Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 85 of 199
Found at i:30066929 original size:44 final size:44
Alignment explanation
Indices: 30066866--30066956 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
30066856 ATAGGTTAAA
* *
30066866 TAATATTAAAATAAACTACATTAATTAAAGTTTAAGTGGGAAAC
1 TAATATTAAAATAAACTACACTAATCAAAGTTTAAGTGGGAAAC
* *
30066910 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAAACTACACTAATCAAAGTTTAAGTGGGAAAC
30066954 TAA
1 TAA
30066957 AAACTATAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (44 bp):
TAATATTAAAATAAACTACACTAATCAAAGTTTAAGTGGGAAAC
Found at i:30068754 original size:23 final size:22
Alignment explanation
Indices: 30068708--30068754 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
30068698 AGATAAAACT
*
30068708 AAACCCCAAAACCTAAAAATAA
1 AAACCCCAAAACCTAAAAACAA
* *
30068730 AAACCCTCAAAACGTAAACACAA
1 AAACCC-CAAAACCTAAAAACAA
30068753 AA
1 AA
30068755 TTCTCTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.62, C:0.28, G:0.02, T:0.09
Consensus pattern (22 bp):
AAACCCCAAAACCTAAAAACAA
Found at i:30069939 original size:107 final size:107
Alignment explanation
Indices: 30069737--30070023 Score: 443
Period size: 107 Copynumber: 2.7 Consensus size: 107
30069727 TTTAAGAGTG
* * * *
30069737 TATTTGG-CTAAACG-AGAAATCGAAACCCAGCGCATTAGGGCACGTTTTCTTGAATTTCCAAAT
1 TATTTGGTC-AAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAAC
* * * *
30069800 ACAAAATATTGCCTTACTTTGAAATTTTAAAAGTATATTTGGC
65 GCAAAATATTACCATACTTTGAAATTTTAAAAGGATATTTGGC
* *
30069843 TATTTGGTCGAACGAAAAAATCAAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
1 TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
30069908 CAAAATATTACCATACTTTGAAATTTTAAAAGGATATTTGGC
66 CAAAATATTACCATACTTTGAAATTTTAAAAGGATATTTGGC
* *
30069950 TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTTCAAACG
1 TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
30070015 CAAAATATT
66 CAAAATATT
30070024 GCCTTTATTA
Statistics
Matches: 165, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
106 11 0.07
107 154 0.93
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (107 bp):
TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
CAAAATATTACCATACTTTGAAATTTTAAAAGGATATTTGGC
Found at i:30071729 original size:20 final size:20
Alignment explanation
Indices: 30071696--30071733 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30071686 TCTAAGTAAA
30071696 AAAATAAAAGAAATAAAAGT
1 AAAATAAAAGAAATAAAAGT
30071716 AAAATGAAAA-AAATAAAA
1 AAAAT-AAAAGAAATAAAA
30071734 AAACAGAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (20 bp):
AAAATAAAAGAAATAAAAGT
Found at i:30072907 original size:183 final size:183
Alignment explanation
Indices: 30072565--30073062 Score: 703
Period size: 183 Copynumber: 2.7 Consensus size: 183
30072555 CTATCTACTG
* * * * * * *
30072565 TCCGCTCCACTACAAATTTAGGGAGACACGACTT-GTTGTTTTCAGTCTACTCCACTGCATCTTC
1 TCCGCTCCACTACAACTTTAGGGAGATAGGA-TTAGTAG-CTTCAGTCTACTCCACTGTAACTTC
* * * * * * * * ** *
30072629 AAGGAAATAGGA-TTCATATCTTCAAACTTGCCCCACTGCAACTTCAGGGGGATAAGACTTGCTA
64 AAGGAGATAAGACTT-GTATCTTC-AACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATA
*
30072693 TGATAAGATTTAATCCGACCCTCTGCAACTTCAAAGGTATAGGATTCATCGTTTTAA
127 TGATAAGATTTAATCCAACCCTCTGCAACTTCAAAGGTATAGGATTCATCGTTTTAA
* *
30072750 TCCGCTCCACTGCAACTTTAGGGAGATAGGATTAGTAGCTTCAGTCTATTCCACTGTAACTTCAA
1 TCCGCTCCACTACAACTTTAGGGAGATAGGATTAGTAGCTTCAGTCTACTCCACTGTAACTTCAA
30072815 GGAGATAAGACTTGTATCTTCAACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATATGAT
66 GGAGATAAGACTTGTATCTTCAACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATATGAT
* *
30072880 AAGATTTAATCCAACCTTTTGCAACTTCAAAGGTATAGGATTCATCGTTTTAA
131 AAGATTTAATCCAACCCTCTGCAACTTCAAAGGTATAGGATTCATCGTTTTAA
* *
30072933 TCCGCTCCACTACAACTTTAGGGAGATAGGATTAGTAGCTTCAGTCTGCTCCACTGTAACTTCAG
1 TCCGCTCCACTACAACTTTAGGGAGATAGGATTAGTAGCTTCAGTCTACTCCACTGTAACTTCAA
* *
30072998 GGAGATAAGACTTGTATCTTCAACCTGTTCCACTACGACCTCAGGGAGATAAGGTTTGATATGAT
66 GGAGATAAGACTTGTATCTTCAACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATATGAT
30073063 CTGCTTTCTA
Statistics
Matches: 282, Mismatches: 29, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
183 210 0.74
184 40 0.14
185 32 0.11
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (183 bp):
TCCGCTCCACTACAACTTTAGGGAGATAGGATTAGTAGCTTCAGTCTACTCCACTGTAACTTCAA
GGAGATAAGACTTGTATCTTCAACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATATGAT
AAGATTTAATCCAACCCTCTGCAACTTCAAAGGTATAGGATTCATCGTTTTAA
Found at i:30072984 original size:44 final size:44
Alignment explanation
Indices: 30072936--30073050 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
30072926 GTTTTAATCC
* * **
30072936 GCTCCACTACAACTTTAGGGAGATAGGA-TTAGTAGCTTCAGTCT
1 GCTCCACTACAACTTCAGGGAGATAAGACTT-GTAGCTTCAACCT
** *
30072980 GCTCCACTGTAACTTCAGGGAGATAAGACTTGTATCTTCAACCT
1 GCTCCACTACAACTTCAGGGAGATAAGACTTGTAGCTTCAACCT
* * *
30073024 GTTCCACTACGACCTCAGGGAGATAAG
1 GCTCCACTACAACTTCAGGGAGATAAG
30073051 GTTTGATATG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
44 56 0.97
45 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (44 bp):
GCTCCACTACAACTTCAGGGAGATAAGACTTGTAGCTTCAACCT
Found at i:30073543 original size:104 final size:104
Alignment explanation
Indices: 30073406--30073640 Score: 355
Period size: 104 Copynumber: 2.3 Consensus size: 104
30073396 TCAACTTGCC
* * * *
30073406 CCACTACAACTTTAAGGG-CATAAGACTTGTAATTTTCAATAAAGTCTGATGTGATCCATTCTAC
1 CCACTGCAACTTT-AGGGAAATAGGACTTATAATTTTCAATAAAGTCTGATGTGATCCATTCTAC
30073470 TGCAAATTCAGAGAGATAAGATCCATCATTTTGACCCGCT
65 TGCAAATTCAGAGAGATAAGATCCATCATTTTGACCCGCT
* * *
30073510 CCACTGCAACTTTAGGGAGATAGGACTTATAATTTTCAATAAAGTTTGATGTGATCCGTTCTACT
1 CCACTGCAACTTTAGGGAAATAGGACTTATAATTTTCAATAAAGTCTGATGTGATCCATTCTACT
* * *
30073575 GTAACTTTAGAGAGATAAGATCCATCATTTTGACCCGCT
66 GCAAATTCAGAGAGATAAGATCCATCATTTTGACCCGCT
*
30073614 CCACTGCAACTTCAGGGAAATAGGACT
1 CCACTGCAACTTTAGGGAAATAGGACT
30073641 CGTATCTTCA
Statistics
Matches: 119, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
103 4 0.03
104 115 0.97
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (104 bp):
CCACTGCAACTTTAGGGAAATAGGACTTATAATTTTCAATAAAGTCTGATGTGATCCATTCTACT
GCAAATTCAGAGAGATAAGATCCATCATTTTGACCCGCT
Found at i:30074065 original size:24 final size:24
Alignment explanation
Indices: 30074010--30074068 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
30074000 ACGGATTGCC
30074010 TCCACTGTAATATTCAAAGTTCAA
1 TCCACTGTAATATTCAAAGTTCAA
* * * * *
30074034 TTCGCTGTAATCTTCAAAGTTTAG
1 TCCACTGTAATATTCAAAGTTCAA
30074058 TCCACTGTAAT
1 TCCACTGTAAT
30074069 TTTGGGACAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (24 bp):
TCCACTGTAATATTCAAAGTTCAA
Found at i:30074715 original size:108 final size:108
Alignment explanation
Indices: 30074540--30074745 Score: 331
Period size: 108 Copynumber: 1.9 Consensus size: 108
30074530 GAAAAATGCT
30074540 TGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAGCAAAACTCCAAACAAATAAAT
1 TGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAGCAAAACTCCAAACAAATAAAT
* *
30074605 TAATCAGGATAGCAAATTTTGCTAAAATTCAAAGTGAATAAGA
66 TAATCAAGATAGCAAATTTTGCTAAAATACAAAGTGAATAAGA
* * * * * *
30074648 TGAAAAAGATTATCACAATGGACAAGATGAAATTTTGTTGAGAGCAAAGCTCGAGACGAATAGAT
1 TGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAGCAAAACTCCAAACAAATAAAT
*
30074713 TAATCAAGATAGCAAATTTTGCTAGAATACAAA
66 TAATCAAGATAGCAAATTTTGCTAAAATACAAA
30074746 AATGATAATA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 89 1.00
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (108 bp):
TGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAGCAAAACTCCAAACAAATAAAT
TAATCAAGATAGCAAATTTTGCTAAAATACAAAGTGAATAAGA
Found at i:30075114 original size:12 final size:11
Alignment explanation
Indices: 30075070--30075128 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
30075060 TGGCCTGTCC
30075070 TTTTTATTTTT
1 TTTTTATTTTT
* *
30075081 CTTTTCTTTTCT
1 TTTTTATTTT-T
* *
30075093 TTATTCTTTTCT
1 TTTTTATTTT-T
30075105 TTTTTATTTTT
1 TTTTTATTTTT
*
30075116 TTTCTATTTTT
1 TTTTTATTTTT
30075127 TT
1 TT
30075129 AACATTCTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
11 21 0.52
12 19 0.47
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTATTTTT
Found at i:30075125 original size:17 final size:16
Alignment explanation
Indices: 30075070--30075126 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 16
30075060 TGGCCTGTCC
30075070 TTTTTATTTTTCTTTTCT
1 TTTTTA-TTTT-TTTTCT
*
30075088 TTTCTT-TATTCTTTTCT
1 TTT-TTAT-TTTTTTTCT
30075105 TTTTTATTTTTTTTCT
1 TTTTTATTTTTTTTCT
30075121 ATTTTT
1 -TTTTT
30075127 TTAACATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
16 10 0.30
17 16 0.48
18 5 0.15
19 2 0.06
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTATTTTTTTTCT
Found at i:30079081 original size:107 final size:107
Alignment explanation
Indices: 30078879--30079170 Score: 428
Period size: 107 Copynumber: 2.7 Consensus size: 107
30078869 TTTAAGAGGG
* * * * *
30078879 TATTTGG-CTAAACG-AGAAATCGAAACCCAGCGCATTAGGGCACGTTTTCTCAAATTTCCAAAT
1 TATTTGGTC-AAACGAAAAAATCGAAACCCAGCACATTAGGGCACATTTTCTCGAATTTCCAAAC
* *
30078942 GCAAAATATTGTCTTACTTTGAAATTTTAAAAGTATATTTGGC
65 GCAAAATATTGCCTTACTTTGAAATTTTAAAAGGATATTTGGC
* * *
30078985 TATTTGGTCGAACGAAAAAATCAAAACCCAGCACATTAGGACACATTTTCTCGAATTTCCAAACG
1 TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACATTTTCTCGAATTTCCAAACG
*
30079050 TAAAATATTGCCTTACTTTGAAATTTTAAAAGGATATTTGGC
66 CAAAATATTGCCTTACTTTGAAATTTTAAAAGGATATTTGGC
*
30079092 TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCA-AGTTTTCTCGAATTTTCAAAC
1 TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACA-TTTTCTCGAATTTCCAAAC
*
30079156 GCAAAATATTACCTT
65 GCAAAATATTGCCTT
30079171 TATTATTTTT
Statistics
Matches: 166, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
106 12 0.07
107 154 0.93
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (107 bp):
TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACATTTTCTCGAATTTCCAAACG
CAAAATATTGCCTTACTTTGAAATTTTAAAAGGATATTTGGC
Found at i:30086234 original size:6 final size:6
Alignment explanation
Indices: 30086225--30086259 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
30086215 AAATAAAATT
30086225 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
30086260 GTCTAAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:30086270 original size:8 final size:8
Alignment explanation
Indices: 30086257--30086283 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
30086247 AACTAAAACT
30086257 AAAGTCTA
1 AAAGTCTA
30086265 AAAGTCTA
1 AAAGTCTA
30086273 AAAGTCTA
1 AAAGTCTA
30086281 AAA
1 AAA
30086284 ATAATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (8 bp):
AAAGTCTA
Found at i:30086354 original size:18 final size:18
Alignment explanation
Indices: 30086307--30086354 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
30086297 GTAGTGATTC
*
30086307 AATTCGGTTAATTCGGGT
1 AATTCGATTAATTCGGGT
* *
30086325 AA-TCTGAGTAATTCGGTT
1 AATTC-GATTAATTCGGGT
30086343 AATTCGATTAAT
1 AATTCGATTAAT
30086355 CAACCGAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (18 bp):
AATTCGATTAATTCGGGT
Found at i:30095036 original size:19 final size:18
Alignment explanation
Indices: 30095001--30095036 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30094991 TTTTAAAAAA
*
30095001 ATAAAAAATATATATTTT
1 ATAAAAAATATAAATTTT
30095019 ATAAAAAATAATAAATTT
1 ATAAAAAAT-ATAAATTT
30095037 GTAAAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAAAAATATAAATTTT
Found at i:30095041 original size:18 final size:18
Alignment explanation
Indices: 30095001--30095042 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
30094991 TTTTAAAAAA
*
30095001 ATAAAAAATATATATTTT
1 ATAAAAAATATATAATTT
30095019 ATAAAAAATA-ATAAATTT
1 ATAAAAAATATAT-AATTT
*
30095037 GTAAAA
1 ATAAAA
30095043 CATTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAAAAAATATATAATTT
Found at i:30095086 original size:19 final size:21
Alignment explanation
Indices: 30095049--30095088 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30095039 AAAACATTAT
30095049 TAAAATTCATAAAATATTAAA
1 TAAAATTCATAAAATATTAAA
*
30095070 TAAAGTTCA-AAAA-ATTAAA
1 TAAAATTCATAAAATATTAAA
30095089 AACTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (21 bp):
TAAAATTCATAAAATATTAAA
Found at i:30101975 original size:50 final size:50
Alignment explanation
Indices: 30101851--30102099 Score: 277
Period size: 50 Copynumber: 4.8 Consensus size: 50
30101841 GATAATAACA
* * ** * *
30101851 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
30101902 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
30101952 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
30102002 TGTCC-ATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
30102057 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
30102100 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 19, Indels: 13
0.84 0.09 0.06
Matches are distributed among these distances:
49 1 0.01
50 90 0.53
51 35 0.21
53 2 0.01
54 1 0.01
55 4 0.02
56 37 0.22
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:30102037 original size:100 final size:104
Alignment explanation
Indices: 30101850--30102099 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
30101840 TGATAATAAC
**
30101850 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
30101915 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* * *
30101952 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGTCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
30102015 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
30102057 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
30102100 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:30102215 original size:13 final size:13
Alignment explanation
Indices: 30102194--30102225 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
30102184 GCTTGGATCA
*
30102194 TCATCAAATAAAT
1 TCATAAAATAAAT
30102207 TCATAAAATAAAT
1 TCATAAAATAAAT
30102220 TCATAA
1 TCATAA
30102226 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:30102472 original size:30 final size:30
Alignment explanation
Indices: 30102437--30102494 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
30102427 CCTCGACTCT
*
30102437 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
30102467 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
30102495 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:30105296 original size:16 final size:15
Alignment explanation
Indices: 30105277--30105327 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
30105267 TATAAAATTG
30105277 TAAAAAGATATATATA
1 TAAAAA-ATATATATA
*
30105293 TAAAAAATTATAAAATA
1 TAAAAAA-TAT-ATATA
*
30105310 TAAAAATTATATATA
1 TAAAAAATATATATA
30105325 TAA
1 TAA
30105328 GTTAATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 8 0.27
16 12 0.40
17 10 0.33
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
TAAAAAATATATATA
Found at i:30105306 original size:34 final size:33
Alignment explanation
Indices: 30105257--30105327 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 33
30105247 ATGTAAATAA
*
30105257 ATAAATAAAATATAAAATTGTAAAAAGATATATAT
1 ATAAATAAAATATAAAA-TATAAAAA-ATATATAT
* *
30105292 ATAAA-AAATTATAAAATATAAAAATTATATAT
1 ATAAATAAAATATAAAATATAAAAAATATATAT
30105324 ATAA
1 ATAA
30105328 GTTAATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 11 0.33
33 7 0.21
34 10 0.30
35 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (33 bp):
ATAAATAAAATATAAAATATAAAAAATATATAT
Found at i:30108918 original size:32 final size:32
Alignment explanation
Indices: 30108882--30108942 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
30108872 GTAAAACACT
30108882 AAAATGGGTTTTAGATTCC-TTAAAAGTTAGAG
1 AAAATGGGTTTTAGA-TCCTTTAAAAGTTAGAG
***
30108914 AAAATTTTTTTTAGATCCTTTAAAAGTTA
1 AAAATGGGTTTTAGATCCTTTAAAAGTTA
30108943 ATAAAAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 3 0.12
32 22 0.88
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.41
Consensus pattern (32 bp):
AAAATGGGTTTTAGATCCTTTAAAAGTTAGAG
Found at i:30109368 original size:3 final size:3
Alignment explanation
Indices: 30109360--30109392 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
30109350 TGACTCAAAT
30109360 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30109393 CCATAAGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:30111103 original size:56 final size:53
Alignment explanation
Indices: 30111020--30111173 Score: 189
Period size: 46 Copynumber: 3.0 Consensus size: 53
30111010 GTCCCTGATC
30111020 AGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGA
1 AGATAAG-GTAGCTAAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGA
*
30111073 GTAGATAAGAGTAGCTAAGGCTACCACTTATCACTTTCTCACTTGATCAGAT---A
1 --AGATAAG-GTAGCTAAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGA
* *
30111126 A-CT---GTAGCTAAGGCTAACACTTATCACTTTGTCACTTGATCAGATAAG
1 AGATAAGGTAGCTAAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAG
30111174 TATAGCACTT
Statistics
Matches: 90, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
46 40 0.44
50 1 0.01
51 1 0.01
53 1 0.01
55 13 0.14
56 34 0.38
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (53 bp):
AGATAAGGTAGCTAAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGA
Found at i:30111126 original size:46 final size:45
Alignment explanation
Indices: 30111075--30111379 Score: 358
Period size: 46 Copynumber: 7.1 Consensus size: 45
30111065 AGATAAGAGT
*
30111075 AGATAAGAGTAGCTAAGGCTACCACTTATCACTTTCTCACTTGATC
1 AGATAAGTGTAGCTAA-GCTACCACTTATCACTTTCTCACTTGATC
* * *
30111121 AGATAACTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTGATC
1 AGATAAGTGTAGCTAA-GCTACCACTTATCACTTTCTCACTTGATC
*
30111167 AGATAA--GTA--T-AG----CACTTATCACTTTTTCACTTGATC
1 AGATAAGTGTAGCTAAGCTACCACTTATCACTTTCTCACTTGATC
* *
30111203 AGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGATC
1 AGATAAGTGTAGCT-AAGCTACCACTTATCACTTTCTCACTTGATC
*
30111249 AGATAA--GT-G-T-AG----CACTTATCACTTTTTCACTTGATC
1 AGATAAGTGTAGCTAAGCTACCACTTATCACTTTCTCACTTGATC
30111285 AGATAAGTGTAGCTAATGCTACCACTTATCACTTTCTCACTTGATC
1 AGATAAGTGTAGCTAA-GCTACCACTTATCACTTTCTCACTTGATC
*
30111331 AGATAAGTGTAGCTAATGCTACCACTTATCACTTTATCACTTGATC
1 AGATAAGTGTAGCTAA-GCTACCACTTATCACTTTCTCACTTGATC
30111377 AGA
1 AGA
30111380 AGTACTCAAA
Statistics
Matches: 228, Mismatches: 11, Indels: 40
0.82 0.04 0.14
Matches are distributed among these distances:
36 57 0.25
38 5 0.02
39 1 0.00
40 5 0.02
41 2 0.01
42 5 0.02
43 1 0.00
44 5 0.02
46 147 0.64
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (45 bp):
AGATAAGTGTAGCTAAGCTACCACTTATCACTTTCTCACTTGATC
Found at i:30111184 original size:36 final size:36
Alignment explanation
Indices: 30111143--30111297 Score: 175
Period size: 36 Copynumber: 4.0 Consensus size: 36
30111133 CTAAGGCTAA
30111143 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
30111179 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
* *
30111221 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
30111261 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
30111297 C
1 C
30111298 TAATGCTACC
Statistics
Matches: 103, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
36 64 0.62
38 3 0.03
40 3 0.03
42 3 0.03
44 2 0.02
46 28 0.27
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:30111234 original size:82 final size:82
Alignment explanation
Indices: 30111097--30111343 Score: 422
Period size: 82 Copynumber: 3.0 Consensus size: 82
30111087 CTAAGGCTAC
* * * *
30111097 CACTTATCACTTTCTCACTTGATCAGATAACTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
*
30111162 TGATCAGATAAGTATAG
66 TGATCAGATAAGTGTAG
*
30111179 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
30111244 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
* *
30111261 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTCTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
30111326 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
30111343 C
1 C
30111344 TAATGCTACC
Statistics
Matches: 156, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 156 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
TGATCAGATAAGTGTAG
Found at i:30114439 original size:24 final size:23
Alignment explanation
Indices: 30114407--30114467 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
30114397 ACATAGACAA
*
30114407 AAACTGATACTTCCCTGAAAGTGG
1 AAACTGATACTTCCCAG-AAGTGG
*
30114431 AAACTGATACTTCCCAGAGGTGG
1 AAACTGATACTTCCCAGAAGTGG
* *
30114454 AAAATGAAACTTCC
1 AAACTGATACTTCC
30114468 TAAGGGATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 17 0.52
24 16 0.48
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (23 bp):
AAACTGATACTTCCCAGAAGTGG
Found at i:30114554 original size:19 final size:19
Alignment explanation
Indices: 30114513--30114554 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
30114503 CTAAAAACGA
*
30114513 AATTTAATTTTCTAAATTTG
1 AATTTAATTTTC-AAATTAG
30114533 AATTATAATTTTC-AATTAG
1 AATT-TAATTTTCAAATTAG
30114552 AAT
1 AAT
30114555 GAAACTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
AATTTAATTTTCAAATTAG
Found at i:30115817 original size:51 final size:51
Alignment explanation
Indices: 30115741--30115843 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
30115731 AAATAGGGTA
30115741 AGATATCCAACAATTATAAATTGCCACGTGGCATAC-ACTGATGCTATGATG
1 AGATATCCAACAATTATAAATTGCCACGTGGCATACTA-TGATGCTATGATG
30115792 AGATATCCAACAATTATAAATTGCCACGTGGCATACTATGATGCTATGATG
1 AGATATCCAACAATTATAAATTGCCACGTGGCATACTATGATGCTATGATG
30115843 A
1 A
30115844 CATCATCACT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 50 0.98
52 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (51 bp):
AGATATCCAACAATTATAAATTGCCACGTGGCATACTATGATGCTATGATG
Found at i:30121740 original size:17 final size:16
Alignment explanation
Indices: 30121711--30121752 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
30121701 CTGTCAACGT
30121711 CACACGG-CTGTGTGCAA
1 CACACGGTCTGTGT--AA
30121728 CACACGGTC-GTGTAA
1 CACACGGTCTGTGTAA
30121743 CACACGGTCT
1 CACACGGTCT
30121753 AGGCCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 11 0.48
18 1 0.04
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (16 bp):
CACACGGTCTGTGTAA
Found at i:30132516 original size:21 final size:22
Alignment explanation
Indices: 30132484--30132524 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
30132474 GTCAAAGTCA
30132484 AATGTGTTTTTAATTTAAATTT
1 AATGTGTTTTTAATTTAAATTT
*
30132506 AATGT-TTTTTATTTTAAAT
1 AATGTGTTTTTAATTTAAAT
30132525 AAGCTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
AATGTGTTTTTAATTTAAATTT
Found at i:30140255 original size:29 final size:30
Alignment explanation
Indices: 30140210--30140279 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
30140200 TTATATTATC
*
30140210 TAAATATATTTTA-TTTTGTGATTTAA-AAAT
1 TAAA-ATATTTTATTTTTGTG-GTTAAGAAAT
30140240 TAAAATATTTTATTTTTGTGGTTAAGAAAT
1 TAAAATATTTTATTTTTGTGGTTAAGAAAT
*
30140270 TCAAATATTT
1 TAAAATATTT
30140280 GAATTTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 12 0.33
30 24 0.67
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (30 bp):
TAAAATATTTTATTTTTGTGGTTAAGAAAT
Found at i:30150804 original size:3 final size:3
Alignment explanation
Indices: 30150796--30150831 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
30150786 AGTCTTTGCT
30150796 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
30150832 ATTTCATTGA
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:30155418 original size:22 final size:22
Alignment explanation
Indices: 30155393--30155482 Score: 103
Period size: 22 Copynumber: 4.1 Consensus size: 22
30155383 GAAACAGAAA
*
30155393 CAGAGCATATCAAGTACTGATG
1 CAGAGCATATCAAGTACAGATG
30155415 CAGAGCATATC-AGATACAGATG
1 CAGAGCATATCAAG-TACAGATG
*
30155437 CAGAGCATATCAAATACAGATG
1 CAGAGCATATCAAGTACAGATG
* * *
30155459 CGGAGTATAT-TAGATACAGATG
1 CAGAGCATATCAAG-TACAGATG
30155481 CA
1 CA
30155483 AAATCCTACC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.05
22 54 0.93
23 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (22 bp):
CAGAGCATATCAAGTACAGATG
Found at i:30155479 original size:44 final size:44
Alignment explanation
Indices: 30155379--30155482 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 44
30155369 AGATTTTAGA
* ** * *
30155379 ATCAGAAACAGAAACAGAGCATATCAAGTACTGATGCAGAGCAT
1 ATCAGATACAGATGCAGAGCATATCAAATACAGATGCAGAGCAT
* *
30155423 ATCAGATACAGATGCAGAGCATATCAAATACAGATGCGGAGTAT
1 ATCAGATACAGATGCAGAGCATATCAAATACAGATGCAGAGCAT
*
30155467 ATTAGATACAGATGCA
1 ATCAGATACAGATGCA
30155483 AAATCCTACC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.19
Consensus pattern (44 bp):
ATCAGATACAGATGCAGAGCATATCAAATACAGATGCAGAGCAT
Found at i:30156051 original size:42 final size:42
Alignment explanation
Indices: 30155977--30156059 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
30155967 CCTCACACGG
* ** *
30155977 CCTGGCACAAGGCCGTGTGGCTTAAGTCAGTGAGTTACACAT
1 CCTGACACAAGGCCGTGTAACTTAAGTCAGTGACTTACACAT
* *
30156019 CCTGACACATGGCCGTGTAACTTAAGTTAGTGACTTACACA
1 CCTGACACAAGGCCGTGTAACTTAAGTCAGTGACTTACACA
30156060 AGCTGTGCAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (42 bp):
CCTGACACAAGGCCGTGTAACTTAAGTCAGTGACTTACACAT
Found at i:30158872 original size:18 final size:17
Alignment explanation
Indices: 30158845--30158879 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
30158835 GCTACAGTAA
30158845 TTAACCATTTTAATTTAG
1 TTAACCA-TTTAATTTAG
*
30158863 TTAACTATTTAATTTAG
1 TTAACCATTTAATTTAG
30158880 CAATACTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (17 bp):
TTAACCATTTAATTTAG
Found at i:30164496 original size:12 final size:12
Alignment explanation
Indices: 30164479--30164505 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
30164469 AATAAATCAT
30164479 ATATGTATATTA
1 ATATGTATATTA
30164491 ATATGTATATTA
1 ATATGTATATTA
30164503 ATA
1 ATA
30164506 GAAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
ATATGTATATTA
Found at i:30164890 original size:21 final size:21
Alignment explanation
Indices: 30164866--30164918 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
30164856 CATTGTTTCT
*
30164866 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
30164887 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
30164908 AATCTCACCGC
1 AATCTCACCGC
30164919 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:30165738 original size:21 final size:21
Alignment explanation
Indices: 30165712--30165764 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
30165702 AGTGGTGGCG
* *
30165712 GTGAGATTAGTTGCTGTAGCA
1 GTGAGATTAGATACTGTAGCA
* *
30165733 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCA
30165754 GTGAGATTAGA
1 GTGAGATTAGA
30165765 AACAATGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.08, G:0.36, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:30166940 original size:16 final size:16
Alignment explanation
Indices: 30166919--30166951 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
30166909 GGGTATAGGA
30166919 ATTAGTGTTTCAATCT
1 ATTAGTGTTTCAATCT
30166935 ATTAGTGTTTCAATCT
1 ATTAGTGTTTCAATCT
30166951 A
1 A
30166952 CTCCACTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (16 bp):
ATTAGTGTTTCAATCT
Found at i:30167033 original size:51 final size:51
Alignment explanation
Indices: 30166978--30167077 Score: 137
Period size: 51 Copynumber: 2.0 Consensus size: 51
30166968 AGGAGATTAG
* * *
30166978 ACTCGCATCTACAATCTGCTCCACTGGAACTTTAAGGAAATAAGATTTGTA
1 ACTCGCAGCTACAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTTGTA
** * *
30167029 ACTCGCAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTG
1 ACTCGCAGCTACAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTTG
30167078 CATCTCCAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (51 bp):
ACTCGCAGCTACAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTTGTA
Found at i:30167132 original size:44 final size:44
Alignment explanation
Indices: 30167033--30167148 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
30167023 TTTGTAACTC
* * *
30167033 GCAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTT
1 GCAGCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTG
* * * * *
30167077 GCATCTCCAATCTGCTCCATTGCGACTTCAGGGATATAAGATTG
1 GCAGCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTG
** * *
30167121 GTGGCTTCAATCTTCCCCACTGCAACTT
1 GCAGCTTCAATCTGCTCCACTGCAACTT
30167149 TAAAGAGATA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (44 bp):
GCAGCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTG
Found at i:30167349 original size:190 final size:189
Alignment explanation
Indices: 30167037--30167544 Score: 743
Period size: 190 Copynumber: 2.7 Consensus size: 189
30167027 TAACTCGCAG
* * * * *
30167037 CTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGC-ATCTCCAATCTGCTCCATTGCG
1 CTTTAATCTGTTCCACTGCAACTTCAGGGAAATGAGATTTGCTATCTTCAATTTGCTCCACTGCA
* * *
30167101 ACTTCAGGGATATAAGATTGGTGGCTTCAATC-TTCCCCACTGCAACTTTAAAGAGATAAGATTC
66 ACTTCAGGGAGATGAGATTGGTGGCTTCAATCGTT--CCACTGCAACTTTAAGGAGATAAGATTC
*
30167165 GCCATGGTAGATTTAATCCGACCTATTACAACTCTAAAGGTATAGGATTTGTGACTTGTAA
129 GCCATGGTAGATTTAATCCGACCTACTACAACTCTAAAGGTATAGGATTTGTGACTTGTAA
** **
30167226 CTTTAATCTGTTCCACTGCAACTTCAGGGAAATGAGATTCACTATCTTCAATTTGCTCCACTAAA
1 CTTTAATCTGTTCCACTGCAACTTCAGGGAAATGAGATTTGCTATCTTCAATTTGCTCCACTGCA
* *
30167291 ACTTCAGGGAGATGAGATTGGTGGCTTTAATCAGTTCCACTACAACTTTAAGGAGATAAGATTCG
66 ACTTCAGGGAGATGAGATTGGTGGCTTCAATC-GTTCCACTGCAACTTTAAGGAGATAAGATTCG
* *
30167356 CCATGGTAGATTTAATCTGACCTACTACAACTCTAAAGGTATAGGATTTGTGACTTGTAG
130 CCATGGTAGATTTAATCCGACCTACTACAACTCTAAAGGTATAGGATTTGTGACTTGTAA
* *
30167416 CTTTAATCTGTTCTAATGCAACTTCAGGGAAATGAGATTTGCTATCTTCAATTTGCTCCACTGCA
1 CTTTAATCTGTTCCACTGCAACTTCAGGGAAATGAGATTTGCTATCTTCAATTTGCTCCACTGCA
* * **
30167481 ACTTCAAGGAGATGAGATTTGTGGCTTCAATCTGCCCCACTGCAACTTT-AGAGAGATAAGATTC
66 ACTTCAGGGAGATGAGATTGGTGGCTTCAATC-GTTCCACTGCAACTTTAAG-GAGATAAGATTC
30167545 ACTACTATGA
Statistics
Matches: 285, Mismatches: 30, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
189 41 0.14
190 242 0.85
192 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (189 bp):
CTTTAATCTGTTCCACTGCAACTTCAGGGAAATGAGATTTGCTATCTTCAATTTGCTCCACTGCA
ACTTCAGGGAGATGAGATTGGTGGCTTCAATCGTTCCACTGCAACTTTAAGGAGATAAGATTCGC
CATGGTAGATTTAATCCGACCTACTACAACTCTAAAGGTATAGGATTTGTGACTTGTAA
Found at i:30167524 original size:44 final size:45
Alignment explanation
Indices: 30167432--30167528 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 45
30167422 TCTGTTCTAA
* * * *
30167432 TGCAACTTCAGGGAAATGAGATTTGCTATCTTCAATTTGCTCCAC
1 TGCAACTTCAAGGAAATGAGATTTGCTAGCTTCAATCTGCCCCAC
* *
30167477 TGCAACTTCAAGGAGATGAGATTTG-TGGCTTCAATCTGCCCCAC
1 TGCAACTTCAAGGAAATGAGATTTGCTAGCTTCAATCTGCCCCAC
30167521 TGCAACTT
1 TGCAACTT
30167529 TAGAGAGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 23 0.50
45 23 0.50
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (45 bp):
TGCAACTTCAAGGAAATGAGATTTGCTAGCTTCAATCTGCCCCAC
Found at i:30167537 original size:44 final size:45
Alignment explanation
Indices: 30167432--30167543 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 45
30167422 TCTGTTCTAA
* * * * *
30167432 TGCAACTTCAGGGAAATGAGATTTGCTATCTTCAATTTGCTCCAC
1 TGCAACTTCAGAGAGATGAGATTTGCTAGCTTCAATCTGCCCCAC
*
30167477 TGCAACTTCA-AGGAGATGAGATTTG-TGGCTTCAATCTGCCCCAC
1 TGCAACTTCAGA-GAGATGAGATTTGCTAGCTTCAATCTGCCCCAC
* *
30167521 TGCAACTTTAGAGAGATAAGATT
1 TGCAACTTCAGAGAGATGAGATT
30167544 CACTACTATG
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
44 34 0.60
45 23 0.40
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (45 bp):
TGCAACTTCAGAGAGATGAGATTTGCTAGCTTCAATCTGCCCCAC
Found at i:30175674 original size:19 final size:20
Alignment explanation
Indices: 30175658--30175700 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
30175648 TTATGAAACT
*
30175658 TAATGCATATG-ATGAAATG
1 TAATGCAGATGAATGAAATG
30175677 TAATGCAGATGAATGAAATG
1 TAATGCAGATGAATGAAATG
30175697 -AATG
1 TAATG
30175701 TAAAAATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.28
Consensus pattern (20 bp):
TAATGCAGATGAATGAAATG
Found at i:30179250 original size:3 final size:3
Alignment explanation
Indices: 30179242--30179318 Score: 57
Period size: 3 Copynumber: 25.3 Consensus size: 3
30179232 ATGCATAAAC
* * * * *
30179242 AAT AAT AAT AAT GAT GAA- AAT GAT AAC AAT AAT AAT GAT AAT AAC
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
30179287 AAT AAC ATT AAT AAT ATT AAT AAT GAAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT A
30179319 TAAATATTTG
Statistics
Matches: 55, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
2 2 0.04
3 49 0.89
4 4 0.07
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:30179291 original size:24 final size:24
Alignment explanation
Indices: 30179245--30179309 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
30179235 CATAAACAAT
**
30179245 AATAATAATGATGAA-AATGATAAC
1 AATAATAATGAT-AATAACAATAAC
30179269 AATAATAATGATAATAACAATAAC
1 AATAATAATGATAATAACAATAAC
*
30179293 ATTAATAAT-ATTAATAA
1 AATAATAATGA-TAATAA
30179310 TGAATAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 3 0.08
24 33 0.92
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AATAATAATGATAATAACAATAAC
Found at i:30186595 original size:17 final size:18
Alignment explanation
Indices: 30186562--30186595 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30186552 TAGTCCACAC
*
30186562 ATGTTCAATCTATTTGAA
1 ATGTTCAATCGATTTGAA
30186580 ATGTTC-ATCGATTTGA
1 ATGTTCAATCGATTTGA
30186596 TTTTATCAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (18 bp):
ATGTTCAATCGATTTGAA
Found at i:30187717 original size:9 final size:9
Alignment explanation
Indices: 30187673--30187770 Score: 65
Period size: 9 Copynumber: 10.3 Consensus size: 9
30187663 TTTTAGAAAA
30187673 TTTTTAAATT
1 TTTTTAAA-T
30187683 TGTTTTATATAT
1 T-TTTTA-A-AT
30187695 TTTTTAGAATT
1 TTTTTA-AA-T
30187706 TTTTTAAAT
1 TTTTTAAAT
30187715 TTTTTAAA-
1 TTTTTAAAT
*
30187723 TTTTTAAAA
1 TTTTTAAAT
** *
30187732 AATATAAA-
1 TTTTTAAAT
30187740 TTTTTAAAT
1 TTTTTAAAT
30187749 TTTTATAAAT
1 TTTT-TAAAT
* *
30187759 ATTTTGAAT
1 TTTTTAAAT
30187768 TTT
1 TTT
30187771 AAAAACTATT
Statistics
Matches: 71, Mismatches: 10, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
8 13 0.18
9 24 0.34
10 12 0.17
11 18 0.25
12 3 0.04
13 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:30187768 original size:19 final size:20
Alignment explanation
Indices: 30187741--30187805 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
30187731 AAATATAAAT
*
30187741 TTTTAAATTTTTATAAA-TA
1 TTTTGAATTTTTATAAACTA
*
30187760 TTTTGAA-TTTTAAAAACTA
1 TTTTGAATTTTTATAAACTA
*
30187779 TTTTGAATTTTTGA-AAATTA
1 TTTTGAATTTTT-ATAAACTA
30187799 TTTTGAA
1 TTTTGAA
30187806 ACTTTTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
18 8 0.20
19 15 0.38
20 16 0.40
21 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTTGAATTTTTATAAACTA
Found at i:30187795 original size:20 final size:18
Alignment explanation
Indices: 30187737--30187805 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 18
30187727 TAAAAAATAT
*
30187737 AAAT-TTTTAAATTTTTA
1 AAATATTTTGAATTTTTA
*
30187754 TAAATATTTTGAATTTTAA
1 -AAATATTTTGAATTTTTA
30187773 AAACTATTTTGAATTTTTGA
1 AAA-TATTTTGAATTTTT-A
30187793 AAATTATTTTGAA
1 AAA-TATTTTGAA
30187806 ACTTTTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.16
19 24 0.55
20 13 0.30
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (18 bp):
AAATATTTTGAATTTTTA
Found at i:30189273 original size:17 final size:17
Alignment explanation
Indices: 30189251--30189310 Score: 93
Period size: 17 Copynumber: 3.5 Consensus size: 17
30189241 CCCAAAACCC
*
30189251 ACACGCTCATGTGGCCT
1 ACACGCCCATGTGGCCT
30189268 ACACGCCCATGTGGCCT
1 ACACGCCCATGTGGCCT
* *
30189285 ACACGCCCGTGTGGCCC
1 ACACGCCCATGTGGCCT
30189302 ACACGCCCA
1 ACACGCCCA
30189311 ATCTGGCGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.18, C:0.43, G:0.23, T:0.15
Consensus pattern (17 bp):
ACACGCCCATGTGGCCT
Found at i:30189445 original size:40 final size:40
Alignment explanation
Indices: 30189356--30189447 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
30189346 TCACGTCGTT
* * * *
30189356 ACACGGCCGTGTCTTGCACACGGCCACATCTTCATCAGTC
1 ACACGGCCGTGTCTCGCACACGGCCACACCTACAGCAGTC
30189396 ACACGGCCGTGTCTCGCACACGGCCA-ACCATACAGCAGGTC
1 ACACGGCCGTGTCTCGCACACGGCCACACC-TACAGCA-GTC
30189437 ACAC-GCCGTGT
1 ACACGGCCGTGT
30189448 GGCATCGACA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 2 0.04
40 37 0.80
41 7 0.15
ACGTcount: A:0.22, C:0.38, G:0.23, T:0.17
Consensus pattern (40 bp):
ACACGGCCGTGTCTCGCACACGGCCACACCTACAGCAGTC
Found at i:30191988 original size:51 final size:51
Alignment explanation
Indices: 30191904--30192012 Score: 166
Period size: 51 Copynumber: 2.1 Consensus size: 51
30191894 AATAGAAATG
* *
30191904 ATGAAAATGGAGAAATGGAAAACATTTAGAATGATTATGGTTTTCTCCAAA
1 ATGAAAATGGAGAAATGGAAAACATTTAAAATGAATATGGTTTTCTCCAAA
* *
30191955 ATGAAAATGGAGAAAT-GAAATCATTTGAAAATGAATGTGGTTTTCTCCAAA
1 ATGAAAATGGAGAAATGGAAAACATTT-AAAATGAATATGGTTTTCTCCAAA
30192006 ATGAAAA
1 ATGAAAA
30192013 ATAAAAATGA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 9 0.17
51 44 0.83
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.28
Consensus pattern (51 bp):
ATGAAAATGGAGAAATGGAAAACATTTAAAATGAATATGGTTTTCTCCAAA
Found at i:30195873 original size:25 final size:25
Alignment explanation
Indices: 30195813--30195875 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 25
30195803 ATCGGATTCG
*
30195813 TTAT-TGTAAAGGAAATGTCATGGT
1 TTATATGTAAAGGAAATGTCACGGT
*
30195837 TATATATGTAAAGGAAATGTTACGGT
1 T-TATATGTAAAGGAAATGTCACGGT
30195863 TTATATGTAAAGG
1 TTATATGTAAAGG
30195876 TACACTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
24 1 0.03
25 15 0.43
26 19 0.54
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (25 bp):
TTATATGTAAAGGAAATGTCACGGT
Found at i:30200598 original size:30 final size:30
Alignment explanation
Indices: 30200562--30200623 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
30200552 AAGTAGCAAG
30200562 CTCATTCTATTTTTAAAACGCGAAAACTAA
1 CTCATTCTATTTTTAAAACGCGAAAACTAA
30200592 CTCATTCTATTTTTAAAACGCGAAAACTAA
1 CTCATTCTATTTTTAAAACGCGAAAACTAA
30200622 CT
1 CT
30200624 TAAAGGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (30 bp):
CTCATTCTATTTTTAAAACGCGAAAACTAA
Found at i:30201517 original size:20 final size:20
Alignment explanation
Indices: 30201492--30201529 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30201482 AAATGAAAAT
*
30201492 AAATAAAATTATCATAAAGC
1 AAATAAAATCATCATAAAGC
*
30201512 AAATAATATCATCATAAA
1 AAATAAAATCATCATAAA
30201530 TATAATATTA
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:0.61, C:0.11, G:0.03, T:0.26
Consensus pattern (20 bp):
AAATAAAATCATCATAAAGC
Found at i:30204716 original size:13 final size:13
Alignment explanation
Indices: 30204698--30204723 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30204688 AAAGTGCGAG
30204698 CCTGTTGAAGACA
1 CCTGTTGAAGACA
30204711 CCTGTTGAAGACA
1 CCTGTTGAAGACA
30204724 ATATGCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
CCTGTTGAAGACA
Found at i:30205786 original size:13 final size:13
Alignment explanation
Indices: 30205768--30205793 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30205758 AAAGTACGAG
30205768 CCTGTTGAAGACA
1 CCTGTTGAAGACA
30205781 CCTGTTGAAGACA
1 CCTGTTGAAGACA
30205794 ATATGCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
CCTGTTGAAGACA
Found at i:30210879 original size:5 final size:6
Alignment explanation
Indices: 30210865--30210889 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30210855 GGCTCTATTT
30210865 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
30210890 TTCAAGTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:30211833 original size:5 final size:5
Alignment explanation
Indices: 30211806--30211867 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
30211796 ATTATAAATA
*
30211806 AAAAG -AAAG AAACG AAACA- AAAAG AAAA- AGAAAG -AAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG A-AAAG AAAAG AAAAG AAAAG
*
30211854 AAAAAG GAAAG AAA
1 -AAAAG AAAAG AAA
30211868 GGAAGGAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
4 10 0.22
5 31 0.67
6 5 0.11
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:30211839 original size:25 final size:24
Alignment explanation
Indices: 30211805--30211868 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 24
30211795 TATTATAAAT
30211805 AAAAAGAAAGAAACGAAACA-AAAAG
1 AAAAAGAAAGAAA-GAAA-AGAAAAG
30211830 AAAAAGAAAGAAAGAAAAGAAAAG
1 AAAAAGAAAGAAAGAAAAGAAAAG
30211854 AAAAAGGAAAGAAAG
1 AAAAA-GAAAGAAAG
30211869 GAAGGAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
23 1 0.03
24 14 0.38
25 22 0.59
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (24 bp):
AAAAAGAAAGAAAGAAAAGAAAAG
Found at i:30211844 original size:29 final size:29
Alignment explanation
Indices: 30211807--30211868 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
30211797 TTATAAATAA
*
30211807 AAAGAAAGAAACG-AAACAAAAAGAAAAAG
1 AAAGAAAGAAAAGAAAACAAAAAG-AAAAG
* *
30211836 AAAGAAAGAAAAGAAAAGAAAAAGGAAAG
1 AAAGAAAGAAAAGAAAACAAAAAGAAAAG
30211865 AAAG
1 AAAG
30211869 GAAGGAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (29 bp):
AAAGAAAGAAAAGAAAACAAAAAGAAAAG
Found at i:30214880 original size:27 final size:25
Alignment explanation
Indices: 30214850--30214909 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 25
30214840 TGATATAAAC
30214850 TTATAAAAACTATGAAAAAATAAAATA
1 TTATAAAAACTAT-AAAAAATAAAA-A
* * *
30214877 TTATAAATATTATAAAATATAAAAA
1 TTATAAAAACTATAAAAAATAAAAA
30214902 -TATAAAAA
1 TTATAAAAA
30214910 ATTCTAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.24
25 1 0.03
26 10 0.34
27 11 0.38
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (25 bp):
TTATAAAAACTATAAAAAATAAAAA
Found at i:30215007 original size:11 final size:10
Alignment explanation
Indices: 30214835--30215056 Score: 73
Period size: 10 Copynumber: 23.3 Consensus size: 10
30214825 AAAAAATACT
*
30214835 AAAATTGATAT
1 AAAATT-ATAA
*
30214846 AAACTTAT-A
1 AAAATTATAA
* *
30214855 AAAACTATGA
1 AAAATTATAA
30214865 AAAA--ATAA
1 AAAATTATAA
*
30214873 AATATTAT-A
1 AAAATTATAA
*
30214882 AATATTAT--
1 AAAATTATAA
30214890 AAAA-TAT-A
1 AAAATTATAA
30214898 AAAA-TATAA
1 AAAATTATAA
*
30214907 AAAATTCTAA
1 AAAATTATAA
*
30214917 TAAATTATAA
1 AAAATTATAA
30214927 AATCAA-TA-AA
1 AA--AATTATAA
*
30214937 ACATATT-TAA
1 A-AAATTATAA
* *
30214947 AACACT-TAA
1 AAAATTATAA
**
30214956 AATGTTATAA
1 AAAATTATAA
*
30214966 AAAAGTATAA
1 AAAATTATAA
*
30214976 AAAATCATAA
1 AAAATTATAA
30214986 AAAATTATAA
1 AAAATTATAA
* *
30214996 AAAATTGT-T
1 AAAATTATAA
* *
30215005 AAAAGTAT-T
1 AAAATTATAA
*
30215014 AAAATTGATAT
1 AAAATT-ATAA
*
30215025 AAATTTAT-A
1 AAAATTATAA
30215034 AAAA-TATTAA
1 AAAATTA-TAA
*
30215044 AAAATCATAA
1 AAAATTATAA
30215054 AAA
1 AAA
30215057 CTTGAGCTAG
Statistics
Matches: 162, Mismatches: 32, Indels: 35
0.71 0.14 0.15
Matches are distributed among these distances:
7 3 0.02
8 18 0.11
9 46 0.28
10 78 0.48
11 15 0.09
12 2 0.01
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (10 bp):
AAAATTATAA
Found at i:30215018 original size:28 final size:28
Alignment explanation
Indices: 30214986--30215045 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
30214976 AAAATCATAA
*
30214986 AAAATT-ATAAAAAATTGT-TAAAAGTATT
1 AAAATTGAT-AAAAATT-TATAAAAATATT
*
30215014 AAAATTGATATAAATTTATAAAAATATT
1 AAAATTGATAAAAATTTATAAAAATATT
30215042 AAAA
1 AAAA
30215046 AATCATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 25 0.89
29 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (28 bp):
AAAATTGATAAAAATTTATAAAAATATT
Found at i:30215614 original size:18 final size:18
Alignment explanation
Indices: 30215575--30215616 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
30215565 ATATATATAT
* *
30215575 ATTTTTATAATTTATTAG
1 ATTTTTATAAGTTATTAA
30215593 ATTTTTATAAGTT-TTACA
1 ATTTTTATAAGTTATTA-A
30215611 ATTTTT
1 ATTTTT
30215617 TATCACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (18 bp):
ATTTTTATAAGTTATTAA
Found at i:30216534 original size:18 final size:18
Alignment explanation
Indices: 30216499--30216532 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30216489 GTTCACTCTG
30216499 TTTTTCAGTTTTACTTTA
1 TTTTTCAGTTTTACTTTA
*
30216517 TTTTT-AGTTTTGCTTT
1 TTTTTCAGTTTTACTTT
30216533 TAAAAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.71
Consensus pattern (18 bp):
TTTTTCAGTTTTACTTTA
Found at i:30219387 original size:102 final size:101
Alignment explanation
Indices: 30219211--30219554 Score: 458
Period size: 102 Copynumber: 3.4 Consensus size: 101
30219201 TATCGATGAA
* * * *
30219211 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGTATTGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
30219276 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGA-AAGCTTTGGT
*
30219313 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
30219378 TAAGTGAAGGCTACTATGTGTACTGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* *** * *
30219415 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* * * * *
30219479 TATGTGAAGGCTACTACGTGAACCGTAAAAC-TTGAT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* * *
30219515 CATGTGTGTAGTACTATGTGAAGGTTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
30219555 ATGATAAAAG
Statistics
Matches: 217, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
100 39 0.18
101 45 0.21
102 132 0.61
103 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAGCTTTGGT
Found at i:30219481 original size:50 final size:50
Alignment explanation
Indices: 30219211--30219548 Score: 356
Period size: 51 Copynumber: 6.7 Consensus size: 50
30219201 TATCGATGAA
* * * ** ***
30219211 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGTATTGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* * * * * *
30219262 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGGT
* * ***
30219313 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* * * * *
30219364 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACTG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGGT
*
30219415 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
*
30219465 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
* *
30219515 CATGTGTGTAGTACTATGTGAAGGTTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
30219549 TATCGAATGA
Statistics
Matches: 243, Mismatches: 37, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
49 4 0.02
50 88 0.36
51 144 0.59
52 6 0.02
53 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
Found at i:30220686 original size:24 final size:24
Alignment explanation
Indices: 30220659--30220710 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
30220649 TTAGTAAGTC
*
30220659 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
30220683 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
30220707 AAAT
1 AAAT
30220711 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:30221703 original size:56 final size:56
Alignment explanation
Indices: 30221617--30221727 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 56
30221607 CTTTTTACAA
30221617 TAGCGACACCTTTTGTCTCGTTTCTTTGATGCTACCAAAAAGGAAGCTTGTCTATC
1 TAGCGACACCTTTTGTCTCGTTTCTTTGATGCTACCAAAAAGGAAGCTTGTCTATC
* *
30221673 TAGCGACACCTTTTGTCTCGTTTCTTTGATGCTACCAAAACGGAAGCTTTTCTAT
1 TAGCGACACCTTTTGTCTCGTTTCTTTGATGCTACCAAAAAGGAAGCTTGTCTAT
30221728 TTGCTTTGCT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (56 bp):
TAGCGACACCTTTTGTCTCGTTTCTTTGATGCTACCAAAAAGGAAGCTTGTCTATC
Found at i:30222695 original size:24 final size:24
Alignment explanation
Indices: 30222668--30222719 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
30222658 TTAGTAAGTC
*
30222668 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
30222692 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
30222716 AAAT
1 AAAT
30222720 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:30226610 original size:16 final size:16
Alignment explanation
Indices: 30226589--30226624 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
30226579 TTTTACATAA
*
30226589 ATATAAATATTTGTTT
1 ATATAAATATTTGCTT
30226605 ATATAAATATTTGCTT
1 ATATAAATATTTGCTT
30226621 ATAT
1 ATAT
30226625 TAATTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
ATATAAATATTTGCTT
Found at i:30226904 original size:17 final size:17
Alignment explanation
Indices: 30226879--30226916 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
30226869 ATCATTCACT
* *
30226879 CTTTCTTTTTCAATTTA
1 CTTTATTTTTAAATTTA
30226896 CTTTATTTTTAAATTTA
1 CTTTATTTTTAAATTTA
30226913 CTTT
1 CTTT
30226917 TAAAAATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (17 bp):
CTTTATTTTTAAATTTA
Found at i:30230063 original size:43 final size:44
Alignment explanation
Indices: 30229988--30230165 Score: 236
Period size: 45 Copynumber: 4.0 Consensus size: 44
30229978 GGATTAGACT
* * *
30229988 GGATATCCATATAAATAAAGGTTGTTGCTAAGTGCTGATTCCACC
1 GGATATCCATGTAAGT-AAGGTGGTTGCTAAGTGCTGATTCCACC
30230033 GGATATCCATGTAAGT-AGGTGGTTGCTAAGTGCTGATTCCACC
1 GGATATCCATGTAAGTAAGGTGGTTGCTAAGTGCTGATTCCACC
* * * *
30230076 AGATATCC-TCG-AATCTAAAGATGGTTGCTAAGTGCTAATTCCACC
1 GGATATCCAT-GTAA-GT-AAGGTGGTTGCTAAGTGCTGATTCCACC
30230121 GGATATCCATGTAAGTAAGGTGGTTGCTAAGTGCTGATTCCACC
1 GGATATCCATGTAAGTAAGGTGGTTGCTAAGTGCTGATTCCACC
30230165 G
1 G
30230166 TGTAATTATT
Statistics
Matches: 116, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
42 3 0.03
43 35 0.30
44 27 0.23
45 48 0.41
46 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (44 bp):
GGATATCCATGTAAGTAAGGTGGTTGCTAAGTGCTGATTCCACC
Found at i:30232470 original size:32 final size:32
Alignment explanation
Indices: 30232433--30232497 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
30232423 CCGATTTAAG
*
30232433 TGGATCTCTCCCCTTTTATTAAAATTAAAATA
1 TGGATCCCTCCCCTTTTATTAAAATTAAAATA
30232465 TGGATCCCTCCCCTTTTATTAAAATTAAAATA
1 TGGATCCCTCCCCTTTTATTAAAATTAAAATA
30232497 T
1 T
30232498 ACTTTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (32 bp):
TGGATCCCTCCCCTTTTATTAAAATTAAAATA
Found at i:30232934 original size:30 final size:31
Alignment explanation
Indices: 30232900--30232959 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
30232890 AAACATTTTA
*
30232900 TTTTCCCCTAAAATTTTTACTTCC-TCCCAC
1 TTTTCCCCTAAAACTTTTACTTCCTTCCCAC
*
30232930 TTTTCCCCTAAAACTTTTATTTCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTTCCTTCCCA
30232960 TCCCACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTTCCTTCCCAC
Found at i:30234398 original size:21 final size:22
Alignment explanation
Indices: 30234368--30234408 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
30234358 ATATCTAAAT
30234368 TACCACACACACATA-TATATA
1 TACCACACACACATACTATATA
*
30234389 TACCATACACACATACTATA
1 TACCACACACACATACTATA
30234409 AAACTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (22 bp):
TACCACACACACATACTATATA
Found at i:30258222 original size:23 final size:25
Alignment explanation
Indices: 30258146--30258224 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
30258136 AAACTCTTTC
* * *
30258146 GAGCCACGTAACGGGAAACTCATGT
1 GAGCCATGTAACGGGAAGCTCATAT
* *
30258171 GATCCATGTAACGGGAAGCTCCAGA-
1 GAGCCATGTAACGGGAAGCT-CATAT
30258196 GAGCCAT-T-ACGGGAAGCTCATAT
1 GAGCCATGTAACGGGAAGCTCATAT
30258219 GAGCCA
1 GAGCCA
30258225 ATGTCAGGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
22 3 0.07
23 16 0.36
24 1 0.02
25 23 0.51
26 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (25 bp):
GAGCCATGTAACGGGAAGCTCATAT
Found at i:30260059 original size:22 final size:22
Alignment explanation
Indices: 30260034--30260075 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30260024 AAAAGGAAAG
30260034 AAATATCATAAAAC-ATAAAACA
1 AAAT-TCATAAAACAATAAAACA
*
30260056 AAATTGATAAAACAATAAAA
1 AAATTCATAAAACAATAAAA
30260076 TGTTATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.19
Consensus pattern (22 bp):
AAATTCATAAAACAATAAAACA
Found at i:30261191 original size:21 final size:23
Alignment explanation
Indices: 30261149--30261191 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
30261139 TAATTAATCA
*
30261149 TAAACAGAAGCAAATCTCTTTTC
1 TAAACAGAAGCAAATATCTTTTC
*
30261172 TAAA-AGAAG-AAATATGTTTT
1 TAAACAGAAGCAAATATCTTTT
30261192 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (23 bp):
TAAACAGAAGCAAATATCTTTTC
Found at i:30261236 original size:21 final size:21
Alignment explanation
Indices: 30261212--30261267 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
30261202 CTGAACAATT
*
30261212 AAGAAAAAGA-GAAATACAAAA
1 AAGAAAAAGATCAAAT-CAAAA
*
30261233 AAG-AATAGATCAAATCAAAA
1 AAGAAAAAGATCAAATCAAAA
*
30261253 AAGAAATAGAATCAA
1 AAGAAAAAG-ATCAA
30261268 CAATTTGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (21 bp):
AAGAAAAAGATCAAATCAAAA
Found at i:30261253 original size:20 final size:23
Alignment explanation
Indices: 30261223--30261267 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
30261213 AGAAAAAGAG
30261223 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
30261244 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
30261266 AA
1 AA
30261268 CAATTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:30264111 original size:34 final size:34
Alignment explanation
Indices: 30264057--30264270 Score: 286
Period size: 34 Copynumber: 6.3 Consensus size: 34
30264047 GAAGAAATGA
*
30264057 TGCAAGAAAAT-ATGTGTGAACAGGAAAGATTCCC
1 TGCAAG-AAATGATGCGTGAACAGGAAAGATTCCC
* * *
30264091 TGTAAGGAATGATGTGTGAACAGGAAAGATTCCC
1 TGCAAGAAATGATGCGTGAACAGGAAAGATTCCC
* *
30264125 TGCAAGGAATGATGCATGAACAGGAAAGATTCCC
1 TGCAAGAAATGATGCGTGAACAGGAAAGATTCCC
* *
30264159 TGCAAGAAATGATGCATGAACAGGAAAGATTCTC
1 TGCAAGAAATGATGCGTGAACAGGAAAGATTCCC
* * * *
30264193 TGCAAGAAAAGACGAGGTGAACATGAAAGATTCCC
1 TGCAAGAAATGATG-CGTGAACAGGAAAGATTCCC
*
30264228 TGCAAGAAATGATGCGTGAACAGGAAATATTCCC
1 TGCAAGAAATGATGCGTGAACAGGAAAGATTCCC
30264262 TGCAAGAAA
1 TGCAAGAAA
30264271 AGACAAGAAA
Statistics
Matches: 160, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
33 3 0.02
34 129 0.81
35 28 0.17
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.19
Consensus pattern (34 bp):
TGCAAGAAATGATGCGTGAACAGGAAAGATTCCC
Found at i:30264132 original size:17 final size:17
Alignment explanation
Indices: 30264112--30264204 Score: 57
Period size: 17 Copynumber: 5.5 Consensus size: 17
30264102 ATGTGTGAAC
30264112 AGGAAAGATTCCCTGCA
1 AGGAAAGATTCCCTGCA
* * * *
30264129 AGGAATGA-TGCATGAA
1 AGGAAAGATTCCCTGCA
30264145 CAGGAAAGATTCCCTGCA
1 -AGGAAAGATTCCCTGCA
* * *
30264163 A-GAAATGA-TGCATGAA
1 AGGAAA-GATTCCCTGCA
*
30264179 CAGGAAAGATTCTCTGCA
1 -AGGAAAGATTCCCTGCA
*
30264197 AGAAAAGA
1 AGGAAAGA
30264205 CGAGGTGAAC
Statistics
Matches: 54, Mismatches: 16, Indels: 12
0.66 0.20 0.15
Matches are distributed among these distances:
16 14 0.26
17 27 0.50
18 13 0.24
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.17
Consensus pattern (17 bp):
AGGAAAGATTCCCTGCA
Found at i:30264239 original size:103 final size:102
Alignment explanation
Indices: 30264073--30264270 Score: 297
Period size: 103 Copynumber: 1.9 Consensus size: 102
30264063 AAAATATGTG
* * * * * *
30264073 TGAACAGGAAAGATTCCCTGTAAGGAATGATGTGTGAACAGGAAAGATTCCCTGCAAGGAATGAT
1 TGAACAGGAAAGATTCCCTGCAAGAAAAGACGGGTGAACAGGAAAGATTCCCTGCAAGAAATGAT
30264138 GCATGAACAGGAAAGATTCCCTGCAAGAAATGATGCA
66 GCATGAACAGGAAAGATTCCCTGCAAGAAATGATGCA
* *
30264175 TGAACAGGAAAGATTCTCTGCAAGAAAAGACGAGGTGAACATGAAAGATTCCCTGCAAGAAATGA
1 TGAACAGGAAAGATTCCCTGCAAGAAAAGACG-GGTGAACAGGAAAGATTCCCTGCAAGAAATGA
* *
30264240 TGCGTGAACAGGAAATATTCCCTGCAAGAAA
65 TGCATGAACAGGAAAGATTCCCTGCAAGAAA
30264271 AGACAAGAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
102 27 0.32
103 58 0.68
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.19
Consensus pattern (102 bp):
TGAACAGGAAAGATTCCCTGCAAGAAAAGACGGGTGAACAGGAAAGATTCCCTGCAAGAAATGAT
GCATGAACAGGAAAGATTCCCTGCAAGAAATGATGCA
Found at i:30264240 original size:69 final size:69
Alignment explanation
Indices: 30264072--30264274 Score: 293
Period size: 69 Copynumber: 3.0 Consensus size: 69
30264062 GAAAATATGT
* * * * *
30264072 GTGAACAGGAAAGATTCCCTGTAAGGAATGATGTGTGAACAGGAAAGATTCCCTGCAAGGAATGA
1 GTGAACAGGAAAGATTCCCTGCAAGAAATGATGCGTGAACAGGAAAGATTCCCTGCAAGAAAAGA
*
30264137 TGCA
66 CGCA
* *
30264141 -TGAACAGGAAAGATTCCCTGCAAGAAATGATGCATGAACAGGAAAGATTCTCTGCAAGAAAAGA
1 GTGAACAGGAAAGATTCCCTGCAAGAAATGATGCGTGAACAGGAAAGATTCCCTGCAAGAAAAGA
30264205 CG-A
66 CGCA
* *
30264208 GGTGAACATGAAAGATTCCCTGCAAGAAATGATGCGTGAACAGGAAATATTCCCTGCAAGAAAAG
1 -GTGAACAGGAAAGATTCCCTGCAAGAAATGATGCGTGAACAGGAAAGATTCCCTGCAAGAAAAG
30264273 AC
65 AC
30264275 AAGAAAAAGA
Statistics
Matches: 120, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
67 1 0.01
68 58 0.48
69 61 0.51
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.18
Consensus pattern (69 bp):
GTGAACAGGAAAGATTCCCTGCAAGAAATGATGCGTGAACAGGAAAGATTCCCTGCAAGAAAAGA
CGCA
Found at i:30267223 original size:17 final size:18
Alignment explanation
Indices: 30267185--30267224 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
30267175 TAAGTTCAAA
*
30267185 TAAAACTCTTAAGTATAC
1 TAAAACTCTTAAGTAAAC
*
30267203 TAAAACTC-TAATTAAAC
1 TAAAACTCTTAAGTAAAC
30267220 TAAAA
1 TAAAA
30267225 TTTCTTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.30
Consensus pattern (18 bp):
TAAAACTCTTAAGTAAAC
Found at i:30270370 original size:26 final size:26
Alignment explanation
Indices: 30270334--30270385 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
30270324 ACTCAGAGTG
30270334 ATAGTTTCTTTTATTGATAATCAAAT
1 ATAGTTTCTTTTATTGATAATCAAAT
30270360 ATAGTTTCTTTTATTGATAATCAAAT
1 ATAGTTTCTTTTATTGATAATCAAAT
30270386 TTATCCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (26 bp):
ATAGTTTCTTTTATTGATAATCAAAT
Found at i:30271412 original size:106 final size:106
Alignment explanation
Indices: 30271226--30271639 Score: 594
Period size: 106 Copynumber: 3.9 Consensus size: 106
30271216 GAGATTTATG
* * * * * *
30271226 AGGATATTCGGCTATTTGGTCGAACGAAAAATCGAAACCTAACACGTTAGGGTACGTTTTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGA
* *
30271291 ATTTCCAAACACAAAATATTGCTTTACTTTGAAATTTTAAA
66 ATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
* * * *
30271332 AGGATATTTGGCTATTTGGTCTAACGAGAACTCGAAACCCAGCATGTTAGGACACGTTTCCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGA
* *
30271397 ATTTCTAAACGCAAAATATCGCCTTACTTTGAAATTTTAAA
66 ATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
* * * *
30271438 AGGATATTTAGCTATTTGGTCGAACAAGAACTCGAAACCCAGCACATTAGGGCACGTTTCCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGA
30271503 ATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
66 ATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
* *
30271544 AGGATATTTGGCTATAATTTGGTCGAACGAGAGAAATCGAAACCCAGCACGTTAGGGCACATTTT
1 AGGATATTTGGC--T-ATTTGGTCGAAC--GAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
*
30271609 CTCGAATTTCTAAACGCAAAATATTGCCTTA
61 CTCGAATTTCCAAACGCAAAATATTGCCTTA
30271640 TTTTAAAACT
Statistics
Matches: 274, Mismatches: 29, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
106 201 0.73
108 1 0.00
109 12 0.04
111 60 0.22
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (106 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGA
ATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
Found at i:30280065 original size:31 final size:31
Alignment explanation
Indices: 30280030--30280088 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
30280020 TAAGATCATC
30280030 GTTTCACAAACATTAACCATTTTAGAACATT
1 GTTTCACAAACATTAACCATTTTAGAACATT
30280061 GTTTCACAAACATTAACCATTTTAGAAC
1 GTTTCACAAACATTAACCATTTTAGAAC
30280089 TATCACCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (31 bp):
GTTTCACAAACATTAACCATTTTAGAACATT
Found at i:30286371 original size:42 final size:42
Alignment explanation
Indices: 30286312--30286417 Score: 151
Period size: 42 Copynumber: 2.5 Consensus size: 42
30286302 TCTTTAGCGG
*
30286312 CATGTTCTTTAGTGGCGTTTTTCCT-TAAGTGCCGCTAAAGAA
1 CATGTTCTTTAGTGGCGTTTTT-CTATAAATGCCGCTAAAGAA
* *
30286354 CATGTTCTTTAGCGGCGTTTTTTTATAAATGCCGCTAAAGAA
1 CATGTTCTTTAGTGGCGTTTTTCTATAAATGCCGCTAAAGAA
* *
30286396 CATATTCTTTAGTGGCGCTTTT
1 CATGTTCTTTAGTGGCGTTTTT
30286418 ATACAAAAAC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.02
42 56 0.98
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (42 bp):
CATGTTCTTTAGTGGCGTTTTTCTATAAATGCCGCTAAAGAA
Found at i:30286502 original size:14 final size:14
Alignment explanation
Indices: 30286483--30286516 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
30286473 GCCCTCTTGT
30286483 AGCAACAATTCAAA
1 AGCAACAATTCAAA
30286497 AGCAACAATTCAAA
1 AGCAACAATTCAAA
30286511 AGCAAC
1 AGCAAC
30286517 CAATAGCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.24, G:0.09, T:0.12
Consensus pattern (14 bp):
AGCAACAATTCAAA
Found at i:30286801 original size:21 final size:21
Alignment explanation
Indices: 30286738--30286803 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
30286728 CTCTGCTCCA
* *
30286738 CTTCTCTCGCTGCAGCCTCCG
1 CTTCCCTCGCTGCAGCCTCTG
*
30286759 CTTCCCTCGCTGCAGCCGCTG
1 CTTCCCTCGCTGCAGCCTCTG
* *
30286780 CTTCCCTCGCTTCCGCCTCTG
1 CTTCCCTCGCTGCAGCCTCTG
30286801 CTT
1 CTT
30286804 TAAGTTGTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.03, C:0.48, G:0.18, T:0.30
Consensus pattern (21 bp):
CTTCCCTCGCTGCAGCCTCTG
Found at i:30292326 original size:16 final size:17
Alignment explanation
Indices: 30292305--30292383 Score: 65
Period size: 16 Copynumber: 4.6 Consensus size: 17
30292295 TGATATATAT
30292305 TTATGTA-TTAAGTAAA
1 TTATGTAGTTAAGTAAA
* *
30292321 TTATGTAAGTTATGTACA
1 TTATGT-AGTTAAGTAAA
* *
30292339 TGTAT-AAGTTAAGTAAG
1 T-TATGTAGTTAAGTAAA
*
30292356 TTATGTA-TTAAGTAAG
1 TTATGTAGTTAAGTAAA
30292372 TTATGTAAGTTA
1 TTATGT-AGTTA
30292384 TGAAAGTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
16 24 0.48
17 12 0.24
18 11 0.22
19 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.43
Consensus pattern (17 bp):
TTATGTAGTTAAGTAAA
Found at i:30292333 original size:9 final size:9
Alignment explanation
Indices: 30292316--30292522 Score: 128
Period size: 9 Copynumber: 23.4 Consensus size: 9
30292306 TATGTATTAA
*
30292316 GTAAATTAT
1 GTAAGTTAT
30292325 GTAAGTTAT
1 GTAAGTTAT
30292334 GTACA-TGTA-
1 GTA-AGT-TAT
*
30292343 -TAAGTTAA
1 GTAAGTTAT
30292351 GTAAGTTAT
1 GTAAGTTAT
*
30292360 GT-A-TTAA
1 GTAAGTTAT
30292367 GTAAGTTAT
1 GTAAGTTAT
30292376 GTAAGTTAT
1 GTAAGTTAT
* *
30292385 GAAAGTAAT
1 GTAAGTTAT
* *
30292394 GTATGTAAT
1 GTAAGTTAT
30292403 GTAAG-T-T
1 GTAAGTTAT
30292410 GTAAGTTAT
1 GTAAGTTAT
*
30292419 -TATGTATTAT
1 GTAAG--TTAT
30292429 GTAAGTTAT
1 GTAAGTTAT
30292438 GTAAGTTAAAT
1 GTAAGTT--AT
30292449 GT-A-TTAT
1 GTAAGTTAT
*
30292456 GTAGGTTAT
1 GTAAGTTAT
*
30292465 GTAAGTTGT
1 GTAAGTTAT
* **
30292474 GAAAGAGAT
1 GTAAGTTAT
*
30292483 TTAAGTTAT
1 GTAAGTTAT
*
30292492 GTAGGTTAT
1 GTAAGTTAT
* *
30292501 TTAGGTTAT
1 GTAAGTTAT
*
30292510 GTAAGTTTT
1 GTAAGTTAT
30292519 GTAA
1 GTAA
30292523 TGTGCAAGTG
Statistics
Matches: 153, Mismatches: 29, Indels: 32
0.71 0.14 0.15
Matches are distributed among these distances:
7 18 0.12
8 9 0.06
9 111 0.73
10 8 0.05
11 7 0.05
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:30292335 original size:25 final size:25
Alignment explanation
Indices: 30292305--30292385 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 25
30292295 TGATATATAT
30292305 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* * *
30292330 TTATGTA-CATGTATAAGTTAAGTAAG
1 TTATGTATTAAGTA-AA-TTATGTAAG
*
30292356 TTATGTATTAAGTAAGTTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
30292381 TTATG
1 TTATG
30292386 AAAGTAATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
24 4 0.09
25 22 0.48
26 16 0.35
27 4 0.09
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.43
Consensus pattern (25 bp):
TTATGTATTAAGTAAATTATGTAAG
Found at i:30292398 original size:22 final size:24
Alignment explanation
Indices: 30292305--30292471 Score: 97
Period size: 25 Copynumber: 7.1 Consensus size: 24
30292295 TGATATATAT
*
30292305 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTA-TAAGTAAGTTATGTAAG
* * *
30292330 TTATGTACATGTATAAGTTAAGTAAG
1 TTATGTATAAG--TAAGTTATGTAAG
30292356 TTATGTATTAAGTAAGTTATGTAAG
1 TTATGTA-TAAGTAAGTTATGTAAG
30292381 TTATG-A-AAGTAA-TGTATGTAA-
1 TTATGTATAAGTAAGT-TATGTAAG
* *
30292402 TGTAAGT-T--GTAAGTTAT-TATG
1 T-TATGTATAAGTAAGTTATGTAAG
30292423 -TAT-TAT--GTAAGTTATGTAAG
1 TTATGTATAAGTAAGTTATGTAAG
* *
30292443 TTAAATGTATTATGTAGGTTATGTAAG
1 TT--ATGTA-TAAGTAAGTTATGTAAG
30292470 TT
1 TT
30292472 GTGAAAGAGA
Statistics
Matches: 112, Mismatches: 12, Indels: 34
0.71 0.08 0.22
Matches are distributed among these distances:
18 1 0.01
19 12 0.11
20 5 0.04
21 10 0.09
22 17 0.15
23 2 0.02
24 5 0.04
25 25 0.22
26 18 0.16
27 17 0.15
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.44
Consensus pattern (24 bp):
TTATGTATAAGTAAGTTATGTAAG
Found at i:30292458 original size:62 final size:61
Alignment explanation
Indices: 30292356--30292473 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 61
30292346 GTTAAGTAAG
*
30292356 TTATGTATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTAAGTTGTAAGTTA
1 TTATGTATTAAGTAAGTTATGTAAGTTA-GAAAGTAATGTAGGTAATGTAAGTTGTAAGTTA
* * *
30292418 TTATGTATTATGTAAGTTATGTAAGTTA-AATGTATTATGTAGGTTATGTAAGTTGT
1 TTATGTATTAAGTAAGTTATGTAAGTTAGAAAGTA--ATGTAGGTAATGTAAGTTGT
30292474 GAAAGAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 5 0.10
62 45 0.90
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (61 bp):
TTATGTATTAAGTAAGTTATGTAAGTTAGAAAGTAATGTAGGTAATGTAAGTTGTAAGTTA
Found at i:30295030 original size:84 final size:83
Alignment explanation
Indices: 30294929--30295096 Score: 273
Period size: 84 Copynumber: 2.0 Consensus size: 83
30294919 AAATCTTACA
* * *
30294929 AATTTCAATTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTGTTTGCGGCGTTTTTGT
1 AATTTCAATTCACGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTATTTGCGGCGTTTGT-T
30294994 AAAAAAACGCCACTAAATT
65 AAAAAAACGCCACTAAATT
* *
30295013 AATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTGTTA
1 AATTTCAATTCACGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTATTTGCGGCGTTTGTTA
*
30295078 CAAAAACGCCACTAAATT
66 AAAAAACGCCACTAAATT
30295096 A
1 A
30295097 TTTATATTTA
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
83 20 0.26
84 58 0.74
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (83 bp):
AATTTCAATTCACGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTATTTGCGGCGTTTGTTA
AAAAAACGCCACTAAATT
Found at i:30295429 original size:83 final size:83
Alignment explanation
Indices: 30295337--30295503 Score: 275
Period size: 83 Copynumber: 2.0 Consensus size: 83
30295327 AAATCTTACA
*
30295337 AATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTGTTTGCGGCGATTT-TG
1 AATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTATTTGCGGCG-TTTGT-
30295401 TA-AAAAACGCCACTAAATT
64 TACAAAAACGCCACTAAATT
*
30295420 AATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTGTTA
1 AATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTATTTGCGGCGTTTGTTA
*
30295485 CAAAAACGCCATTAAATT
66 CAAAAACGCCACTAAATT
30295503 A
1 A
30295504 TTTATATTTA
Statistics
Matches: 79, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
82 5 0.06
83 74 0.94
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.40
Consensus pattern (83 bp):
AATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTATTTGCGGCGTTTGTTA
CAAAAACGCCACTAAATT
Found at i:30295596 original size:407 final size:406
Alignment explanation
Indices: 30294800--30295827 Score: 1912
Period size: 407 Copynumber: 2.5 Consensus size: 406
30294790 AATTATTGAT
30294800 ATTATTCAAATAATGTATTACAATTTTAAATTTATGCTATATTTTTAAGTTAAATTGGGTTGATG
1 ATTATTCAAATAATGTATTACAATTTTAAATTTATGCTATATTTTTAAGTTAAATTGGGTTGATG
** * *
30294865 GAGATATGCCAATATAATTTCATTTCATTTAGCGGCGCTTAAAGAAAACGCCACAAATCTTACAA
66 GAGATATGCCGGTGTAATTTCATTTCATGTAGCGGCGCTTAAAGAAAACGCCACAAATCTTACAA
*
30294930 ATTTCAATTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTGTTTGCGGCGTTTTTGTA
131 ATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTGTTTGCGGCG-TTTTGT-
30294995 AAAAAACGCCACTAAATTAATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATAT
194 AAAAAACGCCACTAAATTAATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATAT
30295060 TATTTGCGGCGTTTGTTACAAAAACGCCACTAAATTATTTATATTTATTTATAAGTAATTGCGGA
259 TATTTGCGGCGTTTGTTACAAAAACGCCACTAAATTATTTATATTTATTTATAAGTAATTGCGGA
30295125 TATTATTCATATTTGCGGCGTTTTAGTATAAAACGCCACTAAAATTTCATGTACAGAAACAAACG
324 TATTATTCATATTTGCGGCGTTTTAGTATAAAACGCCACTAAAATTTCATGTACAGAAACAAACG
30295190 GTGCCGTTTTATTAAAAC
389 GTGCCGTTTTATTAAAAC
30295208 ATTATTCAAATAATGTATTACAATTTTAAATTTATGCTATATTTTTAAGTTAAATTGGGTTGATG
1 ATTATTCAAATAATGTATTACAATTTTAAATTTATGCTATATTTTTAAGTTAAATTGGGTTGATG
30295273 GAGATATGCCGGTGTAATTTCATTTCATGTAGCGGCGCTTAAAGAAAACGCCACAAATCTTACAA
66 GAGATATGCCGGTGTAATTTCATTTCATGTAGCGGCGCTTAAAGAAAACGCCACAAATCTTACAA
30295338 ATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTGTTTGCGGCGATTTTGTA
131 ATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTGTTTGCGGCG-TTTTGTA
*
30295403 AAAAACGCCACTAAATTAATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTTCAAATATT
195 AAAAACGCCACTAAATTAATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATT
*
30295468 ATTTGCGGCGTTTGTTACAAAAACGCCATTAAATTATTTATATTTATTTATAAGTAATTGCGGAT
260 ATTTGCGGCGTTTGTTACAAAAACGCCACTAAATTATTTATATTTATTTATAAGTAATTGCGGAT
30295533 ATTATTCATATTTGCGGCGTTTTAGTATAAAACGCCACTAAAATTTCATGTACAGAAACAAACGG
325 ATTATTCATATTTGCGGCGTTTTAGTATAAAACGCCACTAAAATTTCATGTACAGAAACAAACGG
30295598 TGCCGTTTTATTAAAAC
390 TGCCGTTTTATTAAAAC
30295615 ATTATTCAAATAATGTATTACAATTTTAAATTTATGCTATATTTTTAAGTTAAATTGGGTTGATG
1 ATTATTCAAATAATGTATTACAATTTTAAATTTATGCTATATTTTTAAGTTAAATTGGGTTGATG
*
30295680 GAGATATGCCGGTGTAATTTCATTTCATGTAGCGGGGCTTAAAGAAAACGCCACAAATCTTACAA
66 GAGATATGCCGGTGTAATTTCATTTCATGTAGCGGCGCTTAAAGAAAACGCCACAAATCTTACAA
* * * *
30295745 ATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTTCAAATACTATTTGCGGCGTTTTATAC
131 ATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTGTTTGCGGCGTTTTGTA-
30295810 AAAAACGCCACTAAATTA
195 AAAAACGCCACTAAATTA
30295828 TTTATATTTA
Statistics
Matches: 606, Mismatches: 13, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
406 6 0.01
407 412 0.68
408 188 0.31
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (406 bp):
ATTATTCAAATAATGTATTACAATTTTAAATTTATGCTATATTTTTAAGTTAAATTGGGTTGATG
GAGATATGCCGGTGTAATTTCATTTCATGTAGCGGCGCTTAAAGAAAACGCCACAAATCTTACAA
ATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTGTTTGCGGCGTTTTGTAA
AAAACGCCACTAAATTAATTTCATTTCACGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTA
TTTGCGGCGTTTGTTACAAAAACGCCACTAAATTATTTATATTTATTTATAAGTAATTGCGGATA
TTATTCATATTTGCGGCGTTTTAGTATAAAACGCCACTAAAATTTCATGTACAGAAACAAACGGT
GCCGTTTTATTAAAAC
Found at i:30296463 original size:15 final size:16
Alignment explanation
Indices: 30296438--30296469 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
30296428 TTAAATAATA
30296438 TAAACTATATTAAATT
1 TAAACTATATTAAATT
30296454 TAAA-TATATTAAATT
1 TAAACTATATTAAATT
30296469 T
1 T
30296470 CTTATTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAACTATATTAAATT
Found at i:30296576 original size:15 final size:15
Alignment explanation
Indices: 30296556--30296606 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
30296546 CGTTCAAACT
30296556 CTAAACCCCAAATCC
1 CTAAACCCCAAATCC
30296571 CTAAACCCCTAAA-CC
1 CTAAACCCC-AAATCC
* *
30296586 CTAAATCTCTAAATCC
1 CTAAA-CCCCAAATCC
30296602 CTAAA
1 CTAAA
30296607 TCCTAACTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 19 0.61
16 12 0.39
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (15 bp):
CTAAACCCCAAATCC
Found at i:30296582 original size:8 final size:8
Alignment explanation
Indices: 30296556--30296609 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
30296546 CGTTCAAACT
30296556 CTAAA-CC
1 CTAAATCC
*
30296563 CCAAATCC
1 CTAAATCC
*
30296571 CTAAACCC
1 CTAAATCC
30296579 CTAAA-CC
1 CTAAATCC
*
30296586 CTAAATCT
1 CTAAATCC
30296594 CTAAATCC
1 CTAAATCC
30296602 CTAAATCC
1 CTAAATCC
30296610 TAACTCTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
7 11 0.28
8 29 0.73
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (8 bp):
CTAAATCC
Found at i:30296582 original size:23 final size:23
Alignment explanation
Indices: 30296556--30296606 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
30296546 CGTTCAAACT
30296556 CTAAACCCCAAATCCCTAAACCC
1 CTAAACCCCAAATCCCTAAACCC
* * *
30296579 CTAAACCCTAAATCTCTAAATCC
1 CTAAACCCCAAATCCCTAAACCC
30296602 CTAAA
1 CTAAA
30296607 TCCTAACTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (23 bp):
CTAAACCCCAAATCCCTAAACCC
Found at i:30296612 original size:15 final size:15
Alignment explanation
Indices: 30296565--30296612 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
30296555 TCTAAACCCC
*
30296565 AAATCCCTAAACCCCT
1 AAATCCCTAAA-TCCT
30296581 AAA-CCCTAAATCTCT
1 AAATCCCTAAATC-CT
30296596 AAATCCCTAAATCCT
1 AAATCCCTAAATCCT
30296611 AA
1 AA
30296613 CTCTTAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 1 0.03
15 16 0.55
16 12 0.41
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATCCCTAAATCCT
Found at i:30296680 original size:14 final size:13
Alignment explanation
Indices: 30296656--30296689 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
30296646 CCTAAACCCT
30296656 AAACCCTAAATCTC
1 AAACCCTAAAT-TC
30296670 AAACCCTAAATTC
1 AAACCCTAAATTC
*
30296683 ATACCCT
1 AAACCCT
30296690 GACCTACTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (13 bp):
AAACCCTAAATTC
Found at i:30297168 original size:114 final size:109
Alignment explanation
Indices: 30296965--30297337 Score: 383
Period size: 114 Copynumber: 3.3 Consensus size: 109
30296955 AAATTGGGCT
* * * *
30296965 TAGGTTTTTAGCGGCGCTTTTACAAAAAACGCCGCTAAAAACCTGAGCATTAGTGGCGCTTT-AT
1 TAGGTTTTTTGCGGCGC-TTTCCCAGAAACGCCGCTAAAAACCTGAGCATTAGTGGCGCTTTCAT
** * * * *
30297029 ATAAAGGGCCACTAAATCCCTGAAAGCTGGCGAGACGACGTCGTTGCGC
65 A-AAAACGCCGCTAAATCCCAGAAAGCT--CGAAACGGCGTCGTTG-GC
* * *
30297078 TAGATTTTTTTGCGGCGCTTTCCCAGAAACGCCTCTAAAAGACATGAGCATTAGTGGCGCTTTCA
1 TAG-GTTTTTTGCGGCGCTTTCCCAGAAACGCCGCTAAAA-ACCTGAGCATTAGTGGCGCTTTCA
*
30297143 TAAAAACGCCGCTAAATCCCAGAAAGCTCAGAAAACGGCGACGTTGGCC
64 TAAAAACGCCGCTAAATCCCAGAAAGCTC-G-AAACGGCGTCGTTGG-C
* ** * * * *
30297192 TTAGGTTTTTAGCGGCGCTTTCTTAAAAACGCCGCTAAAAACCTGAGCATTAGCGGCGCTTACTT
1 -TAGGTTTTTTGCGGCGCTTTCCCAGAAACGCCGCTAAAAACCTGAGCATTAGTGGCGCTTTCAT
*
30297257 AAAAACGCCGCTAAATCACCA-AATGCTCTTGAAACGGCGTCGTTGTGC
65 AAAAACGCCGCTAAATC-CCAGAAAGCTC--GAAACGGCGTCGTTG-GC
30297305 TAGGTTTTTTGCGGCGCTTTCCC-GAAAACGCCG
1 TAGGTTTTTTGCGGCGCTTTCCCAG-AAACGCCG
30297338 GTAATGTTTA
Statistics
Matches: 218, Mismatches: 31, Indels: 23
0.80 0.11 0.08
Matches are distributed among these distances:
112 29 0.13
113 81 0.37
114 102 0.47
115 6 0.03
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (109 bp):
TAGGTTTTTTGCGGCGCTTTCCCAGAAACGCCGCTAAAAACCTGAGCATTAGTGGCGCTTTCATA
AAAACGCCGCTAAATCCCAGAAAGCTCGAAACGGCGTCGTTGGC
Found at i:30316636 original size:18 final size:18
Alignment explanation
Indices: 30316596--30316638 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
30316586 GTTCAAGGTG
30316596 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
30316614 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
30316632 TAATTAA
1 TAATTAA
30316639 AAATCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:30336547 original size:5 final size:5
Alignment explanation
Indices: 30336537--30336587 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
30336527 ACTTACTAAG
* * *
30336537 AAAAT AAAAT AAAAT AAAACCT AAATT AAAAC AAAAC AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA--T AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
30336588 CTTAATCTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
5 36 0.90
7 4 0.10
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:30336592 original size:27 final size:26
Alignment explanation
Indices: 30336537--30336586 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
30336527 ACTTACTAAG
* *
30336537 AAAATAAAATAAAATAAAACCTAAATT
1 AAAACAAAACAAAATAAAA-CTAAATT
30336564 AAAACAAAACAAAATAAAA-TAAA
1 AAAACAAAACAAAATAAAACTAAA
30336587 ACTTAATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
27 17 0.81
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (26 bp):
AAAACAAAACAAAATAAAACTAAATT
Found at i:30340000 original size:15 final size:15
Alignment explanation
Indices: 30339980--30340087 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
30339970 TTTATGGAAA
30339980 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
30339995 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
30340009 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
30340025 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
30340039 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
30340055 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
30340069 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
30340085 ATC
1 ATC
30340088 GATATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Done.