Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 102 of 318
Found at i:33202744 original size:42 final size:42
Alignment explanation
Indices: 33202697--33202780 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
33202687 ATTATGTTAG
33202697 TATATTAATCAAAGTAATGTATTTTAATATTCAAAGTACAAA
1 TATATTAATCAAAGTAATGTATTTTAATATTCAAAGTACAAA
33202739 TATATTAATCAAAGTAATGTATTTTAATATTCAAAGTACAAA
1 TATATTAATCAAAGTAATGTATTTTAATATTCAAAGTACAAA
33202781 ATAAGCGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (42 bp):
TATATTAATCAAAGTAATGTATTTTAATATTCAAAGTACAAA
Found at i:33207966 original size:26 final size:26
Alignment explanation
Indices: 33207937--33207988 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
33207927 TAGTGCTACG
*
33207937 TGGTGTGCAACCATTAGAGGTGCAAA
1 TGGTGTGCAACCATTAGAAGTGCAAA
* * *
33207963 TGGTTTGTAACCATTGGAAGTGCAAA
1 TGGTGTGCAACCATTAGAAGTGCAAA
33207989 AGGTTGCTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (26 bp):
TGGTGTGCAACCATTAGAAGTGCAAA
Found at i:33212416 original size:11 final size:12
Alignment explanation
Indices: 33212376--33212440 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 12
33212366 CTTGAACTAA
*
33212376 AATTA-AAATTT
1 AATTATAAATAT
33212387 AA-TAT-AATAT
1 AATTATAAATAT
*
33212397 AA-TAAAAATAT
1 AATTATAAATAT
*
33212408 AATT-TAAATTT
1 AATTATAAATAT
33212419 AATTATAAA-AT
1 AATTATAAATAT
*
33212430 ATTTATAAATA
1 AATTATAAATA
33212441 ATATTTTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
10 10 0.23
11 27 0.63
12 6 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATTATAAATAT
Found at i:33216661 original size:14 final size:14
Alignment explanation
Indices: 33216642--33216672 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
33216632 TAGAGCATAT
*
33216642 TTTTAATTTTTTAA
1 TTTTAATTTTATAA
33216656 TTTTAATTTTATAA
1 TTTTAATTTTATAA
33216670 TTT
1 TTT
33216673 AACACATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTAATTTTATAA
Found at i:33224857 original size:17 final size:17
Alignment explanation
Indices: 33224831--33224866 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
33224821 AATTTTGATG
* *
33224831 GTGTTTGATATTGGTAT
1 GTGTTCGATATAGGTAT
33224848 GTGTTCGATATAGGTAT
1 GTGTTCGATATAGGTAT
33224865 GT
1 GT
33224867 TCAAATTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.31, T:0.47
Consensus pattern (17 bp):
GTGTTCGATATAGGTAT
Found at i:33229003 original size:12 final size:12
Alignment explanation
Indices: 33228988--33229152 Score: 79
Period size: 12 Copynumber: 13.8 Consensus size: 12
33228978 TGTTATTTCA
*
33228988 ATTTCAATTTTG
1 ATTTCGATTTTG
*
33229000 ATTTCGATTCTG
1 ATTTCGATTTTG
*
33229012 A-TTCTGATTCTG
1 ATTTC-GATTTTG
*
33229024 ATTTTGATTTCT-
1 ATTTCGATTT-TG
*
33229036 ATTTCGCTTTTG
1 ATTTCGATTTTG
*
33229048 ATTTCAATTTTG
1 ATTTCGATTTTG
** **
33229060 A-AAC-ACTCACTG
1 ATTTCGA-T-TTTG
*
33229072 ATTTTGATTTTG
1 ATTTCGATTTTG
*
33229084 ATTTTGATTTTG
1 ATTTCGATTTTG
* *
33229096 ATTTC-AATTCG
1 ATTTCGATTTTG
*
33229107 ATCTCGATTTTG
1 ATTTCGATTTTG
*
33229119 ATTTAGATTTTG
1 ATTTCGATTTTG
* * *
33229131 GTTTTGATTTCG
1 ATTTCGATTTTG
*
33229143 ATTTGGATTT
1 ATTTCGATTT
33229153 CAATTTAGGA
Statistics
Matches: 114, Mismatches: 30, Indels: 18
0.70 0.19 0.11
Matches are distributed among these distances:
10 1 0.01
11 14 0.12
12 94 0.82
13 4 0.04
14 1 0.01
ACGTcount: A:0.20, C:0.11, G:0.15, T:0.55
Consensus pattern (12 bp):
ATTTCGATTTTG
Found at i:33229019 original size:18 final size:19
Alignment explanation
Indices: 33228994--33229052 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 19
33228984 TTCAATTTCA
33228994 ATTT-TGATTTCGATTCTG
1 ATTTCTGATTTCGATTCTG
*
33229012 A-TTCTGA-TTCTGATTTTG
1 ATTTCTGATTTC-GATTCTG
* *
33229030 ATTTCT-ATTTCGCTTTTG
1 ATTTCTGATTTCGATTCTG
33229048 ATTTC
1 ATTTC
33229053 AATTTTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 5 0.14
18 23 0.66
19 7 0.20
ACGTcount: A:0.15, C:0.14, G:0.14, T:0.58
Consensus pattern (19 bp):
ATTTCTGATTTCGATTCTG
Found at i:33229081 original size:6 final size:6
Alignment explanation
Indices: 33229070--33229152 Score: 78
Period size: 6 Copynumber: 14.0 Consensus size: 6
33229060 AAACACTCAC
* * * * *
33229070 TGATTT TGATTT TGATTT TGATTT TGA-TT TCAATT CGATCT CGATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
* * * *
33229117 TGATTT AGATTT TGGTTT TGATTT CGATTT GGATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
33229153 CAATTTAGGA
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
5 4 0.06
6 59 0.94
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.58
Consensus pattern (6 bp):
TGATTT
Found at i:33229170 original size:16 final size:16
Alignment explanation
Indices: 33229149--33229190 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
33229139 TTCGATTTGG
33229149 ATTTCAATTTAGGATT
1 ATTTCAATTTAGGATT
*
33229165 ATTTCAATTTAGGGTT
1 ATTTCAATTTAGGATT
*
33229181 ATTTCGATTT
1 ATTTCAATTT
33229191 GTATGACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.52
Consensus pattern (16 bp):
ATTTCAATTTAGGATT
Found at i:33229273 original size:25 final size:25
Alignment explanation
Indices: 33229235--33229285 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
33229225 ATGATGTTTT
*
33229235 TTGTTTGTAACTGCTATTGTATGGA
1 TTGTTTGTAACTGCCATTGTATGGA
*
33229260 TTGTTTGTATCTGCCATTGTATGGA
1 TTGTTTGTAACTGCCATTGTATGGA
33229285 T
1 T
33229286 GCCATTGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.18, C:0.10, G:0.24, T:0.49
Consensus pattern (25 bp):
TTGTTTGTAACTGCCATTGTATGGA
Found at i:33230672 original size:15 final size:15
Alignment explanation
Indices: 33230652--33230681 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33230642 TGAAGAAGAC
*
33230652 ATGTCTGGTAGTGAT
1 ATGTCTAGTAGTGAT
33230667 ATGTCTAGTAGTGAT
1 ATGTCTAGTAGTGAT
33230682 GCATCTGAAA
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:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (15 bp):
ATGTCTAGTAGTGAT
Found at i:33232334 original size:377 final size:379
Alignment explanation
Indices: 33231623--33232383 Score: 1346
Period size: 377 Copynumber: 2.0 Consensus size: 379
33231613 TGGAAATTGT
* *
33231623 GAGCTCGTACCAAATATCTTTCATGTTTGACAAACAAAAGGTAAAACTCCATTTATTTATTTATT
1 GAGCTCATACCAAATATCTTTCATGTCTGACAAACAAAAGGTAAAACTCCATTTATTTATTTATT
*
33231688 TTATGTTGATTCTATTTAGGGATTGTCAAATAATTAAACTATTTTTTTCCTAATTGCAGGGACTT
66 TTATGTTGATTCTATTTAGGGATTGTCAAAGAATTAAACTATTTTTTTCCTAATTGCAGGGACTT
33231753 TTAGAAGCAATATGTATGTTGTTTCCTAATACAGAAACAAGACACTGTGTTAGACACCTACATGC
131 TTAGAAGCAATATGTATGTTGTTTCCTAATACAGAAACAAGA-ACTGTGTTAGACACCTACATGC
*
33231818 CAATTTTAAGAAGGCTAGTTTTCGAACAAAGGAATTAAAAGATTCGCTTTGGAAAGCTGCCAGAA
195 CAATTTCAAGAAGGCTAGTTTTCGAACAAAGGAATTAAAAGATTCGCTTTGGAAAGCTGCCAGAA
*
33231883 CAAGTACTACAAGGGATTTGAGGATGCCATGGATAAAATGAGGAAAACCAATCAACATGCTTATG
260 CAAGTACTACAAGGGATTTAAGGATGCCATGGATAAAATGAGGAAAACCAATCAACATGCTTATG
*
33231948 ATCGGTTGAAGGAAAAGAACCCTACTCATTGGTCAAGGTCTCACTTCTCAATTAG
325 ATCGGTTGAAGGAAAAGAACCCTACTCACTGGTCAAGGTCTCACTTCTCAATTAG
33232003 GAGCTCATACCAAATATCTTTCATGTCTGACAAACAAAAGGTAAAACTCCATTTATTTATTTATT
1 GAGCTCATACCAAATATCTTTCATGTCTGACAAACAAAAGGTAAAACTCCATTTATTTATTTATT
* *
33232068 TTATGTTGTTTCTATTTAGGGATTGTCAAAGAATTAAACTATTTTTTTTCTAA-TGCAGGGACTT
66 TTATGTTGATTCTATTTAGGGATTGTCAAAGAATTAAACTATTTTTTTCCTAATTGCAGGGACTT
* **
33232132 TTAGAAGCAATATGTATGTTGTTTCTTAATGTAGAAACAAG-ACTGTGTTAGACACCTACATGCC
131 TTAGAAGCAATATGTATGTTGTTTCCTAATACAGAAACAAGAACTGTGTTAGACACCTACATGCC
* *
33232196 AATTTCAAGAAGGCTAGTTTTCGAACAAAGGAATTGAAATATTCGCTTTGGAAAGCTGCCAGAAC
196 AATTTCAAGAAGGCTAGTTTTCGAACAAAGGAATTAAAAGATTCGCTTTGGAAAGCTGCCAGAAC
* *
33232261 AAGTACTACAAGGGATTTAAGGATGCCATGGATGAACTGAGGAAAACCAATCAACATGCTTATGA
261 AAGTACTACAAGGGATTTAAGGATGCCATGGATAAAATGAGGAAAACCAATCAACATGCTTATGA
* *
33232326 TTGGTTGAAGGAAAAGAACCCTACTCACTGGTTAAGGTCTCACTTCTCAATTAG
326 TCGGTTGAAGGAAAAGAACCCTACTCACTGGTCAAGGTCTCACTTCTCAATTAG
33232380 GAGC
1 GAGC
33232384 CATTCTGACA
Statistics
Matches: 364, Mismatches: 17, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
377 202 0.55
379 49 0.13
380 113 0.31
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (379 bp):
GAGCTCATACCAAATATCTTTCATGTCTGACAAACAAAAGGTAAAACTCCATTTATTTATTTATT
TTATGTTGATTCTATTTAGGGATTGTCAAAGAATTAAACTATTTTTTTCCTAATTGCAGGGACTT
TTAGAAGCAATATGTATGTTGTTTCCTAATACAGAAACAAGAACTGTGTTAGACACCTACATGCC
AATTTCAAGAAGGCTAGTTTTCGAACAAAGGAATTAAAAGATTCGCTTTGGAAAGCTGCCAGAAC
AAGTACTACAAGGGATTTAAGGATGCCATGGATAAAATGAGGAAAACCAATCAACATGCTTATGA
TCGGTTGAAGGAAAAGAACCCTACTCACTGGTCAAGGTCTCACTTCTCAATTAG
Found at i:33232844 original size:28 final size:27
Alignment explanation
Indices: 33232780--33232844 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 27
33232770 GTTGGTGTGT
33232780 TGACTATA--TTTTAATATGCATGCAG
1 TGACTATATTTTTTAATATGCATGCAG
* * * * *
33232805 TGATTTTTTTTTTATAATTTGCATGTAG
1 TGACTATATTTTT-TAATATGCATGCAG
33232833 TGACTATATTTT
1 TGACTATATTTT
33232845 AGGGTTGTGT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
25 5 0.17
27 3 0.10
28 21 0.72
ACGTcount: A:0.26, C:0.08, G:0.14, T:0.52
Consensus pattern (27 bp):
TGACTATATTTTTTAATATGCATGCAG
Found at i:33233533 original size:21 final size:21
Alignment explanation
Indices: 33233503--33233548 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
33233493 AAGTTGGTGT
*
33233503 CCCAACTCAGCAACAGGCTAC
1 CCCAAATCAGCAACAGGCTAC
* * *
33233524 CCCAAATCAGTAAGAGGGTAC
1 CCCAAATCAGCAACAGGCTAC
33233545 CCCA
1 CCCA
33233549 GCTCAATAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.17, T:0.11
Consensus pattern (21 bp):
CCCAAATCAGCAACAGGCTAC
Found at i:33234340 original size:36 final size:36
Alignment explanation
Indices: 33234268--33234343 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
33234258 TAAAATATGT
* * * *
33234268 TAAGCAACAATATGCCAGCAGCCATACATACCAACA
1 TAAGCAACAATATACCAGCAACAATACATACAAACA
*
33234304 TAAGCAACAATATACCAGCAACAATA-TTACAAAACA
1 TAAGCAACAATATACCAGCAACAATACATAC-AAACA
33234340 TAAG
1 TAAG
33234344 TTGGTTTTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 3 0.09
36 31 0.91
ACGTcount: A:0.50, C:0.25, G:0.09, T:0.16
Consensus pattern (36 bp):
TAAGCAACAATATACCAGCAACAATACATACAAACA
Found at i:33235805 original size:38 final size:40
Alignment explanation
Indices: 33235736--33235810 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
33235726 TTTGGAAATT
33235736 TCAAAAATTTTAATTCTGTTTTTATTTTATTTTTTTCAGA
1 TCAAAAATTTTAATTCTGTTTTTATTTTATTTTTTTCAGA
*
33235776 TCAAAACTTTTAATTCT-TTTTT-TTTTATTTTTTTC
1 TCAAAAATTTTAATTCTGTTTTTATTTTATTTTTTTC
33235811 TAGGTACGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 13 0.38
39 5 0.15
40 16 0.47
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.64
Consensus pattern (40 bp):
TCAAAAATTTTAATTCTGTTTTTATTTTATTTTTTTCAGA
Found at i:33238088 original size:68 final size:68
Alignment explanation
Indices: 33237979--33238115 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
33237969 TGACATCCTC
33237979 ACTAAAGATTCACTCAAATCACTCAAAGTGTTTAAGGTTCAAGATTAAGCACTTGATTGTCTAAC
1 ACTAAAGATTCACTCAAATCACTCAAAGTGTTTAAGGTTCAAGATTAAGCACTTGATTGTCTAAC
33238044 ATA
66 ATA
33238047 ACTAAAGATTCACTCAAATCACTCAAAGTGTTTAAGGTTCAAGATTAAGCACTTGATTGTCTAAC
1 ACTAAAGATTCACTCAAATCACTCAAAGTGTTTAAGGTTCAAGATTAAGCACTTGATTGTCTAAC
33238112 ATA
66 ATA
33238115 A
1 A
33238116 GAAGTTATTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.31
Consensus pattern (68 bp):
ACTAAAGATTCACTCAAATCACTCAAAGTGTTTAAGGTTCAAGATTAAGCACTTGATTGTCTAAC
ATA
Found at i:33257894 original size:11 final size:11
Alignment explanation
Indices: 33257878--33257902 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33257868 AACCAAAAAG
33257878 AAAGAAAGAAA
1 AAAGAAAGAAA
33257889 AAAGAAAGAAA
1 AAAGAAAGAAA
33257900 AAA
1 AAA
33257903 TAAAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:33259857 original size:178 final size:179
Alignment explanation
Indices: 33259615--33259980 Score: 509
Period size: 178 Copynumber: 2.1 Consensus size: 179
33259605 GGGTAACAGG
* * *
33259615 CTGAAAATTACAAATCTTTATCTCCATGTCTCGGCTATGGAGCAGATTAAAAATGGCAAGTCTTA
1 CTGAAAATTACAAATCTTTATCTCCATGTATCGGCTATCGAGCAGATCAAAAATGGCAAGTCTTA
* * * * *
33259680 TCTCTATGTATTGGCTATGGAGTAGATTTTAGCCACCGGCCTTATCTCTCTGAGGTAACAAAAGA
66 TCTCTATGTATCGGCTATGAAGCAAATTTTAGCCACCGGCCTTATCTCTCTAAGGTAACAAAAGA
* *
33259745 GCAAGTTGAAGATACAAGTCTTATCTTCATGAGATAGTAAGGAAGCAGA
131 GCAAGTCGAAGATACAAGTCTTATCTTCATGAGATAGAAAGGAAGCAGA
* * ** **
33259794 CTGAAAATTATAGATC-TTATCTCCATGTATCGGCTATCGAGCAGATCGGAAATGGTGAGTCTTA
1 CTGAAAATTACAAATCTTTATCTCCATGTATCGGCTATCGAGCAGATCAAAAATGGCAAGTCTTA
* * *
33259858 TCTCTATGTATCGGCTATGAAGCAAATTTTAGCCATCGGCCTTATCTCTCTAAGGTAGCAAGAGA
66 TCTCTATGTATCGGCTATGAAGCAAATTTTAGCCACCGGCCTTATCTCTCTAAGGTAACAAAAGA
* * * * *
33259923 GTAGGTCGAAGATACAAGTCTTATCTTCTTGAGGTAGAAAGGAAGTAGA
131 GCAAGTCGAAGATACAAGTCTTATCTTCATGAGATAGAAAGGAAGCAGA
33259972 CTGAAAATT
1 CTGAAAATT
33259981 CCAAGCCTTA
Statistics
Matches: 163, Mismatches: 24, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
178 149 0.91
179 14 0.09
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (179 bp):
CTGAAAATTACAAATCTTTATCTCCATGTATCGGCTATCGAGCAGATCAAAAATGGCAAGTCTTA
TCTCTATGTATCGGCTATGAAGCAAATTTTAGCCACCGGCCTTATCTCTCTAAGGTAACAAAAGA
GCAAGTCGAAGATACAAGTCTTATCTTCATGAGATAGAAAGGAAGCAGA
Found at i:33260096 original size:88 final size:88
Alignment explanation
Indices: 33259984--33260782 Score: 1258
Period size: 88 Copynumber: 9.1 Consensus size: 88
33259974 GAAAATTCCA
* * *
33259984 AGCCTTAACCCCTTAAGCAATAGGGTAACAGGCTGAAAATTACAGATCGTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
*
33260049 AGTGGAGCAGATCAAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
*
33260072 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCT-AGAAATTATAGATCTTATCTCCCTAAGCAG
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGA-AAATTACAGATCTTATCTCCCTAAGCAG
* * * *
33260136 TAGGGGAACAGATCAAAGATGGTG
65 TAGTGGAGCAGATCGAAGACGGTG
* * *
33260160 AGCCTTAAACCCCTAAGCACTAGGGTAACAGGCTGAAAATTATAGATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
* * *
33260225 AGTAGAGCAGATCAAAGATGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* *
33260248 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTCTCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
*
33260313 AGTGGAGTAGATCGAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* * *
33260336 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTCTCTAAGTAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
*
33260401 AGGGGAGCAGATCGAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
33260424 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
33260489 AGTGGAGCAGATCGAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* * * * *
33260512 AGCCTTAACCTCCTAAACAGTAGGGTAACAGGTTAAAAATTACAAATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
*
33260577 AGCGGAGCAGATCGAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* * *
33260600 AACCTTAACCCCCTAAGCAGTAGGGTAACAGGTTAAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
*
33260665 AGTGGAGCAGATCGAAAACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
*
33260688 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
* **
33260753 AGCGGAGCAGATCGAAGATAGTG
66 AGTGGAGCAGATCGAAGACGGTG
33260776 AGCCTTA
1 AGCCTTA
33260783 TCTCCCTGAA
Statistics
Matches: 661, Mismatches: 48, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
87 1 0.00
88 659 1.00
89 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (88 bp):
AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGACGGTG
Found at i:33264427 original size:36 final size:36
Alignment explanation
Indices: 33264387--33264459 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
33264377 ACATCAATTC
33264387 ACCCATTCTTAGTGATTATTGAACGTGACAATTTAT
1 ACCCATTCTTAGTGATTATTGAACGTGACAATTTAT
*
33264423 ACCCATTCTTGGTGATTATTGAACGTGACAATTTAT
1 ACCCATTCTTAGTGATTATTGAACGTGACAATTTAT
33264459 A
1 A
33264460 GAGAAAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (36 bp):
ACCCATTCTTAGTGATTATTGAACGTGACAATTTAT
Found at i:33269924 original size:26 final size:26
Alignment explanation
Indices: 33269879--33269948 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
33269869 TTTATCATAA
33269879 AAAATA-TAAAAAATATAAAAATTAT
1 AAAATATTAAAAAATATAAAAATTAT
* *
33269904 TAAATATTAAAAAA-ATGAAAATTTAT
1 AAAATATTAAAAAATAT-AAAAATTAT
*
33269930 AAAAAATTATAAAACATAT
1 AAAATATTA-AAAA-ATAT
33269949 CTAAAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 7 0.19
26 22 0.61
27 4 0.11
28 1 0.03
29 2 0.06
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (26 bp):
AAAATATTAAAAAATATAAAAATTAT
Found at i:33269960 original size:21 final size:21
Alignment explanation
Indices: 33269936--33269986 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
33269926 TTATAAAAAA
*
33269936 TTATAAAACA-TATCTAAAATT
1 TTATAAAAAATTAT-TAAAATT
33269957 TTATAAAAAATTATTAAAATT
1 TTATAAAAAATTATTAAAATT
*
33269978 CTATAAAAA
1 TTATAAAAA
33269987 TAATAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (21 bp):
TTATAAAAAATTATTAAAATT
Found at i:33269987 original size:11 final size:10
Alignment explanation
Indices: 33269921--33270042 Score: 63
Period size: 10 Copynumber: 12.4 Consensus size: 10
33269911 TAAAAAAATG
33269921 AAAATTTATA
1 AAAATTTATA
*
33269931 AAAAATTATA
1 AAAATTTATA
* *
33269941 AAACATATCTA
1 AAA-ATTTATA
*
33269952 AAATTTTATA
1 AAAATTTATA
* *
33269962 AAAAATTATT
1 AAAATTTATA
33269972 AAAATTCTATA
1 AAAATT-TATA
*
33269983 AAAA-TAATA
1 AAAATTTATA
*
33269992 AAAA-ATATA
1 AAAATTTATA
* * *
33270001 AAGA-GTATT
1 AAAATTTATA
* *
33270010 AAGATTGATA
1 AAAATTTATA
* *
33270020 TAAACTTATA
1 AAAATTTATA
33270030 AAAA-TTATA
1 AAAATTTATA
33270039 AAAA
1 AAAA
33270043 AATCGCAAAA
Statistics
Matches: 83, Mismatches: 26, Indels: 7
0.72 0.22 0.06
Matches are distributed among these distances:
9 29 0.35
10 40 0.48
11 14 0.17
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (10 bp):
AAAATTTATA
Found at i:33270039 original size:9 final size:9
Alignment explanation
Indices: 33269875--33270042 Score: 90
Period size: 9 Copynumber: 17.8 Consensus size: 9
33269865 CTTTTTTATC
*
33269875 ATAAAAAAT
1 ATAAAAATT
*
33269884 ATAAAAAAT
1 ATAAAAATT
33269893 ATAAAAATT
1 ATAAAAATT
*
33269902 ATTAAATATT
1 A-TAAAAATT
33269912 A-AAAAA--
1 ATAAAAATT
*
33269918 ATGAAAATTT
1 AT-AAAAATT
33269928 ATAAAAAATT
1 AT-AAAAATT
33269938 ATAAAACATAT
1 ATAAAA-AT-T
* *
33269949 CTAAAATTTT
1 ATAAAA-ATT
33269959 ATAAAAAATT
1 AT-AAAAATT
*
33269969 ATTAAAATTCT
1 A-TAAAAAT-T
*
33269980 ATAAAAATA
1 ATAAAAATT
*
33269989 ATAAAAAAT
1 ATAAAAATT
* *
33269998 ATAAAGAGT
1 ATAAAAATT
* *
33270007 ATTAAGATT
1 ATAAAAATT
*
33270016 GATATAAACTT
1 -ATA-AAAATT
33270027 ATAAAAATT
1 ATAAAAATT
33270036 ATAAAAA
1 ATAAAAA
33270043 AATCGCAAAA
Statistics
Matches: 123, Mismatches: 24, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
6 1 0.01
8 8 0.07
9 55 0.45
10 41 0.33
11 18 0.15
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:33270363 original size:29 final size:30
Alignment explanation
Indices: 33270331--33270394 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
33270321 AATAAGTTTT
*
33270331 AAAAA-AAAGTTA-AAATACTT-AAAATAAA
1 AAAAATAAAATTAGAAAT-CTTAAAAATAAA
* *
33270359 AAAAATAACATTAGAAATCTTAAAAATAAT
1 AAAAATAAAATTAGAAATCTTAAAAATAAA
33270389 AAAAAT
1 AAAAAT
33270395 TGTAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 5 0.17
29 8 0.27
30 17 0.57
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (30 bp):
AAAAATAAAATTAGAAATCTTAAAAATAAA
Found at i:33271548 original size:16 final size:17
Alignment explanation
Indices: 33271519--33271559 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
33271509 ATATATATAT
*
33271519 AAAGTAAAAGGAATA-AA
1 AAAG-AAAAAGAATAGAA
33271536 AAAGAAAAAGAATAGAA
1 AAAGAAAAAGAATAGAA
33271553 AAAGAAA
1 AAAGAAA
33271560 GGAAGGATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (17 bp):
AAAGAAAAAGAATAGAA
Found at i:33271628 original size:16 final size:16
Alignment explanation
Indices: 33271590--33271622 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
33271580 AGAGCAGGGG
33271590 AAAGAAAGAAGGAAAA
1 AAAGAAAGAAGGAAAA
33271606 AAAGAAAGAAGGAAAA
1 AAAGAAAGAAGGAAAA
33271622 A
1 A
33271623 GGGAAAAATC
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAGGAAAA
Found at i:33273409 original size:19 final size:18
Alignment explanation
Indices: 33273385--33273426 Score: 68
Period size: 17 Copynumber: 2.3 Consensus size: 18
33273375 CGGTTGAATG
33273385 AAAGGAAAATTGACGGTAA
1 AAAGG-AAATTGACGGTAA
33273404 AAAGG-AATTGACGGTAA
1 AAAGGAAATTGACGGTAA
33273421 AAAGGA
1 AAAGGA
33273427 TCTAGCCCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 17 0.77
19 5 0.23
ACGTcount: A:0.52, C:0.05, G:0.29, T:0.14
Consensus pattern (18 bp):
AAAGGAAATTGACGGTAA
Found at i:33273414 original size:17 final size:17
Alignment explanation
Indices: 33273392--33273426 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
33273382 ATGAAAGGAA
33273392 AATTGACGGTAAAAAGG
1 AATTGACGGTAAAAAGG
33273409 AATTGACGGTAAAAAGG
1 AATTGACGGTAAAAAGG
33273426 A
1 A
33273427 TCTAGCCCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.29, T:0.17
Consensus pattern (17 bp):
AATTGACGGTAAAAAGG
Found at i:33273745 original size:46 final size:46
Alignment explanation
Indices: 33273693--33273968 Score: 435
Period size: 46 Copynumber: 6.0 Consensus size: 46
33273683 AGTGTGCTCT
**
33273693 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
**
33273739 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
*
33273785 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
33273831 GTGACATGAAAAGAATAAGACCATAGTTGCAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
33273877 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
33273923 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
33273969 ATGACAGAAA
Statistics
Matches: 215, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 215 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:33273946 original size:138 final size:141
Alignment explanation
Indices: 33273707--33274016 Score: 493
Period size: 138 Copynumber: 2.2 Consensus size: 141
33273697 TATGAAATGT
* **
33273707 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAG
1 GTAAGACCATAGTTGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAG
* * *
33273772 ATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACA
66 ATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA
33273837 TGAAAA-G-A-A
131 -GAAAATGAAGA
*
33273846 -TAAGACCATAGTTGCAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAG
1 GTAAGACCATAGTTGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAG
33273910 ATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA
66 ATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA
33273975 GAAAATGAATGA
131 GAAAATGAA-GA
* *
33273987 GTAAGACCATAGTTGAAAGACACTATGGCA
1 GTAAGACCATAGTTGAAAGATACCATGGCA
33274017 TCATGTCAAA
Statistics
Matches: 156, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
137 5 0.03
138 123 0.79
139 1 0.01
141 1 0.01
142 26 0.17
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (141 bp):
GTAAGACCATAGTTGAAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAG
ATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA
GAAAATGAAGA
Found at i:33273974 original size:46 final size:46
Alignment explanation
Indices: 33273708--33274016 Score: 422
Period size: 46 Copynumber: 6.6 Consensus size: 46
33273698 ATGAAATGTG
* * * **
33273708 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTG
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
* *
33273754 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
33273800 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
* * * * *
33273846 TAAGACCATAGTTGCAAGATACCATGGCAACCTGATATGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
33273892 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
*
33273938 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAATGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA-G-A--A
* * *
33273987 GTAAGACCATAGTTGAAAGACACTATGGCA
1 -TAAGACCATGGTTGAAAGATACCATGGCA
33274017 TCATGTCAAA
Statistics
Matches: 239, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
45 5 0.02
46 206 0.86
47 1 0.00
49 1 0.00
50 26 0.11
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAA
Found at i:33275847 original size:51 final size:51
Alignment explanation
Indices: 33275772--33275879 Score: 171
Period size: 51 Copynumber: 2.1 Consensus size: 51
33275762 CTGGTGGGGT
* * *
33275772 TGGTTTTGATTCAGAGGGAGGATTCGGTTTAGCCACTGATGGGGATGGTTG
1 TGGTTTTGATTCAGAGGAAAGATTCGGTGTAGCCACTGATGGGGATGGTTG
* *
33275823 TGGTTTTGGTTCAGAGGAAAGATTCGGTGTAGCCACTGATGGGGGTGGTTG
1 TGGTTTTGATTCAGAGGAAAGATTCGGTGTAGCCACTGATGGGGATGGTTG
33275874 TGGTTT
1 TGGTTT
33275880 GTTTTGAGGC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.17, C:0.09, G:0.40, T:0.34
Consensus pattern (51 bp):
TGGTTTTGATTCAGAGGAAAGATTCGGTGTAGCCACTGATGGGGATGGTTG
Found at i:33275878 original size:45 final size:45
Alignment explanation
Indices: 33275756--33275878 Score: 129
Period size: 51 Copynumber: 2.6 Consensus size: 45
33275746 GAGCTTGGTT
* * * * * *
33275756 TAGCCACTGGTGGGGTTGGTTTTGATTCAGAGGGAGGATTCGGTT
1 TAGCCACTGATGGGGGTGGTTTTGGTTCAGAGGAAAGATTCGGTG
33275801 TAGCCACTGATGGGGATGGTTGTGGTTTTGGTTCAGAGGAAAGATTCGGTG
1 TAGCCACTGAT--GG--GG--GTGGTTTTGGTTCAGAGGAAAGATTCGGTG
*
33275852 TAGCCACTGATGGGGGTGGTTGTGGTT
1 TAGCCACTGATGGGGGTGGTTTTGGTT
33275879 TGTTTTGAGG
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
45 21 0.32
47 4 0.06
49 4 0.06
51 36 0.55
ACGTcount: A:0.16, C:0.11, G:0.41, T:0.33
Consensus pattern (45 bp):
TAGCCACTGATGGGGGTGGTTTTGGTTCAGAGGAAAGATTCGGTG
Found at i:33280277 original size:12 final size:13
Alignment explanation
Indices: 33280262--33280312 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
33280252 AAAAAGGAGT
33280262 AATAAATAAAT-G
1 AATAAATAAATAG
*
33280274 AATAAACAAAATAG
1 AATAAA-TAAATAG
*
33280288 TAATAAAT-AATAA
1 -AATAAATAAATAG
33280301 AATAAATAAATA
1 AATAAATAAATA
33280313 ATCAAAGGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 13 0.41
13 12 0.38
14 1 0.03
15 6 0.19
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (13 bp):
AATAAATAAATAG
Found at i:33280314 original size:23 final size:23
Alignment explanation
Indices: 33280261--33280314 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
33280251 TAAAAAGGAG
33280261 TAATAAATAAATGAATAAACAAAA
1 TAAT-AATAAATGAATAAACAAAA
*
33280285 TAGTAATAAAT-AATAAA-ATAAA
1 TAATAATAAATGAATAAACA-AAA
33280307 TAAATAAT
1 T-AATAAT
33280315 CAAAGGCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.04
22 10 0.38
23 12 0.46
24 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.26
Consensus pattern (23 bp):
TAATAATAAATGAATAAACAAAA
Found at i:33281903 original size:15 final size:15
Alignment explanation
Indices: 33281883--33281911 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33281873 ACTGTGGACT
33281883 TTAATATTTTATTTA
1 TTAATATTTTATTTA
33281898 TTAATATTTTATTT
1 TTAATATTTTATTT
33281912 TGGTTATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTAATATTTTATTTA
Found at i:33282350 original size:44 final size:44
Alignment explanation
Indices: 33282302--33282662 Score: 245
Period size: 44 Copynumber: 8.0 Consensus size: 44
33282292 GACTTGTTGT
* * *
33282302 TTCAATATACTCCACTGTAACTTCAGGGAGATAAGATTAGTAGC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * * * ** *
33282346 TTCAATCTGCTCTACTGTAACATCAAAGAGATAAGATTTGCTATC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* * * ** * *
33282391 TTCGATCTACTCTACTACAACTTTTGGGAGATAAGATCTGTAAC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * * *
33282435 TTCAATCTGCTCCACTGTAACTTTAGGGAGATAAGATTTATAGC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * * * * ** *
33282479 TTTAATTTGCTCTACTGCAACTTTAGATAGATAAGATTTGCTATC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* * * * * *
33282524 TTCAACCTAATTCGCTGTAACTTTAGGGAGATAAGATTTGTAACTTGTAGC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGA----T---TTGTAGC
* * * * *
33282575 TTTAATTTATTCCACTGCAACTTCAGGGAAATAAGATTTGCTATC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* * *
33282620 TTCCATCTGCTCCACTGCAACTTCAGGGAGATGAGATTTGTAG
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAG
33282663 TTACTCCATT
Statistics
Matches: 241, Mismatches: 66, Indels: 20
0.74 0.20 0.06
Matches are distributed among these distances:
44 109 0.45
45 97 0.40
47 1 0.00
49 1 0.00
51 30 0.12
52 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (44 bp):
TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
Found at i:33282546 original size:133 final size:133
Alignment explanation
Indices: 33282302--33282659 Score: 342
Period size: 133 Copynumber: 2.6 Consensus size: 133
33282292 GACTTGTTGT
*
33282302 TTCAATATACTCCACTGTAACTTCAGGGAGATAAGATTAGTAGCTTCAATCTGCTCTACTGTAAC
1 TTCAATATACTCCACTGTAACTTCAGGGAGATAAGATTAGTAGCTTCAATCTGCTCTACTGCAAC
* * *
33282367 ATCAAAGAGATAAGATTTGCTATCTTCGATCTACTCTACTACAACTTTTGGGAGATAAGATCTGT
66 ATCAAAGAGATAAGATTTGCTATCTTCAACCTACTCTACTACAACTTTAGGGAGATAAGATCTGT
33282432 AAC
131 AAC
* * * * *
33282435 TTCAATCTGCTCCACTGTAACTTTAGGGAGATAAGATTTA-TAGCTTTAATTTGCTCTACTGCAA
1 TTCAATATACTCCACTGTAACTTCAGGGAGATAAGA-TTAGTAGCTTCAATCTGCTCTACTGCAA
* * * * * * ** *
33282499 CTTTAGATAGATAAGATTTGCTATCTTCAACCTAAT-TCGCTGTAACTTTAGGGAGATAAGATTT
65 CATCAAAGAGATAAGATTTGCTATCTTCAACCTACTCT-ACTACAACTTTAGGGAGATAAGATCT
33282563 GTAAC
129 GTAAC
* * * * * * * *
33282568 TTGTAGCTTTAATTTATTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCCATCTGCTCC
1 -T-T--C---AATATACTCCACTGTAACTTCAGGGAGATAAGATTAG-TAGCTTCAATCTGCTCT
* ** *
33282633 ACTGCAACTTCAGGGAGATGAGATTTG
58 ACTGCAACATCAAAGAGATAAGATTTG
33282660 TAGTTACTCC
Statistics
Matches: 180, Mismatches: 34, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
132 1 0.01
133 109 0.61
134 4 0.02
135 1 0.01
137 1 0.01
139 2 0.01
140 27 0.15
141 35 0.19
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (133 bp):
TTCAATATACTCCACTGTAACTTCAGGGAGATAAGATTAGTAGCTTCAATCTGCTCTACTGCAAC
ATCAAAGAGATAAGATTTGCTATCTTCAACCTACTCTACTACAACTTTAGGGAGATAAGATCTGT
AAC
Found at i:33282613 original size:96 final size:89
Alignment explanation
Indices: 33282449--33282622 Score: 222
Period size: 96 Copynumber: 1.9 Consensus size: 89
33282439 ATCTGCTCCA
* * * * *
33282449 CTGTAACTTTAGGGAGATAAGATTTATAGCTTTAATTTGCTCTACTGCAACTTTAGATAGATAAG
1 CTGTAACTTTAGGGAGATAAGATTTATAGCTTTAATTTACTCCACTGCAACTTCAGAGAAATAAG
33282514 ATTTGCTATCTTCAACCTAATTCG
66 ATTTGCTATCTTCAACCTAATTCG
* *
33282538 CTGTAACTTTAGGGAGATAAGATTTGTAACTTGTAGCTTTAATTTATTCCACTGCAACTTCAGGG
1 CTGTAACTTTAGGGAGATAAGA-TT-T-A----TAGCTTTAATTTACTCCACTGCAACTTCAGAG
33282603 AAATAAGATTTGCTATCTTC
59 AAATAAGATTTGCTATCTTC
33282623 CATCTGCTCC
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
89 22 0.31
90 2 0.03
91 1 0.01
92 1 0.01
96 45 0.63
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (89 bp):
CTGTAACTTTAGGGAGATAAGATTTATAGCTTTAATTTACTCCACTGCAACTTCAGAGAAATAAG
ATTTGCTATCTTCAACCTAATTCG
Found at i:33282642 original size:96 final size:92
Alignment explanation
Indices: 33282309--33282661 Score: 308
Period size: 89 Copynumber: 3.9 Consensus size: 92
33282299 TGTTTCAATA
* * * * * * **
33282309 TACTCCACTGTAACTTCAGGGAGATAAGATTAG-TAGCTTCAATCTGCTCTACTGTAACATCAAA
1 TACTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGTAACTTTAGG
** *
33282373 GAGATAAGATTTGCT-AT--CTTCGATC
66 GAGATAAGATTTG-TAATAGCTTTAATT
* * ** * *
33282398 TACTCTACTACAACTTTTGGGAGATAAGATCTG-TAACTTCAATCTGCTCCACTGTAACTTTAGG
1 TACTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGTAACTTTAGG
33282462 GAGATAAGA-TT-T-ATAGCTTTAATT
66 GAGATAAGATTTGTAATAGCTTTAATT
* * * ** * ** * *
33282486 TGCTCTACTGCAACTTTAGATAGATAAGATTTGCTATCTTCAACCTAATTCGCTGTAACTTTAGG
1 TACTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGTAACTTTAGG
33282551 GAGATAAGATTTGTAACTTGTAGCTTTAATT
66 GAGATAAGATTTGTAA----TAGCTTTAATT
* * * * *
33282582 TATTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCCATCTGCTCCACTGCAACTTCAGG
1 TACTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGTAACTTTAGG
*
33282647 GAGATGAGATTTGTA
66 GAGATAAGATTTGTA
33282662 GTTACTCCAT
Statistics
Matches: 210, Mismatches: 44, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
86 3 0.01
88 34 0.16
89 94 0.45
90 2 0.01
91 1 0.00
92 1 0.00
96 75 0.36
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (92 bp):
TACTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGTAACTTTAGG
GAGATAAGATTTGTAATAGCTTTAATT
Found at i:33296001 original size:12 final size:11
Alignment explanation
Indices: 33295983--33296031 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
33295973 TAAAAAGGAG
33295983 TAATAAATAAA
1 TAATAAATAAA
*
33295994 TGAATAAACAAAA
1 T-AATAAA-TAAA
33296007 TAAT-AATAAA
1 TAATAAATAAA
33296017 TAATAAAATAAA
1 TAAT-AAATAAA
33296029 TAA
1 TAA
33296032 ATAATCAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 7 0.22
11 3 0.09
12 18 0.56
13 4 0.12
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (11 bp):
TAATAAATAAA
Found at i:33296026 original size:27 final size:26
Alignment explanation
Indices: 33295983--33296036 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
33295973 TAAAAAGGAG
*
33295983 TAATAAATAAATGAATAAACAAAATAA
1 TAATAAATAAATAAATAAA-AAAATAA
*
33296010 TAATAAAT-AATAAAATAAATAAATAA
1 TAATAAATAAAT-AAATAAAAAAATAA
33296036 T
1 T
33296037 CAAAGGCTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (26 bp):
TAATAAATAAATAAATAAAAAAATAA
Found at i:33299672 original size:28 final size:26
Alignment explanation
Indices: 33299628--33299686 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
33299618 ATATTTATAT
33299628 TATATTATTTTAGTATTTGATAATTTTA
1 TATATTATTTTAGTA-TTGA-AATTTTA
* *
33299656 TATATT-TTTTACTTATTGAAATTTTT
1 TATATTATTTTA-GTATTGAAATTTTA
33299682 TATAT
1 TATAT
33299687 AGTTATCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 11 0.39
27 9 0.32
28 8 0.29
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (26 bp):
TATATTATTTTAGTATTGAAATTTTA
Found at i:33301736 original size:26 final size:23
Alignment explanation
Indices: 33301703--33301752 Score: 55
Period size: 26 Copynumber: 2.0 Consensus size: 23
33301693 TTTTTTTAAA
*
33301703 TTTTAAATATATATATTTAATTTTT
1 TTTTAAATATAAATA-TT-ATTTTT
*
33301728 TTTTAAAATTTAAATATTATTTTT
1 TTTT-AAATATAAATATTATTTTT
33301752 T
1 T
33301753 AAATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTAAATATAAATATTATTTTT
Found at i:33301754 original size:32 final size:32
Alignment explanation
Indices: 33301693--33301759 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
33301683 TGTTTTATAA
* *
33301693 TTTTTTTAAATTTTAAATATATATATTTAATT
1 TTTTTTTAAAATTTAAATATATATATTTAAAT
*
33301725 TTTTTTTAAAATTTAAATAT-TATTTTTTAAAT
1 TTTTTTTAAAATTTAAATATATA-TATTTAAAT
33301757 TTT
1 TTT
33301760 AAATATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 2 0.06
32 29 0.94
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
TTTTTTTAAAATTTAAATATATATATTTAAAT
Found at i:33301782 original size:20 final size:20
Alignment explanation
Indices: 33301724--33301771 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
33301714 TATATTTAAT
33301724 TTTTTTTTAAAATTTAAATA
1 TTTTTTTTAAAATTTAAATA
*
33301744 TTATTTTTTAAATTTTAAATA
1 TT-TTTTTTAAAATTTAAATA
33301765 TTTTTTT
1 TTTTTTT
33301772 AATAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTTTTAAAATTTAAATA
Found at i:33301929 original size:29 final size:30
Alignment explanation
Indices: 33301814--33301929 Score: 95
Period size: 29 Copynumber: 4.0 Consensus size: 30
33301804 ATAACCTTTC
*
33301814 AAATTTATTATTAT--T-TTTATAATATTTT
1 AAATTTATT-TTATAATATTTAAAATATTTT
33301842 AAATGTATATTTTA-AAT-TTTAAAA-ATTTT
1 AAAT-T-TATTTTATAATATTTAAAATATTTT
* * * *
33301871 TAATTTGTTTTATAATATTTTTAAGT-TTTT
1 AAATTTATTTTATAATA-TTTAAAATATTTT
33301901 AAATTT-TTTTATAATATTTAAAATATTTT
1 AAATTTATTTTATAATATTTAAAATATTTT
33301930 TAAAATATAT
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
27 6 0.08
28 14 0.20
29 26 0.37
30 25 0.35
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (30 bp):
AAATTTATTTTATAATATTTAAAATATTTT
Found at i:33302021 original size:31 final size:29
Alignment explanation
Indices: 33301977--33302065 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 29
33301967 TTATTGTTTG
* *
33301977 TTTTATAATATTTTAAATGTATATTTTAAATA
1 TTTT-TAAAATTTTAAAT-TA-ATTTTAAAAA
33302009 TTTTTAAAATTTTAAATATAATTTTTAAAAA
1 TTTTTAAAATTTTAAAT-TAA-TTTTAAAAA
*
33302040 TTTTT-AATTTTTAAATTAATTTTAAA
1 TTTTTAAAATTTTAAATTAATTTTAAA
33302066 GATATTCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.13
29 3 0.06
30 11 0.21
31 27 0.52
32 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
TTTTTAAAATTTTAAATTAATTTTAAAAA
Found at i:33302098 original size:149 final size:148
Alignment explanation
Indices: 33301791--33302071 Score: 365
Period size: 149 Copynumber: 1.9 Consensus size: 148
33301781 AAACATTTAA
*
33301791 ATAT-TTTAAAGATATAACCTTTCAAATTTATTATTATTTTTATAATATTTTAAATGTATATTTT
1 ATATATTTAAAGATATAACATTTCAAATTTATTATTATTTTTATAATATTTTAAATGTATATTTT
* * * *
33301855 AAATTTTAAAAATTTTTAATTTGTTTTATAATATTTTTAAGTTTTTAAATTTTTTTATAATATTT
66 AAATTTTAAAAATTTTAAATTTGTTTTATAAAATTTTTAAGTTTTTAAATTATTTTAAAATATTT
33301920 AAAATATTTTTAAAATAT
131 AAAATATTTTTAAAATAT
* * *
33301938 ATTATTTTTAAAGATATGACATTTCAAATTTATTGTT-TGTTTTATAATATTTTAAATGTATATT
1 A-TATATTTAAAGATATAACATTTCAAATTTATTATTAT-TTTTATAATATTTTAAATGTATATT
*
33302002 TTAAATATTTTTAAAATTTTAAATATAAT-TTTTA-AAAATTTTTAA-TTTTTAAATTAATTTTA
64 TT-AA-ATTTTAAAAATTTTAAAT-T--TGTTTTATAAAATTTTTAAGTTTTTAAATT-ATTTTA
33302064 AAGATATT
123 AA-ATATT
33302072 CAAATGTTTT
Statistics
Matches: 116, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
147 1 0.01
148 4 0.03
149 55 0.47
150 2 0.02
151 26 0.22
152 17 0.15
153 10 0.09
154 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (148 bp):
ATATATTTAAAGATATAACATTTCAAATTTATTATTATTTTTATAATATTTTAAATGTATATTTT
AAATTTTAAAAATTTTAAATTTGTTTTATAAAATTTTTAAGTTTTTAAATTATTTTAAAATATTT
AAAATATTTTTAAAATAT
Found at i:33302118 original size:33 final size:33
Alignment explanation
Indices: 33302043--33302118 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
33302033 TTAAAAATTT
* *
33302043 TTAATTTTTAAATTAATTTTAAAGATATTCAAA
1 TTAATTTTTAAATTAAATTTAAAGATATTAAAA
* *
33302076 TGT-TTTTTTAAATTAAATTTAAA-ATTTTAAAA
1 T-TAATTTTTAAATTAAATTTAAAGATATTAAAA
33302108 TTAATATTTTA
1 TTAAT-TTTTA
33302119 TTTGGTGGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
31 1 0.03
32 9 0.26
33 24 0.69
34 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (33 bp):
TTAATTTTTAAATTAAATTTAAAGATATTAAAA
Found at i:33305037 original size:48 final size:48
Alignment explanation
Indices: 33304977--33305174 Score: 279
Period size: 48 Copynumber: 4.1 Consensus size: 48
33304967 CCTCAGATGG
** * *
33304977 TGGTTGCGGTTTTGGTTTTGAAGGAGGGTTAGGTTTAGGCACTGGTGA
1 TGGTTGCGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGGCACTGGTGA
* * * *
33305025 TGGTTGTGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGTCACTGTTAA
1 TGGTTGCGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGGCACTGGTGA
* *
33305073 TGGTTGCGGTTTTGGTTCAGAGGGCGGATTAGGTTTAGGCACTGGTGG
1 TGGTTGCGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGGCACTGGTGA
* * *
33305121 TGGTTGCGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGCCACTGTTGG
1 TGGTTGCGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGGCACTGGTGA
33305169 TGGTTG
1 TGGTTG
33305175 TGGCTGCGGA
Statistics
Matches: 133, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 133 1.00
ACGTcount: A:0.13, C:0.09, G:0.41, T:0.37
Consensus pattern (48 bp):
TGGTTGCGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGGCACTGGTGA
Found at i:33305173 original size:96 final size:96
Alignment explanation
Indices: 33304974--33305174 Score: 312
Period size: 96 Copynumber: 2.1 Consensus size: 96
33304964 GCTCCTCAGA
** * *
33304974 TGGTGGTTGCGGTTTTGGTTTTGAAGGAGGGTTAGGTTTAGGCACTGGTGATGGTTGTGGTTTTG
1 TGGTGGTTGCGGTTTTGGTTCAGAAGGAGGATTAGGTTTAGGCACTGGTGATGGTTGCGGTTTTG
*
33305039 GTTCAGAGGGCGGGTTAGGTTTAGTCACTGT
66 GTTCAGAGGGCGGGTTAGGTTTAGCCACTGT
** * * *
33305070 TAATGGTTGCGGTTTTGGTTCAGAGGGCGGATTAGGTTTAGGCACTGGTGGTGGTTGCGGTTTTG
1 TGGTGGTTGCGGTTTTGGTTCAGAAGGAGGATTAGGTTTAGGCACTGGTGATGGTTGCGGTTTTG
33305135 GTTCAGAGGGCGGGTTAGGTTTAGCCACTGT
66 GTTCAGAGGGCGGGTTAGGTTTAGCCACTGT
33305166 TGGTGGTTG
1 TGGTGGTTG
33305175 TGGCTGCGGA
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.12, C:0.09, G:0.42, T:0.37
Consensus pattern (96 bp):
TGGTGGTTGCGGTTTTGGTTCAGAAGGAGGATTAGGTTTAGGCACTGGTGATGGTTGCGGTTTTG
GTTCAGAGGGCGGGTTAGGTTTAGCCACTGT
Found at i:33305184 original size:84 final size:84
Alignment explanation
Indices: 33305096--33305314 Score: 305
Period size: 84 Copynumber: 2.6 Consensus size: 84
33305086 GGTTCAGAGG
* * *
33305096 GCGGATTAGGTTTAGGCACTGGTGGTGGTTGCGGTTTTGGTTCAGAGGGCGGGTTAGGTTTAGCC
1 GCGGATTTGGTTTAGGCACTGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTCAGGTTTAGCC
* *
33305161 ACTGTTGGTGGTTGTGGCT
66 ACCGGTGGTGGTTGTGGCT
* * * *
33305180 GCGGATTTGGTTTAGGAATTGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTCCGGTTTAGCT
1 GCGGATTTGGTTTAGGCACTGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTCAGGTTTAGCC
33305245 ACCGGTGGTGGTTGTGGCT
66 ACCGGTGGTGGTTGTGGCT
* * * *
33305264 GCGGTTTTGGTTCAGGCACTGGTGGCT-GCTGTGGTTTTGGTTCAGACGGCG
1 GCGGATTTGGTTTAGGCACTGGTGG-TGGTTGTGGTTTTGGTTCAGAGGGCG
33305315 AGTTTAGTGG
Statistics
Matches: 119, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
84 118 0.99
85 1 0.01
ACGTcount: A:0.10, C:0.13, G:0.43, T:0.35
Consensus pattern (84 bp):
GCGGATTTGGTTTAGGCACTGGTGGTGGTTGTGGTTTTGGTTCAGAGGGCGGGTCAGGTTTAGCC
ACCGGTGGTGGTTGTGGCT
Found at i:33305819 original size:25 final size:27
Alignment explanation
Indices: 33305791--33305848 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
33305781 ACGTTTTGAA
33305791 ATTATAATTTT-GTA-AAAATAATTAT
1 ATTATAATTTTGGTACAAAATAATTAT
*
33305816 ATTA-ATTTTTGGTACCTAAAATAATTAT
1 ATTATAATTTTGGTA-C-AAAATAATTAT
33305844 ATTAT
1 ATTAT
33305849 TTGTGTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 5 0.19
25 7 0.26
28 15 0.56
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (27 bp):
ATTATAATTTTGGTACAAAATAATTAT
Found at i:33315455 original size:6 final size:6
Alignment explanation
Indices: 33315437--33315556 Score: 77
Period size: 6 Copynumber: 19.3 Consensus size: 6
33315427 AAGAAACATT
* *
33315437 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * * *
33315486 ATCAAA ATCAGC ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAGGTA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
*
33315537 A-CAGA ATCAAA AGTCAGA AT
1 ATCAGA ATCAGA A-TCAGA AT
33315557 GTGAATGCAA
Statistics
Matches: 88, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
5 6 0.07
6 65 0.74
7 14 0.16
8 3 0.03
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.18
Consensus pattern (6 bp):
ATCAGA
Found at i:33315482 original size:31 final size:31
Alignment explanation
Indices: 33315446--33315556 Score: 150
Period size: 31 Copynumber: 3.5 Consensus size: 31
33315436 TATCAGAACT
* * *
33315446 AGAATCAGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
* * *
33315477 AGAATCAGAATCAAAATCAGCATCAGGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
*
33315508 AGAATCAAAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
33315539 AGAATCAAAAGTCAGAAT
1 AGAATCAAAA-TCAGAAT
33315557 GTGAATGCAA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
31 65 0.90
32 7 0.10
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGAATCAGGTAAC
Found at i:33315735 original size:27 final size:26
Alignment explanation
Indices: 33315693--33315794 Score: 132
Period size: 27 Copynumber: 3.8 Consensus size: 26
33315683 GCTCAGTTAT
* *
33315693 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
33315720 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
33315746 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
33315774 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
33315795 TTAACAGAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
26 7 0.10
27 53 0.78
28 8 0.12
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:33315977 original size:22 final size:22
Alignment explanation
Indices: 33315952--33316016 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
33315942 GCAAATACGT
* *
33315952 TTGGCATACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
33315974 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
33315996 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
33316017 AAAGCTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:33316500 original size:27 final size:27
Alignment explanation
Indices: 33316461--33316735 Score: 374
Period size: 27 Copynumber: 10.3 Consensus size: 27
33316451 TACCCCATAA
* *
33316461 GGTATCTCGGTAATTCCACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
**
33316488 GGTATTTTAGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
33316515 AGTATTTCGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* * *
33316542 GATATTGCGATAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* * *
33316569 GATATTGCGATAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
33316596 GGTATTTCGATAATTCTACCCTACAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
33316623 GGTATTTCGGTAATT-TACCATACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
33316649 GGTATTTCGGTAATTCTACCTTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
33316676 GGTATTTCGGTAATTGTACCTTACA-G
1 GGTATTTCGGTAATTCTACCCTACAGG
*
33316702 GGTATTTCGGTAATTCTACCCTACAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
33316729 GGTATTT
1 GGTATTT
33316736 TGATATTTTA
Statistics
Matches: 225, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
26 48 0.21
27 177 0.79
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTATTTCGGTAATTCTACCCTACAGG
Found at i:33316760 original size:53 final size:50
Alignment explanation
Indices: 33316498--33316769 Score: 199
Period size: 53 Copynumber: 5.1 Consensus size: 50
33316488 GGTATTTTAG
* * *
33316498 TAATTCTACCCTAC-AGGAGTATTTCGGTAATTCTACCCTACAGGGATATTGCGA
1 TAATTCTACCCTACAAGG-GTATTTCGGT-ATTTTA-CATACA-GG-TATTTCGA
* * * *
33316552 TAATTCTACCCTAC-AGGGATATTGCGATAATTCTACCCTACAGGGGTATTTCGA
1 TAATTCTACCCTACAAGGG-TATTTCGGT-ATTTTA-CATACA--GGTATTTCGA
* *
33316606 TAATTCTACCCTACAAGGGTATTTCGGTAATTTACCATACAGGGGTATTTCGG
1 TAATTCTACCCTACAAGGGTATTTCGGTATTTTA-CATACA--GGTATTTCGA
* * * * *
33316659 TAATTCTACCTTACAGGGGTATTTCGGTAATTGTACCTTACAGGGTATTTCGG
1 TAATTCTACCCTACAAGGGTATTTCGGT-ATTTTA-CATACA-GGTATTTCGA
* *
33316712 TAATTCTACCCTACAAGGGTATTTTGATATTTTACAAATCGACA-GTATTTCGA
1 TAATTCTACCCTACAAGGGTATTTCGGTATTTTAC--AT--ACAGGTATTTCGA
33316765 TAATT
1 TAATT
33316770 TCACAAATCA
Statistics
Matches: 189, Mismatches: 21, Indels: 17
0.83 0.09 0.07
Matches are distributed among these distances:
51 1 0.01
52 5 0.03
53 97 0.51
54 76 0.40
55 10 0.05
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (50 bp):
TAATTCTACCCTACAAGGGTATTTCGGTATTTTACATACAGGTATTTCGA
Found at i:33316786 original size:27 final size:27
Alignment explanation
Indices: 33316756--33317063 Score: 393
Period size: 27 Copynumber: 11.4 Consensus size: 27
33316746 CAAATCGACA
* * * *
33316756 GTATTTCGATAATTTCACAAATCAGGG
1 GTATTTTGGTAATTTTACAAACCAGGG
* *
33316783 GTATTTTGGTAATTTTACAAGCCAAGG
1 GTATTTTGGTAATTTTACAAACCAGGG
*
33316810 GTATTTTGGTAATTTTACAAACTAGGG
1 GTATTTTGGTAATTTTACAAACCAGGG
** *
33316837 GTATTTTGGTAATTTTGTAAACCAAGG
1 GTATTTTGGTAATTTTACAAACCAGGG
*
33316864 GTATTTTAGTAATTTTACAAACCAGGG
1 GTATTTTGGTAATTTTACAAACCAGGG
** * *
33316891 GTATTTTGGTAATTTTGTAAACAAAGG
1 GTATTTTGGTAATTTTACAAACCAGGG
*
33316918 GTATTTTGGTAATTTTACAAACTAGGG
1 GTATTTTGGTAATTTTACAAACCAGGG
** * *
33316945 GTATTTTGGTAATTTTGTAAACTAAGG
1 GTATTTTGGTAATTTTACAAACCAGGG
33316972 GTATTTTGGTAATTTTACAAACCAGGG
1 GTATTTTGGTAATTTTACAAACCAGGG
* *
33316999 GTATTTTGGTAATTTTATAAACCAAGG
1 GTATTTTGGTAATTTTACAAACCAGGG
* *
33317026 GTATTCTAGTAA-TTTACAAACCAGGG
1 GTATTTTGGTAATTTTACAAACCAGGG
33317052 GTATTTTGGTAA
1 GTATTTTGGTAA
33317064 AAGGGTATTT
Statistics
Matches: 240, Mismatches: 41, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 0.09
27 218 0.91
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (27 bp):
GTATTTTGGTAATTTTACAAACCAGGG
Found at i:33316823 original size:54 final size:54
Alignment explanation
Indices: 33316756--33317063 Score: 474
Period size: 54 Copynumber: 5.7 Consensus size: 54
33316746 CAAATCGACA
* * * * ** *
33316756 GTATTTCGATAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAGCCAAGG
1 GTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGG
*
33316810 GTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTGTAAACCAAGG
1 GTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGG
* *
33316864 GTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACAAAGG
1 GTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGG
* *
33316918 GTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTGTAAACTAAGG
1 GTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGG
*
33316972 GTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCAAGG
1 GTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGG
* *
33317026 GTATTCTAGTAA-TTTACAAACCAGGGGTATTTTGGTAA
1 GTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAA
33317064 AAGGGTATTT
Statistics
Matches: 235, Mismatches: 19, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
53 26 0.11
54 209 0.89
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (54 bp):
GTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGG
Found at i:33317100 original size:25 final size:25
Alignment explanation
Indices: 33317067--33317149 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 25
33317057 TTGGTAAAAG
*
33317067 GGTATTTTGATAATTTTGTAAACCAA
1 GGTA-TTTGGTAATTTTGTAAACCAA
** *
33317093 GGTATTTGGTAATTTTACAAACCAGG
1 GGTATTTGGTAATTTTGTAAACCA-A
* *
33317119 GGTATTTGGTAATTTGGTAAACTAA
1 GGTATTTGGTAATTTTGTAAACCAA
*
33317144 AGTATT
1 GGTATT
33317150 CTAAACAGGG
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
25 22 0.48
26 24 0.52
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (25 bp):
GGTATTTGGTAATTTTGTAAACCAA
Found at i:33318423 original size:27 final size:26
Alignment explanation
Indices: 33318386--33318437 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
33318376 AATATTTTTT
*
33318386 GTTTTTATTTTCTAGTTTTTAAAAATA
1 GTTTTCATTTTCTA-TTTTTAAAAATA
*
33318413 GTTTTCATTTTCTATTTTTAGAAAT
1 GTTTTCATTTTCTATTTTTAAAAAT
33318438 TGAAGGGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.60
Consensus pattern (26 bp):
GTTTTCATTTTCTATTTTTAAAAATA
Found at i:33318774 original size:16 final size:16
Alignment explanation
Indices: 33318753--33318803 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
33318743 CATTTTCAAA
33318753 ATTTTCAACCGAACAC
1 ATTTTCAACCGAACAC
***
33318769 ATTTTCCTTC-AA-A-
1 ATTTTCAACCGAACAC
33318782 ATTTTCAACCGAACAC
1 ATTTTCAACCGAACAC
33318798 ATTTTC
1 ATTTTC
33318804 CTTATTGTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 7 0.27
14 3 0.12
15 3 0.12
16 13 0.50
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTTTCAACCGAACAC
Found at i:33318779 original size:29 final size:29
Alignment explanation
Indices: 33318747--33318806 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
33318737 AAAAATCATT
33318747 TTCAAAATTTTCAACCGAACACATTTTCC
1 TTCAAAATTTTCAACCGAACACATTTTCC
33318776 TTCAAAATTTTCAACCGAACACATTTTCC
1 TTCAAAATTTTCAACCGAACACATTTTCC
33318805 TT
1 TT
33318807 ATTGTTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (29 bp):
TTCAAAATTTTCAACCGAACACATTTTCC
Found at i:33319619 original size:14 final size:14
Alignment explanation
Indices: 33319600--33319626 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33319590 TCTCCTCTGG
33319600 TTTTATTTTCCTTA
1 TTTTATTTTCCTTA
33319614 TTTTATTTTCCTT
1 TTTTATTTTCCTT
33319627 CTTATTTGGA
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:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATTTTCCTTA
Found at i:33320225 original size:21 final size:21
Alignment explanation
Indices: 33320200--33320255 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
33320190 ATAAGGATCC
**
33320200 CACACGGGCGTGTGTTTTGGA
1 CACACGGGCGTGTGTGGTGGA
* * *
33320221 CACACGGCCGTGTCTGGTGGG
1 CACACGGGCGTGTGTGGTGGA
33320242 CACACGGGCGTGTG
1 CACACGGGCGTGTG
33320256 AGACCCTCAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.12, C:0.25, G:0.41, T:0.21
Consensus pattern (21 bp):
CACACGGGCGTGTGTGGTGGA
Found at i:33321790 original size:20 final size:20
Alignment explanation
Indices: 33321765--33321804 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
33321755 CTAAAAGTTG
33321765 ATACGTTAGGTATATGACTT
1 ATACGTTAGGTATATGACTT
33321785 ATACGTTAGGTATATGACTT
1 ATACGTTAGGTATATGACTT
33321805 TTGCATGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (20 bp):
ATACGTTAGGTATATGACTT
Found at i:33325959 original size:21 final size:21
Alignment explanation
Indices: 33325933--33325979 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
33325923 TATTGTTATT
33325933 AAATTATCCATTGTTCAAGTA
1 AAATTATCCATTGTTCAAGTA
33325954 AAATTATCCATTGTTCAAGTA
1 AAATTATCCATTGTTCAAGTA
33325975 AAATT
1 AAATT
33325980 CTAGTACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (21 bp):
AAATTATCCATTGTTCAAGTA
Found at i:33327918 original size:41 final size:40
Alignment explanation
Indices: 33327850--33328057 Score: 263
Period size: 41 Copynumber: 5.1 Consensus size: 40
33327840 GTAAAAATTG
** * * *
33327850 TAAAACACAGAGCAATAGCGATGTTTTTGTTAACACGCCGC
1 TAAAA-ACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* *
33327891 TAAAAACAGAGCAATAGCGGCGTTTTTTGTTAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCG-CTTTTGGTAAAACGCCGC
33327932 TAAAAACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
** * * *
33327972 TAAAGTCGGAGCATTAGCGGCGCTTTTGGTAAAACGCAGC
1 TAAAAACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* *
33328012 TAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCAC
1 TAAAAA-CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
33328053 TAAAA
1 TAAAA
33328058 GTCATATAAC
Statistics
Matches: 150, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
40 70 0.47
41 80 0.53
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (40 bp):
TAAAAACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
Found at i:33327991 original size:81 final size:80
Alignment explanation
Indices: 33327850--33328057 Score: 263
Period size: 81 Copynumber: 2.6 Consensus size: 80
33327840 GTAAAAATTG
** * * * *
33327850 TAAAACACAGAGCAATAGCGATGTTTTTGTTAACACGCCGCTAAAAACAGAGCAATAGCGGCGTT
1 TAAAA-ACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACAGAGCAATAGCGGCG-C
* *
33327915 TTTTGTTAAAACGCCGC
64 TTTTGGTAAAACGCAGC
** * *
33327932 TAAAAACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAGTCGGAGCATTAGCGGCGCTT
1 TAAAAACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACAGAGCAATAGCGGCGCTT
33327997 TTGGTAAAACGCAGC
66 TTGGTAAAACGCAGC
* *
33328012 TAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCACTAAAA
1 TAAAAA-CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
33328058 GTCATATAAC
Statistics
Matches: 110, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
80 21 0.19
81 84 0.76
82 5 0.05
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (80 bp):
TAAAAACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACAGAGCAATAGCGGCGCTT
TTGGTAAAACGCAGC
Found at i:33328306 original size:7 final size:7
Alignment explanation
Indices: 33328294--33328357 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
33328284 TTTATTTTTT
*
33328294 GGTTTAC
1 GGTTTAA
33328301 GGTTTAA
1 GGTTTAA
**
33328308 TATTTAA
1 GGTTTAA
33328315 GGTTTAA
1 GGTTTAA
* *
33328322 GGTCTAT
1 GGTTTAA
*
33328329 GGTTTAG
1 GGTTTAA
*
33328336 GGTTTTAT
1 GG-TTTAA
33328344 GGTTTAA
1 GGTTTAA
33328351 GGTTTAA
1 GGTTTAA
33328358 TGGCCATGGG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 39 0.87
8 6 0.13
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (7 bp):
GGTTTAA
Found at i:33328346 original size:15 final size:15
Alignment explanation
Indices: 33328310--33328360 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
33328300 CGGTTTAATA
*
33328310 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* *
33328324 TCTATGGTTTAGGGT
1 TTTATGGTTTAAGGT
33328339 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
33328354 TTAATGG
1 TTTATGG
33328361 CCATGGGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:33328892 original size:8 final size:8
Alignment explanation
Indices: 33328881--33328935 Score: 55
Period size: 8 Copynumber: 7.4 Consensus size: 8
33328871 TCAAAAAAAA
33328881 TAAAAATT
1 TAAAAATT
33328889 T-AAAATT
1 TAAAAATT
33328896 TAAAAA--
1 TAAAAATT
*
33328902 TAAAAAGT
1 TAAAAATT
*
33328910 TAAAAA-A
1 TAAAAATT
*
33328917 TAAAAACT
1 TAAAAATT
33328925 TAAAAATT
1 TAAAAATT
33328933 TAA
1 TAA
33328936 TATTTAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 6 0.15
7 13 0.32
8 21 0.52
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (8 bp):
TAAAAATT
Found at i:33328942 original size:15 final size:15
Alignment explanation
Indices: 33328881--33328942 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
33328871 TCAAAAAAAA
*
33328881 TAAAAATTTAAAATT
1 TAAAAATTAAAAATT
*
33328896 TAAAAA-TAAAAAGT
1 TAAAAATTAAAAATT
* *
33328910 TAAAAAATAAAAACT
1 TAAAAATTAAAAATT
* *
33328925 TAAAAATTTAATATT
1 TAAAAATTAAAAATT
33328940 TAA
1 TAA
33328943 TATTTTAGTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 12 0.31
15 27 0.69
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
TAAAAATTAAAAATT
Found at i:33329027 original size:18 final size:16
Alignment explanation
Indices: 33329006--33329043 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
33328996 TTCAAAAGAG
33329006 AAAAATAAAAAATATGTT
1 AAAAATAAAAAA-AT-TT
33329024 AAAAATAAAAAAATTT
1 AAAAATAAAAAAATTT
33329040 AAAA
1 AAAA
33329044 TTAATCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 12 0.60
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAAATAAAAAAATTT
Found at i:33329028 original size:26 final size:25
Alignment explanation
Indices: 33328981--33329037 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
33328971 TTCAATATTC
* * *
33328981 AAAATTAAAAAAAATTTCAAAAGAG
1 AAAAATAAAAAAAATTTAAAAAGAA
* *
33329006 AAAAATAAAAAATATGTTAAAAATAA
1 AAAAATAAAAAAAAT-TTAAAAAGAA
33329032 AAAAAT
1 AAAAAT
33329038 TTAAAATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (25 bp):
AAAAATAAAAAAAATTTAAAAAGAA
Found at i:33333525 original size:18 final size:19
Alignment explanation
Indices: 33333504--33333544 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
33333494 TTATTGATAT
33333504 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
33333522 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
33333541 TTTT
1 TTTT
33333545 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:33333989 original size:43 final size:43
Alignment explanation
Indices: 33333796--33333987 Score: 240
Period size: 43 Copynumber: 4.3 Consensus size: 43
33333786 ATTTTATGAC
* *
33333796 CTTTAGCGGCGTTTGTGGGATAAGCGCCACTAAAGGTCATGACCT
1 CTTTAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGGTCACGA--T
* * * * *
33333841 TTAGCTTAGCGGCGCTTGTGGGATAAAACGCCGCTAAAGGTCATGAC
1 CT---TTAGCGGCGTTTGTGGGAT-AAGCGCCGCTAAAGGTCACGAT
33333888 CTTTAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGGTCACGAT
1 CTTTAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGGTCACGAT
* * *
33333931 CTTTAGCGGCATTTTTGGGATAAGCGCCGCTAAAAGTCACGAT
1 CTTTAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGGTCACGAT
33333974 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
33333988 TTTTCAAATA
Statistics
Matches: 129, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
43 72 0.56
44 18 0.14
45 1 0.01
47 1 0.01
48 18 0.14
49 19 0.15
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGGTCACGAT
Found at i:33339479 original size:43 final size:43
Alignment explanation
Indices: 33339422--33339583 Score: 170
Period size: 43 Copynumber: 3.8 Consensus size: 43
33339412 ATCAAGATGT
*
33339422 GATTACATGT-AGACCATGTCTGGGACATTGGCATTG-TATTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGATATT-A
* * * *
33339464 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATC
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGATATTA
* * * *
33339507 GATTTCGTGTAAGACCCTGTCTGGGACAATGGCATCGATATATA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGATAT-TA
* * *
33339551 -ATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCAT
33339584 TGTACGAGCT
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 15 0.15
43 82 0.81
44 4 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATCGATATTA
Found at i:33348296 original size:16 final size:16
Alignment explanation
Indices: 33348268--33348301 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
33348258 CATGCTTCAT
33348268 TATTTATTTTTAATTA
1 TATTTATTTTTAATTA
33348284 TATTT-TTTATTAATTA
1 TATTTATTT-TTAATTA
33348300 TA
1 TA
33348302 GCGAGAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTATTTTTAATTA
Found at i:33349773 original size:33 final size:33
Alignment explanation
Indices: 33349735--33349824 Score: 90
Period size: 41 Copynumber: 2.5 Consensus size: 33
33349725 ACAAAATAAG
*
33349735 AATGTAGTCATTTTAATAGATACACATAATACA
1 AATGTAATCATTTTAATAGATACACATAATACA
33349768 AATGTAATCATATTAACATATTAATAGATACACATAATACA
1 AATGTAATC--A-T----T-TTAATAGATACACATAATACA
*
33349809 AATGTAATCATATTAA
1 AATGTAATCATTTTAA
33349825 CATATATACA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
33 12 0.26
35 1 0.02
36 1 0.02
38 1 0.02
39 1 0.02
40 1 0.02
41 30 0.64
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (33 bp):
AATGTAATCATTTTAATAGATACACATAATACA
Found at i:33349794 original size:41 final size:41
Alignment explanation
Indices: 33349747--33349829 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
33349737 TGTAGTCATT
33349747 TTAATAGATACACATAATACAAATGTAATCATATTAACATA
1 TTAATAGATACACATAATACAAATGTAATCATATTAACATA
33349788 TTAATAGATACACATAATACAAATGTAATCATATTAACATA
1 TTAATAGATACACATAATACAAATGTAATCATATTAACATA
33349829 T
1 T
33349830 ATACAGAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.33
Consensus pattern (41 bp):
TTAATAGATACACATAATACAAATGTAATCATATTAACATA
Found at i:33351922 original size:31 final size:31
Alignment explanation
Indices: 33351886--33351949 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
33351876 CTCTACTAAC
33351886 TTTTGACTTTTAACAAGTATTCTGAATGGTT
1 TTTTGACTTTTAACAAGTATTCTGAATGGTT
33351917 TTTTGACTTTTAACAAGTATTCTGAATGGTT
1 TTTTGACTTTTAACAAGTATTCTGAATGGTT
33351948 TT
1 TT
33351950 GTAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (31 bp):
TTTTGACTTTTAACAAGTATTCTGAATGGTT
Found at i:33355030 original size:10 final size:10
Alignment explanation
Indices: 33355005--33355054 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
33354995 TAATTTTAGG
33355005 ATTTAT-TTT
1 ATTTATCTTT
33355014 CATTTATCTTT
1 -ATTTATCTTT
* *
33355025 AATTATCTAT
1 ATTTATCTTT
33355035 ATTTAT-TTGT
1 ATTTATCTT-T
33355045 ATTTATCTTT
1 ATTTATCTTT
33355055 TAGAATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 1 0.03
10 27 0.82
11 5 0.15
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.66
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:33358881 original size:17 final size:18
Alignment explanation
Indices: 33358859--33358898 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
33358849 TCTGCATTGA
33358859 TTACAAGAAGTTGAATT-
1 TTACAAGAAGTTGAATTC
33358876 TTACAAGAAGTTGAATTC
1 TTACAAGAAGTTGAATTC
33358894 TTACA
1 TTACA
33358899 CTAGAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (18 bp):
TTACAAGAAGTTGAATTC
Found at i:33361329 original size:10 final size:10
Alignment explanation
Indices: 33361314--33361374 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
33361304 TAATTTTAGG
33361314 ATTTAT-TTT
1 ATTTATCTTT
33361323 CATTTATCTTT
1 -ATTTATCTTT
33361334 ATTTATCTTT
1 ATTTATCTTT
*
33361344 AATTATCTTT
1 ATTTATCTTT
*
33361354 ATTTATTTATT
1 ATTTATCT-TT
33361365 ATTTATCTTT
1 ATTTATCTTT
33361375 TAGAATTTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
10 33 0.73
11 12 0.27
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:33367143 original size:28 final size:28
Alignment explanation
Indices: 33367103--33367162 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
33367093 TGTAACATAA
33367103 CTCAAAGACATACTCACCAATGGCTTAT
1 CTCAAAGACATACTCACCAATGGCTTAT
33367131 CTCAAAGACATACTCACCAATGGCTTAT
1 CTCAAAGACATACTCACCAATGGCTTAT
33367159 CTCA
1 CTCA
33367163 TTGAGATCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (28 bp):
CTCAAAGACATACTCACCAATGGCTTAT
Found at i:33370988 original size:7 final size:7
Alignment explanation
Indices: 33370976--33371063 Score: 151
Period size: 7 Copynumber: 12.7 Consensus size: 7
33370966 GAGGCAACCC
33370976 AATTTTT
1 AATTTTT
33370983 AATTTTT
1 AATTTTT
33370990 -ATTTTT
1 AATTTTT
*
33370996 ATTTTTT
1 AATTTTT
33371003 AATTTTT
1 AATTTTT
*
33371010 ATTTTTT
1 AATTTTT
33371017 AATTTTT
1 AATTTTT
33371024 AATTTTT
1 AATTTTT
33371031 AATTTTT
1 AATTTTT
33371038 AATTTTT
1 AATTTTT
33371045 AATTTTT
1 AATTTTT
33371052 AATTTTT
1 AATTTTT
33371059 AATTT
1 AATTT
33371064 ATTTTATTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
6 6 0.08
7 70 0.92
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
AATTTTT
Found at i:33371000 original size:5 final size:6
Alignment explanation
Indices: 33370977--33371105 Score: 84
Period size: 7 Copynumber: 19.5 Consensus size: 6
33370967 AGGCAACCCA
33370977 ATTTTT AATTTTT ATTTTT ATTTTTT AATTTTT ATTTTTT AATTTTT AATTTTT
1 ATTTTT -ATTTTT ATTTTT A-TTTTT -ATTTTT A-TTTTT -ATTTTT -ATTTTT
* *
33371031 AATTTTT AATTTTT AATTTTT AATTTTT A-ATTT A-TTTT ATTTTAT TTATTTT
1 -ATTTTT -ATTTTT -ATTTTT -ATTTTT ATTTTT ATTTTT ATTTT-T AT-TTTT
33371083 ATCTTATT A-TTTT ATTATTT ATT
1 AT-TT-TT ATTTTT ATT-TTT ATT
33371106 ATTTCCAGAT
Statistics
Matches: 107, Mismatches: 5, Indels: 20
0.81 0.04 0.15
Matches are distributed among these distances:
5 11 0.10
6 15 0.14
7 73 0.68
8 8 0.07
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:33371002 original size:14 final size:14
Alignment explanation
Indices: 33370985--33371109 Score: 94
Period size: 14 Copynumber: 8.6 Consensus size: 14
33370975 CAATTTTTAA
33370985 TTTTTATTTTTATT
1 TTTTTATTTTTATT
*
33370999 TTTTAATTTTTATT
1 TTTTTATTTTTATT
* *
33371013 TTTTAATTTTTAAT
1 TTTTTATTTTTATT
* *
33371027 TTTTAATTTTTAAT
1 TTTTTATTTTTATT
*
33371041 TTTTAATTTTTAATT
1 TTTTTATTTTT-ATT
33371056 TTTAATT-TATTTTATT
1 TTT--TTAT-TTTTATT
*
33371072 TTATTTA-TTTTATC
1 TT-TTTATTTTTATT
*
33371086 TTATTA-TTTTATT
1 TTTTTATTTTTATT
33371099 ATTTATTATTT
1 -TTT-TTATTT
33371110 CCAGATATGA
Statistics
Matches: 94, Mismatches: 8, Indels: 16
0.80 0.07 0.14
Matches are distributed among these distances:
13 9 0.10
14 61 0.65
15 10 0.11
16 8 0.09
17 6 0.06
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:33371009 original size:21 final size:21
Alignment explanation
Indices: 33370978--33371109 Score: 110
Period size: 21 Copynumber: 6.1 Consensus size: 21
33370968 GGCAACCCAA
33370978 TTTTTAA-TTTTTATTTTTAT
1 TTTTTAATTTTTTATTTTTAT
*
33370998 TTTTTAA-TTTTTATTTTTTAA
1 TTTTTAATTTTTTA-TTTTTAT
* *
33371019 TTTTTAATTTTTAATTTTTAA
1 TTTTTAATTTTTTATTTTTAT
*
33371040 TTTTTAATTTTTAATTTTTAAT
1 TTTTTAATTTTTTATTTTT-AT
*
33371062 TTATTTTATTTTATT-TATTTTAT
1 TT-TTTAATTTT-TTAT-TTTTAT
*
33371085 CTTATT-ATTTTATTATTTATTAT
1 -TTTTTAATTTT-TTATTT-TTAT
33371108 TT
1 TT
33371110 CCAGATATGA
Statistics
Matches: 97, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
20 13 0.13
21 39 0.40
22 20 0.21
23 18 0.19
24 7 0.07
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTAATTTTTTATTTTTAT
Found at i:33372657 original size:101 final size:98
Alignment explanation
Indices: 33372493--33372723 Score: 284
Period size: 100 Copynumber: 2.3 Consensus size: 98
33372483 CTGGTACGCA
* *
33372493 TAGTAGCCTGCACTTAG-ACTACACATGTGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
* *
33372557 GTACTACACACGTGACCTAACCATCTGACACACG
66 GTACTACACACGCGACC-AACCATCCGACACACG
* * * **
33372591 TAGTAGCCAGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTATGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACATAGTAGCCTGCACT
* * ** **
33372656 TAGTACTACACATGCGGCCAATTATCCGGTACACG
64 TAGTACTACACACGCGACCAACCATCCGACACACG
*
33372691 TAGTAGTCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
33372724 TCACAATAGA
Statistics
Matches: 112, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
98 16 0.14
99 13 0.12
100 43 0.38
101 40 0.36
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCAACCATCCGACACACG
Found at i:33372702 original size:49 final size:49
Alignment explanation
Indices: 33372493--33372723 Score: 284
Period size: 49 Copynumber: 4.7 Consensus size: 49
33372483 CTGGTACGCA
*
33372493 TAGTAGCCTGCACTTAG-ACTACACATGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
** * **
33372541 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGACACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * * ** *
33372591 TAGTAGCCAGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACG
* * *
33372642 TAGTAGCCTGCACTTAGTACTACACATGCGGCCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
*
33372691 TAGTAGTCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
33372724 TCACAATAGA
Statistics
Matches: 150, Mismatches: 29, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
48 17 0.11
49 53 0.35
50 46 0.31
51 34 0.23
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:33372982 original size:27 final size:27
Alignment explanation
Indices: 33372942--33372995 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
33372932 AGGTACAACC
* *
33372942 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
33372969 CATGTAACAATAATTTGTCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
33372996 TCCCATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:33374223 original size:22 final size:22
Alignment explanation
Indices: 33374198--33374240 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
33374188 CCTTGGACCA
*
33374198 CCCTAATCCTGCAGCCAAACAG
1 CCCTAATCCTGCAACCAAACAG
* *
33374220 CCCTACTCCTGGAACCAAACA
1 CCCTAATCCTGCAACCAAACA
33374241 CCACCTTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.42, G:0.12, T:0.14
Consensus pattern (22 bp):
CCCTAATCCTGCAACCAAACAG
Found at i:33374577 original size:11 final size:12
Alignment explanation
Indices: 33374552--33374585 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
33374542 GTCGTTTTAT
*
33374552 CTGTTGCTTTTA
1 CTGTTGCTGTTA
33374564 CTGTTG-TGTTA
1 CTGTTGCTGTTA
33374575 CTGTTGCTGTT
1 CTGTTGCTGTT
33374586 GCCTTATGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.06, C:0.15, G:0.24, T:0.56
Consensus pattern (12 bp):
CTGTTGCTGTTA
Found at i:33376089 original size:26 final size:26
Alignment explanation
Indices: 33376064--33376121 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
33376054 TTTATTTAAT
*
33376064 TAAAT-AAAAAAATTTAAAAATATAA
1 TAAATCAAAAAAATTTAAAAACATAA
* *
33376089 TAAATCAAATATATTTAAAAACATAA
1 TAAATCAAAAAAATTTAAAAACATAA
33376115 -AAA-CAAA
1 TAAATCAAA
33376122 TATTAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 8 0.28
26 17 0.59
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (26 bp):
TAAATCAAAAAAATTTAAAAACATAA
Found at i:33376144 original size:21 final size:20
Alignment explanation
Indices: 33376103--33376150 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
33376093 TCAAATATAT
* *
33376103 TTAAAAACATAAAAACAAATA
1 TTAAAAAAATAAAAA-TAATA
33376124 TTAAAACAAATAAAAATAATA
1 TTAAAA-AAATAAAAATAATA
*
33376145 CTAAAA
1 TTAAAA
33376151 TAATTCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TTAAAAAAATAAAAATAATA
Found at i:33376227 original size:15 final size:16
Alignment explanation
Indices: 33376197--33376229 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
33376187 AAATAGTTAT
33376197 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
33376214 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
33376229 A
1 A
33376230 AAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:33376273 original size:15 final size:16
Alignment explanation
Indices: 33376253--33376283 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
33376243 AATATATAAT
33376253 TCGGGCCGGGC-CGGG
1 TCGGGCCGGGCTCGGG
33376268 TCGGGCCGGGCTCGGG
1 TCGGGCCGGGCTCGGG
33376284 CCAAAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.00, C:0.32, G:0.58, T:0.10
Consensus pattern (16 bp):
TCGGGCCGGGCTCGGG
Found at i:33376502 original size:10 final size:10
Alignment explanation
Indices: 33376487--33376539 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
33376477 TAATTTTAGG
33376487 ATTTATTTTT
1 ATTTATTTTT
*
33376497 ATTTATCTTT
1 ATTTATTTTT
*
33376507 ATTTATCTTT
1 ATTTATTTTT
*
33376517 AATTATTTATT
1 ATTTATTT-TT
33376528 ATTTATCTTTT
1 ATTTAT-TTTT
33376539 A
1 A
33376540 GAATTTCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
10 25 0.68
11 10 0.27
12 2 0.05
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:33376545 original size:21 final size:22
Alignment explanation
Indices: 33376505--33376550 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
33376495 TTATTTATCT
**
33376505 TTATTTATCTTTAATTATTT-A
1 TTATTTATCTTTAAGAATTTCA
*
33376526 TTATTTATCTTTTAGAATTTCA
1 TTATTTATCTTTAAGAATTTCA
33376548 TTA
1 TTA
33376551 GGAATAGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTTATCTTTAAGAATTTCA
Found at i:33377853 original size:6 final size:6
Alignment explanation
Indices: 33377842--33377925 Score: 68
Period size: 6 Copynumber: 14.0 Consensus size: 6
33377832 TTGCAACTCA
* * *
33377842 ATTTTT ATTTTT ATTTTT ATTTTT ATCTTT ATTAATT -TTTTT -GTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT-TTT ATTTTT ATTTTT
*
33377889 ATTCTT A-TTTT A-TTTT ATTATTT ACTATTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATT-TTT A-T-TTTT ATTTTT
33377926 GAATGTTAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
5 15 0.23
6 36 0.56
7 7 0.11
8 5 0.08
9 1 0.02
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:33377889 original size:29 final size:27
Alignment explanation
Indices: 33377848--33377902 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
33377838 CTCAATTTTT
*
33377848 ATTTTTATTTTTATTTTTATCTTTATTA
1 ATTTTTATTTTTATTCTTAT-TTTATTA
*
33377876 ATTTTTTTGTTTTATTCTTATTTTATT
1 ATTTTTAT-TTTTATTCTTATTTTATT
33377903 TTATTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (27 bp):
ATTTTTATTTTTATTCTTATTTTATTA
Found at i:33390204 original size:96 final size:95
Alignment explanation
Indices: 33390040--33390226 Score: 257
Period size: 96 Copynumber: 2.0 Consensus size: 95
33390030 AATTAATTTT
* * *
33390040 TAAGAATATGTTGGGCTAAGTAATCGGGGTGAGGTGCTTGGCTGTAATCTTTTTTCACGTCAAAA
1 TAAGAATATGTTGGGCTAAGTAACCGGGGTGAGGTGCTTGGCTGTAATCTCTCTTCACGTCAAAA
* *
33390105 GGTTCGATATGTTCTTAAGAAAAATAAAAAC
66 GGTTCCATATATTCTTAA-AAAAATAAAAAC
* * * * * **
33390136 TAAGAGTATGTTGGGCTGAGTAACCGGGGTGGGGTGCTTGGTTGTCATCTCTCTTCGTGTCAAAA
1 TAAGAATATGTTGGGCTAAGTAACCGGGGTGAGGTGCTTGGCTGTAATCTCTCTTCACGTCAAAA
33390201 GGTTCCATATATTCTTAAAAAAATAA
66 GGTTCCATATATTCTTAAAAAAATAA
33390227 TAATTAATTA
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
95 8 0.10
96 71 0.90
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (95 bp):
TAAGAATATGTTGGGCTAAGTAACCGGGGTGAGGTGCTTGGCTGTAATCTCTCTTCACGTCAAAA
GGTTCCATATATTCTTAAAAAAATAAAAAC
Found at i:33390893 original size:10 final size:10
Alignment explanation
Indices: 33390878--33390925 Score: 69
Period size: 10 Copynumber: 4.8 Consensus size: 10
33390868 ATTTTAGGAT
33390878 TTATCTTTAA
1 TTATCTTTAA
33390888 TTATCTTTAA
1 TTATCTTTAA
*
33390898 TTATCTTTAT
1 TTATCTTTAA
* *
33390908 TTATCTGTAT
1 TTATCTTTAA
33390918 TTATCTTT
1 TTATCTTT
33390926 TAGAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.65
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:33391174 original size:38 final size:38
Alignment explanation
Indices: 33391132--33391212 Score: 121
Period size: 39 Copynumber: 2.2 Consensus size: 38
33391122 AATTTTCAAA
33391132 TTCCA-ATCAAAACTTTTAATTCTATTTTTATTTTATTT
1 TTCCAGATCAAAACTTTTAATTCTATTTTT-TTTTATTT
* *
33391170 TTCCAGATCAAAACTTTTAATTCTGTTTTTTTTT-CTT
1 TTCCAGATCAAAACTTTTAATTCTATTTTTTTTTATTT
33391207 TTCCAG
1 TTCCAG
33391213 GTACGCAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
37 8 0.20
38 9 0.22
39 23 0.57
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.56
Consensus pattern (38 bp):
TTCCAGATCAAAACTTTTAATTCTATTTTTTTTTATTT
Found at i:33395783 original size:14 final size:14
Alignment explanation
Indices: 33395764--33395794 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
33395754 ACTTATTTTG
33395764 AAAAATAAAATAAT
1 AAAAATAAAATAAT
33395778 AAAAATAAAATAAT
1 AAAAATAAAATAAT
33395792 AAA
1 AAA
33395795 TAAGAAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAAATAAAATAAT
Found at i:33397594 original size:7 final size:7
Alignment explanation
Indices: 33397570--33397605 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
33397560 GTCCGGATTT
33397570 ATTTT-A
1 ATTTTCA
33397576 ATTTTCA
1 ATTTTCA
33397583 A--TTCA
1 ATTTTCA
33397588 ATTTTCA
1 ATTTTCA
33397595 ATTTTCA
1 ATTTTCA
33397602 ATTT
1 ATTT
33397606 ATTACTTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.19
6 5 0.19
7 17 0.63
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTTCA
Found at i:33407496 original size:18 final size:18
Alignment explanation
Indices: 33407458--33407490 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33407448 TATTTTTAGG
33407458 AATTAAATATTATATTAA
1 AATTAAATATTATATTAA
33407476 AATTAAA-ATT-TATTA
1 AATTAAATATTATATTA
33407491 TTAAATATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTAAATATTATATTAA
Found at i:33408829 original size:3 final size:3
Alignment explanation
Indices: 33408821--33408863 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
33408811 ATCTCCATTT
* * *
33408821 TTC TTC TTC TTC TTA TTC -TC CTC TTC CTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
33408864 TTGTATAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:33408851 original size:20 final size:20
Alignment explanation
Indices: 33408822--33408859 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33408812 TCTCCATTTT
*
33408822 TCTTCTTCTTCTTATTCTCC
1 TCTTCCTCTTCTTATTCTCC
*
33408842 TCTTCCTCTTCTTCTTCT
1 TCTTCCTCTTCTTATTCT
33408860 TCTTTTGTAT
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:0.03, C:0.37, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCCTCTTCTTATTCTCC
Found at i:33411119 original size:21 final size:21
Alignment explanation
Indices: 33411093--33411134 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
33411083 ATGGAAATAT
33411093 CGGTTCAAAGTAAGAGATTAG
1 CGGTTCAAAGTAAGAGATTAG
33411114 CGGTTCAAAGTAAGAGATTAG
1 CGGTTCAAAGTAAGAGATTAG
33411135 GTTGATTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.29, T:0.24
Consensus pattern (21 bp):
CGGTTCAAAGTAAGAGATTAG
Found at i:33413992 original size:20 final size:18
Alignment explanation
Indices: 33413950--33413988 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
33413940 TATATATAAC
*
33413950 ATTATATATTAACTTAAA
1 ATTATATATTAAATTAAA
33413968 ATTATATATTAAATTAAA
1 ATTATATATTAAATTAAA
33413986 ATT
1 ATT
33413989 TTATGTATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTATATATTAAATTAAA
Found at i:33414038 original size:47 final size:47
Alignment explanation
Indices: 33413982--33414075 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
33413972 TATATTAAAT
33413982 TAAAATTTTATGTATAGTTTTAATATTTATTTCTTAATTCAATCTAG
1 TAAAATTTTATGTATAGTTTTAATATTTATTTCTTAATTCAATCTAG
33414029 TAAAATTTTATGTATAGTTTTAATATTTATTTCTTAATTCAATCTAG
1 TAAAATTTTATGTATAGTTTTAATATTTATTTCTTAATTCAATCTAG
33414076 CAACAAGACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (47 bp):
TAAAATTTTATGTATAGTTTTAATATTTATTTCTTAATTCAATCTAG
Found at i:33415195 original size:19 final size:19
Alignment explanation
Indices: 33415173--33415213 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
33415163 TATATTATTA
* *
33415173 ATGTAAATATGATTCTAGC
1 ATGTAAATATAATTCGAGC
*
33415192 ATGTAAATTTAATTCGAGC
1 ATGTAAATATAATTCGAGC
33415211 ATG
1 ATG
33415214 ATTCTAGCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (19 bp):
ATGTAAATATAATTCGAGC
Done.