Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 67 of 109
Found at i:21689306 original size:45 final size:46
Alignment explanation
Indices: 21689257--21689354 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
21689247 AGATAGAAAC
*
21689257 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
21689302 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
21689348 GAAAATA
1 CAAAATA
21689355 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:21693908 original size:45 final size:46
Alignment explanation
Indices: 21693859--21693956 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
21693849 AGATAGAAAC
*
21693859 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
21693904 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
21693950 GAAAATA
1 CAAAATA
21693957 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:21702673 original size:8 final size:8
Alignment explanation
Indices: 21702660--21702722 Score: 58
Period size: 8 Copynumber: 7.8 Consensus size: 8
21702650 GTTTATTTAA
21702660 AATATAAT
1 AATATAAT
21702668 AATATAAT
1 AATATAAT
21702676 AATA-ATAT
1 AATATA-AT
21702684 AATATAAT
1 AATATAAT
* *
21702692 -ATAATTTAC
1 AAT-A-TAAT
21702701 AATATAAT
1 AATATAAT
*
21702709 AAAATAAT
1 AATATAAT
21702717 AATATA
1 AATATA
21702723 CTTCAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
7 3 0.07
8 35 0.80
9 4 0.09
10 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (8 bp):
AATATAAT
Found at i:21702674 original size:5 final size:5
Alignment explanation
Indices: 21702666--21702722 Score: 60
Period size: 5 Copynumber: 10.6 Consensus size: 5
21702656 TTAAAATATA
* *
21702666 ATAAT ATAAT AATAAT ATAAT ATAAT ATAATTT ACAAT ATAAT AAAAT
1 ATAAT ATAAT -ATAAT ATAAT ATAAT ATAA--T ATAAT ATAAT ATAAT
21702714 AATAAT ATA
1 -ATAAT ATA
21702723 CTTCAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 31 0.70
6 9 0.20
7 4 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:21705745 original size:25 final size:24
Alignment explanation
Indices: 21705708--21705756 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
21705698 TTGTAAATCA
21705708 GAAAAATATCTTT-AGAAATTTTCT
1 GAAAAATATCTTTAAG-AATTTTCT
*
21705732 GAAATAATCTCTTTAAGAATTTTCT
1 GAAA-AATATCTTTAAGAATTTTCT
21705757 CTTTGCAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 16 0.73
26 2 0.09
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (24 bp):
GAAAAATATCTTTAAGAATTTTCT
Found at i:21705895 original size:28 final size:29
Alignment explanation
Indices: 21705864--21705921 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
21705854 TAATCACTTT
* *
21705864 AATATTAAATTTAATTTAATA-CAAGATA
1 AATATGAAATTAAATTTAATATCAAGATA
*
21705892 AATATGAAATTAAATTTAATATTAAGATA
1 AATATGAAATTAAATTTAATATCAAGATA
21705921 A
1 A
21705922 TCACTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (29 bp):
AATATGAAATTAAATTTAATATCAAGATA
Found at i:21705980 original size:67 final size:65
Alignment explanation
Indices: 21705854--21705983 Score: 183
Period size: 67 Copynumber: 2.0 Consensus size: 65
21705844 TGATTAAACC
**
21705854 TAATCACTTTAATATTAAATTTAATTTAATACAAGATAAATATGAAATTAAATTTAATATTAAGA
1 TAATCACTTTAATATTAAATTTAATAAAATACAAGATAAATATGAAATTAAATTTAATATTAAGA
*
21705919 TAATCACTTTAATATTAAA-TTAATAAAATACTATTAAGAT-AATATTAAATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTTAATAAAATAC----AAGATAAATATGAAATTAAATTTAATATT
21705982 AA
62 AA
21705984 ATCTATTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
64 10 0.17
65 19 0.33
67 24 0.41
68 5 0.09
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (65 bp):
TAATCACTTTAATATTAAATTTAATAAAATACAAGATAAATATGAAATTAAATTTAATATTAAGA
Found at i:21705998 original size:37 final size:36
Alignment explanation
Indices: 21705927--21706002 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
21705917 GATAATCACT
*
21705927 TTAATATTAAATTAATAAAATACTATTAAGATAATA
1 TTAATATTAAATTAATAAAATACTATTAAAATAATA
21705963 TTAA-ATTAAATTTAATATTAAAT-CTATTAAAATAATA
1 TTAATATTAAA-TTAATA--AAATACTATTAAAATAATA
21706000 TTA
1 TTA
21706003 TTTTTGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
35 6 0.17
36 10 0.28
37 16 0.44
38 4 0.11
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:21710322 original size:8 final size:8
Alignment explanation
Indices: 21710309--21710371 Score: 58
Period size: 8 Copynumber: 7.8 Consensus size: 8
21710299 GTTTATTTAA
21710309 AATATAAT
1 AATATAAT
21710317 AATATAAT
1 AATATAAT
21710325 AATA-ATAT
1 AATATA-AT
21710333 AATATAAT
1 AATATAAT
* *
21710341 -ATAATTTAC
1 AAT-A-TAAT
21710350 AATATAAT
1 AATATAAT
*
21710358 AAAATAAT
1 AATATAAT
21710366 AATATA
1 AATATA
21710372 CTTCAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
7 3 0.07
8 35 0.80
9 4 0.09
10 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (8 bp):
AATATAAT
Found at i:21710323 original size:5 final size:5
Alignment explanation
Indices: 21710315--21710371 Score: 60
Period size: 5 Copynumber: 10.6 Consensus size: 5
21710305 TTAAAATATA
* *
21710315 ATAAT ATAAT AATAAT ATAAT ATAAT ATAATTT ACAAT ATAAT AAAAT
1 ATAAT ATAAT -ATAAT ATAAT ATAAT ATAA--T ATAAT ATAAT ATAAT
21710363 AATAAT ATA
1 -ATAAT ATA
21710372 CTTCAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 31 0.70
6 9 0.20
7 4 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:21713394 original size:25 final size:24
Alignment explanation
Indices: 21713357--21713405 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
21713347 TTGTAAATCA
21713357 GAAAAATATCTTT-AGAAATTTTCT
1 GAAAAATATCTTTAAG-AATTTTCT
*
21713381 GAAATAATCTCTTTAAGAATTTTCT
1 GAAA-AATATCTTTAAGAATTTTCT
21713406 CTTTGCAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 16 0.73
26 2 0.09
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (24 bp):
GAAAAATATCTTTAAGAATTTTCT
Found at i:21713573 original size:25 final size:24
Alignment explanation
Indices: 21713511--21713584 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 24
21713501 CCTAATCACT
* * *
21713511 TTAATATTAAATTAATAAATACTA
1 TTAATATTAAACTATTAAATAATA
* *
21713535 TTAAGA-T-AAGTATTAAATTAATA
1 TTAATATTAAACTATTAAA-TAATA
21713558 TTAATATTAAACTATTAAAATAATA
1 TTAATATTAAACTATT-AAATAATA
21713583 TT
1 TT
21713585 TTTTTTGGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
22 8 0.20
23 10 0.25
24 6 0.15
25 13 0.32
26 3 0.08
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (24 bp):
TTAATATTAAACTATTAAATAATA
Found at i:21715209 original size:5 final size:6
Alignment explanation
Indices: 21715194--21715218 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21715184 TCTTAGGCTA
21715194 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
21715219 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:21729396 original size:41 final size:41
Alignment explanation
Indices: 21729345--21729464 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 41
21729335 ACAAATCTTA
**
21729345 ATATGATACACCGGCACGAAGCCTGCTAGGCATAAAGCCTG
1 ATATGATACACCGGCATAAAGCCTGCTAGGCATAAAGCCTG
* * * **
21729386 ATATGGTACACCGGCATTAAGCCTGCTAGGCGTAAAATCTG
1 ATATGATACACCGGCATAAAGCCTGCTAGGCATAAAGCCTG
* * * *
21729427 ATATAATTCACCGGCATAAAGCCTACTAGGCACAAAGC
1 ATATGATACACCGGCATAAAGCCTGCTAGGCATAAAGC
21729465 TCGATTATCA
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (41 bp):
ATATGATACACCGGCATAAAGCCTGCTAGGCATAAAGCCTG
Found at i:21731538 original size:11 final size:11
Alignment explanation
Indices: 21731516--21731549 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
21731506 CTTCAATTAT
21731516 TTAATT-ATAA
1 TTAATTAATAA
21731526 TTAATTAATAA
1 TTAATTAATAA
21731537 TTAATTAATAA
1 TTAATTAATAA
21731548 TT
1 TT
21731550 CAAAAACCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTAATTAATAA
Found at i:21735612 original size:38 final size:38
Alignment explanation
Indices: 21735540--21735655 Score: 124
Period size: 38 Copynumber: 3.1 Consensus size: 38
21735530 AACTTTAATT
* * * * *
21735540 ACACCAGCAATAAACCTGCTAGGCACTAAGCCTGAATA
1 ACACCAGCACTAAGCATGCTAGGCACAAAACCTGAATA
** *
21735578 ACACTGGCACTAAGCATGCTAGGCACAAATCCTGAATA
1 ACACCAGCACTAAGCATGCTAGGCACAAAACCTGAATA
* * * *
21735616 TCACCAGCACTAAGCCTGCTATGCACAAAACTTGAATA
1 ACACCAGCACTAAGCATGCTAGGCACAAAACCTGAATA
21735654 AC
1 AC
21735656 GATATAACTC
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 63 1.00
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.18
Consensus pattern (38 bp):
ACACCAGCACTAAGCATGCTAGGCACAAAACCTGAATA
Found at i:21741201 original size:30 final size:30
Alignment explanation
Indices: 21741167--21741303 Score: 122
Period size: 30 Copynumber: 4.6 Consensus size: 30
21741157 TTATTTTTTG
* *
21741167 CATTTTAACCCCTATACTTTTC-AAAATTTA
1 CATTTTGACCCC-AAACTTTTCTAAAATTTA
21741197 CATTTTGACCCCAAACTTTTCTAAAATTTA
1 CATTTTGACCCCAAACTTTTCTAAAATTTA
*
21741227 CATTTTGACCCTAAAAC-TTTCTAAAA-TTA
1 CATTTTGACCC-CAAACTTTTCTAAAATTTA
* * * *
21741256 TATTTCGACCCTTAAAC-TTTCTCAAAA-TTG
1 CATTTTGACCC-CAAACTTTTCT-AAAATTTA
*
21741286 CACTTTGACCCCTAAACT
1 CATTTTGACCCC-AAACT
21741304 CTCAAGAAAT
Statistics
Matches: 91, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
29 30 0.33
30 57 0.63
31 4 0.04
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (30 bp):
CATTTTGACCCCAAACTTTTCTAAAATTTA
Found at i:21741303 original size:59 final size:60
Alignment explanation
Indices: 21741163--21741320 Score: 148
Period size: 59 Copynumber: 2.6 Consensus size: 60
21741153 TTTTTTATTT
* * *
21741163 TTTGCATTTTAACCCCTATACTTTTCAAAATTTACATTTTGACCCCAAACTTTTCTAAAA
1 TTTGCATTTTGACCCCTAAACTTTTCAAAATTTACATTTCGACCCCAAACTTTTCTAAAA
* * *
21741223 TTTACATTTTGA-CCCTAAAAC-TTTCTAAAA-TTATATTTCGACCCTTAAAC-TTTCTCAAAA
1 TTTGCATTTTGACCCCT-AAACTTTTC-AAAATTTACATTTCGACCC-CAAACTTTTCT-AAAA
* * *
21741283 -TTGCACTTTGACCCCTAAAC-TCTCAAGAAATTACATTT
1 TTTGCATTTTGACCCCTAAACTTTTCAA-AATTTACATTT
21741321 TGGCCCATAT
Statistics
Matches: 81, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
58 2 0.02
59 43 0.53
60 36 0.44
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.39
Consensus pattern (60 bp):
TTTGCATTTTGACCCCTAAACTTTTCAAAATTTACATTTCGACCCCAAACTTTTCTAAAA
Found at i:21741765 original size:20 final size:20
Alignment explanation
Indices: 21741742--21741782 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21741732 AGAAATCAAC
21741742 AAAAAAAACAACCAAGAAGA
1 AAAAAAAACAACCAAGAAGA
* * *
21741762 AAAAGAAGCAGCCAAGAAGA
1 AAAAAAAACAACCAAGAAGA
21741782 A
1 A
21741783 GGAGAAGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.15, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAAAAACAACCAAGAAGA
Found at i:21741788 original size:20 final size:19
Alignment explanation
Indices: 21741753--21741808 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
21741743 AAAAAAACAA
* *
21741753 CCAAGAAGAAAAAGAAGCAG
1 CCAAGAAG-AAGAGAAGAAG
21741773 CCAAGAAGAAGGAGAAGAAG
1 CCAAGAAGAA-GAGAAGAAG
*
21741793 -AAAGAAGAAGAGAAGA
1 CCAAGAAGAAGAGAAGA
21741809 GGAGACGCCG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 7 0.22
19 10 0.31
20 15 0.47
ACGTcount: A:0.61, C:0.09, G:0.30, T:0.00
Consensus pattern (19 bp):
CCAAGAAGAAGAGAAGAAG
Found at i:21741891 original size:4 final size:4
Alignment explanation
Indices: 21741884--21741953 Score: 72
Period size: 4 Copynumber: 17.5 Consensus size: 4
21741874 GGGAAGGAAG
* *
21741884 AAGA AAGA AAGA AAGA AA-A AAGA GAAAA AAGA AAGA AA-A AAGA GAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA -AAGA AAGA AAGA AAGA AAGA AAGA
* *
21741931 AAGA AAAA GAAGA AAAA AAGA AA
1 AAGA AAGA -AAGA AAGA AAGA AA
21741954 TACATTACAG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
3 6 0.11
4 42 0.78
5 6 0.11
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:21741911 original size:9 final size:9
Alignment explanation
Indices: 21741897--21741951 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
21741887 AAAGAAAGAA
21741897 AGAAAAAAG
1 AGAAAAAAG
21741906 AGAAAAAAG
1 AGAAAAAAG
21741915 AAAGAAAAAAG
1 --AGAAAAAAG
*
21741926 AG-AGAAAG
1 AGAAAAAAG
21741934 A-AAAAGAAG
1 AGAAAA-AAG
21741943 A-AAAAAAG
1 AGAAAAAAG
21741951 A
1 A
21741952 AATACATTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 12 0.30
9 19 0.47
11 9 0.22
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:21741914 original size:24 final size:23
Alignment explanation
Indices: 21741882--21741953 Score: 87
Period size: 22 Copynumber: 3.2 Consensus size: 23
21741872 AAGGGAAGGA
*
21741882 AGAAGAAAGAAAGAAAGAAAAAAG
1 AGAAAAAAGAAAG-AAGAAAAAAG
*
21741906 AGAAAAAAGAAAGAA-AAAAGAG
1 AGAAAAAAGAAAGAAGAAAAAAG
*
21741928 AGAAAGAA-AAAGAAGAAAAAA-
1 AGAAAAAAGAAAGAAGAAAAAAG
21741949 AGAAA
1 AGAAA
21741954 TACATTACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
21 11 0.26
22 18 0.42
23 2 0.05
24 12 0.28
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (23 bp):
AGAAAAAAGAAAGAAGAAAAAAG
Found at i:21741915 original size:28 final size:29
Alignment explanation
Indices: 21741881--21741953 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 29
21741871 GAAGGGAAGG
21741881 AAGAAGAAAGAAAGAAAGA-AAAAAGAGAA
1 AAGAAGAAAGAAAGAAAGAGAAAAAGA-AA
*
21741910 AA-AAGAAAGAAA-AAAGAGAGAAAGAAA
1 AAGAAGAAAGAAAGAAAGAGAAAAAGAAA
*
21741937 AAGAAGAAAAAAAGAAA
1 AAGAAGAAAGAAAGAAA
21741954 TACATTACAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 9 0.23
28 25 0.64
29 5 0.13
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (29 bp):
AAGAAGAAAGAAAGAAAGAGAAAAAGAAA
Found at i:21741926 original size:35 final size:36
Alignment explanation
Indices: 21741881--21741953 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 36
21741871 GAAGGGAAGG
*
21741881 AAGAAGAAAGAAAGAAAG-AAAA-AAGAGAAAAAAGA
1 AAGAAAAAAGAAAGAAAGAAAAAGAAGA-AAAAAAGA
*
21741916 AAGAAAAAAGAGAGAAAGAAAAAGAAGAAAAAAAGA
1 AAGAAAAAAGAAAGAAAGAAAAAGAAGAAAAAAAGA
21741952 AA
1 AA
21741954 TACATTACAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 16 0.47
36 14 0.41
37 4 0.12
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (36 bp):
AAGAAAAAAGAAAGAAAGAAAAAGAAGAAAAAAAGA
Found at i:21742078 original size:18 final size:20
Alignment explanation
Indices: 21742043--21742079 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
21742033 AAAAAAGAAA
*
21742043 AAAAAAGAAATAGTAGCAGC
1 AAAAAAGAAATAGCAGCAGC
21742063 AAAAAA-AAA-AGCAGCAG
1 AAAAAAGAAATAGCAGCAG
21742080 GCCAGGCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 3 0.19
20 6 0.38
ACGTcount: A:0.65, C:0.11, G:0.19, T:0.05
Consensus pattern (20 bp):
AAAAAAGAAATAGCAGCAGC
Found at i:21742901 original size:18 final size:18
Alignment explanation
Indices: 21742873--21743103 Score: 149
Period size: 18 Copynumber: 13.1 Consensus size: 18
21742863 TTCTGTATTT
*
21742873 TCTTCCGTGTTTTAAAAAA
1 TCTT-CGTGTTTTCAAAAA
*
21742892 TCTTCGTGTTTTCAAGAA
1 TCTTCGTGTTTTCAAAAA
*
21742910 TCCTCGTGTTTTC-AAAA
1 TCTTCGTGTTTTCAAAAA
*
21742927 T-TCCG-GTGTTTCAAAAA
1 TCTTCGTGT-TTTCAAAAA
* *
21742944 TTTTCATGTTTTCAAAAA
1 TCTTCGTGTTTTCAAAAA
*
21742962 T-TCCTGTGTTTT-AAAAA
1 TCTTC-GTGTTTTCAAAAA
21742979 T-TTCCGTGTTTTCAAAAA
1 TCTT-CGTGTTTTCAAAAA
* * * *
21742997 TTTTCGTATTTTTAAGAA
1 TCTTCGTGTTTTCAAAAA
* * *
21743015 TTTTCGTG-TCTCTAAAA
1 TCTTCGTGTTTTCAAAAA
21743032 T-TCTCGTGTTTT-AAAAA
1 TCT-TCGTGTTTTCAAAAA
*
21743049 TTTTTCGTGTTTTCAAAAA
1 -TCTTCGTGTTTTCAAAAA
** ***
21743068 AATAAATG-TTTCAAAAA
1 TCTTCGTGTTTTCAAAAA
*
21743085 TCTTCGTGTTTTTAAAAA
1 TCTTCGTGTTTTCAAAAA
21743103 T
1 T
21743104 TCTCGTATTT
Statistics
Matches: 166, Mismatches: 32, Indels: 29
0.73 0.14 0.13
Matches are distributed among these distances:
15 2 0.01
16 7 0.04
17 52 0.31
18 91 0.55
19 14 0.08
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (18 bp):
TCTTCGTGTTTTCAAAAA
Found at i:21742936 original size:35 final size:34
Alignment explanation
Indices: 21742897--21743066 Score: 118
Period size: 35 Copynumber: 4.9 Consensus size: 34
21742887 AAAAATCTTC
* *
21742897 GTGTTTTCAAGAATCCTCGTGTTTTCAAAATTCCG
1 GTGTTTTCAAAAAT-TTCGTGTTTTCAAAATTCCG
* *
21742932 GTG-TTTCAAAAATTTTCATGTTTTCAAAAATTCCT
1 GTGTTTTCAAAAA-TTTCGTGTTTTC-AAAATTCCG
*
21742967 GTGTTTT-AAAAATTTCCGTGTTTTCAAAAATTTTC-
1 GTGTTTTCAAAAATTT-CGTGTTTTC-AAAA-TTCCG
* * * *
21743002 GTATTTTTAAGAATTTTCGTG-TCTCTAAAATTCTC-
1 GTGTTTTCAA-AAATTTCGTGTTTTC-AAAATTC-CG
21743037 GTGTTTT-AAAAATTTTTCGTGTTTTCAAAA
1 GTGTTTTCAAAAA--TTTCGTGTTTTCAAAA
21743067 AAATAAATGT
Statistics
Matches: 110, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
33 2 0.02
34 24 0.22
35 64 0.58
36 15 0.14
37 5 0.05
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (34 bp):
GTGTTTTCAAAAATTTCGTGTTTTCAAAATTCCG
Found at i:21743032 original size:53 final size:52
Alignment explanation
Indices: 21742875--21743064 Score: 199
Period size: 53 Copynumber: 3.6 Consensus size: 52
21742865 CTGTATTTTC
* * ** *
21742875 TTCCGTGTTTTAAAAAATCTTCGTGTTTTCAAGAATCCTCGTGTTTTCAAAA
1 TTCCGTGTTTTCAAAAATTTTCGTGTTTTCAAGAATTTTCGTGTTTTAAAAA
* * *
21742927 TTCCG-GTGTTTCAAAAATTTTCATGTTTTCAA-AAATTCCTGTGTTTTAAAAA
1 TTCCGTGT-TTTCAAAAATTTTCGTGTTTTCAAGAATTTTC-GTGTTTTAAAAA
* * *
21742979 TTTCCGTGTTTTCAAAAATTTTCGTATTTTTAAGAATTTTCGTGTCTCT-AAAA
1 -TTCCGTGTTTTCAAAAATTTTCGTGTTTTCAAGAATTTTCGTGT-TTTAAAAA
21743032 TTCTCGTGTTTT-AAAAATTTTTCGTGTTTTCAA
1 TTC-CGTGTTTTCAAAAA-TTTTCGTGTTTTCAA
21743065 AAAAATAAAT
Statistics
Matches: 114, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
51 5 0.04
52 45 0.39
53 55 0.48
54 9 0.08
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (52 bp):
TTCCGTGTTTTCAAAAATTTTCGTGTTTTCAAGAATTTTCGTGTTTTAAAAA
Found at i:21749074 original size:17 final size:17
Alignment explanation
Indices: 21749052--21749086 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21749042 TTGATATTTG
21749052 CACATTACATGGCACCC
1 CACATTACATGGCACCC
21749069 CACATTACATGGCACCC
1 CACATTACATGGCACCC
21749086 C
1 C
21749087 TGAAGCCCCC
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:0.29, C:0.43, G:0.11, T:0.17
Consensus pattern (17 bp):
CACATTACATGGCACCC
Found at i:21754958 original size:1 final size:1
Alignment explanation
Indices: 21754952--21755046 Score: 73
Period size: 1 Copynumber: 95.0 Consensus size: 1
21754942 TATTATGCTT
* * * * * * * * * *
21754952 AAAAAAAACAAACAAAAAAAACAAAAAAAACAAAAAAACAAAAAACAGACAAAACAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
21755017 AAAAACAAAAAAAACAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21755047 TCAAGATGAA
Statistics
Matches: 68, Mismatches: 26, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:21754973 original size:9 final size:9
Alignment explanation
Indices: 21754955--21755046 Score: 113
Period size: 9 Copynumber: 10.7 Consensus size: 9
21754945 TATGCTTAAA
21754955 AAAAACAAAC
1 AAAAA-AAAC
21754965 AAAAAAAAC
1 AAAAAAAAC
21754974 AAAAAAAAC
1 AAAAAAAAC
21754983 -AAAAAAAC
1 AAAAAAAAC
21754991 --AAAAAAC
1 AAAAAAAAC
* *
21754998 AGACAAAAC
1 AAAAAAAAC
21755007 -AAAAAAAC
1 AAAAAAAAC
21755015 -AAAAAAAC
1 AAAAAAAAC
21755023 AAAAAAAAC
1 AAAAAAAAC
*
21755032 AAAAAAAAG
1 AAAAAAAAC
21755041 AAAAAA
1 AAAAAA
21755047 TCAAGATGAA
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
7 7 0.09
8 22 0.29
9 41 0.55
10 5 0.07
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:21754986 original size:17 final size:17
Alignment explanation
Indices: 21754955--21755038 Score: 111
Period size: 17 Copynumber: 4.9 Consensus size: 17
21754945 TATGCTTAAA
21754955 AAAAACAAACAAAAAAAAC
1 AAAAA-AAAC-AAAAAAAC
21754974 AAAAAAAACAAAAAAAC
1 AAAAAAAACAAAAAAAC
*
21754991 --AAAAAACAGACAAAAC
1 AAAAAAAACA-AAAAAAC
21755007 -AAAAAAACAAAAAAAC
1 AAAAAAAACAAAAAAAC
21755023 AAAAAAAACAAAAAAA
1 AAAAAAAACAAAAAAA
21755039 AGAAAAAATC
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
15 8 0.13
16 12 0.20
17 31 0.52
18 4 0.07
19 5 0.08
ACGTcount: A:0.86, C:0.13, G:0.01, T:0.00
Consensus pattern (17 bp):
AAAAAAAACAAAAAAAC
Found at i:21756021 original size:74 final size:74
Alignment explanation
Indices: 21755925--21756736 Score: 1581
Period size: 74 Copynumber: 11.0 Consensus size: 74
21755915 TTTTTCAAAA
21755925 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
1 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
21755990 CTTTTTTTT
66 CTTTTTTTT
21755999 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
1 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
21756064 CTTTTTTTT
66 CTTTTTTTT
21756073 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
1 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
21756138 CTTTTTTTT
66 CTTTTTTTT
21756147 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
1 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
21756212 CTTTTTTTT
66 CTTTTTTTT
21756221 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
1 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
21756286 CTTTTTTTT
66 CTTTTTTTT
21756295 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
1 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
21756360 CTTTTTTTT
66 CTTTTTTTT
21756369 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
1 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
21756434 CTTTTTTTT
66 CTTTTTTTT
21756443 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
1 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
21756508 CTTTTTTTT
66 CTTTTTTTT
21756517 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
1 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
21756582 CTTTTTTTT
66 CTTTTTTTT
* * *
21756591 AAATCAACTCATAATACAGAGGTGAGTTGAGCATCGGGTCACACTGAGGTATTTTTAATTTATGT
1 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
21756656 CTTTTTTTT
66 CTTTTTTTT
*
21756665 -AATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTATGT
1 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
21756729 CTTTTTTT
66 CTTTTTTT
21756737 NNNNNNNNNN
Statistics
Matches: 733, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
73 70 0.10
74 663 0.90
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (74 bp):
AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTTAATTTATGT
CTTTTTTTT
Found at i:21757578 original size:30 final size:30
Alignment explanation
Indices: 21757543--21757698 Score: 140
Period size: 30 Copynumber: 5.2 Consensus size: 30
21757533 TAAAAAATTG
*
21757543 CATTTTGACCCCTGTACTTTTCAAAATTTA
1 CATTTTGACCCCTATACTTTTCAAAATTTA
**
21757573 CATTTTGACCCCTATACTTTTTGAAATTTA
1 CATTTTGACCCCTATACTTTTCAAAATTTA
*
21757603 CATTTTGACCCC-AAACTTTTCTAAAA-TTA
1 CATTTTGACCCCTATACTTTTC-AAAATTTA
** ** *
21757632 CATTTCAACCTTTAAACTTTCTCAAAATTT-
1 CATTTTGACCCCTATACTTT-TCAAAATTTA
* * * *
21757662 CACTTTAACCCCTAAAC-TTTCAAGAAATTA
1 CATTTTGACCCCTATACTTTTCAA-AATTTA
21757692 CATTTTG
1 CATTTTG
21757699 GCCCATATTT
Statistics
Matches: 103, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
28 4 0.04
29 24 0.23
30 71 0.69
31 4 0.04
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.41
Consensus pattern (30 bp):
CATTTTGACCCCTATACTTTTCAAAATTTA
Found at i:21757651 original size:59 final size:59
Alignment explanation
Indices: 21757536--21757696 Score: 148
Period size: 59 Copynumber: 2.7 Consensus size: 59
21757526 AAAAAATTAA
* ** ** * *
21757536 AAAATTGCATTTTGACCCCTGTACTTTTCAAAATTTACATTTTGACCCCTATACTTT-TT
1 AAAATTTCATTTTGACCCCTAAACTTTTCAAAA-TTACATTTCAACCCCTAAACTTTCTC
* **
21757595 GAAATTTACATTTTGACCCC-AAACTTTTCTAAAATTACATTTCAACCTTTAAACTTTCTC
1 AAAATTT-CATTTTGACCCCTAAACTTTTC-AAAATTACATTTCAACCCCTAAACTTTCTC
* *
21757655 AAAATTTCACTTTAACCCCTAAAC-TTTCAAGAAATTACATTT
1 AAAATTTCATTTTGACCCCTAAACTTTTC-A-AAATTACATTT
21757697 TGGCCCATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 9
0.78 0.13 0.08
Matches are distributed among these distances:
59 45 0.54
60 38 0.46
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (59 bp):
AAAATTTCATTTTGACCCCTAAACTTTTCAAAATTACATTTCAACCCCTAAACTTTCTC
Found at i:21758274 original size:4 final size:4
Alignment explanation
Indices: 21758267--21758316 Score: 57
Period size: 4 Copynumber: 12.5 Consensus size: 4
21758257 GGGAAGGAAG
* * *
21758267 AAGA AAGA AAGA AAGA AA-A AAGA GAGA AAGA AAAA GAAGA AAAA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA -AAGA AAGA AAGA
21758315 AA
1 AA
21758317 TACATTACAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 3 0.08
4 32 0.84
5 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:21758288 original size:15 final size:15
Alignment explanation
Indices: 21758264--21758316 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
21758254 GAAGGGAAGG
*
21758264 AAGAAGAAAGAAAGA
1 AAGAAAAAAGAAAGA
*
21758279 AAGAAAAAAGAGAGA
1 AAGAAAAAAGAAAGA
*
21758294 AAGAAAAAGAAGAAAAA
1 AAG-AAAA-AAGAAAGA
21758311 AAGAAA
1 AAGAAA
21758317 TACATTACAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 16 0.50
16 7 0.22
17 9 0.28
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAGAAAGA
Found at i:21758433 original size:18 final size:20
Alignment explanation
Indices: 21758401--21758437 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
21758391 AAAAAAAGAA
21758401 AAAAAAGAAATAGCAGCAGC
1 AAAAAAGAAATAGCAGCAGC
21758421 AAAAAA-AAA-AGCAGCAG
1 AAAAAAGAAATAGCAGCAG
21758438 GCCAGGCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.65, C:0.14, G:0.19, T:0.03
Consensus pattern (20 bp):
AAAAAAGAAATAGCAGCAGC
Found at i:21758581 original size:13 final size:13
Alignment explanation
Indices: 21758565--21758589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21758555 GAAAAAAGAA
21758565 AAAAAACAAAAAC
1 AAAAAACAAAAAC
21758578 AAAAAACAAAAA
1 AAAAAACAAAAA
21758590 AGGCCCGAAT
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:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:21759277 original size:53 final size:52
Alignment explanation
Indices: 21759198--21759384 Score: 193
Period size: 53 Copynumber: 3.5 Consensus size: 52
21759188 CTGTATTTTC
* *
21759198 TTCCGTGTTTTAAAAAATTTCGTGTTTTTCAAGAATCCTCGTGTTTTCAAAA
1 TTCCGTGTTTCAAAAATTTTCGTGTTTTTCAAGAATCCTCGTGTTTTCAAAA
* * *
21759250 TTCCGGTGTTTCAAAAATTTTCATG-TTTTCAAAAATTCCT-GTGTTTTAAAAA
1 TTCC-GTGTTTCAAAAATTTTCGTGTTTTTCAAGAA-TCCTCGTGTTTTCAAAA
* ** *
21759302 TTTCCGTGTTTTCAAAAATTTTCGTATTTTT-AAGAATTTTCGTG-TCTCTAAAA
1 -TTCCGTG-TTTCAAAAATTTTCGTGTTTTTCAAGAATCCTCGTGTTTTC-AAAA
*
21759355 TTCTCGTGTTTTAAAAATTTTTCGTGTTTT
1 TTC-CGTGTTTCAAAAA-TTTTCGTGTTTT
21759385 CAAAAAAATA
Statistics
Matches: 112, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
52 42 0.38
53 66 0.59
54 4 0.04
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.48
Consensus pattern (52 bp):
TTCCGTGTTTCAAAAATTTTCGTGTTTTTCAAGAATCCTCGTGTTTTCAAAA
Found at i:21759281 original size:18 final size:18
Alignment explanation
Indices: 21759201--21759437 Score: 168
Period size: 18 Copynumber: 13.4 Consensus size: 18
21759191 TATTTTCTTC
*
21759201 CGTGTTTT-AAAAAATTT
1 CGTGTTTTCAAAAATTTT
* **
21759218 CGTGTTTTTCAAGAATCCT
1 CGTG-TTTTCAAAAATTTT
*
21759237 CGTGTTTTC-AAAA-TTC
1 CGTGTTTTCAAAAATTTT
21759253 CG-GTGTTTCAAAAATTTT
1 CGTGT-TTTCAAAAATTTT
* *
21759271 CATGTTTTCAAAAA-TTC
1 CGTGTTTTCAAAAATTTT
*
21759288 CTGTGTTTT-AAAAATTTC
1 C-GTGTTTTCAAAAATTTT
21759306 CGTGTTTTCAAAAATTTT
1 CGTGTTTTCAAAAATTTT
* * *
21759324 CGTATTTTTAAGAATTTT
1 CGTGTTTTCAAAAATTTT
* * *
21759342 CGTG-TCTCTAAAATTCT
1 CGTGTTTTCAAAAATTTT
21759359 CGTGTTTT-AAAAATTTTT
1 CGTGTTTTCAAAAA-TTTT
** *
21759377 CGTGTTTTCAAAAAAATA
1 CGTGTTTTCAAAAATTTT
** *
21759395 AATG-TTTCAAAAATCTT
1 CGTGTTTTCAAAAATTTT
* *
21759412 CGTGTTTTTAAAAATTCT
1 CGTGTTTTCAAAAATTTT
*
21759430 CGTATTTT
1 CGTGTTTT
21759438 GATCTGATCG
Statistics
Matches: 168, Mismatches: 39, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
15 2 0.01
16 6 0.04
17 54 0.32
18 90 0.54
19 16 0.10
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (18 bp):
CGTGTTTTCAAAAATTTT
Found at i:21759285 original size:35 final size:34
Alignment explanation
Indices: 21759201--21759437 Score: 181
Period size: 35 Copynumber: 6.7 Consensus size: 34
21759191 TATTTTCTTC
* * * **
21759201 CGTGTTTTAAAAAATTTCGTGTTTTTCAAGAATCCT
1 CGTGTTTTCAAAAATTCCGTG-TTTT-AAAAATTTT
*
21759237 CGTGTTTTC-AAAATTCCGGTGTTTCAAAAATTTT
1 CGTGTTTTCAAAAATTCC-GTGTTTTAAAAATTTT
* *
21759271 CATGTTTTCAAAAATTCCTGTGTTTTAAAAATTTC
1 CGTGTTTTCAAAAATTCC-GTGTTTTAAAAATTTT
* * *
21759306 CGTGTTTTCAAAAATTTTCGTATTTTTAAGAATTTT
1 CGTGTTTTCAAAAA-TTCCGT-GTTTTAAAAATTTT
* *
21759342 CGTG-TCTCTAAAATTCTCGTGTTTTAAAAATTTTT
1 CGTGTTTTCAAAAATTC-CGTGTTTTAAAAA-TTTT
* *** * *
21759377 CGTGTTTTCAAAAAAATAAATGTTTCAAAAATCTT
1 CGTGTTTTC-AAAAATTCCGTGTTTTAAAAATTTT
* *
21759412 CGTGTTTTTAAAAATTCTCGTATTTT
1 CGTGTTTTCAAAAATTC-CGTGTTTT
21759438 GATCTGATCG
Statistics
Matches: 157, Mismatches: 35, Indels: 19
0.74 0.17 0.09
Matches are distributed among these distances:
34 30 0.19
35 80 0.51
36 42 0.27
37 5 0.03
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (34 bp):
CGTGTTTTCAAAAATTCCGTGTTTTAAAAATTTT
Found at i:21760048 original size:54 final size:54
Alignment explanation
Indices: 21759937--21760053 Score: 146
Period size: 54 Copynumber: 2.2 Consensus size: 54
21759927 AATGAATTGT
* * * * *
21759937 CTTTGTGGCATACTCTGTATATATCACCTTTGTGGCATACTCTGTATATGTCGC
1 CTTTGTGGCATACTCTCTATATATAACCTTTGTGACATACTCTGTATAGGTCAC
* **
21759991 CTTTGTGGTATACTCTCTATATATAACCTTTGTGATGTACTCTGTAT-GGATCAC
1 CTTTGTGGCATACTCTCTATATATAACCTTTGTGACATACTCTGTATAGG-TCAC
21760045 CTTTGTGGC
1 CTTTGTGGC
21760054 GTATTCTGTA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.02
54 52 0.98
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (54 bp):
CTTTGTGGCATACTCTCTATATATAACCTTTGTGACATACTCTGTATAGGTCAC
Found at i:21760061 original size:27 final size:27
Alignment explanation
Indices: 21759937--21760063 Score: 130
Period size: 27 Copynumber: 4.7 Consensus size: 27
21759927 AATGAATTGT
*
21759937 CTTTGTGGCATACTCTGTATATATCAC
1 CTTTGTGGCATACTCTGTATAGATCAC
*
21759964 CTTTGTGGCATACTCTGTATATG-TCGC
1 CTTTGTGGCATACTCTGTATA-GATCAC
* * * *
21759991 CTTTGTGGTATACTCTCTATATATAAC
1 CTTTGTGGCATACTCTGTATAGATCAC
*** *
21760018 CTTTGTGATGTACTCTGTATGGATCAC
1 CTTTGTGGCATACTCTGTATAGATCAC
* *
21760045 CTTTGTGGCGTATTCTGTA
1 CTTTGTGGCATACTCTGTA
21760064 ATAAGGACTT
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (27 bp):
CTTTGTGGCATACTCTGTATAGATCAC
Found at i:21762211 original size:17 final size:17
Alignment explanation
Indices: 21762179--21762273 Score: 63
Period size: 16 Copynumber: 5.5 Consensus size: 17
21762169 ATCAATAATT
*
21762179 ATTTAAAAAAAT-TAAA
1 ATTTAAAAAATTATAAA
21762195 ATTTAAAAAATTATAAA
1 ATTTAAAAAATTATAAA
*
21762212 ATTTTATAAAAAAATTTTAATA
1 A--TT-T-AAAAAATTATAA-A
* *
21762234 ATATAAAAAATTAT-GA
1 ATTTAAAAAATTATAAA
*
21762250 A-TTATAAAA-TATAAA
1 ATTTAAAAAATTATAAA
21762265 GATTTAAAA
1 -ATTTAAAA
21762274 GTAAAAAATA
Statistics
Matches: 61, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
14 3 0.05
15 7 0.11
16 14 0.23
17 10 0.16
18 9 0.15
19 3 0.05
20 2 0.03
21 11 0.18
22 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATTTAAAAAATTATAAA
Found at i:21764314 original size:15 final size:15
Alignment explanation
Indices: 21764294--21764329 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
21764284 CTTGTGGATT
21764294 TGAACTAGTACATAA
1 TGAACTAGTACATAA
21764309 TGAACTAGTACATAA
1 TGAACTAGTACATAA
21764324 TGAACT
1 TGAACT
21764330 GAGTGAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (15 bp):
TGAACTAGTACATAA
Found at i:21766536 original size:30 final size:30
Alignment explanation
Indices: 21766500--21766560 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
21766490 ACAAAAGAAG
*
21766500 TAAGGAAATTAGGTCCGAAACTAGTGACAA
1 TAAGGAAATTAGGTCCAAAACTAGTGACAA
21766530 TAAGGAAATTAGGTCCAAAACTAGTGACAA
1 TAAGGAAATTAGGTCCAAAACTAGTGACAA
21766560 T
1 T
21766561 CCTTTGTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.21
Consensus pattern (30 bp):
TAAGGAAATTAGGTCCAAAACTAGTGACAA
Found at i:21769927 original size:16 final size:16
Alignment explanation
Indices: 21769906--21769940 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
21769896 AAAAAATTAA
21769906 TTAATTTTTATCATTT
1 TTAATTTTTATCATTT
*
21769922 TTAATTTTTATTATTT
1 TTAATTTTTATCATTT
21769938 TTA
1 TTA
21769941 TATAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTAATTTTTATCATTT
Found at i:21769991 original size:18 final size:18
Alignment explanation
Indices: 21769962--21770017 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
21769952 AAAAATTTAT
*
21769962 ATTTTTTAAATTGTTAACA
1 ATTTTTT-AATTATTAACA
* *
21769981 ATTTTTTAATTTTTAAAA
1 ATTTTTTAATTATTAACA
*
21769999 ATTTAATTAATTATTAACA
1 ATTT-TTTAATTATTAACA
21770018 TGACTTACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTTTTTAATTATTAACA
Found at i:21770557 original size:26 final size:27
Alignment explanation
Indices: 21770512--21770563 Score: 88
Period size: 26 Copynumber: 1.9 Consensus size: 27
21770502 TAATATTGAA
21770512 AAAGAGATATTAAATTTTTAAATTTTCT
1 AAAGAGATA-TAAATTTTTAAATTTTCT
21770540 AAAGAGATA-AAATTTTTAAATTTT
1 AAAGAGATATAAATTTTTAAATTTT
21770564 TTGAGACCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 15 0.62
28 9 0.38
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (27 bp):
AAAGAGATATAAATTTTTAAATTTTCT
Found at i:21771804 original size:42 final size:42
Alignment explanation
Indices: 21771749--21771930 Score: 249
Period size: 42 Copynumber: 4.3 Consensus size: 42
21771739 ATTTGCAGCG
21771749 TTTTTTCTAAGCGCCTCTAAAGAACATGGTCTTTAGCGGCGT
1 TTTTTTCTAAGCGCCTCTAAAGAACATGGTCTTTAGCGGCGT
* *
21771791 TTTTTTCTAAGCGCCGT-GAAAGAACATGGTCTTTAGTGGCGT
1 TTTTTTCTAAGCGCC-TCTAAAGAACATGGTCTTTAGCGGCGT
* * * * *
21771833 TTCTTTCTAAGCGCCACTAAAGAACATTGCCTTTAGCTGCGTT
1 TTTTTTCTAAGCGCCTCTAAAGAACATGGTCTTTAGCGGCG-T
* **
21771876 TTTTTTCTAAGCGCCGCTAAAGAACATTATCTTTAGCGGCGT
1 TTTTTTCTAAGCGCCTCTAAAGAACATGGTCTTTAGCGGCGT
21771918 TTTTTTCTAAGCG
1 TTTTTTCTAAGCG
21771931 TCATGTTCTT
Statistics
Matches: 123, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
42 85 0.69
43 38 0.31
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (42 bp):
TTTTTTCTAAGCGCCTCTAAAGAACATGGTCTTTAGCGGCGT
Found at i:21771919 original size:85 final size:83
Alignment explanation
Indices: 21771746--21771930 Score: 264
Period size: 85 Copynumber: 2.2 Consensus size: 83
21771736 AACATTTGCA
* *
21771746 GCGTTTTTTCTAAGCGCCTCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGTGAA
1 GCGTTTTTTCTAAGCGCCACTAAAGAACATGGCCTTTAGCGGCGTTTTTTTCTAAGCGCCGTGAA
* *
21771811 AGAACATGGTCTTTAGTG
66 AGAACATGATCTTTAGCG
* *
21771829 GCGTTTCTTTCTAAGCGCCACTAAAGAACATTGCCTTTAGCTGCGTTTTTTTTCTAAGCGCCGCT
1 GCGTTT-TTTCTAAGCGCCACTAAAGAACATGGCCTTTAGCGGCG-TTTTTTTCTAAGCGCCG-T
*
21771894 -AAAGAACATTATCTTTAGCG
63 GAAAGAACATGATCTTTAGCG
21771914 GCGTTTTTTTCTAAGCG
1 GCG-TTTTTTCTAAGCG
21771931 TCATGTTCTT
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
83 6 0.07
84 34 0.37
85 47 0.52
86 4 0.04
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (83 bp):
GCGTTTTTTCTAAGCGCCACTAAAGAACATGGCCTTTAGCGGCGTTTTTTTCTAAGCGCCGTGAA
AGAACATGATCTTTAGCG
Found at i:21779190 original size:23 final size:23
Alignment explanation
Indices: 21779151--21779206 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
21779141 TGTAAGATTG
21779151 TAATTTTTTA-AATATTTT-AAT
1 TAATTTTTTATAATATTTTAAAT
21779172 TAATTTTTTATAATCATTTTAAAT
1 TAATTTTTTATAAT-ATTTTAAAT
*
21779196 T-ATTTATTATA
1 TAATTTTTTATA
21779207 TGAAATGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 10 0.32
22 3 0.10
23 14 0.45
24 4 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TAATTTTTTATAATATTTTAAAT
Found at i:21781659 original size:16 final size:18
Alignment explanation
Indices: 21781629--21781661 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21781619 ATACGACACC
21781629 AAAATAATAATATGATAA
1 AAAATAATAATATGATAA
21781647 AAAATAA-AA-ATGATA
1 AAAATAATAATATGATA
21781662 TTTTTGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (18 bp):
AAAATAATAATATGATAA
Found at i:21789540 original size:37 final size:37
Alignment explanation
Indices: 21789499--21789575 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
21789489 GATTAATTTG
*
21789499 TCTATTTTTAAATAAAAACGATAAAATATAATCTAAC
1 TCTATTTTTAAATAAAAACGACAAAATATAATCTAAC
21789536 TCTATTTTTAAATAAAAACGACAAAATATAATCTAAC
1 TCTATTTTTAAATAAAAACGACAAAATATAATCTAAC
21789573 TCT
1 TCT
21789576 TAATACAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (37 bp):
TCTATTTTTAAATAAAAACGACAAAATATAATCTAAC
Found at i:21796785 original size:41 final size:43
Alignment explanation
Indices: 21796696--21796835 Score: 103
Period size: 41 Copynumber: 3.3 Consensus size: 43
21796686 GTCCCGGATG
*
21796696 TGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGATA
1 TGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACA
* ** **
21796739 GGGTCTTACATG-AATCGTATA-CGATGCCGA-TGTCTTAGACA
1 TGGTCTTACATGTAATCAAATATCGATGCC-ACTGTCCCAGACA
* * **
21796780 TGGTCTCACACGTAAATCTCAAAT-T-GATGCCAAC-GTCCCAGATG
1 TGGTCTTACATGT-AA--TCAAATATCGATGCC-ACTGTCCCAGACA
21796824 TGGTCTTACATG
1 TGGTCTTACATG
21796836 ATAACTCATA
Statistics
Matches: 72, Mismatches: 18, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
41 24 0.33
42 8 0.11
43 13 0.18
44 23 0.32
45 4 0.06
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
TGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACA
Found at i:21799665 original size:11 final size:10
Alignment explanation
Indices: 21799644--21799677 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
21799634 TTTATTTAAA
21799644 ATATACATAT
1 ATATACATAT
21799654 ATATAGCATAT
1 ATATA-CATAT
*
21799665 ATATATATAT
1 ATATACATAT
21799675 ATA
1 ATA
21799678 AATGTACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (10 bp):
ATATACATAT
Found at i:21800399 original size:7 final size:7
Alignment explanation
Indices: 21800387--21800422 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
21800377 ATTATATGAT
21800387 TTTATTA
1 TTTATTA
21800394 TTTATTA
1 TTTATTA
21800401 TTTATTA
1 TTTATTA
21800408 TTTATTA
1 TTTATTA
21800415 TTTATTA
1 TTTATTA
21800422 T
1 T
21800423 GTCCTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:21806461 original size:37 final size:36
Alignment explanation
Indices: 21806393--21806654 Score: 235
Period size: 37 Copynumber: 7.1 Consensus size: 36
21806383 ATCTTCTACT
** *
21806393 AAGGTTGTATTAGAC-GGCTCTATCTCAACCTTTTTA
1 AAGGTTGCCTTAGACAGG-TCTATCCCAACCTTTTTA
21806429 AAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTA
1 AAGGTTGCCTTAGAC-AGGTCTATCCCAACCTTTTTA
* *
21806466 AGGGTTGCCTTAGACAAGATTCTATCCCAACCTTTTT-
1 AAGGTTGCCTTAGAC-AG-GTCTATCCCAACCTTTTTA
* ** * **
21806503 AAGGTTGCCATAGAC-GGCTCCGTCTCAAATTTTTTTA
1 AAGGTTGCCTTAGACAGG-TCTATC-CCAACCTTTTTA
* * **
21806540 AAGGCTGCCTTAGACAAGGTCTATGCCGGCCTTTTT-
1 AAGGTTGCCTTAGAC-AGGTCTATCCCAACCTTTTTA
* *
21806576 AAGGTTGTCTTAGACAGGTCTATCCTAACCTTTTTTA
1 AAGGTTGCCTTAGACAGGTCTATCCCAACC-TTTTTA
* * *
21806613 AAGGTTACCTTAGACGGGTCTATCTCAACCTTTTTTA
1 AAGGTTGCCTTAGACAGGTCTATCCCAACC-TTTTTA
21806650 AAGGT
1 AAGGT
21806655 CGACCTTGAC
Statistics
Matches: 182, Mismatches: 34, Indels: 19
0.77 0.14 0.08
Matches are distributed among these distances:
35 16 0.09
36 39 0.21
37 103 0.57
38 22 0.12
39 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.35
Consensus pattern (36 bp):
AAGGTTGCCTTAGACAGGTCTATCCCAACCTTTTTA
Found at i:21806611 original size:74 final size:73
Alignment explanation
Indices: 21806411--21806647 Score: 248
Period size: 73 Copynumber: 3.2 Consensus size: 73
21806401 ATTAGACGGC
* * *
21806411 TCTATCTCAACCTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACC-TTTTTAAGGGTTGCC
1 TCTATCCCAACCTTTTT-AAGGTTGCCTTAGAC-AGGTCTATCCTAACCTTTTTTAAAGGTTGCC
*
21806475 TTAGACAAGAT
64 TTAGACAAG-G
* ** ** *
21806486 TCTATCCCAACCTTTTTAAGGTTGCCATAGAC-GGCTCCGT-CTCAAATTTTTTTAAAGGCTGCC
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGG-TCTATCCT-AACCTTTTTTAAAGGTTGCC
21806549 TTAGACAAGG
64 TTAGACAAGG
* ** * *
21806559 TCTATGCCGGCCTTTTTAAGGTTGTCTTAGACAGGTCTATCCTAACCTTTTTTAAAGGTTACCTT
1 TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCTAACCTTTTTTAAAGGTTGCCTT
*
21806624 AGAC-GGG
66 AGACAAGG
*
21806631 TCTATCTCAACCTTTTT
1 TCTATCCCAACCTTTTT
21806648 TAAAGGTCGA
Statistics
Matches: 131, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
72 18 0.14
73 57 0.44
74 40 0.31
75 16 0.12
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (73 bp):
TCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCTAACCTTTTTTAAAGGTTGCCTT
AGACAAGG
Found at i:21807098 original size:11 final size:11
Alignment explanation
Indices: 21807082--21807121 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
21807072 CTTTCAATAA
21807082 TAATAATAATT
1 TAATAATAATT
*
21807093 TAATAATTATT
1 TAATAATAATT
21807104 TAAATAATAATT
1 T-AATAATAATT
*
21807116 TGATAA
1 TAATAA
21807122 ACGTAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (11 bp):
TAATAATAATT
Found at i:21810751 original size:29 final size:31
Alignment explanation
Indices: 21810717--21810780 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
21810707 TCCTAAAATT
21810717 AAAATTTGAGAA-GTTTAATAA-AATT-TTTA
1 AAAATTTGA-AAGGTTTAATAATAATTATTTA
* *
21810746 AAAATTTTAAAGGTTTAGTAATAATTATTTA
1 AAAATTTGAAAGGTTTAATAATAATTATTTA
21810777 AAAA
1 AAAA
21810781 AATAAATGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 16 0.53
30 4 0.13
31 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (31 bp):
AAAATTTGAAAGGTTTAATAATAATTATTTA
Found at i:21811714 original size:28 final size:28
Alignment explanation
Indices: 21811669--21811722 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
21811659 AATCCTTGAA
*
21811669 CCTAAACCTTAAACTCTGAATCCAAAAC
1 CCTAAACCTTAAACTCTGAACCCAAAAC
**
21811697 CCTAAACCTTAAGTTCTGAACCCAAA
1 CCTAAACCTTAAACTCTGAACCCAAA
21811723 TCCTGAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.41, C:0.31, G:0.06, T:0.22
Consensus pattern (28 bp):
CCTAAACCTTAAACTCTGAACCCAAAAC
Found at i:21821998 original size:60 final size:60
Alignment explanation
Indices: 21821878--21821999 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 60
21821868 CCAATGTAAA
* * *
21821878 AACAATTGCTAAGTCCAGGGCCTAACTTGGACAAAAAAAAAGTTTACACCTCAATGTGGG
1 AACAATTGCTAAGTCCAGGGCCTAACTTGAACAAAAAAAAAGTTCACACCTAAATGTGGG
* * * * * ** *
21821938 AACAATTGTTAAGTTCAGGGCTTAACTTGAACCAATAAAAAGTTCAGGCCTAAATTTGGG
1 AACAATTGCTAAGTCCAGGGCCTAACTTGAACAAAAAAAAAGTTCACACCTAAATGTGGG
21821998 AA
1 AA
21822000 AAGTTGTCAA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.25
Consensus pattern (60 bp):
AACAATTGCTAAGTCCAGGGCCTAACTTGAACAAAAAAAAAGTTCACACCTAAATGTGGG
Found at i:21823499 original size:17 final size:20
Alignment explanation
Indices: 21823449--21823493 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
21823439 AAAAACTGTA
*
21823449 TTTTTACTATTTTCTTGTTG
1 TTTTTATTATTTTCTTGTTG
21823469 TTTTTATTATTTTCTTGTTG
1 TTTTTATTATTTTCTTGTTG
21823489 TTTTT
1 TTTTT
21823494 TTTTTCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.09, C:0.07, G:0.09, T:0.76
Consensus pattern (20 bp):
TTTTTATTATTTTCTTGTTG
Found at i:21823551 original size:9 final size:11
Alignment explanation
Indices: 21823521--21823552 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
21823511 ATTATTTCAC
21823521 TACTATATTGT
1 TACTATATTGT
21823532 TACTATATTGT
1 TACTATATTGT
21823543 TA-T-TATTGT
1 TACTATATTGT
21823552 T
1 T
21823553 TGGATATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 7 0.33
10 1 0.05
11 13 0.62
ACGTcount: A:0.25, C:0.06, G:0.09, T:0.59
Consensus pattern (11 bp):
TACTATATTGT
Found at i:21831009 original size:9 final size:10
Alignment explanation
Indices: 21830993--21831049 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
21830983 AGCTCTAAAC
21830993 TATAAAAAAT
1 TATAAAAAAT
21831003 T-T-AAAAAT
1 TATAAAAAAT
21831011 TAT-AAAAA-
1 TATAAAAAAT
* *
21831019 TATTAATAAT
1 TATAAAAAAT
**
21831029 TATTTAAAAT
1 TATAAAAAAT
21831039 TATAAAAAAT
1 TATAAAAAAT
21831049 T
1 T
21831050 GAAACGAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 10 0.26
9 11 0.28
10 18 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TATAAAAAAT
Found at i:21831016 original size:18 final size:17
Alignment explanation
Indices: 21830997--21831046 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
21830987 CTAAACTATA
21830997 AAAAATTTAAAAATTAT
1 AAAAATTTAAAAATTAT
*
21831014 AAAAATATTAATAATTATT
1 AAAAAT-TTAAAAATTA-T
*
21831033 TAAAATTATAAAAA
1 AAAAATT-TAAAAA
21831047 ATTGAAACGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 6 0.22
18 10 0.37
19 11 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAATTTAAAAATTAT
Found at i:21831049 original size:10 final size:9
Alignment explanation
Indices: 21830997--21831046 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
21830987 CTAAACTATA
21830997 AAAAATT-T
1 AAAAATTAT
21831005 AAAAATTAT
1 AAAAATTAT
21831014 AAAAA-TATT
1 AAAAATTA-T
*
21831023 AATAATTATT
1 AAAAATTA-T
*
21831033 TAAAATTAT
1 AAAAATTAT
21831042 AAAAA
1 AAAAA
21831047 ATTGAAACGA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 9 0.26
9 16 0.46
10 10 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAAATTAT
Found at i:21832791 original size:17 final size:18
Alignment explanation
Indices: 21832769--21832802 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
21832759 AGGCCAGAAT
21832769 GGGCGTGTGGG-CTACAC
1 GGGCGTGTGGGCCTACAC
21832786 GGGCGTGTGGGCCTACA
1 GGGCGTGTGGGCCTACA
21832803 AGGGTGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.12, C:0.24, G:0.47, T:0.18
Consensus pattern (18 bp):
GGGCGTGTGGGCCTACAC
Found at i:21834148 original size:30 final size:30
Alignment explanation
Indices: 21834114--21834175 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
21834104 ATTTTTTTAA
21834114 TAAATTTAATATTTATTATTATTGATGTGG
1 TAAATTTAATATTTATTATTATTGATGTGG
21834144 TAAATTTAATATTTATTATTATTGATGTGG
1 TAAATTTAATATTTATTATTATTGATGTGG
21834174 TA
1 TA
21834176 TACTTTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (30 bp):
TAAATTTAATATTTATTATTATTGATGTGG
Found at i:21834364 original size:15 final size:15
Alignment explanation
Indices: 21834344--21834373 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21834334 CATACATTAA
21834344 ACAACAAGATTATCC
1 ACAACAAGATTATCC
21834359 ACAACAAGATTATCC
1 ACAACAAGATTATCC
21834374 CATACTAAAT
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:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (15 bp):
ACAACAAGATTATCC
Found at i:21835159 original size:19 final size:19
Alignment explanation
Indices: 21835135--21835171 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
21835125 ATATATTTTC
21835135 AAAAA-TAATAAATAATTAA
1 AAAAATTAATAAA-AATTAA
21835154 AAAAATTAATAAAAATTA
1 AAAAATTAATAAAAATTA
21835172 CATCTTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATTAATAAAAATTAA
Found at i:21835169 original size:10 final size:10
Alignment explanation
Indices: 21835135--21835171 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
21835125 ATATATTTTC
21835135 AAAAA-TAAT
1 AAAAATTAAT
21835144 AAATAATTAA-
1 AAA-AATTAAT
21835154 AAAAATTAAT
1 AAAAATTAAT
21835164 AAAAATTA
1 AAAAATTA
21835172 CATCTTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.36
10 13 0.52
11 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATTAAT
Found at i:21835306 original size:19 final size:19
Alignment explanation
Indices: 21835260--21835299 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
21835250 AACTTCAAAC
21835260 TATAAAAAA-ATTAAAAAT
1 TATAAAAAATATTAAAAAT
*
21835278 TATAAAAAATATTAATAAT
1 TATAAAAAATATTAAAAAT
21835297 TAT
1 TAT
21835300 TTAAAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TATAAAAAATATTAAAAAT
Found at i:21835818 original size:20 final size:20
Alignment explanation
Indices: 21835773--21835821 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
21835763 ATGTTTCTTA
21835773 TAAT-ATTTTTTAAATATTT
1 TAATAATTTTTTAAATATTT
* *
21835792 CATTAATTTTTT-AATATTTT
1 TAATAATTTTTTAAATA-TTT
21835812 TAATAATTTT
1 TAATAATTTT
21835822 ATATATATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TAATAATTTTTTAAATATTT
Found at i:21836049 original size:20 final size:21
Alignment explanation
Indices: 21836014--21836053 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
21836004 TTTTATAATT
*
21836014 TTTAATTTTTTTATGATTTTC
1 TTTAATTTTTTAATGATTTTC
21836035 TTTAA-TTTTTAATGATTTT
1 TTTAATTTTTTAATGATTTT
21836054 AAATATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTAATTTTTTAATGATTTTC
Found at i:21836949 original size:2 final size:2
Alignment explanation
Indices: 21836942--21836968 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21836932 TTTTGTCAGC
21836942 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 T
21836969 TTGTTTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21843380 original size:17 final size:18
Alignment explanation
Indices: 21843352--21843386 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
21843342 CCCCCCAAAA
21843352 AAAATAATTATTGCATTT
1 AAAATAATTATTGCATTT
*
21843370 AAAAT-ATTATTTCATTT
1 AAAATAATTATTGCATTT
21843387 TGACTAATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (18 bp):
AAAATAATTATTGCATTT
Found at i:21851421 original size:25 final size:24
Alignment explanation
Indices: 21851392--21851500 Score: 101
Period size: 25 Copynumber: 4.4 Consensus size: 24
21851382 CCAAACCAAG
* * *
21851392 CCTTTATGGTGAATATTCTGTAAAA
1 CCTTTGTGGCGAAT-TTCTATAAAA
*
21851417 CCTTTGTGGCGAATTCTCTATAAAG
1 CCTTTGTGGCGAATT-TCTATAAAA
* *
21851442 CCTTTATGGCGAATATTCTATAAAG
1 CCTTTGTGGCGAAT-TTCTATAAAA
* * *
21851467 CCTTTGTGGCGAGCTCTCTGTAAAA
1 CCTTTGTGGCGA-ATTTCTATAAAA
21851492 CCTTTGTGG
1 CCTTTGTGG
21851501 TGGACTCTCT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.01
25 68 0.96
26 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (24 bp):
CCTTTGTGGCGAATTTCTATAAAA
Found at i:21851471 original size:50 final size:50
Alignment explanation
Indices: 21851389--21851496 Score: 153
Period size: 50 Copynumber: 2.2 Consensus size: 50
21851379 AAACCAAACC
* * *
21851389 AAGCCTTTATGGTGAATATTCTGTAAAACCTTTGTGGCGAATTCTCTATA
1 AAGCCTTTATGGCGAATATTCTATAAAACCTTTGTGGCGAACTCTCTATA
* * *
21851439 AAGCCTTTATGGCGAATATTCTATAAAGCCTTTGTGGCGAGCTCTCTGTA
1 AAGCCTTTATGGCGAATATTCTATAAAACCTTTGTGGCGAACTCTCTATA
*
21851489 AAACCTTT
1 AAGCCTTT
21851497 GTGGTGGACT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (50 bp):
AAGCCTTTATGGCGAATATTCTATAAAACCTTTGTGGCGAACTCTCTATA
Found at i:21851508 original size:25 final size:24
Alignment explanation
Indices: 21851408--21851596 Score: 99
Period size: 25 Copynumber: 7.5 Consensus size: 24
21851398 TGGTGAATAT
*
21851408 TCTGTAAAACCTTTGTGGCGAATTC
1 TCTGTAAAACCTTTGTGGCG-ACTC
* * * * *
21851433 TCTATAAAGCCTTTATGGCGAATAT
1 TCTGTAAAACCTTTGTGGCGACT-C
* *
21851458 TCTATAAAGCCTTTGTGGCGAGCTC
1 TCTGTAAAACCTTTGTGGCGA-CTC
*
21851483 TCTGTAAAACCTTTGTGGTGGACTC
1 TCTGTAAAACCTTTGTGG-CGACTC
* ** * * *
21851508 TCTGTTAAGTCTTTGTGGCAAATAT
1 TCTGTAAAACCTTTGTGGCGACT-C
* *
21851533 TTTGTAAAGCCTTTTGTGGCGAACTC
1 TCTGTAAAACC-TTTGTGGCG-ACTC
* *** *
21851559 TCTATAAAGGATTTTTGGCGAGCTC
1 TCTGTAAAACCTTTGTGGCGA-CTC
*
21851584 TCTATAAAACCTT
1 TCTGTAAAACCTT
21851597 CTTAGCGTAT
Statistics
Matches: 125, Mismatches: 32, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
24 5 0.04
25 100 0.80
26 18 0.14
27 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (24 bp):
TCTGTAAAACCTTTGTGGCGACTC
Found at i:21851532 original size:75 final size:76
Alignment explanation
Indices: 21851408--21851596 Score: 209
Period size: 75 Copynumber: 2.5 Consensus size: 76
21851398 TGGTGAATAT
* *
21851408 TCTGTAAAACCTTTGTGGCGAATTCTCTATAAAGCCTTTATGGCGAATATTCTATAAAGCC-TTT
1 TCTGTAAAACCTTTGTGGCGAACTCTCTATAAAGCCTTTATGGCAAATATTCTATAAAGCCTTTT
*
21851472 GTGGCGAGCTC
66 GTGGCGAACTC
* * * * * * * *
21851483 TCTGTAAAACCTTTGTGGTGGACTCTCTGTTAAGTCTTTGTGGCAAATATTTTGTAAAGCCTTTT
1 TCTGTAAAACCTTTGTGGCGAACTCTCTATAAAGCCTTTATGGCAAATATTCTATAAAGCCTTTT
21851548 GTGGCGAACTC
66 GTGGCGAACTC
* *** * * *
21851559 TCTATAAAGGATTTTTGGCGAGCTCTCTATAAAACCTT
1 TCTGTAAAACCTTTGTGGCGAACTCTCTATAAAGCCTT
21851597 CTTAGCGTAT
Statistics
Matches: 90, Mismatches: 23, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
75 51 0.57
76 39 0.43
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (76 bp):
TCTGTAAAACCTTTGTGGCGAACTCTCTATAAAGCCTTTATGGCAAATATTCTATAAAGCCTTTT
GTGGCGAACTC
Found at i:21856309 original size:1 final size:1
Alignment explanation
Indices: 21856303--21856346 Score: 61
Period size: 1 Copynumber: 44.0 Consensus size: 1
21856293 GTGAGTAAAT
* **
21856303 AAAAAAAAAAAAAAAAAACAAGGAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21856347 GCAAGGAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.93, C:0.02, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:21856341 original size:27 final size:27
Alignment explanation
Indices: 21856303--21856355 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
21856293 GTGAGTAAAT
21856303 AAAAAAAAAAAAAAAAAACAAGGAAAA
1 AAAAAAAAAAAAAAAAAACAAGGAAAA
*
21856330 AAAAAAAAAAAAAAAAAGCAAGGAAA
1 AAAAAAAAAAAAAAAAAACAAGGAAA
21856356 CAAGAATACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAAAAAAAAAACAAGGAAAA
Found at i:21856774 original size:20 final size:21
Alignment explanation
Indices: 21856736--21856774 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
21856726 TCAGTTCAGC
* *
21856736 TTGTAAAGATTGAACTTGCTG
1 TTGTAAAGACTGAAATTGCTG
21856757 TTGTAAAG-CTGAAATTGC
1 TTGTAAAGACTGAAATTGC
21856775 ACCCATGCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (21 bp):
TTGTAAAGACTGAAATTGCTG
Found at i:21858977 original size:15 final size:16
Alignment explanation
Indices: 21858953--21858986 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21858943 TAGTTGGACC
21858953 AATTTATATATTT-TT
1 AATTTATATATTTCTT
*
21858968 AATTTTTATATTTCTT
1 AATTTATATATTTCTT
21858984 AAT
1 AAT
21858987 AATTCATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTTATATATTTCTT
Found at i:21864447 original size:3 final size:3
Alignment explanation
Indices: 21864441--21864465 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
21864431 AAAATAATAA
21864441 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
21864466 GATACAAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:21864906 original size:17 final size:17
Alignment explanation
Indices: 21864884--21864917 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
21864874 TAAGGTATAA
21864884 GTTTTATAGTTTCCATC
1 GTTTTATAGTTTCCATC
21864901 GTTTTATAGTTTCCATC
1 GTTTTATAGTTTCCATC
21864918 TCATTTATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.53
Consensus pattern (17 bp):
GTTTTATAGTTTCCATC
Found at i:21867851 original size:43 final size:42
Alignment explanation
Indices: 21867716--21867851 Score: 140
Period size: 43 Copynumber: 3.2 Consensus size: 42
21867706 GCATGTAATC
* *
21867716 ACAT-ATCGATGCC-ACTGTCCCAGACAGGGTCTTCCACGAATTA
1 ACATAATCGATGCCAAC-GTCCCAGACATGGTCTTACACGAA--A
* *
21867759 A-AT-A-CGATGCCAATGTCCCAGACATGGTCTTATACGTAAA
1 ACATAATCGATGCCAACGTCCCAGACATGGTCTTACACG-AAA
21867799 CACA-AATCGATGCCAACGTCCCAGACATGGTCTTACACGAAA
1 -ACATAATCGATGCCAACGTCCCAGACATGGTCTTACACGAAA
21867841 ACATACATCGA
1 ACATA-ATCGA
21867852 AAATCCTACG
Statistics
Matches: 79, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
40 1 0.01
41 30 0.38
42 12 0.15
43 36 0.46
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (42 bp):
ACATAATCGATGCCAACGTCCCAGACATGGTCTTACACGAAA
Found at i:21870472 original size:28 final size:28
Alignment explanation
Indices: 21870422--21870479 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
21870412 AAAAATATGT
** *
21870422 TTTTTTATAATTTTTAATTTTTTAATAA
1 TTTTTTATAATTTTTAAAATTTTAAAAA
* *
21870450 TTTTTTCTTATTTTTAAAATTTTAAAAA
1 TTTTTTATAATTTTTAAAATTTTAAAAA
21870478 TT
1 TT
21870480 AATTAATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTTTATAATTTTTAAAATTTTAAAAA
Found at i:21873434 original size:15 final size:16
Alignment explanation
Indices: 21873398--21873436 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
21873388 TTATTCTAAC
*
21873398 TCGATTTGAAATCGAG
1 TCGAATTGAAATCGAG
21873414 TCGAATTGAAAT-GAG
1 TCGAATTGAAATCGAG
*
21873429 TGGAATTG
1 TCGAATTG
21873437 TTCGAGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (16 bp):
TCGAATTGAAATCGAG
Found at i:21873682 original size:20 final size:20
Alignment explanation
Indices: 21873654--21873712 Score: 84
Period size: 21 Copynumber: 3.0 Consensus size: 20
21873644 TTATATATTC
*
21873654 TTTAGAATTTTTTTAAAAAA
1 TTTATAATTTTTTTAAAAAA
*
21873674 TTTATAATTTTTTTTTAAAAA
1 TTTATAA-TTTTTTTAAAAAA
21873695 TTTATAA-TTTTTTAAAAA
1 TTTATAATTTTTTTAAAAA
21873713 TATAAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.29
20 6 0.17
21 19 0.54
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTATAATTTTTTTAAAAAA
Found at i:21873687 original size:21 final size:21
Alignment explanation
Indices: 21873661--21873707 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
21873651 TTCTTTAGAA
21873661 TTTTTTTAAAAAATTTATAAT
1 TTTTTTTAAAAAATTTATAAT
*
21873682 TTTTTTTTAAAAATTTATAAT
1 TTTTTTTAAAAAATTTATAAT
21873703 TTTTT
1 TTTTT
21873708 AAAAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTTTAAAAAATTTATAAT
Found at i:21873707 original size:18 final size:19
Alignment explanation
Indices: 21873654--21873713 Score: 77
Period size: 18 Copynumber: 3.1 Consensus size: 19
21873644 TTATATATTC
*
21873654 TTTAGAATTTTTTTAAAAAA
1 TTTATAATTTTTTT-AAAAA
21873674 TTTATAATTTTTTTTTAAAAA
1 TTTATAA--TTTTTTTAAAAA
21873695 TTTATAA-TTTTTTAAAAA
1 TTTATAATTTTTTTAAAAA
21873713 T
1 T
21873714 ATAAAATTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 12 0.32
20 6 0.16
21 12 0.32
22 7 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTATAATTTTTTTAAAAA
Found at i:21873721 original size:18 final size:18
Alignment explanation
Indices: 21873684--21873722 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
21873674 TTTATAATTT
* *
21873684 TTTTTTAAAAATTTATAA
1 TTTTTTAAAAATATAAAA
21873702 TTTTTTAAAAATATAAAA
1 TTTTTTAAAAATATAAAA
21873720 TTT
1 TTT
21873723 GAAATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTTTAAAAATATAAAA
Found at i:21873762 original size:19 final size:21
Alignment explanation
Indices: 21873727--21873771 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
21873717 AAATTTGAAA
*
21873727 TTTTAAAAATTACTTTGT-AT
1 TTTTGAAAATTACTTTGTAAT
21873747 TTTTGAAAATTA-TTTGTAAT
1 TTTTGAAAATTACTTTGTAAT
21873767 TTTTG
1 TTTTG
21873772 TTGAGAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.31, C:0.02, G:0.09, T:0.58
Consensus pattern (21 bp):
TTTTGAAAATTACTTTGTAAT
Found at i:21874134 original size:25 final size:25
Alignment explanation
Indices: 21874100--21874149 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
21874090 TTCCCGTCTT
21874100 TGTTGTTAAGTCAAGGAGGGCAGAG
1 TGTTGTTAAGTCAAGGAGGGCAGAG
* **
21874125 TGTTTTTAAGTTGAGGAGGGCAGAG
1 TGTTGTTAAGTCAAGGAGGGCAGAG
21874150 CTAGGATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.26, C:0.06, G:0.40, T:0.28
Consensus pattern (25 bp):
TGTTGTTAAGTCAAGGAGGGCAGAG
Found at i:21877657 original size:29 final size:28
Alignment explanation
Indices: 21877610--21877706 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 28
21877600 TGTACTCTAC
* *
21877610 AAAATTTACATTTTAACCCAAAAACTTTCT
1 AAAA-TTACA-TTTGACCCATAAACTTTCT
* *
21877640 AAAATTACATTTCGACCCTTAGACTTTCT
1 AAAATTACATTT-GACCCATAAACTTTCT
* * *
21877669 CACAATTGCACTTTGACCCCTAAACTTTCTT
1 -AAAATTACA-TTTGACCCATAAACTTTC-T
21877700 AAAATTA
1 AAAATTA
21877707 TGTTTTGGCC
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
28 3 0.06
29 17 0.32
30 29 0.55
31 4 0.08
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATTACATTTGACCCATAAACTTTCT
Found at i:21877696 original size:30 final size:29
Alignment explanation
Indices: 21877631--21877706 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
21877621 TTTAACCCAA
*
21877631 AAACTTTCTAAAATTACATTTCGACCCTT
1 AAACTTTCTAAAATTACATTTCGACCCCT
* * *
21877660 AGACTTTCTCACAATTGCACTTT-GACCCCT
1 AAACTTTCT-AAAATTACA-TTTCGACCCCT
21877690 AAACTTTCTTAAAATTA
1 AAACTTTC-TAAAATTA
21877707 TGTTTTGGCC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 8 0.22
30 25 0.68
31 4 0.11
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (29 bp):
AAACTTTCTAAAATTACATTTCGACCCCT
Found at i:21878449 original size:12 final size:12
Alignment explanation
Indices: 21878424--21878472 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
21878414 GAAGAAGAAG
21878424 AAGAAGAAAGGAGA
1 AAGAA-AAA-GAGA
21878438 AAGAAAAAGAG-
1 AAGAAAAAGAGA
21878449 -AGAAAAA-AGA
1 AAGAAAAAGAGA
*
21878459 AAGAAAAAAAGA
1 AAGAAAAAGAGA
21878471 AA
1 AA
21878473 ATAAAAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 2 0.06
10 7 0.22
11 7 0.22
12 8 0.25
13 3 0.09
14 5 0.16
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAGA
Found at i:21878455 original size:11 final size:11
Alignment explanation
Indices: 21878435--21878472 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
21878425 AGAAGAAAGG
21878435 AGAAAG-AAAA
1 AGAAAGAAAAA
*
21878445 AGAGAGAAAAA
1 AGAAAGAAAAA
21878456 AGAAAGAAAAAA
1 AGAAAG-AAAAA
21878468 AGAAA
1 AGAAA
21878473 ATAAAAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 5 0.21
11 9 0.38
12 10 0.42
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:21878459 original size:21 final size:20
Alignment explanation
Indices: 21878418--21878473 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
21878408 CAAAGGGAAG
* **
21878418 AAGAAGAAGAAGAAAGGAGA
1 AAGAAAAAGAAGAAAAAAGA
21878438 AAGAAAAAGAGAGAAAAAAGA
1 AAGAAAAAGA-AGAAAAAAGA
21878459 AAGAAAAA-AAGAAAA
1 AAGAAAAAGAAGAAAA
21878474 TAAAAAGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.19
20 10 0.31
21 16 0.50
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
AAGAAAAAGAAGAAAAAAGA
Found at i:21878480 original size:19 final size:19
Alignment explanation
Indices: 21878437--21878498 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
21878427 AAGAAAGGAG
21878437 AAAGAAAAAGAGAGAAAA-AA
1 AAAGAAAAA-A-AGAAAATAA
21878457 GAAAGAAAAAAAGAAAATAA
1 -AAAGAAAAAAAGAAAATAA
**
21878477 AAAGTAGTAAAA-AAAATAA
1 AAAG-AAAAAAAGAAAATAA
21878496 AAA
1 AAA
21878499 CAGCAGCCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 20 0.54
20 8 0.22
21 9 0.24
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (19 bp):
AAAGAAAAAAAGAAAATAA
Found at i:21878936 original size:20 final size:20
Alignment explanation
Indices: 21878911--21878948 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21878901 AAAAATATTC
21878911 AAAAATCCTCGTATTTTAAT
1 AAAAATCCTCGTATTTTAAT
* *
21878931 AAAAATTCTCGTGTTTTA
1 AAAAATCCTCGTATTTTA
21878949 TTAGAATCCC
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:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAAATCCTCGTATTTTAAT
Found at i:21879197 original size:17 final size:17
Alignment explanation
Indices: 21879169--21879303 Score: 72
Period size: 17 Copynumber: 8.2 Consensus size: 17
21879159 CTTTCTTTAA
21879169 AAAAATTC-CGTGTTTC
1 AAAAATTCTCGTGTTTC
** *
21879185 AAAAATTCTCGTGAATA
1 AAAAATTCTCGTGTTTC
* *
21879202 AAAAATTTTTGTGTTTTC
1 AAAAATTCTCGTG-TTTC
*
21879220 AAAAATTCCCGTGTTT-
1 AAAAATTCTCGTGTTTC
21879236 -AAAATT-T--T-TTTC
1 AAAAATTCTCGTGTTTC
*** *
21879248 --GTGTTTTCGTGTTTTC
1 AAAAATTCTCGTG-TTTC
21879264 AAAAAATTCTCGTGTTTC
1 -AAAAATTCTCGTGTTTC
*
21879282 AAAAATTTTCGTGGTTTC
1 AAAAATTCTCGT-GTTTC
21879300 AAAA
1 AAAA
21879304 TTTTCATGTT
Statistics
Matches: 87, Mismatches: 20, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
11 5 0.06
12 2 0.02
14 1 0.01
15 6 0.07
16 12 0.14
17 30 0.34
18 24 0.28
19 7 0.08
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (17 bp):
AAAAATTCTCGTGTTTC
Found at i:21879220 original size:35 final size:36
Alignment explanation
Indices: 21879177--21879255 Score: 99
Period size: 35 Copynumber: 2.2 Consensus size: 36
21879167 AAAAAAATTC
*
21879177 CGTG-TTTCAAAAATTCTCGTGAATAAAAAATTTTT
1 CGTGTTTTCAAAAATTCCCGTGAATAAAAAATTTTT
** **
21879212 -GTGTTTTCAAAAATTCCCGTGTTTAAAATTTTTTT
1 CGTGTTTTCAAAAATTCCCGTGAATAAAAAATTTTT
21879247 CGTGTTTTC
1 CGTGTTTTC
21879256 GTGTTTTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 3 0.08
35 26 0.70
36 8 0.22
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (36 bp):
CGTGTTTTCAAAAATTCCCGTGAATAAAAAATTTTT
Found at i:21879286 original size:62 final size:61
Alignment explanation
Indices: 21879201--21879342 Score: 180
Period size: 61 Copynumber: 2.3 Consensus size: 61
21879191 TCTCGTGAAT
* * *
21879201 AAAAAATTTTTGTGTTTTCAAAAATTCCCGT-GTTT-AAAATTTTTTTCGTGTTTTCGTGTTTTC
1 AAAAAATTCTCGTG-TTTCAAAAATTCCCGTGGTTTCAAAA---TTTTCATGTTTTCGTGTTTTC
**
21879264 AAAAAATTCTCGTGTTTCAAAAATTTTCGTGGTTTCAAAATTTTCATGTTTTCGTGTTTTC
1 AAAAAATTCTCGTGTTTCAAAAATTCCCGTGGTTTCAAAATTTTCATGTTTTCGTGTTTTC
21879325 AAAAAATTTCTCGTGTTT
1 AAAAAA-TTCTCGTGTTT
21879343 TTTTAAAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
61 26 0.37
62 25 0.35
63 16 0.23
64 4 0.06
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (61 bp):
AAAAAATTCTCGTGTTTCAAAAATTCCCGTGGTTTCAAAATTTTCATGTTTTCGTGTTTTC
Found at i:21879291 original size:44 final size:43
Alignment explanation
Indices: 21879207--21879299 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 43
21879197 GAATAAAAAA
* *
21879207 TTTTTGTGTTTTCAAAAATTCCCGTGTTTAAAATTTTTTTCGTG
1 TTTTCGTGTTTTCAAAAATTCCCGTGTTTAAAA-TATTTTCGTG
*
21879251 TTTTCGTGTTTTCAAAAAATTCTCGTGTTTCAAAA-ATTTTCGTG
1 TTTTCGTGTTTTC-AAAAATTCCCGTGTTT-AAAATATTTTCGTG
*
21879295 GTTTC
1 TTTTC
21879300 AAAATTTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 24 0.56
45 15 0.35
46 4 0.09
ACGTcount: A:0.22, C:0.13, G:0.14, T:0.52
Consensus pattern (43 bp):
TTTTCGTGTTTTCAAAAATTCCCGTGTTTAAAATATTTTCGTG
Found at i:21879304 original size:17 final size:18
Alignment explanation
Indices: 21879251--21879308 Score: 75
Period size: 17 Copynumber: 3.3 Consensus size: 18
21879241 TTTTTTCGTG
*
21879251 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGGTTTC-AAAAA
*
21879270 TTCTCGT-GTTTCAAAAA
1 TTTTCGTGGTTTCAAAAA
21879287 TTTTCGTGGTTTC-AAAA
1 TTTTCGTGGTTTCAAAAA
21879304 TTTTC
1 TTTTC
21879309 ATGTTTTCGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 20 0.57
18 9 0.26
19 6 0.17
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (18 bp):
TTTTCGTGGTTTCAAAAA
Found at i:21879316 original size:17 final size:17
Alignment explanation
Indices: 21879251--21879316 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
21879241 TTTTTTCGTG
21879251 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC--AAAA
*
21879270 TTCTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTC-AAAA
*
21879287 TTTTCGTGGTTTCAAAA
1 TTTTCGTGTTTTCAAAA
*
21879304 TTTTCATGTTTTC
1 TTTTCGTGTTTTC
21879317 GTGTTTTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 27 0.64
18 8 0.19
19 7 0.17
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (17 bp):
TTTTCGTGTTTTCAAAA
Found at i:21879365 original size:17 final size:18
Alignment explanation
Indices: 21879342--21879382 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
21879332 TTCTCGTGTT
*
21879342 TTTTTAAAAAAATTCATG
1 TTTTAAAAAAAATTCATG
21879360 TTTTAAAAAAAAATTCATG
1 TTTT-AAAAAAAATTCATG
21879379 TTTT
1 TTTT
21879383 CGAAATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TTTTAAAAAAAATTCATG
Found at i:21879399 original size:17 final size:18
Alignment explanation
Indices: 21879377--21879510 Score: 64
Period size: 17 Copynumber: 7.6 Consensus size: 18
21879367 AAAAAATTCA
*
21879377 TGTTTTCGAAA-TTTTCG
1 TGTTTTCAAAATTTTTCG
21879394 TGTTTTCAAAATTTTTCG
1 TGTTTTCAAAATTTTTCG
*** * *
21879412 TG-TCAAAAAATTCTT-A
1 TGTTTTCAAAATTTTTCG
* * *
21879428 TG-TATCGAAAA-TTTCCT
1 TGTTTTC-AAAATTTTTCG
***
21879445 TGTTTTCAAAAAAATTCTG
1 TGTTTTCAAAATTTTTC-G
*
21879464 TGTTTTCAAAAAATTTTCG
1 TGTTTTC-AAAATTTTTCG
* *
21879483 TG-TTTCAAAAATCTTCG
1 TGTTTTCAAAATTTTTCG
21879500 TGTTTTCAAAA
1 TGTTTTCAAAA
21879511 ATTATTATTG
Statistics
Matches: 89, Mismatches: 20, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
16 5 0.06
17 41 0.46
18 25 0.28
19 10 0.11
20 8 0.09
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (18 bp):
TGTTTTCAAAATTTTTCG
Found at i:21879411 original size:18 final size:18
Alignment explanation
Indices: 21879251--21879513 Score: 137
Period size: 18 Copynumber: 14.1 Consensus size: 18
21879241 TTTTTTCGTG
21879251 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
21879270 TTCTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
21879287 TTTTCGTGGTTTCAAAATTTTCA
1 TTTTCGTGTTTTCAAAA-----A
21879310 TGTTTTCGTGTTTTCAAAAAA
1 --TTTTCGTGTTTTC-AAAAA
*
21879331 TTTCTCGTGTTTTTTTAAAAA
1 TTT-TCGTG--TTTTCAAAAA
** * *
21879352 AATTCATGTTTTAAAAAAA
1 TTTTCGTGTTTT-CAAAAA
** * *
21879371 AATTCATGTTTTC-GAAA
1 TTTTCGTGTTTTCAAAAA
*
21879388 TTTTCGTGTTTTCAAAAT
1 TTTTCGTGTTTTCAAAAA
21879406 TTTTCGTG---TCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* * *
21879422 TTCTT-ATG-TATCGAAAA
1 TT-TTCGTGTTTTCAAAAA
* *
21879439 TTTCCTTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
**
21879457 AATTCTGTGTTTTCAAAAAA
1 TTTTC-GTGTTTTC-AAAAA
21879477 TTTTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
21879494 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
21879512 TT
1 TT
21879514 ATTATTGTGT
Statistics
Matches: 191, Mismatches: 30, Indels: 47
0.71 0.11 0.18
Matches are distributed among these distances:
15 2 0.01
16 9 0.05
17 47 0.25
18 51 0.27
19 37 0.19
20 17 0.09
21 7 0.04
22 4 0.02
23 1 0.01
25 12 0.06
26 4 0.02
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:21886307 original size:1 final size:1
Alignment explanation
Indices: 21886301--21886399 Score: 54
Period size: 1 Copynumber: 99.0 Consensus size: 1
21886291 TATTATGCTT
* * * * * * * * * * *
21886301 AAAAAAATAAAAAAATAGAAAAAAACAAAAAAACAGAAAAAAATAGACAAAACAAAAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
21886366 AACAAAAACAAAAAAACAAAGAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21886400 TCAAGATGAA
Statistics
Matches: 66, Mismatches: 32, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.84, C:0.07, G:0.05, T:0.04
Consensus pattern (1 bp):
A
Found at i:21886373 original size:8 final size:8
Alignment explanation
Indices: 21886319--21886398 Score: 69
Period size: 8 Copynumber: 9.9 Consensus size: 8
21886309 AAAAAAATAG
21886319 AAAAAAAC
1 AAAAAAAC
21886327 AAAAAAAC
1 AAAAAAAC
21886335 AGAAAAAA-
1 A-AAAAAAC
21886343 ATAGACAAAAC
1 A-A-A-AAAAC
21886354 AAAAAAA-
1 AAAAAAAC
*
21886361 TAAAAAAC
1 AAAAAAAC
21886369 --AAAAAC
1 AAAAAAAC
21886375 AAAAAAAC
1 AAAAAAAC
*
21886383 AAAGAAAAG
1 AAA-AAAAC
21886392 AAAAAAA
1 AAAAAAA
21886399 ATCAAGATGA
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
6 6 0.10
7 6 0.10
8 28 0.46
9 15 0.25
10 5 0.08
11 1 0.02
ACGTcount: A:0.84, C:0.09, G:0.05, T:0.03
Consensus pattern (8 bp):
AAAAAAAC
Found at i:21886390 original size:18 final size:17
Alignment explanation
Indices: 21886301--21886399 Score: 72
Period size: 18 Copynumber: 5.4 Consensus size: 17
21886291 TATTATGCTT
* *
21886301 AAAAAAATAAAAAAATA
1 AAAAAAACAAAAAAACA
21886318 GAAAAAAACAAAAAAACA
1 -AAAAAAACAAAAAAACA
* *
21886336 GAAAAAAATAGACAAAACA
1 -AAAAAAACA-AAAAAACA
* *
21886355 AAAAAATAAAAAACAAAAA
1 AAAAAA-ACAAAA-AAACA
*
21886374 CAAAAAAACAAAGAAAAGA
1 -AAAAAAACAAA-AAAACA
21886393 AAAAAAA
1 AAAAAAA
21886400 TCAAGATGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
18 39 0.58
19 21 0.31
20 7 0.10
ACGTcount: A:0.84, C:0.07, G:0.05, T:0.04
Consensus pattern (17 bp):
AAAAAAACAAAAAAACA
Found at i:21887415 original size:83 final size:77
Alignment explanation
Indices: 21887318--21887679 Score: 359
Period size: 78 Copynumber: 4.6 Consensus size: 77
21887308 ATTCTGTTTT
21887318 TTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
1 TTTTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
21887382 TTTAATTTAATTTCTG
66 TTT-A---AATTTCTG
*
21887398 TTTTTTCAAAAGAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACATCCTGAGGT
1 -TTTTTC-AAA-AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCAC--GCTGAGGT
21887462 A---TTTTAAATTTCTG
61 ATTTTTTTAAATTTCTG
** * * * *
21887476 CTTTTGAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATT
1 -TTTT-TCAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
21887541 TCTTTTAAATTTATG
64 T-TTTTAAATTTCTG
* * * * * *
21887556 TGTTTCAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCTTCGGGTCACGCTAAGGTA--TT
1 TTTTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
*
21887619 TTTCAA-TTCATG
66 TTTAAATTTC-TG
* *
21887631 TTTTTC-AAAAATCAACTCAT-AT-CGCTAGAAGTGAGTTGAGTCTCGGGTC
1 TTTTTCAAAAAATCAACTCATAATACG--AGAGGTGAGTTGAGCCTCGGGTC
21887680 GCACGCCGAG
Statistics
Matches: 242, Mismatches: 26, Indels: 33
0.80 0.09 0.11
Matches are distributed among these distances:
72 2 0.01
73 1 0.00
74 35 0.14
75 13 0.05
76 8 0.03
77 15 0.06
78 89 0.37
79 3 0.01
80 12 0.05
81 7 0.03
82 7 0.03
83 42 0.17
85 8 0.03
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (77 bp):
TTTTTCAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
TTTAAATTTCTG
Found at i:21887894 original size:49 final size:49
Alignment explanation
Indices: 21887841--21887940 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
21887831 GATTAATTTC
*
21887841 GTGTTTGAAAAAAAAAGATTTTTTTTTATTTTTTTGCATTTTGACCCCT
1 GTGTTTGAAAAAAAAAGATTTTTTTTTATTTTTTTGCATTTTAACCCCT
21887890 GTGTTTGAAAAAAAAAGATTTTTTTTTATTTTTTTGCATTTTAACCCCT
1 GTGTTTGAAAAAAAAAGATTTTTTTTTATTTTTTTGCATTTTAACCCCT
21887939 GT
1 GT
21887941 ACTCTTCAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (49 bp):
GTGTTTGAAAAAAAAAGATTTTTTTTTATTTTTTTGCATTTTAACCCCT
Done.