Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 154 of 427
Found at i:42449254 original size:37 final size:37
Alignment explanation
Indices: 42449204--42449305 Score: 152
Period size: 37 Copynumber: 2.8 Consensus size: 37
42449194 GGAAATATAT
42449204 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
42449241 TCCGGGTAAGACCCGATGACTATGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
42449278 TCC-AGTAATACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
42449306 GGACTATTCG
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 21 0.36
37 38 0.64
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:42454710 original size:40 final size:39
Alignment explanation
Indices: 42454655--42454922 Score: 315
Period size: 40 Copynumber: 6.7 Consensus size: 39
42454645 ATAACCACAA
* * *
42454655 GCACAATTGCCTTCGGGTCTTAACCCGAGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCG-GTATAACAACTC
* *
42454695 GCACAAATGCCTTCGGGTCTTAGCCCGAATATAACCACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCG-GTATAACAACTC
*
42454735 GCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGG-TATAACAACTC
*
42454775 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGG-TATAA-CAACTC
* * * * *
42454815 GTATAAATGCCTTCGGGTCTTAACTCTGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAGC-CCGGTATAACAACTC
*
42454855 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGG-TATAA-CAACTC
* *
42454895 GCATAAATGCCTTCGGGGCTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAGCCCGG
42454923 GTATCATTCA
Statistics
Matches: 198, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.02
40 191 0.96
41 4 0.02
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGTATAACAACTC
Found at i:42454776 original size:80 final size:80
Alignment explanation
Indices: 42454635--42454922 Score: 427
Period size: 80 Copynumber: 3.6 Consensus size: 80
42454625 TCTTTGGAAT
* * *
42454635 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCC-GAGTATAGCAACTCGCA
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGGA-TATAACAACTCGCA
42454698 CAAATGCCTTCGGGTC
65 CAAATGCCTTCGGGTC
* *
42454714 TTAGCCCGAATATAACCACTCGCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTCGCAC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTCGCAC
42454779 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* * * * *
42454794 TTAGCCCGGATATAATCACTAGTATAAATGCCTTCGGGTCTTAACTCTGATATAACAACTCGCAC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTCGCAC
42454859 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* * * *
42454874 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGGCTTAGCCCGG
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGG
42454923 GTATCATTCA
Statistics
Matches: 190, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
79 4 0.02
80 184 0.97
81 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (80 bp):
TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTCGCAC
AAATGCCTTCGGGTC
Found at i:42454855 original size:120 final size:120
Alignment explanation
Indices: 42454639--42454926 Score: 370
Period size: 120 Copynumber: 2.4 Consensus size: 120
42454629 TGGAATTTAG
* * * *
42454639 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCC-GAGTATAGCAACTCGCACAAAT
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAGCCCGGAGTATAGCAACTAGCACAAAT
* *
42454703 GCCTTCGGGTCTTAGCCCGAATATAACCACTCGCACAAATGCCTTCGGGTCTTAAC
65 GCCTTCGGGTCTTAACCCGAATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* * * *
42454759 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGA-TATAATC-ACTAGTATAAA
1 CCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAGCCCGGAGTAT-AGCAACTAGCACAAA
* *
42454822 TGCCTTCGGGTCTTAACTCTG-ATATAACAACTCGCACAAATGCCTTCGGGTCTTAGC
64 TGCCTTCGGGTCTTAAC-CCGAATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* *
42454879 CCGGATATAATCACTAGCATAAATGCCTTCGGGGCTTAGCCCGG-GTAT
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAGCCCGGAGTAT
42454927 CATTCAAATG
Statistics
Matches: 147, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
119 1 0.01
120 139 0.95
121 7 0.05
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (120 bp):
CCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAGCCCGGAGTATAGCAACTAGCACAAATG
CCTTCGGGTCTTAACCCGAATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
Found at i:42458481 original size:6 final size:6
Alignment explanation
Indices: 42458466--42458622 Score: 153
Period size: 6 Copynumber: 25.8 Consensus size: 6
42458456 AACCAAAATG
* *
42458466 AGAATC AGAATT AGAATC AGTAA-C AGAATC AGAATC AGAATC AGAATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
*
42458514 AG-GTGAC AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC
1 AGAAT--C AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC
* * * *
42458563 AGTATT AGTAA-C AGAATC AGAATC AGAATC AGAATT ACGTGA-C AGAATC
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC
42458612 AGAATC AGAAT
1 AGAATC AGAAT
42458623 GTGAATGCAA
Statistics
Matches: 125, Mismatches: 14, Indels: 24
0.77 0.09 0.15
Matches are distributed among these distances:
5 8 0.06
6 106 0.85
7 9 0.07
8 2 0.02
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:42458590 original size:85 final size:85
Alignment explanation
Indices: 42458466--42458622 Score: 278
Period size: 85 Copynumber: 1.8 Consensus size: 85
42458456 AACCAAAATG
* *
42458466 AGAATCAGAATTAGAATCAGTAACAGAATCAGAATCAGAATCAGAATTAGGTGACAGAATCAGAA
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATTACGTGACAGAATCAGAA
42458531 TCAGAATCAGTAACAGAATC
66 TCAGAATCAGTAACAGAATC
* *
42458551 AGAATCAGAATCAGTATTAGTAACAGAATCAGAATCAGAATCAGAATTACGTGACAGAATCAGAA
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATTACGTGACAGAATCAGAA
42458616 TCAGAAT
66 TCAGAAT
42458623 GTGAATGCAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 68 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (85 bp):
AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATTACGTGACAGAATCAGAA
TCAGAATCAGTAACAGAATC
Found at i:42458788 original size:27 final size:27
Alignment explanation
Indices: 42458758--42458812 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
42458748 ATATCGTGAT
* *
42458758 AGAGTCACCAG-ATACAGATATTGTGGC
1 AGAGCCACCAGAAT-CAGATAATGTGGC
42458785 AGAGCCACCAGAATCAGATAATGTGGC
1 AGAGCCACCAGAATCAGATAATGTGGC
42458812 A
1 A
42458813 AACGCACCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.18
Consensus pattern (27 bp):
AGAGCCACCAGAATCAGATAATGTGGC
Found at i:42459024 original size:22 final size:22
Alignment explanation
Indices: 42458976--42459034 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
42458966 GTAAATACGT
*
42458976 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
42458998 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
42459020 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
42459035 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:42459200 original size:27 final size:26
Alignment explanation
Indices: 42459121--42459203 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
42459111 TCGATCGGTC
* * * *
42459121 AACAGATACTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
42459147 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
42459174 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
42459201 AAC
1 AAC
42459204 GCTTCCTTCG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 8 0.16
27 42 0.84
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:42459432 original size:27 final size:26
Alignment explanation
Indices: 42459402--42459597 Score: 212
Period size: 27 Copynumber: 7.3 Consensus size: 26
42459392 GGGGCAAAAT
* * *
42459402 GGTAATTTTACCCCACATGGGTATCTC
1 GGTAATTCTACCCTACA-GGGTATTTC
42459429 GGTAATTCTACCCTACAGGAGTATTTC
1 GGTAATTCTACCCTACAGG-GTATTTC
*
42459456 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTAC-AGGGTATTTC
* *
42459483 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACA-GGGTATTTC
* *
42459510 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTA-CAGGGTATTTC
* * *
42459537 AGTAATTCTACGCTATAGGGGTATTTC
1 GGTAATTCTACCCTACA-GGGTATTTC
*
42459564 GGAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACA-GGGTATTTC
*
42459591 AGTAATT
1 GGTAATT
42459598 TCATAATCAA
Statistics
Matches: 143, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.03
27 135 0.94
28 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (26 bp):
GGTAATTCTACCCTACAGGGTATTTC
Found at i:42459478 original size:54 final size:54
Alignment explanation
Indices: 42459402--42459597 Score: 250
Period size: 54 Copynumber: 3.6 Consensus size: 54
42459392 GGGGCAAAAT
* * * * * *
42459402 GGTAATTTTACCCCACATGGGTATCTCGGTAATTCTACCCTACAGGAGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
* *
42459456 GGTATTTCTACCCTACAAGGGTATTTC-GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTCAG-TAATTCTACCCTACAGGGGTATTTC
* * * *
42459510 GGTAATTCTATCCTATAAGGGTATTTCAGTAATTCTACGCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
* *
42459564 GGAAATTCTACCCTACAGGGGTATTTCAGTAATT
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAATT
42459598 TCATAATCAA
Statistics
Matches: 123, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 121 0.98
55 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
Found at i:42459546 original size:81 final size:82
Alignment explanation
Indices: 42459404--42459597 Score: 241
Period size: 81 Copynumber: 2.4 Consensus size: 82
42459394 GGCAAAATGG
* * * * * * *
42459404 TAATTTTACCCCACATGGGTATCTCGGTAATTCTACCCTACAGGAGTATTTCGGTATTTCTACCC
1 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTAAAGGAGTATTTCAGTAATTCTACCC
42459469 TACAAGGGTATTTC-GA
66 TACAAGGGTATTTCGGA
* * *
42459485 TAATTCTACCCTACAGGGGTATTTTGGTAATTCTATCCTATAAGG-GTATTTCAGTAATTCTACG
1 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTA-AAGGAGTATTTCAGTAATTCTACC
* *
42459549 CTATAGGGGTATTTCGGA
65 CTACAAGGGTATTTCGGA
*
42459567 -AATTCTACCCTACAGGGGTATTTCAGTAATT
1 TAATTCTACCCTACAGGGGTATTTCGGTAATT
42459598 TCATAATCAA
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
81 92 0.95
82 5 0.05
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (82 bp):
TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTAAAGGAGTATTTCAGTAATTCTACCC
TACAAGGGTATTTCGGA
Found at i:42459632 original size:27 final size:27
Alignment explanation
Indices: 42459602--42459983 Score: 490
Period size: 27 Copynumber: 14.2 Consensus size: 27
42459592 GTAATTTCAT
*
42459602 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
42459629 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
42459656 AA-CTGAGGGT-AAACTAGTAATTCTGTA
1 AATC-GAGGGTAAAAC-GGTAATTCTGTA
* **
42459683 AATC-ATGGGTAAAACGGTAATTTTACA
1 AATCGA-GGGTAAAACGGTAATTCTGTA
* *
42459710 AATCGAGGGTAAAACAGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
42459737 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
42459764 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
**
42459791 AATCGAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
42459818 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
42459845 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
42459872 AA-CTGAGGGTAAAACAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * **
42459899 AATCGAGGGTAAAATGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
42459926 AATTGAGGGTAAAACGGTAATTCTGT-
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
42459952 AATTGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
42459979 AATCG
1 AATCG
42459984 GGAGTACTTT
Statistics
Matches: 311, Mismatches: 31, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
26 35 0.11
27 267 0.86
28 9 0.03
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:42462010 original size:6 final size:6
Alignment explanation
Indices: 42461999--42462155 Score: 153
Period size: 6 Copynumber: 25.8 Consensus size: 6
42461989 AACCAAAATG
*
42461999 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC AGAATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
* *
42462047 AG-GTGAC AGAATC AGAATC AGAATC AGTAA-C AAAATC AGAATC AGAATC
1 AGAAT--C AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC
* * * *
42462096 AGTATT AGTAA-C AGAATC AGAATC AGAATC AGAATT ACGTGA-C AGAATC
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC
42462145 AGAATC AGAAT
1 AGAATC AGAAT
42462156 GTGAATGCAA
Statistics
Matches: 125, Mismatches: 14, Indels: 24
0.77 0.09 0.15
Matches are distributed among these distances:
5 8 0.06
6 106 0.85
7 9 0.07
8 2 0.02
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:42462088 original size:85 final size:85
Alignment explanation
Indices: 42461992--42462155 Score: 292
Period size: 85 Copynumber: 1.9 Consensus size: 85
42461982 GAATTGGAAC
* *
42461992 CAAAATGAGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATTAGGTGACAGA
1 CAAAATCAGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATTACGTGACAGA
42462057 ATCAGAATCAGAATCAGTAA
66 ATCAGAATCAGAATCAGTAA
* *
42462077 CAAAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAATCAGAATCAGAATTACGTGACAGA
1 CAAAATCAGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATTACGTGACAGA
42462142 ATCAGAATCAGAAT
66 ATCAGAATCAGAAT
42462156 GTGAATGCAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 75 1.00
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.19
Consensus pattern (85 bp):
CAAAATCAGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATTACGTGACAGA
ATCAGAATCAGAATCAGTAA
Found at i:42462310 original size:27 final size:26
Alignment explanation
Indices: 42462273--42462338 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
42462263 AGCATGGCTG
*
42462273 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
42462299 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
42462326 CCAGAATCAGATA
1 CCAGAA-CAGATA
42462339 ATGTGGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:42462343 original size:27 final size:27
Alignment explanation
Indices: 42462273--42462346 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
42462263 AGCATGGCTG
* *
42462273 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
*
42462299 CCAG-ATACAGATATTGTGGCAGAGCCA
1 CCAGAAT-CAGATAATGTGGCAGAGCCA
42462326 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
42462347 AACGCACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.10
27 32 0.80
28 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:42462559 original size:22 final size:22
Alignment explanation
Indices: 42462511--42462569 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
42462501 GTAAATACGT
*
42462511 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
42462533 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
42462555 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
42462570 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:42462736 original size:27 final size:26
Alignment explanation
Indices: 42462657--42462739 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 26
42462647 TCGATCGGTC
* * * * *
42462657 AACAGATACTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCACAGCCACCAG
42462683 ATACAGATATTGTGGCACAGCCACCAG
1 A-ACAGATATTGTGGCACAGCCACCAG
*
42462710 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCACAGCCACCAG
42462737 AAC
1 AAC
42462740 GCTTCCTCCG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
26 8 0.16
27 41 0.84
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (26 bp):
AACAGATATTGTGGCACAGCCACCAG
Found at i:42463295 original size:27 final size:27
Alignment explanation
Indices: 42462933--42463278 Score: 439
Period size: 27 Copynumber: 12.8 Consensus size: 27
42462923 CCCTAGGGGC
* *
42462933 AAAATGGTAATTTTGTAAA-CTGAGGGT
1 AAAACGGTAATTCTGTAAATC-GAGGGT
* * *
42462960 AAACCAGTAATTCTGTAAATCAAGGGT
1 AAAACGGTAATTCTGTAAATCGAGGGT
* * **
42462987 AAAATGGTAATTTTACAAATCGAGGGT
1 AAAACGGTAATTCTGTAAATCGAGGGT
* *
42463014 AAAACAGTAATTTTGTAAATCGAGGGT
1 AAAACGGTAATTCTGTAAATCGAGGGT
*
42463041 AAAACAGTAATTCTGTAAA-CTGAGGGT
1 AAAACGGTAATTCTGTAAATC-GAGGGT
42463068 AAAACGGTAATTCTGTAAATCGAGGGT
1 AAAACGGTAATTCTGTAAATCGAGGGT
** *
42463095 AAAATAGTAATTCTGTAAA-CTAAGGGT
1 AAAACGGTAATTCTGTAAATC-GAGGGT
42463122 AAAACGGTAATTCTGTAAATCGAGGGT
1 AAAACGGTAATTCTGTAAATCGAGGGT
42463149 AAAACGGTAATTCTGTAAA-CTGAGGGT
1 AAAACGGTAATTCTGTAAATC-GAGGGT
* *
42463176 AAAACAGTAATTCTGTAAATTGAGGGT
1 AAAACGGTAATTCTGTAAATCGAGGGT
* * **
42463203 AAAATGGTAATTTTAAAAATCGAGGGT
1 AAAACGGTAATTCTGTAAATCGAGGGT
42463230 AAAACGGTAATTCTGTAAATCGAGGGT
1 AAAACGGTAATTCTGTAAATCGAGGGT
42463257 AAAACGGTAATTCTGTAAATCG
1 AAAACGGTAATTCTGTAAATCG
42463279 GGAGTACTTT
Statistics
Matches: 276, Mismatches: 36, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
26 3 0.01
27 270 0.98
28 3 0.01
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (27 bp):
AAAACGGTAATTCTGTAAATCGAGGGT
Found at i:42463322 original size:81 final size:81
Alignment explanation
Indices: 42463008--42463311 Score: 305
Period size: 81 Copynumber: 3.8 Consensus size: 81
42462998 TTTACAAATC
* ** * *
42463008 GAGGGTAAAACAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGT-AAACT-GAGGGTAAA
1 GAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATGGTAATT-T-TAAAAATCGAGGGCAAA
*
42463071 ACGGTAATTCTGTAAA-T
64 ACAGTAATTCTGTAAACT
* * * * ** *
42463088 CGAGGGTAAAATAGTAATTCTGTAAA-CTAAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAA
1 -GAGGGTAAAACAGTAATTCTGTAAATC-GAGGGTAAAATGGTAATTTTAAAAATCGAGGGCAAA
*
42463152 ACGGTAATTCTGTAAACT
64 ACAGTAATTCTGTAAACT
* *
42463170 GAGGGTAAAACAGTAATTCTGTAAATTGAGGGTAAAATGGTAATTTTAAAAATCGAGGGTAAAAC
1 GAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTAAAAATCGAGGGCAAAAC
*
42463235 GGTAATTCTGTAAA-T
66 AGTAATTCTGTAAACT
* *** * *
42463250 CGAGGGTAAAACGGTAATTCTGTAAATCG-GGAGTACTTTGGTAATTTTACAAGTCGAGGGCA
1 -GAGGGTAAAACAGTAATTCTGTAAATCGAGG-GTAAAATGGTAATTTTAAAAATCGAGGGCA
42463312 TTTCAGTAAT
Statistics
Matches: 194, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
79 1 0.01
80 7 0.04
81 185 0.95
82 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (81 bp):
GAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATGGTAATTTTAAAAATCGAGGGCAAAAC
AGTAATTCTGTAAACT
Found at i:42469166 original size:40 final size:39
Alignment explanation
Indices: 42469101--42469387 Score: 335
Period size: 40 Copynumber: 7.2 Consensus size: 39
42469091 TCTTCGGAAT
** *
42469101 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAA-CACTCGCACAAATGCCTTCGGGTC
* * *
42469140 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAAC-ACTCGCACAAATGCCTTCGGGTC
* *
42469180 TTAGCTCGGATATAACACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACACTCGCACAAATGCCTTCGGGTC
* *
42469219 TTAACCCGGATATAACAACTCACACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAAC-ACTCGCACAAATGCCTTCGGGTC
* * *
42469259 TTAGCCTGGATATAATCACTAGCATAAATGCCTTCGGGTC
1 TTAGCCCGGATATAA-CACTCGCACAAATGCCTTCGGGTC
* * *
42469299 TTAACCCAGTTATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAAC-ACTCGCACAAATGCCTTCGGGTC
* *
42469339 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCAGGG-C
1 TTAGCCCGGATATAA-CACTCGCACAAATGCCTTC-GGGTC
42469379 TTAGCCCGG
1 TTAGCCCGG
42469388 GTATCATTCA
Statistics
Matches: 210, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
39 41 0.20
40 164 0.78
41 5 0.02
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
TTAGCCCGGATATAACACTCGCACAAATGCCTTCGGGTC
Found at i:42469318 original size:80 final size:80
Alignment explanation
Indices: 42469101--42469387 Score: 411
Period size: 80 Copynumber: 3.6 Consensus size: 80
42469091 TCTTCGGAAT
* * * * *
42469101 TTAGCC-GGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCTGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTCGCAC
42469165 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* *
42469180 TTAG-CTCGGATATAA-CACTTGCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTCACA
1 TTAGCCT-GGATATAATCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTCGCA
42469243 CAAATGCCTTCGGGTC
65 CAAATGCCTTCGGGTC
* * *
42469259 TTAGCCTGGATATAATCACTAGCATAAATGCCTTCGGGTCTTAACCCAGTTATAACAACTCGCAC
1 TTAGCCTGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTCGCAC
42469324 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* * *
42469339 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCAGGG-CTTAGCCCGG
1 TTAGCCTGGATATAATCACTAGCACAAATGCCTTC-GGGTCTTAACCCGG
42469388 GTATCATTCA
Statistics
Matches: 189, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
78 1 0.01
79 74 0.39
80 111 0.59
81 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (80 bp):
TTAGCCTGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTCGCAC
AAATGCCTTCGGGTC
Found at i:42472680 original size:41 final size:43
Alignment explanation
Indices: 42472598--42472704 Score: 121
Period size: 41 Copynumber: 2.5 Consensus size: 43
42472588 TGGTATTGAT
* * *
42472598 ATATGTGGTTACGTGTAAGACCATGTCTGGGACATCAGCATCG
1 ATATGTGATTACGTGTAAGACCATGTATGAGACATCAGCATCG
* * *
42472641 -TATTTGATT-CGTGTAAGACCCTGTATGAGACAGT-GGCATCG
1 ATATGTGATTACGTGTAAGACCATGTATGAGACA-TCAGCATCG
*
42472682 ATATGTGATTACATGTAAGACCA
1 ATATGTGATTACGTGTAAGACCA
42472705 CGTCTGGGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
41 26 0.50
42 16 0.31
43 10 0.19
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (43 bp):
ATATGTGATTACGTGTAAGACCATGTATGAGACATCAGCATCG
Found at i:42489319 original size:40 final size:41
Alignment explanation
Indices: 42489235--42489376 Score: 134
Period size: 40 Copynumber: 3.5 Consensus size: 41
42489225 ACATTCAAAT
* * * * *
42489235 GCCTTCGGGACATAGCCCGG-TTACAGTAAC-TCGCACGAAT
1 GCCTTCGGGACTTAGCCCGGATT-TAGTCACTTAGCACGAAA
* * *
42489275 GCCTTCGGGACTCAACCCGGATTTAGT-AGCTT-GCTCGAAA
1 GCCTTCGGGACTTAGCCCGGATTTAGTCA-CTTAGCACGAAA
*
42489315 GCCTTC-GGATCTTAGTCCGGATTTAGTCACTTAGCAC-AAA
1 GCCTTCGGGA-CTTAGCCCGGATTTAGTCACTTAGCACGAAA
42489355 GCCTTCGGGACTTAGCCCGGAT
1 GCCTTCGGGACTTAGCCCGGAT
42489377 ATCATTCGAA
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
39 4 0.05
40 70 0.83
41 10 0.12
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (41 bp):
GCCTTCGGGACTTAGCCCGGATTTAGTCACTTAGCACGAAA
Found at i:42497614 original size:40 final size:40
Alignment explanation
Indices: 42497554--42497655 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 40
42497544 TCGCACGAAT
* * *
42497554 GCCTTCGGGACTCAACCCGGATTTAGT-AGCTT-GCTCGAAA
1 GCCTTCGGGACTTAGCCCGGATTTAGTCA-CTTAGCAC-AAA
*
42497594 GCCTTC-GGATCTTAGTCCGGATTTAGTCACTTAGCACAAA
1 GCCTTCGGGA-CTTAGCCCGGATTTAGTCACTTAGCACAAA
42497634 GCCTTCGGGACTTAGCCCGGAT
1 GCCTTCGGGACTTAGCCCGGAT
42497656 ATCATTCGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
39 3 0.06
40 43 0.81
41 7 0.13
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATTTAGTCACTTAGCACAAA
Found at i:42506589 original size:27 final size:27
Alignment explanation
Indices: 42506559--42506619 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
42506549 GTCATTTCAG
*
42506559 TCATTTTACCATATAAGGACAAAATAA
1 TCATTTTACCATATAAGGACAAAACAA
* * *
42506586 TCATTTTACCATATGAGGGCAAAACAG
1 TCATTTTACCATATAAGGACAAAACAA
42506613 TCATTTT
1 TCATTTT
42506620 GATCAATCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.33
Consensus pattern (27 bp):
TCATTTTACCATATAAGGACAAAACAA
Found at i:42510793 original size:21 final size:21
Alignment explanation
Indices: 42510766--42510812 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
42510756 CCCTGCATTG
*
42510766 ATTTA-TTCATTTATTTTGTTT
1 ATTTATTTC-TTTATTTAGTTT
*
42510787 TTTTATTTCTTTATTTAGTTT
1 ATTTATTTCTTTATTTAGTTT
42510808 ATTTA
1 ATTTA
42510813 ATACTTTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (21 bp):
ATTTATTTCTTTATTTAGTTT
Found at i:42510819 original size:21 final size:21
Alignment explanation
Indices: 42510775--42510819 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42510765 GATTTATTCA
* * * *
42510775 TTTATTTTGTTTTTTTATTTC
1 TTTATTTAGTTTATTTAATAC
42510796 TTTATTTAGTTTATTTAATAC
1 TTTATTTAGTTTATTTAATAC
42510817 TTT
1 TTT
42510820 TACTTAACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTATTTAGTTTATTTAATAC
Found at i:42513599 original size:16 final size:18
Alignment explanation
Indices: 42513578--42513610 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
42513568 TGCATGAATA
42513578 TTTAGG-AAC-TTTTATT
1 TTTAGGTAACATTTTATT
42513594 TTTAGGTAACATTTTAT
1 TTTAGGTAACATTTTAT
42513611 ACAATTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (18 bp):
TTTAGGTAACATTTTATT
Found at i:42515668 original size:27 final size:27
Alignment explanation
Indices: 42515638--42515691 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
42515628 ATTACCAGTG
42515638 ATTGGCTAAGAAAAATTAGGAGATTAT
1 ATTGGCTAAGAAAAATTAGGAGATTAT
*
42515665 ATTGGCTAAGAAAAATTGGGAGATTAT
1 ATTGGCTAAGAAAAATTAGGAGATTAT
42515692 GTATAAGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.30
Consensus pattern (27 bp):
ATTGGCTAAGAAAAATTAGGAGATTAT
Found at i:42516590 original size:67 final size:66
Alignment explanation
Indices: 42516448--42516617 Score: 205
Period size: 67 Copynumber: 2.5 Consensus size: 66
42516438 CAGGAGTTTG
* * *
42516448 CTAGGACATTAAACATGGGGTACATTTGTAAGACCAAAGCTTAGCTATGGCAACATGTGGAGTCC
1 CTAGGACATTAAACATGGGGTACATTTGTAAGACCAAAGCTTAGCTATGGAAACATATGGAATCC
42516513 T
66 T
* * * * ** *
42516514 CCAGAACATTAAACATTGGGTACATTATGTAAGATCGTATCTTAGCTATGGAAACATATGGAATC
1 CTAGGACATTAAACATGGGGTACATT-TGTAAGACCAAAGCTTAGCTATGGAAACATATGGAATC
*
42516579 TT
65 CT
* *
42516581 CTAGGACATTACATATGGGGTACATTGTGTAAGACCA
1 CTAGGACATTAAACATGGGGTACATT-TGTAAGACCA
42516618 TCGCTCAGTT
Statistics
Matches: 84, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
66 23 0.27
67 61 0.73
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (66 bp):
CTAGGACATTAAACATGGGGTACATTTGTAAGACCAAAGCTTAGCTATGGAAACATATGGAATCC
T
Found at i:42518288 original size:26 final size:26
Alignment explanation
Indices: 42518252--42518315 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
42518242 GGAAAGGTAT
42518252 GTATATGAAATGAGCTATAATGTTGA
1 GTATATGAAATGAGCTATAATGTTGA
* *
42518278 GTATATGAAATGAGTTATGATGTTGA
1 GTATATGAAATGAGCTATAATGTTGA
*
42518304 GTATATAAAATG
1 GTATATGAAATG
42518316 GATAGTATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (26 bp):
GTATATGAAATGAGCTATAATGTTGA
Found at i:42519674 original size:34 final size:34
Alignment explanation
Indices: 42519634--42519702 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
42519624 ATAAAAAGAG
42519634 AAAAGAGTTTCTTGAATGAAAATAGGGTCGTAGA
1 AAAAGAGTTTCTTGAATGAAAATAGGGTCGTAGA
42519668 AAAAGAGTTTCTTGAATGAAAATAGGGTCGTAGA
1 AAAAGAGTTTCTTGAATGAAAATAGGGTCGTAGA
42519702 A
1 A
42519703 CCGTAGCTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (34 bp):
AAAAGAGTTTCTTGAATGAAAATAGGGTCGTAGA
Found at i:42526176 original size:28 final size:28
Alignment explanation
Indices: 42526136--42526227 Score: 112
Period size: 28 Copynumber: 3.3 Consensus size: 28
42526126 TGGGAAGTAG
* *
42526136 TTGGGTCTGATGGGCCATATGAATGTGA
1 TTGGGCCTGATGGGCCATATGAATGAGA
* * *
42526164 TTGGGCCTGATGGGCCATACGAGTGGGA
1 TTGGGCCTGATGGGCCATATGAATGAGA
* * *
42526192 TTGGGCCAGATGGGCCATGTGAACGAGA
1 TTGGGCCTGATGGGCCATATGAATGAGA
42526220 TTGGGCCT
1 TTGGGCCT
42526228 AAAGGGGCCG
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.20, C:0.16, G:0.39, T:0.25
Consensus pattern (28 bp):
TTGGGCCTGATGGGCCATATGAATGAGA
Found at i:42526582 original size:27 final size:27
Alignment explanation
Indices: 42526544--42527040 Score: 447
Period size: 27 Copynumber: 18.7 Consensus size: 27
42526534 TAATAAAGAG
* * *
42526544 AAATTACTGAAATATCCTCAATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
*
42526571 AAATTACCGAAATACCCTCGA-TTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
* * *
42526597 AAATTACTGAAATACTCTTGATTTG-A
1 AAATTACCGAAATACCCTCGATTTGTA
* *
42526623 AAATTACCTAAATACCCTCGA-TTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
** * *
42526649 AAATTTTCAAAATATCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * *
42526676 AAATTACCAAAATA-CC-CAATTTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
*
42526701 AAATTACCGAAACACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
***
42526728 AAATTATTAAAATACCC-CTGATTTGTA
1 AAATTACCGAAATACCCTC-GATTTGTA
* *
42526755 AAATTACCGAAATACCCTC-AATTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
* ** *
42526781 AAATTACTGAAATA-CCTTTACTTTATA
1 AAATTACCGAAATACCCTCGA-TTTGTA
*
42526808 AAATTATCGAAATACCC-CGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * *
42526834 AAATTATCGAAACACCTTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * * *
42526861 AAGTTATCGAAACACCCTCAATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
** *
42526888 AAATTACTAAAACACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
42526915 AAAGTATCGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
42526942 AAATTATCGAAATACCCTCAATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
** ** *
42526969 AAATTACTAAAATACCCTAAACTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * * *
42526996 AAATTATCAAAATACCCTTG-TAGTGTA
1 AAATTACCGAAATACCCTCGAT-TTGTA
42527023 AAATTACCGAAATACCCT
1 AAATTACCGAAATACCCT
42527041 TCTAGTGTAA
Statistics
Matches: 383, Mismatches: 75, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
25 25 0.07
26 100 0.26
27 255 0.67
28 3 0.01
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGATTTGTA
Found at i:42527041 original size:27 final size:27
Alignment explanation
Indices: 42526992--42527079 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
42526982 ACCCTAAACT
* *
42526992 TGTAAAATTATCAAAATACCCTTGTAG
1 TGTAAAATTACCGAAATACCCTTGTAG
*
42527019 TGTAAAATTACCGAAATACCCTTCTAG
1 TGTAAAATTACCGAAATACCCTTGTAG
* *
42527046 TGTAAAATGACCG-CATA-CCTCTGTAG
1 TGTAAAATTACCGAAATACCCT-TGTAG
*
42527072 GGTAAAAT
1 TGTAAAAT
42527080 AATTATTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
25 3 0.06
26 14 0.26
27 36 0.68
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Consensus pattern (27 bp):
TGTAAAATTACCGAAATACCCTTGTAG
Found at i:42527302 original size:50 final size:50
Alignment explanation
Indices: 42527227--42527329 Score: 170
Period size: 50 Copynumber: 2.1 Consensus size: 50
42527217 TGTTATTGAG
* * * *
42527227 TATGGTCATTCTGCATATACGTGTGATGATTGAGCATGACATTCACGACA
1 TATGGTCATTCTACATACACATGTGATGATTGAACATGACATTCACGACA
42527277 TATGGTCATTCTACATACACATGTGATGATTGAACATGACATTCACGACA
1 TATGGTCATTCTACATACACATGTGATGATTGAACATGACATTCACGACA
42527327 TAT
1 TAT
42527330 TGCATGGGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (50 bp):
TATGGTCATTCTACATACACATGTGATGATTGAACATGACATTCACGACA
Found at i:42538037 original size:20 final size:20
Alignment explanation
Indices: 42538014--42538051 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42538004 CACATCCAAA
*
42538014 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
42538034 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
42538052 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:42547187 original size:31 final size:31
Alignment explanation
Indices: 42547149--42547212 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
42547139 CCTTTTCATA
42547149 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
42547180 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
42547211 TT
1 TT
42547213 ACTGTAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:42547446 original size:24 final size:24
Alignment explanation
Indices: 42547400--42547494 Score: 124
Period size: 24 Copynumber: 4.0 Consensus size: 24
42547390 GCTTTATCAT
*
42547400 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
42547425 ATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGGGG-CATAAGCCCTTTTA
42547449 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
42547472 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
42547495 TCACTTCCTC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
23 25 0.39
24 26 0.41
25 13 0.20
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:42547479 original size:47 final size:49
Alignment explanation
Indices: 42547400--42547493 Score: 133
Period size: 47 Copynumber: 2.0 Consensus size: 49
42547390 GCTTTATCAT
*
42547400 ATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGGAGGCATAGCCTCTTTTAATAACTGGGG-CATAAGCCCTTTCA
42547449 ATAACTGG-GGCATAAGCC-CTTTT-ATAACTGGGGCATAAGCCCTTT
1 ATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCATAAGCCCTTT
42547494 TTCACTTCCT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
46 2 0.05
47 19 0.45
48 9 0.21
49 12 0.29
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (49 bp):
ATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:42547570 original size:20 final size:20
Alignment explanation
Indices: 42547545--42547604 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
42547535 TATGATTACC
42547545 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
42547565 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
42547585 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
42547605 CCATCTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:42547575 original size:11 final size:11
Alignment explanation
Indices: 42547545--42547599 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
42547535 TATGATTACC
42547545 TCATGTGCATA
1 TCATGTGCATA
*
42547556 TCA--TACATA
1 TCATGTGCATA
42547565 TCATGTGCATA
1 TCATGTGCATA
* *
42547576 TCA--TACATT
1 TCATGTGCATA
42547585 TCATGTGCATA
1 TCATGTGCATA
42547596 TCAT
1 TCAT
42547600 ACATACCATC
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:42547792 original size:63 final size:63
Alignment explanation
Indices: 42547719--42547844 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
42547709 AATCTTGCAA
42547719 TTTTACCAAAAATTAGGGTTTCCATGTTTATTAATGATTACTTAACAATTCATGGGTGCAACC
1 TTTTACCAAAAATTAGGGTTTCCATGTTTATTAATGATTACTTAACAATTCATGGGTGCAACC
42547782 TTTTACCAAAAATTAGGGTTTCCATGTTTATTAATGATTACTTAACAATTCATGGGTGCAACC
1 TTTTACCAAAAATTAGGGTTTCCATGTTTATTAATGATTACTTAACAATTCATGGGTGCAACC
42547845 AGTGATTCTG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (63 bp):
TTTTACCAAAAATTAGGGTTTCCATGTTTATTAATGATTACTTAACAATTCATGGGTGCAACC
Found at i:42549572 original size:39 final size:38
Alignment explanation
Indices: 42549529--42549656 Score: 114
Period size: 39 Copynumber: 3.3 Consensus size: 38
42549519 ACCAGCTCGA
* * * *
42549529 AGCCTGCAGGACTTTAGCCCGGACATATTTCCATCACGT
1 AGCCTGC-GGACTTAAGCCCGGACATAATTCCAGCACAT
* * *
42549568 AGCCTGTGGACCTTAAGTCCGGATATAATTCCAGCACAT
1 AGCCTGCGGA-CTTAAGCCCGGACATAATTCCAGCACAT
* * *
42549607 AGCCTGCGGACCCTAAGTCCGGATATAATTCCA-CTACAT
1 AGCCTGCGGA-CTTAAGCCCGGACATAATTCCAGC-ACAT
*
42549646 AACCTGCGGAC
1 AGCCTGCGGAC
42549657 CCTAAGTCCG
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
38 5 0.06
39 72 0.94
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (38 bp):
AGCCTGCGGACTTAAGCCCGGACATAATTCCAGCACAT
Found at i:42549657 original size:39 final size:39
Alignment explanation
Indices: 42549547--42549672 Score: 164
Period size: 39 Copynumber: 3.2 Consensus size: 39
42549537 GGACTTTAGC
* * * * * * *
42549547 CCGGACATATTTCCATCACGTAGCCTGTGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAACCTGCGGACCCTAAGT
*
42549586 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAACCTGCGGACCCTAAGT
42549625 CCGGATATAATTCCA-CTACATAACCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGC-ACATAACCTGCGGACCCTAAGT
42549664 CCGGATATA
1 CCGGATATA
42549673 CATCACTGAA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 1 0.01
39 78 0.99
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAACCTGCGGACCCTAAGT
Found at i:42553721 original size:38 final size:39
Alignment explanation
Indices: 42553651--42553728 Score: 149
Period size: 38 Copynumber: 2.0 Consensus size: 39
42553641 TTTATGCTTA
42553651 CTTAGTTTTATTTCCCTATTTTATAGTAAATCGAAAGCT
1 CTTAGTTTTATTTCCCTATTTTATAGTAAATCGAAAGCT
42553690 CTTAGTTTTATTTCCCTA-TTTATAGTAAATCGAAAGCT
1 CTTAGTTTTATTTCCCTATTTTATAGTAAATCGAAAGCT
42553728 C
1 C
42553729 GTTGGATTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
38 21 0.54
39 18 0.46
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (39 bp):
CTTAGTTTTATTTCCCTATTTTATAGTAAATCGAAAGCT
Found at i:42560095 original size:17 final size:17
Alignment explanation
Indices: 42560073--42560117 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
42560063 GGTTGCAATT
*
42560073 CATGCATGTCCTACATG
1 CATGCACGTCCTACATG
42560090 CATGCACGTCCTACATG
1 CATGCACGTCCTACATG
42560107 CATGCACGTCC
1 CATGCACGTCC
42560118 AAGGGAGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (17 bp):
CATGCACGTCCTACATG
Found at i:42561707 original size:20 final size:20
Alignment explanation
Indices: 42561684--42561723 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42561674 ATTTTTTATC
42561684 ACATTTTCTTTAATTTTTAA
1 ACATTTTCTTTAATTTTTAA
42561704 ACATTTTCTTTAATTTTTAA
1 ACATTTTCTTTAATTTTTAA
42561724 CTTAAGCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (20 bp):
ACATTTTCTTTAATTTTTAA
Found at i:42581682 original size:26 final size:26
Alignment explanation
Indices: 42581653--42581707 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
42581643 GATCATAACA
42581653 ATTCTTTAAGTTCTTAGATGAAAATG
1 ATTCTTTAAGTTCTTAGATGAAAATG
*
42581679 ATTCTTTAAGTTCTTAGATGCAAATG
1 ATTCTTTAAGTTCTTAGATGAAAATG
42581705 ATT
1 ATT
42581708 GTGACTTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.44
Consensus pattern (26 bp):
ATTCTTTAAGTTCTTAGATGAAAATG
Found at i:42586716 original size:13 final size:13
Alignment explanation
Indices: 42586698--42586728 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
42586688 TGGACTTCCT
42586698 TACACGGGCAGAC
1 TACACGGGCAGAC
42586711 TACACGGGCAGAC
1 TACACGGGCAGAC
42586724 TACAC
1 TACAC
42586729 AGTCGTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.26, T:0.10
Consensus pattern (13 bp):
TACACGGGCAGAC
Found at i:42592494 original size:43 final size:43
Alignment explanation
Indices: 42592443--42592574 Score: 167
Period size: 43 Copynumber: 3.1 Consensus size: 43
42592433 AAGTCTGAAT
* * *
42592443 TCAT-TCACCGGCATTATAGCCTGCTAAGCCCGAGGCCCGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATA
* * *
42592485 TTATCTCACCGGCATTATAACCTGCTAGGCTCGAAGCCCGTTA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATA
* * *
42592528 TCATTTCACTGGAATTATAGCCTGCTAGGCTCGAAGCCCGTATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCG-ATA
42592572 TCA
1 TCA
42592575 CATTTCGATA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
42 3 0.04
43 68 0.89
44 5 0.07
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.27
Consensus pattern (43 bp):
TCATCTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATA
Found at i:42593326 original size:70 final size:70
Alignment explanation
Indices: 42593209--42593343 Score: 216
Period size: 70 Copynumber: 1.9 Consensus size: 70
42593199 TAGCACATAA
* * * *
42593209 CACCATGATTTTGTCCTAATTTGGACAGCCAATAATTTACAATATTACAGCAGCATATTAATTAG
1 CACCATAAATTTGTCCTAATTTGGACAGCCAATAATTTACAACATTACAGCAGCAAATTAATTAG
42593274 CTAAG
66 CTAAG
* *
42593279 CACCATAAATTTGTCCTAATTTGGACAGCTAATAATTTACAGCATTACAGCAGCAAATTAATTAG
1 CACCATAAATTTGTCCTAATTTGGACAGCCAATAATTTACAACATTACAGCAGCAAATTAATTAG
42593344 TAATAAACTA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (70 bp):
CACCATAAATTTGTCCTAATTTGGACAGCCAATAATTTACAACATTACAGCAGCAAATTAATTAG
CTAAG
Found at i:42596526 original size:40 final size:40
Alignment explanation
Indices: 42596469--42596648 Score: 249
Period size: 40 Copynumber: 4.5 Consensus size: 40
42596459 CCCAAGTTTT
* * * *
42596469 CTTCGGGAT-TTAG-CCGGATATAACCACACGCCCAATTGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAATGC
* * *
42596508 CTTCGGGTCTTAACCCGGACATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
42596548 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATG-
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
42596587 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
* *
42596627 CTTCGGGGCTTAGCCCTGATAT
1 CTTCGGGTCTTAGCCCGGATAT
42596649 CATTCAAATG
Statistics
Matches: 126, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
38 1 0.01
39 49 0.39
40 76 0.60
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
Found at i:42596604 original size:79 final size:80
Alignment explanation
Indices: 42596469--42596648 Score: 249
Period size: 79 Copynumber: 2.3 Consensus size: 80
42596459 CCCAAGTTTT
* * * *
42596469 CTTCGGGAT-TTAG-CCGGATATAACCACACGCCCAATTGCCTTCGGGTCTTAACCCGGACATAG
1 CTTCGGG-TCTTAGCCCGGATATAACAACACGCACAAATGCCTTCGGGTCTTAACCCGGACATAA
42596532 CAACTCGCACAAATGC
65 CAACTCGCACAAATGC
* * *
42596548 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATG-CTTCGGGTCTTAGCCCGGATATAAC
1 CTTCGGGTCTTAGCCCGGATATAACAACACGCACAAATGCCTTCGGGTCTTAACCCGGACATAAC
42596612 AACTCGCACAAATGC
66 AACTCGCACAAATGC
* *
42596627 CTTCGGGGCTTAGCCCTGATAT
1 CTTCGGGTCTTAGCCCGGATAT
42596649 CATTCAAATG
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 1 0.01
79 68 0.76
80 21 0.23
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (80 bp):
CTTCGGGTCTTAGCCCGGATATAACAACACGCACAAATGCCTTCGGGTCTTAACCCGGACATAAC
AACTCGCACAAATGC
Found at i:42603142 original size:40 final size:40
Alignment explanation
Indices: 42603048--42603232 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
42603038 TATTCGAATG
42603048 ATATCCGGGCTAAG-TCCCGAAGGC-TTTGGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTT-GTGCTA-GTGACT
* * * *
42603089 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* * *
42603129 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* *
42603169 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* *
42603209 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
42603233 CTTGTGCAAG
Statistics
Matches: 120, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
39 1 0.01
40 89 0.74
41 27 0.22
42 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:42603223 original size:80 final size:81
Alignment explanation
Indices: 42603050--42603232 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
42603040 TTCGAATGAT
* *
42603050 ATCCGGGCTAAGTCCCGAAGGCTTTGGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGCAT
1 ATCCGGGCTAAGACCCGAAGGCTTTGGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGCAT
* * *
42603115 TCGTGCGAGTTGCTAT
66 TCATGCGAGTTGCCAC
* * *
42603131 ATCCGGGCTAAGACCCGAAGGCATTT-GTGCTA-GCGATTATATCCGGGCTAAG-TCCCGAAGGC
1 ATCCGGGCTAAGACCCGAAGGC-TTTGGTGCTAGGCGACTATAACCGGACTAAGAT-CCGAAGGC
* *
42603193 ATTTATGCTAG-TGACCAC
64 ATTCATGCGAGTTG-CCAC
42603211 ATCCGGGCTAAGACCCGAAGGC
1 ATCCGGGCTAAGACCCGAAGGC
42603233 CTTGTGCAAG
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
79 3 0.03
80 56 0.63
81 27 0.30
82 3 0.03
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (81 bp):
ATCCGGGCTAAGACCCGAAGGCTTTGGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGCAT
TCATGCGAGTTGCCAC
Found at i:42606455 original size:31 final size:30
Alignment explanation
Indices: 42606420--42606485 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
42606410 CTTCTTGCAT
42606420 TAAAATCCAACC-AAATACAACAAATATAGCA
1 TAAAATCCAACCAAAATAC--CAAATATAGCA
* * *
42606451 TAAAATGCAGCCAAAATACCAAATTTAGCA
1 TAAAATCCAACCAAAATACCAAATATAGCA
42606481 TAAAA
1 TAAAA
42606486 AAATACAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 15 0.48
31 10 0.32
32 6 0.19
ACGTcount: A:0.56, C:0.20, G:0.06, T:0.18
Consensus pattern (30 bp):
TAAAATCCAACCAAAATACCAAATATAGCA
Found at i:42606746 original size:21 final size:21
Alignment explanation
Indices: 42606720--42606781 Score: 115
Period size: 21 Copynumber: 3.0 Consensus size: 21
42606710 TTCCTATGCT
42606720 CTGCCTCCCTCGCTGCTGCCG
1 CTGCCTCCCTCGCTGCTGCCG
42606741 CTGCCTCCCTCGCTGCTGCCG
1 CTGCCTCCCTCGCTGCTGCCG
*
42606762 CTGCCTCCCTCTCTGCTGCC
1 CTGCCTCCCTCGCTGCTGCC
42606782 TCCGCTCTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.00, C:0.53, G:0.21, T:0.26
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCTGCCG
Found at i:42607217 original size:13 final size:14
Alignment explanation
Indices: 42607192--42607220 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42607182 TGATGAATTG
42607192 AATTAAACAATTAT
1 AATTAAACAATTAT
42607206 AATTAAAC-ATTAT
1 AATTAAACAATTAT
42607219 AA
1 AA
42607221 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:42607423 original size:16 final size:17
Alignment explanation
Indices: 42607386--42607424 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
42607376 AAAATATTAT
*
42607386 TTAATATTAGAAAGTTA
1 TTAATATTAGAAAGTAA
*
42607403 TTAATATTTGAAAG-AA
1 TTAATATTAGAAAGTAA
42607419 TTAATA
1 TTAATA
42607425 AAATTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (17 bp):
TTAATATTAGAAAGTAA
Found at i:42613769 original size:40 final size:39
Alignment explanation
Indices: 42613604--42613787 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
42613594 AAATTGAATG
* * *
42613604 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
42613644 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
42613684 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
42613724 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
42613763 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
42613788 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:42613812 original size:80 final size:81
Alignment explanation
Indices: 42613644--42613832 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
42613634 GCTGGAAATT
* * * *
42613644 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
42613709 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
42613725 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
42613788 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
42613804 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
42613833 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:42615737 original size:9 final size:9
Alignment explanation
Indices: 42615723--42615912 Score: 107
Period size: 9 Copynumber: 20.6 Consensus size: 9
42615713 TATTTAAGTA
42615723 TTATGTAAG
1 TTATGTAAG
42615732 TTATGTAAG
1 TTATGTAAG
*
42615741 TTATGATATG
1 TTATG-TAAG
* * *
42615751 ATATAT-AT
1 TTATGTAAG
*
42615759 TTATGTAAA
1 TTATGTAAG
* *
42615768 TTATAT-AT
1 TTATGTAAG
*
42615776 TTATCTAAG
1 TTATGTAAG
*
42615785 TTATATAAG
1 TTATGTAAG
42615794 TTATGTAAG
1 TTATGTAAG
*
42615803 TTATGTAAA
1 TTATGTAAG
*
42615812 TTATGATATAAAA
1 TTATG---T-AAG
*
42615825 TATATTTAAG
1 T-TATGTAAG
42615835 TATTATGTAAG
1 --TTATGTAAG
42615846 TTATGTAAG
1 TTATGTAAG
* *
42615855 TTATAT-AT
1 TTATGTAAG
*
42615863 TTATCTAAG
1 TTATGTAAG
*
42615872 TTATATAAG
1 TTATGTAAG
*
42615881 TTATGTACG
1 TTATGTAAG
*
42615890 TTTTGTAAG
1 TTATGTAAG
* *
42615899 TTATATAAA
1 TTATGTAAG
42615908 TTATG
1 TTATG
42615913 ATATCAAATA
Statistics
Matches: 139, Mismatches: 31, Indels: 22
0.72 0.16 0.11
Matches are distributed among these distances:
8 16 0.12
9 98 0.71
10 8 0.06
11 8 0.06
12 2 0.01
13 4 0.03
14 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:42615805 original size:71 final size:69
Alignment explanation
Indices: 42615723--42615885 Score: 202
Period size: 71 Copynumber: 2.3 Consensus size: 69
42615713 TATTTAAGTA
* * * *
42615723 TTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAATTATAT-ATTTATCTAAGTT
1 TTATGTAAGTTATGTAAGTTATGATATAAAATATATTTAAGT--ATTATATAAGTTATCTAAGTT
42615787 ATATAAG
64 ATAT-AG
* * *
42615794 TTATGTAAGTTATGTAAATTATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT
1 TTATGTAAGTTATGTAAGTTATGATATAAAATATATTTAAGTATTATATAAGTTATCTAAGTTAT
*
42615859 ATAT
66 ATAG
* *
42615863 TTATCTAAGTTATATAAGTTATG
1 TTATGTAAGTTATGTAAGTTATG
42615886 TACGTTTTGT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
69 27 0.34
70 15 0.19
71 38 0.47
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (69 bp):
TTATGTAAGTTATGTAAGTTATGATATAAAATATATTTAAGTATTATATAAGTTATCTAAGTTAT
ATAG
Found at i:42615861 original size:87 final size:90
Alignment explanation
Indices: 42615759--42615943 Score: 259
Period size: 96 Copynumber: 2.0 Consensus size: 90
42615749 TGATATATAT
*
42615759 TTATGTAAATTATATATTTATCTAAGTTATATAAG-T-TA-TGTAAGTTATGTAAATTATGATAT
1 TTATGTAAATTATATATTTATCTAAGTTATATAAGTTGTATTGTAAGTTATATAAATTATGATAT
42615821 AAAATATATTTAAGTATTATGTAAG
66 AAAATATATTTAAGTATTATGTAAG
*
42615846 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTACGTTTTGTAAGTTATATAAATTA
1 TTATGTAAATTATATATTTATCTAAGTTATATAAG-T-TGTA----TTGTAAGTTATATAAATTA
* *
42615911 TGATATCAAATATATTTATGTATTATGTAAG
60 TGATATAAAATATATTTAAGTATTATGTAAG
42615942 TT
1 TT
42615944 TTTTATTTCA
Statistics
Matches: 85, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
87 34 0.40
90 1 0.01
91 2 0.02
96 48 0.56
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (90 bp):
TTATGTAAATTATATATTTATCTAAGTTATATAAGTTGTATTGTAAGTTATATAAATTATGATAT
AAAATATATTTAAGTATTATGTAAG
Found at i:42615899 original size:114 final size:114
Alignment explanation
Indices: 42615699--42615912 Score: 290
Period size: 114 Copynumber: 1.9 Consensus size: 114
42615689 ACTAGTTATG
* * * *
42615699 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATG
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATAGTTATA
*
42615764 TAAATTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
66 TAAATTATATATTTATCTAAGTTATATAAATTATGTAAGTTATGTAAAT
* *
42615813 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT-ATAT-TTATCTAAGTTAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATAT-AGTTAT
* * *
42615876 ATAAGTTATGTACGTTT-TGTAAGTTATATAAATTATG
65 ATAAATTATATA--TTTATCTAAGTTATATAAATTATG
42615913 ATATCAAATA
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
112 4 0.05
113 18 0.21
114 62 0.71
115 3 0.03
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.47
Consensus pattern (114 bp):
TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATAGTTATA
TAAATTATATATTTATCTAAGTTATATAAATTATGTAAGTTATGTAAAT
Found at i:42615951 original size:87 final size:87
Alignment explanation
Indices: 42615759--42615943 Score: 234
Period size: 87 Copynumber: 2.1 Consensus size: 87
42615749 TGATATATAT
*
42615759 TTATGTAAATTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAAA
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAAA
** *
42615824 ATATATTTAAGTATTATGTAAG
66 ATATATCAAAATATTATGTAAG
* * *
42615846 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTACGTTTTGTAAGTTAT-ATA-AAT
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAA-
*
42615909 TATGATATCAAATATATTTATGT-A-
65 AAT-ATATCAAA-ATA-TTATGTAAG
42615933 TTATGTAAGTT
1 TTATGTAAGTT
42615944 TTTTATTTCA
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
85 2 0.02
86 5 0.06
87 70 0.81
88 3 0.03
89 6 0.07
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (87 bp):
TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAAA
ATATATCAAAATATTATGTAAG
Found at i:42616037 original size:15 final size:15
Alignment explanation
Indices: 42616017--42616072 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
42616007 AAGTAGCGGG
42616017 ATTAAATAATATTTA
1 ATTAAATAATATTTA
42616032 ATTAAATAATATTT-
1 ATTAAATAATATTTA
42616046 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
*
42616061 ATTAAGTAATAT
1 ATTAAATAATAT
42616073 ACATGTCGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.46
16 5 0.14
17 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:42617154 original size:358 final size:358
Alignment explanation
Indices: 42616282--42617522 Score: 2428
Period size: 358 Copynumber: 3.5 Consensus size: 358
42616272 ATAAAACGGA
*
42616282 GAATTTTTTAAGATTCATCATACGCGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
1 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
42616347 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
66 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
42616412 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
131 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
*
42616477 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATTGTAATTTGAATATAA
196 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
42616542 TAATATAAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTA
261 TAATAT-AAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTA
42616607 AATGAGCTCGATAGAACTTTTTTCAAGTCTTTTT
325 AATGAGCTCGATAGAACTTTTTTCAAGTCTTTTT
42616641 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
1 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
42616706 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
66 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
42616771 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
131 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
42616836 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
196 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
42616901 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
261 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
42616966 ATGAGCTCGATAGAACTTTTTTCAAGTCTTTTT
326 ATGAGCTCGATAGAACTTTTTTCAAGTCTTTTT
*
42616999 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACTTAGGGAGGATCCATTATATCTTGCAG
1 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
42617064 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
66 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
42617129 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
131 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
42617194 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
196 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
42617259 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
261 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
42617324 ATGAGCTCGATAGAACTTTTTTCAAGTCTTTTT
326 ATGAGCTCGATAGAACTTTTTTCAAGTCTTTTT
*
42617357 GAATTTTTTAAGATTCATCATACGTGACGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
1 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
42617422 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
66 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
*
42617487 AAGGTTGGAGAGAAGGTCATCCATTGTTGTAATTTT
131 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTT
42617523 AATAGACAAG
Statistics
Matches: 876, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
358 612 0.70
359 264 0.30
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (358 bp):
GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
ATGAGCTCGATAGAACTTTTTTCAAGTCTTTTT
Found at i:42617766 original size:15 final size:15
Alignment explanation
Indices: 42617746--42617774 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42617736 AGAATTTTGA
42617746 AATAAAACGTACCTT
1 AATAAAACGTACCTT
42617761 AATAAAACGTACCT
1 AATAAAACGTACCT
42617775 GGTCTACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
AATAAAACGTACCTT
Found at i:42618284 original size:183 final size:183
Alignment explanation
Indices: 42617976--42618344 Score: 684
Period size: 183 Copynumber: 2.0 Consensus size: 183
42617966 CCTAGAACAG
42617976 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
42618041 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
66 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
* *
42618106 AGTAGGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
131 AGCAGGAAGCAGTAACTGAAACACATACAACATTAATTCACTAATACAGACAC
*
42618159 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATGAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
*
42618224 ATTAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
66 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
* *
42618289 AGCAGGAAGCAGTAACTGAAACATATACAACATTAATTCACTAATATAGACAC
131 AGCAGGAAGCAGTAACTGAAACACATACAACATTAATTCACTAATACAGACAC
42618342 ATG
1 ATG
42618345 GAACTATATC
Statistics
Matches: 180, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 180 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (183 bp):
ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
AGCAGGAAGCAGTAACTGAAACACATACAACATTAATTCACTAATACAGACAC
Found at i:42618434 original size:14 final size:13
Alignment explanation
Indices: 42618415--42618444 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
42618405 CAATATAATT
42618415 TTACTTCATATATA
1 TTACTTCATATA-A
42618429 TTACTTCATATAA
1 TTACTTCATATAA
42618442 TTA
1 TTA
42618445 TTATAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (13 bp):
TTACTTCATATAA
Found at i:42621340 original size:28 final size:28
Alignment explanation
Indices: 42621308--42621365 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
42621298 AATCAAAACT
*
42621308 CTAT-ACCTTAAACCATTAAACTATATCC
1 CTATAACCTTAAACC-CTAAACTATATCC
* *
42621336 CTATAACCTTAATCCCTAAAGTATATCC
1 CTATAACCTTAAACCCTAAACTATATCC
42621364 CT
1 CT
42621366 TAAACCCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (28 bp):
CTATAACCTTAAACCCTAAACTATATCC
Found at i:42621366 original size:21 final size:21
Alignment explanation
Indices: 42621342--42621385 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
42621332 ATCCCTATAA
* * *
42621342 CCTTAATCCCTAAAGTATATC
1 CCTTAAACCCAAAACTATATC
42621363 CCTTAAACCCAAAACTATATC
1 CCTTAAACCCAAAACTATATC
42621384 CC
1 CC
42621386 CTAACCATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.34, G:0.02, T:0.27
Consensus pattern (21 bp):
CCTTAAACCCAAAACTATATC
Found at i:42621397 original size:20 final size:22
Alignment explanation
Indices: 42621352--42621397 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
42621342 CCTTAATCCC
* *
42621352 TAAAGTATATCCCTTAAACCCA
1 TAAACTATATCCCCTAAACCCA
42621374 -AAACTATATCCCCT-AA-CCA
1 TAAACTATATCCCCTAAACCCA
42621393 TAAAC
1 TAAAC
42621398 CACAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.14
20 6 0.29
21 12 0.57
ACGTcount: A:0.43, C:0.30, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAACTATATCCCCTAAACCCA
Found at i:42621414 original size:28 final size:27
Alignment explanation
Indices: 42621366--42621433 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
42621356 GTATATCCCT
*
42621366 TAAACC-CAAAACTATATCCCCTAA-CC
1 TAAACCACAAAA-TATAACCCCTAAGCC
42621392 ATAAACCACAAAATAATAACCCCTAAGCC
1 -TAAACCACAAAAT-ATAACCCCTAAGCC
*
42621421 TTAACCACAAAAT
1 TAAACCACAAAAT
42621434 GTATAGATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 7 0.19
28 27 0.75
29 2 0.06
ACGTcount: A:0.49, C:0.32, G:0.01, T:0.18
Consensus pattern (27 bp):
TAAACCACAAAATATAACCCCTAAGCC
Found at i:42621625 original size:28 final size:28
Alignment explanation
Indices: 42621594--42621647 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
42621584 ACAAAATAAA
* *
42621594 AACCCTTAAGT-ATTAACCCCTAACCCCT
1 AACCCTTAAATCATAAACCCC-AACCCCT
42621622 AACCCTTAAATCATAAACCCCAACCC
1 AACCCTTAAATCATAAACCCCAACCC
42621648 TTAAACCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.37, C:0.41, G:0.02, T:0.20
Consensus pattern (28 bp):
AACCCTTAAATCATAAACCCCAACCCCT
Found at i:42621646 original size:21 final size:22
Alignment explanation
Indices: 42621615--42621658 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
42621605 ATTAACCCCT
*
42621615 AACCCCTAACCCTTAAATCATA
1 AACCCCTAACCCTTAAACCATA
42621637 AACCCC-AACCCTTAAACCATA
1 AACCCCTAACCCTTAAACCATA
42621658 A
1 A
42621659 TACATAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (22 bp):
AACCCCTAACCCTTAAACCATA
Found at i:42621789 original size:41 final size:41
Alignment explanation
Indices: 42621732--42621910 Score: 279
Period size: 41 Copynumber: 4.4 Consensus size: 41
42621722 AACCCTAAAC
* *
42621732 TTTTTAGCGGCATTTTACCAAAAGCGTCGCTAATGCTCTTA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
42621773 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
*
42621814 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTTTTA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
* * *
42621855 TTTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTC-TG
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
* *
42621895 TTTTTAGTGACGTTTT
1 TTTTTAGCGGCGTTTT
42621911 TGGTAAAACG
Statistics
Matches: 129, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 15 0.12
41 114 0.88
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (41 bp):
TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
Found at i:42621910 original size:40 final size:40
Alignment explanation
Indices: 42621732--42621941 Score: 260
Period size: 41 Copynumber: 5.2 Consensus size: 40
42621722 AACCCTAAAC
* *
42621732 TTTTTAGCGGCATTTTACCAAAAGCGTCGCTAATGCTCTTA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTC-TA
42621773 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTC-TA
*
42621814 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTTTTA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGC-TCTA
* * *
42621855 TTTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTG
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTA
* * *** *
42621895 TTTTTAGTGACGTTTTTGGTAAAA-CGCCGCTATTGCTCTA
1 TTTTTAGCGGCG-TTTTACCAAAAGCGCCGCTAATGCTCTA
42621935 TGTTTTA
1 T-TTTTA
42621942 CAATTTTTTT
Statistics
Matches: 153, Mismatches: 13, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
40 28 0.18
41 124 0.81
42 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTA
Found at i:42621980 original size:12 final size:12
Alignment explanation
Indices: 42621965--42621990 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42621955 GTTTTTTGAT
42621965 AAAACGCCGCTA
1 AAAACGCCGCTA
42621977 AAAACGCCGCTA
1 AAAACGCCGCTA
42621989 AA
1 AA
42621991 GACCTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:42633434 original size:3 final size:3
Alignment explanation
Indices: 42633426--42633456 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
42633416 TGTAATTTTG
*
42633426 TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
42633457 TTTTCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:42633443 original size:9 final size:9
Alignment explanation
Indices: 42633426--42633468 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
42633416 TGTAATTTTG
*
42633426 TCTTCTTCT
1 TCTTTTTCT
42633435 TCTTTTTCT
1 TCTTTTTCT
*
42633444 TCTTCTTCT
1 TCTTTTTCT
42633453 TCTTTTTTCT
1 TC-TTTTTCT
42633463 T-TTTTT
1 TCTTTTT
42633469 TTTTTTGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
8 5 0.17
9 18 0.60
10 7 0.23
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TCTTTTTCT
Found at i:42634597 original size:40 final size:40
Alignment explanation
Indices: 42634542--42634620 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
42634532 AACATAAGAG
42634542 TCTAATTTCACAATTTAAACATACCTTAATTAATCATGCA
1 TCTAATTTCACAATTTAAACATACCTTAATTAATCATGCA
42634582 TCTAATTTCACAATTTAAACATACCTTAATTAATCATGC
1 TCTAATTTCACAATTTAAACATACCTTAATTAATCATGC
42634621 TTTTAACCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (40 bp):
TCTAATTTCACAATTTAAACATACCTTAATTAATCATGCA
Found at i:42637752 original size:13 final size:13
Alignment explanation
Indices: 42637721--42637759 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
42637711 TCAAATAAAA
*
42637721 AAATGATTTA-AT
1 AAATGATATATAT
*
42637733 TAATGATATATAT
1 AAATGATATATAT
42637746 AAATGATATATAT
1 AAATGATATATAT
42637759 A
1 A
42637760 TAAAGATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (13 bp):
AAATGATATATAT
Found at i:42637758 original size:15 final size:14
Alignment explanation
Indices: 42637738--42637781 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
42637728 TTAATTAATG
42637738 ATATATATAAATGAT
1 ATATATATAAA-GAT
42637753 ATATATATAAAGAT
1 ATATATATAAAGAT
42637767 ACTAATATATGAAAG
1 A-T-ATATAT-AAAG
42637782 TATTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.15
15 12 0.46
16 6 0.23
17 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (14 bp):
ATATATATAAAGAT
Found at i:42637775 original size:14 final size:15
Alignment explanation
Indices: 42637738--42637767 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42637728 TTAATTAATG
42637738 ATATATATAAATGAT
1 ATATATATAAATGAT
42637753 ATATATATAAA-GAT
1 ATATATATAAATGAT
42637767 A
1 A
42637768 CTAATATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (15 bp):
ATATATATAAATGAT
Found at i:42637880 original size:27 final size:26
Alignment explanation
Indices: 42637837--42637901 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
42637827 GGAAACAAAT
*
42637837 TATACATAAATAAATTTAAAAGAATA
1 TATACATAAATAAATTTAAAAGAAAA
* *
42637863 TATATATATAATAGATTTAAAAGAAAA
1 TATACATA-AATAAATTTAAAAGAAAA
42637890 TATTTACATAAA
1 TA--TACATAAA
42637902 ATAATATGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 7 0.22
27 18 0.56
28 2 0.06
29 5 0.16
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (26 bp):
TATACATAAATAAATTTAAAAGAAAA
Found at i:42640076 original size:44 final size:45
Alignment explanation
Indices: 42640015--42640111 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 45
42640005 ACTGCTTAGG
* ** **
42640015 GAGATAAGATCTTCAATCTTCAGTCTACTTC-CTTGCTACCTCAG-
1 GAGATAAGATCTACAATCGCCAACCTA-TTCTCTTGCTACCTCAGA
42640059 GAAGATAAGA-CTACAATCGCCAACCTATTCTCTTGCTACCTCAGA
1 G-AGATAAGATCTACAATCGCCAACCTATTCTCTTGCTACCTCAGA
42640104 GAGATAAG
1 GAGATAAG
42640112 GCTGGTGGCT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
43 3 0.07
44 33 0.73
45 9 0.20
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (45 bp):
GAGATAAGATCTACAATCGCCAACCTATTCTCTTGCTACCTCAGA
Found at i:42640134 original size:177 final size:176
Alignment explanation
Indices: 42639674--42640200 Score: 682
Period size: 177 Copynumber: 3.0 Consensus size: 176
42639664 CAGGGAGATA
* * * * *
42639674 CAATCTTTAGTCTGCTTCCTTGCTACCTCAAGAAGATAAGACTATAATCGTCAATCTGTTCTCTT
1 CAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCCAACCTGTTCTCTT
* * * *
42639739 GCTACCTCAGAAAGATAAGGCTGGTGGCTAAAATCTGCTCC---CCTACTACCTCGGAAAGATAA
66 GCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATTCCGA-TACAT---AGAGATAA
* ** * *
42639801 GATTCACCATCTTCGATCTATTTAACAACTGCTTAGGGAGATAAGATCTT
127 GATTCACCGTCTTCGATCTGCTTCACTACTGCTTAGGGAGATAAGATCTT
* * * * *
42639851 CAATCTTCAGTTTGCTTCCTTACTACCTCAGGAAGATAAGACTACAACCGCCAACCCGCTCTCTT
1 CAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCCAACCTGTTCTCTT
* *
42639916 GCTACCTCAGTGAGATAAGGCTGGTGGCTAGAATCTGCTCCATTGCCGATACATAGAGATAAGAT
66 GCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATT-CCGATACATAGAGATAAGAT
*
42639981 TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTT
130 TCACCGTCTTCGATCTGCTTCACTACTGCTTAGGGAGATAAGATCTT
* *
42640028 CAATCTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCCAACCTATTCTCTT
1 CAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCCAACCTGTTCTCTT
* * * *
42640093 GCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATTTGCTCCATTATCGACACATGGAGATAAGAT
66 GCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATT-CCGATACATAGAGATAAGAT
* * * * *
42640158 TCGCCGTCTTCAATTTGCTTCACTACTACTTAGGGAGACAAGA
130 TCACCGTCTTCGATCTGCTTCACTACTGCTTAGGGAGATAAGA
42640201 CCTATGAATT
Statistics
Matches: 304, Mismatches: 42, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
177 297 0.98
180 4 0.01
181 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (176 bp):
CAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCGCCAACCTGTTCTCTT
GCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATTCCGATACATAGAGATAAGATT
CACCGTCTTCGATCTGCTTCACTACTGCTTAGGGAGATAAGATCTT
Found at i:42640387 original size:64 final size:63
Alignment explanation
Indices: 42640274--42640395 Score: 190
Period size: 64 Copynumber: 1.9 Consensus size: 63
42640264 TGTATCTATG
** * *
42640274 CTTATGCCAAAAATTAGGATGCTATGATTGAAATGAATCAAATGTTCCTAACTAGATGCAATA
1 CTTATGCCAAAAATTAGGACACTATGATCGAAATGAATCAAATGCTCCTAACTAGATGCAATA
*
42640337 CTTATGTCAAATAATTAGGACACTATGATCGAAATGAATCAAATGCTCCTAACTAGATG
1 CTTATGCCAAA-AATTAGGACACTATGATCGAAATGAATCAAATGCTCCTAACTAGATG
42640396 TGTTATGATA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
63 10 0.19
64 43 0.81
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (63 bp):
CTTATGCCAAAAATTAGGACACTATGATCGAAATGAATCAAATGCTCCTAACTAGATGCAATA
Found at i:42652976 original size:13 final size:13
Alignment explanation
Indices: 42652958--42652983 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42652948 TGATTTAATT
42652958 AATGATATATATA
1 AATGATATATATA
42652971 AATGATATATATA
1 AATGATATATATA
42652984 TATAAATACT
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
AATGATATATATA
Found at i:42653123 original size:2 final size:2
Alignment explanation
Indices: 42653118--42653148 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42653108 ACACACACAC
42653118 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 A
42653149 ATAGATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42656242 original size:49 final size:50
Alignment explanation
Indices: 42656170--42656347 Score: 268
Period size: 52 Copynumber: 3.5 Consensus size: 50
42656160 ATTAGTGACT
*
42656170 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AGATAGCTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTGGTCA
42656219 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGC-TTGGTCA
* * *
42656271 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGGTAGCTTTGACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTGGTC-A
* *
42656322 CAAGGGTGGTACTATGTGTAGGCCAC
1 CAAGTGTGGTACTATGTGAAGGCCAC
42656348 CAGGTATCCA
Statistics
Matches: 119, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
49 34 0.29
50 4 0.03
51 39 0.33
52 42 0.35
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (50 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTGGTCA
Found at i:42656290 original size:52 final size:51
Alignment explanation
Indices: 42656170--42656347 Score: 272
Period size: 51 Copynumber: 3.5 Consensus size: 51
42656160 ATTAGTGACT
*
42656170 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AGATAGC-TTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTCA
42656219 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTTTGGTCA
* *
42656271 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGGTAGCTTT-GACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTC-A
* *
42656322 CAAGGGTGGTACTATGTGTAGGCCAC
1 CAAGTGTGGTACTATGTGAAGGCCAC
42656348 CAGGTATCCA
Statistics
Matches: 120, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
49 34 0.28
50 2 0.02
51 42 0.35
52 42 0.35
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (51 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTCA
Found at i:42658519 original size:27 final size:27
Alignment explanation
Indices: 42658481--42658608 Score: 202
Period size: 27 Copynumber: 4.7 Consensus size: 27
42658471 CGTACCTGAA
*
42658481 CCCTCATGTGATAAAATGATGATTTTG
1 CCCTTATGTGATAAAATGATGATTTTG
*
42658508 CCCTTATGTGATAAAATGACGATTTTG
1 CCCTTATGTGATAAAATGATGATTTTG
* *
42658535 CCCTTATATGATAAAATGACGATTTTG
1 CCCTTATGTGATAAAATGATGATTTTG
*
42658562 CCCTTATGTGATAAAATGATGATTTTC
1 CCCTTATGTGATAAAATGATGATTTTG
*
42658589 CCCTTATGTGATGAAATGAT
1 CCCTTATGTGATAAAATGAT
42658609 CGAAATACCC
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 94 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (27 bp):
CCCTTATGTGATAAAATGATGATTTTG
Found at i:42658619 original size:27 final size:27
Alignment explanation
Indices: 42658480--42658672 Score: 94
Period size: 27 Copynumber: 7.1 Consensus size: 27
42658470 GCGTACCTGA
* **
42658480 ACCCTCATGTGATAAAATGAT-GATTTT
1 ACCCTTATGTGATAAAATGATCGA-AAT
* **
42658507 GCCCTTATGTGATAAAATGA-CGATTTT
1 ACCCTTATGTGATAAAATGATCGA-AAT
* * **
42658534 GCCCTTATATGATAAAATGA-CGATTTT
1 ACCCTTATGTGATAAAATGATCGA-AAT
* **
42658561 GCCCTTATGTGATAAAATGAT-GATTTT
1 ACCCTTATGTGATAAAATGATCGA-AAT
* *
42658588 CCCCTTATGTGATGAAATGATCGAAAT
1 ACCCTTATGTGATAAAATGATCGAAAT
* *
42658615 ACCCTCATAG-GGTAAAATGA-CTGAAAT
1 ACCCTTAT-GTGATAAAATGATC-GAAAT
* * *
42658642 ACCCTTATAG-GGTAGAATGACCGAAAT
1 ACCCTTAT-GTGATAAAATGATCGAAAT
42658669 ACCC
1 ACCC
42658673 CTGTAGGGTA
Statistics
Matches: 146, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
26 1 0.01
27 141 0.97
28 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (27 bp):
ACCCTTATGTGATAAAATGATCGAAAT
Found at i:42658631 original size:81 final size:81
Alignment explanation
Indices: 42658481--42658635 Score: 213
Period size: 81 Copynumber: 1.9 Consensus size: 81
42658471 CGTACCTGAA
* ** * * *
42658481 CCCTCATGTGATAAAATGATGATTTTGCCCTTATGTGATAAAATGACGATTTTGCCCTTATATGA
1 CCCTCATGTGATAAAATGATGATTTTCCCCTTATGTGATAAAATGACGATAATACCCTCATAGGA
42658546 TAAAATGACGATTTTG
66 TAAAATGACGATTTTG
* *
42658562 CCCTTATGTGATAAAATGATGATTTTCCCCTTATGTGATGAAATGATCGA-AATACCCTCATAGG
1 CCCTCATGTGATAAAATGATGATTTTCCCCTTATGTGATAAAATGA-CGATAATACCCTCATAGG
*
42658626 GTAAAATGAC
65 ATAAAATGAC
42658636 TGAAATACCC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
81 61 0.95
82 3 0.05
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (81 bp):
CCCTCATGTGATAAAATGATGATTTTCCCCTTATGTGATAAAATGACGATAATACCCTCATAGGA
TAAAATGACGATTTTG
Found at i:42658679 original size:27 final size:27
Alignment explanation
Indices: 42658602--42658716 Score: 124
Period size: 27 Copynumber: 4.3 Consensus size: 27
42658592 TTATGTGATG
*
42658602 AAATGATCGAAATA-CCCTCATAGGGTA
1 AAATGACCGAAATACCCCT-ATAGGGTA
* *
42658629 AAATGACTGAAATACCCTTATAGGGTA
1 AAATGACCGAAATACCCCTATAGGGTA
* *
42658656 GAATGACCGAAATACCCCTGTAGGGTA
1 AAATGACCGAAATACCCCTATAGGGTA
* * ** *
42658683 AAATGACTGTAATACCCCGGTAAGGTA
1 AAATGACCGAAATACCCCTATAGGGTA
42658710 AAATGAC
1 AAATGAC
42658717 AGATTTGTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
27 72 0.96
28 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (27 bp):
AAATGACCGAAATACCCCTATAGGGTA
Found at i:42658715 original size:54 final size:54
Alignment explanation
Indices: 42658602--42658716 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
42658592 TTATGTGATG
* ** *
42658602 AAATGATCGAAATACCCTCATAGGGTAAAATGACTGAAATACCCTTATAGGGTA
1 AAATGACCGAAATACCCTCATAGGGTAAAATGACTGAAATACCCCGATAAGGTA
* * * *
42658656 GAATGACCGAAATACCC-CTGTAGGGTAAAATGACTGTAATACCCCGGTAAGGTA
1 AAATGACCGAAATACCCTC-ATAGGGTAAAATGACTGAAATACCCCGATAAGGTA
42658710 AAATGAC
1 AAATGAC
42658717 AGATTTGTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 1 0.02
54 50 0.98
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (54 bp):
AAATGACCGAAATACCCTCATAGGGTAAAATGACTGAAATACCCCGATAAGGTA
Found at i:42659081 original size:18 final size:19
Alignment explanation
Indices: 42659058--42659109 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
42659048 TCTGCTTGCA
42659058 TACTGCACTGATTACT-GT
1 TACTGCACTGATTACTGGT
* *
42659076 TACTGCATTGATCA-TGGT
1 TACTGCACTGATTACTGGT
*
42659094 TGCTGCACTGATTACT
1 TACTGCACTGATTACT
42659110 ATTGCTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (19 bp):
TACTGCACTGATTACTGGT
Found at i:42659114 original size:18 final size:18
Alignment explanation
Indices: 42659060--42659115 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
42659050 TGCTTGCATA
*
42659060 CTGCACTGATTACTGTTA
1 CTGCACTGATTACTGTTG
* *
42659078 CTGCATTGATCA-TGGTTG
1 CTGCACTGATTACT-GTTG
*
42659096 CTGCACTGATTACTATTG
1 CTGCACTGATTACTGTTG
42659114 CT
1 CT
42659116 AAAATGGGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 1 0.03
18 28 0.93
19 1 0.03
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (18 bp):
CTGCACTGATTACTGTTG
Found at i:42660682 original size:10 final size:10
Alignment explanation
Indices: 42660669--42660693 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42660659 TTTTAATAAA
42660669 TTTTCCAATG
1 TTTTCCAATG
42660679 TTTTCCAATG
1 TTTTCCAATG
42660689 TTTTC
1 TTTTC
42660694 GGTTTAGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (10 bp):
TTTTCCAATG
Found at i:42663712 original size:43 final size:43
Alignment explanation
Indices: 42663665--42663765 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 43
42663655 TGGGTCACTC
* * *
42663665 GAGACGACTGTGGACTATTTTGTTAAGGTTGCACAGGTCGCAT
1 GAGACAACTGTGGACTATTCTGTTAAGGTCGCACAGGTCGCAT
* * *
42663708 GAGACAACTGTGGACTGTTCTGTTAAGGTCGCACGGGTCGCGT
1 GAGACAACTGTGGACTATTCTGTTAAGGTCGCACAGGTCGCAT
*
42663751 GAGACAATTGTGGAC
1 GAGACAACTGTGGAC
42663766 CGACCGATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.27
Consensus pattern (43 bp):
GAGACAACTGTGGACTATTCTGTTAAGGTCGCACAGGTCGCAT
Found at i:42667778 original size:27 final size:27
Alignment explanation
Indices: 42667740--42667826 Score: 106
Period size: 27 Copynumber: 3.2 Consensus size: 27
42667730 GATCATTAAG
*
42667740 ACCCCATA-TTTGTAAGATTACCGAAAT
1 ACCCC-TAGTTTGTAAAATTACCGAAAT
*
42667767 ACCCCTAGTTTGTAAAATTACCGAAAC
1 ACCCCTAGTTTGTAAAATTACCGAAAT
* *
42667794 ACCTCC-GGTTTGTAAAATTACTGAAAT
1 ACC-CCTAGTTTGTAAAATTACCGAAAT
42667821 ACCCCT
1 ACCCCT
42667827 GTAAGATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
26 4 0.08
27 46 0.88
28 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.29
Consensus pattern (27 bp):
ACCCCTAGTTTGTAAAATTACCGAAAT
Found at i:42668132 original size:43 final size:43
Alignment explanation
Indices: 42668082--42668197 Score: 169
Period size: 43 Copynumber: 2.7 Consensus size: 43
42668072 TCTGATAGGA
*
42668082 TCGTACGGGTCGCACGAGACGACTGTGGACTATTCTGTTAAGG
1 TCGTACGGGTCGTACGAGACGACTGTGGACTATTCTGTTAAGG
* *
42668125 TTGTACGGGTCGTACGAGACGACTGTGGACTATTTTGTTAAGG
1 TCGTACGGGTCGTACGAGACGACTGTGGACTATTCTGTTAAGG
* ** *
42668168 TCGCATAGGTCGTGCGAGACGACTGTGGAC
1 TCGTACGGGTCGTACGAGACGACTGTGGAC
42668198 ATACCAATGG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.27
Consensus pattern (43 bp):
TCGTACGGGTCGTACGAGACGACTGTGGACTATTCTGTTAAGG
Found at i:42678759 original size:13 final size:13
Alignment explanation
Indices: 42678741--42678765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42678731 GAATTAGCAT
42678741 GTGTGAAAGTTTC
1 GTGTGAAAGTTTC
42678754 GTGTGAAAGTTT
1 GTGTGAAAGTTT
42678766 AATTGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.32, T:0.40
Consensus pattern (13 bp):
GTGTGAAAGTTTC
Found at i:42681118 original size:55 final size:54
Alignment explanation
Indices: 42681002--42681121 Score: 129
Period size: 55 Copynumber: 2.2 Consensus size: 54
42680992 CCCTATGATT
* *
42681002 TTAAGTCAGTCTTGACCACGGCCAAGGTACACGAGCGTGTGGCTAGCCGTGTGAC
1 TTAAGTCAGTCTTGACCACGGCCAAGGCACACGAGCATGT-GCTAGCCGTGTGAC
** *
42681057 CCAAGTCAGTCTCT-ACTACGGCCAAGGCACACGAGCATGT-CTTATGGCCGTGTGA-
1 TTAAGTCAGTCT-TGACCACGGCCAAGGCACACGAGCATGTGC-TA--GCCGTGTGAC
42681112 TTAAGTCAGT
1 TTAAGTCAGT
42681122 ATGTATCCCT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
53 1 0.02
54 2 0.04
55 41 0.76
56 10 0.19
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (54 bp):
TTAAGTCAGTCTTGACCACGGCCAAGGCACACGAGCATGTGCTAGCCGTGTGAC
Found at i:42682006 original size:909 final size:911
Alignment explanation
Indices: 42680241--42682047 Score: 3010
Period size: 909 Copynumber: 2.0 Consensus size: 911
42680231 TTTGGTTAAG
* *
42680241 AATTATATGCAAATTGATGATGATTATATGATTTAAATTATAAGATTATTTGTATATGGCTTACT
1 AATTATATGAAAATTGATGATGATTATATGATTTAAATGATAAGATTATTTGTATATGGCTTACT
* * * * *
42680306 AAGCTTTTGAAAGCTTATTTTGTGTGTGTTTACATTGTTTTATAGATATCGTAGCTATCGGGTGC
66 AAGCTTTTGAAAGCTTACTTTATATGTGTTTACATTATTTTATAGATATCGTAGCTATCGGGAGC
* *
42680371 TCGGGGATCGTAAAGGATTGTCACCACACTATCGTACCTTGTTTTGGTACCTTTTAACATTGTGA
131 TCGGGGATCGTAAAGGATTGTCACCACACTATCGAACCTTGTTTTGGCACCTTTTAACATTGTGA
*
42680436 ATATAATAGTATGGCATGTATAGGTTAGAAGTACTTTGAGGTATGTTTTGTAATGTGTATATCAT
196 ATATAATAGTATGGCATGTATAGGCTAGAAGTACTTTGAGGTATGTTTTGTAATGTGTATATCAT
*
42680501 GCCATGAGATATGGCTAAATTATGGTTGAACTTATGGTTTGATTTTGGTATATGATATGTGATGC
261 ACCATGAGATATGGCTAAATTATGGTTGAACTTATGGTTTGATTTTGGTATATGATATGTGATGC
42680566 AAATTATGCTTATGTGATGTGTTTATAAATAACCAAATGAAATGGTCAATATTGGTAAATTTTGG
326 AAATTATGCTTATGTGATGTGTTTATAAATAACCAAATGAAATGGTCAATATTGGTAAATTTTGG
42680631 CATATGCAAATTTGAGATATTGGTAAGTTTATAGCATGTGATTGAATGAAAATAAAATGAGGATA
391 CATATGCAAATTTGAGATATTGGTAAGTTTATAGCATGTGATTGAATGAAAATAAAATGAGGATA
* * *
42680696 TGAAACAAATGTTTCGTTATGATTTTGTCTTATGTTTTGGCATCATTTGGTATGATTATTAAGCA
456 TGAAACAAATGTTTCGATATGATTTTGTATTATGTTTTGGCATAATTTGGTATGATTATTAAGCA
42680761 TGAAATTGGTTGATAATGTTATGGCATGATTGGTGTAAGTTTTGGTATTGAAATTGGTTGAAGTT
521 TGAAATTGGTTGATAATGTTATGGCATGATTGGTGTAAGTTTTGGTATTGAAATTGGTTGAAGTT
* *
42680826 ATAGTGAAAATATGGTTGGTTTGATGCTTGTAGGTTTGACCCAAATTGGGTGGCAAATTGGCTTT
586 ATAGTGAAAATATGGTTGGTTTGATGCTTGTAGGTTTGACCCAAATTGGCTGGAAAATTGGCTTT
* * * * **
42680891 TCAAATGGCCTATTTTTGTCCATACGGGCAGAGACACGGGCATCTGTCTCAGTCGTGTGTGACAC
651 TCAAATGGCCTATTTTTGTCCACACGGGCAGAGACACAGGCATCTGTCTCAGCCATGTGCAACAC
** * * *
42680956 ATGGTGATGTTGCACGACCATGTGTCCCCTGGGGTACCCTATGATTTTAAGTCAGTCTTGACCAC
716 ACAGTCATGTTGAACGACCATGTGTCCCCTGGGGTACCCTACGATTTTAAGTCAGTCTTGACCAC
* * * * *
42681021 GGCCAAGGTACACGAGCGTGTGGCTAGCCGTGTGACCCAAGTCAGTCTCTACTACGGCCAAGGCA
781 GGCCAACGCACACGAGCGTATGGCTAGCCGTGTGACCCAAGTCAGTCTCTACCACAGCCAAGGCA
*
42681086 CACGAGCATGTCTTATGGCCGTGTGATTAAGTCAGTATGTAT-CCCTGTTTTGTGGCCTTATGGC
846 CACGAGCATGTCTTATGGCCGTGTGATTAAGTCAGTATCTATGCCCTGTTTTGTGGCCTTATGGC
42681150 A
911 A
*
42681151 AATTATATGAAAATTGATGATGATTATATGATTTAAATGATAA-ATTTATTTGTCTATGGCTTAC
1 AATTATATGAAAATTGATGATGATTATATGATTTAAATGATAAGA-TTATTTGTATATGGCTTAC
* *
42681215 TAAGCTTTTGAAAGCTTACTTTATATGTGTTTGCATTATTTTATAGATATCGTAGCTGTCGGGAG
65 TAAGCTTTTGAAAGCTTACTTTATATGTGTTTACATTATTTTATAGATATCGTAGCTATCGGGAG
* * *
42681280 CTCGGGGTTCGTATAGGATTGTCACCACACTATCGAACCTTGTTTTGGCACCTTTTGACA-TGTG
130 CTCGGGGATCGTAAAGGATTGTCACCACACTATCGAACCTTGTTTTGGCACCTTTTAACATTGTG
42681344 AATATAATAGTATGGCATGTATAGGCTAGAAGTACTTTGAGGTATGTTTTGTAATGTGTATATCA
195 AATATAATAGTATGGCATGTATAGGCTAGAAGTACTTTGAGGTATGTTTTGTAATGTGTATATCA
*
42681409 TACCATGAGATATGGCTAGATTATGGTTGAACTTATGGTTTGATTTTGGTATATGATATGTGATG
260 TACCATGAGATATGGCTAAATTATGGTTGAACTTATGGTTTGATTTTGGTATATGATATGTGATG
*
42681474 CAAATTATGCTTATGTGATGTGTTTATAAATGACCAAATGAAATGGTCAATATTGGTAAATTTTG
325 CAAATTATGCTTATGTGATGTGTTTATAAATAACCAAATGAAATGGTCAATATTGGTAAATTTTG
* * * * *
42681539 GTATGTGCAAGTTTGAGATATTGGTAAGTTTATAGCATGTGATTGAATGAAATTAAAATGAGGTT
390 GCATATGCAAATTTGAGATATTGGTAAGTTTATAGCATGTGATTGAATGAAAATAAAATGAGGAT
42681604 ATGAAACAAATGTTTAC-ATATGATTTTGTATTATGTTTTGGCATAATTTGGTATGATTATTAAG
455 ATGAAACAAATGTTT-CGATATGATTTTGTATTATGTTTTGGCATAATTTGGTATGATTATTAAG
*
42681668 CATGAAATTGGTTGATAATGTTATGGCATGATTGGTGTAAGTTTTGGTATTGACATTGGTTGAAG
519 CATGAAATTGGTTGATAATGTTATGGCATGATTGGTGTAAGTTTTGGTATTGAAATTGGTTGAAG
* * *
42681733 TTATATTGCAAATGTGGTTGGTTTGATGCTTGTAGGTTTGACCCAAATTGGCTGGAAAATTGGCT
584 TTATAGTGAAAATATGGTTGGTTTGATGCTTGTAGGTTTGACCCAAATTGGCTGGAAAATTGGCT
** *
42681798 TTTCAAATGGCCTATTTTTGTCCACACGGGCAGAGACACAGGTTTGTGTCTCAGCCATGTGCAAC
649 TTTCAAATGGCCTATTTTTGTCCACACGGGCAGAGACACAGGCATCTGTCTCAGCCATGTGCAAC
* *
42681863 ACACAGTCATGTTGAACGGCCATGTGTCCCCTGGGGTACCCTACGATTTTAAGTCAGTGTTGACC
714 ACACAGTCATGTTGAACGACCATGTGTCCCCTGGGGTACCCTACGATTTTAAGTCAGTCTTGACC
* * *
42681928 ACGGCCAACGCACACGGGCGTATGGCTAGCTGTGTGATCCAAGTCAGTCTCTACCACAGCCAAGG
779 ACGGCCAACGCACACGAGCGTATGGCTAGCCGTGTGACCCAAGTCAGTCTCTACCACAGCCAAGG
* * * *
42681993 CACACGGGCATGTCTTGTGGCTGTGTTATTAAGTCAGTATCTATGCCCTGTTTTG
844 CACACGAGCATGTCTTATGGCCGTGTGATTAAGTCAGTATCTATGCCCTGTTTTG
42682048 ACACGGCTTA
Statistics
Matches: 832, Mismatches: 62, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
909 649 0.78
910 183 0.22
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (911 bp):
AATTATATGAAAATTGATGATGATTATATGATTTAAATGATAAGATTATTTGTATATGGCTTACT
AAGCTTTTGAAAGCTTACTTTATATGTGTTTACATTATTTTATAGATATCGTAGCTATCGGGAGC
TCGGGGATCGTAAAGGATTGTCACCACACTATCGAACCTTGTTTTGGCACCTTTTAACATTGTGA
ATATAATAGTATGGCATGTATAGGCTAGAAGTACTTTGAGGTATGTTTTGTAATGTGTATATCAT
ACCATGAGATATGGCTAAATTATGGTTGAACTTATGGTTTGATTTTGGTATATGATATGTGATGC
AAATTATGCTTATGTGATGTGTTTATAAATAACCAAATGAAATGGTCAATATTGGTAAATTTTGG
CATATGCAAATTTGAGATATTGGTAAGTTTATAGCATGTGATTGAATGAAAATAAAATGAGGATA
TGAAACAAATGTTTCGATATGATTTTGTATTATGTTTTGGCATAATTTGGTATGATTATTAAGCA
TGAAATTGGTTGATAATGTTATGGCATGATTGGTGTAAGTTTTGGTATTGAAATTGGTTGAAGTT
ATAGTGAAAATATGGTTGGTTTGATGCTTGTAGGTTTGACCCAAATTGGCTGGAAAATTGGCTTT
TCAAATGGCCTATTTTTGTCCACACGGGCAGAGACACAGGCATCTGTCTCAGCCATGTGCAACAC
ACAGTCATGTTGAACGACCATGTGTCCCCTGGGGTACCCTACGATTTTAAGTCAGTCTTGACCAC
GGCCAACGCACACGAGCGTATGGCTAGCCGTGTGACCCAAGTCAGTCTCTACCACAGCCAAGGCA
CACGAGCATGTCTTATGGCCGTGTGATTAAGTCAGTATCTATGCCCTGTTTTGTGGCCTTATGGC
A
Found at i:42686769 original size:30 final size:29
Alignment explanation
Indices: 42686714--42686873 Score: 207
Period size: 29 Copynumber: 5.5 Consensus size: 29
42686704 ATAGTGAATC
42686714 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
*
42686743 CTCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
42686773 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
* *
42686802 CGCACACTTAGTGCTATATA--ATCAAACT
1 CGCACACTTAGTGCTATATATTTTC-AGCT
* * * * *
42686830 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATA-TATTTTCAGCT
42686860 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42686874 CAATCTTGTC
Statistics
Matches: 117, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.02
28 20 0.17
29 49 0.42
30 45 0.38
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:42686808 original size:59 final size:57
Alignment explanation
Indices: 42686714--42686873 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
42686704 ATAGTGAATC
* *
42686714 CGCACACTTAGTGCTATATATTTTCAGCTCTCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
42686773 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
42686830 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
42686874 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 49 0.53
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:42694214 original size:30 final size:30
Alignment explanation
Indices: 42694159--42694316 Score: 229
Period size: 29 Copynumber: 5.5 Consensus size: 30
42694149 ATAGTGAATC
42694159 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42694188 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42694218 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42694247 CGCACACTTAGTGCTATATAA---TCA-CT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
* * * * *
42694273 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42694303 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42694317 CAATCTTGTC
Statistics
Matches: 119, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
26 21 0.18
27 3 0.03
29 50 0.42
30 45 0.38
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:42694251 original size:59 final size:55
Alignment explanation
Indices: 42694159--42694316 Score: 226
Period size: 59 Copynumber: 2.8 Consensus size: 55
42694149 ATAGTGAATC
42694159 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCA-CT
42694218 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCACT
* * * * *
42694273 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
42694317 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
55 19 0.20
56 24 0.26
59 50 0.54
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (55 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCACT
Found at i:42699579 original size:40 final size:41
Alignment explanation
Indices: 42699535--42699640 Score: 137
Period size: 40 Copynumber: 2.6 Consensus size: 41
42699525 GCTACTTGTT
* * * *
42699535 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAGC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTTAGCA
*
42699575 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTAGCA
42699616 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42699641 CATCATTCGA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
40 48 0.83
41 10 0.17
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTAGCA
Found at i:42707534 original size:40 final size:39
Alignment explanation
Indices: 42707484--42707587 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 39
42707474 AGCTACTCTT
* * *
42707484 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAGC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAG-A-CTTAGCA
*
42707524 CAAATGCCTTCGGGACTTAACCCGGATTTAGACTTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGACTTAGCA
42707563 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42707588 CATCATTCGA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 21 0.37
39 9 0.16
40 25 0.44
41 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGACTTAGCA
Found at i:42709547 original size:15 final size:15
Alignment explanation
Indices: 42709527--42709557 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42709517 GTAATCCAGG
42709527 TACTCGAAGATATGC
1 TACTCGAAGATATGC
42709542 TACTCGAAGATATGC
1 TACTCGAAGATATGC
42709557 T
1 T
42709558 TAGATGTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (15 bp):
TACTCGAAGATATGC
Found at i:42711663 original size:41 final size:41
Alignment explanation
Indices: 42711618--42711735 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
42711608 TGAAAGATAA
42711618 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
42711659 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
42711689 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
42711730 ATGTAG
1 ATGTAG
42711736 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:42711673 original size:71 final size:71
Alignment explanation
Indices: 42711586--42711749 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
42711576 GAGATGTATC
42711586 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
42711651 AGGACA
66 AGGACA
42711657 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
42711722 AGGACA
66 AGGACA
42711728 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
42711750 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Done.