Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 134 of 161
Found at i:41714533 original size:42 final size:42
Alignment explanation
Indices: 41714486--41714607 Score: 149
Period size: 42 Copynumber: 2.9 Consensus size: 42
41714476 AAGTTTCAAT
*
41714486 TTAACCC-TATTGGGTTTCCGTTCAGCTCTTTTGAGCTTTAGC
1 TTAACCCTTA-TGGGTTTCCGTTCAGCTCTTATGAGCTTTAGC
**
41714528 TTAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTCCG-
1 TTAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTTAGC
* * * *
41714569 TTAAACCCTTATGGGTTTCTGTTTAGCACTTATGTGCTT
1 TT-AACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTT
41714608 CTGTATAGCC
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
41 2 0.03
42 67 0.94
43 2 0.03
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (42 bp):
TTAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTTAGC
Found at i:41714560 original size:21 final size:21
Alignment explanation
Indices: 41714534--41714602 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
41714524 TAGCTTAACC
* *
41714534 CTTATGGGTTTCCGTTCAGCT
1 CTTATGGGTTTCCGTTAAGCA
* * * *
41714555 CTTATGAGCTTCCGTTAAACC
1 CTTATGGGTTTCCGTTAAGCA
* *
41714576 CTTATGGGTTTCTGTTTAGCA
1 CTTATGGGTTTCCGTTAAGCA
41714597 CTTATG
1 CTTATG
41714603 TGCTTCTGTA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (21 bp):
CTTATGGGTTTCCGTTAAGCA
Found at i:41714609 original size:21 final size:21
Alignment explanation
Indices: 41714576--41714616 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41714566 CCGTTAAACC
* *
41714576 CTTATGGGTTTCTGTTTAGCA
1 CTTATGGGCTTCTGTATAGCA
*
41714597 CTTATGTGCTTCTGTATAGC
1 CTTATGGGCTTCTGTATAGC
41714617 CTTCGGGCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (21 bp):
CTTATGGGCTTCTGTATAGCA
Found at i:41718872 original size:25 final size:25
Alignment explanation
Indices: 41718844--41718893 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
41718834 GGGAAGATCT
*
41718844 TTCGAGCCATATAGTGAGAAGCTCA
1 TTCGAGCCATATAATGAGAAGCTCA
** *
41718869 TTCGAGCTGTATAATGGGAAGCTCA
1 TTCGAGCCATATAATGAGAAGCTCA
41718894 AAAGAGCTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (25 bp):
TTCGAGCCATATAATGAGAAGCTCA
Found at i:41718900 original size:25 final size:24
Alignment explanation
Indices: 41718878--41719012 Score: 67
Period size: 24 Copynumber: 5.5 Consensus size: 24
41718868 ATTCGAGCTG
41718878 TATAAT-GGGAAGCTCAAAAGAGC
1 TATAATCGGGAAGCTCAAAAGAGC
* ** *
41718901 TATAATCGGGAAGTTCAAGCGGGC
1 TATAATCGGGAAGCTCAAAAGAGC
* ***
41718925 CA-ATATCGGGAAGCTCCGGAGAGC
1 TATA-ATCGGGAAGCTCAAAAGAGC
* * *
41718949 CATTAATCGAGAAGCTCATGAAAAAGCC
1 TA-TAATCGGGAAGCTCA--AAAGAG-C
* ***
41718977 TTTAATCGGGAAGCTCTGGAGAGC
1 TATAATCGGGAAGCTCAAAAGAGC
41719001 TATATATCGGGA
1 TATA-ATCGGGA
41719013 TGATCATAAG
Statistics
Matches: 81, Mismatches: 23, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
23 7 0.09
24 35 0.43
25 21 0.26
26 1 0.01
27 16 0.20
28 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (24 bp):
TATAATCGGGAAGCTCAAAAGAGC
Found at i:41719147 original size:25 final size:24
Alignment explanation
Indices: 41719119--41719166 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
41719109 ATAACGGGAA
*
41719119 GCTCGTGAGAGCCAAATATCAGGAT
1 GCTCATGAGAG-CAAATATCAGGAT
* *
41719144 GCTCATGATAGCTAATATCAGGA
1 GCTCATGAGAGCAAATATCAGGA
41719167 CGCCCTTTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (24 bp):
GCTCATGAGAGCAAATATCAGGAT
Found at i:41728633 original size:4 final size:4
Alignment explanation
Indices: 41728624--41728656 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
41728614 GTGAAAGAAT
41728624 AATA AATA AATA AATAA AATA AAT- AATA AATA A
1 AATA AATA AATA AAT-A AATA AATA AATA AATA A
41728657 CATCAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.11
4 20 0.74
5 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:41728750 original size:74 final size:73
Alignment explanation
Indices: 41728649--41728840 Score: 187
Period size: 73 Copynumber: 2.6 Consensus size: 73
41728639 AAAATAAATA
* *
41728649 ATAAATAACA-TCAAATTTAAATGTTTAAAAAGTAAAAGAA-AA-AACGAACAAACAAATAAACA
1 ATAAATAACATTC-AATTTAAGTATTTAAAAAGTAAAAGAATAATAA-G--CAAACAAATAAACA
41728711 GATAAAACACAT
62 GATAAAACACAT
* * * * * *
41728723 ATAAATAACATTCAATTTAAGTATTTAAAAGGTAATAGAATAATAAGTAAATAGATAAATAGATA
1 ATAAATAACATTCAATTTAAGTATTTAAAAAGTAAAAGAATAATAAGCAAACAAATAAACAGATA
* **
41728788 AAGCTGAT
66 AAACACAT
* *
41728796 ATAAATAAGATTAAATTT-AGATATTTAAAAAGT-AAAGAATAATAA
1 ATAAATAACATTCAATTTAAG-TATTTAAAAAGTAAAAGAATAATAA
41728841 ATAAATGAAT
Statistics
Matches: 99, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
72 13 0.13
73 46 0.46
74 33 0.33
75 5 0.05
76 2 0.02
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (73 bp):
ATAAATAACATTCAATTTAAGTATTTAAAAAGTAAAAGAATAATAAGCAAACAAATAAACAGATA
AAACACAT
Found at i:41731398 original size:101 final size:101
Alignment explanation
Indices: 41731202--41731464 Score: 323
Period size: 101 Copynumber: 2.6 Consensus size: 101
41731192 CAATTATTCA
* * * *
41731202 AACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGGTCATAGCTGGGCTAAGGCATT
1 AACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGATCATAGTTGGGCTATGGCATT
* * * * *
41731267 CTAATGATAATATCATATCTAGGTTTTGGCACTATG
66 CTAATGATAAGACCATAACTAGGTTATGGCACTACG
*
41731303 GACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGATCATAGTTGGGCTATGGCATT
1 AACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGATCATAGTTGGGCTATGGCATT
* *
41731368 CTGATGATAAGACCATAACTGGGTTATGGCACTACG
66 CTAATGATAAGACCATAACTAGGTTATGGCACTACG
* ** * * * * * *
41731404 AATGTAAGACCATGGCAGGGCCATGATAATG--CATATGTAAGACCATAGTTGGACTATGGCA
1 AACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGATCATAGTTGGGCTATGGCA
41731465 CAAAGGAAAC
Statistics
Matches: 140, Mismatches: 22, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
99 27 0.19
101 113 0.81
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (101 bp):
AACGTAAGACCATGGTTGGACCATGACAGTGTTTATATGTAAGATCATAGTTGGGCTATGGCATT
CTAATGATAAGACCATAACTAGGTTATGGCACTACG
Found at i:41740556 original size:16 final size:16
Alignment explanation
Indices: 41740535--41740603 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
41740525 TTTGGTTCGC
41740535 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41740551 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41740567 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
41740584 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41740600 TGTA
1 TGTA
41740604 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:41740581 original size:33 final size:32
Alignment explanation
Indices: 41740535--41740603 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
41740525 TTTGGTTCGC
41740535 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
41740567 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
41740600 TGTA
1 TGTA
41740604 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:41740668 original size:44 final size:45
Alignment explanation
Indices: 41740584--41740674 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
41740574 GGATTAGAGG
* * *
41740584 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
41740629 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
41740673 TG
1 TG
41740675 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:41740856 original size:16 final size:16
Alignment explanation
Indices: 41740819--41740873 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
41740809 TTAATCATAT
*
41740819 TTAAACATA-ATTATAA
1 TTAAA-ATATATTTTAA
41740835 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
41740850 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
41740868 -TAAAAT
1 TTAAAAT
41740874 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:41740866 original size:18 final size:18
Alignment explanation
Indices: 41740825--41740873 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
41740815 ATATTTAAAC
41740825 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
41740843 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
41740859 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
41740874 TCTTAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:41747108 original size:59 final size:60
Alignment explanation
Indices: 41747037--41747153 Score: 157
Period size: 59 Copynumber: 2.0 Consensus size: 60
41747027 TTGGATAACT
* * *
41747037 ATTTTGTAACTTTTCATAGTT-GGTGGCTAAAAAAAG-AATTTACTAATAGTTGGGTGATC
1 ATTTTGTAACTTTCCATAGTTAGGTGAC-AAAAAAAGAAATTCACTAATAGTTGGGTGATC
* * *
41747096 ATTTTGTAACTTTCCATAGTTAGGTGACCAAAAAAGAAATTCATTGATAGTTGGGTGA
1 ATTTTGTAACTTTCCATAGTTAGGTGACAAAAAAAGAAATTCACTAATAGTTGGGTGA
41747154 CTACTAGTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 27 0.54
60 23 0.46
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (60 bp):
ATTTTGTAACTTTCCATAGTTAGGTGACAAAAAAAGAAATTCACTAATAGTTGGGTGATC
Found at i:41767680 original size:24 final size:24
Alignment explanation
Indices: 41767633--41767677 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41767623 ACATTTTTAG
41767633 AAAAATATAAGAAATATATATTAT
1 AAAAATATAAGAAATATATATTAT
41767657 AAAAATA-AA-AAATAT-TATTAT
1 AAAAATATAAGAAATATATATTAT
41767678 TATGAATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
23 2 0.10
24 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAAATATAAGAAATATATATTAT
Found at i:41771015 original size:24 final size:24
Alignment explanation
Indices: 41770988--41771035 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
41770978 ATAAATACTC
41770988 CCCGTTACAATTGGTTTTTGACCA
1 CCCGTTACAATTGGTTTTTGACCA
41771012 CCCGTTACAATTGGTTTTTGACCA
1 CCCGTTACAATTGGTTTTTGACCA
41771036 AGAGCTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (24 bp):
CCCGTTACAATTGGTTTTTGACCA
Found at i:41771046 original size:23 final size:24
Alignment explanation
Indices: 41770993--41771046 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
41770983 TACTCCCCGT
* * *
41770993 TACAATTGGTTTTTGACCACCCGT
1 TACAATTGGTTTTTGACCAACAGC
*
41771017 TACAATTGGTTTTTGACCAAGAGC
1 TACAATTGGTTTTTGACCAACAGC
41771041 TA-AATT
1 TACAATT
41771047 TTTCTCATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (24 bp):
TACAATTGGTTTTTGACCAACAGC
Found at i:41773099 original size:19 final size:20
Alignment explanation
Indices: 41773077--41773119 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
41773067 TTTTCTAAAA
*
41773077 TTTTAACTATAT-TTTTATT
1 TTTTAACTATATATTTAATT
*
41773096 TTTTAATTATATATTTAATT
1 TTTTAACTATATATTTAATT
41773116 TTTT
1 TTTT
41773120 GAATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTAACTATATATTTAATT
Found at i:41773108 original size:21 final size:21
Alignment explanation
Indices: 41773084--41773124 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
41773074 AAATTTTAAC
*
41773084 TATAT-TTTTATTTTTT-AAT
1 TATATATTTAATTTTTTGAAT
41773103 TATATATTTAATTTTTTGAAT
1 TATATATTTAATTTTTTGAAT
41773124 T
1 T
41773125 TTTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
TATATATTTAATTTTTTGAAT
Found at i:41773676 original size:4 final size:4
Alignment explanation
Indices: 41773667--41773693 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
41773657 TTTTCATTAA
41773667 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
41773694 GAGCATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:41776611 original size:5 final size:5
Alignment explanation
Indices: 41776601--41776633 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
41776591 ATTTTCTCTC
41776601 CTTCT CTTCT CTTCT CTTTCT CTTCT CTTCT CT
1 CTTCT CTTCT CTTCT C-TTCT CTTCT CTTCT CT
41776634 GTAAAACCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
CTTCT
Found at i:41776621 original size:16 final size:16
Alignment explanation
Indices: 41776597--41776633 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
41776587 CACCATTTTC
*
41776597 TCTCCTTCTCTTCTCT
1 TCTCTTTCTCTTCTCT
41776613 TCTCTTTCTCTTCTCT
1 TCTCTTTCTCTTCTCT
41776629 TCTCT
1 TCTCT
41776634 GTAAAACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (16 bp):
TCTCTTTCTCTTCTCT
Found at i:41778959 original size:126 final size:126
Alignment explanation
Indices: 41778734--41778987 Score: 499
Period size: 126 Copynumber: 2.0 Consensus size: 126
41778724 TTTTAGTTGA
*
41778734 GCTTGGAGTAGCCACACATTTTTCTAGACTGGGCTTGAGGTCTGGTTACCATCAGACTAGAATGT
1 GCTTGGAGTAGCCACACATTTTTCTAGACTGGGCTTGAGGTCTGGTTACCATCAGACTAGAATGC
41778799 GGGTCAAGGATGTTCACAAAACATCTAAAACTCATGAGGGGCATTATGATTTCTTGGTCAT
66 GGGTCAAGGATGTTCACAAAACATCTAAAACTCATGAGGGGCATTATGATTTCTTGGTCAT
41778860 GCTTGGAGTAGCCACACATTTTTCTAGACTGGGCTTGAGGTCTGGTTACCATCAGACTAGAATGC
1 GCTTGGAGTAGCCACACATTTTTCTAGACTGGGCTTGAGGTCTGGTTACCATCAGACTAGAATGC
41778925 GGGTCAAGGATGTTCACAAAACATCTAAAACTCATGAGGGGCATTATGATTTCTTGGTCAT
66 GGGTCAAGGATGTTCACAAAACATCTAAAACTCATGAGGGGCATTATGATTTCTTGGTCAT
41778986 GC
1 GC
41778988 CCTTTGGTTT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 127 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (126 bp):
GCTTGGAGTAGCCACACATTTTTCTAGACTGGGCTTGAGGTCTGGTTACCATCAGACTAGAATGC
GGGTCAAGGATGTTCACAAAACATCTAAAACTCATGAGGGGCATTATGATTTCTTGGTCAT
Found at i:41788609 original size:21 final size:22
Alignment explanation
Indices: 41788570--41788614 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
41788560 AAGCATTATA
*
41788570 TTCTTCTCTTATTTTTCTT-TT
1 TTCTTCTCTTATTTCTCTTCTT
41788591 TTCTTCT-TTATTTACTCTTCTT
1 TTCTTCTCTTATTT-CTCTTCTT
41788613 TT
1 TT
41788615 TAATTAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 11 0.52
22 4 0.19
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (22 bp):
TTCTTCTCTTATTTCTCTTCTT
Found at i:41791126 original size:16 final size:16
Alignment explanation
Indices: 41791105--41791136 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41791095 TCAGCTCATG
*
41791105 TCATTTCAGCTTTGAA
1 TCATTTAAGCTTTGAA
41791121 TCATTTAAGCTTTGAA
1 TCATTTAAGCTTTGAA
41791137 CCCTTATCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (16 bp):
TCATTTAAGCTTTGAA
Found at i:41796498 original size:15 final size:15
Alignment explanation
Indices: 41796478--41796507 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41796468 AAGTATATTA
41796478 AAAATATAATATAAT
1 AAAATATAATATAAT
*
41796493 AAAATATAGTATAAT
1 AAAATATAATATAAT
41796508 CATTAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AAAATATAATATAAT
Found at i:41797847 original size:21 final size:20
Alignment explanation
Indices: 41797809--41797847 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
41797799 TAAGACATGG
*
41797809 AATTAATTAGAAATTAAATC
1 AATTAATTAGAAAATAAATC
*
41797829 AATTAGATTATAAAATAAA
1 AATTA-ATTAGAAAATAAA
41797848 CAGTACAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (20 bp):
AATTAATTAGAAAATAAATC
Found at i:41799631 original size:20 final size:19
Alignment explanation
Indices: 41799606--41799645 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
41799596 TAGCTGCACG
41799606 AAGGAGAAGAAAGAAAAAGA
1 AAGGAGAAG-AAGAAAAAGA
*
41799626 AAGGAGAAGAAGAAGAAGA
1 AAGGAGAAGAAGAAAAAGA
41799645 A
1 A
41799646 GAAGAGGGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (19 bp):
AAGGAGAAGAAGAAAAAGA
Found at i:41799718 original size:20 final size:20
Alignment explanation
Indices: 41799681--41799719 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
41799671 AAGTAAAAGA
*
41799681 GAGAAAGAGAATAGAGAAAC
1 GAGAAAGAGAAGAGAGAAAC
41799701 GAGAAAGA-AAGAGAAGAAA
1 GAGAAAGAGAAGAG-AGAAA
41799720 AAAATAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.64, C:0.03, G:0.31, T:0.03
Consensus pattern (20 bp):
GAGAAAGAGAAGAGAGAAAC
Found at i:41800134 original size:25 final size:25
Alignment explanation
Indices: 41800086--41800134 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
41800076 CATAATTGAA
* * *
41800086 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
41800111 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
41800135 AAGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:41803108 original size:49 final size:49
Alignment explanation
Indices: 41803026--41803119 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
41803016 TCAAGTAGGG
* * *
41803026 ATAAATAGTGATAAGAGTGTAGACAGTGAAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGCAGACAATGAAAGACCAAGTTTAGCAATGT
* *
41803075 ATAAATAGTGATAAGAGTGCGGACAATGGAAGACCAAGTTTAGCA
1 ATAAATAGTGATAAGAGTGCAGACAATGAAAGACCAAGTTTAGCA
41803120 TAGCATAGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.23
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGCAGACAATGAAAGACCAAGTTTAGCAATGT
Found at i:41804030 original size:23 final size:23
Alignment explanation
Indices: 41804004--41804084 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
41803994 TTGGTGGAAG
* **
41804004 CATTCTAACACTACGGTGCAATT
1 CATTCTAGCACTATAGTGCAATT
41804027 CATTCTAGCACTATAGTGCAATT
1 CATTCTAGCACTATAGTGCAATT
* *
41804050 CATTCTGGCGCTATAGTGCAATT
1 CATTCTAGCACTATAGTGCAATT
*
41804073 CATTCTGGCACT
1 CATTCTAGCACT
41804085 TTGATGCGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (23 bp):
CATTCTAGCACTATAGTGCAATT
Found at i:41810338 original size:68 final size:69
Alignment explanation
Indices: 41810251--41810412 Score: 177
Period size: 68 Copynumber: 2.4 Consensus size: 69
41810241 ATAGTTTTAT
* * * * * * *
41810251 ACCTTATAATCTCCATGTTTATTGTCTCGATGGACTTTGTTGGTCGCTATAG-CGGAGCTATGGT
1 ACCTTGTAATCTTCGTGTTTATTGTCCCGACGGACTTTGTTAGTCGCCATAGTC-GAGCTATGGT
41810315 C-TAC
65 CTTAC
* * * *
41810319 ACCTTGTAATCTTCGTGTTTACTGTCCCGGCGGGCTTTGTTAGTTGCCATAGTCGAGCTATGGTC
1 ACCTTGTAATCTTCGTGTTTATTGTCCCGACGGACTTTGTTAGTCGCCATAGTCGAGCTATGGTC
41810384 TTAC
66 TTAC
*
41810388 ACCTCGTAATACTT-GTGTTTATTGT
1 ACCTTGTAAT-CTTCGTGTTTATTGT
41810413 TCTGATAGAC
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
68 52 0.67
69 23 0.29
70 3 0.04
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (69 bp):
ACCTTGTAATCTTCGTGTTTATTGTCCCGACGGACTTTGTTAGTCGCCATAGTCGAGCTATGGTC
TTAC
Found at i:41816085 original size:43 final size:43
Alignment explanation
Indices: 41816019--41816133 Score: 117
Period size: 43 Copynumber: 2.7 Consensus size: 43
41816009 AGTTTGTACA
* ** * * * *
41816019 ATGCCAACGTCCCAGGCCTGGTCTTACATGTGATCAC-CGATTG
1 ATGCCAACGTCCCAGACAGGGTCTTACACGTAAACACAAG-TTG
41816062 ATGCC-ACTGTCCCAGACAGGGTCTTACACGTAAACACAAGTTG
1 ATGCCAAC-GTCCCAGACAGGGTCTTACACGTAAACACAAGTTG
**
41816105 ATGCCAACGTCCCAGACATAGTCTTACAC
1 ATGCCAACGTCCCAGACAGGGTCTTACAC
41816134 AAAATCACAT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
42 2 0.03
43 55 0.92
44 3 0.05
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACACGTAAACACAAGTTG
Found at i:41820129 original size:30 final size:30
Alignment explanation
Indices: 41820065--41820129 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
41820055 ATTATATATT
** *
41820065 TTTATTTTTATTTTTTAAAATACATTTCCCA
1 TTTATTTTTATTTTTTAAAATA-ATTAACAA
41820096 TTTATTTTTATTTTTTAAAAGT-ATTAACAA
1 TTTATTTTTATTTTTTAAAA-TAATTAACAA
41820126 TTTA
1 TTTA
41820130 ACTTTAACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 9 0.30
31 20 0.67
32 1 0.03
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTATTTTTATTTTTTAAAATAATTAACAA
Found at i:41820836 original size:25 final size:25
Alignment explanation
Indices: 41820775--41820837 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
41820765 GGAATTTTAG
*
41820775 AATCTGTATTCTAGATTGTATATTC
1 AATCTGTATTCTGGATTGTATATTC
*
41820800 AAGT-TGTATTCTGGATTGTATGTTC
1 AA-TCTGTATTCTGGATTGTATATTC
*
41820825 AATCTGTCTTCTG
1 AATCTGTATTCTG
41820838 CTTAGTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 1 0.03
25 31 0.94
26 1 0.03
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (25 bp):
AATCTGTATTCTGGATTGTATATTC
Found at i:41821009 original size:30 final size:30
Alignment explanation
Indices: 41820973--41821033 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
41820963 AATGAAAATA
41820973 TTTGGGAATTAGTTCCCCTTCTTTAATCAG
1 TTTGGGAATTAGTTCCCCTTCTTTAATCAG
41821003 TTTGGGAATTAGTTCCCCTTCTTTAATCAG
1 TTTGGGAATTAGTTCCCCTTCTTTAATCAG
41821033 T
1 T
41821034 CTCATAGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (30 bp):
TTTGGGAATTAGTTCCCCTTCTTTAATCAG
Found at i:41822210 original size:80 final size:80
Alignment explanation
Indices: 41822124--41822282 Score: 273
Period size: 80 Copynumber: 2.0 Consensus size: 80
41822114 TATAAGCATG
* * * *
41822124 GATGAACACAACATTTATTCATGTATTAAACTTAACAACATATGTTAATTCATAAACTATTCATG
1 GATGAACACAACATTTATTCATATATCAAACTTAACAACACATGTTAATTCATAAACCATTCATG
41822189 ACATTACTTCATGCA
66 ACATTACTTCATGCA
*
41822204 GATGAACACAACATTTATTCATATATCAAACTTACCAACACATGTTAATTCATAAACCATTCATG
1 GATGAACACAACATTTATTCATATATCAAACTTAACAACACATGTTAATTCATAAACCATTCATG
41822269 ACATTACTTCATGC
66 ACATTACTTCATGC
41822283 CAAATCATAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (80 bp):
GATGAACACAACATTTATTCATATATCAAACTTAACAACACATGTTAATTCATAAACCATTCATG
ACATTACTTCATGCA
Found at i:41823202 original size:38 final size:37
Alignment explanation
Indices: 41823132--41823204 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
41823122 TTTTCATAAT
* *
41823132 TTCACTTTTTTACTTTTAATCACTATTCAATTCAAAA
1 TTCACTTTTTCACTTTTAATCAATATTCAATTCAAAA
41823169 TTCACTTTTTCA-TTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTTTCACTTTT-AA-TCAATATTCAATTCAA
41823205 TTCCACACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.32, C:0.19, G:0.01, T:0.48
Consensus pattern (37 bp):
TTCACTTTTTCACTTTTAATCAATATTCAATTCAAAA
Found at i:41823378 original size:45 final size:45
Alignment explanation
Indices: 41823305--41823626 Score: 414
Period size: 45 Copynumber: 7.2 Consensus size: 45
41823295 AATAATAACA
* * * *
41823305 GTACACGGTGG-ATCAGCACACAGC-ACCACCCTTATAGTCAATG
1 GTACTCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATG
* * * *
41823348 ATACTCGGTGTAATCCGCACATGGCAACCACCTTTATAATCAATG
1 GTACTCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATG
* * *
41823393 GTACCCAGTGGAATCAACACATAGCAACCACCTTTATAATCAATG
1 GTACTCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATG
* * * *
41823438 GTACCCGGTAGAATTAGCACATAACAACCACCTTTATAATCAATG
1 GTACTCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATG
*
41823483 GTACCCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATG
1 GTACTCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATG
* *
41823528 GTACTTGGTGGAATCAACACATAGCAACCACCTTTATAATCAATG
1 GTACTCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATG
* * * * *
41823573 GTATTCAGTGGAATCAGTACATAGCAACCACCGTTACAATCAATG
1 GTACTCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATG
*
41823618 ATACTCGGT
1 GTACTCGGT
41823627 ACACGTAGTA
Statistics
Matches: 241, Mismatches: 36, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
43 8 0.03
44 10 0.04
45 223 0.93
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (45 bp):
GTACTCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATG
Found at i:41830605 original size:32 final size:32
Alignment explanation
Indices: 41830564--41830628 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
41830554 CTGAAGAAAA
41830564 GAATCTGATATGGATAATTATAGGAGTTAGTG
1 GAATCTGATATGGATAATTATAGGAGTTAGTG
41830596 GAATCTGATATGGATAATTATAGGAGTTAGTG
1 GAATCTGATATGGATAATTATAGGAGTTAGTG
41830628 G
1 G
41830629 GTGGGTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (32 bp):
GAATCTGATATGGATAATTATAGGAGTTAGTG
Found at i:41831322 original size:34 final size:35
Alignment explanation
Indices: 41831260--41831333 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
41831250 GCACAGTTGA
* ** *
41831260 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATTAGTG
1 ACAGTCTTGGGCCTAAGCCCATCACAGTATCAGTG
*
41831295 ACAGT-TTGGGCCTTAGCCCATCACAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATCACAGTATCAGTG
*
41831329 GCAGT
1 ACAGT
41831334 AACAGTTATG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 28 0.85
35 5 0.15
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (35 bp):
ACAGTCTTGGGCCTAAGCCCATCACAGTATCAGTG
Found at i:41835444 original size:22 final size:21
Alignment explanation
Indices: 41835409--41835460 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
41835399 AAAATTTTTA
*
41835409 ATTTTTT-AATTTTTTATATAT
1 ATTTTTTAAATTTTCTA-ATAT
41835430 ATTTTTTAGAATTTTCTAATAT
1 ATTTTTTA-AATTTTCTAATAT
41835452 -TTTTTTAAA
1 ATTTTTTAAA
41835461 AAAATACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 14 0.50
22 4 0.14
23 8 0.29
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTTTAAATTTTCTAATAT
Found at i:41837845 original size:6 final size:6
Alignment explanation
Indices: 41837831--41837868 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
41837821 CGGCTGATAC
*
41837831 CGCCTT CGCCAT CGCCAT CGCCAT CGCCAT CGCCAT CG
1 CGCCAT CGCCAT CGCCAT CGCCAT CGCCAT CGCCAT CG
41837869 TCATGTCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.13, C:0.50, G:0.18, T:0.18
Consensus pattern (6 bp):
CGCCAT
Found at i:41846348 original size:20 final size:20
Alignment explanation
Indices: 41846323--41846360 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41846313 CGTAAAATTA
*
41846323 TTTCTGGAAAATGCTTTACT
1 TTTCTGGAAAATGATTTACT
*
41846343 TTTCTGTAAAATGATTTA
1 TTTCTGGAAAATGATTTA
41846361 TTGGAAAATA
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:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:41849161 original size:3 final size:3
Alignment explanation
Indices: 41849134--41849197 Score: 51
Period size: 3 Copynumber: 20.7 Consensus size: 3
41849124 GAATATGCTG
* * *
41849134 AGA AG- AGA AGA TGA AGA A-C AGA AGA AGA AAA AGGA ATGA AGA ATGGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA A-GA AGA A--GA
41849181 AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AG
41849198 GAGCCTTACC
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
2 3 0.06
3 38 0.78
4 5 0.10
5 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.33, T:0.05
Consensus pattern (3 bp):
AGA
Found at i:41849162 original size:25 final size:25
Alignment explanation
Indices: 41849134--41849195 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
41849124 GAATATGCTG
41849134 AGAAGAGAAGATGAAGAACAGAAGA
1 AGAAGAGAAGATGAAGAACAGAAGA
**
41849159 AGAA-A-AAGGAATGAAGAATGGAAGA
1 AGAAGAGAA-G-ATGAAGAACAGAAGA
41849184 AGAAGAAGAAGA
1 AGAAG-AGAAGA
41849196 AGGAGCCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
23 2 0.07
24 2 0.07
25 21 0.70
26 1 0.03
27 2 0.07
28 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.32, T:0.05
Consensus pattern (25 bp):
AGAAGAGAAGATGAAGAACAGAAGA
Found at i:41850703 original size:27 final size:27
Alignment explanation
Indices: 41850665--41850733 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
41850655 GAGGAGGGTA
*
41850665 TCCCATGGGCGGCACCAAAGGTGCCTT
1 TCCCATGGGCGGCACCAAAGGTGCCAT
* * *
41850692 TCCCATAGGCGGCACCGATGGTGCCAT
1 TCCCATGGGCGGCACCAAAGGTGCCAT
*
41850719 TCCCATGGGCAGCAC
1 TCCCATGGGCGGCAC
41850734 TGCCCATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.19, C:0.35, G:0.29, T:0.17
Consensus pattern (27 bp):
TCCCATGGGCGGCACCAAAGGTGCCAT
Found at i:41850803 original size:4 final size:4
Alignment explanation
Indices: 41850786--41850928 Score: 65
Period size: 4 Copynumber: 36.2 Consensus size: 4
41850776 GAAGGAGAGG
*
41850786 GAAA G-AA G-AA GAAA GAAA GAAA G-AA -AAA GAAA GAAAA GGAAA GGAGAG
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA -GA-AA
* *
41850834 GAAA GAAA G-AA -AAA GAAG GAAA GGAAA GGAAA G-GA GAAGA GAAA -AAA
1 GAAA GAAA GAAA GAAA GAAA GAAA -GAAA -GAAA GAAA GAA-A GAAA GAAA
* * * *
41850881 AAAA GAAA G-AA G-AA GAAGA GGGAA GGAA GGAA -AAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAA-A -GAAA GAAA GAAA GAAA GAAA GAAA GAAA
41850928 G
1 G
41850929 GTAATTTTTT
Statistics
Matches: 114, Mismatches: 9, Indels: 32
0.74 0.06 0.21
Matches are distributed among these distances:
3 27 0.24
4 57 0.50
5 26 0.23
6 4 0.04
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:41850828 original size:5 final size:5
Alignment explanation
Indices: 41850796--41850868 Score: 64
Period size: 5 Copynumber: 15.4 Consensus size: 5
41850786 GAAAGAAGAA
* * * *
41850796 GAAA- GAAA- GAAAG AAAAA GAAAG AAAAG GAAAG GAGAG GAAA- GAAAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
* *
41850843 AAAAA G-AAG GAAAG GAAAG GAAAG GA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GA
41850869 GAAGAGAAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
4 15 0.28
5 39 0.72
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:41850838 original size:38 final size:38
Alignment explanation
Indices: 41850785--41850927 Score: 141
Period size: 38 Copynumber: 3.7 Consensus size: 38
41850775 AGAAGGAGAG
* *
41850785 GGAAAGAAGAAGAAAGAAAGAAAGAAAAAGAAAGAAAA
1 GGAAAGGAGAGGAAAGAAAGAAAGAAAAAGAAAGAAAA
* *
41850823 GGAAAGGAGAGGAAAGAAAGAAA-AAGAAGGAAAGGAAA
1 GGAAAGGAGAGGAAAGAAAGAAAGAA-AAAGAAAGAAAA
* *
41850861 GGAAAGGAGAAGAGAAA-AAAAAAAGAAAGAAG-AAGAAGA
1 GGAAAGGAG-AG-GAAAGAAAGAAAGAAA-AAGAAAGAAAA
*
41850900 GGGAAGGA-AGGAAAAAGAAAGAAAGAAA
1 GGAAAGGAGAGG--AAAGAAAGAAAGAAA
41850928 GGTAATTTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
36 1 0.01
37 4 0.05
38 43 0.49
39 31 0.36
40 8 0.09
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (38 bp):
GGAAAGGAGAGGAAAGAAAGAAAGAAAAAGAAAGAAAA
Found at i:41850923 original size:10 final size:10
Alignment explanation
Indices: 41850786--41850923 Score: 72
Period size: 10 Copynumber: 13.8 Consensus size: 10
41850776 GAAGGAGAGG
*
41850786 GAAAGAAGAA
1 GAAAGAAAAA
41850796 GAAAG--AAA
1 GAAAGAAAAA
41850804 GAAAGAAAAA
1 GAAAGAAAAA
*
41850814 GAAAGAAAAG
1 GAAAGAAAAA
41850824 GAAAGGAGAGGAAA
1 GAAA-GA-A--AAA
41850838 GAAAGAAAAA
1 GAAAGAAAAA
* *
41850848 G-AAGGAAAG
1 GAAAGAAAAA
* *
41850857 GAAAGGAAAG
1 GAAAGAAAAA
*
41850867 GAGAAG-AGAA
1 GA-AAGAAAAA
41850877 -AAA-AAAAA
1 GAAAGAAAAA
*
41850885 GAAAGAAGAA
1 GAAAGAAAAA
** *
41850895 GAAGAGGGAAG
1 GAA-AGAAAAA
*
41850906 GAAGGAAAAA
1 GAAAGAAAAA
41850916 GAAAGAAA
1 GAAAGAAA
41850924 GAAAGGTAAT
Statistics
Matches: 98, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
8 12 0.12
9 11 0.11
10 54 0.55
11 11 0.11
12 2 0.02
13 2 0.02
14 6 0.06
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
GAAAGAAAAA
Found at i:41851443 original size:158 final size:159
Alignment explanation
Indices: 41851253--41851811 Score: 612
Period size: 158 Copynumber: 3.5 Consensus size: 159
41851243 TATTTAATAA
* * * *
41851253 ATTTCAAACATAATGCATTGAAATAAAGTAAAATTATAAAATTAGAAATTATGATATTTT-TT-A
1 ATTTCAAACAAAATGCACTGAAATAAAGTAAAATAATAAAATTAGAAATAAT-ATATTTTATTGA
*
41851316 AAATAATAAAATGCGGAGAAAAAAATACGAACAAATGACCGAAGTAAGAGTGTTTTACTAAATTT
65 AAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACTAAATTT
41851381 TTTAAAAATTCAGAAATAATTAATACAAAT
130 TTTAAAAATTCAGAAATAATTAATACAAAT
* * *
41851411 ATTTCAAACAAAATGTACTGAAATAATA-TAAAATAATAAAATACAAAAATAATATATTTTTATT
1 ATTTCAAACAAAATGCACTGAAATAA-AGTAAAATAATAAAAT-TAGAAATAATATA-TTTTATT
* * * * * * * * *
41851475 GAAAGTAATAAAATTC-GA-AAAAATAATACGAGCAGAGGGCAGGAA-TACGGGTTTTTTACACT
63 GAAAATAATAAAATGCGGAGAAAAA-AATACGAACAAATGGC-CGAAGTAAGAGTGTTTT--ACT
* * **
41851537 AAATTAATTTAAAAATACA-CTA-AATTAAT---AA-
124 AAATT-TTTTAAAAATTCAGAAATAATTAATACAAAT
* * * * *
41851568 ATTTCAAACATAATACATTGAAATAAAGTAAAATTATAAAATTAGAAATTATGATATTTT-TT-A
1 ATTTCAAACAAAATGCACTGAAATAAAGTAAAATAATAAAATTAGAAATAAT-ATATTTTATTGA
*
41851631 AAATAATAAAATGCAGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACTAAATTT
65 AAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACTAAATTT
41851696 TTTAAAAATTCAGAAATAATTAATACAAAT
130 TTTAAAAATTCAGAAATAATTAATACAAAT
*
41851726 ATTTCAAACAAAATGTACTGAAATAATA-TAAAATAATAAAA-TACGAAAATAATATATTTTATT
1 ATTTCAAACAAAATGCACTGAAATAA-AGTAAAATAATAAAATTA-G-AAATAATATATTTTATT
* *
41851789 GAAAGTAATAAAATTCGG-GAAAA
63 GAAAATAATAAAATGCGGAGAAAA
41851812 TAAGAAATTA
Statistics
Matches: 324, Mismatches: 51, Indels: 51
0.76 0.12 0.12
Matches are distributed among these distances:
152 11 0.03
153 9 0.03
154 23 0.07
155 26 0.08
156 17 0.05
157 42 0.13
158 83 0.26
159 31 0.10
160 39 0.12
161 23 0.07
162 9 0.03
163 11 0.03
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.30
Consensus pattern (159 bp):
ATTTCAAACAAAATGCACTGAAATAAAGTAAAATAATAAAATTAGAAATAATATATTTTATTGAA
AATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTTTTACTAAATTTT
TTAAAAATTCAGAAATAATTAATACAAAT
Found at i:41851812 original size:45 final size:44
Alignment explanation
Indices: 41851763--41851855 Score: 109
Period size: 43 Copynumber: 2.1 Consensus size: 44
41851753 ATAAAATAAT
* *
41851763 AAAATACGAAAATAAT-ATATTTTATTGAAAGTAATAAAATTCGG-G
1 AAAATAAG-AAATAATGATATTTT-TT-AAAGTAATAAAATGCGGAG
* *
41851808 AAAATAAGAAATTATGATATTTTTTAAATTAATAAAATGCGGAG
1 AAAATAAGAAATAATGATATTTTTTAAAGTAATAAAATGCGGAG
41851852 AAAA
1 AAAA
41851856 AAATACGAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 15 0.36
44 13 0.31
45 14 0.33
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.31
Consensus pattern (44 bp):
AAAATAAGAAATAATGATATTTTTTAAAGTAATAAAATGCGGAG
Found at i:41853566 original size:6 final size:6
Alignment explanation
Indices: 41853557--41853607 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
41853547 GCCGAGCAGG
* * *
41853557 AGCCCC AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC AGCCAG AGCCCC
1 AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC
41853605 AGC
1 AGC
41853608 TAGATCCGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.29, C:0.51, G:0.20, T:0.00
Consensus pattern (6 bp):
AGCCAC
Found at i:41857198 original size:40 final size:39
Alignment explanation
Indices: 41857148--41857253 Score: 113
Period size: 42 Copynumber: 2.6 Consensus size: 39
41857138 ATAACAATAA
* *
41857148 TACTCAAAATAATACTAACTAACAATAATAATTAGGGTTT
1 TACTAAAAATAATACTAACTAACAATAAT-ACTAGGGTTT
* **
41857188 TACTAAAAATAATAACTAACCATAATAATAATACTAGTTTTT
1 TACTAAAAATAAT-ACTAA-C-TAACAATAATACTAGGGTTT
* *
41857230 TACTAACAATAATACTAAGTAACA
1 TACTAAAAATAATACTAACTAACA
41857254 TCTAAACCCT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 4 0.07
40 12 0.22
41 10 0.18
42 20 0.36
43 9 0.16
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (39 bp):
TACTAAAAATAATACTAACTAACAATAATACTAGGGTTT
Found at i:41863586 original size:19 final size:18
Alignment explanation
Indices: 41863551--41863589 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
41863541 TACTTTTTTA
41863551 TAATTTTTATTTAATATT
1 TAATTTTTATTTAATATT
41863569 TAATTTTTGAATTT-ATATT
1 TAATTTTT--ATTTAATATT
41863588 TA
1 TA
41863590 TTAAATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TAATTTTTATTTAATATT
Found at i:41864288 original size:30 final size:30
Alignment explanation
Indices: 41864252--41864311 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
41864242 ACTTAGCAAG
41864252 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
41864282 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
41864312 TAATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:41864367 original size:14 final size:14
Alignment explanation
Indices: 41864348--41864374 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41864338 CAAACAATAA
41864348 CAACATAATAGTAT
1 CAACATAATAGTAT
41864362 CAACATAATAGTA
1 CAACATAATAGTA
41864375 AAATGGTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (14 bp):
CAACATAATAGTAT
Found at i:41870619 original size:25 final size:25
Alignment explanation
Indices: 41870580--41870629 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
41870570 CTCTGCGCAG
* *
41870580 CTCTGTTCTATTTTGTTATGCTCTA
1 CTCTGTTCTACTTTGCTATGCTCTA
* *
41870605 CTCTGTTCTGCTTTGCTCTGCTCTA
1 CTCTGTTCTACTTTGCTATGCTCTA
41870630 TTTTGCTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.08, C:0.26, G:0.14, T:0.52
Consensus pattern (25 bp):
CTCTGTTCTACTTTGCTATGCTCTA
Found at i:41870621 original size:20 final size:20
Alignment explanation
Indices: 41870598--41870639 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41870588 TATTTTGTTA
*
41870598 TGCTCTACTCTGTTCTGCTT
1 TGCTCTACTCTATTCTGCTT
* *
41870618 TGCTCTGCTCTATTTTGCTT
1 TGCTCTACTCTATTCTGCTT
41870638 TG
1 TG
41870640 TCCTATTCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.26, G:0.17, T:0.52
Consensus pattern (20 bp):
TGCTCTACTCTATTCTGCTT
Found at i:41876483 original size:8 final size:8
Alignment explanation
Indices: 41876466--41876498 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
41876456 AAAAAAAGGT
41876466 ATTA-AAA
1 ATTATAAA
41876473 ATTATAAA
1 ATTATAAA
41876481 ATTATAAAA
1 ATTAT-AAA
41876490 ATTATAAA
1 ATTATAAA
41876498 A
1 A
41876499 AAATTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 4 0.17
8 12 0.50
9 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
ATTATAAA
Found at i:41876490 original size:9 final size:9
Alignment explanation
Indices: 41876468--41876499 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
41876458 AAAAAGGTAT
41876468 TAAAAATTA
1 TAAAAATTA
41876477 T-AAAATTA
1 TAAAAATTA
41876485 TAAAAATTA
1 TAAAAATTA
41876494 TAAAAA
1 TAAAAA
41876500 AATTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:41881473 original size:36 final size:36
Alignment explanation
Indices: 41881426--41881497 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
41881416 AATTGTGCCT
*
41881426 TCATTTCCATTTCCATCACCACCAAATACATAAAAA
1 TCATTTCCATTTCCATCACCACCAAATAAATAAAAA
41881462 TCATTTCCATTTCCATCACCACCAAATAAATAAAAA
1 TCATTTCCATTTCCATCACCACCAAATAAATAAAAA
41881498 CTTTTAGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.28
Consensus pattern (36 bp):
TCATTTCCATTTCCATCACCACCAAATAAATAAAAA
Found at i:41882475 original size:2 final size:2
Alignment explanation
Indices: 41882468--41882506 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41882458 GAGCTAATAT
41882468 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
41882507 GGACAAGAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41883047 original size:3 final size:3
Alignment explanation
Indices: 41883039--41883076 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
41883029 ACACATAGAA
41883039 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41883077 AGTAATGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:41883658 original size:3 final size:3
Alignment explanation
Indices: 41883650--41883685 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
41883640 TAAAATAGAT
41883650 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41883686 AAGCATGCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41887853 original size:39 final size:39
Alignment explanation
Indices: 41887805--41887908 Score: 104
Period size: 39 Copynumber: 2.7 Consensus size: 39
41887795 TATAAAGATG
* * * *
41887805 TTTTAGAGTATTGTGGTATATGCTTGAA-TGTTATGTGA
1 TTTTAGAGTATTGTGATATATGCTTGAAGCGTCATGAGA
* *
41887843 TTTTACGAGTATTATGACATATGCTT-AAGCGTCATGAGA
1 TTTTA-GAGTATTGTGATATATGCTTGAAGCGTCATGAGA
* *
41887882 TTATATGAGTATGGTGATATATGCTTG
1 TTTTA-GAGTATTGTGATATATGCTTG
41887909 TATCTTAGGT
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
38 7 0.13
39 45 0.87
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.42
Consensus pattern (39 bp):
TTTTAGAGTATTGTGATATATGCTTGAAGCGTCATGAGA
Found at i:41891699 original size:69 final size:69
Alignment explanation
Indices: 41891625--41892006 Score: 343
Period size: 69 Copynumber: 5.5 Consensus size: 69
41891615 CTATGCTTGC
** * *
41891625 GAGCCTTAATATGGCAGTTAGGAGCTTTGCTCTCGCTAACTGTATTTGAAGCTGTAACTCTTCGC
1 GAGCCTTAATATAACAGTTAGGAGCTTTGCTCTCGCTAACTGTATTGGAAGCTGTGACTCTTCGC
41891690 CTGT
66 CTGT
* * * *
41891694 AAGCCTTAATATAACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTCGGAAGCTGTGACTCTTCGC
1 GAGCCTTAATATAACAGTTAGGAGCTTTGCTCTCGCTAACTGTATTGGAAGCTGTGACTCTTCGC
*
41891759 CTGC
66 CTGT
* * ** * * *
41891763 GAGCTTTAGTATAACAACTAGGAGCTTTGCTCTCGCTAACTGTATTGGAGGCTGCGGCTCTTCGC
1 GAGCCTTAATATAACAGTTAGGAGCTTTGCTCTCGCTAACTGTATTGGAAGCTGTGACTCTTCGC
*
41891828 CAGT
66 CTGT
* * * ** * *** * * *
41891832 GAGCCTTAATATAATAGCTGGGAGCTTTATTCTCGATAACTACGTTAG-AGACTGTGATTCTTTG
1 GAGCCTTAATATAACAGTTAGGAGCTTTGCTCTCGCTAACTGTATTGGAAG-CTGTGACTCTTCG
* **
41891896 CATAC
65 CCTGT
* * * * * *
41891901 GAGCCTTAATATGACAGTTGGGAGCTTTGCTCTTGCTAACTGCATTGGAGGCTGTGGCTCTTCGC
1 GAGCCTTAATATAACAGTTAGGAGCTTTGCTCTCGCTAACTGTATTGGAAGCTGTGACTCTTCGC
*
41891966 CTGC
66 CTGT
* * * * * *
41891970 GAGCTTTAATATGATAGTTGGGAGCTTTACTGTCGCT
1 GAGCCTTAATATAACAGTTAGGAGCTTTGCTCTCGCT
41892007 GACTCTGCTA
Statistics
Matches: 247, Mismatches: 64, Indels: 4
0.78 0.20 0.01
Matches are distributed among these distances:
68 1 0.00
69 245 0.99
70 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (69 bp):
GAGCCTTAATATAACAGTTAGGAGCTTTGCTCTCGCTAACTGTATTGGAAGCTGTGACTCTTCGC
CTGT
Found at i:41892019 original size:138 final size:139
Alignment explanation
Indices: 41891624--41892119 Score: 459
Period size: 138 Copynumber: 3.6 Consensus size: 139
41891614 TCTATGCTTG
* * * **
41891624 CGAGCCTTAATATGGCAGTTAGGAGCTTTGCTCTCGCTAACTGTATTTGAAGCTGTAACTCTTCG
1 CGAGCCTTAATATGACAGTTAGGAGCTTTGCTCTCGCTAACTGTATTGGAGGCTGTGGCTCTTCG
* * * * *
41891689 CCTGTAAGCCTTAATATAACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTCG-GAAGCTGTGACT
66 CCTGTGAGCCTTAATATAATAGTTGGGAGCTTTACTCTCGCTAACTCTGTAGAGAAGCTGTGACT
* *
41891753 CTTCGCCTG
131 CTTCGCATA
* * * ** *
41891762 CGAGCTTTAGTATAACAACTAGGAGCTTTGCTCTCGCTAACTGTATTGGAGGCTGCGGCTCTTCG
1 CGAGCCTTAATATGACAGTTAGGAGCTTTGCTCTCGCTAACTGTATTGGAGGCTGTGGCTCTTCG
* * * *
41891827 CCAGTGAGCCTTAATATAATAGCTGGGAGCTTTATTCTCGATAACTAC-GTTAGAG-A-CTGTGA
66 CCTGTGAGCCTTAATATAATAGTTGGGAGCTTTACTCTCGCTAACT-CTG-TAGAGAAGCTGTGA
* *
41891889 TTCTTTGCATA
129 CTCTTCGCATA
* * *
41891900 CGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTTGCTAACTGCATTGGAGGCTGTGGCTCTTCG
1 CGAGCCTTAATATGACAGTTAGGAGCTTTGCTCTCGCTAACTGTATTGGAGGCTGTGGCTCTTCG
* * * * * * *
41891965 CCTGCGAGCTTTAATATGATAGTTGGGAGCTTTACTGTCGCTGACTCTGCTAGAG--GTTGTGGC
66 CCTGTGAGCCTTAATATAATAGTTGGGAGCTTTACTCTCGCTAACTCTG-TAGAGAAGCTGTGAC
* * *
41892028 TTTTTGTC-TG
130 TCTTCG-CATA
* * * * * * * * **
41892038 CTAACCTTAATACGATAGCT-GGAAGCTTTGCTCTCACTAACTGTGTTAGAGGCTACGGCTCTTC
1 CGAGCCTTAATATGACAGTTAGG-AGCTTTGCTCTCGCTAACTGTATTGGAGGCTGTGGCTCTTC
*
41892102 GCTTGTGAGCCTTAATAT
65 GCCTGTGAGCCTTAATAT
41892120 GACACGAATT
Statistics
Matches: 288, Mismatches: 63, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
137 3 0.01
138 280 0.97
139 4 0.01
140 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (139 bp):
CGAGCCTTAATATGACAGTTAGGAGCTTTGCTCTCGCTAACTGTATTGGAGGCTGTGGCTCTTCG
CCTGTGAGCCTTAATATAATAGTTGGGAGCTTTACTCTCGCTAACTCTGTAGAGAAGCTGTGACT
CTTCGCATA
Found at i:41892026 original size:69 final size:68
Alignment explanation
Indices: 41891622--41892123 Score: 322
Period size: 69 Copynumber: 7.3 Consensus size: 68
41891612 AGTCTATGCT
* * * * * * **
41891622 TGCGAGCCTTAATATGGCAGTTAGGAGCTTTGCTCTCGCTAACTGTATTTGAAGCTGTAACTCTT
1 TGCGAGCCTTAATATGACAGTTGGGAGCTTTACTCTCGCTAACTGCA-TAGAGGCTGTGGCTCTT
41891687 CGCC
65 CGCC
** * * ** * * *
41891691 TGTAAGCCTTAATATAACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTCGGAAGCTGTGACTCTT
1 TGCGAGCCTTAATATGACAGTTGGGAGCTTTACTCTCGCTAACTGCAT-AGAGGCTGTGGCTCTT
41891756 CGCC
65 CGCC
* * * ** * * * * *
41891760 TGCGAGCTTTAGTATAACAACTAGGAGCTTTGCTCTCGCTAACTGTATTGGAGGCTGCGGCTCTT
1 TGCGAGCCTTAATATGACAGTTGGGAGCTTTACTCTCGCTAACTGCA-TAGAGGCTGTGGCTCTT
41891825 CGCC
65 CGCC
* * * * * * * * * * **
41891829 AGTGAGCCTTAATATAATAGCTGGGAGCTTTATTCTCGATAACTACGTTAGAGACTGTGATTCTT
1 TGCGAGCCTTAATATGACAGTTGGGAGCTTTACTCTCGCTAACTGC-ATAGAGGCTGTGGCTCTT
* *
41891894 TGCA
65 CGCC
* * * *
41891898 TACGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTTGCTAACTGCATTGGAGGCTGTGGCTCTT
1 TGCGAGCCTTAATATGACAGTTGGGAGCTTTACTCTCGCTAACTGCA-TAGAGGCTGTGGCTCTT
41891963 CGCC
65 CGCC
* * * * * *
41891967 TGCGAGCTTTAATATGATAGTTGGGAGCTTTACTGTCGCTGACTCTGC-TAGAGGTTGTGGCTTT
1 TGCGAGCCTTAATATGACAGTTGGGAGCTTTACTCTCGCT-A-ACTGCATAGAGGCTGTGGCTCT
* *
41892031 TTGTC
64 TCGCC
* * * * * * * * ** **
41892036 TGCTAACCTTAATACGATAGCTGGAAGCTTTGCTCTCACTAACTGTGTTAGAGGCTACGGCTCTT
1 TGCGAGCCTTAATATGACAGTTGGGAGCTTTACTCTCGCTAACTG-CATAGAGGCTGTGGCTCTT
*
41892101 CGCT
65 CGCC
*
41892105 TGTGAGCCTTAATATGACA
1 TGCGAGCCTTAATATGACA
41892124 CGAATTTTGT
Statistics
Matches: 333, Mismatches: 92, Indels: 16
0.76 0.21 0.04
Matches are distributed among these distances:
67 3 0.01
68 2 0.01
69 322 0.97
70 2 0.01
71 4 0.01
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (68 bp):
TGCGAGCCTTAATATGACAGTTGGGAGCTTTACTCTCGCTAACTGCATAGAGGCTGTGGCTCTTC
GCC
Found at i:41892088 original size:207 final size:207
Alignment explanation
Indices: 41891695--41892072 Score: 452
Period size: 207 Copynumber: 1.8 Consensus size: 207
41891685 TTCGCCTGTA
**
41891695 AGCCTTAATATAACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTCGGAAGCTGTGACTCTTCGCC
1 AGCCTTAATATAACAGTTGGGAGCTTTGCTCTCGCTAACTGCATCGGAAGCTGTGACTCTTCGCC
* * * * *
41891760 TGCGAGCTTTAGTATAACAACTAGGAGCTTTGCTCTCGCTAACTGTATTGGAGGCTGCGGCTCTT
66 TGCGAGCTTTAATATAACAACTAGGAGCTTTACTCTCGCTAACTCTACTAGAGGCTGCGGCTCTT
* * * *
41891825 CGCCAGTGAGCCTTAATATAATAGCTGGGAGCTTTATTCTCGATAACTACGTTAGAGACTGTGAT
131 CGCCAGTGAACCTTAATACAATAGCTGGAAGCTTTACTCTCGATAACTACGTTAGAGACTGTGAT
41891890 TCTTTGCATACG
196 TCTTTGCATACG
* * * * *
41891902 AGCCTTAATATGACAGTTGGGAGCTTTGCTCTTGCTAACTGCATTGGAGGCTGTGGCTCTTCGCC
1 AGCCTTAATATAACAGTTGGGAGCTTTGCTCTCGCTAACTGCATCGGAAGCTGTGACTCTTCGCC
* * ** * * * * * * *
41891967 TGCGAGCTTTAATATGATAGTTGGGAGCTTTACTGTCGCTGACTCTGCTAGAGGTTGTGGCTTTT
66 TGCGAGCTTTAATATAACAACTAGGAGCTTTACTCTCGCTAACTCTACTAGAGGCTGCGGCTCTT
* * * * *
41892032 TGTCTGCT-AACCTTAATACGATAGCTGGAAGCTTTGCTCTC
131 CGCCAG-TGAACCTTAATACAATAGCTGGAAGCTTTACTCTC
41892073 ACTAACTGTG
Statistics
Matches: 138, Mismatches: 32, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
207 137 0.99
208 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.33
Consensus pattern (207 bp):
AGCCTTAATATAACAGTTGGGAGCTTTGCTCTCGCTAACTGCATCGGAAGCTGTGACTCTTCGCC
TGCGAGCTTTAATATAACAACTAGGAGCTTTACTCTCGCTAACTCTACTAGAGGCTGCGGCTCTT
CGCCAGTGAACCTTAATACAATAGCTGGAAGCTTTACTCTCGATAACTACGTTAGAGACTGTGAT
TCTTTGCATACG
Found at i:41892114 original size:207 final size:207
Alignment explanation
Indices: 41891681--41892123 Score: 449
Period size: 207 Copynumber: 2.1 Consensus size: 207
41891671 TGAAGCTGTA
* * * **
41891681 ACTCTTCGCCTGTAAGCCTTAATATAACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTCGGAAGC
1 ACTCTTCGCATGTGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGCATCGGAAGC
* * * * *
41891746 TGTGACTCTTCGCCTGCGAGCTTTAGTATAACAACTAGGAGCTTTGCTCTCGCTAACTGTATTGG
66 TGTGACTCTTCGCCTGCGAGCTTTAATATAACAACTAGGAGCTTTACTCTCGCTAACTCTACTAG
* * * *
41891811 AGGCTGCGGCTCTTCGCCAGTGAGCCTTAATATAATAGCTGGGAGCTTTATTCTCGATAACTACG
131 AGGCTGCGGCTCTTCGCCAGTGAACCTTAATACAATAGCTGGAAGCTTTACTCTCGATAACTACG
**
41891876 TTAGAGACTGTG
196 TTAGAGACTACG
* * ** * * *
41891888 ATTCTTTGCATACGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTTGCTAACTGCATTGGAGGC
1 ACTCTTCGCATGTGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGCATCGGAAGC
* * * ** * * * *
41891953 TGTGGCTCTTCGCCTGCGAGCTTTAATATGATAGTTGGGAGCTTTACTGTCGCTGACTCTGCTAG
66 TGTGACTCTTCGCCTGCGAGCTTTAATATAACAACTAGGAGCTTTACTCTCGCTAACTCTACTAG
* * * * * * * * *
41892018 AGGTTGTGGCTTTTTGTCTGCT-AACCTTAATACGATAGCTGGAAGCTTTGCTCTC-ACTAACTG
131 AGGCTGCGGCTCTTCGCCAG-TGAACCTTAATACAATAGCTGGAAGCTTTACTCTCGA-TAACTA
* *
41892081 TGTTAGAGGCTACG
194 CGTTAGAGACTACG
* *
41892095 GCTCTTCGCTTGTGAGCCTTAATATGACA
1 ACTCTTCGCATGTGAGCCTTAATATGACA
41892124 CGAATTTTGT
Statistics
Matches: 185, Mismatches: 49, Indels: 4
0.78 0.21 0.02
Matches are distributed among these distances:
206 1 0.01
207 183 0.99
208 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.33
Consensus pattern (207 bp):
ACTCTTCGCATGTGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTAACTGCATCGGAAGC
TGTGACTCTTCGCCTGCGAGCTTTAATATAACAACTAGGAGCTTTACTCTCGCTAACTCTACTAG
AGGCTGCGGCTCTTCGCCAGTGAACCTTAATACAATAGCTGGAAGCTTTACTCTCGATAACTACG
TTAGAGACTACG
Found at i:41900409 original size:26 final size:26
Alignment explanation
Indices: 41900373--41900423 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
41900363 TTTTCTTATT
41900373 CAGATTTTCAGATAACTCAAATTGTC
1 CAGATTTTCAGATAACTCAAATTGTC
41900399 CAGATTTTCAGATAACTCAAATTGT
1 CAGATTTTCAGATAACTCAAATTGT
41900424 GTAATTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (26 bp):
CAGATTTTCAGATAACTCAAATTGTC
Found at i:41905859 original size:39 final size:38
Alignment explanation
Indices: 41905816--41905890 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 38
41905806 TTTTTAATTT
*
41905816 TTAAAAAT-TTAAAATTATTATAAAAAGTATTTTTAAGAG
1 TTAAAAATATCAAAATTATTA-AAAAA-TATTTTTAAGAG
41905855 TTAAAAATAATCAAAATTATTAAAAAATATTTTTAA
1 TTAAAAAT-ATCAAAATTATTAAAAAATATTTTTAA
41905891 AATTTCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
39 17 0.52
40 5 0.15
41 11 0.33
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (38 bp):
TTAAAAATATCAAAATTATTAAAAAATATTTTTAAGAG
Found at i:41907085 original size:6 final size:6
Alignment explanation
Indices: 41907074--41907099 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
41907064 AAAACTTAAT
41907074 CCAAAA CCAAAA CCAAAA CCAAAA CC
1 CCAAAA CCAAAA CCAAAA CCAAAA CC
41907100 CTCAAGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAAAA
Found at i:41909026 original size:31 final size:31
Alignment explanation
Indices: 41908988--41909085 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 31
41908978 TTTGGTCTGG
41908988 GTACCAAATTAAACATTAAAGCCAAACTCAA
1 GTACCAAATTAAACATTAAAGCCAAACTCAA
*
41909019 GTACCAAATTGAAA-A--AAA--AAAACTC-A
1 GTACCAAATT-AAACATTAAAGCCAAACTCAA
* * *
41909045 GATACCAAATTGAACATTGAAGCCAGACTCAA
1 G-TACCAAATTAAACATTAAAGCCAAACTCAA
*
41909077 GTACGAAAT
1 GTACCAAAT
41909086 GTTATGGTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
26 4 0.08
27 16 0.30
29 5 0.09
31 23 0.43
32 5 0.09
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.18
Consensus pattern (31 bp):
GTACCAAATTAAACATTAAAGCCAAACTCAA
Found at i:41910310 original size:30 final size:30
Alignment explanation
Indices: 41910245--41910311 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
41910235 TTATTACACT
* * *
41910245 CAAATAAGTCCTTCACCCTTCATTTGTATC
1 CAAATAAGTCCTCCAACCTTCATTTATATC
41910275 CAAATAAGT-CTCCAACCTTCAATTTATA-C
1 CAAATAAGTCCTCCAACCTTC-ATTTATATC
41910304 CTAAATAA
1 C-AAATAA
41910312 ACCCTTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 11 0.34
30 21 0.66
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (30 bp):
CAAATAAGTCCTCCAACCTTCATTTATATC
Found at i:41916191 original size:61 final size:62
Alignment explanation
Indices: 41916077--41916206 Score: 228
Period size: 61 Copynumber: 2.1 Consensus size: 62
41916067 TTTGACAAAA
* *
41916077 CTTAT-ATATTTTGGTACTTAAGAGTAACAATGTTAACTTTTTTTTTGTCTTTATTTTGGGT
1 CTTATGATATTTTGGTACTTAAGAGTAACAATGCTAACTTTTTTTTAGTCTTTATTTTGGGT
41916138 CTTATGATATTTTGGTACTTAAGAGTAACAATGCTAAC-TTTTTTTAGTCTTTATTTTGGGT
1 CTTATGATATTTTGGTACTTAAGAGTAACAATGCTAACTTTTTTTTAGTCTTTATTTTGGGT
41916199 CTTATGAT
1 CTTATGAT
41916207 TAATGAAATT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 35 0.53
62 31 0.47
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (62 bp):
CTTATGATATTTTGGTACTTAAGAGTAACAATGCTAACTTTTTTTTAGTCTTTATTTTGGGT
Found at i:41917172 original size:195 final size:196
Alignment explanation
Indices: 41916805--41917182 Score: 573
Period size: 195 Copynumber: 1.9 Consensus size: 196
41916795 TATCACGGTA
* * *
41916805 TTGTTATCAATCTTTAATTAGTGTCGAGTTAACTTGTGGCATCAACTCAATCAAATACATTAATA
1 TTGTTATCAATCTTTAATTAGTGTCAAGTTAACTTGTGACACCAACTCAATCAAATACATTAATA
* * * *
41916870 TAGATAATATACAATTGATGAATGTAATAAAGTGTGCATAATGAAAATTGATATGTTCAAAAAGA
66 TAGATAATATACAATTGATGAAGGTAATAAAGTGTGCATAATAAAAATTGAAATGTACAAAAAGA
* *
41916935 TCAAAACAAAGTTTTAGTTGAGTGGTAAATTAAAGATTTTACTAATGTAATTGGTCCGGGTTGGT
131 TCAAAACAAAATTTTAGTTGAGTGGTAAATTAAAGATTTTACTAAAGTAATTGGTCCGGGTTGGT
41917000 G
196 G
* *
41917001 TTGTTATCAATCTTTAGTTGGTGTCAAGTTAACTTGTGACACCAACTCAATCAAATACATTAATA
1 TTGTTATCAATCTTTAATTAGTGTCAAGTTAACTTGTGACACCAACTCAATCAAATACATTAATA
*
41917066 TAGAT-ATATACAATTGATTG-AGGTAATAAAGTGTGCATAATAAAAATTGAAATGTACAAAAAT
66 TAGATAATATACAATTGA-TGAAGGTAATAAAGTGTGCATAATAAAAATTGAAATGTACAAAAAG
* * * *
41917129 ATTAAAATAAAATTTTATTTGAGTGTTAAATTAAATG-TTTTACTAAAGTAATTG
130 ATCAAAACAAAATTTTAGTTGAGTGGTAAATTAAA-GATTTTACTAAAGTAATTG
41917183 TTCTTGGTTC
Statistics
Matches: 164, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
195 96 0.59
196 68 0.41
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (196 bp):
TTGTTATCAATCTTTAATTAGTGTCAAGTTAACTTGTGACACCAACTCAATCAAATACATTAATA
TAGATAATATACAATTGATGAAGGTAATAAAGTGTGCATAATAAAAATTGAAATGTACAAAAAGA
TCAAAACAAAATTTTAGTTGAGTGGTAAATTAAAGATTTTACTAAAGTAATTGGTCCGGGTTGGT
G
Found at i:41920067 original size:25 final size:24
Alignment explanation
Indices: 41920037--41920092 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
41920027 AAAATATAAT
* *
41920037 TAAAAATATTTTATATTAATATTAAA
1 TAAAAATA-ATTATATCAAT-TTAAA
41920063 TAAAAATAATTATATCAATTTAAA
1 TAAAAATAATTATATCAATTTAAA
41920087 TAAAAA
1 TAAAAA
41920093 ATTACGTCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 11 0.39
25 9 0.32
26 8 0.29
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAAAATAATTATATCAATTTAAA
Found at i:41920094 original size:25 final size:26
Alignment explanation
Indices: 41920029--41920092 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 26
41920019 ACACCATTAA
* * *
41920029 AATA-TAATTAAAAATATTTTATATT
1 AATATTAAATAAAAATATATTATATC
41920054 AATATTAAATAAAAATA-ATTATATC
1 AATATTAAATAAAAATATATTATATC
41920079 AAT-TTAAATAAAAA
1 AATATTAAATAAAAA
41920093 ATTACGTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 11 0.31
25 13 0.37
26 11 0.31
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
AATATTAAATAAAAATATATTATATC
Found at i:41925126 original size:16 final size:16
Alignment explanation
Indices: 41925105--41925139 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41925095 TGAATTACTG
41925105 ATTACAG-CTCTATTCC
1 ATTACAGCCT-TATTCC
41925121 ATTACAGCCTTATTCC
1 ATTACAGCCTTATTCC
41925137 ATT
1 ATT
41925140 CCAATAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACAGCCTTATTCC
Found at i:41929801 original size:7 final size:7
Alignment explanation
Indices: 41929769--41929800 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
41929759 TTACTCTAGT
41929769 GGAGCTG
1 GGAGCTG
41929776 GGAGCTG
1 GGAGCTG
41929783 GGAGCTG
1 GGAGCTG
*
41929790 GGAGTTG
1 GGAGCTG
41929797 GGAG
1 GGAG
41929801 TGACGGTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.09, G:0.59, T:0.16
Consensus pattern (7 bp):
GGAGCTG
Found at i:41932785 original size:34 final size:34
Alignment explanation
Indices: 41932712--41932803 Score: 105
Period size: 34 Copynumber: 2.7 Consensus size: 34
41932702 CATATCATTC
* *
41932712 CAGTAGCATTTAATATGCTTTTAATAAAATAATA
1 CAGTAGCAATTAATATGCTTATAATAAAATAATA
* * **
41932746 TAGTAGCAATTAATATGCTTATAAT-AATTCGTTA
1 CAGTAGCAATTAATATGCTTATAATAAAAT-AATA
*
41932780 CAGTAGCCATTAATATGCTTATAA
1 CAGTAGCAATTAATATGCTTATAA
41932804 GAGATCAACT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 3 0.06
34 46 0.94
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (34 bp):
CAGTAGCAATTAATATGCTTATAATAAAATAATA
Found at i:41936950 original size:17 final size:17
Alignment explanation
Indices: 41936914--41936951 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
41936904 ATGATGAAAT
41936914 AAAAG-GGGAAAAAAAG
1 AAAAGAGGGAAAAAAAG
*
41936930 -AAAGAGGGAAAAATAG
1 AAAAGAGGGAAAAAAAG
41936946 AAAAGA
1 AAAAGA
41936952 TGAAAGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 4 0.21
16 10 0.53
17 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (17 bp):
AAAAGAGGGAAAAAAAG
Found at i:41943832 original size:6 final size:6
Alignment explanation
Indices: 41943823--41943850 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41943813 AGTTTTAATT
41943823 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
41943851 TCTCTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:41943834 original size:14 final size:14
Alignment explanation
Indices: 41943805--41943851 Score: 62
Period size: 12 Copynumber: 3.4 Consensus size: 14
41943795 TGGAGTGGGG
*
41943805 ATTTTGTAAGTTTTA
1 ATTTTTTAA-TTTTA
41943820 ATTTTTTAATTTTA
1 ATTTTTTAATTTTA
41943834 A--TTTTAATTTTA
1 ATTTTTTAATTTTA
41943846 ATTTTT
1 ATTTTT
41943852 CTCTCTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 12 0.41
14 9 0.31
15 8 0.28
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (14 bp):
ATTTTTTAATTTTA
Found at i:41948115 original size:43 final size:43
Alignment explanation
Indices: 41948003--41948155 Score: 171
Period size: 43 Copynumber: 3.6 Consensus size: 43
41947993 GTGGAAAAAT
* * * * * *
41948003 GCCGCTATAGAACACGATTTTTAGCGACACTTCTCATAAAAAC
1 GCCGCTAAAGAACATGATTTTTAGCGGCGCTTTTCATACAAAC
* * *
41948046 GCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCTACAAAT
1 GCCGCTAAAGAACATGATTTTTAGCGGCGCTTTTCATACAAAC
* **
41948089 GCCGCTATAGAACATGATTTTTAGCGGCGCTTTTTTTACAAAC
1 GCCGCTAAAGAACATGATTTTTAGCGGCGCTTTTCATACAAAC
* * *
41948132 GCCGCAAAAGATCATGTTTTTTAG
1 GCCGCTAAAGAACATGATTTTTAG
41948156 TGGCATTTTT
Statistics
Matches: 92, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 92 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (43 bp):
GCCGCTAAAGAACATGATTTTTAGCGGCGCTTTTCATACAAAC
Found at i:41948294 original size:43 final size:42
Alignment explanation
Indices: 41948039--41948292 Score: 210
Period size: 43 Copynumber: 5.9 Consensus size: 42
41948029 ACACTTCTCA
* * * **
41948039 TAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCC
1 TAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCG-TTTTTG
* * * *
41948082 TACAAA-TGCCGCTATAGAACATGATT-TTTAGCGGCGCTTTTTT
1 TA-AAAGCGCCGCTAAAGATCATG-TTCTTTAGCGGCG-TTTTTG
* * * *
41948125 TACAAA-CGCCGCAAAAGATCATGTTTTTTAGTGGCATTTTTAG
1 TA-AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTT-G
* * **
41948168 TAAAAGCGCAGCTAAAGATCATGTTCTATAGCGGCGTTTCTAA
1 TAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT-TTG
* *
41948211 TAAAAGCGTCGCTAAAGATCATG-TCATTTAACGGCGTTTGTTG
1 TAAAAGCGCCGCTAAAGATCATGTTC-TTTAGCGGCGTTT-TTG
* *
41948254 TAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGCGTTT
1 TAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
41948293 GTGGGAAAAT
Statistics
Matches: 172, Mismatches: 31, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
42 12 0.07
43 153 0.89
44 7 0.04
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (42 bp):
TAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTG
Found at i:41951952 original size:24 final size:24
Alignment explanation
Indices: 41951904--41951950 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41951894 ACTGGTCACA
*
41951904 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
41951928 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
41951951 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:41952621 original size:27 final size:26
Alignment explanation
Indices: 41952590--41952810 Score: 217
Period size: 27 Copynumber: 8.2 Consensus size: 26
41952580 TTACACTGTT
* *
41952590 ATGACCGAAATAGCCCCATAAGGTAGA
1 ATGACCGAAATA-CCCCATAGGGTAAA
*
41952617 ATGACTGAAATACCCTCATAGGGTAAA
1 ATGACCGAAATACCC-CATAGGGTAAA
*
41952644 ATGACTGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATA-CCCCATAGGGTAAA
41952671 ATGACCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATA-CCCCATAGGGTAAA
* ** * *
41952698 ATAACTAAAATACCCTCACAGGGTAGA
1 ATGACCGAAATACCC-CATAGGGTAAA
*
41952725 ATGACTGAAATACCCCTATAGGGTAAA
1 ATGACCGAAATACCCC-ATAGGGTAAA
* * * * *
41952752 ATGATCGAAATACCCTCACAAGATAGA
1 ATGACCGAAATACCC-CATAGGGTAAA
* *
41952779 ATGATCGAAATACCCCCATAGGTTAAA
1 ATGACCGAAATA-CCCCATAGGGTAAA
41952806 ATGAC
1 ATGAC
41952811 TGTTATATCC
Statistics
Matches: 164, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
26 7 0.04
27 150 0.91
28 7 0.04
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.19
Consensus pattern (26 bp):
ATGACCGAAATACCCCATAGGGTAAA
Found at i:41952674 original size:54 final size:54
Alignment explanation
Indices: 41952590--41952812 Score: 270
Period size: 54 Copynumber: 4.1 Consensus size: 54
41952580 TTACACTGTT
* * * *
41952590 ATGACCGAAATAGCCCCATAAGGTAGAATGACTGAAATACCCTCATAGGGTAAA
1 ATGACTGAAATACCCCCACAAGGTAGAATGACTGAAATACCCCCATAGGGTAAA
* * * *
41952644 ATGACTGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAA
1 ATGACTGAAATACCCCCACAAGGTAGAATGACTGAAATACCCCCATAGGGTAAA
* * * * *
41952698 ATAACTAAAATACCCTCACAGGGTAGAATGACTGAAATACCCCTATAGGGTAAA
1 ATGACTGAAATACCCCCACAAGGTAGAATGACTGAAATACCCCCATAGGGTAAA
* * *
41952752 ATGA-TCGAAATACCCTCACAAGATAGAATGA-TCGAAATACCCCCATAGGTTAAA
1 ATGACT-GAAATACCCCCACAAGGTAGAATGACT-GAAATACCCCCATAGGGTAAA
41952806 ATGACTG
1 ATGACTG
41952813 TTATATCCCT
Statistics
Matches: 147, Mismatches: 19, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
53 2 0.01
54 144 0.98
55 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (54 bp):
ATGACTGAAATACCCCCACAAGGTAGAATGACTGAAATACCCCCATAGGGTAAA
Found at i:41952823 original size:81 final size:80
Alignment explanation
Indices: 41952590--41952812 Score: 295
Period size: 81 Copynumber: 2.8 Consensus size: 80
41952580 TTACACTGTT
41952590 ATGACCGAAATAGCCCCATAAGGTAGAATGACTGAAATACCCTCATAGGGTAAAATGACTGAAAT
1 ATGACCGAAATA-CCCCATAAGGTAGAATGACTGAAATACCCTCATAGGGTAAAATGACTGAAAT
*
41952655 ACCCCCATAGGGTAAA
65 ACCCCTATAGGGTAAA
* * * * * *
41952671 ATGACCGAAATACCCCCATAGGGTAAAATAACTAAAATACCCTCACAGGGTAGAATGACTGAAAT
1 ATGACCGAAATA-CCCCATAAGGTAGAATGACTGAAATACCCTCATAGGGTAAAATGACTGAAAT
41952736 ACCCCTATAGGGTAAA
65 ACCCCTATAGGGTAAA
* * * * *
41952752 ATGATCGAAATACCCTCACAAGATAGAATGA-TCGAAATACCCCCATAGGTTAAAATGACTG
1 ATGACCGAAATACCC-CATAAGGTAGAATGACT-GAAATACCCTCATAGGGTAAAATGACTG
41952813 TTATATCCCT
Statistics
Matches: 121, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
80 4 0.03
81 117 0.97
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (80 bp):
ATGACCGAAATACCCCATAAGGTAGAATGACTGAAATACCCTCATAGGGTAAAATGACTGAAATA
CCCCTATAGGGTAAA
Found at i:41961747 original size:42 final size:42
Alignment explanation
Indices: 41961629--41961783 Score: 127
Period size: 42 Copynumber: 3.7 Consensus size: 42
41961619 ACATGGCTTG
* * * ***
41961629 GACACATGCCCATGTCCTTGTCCGTGTGGCTT-ACATGGCCTA
1 GACACACGCCCATATCCTTGCCCGTGTGG-TTCACACAACCTA
* * * * * *
41961671 GACATACACCTATATCCTTGCCCGTATAGCTCACACAACCT-
1 GACACACGCCCATATCCTTGCCCGTGTGGTTCACACAACCTA
*
41961712 GAACACACGCCCATATCCTTGCCCGTGTGGTTCACACAGCCTA
1 G-ACACACGCCCATATCCTTGCCCGTGTGGTTCACACAACCTA
* * *
41961755 GGCACACGCCCATGTCCCTG-CCGTGTGGT
1 GACACACGCCCATATCCTTGCCCGTGTGGT
41961784 CTTAAATCAT
Statistics
Matches: 88, Mismatches: 22, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
41 11 0.12
42 76 0.86
43 1 0.01
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.24
Consensus pattern (42 bp):
GACACACGCCCATATCCTTGCCCGTGTGGTTCACACAACCTA
Found at i:41961891 original size:61 final size:61
Alignment explanation
Indices: 41961811--41961943 Score: 230
Period size: 61 Copynumber: 2.2 Consensus size: 61
41961801 AAGTTACAAG
* *
41961811 GCCTAGACACATGCCCGTGTCTATTTCCTGTGTGAACCTTGTACTAACATGGCCACACACA
1 GCCTGGACACATGCCCGTGTCTATTTCCTGTGTGAACCCTGTACTAACATGGCCACACACA
* *
41961872 GCCTGGACACATGCCCGTGTCTGTTTCCTGTGTGAACCCTGTACTAACATTGCCACACACA
1 GCCTGGACACATGCCCGTGTCTATTTCCTGTGTGAACCCTGTACTAACATGGCCACACACA
41961933 GCCTGGACACA
1 GCCTGGACACA
41961944 CGTTCGTGTC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (61 bp):
GCCTGGACACATGCCCGTGTCTATTTCCTGTGTGAACCCTGTACTAACATGGCCACACACA
Found at i:41961966 original size:61 final size:61
Alignment explanation
Indices: 41961811--41961966 Score: 177
Period size: 61 Copynumber: 2.6 Consensus size: 61
41961801 AAGTTACAAG
* * ** * * *
41961811 GCCTAGACACATGCCCGTGTCTATTTCCTGTGTGAACCTTGTACTAACATGGCCACACACA
1 GCCTGGACACACGCCCGTGTCCCTTGCCCGTGTGAACCCTGTACTAACATGGCCACACACA
* ** * * *
41961872 GCCTGGACACATGCCCGTGTCTGTTTCCTGTGTGAACCCTGTACTAACATTGCCACACACA
1 GCCTGGACACACGCCCGTGTCCCTTGCCCGTGTGAACCCTGTACTAACATGGCCACACACA
**
41961933 GCCTGGACACACGTTCGTGTCCCTTGCCCGTGTG
1 GCCTGGACACACGCCCGTGTCCCTTGCCCGTGTG
41961967 TTCAAATTCA
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 84 1.00
ACGTcount: A:0.20, C:0.33, G:0.21, T:0.26
Consensus pattern (61 bp):
GCCTGGACACACGCCCGTGTCCCTTGCCCGTGTGAACCCTGTACTAACATGGCCACACACA
Found at i:41967027 original size:61 final size:61
Alignment explanation
Indices: 41966932--41967055 Score: 194
Period size: 61 Copynumber: 2.0 Consensus size: 61
41966922 TGCATTGTAA
* * *
41966932 CACCCCATACCCGGCCTAGATACCGGGCTGAATATCGAGATGCCACACCATCGTCTCATGT
1 CACCCCATACCCGGCCTAGATACCAGGCTAAATATCGAGATGCCACACCATCATCTCATGT
* * *
41966993 CACCCCATACCCGGCTTGGATGCCAGGCTAAATATCGAGATGCCACACCATCATCTCATGT
1 CACCCCATACCCGGCCTAGATACCAGGCTAAATATCGAGATGCCACACCATCATCTCATGT
41967054 CA
1 CA
41967056 ACTTCATTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.20
Consensus pattern (61 bp):
CACCCCATACCCGGCCTAGATACCAGGCTAAATATCGAGATGCCACACCATCATCTCATGT
Found at i:41980217 original size:13 final size:13
Alignment explanation
Indices: 41980199--41980224 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41980189 CTATACTTAA
41980199 GGGAAATAAATTC
1 GGGAAATAAATTC
41980212 GGGAAATAAATTC
1 GGGAAATAAATTC
41980225 TAAGTGACAA
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:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (13 bp):
GGGAAATAAATTC
Found at i:41986892 original size:5 final size:5
Alignment explanation
Indices: 41986882--41986910 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
41986872 CCAGACTATT
41986882 CTTTC CTTTC CTTTC CTTTC CTTTC CTTT
1 CTTTC CTTTC CTTTC CTTTC CTTTC CTTT
41986911 GCTTCTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
CTTTC
Found at i:41996680 original size:72 final size:72
Alignment explanation
Indices: 41996563--41996706 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
41996553 AAGCCAGGAG
41996563 AAAGTGAAATTCAGTGGTTTAACTATGGCAGAATAGAAGATGACTCATGCTTGACCACAAAAACA
1 AAAGTGAAATTCAGTGGTTTAACTATGGCAGAATAGAAGATGACTCATGCTTGACCACAAAAACA
41996628 AGTGGAA
66 AGTGGAA
* *
41996635 AAAGTGAAATTCAGTGGTTTAACTATGGTAGAATAGAAGATGACTCATGCTTGACCACAAAACCA
1 AAAGTGAAATTCAGTGGTTTAACTATGGCAGAATAGAAGATGACTCATGCTTGACCACAAAAACA
41996700 AGTGGAA
66 AGTGGAA
41996707 CTTGCCTGAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (72 bp):
AAAGTGAAATTCAGTGGTTTAACTATGGCAGAATAGAAGATGACTCATGCTTGACCACAAAAACA
AGTGGAA
Found at i:41996841 original size:30 final size:31
Alignment explanation
Indices: 41996805--41996877 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
41996795 TGTAATACAC
* **
41996805 AAACTTTAATTT-GATACAATTATACACATG
1 AAACTTTGATTTGGATACAACCATACACATG
*
41996835 AAACTTTGATTTGGATTCAACCATACACATG
1 AAACTTTGATTTGGATACAACCATACACATG
*
41996866 AAAATTTGATTT
1 AAACTTTGATTT
41996878 TGATTTTGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 11 0.30
31 26 0.70
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (31 bp):
AAACTTTGATTTGGATACAACCATACACATG
Found at i:41996904 original size:21 final size:21
Alignment explanation
Indices: 41996874--41996913 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41996864 TGAAAATTTG
41996874 ATTTTGATTTTG-ATTCAATAA
1 ATTTTGA-TTTGAATTCAATAA
*
41996895 ATTTTTATTTGAATTCAAT
1 ATTTTGATTTGAATTCAAT
41996914 TATACACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTTTGATTTGAATTCAATAA
Found at i:41999354 original size:20 final size:20
Alignment explanation
Indices: 41999329--41999369 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41999319 AGTCTTCCTT
41999329 AGTTCATTCTTAAAACCCTG
1 AGTTCATTCTTAAAACCCTG
41999349 AGTTCATTCTTAAAACCCTG
1 AGTTCATTCTTAAAACCCTG
41999369 A
1 A
41999370 TAAATAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (20 bp):
AGTTCATTCTTAAAACCCTG
Found at i:42005945 original size:24 final size:23
Alignment explanation
Indices: 42005870--42005951 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 23
42005860 CTCGAGGTCA
* * * *
42005870 AATGATTGTTTTGTCTGTGGTTA
1 AATGATTGATTTGTCTATGTTTG
42005893 AATGATTGATTTGTCTATGTTTGG
1 AATGATTGATTTGTCTATGTTT-G
*
42005917 TATGATTGATTTGTCTATGATTTG
1 AATGATTGATTTGTCTATG-TTTG
*
42005941 AATGACTGATT
1 AATGATTGATT
42005952 CTGAGTATGG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
23 19 0.38
24 28 0.56
25 3 0.06
ACGTcount: A:0.22, C:0.05, G:0.23, T:0.50
Consensus pattern (23 bp):
AATGATTGATTTGTCTATGTTTG
Found at i:42006132 original size:26 final size:26
Alignment explanation
Indices: 42006077--42006132 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
42006067 ATACTATTAC
* * ** *
42006077 TGGCTGCTTTACTGCGATATTGTTGC
1 TGGCAGCTTTACTGCGATACTACTGA
42006103 TGGCAGCTTTACTGCGATACTACTGA
1 TGGCAGCTTTACTGCGATACTACTGA
42006129 TGGC
1 TGGC
42006133 TTTGTGCCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.16, C:0.21, G:0.27, T:0.36
Consensus pattern (26 bp):
TGGCAGCTTTACTGCGATACTACTGA
Found at i:42006344 original size:32 final size:32
Alignment explanation
Indices: 42006123--42006346 Score: 254
Period size: 32 Copynumber: 7.0 Consensus size: 32
42006113 ACTGCGATAC
* * *
42006123 TACTGATGGCTTTGTGCCGATCATAGTACCGA
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* *
42006155 TACTGATGGCTTTATGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * *
42006187 TACTGATGGCTATGTACCGATCAT-TTCATTGT
1 TACTGATGGCTTTGTGCCGATCATATT-ACTGT
* *
42006219 TACTGATGG-TTGTGTCCCGATCATATCACTGT
1 TACTGATGGCTT-TGTGCCGATCATATTACTGT
* *
42006251 TACTAATGGCTTTGTGCCGATCATGTTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * **
42006283 TATTGATGGCTATGTGCCGATCATATTACTAC
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* *
42006315 TACTGATGGCTTTGTGCCAATCACATTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
42006347 ACTTATGACT
Statistics
Matches: 160, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
31 3 0.02
32 154 0.96
33 3 0.02
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACTGT
Found at i:42006436 original size:26 final size:26
Alignment explanation
Indices: 42006407--42006459 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
42006397 AGCTCTTAGC
* *
42006407 CATTCTGACTACTGACAGCTCTGCTG
1 CATTATGACTACTGACAGCTATGCTG
* *
42006433 CATTATTACTACTGGCAGCTATGCTG
1 CATTATGACTACTGACAGCTATGCTG
42006459 C
1 C
42006460 GATATTAGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (26 bp):
CATTATGACTACTGACAGCTATGCTG
Found at i:42011294 original size:79 final size:83
Alignment explanation
Indices: 42011140--42011299 Score: 229
Period size: 85 Copynumber: 1.9 Consensus size: 83
42011130 TAAGACTTTG
*
42011140 AACATTCGGCCTTTGGTGTTGCTCAATTAAGGTATGTTTAGGTTTCAATTTTTGATAATTTTTAC
1 AACATTCGGCCTTTGGTGTTGCTCAATTAAGGTACGTTTAGG-TT--ATTTTTGATAATTTTTAC
42011205 ATTTCTGAGATTGTTGATTTA
63 ATTTCTGAGATTGTTGATTTA
* *
42011226 AACATTCGGCC-TTGGTGTTGCTCAATTAAGGTACGTTTCGG-T-TTTTT-ATAATTTTTACGTT
1 AACATTCGGCCTTTGGTGTTGCTCAATTAAGGTACGTTTAGGTTATTTTTGATAATTTTTACATT
*
42011287 TTTGAGATTGTTG
66 TCTGAGATTGTTG
42011300 CTTTGTGTTC
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
79 25 0.36
80 5 0.07
83 1 0.01
85 28 0.40
86 11 0.16
ACGTcount: A:0.21, C:0.11, G:0.20, T:0.47
Consensus pattern (83 bp):
AACATTCGGCCTTTGGTGTTGCTCAATTAAGGTACGTTTAGGTTATTTTTGATAATTTTTACATT
TCTGAGATTGTTGATTTA
Found at i:42012072 original size:43 final size:43
Alignment explanation
Indices: 42012010--42012124 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
42012000 AAGCGTTTCT
* * *
42012010 ATGTAAGACCACGTCTGGGACGTTGGCATAGA-CTTGTGTTTTC
1 ATGTAAGACCACGTCTGGGACGTTGGCATAGATC-AGTGATTAC
* * *
42012053 GTGTAAGACC-CTGTTTGGGACAG-TGGCATCGATCAGTGATTAC
1 ATGTAAGACCAC-GTCTGGGAC-GTTGGCATAGATCAGTGATTAC
42012096 ATGTAAGACCACGTCTGGGACGTTGGCAT
1 ATGTAAGACCACGTCTGGGACGTTGGCAT
42012125 TGTACGAGCT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.03
43 54 0.92
44 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.29
Consensus pattern (43 bp):
ATGTAAGACCACGTCTGGGACGTTGGCATAGATCAGTGATTAC
Found at i:42015509 original size:17 final size:18
Alignment explanation
Indices: 42015477--42015510 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42015467 AATTTCTTTT
42015477 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
42015495 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
42015511 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:42016006 original size:3 final size:3
Alignment explanation
Indices: 42015988--42016046 Score: 54
Period size: 3 Copynumber: 20.7 Consensus size: 3
42015978 ATATATTAGT
* * *
42015988 TAA TAA TAT TAT TAA TAA TAA TACA TTA TAA TAA T-A TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
42016032 T-A TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TA
42016047 TTTAATTCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
2 8 0.17
3 37 0.79
4 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:42016020 original size:10 final size:8
Alignment explanation
Indices: 42015988--42016047 Score: 52
Period size: 8 Copynumber: 7.1 Consensus size: 8
42015978 ATATATTAGT
42015988 TAATAATA
1 TAATAATA
*
42015996 TTATTAATAA
1 -TAATAAT-A
42016006 TAATACATTA
1 TAATA-A-TA
42016016 TAATAATA
1 TAATAATA
42016024 TAAT-ATA
1 TAATAATA
42016031 -ATATAATA
1 TA-ATAATA
42016039 TAATAATA
1 TAATAATA
42016047 T
1 T
42016048 TTAATTCATA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
6 1 0.02
7 5 0.12
8 16 0.37
9 12 0.28
10 8 0.19
11 1 0.02
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (8 bp):
TAATAATA
Found at i:42016020 original size:13 final size:13
Alignment explanation
Indices: 42015978--42016047 Score: 65
Period size: 13 Copynumber: 5.3 Consensus size: 13
42015968 TTTATTTTAT
42015978 ATATATTAGTTAATA
1 ATATATTA--TAATA
42015993 ATATTATTAATAATA
1 ATA-TATT-ATAATA
*
42016008 ATACATTATAATA
1 ATATATTATAATA
42016021 ATATA--AT-ATA
1 ATATATTATAATA
*
42016031 ATATAATATAATA
1 ATATATTATAATA
42016044 ATAT
1 ATAT
42016048 TTAATTCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
10 8 0.17
11 2 0.04
12 2 0.04
13 17 0.35
14 3 0.06
15 11 0.23
16 4 0.08
17 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (13 bp):
ATATATTATAATA
Found at i:42016028 original size:5 final size:5
Alignment explanation
Indices: 42016018--42016043 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42016008 ATACATTATA
42016018 ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT A
42016044 ATATTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:42031423 original size:12 final size:13
Alignment explanation
Indices: 42031406--42031437 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
42031396 AGAGAAATAA
42031406 AATTTAAGTA-AG
1 AATTTAAGTAGAG
42031418 AATTTAA-TAGAG
1 AATTTAAGTAGAG
42031430 AATTTAAG
1 AATTTAAG
42031438 ATATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 16 0.89
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (13 bp):
AATTTAAGTAGAG
Found at i:42040471 original size:178 final size:178
Alignment explanation
Indices: 42040261--42040617 Score: 696
Period size: 178 Copynumber: 2.0 Consensus size: 178
42040251 ATGAATTTAC
*
42040261 AAAAGTACATGATAAATTCGAATATGTATATATATACATGTATAATTTCTTGTATTGAAATTAGG
1 AAAAGTACATGATAAATTCGAATATATATATATATACATGTATAATTTCTTGTATTGAAATTAGG
42040326 TATGGAATTATATATTGATATATATGGTTGAAAGTATATGTATATATATGTTTAAGATTTGCATT
66 TATGGAATTATATATTGATATATATGGTTGAAAGTATATGTATATATATGTTTAAGATTTGCATT
42040391 GAATCAAAAGTATGAAATTGTTAGCTTAAATTATTTTAATATGTTCGA
131 GAATCAAAAGTATGAAATTGTTAGCTTAAATTATTTTAATATGTTCGA
*
42040439 AAAAGTACATGATAAATTCGAATATATATATATGTACATGTATAATTTCTTGTATTGAAATTAGG
1 AAAAGTACATGATAAATTCGAATATATATATATATACATGTATAATTTCTTGTATTGAAATTAGG
42040504 TATGGAATTATATATTGATATATATGGTTGAAAGTATATGTATATATATGTTTAAGATTTGCATT
66 TATGGAATTATATATTGATATATATGGTTGAAAGTATATGTATATATATGTTTAAGATTTGCATT
42040569 GAATCAAAAGTATGAAATTGTTAGCTTAAATTATTTTAATATGTTCGA
131 GAATCAAAAGTATGAAATTGTTAGCTTAAATTATTTTAATATGTTCGA
42040617 A
1 A
42040618 TGTGAAATGT
Statistics
Matches: 177, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
178 177 1.00
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.41
Consensus pattern (178 bp):
AAAAGTACATGATAAATTCGAATATATATATATATACATGTATAATTTCTTGTATTGAAATTAGG
TATGGAATTATATATTGATATATATGGTTGAAAGTATATGTATATATATGTTTAAGATTTGCATT
GAATCAAAAGTATGAAATTGTTAGCTTAAATTATTTTAATATGTTCGA
Found at i:42040953 original size:41 final size:40
Alignment explanation
Indices: 42040903--42041106 Score: 209
Period size: 41 Copynumber: 5.0 Consensus size: 40
42040893 GCATGTATAT
* *
42040903 TGCCAGTGAATCAATTCAGGCTTAAAGCTTAGCAGGCTAAG
1 TGCCGGTGAATCAA-TCAGGCTTAAAGCCTAGCAGGCTAAG
*
42040944 TGCCGGTGAACTGAATCAGG-TTATAAGCCTAGCAGGCTAAG
1 TGCCGGTGAA-TCAATCAGGCTTA-AAGCCTAGCAGGCTAAG
*
42040985 TGCCGGTG-ATCTGAATCAGGCTTTAAGCCTAGCAGGCTAAG
1 TGCCGGTGAATC--AATCAGGCTTAAAGCCTAGCAGGCTAAG
* *
42041026 TGCCGGTAAACTGAATCAGGC-TATAAGCCTAGCAGGCTAAG
1 TGCCGGTGAA-TCAATCAGGCTTA-AAGCCTAGCAGGCTAAG
* * * *
42041067 TGCCGGTG-ATCTGAATCAGACTTTAAGCTTAGTAGGCTAA
1 TGCCGGTGAATC--AATCAGGCTTAAAGCCTAGCAGGCTAA
42041107 CTGTCAGTGA
Statistics
Matches: 138, Mismatches: 14, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
39 2 0.01
40 6 0.04
41 122 0.88
42 7 0.05
43 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (40 bp):
TGCCGGTGAATCAATCAGGCTTAAAGCCTAGCAGGCTAAG
Found at i:42041018 original size:82 final size:82
Alignment explanation
Indices: 42040918--42041106 Score: 324
Period size: 82 Copynumber: 2.3 Consensus size: 82
42040908 GTGAATCAAT
* * *
42040918 TCAGGCTTAAAGCTTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAGCAGGCTA
1 TCAGGCTTTAAGCTTAGCAGGCTAAGTGCCGGTAAACTGAATCAGGCTATAAGCCTAGCAGGCTA
42040983 AGTGCCGGTGATCTGAA
66 AGTGCCGGTGATCTGAA
*
42041000 TCAGGCTTTAAGCCTAGCAGGCTAAGTGCCGGTAAACTGAATCAGGCTATAAGCCTAGCAGGCTA
1 TCAGGCTTTAAGCTTAGCAGGCTAAGTGCCGGTAAACTGAATCAGGCTATAAGCCTAGCAGGCTA
42041065 AGTGCCGGTGATCTGAA
66 AGTGCCGGTGATCTGAA
* *
42041082 TCAGACTTTAAGCTTAGTAGGCTAA
1 TCAGGCTTTAAGCTTAGCAGGCTAA
42041107 CTGTCAGTGA
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 100 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (82 bp):
TCAGGCTTTAAGCTTAGCAGGCTAAGTGCCGGTAAACTGAATCAGGCTATAAGCCTAGCAGGCTA
AGTGCCGGTGATCTGAA
Done.