Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 272 of 325
Found at i:89071357 original size:20 final size:21
Alignment explanation
Indices: 89071322--89071364 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
89071312 AAGAAAAGTT
**
89071322 ATAAAAAATATTAAAT-TTTA
1 ATAAAAAATAAGAAATATTTA
89071342 ATAAAAAATAAGAAATATTTA
1 ATAAAAAATAAGAAATATTTA
89071363 AT
1 AT
89071365 TTAATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAAAAATAAGAAATATTTA
Found at i:89071382 original size:26 final size:27
Alignment explanation
Indices: 89071322--89071376 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
89071312 AAGAAAAGTT
*
89071322 ATAAAAAATATTAAATTTTAATAAAAA
1 ATAAGAAATATTAAATTTTAATAAAAA
* *
89071349 ATAAGAAATATTTAA-TTTAATTAAAA
1 ATAAGAAATATTAAATTTTAATAAAAA
89071375 AT
1 AT
89071377 TGGAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
ATAAGAAATATTAAATTTTAATAAAAA
Found at i:89071395 original size:20 final size:20
Alignment explanation
Indices: 89071370--89071414 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
89071360 TTAATTTAAT
* *
89071370 TAAAAATTGGAAAAAGATTA
1 TAAAAATTGGAAAAAAAATA
*
89071390 TAAAAATTGTAAAAAAAATA
1 TAAAAATTGGAAAAAAAATA
89071410 TAAAA
1 TAAAA
89071415 TATATAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (20 bp):
TAAAAATTGGAAAAAAAATA
Found at i:89071420 original size:29 final size:29
Alignment explanation
Indices: 89071388--89071444 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
89071378 GGAAAAAGAT
*
89071388 TATAAAAATTGTA-AAAAAAATATAAAATA
1 TATAAAAA-TATAGAAAAAAATATAAAATA
*
89071417 TATAGAAATATAGAAAAAAATATAAAAT
1 TATAAAAATATAGAAAAAAATATAAAAT
89071445 TTTATAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (29 bp):
TATAAAAATATAGAAAAAAATATAAAATA
Found at i:89071700 original size:10 final size:9
Alignment explanation
Indices: 89071685--89071815 Score: 57
Period size: 10 Copynumber: 13.6 Consensus size: 9
89071675 TTTTTATGCA
89071685 TTTTATAAT
1 TTTTATAAT
*
89071694 TTCTTATGAT
1 TT-TTATAAT
*
89071704 TTTTATAAAA
1 TTTTAT-AAT
*
89071714 TTTTACAAATT
1 TTTTA-TAA-T
*
89071725 TTTTATATT
1 TTTTATAAT
89071734 TTTTACT-AT
1 TTTTA-TAAT
*
89071743 TTATATATAT
1 TTTTATA-AT
* *
89071753 ATTTCTAATT
1 TTTTATAA-T
* *
89071763 TTTTGTAAA
1 TTTTATAAT
*
89071772 TTTTAAATAT
1 TTTTATA-AT
89071782 TTTTATAAT
1 TTTTATAAT
*
89071791 TTTTATTAAAG
1 TTTTA-T-AAT
*
89071802 TTTAATAAT
1 TTTTATAAT
89071811 TTTTA
1 TTTTA
89071816 AAACGTTTAT
Statistics
Matches: 88, Mismatches: 23, Indels: 22
0.66 0.17 0.17
Matches are distributed among these distances:
8 1 0.01
9 36 0.41
10 40 0.45
11 11 0.12
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:89071800 original size:29 final size:29
Alignment explanation
Indices: 89071684--89071815 Score: 87
Period size: 29 Copynumber: 4.6 Consensus size: 29
89071674 TTTTTTATGC
* * *
89071684 ATTTTATAAT-TTCTTATGATTTTTATAAA
1 ATTTTA-AATATTTTTATAATTTTTATTAA
* *
89071713 ATTTTACAA-ATTTTTTATATTTTTTACT--
1 ATTTTA-AATA-TTTTTATAATTTTTATTAA
* * *
89071741 ATTTATATATATATTTCTAATTTTT-TGTAA
1 ATTT-TAAATATTTTTATAATTTTTAT-TAA
89071771 ATTTTAAATATTTTTATAATTTTTATTAA
1 ATTTTAAATATTTTTATAATTTTTATTAA
*
89071800 AGTTT-AATAATTTTTA
1 ATTTTAAAT-ATTTTTA
89071816 AAACGTTTAT
Statistics
Matches: 79, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
28 20 0.25
29 42 0.53
30 17 0.22
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTAAATATTTTTATAATTTTTATTAA
Found at i:89071823 original size:19 final size:19
Alignment explanation
Indices: 89071786--89071834 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
89071776 AAATATTTTT
89071786 ATAATTTTTATTAAAGTTTA
1 ATAATTTTTA-TAAAGTTTA
89071806 ATAATTTTTA-AAACGTTTA
1 ATAATTTTTATAAA-GTTTA
* *
89071825 TTGATTTTTA
1 ATAATTTTTA
89071835 CTTTTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 3 0.12
19 13 0.50
20 10 0.38
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (19 bp):
ATAATTTTTATAAAGTTTA
Found at i:89075518 original size:16 final size:16
Alignment explanation
Indices: 89075482--89075520 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
89075472 GTTTGGTTCA
*
89075482 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
* *
89075498 TTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
89075514 CTGTAAT
1 CTGTAAT
89075521 CAATAATTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.33
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:89075681 original size:26 final size:25
Alignment explanation
Indices: 89075632--89075682 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
89075622 ATGATTATTG
*
89075632 TTATTGTTATTAAATTTTAATAAAA
1 TTATTGTTAATAAATTTTAATAAAA
* *
89075657 TTATTGTTAAATATATTTTATTAAAA
1 TTATTGTT-AATAAATTTTAATAAAA
89075683 ATAATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
TTATTGTTAATAAATTTTAATAAAA
Found at i:89075717 original size:58 final size:57
Alignment explanation
Indices: 89075643--89075784 Score: 178
Period size: 58 Copynumber: 2.5 Consensus size: 57
89075633 TATTGTTATT
* * * * *
89075643 AAATTTTAATAAAATTATTGTTAAATATATTTTATTAAAAATAATAA-ATAATTTAACC
1 AAATTTTAATATAATTATTATTAAATATAATTTAAT-AAAATAA-AATATAATTTAACA
* * *
89075701 ATATTTTAACATAATTATTATTAAATATAATTTAATAAAATAAAATATAATTTAATA
1 AAATTTTAATATAATTATTATTAAATATAATTTAATAAAATAAAATATAATTTAACA
89075758 AAATTCTTAATATAATTATTATTAAAT
1 AAATT-TTAATATAATTATTATTAAAT
89075785 GAATTAAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
56 2 0.03
57 20 0.28
58 50 0.69
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (57 bp):
AAATTTTAATATAATTATTATTAAATATAATTTAATAAAATAAAATATAATTTAACA
Found at i:89075748 original size:20 final size:20
Alignment explanation
Indices: 89075723--89075761 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
89075713 AATTATTATT
89075723 AAATATAATTTAATAAAATA
1 AAATATAATTTAATAAAATA
89075743 AAATATAATTTAATAAAAT
1 AAATATAATTTAATAAAAT
89075762 TCTTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATATAATTTAATAAAATA
Found at i:89075808 original size:57 final size:57
Alignment explanation
Indices: 89075643--89075808 Score: 158
Period size: 58 Copynumber: 2.9 Consensus size: 57
89075633 TATTGTTATT
* * * * * * * *
89075643 AAATTTTAATAAAATTATTGTTAAATATATTTTATTAAAAATAATAAATAATTTAACC
1 AAATTTTAACATAATTATTATTAAATAGAATTTAAT-AAAATAATATATAATTTAACA
* * * *
89075701 ATATTTTAACATAATTATTATTAAATATAATTTAATAAAATAAAATATAATTTAATA
1 AAATTTTAACATAATTATTATTAAATAGAATTTAATAAAATAATATATAATTTAACA
*
89075758 AAATTCTTAATATAATTATTATTAAAT-GAA-TTAA-AAATCATAATATATAAT
1 AAATT-TTAACATAATTATTATTAAATAGAATTTAATAAA--ATAATATATAAT
89075809 ACTATAAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
55 3 0.03
56 4 0.04
57 34 0.37
58 50 0.55
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (57 bp):
AAATTTTAACATAATTATTATTAAATAGAATTTAATAAAATAATATATAATTTAACA
Found at i:89081269 original size:32 final size:32
Alignment explanation
Indices: 89081200--89081277 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
89081190 CATATATTAG
*
89081200 AAATAC-TAAAATATATATATATATTAATAAT
1 AAATACATAAAATATACATATATATTAATAAT
** *
89081231 -GCTACATAAATATGTACATATATATTAA-AAT
1 AAATACATAAA-ATATACATATATATTAATAAT
89081262 AAATACATAATAATAT
1 AAATACATAA-AATAT
89081278 TGAAAGTATG
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
30 3 0.08
31 7 0.19
32 25 0.69
33 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (32 bp):
AAATACATAAAATATACATATATATTAATAAT
Found at i:89081292 original size:23 final size:22
Alignment explanation
Indices: 89081238--89081337 Score: 87
Period size: 23 Copynumber: 4.4 Consensus size: 22
89081228 AATGCTACAT
*
89081238 AAATATGTACAT-AT-ATATTA
1 AAATATATACATAATAATATTA
*
89081258 AAATAAATACATAATAATATTGA
1 AAATATATACATAATAATATT-A
* * * *
89081281 AAGTATGTACATAATAGTGTTAA
1 AAATATATACATAATAATATT-A
89081304 AAATATATACATAATATAGCTATTA
1 AAATATATACATAATA-A--TATTA
89081329 AAATATATA
1 AAATATATA
89081338 TATACGTACG
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
20 10 0.16
21 2 0.03
22 5 0.08
23 32 0.52
25 10 0.16
26 3 0.05
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (22 bp):
AAATATATACATAATAATATTA
Found at i:89081407 original size:25 final size:26
Alignment explanation
Indices: 89081365--89081435 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
89081355 GTAAAAAATG
* * *
89081365 TAAT-ATAGTATTAGAAATATATACC
1 TAATAATAGTATAAAAAATATATAAC
*
89081390 TGA-AATAGTATAAAAAATATATAAC
1 TAATAATAGTATAAAAAATATATAAC
*
89081415 TAATAATA-TTTAAAAAATATA
1 TAATAATAGTATAAAAAATATA
89081436 CATAATATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
25 34 0.89
26 4 0.11
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (26 bp):
TAATAATAGTATAAAAAATATATAAC
Found at i:89081419 original size:23 final size:23
Alignment explanation
Indices: 89081369--89081450 Score: 62
Period size: 25 Copynumber: 3.5 Consensus size: 23
89081359 AAAATGTAAT
* * *
89081369 ATAGTATTAGAAATATATACCTGAA
1 ATAGTATAAAAAATATATAACT--A
89081394 ATAGTATAAAAAATATATAACTA
1 ATAGTATAAAAAATATATAACTA
* *
89081417 ATAATATTTAAAAA-ATAT-ACATA
1 ATAGTA-TAAAAAATATATAAC-TA
89081440 ATA-TATAAAAA
1 ATAGTATAAAAA
89081451 TATGATATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
21 5 0.10
22 4 0.08
23 15 0.31
24 6 0.12
25 19 0.39
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (23 bp):
ATAGTATAAAAAATATATAACTA
Found at i:89081611 original size:23 final size:22
Alignment explanation
Indices: 89081580--89081635 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
89081570 TAATACTACC
* *
89081580 TAAATATATACGTATATATATAT
1 TAAACATATACGCATATATA-AT
* *
89081603 TAAAGATATATGCATATATAAT
1 TAAACATATACGCATATATAAT
*
89081625 AAAACATATAC
1 TAAACATATAC
89081636 TAATAATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (22 bp):
TAAACATATACGCATATATAAT
Found at i:89081642 original size:3 final size:3
Alignment explanation
Indices: 89081636--89081685 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
89081626 AAACATATAC
89081636 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
89081684 TA
1 TA
89081686 TTGAAATACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:89083707 original size:88 final size:87
Alignment explanation
Indices: 89083498--89083708 Score: 255
Period size: 88 Copynumber: 2.4 Consensus size: 87
89083488 GTAATCCTGA
* * *
89083498 GCTCAACTCATTTCTCGCAATATGAGTTGACTCTTTAAAAATAGACATTAAAAACAGAAATTGAA
1 GCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTAAAAACAGACATTAAAAACAGAAATTGAA
* *
89083563 AATAGCTCAGCACGTGAGCCAAG
65 AATACCTCAGCACGTGACCCAAG
* * * * **
89083586 GCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAACAGA-ATTTGAAAAATAGATTTTGA
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAACAGACA-TT-AAAAACAGAAATTGA
* *
89083650 AAATACCTC-GACATGTTACCCAAG
64 AAATACCTCAG-CACGTGACCCAAG
89083674 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
1 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
89083709 TTTTTGAAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
86 1 0.01
87 14 0.13
88 90 0.86
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (87 bp):
GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAACAGACATTAAAAACAGAAATTGAAA
ATACCTCAGCACGTGACCCAAG
Found at i:89083841 original size:73 final size:73
Alignment explanation
Indices: 89083674--89084096 Score: 329
Period size: 73 Copynumber: 5.5 Consensus size: 73
89083664 GTTACCCAAG
* *
89083674 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTGAAAAACATAAATTAAAGTAATACC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTG--AAACATAAATTGAA--AATACC
*** *
89083739 TCAGTGTATGATCTGAA
57 TCAGTACGTGATTTGAA
*
89083756 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAATCATAAATTGAAAATACCTCAGTGCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA-CATAAATTGAAAATACCTCAGTACG
89083820 TGATTTGAA
65 TGATTTGAA
* * * *
89083829 GCTCAACTCACCTCTCCCAATATGAGTTGATTTTTGAAACAAAAATTGAAAA-ACAGAATTTGAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAAATAC-----CT--C
* * *
89083893 AATACCTCGGCATTCTGAG
59 AGTACGT--G-ATT-TGAA
* * * * *
89083912 GTTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAACATTAATTTTAGAATACATCAGT--
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAACA-TAAATTGAAAATACCTCAGTAC
* *
89083975 GTGACTTGAG
64 GTGATTTGAA
*
89083985 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGATAGAAATTGAAAATACCTCA--AC
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACAT--AAATTGAAAATACCTCAGTAC
89084048 GTG-TCTTGAA
64 GTGAT-TTGAA
* * * *
89084058 GATCAACTCAACTCTCGCAATATGAGTTAATTTCTGAAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
89084097 ATAGAAATAA
Statistics
Matches: 284, Mismatches: 36, Indels: 51
0.77 0.10 0.14
Matches are distributed among these distances:
71 1 0.00
72 12 0.04
73 154 0.54
74 8 0.03
75 11 0.04
77 7 0.02
79 6 0.02
81 2 0.01
82 32 0.11
83 31 0.11
84 11 0.04
85 7 0.02
86 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (73 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAAATACCTCAGTACGT
GATTTGAA
Found at i:89096326 original size:20 final size:22
Alignment explanation
Indices: 89096303--89096358 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
89096293 AATGCTACAT
89096303 AAATATGTACATAT-ATATT-A
1 AAATATGTACATATAATATTGA
**
89096323 AAATAAATACATAATAATATTGA
1 AAATATGTACAT-ATAATATTGA
*
89096346 AAGTATGTACATA
1 AAATATGTACATA
89096359 ATAGTGTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 10 0.36
21 2 0.07
22 6 0.21
23 10 0.36
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (22 bp):
AAATATGTACATATAATATTGA
Found at i:89096357 original size:23 final size:22
Alignment explanation
Indices: 89096303--89096384 Score: 69
Period size: 23 Copynumber: 3.7 Consensus size: 22
89096293 AATGCTACAT
89096303 AAATATGTACAT-AT-ATATTA
1 AAATATGTACATAATAATATTA
**
89096323 AAATAAATACATAATAATATTGA
1 AAATATGTACATAATAATATT-A
* * *
89096346 AAGTATGTACATAATAGTGTTAA
1 AAATATGTACATAATAATATT-A
**
89096369 AAATACATACATAATA
1 AAATATGTACATAATA
89096385 TAGCTATTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
20 10 0.21
21 2 0.04
22 5 0.10
23 31 0.65
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (22 bp):
AAATATGTACATAATAATATTA
Found at i:89096484 original size:24 final size:23
Alignment explanation
Indices: 89096443--89096515 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 23
89096433 ATAGTATTAG
*
89096443 AAATATATACCTGAAATAGTATAAAA
1 AAATATATAACT--AATA-TATAAAA
**
89096469 AAATATATAACTAATAATATTTAA
1 AAATATATAACTAAT-ATATAAAA
89096493 AAA-ATAT-ACATAATATATAAAA
1 AAATATATAAC-TAATATATAAAA
89096515 A
1 A
89096516 TATGATATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
22 9 0.22
23 8 0.20
24 11 0.28
25 1 0.03
26 11 0.28
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (23 bp):
AAATATATAACTAATATATAAAA
Found at i:89096499 original size:23 final size:21
Alignment explanation
Indices: 89096462--89096609 Score: 68
Period size: 20 Copynumber: 7.3 Consensus size: 21
89096452 CCTGAAATAG
*
89096462 TATAAAAAAATATATAACTAATAA
1 TATATAAAAATATAT-AC--ATAA
*
89096486 TATTTAAAAA-ATATACATAA
1 TATATAAAAATATATACATAA
89096506 TATATAAAAATATGAT--AT--
1 TATATAAAAATAT-ATACATAA
*
89096524 TA-A-AAACATATATACATAACA
1 TATATAAAAATATATACAT-A-A
*
89096545 TATATGAAAATATAT--AT-A
1 TATATAAAAATATATACATAA
* *
89096563 TATATATATATATATA-A-AA
1 TATATAAAAATATATACATAA
* * *
89096582 TAGTATTAGAATATTTACATAA
1 TA-TATAAAAATATATACATAA
89096604 TATATA
1 TATATA
89096610 CATATTAGAA
Statistics
Matches: 94, Mismatches: 15, Indels: 33
0.66 0.11 0.23
Matches are distributed among these distances:
15 2 0.02
16 7 0.07
17 3 0.03
18 15 0.16
19 4 0.04
20 24 0.26
21 10 0.11
22 9 0.10
23 12 0.13
24 8 0.09
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (21 bp):
TATATAAAAATATATACATAA
Found at i:89096536 original size:13 final size:12
Alignment explanation
Indices: 89096505--89096562 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
89096495 AATATACATA
*
89096505 ATATATAAAAAT
1 ATATATAAAAAC
89096517 ATGATATTAAAAAC
1 AT-ATA-TAAAAAC
*
89096531 ATATATACATAAC
1 ATATATA-AAAAC
* *
89096544 ATATATGAAAAT
1 ATATATAAAAAC
89096556 ATATATA
1 ATATATA
89096563 TATATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 13 0.35
13 16 0.43
14 8 0.22
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (12 bp):
ATATATAAAAAC
Found at i:89096559 original size:2 final size:2
Alignment explanation
Indices: 89096554--89096578 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89096544 ATATATGAAA
89096554 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
89096579 AAATAGTATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:89096798 original size:36 final size:35
Alignment explanation
Indices: 89096720--89096799 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 35
89096710 ATATACTAAT
* *
89096720 AATAATAATAATAATAATATTGAAATAAAAAAGTAA
1 AATAAT-ATAACAATAATATTAAAATAAAAAAGTAA
* *
89096756 ATATAATATAACAATAATATTAAAATAAAGTAATTAA
1 A-ATAATATAACAATAATATTAAAATAAA-AAAGTAA
89096793 AATAATA
1 AATAATA
89096800 CTATATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 27 0.71
37 11 0.29
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (35 bp):
AATAATATAACAATAATATTAAAATAAAAAAGTAA
Found at i:89100623 original size:27 final size:27
Alignment explanation
Indices: 89100592--89100648 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
89100582 AGCATCATGG
89100592 TATTAATTTCCCTTGAATTTGCTTCTT
1 TATTAATTTCCCTTGAATTTGCTTCTT
89100619 TATTAATTTCCCTTGAATTTGCTTCTT
1 TATTAATTTCCCTTGAATTTGCTTCTT
89100646 TAT
1 TAT
89100649 CTTCATCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.18, G:0.07, T:0.56
Consensus pattern (27 bp):
TATTAATTTCCCTTGAATTTGCTTCTT
Found at i:89112009 original size:20 final size:20
Alignment explanation
Indices: 89111986--89112043 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
89111976 ATTTAAGTTA
89111986 AAAAATTATTAAAATATTAT
1 AAAAATTATTAAAATATTAT
* * *
89112006 AAAAATTATAAAAAAACTAT
1 AAAAATTATTAAAATATTAT
**
89112026 AAATTTTATT-AAATATTA
1 AAAAATTATTAAAATATTA
89112044 GAATTTTTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATTATTAAAATATTAT
Found at i:89112013 original size:9 final size:9
Alignment explanation
Indices: 89111986--89112019 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
89111976 ATTTAAGTTA
89111986 AAAAATTATT
1 AAAAATTA-T
89111996 AAAATATTAT
1 AAAA-ATTAT
89112006 AAAAATTAT
1 AAAAATTAT
89112015 AAAAA
1 AAAAA
89112020 AACTATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 10 0.43
10 9 0.39
11 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:89112660 original size:59 final size:59
Alignment explanation
Indices: 89112568--89112693 Score: 191
Period size: 59 Copynumber: 2.1 Consensus size: 59
89112558 TACATGATTT
* * * * *
89112568 AATTAAGTGCTAACTTTCTATTAAAGGTTTAATTGATTGCATTTTTTGACAA-GAGGCTC
1 AATTAATTGCTAACTTTCGATTAAAGGTTTAATTGATTGCACTTTTTAACAATG-GGATC
89112627 AATTAATTGCTAACTTTCGATTAAAGGTTTAATTGATTGCACTTTTTAACAATGGGATC
1 AATTAATTGCTAACTTTCGATTAAAGGTTTAATTGATTGCACTTTTTAACAATGGGATC
89112686 AATTAATT
1 AATTAATT
89112694 TTTAAAGACT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 60 0.98
60 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (59 bp):
AATTAATTGCTAACTTTCGATTAAAGGTTTAATTGATTGCACTTTTTAACAATGGGATC
Found at i:89113838 original size:27 final size:26
Alignment explanation
Indices: 89113795--89113847 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
89113785 TTATGTTATT
*
89113795 TTAAATACTTTTTAAGG-CTTTTTAA
1 TTAAATACTTTTCAAGGTCTTTTTAA
89113820 TTAAATAAGCTTTTCAAGGTCTTTTTAA
1 TTAAAT-A-CTTTTCAAGGTCTTTTTAA
89113848 AGGCATTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 6 0.25
26 1 0.04
27 9 0.38
28 8 0.33
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.49
Consensus pattern (26 bp):
TTAAATACTTTTCAAGGTCTTTTTAA
Found at i:89124418 original size:12 final size:12
Alignment explanation
Indices: 89124401--89124433 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
89124391 TGGCCCGCCC
89124401 ATATTAATTTTT
1 ATATTAATTTTT
89124413 ATATT-ATTTTT
1 ATATTAATTTTT
89124424 ATA-TAATTTT
1 ATATTAATTTT
89124434 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:89124592 original size:28 final size:27
Alignment explanation
Indices: 89124561--89124615 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
89124551 TAAGAAAATG
89124561 TTTC-TAAAATAATAACAAAATTAACAAA
1 TTTCTTAAAATAAT-A-AAAATTAACAAA
89124589 TTTCTTTAAAATAATAAAAATTAACAA
1 TTTC-TTAAAATAATAAAAATTAACAA
89124616 TAAAATAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 15 0.60
29 1 0.04
30 9 0.36
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (27 bp):
TTTCTTAAAATAATAAAAATTAACAAA
Found at i:89124687 original size:11 final size:11
Alignment explanation
Indices: 89124653--89124692 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
89124643 CAATAATAAC
*
89124653 AAAATAGTAGC
1 AAAATAGTAGT
* *
89124664 AACATAATAGT
1 AAAATAGTAGT
89124675 AAAATAGTAGT
1 AAAATAGTAGT
89124686 AAAATAG
1 AAAATAG
89124693 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (11 bp):
AAAATAGTAGT
Found at i:89125750 original size:6 final size:6
Alignment explanation
Indices: 89125724--89125780 Score: 71
Period size: 6 Copynumber: 9.7 Consensus size: 6
89125714 AGTTCAAAAT
* * * *
89125724 ATAAAG ACAAA- ATAAAC ATAAAA ATAAAA ATAAAG ATAAAG ATAAAG
1 ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG
89125771 ATAAAG ATAA
1 ATAAAG ATAA
89125781 TCGAACTCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
5 4 0.09
6 42 0.91
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.16
Consensus pattern (6 bp):
ATAAAG
Found at i:89127375 original size:8 final size:7
Alignment explanation
Indices: 89127341--89127374 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
89127331 ACTAAAATAG
*
89127341 AATAACA
1 AATAAGA
89127348 AATAAGA
1 AATAAGA
89127355 AATAAGA
1 AATAAGA
89127362 AATAAAGA
1 AAT-AAGA
89127370 AATAA
1 AATAA
89127375 AAAACTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.15
Consensus pattern (7 bp):
AATAAGA
Found at i:89131947 original size:26 final size:26
Alignment explanation
Indices: 89131918--89132025 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
89131908 TGATACAAAT
*
89131918 TGATAATGGGTTAGTTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
89131944 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
89131970 TGATAATGGGTTTGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89131996 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89132022 TGAT
1 TGAT
89132026 GGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:89133656 original size:27 final size:27
Alignment explanation
Indices: 89133616--89133756 Score: 155
Period size: 27 Copynumber: 5.2 Consensus size: 27
89133606 AGGAAGCGTC
89133616 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCACAATTATCTGAT
* *
89133643 ATGGTGGCTTTGCCAC-ATATATCTG-T
1 CTGGTGGCTATGCCACAAT-TATCTGAT
* *
89133669 CCTGGTTGCTATGCCACAATTATCTAAT
1 -CTGGTGGCTATGCCACAATTATCTGAT
* *
89133697 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTATGCCACAAT-TATCTGAT
*
89133724 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTATGCCACAATTATCTG-AT
89133751 CTGGTG
1 CTGGTG
89133757 ACTTCGTCAC
Statistics
Matches: 96, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
26 11 0.11
27 81 0.84
28 4 0.04
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTATGCCACAATTATCTGAT
Found at i:89133702 original size:54 final size:54
Alignment explanation
Indices: 89133613--89133774 Score: 211
Period size: 54 Copynumber: 3.0 Consensus size: 54
89133603 TGGAGGAAGC
* *
89133613 GTCCTGGTGGCTATGCCACAATTATCTGATATGGTGGCTTTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTAATCTGGTGGCTTTGCCACATATATCT
* *
89133667 GTCCTGGTTGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTAATCTGGTGGCTTTGCCACATATATCT
* * * * * *
89133721 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTGACTTCGTCACA-ATATCT
1 GTCCTGGTGGCTATGCCACAATTATCT-AATCTGGTGGCTTTGCCACATATATCT
89133774 G
1 G
89133775 GCAGCTTCGC
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 12 0.13
54 83 0.87
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTAATCTGGTGGCTTTGCCACATATATCT
Found at i:89133767 original size:27 final size:26
Alignment explanation
Indices: 89133616--89133774 Score: 124
Period size: 27 Copynumber: 5.9 Consensus size: 26
89133606 AGGAAGCGTC
* * *
89133616 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGACTCTGCCACAA-TATCTGTT
* * * *
89133643 ATGGTGGCTTTGCCACATATATCTGTC
1 CTGGTGACTCTGCCACA-ATATCTGTT
* **
89133670 CTGGTTG-CTATGCCACAATTATCTAAT
1 CTGG-TGACTCTGCCACAA-TATCTGTT
*
89133697 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGACTCTGCCACA-ATATCTGTT
*
89133724 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGACTCTGCCACAATATCTGT-T
*
89133751 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGACTCT-GCCACAATATCTG
89133775 GCAGCTTCGC
Statistics
Matches: 111, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
26 12 0.11
27 95 0.86
28 4 0.04
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (26 bp):
CTGGTGACTCTGCCACAATATCTGTT
Found at i:89139343 original size:40 final size:39
Alignment explanation
Indices: 89139298--89139435 Score: 140
Period size: 40 Copynumber: 3.6 Consensus size: 39
89139288 GTATTTGTCA
*
89139298 GTTTATCCGATTAGTGCTGGGCACACATTTGATATCTTCG
1 GTTTATCCGACTAGTGCTGGGCACACATTTGATAT-TTCG
* * * * *
89139338 GTTTATCTGACTAGTGTTGGGCAGAC--CT-A-ATTGTTG
1 GTTTATCCGACTAGTGCTGGGCACACATTTGATATT-TCG
* *
89139374 TTTTATCCGACTAGTGCTGGGTACACATTTGATATTGTCG
1 GTTTATCCGACTAGTGCTGGGCACACATTTGATATT-TCG
*
89139414 GTTTATCCGACTAGCGCTGGGC
1 GTTTATCCGACTAGTGCTGGGC
89139436 GTAAAACGTT
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
35 1 0.01
36 25 0.32
37 1 0.01
38 2 0.03
39 1 0.01
40 47 0.61
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (39 bp):
GTTTATCCGACTAGTGCTGGGCACACATTTGATATTTCG
Found at i:89139448 original size:76 final size:75
Alignment explanation
Indices: 89139298--89139466 Score: 191
Period size: 76 Copynumber: 2.2 Consensus size: 75
89139288 GTATTTGTCA
* * * *
89139298 GTTTATCCGATTAGTGCTGGGCACACATTTGATATCTTCGGTTTATCTGACTAGTGTTGGGCAGA
1 GTTTATCCGACTAGTGCTGGGCACACATTTGATATCTTCGGTTTATCCGACTAGCGCTGGGCAGA
*
89139363 CCTAATTGTTG
66 -CAAATTGTTG
* *
89139374 TTTTATCCGACTAGTGCTGGGTACACATTTGATAT-TGTCGGTTTATCCGACTAGCGCTGGGC-G
1 GTTTATCCGACTAGTGCTGGGCACACATTTGATATCT-TCGGTTTATCCGACTAGCGCTGGGCAG
89139437 TA-AAACGTTGTTG
65 -ACAAA--TTGTTG
* *
89139450 GTTTATCCAACCAGTGC
1 GTTTATCCGACTAGTGC
89139467 AGGACATACC
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
74 2 0.03
75 2 0.03
76 75 0.95
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (75 bp):
GTTTATCCGACTAGTGCTGGGCACACATTTGATATCTTCGGTTTATCCGACTAGCGCTGGGCAGA
CAAATTGTTG
Found at i:89141037 original size:40 final size:40
Alignment explanation
Indices: 89140973--89141049 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
89140963 ACTATGTTTG
* **
89140973 GCACTTAGTGTGCTATTCGAAATAGCTTTGGCTATATAAA
1 GCACTTAGTGTGCAATTCGAAATAGCTTCAGCTATATAAA
*
89141013 GCACTTAGTGTGCGAATT-GGAATAGCTTCAGCTATAT
1 GCACTTAGTGTGC-AATTCGAAATAGCTTCAGCTATAT
89141050 GTGGCACTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 29 0.91
41 3 0.09
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (40 bp):
GCACTTAGTGTGCAATTCGAAATAGCTTCAGCTATATAAA
Found at i:89141057 original size:40 final size:40
Alignment explanation
Indices: 89140971--89141063 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
89140961 CGACTATGTT
* **
89140971 TGGCACTTAGTGTGCTATTCGAAATAGCTTTGGCTATATA
1 TGGCACTTAGTGTGCAATTCGAAATAGCTTCAGCTATATA
** * *
89141011 AAGCACTTAGTGTGCGAATT-GGAATAGCTTCAGCTATATG
1 TGGCACTTAGTGTGC-AATTCGAAATAGCTTCAGCTATATA
*
89141051 TGGCACTAAGTGT
1 TGGCACTTAGTGT
89141064 TTGATACCGT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
40 39 0.93
41 3 0.07
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (40 bp):
TGGCACTTAGTGTGCAATTCGAAATAGCTTCAGCTATATA
Found at i:89147892 original size:29 final size:29
Alignment explanation
Indices: 89147841--89147901 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
89147831 TAGAGTGATT
*
89147841 TTGAGTAAAAATGCATATTAGGGACTAAA
1 TTGAGTAAAAATGCAAATTAGGGACTAAA
* **
89147870 TTGAGT-AAAATGTAAATTGAGGGGTTAAA
1 TTGAGTAAAAATGCAAATT-AGGGACTAAA
89147899 TTG
1 TTG
89147902 TGAAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (29 bp):
TTGAGTAAAAATGCAAATTAGGGACTAAA
Found at i:89148404 original size:40 final size:41
Alignment explanation
Indices: 89148318--89148414 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 41
89148308 CGACTATGTT
* *
89148318 TGGCACTTATTGTGCG-ATTCAAAATAGCTTTGCCTATATG
1 TGGCACTTAATGTGCGAATTCAAAATAGCTTCGCCTATATG
** * ** *
89148358 AAGCACTTAGTGTGCGAATT-GGAATAGCTTCGGCTATATG
1 TGGCACTTAATGTGCGAATTCAAAATAGCTTCGCCTATATG
*
89148398 TGGCACTGAATGTGCGA
1 TGGCACTTAATGTGCGA
89148415 TACCGTGATA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
40 42 0.93
41 3 0.07
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (41 bp):
TGGCACTTAATGTGCGAATTCAAAATAGCTTCGCCTATATG
Found at i:89148778 original size:31 final size:30
Alignment explanation
Indices: 89148721--89148779 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
89148711 GTATATACTC
*
89148721 AAAATTTAAGGGATTAAAGTGTAAATATGA
1 AAAATTTAAGGGATTAAAGTGCAAATATGA
89148751 AAAATTTGAAGGG-TTAATAGTGCAAATAT
1 AAAATTT-AAGGGATTAA-AGTGCAAATAT
89148780 TTTAAGGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.47, C:0.02, G:0.20, T:0.31
Consensus pattern (30 bp):
AAAATTTAAGGGATTAAAGTGCAAATATGA
Found at i:89153516 original size:26 final size:26
Alignment explanation
Indices: 89153435--89153516 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
89153425 TGGTACAAAT
*
89153435 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
89153461 TGAGAATGGATTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
* *
89153487 TGATAATAGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
89153513 TGAT
1 TGAT
89153517 GGGCATTTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:89155977 original size:10 final size:10
Alignment explanation
Indices: 89155962--89156000 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
89155952 AGAACCCATC
89155962 ACACACACAT
1 ACACACACAT
89155972 ACACACA-A-
1 ACACACACAT
89155980 ACACACACAT
1 ACACACACAT
*
89155990 ACACATACAT
1 ACACACACAT
89156000 A
1 A
89156001 TGACACAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 7 0.27
9 2 0.08
10 17 0.65
ACGTcount: A:0.54, C:0.36, G:0.00, T:0.10
Consensus pattern (10 bp):
ACACACACAT
Found at i:89157190 original size:26 final size:26
Alignment explanation
Indices: 89157161--89157268 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
89157151 TGGTACAAAT
89157161 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
89157187 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
89157213 TGATAATGTGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89157239 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89157265 TGAT
1 TGAT
89157269 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:89158900 original size:27 final size:27
Alignment explanation
Indices: 89158862--89158998 Score: 167
Period size: 27 Copynumber: 5.1 Consensus size: 27
89158852 AGCGTCCGGA
*
89158862 TGGCTATGCCACAATTATCTGATCTGG
1 TGGCTCTGCCACAATTATCTGATCTGG
*
89158889 TGGCTCTGCCAC-ATATATCTG-TCCTAG
1 TGGCTCTGCCACAAT-TATCTGAT-CTGG
*
89158916 TGGCTATGCCACAATTATCTGATCTGG
1 TGGCTCTGCCACAATTATCTGATCTGG
89158943 TGGCTCTGCCAC-ATATATCT-ATTCTGG
1 TGGCTCTGCCACAAT-TATCTGA-TCTGG
89158970 TGGCTCTGCCACAA-TATCTGTATCTGG
1 TGGCTCTGCCACAATTATCTG-ATCTGG
89158997 TG
1 TG
89158999 ACTTCGTCAC
Statistics
Matches: 96, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
26 11 0.11
27 80 0.83
28 5 0.05
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (27 bp):
TGGCTCTGCCACAATTATCTGATCTGG
Found at i:89158944 original size:54 final size:54
Alignment explanation
Indices: 89158862--89158998 Score: 222
Period size: 54 Copynumber: 2.5 Consensus size: 54
89158852 AGCGTCCGGA
*
89158862 TGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTAG
1 TGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTATCCTAG
* *
89158916 TGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTATTCTGG
1 TGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTATCCTAG
*
89158970 TGGCTCTGCCACAA-TATCTGTATCTGGTG
1 TGGCTATGCCACAATTATCTG-ATCTGGTG
89158999 ACTTCGTCAC
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 6 0.08
54 72 0.92
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (54 bp):
TGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTATCCTAG
Found at i:89159010 original size:81 final size:80
Alignment explanation
Indices: 89158862--89159016 Score: 192
Period size: 81 Copynumber: 1.9 Consensus size: 80
89158852 AGCGTCCGGA
*
89158862 TGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTAGTGGCTATGCCA
1 TGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTAGTGACTATGCCA
89158927 CAATTATCTGATCTGG
66 CAA-TATCTGATCTGG
* * *
89158943 TGGCTCTGCCAC-ATATATCT-ATTCTGGTGGCTCTGCCACA-ATATCTGTATCTGGTGACT-TC
1 TGGCTATGCCACAAT-TATCTGA-TCTGGTGGCTCTGCCACATATATCTGT-CCTAGTGACTAT-
*
89159004 GTCACAATATCTG
62 GCCACAATATCTG
89159017 GCAGCCTCGC
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
80 18 0.28
81 47 0.72
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (80 bp):
TGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTAGTGACTATGCCA
CAATATCTGATCTGG
Found at i:89167931 original size:38 final size:35
Alignment explanation
Indices: 89167868--89167944 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 35
89167858 TGAGTTCTTT
* *
89167868 TTTTTTATTTGTTCTTTAATGTGTTGGGTTCTCTG
1 TTTTTTATTTGTTCTTTAAAGTGTTGGGTCCTCTG
* *
89167903 TTTTTTATTTGTTTTTTTTAAAGATGTTGGGTCCTTTG
1 TTTTTTATTTG--TTCTTTAAAG-TGTTGGGTCCTCTG
89167941 TTTT
1 TTTT
89167945 AAAGATTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 11 0.31
37 8 0.23
38 16 0.46
ACGTcount: A:0.10, C:0.06, G:0.18, T:0.65
Consensus pattern (35 bp):
TTTTTTATTTGTTCTTTAAAGTGTTGGGTCCTCTG
Found at i:89170329 original size:36 final size:37
Alignment explanation
Indices: 89170289--89170365 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
89170279 GACTAAATAA
* * *
89170289 TAAAAATTGTAAAATTTGA-ATTTAGGGGTTGTTTTG
1 TAAAAACTATAAAATTTGAGATATAGGGGTTGTTTTG
** *
89170325 TAAAAACTATAATTTTTGAGGTATAGGGGTTGTTTTG
1 TAAAAACTATAAAATTTGAGATATAGGGGTTGTTTTG
89170362 TAAA
1 TAAA
89170366 TGCTGAAACA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 15 0.44
37 19 0.56
ACGTcount: A:0.34, C:0.01, G:0.22, T:0.43
Consensus pattern (37 bp):
TAAAAACTATAAAATTTGAGATATAGGGGTTGTTTTG
Found at i:89171290 original size:54 final size:55
Alignment explanation
Indices: 89171181--89171309 Score: 161
Period size: 54 Copynumber: 2.4 Consensus size: 55
89171171 AATTGTTTAG
* * * *
89171181 TTTGATTCCTTTAGACTATGGAGAACTTATATTACCTACCAATATAATTACTCAA
1 TTTGATTCCTTTAGACTATGGAGAACTTAAACTACCAACCAATACAATTACTCAA
* * * * **
89171236 TTTGACTCC-TTAGACTATGGATAACTTAAACTACCAACTAATACATTTGGTCAA
1 TTTGATTCCTTTAGACTATGGAGAACTTAAACTACCAACCAATACAATTACTCAA
89171290 TTTGATTCCTTTAGACTATG
1 TTTGATTCCTTTAGACTATG
89171310 TATTATGATT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
54 44 0.71
55 18 0.29
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (55 bp):
TTTGATTCCTTTAGACTATGGAGAACTTAAACTACCAACCAATACAATTACTCAA
Found at i:89172664 original size:39 final size:39
Alignment explanation
Indices: 89172610--89172692 Score: 141
Period size: 39 Copynumber: 2.1 Consensus size: 39
89172600 GATTTAGGCT
89172610 GTGTGGGCTACACGAGCGTGTAGGATTTTGGGTCA-GTCC
1 GTGTGGGCTACACGAGCGTGTAGGATTTTGGGTCAGGT-C
*
89172649 GTGTGTGCTACACGAGCGTGTAGGATTTTGGGTCAGGTC
1 GTGTGGGCTACACGAGCGTGTAGGATTTTGGGTCAGGTC
89172688 GTGTG
1 GTGTG
89172693 ATCCACACGA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
39 40 0.95
40 2 0.05
ACGTcount: A:0.14, C:0.16, G:0.40, T:0.30
Consensus pattern (39 bp):
GTGTGGGCTACACGAGCGTGTAGGATTTTGGGTCAGGTC
Found at i:89172701 original size:39 final size:39
Alignment explanation
Indices: 89172610--89172702 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 39
89172600 GATTTAGGCT
* *
89172610 GTGTGGGCTACACGAGCGTGTAGGATTTTGGGTCAGTCC
1 GTGTGTGCCACACGAGCGTGTAGGATTTTGGGTCAGTCC
*
89172649 GTGTGTGCTACACGAGCGTGTAGGATTTTGGGTCAGGT-C
1 GTGTGTGCCACACGAGCGTGTAGGATTTTGGGTCA-GTCC
89172688 GTGTGAT-CCACACGA
1 GTGTG-TGCCACACGA
89172703 CCAAGAAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
39 47 0.94
40 3 0.06
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.28
Consensus pattern (39 bp):
GTGTGTGCCACACGAGCGTGTAGGATTTTGGGTCAGTCC
Found at i:89185812 original size:20 final size:19
Alignment explanation
Indices: 89185773--89185834 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
89185763 ATCTACACTA
*
89185773 AATT-GGTTAATTAAAATT
1 AATTAGGTTAATTATAATT
*
89185791 AAGGTTA-GTTAATTATAGTT
1 AA--TTAGGTTAATTATAATT
*
89185811 AATTAGGTTAATTATAAAT
1 AATTAGGTTAATTATAATT
89185830 AATTA
1 AATTA
89185835 TAATTTTAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 5 0.14
19 16 0.44
20 15 0.42
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (19 bp):
AATTAGGTTAATTATAATT
Found at i:89189741 original size:5 final size:5
Alignment explanation
Indices: 89189731--89189769 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
89189721 AATTTGTGTG
*
89189731 TTATT TTATTT TTTTCT TTATT TTATT TTATT TTATT TT
1 TTATT TTA-TT TTAT-T TTATT TTATT TTATT TTATT TT
89189770 TTTCACAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 22 0.73
6 8 0.27
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTATT
Found at i:89194208 original size:17 final size:17
Alignment explanation
Indices: 89194186--89194218 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
89194176 AATTTGTGTG
89194186 TTATTTTATTTTTTTCT
1 TTATTTTATTTTTTTCT
89194203 TTATTTTATTTTTTTC
1 TTATTTTATTTTTTTC
89194219 ACATTGTCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (17 bp):
TTATTTTATTTTTTTCT
Found at i:89197334 original size:10 final size:10
Alignment explanation
Indices: 89197319--89197357 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
89197309 AGAACCCATC
89197319 ACACACACAT
1 ACACACACAT
89197329 ACACACA-A-
1 ACACACACAT
89197337 ACACACACAT
1 ACACACACAT
*
89197347 ACACATACAT
1 ACACACACAT
89197357 A
1 A
89197358 TGACACAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 7 0.27
9 2 0.08
10 17 0.65
ACGTcount: A:0.54, C:0.36, G:0.00, T:0.10
Consensus pattern (10 bp):
ACACACACAT
Found at i:89198549 original size:26 final size:26
Alignment explanation
Indices: 89198520--89198627 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
89198510 TGGTACAAAT
89198520 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
89198546 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
89198572 TGATAATGTGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89198598 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89198624 TGAT
1 TGAT
89198628 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:89202086 original size:37 final size:37
Alignment explanation
Indices: 89202025--89202103 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
89202015 TTATTACGAA
* * *
89202025 GTCTTACCCGAACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
* *
89202062 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
89202099 GTCTT
1 GTCTT
89202104 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
Found at i:89202300 original size:47 final size:47
Alignment explanation
Indices: 89202222--89202406 Score: 289
Period size: 47 Copynumber: 3.9 Consensus size: 47
89202212 CCCTTCGGGA
* * * * * *
89202222 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
89202269 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
89202316 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
89202363 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
89202407 CAAAGCTTCA
Statistics
Matches: 127, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 127 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:89205904 original size:27 final size:27
Alignment explanation
Indices: 89205866--89205921 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
89205856 TAAGGTCAGG
89205866 TATCGATACTAGATGTAAAAATATCCA
1 TATCGATACTAGATGTAAAAATATCCA
89205893 TATCGATACTAGATGTAAAAATATCCA
1 TATCGATACTAGATGTAAAAATATCCA
89205920 TA
1 TA
89205922 CTTGAGTTCA
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:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (27 bp):
TATCGATACTAGATGTAAAAATATCCA
Found at i:89207643 original size:16 final size:16
Alignment explanation
Indices: 89207622--89207656 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
89207612 TGCTACTTGT
89207622 TTTCATT-TTATTTTTA
1 TTTCATTGTTA-TTTTA
89207638 TTTCATTGTTATTTTA
1 TTTCATTGTTATTTTA
89207654 TTT
1 TTT
89207657 ACTCATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTCATTGTTATTTTA
Found at i:89208172 original size:6 final size:6
Alignment explanation
Indices: 89208157--89208241 Score: 50
Period size: 6 Copynumber: 13.8 Consensus size: 6
89208147 ATTCTGTTAC
* * * *
89208157 CTGATA CTGATT CTGATT TTGATT CTG-TT ACCTGATA CTGATT CTG-TCAC
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGAT--T
* *
89208207 CTAATT CTGATT CTGATT TTGATT CT-AGTT CTGAT
1 CTGATT CTGATT CTGATT CTGATT CTGA-TT CTGAT
89208242 AATGTTTCTT
Statistics
Matches: 60, Mismatches: 11, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
5 4 0.07
6 48 0.80
7 6 0.10
8 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.47
Consensus pattern (6 bp):
CTGATT
Found at i:89208185 original size:31 final size:32
Alignment explanation
Indices: 89208134--89208202 Score: 122
Period size: 31 Copynumber: 2.2 Consensus size: 32
89208124 CGAAACTACC
*
89208134 ATTCTGATTTTTTATTCTGTTACCTGATACTG
1 ATTCTGATTTTTGATTCTGTTACCTGATACTG
89208166 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTTGATTCTGTTACCTGATACTG
89208197 ATTCTG
1 ATTCTG
89208203 TCACCTAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 29 0.81
32 7 0.19
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (32 bp):
ATTCTGATTTTTGATTCTGTTACCTGATACTG
Found at i:89208198 original size:19 final size:19
Alignment explanation
Indices: 89208176--89208221 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
89208166 ATTCTGATTT
* *
89208176 TGATTCTGTTACCTGATAC
1 TGATTCTGTCACCTAATAC
*
89208195 TGATTCTGTCACCTAATTC
1 TGATTCTGTCACCTAATAC
89208214 TGATTCTG
1 TGATTCTG
89208222 ATTTTGATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (19 bp):
TGATTCTGTCACCTAATAC
Found at i:89209065 original size:87 final size:87
Alignment explanation
Indices: 89208927--89209374 Score: 513
Period size: 87 Copynumber: 5.2 Consensus size: 87
89208917 CCGGCACGTA
** ** * * * * * **
89208927 AGTGCATCATCGGAT-AAATTGAAGAAAATATACTGGCACAAATAGTGCATCATCAGATATACTG
1 AGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACACAGTGCATCATCGGATAAACCA
* **
89208991 AAGCAAATATACTAACACACAC
66 AAGAAAATATACTGGCACACAC
* * * *
89209013 AGTGCATCATTGGATGAAACTGAAACTACTATATTGGCACACACAGTGCATCATCGGATAAACCA
1 AGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACACAGTGCATCATCGGATAAACCA
*
89209078 AAGAAAATATACTGGTACACAC
66 AAGAAAATATACTGGCACACAC
*
89209100 AGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACACAGTGCATCATCGGATAAATCA
1 AGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACACAGTGCATCATCGGATAAACCA
*
89209165 AAGAAAATATACTGGTACACAC
66 AAGAAAATATACTGGCACACAC
* *
89209187 AGTGCATCATCGGATGAAACCGAAGCTACTATATTGGCACACACAATGCATCATCGGATAAACCA
1 AGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACACAGTGCATCATCGGATAAACCA
89209252 AAGAAAATATACTGGCACACAC
66 AAGAAAATATACTGGCACACAC
* * ** * * * * * * * * * **
89209274 AGTGCATCATCAGCT-ATGCTGAAGCAAATATACTTGCATACATAATGCATCATTGGATATACTG
1 AGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACACAGTGCATCATCGGATAAACCA
* **
89209338 AAGCAAATATACTGGCACATGC
66 AAGAAAATATACTGGCACACAC
89209360 AGTGCATCATCGGAT
1 AGTGCATCATCGGAT
89209375 ATACCAAAGT
Statistics
Matches: 315, Mismatches: 46, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
86 82 0.26
87 233 0.74
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (87 bp):
AGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACACAGTGCATCATCGGATAAACCA
AAGAAAATATACTGGCACACAC
Found at i:89209303 original size:130 final size:128
Alignment explanation
Indices: 89208927--89209383 Score: 425
Period size: 130 Copynumber: 3.5 Consensus size: 128
89208917 CCGGCACGTA
** * * * * * **
89208927 AGTGCATCATCGGATAAATTGAAGAAAATATACTGGCACAAATAGTGCATCATCAGATATACTGA
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACACAGTGCATCATCGGATAAACCAA
* ** ** ** *
89208992 AGCAAATATACTAACACACACAGTGCATCATTGGATGAA--ACTGAAACTACTATATTGGCACAC
66 AGAAAATATACTGGCACACACAGTGCATCATCAGAT-AATCAAAGAAA--A-TATACTGGCACAC
89209055 AC
127 AC
* * * *
89209057 AGTGCATCATCGGATAAACCAAAGAAAATATACTGGTACACACAGTGCATCATCGGATGAAACCG
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACACAGTGCATCATCGGAT-AAACCA
** * * *
89209122 AAGCTACTATACTGGCACACACAGTGCATCATCGGATAAATCAAAGAAAATATACTGGTACACAC
65 AAGAAAATATACTGGCACACACAGTGCATCATCAGAT-AATCAAAGAAAATATACTGGCACACAC
* * * *
89209187 AGTGCATCATCGGATGAAACCGAAGCTACTATATTGGCACACACAATGCATCATCGGATAAACCA
1 AGTGCATCATCGGAT-AAACCGAAGCAAATATACTGGCACACACAGTGCATCATCGGATAAACCA
* * * * *
89209252 AAGAAAATATACTGGCACACACAGTGCATCATCAGCT-ATGCTGAAGCAAATATACTTGCATACA
65 AAGAAAATATACTGGCACACACAGTGCATCATCAGATAAT-C-AAAGAAAATATACTGGCACACA
*
89209316 T
128 C
* * * * ** *
89209317 AATGCATCATTGGATATACTGAAGCAAATATACTGGCACATGCAGTGCATCATCGGATATACCAA
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACACAGTGCATCATCGGATAAACCAA
89209382 AG
66 AG
89209384 TATAACCTGT
Statistics
Matches: 272, Mismatches: 49, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
128 2 0.01
129 44 0.16
130 146 0.54
131 75 0.28
133 5 0.02
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (128 bp):
AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACACAGTGCATCATCGGATAAACCAA
AGAAAATATACTGGCACACACAGTGCATCATCAGATAATCAAAGAAAATATACTGGCACACAC
Found at i:89209378 original size:43 final size:43
Alignment explanation
Indices: 89208927--89209375 Score: 468
Period size: 43 Copynumber: 10.4 Consensus size: 43
89208917 CCGGCACGTA
* * * *
89208927 AGTGCATCATCGGATAAATTGAAGAAAATATACTGGCACAAAT
1 AGTGCATCATCGGATAAACTGAAGCAAATATACTGGCACACAC
* * **
89208970 AGTGCATCATCAGATATACTGAAGCAAATATACTAACACACAC
1 AGTGCATCATCGGATAAACTGAAGCAAATATACTGGCACACAC
* * * * *
89209013 AGTGCATCATTGGATGAAACTGAAACTACTATATTGGCACACAC
1 AGTGCATCATCGGAT-AAACTGAAGCAAATATACTGGCACACAC
** * *
89209057 AGTGCATCATCGGATAAACCAAAGAAAATATACTGGTACACAC
1 AGTGCATCATCGGATAAACTGAAGCAAATATACTGGCACACAC
* * *
89209100 AGTGCATCATCGGATGAAACCGAAGCTACTATACTGGCACACAC
1 AGTGCATCATCGGAT-AAACTGAAGCAAATATACTGGCACACAC
* * *
89209144 AGTGCATCATCGGATAAA-TCAAAGAAAATATACTGGTACACAC
1 AGTGCATCATCGGATAAACT-GAAGCAAATATACTGGCACACAC
* * * *
89209187 AGTGCATCATCGGATGAAACCGAAGCTACTATATTGGCACACAC
1 AGTGCATCATCGGAT-AAACTGAAGCAAATATACTGGCACACAC
* ** *
89209231 AATGCATCATCGGATAAACCAAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACTGAAGCAAATATACTGGCACACAC
* * ** * * *
89209274 AGTGCATCATCAGCTATGCTGAAGCAAATATACTTGCATACAT
1 AGTGCATCATCGGATAAACTGAAGCAAATATACTGGCACACAC
* * * **
89209317 AATGCATCATTGGATATACTGAAGCAAATATACTGGCACATGC
1 AGTGCATCATCGGATAAACTGAAGCAAATATACTGGCACACAC
89209360 AGTGCATCATCGGATA
1 AGTGCATCATCGGATA
89209376 TACCAAAGTA
Statistics
Matches: 328, Mismatches: 73, Indels: 10
0.80 0.18 0.02
Matches are distributed among these distances:
43 221 0.67
44 107 0.33
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (43 bp):
AGTGCATCATCGGATAAACTGAAGCAAATATACTGGCACACAC
Found at i:89216202 original size:21 final size:20
Alignment explanation
Indices: 89216178--89216228 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
89216168 CAAGAGATTA
89216178 TTTAGAATT-TAATTTAATTT
1 TTTA-AATTATAATTTAATTT
*
89216198 CTTTAAATTATCATTTAATTT
1 -TTTAAATTATAATTTAATTT
89216219 TTTATAATTA
1 TTTA-AATTA
89216229 AATAATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTAAATTATAATTTAATTT
Found at i:89217122 original size:24 final size:24
Alignment explanation
Indices: 89217077--89217123 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
89217067 ATAAAAACTA
* *
89217077 AACCCTGAAAACCTGAAAACAAAG
1 AACCCTCAAAACATGAAAACAAAG
89217101 AACCCTCAAAACAT-AAACACAAA
1 AACCCTCAAAACATGAAA-ACAAA
89217124 ATTCTCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.57, C:0.28, G:0.06, T:0.09
Consensus pattern (24 bp):
AACCCTCAAAACATGAAAACAAAG
Found at i:89217201 original size:88 final size:88
Alignment explanation
Indices: 89217089--89217264 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
89217079 CCCTGAAAAC
89217089 CTGAAAACAAAGAACCCTCAAAACATAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATCT
1 CTGAAAACAAAGAACCCTCAAAACATAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATCT
89217154 CTAATGGATTTTTTTCTAATGTT
66 CTAATGGATTTTTTTCTAATGTT
89217177 CTGAAAACAAAGAACCCTCAAAACATAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATCT
1 CTGAAAACAAAGAACCCTCAAAACATAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATCT
89217242 CTAATGGATTTTTTTCTAATGTT
66 CTAATGGATTTTTTTCTAATGTT
89217265 GTAAAAGAGC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (88 bp):
CTGAAAACAAAGAACCCTCAAAACATAAACACAAAATTCTCTAAATGTGTTATGAGTTCTAATCT
CTAATGGATTTTTTTCTAATGTT
Found at i:89221157 original size:40 final size:40
Alignment explanation
Indices: 89221092--89221188 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 40
89221082 CCATCTCCGT
* *
89221092 CCAACCCAACACACC-AG-GTGGGGATAAAATAAACCCAC
1 CCAACCCTACACACCAAGTATGGGGATAAAATAAACCCAC
* * * * *
89221130 CCAGCTCTACACACCAAGTATGGGGATAGAATCAACCCAT
1 CCAACCCTACACACCAAGTATGGGGATAAAATAAACCCAC
89221170 CCAACCCTACACACCAAGT
1 CCAACCCTACACACCAAGT
89221189 GGTACCGTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
38 12 0.25
39 2 0.04
40 34 0.71
ACGTcount: A:0.38, C:0.35, G:0.14, T:0.12
Consensus pattern (40 bp):
CCAACCCTACACACCAAGTATGGGGATAAAATAAACCCAC
Found at i:89223319 original size:33 final size:33
Alignment explanation
Indices: 89223258--89223416 Score: 144
Period size: 33 Copynumber: 4.8 Consensus size: 33
89223248 GAACATTGAA
* *
89223258 AGTCCACT-AGGACAGTAAGCACATAATAGAGAT
1 AGTCCACTGA-GACAGTAAACACATAATAGAAAT
* ** *
89223291 AATCTGCTGAGACAGTAAACACAAAATAGAAAT
1 AGTCCACTGAGACAGTAAACACATAATAGAAAT
* *
89223324 AGTCCGCT-AGGACAGTAAACACATAATAAAAAT
1 AGTCCACTGA-GACAGTAAACACATAATAGAAAT
* * * * *
89223357 AGTCTACTGTGACATTAAACACATAACAGAGAT
1 AGTCCACTGAGACAGTAAACACATAATAGAAAT
* *
89223390 AGTCCACTGGGAAAGTAAACACA-AATA
1 AGTCCACTGAGACAGTAAACACATAATA
89223417 AAGTTTATCG
Statistics
Matches: 101, Mismatches: 22, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
32 4 0.04
33 96 0.95
34 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.17, T:0.19
Consensus pattern (33 bp):
AGTCCACTGAGACAGTAAACACATAATAGAAAT
Found at i:89223376 original size:66 final size:66
Alignment explanation
Indices: 89223258--89223418 Score: 198
Period size: 66 Copynumber: 2.5 Consensus size: 66
89223248 GAACATTGAA
* * * * *
89223258 AGTCCACTAGGACAGTAAGCACATAATAGAGATAATCTGCTGAGACAGTAAACACAAAATAGAAA
1 AGTCCACTAGGACAGTAAACACATAATAAAAATAATCTACTGAGACAGTAAACACAAAACAGAAA
89223323 T
66 T
* * * * * *
89223324 AGTCCGCTAGGACAGTAAACACATAATAAAAATAGTCTACTGTGACATTAAACACATAACAGAGA
1 AGTCCACTAGGACAGTAAACACATAATAAAAATAATCTACTGAGACAGTAAACACAAAACAGAAA
89223389 T
66 T
* *
89223390 AGTCCACTGGGAAAGTAAACACA-AATAAA
1 AGTCCACTAGGACAGTAAACACATAATAAA
89223419 GTTTATCGGG
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
65 6 0.07
66 75 0.93
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (66 bp):
AGTCCACTAGGACAGTAAACACATAATAAAAATAATCTACTGAGACAGTAAACACAAAACAGAAA
T
Found at i:89224522 original size:17 final size:17
Alignment explanation
Indices: 89224489--89224523 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
89224479 TCTATAATAA
*
89224489 ACTCCATACAATTACAT
1 ACTCCATACAATCACAT
*
89224506 ACTCCATACCATCACAT
1 ACTCCATACAATCACAT
89224523 A
1 A
89224524 TATCTCGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (17 bp):
ACTCCATACAATCACAT
Found at i:89234870 original size:243 final size:244
Alignment explanation
Indices: 89234428--89234912 Score: 819
Period size: 243 Copynumber: 2.0 Consensus size: 244
89234418 TTCTCGAGGT
*
89234428 AGACCCCCGAGACATCCCAGAAATGCAAGTGGCAGTTGAACTGTTGCTAAGGATGCTACTGTAAA
1 AGACCCCCGAGACATCCCAGAAATGCAAGTGGCAGTCGAACTGTTGCTAAGGATGCTACTGTAAA
* *
89234493 ACCAGAGGCTCGAGCCCCGGAAAGAACTTATGCAATACGCGCTCGAGATGAAGCCACTACTCCCG
66 ACCAGAGGCTCGAGCCCCGGAAAGAACTTATGCAATAAGCGCTCGAGAGGAAGCCACTACTCCCG
*
89234558 ATGTCATCAGGGTACATTTTATATCTGTAATACTCGTGTCATTGCCTTAATTGATCTAGGGTCAA
131 ATGTCATCAGGGTACATTTTATATCTGTAATACTCGTGTCATTGCCTTAATTGATCCAGGGTCAA
* **
89234623 TCCATTCATACATTTGTATGGACTTGGTGTCTAGTATGGATATGTCTGC
196 TCCATTCATAAATTTGTATAAACTTGGTGTCTAGTATGGATATGTCTGC
* * *
89234672 AGACCCCCGAGACATCCTAGAAGTGCAAGTGGCAGTCGAACTGTTGCTAAGGATGCTACTG-CAA
1 AGACCCCCGAGACATCCCAGAAATGCAAGTGGCAGTCGAACTGTTGCTAAGGATGCTACTGTAAA
*
89234736 ACCAGAGGCTCGAGCCCCGGCAAGAACTTATGCAATAAGCGCTCGAGAGGAAGCCACTACTCCCG
66 ACCAGAGGCTCGAGCCCCGGAAAGAACTTATGCAATAAGCGCTCGAGAGGAAGCCACTACTCCCG
* * * *
89234801 ATGTCATCATGGTACATTTTATATTTGTAATACTTGTGTCATTGCCTTAATTGATCCAGGGTTAA
131 ATGTCATCAGGGTACATTTTATATCTGTAATACTCGTGTCATTGCCTTAATTGATCCAGGGTCAA
*
89234866 TCCATTCGTAAATTTGTATAAACTTGGTGTCTAGTATGGATATGTCT
196 TCCATTCATAAATTTGTATAAACTTGGTGTCTAGTATGGATATGTCT
89234913 ATAGAACCTA
Statistics
Matches: 225, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
243 167 0.74
244 58 0.26
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (244 bp):
AGACCCCCGAGACATCCCAGAAATGCAAGTGGCAGTCGAACTGTTGCTAAGGATGCTACTGTAAA
ACCAGAGGCTCGAGCCCCGGAAAGAACTTATGCAATAAGCGCTCGAGAGGAAGCCACTACTCCCG
ATGTCATCAGGGTACATTTTATATCTGTAATACTCGTGTCATTGCCTTAATTGATCCAGGGTCAA
TCCATTCATAAATTTGTATAAACTTGGTGTCTAGTATGGATATGTCTGC
Found at i:89240888 original size:28 final size:29
Alignment explanation
Indices: 89240857--89240911 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
89240847 CACGAGTGAT
89240857 GACAC-GA-GTGTGTCTAGGCCGTGTGAGG
1 GACACGGACGTGTG-CTAGGCCGTGTGAGG
*
89240885 GACACGGACGTGTGCTTGGCCGTGTGA
1 GACACGGACGTGTGCTAGGCCGTGTGA
89240912 AAACCTCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 5 0.21
29 14 0.58
30 5 0.21
ACGTcount: A:0.16, C:0.20, G:0.42, T:0.22
Consensus pattern (29 bp):
GACACGGACGTGTGCTAGGCCGTGTGAGG
Found at i:89241716 original size:43 final size:43
Alignment explanation
Indices: 89241668--89241823 Score: 215
Period size: 43 Copynumber: 3.6 Consensus size: 43
89241658 GGTACTGGTT
* *
89241668 TAAAGAACATGATCTTTAGTGGTGCTTTTCCTACAAACGCTGC
1 TAAAGAACATGATCTTTAGCGGCGCTTTTCCTACAAACGCTGC
* *
89241711 TAAAGAACATGATTTTTAGCGGCGTTTTTCCTACAAACGCTGC
1 TAAAGAACATGATCTTTAGCGGCGCTTTTCCTACAAACGCTGC
* * * *
89241754 TAAAGAACATGATCTTTAACGGCGCTTTTACTA-ATAATGCCGC
1 TAAAGAACATGATCTTTAGCGGCGCTTTTCCTACA-AACGCTGC
*
89241797 TATAGAACATGATCTTTAGCGGCGCTT
1 TAAAGAACATGATCTTTAGCGGCGCTT
89241824 CTTAAAAAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
42 1 0.01
43 99 0.99
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (43 bp):
TAAAGAACATGATCTTTAGCGGCGCTTTTCCTACAAACGCTGC
Found at i:89242383 original size:30 final size:27
Alignment explanation
Indices: 89242333--89242388 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
89242323 TTGGGTTAAG
89242333 GAATTGTATAAGATTTGTTGTTATTAT
1 GAATTGTATAAGATTTGTTGTTATTAT
*
89242360 GAATTGTATAAGATTTGTTGTTGTTAT
1 GAATTGTATAAGATTTGTTGTTATTAT
89242387 GA
1 GA
89242389 TCATCATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (27 bp):
GAATTGTATAAGATTTGTTGTTATTAT
Found at i:89244201 original size:31 final size:31
Alignment explanation
Indices: 89244163--89244224 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
89244153 TATTTTGGAG
89244163 TTAGCAGCTTAAAGGAGCCAAACCCAACGAC
1 TTAGCAGCTTAAAGGAGCCAAACCCAACGAC
89244194 TTAGCAGCTTAAAGGAGCCAAACCCAACGAC
1 TTAGCAGCTTAAAGGAGCCAAACCCAACGAC
89244225 GGCTTTGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.29, G:0.19, T:0.13
Consensus pattern (31 bp):
TTAGCAGCTTAAAGGAGCCAAACCCAACGAC
Found at i:89250009 original size:20 final size:21
Alignment explanation
Indices: 89249972--89250018 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
89249962 ACGACAAAAA
89249972 GAAAAAAAGAAGATTAGAACAC
1 GAAAAAAAGAAGATTAG-ACAC
89249994 -AAAAAAA-AA-ATGTAGACAC
1 GAAAAAAAGAAGAT-TAGACAC
89250013 GAAAAA
1 GAAAAA
89250019 TACGAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.68, C:0.09, G:0.15, T:0.09
Consensus pattern (21 bp):
GAAAAAAAGAAGATTAGACAC
Found at i:89251566 original size:13 final size:13
Alignment explanation
Indices: 89251550--89251581 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
89251540 TGTCCTTGCC
89251550 CTTTTTCCTTTTT
1 CTTTTTCCTTTTT
*
89251563 CTTTTTCTTTTTT
1 CTTTTTCCTTTTT
89251576 CTTTTT
1 CTTTTT
89251582 GTACTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
CTTTTTCCTTTTT
Found at i:89252922 original size:22 final size:20
Alignment explanation
Indices: 89252885--89252925 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
89252875 CTCTCTTTAA
89252885 ATTTTTTTTATTTTCCTTTT
1 ATTTTTTTTATTTTCCTTTT
*
89252905 ATTTTTCTTTTTTCTTCCTTT
1 ATTTTT-TTTATT-TTCCTTT
89252926 ATAATGTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (20 bp):
ATTTTTTTTATTTTCCTTTT
Found at i:89263206 original size:46 final size:46
Alignment explanation
Indices: 89263156--89263331 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
89263146 TGGTTGAGCA
89263156 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
89263202 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
89263247 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
89263295 -CCTGAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
89263332 GCGAGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 60 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:89263312 original size:93 final size:93
Alignment explanation
Indices: 89263153--89263324 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
89263143 GGATGGTTGA
*
89263153 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
89263218 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
89263246 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
*
89263310 TTGAGTCTGAGTTCG
65 TTGAGTCCGAGTTCG
89263325 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:89268198 original size:12 final size:12
Alignment explanation
Indices: 89268179--89268215 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
89268169 AGTTGTTAAA
89268179 TTGTTAG-TAGT
1 TTGTTAGTTAGT
89268190 TTGGTTAGTTAGT
1 TT-GTTAGTTAGT
89268203 TTGTTAGTTAGT
1 TTGTTAGTTAGT
89268215 T
1 T
89268216 AAATATGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 2 0.08
12 16 0.67
13 6 0.25
ACGTcount: A:0.16, C:0.00, G:0.27, T:0.57
Consensus pattern (12 bp):
TTGTTAGTTAGT
Found at i:89271372 original size:13 final size:13
Alignment explanation
Indices: 89271354--89271403 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
89271344 GTGTGTGGAG
89271354 AAGAAAAGAGAGA
1 AAGAAAAGAGAGA
*
89271367 AAGAAAGGAGAGA
1 AAGAAAAGAGAGA
* *
89271380 AAGGAAAAGAAAAA
1 AA-GAAAAGAGAGA
89271394 AAGAAGAAGA
1 AAGAA-AAGA
89271404 AGTTTTTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 17 0.55
14 14 0.45
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAGAGA
Found at i:89271376 original size:23 final size:24
Alignment explanation
Indices: 89271350--89271404 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
89271340 ACTGGTGTGT
* *
89271350 GGAGAAGAAAAG-AGAGAAAGAAA
1 GGAGAAGAAAAGAAAAGAAAAAAA
*
89271373 GGAG-AGAAAGGAAAAGAAAAAAA
1 GGAGAAGAAAAGAAAAGAAAAAAA
*
89271396 GAAGAAGAA
1 GGAGAAGAA
89271405 GTTTTTAGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 6 0.23
23 16 0.62
24 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (24 bp):
GGAGAAGAAAAGAAAAGAAAAAAA
Found at i:89272113 original size:22 final size:20
Alignment explanation
Indices: 89272064--89272116 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
89272054 TTGTGATTCT
*
89272064 TTAGTAATTTA-ATTTTTTT
1 TTAGTAATTTATATTTTTTG
**
89272083 TTAAAAATTTATAGTTATTTTG
1 TTAGTAATTTATA-TT-TTTTG
89272105 TTAGTAATTTAT
1 TTAGTAATTTAT
89272117 GATTAGGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 9 0.35
20 1 0.04
21 2 0.08
22 14 0.54
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (20 bp):
TTAGTAATTTATATTTTTTG
Found at i:89272245 original size:205 final size:207
Alignment explanation
Indices: 89271739--89272281 Score: 727
Period size: 205 Copynumber: 2.6 Consensus size: 207
89271729 ATAAATTGTT
* * *
89271739 GTGTTTTGTGAGTTTTTAGTAATATAATTT-AAAAAAATAATTTTATAGTTATTTTGTTAGTAGT
1 GTGTTTTGTGATTTTTTAGTAATGTAATTTAAAAAAAATAATTTTATAGTTATTTTGTTAGTAAT
* * * *
89271803 TTATGATTAGGTT-ATAAATTGTTAG--TGT--TTT-CTGTTTTGTTATTTTTTAGTAATGTAAT
66 TTATGATTAGGTTAATAAATTGTTAGTATTTAATTTAGTGTTTTGTGATTCTTTAGTAATGTAAT
**
89271862 TTCTTTTTTTTTAAATGTTATAGTTATTTATTTTGTTAGTAATTTATGGGATTACGTTATAAATT
131 TTCTTTTTTTAAAAATGTTATAG---TTTATTTTGTTAGTAATTTAT-GGATTACGTTATAAATT
*
89271927 GTTAGTGTTTAGTTTC
192 GTTAGTGTTTAGTTTA
* *
89271943 GAGTTTTGTGATTTTTTTAGTAATGTAATTTTTAAAAAAAATAATTTTATCGTTATTTTGTTAGT
1 GTGTTTTGTGA-TTTTTTAGTAATGTAA--TTTAAAAAAAATAATTTTATAGTTATTTTGTTAGT
* *
89272008 AATTTATGATTATGTTATATAAATTGTTAGTATTTAATTTAGTGTTTTGTGATTCTTTAGTAATT
63 AATTTATGATTAGGTTA-ATAAATTGTTAGTATTTAATTTAGTGTTTTGTGATTCTTTAGTAATG
*
89272073 TAA-TT-TTTTTTTAAAAAT-TTATAG-TTATTTTGTTAGTAATTTAT-GATTAGGTTATATAAA
127 TAATTTCTTTTTTTAAAAATGTTATAGTTTATTTTGTTAGTAATTTATGGATTACG-T-TATAAA
89272133 TTGTTAGTGTTTAGTTTA
190 TTGTTAGTGTTTAGTTTA
*
89272151 GTGTTTTGTGATTTTTTAGTAATGTAATTTAAAAAAAATAATTTTATAGTTATTTTTTTAGTAAT
1 GTGTTTTGTGATTTTTTAGTAATGTAATTTAAAAAAAATAATTTTATAGTTATTTTGTTAGTAAT
* *
89272216 TTATGATTAGGTTAAATAAATTTTTAGTATTTAATTTAGTGTTTTGTGATT-TTT-TTAATGTAA
66 TTATGATTAGGTT-AATAAATTGTTAGTATTTAATTTAGTGTTTTGTGATTCTTTAGTAATGTAA
89272279 TTT
130 TTT
89272282 ATATCTAATG
Statistics
Matches: 302, Mismatches: 22, Indels: 30
0.85 0.06 0.08
Matches are distributed among these distances:
203 7 0.02
204 15 0.05
205 97 0.32
206 7 0.02
207 20 0.07
208 97 0.32
210 12 0.04
212 8 0.03
213 11 0.04
214 5 0.02
215 23 0.08
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (207 bp):
GTGTTTTGTGATTTTTTAGTAATGTAATTTAAAAAAAATAATTTTATAGTTATTTTGTTAGTAAT
TTATGATTAGGTTAATAAATTGTTAGTATTTAATTTAGTGTTTTGTGATTCTTTAGTAATGTAAT
TTCTTTTTTTAAAAATGTTATAGTTTATTTTGTTAGTAATTTATGGATTACGTTATAAATTGTTA
GTGTTTAGTTTA
Found at i:89272282 original size:208 final size:208
Alignment explanation
Indices: 89271739--89272282 Score: 729
Period size: 208 Copynumber: 2.6 Consensus size: 208
89271729 ATAAATTGTT
* * *
89271739 GTGTTTTGTGAGTTTTTAGTAATATAATTT-AAAAAAATAATTTTATAGTTATTTTGTTAGTAGT
1 GTGTTTTGTGATTTTTTAGTAATGTAATTTAAAAAAAATAATTTTATAGTTATTTTGTTAGTAAT
* * *
89271803 TTATGATTAGGTT-ATAAATTGTTAG--TGT--TTT-CTGTTTTGTTATTTTTTAGTAATGTAAT
66 TTATGATTAGGTTAATAAATTGTTAGTATTTAATTTAGTGTTTTGTGATTTTTT--TAATGTAAT
* ** *
89271862 TT-CTTTTTTTTTAAATGTTATAGTTATTTATTTTGTTAGTAATTTATGGGATTACGTTATAAAT
129 TTAATTTTTTTTTAAAAATTATAG-TAGTTATTTTGTTAGTAATTTAT-GGATTACGTTATAAAT
*
89271926 TGTTAGTGTTTAGTTTC
192 TGTTAGTGTTTAGTTTA
* *
89271943 GAGTTTTGTGATTTTTTTAGTAATGTAATTTTTAAAAAAAATAATTTTATCGTTATTTTGTTAGT
1 GTGTTTTGTGA-TTTTTTAGTAATGTAA--TTTAAAAAAAATAATTTTATAGTTATTTTGTTAGT
* *
89272008 AATTTATGATTATGTTATATAAATTGTTAGTATTTAATTTAGTGTTTTGTGA-TTCTTT-A-GTA
63 AATTTATGATTAGGTTA-ATAAATTGTTAGTATTTAATTTAGTGTTTTGTGATTTTTTTAATGTA
*
89272070 ATTTAATTTTTTTTTAAAAATT-TA-TAGTTATTTTGTTAGTAATTTAT-GATTAGGTTATATAA
127 ATTTAATTTTTTTTTAAAAATTATAGTAGTTATTTTGTTAGTAATTTATGGATTACG-T-TATAA
89272132 ATTGTTAGTGTTTAGTTTA
190 ATTGTTAGTGTTTAGTTTA
*
89272151 GTGTTTTGTGATTTTTTAGTAATGTAATTTAAAAAAAATAATTTTATAGTTATTTTTTTAGTAAT
1 GTGTTTTGTGATTTTTTAGTAATGTAATTTAAAAAAAATAATTTTATAGTTATTTTGTTAGTAAT
*
89272216 TTATGATTAGGTTAAATAAATTTTTAGTATTTAATTTAGTGTTTTGTGATTTTTTTAATGTAATT
66 TTATGATTAGGTT-AATAAATTGTTAGTATTTAATTTAGTGTTTTGTGATTTTTTTAATGTAATT
89272281 TA
130 TA
89272283 TATCTAATGT
Statistics
Matches: 300, Mismatches: 22, Indels: 32
0.85 0.06 0.09
Matches are distributed among these distances:
204 10 0.03
205 95 0.32
206 12 0.04
207 21 0.07
208 107 0.36
210 21 0.07
211 15 0.05
212 3 0.01
214 7 0.02
215 9 0.03
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (208 bp):
GTGTTTTGTGATTTTTTAGTAATGTAATTTAAAAAAAATAATTTTATAGTTATTTTGTTAGTAAT
TTATGATTAGGTTAATAAATTGTTAGTATTTAATTTAGTGTTTTGTGATTTTTTTAATGTAATTT
AATTTTTTTTTAAAAATTATAGTAGTTATTTTGTTAGTAATTTATGGATTACGTTATAAATTGTT
AGTGTTTAGTTTA
Found at i:89272308 original size:103 final size:104
Alignment explanation
Indices: 89271739--89272285 Score: 538
Period size: 102 Copynumber: 5.3 Consensus size: 104
89271729 ATAAATTGTT
* *
89271739 GTGTTTTGTGAGTTTTTAGTAATATAA-TT-TA-AAAAAATAATTTTATAGTTATTTTGTTAGTA
1 GTGTTTTGTGATTTTTTA-TAATGTAATTTATATAAAAAATAATTTTATAGTTATTTTGTTAGTA
* *
89271801 GTTTATGATTAGG-T-TATAAATTGTTAG--TGT--TTT-
65 ATTTATGATTAGGTTATATAAATTGTTAGTATTTAATTTA
* * * * *** * * *
89271834 CTGTTTTGTTATTTTTTAGTAATGTAATTTCTTTTTTTTTAAAT-GTTATAGTTATTTATTTTGT
1 GTGTTTTGTGATTTTTTA-TAATGTAA--T-TTATATAAAAAATAATTTTA--TAGTTATTTTGT
* * * *
89271898 TAGTAATTTATGGGATTACG-T-TATAAATTGTTAGTGTTTAGTTTC
60 TAGTAATTTAT--GATTAGGTTATATAAATTGTTAGTATTTAATTTA
* * * *
89271943 GAGTTTTGTGATTTTTTTAGTAATGTAATTTTTAAAAAAAATAATTTTATCGTTATTTTGTTAGT
1 GTGTTTTGTGA-TTTTTTA-TAATGTAATTTATATAAAAAATAATTTTATAGTTATTTTGTTAGT
*
89272008 AATTTATGATTATGTTATATAAATTGTTAGTATTTAATTTA
64 AATTTATGATTAGGTTATATAAATTGTTAGTATTTAATTTA
* * * ***
89272049 GTGTTTTGTGATTCTTTAGTAATTTAATTT-TTTTTTAAA-AA-TTTATAGTTATTTTGTTAGTA
1 GTGTTTTGTGATTTTTTA-TAATGTAATTTATATAAAAAATAATTTTATAGTTATTTTGTTAGTA
* *
89272111 ATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTA
65 ATTTATGATTAGGTTATATAAATTGTTAGTATTTAATTTA
*
89272151 GTGTTTTGTGATTTTTTAGTAATGTAATTTA-A-AAAAAATAATTTTATAGTTATTTTTTTAGTA
1 GTGTTTTGTGATTTTTTA-TAATGTAATTTATATAAAAAATAATTTTATAGTTATTTTGTTAGTA
* *
89272214 ATTTATGATTAGGTTAAATAAATTTTTAGTATTTAATTTA
65 ATTTATGATTAGGTTATATAAATTGTTAGTATTTAATTTA
89272254 GTGTTTTGTGATTTTTT-TAATGTAATTTATAT
1 GTGTTTTGTGATTTTTTATAATGTAATTTATAT
89272286 CTAATGTAAT
Statistics
Matches: 375, Mismatches: 53, Indels: 40
0.80 0.11 0.09
Matches are distributed among these distances:
95 23 0.06
99 2 0.01
100 5 0.01
101 19 0.05
102 109 0.29
103 75 0.20
104 30 0.08
105 18 0.05
106 54 0.14
107 8 0.02
108 8 0.02
109 8 0.02
110 16 0.04
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (104 bp):
GTGTTTTGTGATTTTTTATAATGTAATTTATATAAAAAATAATTTTATAGTTATTTTGTTAGTAA
TTTATGATTAGGTTATATAAATTGTTAGTATTTAATTTA
Found at i:89274415 original size:46 final size:46
Alignment explanation
Indices: 89274352--89274452 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 46
89274342 TATCCCGACT
*
89274352 TGTA-TCCACCTCAGTACTCCACTCCTCCCGGTCC-GTATCCA-TCGC
1 TGTACTCCACCTCAGTACTCCACTCCTCCCGG-CCTGTATCCACT-AC
89274397 TGTACTCCACCATC-GTACTCCACTCCTCCCGGCCTGTATCCACTAC
1 TGTACTCCACC-TCAGTACTCCACTCCTCCCGGCCTGTATCCACTAC
89274443 TGTACTCCAC
1 TGTACTCCAC
89274453 TACTTTTGGC
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
45 6 0.12
46 42 0.82
47 3 0.06
ACGTcount: A:0.17, C:0.45, G:0.12, T:0.27
Consensus pattern (46 bp):
TGTACTCCACCTCAGTACTCCACTCCTCCCGGCCTGTATCCACTAC
Found at i:89274738 original size:75 final size:73
Alignment explanation
Indices: 89274620--89274810 Score: 217
Period size: 75 Copynumber: 2.6 Consensus size: 73
89274610 TCAAACCATC
* * * * *
89274620 AATTTTAGGGG-GTTTTGTAATTT-AA-ATAACTTTATATTTATGTAATGAATTTTTTTCCATTT
1 AATTTTAGGGGTTTTTTGAAATTTAAATATAACTTTGTATTTATGTAATGAATTTTTTGCCACTT
89274682 TAGTTATT
66 TAGTTATT
* *
89274690 AATTTTAGGGGTTTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCCAC
1 AATTTTAGGGGTTTTTTGAAATTTAAATA-T-AACTTTGTATTTATGTAATGAATTTTTTGCCAC
89274755 TTTAGTTATT
64 TTTAGTTATT
**
89274765 AATTTTTAGGATTTTTTTTTGAAATTTAAATAATAAACTTTGTATT
1 AA-TTTTAGG--GGTTTTTTGAAATTTAAAT-AT-AACTTTGTATT
89274811 ATTTACATAA
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
70 11 0.11
71 10 0.10
72 2 0.02
73 1 0.01
74 1 0.01
75 41 0.40
76 7 0.07
78 28 0.27
79 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.53
Consensus pattern (73 bp):
AATTTTAGGGGTTTTTTGAAATTTAAATATAACTTTGTATTTATGTAATGAATTTTTTGCCACTT
TAGTTATT
Found at i:89278088 original size:25 final size:25
Alignment explanation
Indices: 89278054--89278110 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
89278044 CCCATACCAC
*
89278054 ATTCGTACATATACACGGGTCATGT
1 ATTCGTACATATACACGAGTCATGT
89278079 ATTCGTACATATACACGAGTCATGT
1 ATTCGTACATATACACGAGTCATGT
89278104 ATT-GTAC
1 ATTCGTAC
89278111 TAGAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (25 bp):
ATTCGTACATATACACGAGTCATGT
Found at i:89278189 original size:21 final size:22
Alignment explanation
Indices: 89278160--89278200 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
89278150 CAATACTAAT
*
89278160 AAAATAATATT-TAAAAAAACA
1 AAAAAAATATTATAAAAAAACA
89278181 AAAAAAATATTATAAAAAAA
1 AAAAAAATATTATAAAAAAA
89278201 GGTGGTGGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAAAAATATTATAAAAAAACA
Found at i:89279119 original size:2 final size:2
Alignment explanation
Indices: 89279107--89279141 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
89279097 CGTGTAATAG
* *
89279107 TA TA CA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
89279142 TATTCTTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:89281538 original size:21 final size:22
Alignment explanation
Indices: 89281497--89281542 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
89281487 CAGTATGCTT
* *
89281497 ATCTTCAGGGGTATGTTGCGAC
1 ATCTTCAGGGCTATGTCGCGAC
89281519 ATCTTCA-GGCTATGTCGCGAC
1 ATCTTCAGGGCTATGTCGCGAC
89281540 ATC
1 ATC
89281543 GAAGGCAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (22 bp):
ATCTTCAGGGCTATGTCGCGAC
Found at i:89287470 original size:18 final size:18
Alignment explanation
Indices: 89287447--89287482 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
89287437 CCTTCTAAGG
89287447 AGCACTTTTGGGACAAAA
1 AGCACTTTTGGGACAAAA
*
89287465 AGCACTTTTGGGATAAAA
1 AGCACTTTTGGGACAAAA
89287483 GTATTGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (18 bp):
AGCACTTTTGGGACAAAA
Found at i:89289857 original size:7 final size:7
Alignment explanation
Indices: 89289838--89289866 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
89289828 TATGTCGCAT
89289838 TTTAAAA
1 TTTAAAA
89289845 -TTAAAA
1 TTTAAAA
89289851 TTTAAAA
1 TTTAAAA
89289858 TTTAAAA
1 TTTAAAA
89289865 TT
1 TT
89289867 ATATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TTTAAAA
Found at i:89290585 original size:17 final size:16
Alignment explanation
Indices: 89290551--89290607 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
89290541 ATAGTAAAAG
* *
89290551 AAAGAATATAGGATGAA
1 AAAGAA-ATAGAAAGAA
89290568 AAAGAAATAGAAAGGAA
1 AAAGAAATAGAAA-GAA
*
89290585 AGAA-AAATGGAAAGAA
1 A-AAGAAATAGAAAGAA
89290601 AAAGAAA
1 AAAGAAA
89290608 GGAAAAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 2 0.06
16 12 0.35
17 18 0.53
18 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.09
Consensus pattern (16 bp):
AAAGAAATAGAAAGAA
Found at i:89292461 original size:22 final size:22
Alignment explanation
Indices: 89292433--89292488 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
89292423 ACGGGTGATG
*
89292433 ACACGGGCGTGTCACA-TCATCC
1 ACACGGGCGTGTCACACT-AGCC
*
89292455 ACACGGGCGTGTTACACTAGCC
1 ACACGGGCGTGTCACACTAGCC
*
89292477 ACACGGACGTGT
1 ACACGGGCGTGT
89292489 GGCACTATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (22 bp):
ACACGGGCGTGTCACACTAGCC
Found at i:89292494 original size:22 final size:22
Alignment explanation
Indices: 89292453--89292495 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
89292443 GTCACATCAT
* *
89292453 CCACACGGGCGTGTTACACTAG
1 CCACACGGACGTGTGACACTAG
*
89292475 CCACACGGACGTGTGGCACTA
1 CCACACGGACGTGTGACACTA
89292496 TTCAAAGGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.33, G:0.28, T:0.16
Consensus pattern (22 bp):
CCACACGGACGTGTGACACTAG
Found at i:89294832 original size:21 final size:22
Alignment explanation
Indices: 89294780--89294832 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
89294770 AAATAAAGTC
*
89294780 CATGTA-CAAATATCATCATCT
1 CATGTATCATATATCATCATCT
* *
89294801 CATGTTTTCATATATCAT-ATGT
1 CATG-TATCATATATCATCATCT
89294823 CATGTATCAT
1 CATGTATCAT
89294833 CGTTTACTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.35
22 8 0.31
23 9 0.35
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.42
Consensus pattern (22 bp):
CATGTATCATATATCATCATCT
Found at i:89295141 original size:57 final size:58
Alignment explanation
Indices: 89295080--89295189 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 58
89295070 GATCCTTTTT
* *
89295080 ATGACATATGCTCTAAA-GAGCTT-GATCTGGATTACCCGTCCGGGCTAAATCCAATAC
1 ATGACATATGCTCGAAAGGA-CTTAGATCAGGATTACCCGTCCGGGCTAAATCCAATAC
* * * * *
89295137 ATGACATTTGCTCGAGAGGACTTATATCAGGATTACTCGTTCGGGCTAAATCC
1 ATGACATATGCTCGAAAGGACTTAGATCAGGATTACCCGTCCGGGCTAAATCC
89295190 TTTCTATCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
57 17 0.39
58 27 0.61
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (58 bp):
ATGACATATGCTCGAAAGGACTTAGATCAGGATTACCCGTCCGGGCTAAATCCAATAC
Found at i:89295478 original size:17 final size:18
Alignment explanation
Indices: 89295433--89295478 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
89295423 TATCATTTAG
89295433 CATTTATCGGGCATTATT
1 CATTTATCGGGCATTATT
* *
89295451 -ATTGATTGGGCATT-TT
1 CATTTATCGGGCATTATT
89295467 CATTTATCGGGC
1 CATTTATCGGGC
89295479 TGTAACGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (18 bp):
CATTTATCGGGCATTATT
Found at i:89303964 original size:25 final size:25
Alignment explanation
Indices: 89303921--89303969 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
89303911 GAAGGTCAGT
* **
89303921 ATGCTCTCACGTGTTATAAATCGGC
1 ATGCTCTCACGAGCCATAAATCGGC
89303946 ATGCTCTCACGAGCCATAAATCGG
1 ATGCTCTCACGAGCCATAAATCGG
89303970 TAACCCTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (25 bp):
ATGCTCTCACGAGCCATAAATCGGC
Found at i:89306806 original size:28 final size:28
Alignment explanation
Indices: 89306741--89306839 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
89306731 CATGAGATTG
* * *
89306741 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTT-AGATTATATA
*
89306770 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTAGATTATATA
* *
89306798 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTAGATTATAT-A
89306826 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
89306840 GGCTTATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.71
29 17 0.27
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTAGATTATATA
Found at i:89309625 original size:16 final size:17
Alignment explanation
Indices: 89309604--89309636 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
89309594 TTAGATTGAG
89309604 AAAATT-ATTTAATTAA
1 AAAATTAATTTAATTAA
*
89309620 AAAATTAATTTAGTTAA
1 AAAATTAATTTAATTAA
89309637 CTTAATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AAAATTAATTTAATTAA
Found at i:89309629 original size:4 final size:4
Alignment explanation
Indices: 89309606--89309658 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
89309596 AGATTGAGAA
* ** *
89309606 AATT ATTT AATT AAAA AATT AATTT AGTT AACTT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AA-TT AATT AA-TT AATT AATT AATT AATT
89309656 AAT
1 AAT
89309659 ATCTATTTGT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
4 32 0.82
5 7 0.18
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:89313571 original size:61 final size:61
Alignment explanation
Indices: 89313477--89313595 Score: 177
Period size: 61 Copynumber: 2.0 Consensus size: 61
89313467 CGACAGCCAG
* * * *
89313477 GGGCATGTGGTGGCTTTTAGGACGTGTGCGAGGCA-AGGGCTCATGCACGGGTGAATCATAT
1 GGGCATGTGATGGCTTTTAGGACGTGTGCGAGGCACA-AGCTCAGGCACGAGTGAATCATAT
*
89313538 GGGCATGTGATGGCTTTTAGGACGTGTGTGAGGCACAAGCTCAGGCACGAGTGAATCA
1 GGGCATGTGATGGCTTTTAGGACGTGTGCGAGGCACAAGCTCAGGCACGAGTGAATCA
89313596 CACGGGCGTG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
61 51 0.98
62 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.38, T:0.24
Consensus pattern (61 bp):
GGGCATGTGATGGCTTTTAGGACGTGTGCGAGGCACAAGCTCAGGCACGAGTGAATCATAT
Found at i:89322131 original size:23 final size:23
Alignment explanation
Indices: 89322105--89322148 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
89322095 GACTTTTAAA
89322105 TCTTATTTGACAAA-ATTTCTAGG
1 TCTT-TTTGACAAATATTTCTAGG
* *
89322128 TCTTTTTTATAAATATTTCTA
1 TCTTTTTGACAAATATTTCTA
89322149 AAAAACAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (23 bp):
TCTTTTTGACAAATATTTCTAGG
Found at i:89323309 original size:33 final size:33
Alignment explanation
Indices: 89323267--89323336 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
89323257 TGTTAAACGA
89323267 CTGATCAATTTAGGTTTGACCATCTCAATCAAG
1 CTGATCAATTTAGGTTTGACCATCTCAATCAAG
**
89323300 CTGATCAATTTAGGTTTGATTATCTCAATCAAG
1 CTGATCAATTTAGGTTTGACCATCTCAATCAAG
89323333 CTGA
1 CTGA
89323337 CTTTATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (33 bp):
CTGATCAATTTAGGTTTGACCATCTCAATCAAG
Found at i:89325820 original size:50 final size:50
Alignment explanation
Indices: 89325742--89325918 Score: 273
Period size: 50 Copynumber: 3.5 Consensus size: 50
89325732 CCATGGCAAC
*
89325742 AAGTGATAAGTGATAGCTTCGGCAACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
89325792 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
89325842 AAGTGAGAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATAA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
89325892 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
89325919 CTGATCAGTG
Statistics
Matches: 116, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 92 0.79
51 24 0.21
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Done.