Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 24 of 135
Found at i:10000363 original size:21 final size:21
Alignment explanation
Indices: 10000339--10000396 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
10000329 TGGGTTCAAA
10000339 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
10000360 TGGGTTTGGTTTAAATGAATT
1 TGGGTTTGGTTTAAATGAATT
10000381 TGGGTTTGGTTTAAAT
1 TGGGTTTGGTTTAAAT
10000397 AGGATTTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.48
Consensus pattern (21 bp):
TGGGTTTGGTTTAAATGAATT
Found at i:10000808 original size:18 final size:16
Alignment explanation
Indices: 10000783--10000829 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 16
10000773 GAAGAAAAAT
10000783 AGAAAAGAAAAGAATG
1 AGAAAAGAAAAGAATG
*
10000799 AGAAATAAGAAATGAATG
1 AG-AA-AAGAAAAGAATG
10000817 AGAAAAGAAAAGA
1 AGAAAAGAAAAGA
10000830 GAAAGGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 10 0.37
17 4 0.15
18 13 0.48
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.09
Consensus pattern (16 bp):
AGAAAAGAAAAGAATG
Found at i:10007612 original size:13 final size:13
Alignment explanation
Indices: 10007594--10007619 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10007584 TTTTATTTAA
10007594 CCTTATAGAATTT
1 CCTTATAGAATTT
10007607 CCTTATAGAATTT
1 CCTTATAGAATTT
10007620 AGAACTGCTG
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:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
CCTTATAGAATTT
Found at i:10009861 original size:14 final size:14
Alignment explanation
Indices: 10009842--10009870 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10009832 ACAGATGGAT
10009842 TCGTATAATTCTTA
1 TCGTATAATTCTTA
10009856 TCGTATAATTCTTA
1 TCGTATAATTCTTA
10009870 T
1 T
10009871 ATATATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TCGTATAATTCTTA
Found at i:10014103 original size:20 final size:21
Alignment explanation
Indices: 10014037--10014105 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
10014027 TCACTTCGTT
10014037 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
10014058 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
* * *
10014079 TCTTTTTGTCTAACTCACTTC
1 TCTTTTTGTCCAAGTTACTTC
10014100 -CTTTTT
1 TCTTTTT
10014106 TCTTTGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:10016504 original size:18 final size:18
Alignment explanation
Indices: 10016471--10016564 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
10016461 AAGGTTTTCT
10016471 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
10016486 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
*
10016504 TATTGATGCTAGTGACGA
1 TATTGATGATAGTGACGA
* *
10016522 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
*
10016540 TATTGATGATAGTGACGC
1 TATTGATGATAGTGACGA
10016558 TATTGAT
1 TATTGAT
10016565 CGTGACCTTG
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:10024826 original size:14 final size:14
Alignment explanation
Indices: 10024807--10024834 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10024797 TATATTAGTA
10024807 TTTTCTATTCTATT
1 TTTTCTATTCTATT
10024821 TTTTCTATTCTATT
1 TTTTCTATTCTATT
10024835 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:10024846 original size:5 final size:6
Alignment explanation
Indices: 10024831--10024881 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
10024821 TTTTCTATTC
* *
10024831 TATTAG TATTAG -ATTAG TATT-C TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
10024875 TATTAG T
1 TATTAG T
10024882 TAGTGATCCC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 19 0.47
6 21 0.52
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:10024846 original size:11 final size:12
Alignment explanation
Indices: 10024831--10024881 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 12
10024821 TTTTCTATTC
10024831 TATTAGTATTAG
1 TATTAGTATTAG
*
10024843 -ATTAGTATT-C
1 TATTAGTATTAG
*
10024853 TATT-CTATTAG
1 TATTAGTATTAG
10024864 TATTAG-ATTAG
1 TATTAGTATTAG
10024875 TATTAGT
1 TATTAGT
10024882 TAGTGATCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
10 4 0.13
11 27 0.87
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (12 bp):
TATTAGTATTAG
Found at i:10024853 original size:27 final size:27
Alignment explanation
Indices: 10024823--10024878 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
10024813 ATTCTATTTT
10024823 TTCTATTCTATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTAGTA
10024850 TTCTATTCTATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTAGTA
10024877 TT
1 TT
10024879 AGTTAGTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54
Consensus pattern (27 bp):
TTCTATTCTATTAGTATTAGATTAGTA
Found at i:10033098 original size:32 final size:32
Alignment explanation
Indices: 10033057--10033118 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
10033047 CATCTATTTT
10033057 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
10033089 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
10033119 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:10040421 original size:13 final size:13
Alignment explanation
Indices: 10040403--10040430 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
10040393 TGAAAATTCG
10040403 TTAATGGTACATT
1 TTAATGGTACATT
10040416 TTAATGGTACATT
1 TTAATGGTACATT
10040429 TT
1 TT
10040431 CCCCTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (13 bp):
TTAATGGTACATT
Found at i:10046663 original size:10 final size:10
Alignment explanation
Indices: 10046641--10046670 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
10046631 GTTGAATAAG
10046641 TAATATT-AA
1 TAATATTAAA
10046650 TAATATTAAA
1 TAATATTAAA
10046660 TAATATTAAA
1 TAATATTAAA
10046670 T
1 T
10046671 TATAAGATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.35
10 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TAATATTAAA
Found at i:10060291 original size:27 final size:27
Alignment explanation
Indices: 10060253--10060308 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
10060243 ATCACTAACT
10060253 AATACTAATCTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
10060280 AATACTAATCTAATACTAATAGAATAG
1 AATACTAATCTAATACTAATAGAATAG
10060307 AA
1 AA
10060309 AAAATAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.29
Consensus pattern (27 bp):
AATACTAATCTAATACTAATAGAATAG
Found at i:10060293 original size:5 final size:6
Alignment explanation
Indices: 10060250--10060300 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
10060240 GGGATCACTA
* *
10060250 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT A-GAAT ACTAAT -CTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
10060294 ACTAAT A
1 ACTAAT A
10060301 GAATAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 19 0.47
6 21 0.52
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (6 bp):
ACTAAT
Found at i:10060316 original size:14 final size:14
Alignment explanation
Indices: 10060297--10060324 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10060287 ATCTAATACT
10060297 AATAGAATAGAAAA
1 AATAGAATAGAAAA
10060311 AATAGAATAGAAAA
1 AATAGAATAGAAAA
10060325 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:10068646 original size:18 final size:18
Alignment explanation
Indices: 10068567--10068660 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
10068557 CAAGGTCACG
*
10068567 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
10068585 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
*
10068603 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
10068621 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
10068639 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
10068654 ATCAATA
1 ATCAATA
10068661 AGAAAACCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (18 bp):
ATCAATATCGTCACTATC
Found at i:10068647 original size:9 final size:9
Alignment explanation
Indices: 10068567--10068647 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
10068557 CAAGGTCACG
*
10068567 ATCAATAGC
1 ATCAATATC
* *
10068576 GTCACTATC
1 ATCAATATC
*
10068585 ATCAATAGC
1 ATCAATATC
* * *
10068594 GTCACTAGC
1 ATCAATATC
10068603 ATCAATATC
1 ATCAATATC
* * *
10068612 GTCACTAGC
1 ATCAATATC
10068621 ATCAATATC
1 ATCAATATC
* *
10068630 GTCACTATC
1 ATCAATATC
10068639 ATCAATATC
1 ATCAATATC
10068648 GATATCATCA
Statistics
Matches: 51, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (9 bp):
ATCAATATC
Found at i:10071056 original size:21 final size:21
Alignment explanation
Indices: 10071026--10071114 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
10071016 CTCACAAAGA
* *
10071026 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
10071046 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
10071067 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
10071088 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
10071112 AAA
1 AAA
10071115 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:10071107 original size:24 final size:21
Alignment explanation
Indices: 10071026--10071094 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
10071016 CTCACAAAGA
* * *
10071026 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
10071046 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
10071067 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
10071088 AAAAAGA
1 AAAAAGA
10071095 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:10075280 original size:14 final size:14
Alignment explanation
Indices: 10075261--10075289 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10075251 TACAATATAT
10075261 ATAAGAATTATACG
1 ATAAGAATTATACG
10075275 ATAAGAATTATACG
1 ATAAGAATTATACG
10075289 A
1 A
10075290 ATCCATCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:10077531 original size:13 final size:13
Alignment explanation
Indices: 10077513--10077538 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10077503 CAGCAGTTCT
10077513 AAATTCTATAAGG
1 AAATTCTATAAGG
10077526 AAATTCTATAAGG
1 AAATTCTATAAGG
10077539 TTAAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AAATTCTATAAGG
Found at i:10089042 original size:12 final size:12
Alignment explanation
Indices: 10089027--10089051 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10089017 TTTCTATATT
10089027 ATAGATTATAGG
1 ATAGATTATAGG
10089039 ATAGATTATAGG
1 ATAGATTATAGG
10089051 A
1 A
10089052 AAACGGGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
ATAGATTATAGG
Found at i:10089847 original size:12 final size:12
Alignment explanation
Indices: 10089830--10089854 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10089820 CAGAGGCTAT
10089830 TAACAATATTTA
1 TAACAATATTTA
10089842 TAACAATATTTA
1 TAACAATATTTA
10089854 T
1 T
10089855 GTTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:10092489 original size:21 final size:20
Alignment explanation
Indices: 10092460--10092498 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
10092450 ACGCCTACGA
10092460 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
10092480 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
10092499 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:10092654 original size:18 final size:15
Alignment explanation
Indices: 10092615--10092649 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
10092605 ATTTGGTTTG
10092615 TTTATTTTATTATTT
1 TTTATTTTATTATTT
*
10092630 TTTATTTTATTATTA
1 TTTATTTTATTATTT
10092645 TTTAT
1 TTTAT
10092650 CATTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTTATTATTT
Found at i:10092686 original size:13 final size:13
Alignment explanation
Indices: 10092656--10092754 Score: 55
Period size: 11 Copynumber: 8.6 Consensus size: 13
10092646 TTATCATTTA
*
10092656 AATATATATATTT
1 AATATATATAATT
10092669 AATATATATAA--
1 AATATATATAATT
*
10092680 ATTATATA-AATT
1 AATATATATAATT
10092692 AA-A-ATAT-ATT
1 AATATATATAATT
*
10092702 AATA-ATATAGAAT
1 AATATATATA-ATT
10092715 AATATATA-AA-T
1 AATATATATAATT
10092726 -A-ATAT-TAA-T
1 AATATATATAATT
*
10092735 AATATATA-AATA
1 AATATATATAATT
10092747 AATATATA
1 AATATATA
10092755 AAGAAAATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
9 7 0.10
10 12 0.17
11 20 0.29
12 10 0.14
13 17 0.25
14 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (13 bp):
AATATATATAATT
Found at i:10092693 original size:23 final size:22
Alignment explanation
Indices: 10092654--10092756 Score: 77
Period size: 23 Copynumber: 4.6 Consensus size: 22
10092644 ATTTATCATT
**
10092654 TAAATATATATATTTAATATATA
1 TAAAT-TATATAAATAATATATA
*
10092677 TAAATTATATAAATTAAAATATA
1 TAAATTATATAAA-TAATATATA
* *
10092700 TTAATAATATAGAAT-A-ATATA
1 TAAATTATATA-AATAATATATA
* *
10092721 TAAATAATATTAATAATATATAAA
1 TAAATTATATAAATAATATAT--A
10092745 TAAA-TATATAAA
1 TAAATTATATAAA
10092757 GAAAATATGC
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
20 3 0.05
21 15 0.23
22 11 0.17
23 29 0.45
24 7 0.11
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (22 bp):
TAAATTATATAAATAATATATA
Found at i:10092709 original size:9 final size:9
Alignment explanation
Indices: 10092676--10092739 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
10092666 TTTAATATAT
10092676 ATAA-ATTA
1 ATAATATTA
10092684 TATAA-ATTA
1 -ATAATATTA
*
10092693 AAATATATTA
1 ATA-ATATTA
*
10092703 ATAATATAGA
1 ATAATAT-TA
10092713 ATAATATATAA
1 ATAATAT-T-A
10092724 ATAATATTA
1 ATAATATTA
10092733 ATAATAT
1 ATAATAT
10092740 ATAAATAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
8 2 0.04
9 21 0.45
10 16 0.34
11 8 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (9 bp):
ATAATATTA
Found at i:10092718 original size:21 final size:21
Alignment explanation
Indices: 10092672--10092752 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 21
10092662 TATATTTAAT
*
10092672 ATATATAAATTATATA-AATTAAA
1 ATATATAAATAATATAGAA-T--A
*
10092695 ATATATTAATAATATAGAATA
1 ATATATAAATAATATAGAATA
*
10092716 ATATATAAATAATAT-TAATA
1 ATATATAAATAATATAGAATA
10092736 ATATATAAATAAATATA
1 ATATATAAAT-AATATA
10092753 TAAAGAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
20 14 0.27
21 20 0.39
23 15 0.29
24 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (21 bp):
ATATATAAATAATATAGAATA
Found at i:10092733 original size:30 final size:31
Alignment explanation
Indices: 10092654--10092756 Score: 101
Period size: 30 Copynumber: 3.4 Consensus size: 31
10092644 ATTTATCATT
10092654 TAAATATAT--ATAT-TTAAT-ATATATAAA
1 TAAATATATAAATATATTAATAATATATAAA
* * *
10092681 TTATATAAATTAAAATATATTAATAATATA-GAA
1 -TAAATATA-T-AAATATATTAATAATATATAAA
10092714 T-AATATATAAATAATATTAATAATATATAAA
1 TAAATATATAAAT-ATATTAATAATATATAAA
10092745 TAAATATATAAA
1 TAAATATATAAA
10092757 GAAAATATGC
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
28 6 0.10
29 5 0.08
30 15 0.25
31 7 0.12
32 15 0.25
33 7 0.12
34 5 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
TAAATATATAAATATATTAATAATATATAAA
Found at i:10093219 original size:13 final size:13
Alignment explanation
Indices: 10093203--10093227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10093193 GATTTCGTTG
10093203 AAATCAATATAGT
1 AAATCAATATAGT
10093216 AAATCAATATAG
1 AAATCAATATAG
10093228 ATTTATAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (13 bp):
AAATCAATATAGT
Found at i:10094539 original size:23 final size:23
Alignment explanation
Indices: 10094510--10094554 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
10094500 GGGTCAGTCA
10094510 AAAAAAGGTATGTTAATTAATCC
1 AAAAAAGGTATGTTAATTAATCC
10094533 AAAAAAGGTATGTTAATTAATC
1 AAAAAAGGTATGTTAATTAATC
10094555 AAAGGTCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (23 bp):
AAAAAAGGTATGTTAATTAATCC
Found at i:10101155 original size:12 final size:12
Alignment explanation
Indices: 10101138--10101164 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
10101128 CTAGTACTTT
10101138 TTTGATATGAAC
1 TTTGATATGAAC
10101150 TTTGATATGAAC
1 TTTGATATGAAC
10101162 TTT
1 TTT
10101165 TAGAAGGAAT
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:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (12 bp):
TTTGATATGAAC
Found at i:10101682 original size:17 final size:17
Alignment explanation
Indices: 10101662--10101696 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10101652 TCCGTATATT
*
10101662 ATACTAATTATATCTAA
1 ATACTAAGTATATCTAA
10101679 ATACTAAGTATATCTAA
1 ATACTAAGTATATCTAA
10101696 A
1 A
10101697 CGAGTCTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (17 bp):
ATACTAAGTATATCTAA
Found at i:10106252 original size:21 final size:21
Alignment explanation
Indices: 10106226--10106267 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
10106216 ATATATTAGA
10106226 AATAAAATATATAAAAAAATT
1 AATAAAATATATAAAAAAATT
*
10106247 AATAAAATATATAAATAAATT
1 AATAAAATATATAAAAAAATT
10106268 CTAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AATAAAATATATAAAAAAATT
Found at i:10106266 original size:12 final size:12
Alignment explanation
Indices: 10106225--10106309 Score: 51
Period size: 12 Copynumber: 7.4 Consensus size: 12
10106215 AATATATTAG
10106225 AAATAAAATATAT
1 AAAT-AAATATAT
10106238 AAA-AAA-AT-T
1 AAATAAATATAT
10106247 -AATAAAATATAT
1 AAAT-AAATATAT
*
10106259 AAATAAAT-TCT
1 AAATAAATATAT
*
10106270 -AATATATAT-T
1 AAATAAATATAT
*
10106280 AGAATATATATAT
1 A-AATAAATATAT
10106293 -AATAGAATATAT
1 AAATA-AATATAT
10106305 AAATA
1 AAATA
10106310 TATAATAGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 22
0.70 0.04 0.27
Matches are distributed among these distances:
8 2 0.03
9 1 0.02
10 12 0.21
11 12 0.21
12 20 0.34
13 11 0.19
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (12 bp):
AAATAAATATAT
Found at i:10106290 original size:14 final size:15
Alignment explanation
Indices: 10106271--10106316 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
10106261 ATAAATTCTA
10106271 ATATATAT-TAGAAT
1 ATATATATATAGAAT
10106285 ATATATATAATAGAAT
1 ATATATAT-ATAGAAT
* *
10106301 ATATAAATATATAAT
1 ATATATATATAGAAT
10106316 A
1 A
10106317 GAATTAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (15 bp):
ATATATATATAGAAT
Found at i:10106290 original size:16 final size:16
Alignment explanation
Indices: 10106271--10106310 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
10106261 ATAAATTCTA
10106271 ATATATATTAGAATAT
1 ATATATATTAGAATAT
*
10106287 ATATATAATAGAATAT
1 ATATATATTAGAATAT
*
10106303 ATAAATAT
1 ATATATAT
10106311 ATAATAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
ATATATATTAGAATAT
Found at i:10106355 original size:21 final size:21
Alignment explanation
Indices: 10106329--10106372 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
10106319 ATTAATATTC
10106329 TAACATCTAATATAAATTATA
1 TAACATCTAATATAAATTATA
10106350 TAACATCTAATATAAATTATA
1 TAACATCTAATATAAATTATA
10106371 TA
1 TA
10106373 TTATAAGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (21 bp):
TAACATCTAATATAAATTATA
Found at i:10106364 original size:12 final size:12
Alignment explanation
Indices: 10106329--10106364 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10106319 ATTAATATTC
10106329 TAACATCTAATA
1 TAACATCTAATA
10106341 TAA-AT-T-ATA
1 TAACATCTAATA
10106350 TAACATCTAATA
1 TAACATCTAATA
10106362 TAA
1 TAA
10106365 ATTATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
9 6 0.29
10 3 0.14
11 3 0.14
12 9 0.43
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (12 bp):
TAACATCTAATA
Found at i:10109796 original size:15 final size:15
Alignment explanation
Indices: 10109776--10109806 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
10109766 CTGTATCAGT
10109776 AATGAATCAGAGCAC
1 AATGAATCAGAGCAC
10109791 AATGAATCAGAGCAC
1 AATGAATCAGAGCAC
10109806 A
1 A
10109807 CGGAACCGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (15 bp):
AATGAATCAGAGCAC
Found at i:10114802 original size:18 final size:18
Alignment explanation
Indices: 10114779--10114814 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10114769 ATTAGGATGC
10114779 CCCTCCTTCCCCCTTTTT
1 CCCTCCTTCCCCCTTTTT
10114797 CCCTCCTTCCCCCTTTTT
1 CCCTCCTTCCCCCTTTTT
10114815 TCCCCCCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (18 bp):
CCCTCCTTCCCCCTTTTT
Found at i:10114817 original size:11 final size:11
Alignment explanation
Indices: 10114803--10114838 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
10114793 TTTTCCCTCC
*
10114803 TTCCCCCTTTT
1 TTCCCCCTTCT
*
10114814 TTCCCCCCTCT
1 TTCCCCCTTCT
10114825 TTCCCCCTTCT
1 TTCCCCCTTCT
10114836 TTC
1 TTC
10114839 ATTTGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (11 bp):
TTCCCCCTTCT
Found at i:10114855 original size:18 final size:18
Alignment explanation
Indices: 10114832--10114874 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
10114822 TCTTTCCCCC
*
10114832 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
10114850 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
*
10114868 TGCTTTC
1 TTCTTTC
10114875 TTTTTATGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Found at i:10115406 original size:27 final size:28
Alignment explanation
Indices: 10115361--10115417 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
10115351 ATTATTTTTT
*
10115361 TTTATAGTATAATAGCTAGAACTAATTA
1 TTTATAGTATAATAACTAGAACTAATTA
*
10115389 TTTATA-TTTAATAACTAGAACTAATTA
1 TTTATAGTATAATAACTAGAACTAATTA
10115416 TT
1 TT
10115418 CCATTCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (28 bp):
TTTATAGTATAATAACTAGAACTAATTA
Found at i:10115535 original size:15 final size:17
Alignment explanation
Indices: 10115515--10115546 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10115505 TCATTTCATT
10115515 TATAT-AATG-ATAAAA
1 TATATAAATGCATAAAA
10115530 TATATAAATGCATAAAA
1 TATATAAATGCATAAAA
10115547 AGATTTTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (17 bp):
TATATAAATGCATAAAA
Found at i:10115704 original size:17 final size:17
Alignment explanation
Indices: 10115682--10115720 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
10115672 AATTTAGATG
*
10115682 TAAAATATACTA-AAATA
1 TAAAATAAACTAGAAA-A
10115699 TAAAATAAACTAGAAAA
1 TAAAATAAACTAGAAAA
10115716 TAAAA
1 TAAAA
10115721 ATGGAGTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAATAAACTAGAAAA
Found at i:10115822 original size:23 final size:23
Alignment explanation
Indices: 10115779--10115821 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
10115769 TAATAAAATC
10115779 AATATAACATATAATATAAAAGA
1 AATATAACATATAATATAAAAGA
10115802 AATATAAC-TA-AGATATAAAA
1 AATATAACATATA-ATATAAAA
10115822 AAAGATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.05
22 10 0.53
23 8 0.42
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (23 bp):
AATATAACATATAATATAAAAGA
Found at i:10116514 original size:29 final size:28
Alignment explanation
Indices: 10116482--10116612 Score: 83
Period size: 29 Copynumber: 4.5 Consensus size: 28
10116472 TATTCAATTT
*
10116482 TTTTATATATTATTTATATATCTATTTTA
1 TTTTATATATTATTTAT-TATATATTTTA
10116511 TTTTATATA-TATTCTAAATATTTGATATATTTTTA
1 TTTTATATATTA-T-T---TA-TT-ATATA-TTTTA
10116546 TATTTATATATTATTT-TTATATATTATTA
1 T-TTTATATATTATTTATTATATATT-TTA
* *
10116575 TTATATATATT-TTTATT-TCTATTTT-
1 TTTTATATATTATTTATTATATATTTTA
* *
10116600 TTGTATACATTAT
1 TTTTATATATTAT
10116613 ATACAATACA
Statistics
Matches: 84, Mismatches: 5, Indels: 29
0.71 0.04 0.25
Matches are distributed among these distances:
25 9 0.11
26 3 0.04
27 8 0.10
28 15 0.18
29 19 0.23
30 3 0.04
32 1 0.01
33 3 0.04
34 5 0.06
35 7 0.08
36 9 0.11
37 2 0.02
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTATATATTATTTATTATATATTTTA
Found at i:10116556 original size:18 final size:18
Alignment explanation
Indices: 10116492--10116572 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
10116482 TTTTATATAT
*
10116492 TATTTATATATCTATTTTA
1 TATTTATATATAT-TTTTA
**
10116511 T-TTTATATATATTCTAAA
1 TATTTATATATATT-TTTA
*
10116529 TATTT-GATATATTTTTA
1 TATTTATATATATTTTTA
10116546 TATTTATATATTATTTTTA
1 TATTTATATA-TATTTTTA
10116565 TATATTAT
1 TAT-TTAT
10116573 TATTATATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
17 8 0.16
18 23 0.46
19 15 0.30
20 4 0.08
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (18 bp):
TATTTATATATATTTTTA
Found at i:10119217 original size:16 final size:16
Alignment explanation
Indices: 10119196--10119246 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
10119186 AAGAAAGAGC
10119196 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
10119212 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
*
10119228 AAACACGCTAGTAAAT
1 AAATACGCTAGTAAAT
10119244 AAA
1 AAA
10119247 ATACTAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.22
Consensus pattern (16 bp):
AAATACGCTAGTAAAT
Found at i:10120906 original size:15 final size:15
Alignment explanation
Indices: 10120867--10120896 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10120857 ATAACTAAAG
10120867 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
10120882 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
10120897 GAGAGATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (15 bp):
AAAAAATAGATAGAT
Found at i:10122443 original size:11 final size:11
Alignment explanation
Indices: 10122427--10122454 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
10122417 TTTTTAAAAT
10122427 TTTAAAATTAA
1 TTTAAAATTAA
10122438 TTTAAAATTAA
1 TTTAAAATTAA
10122449 TTTAAA
1 TTTAAA
10122455 CTCAAAGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TTTAAAATTAA
Found at i:10123105 original size:67 final size:68
Alignment explanation
Indices: 10122843--10123509 Score: 853
Period size: 68 Copynumber: 9.9 Consensus size: 68
10122833 GAAATGATCC
* *
10122843 TGCTCTTTACTTCAAATTCAGAGAT--A-A--TGTTATCCACTCTTCTTCAATTTCAAGAGGATG
1 TGCTC-TTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
*
10122903 ACAT
65 ACGT
* * * *
10122907 TGCTCTTACTTCAATTTCAAAGATAAACACATGTTATCCACTCTACTTCAATTTCAAGAGGACGA
1 TGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGA
*
10122972 CAT
66 CGT
* * *
10122975 TGCTCTTACTTCAACTTCAGAGATAAAGACGTATTATCCACTCTACTTCAACTTCAAGAGGATGA
1 TGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGA
10123040 CGT
66 CGT
* * * * * *
10123043 TGCTCTTACTTCAATTTCAAATATGAAGACTTG-TATCCACTCAACTTCAATTTCAAGCGGATGA
1 TGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGA
10123107 CGT
66 CGT
*
10123110 TGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTC-AGGGGATTG
1 TGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGA-TG
10123174 ACGT
65 ACGT
* * *
10123178 TGCTCTTACTTCAATTTCAGAGATAAAGACATGTTAT-CACTCTATACTTCAATTTCAAGCGGAC
1 TGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC--TACTTCAATTTCAAGAGGAT
*
10123242 GACAT
64 GACGT
* *
10123247 TGCTCTTACTTCAATTTCAGAGAAAAAGACGTG-TATCCACTCTACTTCAATTTCAAGGGGATGA
1 TGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGA
10123311 CGT
66 CGT
10123314 TGCTCTTACTTCAA-TTCAGAGAT-AAGAC-TCGTTATCCACTCTACTTCAATTTCAAGAGGA--
1 TGCTCTTACTTCAATTTCAGAGATAAAGACGT-GTTATCCACTCTACTTCAATTTCAAGAGGATG
10123374 ACGT
65 ACGT
* * * * *
10123378 TGCTTTTACTTCAATTTCAGAGAAAAGAGACGTGTTATCCGCTTTACTTCAATTTCAAGGGGATG
1 TGCTCTTACTTCAATTTCAGAGATAA-AGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
10123443 ACGT
65 ACGT
** * *
10123447 TGCTCTTACTTCAATTTCAGAGATATGATTAC-TGTTATCCACTCTTCTTCAA-TTCAAGCGGAT
1 TGCTCTTACTTCAATTTCAGAGATA--AAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGAT
10123510 TGGAAATGAT
Statistics
Matches: 531, Mismatches: 51, Indels: 38
0.86 0.08 0.06
Matches are distributed among these distances:
63 17 0.03
64 23 0.04
65 15 0.03
66 37 0.07
67 137 0.26
68 198 0.37
69 96 0.18
70 7 0.01
71 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (68 bp):
TGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGA
CGT
Found at i:10123139 original size:135 final size:136
Alignment explanation
Indices: 10122870--10123508 Score: 886
Period size: 135 Copynumber: 4.7 Consensus size: 136
10122860 TCAGAGATAA
* * * *
10122870 TGTTATCCACTCTTCTTCAATTTCAAGAGGATGACATTGCTCTTACTTCAATTTCAAAGATAAAC
1 TGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAAAGATAAAG
* * *
10122935 ACATGTTATCCACTCTACTTCAATTTCAAGAGGACGACATTGCTCTTACTTCAACTTCAGAGATA
66 ACATGTTATCCACTCTACTTCAATTTCAAGCGGACGACATTGCTCTTACTTCAATTTCAGAGAAA
10123000 AAGACG
131 AAGACG
* * * * *
10123006 TATTATCCACTCTACTTCAACTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAAATATGAAG
1 TGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAAAGATAAAG
* * * * *
10123071 ACTTG-TATCCACTCAACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATA
66 ACATGTTATCCACTCTACTTCAATTTCAAGCGGACGACATTGCTCTTACTTCAATTTCAGAGAAA
10123135 AAGACG
131 AAGACG
*
10123141 TGTTATCCACTCTACTTCAATTTC-AGGGGATTGACGTTGCTCTTACTTCAATTTCAGAGATAAA
1 TGTTATCCACTCTACTTCAATTTCAAGGGGA-TGACGTTGCTCTTACTTCAATTTCAAAGATAAA
10123205 GACATGTTAT-CACTCTATACTTCAATTTCAAGCGGACGACATTGCTCTTACTTCAATTTCAGAG
65 GACATGTTATCCACTC--TACTTCAATTTCAAGCGGACGACATTGCTCTTACTTCAATTTCAGAG
10123269 AAAAAGACG
128 AAAAAGACG
*
10123278 TG-TATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAA-TTCAGAGAT-AAG
1 TGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAAAGATAAAG
* * *
10123340 AC-TCGTTATCCACTCTACTTCAATTTCAAGAGGA--ACGTTGCTTTTACTTCAATTTCAGAGAA
66 ACAT-GTTATCCACTCTACTTCAATTTCAAGCGGACGACATTGCTCTTACTTCAATTTCAGAGAA
10123402 AAGAGACG
130 AA-AGACG
* * * *
10123410 TGTTATCCGCTTTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAT-ATG
1 TGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAAAGATAAAG
* *
10123474 ATTACTGTTATCCACTCTTCTTCAA-TTCAAGCGGA
66 A-CA-TGTTATCCACTCTACTTCAATTTCAAGCGGA
10123509 TTGGAAATGA
Statistics
Matches: 457, Mismatches: 33, Indels: 27
0.88 0.06 0.05
Matches are distributed among these distances:
131 28 0.06
132 7 0.02
133 65 0.14
134 27 0.06
135 145 0.32
136 124 0.27
137 61 0.13
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (136 bp):
TGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAAAGATAAAG
ACATGTTATCCACTCTACTTCAATTTCAAGCGGACGACATTGCTCTTACTTCAATTTCAGAGAAA
AAGACG
Found at i:10135285 original size:29 final size:28
Alignment explanation
Indices: 10135246--10135389 Score: 94
Period size: 29 Copynumber: 4.9 Consensus size: 28
10135236 TTTGGTGAAA
10135246 TCGGGGTTAAAAATGGAATTTTGGAAAGT
1 TCGGGG-TAAAAATGGAATTTTGGAAAGT
* *
10135275 TCGAGGGT-AAAATGGTAATTTTTGAAAATT
1 TCG-GGGTAAAAATGG-AA-TTTTGGAAAGT
** *
10135305 TCGGGGTAAAAATATAATTTTTGGAAATT
1 TCGGGGTAAAAATGGAA-TTTTGGAAAGT
** * *
10135334 TTAGGGTCAAAATAT-GATTTTTGAAAAGTT
1 TCGGGGT-AAAA-ATGGAATTTTGGAAAG-T
* * *
10135364 TTGGGGTCAAAATGTAATTTTGGAAA
1 TCGGGGTAAAAATGGAATTTTGGAAA
10135390 AGTTTTTAGG
Statistics
Matches: 91, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
28 9 0.10
29 48 0.53
30 32 0.35
31 2 0.02
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (28 bp):
TCGGGGTAAAAATGGAATTTTGGAAAGT
Found at i:10135503 original size:30 final size:29
Alignment explanation
Indices: 10135255--10135515 Score: 213
Period size: 30 Copynumber: 8.8 Consensus size: 29
10135245 ATCGGGGTTA
* *
10135255 AAAATGGAATTTTGGAAAG-TTCGAGGGT-
1 AAAATGTAATTTTGGAAAGTTTTG-GGGTC
* * * *
10135283 AAAATGGTAATTTTTGAAAATTTCGGGGTA
1 AAAAT-GTAATTTTGGAAAGTTTTGGGGTC
* *
10135313 AAAATATAATTTTTGGAAA-TTTTAGGGTC
1 AAAATGTAA-TTTTGGAAAGTTTTGGGGTC
* * *
10135342 AAAATATGATTTTTGAAAAGTTTTGGGGTC
1 AAAATGT-AATTTTGGAAAGTTTTGGGGTC
**
10135372 AAAATGTAATTTTGGAAAAGTTTTTAGGTC
1 AAAATGTAATTTTGG-AAAGTTTTGGGGTC
* * *
10135402 AAAATATAATTTTGGAAAAGTTTAGAGGTC
1 AAAATGTAATTTTGG-AAAGTTTTGGGGTC
* * * *
10135432 AAAATATAATTTTGAAAAAGCTTAGGGGTC
1 AAAATGTAATTTTG-GAAAGTTTTGGGGTC
* *
10135462 AAAATGTAATTATTAGAAAGTTTTGGGGTT
1 AAAATGTAATT-TTGGAAAGTTTTGGGGTC
*
10135492 AAAATGTAATTATTAGAAAGTTTT
1 AAAATGTAATT-TTGGAAAGTTTT
10135516 ATTTTTACCC
Statistics
Matches: 196, Mismatches: 28, Indels: 16
0.82 0.12 0.07
Matches are distributed among these distances:
28 5 0.03
29 46 0.23
30 143 0.73
31 2 0.01
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAGTTTTGGGGTC
Found at i:10135512 original size:90 final size:87
Alignment explanation
Indices: 10135261--10135514 Score: 262
Period size: 90 Copynumber: 2.9 Consensus size: 87
10135251 GTTAAAAATG
* * * * *
10135261 GAATTTTGGAAAG-TTCGAGGGT-AAAATGGTAATTTTTGAAAATTTCGGGGTAAAAATATAATT
1 GAATTTTGAAAAGCTTAG-GGGTCAAAAT-GTAATTTTAGAAAGTTTTGGGGTAAAAATATAA-T
*
10135324 TTTGGAAATTTTAGGGTCAAAATAT
63 TTTGGAAAGTTTAGGGTCAAAATAT
* * * * ** *
10135349 GATTTTTGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTTAGGTCAAAATATAATTT
1 GAATTTTGAAAAGCTTAGGGGTCAAAATGTAATTTTAG-AAAGTTTTGGGGTAAAAATATAATTT
10135414 TGGAAAAGTTTAGAGGTCAAAATAT
65 TGG-AAAGTTTAG-GGTCAAAATAT
* *
10135439 -AATTTTGAAAAAGCTTAGGGGTCAAAATGTAATTATTAGAAAGTTTTGGGGTTAAAATGTAATT
1 GAATTTTG-AAAAGCTTAGGGGTCAAAATGTAATT-TTAGAAAGTTTTGGGGTAAAAATATAATT
*
10135503 ATTAGAAAGTTT
64 -TTGGAAAGTTT
10135515 TATTTTTACC
Statistics
Matches: 139, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
88 30 0.22
89 40 0.29
90 63 0.45
91 6 0.04
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (87 bp):
GAATTTTGAAAAGCTTAGGGGTCAAAATGTAATTTTAGAAAGTTTTGGGGTAAAAATATAATTTT
GGAAAGTTTAGGGTCAAAATAT
Found at i:10135702 original size:29 final size:30
Alignment explanation
Indices: 10135663--10136098 Score: 103
Period size: 30 Copynumber: 14.9 Consensus size: 30
10135653 TTTGGTGAAA
*
10135663 TCGGGGTTAAAAATGG-AA-TTTTGGAAAGT
1 TCGGGG-TAAAAATGGTAATTTTTGAAAAGT
*
10135692 TCGAGGGT-AAAATGGTAATTTTTGAAAATT
1 TCG-GGGTAAAAATGGTAATTTTTGAAAAGT
* *
10135722 TCGGGGTAAAAAT-ATAATTTTT-AGAAATT
1 TCGGGGTAAAAATGGTAATTTTTGA-AAAGT
** * * *
10135751 TTAGGGTCAAAAT-ATGATTTTTGAAAAGTT
1 TCGGGGTAAAAATGGTAATTTTTGAAAAG-T
* * *
10135781 TTGGGGTCAAAAT-GTAATTTTGGAAAAGTT
1 TCGGGGTAAAAATGGTAATTTTTGAAAAG-T
*** * * *
10135811 TTTAGGTCAAAAT-ATAATTTTGGAAAAGTT
1 TCGGGGTAAAAATGGTAATTTTTGAAAAG-T
* * * * *
10135841 TAGAGGTCAAAAT-ATAATTTTGGAAAAGCT
1 TCGGGGTAAAAATGGTAATTTTTGAAAAG-T
* * *
10135871 TAGGGGTCAAAAT-GTAATTATT-AGAAAGT
1 TCGGGGTAAAAATGGTAATTTTTGA-AAAGT
** *
10135900 T-TTGG-------GGTAATTTTTGAAAATT
1 TCGGGGTAAAAATGGTAATTTTTGAAAAGT
* * *
10135922 TCGGGGTAAAAAT-ATAATTTTTGGAAATT
1 TCGGGGTAAAAATGGTAATTTTTGAAAAGT
** * * *
10135951 TTAGGGTCAAAAT-ATGATTTTTGAAAAGTT
1 TCGGGGTAAAAATGGTAATTTTTGAAAAG-T
* * *
10135981 TTGGGGTCAAAAT-GTAATTTTGGAAAAGTT
1 TCGGGGTAAAAATGGTAATTTTTGAAAAG-T
*** * * *
10136011 TTTAGGTCAAAAT-ATAATTTTGGAAAAGTT
1 TCGGGGTAAAAATGGTAATTTTTGAAAAG-T
* * * *
10136041 TAGGGGTCAAAAT-ATAATTTTGGAAAAGTT
1 TCGGGGTAAAAATGGTAATTTTTGAAAAG-T
* * *
10136071 TAGAGGTTAAAAT-GTAATTTTTAGAAAA
1 TCGGGGTAAAAATGGTAATTTTT-GAAAA
10136099 TTTTGGGGAC
Statistics
Matches: 337, Mismatches: 50, Indels: 38
0.79 0.12 0.09
Matches are distributed among these distances:
22 13 0.04
23 3 0.01
28 10 0.03
29 83 0.25
30 223 0.66
31 5 0.01
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (30 bp):
TCGGGGTAAAAATGGTAATTTTTGAAAAGT
Found at i:10135726 original size:59 final size:58
Alignment explanation
Indices: 10135663--10136091 Score: 208
Period size: 60 Copynumber: 7.4 Consensus size: 58
10135653 TTTGGTGAAA
* *
10135663 TCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT-AAAATGGTAATTTTTGAAAA-TT
1 TCGGGG-TAAAAATGTAATTTTGGAAA-TTCGAGGGTCAAAAT-ATAATTTTTGAAAAGTT
* * ** *
10135722 TCGGGGTAAAAATATAATTTTTAGAAATTTTAGGGTCAAAATATGATTTTTGAAAAGTT
1 TCGGGGTAAAAATGTAA-TTTTGGAAATTCGAGGGTCAAAATATAATTTTTGAAAAGTT
* * ** *
10135781 TTGGGGTCAAAATGTAATTTTGGAAAAGTTTTTA-GGTCAAAATATAATTTTGGAAAAGTT
1 TCGGGGTAAAAATGTAATTTTGG-AAA--TTCGAGGGTCAAAATATAATTTTTGAAAAGTT
* * * * * * *
10135841 TAGAGGTCAAAATATAATTTTGGAAAAGCTTAG-GGGTCAAAATGTAATTATT-AGAAAGTT
1 TCGGGGTAAAAATGTAATTTTGG-AAA--TTCGAGGGTCAAAATATAATTTTTGA-AAAGTT
* * * *
10135901 TTGGGGT---AA--T--TTTTGAAAATTTCG-GGGTAAAAATATAATTTTTGGAAA-TT
1 TCGGGGTAAAAATGTAATTTTGGAAA-TTCGAGGGTCAAAATATAATTTTTGAAAAGTT
** * * * * *
10135951 TTAGGGTCAAAATATG-ATTTTTGAAAAGTTTTG-GGGTCAAAATGTAATTTTGGAAAAGTT
1 TCGGGGT-AAAA-ATGTAATTTTGGAAA--TTCGAGGGTCAAAATATAATTTTTGAAAAGTT
*** * * * *
10136011 TTTAGGTCAAAATATAATTTTGGAAAAGTT-TAGGGGTCAAAATATAATTTTGGAAAAGTT
1 TCGGGGTAAAAATGTAATTTTGG-AAA-TTCGA-GGGTCAAAATATAATTTTTGAAAAGTT
* * *
10136071 TAGAGGTTAAAATGTAATTTT
1 TCGGGGTAAAAATGTAATTTT
10136092 TAGAAAATTT
Statistics
Matches: 296, Mismatches: 50, Indels: 47
0.75 0.13 0.12
Matches are distributed among these distances:
50 8 0.03
51 22 0.07
52 3 0.01
53 5 0.02
54 1 0.00
55 2 0.01
57 2 0.01
58 44 0.15
59 74 0.25
60 130 0.44
61 5 0.02
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (58 bp):
TCGGGGTAAAAATGTAATTTTGGAAATTCGAGGGTCAAAATATAATTTTTGAAAAGTT
Found at i:10135734 original size:30 final size:30
Alignment explanation
Indices: 10135707--10136106 Score: 380
Period size: 30 Copynumber: 13.7 Consensus size: 30
10135697 GGTAAAATGG
* *
10135707 TAATTTTTGAAAA-TTTCGGGGTAAAAATA
1 TAATTTTTGAAAAGTTTTGGGGTCAAAATA
*
10135736 TAATTTTT-AGAAA-TTTTAGGGTCAAAATA
1 TAATTTTTGA-AAAGTTTTGGGGTCAAAATA
* *
10135765 TGATTTTTGAAAAGTTTTGGGGTCAAAATG
1 TAATTTTTGAAAAGTTTTGGGGTCAAAATA
* **
10135795 TAATTTTGGAAAAGTTTTTAGGTCAAAATA
1 TAATTTTTGAAAAGTTTTGGGGTCAAAATA
* * *
10135825 TAATTTTGGAAAAGTTTAGAGGTCAAAATA
1 TAATTTTTGAAAAGTTTTGGGGTCAAAATA
* * * *
10135855 TAATTTTGGAAAAGCTTAGGGGTCAAAATG
1 TAATTTTTGAAAAGTTTTGGGGTCAAAATA
*
10135885 TAATTATT-AGAAAGTTTTGGGG--------
1 TAATTTTTGA-AAAGTTTTGGGGTCAAAATA
* *
10135907 TAATTTTTGAAAA-TTTCGGGGTAAAAATA
1 TAATTTTTGAAAAGTTTTGGGGTCAAAATA
* *
10135936 TAATTTTTGGAAA-TTTTAGGGTCAAAATA
1 TAATTTTTGAAAAGTTTTGGGGTCAAAATA
* *
10135965 TGATTTTTGAAAAGTTTTGGGGTCAAAATG
1 TAATTTTTGAAAAGTTTTGGGGTCAAAATA
* **
10135995 TAATTTTGGAAAAGTTTTTAGGTCAAAATA
1 TAATTTTTGAAAAGTTTTGGGGTCAAAATA
* *
10136025 TAATTTTGGAAAAGTTTAGGGGTCAAAATA
1 TAATTTTTGAAAAGTTTTGGGGTCAAAATA
* * * * *
10136055 TAATTTTGGAAAAGTTTAGAGGTTAAAATG
1 TAATTTTTGAAAAGTTTTGGGGTCAAAATA
10136085 TAATTTTTAGAAAA-TTTTGGGG
1 TAATTTTT-GAAAAGTTTTGGGG
10136107 ACTTACAAAG
Statistics
Matches: 312, Mismatches: 44, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
21 7 0.02
22 10 0.03
23 1 0.00
28 1 0.00
29 71 0.23
30 217 0.70
31 5 0.02
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (30 bp):
TAATTTTTGAAAAGTTTTGGGGTCAAAATA
Found at i:10135885 original size:417 final size:417
Alignment explanation
Indices: 10135111--10135907 Score: 1576
Period size: 417 Copynumber: 1.9 Consensus size: 417
10135101 ATACGAAGTG
10135111 AAAATAAAATAAACGCAAAGAACGGGGTATAACAATTAAGATTAAATACAAATATTATTAAAGAA
1 AAAATAAAATAAACGCAAAGAACGGGGTATAACAATTAAGATTAAATACAAATATTATTAAAGAA
10135176 ATGAAGCAATCGGTGATTAAAACAAGACTTTTTGGGATACCCGGGGGCAAAATGGTAGATTTTGG
66 ATGAAGCAATCGGTGATTAAAACAAGACTTTTTGGGATACCCGGGGGCAAAATGGTAGATTTTGG
10135241 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGAAAATTT
131 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGAAAATTT
*
10135306 CGGGGTAAAAATATAATTTTTGGAAATTTTAGGGTCAAAATATGATTTTTGAAAAGTTTTGGGGT
196 CGGGGTAAAAATATAATTTTTAGAAATTTTAGGGTCAAAATATGATTTTTGAAAAGTTTTGGGGT
10135371 CAAAATGTAATTTTGGAAAAGTTTTTAGGTCAAAATATAATTTTGGAAAAGTTTAGAGGTCAAAA
261 CAAAATGTAATTTTGGAAAAGTTTTTAGGTCAAAATATAATTTTGGAAAAGTTTAGAGGTCAAAA
10135436 TATAATTTTGAAAAAGCTTAGGGGTCAAAATGTAATTATTAGAAAGTTTTGGGGTTAAAATGTAA
326 TATAATTTTGAAAAAGCTTAGGGGTCAAAATGTAATTATTAGAAAGTTTTGGGGTTAAAATGTAA
10135501 TTATTAGAAAGTTTTATTTTTACCCCA
391 TTATTAGAAAGTTTTATTTTTACCCCA
10135528 AAAATAAAATAAACGCAAAGAACGGGGTATAACAATTAAGATTAAATACAAATATTATTAAAGAA
1 AAAATAAAATAAACGCAAAGAACGGGGTATAACAATTAAGATTAAATACAAATATTATTAAAGAA
10135593 ATGAAGCAATCGGTGATTAAAACAAGACTTTTTGGGATACCCGGGGGCAAAATGGTAGATTTTGG
66 ATGAAGCAATCGGTGATTAAAACAAGACTTTTTGGGATACCCGGGGGCAAAATGGTAGATTTTGG
10135658 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGAAAATTT
131 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGAAAATTT
10135723 CGGGGTAAAAATATAATTTTTAGAAATTTTAGGGTCAAAATATGATTTTTGAAAAGTTTTGGGGT
196 CGGGGTAAAAATATAATTTTTAGAAATTTTAGGGTCAAAATATGATTTTTGAAAAGTTTTGGGGT
10135788 CAAAATGTAATTTTGGAAAAGTTTTTAGGTCAAAATATAATTTTGGAAAAGTTTAGAGGTCAAAA
261 CAAAATGTAATTTTGGAAAAGTTTTTAGGTCAAAATATAATTTTGGAAAAGTTTAGAGGTCAAAA
*
10135853 TATAATTTTGGAAAAGCTTAGGGGTCAAAATGTAATTATTAGAAAGTTTTGGGGT
326 TATAATTTTGAAAAAGCTTAGGGGTCAAAATGTAATTATTAGAAAGTTTTGGGGT
10135908 AATTTTTGAA
Statistics
Matches: 378, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
417 378 1.00
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (417 bp):
AAAATAAAATAAACGCAAAGAACGGGGTATAACAATTAAGATTAAATACAAATATTATTAAAGAA
ATGAAGCAATCGGTGATTAAAACAAGACTTTTTGGGATACCCGGGGGCAAAATGGTAGATTTTGG
TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGAAAATTT
CGGGGTAAAAATATAATTTTTAGAAATTTTAGGGTCAAAATATGATTTTTGAAAAGTTTTGGGGT
CAAAATGTAATTTTGGAAAAGTTTTTAGGTCAAAATATAATTTTGGAAAAGTTTAGAGGTCAAAA
TATAATTTTGAAAAAGCTTAGGGGTCAAAATGTAATTATTAGAAAGTTTTGGGGTTAAAATGTAA
TTATTAGAAAGTTTTATTTTTACCCCA
Found at i:10135927 original size:21 final size:22
Alignment explanation
Indices: 10135884--10135930 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
10135874 GGGTCAAAAT
* *
10135884 GTAATTATTAGAAAGTTTTGGG
1 GTAATTATTAGAAAATTTCGGG
*
10135906 GTAATT-TTTGAAAATTTCGGG
1 GTAATTATTAGAAAATTTCGGG
10135927 GTAA
1 GTAA
10135931 AAATATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.40
Consensus pattern (22 bp):
GTAATTATTAGAAAATTTCGGG
Found at i:10135934 original size:51 final size:51
Alignment explanation
Indices: 10135855--10135957 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 51
10135845 GGTCAAAATA
* * *
10135855 TAATTTTGGAAAAGCTTAGGGGTCAAAATGTAATTATTAGAAAGTTTTGGGG
1 TAATTTTGGAAAAGCTTAGGGGTAAAAATATAATTATTAGAAA-TTTTAGGG
* * * * *
10135907 TAATTTTTGAAAA-TTTCGGGGTAAAAATATAATTTTTGGAAATTTTAGGG
1 TAATTTTGGAAAAGCTTAGGGGTAAAAATATAATTATTAGAAATTTTAGGG
10135957 T
1 T
10135958 CAAAATATGA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 8 0.19
51 23 0.53
52 12 0.28
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (51 bp):
TAATTTTGGAAAAGCTTAGGGGTAAAAATATAATTATTAGAAATTTTAGGG
Found at i:10136051 original size:200 final size:200
Alignment explanation
Indices: 10135705--10136106 Score: 741
Period size: 200 Copynumber: 2.0 Consensus size: 200
10135695 AGGGTAAAAT
10135705 GGTAATTTTTGAAAATTTCGGGGTAAAAATATAATTTTTAGAAATTTTAGGGTCAAAATATGATT
1 GGTAATTTTTGAAAATTTCGGGGTAAAAATATAATTTTTAGAAATTTTAGGGTCAAAATATGATT
10135770 TTTGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTTAGGTCAAAATATAATTTTGGA
66 TTTGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTTAGGTCAAAATATAATTTTGGA
* *
10135835 AAAGTTTAGAGGTCAAAATATAATTTTGGAAAAGCTTAGGGGTCAAAATGTAATTATTAGAAAGT
131 AAAGTTTAGAGGTCAAAATATAATTTTGGAAAAGCTTAGAGGTCAAAATGTAATTATTAGAAAAT
10135900 TTTGG
196 TTTGG
*
10135905 GGTAATTTTTGAAAATTTCGGGGTAAAAATATAATTTTTGGAAATTTTAGGGTCAAAATATGATT
1 GGTAATTTTTGAAAATTTCGGGGTAAAAATATAATTTTTAGAAATTTTAGGGTCAAAATATGATT
10135970 TTTGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTTAGGTCAAAATATAATTTTGGA
66 TTTGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTTAGGTCAAAATATAATTTTGGA
* * * *
10136035 AAAGTTTAGGGGTCAAAATATAATTTTGGAAAAGTTTAGAGGTTAAAATGTAATTTTTAGAAAAT
131 AAAGTTTAGAGGTCAAAATATAATTTTGGAAAAGCTTAGAGGTCAAAATGTAATTATTAGAAAAT
10136100 TTTGG
196 TTTGG
10136105 GG
1 GG
10136107 ACTTACAAAG
Statistics
Matches: 195, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
200 195 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (200 bp):
GGTAATTTTTGAAAATTTCGGGGTAAAAATATAATTTTTAGAAATTTTAGGGTCAAAATATGATT
TTTGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTTAGGTCAAAATATAATTTTGGA
AAAGTTTAGAGGTCAAAATATAATTTTGGAAAAGCTTAGAGGTCAAAATGTAATTATTAGAAAAT
TTTGG
Found at i:10137714 original size:20 final size:20
Alignment explanation
Indices: 10137676--10137714 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10137666 CAGGGCATGG
*
10137676 TGGAGCTTGGTGGTGGCAGA
1 TGGAGCTTGGTGGTAGCAGA
10137696 TGGAGC-TGGTGGTCAGCAG
1 TGGAGCTTGGTGGT-AGCAG
10137715 CAGCAAAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.15, C:0.13, G:0.49, T:0.23
Consensus pattern (20 bp):
TGGAGCTTGGTGGTAGCAGA
Found at i:10137941 original size:11 final size:11
Alignment explanation
Indices: 10137925--10137952 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
10137915 AATTTTAAAT
10137925 TTTAAAATTAA
1 TTTAAAATTAA
10137936 TTTAAAATTAA
1 TTTAAAATTAA
10137947 TTTAAA
1 TTTAAA
10137953 CTCACCCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TTTAAAATTAA
Found at i:10138344 original size:18 final size:18
Alignment explanation
Indices: 10138323--10138357 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10138313 AATTTTTGTT
10138323 TTTTAAAAATATTTTTAG
1 TTTTAAAAATATTTTTAG
* *
10138341 TTTTCATAATATTTTTA
1 TTTTAAAAATATTTTTA
10138358 AGCCAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTAAAAATATTTTTAG
Found at i:10138781 original size:2 final size:2
Alignment explanation
Indices: 10138745--10138769 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10138735 ATATTAACCT
10138745 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10138770 TTTATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10139564 original size:21 final size:22
Alignment explanation
Indices: 10139533--10139577 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
10139523 ACAAATTACT
*
10139533 ATCAACTAAATGCGATAGAAAA
1 ATCAACTAAATGCGATAAAAAA
10139555 ATCAA-TAAATGCGATAAAAAA
1 ATCAACTAAATGCGATAAAAAA
10139576 AT
1 AT
10139578 AATTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (22 bp):
ATCAACTAAATGCGATAAAAAA
Found at i:10146436 original size:731 final size:731
Alignment explanation
Indices: 10145035--10146497 Score: 2854
Period size: 731 Copynumber: 2.0 Consensus size: 731
10145025 TCAAAAGGCG
*
10145035 GCTTTCTTTAGAAATGATTTTTGGCTTCTTCTCCACAGTTGAATTAGATTAGAACGCATGTTCTC
1 GCTTTCTTTAGAAATGATTTTTGGCTTCTTCTCCACAGTTAAATTAGATTAGAACGCATGTTCTC
10145100 TTCAGAACTAATTCGAAGTTCTTTAGAATTTTTCAAGTTTTTGGATTTTCTTCAGAGAATTCTAT
66 TTCAGAACTAATTCGAAGTTCTTTAGAATTTTTCAAGTTTTTGGATTTTCTTCAGAGAATTCTAT
*
10145165 AGATATTTTTCGGGTTTCTTGAACTTGTGAATCTATAAAATGACTTAGGGTGATCCTTTTTTATA
131 AGATATTTTTCGGGTATCTTGAACTTGTGAATCTATAAAATGACTTAGGGTGATCCTTTTTTATA
10145230 ATATCAATTAAATGATTAAAAGAGAGTTTTGTAGAATTTAACTGTTTCGTTTAAATATTCTACAC
196 ATATCAATTAAATGATTAAAAGAGAGTTTTGTAGAATTTAACTGTTTCGTTTAAATATTCTACAC
10145295 CGATTTAAACTATTTTATTTATTATTTTATCAAAAAATTAATTAGAGATCAAATAATAATTGATA
261 CGATTTAAACTATTTTATTTATTATTTTATCAAAAAATTAATTAGAGATCAAATAATAATTGATA
10145360 TCATCACTTAATTATTTTATTTTTAATTAGAGATCAAATAATAATTGATATCATCAATTAAATTA
326 TCATCACTTAATTATTTTATTTTTAATTAGAGATCAAATAATAATTGATATCATCAATTAAATTA
10145425 AATTAATTAAAGAAAAATAATTATAACATAAGTATGATGTCATCATTTTCACTCATGATAACTTC
391 AATTAATTAAAGAAAAATAATTATAACATAAGTATGATGTCATCATTTTCACTCATGATAACTTC
10145490 GGTTTTACTGACAATAATTTCGACTTGACACGTGACAGTCTCGTAATGTGTAATGATTGGAAAAT
456 GGTTTTACTGACAATAATTTCGACTTGACACGTGACAGTCTCGTAATGTGTAATGATTGGAAAAT
10145555 TGGGATTAGACCTTAAATTTAACTAAACTCCACGAGATCCTCCACTCCAAATCTATTAAGTTGTC
521 TGGGATTAGACCTTAAATTTAACTAAACTCCACGAGATCCTCCACTCCAAATCTATTAAGTTGTC
10145620 TTTGAGATTTTGAGACGATGTAATACGACGGATCATTGAGACAATTAATAGGTAGACCAAGTATT
586 TTTGAGATTTTGAGACGATGTAATACGACGGATCATTGAGACAATTAATAGGTAGACCAAGTATT
10145685 GTGGAAACATAAAAATAGAAATTGAGCCTAATGCATCAAAACTGGAATGATGCACTAAGACAAAC
651 GTGGAAACATAAAAATAGAAATTGAGCCTAATGCATCAAAACTGGAATGATGCACTAAGACAAAC
10145750 CTTAGTGCATGATATT
716 CTTAGTGCATGATATT
* *
10145766 GCTTTCTTTAGAGATGATTTTTGGCTTCTTCTCCACAGTTAAATTAGATTAGAACGTATGTTCTC
1 GCTTTCTTTAGAAATGATTTTTGGCTTCTTCTCCACAGTTAAATTAGATTAGAACGCATGTTCTC
10145831 TTCAGAACTAATTCGAAGTTCTTTAGAATTTTTCAAGTTTTTGGATTTTCTTCAGAGAATTCTAT
66 TTCAGAACTAATTCGAAGTTCTTTAGAATTTTTCAAGTTTTTGGATTTTCTTCAGAGAATTCTAT
* *
10145896 AGGTATTTTTCGGGTATCTTGAACTTGTGAATCTATAAAATGGCTTAGGGTGATCCTTTTTTATA
131 AGATATTTTTCGGGTATCTTGAACTTGTGAATCTATAAAATGACTTAGGGTGATCCTTTTTTATA
10145961 ATATCAATTAAATGATTAAAAGAGAGTTTTGTAGAATTTAACTGTTTCGTTTAAATATTCTACAC
196 ATATCAATTAAATGATTAAAAGAGAGTTTTGTAGAATTTAACTGTTTCGTTTAAATATTCTACAC
10146026 CGATTTAAACTATTTTATTTATTATTTTATCAAAAAATTAATTAGAGATCAAATAATAATTGATA
261 CGATTTAAACTATTTTATTTATTATTTTATCAAAAAATTAATTAGAGATCAAATAATAATTGATA
10146091 TCATCACTTAATTATTTTATTTTTAATTAGAGATCAAATAATAATTGATATCATCAATTAAATTA
326 TCATCACTTAATTATTTTATTTTTAATTAGAGATCAAATAATAATTGATATCATCAATTAAATTA
*
10146156 AATTAATTAAAGAAAAATAATTATAACATAAGTATGATGTCATCATTTTCATTCATGATAACTTC
391 AATTAATTAAAGAAAAATAATTATAACATAAGTATGATGTCATCATTTTCACTCATGATAACTTC
*
10146221 GGTTTTATTGACAATAATTTCGACTTGACACGTGACAGTCTCGTAATGTGTAATGATTGGAAAAT
456 GGTTTTACTGACAATAATTTCGACTTGACACGTGACAGTCTCGTAATGTGTAATGATTGGAAAAT
10146286 TGGGATTAGACCTTAAATTTAACTAAACTCCACGAGATCCTCCACTCCAAATCTATTAAGTTGTC
521 TGGGATTAGACCTTAAATTTAACTAAACTCCACGAGATCCTCCACTCCAAATCTATTAAGTTGTC
10146351 TTTGAGATTTTGAGACGATGTAATACGACGGATCATTGAGACAATTAATAGGTAGACCAAGTATT
586 TTTGAGATTTTGAGACGATGTAATACGACGGATCATTGAGACAATTAATAGGTAGACCAAGTATT
10146416 GTGGAAACATAAAAATAGAAATTGAGCCTAATGCATCAAAACTGGAATGATGCACTAAGACAAAC
651 GTGGAAACATAAAAATAGAAATTGAGCCTAATGCATCAAAACTGGAATGATGCACTAAGACAAAC
10146481 CTTAGTGCATGATATT
716 CTTAGTGCATGATATT
10146497 G
1 G
10146498 GGTGTCTATC
Statistics
Matches: 724, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
731 724 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (731 bp):
GCTTTCTTTAGAAATGATTTTTGGCTTCTTCTCCACAGTTAAATTAGATTAGAACGCATGTTCTC
TTCAGAACTAATTCGAAGTTCTTTAGAATTTTTCAAGTTTTTGGATTTTCTTCAGAGAATTCTAT
AGATATTTTTCGGGTATCTTGAACTTGTGAATCTATAAAATGACTTAGGGTGATCCTTTTTTATA
ATATCAATTAAATGATTAAAAGAGAGTTTTGTAGAATTTAACTGTTTCGTTTAAATATTCTACAC
CGATTTAAACTATTTTATTTATTATTTTATCAAAAAATTAATTAGAGATCAAATAATAATTGATA
TCATCACTTAATTATTTTATTTTTAATTAGAGATCAAATAATAATTGATATCATCAATTAAATTA
AATTAATTAAAGAAAAATAATTATAACATAAGTATGATGTCATCATTTTCACTCATGATAACTTC
GGTTTTACTGACAATAATTTCGACTTGACACGTGACAGTCTCGTAATGTGTAATGATTGGAAAAT
TGGGATTAGACCTTAAATTTAACTAAACTCCACGAGATCCTCCACTCCAAATCTATTAAGTTGTC
TTTGAGATTTTGAGACGATGTAATACGACGGATCATTGAGACAATTAATAGGTAGACCAAGTATT
GTGGAAACATAAAAATAGAAATTGAGCCTAATGCATCAAAACTGGAATGATGCACTAAGACAAAC
CTTAGTGCATGATATT
Found at i:10148421 original size:37 final size:39
Alignment explanation
Indices: 10148352--10148430 Score: 135
Period size: 37 Copynumber: 2.1 Consensus size: 39
10148342 AAAAATGATT
10148352 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
1 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
*
10148391 TTAAAATTATT-ATATTATTTTTTT-AAATATAAAATTA
1 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
10148428 TTA
1 TTA
10148431 TATGATTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 16 0.41
38 12 0.31
39 11 0.28
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (39 bp):
TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
Found at i:10148429 original size:20 final size:20
Alignment explanation
Indices: 10148362--10148429 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
10148352 TTAAAATTAT
10148362 TAAAATTATTTTTTTGAAATA
1 TAAAATTATTTTTTT-AAATA
*
10148383 TAAAATTA----TTAAAATTA
1 TAAAATTATTTTTTTAAA-TA
* *
10148400 TTATATTATTTTTTTAAATA
1 TAAAATTATTTTTTTAAATA
10148420 TAAAATTATT
1 TAAAATTATT
10148430 ATATGATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 11
0.68 0.11 0.21
Matches are distributed among these distances:
16 3 0.08
17 10 0.28
20 10 0.28
21 13 0.36
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (20 bp):
TAAAATTATTTTTTTAAATA
Found at i:10149436 original size:27 final size:29
Alignment explanation
Indices: 10149406--10149482 Score: 113
Period size: 27 Copynumber: 2.7 Consensus size: 29
10149396 ATTAGAAATT
10149406 AAAATAATATAATAATTTTATA-TTC-AA
1 AAAATAATATAATAATTTTATATTTCAAA
*
10149433 AAAATAATATAGTAATTTTATATTTCAAA
1 AAAATAATATAATAATTTTATATTTCAAA
*
10149462 AAAATAATTTTAATAATTTTA
1 AAAATAA-TATAATAATTTTA
10149483 AAATCATTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 21 0.48
28 3 0.07
29 9 0.20
30 11 0.25
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (29 bp):
AAAATAATATAATAATTTTATATTTCAAA
Found at i:10150302 original size:19 final size:18
Alignment explanation
Indices: 10150280--10150335 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
10150270 GATTAAAAAA
10150280 TTTATAGTTTTTATTAATT
1 TTTATA-TTTTTATTAATT
*
10150299 TTTATATTTTTA-AAGATTT
1 TTTATATTTTTATTA-A-TT
10150318 TTTATATTTTT-TTAATT
1 TTTATATTTTTATTAATT
10150335 T
1 T
10150336 ATGCTTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 4 0.12
18 8 0.25
19 20 0.62
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTATATTTTTATTAATT
Found at i:10158489 original size:24 final size:24
Alignment explanation
Indices: 10158473--10158547 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
10158463 AGTTTGACTC
10158473 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* * *
10158497 AAACAAATAAATAAAATTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
10158521 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
10158545 AAA
1 AAA
10158548 GATTATTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.57, C:0.08, G:0.09, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:10161099 original size:18 final size:18
Alignment explanation
Indices: 10161076--10161133 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
10161066 AATTCAAAAT
10161076 ATTTATAAAAATTTTAAA
1 ATTTATAAAAATTTTAAA
** **
10161094 ATTTATGTATTTTTTAAA
1 ATTTATAAAAATTTTAAA
* *
10161112 AATTATAAAAATTTCAAA
1 ATTTATAAAAATTTTAAA
10161130 ATTT
1 ATTT
10161134 TTTAAAAAAT
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
ATTTATAAAAATTTTAAA
Found at i:10161123 original size:28 final size:28
Alignment explanation
Indices: 10161051--10161152 Score: 91
Period size: 28 Copynumber: 3.5 Consensus size: 28
10161041 TCTCTCTCAA
* * *
10161051 TAAAAATTACAAAATAATTCAAAATATTTA
1 TAAAAATTATAAAA-ATTTCAAAAT-TTTT
* **
10161081 TAAAAATT-TTAAAATTT-ATGTATTTTT
1 TAAAAATTATAAAAATTTCA-AAATTTTT
10161108 TAAAAATTATAAAAATTTCAAAATTTTT
1 TAAAAATTATAAAAATTTCAAAATTTTT
10161136 TAAAAAATATATAAAAA
1 T-AAAAAT-TATAAAAA
10161153 AAAGTTAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
27 12 0.21
28 20 0.34
29 10 0.17
30 16 0.28
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (28 bp):
TAAAAATTATAAAAATTTCAAAATTTTT
Found at i:10161588 original size:2 final size:2
Alignment explanation
Indices: 10161583--10161625 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
10161573 TTTGTAATCT
10161583 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10161625 T
1 T
10161626 TTGTAATCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10165622 original size:24 final size:24
Alignment explanation
Indices: 10165594--10165652 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
10165584 TAGAGTAATA
**
10165594 AGAGTTTGGCTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
10165618 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
10165642 AGAGTTTAACT
1 AGAGTTTAACT
10165653 AAAAGATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:10168653 original size:17 final size:17
Alignment explanation
Indices: 10168627--10168667 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
10168617 TTAGAATTGG
* *
10168627 ATTGAGAAAATTATTTA
1 ATTGAAAAAATTAATTA
10168644 ATTGAAAAAATTAATTA
1 ATTGAAAAAATTAATTA
10168661 ATT-AAAA
1 ATTGAAAA
10168668 TTAATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (17 bp):
ATTGAAAAAATTAATTA
Found at i:10178535 original size:19 final size:18
Alignment explanation
Indices: 10178491--10178550 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 18
10178481 GTTCATAATA
*
10178491 ATAAAAAATATAAGAATTT
1 ATAAAAAATATAA-AAATT
*
10178510 ATTTAAAAATTAGTAAAAATT
1 A--TAAAAAATA-TAAAAATT
*
10178531 ATAAAAAATATTAAAATT
1 ATAAAAAATATAAAAATT
10178549 AT
1 AT
10178551 TTAAAATTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 9 0.26
19 9 0.26
21 13 0.38
22 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAAAAAATATAAAAATT
Found at i:10180514 original size:21 final size:21
Alignment explanation
Indices: 10180472--10180514 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
10180462 ACAAAGAAAC
**
10180472 AATAATAGATAAATTTTGTTT
1 AATAATAGATAAATTTAATTT
10180493 AATAATA-ACTAAATTTAATTT
1 AATAATAGA-TAAATTTAATTT
10180514 A
1 A
10180515 TGCATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
AATAATAGATAAATTTAATTT
Found at i:10181303 original size:21 final size:20
Alignment explanation
Indices: 10181274--10181312 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
10181264 CATGATTTTT
*
10181274 CAAATTATTAAAATATAATAA
1 CAAAATATTAAAAT-TAATAA
*
10181295 CAAAATATTTAAATTAAT
1 CAAAATATTAAAATTAAT
10181313 CTTAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
CAAAATATTAAAATTAATAA
Found at i:10181698 original size:10 final size:10
Alignment explanation
Indices: 10181685--10181743 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
10181675 ATATAAATTT
10181685 ATTTTTTATA
1 ATTTTTTATA
*
10181695 ATTTCTTATA
1 ATTTTTTATA
10181705 A-TTTTTACTA
1 ATTTTTTA-TA
*
10181715 ATTTTTAAATA
1 ATTTTT-TATA
* *
10181726 AATTCTTAT-
1 ATTTTTTATA
10181735 ATTTTTTAT
1 ATTTTTTAT
10181744 TATTATGAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
9 12 0.32
10 15 0.39
11 10 0.26
12 1 0.03
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:10183347 original size:20 final size:21
Alignment explanation
Indices: 10183322--10183392 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
10183312 TGTCACATAC
10183322 AATATTTAATTAA-TTTTTTA
1 AATATTTAATTAACTTTTTTA
* *
10183342 AATATTATAATAGAACTTTTTTT
1 AATATT-TAAT-TAACTTTTTTA
* *
10183365 AATA-ATAATTAAGTATTTTTA
1 AATATTTAATTAACT-TTTTTA
10183386 ATATATT
1 A-ATATT
10183393 CAACATGCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 9 0.24
21 14 0.37
22 5 0.13
23 10 0.26
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (21 bp):
AATATTTAATTAACTTTTTTA
Found at i:10185954 original size:42 final size:42
Alignment explanation
Indices: 10185907--10185992 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 42
10185897 AAAGAGTTGC
10185907 TTATGAGTATTATTT-AAGAATAAAATTATATTTGAGTTTAAT
1 TTATGAGTATT-TTTGAAGAATAAAATTATATTTGAGTTTAAT
* *
10185949 TTATGAGTGTTTTTGAAGAATGAAATTATATTTGAGTTTAAT
1 TTATGAGTATTTTTGAAGAATAAAATTATATTTGAGTTTAAT
10185991 TT
1 TT
10185993 GTTGATGAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 3 0.07
42 38 0.93
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (42 bp):
TTATGAGTATTTTTGAAGAATAAAATTATATTTGAGTTTAAT
Found at i:10191127 original size:29 final size:29
Alignment explanation
Indices: 10191085--10191143 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
10191075 ACAAGACAAC
10191085 AGGAATCTCTATGATAATGAGATAAAAGT
1 AGGAATCTCTATGATAATGAGATAAAAGT
10191114 AGGAATCTCTATGATAATGAGATAAAAGT
1 AGGAATCTCTATGATAATGAGATAAAAGT
10191143 A
1 A
10191144 CAACCAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (29 bp):
AGGAATCTCTATGATAATGAGATAAAAGT
Found at i:10191192 original size:41 final size:41
Alignment explanation
Indices: 10191147--10191226 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
10191137 AAAAGTACAA
10191147 CCAAGGAACTTAGGACCAATGTATGAAGGATGCCTATCAAG
1 CCAAGGAACTTAGGACCAATGTATGAAGGATGCCTATCAAG
10191188 CCAAGGAACTTAGGACCAATGTATGAAGGATGCCTATCA
1 CCAAGGAACTTAGGACCAATGTATGAAGGATGCCTATCA
10191227 TATATCCTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (41 bp):
CCAAGGAACTTAGGACCAATGTATGAAGGATGCCTATCAAG
Found at i:10199805 original size:2 final size:2
Alignment explanation
Indices: 10199798--10199836 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
10199788 TTTTGTGCTT
10199798 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10199837 TGTAATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10205973 original size:19 final size:19
Alignment explanation
Indices: 10205949--10206008 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
10205939 TTTGGTGATA
10205949 TTTTTTTTACTGTTTTGGT
1 TTTTTTTTACTGTTTTGGT
*
10205968 TTTTTTTTCCTGTTTTTGTGT
1 TTTTTTTTACTG-TTTTG-GT
*
10205989 TATTTTTTACTGTTTTGGT
1 TTTTTTTTACTGTTTTGGT
10206008 T
1 T
10206009 GTTGTTTTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 14 0.39
20 10 0.28
21 12 0.33
ACGTcount: A:0.05, C:0.07, G:0.15, T:0.73
Consensus pattern (19 bp):
TTTTTTTTACTGTTTTGGT
Found at i:10205975 original size:21 final size:20
Alignment explanation
Indices: 10205949--10206008 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
10205939 TTTGGTGATA
10205949 TTTTTTTTACTGTTTTGG-T
1 TTTTTTTTACTGTTTTGGTT
* *
10205968 TTTTTTTTCCTGTTTTTGTGT
1 TTTTTTTTACTGTTTTGGT-T
*
10205989 TATTTTTTACTGTTTTGGTT
1 TTTTTTTTACTGTTTTGGTT
10206009 GTTGTTTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 16 0.47
20 1 0.03
21 17 0.50
ACGTcount: A:0.05, C:0.07, G:0.15, T:0.73
Consensus pattern (20 bp):
TTTTTTTTACTGTTTTGGTT
Found at i:10206014 original size:12 final size:12
Alignment explanation
Indices: 10205999--10206070 Score: 76
Period size: 12 Copynumber: 6.1 Consensus size: 12
10205989 TATTTTTTAC
*
10205999 TGTTTTGGTTGT
1 TGTTTTTGTTGT
*
10206011 TGTTTTCG-TGT
1 TGTTTTTGTTGT
10206022 TGTTTTT-TATGT
1 TGTTTTTGT-TGT
*
10206034 TATTTTTGTTGT
1 TGTTTTTGTTGT
*
10206046 TGTTTTTGTTGC
1 TGTTTTTGTTGT
*
10206058 TATTTTTGTTGT
1 TGTTTTTGTTGT
10206070 T
1 T
10206071 TTTAATGTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
11 9 0.18
12 40 0.80
13 1 0.02
ACGTcount: A:0.04, C:0.03, G:0.22, T:0.71
Consensus pattern (12 bp):
TGTTTTTGTTGT
Found at i:10206016 original size:21 final size:20
Alignment explanation
Indices: 10205950--10206016 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
10205940 TTGGTGATAT
10205950 TTTTTTTACTGTTTTGGTT-
1 TTTTTTTACTGTTTTGGTTG
*
10205969 TTTTTTTCCTGTTTTTGTGTT-
1 TTTTTTTACTG-TTTTG-GTTG
*
10205990 ATTTTTTACTGTTTTGGTTG
1 TTTTTTTACTGTTTTGGTTG
*
10206010 TTGTTTT
1 TTTTTTT
10206017 CGTGTTGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.32
20 15 0.38
21 12 0.30
ACGTcount: A:0.04, C:0.06, G:0.16, T:0.73
Consensus pattern (20 bp):
TTTTTTTACTGTTTTGGTTG
Found at i:10206028 original size:24 final size:22
Alignment explanation
Indices: 10205978--10206127 Score: 94
Period size: 21 Copynumber: 6.8 Consensus size: 22
10205968 TTTTTTTTCC
* **
10205978 TGTTTTTG-TGTTATTTTTTAC
1 TGTTTTTGTTGTTATTTTGTGT
* *
10205999 TGTTTTGGTTGTTGTTTTCGTGT
1 TGTTTTTGTTGTTATTTT-GTGT
10206022 TGTTTTT-TATGTTATTTTTGTTGT
1 TGTTTTTGT-TGTTA-TTTTG-TGT
*
10206046 TGTTTTTGTTGCTATTTT-TGT
1 TGTTTTTGTTGTTATTTTGTGT
** *
10206067 TGTTTTTAATGTTATTTTGCTGC
1 TGTTTTTGTTGTTATTTTG-TGT
* ** *
10206090 TATTTTTGTTACTGTTTTG-GT
1 TGTTTTTGTTGTTATTTTGTGT
10206111 TGTTATTT-TTGTTATTT
1 TGTT-TTTGTTGTTATTT
10206128 AGATGCTATT
Statistics
Matches: 97, Mismatches: 23, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
21 35 0.36
22 12 0.12
23 31 0.32
24 18 0.19
25 1 0.01
ACGTcount: A:0.08, C:0.04, G:0.19, T:0.69
Consensus pattern (22 bp):
TGTTTTTGTTGTTATTTTGTGT
Found at i:10206079 original size:12 final size:10
Alignment explanation
Indices: 10205978--10206073 Score: 50
Period size: 12 Copynumber: 8.7 Consensus size: 10
10205968 TTTTTTTTCC
10205978 TGTTTTTGTGT
1 TGTTTTT-TGT
* **
10205989 TATTTTTTAC
1 TGTTTTTTGT
10205999 TGTTTTGGTTGT
1 TGTTTT--TTGT
*
10206011 TGTTTTCGTGT
1 TGTTTT-TTGT
10206022 TGTTTTTTATGT
1 TG-TTTTT-TGT
*
10206034 T-ATTTTTGT
1 TGTTTTTTGT
10206043 TGTTGTTTTTGT
1 TG-T-TTTTTGT
10206055 TGCTATTTTTGT
1 TG-T-TTTTTGT
10206067 TGTTTTT
1 TGTTTTT
10206074 AATGTTATTT
Statistics
Matches: 65, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
9 4 0.06
10 14 0.22
11 12 0.18
12 35 0.54
ACGTcount: A:0.05, C:0.03, G:0.20, T:0.72
Consensus pattern (10 bp):
TGTTTTTTGT
Found at i:10206099 original size:20 final size:20
Alignment explanation
Indices: 10206076--10206140 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
10206066 TTGTTTTTAA
*
10206076 TGTTATTTTGCTGCTATTTT
1 TGTTATTTTGATGCTATTTT
* *
10206096 TGTTACTGTTTTGGTTGTTATTTT
1 TGTTA---TTTT-GATGCTATTTT
*
10206120 TGTTATTTAGATGCTATTTT
1 TGTTATTTTGATGCTATTTT
10206140 T
1 T
10206141 ATGCGTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
20 15 0.42
21 3 0.08
23 4 0.11
24 14 0.39
ACGTcount: A:0.12, C:0.06, G:0.17, T:0.65
Consensus pattern (20 bp):
TGTTATTTTGATGCTATTTT
Found at i:10206119 original size:12 final size:12
Alignment explanation
Indices: 10206001--10206123 Score: 69
Period size: 12 Copynumber: 10.7 Consensus size: 12
10205991 TTTTTTACTG
* *
10206001 TTTTGGTTGTTG
1 TTTTTGTTGTTA
* *
10206013 TTTTCG-TGTTG
1 TTTTTGTTGTTA
10206024 TTTTT-TATGTTA
1 TTTTTGT-TGTTA
*
10206036 TTTTTGTTGTTG
1 TTTTTGTTGTTA
*
10206048 TTTTTGTTGCTA
1 TTTTTGTTGTTA
10206060 TTTTTGTTG---
1 TTTTTGTTGTTA
**
10206069 TTTTTAATGTTA
1 TTTTTGTTGTTA
* *
10206081 -TTTTGCTGCTA
1 TTTTTGTTGTTA
** *
10206092 TTTTTGTTACTG
1 TTTTTGTTGTTA
*
10206104 TTTTGGTTGTTA
1 TTTTTGTTGTTA
10206116 TTTTTGTT
1 TTTTTGTT
10206124 ATTTAGATGC
Statistics
Matches: 85, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
9 7 0.08
11 17 0.20
12 60 0.71
13 1 0.01
ACGTcount: A:0.07, C:0.04, G:0.20, T:0.69
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:10206135 original size:44 final size:44
Alignment explanation
Indices: 10206048--10206140 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
10206038 TTTGTTGTTG
* * * * *
10206048 TTTTTGTTGCTATTTTTGTTGTTTTTAATGTTATTTTGCTGCTA
1 TTTTTGTTACTATTTTGGTTGTTATTAATGTTATTTAGATGCTA
* **
10206092 TTTTTGTTACTGTTTTGGTTGTTATTTTTGTTATTTAGATGCTA
1 TTTTTGTTACTATTTTGGTTGTTATTAATGTTATTTAGATGCTA
10206136 TTTTT
1 TTTTT
10206141 ATGCGTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.12, C:0.05, G:0.16, T:0.67
Consensus pattern (44 bp):
TTTTTGTTACTATTTTGGTTGTTATTAATGTTATTTAGATGCTA
Found at i:10207797 original size:12 final size:12
Alignment explanation
Indices: 10207769--10207843 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
10207759 TTGTTTATTA
*
10207769 TTCATTAACATTG
1 TTCATGAACA-TG
10207782 TTCATGAACATG
1 TTCATGAACATG
* *
10207794 TTCAAT-TATATG
1 TTC-ATGAACATG
10207806 TTCATGAACATG
1 TTCATGAACATG
* **
10207818 TTCGTTTA-ATG
1 TTCATGAACATG
*
10207829 TTCGTGAACATG
1 TTCATGAACATG
10207841 TTC
1 TTC
10207844 GATTAAGTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
11 11 0.22
12 27 0.55
13 11 0.22
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (12 bp):
TTCATGAACATG
Found at i:10207836 original size:23 final size:23
Alignment explanation
Indices: 10207780--10207867 Score: 115
Period size: 23 Copynumber: 3.8 Consensus size: 23
10207770 TCATTAACAT
*
10207780 TGTTCATGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCGATTA-A
*
10207804 TGTTCATGAACATGTTCGTTTAA
1 TGTTCATGAACATGTTCGATTAA
*
10207827 TGTTCGTGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCGATTAA
*
10207850 -GTTAGATGAACATGTTCG
1 TGTT-CATGAACATGTTCG
10207868 TGAATATTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
22 3 0.05
23 34 0.60
24 20 0.35
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (23 bp):
TGTTCATGAACATGTTCGATTAA
Found at i:10220645 original size:27 final size:26
Alignment explanation
Indices: 10220596--10220646 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
10220586 CTTAAATTAT
* **
10220596 AACATTTTTTTTTATTTTGATACTTA
1 AACATTTTTTTTAATTTAAATACTTA
10220622 AACATTTTTTTTAATTATAAATACT
1 AACATTTTTTTTAATT-TAAATACT
10220647 ACCTAAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (26 bp):
AACATTTTTTTTAATTTAAATACTTA
Found at i:10224529 original size:122 final size:122
Alignment explanation
Indices: 10224387--10224631 Score: 472
Period size: 122 Copynumber: 2.0 Consensus size: 122
10224377 GAGACTGTTA
*
10224387 TCTGGCTATATATATATATATCATGTTTTCTTGTATGGTATTAATTGTTTTTGAATTATGGTTGT
1 TCTGGCTATATATATATATATCATGTTTTCTTGTATGGTATTAATTGTTTTTGAATTATGGTTGC
10224452 TGGAATGTAATGGAAAGTCGTGTGCTTAGAGCAGAACCTCATCCTTAGATGTGTGAG
66 TGGAATGTAATGGAAAGTCGTGTGCTTAGAGCAGAACCTCATCCTTAGATGTGTGAG
10224509 TCTGGCTATATATATATATATCATGTTTTCTTGTATGGTATTAATTGTTTTTGAATTATGGTTGC
1 TCTGGCTATATATATATATATCATGTTTTCTTGTATGGTATTAATTGTTTTTGAATTATGGTTGC
*
10224574 TGGAATGTAATGGAAAGTCGTGTGTTTAGAGCAGAACCTCATCCTTAGATGTGTGAG
66 TGGAATGTAATGGAAAGTCGTGTGCTTAGAGCAGAACCTCATCCTTAGATGTGTGAG
10224631 T
1 T
10224632 TTGCTTGTTT
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 121 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (122 bp):
TCTGGCTATATATATATATATCATGTTTTCTTGTATGGTATTAATTGTTTTTGAATTATGGTTGC
TGGAATGTAATGGAAAGTCGTGTGCTTAGAGCAGAACCTCATCCTTAGATGTGTGAG
Found at i:10225872 original size:10 final size:10
Alignment explanation
Indices: 10225853--10225920 Score: 57
Period size: 10 Copynumber: 6.6 Consensus size: 10
10225843 TAATTTAAAA
10225853 TTTTATTAATT
1 TTTTA-TAATT
10225864 TTTTATAATT
1 TTTTATAATT
* *
10225874 TCTTATACTT
1 TTTTATAATT
*
10225884 TTTAAGT-ATT
1 TTTTA-TAATT
*
10225894 TTTAAATAATT
1 TTT-TATAATT
*
10225905 TTCTATAATT
1 TTTTATAATT
10225915 TTTTAT
1 TTTTAT
10225921 GTCCATTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
10 33 0.72
11 13 0.28
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:10226052 original size:21 final size:22
Alignment explanation
Indices: 10226008--10226052 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
10225998 TGGATGTTTC
* * *
10226008 TTTTATCATTTCTGATATATTT
1 TTTTATAATTTCTGAAATAATT
10226030 TTTTATAATTTCT-AAATAATT
1 TTTTATAATTTCTGAAATAATT
10226051 TT
1 TT
10226053 ATATTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTATAATTTCTGAAATAATT
Found at i:10234791 original size:14 final size:14
Alignment explanation
Indices: 10234763--10234804 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
10234753 AATTCCAACA
* *
10234763 AATAAGTAATAAAT
1 AATAAGTTATTAAT
10234777 AATAAGTTATTAAT
1 AATAAGTTATTAAT
*
10234791 ATTAA-TTATTAAT
1 AATAAGTTATTAAT
10234804 A
1 A
10234805 CCAAATTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (14 bp):
AATAAGTTATTAAT
Found at i:10235393 original size:13 final size:13
Alignment explanation
Indices: 10235375--10235399 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10235365 TAAAAAATCA
10235375 AAAAATTTTAAAT
1 AAAAATTTTAAAT
10235388 AAAAATTTTAAA
1 AAAAATTTTAAA
10235400 ACGGAAAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAATTTTAAAT
Found at i:10243539 original size:21 final size:23
Alignment explanation
Indices: 10243496--10243553 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
10243486 GTTATGAAAG
10243496 TTTTATATAATTTATAAAATATT
1 TTTTATATAATTTATAAAATATT
* *
10243519 TTTTATA-AATTT-TATATTATT
1 TTTTATATAATTTATAAAATATT
10243540 TTTTACT-TAATTTA
1 TTTTA-TATAATTTA
10243554 CGTATTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 12 0.40
22 11 0.37
23 7 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTATATAATTTATAAAATATT
Found at i:10243984 original size:26 final size:27
Alignment explanation
Indices: 10243955--10244041 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 27
10243945 TTATTTTAGA
*
10243955 ATATTTTTTA-AATTTTAACTTTCTTT
1 ATATTTTTTAGAATTTTAAGTTTCTTT
* *
10243981 ATATATTCTTTAGAATTTTTAAGTTTATAT
1 ATAT-TT-TTTAGAA-TTTTAAGTTTCTTT
10244011 ATATTTTTTAGAA-TTT-AGTTTCTTT
1 ATATTTTTTAGAATTTTAAGTTTCTTT
10244036 A-ATTTT
1 ATATTTT
10244042 ATTTTTAGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
24 5 0.10
25 8 0.15
26 7 0.13
27 2 0.04
28 11 0.21
29 4 0.08
30 15 0.29
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (27 bp):
ATATTTTTTAGAATTTTAAGTTTCTTT
Found at i:10259158 original size:31 final size:33
Alignment explanation
Indices: 10259098--10259165 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 33
10259088 AACACATCCA
*
10259098 AGGACTAAATTTTAAAAATCAGAAAATACATAT
1 AGGACTAAATTTGAAAAATCAGAAAATACATAT
*
10259131 AGGACTAAA-TTGAACAAAT-A-AAAATACATCT
1 AGGACTAAATTTGAA-AAATCAGAAAATACATAT
10259162 AGGA
1 AGGA
10259166 ACTTAGTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 14 0.44
32 5 0.16
33 13 0.41
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (33 bp):
AGGACTAAATTTGAAAAATCAGAAAATACATAT
Found at i:10259793 original size:29 final size:30
Alignment explanation
Indices: 10259746--10259826 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
10259736 GAATTGAATC
*
10259746 AAATCAAAATTTCATGTATAAAATTGCACA-
1 AAATC-AAAGTTCATGTATAAAATTGCACAT
* *
10259776 AAATCAAAGTTCGTGTATACAATTGCACATT
1 AAATCAAAGTTCATGTATAAAATTGCACA-T
*
10259807 AAATCATAGTTCATGTATAA
1 AAATCAAAGTTCATGTATAA
10259827 TTTTGAGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 21 0.49
30 5 0.12
31 17 0.40
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTGCACAT
Found at i:10259881 original size:3 final size:3
Alignment explanation
Indices: 10259873--10259898 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10259863 AGTTTAAAAC
10259873 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
10259899 GTAGTAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:10263148 original size:30 final size:32
Alignment explanation
Indices: 10263112--10263179 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 32
10263102 AATTTTTTAT
* *
10263112 ATTTTTATAATTTTTAAA-AGATTAAATTA-A
1 ATTTTTATAATTTTTAAAGAGATCAAAGTATA
*
10263142 ATTTTTATTATTTTTAAAGAGATCAAAGTATA
1 ATTTTTATAATTTTTAAAGAGATCAAAGTATA
10263174 ATTTTT
1 ATTTTT
10263180 TTTATTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 17 0.52
31 9 0.27
32 7 0.21
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (32 bp):
ATTTTTATAATTTTTAAAGAGATCAAAGTATA
Found at i:10274590 original size:31 final size:32
Alignment explanation
Indices: 10274555--10274614 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
10274545 AACAACCTAG
*
10274555 TAACTTAAATAAAAAA-TTTCGAATAATTCAA
1 TAACTTAAATAAAAAACTTTCAAATAATTCAA
10274586 TAACTTAAATAAAAAACTTTCAAATAATT
1 TAACTTAAATAAAAAACTTTCAAATAATT
10274615 TAATCAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (32 bp):
TAACTTAAATAAAAAACTTTCAAATAATTCAA
Found at i:10280746 original size:33 final size:33
Alignment explanation
Indices: 10280704--10280873 Score: 187
Period size: 33 Copynumber: 5.0 Consensus size: 33
10280694 GGAGATCATA
* **
10280704 GAGATCCAACAGAAATTAGAACGCCTGGAAATG
1 GAGATCCAACAGGAATTAGAATACCTGGAAATG
* *
10280737 GAGATCCAACAGGAATTGGAATGCCTGGAAATG
1 GAGATCCAACAGGAATTAGAATACCTGGAAATG
*
10280770 GAGCTCCTACAGCCACGGGAATTAGAATACCTGGAAATG
1 GAGATCC-A-A--CA--GGAATTAGAATACCTGGAAATG
* ** *
10280809 GAGCTCCTTCAGGAATTAGAATACCTGGAAATA
1 GAGATCCAACAGGAATTAGAATACCTGGAAATG
*
10280842 GAGATCCAACAAGAATTAGAATACCTGGAAAT
1 GAGATCCAACAGGAATTAGAATACCTGGAAAT
10280874 CGGGGTCCCG
Statistics
Matches: 118, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
33 85 0.72
34 1 0.01
35 3 0.03
37 2 0.02
39 27 0.23
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (33 bp):
GAGATCCAACAGGAATTAGAATACCTGGAAATG
Found at i:10292858 original size:28 final size:28
Alignment explanation
Indices: 10292818--10292987 Score: 182
Period size: 28 Copynumber: 6.1 Consensus size: 28
10292808 AAAAATCAGG
*
10292818 TGGAAAATCTGATTTGTCATTCTCTTAT
1 TGGAAAATCTGATTTGTCATTCTCCTAT
* * *
10292846 TGGAAAGTCTGATCTGTCATTTTCCTAT
1 TGGAAAATCTGATTTGTCATTCTCCTAT
* *
10292874 TGAAAAATTTGATTTGTCATT-TCCTAT
1 TGGAAAATCTGATTTGTCATTCTCCTAT
*
10292901 TGGAAAATCTGATTTTTCATTCTCCTAT
1 TGGAAAATCTGATTTGTCATTCTCCTAT
* * * **
10292929 TAGAAAATCTGATTTATCGTTCTTTTAT
1 TGGAAAATCTGATTTGTCATTCTCCTAT
* * *
10292957 T-GAAAATTTTGATTTGTCATTATTCTAT
1 TGGAAAA-TCTGATTTGTCATTCTCCTAT
10292985 TGG
1 TGG
10292988 TAAGGGATAT
Statistics
Matches: 118, Mismatches: 21, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
27 29 0.25
28 88 0.75
29 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.48
Consensus pattern (28 bp):
TGGAAAATCTGATTTGTCATTCTCCTAT
Found at i:10292958 original size:83 final size:84
Alignment explanation
Indices: 10292818--10292987 Score: 227
Period size: 83 Copynumber: 2.0 Consensus size: 84
10292808 AAAAATCAGG
* * * *
10292818 TGGAAAATCTGATTTGTCATTCTCTTATTGGAAAGTCTGATCTGTCATTTTCCTATTGAAAAATT
1 TGGAAAATCTGATTTGTCATTCTCCTATTAGAAAATCTGATCTATCATTTTCCTATTGAAAAATT
10292883 TGATTTGTCATT-TCCTAT
66 TGATTTGTCATTATCCTAT
* * * * *
10292901 TGGAAAATCTGATTTTTCATTCTCCTATTAGAAAATCTGATTTATCGTTCTT-TTATTGAAAATT
1 TGGAAAATCTGATTTGTCATTCTCCTATTAGAAAATCTGATCTATCATT-TTCCTATTGAAAAAT
*
10292965 TTGATTTGTCATTATTCTAT
65 TTGATTTGTCATTATCCTAT
10292985 TGG
1 TGG
10292988 TAAGGGATAT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
83 65 0.87
84 10 0.13
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.48
Consensus pattern (84 bp):
TGGAAAATCTGATTTGTCATTCTCCTATTAGAAAATCTGATCTATCATTTTCCTATTGAAAAATT
TGATTTGTCATTATCCTAT
Found at i:10292962 original size:55 final size:55
Alignment explanation
Indices: 10292820--10292986 Score: 185
Period size: 55 Copynumber: 3.0 Consensus size: 55
10292810 AAATCAGGTG
* * *
10292820 GAAAATCTGATTTGTCATTCTCTTATTGGAAAGTCTGATCTGTCATTTTCCTATT
1 GAAAATCTGATTTGTCATTCTCTTATTGGAAAATCTGATTTGTCATTCTCCTATT
* * *
10292875 GAAAAATTTGATTTGTCATT-TCCTATTGGAAAATCTGATTTTTCATTCTCCTATT
1 G-AAAATCTGATTTGTCATTCTCTTATTGGAAAATCTGATTTGTCATTCTCCTATT
* * * * * *
10292930 AGAAAATCTGATTTATCGTTCTTTTATT-GAAAATTTTGATTTGTCATTATTCTATT
1 -GAAAATCTGATTTGTCATTCTCTTATTGGAAAA-TCTGATTTGTCATTCTCCTATT
10292986 G
1 G
10292987 GTAAGGGATA
Statistics
Matches: 93, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
55 52 0.56
56 41 0.44
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (55 bp):
GAAAATCTGATTTGTCATTCTCTTATTGGAAAATCTGATTTGTCATTCTCCTATT
Found at i:10298740 original size:26 final size:24
Alignment explanation
Indices: 10298711--10298775 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
10298701 AAAATTTTGA
*
10298711 GACCCTTAAAAGTTGATAATTTTTTT
1 GACCCTTAAAAATT-A-AATTTTTTT
*
10298737 GACCTTTAAAAATTAAATTTTTTT
1 GACCCTTAAAAATTAAATTTTTTT
* *
10298761 AGATCCTTTAAAATT
1 -GACCCTTAAAAATT
10298776 TTAAAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 9 0.27
25 12 0.36
26 12 0.36
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (24 bp):
GACCCTTAAAAATTAAATTTTTTT
Done.