGGGAAATTGAA
1 ATTTCCTCCATAAAAACCCAAAGATTTATGAAAAGGGAAATTGAA
44570605 GTTTAATAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.26
Consensus pattern (49 bp):
ATTTCCTCCATAAAAACCCAAAGATTTATGAAAAGGGAAATTGAAATTG
Found at i:44572912 original size:6 final size:6
Alignment explanation
Indices: 44572901--44572933 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
44572891 TTAAGGATAT
44572901 ATATAC ATATAC ATATAC ATATAC ATATAC ATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATA
44572934 GGTTGATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:44576074 original size:21 final size:21
Alignment explanation
Indices: 44576048--44576088 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44576038 TAGCAAGATT
44576048 GCTGATGTGGCAAGTTAACTA
1 GCTGATGTGGCAAGTTAACTA
* *
44576069 GCTGATGTTGCCAGTTAACT
1 GCTGATGTGGCAAGTTAACT
44576089 TGCCACATTG
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:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (21 bp):
GCTGATGTGGCAAGTTAACTA
Found at i:44577049 original size:49 final size:49
Alignment explanation
Indices: 44576996--44577089 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
44576986 CCTAATTGAT
*
44576996 ATTTCCTCCATAAAAACCCAAAGATTTATGAAAGGGGAAATTGAAATTG
1 ATTTCCTCCATAAAAACCCAAAGATTTATGAAAAGGGAAATTGAAATTG
*
44577045 ATTTCCTCCATGAAAACCCAAAGATTTATGAAAAGGGAAATTGAA
1 ATTTCCTCCATAAAAACCCAAAGATTTATGAAAAGGGAAATTGAA
44577090 GTTTAATAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.26
Consensus pattern (49 bp):
ATTTCCTCCATAAAAACCCAAAGATTTATGAAAAGGGAAATTGAAATTG
Found at i:44587780 original size:93 final size:93
Alignment explanation
Indices: 44587676--44587862 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
44587666 AGCATATTAA
44587676 TTATCACTTAATTAATATTAGGGTTAATTAGGTTAATTAGTTATTATTTTGAATAATGTTACTTT
1 TTATCACTTAATTAATATTAGGGTTAATTAGGTTAATTAGTTATTATTTTGAATAATGTTACTTT
44587741 ACATTAATTTCATAAAATAAAACTATAT
66 ACATTAATTTCATAAAATAAAACTATAT
44587769 TTATCACTTAATTAATATTAGGGTTAATTAGGTTAATTAGTTATTATTTTGAATAATGTTACTTT
1 TTATCACTTAATTAATATTAGGGTTAATTAGGTTAATTAGTTATTATTTTGAATAATGTTACTTT
44587834 ACATTAATTTCATAAAATAAAACTATAT
66 ACATTAATTTCATAAAATAAAACTATAT
44587862 T
1 T
44587863 GTATGTCCAA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.47
Consensus pattern (93 bp):
TTATCACTTAATTAATATTAGGGTTAATTAGGTTAATTAGTTATTATTTTGAATAATGTTACTTT
ACATTAATTTCATAAAATAAAACTATAT
Found at i:44589070 original size:23 final size:23
Alignment explanation
Indices: 44589043--44589093 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
44589033 GGTTAATTAT
* *
44589043 TGTAATATCCCTAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
44589066 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
44589089 AGTAA
1 TGTAA
44589094 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:44594637 original size:18 final size:18
Alignment explanation
Indices: 44594592--44594638 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
44594582 CCATGTGGAC
* *
44594592 CGCCCGTCTAGGGGCACA
1 CGCCCGTATGGGGGCACA
44594610 CGCCCGTATGGGGGCACA
1 CGCCCGTATGGGGGCACA
*
44594628 TGCCCGTATGG
1 CGCCCGTATGG
44594639 TCACGAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.34, G:0.36, T:0.15
Consensus pattern (18 bp):
CGCCCGTATGGGGGCACA
Found at i:44596135 original size:21 final size:21
Alignment explanation
Indices: 44596109--44596258 Score: 104
Period size: 21 Copynumber: 7.1 Consensus size: 21
44596099 CCGAAGGCTG
*
44596109 AACAGAAGCTCATGAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
44596130 AACAGAAACCCGTAAGGGTTA
1 AACAGAAGCTCATAAGAGCTA
* * *
44596151 AACGGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
* * * *
44596172 AACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTA
* * *
44596193 AACAGAAGCTCAAAATAGCTG
1 AACAGAAGCTCATAAGAGCTA
* * * *
44596214 AACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTA
44596235 AACAGAAGCTCATGAA-AGCTA
1 AACAGAAGCTCAT-AAGAGCTA
44596256 AAC
1 AAC
44596259 GAAAAGTAAA
Statistics
Matches: 91, Mismatches: 37, Indels: 2
0.70 0.28 0.02
Matches are distributed among these distances:
21 90 0.99
22 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:44596160 original size:42 final size:42
Alignment explanation
Indices: 44596109--44596262 Score: 177
Period size: 42 Copynumber: 3.7 Consensus size: 42
44596099 CCGAAGGCTG
* *
44596109 AACAGAAGCTCATGAGAGCTAAACAGAAACCCGTAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
* * *
44596151 AACGGAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
* * * * * * *
44596193 AACAGAAGCTCAAAATAGCTGAACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
44596235 AACAGAAGCTCATGAA-AGCTAAAC-GAAA
1 AACAGAAGCTCAT-AAGAGCTAAACAGAAA
44596263 AGTAAACACG
Statistics
Matches: 96, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
41 4 0.04
42 90 0.94
43 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTA
Found at i:44600065 original size:56 final size:56
Alignment explanation
Indices: 44599998--44600110 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
44599988 AGGAATTGAG
* * *
44599998 CTACGGCCTAAAGATACTGGTAGCTAGGTAGACTTTGGATTAGGGTTTGGTAAGCT
1 CTACGGCCTAAAGATACTGGTAGCTAGGTAGACTCTAGATTAGGGTTTGATAAGCT
44600054 CTACGGCCTAAAGATACTGGTAGCTAGGTAGACTCTAGATTAGGGTTTGATAAGCT
1 CTACGGCCTAAAGATACTGGTAGCTAGGTAGACTCTAGATTAGGGTTTGATAAGCT
44600110 C
1 C
44600111 ACCTTATTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (56 bp):
CTACGGCCTAAAGATACTGGTAGCTAGGTAGACTCTAGATTAGGGTTTGATAAGCT
Found at i:44607539 original size:25 final size:25
Alignment explanation
Indices: 44607511--44607584 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
44607501 CGAGCATGTA
44607511 AACGGGAAGCTCTTTCGAGCCATAT
1 AACGGGAAGCTCTTTCGAGCCATAT
** * *
44607536 AACGAAAAGCTCATGT-GAGCTATAT
1 AACGGGAAGCTC-TTTCGAGCCATAT
* *
44607561 AACGGGAAGCTCATGCGAGCCATA
1 AACGGGAAGCTCTTTCGAGCCATA
44607585 AATTAGGAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
25 35 0.95
26 2 0.05
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (25 bp):
AACGGGAAGCTCTTTCGAGCCATAT
Found at i:44613410 original size:7 final size:7
Alignment explanation
Indices: 44613398--44613431 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
44613388 ATAATAAAAA
44613398 TATATTT
1 TATATTT
44613405 TATA-TT
1 TATATTT
*
44613411 GATATTT
1 TATATTT
44613418 TATATTT
1 TATATTT
44613425 TATATTT
1 TATATTT
44613432 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (7 bp):
TATATTT
Found at i:44613432 original size:13 final size:14
Alignment explanation
Indices: 44613398--44613431 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
44613388 ATAATAAAAA
44613398 TATATTTTATA-TT
1 TATATTTTATATTT
*
44613411 GATATTTTATATTT
1 TATATTTTATATTT
44613425 TATATTT
1 TATATTT
44613432 AATTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TATATTTTATATTT
Found at i:44616080 original size:22 final size:22
Alignment explanation
Indices: 44616049--44616115 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
44616039 TAAAATTAAC
*
44616049 AATAATAAATAGTAATAATAGT
1 AATAATAAATAGTAATAATAAT
* **
44616071 AATAAAAAATAACAATAATAAT
1 AATAATAAATAGTAATAATAAT
*
44616093 AATAATAAAT-GTAATGATAAT
1 AATAATAAATAGTAATAATAAT
44616114 AA
1 AA
44616116 CATTCAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
21 10 0.27
22 27 0.73
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.28
Consensus pattern (22 bp):
AATAATAAATAGTAATAATAAT
Found at i:44616087 original size:19 final size:19
Alignment explanation
Indices: 44616049--44616094 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
44616039 TAAAATTAAC
* * *
44616049 AATAATAAATAGTAATAAT
1 AATAATAAAAAATAACAAT
*
44616068 AGTAATAAAAAATAACAAT
1 AATAATAAAAAATAACAAT
44616087 AATAATAA
1 AATAATAA
44616095 TAATAAATGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
AATAATAAAAAATAACAAT
Found at i:44616115 original size:3 final size:3
Alignment explanation
Indices: 44616049--44616100 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
44616039 TAAAATTAAC
* * *
44616049 AAT AAT AAAT AGT AAT AAT AGT AAT AA- AA- AAT AAC AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
44616093 AAT AAT AA
1 AAT AAT AA
44616101 ATGTAATGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:44626804 original size:17 final size:17
Alignment explanation
Indices: 44626782--44626814 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44626772 AAGCATATAA
*
44626782 TAAAATTTTAAAAAATT
1 TAAAATATTAAAAAATT
44626799 TAAAATATTAAAAAAT
1 TAAAATATTAAAAAAT
44626815 ATTTTCATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATATTAAAAAATT
Found at i:44627437 original size:17 final size:19
Alignment explanation
Indices: 44627396--44627444 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
44627386 TTGCTACTGC
*
44627396 TTTGTTGTTATTGTATAAC
1 TTTGTTGTTATTGTATAAA
44627415 TCTTGTT-TTATTGT-TAAA
1 T-TTGTTGTTATTGTATAAA
*
44627433 TTTGTTGCTATT
1 TTTGTTGTTATT
44627445 TTAGAGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 5 0.19
18 8 0.31
19 8 0.31
20 5 0.19
ACGTcount: A:0.18, C:0.06, G:0.14, T:0.61
Consensus pattern (19 bp):
TTTGTTGTTATTGTATAAA
Found at i:44629299 original size:26 final size:26
Alignment explanation
Indices: 44629270--44629347 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 26
44629260 CAAATACAAT
44629270 AAATGAAAGAGAATAACATATATGTA
1 AAATGAAAGAGAATAACATATATGTA
** *
44629296 AAAT--AA-A-AA-CCCAAATATG-A
1 AAATGAAAGAGAATAACATATATGTA
* *
44629316 GGAAGGAAAGAGAATAACATATATGTA
1 -AAATGAAAGAGAATAACATATATGTA
44629343 AAATG
1 AAATG
44629348 GAGATATTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 14
0.59 0.17 0.24
Matches are distributed among these distances:
20 1 0.03
21 9 0.26
22 2 0.06
23 3 0.09
24 3 0.09
25 2 0.06
26 14 0.40
27 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.19
Consensus pattern (26 bp):
AAATGAAAGAGAATAACATATATGTA
Found at i:44630490 original size:27 final size:27
Alignment explanation
Indices: 44630456--44630515 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
44630446 AAAATAACCT
*
44630456 AAATATTATAACTTTTTTTATTTACCA
1 AAATATTATAAATTTTTTTATTTACCA
44630483 AAATATTATAAATTTTTTTATTTACCA
1 AAATATTATAAATTTTTTTATTTACCA
44630510 AAATAT
1 AAATAT
44630516 ACCAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (27 bp):
AAATATTATAAATTTTTTTATTTACCA
Found at i:44631180 original size:19 final size:19
Alignment explanation
Indices: 44631156--44631214 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
44631146 TCTAATTAAG
*
44631156 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTCATT
* *
44631175 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTCATT
44631193 TAATAACTCTATTTTCATT
1 TAATAACTCTATTTTCATT
44631212 TAA
1 TAA
44631215 AATATAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTCATT
Found at i:44631588 original size:30 final size:29
Alignment explanation
Indices: 44631552--44631608 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
44631542 TGGTTTTTGT
44631552 TTTTTTATATATATTTTAGTAAATAAAATC
1 TTTTTTATA-ATATTTTAGTAAATAAAATC
*
44631582 TTTTTTATAATATTTTGGTAAATAAAA
1 TTTTTTATAATATTTTAGTAAATAAAA
44631609 AAAATTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (29 bp):
TTTTTTATAATATTTTAGTAAATAAAATC
Found at i:44636425 original size:22 final size:22
Alignment explanation
Indices: 44636383--44636425 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
44636373 CACCCCAAAT
**
44636383 TTTGGGGTTAGAAGTTTTGAGC
1 TTTGGGGTTAGAAGTAGTGAGC
44636405 TTTGGGGTTA-AAGTCAGTGAG
1 TTTGGGGTTAGAAGT-AGTGAG
44636426 TAGGTTGTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.21, C:0.05, G:0.37, T:0.37
Consensus pattern (22 bp):
TTTGGGGTTAGAAGTAGTGAGC
Found at i:44636648 original size:21 final size:21
Alignment explanation
Indices: 44636624--44636677 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
44636614 TTTTTTATTA
*
44636624 TTTATTTTTCTTAATGTTTAT
1 TTTATTTTTCTTAATGGTTAT
**
44636645 TTTATTTTT-TATTTTGGTTAT
1 TTTATTTTTCT-TAATGGTTAT
44636666 TTTATTTTTCTT
1 TTTATTTTTCTT
44636678 CCTTGTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.76
Consensus pattern (21 bp):
TTTATTTTTCTTAATGGTTAT
Found at i:44637315 original size:19 final size:20
Alignment explanation
Indices: 44637291--44637330 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
44637281 TTTAAATAAA
44637291 TTTTATTAA-ATTTAT-AGTT
1 TTTTA-TAATATTTATAAGTT
44637310 TTTTATAATATTTATAAGTT
1 TTTTATAATATTTATAAGTT
44637330 T
1 T
44637331 ATATTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.16
19 11 0.58
20 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTATAATATTTATAAGTT
Found at i:44637342 original size:19 final size:17
Alignment explanation
Indices: 44637291--44637342 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 17
44637281 TTTAAATAAA
*
44637291 TTTTATTAAATTTATAG
1 TTTTATTAATTTTATAG
*
44637308 TTTTTTATAATATTTATAAG
1 TTTTAT-TAAT-TTTAT-AG
44637328 TTTATATTAATTTTA
1 TTT-TATTAATTTTA
44637343 ATATTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 5 0.18
18 3 0.11
19 9 0.32
20 9 0.32
21 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTTATTAATTTTATAG
Found at i:44641125 original size:40 final size:40
Alignment explanation
Indices: 44641070--44641152 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 40
44641060 TTTAAAAGAA
* * *
44641070 TTTTCAAGTTATCATTTAGATTTAATAATGTGATTTTCGT
1 TTTTCAAGGTATCATTTAGATTTAATAAAGTGATTTTCAT
* *
44641110 TTTTCAAGGTATCATTTGGATTTAATAAAGTTATTTTCAT
1 TTTTCAAGGTATCATTTAGATTTAATAAAGTGATTTTCAT
44641150 TTT
1 TTT
44641153 CTCTTTCTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (40 bp):
TTTTCAAGGTATCATTTAGATTTAATAAAGTGATTTTCAT
Found at i:44649956 original size:44 final size:44
Alignment explanation
Indices: 44649905--44650036 Score: 264
Period size: 44 Copynumber: 3.0 Consensus size: 44
44649895 TAGTTCAGTG
44649905 ACTAAATTGTAACTTTTCTTAGTTAAGTGATCAAAACGAAAACT
1 ACTAAATTGTAACTTTTCTTAGTTAAGTGATCAAAACGAAAACT
44649949 ACTAAATTGTAACTTTTCTTAGTTAAGTGATCAAAACGAAAACT
1 ACTAAATTGTAACTTTTCTTAGTTAAGTGATCAAAACGAAAACT
44649993 ACTAAATTGTAACTTTTCTTAGTTAAGTGATCAAAACGAAAACT
1 ACTAAATTGTAACTTTTCTTAGTTAAGTGATCAAAACGAAAACT
44650037 TACCCATAAT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 88 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (44 bp):
ACTAAATTGTAACTTTTCTTAGTTAAGTGATCAAAACGAAAACT
Found at i:44659234 original size:16 final size:16
Alignment explanation
Indices: 44659213--44659246 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44659203 CAAAATTTCA
* *
44659213 TCAATCTTTCCAATTT
1 TCAATCCTTCAAATTT
44659229 TCAATCCTTCAAATTT
1 TCAATCCTTCAAATTT
44659245 TC
1 TC
44659247 TTTAGACCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (16 bp):
TCAATCCTTCAAATTT
Found at i:44660127 original size:3 final size:3
Alignment explanation
Indices: 44660121--44660158 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
44660111 ATCATCATCA
44660121 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
44660159 CCCAACGTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:44676285 original size:15 final size:15
Alignment explanation
Indices: 44676236--44676286 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
44676226 TTTCCTCATA
*
44676236 TTACATTTTAGTCAC
1 TTACGTTTTAGTCAC
* *
44676251 TTATGTTTGAGAT-A-
1 TTACGTTTTAG-TCAC
44676265 TTACGTTTTAGTCAC
1 TTACGTTTTAGTCAC
44676280 TTACGTT
1 TTACGTT
44676287 ATCGTGTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 1 0.04
14 10 0.36
15 16 0.57
16 1 0.04
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (15 bp):
TTACGTTTTAGTCAC
Found at i:44678837 original size:7 final size:7
Alignment explanation
Indices: 44678821--44678850 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
44678811 TAACAATACC
44678821 TTTC-TT
1 TTTCTTT
44678827 TTTCTTT
1 TTTCTTT
44678834 TTTCTTT
1 TTTCTTT
44678841 TTTCTTT
1 TTTCTTT
44678848 TTT
1 TTT
44678851 TTTAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTCTTT
Found at i:44689309 original size:7 final size:7
Alignment explanation
Indices: 44689297--44689327 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
44689287 CATAAGAGAG
44689297 CTTGAGC
1 CTTGAGC
44689304 CTTGAGC
1 CTTGAGC
44689311 CTTGAGC
1 CTTGAGC
44689318 CTTGAGC
1 CTTGAGC
44689325 CTT
1 CTT
44689328 AAGCTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.29, G:0.26, T:0.32
Consensus pattern (7 bp):
CTTGAGC
Found at i:44690283 original size:25 final size:25
Alignment explanation
Indices: 44690238--44690287 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
44690228 GGGTAGAGTG
44690238 GAAAAGTGAAAGAATAGAAAGAAAA
1 GAAAAGTGAAAGAATAGAAAGAAAA
44690263 GAAAAGTAGAAA-AAT-GAAAAGAAAA
1 GAAAAGT-GAAAGAATAG-AAAGAAAA
44690288 TTAATTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 1 0.04
25 18 0.78
26 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.08
Consensus pattern (25 bp):
GAAAAGTGAAAGAATAGAAAGAAAA
Found at i:44690466 original size:7 final size:7
Alignment explanation
Indices: 44690454--44690478 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44690444 TTATATTTTT
44690454 TTTTAAA
1 TTTTAAA
44690461 TTTTAAA
1 TTTTAAA
44690468 TTTTAAA
1 TTTTAAA
44690475 TTTT
1 TTTT
44690479 TTCTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:44690897 original size:16 final size:16
Alignment explanation
Indices: 44690876--44690909 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
44690866 TTCCAACTTC
44690876 TTTTTGTTTATTAGGT
1 TTTTTGTTTATTAGGT
44690892 TTTTTGTTTATTAGGT
1 TTTTTGTTTATTAGGT
44690908 TT
1 TT
44690910 GATTGAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.71
Consensus pattern (16 bp):
TTTTTGTTTATTAGGT
Found at i:44693180 original size:36 final size:36
Alignment explanation
Indices: 44693133--44693204 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
44693123 TCTTTTTATC
44693133 TCCATGCGAGACACTGGTTACTTTGGCCATTTCATG
1 TCCATGCGAGACACTGGTTACTTTGGCCATTTCATG
44693169 TCCATGCGAGACACTGGTTACTTTGGCCATTTCATG
1 TCCATGCGAGACACTGGTTACTTTGGCCATTTCATG
44693205 AACTCAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.33
Consensus pattern (36 bp):
TCCATGCGAGACACTGGTTACTTTGGCCATTTCATG
Found at i:44724033 original size:25 final size:25
Alignment explanation
Indices: 44724001--44724049 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
44723991 TAGACAAATG
44724001 AAAAAAAT-ATATACAATATAATACT
1 AAAAAAATAATAT-CAATATAATACT
*
44724026 AAAAAAATAATATGAATATAATAC
1 AAAAAAATAATATCAATATAATAC
44724050 AACTAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAAAAATAATATCAATATAATACT
Found at i:44735157 original size:2 final size:2
Alignment explanation
Indices: 44735152--44735178 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44735142 GTGTGTGTGT
44735152 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
44735179 GAAGTGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:44737134 original size:36 final size:36
Alignment explanation
Indices: 44737087--44737158 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
44737077 TGAAATTGAG
44737087 TTAAATTTCAATCCTTTTAATAATGTGTAAGATTAC
1 TTAAATTTCAATCCTTTTAATAATGTGTAAGATTAC
44737123 TTAAATTTCAATCCTTTTAATAATGTGTAAGATTAC
1 TTAAATTTCAATCCTTTTAATAATGTGTAAGATTAC
44737159 CATTCATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (36 bp):
TTAAATTTCAATCCTTTTAATAATGTGTAAGATTAC
Found at i:44739287 original size:27 final size:27
Alignment explanation
Indices: 44739257--44739310 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
44739247 ATTTTTTCAT
44739257 GTTTATCATTTAAATTTAATTTAAATA
1 GTTTATCATTTAAATTTAATTTAAATA
44739284 GTTTATCATTTAAATTTAATTTAAATA
1 GTTTATCATTTAAATTTAATTTAAATA
44739311 CATATTTAAA
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:0.04, G:0.04, T:0.52
Consensus pattern (27 bp):
GTTTATCATTTAAATTTAATTTAAATA
Found at i:44741332 original size:50 final size:50
Alignment explanation
Indices: 44741250--44741349 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
44741240 TTAAACCCCT
*
44741250 CTTTTTTTTACACTCAATCGAGCACTTGAACTTTCAAAATGCATCAAAAA
1 CTTTTTTTTACACTCAATCGAGCACTTAAACTTTCAAAATGCATCAAAAA
* * *
44741300 CTTTTTTTTTCACTCAATTGAGTACTTAAACTTTCAAAATGCATCAAAAA
1 CTTTTTTTTACACTCAATCGAGCACTTAAACTTTCAAAATGCATCAAAAA
44741350 TACCCTCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (50 bp):
CTTTTTTTTACACTCAATCGAGCACTTAAACTTTCAAAATGCATCAAAAA
Found at i:44741478 original size:38 final size:36
Alignment explanation
Indices: 44741402--44741474 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 36
44741392 ATTAAAAATT
* *
44741402 ATAAAAAGATAAAAATTTAGAAAATTTATTAAATTTTA
1 ATAAAAATATAAAAATTT--AAAATATATTAAATTTTA
44741440 ATAAAAATATAAAAATTT-AAATATATTAGAATTTT
1 ATAAAAATATAAAAATTTAAAATATATTA-AATTTT
44741475 TTAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 9 0.28
36 6 0.19
38 17 0.53
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (36 bp):
ATAAAAATATAAAAATTTAAAATATATTAAATTTTA
Found at i:44741719 original size:18 final size:20
Alignment explanation
Indices: 44741698--44741737 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
44741688 CTTTATAAAA
44741698 TTTTAT-ATTTCTAT-ATAT
1 TTTTATAATTTCTATGATAT
*
44741716 TTTTATAATTTTTATGATAT
1 TTTTATAATTTCTATGATAT
44741736 TT
1 TT
44741738 ATAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 7 0.37
20 6 0.32
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTTATAATTTCTATGATAT
Found at i:44741728 original size:9 final size:9
Alignment explanation
Indices: 44741698--44741784 Score: 52
Period size: 9 Copynumber: 9.4 Consensus size: 9
44741688 CTTTATAAAA
44741698 TTTTAT-AT
1 TTTTATAAT
*
44741706 TTCTATATAT
1 TTTTATA-AT
44741716 TTTTATAAT
1 TTTTATAAT
*
44741725 TTTTATGAT
1 TTTTATAAT
* *
44741734 ATTTATAAAA
1 TTTTAT-AAT
*
44741744 TTTTACAATT
1 TTTTATAA-T
*
44741754 TTTTTTATAT
1 TTTTATA-AT
**
44741764 TTTTACGAT
1 TTTTATAAT
44741773 TTTTAT-AT
1 TTTTATAAT
44741781 TTTT
1 TTTT
44741785 TTTCTAATTT
Statistics
Matches: 59, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
8 11 0.19
9 24 0.41
10 23 0.39
11 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:44741737 original size:20 final size:19
Alignment explanation
Indices: 44741701--44741803 Score: 66
Period size: 20 Copynumber: 5.4 Consensus size: 19
44741691 TATAAAATTT
*
44741701 TATATTTCTATATATTTTTA
1 TATATTTTTATA-ATTTTTA
* *
44741721 TA-ATTTTTATGATATTTA
1 TATATTTTTATAATTTTTA
* * * *
44741739 TAAAATTTTACAATTTTTTT
1 TATATTTTTATAA-TTTTTA
**
44741759 TATATTTTTACGATTTTTA
1 TATATTTTTATAATTTTTA
* *
44741778 TATTTTTTTTCTAATTTTTA
1 TA-TATTTTTATAATTTTTA
44741798 -ATATTT
1 TATATTT
44741804 AAATTTTTTA
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
18 12 0.19
19 22 0.35
20 29 0.46
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TATATTTTTATAATTTTTA
Found at i:44741740 original size:28 final size:28
Alignment explanation
Indices: 44741709--44741785 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
44741699 TTTATATTTC
*
44741709 TATATATTTTTATAATTTTTATGATATT
1 TATAAATTTTTATAATTTTTATGATATT
* * * *
44741737 TATAAAATTTTACAATTTTTTTTATATT
1 TATAAATTTTTATAATTTTTATGATATT
* * *
44741765 TTTACGATTTTTATATTTTTT
1 TATA-AATTTTTATAATTTTT
44741786 TTCTAATTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
28 26 0.68
29 12 0.32
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (28 bp):
TATAAATTTTTATAATTTTTATGATATT
Found at i:44741776 original size:29 final size:27
Alignment explanation
Indices: 44741744--44741822 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 27
44741734 ATTTATAAAA
44741744 TTTTACAATTTTTTTTAT-ATTTTTACGAT
1 TTTTA-AATTTTTTTTATAATTTTTA--AT
* *
44741773 TTTTATATTTTTTTTCTAATTTTTAAT
1 TTTTAAATTTTTTTTATAATTTTTAAT
* *
44741800 ATTTAAATTTTTTATTAAAATTT
1 TTTTAAATTTTTT-TTATAATTT
44741823 AATAATATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
27 13 0.31
28 17 0.40
29 12 0.29
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (27 bp):
TTTTAAATTTTTTTTATAATTTTTAAT
Found at i:44741985 original size:91 final size:91
Alignment explanation
Indices: 44741888--44742065 Score: 218
Period size: 91 Copynumber: 2.0 Consensus size: 91
44741878 GTAAAAGCAT
* * *
44741888 GAGCTTAATTGCATTT-TTTTAAAAAGTTTGAGCATCTTTTTGAT-TCATTTTGAAAGTTCAAGT
1 GAGCTTAATTGC-TTTCTTTGAAAAAGTTTGAGCACCTTTTTGATGT-ATTTTAAAAGTTCAAGT
* * *
44741951 AC-CTAATTGAGTGTAAAAGAAAAAGTAG
64 ACTC-AAATGAGTGGAAAAAAAAAAGTAG
* * * *
44741979 GAGCTTAATTGCTTTCTTTGAAAAGGTTTGAGGACCTTTTTGATGTATTTTAAAATTTTAAGTAC
1 GAGCTTAATTGCTTTCTTTGAAAAAGTTTGAGCACCTTTTTGATGTATTTTAAAAGTTCAAGTAC
44742044 TCAAATGAGTGGAAAAAAAAAA
66 TCAAATGAGTGGAAAAAAAAAA
44742066 CTTAAATACT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
90 3 0.04
91 69 0.93
92 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (91 bp):
GAGCTTAATTGCTTTCTTTGAAAAAGTTTGAGCACCTTTTTGATGTATTTTAAAAGTTCAAGTAC
TCAAATGAGTGGAAAAAAAAAAGTAG
Found at i:44743330 original size:40 final size:40
Alignment explanation
Indices: 44743275--44743428 Score: 299
Period size: 40 Copynumber: 3.9 Consensus size: 40
44743265 GAGAATTGAT
*
44743275 TGTATGAAACAGAGGCACCGTGCTATCTTGTATCAAGGAC
1 TGTATGAAACAGAGGCACTGTGCTATCTTGTATCAAGGAC
44743315 TGTATGAAACAGAGGCACTGTGCTATCTTGTATCAAGGAC
1 TGTATGAAACAGAGGCACTGTGCTATCTTGTATCAAGGAC
44743355 TGTATGAAACAGAGGCACTGTGCTATCTTGTATCAAGGAC
1 TGTATGAAACAGAGGCACTGTGCTATCTTGTATCAAGGAC
44743395 TGTATGAAACAGAGGCACTGTGCTATCTTGTATC
1 TGTATGAAACAGAGGCACTGTGCTATCTTGTATC
44743429 TCTTTCCAAT
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 113 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (40 bp):
TGTATGAAACAGAGGCACTGTGCTATCTTGTATCAAGGAC
Found at i:44743644 original size:7 final size:7
Alignment explanation
Indices: 44743632--44743674 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
44743622 TTTCAAGTTT
44743632 ATGATTC
1 ATGATTC
44743639 ATGATTC
1 ATGATTC
44743646 ATGATTC
1 ATGATTC
44743653 ATGATTC
1 ATGATTC
*
44743660 AAGATTC
1 ATGATTC
*
44743667 AAGATTC
1 ATGATTC
44743674 A
1 A
44743675 AGGTTCAGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (7 bp):
ATGATTC
Found at i:44743675 original size:7 final size:7
Alignment explanation
Indices: 44743615--44743681 Score: 64
Period size: 7 Copynumber: 9.6 Consensus size: 7
44743605 ATAGTTCGAG
44743615 TTCAAGA
1 TTCAAGA
44743622 TTTCAAG-
1 -TTCAAGA
* *
44743629 TTTATGA
1 TTCAAGA
*
44743636 TTCATGA
1 TTCAAGA
*
44743643 TTCATGA
1 TTCAAGA
*
44743650 TTCATGA
1 TTCAAGA
44743657 TTCAAGA
1 TTCAAGA
44743664 TTCAAGA
1 TTCAAGA
*
44743671 TTCAAGG
1 TTCAAGA
44743678 TTCA
1 TTCA
44743682 GGGTAAAAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
6 4 0.08
7 43 0.81
8 6 0.11
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (7 bp):
TTCAAGA
Found at i:44743681 original size:21 final size:21
Alignment explanation
Indices: 44743615--44743674 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
44743605 ATAGTTCGAG
*
44743615 TTCAAGATTTCAAG-TTTATGA
1 TTCAAGA-TTCAAGATTCATGA
* *
44743636 TTCATGATTCATGATTCATGA
1 TTCAAGATTCAAGATTCATGA
44743657 TTCAAGATTCAAGATTCA
1 TTCAAGATTCAAGATTCA
44743675 AGGTTCAGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (21 bp):
TTCAAGATTCAAGATTCATGA
Found at i:44744736 original size:14 final size:13
Alignment explanation
Indices: 44744702--44744739 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
44744692 CGGTTCAAAT
44744702 AATATAA-TTTTA
1 AATATAATTTTTA
44744714 AAT-TAATTTTTA
1 AATATAATTTTTA
44744726 AATTATAATTTTTA
1 AA-TATAATTTTTA
44744740 TTTTAAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.13
12 10 0.43
13 1 0.04
14 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATATAATTTTTA
Found at i:44750172 original size:26 final size:26
Alignment explanation
Indices: 44750140--44750208 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
44750130 ATCAGGAAGC
44750140 TCCCGA-TATATGGCTCTTTGTGAGCT
1 TCCCGATTA-ATGGCTCTTTGTGAGCT
*
44750166 TCCCGATTAAAGGCTCTTTGTGAGCT
1 TCCCGATTAATGGCTCTTTGTGAGCT
*
44750192 TCCTGATTAATGGCTCT
1 TCCCGATTAATGGCTCT
44750209 CCGAAGCTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
26 37 0.95
27 2 0.05
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (26 bp):
TCCCGATTAATGGCTCTTTGTGAGCT
Found at i:44750222 original size:25 final size:24
Alignment explanation
Indices: 44750135--44750281 Score: 84
Period size: 26 Copynumber: 5.9 Consensus size: 24
44750125 CATATATCAG
* *
44750135 GAAGC-TCCCGATATATGGCTCTTT
1 GAAGCTTCCTGATA-ATGGCTCTCT
* * * *
44750159 GTGAGCTTCCCGATTAAAGGCTCTTT
1 G-AAGCTTCCTGA-TAATGGCTCTCT
* *
44750185 GTGAGCTTCCTGATTAATGGCTCTCC
1 G-AAGCTTCCTGA-TAATGGCTCTCT
* *
44750211 GAAGCTTCCTGAT-ATGACTCGCTT
1 GAAGCTTCCTGATAATGGCTCTC-T
* *
44750235 GAA-CTTCCCGATATATGGCTATCT
1 GAAGCTTCCTGATA-ATGGCTCTCT
*
44750259 GAAGCTTCTTGATTAATGGCTCT
1 GAAGCTTCCTGA-TAATGGCTCT
44750282 TTAGAGCTAC
Statistics
Matches: 98, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
23 15 0.15
24 9 0.09
25 32 0.33
26 40 0.41
27 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (24 bp):
GAAGCTTCCTGATAATGGCTCTCT
Found at i:44757001 original size:2 final size:2
Alignment explanation
Indices: 44756994--44757029 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
44756984 CTTCCTTATT
44756994 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
44757030 GTTTTNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:44757548 original size:2 final size:2
Alignment explanation
Indices: 44757501--44757537 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
44757491 CTCCCTTATT
44757501 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
44757538 TGTTTTCTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:44758932 original size:17 final size:17
Alignment explanation
Indices: 44758910--44758948 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
44758900 AGAAAAGTCC
44758910 CTTTTATGAGGTGAGGA
1 CTTTTATGAGGTGAGGA
44758927 CTTTTATGAGGTGAGGA
1 CTTTTATGAGGTGAGGA
44758944 CTTTT
1 CTTTT
44758949 GGTGTGTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.21, C:0.08, G:0.31, T:0.41
Consensus pattern (17 bp):
CTTTTATGAGGTGAGGA
Found at i:44764987 original size:33 final size:33
Alignment explanation
Indices: 44764941--44765024 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 33
44764931 CCCAGATTCT
**
44764941 CCTCCACCACCACCACCTTTGCCACCTTCACCA
1 CCTCCACCACCACCACCTTCACCACCTTCACCA
* * * * * *
44764974 CCTCCGCCCCCACCTCCATCATCTCCTTCACCA
1 CCTCCACCACCACCACCTTCACCACCTTCACCA
* *
44765007 CCTCCTCCTCCACCACCT
1 CCTCCACCACCACCACCT
44765025 CTACCAACAC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.17, C:0.61, G:0.02, T:0.20
Consensus pattern (33 bp):
CCTCCACCACCACCACCTTCACCACCTTCACCA
Found at i:44765020 original size:15 final size:15
Alignment explanation
Indices: 44764996--44765025 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44764986 CCTCCATCAT
*
44764996 CTCCTTCACCACCTC
1 CTCCTCCACCACCTC
44765011 CTCCTCCACCACCTC
1 CTCCTCCACCACCTC
44765026 TACCAACACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.63, G:0.00, T:0.23
Consensus pattern (15 bp):
CTCCTCCACCACCTC
Found at i:44791532 original size:20 final size:21
Alignment explanation
Indices: 44791490--44791535 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
44791480 ATAACAGCTT
* *
44791490 TTAAAATAATTATCTTTTAAA
1 TTAAAAAAATTATCTTATAAA
44791511 TTAAAAAAATTATC-TATAAA
1 TTAAAAAAATTATCTTATAAA
44791531 TTAAA
1 TTAAA
44791536 TTCTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAAAAATTATCTTATAAA
Found at i:44809811 original size:10 final size:9
Alignment explanation
Indices: 44809795--44809860 Score: 51
Period size: 10 Copynumber: 6.7 Consensus size: 9
44809785 AATTATACAA
44809795 ATAAAAATT
1 ATAAAAATT
44809804 ACTAAAAATT
1 A-TAAAAATT
**
44809814 ATTAAATTTT
1 A-TAAAAATT
44809824 AATAAAAATT
1 -ATAAAAATT
44809834 ATAAAAATCGT
1 ATAAAAAT--T
*
44809845 AAAAAAAATT
1 -ATAAAAATT
44809855 ATAAAA
1 ATAAAA
44809861 CATAATATAG
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
9 14 0.31
10 22 0.49
11 2 0.04
12 7 0.16
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:44809841 original size:21 final size:21
Alignment explanation
Indices: 44809806--44809860 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
44809796 TAAAAATTAC
* **
44809806 TAAAAATTAT-TAAATTTTAA
1 TAAAAATTATAAAAATCGTAA
44809826 TAAAAATTATAAAAATCGTAA
1 TAAAAATTATAAAAATCGTAA
*
44809847 AAAAAATTATAAAA
1 TAAAAATTATAAAA
44809861 CATAATATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
TAAAAATTATAAAAATCGTAA
Found at i:44812821 original size:18 final size:17
Alignment explanation
Indices: 44812795--44812828 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
44812785 TTTTTTTCTC
44812795 TCTTTTCCTTGTCCTTG
1 TCTTTTCCTTGTCCTTG
44812812 TCTTTGTCCTTGTCCTT
1 TCTTT-TCCTTGTCCTT
44812829 CTTCTCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.29, G:0.12, T:0.59
Consensus pattern (17 bp):
TCTTTTCCTTGTCCTTG
Found at i:44815005 original size:95 final size:94
Alignment explanation
Indices: 44814820--44815146 Score: 444
Period size: 95 Copynumber: 3.4 Consensus size: 94
44814810 CGGGCAACCT
* * *
44814820 CTTGGGAAACCTACTG-TTTCCTTATGCCAAGCTACTTCAACAATGCCCCAAATAGAAAGATAAT
1 CTTGGGAAACCTACTGCTTT-CTTATGCCAAG---C-T-AACAATTCCCCGAATAGGAAGAT-A-
44814884 TTCAAGAAATGCTCTTTTGATCAATAATTCTAGCTCAGAAA
58 ---AAGAAA-GCTCTTTTGATCAATAATTCTAGCTCAGAAA
44814925 CTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAAAGAAACG
1 CTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAAAGAAA-G
44814990 CTCTTTTGATCAATAATTCTAGCTCAGAAA
65 CTCTTTTGATCAATAATTCTAGCTCAGAAA
*
44815020 CTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAACG-AAGC
1 CTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAAAGAAAGC
*
44815084 TCTTTTGATCAATAATTCTCGCTCAGAAA
66 TCTTTTGATCAATAATTCTAGCTCAGAAA
* *
44815113 CTTAGGG-AACCTACTGTTTTCTTATTCCAAGCTA
1 CTT-GGGAAACCTACTGCTTTCTTATGCCAAGCTA
44815147 CTTCAACAAT
Statistics
Matches: 212, Mismatches: 8, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
93 58 0.27
94 5 0.02
95 96 0.45
99 1 0.00
100 20 0.09
101 1 0.00
102 1 0.00
105 27 0.13
106 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (94 bp):
CTTGGGAAACCTACTGCTTTCTTATGCCAAGCTAACAATTCCCCGAATAGGAAGATAAAGAAAGC
TCTTTTGATCAATAATTCTAGCTCAGAAA
Found at i:44817124 original size:19 final size:19
Alignment explanation
Indices: 44817102--44817153 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
44817092 AAATGATATT
*
44817102 AAATTTATAAAAATTTAGA
1 AAATTTATAAAAATCTAGA
* *
44817121 AAATATAT-ATAATCTAGA
1 AAATTTATAAAAATCTAGA
44817139 AATATATTATAAAAA
1 AA-AT-TTATAAAAA
44817154 ATAAAAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 10 0.40
19 9 0.36
20 3 0.12
21 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
AAATTTATAAAAATCTAGA
Found at i:44827839 original size:39 final size:39
Alignment explanation
Indices: 44827785--44827861 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
44827775 CAAAGACATC
44827785 CACCTCACGCGTTTCGTAATGATTATTAAATGAAAAGTT
1 CACCTCACGCGTTTCGTAATGATTATTAAATGAAAAGTT
* * * *
44827824 CACCTCATGCGTTTCGTAATGATTGTTAGATGATAAGT
1 CACCTCACGCGTTTCGTAATGATTATTAAATGAAAAGT
44827862 CTAACACGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (39 bp):
CACCTCACGCGTTTCGTAATGATTATTAAATGAAAAGTT
Found at i:44836701 original size:1 final size:1
Alignment explanation
Indices: 44836697--44836733 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
44836687 CTTTTTTCTC
*
44836697 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
44836734 CTCTTCATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:44840648 original size:87 final size:87
Alignment explanation
Indices: 44840546--44840721 Score: 192
Period size: 87 Copynumber: 2.0 Consensus size: 87
44840536 CTTTTTTTTT
* * * *
44840546 TTTTTGCACTCAATTGAACAATTTAACTTTCAAAATGAATCAAAAAAACCCTCAAACTTCTTCAA
1 TTTTTCCACTCAATTGAACAATTGAACTTTCAAAACGAATCAAAAAAACCCTCAAAATTCTTCAA
44840611 AACAAGCAATTAAGCCCCTG-TC
66 AA-AAGCAATTAAGCCCCTGCTC
* *** * * * * * * *
44840633 TTTTTCCACTTAATTGGGTACTTGAACTTTTAAAACGCATTAATAAGACCCTCAAAATTTTTCAA
1 TTTTTCCACTCAATTGAACAATTGAACTTTCAAAACGAATCAAAAAAACCCTCAAAATTCTTCAA
*
44840698 AAAAGCAATTAAGCCTCTGCTC
66 AAAAGCAATTAAGCCCCTGCTC
44840720 TT
1 TT
44840722 ATTAAAAATT
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
86 16 0.22
87 56 0.78
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (87 bp):
TTTTTCCACTCAATTGAACAATTGAACTTTCAAAACGAATCAAAAAAACCCTCAAAATTCTTCAA
AAAAGCAATTAAGCCCCTGCTC
Found at i:44840766 original size:19 final size:18
Alignment explanation
Indices: 44840730--44840782 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
44840720 TTATTAAAAA
* *
44840730 TTAGAAATATAATAAATT
1 TTAGAAAAATATTAAATT
44840748 TTAGAAAAATTATTAAATT
1 TTAGAAAAA-TATTAAATT
44840767 TTA-ATAAAATATTAAA
1 TTAGA-AAAATATTAAA
44840783 AATTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 16 0.52
19 15 0.48
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
TTAGAAAAATATTAAATT
Found at i:44840775 original size:20 final size:20
Alignment explanation
Indices: 44840734--44840790 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
44840724 TAAAAATTAG
*
44840734 AAATATAATAAATTTT-AGA
1 AAATATTATAAATTTTAAGA
*
44840753 AAA-ATTATTAAATTTTAATA
1 AAATATTA-TAAATTTTAAGA
*
44840773 AAATATTAAAAATTTTAA
1 AAATATTATAAATTTTAA
44840791 ATTTATTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.09
19 11 0.34
20 14 0.44
21 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATATTATAAATTTTAAGA
Found at i:44840797 original size:18 final size:17
Alignment explanation
Indices: 44840776--44840817 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
44840766 TTTAATAAAA
*
44840776 TATTAAAAATTTTAAATT
1 TATTAAAAATTAT-AATT
44840794 TATTAAAAATTATAATT
1 TATTAAAAATTATAATT
44840811 T-TTAAAA
1 TATTAAAA
44840818 GAAAATCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.26
17 5 0.22
18 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAAAAATTATAATT
Found at i:44840813 original size:25 final size:27
Alignment explanation
Indices: 44840753--44840816 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 27
44840743 AAATTTTAGA
*
44840753 AAAATTATTAAATTTTAATAAAATATT
1 AAAATTTTTAAATTTTAATAAAATATT
* *
44840780 AAAAATTTTAAA-TTTATTAAAA-ATT
1 AAAATTTTTAAATTTTAATAAAATATT
*
44840805 ATAATTTTTAAA
1 AAAATTTTTAAA
44840817 AGAAAATCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 13 0.41
26 9 0.28
27 10 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATTTTTAAATTTTAATAAAATATT
Found at i:44841393 original size:16 final size:16
Alignment explanation
Indices: 44841372--44841404 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44841362 NNNNNNAATT
44841372 TTACAATTTATATATA
1 TTACAATTTATATATA
44841388 TTACAATTTATATATA
1 TTACAATTTATATATA
44841404 T
1 T
44841405 ATATTTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
TTACAATTTATATATA
Found at i:44841970 original size:23 final size:24
Alignment explanation
Indices: 44841925--44841970 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
44841915 TTTATTAAAA
*
44841925 TTTGATATGAAAGTTAAACATTGC
1 TTTGATATGAAAGGTAAACATTGC
44841949 TTTGAT-TGAAATGGTAAA-ATTG
1 TTTGATATGAAA-GGTAAACATTG
44841971 AGAGATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATGAAAGGTAAACATTGC
Found at i:44843297 original size:2 final size:2
Alignment explanation
Indices: 44843290--44843534 Score: 490
Period size: 2 Copynumber: 122.5 Consensus size: 2
44843280 ATCAATTAGC
44843290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44843332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44843374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44843416 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44843458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44843500 AT AT AT 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 AT AT AT A
44843535 ACACATTTAT
Statistics
Matches: 243, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 243 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44844803 original size:19 final size:19
Alignment explanation
Indices: 44844765--44844803 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
44844755 TATGTTTTTT
*
44844765 ATTTTATTTTAAAATTAAA
1 ATTTTATTTTAAAATAAAA
44844784 ATTTTATATTT-AAATAAAA
1 ATTTTAT-TTTAAAATAAAA
44844803 A
1 A
44844804 ATGCATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTATTTTAAAATAAAA
Found at i:44847174 original size:18 final size:19
Alignment explanation
Indices: 44847141--44847177 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
44847131 GTTCTTTTTT
*
44847141 GTGTTTGGGTGATGGGAAA
1 GTGTCTGGGTGATGGGAAA
44847160 GTGTCTGGG-GATGGGAAA
1 GTGTCTGGGTGATGGGAAA
44847178 ATGATGTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.27
Consensus pattern (19 bp):
GTGTCTGGGTGATGGGAAA
Found at i:44848808 original size:3 final size:3
Alignment explanation
Indices: 44848764--44848791 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
44848754 ATTTAAAAAT
44848764 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
44848792 CAAATTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:44852731 original size:17 final size:17
Alignment explanation
Indices: 44852704--44852750 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
44852694 ATATTATCTC
44852704 AATTTTT-AATTTTTAT
1 AATTTTTCAATTTTTAT
*
44852720 AATTTTTCAATTTTTGT
1 AATTTTTCAATTTTTAT
*
44852737 GATTTTTCGAATTT
1 AATTTTTC-AATTT
44852751 CTCTTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 7 0.26
17 15 0.56
18 5 0.19
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (17 bp):
AATTTTTCAATTTTTAT
Found at i:44857970 original size:18 final size:17
Alignment explanation
Indices: 44857947--44857983 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
44857937 TTAAATTTGT
44857947 TTTAAAATTAATTTAAAA
1 TTTAAAATTAA-TTAAAA
*
44857965 TTTAAAATTTATTAAAA
1 TTTAAAATTAATTAAAA
44857982 TT
1 TT
44857984 GATTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAAATTAATTAAAA
Done.