Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, whole genome shotgun sequence
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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 41 of 84
Found at i:9653552 original size:16 final size:16
Alignment explanation
Indices: 9653509--9653558 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
9653499 TATAATTTCG
9653509 ATGTTATTCTTTTGCT
1 ATGTTATTCTTTTGCT
*
9653525 ATGTGA----TTTGCT
1 ATGTTATTCTTTTGCT
9653537 ATGTTATTCTTTTGCT
1 ATGTTATTCTTTTGCT
9653553 ATGTTA
1 ATGTTA
9653559 ATCTCTTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 11 0.39
16 17 0.61
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.58
Consensus pattern (16 bp):
ATGTTATTCTTTTGCT
Found at i:9656111 original size:15 final size:16
Alignment explanation
Indices: 9656066--9656129 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
9656056 ACTAGTGTGG
9656066 TAAATAATATTATCTTTTT
1 TAAAT-ATATTA--TTTTT
*
9656085 TAACTA-ATTTATTTTT
1 TAAATATA-TTATTTTT
*
9656101 TATAT-TATTA-TTTT
1 TAAATATATTATTTTT
9656115 TAAATATATTATTTT
1 TAAATATATTATTTT
9656130 ATGATATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
14 8 0.22
15 8 0.22
16 12 0.32
17 1 0.03
18 4 0.11
19 4 0.11
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TAAATATATTATTTTT
Found at i:9656114 original size:14 final size:15
Alignment explanation
Indices: 9656097--9656129 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
9656087 ACTAATTTAT
*
9656097 TTTTTATAT-TATTA
1 TTTTTAAATATATTA
9656111 TTTTTAAATATATTA
1 TTTTTAAATATATTA
9656126 TTTT
1 TTTT
9656130 ATGATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTAAATATATTA
Found at i:9656127 original size:30 final size:30
Alignment explanation
Indices: 9656072--9656129 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
9656062 GTGGTAAATA
*
9656072 ATATTATCTTTTTTAACTAATTTATTTTTT
1 ATATTATCTTTTTTAAATAATTTATTTTTT
9656102 ATATTAT-TATTTTTAAAT-ATATTATTTT
1 ATATTATCT-TTTTTAAATAAT-TTATTTT
9656130 ATGATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (30 bp):
ATATTATCTTTTTTAAATAATTTATTTTTT
Found at i:9656136 original size:15 final size:14
Alignment explanation
Indices: 9656094--9656142 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
9656084 TTAACTAATT
9656094 TATT-TTTTATAT-
1 TATTATTTTATATA
*
9656106 TATTATTTTTAAATA
1 TATTA-TTTTATATA
9656121 TATTATTTTATGATA
1 TATTATTTTAT-ATA
9656136 T-TTATTT
1 TATTATTT
9656143 ATTCATCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 4 0.13
14 18 0.58
15 9 0.29
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TATTATTTTATATA
Found at i:9658212 original size:8 final size:8
Alignment explanation
Indices: 9658199--9658224 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
9658189 TGGGCCACTA
9658199 TGAGTTTC
1 TGAGTTTC
9658207 TGAGTTTC
1 TGAGTTTC
9658215 TGAGTTTC
1 TGAGTTTC
9658223 TG
1 TG
9658225 GTGATGCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.27, T:0.50
Consensus pattern (8 bp):
TGAGTTTC
Found at i:9660662 original size:18 final size:17
Alignment explanation
Indices: 9660641--9660676 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
9660631 TTGTATTACC
9660641 GTTATATCGGTTATTGTT
1 GTTATATCGGTTA-TGTT
*
9660659 GTTATATTGGTTATGTT
1 GTTATATCGGTTATGTT
9660676 G
1 G
9660677 GTTGTGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (17 bp):
GTTATATCGGTTATGTT
Found at i:9661313 original size:12 final size:12
Alignment explanation
Indices: 9661296--9661342 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
9661286 TATATTTTCA
9661296 TATAATATAAAT
1 TATAATATAAAT
9661308 TATAATA-AAAT
1 TATAATATAAAT
* * *
9661319 TTTTATATAAAA
1 TATAATATAAAT
*
9661331 TATAAAATAAAT
1 TATAATATAAAT
9661343 ACACAAATTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TATAATATAAAT
Found at i:9662197 original size:20 final size:19
Alignment explanation
Indices: 9662169--9662218 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
9662159 AAATTATTTT
9662169 AAAATTTTAATAATTAATA
1 AAAATTTTAATAATTAATA
* **
9662188 AAAATATTTATTAAAAAATA
1 AAAAT-TTTAATAATTAATA
9662208 ATAAATTTTAA
1 A-AAATTTTAA
9662219 ATTTATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 5 0.20
20 16 0.64
21 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTTTAATAATTAATA
Found at i:9670345 original size:11 final size:12
Alignment explanation
Indices: 9670318--9670350 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9670308 AAATATTACT
9670318 AAAAGAAAAACA
1 AAAAGAAAAACA
9670330 AAAAGAAAAA-A
1 AAAAGAAAAACA
9670341 AAAAGTAAAA
1 AAAAG-AAAA
9670351 TCAATGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.85, C:0.03, G:0.09, T:0.03
Consensus pattern (12 bp):
AAAAGAAAAACA
Found at i:9671834 original size:19 final size:19
Alignment explanation
Indices: 9671812--9671858 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
9671802 TATATGTTTT
*
9671812 TTAAAATATATTTAAAAAA
1 TTAAAATATAATTAAAAAA
*
9671831 TTAAAAAATTAATTAAAAAA
1 TTAAAATA-TAATTAAAAAA
9671851 -TAAAATAT
1 TTAAAATAT
9671859 GTATCATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 13 0.54
20 10 0.42
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAAATATAATTAAAAAA
Found at i:9672135 original size:13 final size:13
Alignment explanation
Indices: 9672117--9672141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9672107 TCCCTACCAT
9672117 ATAATAATATGTA
1 ATAATAATATGTA
9672130 ATAATAATATGT
1 ATAATAATATGT
9672142 TTTTAAGATA
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:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
ATAATAATATGTA
Found at i:9672818 original size:14 final size:14
Alignment explanation
Indices: 9672799--9672845 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
9672789 AATTTTATAC
9672799 ATATTTTTAAATAA
1 ATATTTTTAAATAA
*
9672813 ATATTTTTAATAAAA
1 ATATTTTTAA-ATAA
*
9672828 ATATTATTAAATAA
1 ATATTTTTAAATAA
9672842 ATAT
1 ATAT
9672846 AAATCAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATTTTTAAATAA
Found at i:9672866 original size:18 final size:17
Alignment explanation
Indices: 9672839--9672874 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
9672829 TATTATTAAA
*
9672839 TAAATATAAATCAAATT
1 TAAATATAAATAAAATT
9672856 TAAATTATAAATAAAATT
1 TAAA-TATAAATAAAATT
9672874 T
1 T
9672875 TTAACAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATATAAATAAAATT
Found at i:9672952 original size:12 final size:13
Alignment explanation
Indices: 9672937--9672966 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
9672927 TAATTTAATT
9672937 TTTTTATT-AAAA
1 TTTTTATTAAAAA
9672949 TTTTTATTAAAAA
1 TTTTTATTAAAAA
9672962 TTTTT
1 TTTTT
9672967 TTCCAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTATTAAAAA
Found at i:9673847 original size:20 final size:20
Alignment explanation
Indices: 9673824--9673894 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
9673814 AATTTATTGC
*
9673824 ATATAAAAATTAGATAAATT
1 ATATAAAAATTAAATAAATT
** *
9673844 ATATAATTATTAAATAATACAT
1 ATATAAAAATTAAATAA-A-TT
* *
9673866 ATATAATAAATTATATAACTT
1 ATATAA-AAATTAAATAAATT
9673887 AT-TAAAAA
1 ATATAAAAA
9673895 CTTATATCCA
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 4 0.10
22 7 0.18
23 8 0.21
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (20 bp):
ATATAAAAATTAAATAAATT
Found at i:9677850 original size:2 final size:2
Alignment explanation
Indices: 9677843--9677867 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9677833 AATTAGCAAT
9677843 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9677868 TAGAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9684311 original size:21 final size:21
Alignment explanation
Indices: 9684273--9684312 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9684263 CAATGATGCA
* *
9684273 AGGGCTGCTGCAGAGGCTGGC
1 AGGGCAGCTACAGAGGCTGGC
*
9684294 AGGGCAGCTACAGCGGCTG
1 AGGGCAGCTACAGAGGCTG
9684313 CTTTGCAAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.25, G:0.45, T:0.12
Consensus pattern (21 bp):
AGGGCAGCTACAGAGGCTGGC
Found at i:9685211 original size:26 final size:22
Alignment explanation
Indices: 9685157--9685228 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 22
9685147 ATATATAATT
9685157 TTTAAT-AAAAATATATTTATTTTA
1 TTTAATAAAAAATA-ATTTA--TTA
*
9685181 ATTAATTTAAAATAATAATTTTATTA
1 TTTAA--TAAAA-AATAA-TTTATTA
9685207 TTTAATAAAAAATAATTTATTA
1 TTTAATAAAAAATAATTTATTA
9685229 ATTATATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
22 7 0.17
23 5 0.12
24 9 0.22
26 8 0.20
27 4 0.10
28 8 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAATAAAAAATAATTTATTA
Found at i:9685232 original size:26 final size:26
Alignment explanation
Indices: 9685152--9685233 Score: 70
Period size: 23 Copynumber: 3.3 Consensus size: 26
9685142 TATTGATATA
9685152 TAATT-TTTAAT-AAAAATATATTTATTT
1 TAATTATTTAATAAAAAATA-ATTTA--T
*
9685179 TAATTAATTT-A-AAATAATAA-TT-T
1 TAATT-ATTTAATAAAAAATAATTTAT
9685202 T-ATTATTTAATAAAAAATAATTTAT
1 TAATTATTTAATAAAAAATAATTTAT
9685227 TAATTAT
1 TAATTAT
9685234 ATATAAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 17
0.70 0.03 0.27
Matches are distributed among these distances:
21 4 0.09
22 4 0.09
23 10 0.22
24 2 0.04
25 2 0.04
26 7 0.16
27 6 0.13
28 7 0.16
29 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TAATTATTTAATAAAAAATAATTTAT
Found at i:9685242 original size:22 final size:23
Alignment explanation
Indices: 9685158--9685232 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 23
9685148 TATATAATTT
*
9685158 TTAAT-AAAAATATATTTATTTTAA
1 TTAATAAAAAATA-ATTT-TATTAA
*
9685182 TTAATTTAAAATAATAATTTTATTAT
1 TTAA--TAAAA-AATAATTTTATTAA
9685208 TTAATAAAAAATAA-TTTATTAA
1 TTAATAAAAAATAATTTTATTAA
9685230 TTA
1 TTA
9685233 TATATAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
22 10 0.23
23 5 0.11
24 9 0.20
26 9 0.20
27 7 0.16
28 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAATAAAAAATAATTTTATTAA
Found at i:9689573 original size:20 final size:21
Alignment explanation
Indices: 9689550--9689591 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
9689540 TGAATTCTTA
9689550 AAAAAGAAAATTG-TGATTTG
1 AAAAAGAAAATTGATGATTTG
*
9689570 AAAAAGAAATTTGATGATTTG
1 AAAAAGAAAATTGATGATTTG
9689591 A
1 A
9689592 TGAATGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (21 bp):
AAAAAGAAAATTGATGATTTG
Found at i:9698716 original size:2 final size:2
Alignment explanation
Indices: 9698709--9698736 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9698699 ATATGCAGTT
9698709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9698737 GTATTGGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9701709 original size:18 final size:19
Alignment explanation
Indices: 9701686--9701729 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
9701676 TGAATTAGTT
9701686 TATTGTTGT-TGTTAATGA
1 TATTGTTGTATGTTAATGA
**
9701704 TATTGTT-TATGTTGTTGA
1 TATTGTTGTATGTTAATGA
9701722 TATTGTTG
1 TATTGTTG
9701730 ACATTGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.18, C:0.00, G:0.23, T:0.59
Consensus pattern (19 bp):
TATTGTTGTATGTTAATGA
Found at i:9707620 original size:14 final size:14
Alignment explanation
Indices: 9707595--9707621 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9707585 ATGGAAAAGA
9707595 TTTAGATGAAATTT
1 TTTAGATGAAATTT
9707609 TTTAGATGAAATT
1 TTTAGATGAAATT
9707622 CATAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
TTTAGATGAAATTT
Found at i:9711119 original size:20 final size:20
Alignment explanation
Indices: 9711076--9711112 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9711066 TAATCAAAGT
9711076 TTTA-TGATTTTATTTTTAA
1 TTTATTGATTTTATTTTTAA
9711095 TTTATTGATTTTATTTTT
1 TTTATTGATTTTATTTTT
9711113 TTATTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (20 bp):
TTTATTGATTTTATTTTTAA
Found at i:9715473 original size:3 final size:3
Alignment explanation
Indices: 9715465--9715490 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9715455 AGTTTCCTAG
9715465 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
9715491 GGGTTTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:9717892 original size:9 final size:9
Alignment explanation
Indices: 9717865--9717902 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
9717855 GGAGGAAGAG
9717865 GAAGAGGAA
1 GAAGAGGAA
* *
9717874 GAGGAAGAA
1 GAAGAGGAA
9717883 GAAGAGGAA
1 GAAGAGGAA
9717892 GAAGAGGAA
1 GAAGAGGAA
9717901 GA
1 GA
9717903 GCAGATTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (9 bp):
GAAGAGGAA
Found at i:9717916 original size:21 final size:21
Alignment explanation
Indices: 9717859--9717920 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
9717849 TGACTTGGAG
* *
9717859 GAAGAGGAAGAGGAAGAGGAA
1 GAAGAAGAGGAGGAAGAGGAA
*
9717880 GAAGAAGAGGAAGAAGAGGAA
1 GAAGAAGAGGAGGAAGAGGAA
* *
9717901 G-AGCAGATTGAGGAAGAGGA
1 GAAGAAGA-GGAGGAAGAGGA
9717921 GTTAGAGGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 5 0.15
21 29 0.85
ACGTcount: A:0.50, C:0.02, G:0.45, T:0.03
Consensus pattern (21 bp):
GAAGAAGAGGAGGAAGAGGAA
Found at i:9717920 original size:6 final size:6
Alignment explanation
Indices: 9717856--9717893 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
9717846 GGGTGACTTG
*
9717856 GAGGAA GAGGAA GAGGAA GAGGAA GAAGAA GAGGAA GA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GA
9717894 AGAGGAAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:9722956 original size:3 final size:3
Alignment explanation
Indices: 9722950--9723135 Score: 175
Period size: 3 Copynumber: 62.3 Consensus size: 3
9722940 TTTTTTTTAG
* * * * *
9722950 TAT TAT TATT TGT TAT TAT TAT TAC TA- TAG TA- TAG TA- TGT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9722993 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* ** * ** *
9723040 TAG TAT GGT GTAA TAT TAT TAT TAT TAT TAT TAT TAT TAT GGT GTAA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* *
9723087 TAT TA- TAG TAT AAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9723132 TAT T
1 TAT T
9723136 TCTTTCTTTC
Statistics
Matches: 153, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
2 9 0.06
3 140 0.92
4 4 0.03
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:9723261 original size:16 final size:16
Alignment explanation
Indices: 9723242--9723273 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9723232 TTTTTTAGCT
9723242 CAATCTAGACAAATCA
1 CAATCTAGACAAATCA
9723258 CAATCTAGACAAATCA
1 CAATCTAGACAAATCA
9723274 GCAAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (16 bp):
CAATCTAGACAAATCA
Found at i:9723960 original size:18 final size:18
Alignment explanation
Indices: 9723935--9723978 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
9723925 GATCATAGGT
*
9723935 TTTTTTTTCTATTTTAA-
1 TTTTTTTTATATTTTAAG
9723952 TTTTATTTTATATTTTAAG
1 TTTT-TTTTATATTTTAAG
9723971 TTTTTTTT
1 TTTTTTTT
9723979 TAGTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 16 0.67
19 4 0.17
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTTTTTATATTTTAAG
Found at i:9723998 original size:22 final size:22
Alignment explanation
Indices: 9723973--9724020 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
9723963 ATTTTAAGTT
*
9723973 TTTTTTTAG-TTTTATTTATTTA
1 TTTTGTTAGTTTTTA-TTATTTA
*
9723995 TTTTGTTGGTTTTTATTATTTA
1 TTTTGTTAGTTTTTATTATTTA
9724017 TTTT
1 TTTT
9724021 ACCAAGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTGTTAGTTTTTATTATTTA
Found at i:9724103 original size:16 final size:17
Alignment explanation
Indices: 9724084--9724126 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
9724074 AGAAAATAAT
9724084 TAAAAA-AATTTTTTTG
1 TAAAAATAATTTTTTTG
*
9724100 TAAAAATTATTTTTTTG
1 TAAAAATAATTTTTTTG
*
9724117 GAAAAATAAT
1 TAAAAATAAT
9724127 AATATTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
TAAAAATAATTTTTTTG
Found at i:9732153 original size:25 final size:26
Alignment explanation
Indices: 9732107--9732159 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
9732097 ATGGTTCATT
9732107 CACATTCAACCCAAAAAGAACTATAC
1 CACATTCAACCCAAAAAGAACTATAC
*
9732133 CACATTC-ACCTAAAAAGAACTATAC
1 CACATTCAACCCAAAAAGAACTATAC
9732158 CA
1 CA
9732160 ACAATAAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.49, C:0.30, G:0.04, T:0.17
Consensus pattern (26 bp):
CACATTCAACCCAAAAAGAACTATAC
Found at i:9732718 original size:16 final size:14
Alignment explanation
Indices: 9732683--9732710 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9732673 TAAGAAGCAC
9732683 TTCTTTGGATCTAT
1 TTCTTTGGATCTAT
9732697 TTCTTTGGATCTAT
1 TTCTTTGGATCTAT
9732711 ATTTCTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
TTCTTTGGATCTAT
Found at i:9735802 original size:12 final size:12
Alignment explanation
Indices: 9735763--9735804 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
9735753 AATAAAATAT
*
9735763 TTCGAGTCCGAA
1 TTCGAGTTCGAA
* *
9735775 TTCAAGTTTGAA
1 TTCGAGTTCGAA
9735787 TTCGAGTTCGAA
1 TTCGAGTTCGAA
9735799 TTCGAG
1 TTCGAG
9735805 CATGAATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (12 bp):
TTCGAGTTCGAA
Found at i:9735810 original size:24 final size:24
Alignment explanation
Indices: 9735763--9735811 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
9735753 AATAAAATAT
**
9735763 TTCGAGTCCGAATTCAAGTTTGAA
1 TTCGAGTCCGAATTCAAGCATGAA
* *
9735787 TTCGAGTTCGAATTCGAGCATGAA
1 TTCGAGTCCGAATTCAAGCATGAA
9735811 T
1 T
9735812 AATCGAACTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (24 bp):
TTCGAGTCCGAATTCAAGCATGAA
Found at i:9736483 original size:11 final size:12
Alignment explanation
Indices: 9736453--9736480 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
9736443 ATTTAATCAT
9736453 TTTTTATTTTTG
1 TTTTTATTTTTG
9736465 TTTTTATTTTTG
1 TTTTTATTTTTG
9736477 TTTT
1 TTTT
9736481 ATTGAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (12 bp):
TTTTTATTTTTG
Found at i:9737109 original size:4 final size:4
Alignment explanation
Indices: 9737100--9737146 Score: 58
Period size: 4 Copynumber: 11.5 Consensus size: 4
9737090 CATAAACAGT
* * *
9737100 TAAA TAAA TAAAA TAAA CAAA TAAA CAAA GAAA TAAA TAAA TAAA TA
1 TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
9737147 GACAATTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.19
Consensus pattern (4 bp):
TAAA
Found at i:9738042 original size:16 final size:17
Alignment explanation
Indices: 9737996--9738043 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
9737986 CAAAAAAATC
9737996 AAAGATTCACAAAGATTT
1 AAAGATTCACAAA-ATTT
**
9738014 AAAGATTTGCAAAATTT
1 AAAGATTCACAAAATTT
9738031 -AAGATTCACAAAA
1 AAAGATTCACAAAA
9738044 GATTCAAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 11 0.42
17 4 0.15
18 11 0.42
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.27
Consensus pattern (17 bp):
AAAGATTCACAAAATTT
Found at i:9738058 original size:35 final size:37
Alignment explanation
Indices: 9737997--9738108 Score: 124
Period size: 37 Copynumber: 3.1 Consensus size: 37
9737987 AAAAAAATCA
*
9737997 AAGATTCAC-AAAGATTTAAAGATTTGC-AAAATTT-
1 AAGATTCACAAAAGATTCAAAGATTTGCAAAAATTTC
*
9738031 AAGATTCACAAAAGATTCAAAGGTTTGCAAAAATTTC
1 AAGATTCACAAAAGATTCAAAGATTTGCAAAAATTTC
** * **
9738068 AAGATTCGTAAAAGATTTC-AAGATTTACAAAGGTTTC
1 AAGATTCACAAAAGA-TTCAAAGATTTGCAAAAATTTC
9738105 AAGA
1 AAGA
9738109 CTTGCAAAGA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
34 9 0.14
35 16 0.24
36 7 0.11
37 31 0.47
38 3 0.05
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (37 bp):
AAGATTCACAAAAGATTCAAAGATTTGCAAAAATTTC
Found at i:9738104 original size:18 final size:18
Alignment explanation
Indices: 9737997--9738135 Score: 99
Period size: 18 Copynumber: 7.7 Consensus size: 18
9737987 AAAAAAATCA
* *
9737997 AAGATTCACAAAGATTTA
1 AAGATTTACAAAGATTTC
*
9738015 AAGATTTGCAAA-ATTT-
1 AAGATTTACAAAGATTTC
*
9738031 AAGATTCACAAAAGA-TTC
1 AAGATTTAC-AAAGATTTC
* * *
9738049 AAAGGTTTGCAAAAATTTC
1 -AAGATTTACAAAGATTTC
9738068 AAGATTCGTA-AAAGATTTC
1 AAGATT--TACAAAGATTTC
*
9738087 AAGATTTACAAAGGTTTC
1 AAGATTTACAAAGATTTC
* * *
9738105 AAGACTTGCAAAGATTAC
1 AAGATTTACAAAGATTTC
9738123 AAG-TTTAGCAAAG
1 AAGATTTA-CAAAG
9738136 CTTCTAAGAT
Statistics
Matches: 94, Mismatches: 18, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
16 7 0.07
17 13 0.14
18 50 0.53
19 23 0.24
20 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.29
Consensus pattern (18 bp):
AAGATTTACAAAGATTTC
Found at i:9738152 original size:36 final size:36
Alignment explanation
Indices: 9737997--9738154 Score: 105
Period size: 37 Copynumber: 4.4 Consensus size: 36
9737987 AAAAAAATCA
* * *
9737997 AAGATTCACAAAGATTTA-AAGATTTGCAAA-ATTT-
1 AAGATTCGCAAAGA-TTACAAGATTTACAAAGCTTTC
* * * **
9738031 AAGATTCACAAAAGATT-CAAAGGTTTGCAAAAATTTC
1 AAGATTCGC-AAAGATTAC-AAGATTTACAAAGCTTTC
* * *
9738068 AAGATTCGTAAAAGATTTCAAGATTTACAAAGGTTTC
1 AAGATTCG-CAAAGATTACAAGATTTACAAAGCTTTC
9738105 AAGACTT-GCAAAGATTACAAG-TTTAGCAAAGC-TTC
1 AAGA-TTCGCAAAGATTACAAGATTTA-CAAAGCTTTC
9738140 TAAGATTCGCAAAGA
1 -AAGATTCGCAAAGA
9738155 ATTTTAAAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
34 11 0.11
35 25 0.24
36 31 0.30
37 33 0.32
38 3 0.03
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (36 bp):
AAGATTCGCAAAGATTACAAGATTTACAAAGCTTTC
Found at i:9738428 original size:32 final size:33
Alignment explanation
Indices: 9738335--9738414 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 33
9738325 TTTTTAGTTC
* * * * *
9738335 CACAAGAATTTCAAATTCGAAAGGATTAAAGATT
1 CACAAGAATTTTAGATTCGTAAGAATTTAA-ATT
9738369 CACAAGAATTTTAGATTCGTAAGAATTTAAATT
1 CACAAGAATTTTAGATTCGTAAGAATTTAAATT
9738402 CACAAG-ATTTTAG
1 CACAAGAATTTTAG
9738415 TTTTTCAAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
32 7 0.17
33 9 0.22
34 25 0.61
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (33 bp):
CACAAGAATTTTAGATTCGTAAGAATTTAAATT
Found at i:9738455 original size:16 final size:17
Alignment explanation
Indices: 9738320--9738453 Score: 77
Period size: 17 Copynumber: 8.1 Consensus size: 17
9738310 CAAAATTACA
9738320 AAGAATTTTTAG-TTCCAC
1 AAGAA-TTTTAGATT-CAC
* *
9738338 AAGAATTTCAAATTCGA-
1 AAGAATTTTAGATTC-AC
* **
9738355 AAGGATTAAAGATTCAC
1 AAGAATTTTAGATTCAC
**
9738372 AAGAATTTTAGATTCGT
1 AAGAATTTTAGATTCAC
*
9738389 AAGAA-TTTAAATTCAC
1 AAGAATTTTAGATTCAC
* **
9738405 AAG-ATTTTAGTTTTTC
1 AAGAATTTTAGATTCAC
9738421 AAGAA-TTT-GATT-ATC
1 AAGAATTTTAGATTCA-C
9738436 AA-AATTTTAGATTCAC
1 AAGAATTTTAGATTCAC
9738452 AA
1 AA
9738454 AACTCAAATT
Statistics
Matches: 87, Mismatches: 20, Indels: 20
0.69 0.16 0.16
Matches are distributed among these distances:
14 2 0.02
15 10 0.11
16 32 0.37
17 35 0.40
18 8 0.09
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (17 bp):
AAGAATTTTAGATTCAC
Found at i:9738883 original size:109 final size:108
Alignment explanation
Indices: 9738745--9738957 Score: 304
Period size: 109 Copynumber: 2.0 Consensus size: 108
9738735 ATTTCTCATT
* * *
9738745 AAAAACTTTAGGATTTCATCCAAAATTTCAAAACTTCTCATTCGGGTTCAAAGATTTACATTCGA
1 AAAAAATTTAGGATTTCATCCAAAATTTCAAAACTTCTCATTCGAGTTCAAAGATTAACATTCGA
*
9738810 TAAA-TTTAAAGTTTCACATCTAAA-TCTAAAGGTTTTCACTAA
66 TAAATTTTAAAGTTTCACATCTAAATTC-AAAAGTTTTCACTAA
* * * *
9738852 AAAAAATTTAGGGTTTCACATCGAAAATTTCAAAGCTTCTCATTCGAGTTCAAAGATTAATATTC
1 AAAAAATTTAGGATTT--CATCCAAAATTTCAAAACTTCTCATTCGAGTTCAAAGATTAACATTC
*
9738917 GATAAATTTTAGAGTTTCACATCTAAATTCAAAAGTTTTCA
64 GATAAATTTTAAAGTTTCACATCTAAATTCAAAAGTTTTCA
9738958 TTTAAAACTT
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
107 14 0.15
109 48 0.52
110 29 0.31
111 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (108 bp):
AAAAAATTTAGGATTTCATCCAAAATTTCAAAACTTCTCATTCGAGTTCAAAGATTAACATTCGA
TAAATTTTAAAGTTTCACATCTAAATTCAAAAGTTTTCACTAA
Found at i:9738979 original size:24 final size:24
Alignment explanation
Indices: 9738948--9739103 Score: 92
Period size: 24 Copynumber: 6.5 Consensus size: 24
9738938 TCTAAATTCA
9738948 AAAG-TTTTCATTTAAAACTTCTT
1 AAAGATTTTCATTTAAAACTTCTT
**
9738971 AAAGATTTTCATTTAAAA-GAC--
1 AAAGATTTTCATTTAAAACTTCTT
* * *
9738992 AAAGATTCTT-ATTCAAAACTCCGT
1 AAAGATT-TTCATTTAAAACTTCTT
* * **
9739016 AAAGATTCTCATTTAAAGC-TCAAAGAC
1 AAAGATTTTCATTTAAAACTTC----TT
9739043 AAAGATTCTT-ATTTAAAACTTCTT
1 AAAGATT-TTCATTTAAAACTTCTT
* *
9739067 AAAGATTCTCATTTAAAACTTTTT
1 AAAGATTTTCATTTAAAACTTCTT
* *
9739091 TAAGGTTTTCATT
1 AAAGATTTTCATT
9739104 ATTTTTAACT
Statistics
Matches: 100, Mismatches: 20, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
21 14 0.14
22 3 0.03
23 8 0.08
24 57 0.57
27 15 0.15
28 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (24 bp):
AAAGATTTTCATTTAAAACTTCTT
Found at i:9739019 original size:45 final size:45
Alignment explanation
Indices: 9738961--9739084 Score: 158
Period size: 51 Copynumber: 2.6 Consensus size: 45
9738951 GTTTTCATTT
*
9738961 AAAACTTCTTAAAGATTTTCATTTAAAAGACAAAGATTCTTATTC
1 AAAACTTCTTAAAGATTCTCATTTAAAAGACAAAGATTCTTATTC
* * *
9739006 AAAACTCCGTAAAGATTCTCATTTAAAGCTCAAAGACAAAGATTCTTATTT
1 AAAACTTCTTAAAGATTCTCATTT--A----AAAGACAAAGATTCTTATTC
9739057 AAAACTTCTTAAAGATTCTCATTTAAAA
1 AAAACTTCTTAAAGATTCTCATTTAAAA
9739085 CTTTTTTAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
45 24 0.36
47 1 0.01
49 1 0.01
51 41 0.61
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (45 bp):
AAAACTTCTTAAAGATTCTCATTTAAAAGACAAAGATTCTTATTC
Found at i:9739062 original size:51 final size:51
Alignment explanation
Indices: 9738986--9739083 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
9738976 TTTTCATTTA
9738986 AAAGACAAAGATTCTTATTCAAAACTCCGTAAAGATTCTCATTTAAAGCTC
1 AAAGACAAAGATTCTTATTCAAAACTCCGTAAAGATTCTCATTTAAAGCTC
* * *
9739037 AAAGACAAAGATTCTTATTTAAAACTTCTTAAAGATTCTCATTTAAA
1 AAAGACAAAGATTCTTATTCAAAACTCCGTAAAGATTCTCATTTAAA
9739084 ACTTTTTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (51 bp):
AAAGACAAAGATTCTTATTCAAAACTCCGTAAAGATTCTCATTTAAAGCTC
Found at i:9740264 original size:17 final size:19
Alignment explanation
Indices: 9740224--9740269 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
9740214 TCCTTTCACA
*
9740224 TTTTTCTCATTTCTTCATT
1 TTTTTCACATTTCTTCATT
9740243 TTTTTCACATTTC-TCA-T
1 TTTTTCACATTTCTTCATT
9740260 TTTTTCACAT
1 TTTTTCACAT
9740270 GTTCACTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 11 0.42
18 3 0.12
19 12 0.46
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTCACATTTCTTCATT
Found at i:9740316 original size:23 final size:24
Alignment explanation
Indices: 9740286--9740331 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
9740276 TTCTTTCATT
9740286 TTTTTTCACTTTATTT-TTTTTTA
1 TTTTTTCACTTTATTTCTTTTTTA
*
9740309 TTTTTTCACTTTTTTTCTTTTTT
1 TTTTTTCACTTTATTTCTTTTTT
9740332 CTTTCATCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTTCACTTTATTTCTTTTTTA
Found at i:9740321 original size:9 final size:9
Alignment explanation
Indices: 9740217--9740332 Score: 52
Period size: 9 Copynumber: 13.4 Consensus size: 9
9740207 TTTTCTCTCC
9740217 TTTCACATTT
1 TTTCAC-TTT
9740227 TTCTCA-TTT
1 TT-TCACTTT
* *
9740236 CTTCATTTT
1 TTTCACTTT
*
9740245 TTTCACATT
1 TTTCACTTT
*
9740254 TCTCA-TTT
1 TTTCACTTT
*
9740262 TTTCAC-AT
1 TTTCACTTT
* *
9740270 GTTCACTTC
1 TTTCACTTT
*
9740279 TTTCATTTTT
1 TTTCA-CTTT
9740289 TTTCACTTT
1 TTTCACTTT
9740298 ATTT---TTT
1 -TTTCACTTT
9740305 TTT-A-TTT
1 TTTCACTTT
9740312 TTTCACTTT
1 TTTCACTTT
*
9740321 TTT-TCTTT
1 TTTCACTTT
9740329 TTTC
1 TTTC
9740333 TTTCATCCAT
Statistics
Matches: 80, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
6 3 0.04
7 9 0.11
8 23 0.29
9 30 0.38
10 12 0.15
11 3 0.04
ACGTcount: A:0.13, C:0.19, G:0.01, T:0.67
Consensus pattern (9 bp):
TTTCACTTT
Found at i:9746161 original size:30 final size:30
Alignment explanation
Indices: 9746125--9746192 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
9746115 CTAAGCATCA
9746125 GCATCATCGACAACAATAGCAGTGGTACTT
1 GCATCATCGACAACAATAGCAGTGGTACTT
9746155 GCATCATCGACAACAATAGCAGTGGTACTT
1 GCATCATCGACAACAATAGCAGTGGTACTT
9746185 GCATCATC
1 GCATCATC
9746193 AATAGTAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (30 bp):
GCATCATCGACAACAATAGCAGTGGTACTT
Found at i:9747532 original size:956 final size:953
Alignment explanation
Indices: 9746155--9747945 Score: 2791
Period size: 956 Copynumber: 1.9 Consensus size: 953
9746145 AGTGGTACTT
* * * *
9746155 GCATCATCGACAACAATAGCAGTGGTACTTGCATCATCAATAGTAACAGCAACAACATTGACTTG
1 GCATCATCAACAACAATAGCAATGGCACTTGCATCATCAATAGTAACAGCAACAACATTGACTTA
* *
9746220 TGCCTTTCTAACCTCACCCCCTTAGCCTCAGCTCCCAAAGCGACCTCATGCTCGGCATCTAGTGC
66 TGCCTTTCTAACCTCACCCCCTTAGCCTCAACTCCCAAAACGACCTCATGCTCGGCATCTAGTGC
*
9746285 TCCATCTTCATTATATTTTTTTTCCTTCTCGTTGGACTAATTTGGAAAAGGTCTCGATATGATGT
131 TCCATCTTCATTATATTTTTTTTCCTTCTCGTTGGACTAATTTAGAAAAGGTCTCGATATGATGT
* * *
9746350 TGTTGATATCAATATTAAAGAGATTAAGGTTGAGGTTGACAAATTTAAACTGCACCTCCTTGCTT
196 TGTTGATATCAATACTAAAGAGATTAAGGTTGAGGTTGACAAATTTAAACTGCACCTCCTTACCT
* * *
9746415 AGCTCGAAGGCACTGAGCACAATACCCCTAGAGAACTCTACTTGGAACTTGAAGAATTCACTAGA
261 AGCTCGAAGACACTGAGCACAATACCCCTAGAAAACTCTACTTAGAACTTGAAGAATTCACTAGA
* *
9746480 GGCCTTAAAGTCATCCATAGCTTTCTTTTTTACTTTTTCTTTCTCATTTTTCCCAACTTTTAGCT
326 GGCCTTAAAGTCATCCATAGCTTTCTTTTTTACTTCTTCTTTCTCATTTTTCCCAACTTTTAACT
*
9746545 CTAACCTCAGTCTGACTATCTTAGTTTAAGCATCACTAAGGTTTAGCTCGGTCTACTCCATCATA
391 CTAACCTCAGTCTGACTATCTTAGCTTAAGCATCACTAAGGTTTAGCTCGGTCTACTCCATCATA
* * * *
9746610 GATTCCATTAAGGCCTTCTTAATATGGATAATCTCCAGCTTGGCTGTCAGTTCATCGATTCTCTT
456 AATTCCACTAAGGCCTTCTTAATATGGACAATCTCCAGCTTGGCTGTCAGTTCATCAATT-TCTT
* * *
9746675 TATCTGTTAGGCCTTTATCTTGTAAGATACATTAAGGTTAGACCTCATGTTGCCTAGAGCATTCA
520 TATCTGTTAGGCCTTCATCTTATAAGATACACTAAGGTTAGACCTCATGTTGCCTAGAGCATTCA
* *
9746740 AGTTTTTCTTGTGCTCTTCGCTCAGAATAACCATATCCTT-TTCAGCCTTAAGTAAATGGGTCAT
585 AGTTTTTCTTATGCTCTTCACTCAGAATAACCATATCCTTCTT-AGCCTTAAGTAAATGGGTCAT
* * *
9746804 AACATGATAGGCTTGGTGGAAGGCTTCGCTGGTGTTATCAGTAGGCTGAGGTGGGAGCTTTTAAT
649 AACAAGATAGGCTTGGCGAAAGGCTTCGCTGGTGTTATCAGTAGGCTGAGGTGGGAGCTTTTAAT
* *
9746869 GAACTGCATAAAATGAACTTAAATTTAAGCCAAAACAAAAACAAAGAACAATGATAAAATTAAAC
714 GAACTGCATAAAATGAACTTAAACTTAAGCCAAAACAAAAACAAAAAACAATGATAAAATTAAAC
* *
9746934 TAGAATCAAGTAATACTCACCGATATAATGAATTATGACCTTTCAGAACCTCCTGACAAAAGTTT
779 TACAATCAAGCAATACTCACCGATATAATGAATTATGACCTTTCAGAACCTCCTGACAAAAGTTT
9746999 TTGTAGAGTGATTTCTATCAAAGGTCACAACAAAAACTAATCTCATACATCAGCAATCTTGAATA
844 TTGTAGAGTGATTTCTATCAAAGGTCACAACAAAAACTAATCTCATACATCAGCAATCTTGAATA
9747064 AAAATTCATAAAAATTTACAAGTAAAAAAAAAAACCTAAGCATCA
909 AAAATTCATAAAAATTTACAAGTAAAAAAAAAAACCTAAGCATCA
* * * * *
9747109 GCATCATCAACAGCAATAGTAATGGCACTTGCATTATCAGTAGT-AGAGCAACAACATTGACTTA
1 GCATCATCAACAACAATAGCAATGGCACTTGCATCATCAATAGTAACAGCAACAACATTGACTTA
* * *
9747173 TGCCTTTCTAGCCTCACCCTCTTAGCCTCAACTCTCAAAACGACCTCATGCTCGGCATCTAGTGC
66 TGCCTTTCTAACCTCACCCCCTTAGCCTCAACTCCCAAAACGACCTCATGCTCGGCATCTAGTGC
*
9747238 TCCATCTTTATTATATTCCTTATTTTCCTTCTCGTTGGACTAATTTAGAAAAGGTCTCGATATGA
131 TCCATCTTCATTATATT--TT-TTTTCCTTCTCGTTGGACTAATTTAGAAAAGGTCTCGATATGA
* * *
9747303 TGTTGTTGATATCAATACTAAAGAGATTGAGGTTGAGGTTGACAAATTTAAATTGCACCTCTTTA
193 TGTTGTTGATATCAATACTAAAGAGATTAAGGTTGAGGTTGACAAATTTAAACTGCACCTCCTTA
* * * * *
9747368 CCTAGCTCGACA-ACACTGAGCACATTATCCCTAGAAAACTTTACTTAGAGCTTGAGGAATTCAC
258 CCTAGCTCGA-AGACACTGAGCACAATACCCCTAGAAAACTCTACTTAGAACTTGAAGAATTCAC
* * * *
9747432 T-GAAGGCCTTGAAGTCATCCATAGCTTTTTTTTTTACTTCTTCTTTCTCA-TTTTCCCTATTTT
322 TAG-AGGCCTTAAAGTCATCCATAGCTTTCTTTTTTACTTCTTCTTTCTCATTTTTCCCAACTTT
* * * *
9747495 CTAACTCTAACCTCAGTTTGGCTATCTTAGCTTAAGCATCACTAAGTTTTAGCTTGGTCTACTCC
386 -TAACTCTAACCTCAGTCTGACTATCTTAGCTTAAGCATCACTAAGGTTTAGCTCGGTCTACTCC
* * * *
9747560 CTCATAAATTCCACTGAGGCCTTCTTAATATGGACAGTCTCCAGCTTGGCTGTCAGTTCATTAAT
450 ATCATAAATTCCACTAAGGCCTTCTTAATATGGACAATCTCCAGCTTGGCTGTCAGTTCATCAAT
* * * * *
9747625 TTTTTTCTCTGTTAGGCCTTCATCTTATGAGATGCACTAAGGTTAGACCTTATGTTGCCTAGAGC
515 TTCTTTATCTGTTAGGCCTTCATCTTATAAGATACACTAAGGTTAGACCTCATGTTGCCTAGAGC
* *
9747690 ATTCGAGTTTTTCTTATGCTCTTCACTTAGAATAACCATATCCTTCTTAGCCTTAAGTAAATGGG
580 ATTCAAGTTTTTCTTATGCTCTTCACTCAGAATAACCATATCCTTCTTAGCCTTAAGTAAATGGG
* * * *
9747755 TCATAGCAAGATAGGTTTGGCGAAAGGCTTGGCTGGTGTTATCAGTGGGCTGAGGTGGGAGCTTT
645 TCATAACAAGATAGGCTTGGCGAAAGGCTTCGCTGGTGTTATCAGTAGGCTGAGGTGGGAGCTTT
* * *
9747820 TAATGGACTGCATAAAATGAACTTGAACTTAAGCCAAAATAAAAACAAAAAACAATGATAAAATT
710 TAATGAACTGCATAAAATGAACTTAAACTTAAGCCAAAACAAAAACAAAAAACAATGATAAAATT
*
9747885 AAACTACAATCAAGCAATACTCATCGATATAATGAATTATGACCTTTCAGAACCTCCTGAC
775 AAACTACAATCAAGCAATACTCACCGATATAATGAATTATGACCTTTCAGAACCTCCTGAC
9747946 CATTTCAAGG
Statistics
Matches: 754, Mismatches: 76, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
953 94 0.12
954 37 0.05
955 304 0.40
956 318 0.42
957 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (953 bp):
GCATCATCAACAACAATAGCAATGGCACTTGCATCATCAATAGTAACAGCAACAACATTGACTTA
TGCCTTTCTAACCTCACCCCCTTAGCCTCAACTCCCAAAACGACCTCATGCTCGGCATCTAGTGC
TCCATCTTCATTATATTTTTTTTCCTTCTCGTTGGACTAATTTAGAAAAGGTCTCGATATGATGT
TGTTGATATCAATACTAAAGAGATTAAGGTTGAGGTTGACAAATTTAAACTGCACCTCCTTACCT
AGCTCGAAGACACTGAGCACAATACCCCTAGAAAACTCTACTTAGAACTTGAAGAATTCACTAGA
GGCCTTAAAGTCATCCATAGCTTTCTTTTTTACTTCTTCTTTCTCATTTTTCCCAACTTTTAACT
CTAACCTCAGTCTGACTATCTTAGCTTAAGCATCACTAAGGTTTAGCTCGGTCTACTCCATCATA
AATTCCACTAAGGCCTTCTTAATATGGACAATCTCCAGCTTGGCTGTCAGTTCATCAATTTCTTT
ATCTGTTAGGCCTTCATCTTATAAGATACACTAAGGTTAGACCTCATGTTGCCTAGAGCATTCAA
GTTTTTCTTATGCTCTTCACTCAGAATAACCATATCCTTCTTAGCCTTAAGTAAATGGGTCATAA
CAAGATAGGCTTGGCGAAAGGCTTCGCTGGTGTTATCAGTAGGCTGAGGTGGGAGCTTTTAATGA
ACTGCATAAAATGAACTTAAACTTAAGCCAAAACAAAAACAAAAAACAATGATAAAATTAAACTA
CAATCAAGCAATACTCACCGATATAATGAATTATGACCTTTCAGAACCTCCTGACAAAAGTTTTT
GTAGAGTGATTTCTATCAAAGGTCACAACAAAAACTAATCTCATACATCAGCAATCTTGAATAAA
AATTCATAAAAATTTACAAGTAAAAAAAAAAACCTAAGCATCA
Found at i:9760287 original size:17 final size:19
Alignment explanation
Indices: 9760265--9760301 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
9760255 CTTTTTAATT
9760265 ATAAAA-TAATTA-TATAA
1 ATAAAACTAATTATTATAA
*
9760282 ATAAAACTATTTATTATAA
1 ATAAAACTAATTATTATAA
9760301 A
1 A
9760302 ATATATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAACTAATTATTATAA
Found at i:9762698 original size:2 final size:2
Alignment explanation
Indices: 9762686--9762720 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
9762676 TACCACGGAC
9762686 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9762721 TATTGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9762962 original size:2 final size:2
Alignment explanation
Indices: 9762955--9762979 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9762945 AATATCATAC
9762955 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
9762980 GATTTGTTGG
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:9763147 original size:21 final size:21
Alignment explanation
Indices: 9763121--9763166 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
9763111 ATTGATATTT
* *
9763121 ATTTTTATTTAAAATTATTAAA
1 ATTTTAATTT-AAATCATTAAA
*
9763143 ATTTTAATTTTAATCATTAAA
1 ATTTTAATTTAAATCATTAAA
9763164 ATT
1 ATT
9763167 AAAAATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTAATTTAAATCATTAAA
Found at i:9763165 original size:30 final size:31
Alignment explanation
Indices: 9763129--9763189 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
9763119 TTATTTTTAT
*
9763129 TTAAAATTATTAAA-ATTTTAAT-TTTAATCA
1 TTAAAATTA-AAAATATTTTAATATTTAATCA
*
9763159 TTAAAATTAAAAATATTTTAATATTTTATCA
1 TTAAAATTAAAAATATTTTAATATTTAATCA
9763190 ACATATTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 3 0.11
30 17 0.63
31 7 0.26
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (31 bp):
TTAAAATTAAAAATATTTTAATATTTAATCA
Found at i:9765963 original size:18 final size:17
Alignment explanation
Indices: 9765940--9766203 Score: 98
Period size: 15 Copynumber: 16.6 Consensus size: 17
9765930 AATTTTACTT
9765940 ATAAATAATATTATATGA
1 ATAAATAATATTATAT-A
9765958 ATAAATAATA-TAT-T-
1 ATAAATAATATTATATA
*
9765972 AT---TAATATAATA-A
1 ATAAATAATATTATATA
* *
9765985 ATCAAAAAATAATAT-TA
1 AT-AAATAATATTATATA
9766002 ATAAATAATA-TAT-TA
1 ATAAATAATATTATATA
*
9766017 ATAAATATTA-TA-ATA
1 ATAAATAATATTATATA
* *
9766032 ATGTATTAATATTA-ATA
1 AT-AAATAATATTATATA
*
9766049 A-ATAATAA-ACTAT-TA
1 ATA-AATAATATTATATA
* ** *
9766064 ATATAATATTAAGAAATA
1 ATA-AATAATATTATATA
* *
9766082 ATACTATAATA-TGT-TA
1 ATA-AATAATATTATATA
9766098 ATAAATAATATTATATTA
1 ATAAATAATATTATA-TA
9766116 ATAAATAATA-TA-ATA
1 ATAAATAATATTATATA
* *
9766131 ATAAATATTATTAATTTA
1 ATAAATAATATT-ATATA
*
9766149 ATTAATAA-A-TAT-T-
1 ATAAATAATATTATATA
9766162 AT-AATAATA-TAT-TA
1 ATAAATAATATTATATA
9766176 ATAAATAATA-TATTATTA
1 ATAAATAATATTA-TA-TA
9766194 ATAAATAATA
1 ATAAATAATA
9766204 CACTATTAAT
Statistics
Matches: 190, Mismatches: 28, Indels: 56
0.69 0.10 0.20
Matches are distributed among these distances:
11 5 0.03
12 7 0.04
13 9 0.05
14 5 0.03
15 54 0.28
16 34 0.18
17 24 0.13
18 52 0.27
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (17 bp):
ATAAATAATATTATATA
Found at i:9765969 original size:15 final size:15
Alignment explanation
Indices: 9765940--9766227 Score: 165
Period size: 18 Copynumber: 18.2 Consensus size: 15
9765930 AATTTTACTT
9765940 ATAAATAATATTATATGA
1 ATAAATAATA-TAT-T-A
9765958 ATAAATAATATATTA
1 ATAAATAATATATTA
* * *
9765973 TTAATATAATAAATCA
1 ATAA-ATAATATATTA
*
9765989 AAAAAT-A-ATATTA
1 ATAAATAATATATTA
9766002 ATAAATAATATATTA
1 ATAAATAATATATTA
* *
9766017 ATAAATATTATAATA
1 ATAAATAATATATTA
** *
9766032 ATGTATTA-ATATTA
1 ATAAATAATATATTA
9766046 ATAAATAATAAACTATTA
1 ATAAATAAT--A-TATTA
* * *
9766064 ATATAATATTAAGAAATA
1 ATA-AATAAT-A-TATTA
* *
9766082 ATACTATAATATGTTA
1 ATA-AATAATATATTA
9766098 ATAAATAATATTATATTA
1 ATAAAT-A-A-TATATTA
*
9766116 ATAAATAATATAATA
1 ATAAATAATATATTA
*
9766131 ATAAATATTATTAATTTA
1 ATAAATAATA-T-A-TTA
*
9766149 ATTAATAA-ATATT-
1 ATAAATAATATATTA
9766162 AT-AATAATATATTA
1 ATAAATAATATATTA
9766176 ATAAATAATATATTATTA
1 ATAAAT-A-ATA-TATTA
* *
9766194 ATAAATAATACACTA
1 ATAAATAATATATTA
*
9766209 TTAATATAATATATTA
1 ATAA-ATAATATATTA
9766225 ATA
1 ATA
9766228 CGTATTATTG
Statistics
Matches: 208, Mismatches: 41, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
12 5 0.02
13 16 0.08
14 16 0.08
15 56 0.27
16 36 0.17
17 13 0.06
18 61 0.29
19 5 0.02
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (15 bp):
ATAAATAATATATTA
Found at i:9766395 original size:25 final size:26
Alignment explanation
Indices: 9766359--9766440 Score: 89
Period size: 25 Copynumber: 3.2 Consensus size: 26
9766349 AAATTATTTT
9766359 TTAATATT-AATAATTTTAATAATAAA
1 TTAAT-TTCAATAATTTTAATAATAAA
9766385 -TAATTTCAATATATTTTAATAATAAA
1 TTAATTTCAATA-ATTTTAATAATAAA
* * * *
9766411 TTATTTTTAAT-ATTTTAATATTATA
1 TTAATTTCAATAATTTTAATAATAAA
9766436 TTAAT
1 TTAAT
9766441 ATCATTTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
24 2 0.04
25 24 0.50
26 14 0.29
27 8 0.17
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAATTTCAATAATTTTAATAATAAA
Found at i:9766404 original size:26 final size:26
Alignment explanation
Indices: 9766367--9766430 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
9766357 TTTTAATATT
9766367 AATA-ATTTTAATAATAAATAATTTC
1 AATATATTTTAATAATAAATAATTTC
* *
9766392 AATATATTTTAATAATAAATTATTTT
1 AATATATTTTAATAATAAATAATTTC
*
9766418 TA-ATATTTTAATA
1 AATATATTTTAATA
9766431 TTATATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
25 15 0.43
26 20 0.57
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:9766415 original size:16 final size:16
Alignment explanation
Indices: 9766319--9766422 Score: 53
Period size: 17 Copynumber: 6.6 Consensus size: 16
9766309 ATTAACATAA
*
9766319 TATTTTAATATTAAATAT
1 TATTTTAATAAT-AA-AT
9766337 TATTATTAA-AATAAAT
1 TATT-TTAATAATAAAT
*
9766353 TATTTTTTAAT-ATTAAT
1 TA--TTTTAATAATAAAT
*
9766370 AATTTTAATAATAAA-
1 TATTTTAATAATAAAT
* *
9766385 TAATTT--CAAT--A-
1 TATTTTAATAATAAAT
9766396 TATTTTAATAATAAAT
1 TATTTTAATAATAAAT
9766412 TATTTTTAATA
1 TA-TTTTAATA
9766423 TTTTAATATT
Statistics
Matches: 66, Mismatches: 9, Indels: 23
0.67 0.09 0.23
Matches are distributed among these distances:
11 6 0.09
13 6 0.09
15 12 0.18
16 10 0.15
17 20 0.30
18 8 0.12
19 4 0.06
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTTTAATAATAAAT
Found at i:9766561 original size:15 final size:14
Alignment explanation
Indices: 9766541--9766584 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
9766531 AAAATATAAA
9766541 TATTTTTATAAAAAT
1 TATTTTT-TAAAAAT
9766556 TATTTTTTAAAAAT
1 TATTTTTTAAAAAT
*
9766570 CATTTTTTGAAAAAT
1 TATTTTTT-AAAAAT
9766585 AAATGGAGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 14 0.52
15 13 0.48
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (14 bp):
TATTTTTTAAAAAT
Found at i:9768466 original size:12 final size:12
Alignment explanation
Indices: 9768440--9768477 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
9768430 ATAAAGACAT
9768440 AAAAA-CAAA-A
1 AAAAATCAAAGA
9768450 AAAAATCAAAGA
1 AAAAATCAAAGA
*
9768462 AAAAATAAAAGA
1 AAAAATCAAAGA
9768474 AAAA
1 AAAA
9768478 GGGAAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 5 0.20
11 4 0.16
12 16 0.64
ACGTcount: A:0.84, C:0.05, G:0.05, T:0.05
Consensus pattern (12 bp):
AAAAATCAAAGA
Found at i:9769402 original size:24 final size:24
Alignment explanation
Indices: 9769375--9769420 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
9769365 TTTTTATTAA
*
9769375 ATTAAAATATTAA-ATAATAATTTT
1 ATTAAAATAATAATAT-ATAATTTT
*
9769399 ATTAATATAATAATATATAATT
1 ATTAAAATAATAATATATAATT
9769421 ATAAGATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTAAAATAATAATATATAATTTT
Found at i:9771767 original size:22 final size:21
Alignment explanation
Indices: 9771732--9771791 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
9771722 ATTTTATATT
*
9771732 AAAAATTATGAAATTAAATTTATA
1 AAAAATTA--AAATCAAATTT-TA
**
9771756 AAAAATTAAAATCCTATTTTA
1 AAAAATTAAAATCAAATTTTA
9771777 AAATAATTAAAATCA
1 AAA-AATTAAAATCA
9771792 CTTTTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 5 0.16
22 18 0.58
24 8 0.26
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAAATTAAAATCAAATTTTA
Found at i:9771797 original size:22 final size:21
Alignment explanation
Indices: 9771749--9771790 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 21
9771739 ATGAAATTAA
9771749 ATTTATAAAAAATTAAAATCCT
1 ATTT-TAAAAAATTAAAATCCT
9771771 ATTTTAAAATAATTAAAATC
1 ATTTTAAAA-AATTAAAATC
9771791 ACTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTTTAAAAAATTAAAATCCT
Found at i:9772248 original size:15 final size:15
Alignment explanation
Indices: 9772210--9772255 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
9772200 CCTTTAAAAA
*
9772210 TAAAATTTAATATGTT
1 TAAAATTTAAAAT-TT
9772226 TAAAATTTAAAATTT
1 TAAAATTTAAAATTT
* *
9772241 TAACATTTATAATTT
1 TAAAATTTAAAATTT
9772256 ATTTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
TAAAATTTAAAATTT
Found at i:9772571 original size:32 final size:34
Alignment explanation
Indices: 9772534--9772623 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
9772524 TTAATAATAA
*
9772534 TTATATTTAAATTTAATA-AAATAA-AAAATATT
1 TTATATTTAAATTTAATATAAATAATAAAACATT
* *
9772566 TTATATTTCATATTT-ATATAAATAATAATACATT
1 TTATATTT-AAATTTAATATAAATAATAAAACATT
*
9772600 TT-TATATAAATTATAATATAAATA
1 TTATATTTAAATT-TAATATAAATA
9772624 TATTTTTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
32 15 0.31
33 16 0.33
34 17 0.35
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (34 bp):
TTATATTTAAATTTAATATAAATAATAAAACATT
Found at i:9773863 original size:2 final size:2
Alignment explanation
Indices: 9773858--9773882 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9773848 AAAAAGACAA
9773858 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
9773883 AATAAGAGTA
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:9779166 original size:13 final size:14
Alignment explanation
Indices: 9779143--9779175 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9779133 GGGTCAAATA
9779143 TTTTTATTTTATTG
1 TTTTTATTTTATTG
9779157 TTTTTA-TTTATTG
1 TTTTTATTTTATTG
9779170 TATTTT
1 T-TTTT
9779176 TTAAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (14 bp):
TTTTTATTTTATTG
Found at i:9779736 original size:9 final size:9
Alignment explanation
Indices: 9779722--9779754 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
9779712 AAATTAATTT
9779722 ATAAAAAAA
1 ATAAAAAAA
9779731 AT-AAAAAA
1 ATAAAAAAA
*
9779739 ATGAAAAAA
1 ATAAAAAAA
9779748 ATAAAAA
1 ATAAAAA
9779755 CAAAAGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:9779738 original size:8 final size:8
Alignment explanation
Indices: 9779725--9779754 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
9779715 TTAATTTATA
9779725 AAAAAAAT
1 AAAAAAAT
9779733 AAAAAAAT
1 AAAAAAAT
9779741 GAAAAAAAT
1 -AAAAAAAT
9779750 AAAAA
1 AAAAA
9779755 CAAAAGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:9779759 original size:20 final size:18
Alignment explanation
Indices: 9779724--9779768 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
9779714 ATTAATTTAT
* *
9779724 AAAAAAAATAAAAAAATG
1 AAAAAAAAAAAAAAAAGG
9779742 AAAAAAATAAAAACAAAAGG
1 AAAAAAA-AAAAA-AAAAGG
9779762 AAAAAAA
1 AAAAAAA
9779769 GCTTATTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 4 0.17
20 12 0.52
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAGG
Found at i:9780575 original size:19 final size:21
Alignment explanation
Indices: 9780543--9780584 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
9780533 AATGGCACAT
*
9780543 AAAAATTTTAAAATA-TTAAA
1 AAAAATTATAAAATAGTTAAA
9780563 AAAAATTAT-AAATAGTTAAA
1 AAAAATTATAAAATAGTTAAA
9780583 AA
1 AA
9780585 CTTAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAAATTATAAAATAGTTAAA
Found at i:9781487 original size:14 final size:14
Alignment explanation
Indices: 9781468--9781495 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9781458 ATATGTGAAT
9781468 TTTTATTTTTTTTA
1 TTTTATTTTTTTTA
9781482 TTTTATTTTTTTTA
1 TTTTATTTTTTTTA
9781496 AAAAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTATTTTTTTTA
Found at i:9783186 original size:9 final size:8
Alignment explanation
Indices: 9783159--9783197 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
9783149 CTCCATTTTG
9783159 TATTTTAT
1 TATTTTAT
9783167 TATTTTAT
1 TATTTTAT
9783175 TATTTATAT
1 TATTT-TAT
9783184 TATTTCTAT
1 TATTT-TAT
9783193 T-TTTT
1 TATTTT
9783198 TTCTTTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 1 0.03
8 16 0.55
9 12 0.41
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTTTAT
Found at i:9783186 original size:17 final size:17
Alignment explanation
Indices: 9783159--9783197 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
9783149 CTCCATTTTG
9783159 TATTTTATTATTT-TAT
1 TATTTTATTATTTCTAT
9783175 TATTTATATTATTTCTAT
1 TATTT-TATTATTTCTAT
9783193 T-TTTT
1 TATTTT
9783198 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 11 0.52
18 4 0.19
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTTATTATTTCTAT
Found at i:9783405 original size:23 final size:22
Alignment explanation
Indices: 9783375--9783455 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 22
9783365 ATTGAAAGTC
9783375 TGAGATTTGAATATAAAAACATA
1 TGAGATTTGAATATAAAAA-ATA
* * *
9783398 TGAGATTTGAATCTTAGAAAATC
1 TGAGATTTGAAT-ATAAAAAATA
*
9783421 TGAGATTTGAATATCAAAAAATT
1 TGAGATTTGAATAT-AAAAAATA
*
9783444 TGATATTTGAAT
1 TGAGATTTGAAT
9783456 CCCACAAAGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
22 1 0.02
23 43 0.88
24 5 0.10
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (22 bp):
TGAGATTTGAATATAAAAAATA
Found at i:9783426 original size:46 final size:46
Alignment explanation
Indices: 9783368--9783456 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 46
9783358 CACATCGATT
*
9783368 GAAAGTCTGAGATTTGAATAT-AAAAACATATGAGATTTGAATCTTA
1 GAAAATCTGAGATTTGAATATCAAAAA-ATATGAGATTTGAATCTTA
* *
9783414 GAAAATCTGAGATTTGAATATCAAAAAATTTGATATTTGAATC
1 GAAAATCTGAGATTTGAATATCAAAAAATATGAGATTTGAATC
9783457 CCACAAAGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
46 34 0.87
47 5 0.13
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.34
Consensus pattern (46 bp):
GAAAATCTGAGATTTGAATATCAAAAAATATGAGATTTGAATCTTA
Found at i:9785295 original size:10 final size:10
Alignment explanation
Indices: 9785280--9785305 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9785270 AAAAATATCT
9785280 TTTTAATAAA
1 TTTTAATAAA
9785290 TTTTAATAAA
1 TTTTAATAAA
9785300 TTTTAA
1 TTTTAA
9785306 GATTTCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:9785576 original size:11 final size:10
Alignment explanation
Indices: 9785560--9785594 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
9785550 CATTTTTAAC
*
9785560 AAAAAAAGTA
1 AAAAAAAATA
9785570 AAAAAAAATAA
1 AAAAAAAAT-A
9785581 AAAAAAAATA
1 AAAAAAAATA
9785591 AAAA
1 AAAA
9785595 TTCACACACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.09
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:9796750 original size:47 final size:47
Alignment explanation
Indices: 9796678--9797083 Score: 385
Period size: 47 Copynumber: 8.6 Consensus size: 47
9796668 CATATCGAAT
* * *
9796678 TTTAAAGTTGTTGAGCCTTTGCTTAGAGGAAACTTTTCAAGATTAAG
1 TTTAAAGTTGTTGAGCCTCTGCTTAGAGGAACCTTTTCAAGATGAAG
* * * * *
9796725 TTTAAAGTTGTTAAGCCTCTACTTAGAGGAGCCTTTTCAAGATAAAA
1 TTTAAAGTTGTTGAGCCTCTGCTTAGAGGAACCTTTTCAAGATGAAG
* * *
9796772 TTTAAAGTTGTTGAGCCTCTGTTTAGAGGAACTTTTTCAAGATTAAG
1 TTTAAAGTTGTTGAGCCTCTGCTTAGAGGAACCTTTTCAAGATGAAG
* * * *
9796819 TTTGAAGTTGTTGAGCCTCTACTTAGA-GAAGCTTTTTCAAGATGAAA
1 TTTAAAGTTGTTGAGCCTCTGCTTAGAGGAA-CCTTTTCAAGATGAAG
* * * * *
9796866 TTTAAAGTTTTTGAGCCTCTGTTTAGAGGAGCTTTTTCAAGATGAGATT
1 TTTAAAGTTGTTGAGCCTCTGCTTAGAGGAACCTTTTCAAGATGA-A-G
* * * *
9796915 TTTAAAGTTGTTTA-CCTCTGTTTAGAAGAGCCTTTTCAAGATGAAG
1 TTTAAAGTTGTTGAGCCTCTGCTTAGAGGAACCTTTTCAAGATGAAG
** * * *
9796961 TTTAAAGTTGTTGAGCCTCTATTTAGATG-AGCTTTTACAAGATGAGATT
1 TTTAAAGTTGTTGAGCCTCTGCTTAGAGGAACCTTTT-CAAGATGA-A-G
* * * *
9797010 TTTAAAATTGTTGAGCTTCTGCTTAGAGGAACCTTTT-TA-A--AAT
1 TTTAAAGTTGTTGAGCCTCTGCTTAGAGGAACCTTTTCAAGATGAAG
* *
9797053 TTTAAAAGTTATTGAGCCTCTGCTTAAAGGA
1 TTT-AAAGTTGTTGAGCCTCTGCTTAGAGGA
9797084 GCCTATTTAA
Statistics
Matches: 302, Mismatches: 47, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
43 4 0.01
44 24 0.08
45 1 0.00
46 21 0.07
47 177 0.59
48 33 0.11
49 36 0.12
50 6 0.02
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (47 bp):
TTTAAAGTTGTTGAGCCTCTGCTTAGAGGAACCTTTTCAAGATGAAG
Found at i:9796839 original size:94 final size:96
Alignment explanation
Indices: 9796678--9797046 Score: 453
Period size: 94 Copynumber: 3.9 Consensus size: 96
9796668 CATATCGAAT
* * * *
9796678 TTTAAAGTTGTTGAGCCTTTGCTTAGAGGAAAC-TTTTCAAGATTA-A-GTTTAAAGTTGTTAAG
1 TTTAAAGTTGTTGAGCCTCTGTTTAGAGG-AACTTTTTCAAGATGAGATGTTTAAAGTTGTTGAG
*
9796740 CCTCTACTTAGAGGAGCCTTTTCAAGATAAAA
65 CCTCTACTTAGAGGAGCCTTTTCAAGATGAAA
* *
9796772 TTTAAAGTTGTTGAGCCTCTGTTTAGAGGAACTTTTTCAAGATTA-A-GTTTGAAGTTGTTGAGC
1 TTTAAAGTTGTTGAGCCTCTGTTTAGAGGAACTTTTTCAAGATGAGATGTTTAAAGTTGTTGAGC
* *
9796835 CTCTACTTAGAGAAGCTTTTTCAAGATGAAA
66 CTCTACTTAGAGGAGCCTTTTCAAGATGAAA
* * * *
9796866 TTTAAAGTTTTTGAGCCTCTGTTTAGAGGAGCTTTTTCAAGATGAGATTTTTAAAGTTGTTTA-C
1 TTTAAAGTTGTTGAGCCTCTGTTTAGAGGAACTTTTTCAAGATGAGATGTTTAAAGTTGTTGAGC
** * *
9796930 CTCTGTTTAGAAGAGCCTTTTCAAGATGAAG
66 CTCTACTTAGAGGAGCCTTTTCAAGATGAAA
* * * * * *
9796961 TTTAAAGTTGTTGAGCCTCTATTTAGATGAGCTTTTACAAGATGAGATTTTTAAAATTGTTGAGC
1 TTTAAAGTTGTTGAGCCTCTGTTTAGAGGAACTTTTTCAAGATGAGATGTTTAAAGTTGTTGAGC
* * *
9797026 TTCTGCTTAGAGGAACCTTTT
66 CTCTACTTAGAGGAGCCTTTT
9797047 TAAAATTTTA
Statistics
Matches: 242, Mismatches: 29, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
93 3 0.01
94 125 0.52
95 84 0.35
96 30 0.12
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.39
Consensus pattern (96 bp):
TTTAAAGTTGTTGAGCCTCTGTTTAGAGGAACTTTTTCAAGATGAGATGTTTAAAGTTGTTGAGC
CTCTACTTAGAGGAGCCTTTTCAAGATGAAA
Found at i:9797119 original size:44 final size:43
Alignment explanation
Indices: 9797007--9797146 Score: 160
Period size: 44 Copynumber: 3.2 Consensus size: 43
9796997 ACAAGATGAG
* * *
9797007 ATTTTTAAAA-TTGTTGAGCTTCTGCTTAGAGGAACCTTTTTAA
1 ATTTTTAAAAGTTATTGAGCTTCTGCTTAAAGGAGCC-TTTTAA
* *
9797050 AATTTTAAAAGTTATTGAGCCTCTGCTTAAAGGAGCCTATTTAA
1 ATTTTTAAAAGTTATTGAGCTTCTGCTTAAAGGAGCCT-TTTAA
* *
9797094 ATTTTTAAAAGTTATTG-GACTTCTGCTCAGAA-GAGTCTTTTAA
1 ATTTTTAAAAGTTATTGAG-CTTCTGCTTA-AAGGAGCCTTTTAA
9797137 ATTTTTAAAA
1 ATTTTTAAAA
9797147 ATATTGTTAA
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
43 26 0.31
44 56 0.67
45 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (43 bp):
ATTTTTAAAAGTTATTGAGCTTCTGCTTAAAGGAGCCTTTTAA
Found at i:9797333 original size:4 final size:4
Alignment explanation
Indices: 9797314--9797363 Score: 55
Period size: 4 Copynumber: 11.8 Consensus size: 4
9797304 TATTATATAT
* *
9797314 TTTA TTATA TTTTA TTTA TTTA TTTA TTTA TTTT TCTTT TTTA TTTA TTT
1 TTTA TT-TA -TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTT
9797364 TTCTTATCCG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 31 0.76
5 8 0.20
6 2 0.05
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:9797347 original size:21 final size:21
Alignment explanation
Indices: 9797314--9797363 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
9797304 TATTATATAT
9797314 TTTATTATATTTTAT-TTATTTA
1 TTTATT-TATTTT-TCTTATTTA
*
9797336 TTTATTTATTTTTCTTTTTTA
1 TTTATTTATTTTTCTTATTTA
9797357 TTTATTT
1 TTTATTT
9797364 TTCTTATCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.73
22 6 0.23
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATTTATTTTTCTTATTTA
Found at i:9797364 original size:17 final size:17
Alignment explanation
Indices: 9797336--9797368 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9797326 TATTTATTTA
9797336 TTTATTTATTTTTCTTT
1 TTTATTTATTTTTCTTT
9797353 TTTATTTATTTTTCTT
1 TTTATTTATTTTTCTT
9797369 ATCCGATTCA
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):
TTTATTTATTTTTCTTT
Found at i:9799116 original size:10 final size:10
Alignment explanation
Indices: 9799101--9799126 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9799091 AAAATTATCT
9799101 TTTTAATAAA
1 TTTTAATAAA
9799111 TTTTAATAAA
1 TTTTAATAAA
9799121 TTTTAA
1 TTTTAA
9799127 GATTTCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:9801239 original size:20 final size:20
Alignment explanation
Indices: 9801214--9801252 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9801204 TTTGATTGAG
9801214 GAAAGACTCAA-AAGAAGATT
1 GAAAGA-TCAAGAAGAAGATT
*
9801234 GAAAGATTAAGAAGAAGAT
1 GAAAGATCAAGAAGAAGAT
9801253 CTAAGTCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAGATCAAGAAGAAGATT
Found at i:9807274 original size:2 final size:2
Alignment explanation
Indices: 9807267--9807300 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
9807257 ACAAATTCGA
*
9807267 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9807301 CAGGTGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:9807611 original size:7 final size:7
Alignment explanation
Indices: 9807599--9807677 Score: 76
Period size: 7 Copynumber: 11.1 Consensus size: 7
9807589 CCTTCATATC
9807599 TTAAATT
1 TTAAATT
9807606 TTAAATT
1 TTAAATT
9807613 TTAAATT
1 TTAAATT
*
9807620 TTAAATC
1 TTAAATT
9807627 TTAAATT
1 TTAAATT
9807634 TT--ATT
1 TTAAATT
9807639 TT--ATT
1 TTAAATT
9807644 TTAAATCTT
1 TTAAA--TT
9807653 ATTAAAATT
1 -TT-AAATT
9807662 TTAAATCT
1 TTAAAT-T
9807670 TTAAATT
1 TTAAATT
9807677 T
1 T
9807678 GATGATCTGT
Statistics
Matches: 63, Mismatches: 2, Indels: 14
0.80 0.03 0.18
Matches are distributed among these distances:
5 10 0.16
7 35 0.56
8 9 0.14
9 4 0.06
10 2 0.03
11 3 0.05
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (7 bp):
TTAAATT
Found at i:9807627 original size:28 final size:28
Alignment explanation
Indices: 9807596--9807675 Score: 93
Period size: 24 Copynumber: 3.1 Consensus size: 28
9807586 GTACCTTCAT
9807596 ATCTTAAATTTTAAATTTTAAATTTTAA
1 ATCTTAAATTTTAAATTTTAAATTTTAA
9807624 ATCTTAAATTTT--ATTTT--ATTTTAA
1 ATCTTAAATTTTAAATTTTAAATTTTAA
*
9807648 ATCTT--A-TTAAAATTTTAAATCTTTAA
1 ATCTTAAATTTTAAATTTTAAAT-TTTAA
9807674 AT
1 AT
9807676 TTGATGATCT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
21 2 0.04
22 1 0.02
23 5 0.11
24 12 0.26
25 2 0.04
26 12 0.26
28 12 0.26
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (28 bp):
ATCTTAAATTTTAAATTTTAAATTTTAA
Found at i:9808190 original size:13 final size:15
Alignment explanation
Indices: 9808174--9808205 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
9808164 AATTTATATG
9808174 AAAATTT-TAAAA-T
1 AAAATTTATAAAATT
9808187 AAAATTTATAAAATT
1 AAAATTTATAAAATT
9808202 AAAA
1 AAAA
9808206 AAAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAATTTATAAAATT
Found at i:9808381 original size:13 final size:12
Alignment explanation
Indices: 9808344--9808425 Score: 62
Period size: 12 Copynumber: 6.9 Consensus size: 12
9808334 TATTAAATAA
9808344 TAAAAATTTTAT
1 TAAAAATTTTAT
* *
9808356 TAATATTTTTAT
1 TAAAAATTTTAT
9808368 TAAAAATGTTTAT
1 TAAAAAT-TTTAT
* * *
9808381 TTAAAACTATAT
1 TAAAAATTTTAT
*
9808393 ATCAAAA-TTTAT
1 -TAAAAATTTTAT
*
9808405 T--AAATTTTTT
1 TAAAAATTTTAT
9808415 TAAAAATTTTA
1 TAAAAATTTTA
9808426 CATAATTTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
9 3 0.06
10 5 0.09
11 1 0.02
12 30 0.56
13 15 0.28
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (12 bp):
TAAAAATTTTAT
Found at i:9808446 original size:45 final size:48
Alignment explanation
Indices: 9808346--9808456 Score: 122
Period size: 45 Copynumber: 2.4 Consensus size: 48
9808336 TTAAATAATA
** *
9808346 AAAATTTTATTAATATTTTTATTAAAAATGTTTATTTAAAACTATATATC
1 AAAA-TTTATTAA-ATTTTTATTAAAAATGTTTACATAAAACTATATAAC
**
9808396 AAAATTTATTAAATTTTT-TTAAAAAT-TTTACAT-AATTTATATAAC
1 AAAATTTATTAAATTTTTATTAAAAATGTTTACATAAAACTATATAAC
*
9808441 AAAATTT-TTTAATTTT
1 AAAATTTATTAAATTTT
9808457 AATTTTAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
44 8 0.15
45 16 0.29
46 5 0.09
47 8 0.15
48 6 0.11
49 8 0.15
50 4 0.07
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (48 bp):
AAAATTTATTAAATTTTTATTAAAAATGTTTACATAAAACTATATAAC
Found at i:9808969 original size:15 final size:16
Alignment explanation
Indices: 9808943--9808975 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
9808933 TCTTGATGAG
*
9808943 ATTTTGTTATAATAAA
1 ATTTTGTTATAACAAA
9808959 ATTTT-TTATAACAAA
1 ATTTTGTTATAACAAA
9808974 AT
1 AT
9808976 GGTGAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
ATTTTGTTATAACAAA
Found at i:9809933 original size:24 final size:23
Alignment explanation
Indices: 9809888--9809937 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
9809878 TAGAAAATGC
* * *
9809888 TTTAAATAATTATTTTATATATAT
1 TTTAAAAAATTATTTAAGATAT-T
9809912 TTTAAAAAATTATTTAAGATATT
1 TTTAAAAAATTATTTAAGATATT
9809935 TTT
1 TTT
9809938 CAACAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTAAAAAATTATTTAAGATATT
Found at i:9809937 original size:62 final size:61
Alignment explanation
Indices: 9809789--9809947 Score: 151
Period size: 62 Copynumber: 2.5 Consensus size: 61
9809779 TATTTTTTGT
* *
9809789 AAGAGAATTATTTAAGATATTTTCTAATAAAAAACGTTTTAAATAATCTTATGATATTTTTTA
1 AAGA-AATTATTTAAGATATTTT-TAATAAAAAACGCTTTAAATAATCTTATGATATATTTTA
** * * * * *
9809852 AAGAAGATTATTTGTGATGTTTTTATTAGAAAATGCTTTAAATAATTATTTTAT-ATATATTTTA
1 AAGAA-ATTATTTAAGATATTTTTAATAAAAAACGCTTTAAAT-A--ATCTTATGATATATTTTA
*
9809916 AA-AAATTATTTAAGATATTTTTCAACAAAAAA
1 AAGAAATTATTTAAGATATTTTT-AATAAAAAA
9809948 TACCTTAAAT
Statistics
Matches: 76, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
62 32 0.42
63 27 0.36
64 11 0.14
65 6 0.08
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (61 bp):
AAGAAATTATTTAAGATATTTTTAATAAAAAACGCTTTAAATAATCTTATGATATATTTTA
Found at i:9811416 original size:19 final size:19
Alignment explanation
Indices: 9811392--9811428 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
9811382 TATCTAAACC
*
9811392 AATATTCATTTGGCAAATT
1 AATATTCAATTGGCAAATT
9811411 AATATTCAATTGGCAAAT
1 AATATTCAATTGGCAAAT
9811429 GTGAACTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (19 bp):
AATATTCAATTGGCAAATT
Found at i:9818650 original size:40 final size:40
Alignment explanation
Indices: 9818593--9818681 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
9818583 TTCAGTAAAT
* *
9818593 CATTCAGTATACGATTCAGCCTCCC-AATATCATACAAAAC
1 CATTCAGCATACAATTCAGCC-CCCTAATATCATACAAAAC
*
9818633 CATTCAGCATACAATTCAGCCCCCTTATATCATACAAAAC
1 CATTCAGCATACAATTCAGCCCCCTAATATCATACAAAAC
*
9818673 TATTCAGCA
1 CATTCAGCA
9818682 AAATAATATC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 3 0.07
40 41 0.93
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.26
Consensus pattern (40 bp):
CATTCAGCATACAATTCAGCCCCCTAATATCATACAAAAC
Found at i:9818730 original size:80 final size:80
Alignment explanation
Indices: 9818629--9818874 Score: 287
Period size: 80 Copynumber: 3.1 Consensus size: 80
9818619 ATATCATACA
** * * *
9818629 AAACCATTCAGCATACAATTCAGCCCCCTTATATCATACAAAACTATTCAGCAAAATAATATCAG
1 AAACCATTCAGCATATGATTCAGCCCCCTAATATCATACAATACCATTCAGCAAAATAATATCAG
* * *
9818694 ACAATAAGGTTTAAC
66 ACAACAAGATTCAAC
* * * *
9818709 AAACCATTAAGCATATGATTCAGTCCCCTAATATCATACAATACCA-TCCGACAATATAATATCA
1 AAACCATTCAGCATATGATTCAGCCCCCTAATATCATACAATACCATTCAG-CAAAATAATATCA
* *
9818773 GATAACAAGATTCAGC
65 GACAACAAGATTCAAC
* * *
9818789 AAACCATTCACCATATGATTCAGCCCCCCAATATCATACAATACCATTCAGTAAAATAATATCAG
1 AAACCATTCAGCATATGATTCAGCCCCCTAATATCATACAATACCATTCAGCAAAATAATATCAG
* * * *
9818854 ATAACCAGGTTCAGC
66 ACAACAAGATTCAAC
9818869 AAACCA
1 AAACCA
9818875 CAATATTTAA
Statistics
Matches: 141, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
79 3 0.02
80 135 0.96
81 3 0.02
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.24
Consensus pattern (80 bp):
AAACCATTCAGCATATGATTCAGCCCCCTAATATCATACAATACCATTCAGCAAAATAATATCAG
ACAACAAGATTCAAC
Found at i:9820512 original size:62 final size:60
Alignment explanation
Indices: 9820323--9820523 Score: 163
Period size: 62 Copynumber: 3.2 Consensus size: 60
9820313 TCTGGTAGTA
* * * * * *
9820323 TATTGAAGGCATTTTACAATAGAAGAAGCTTTTAATAATCTCAACATATTTTAAAAAAAAAT
1 TATTGAAGGTATTTTTC-ATAGAAGACGCCTTTAATAATTTCAAAATATTTT-AAAAAAAAT
* * ** ** * *
9820385 TATTAAAGGTATTTATTACCA-AGAA-ACGCCTTCAATTTTTATGTAAATAATTTAAAAAAATT
1 TATTGAAGGTATTT-TT--CATAGAAGACGCCTTTAATAATT-TCAAAATATTTTAAAAAAAAT
* *
9820447 TATTGAAGGTATTTTTCAGTAGAAGACGCCTTTAATAATTTCAAAATTTTTTAGAGAAAAAT
1 TATTGAAGGTATTTTTCA-TAGAAGACGCCTTTAATAATTTCAAAATATTTTA-AAAAAAAT
*
9820509 TATTGAAGGTGTTTT
1 TATTGAAGGTATTTT
9820524 GTTATTAACA
Statistics
Matches: 106, Mismatches: 25, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
59 2 0.02
61 15 0.14
62 74 0.70
63 13 0.12
64 1 0.01
65 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.38
Consensus pattern (60 bp):
TATTGAAGGTATTTTTCATAGAAGACGCCTTTAATAATTTCAAAATATTTTAAAAAAAAT
Found at i:9820525 original size:606 final size:608
Alignment explanation
Indices: 9819339--9820558 Score: 2011
Period size: 606 Copynumber: 2.0 Consensus size: 608
9819329 AAATAATTTT
*
9819339 CTAACAAATTTATTAAAGGTGTTTATCATAAAAAAAAAATACCTTTGATAATTCTTAAAAATTAT
1 CTAACAAATTTATTAAAGGCGTTTATCAT--AAAAAAAATACCTTTGATAATTCTTAAAAATTAT
9819404 AAAAAATATTTTAAGTAGAAAATCACCTTCACTAATATCCCCGTGATAAAGGTGGAGGGAATTAT
64 AAAAAATATTTTAAGTAGAAAATCACCTTCACTAATATCCCCGTGATAAAGGTGGAGGGAATTAT
* *
9819469 TGATGGCGTATTATGTAGAAAATGCCTTCAATAATTATGGACTTCAAAAGTTTAGAACAAATTAT
129 TGATGGCGTATTATGTAAAAAATGCCTTCAATAATTATGAACTTCAAAAGTTTAGAACAAATTAT
* *
9819534 TAAATGCATTTTATAATAAAATGTGCCTTTGATAAACCCAAAAATTTTATAAAAGAAATTATTGA
194 TAAATGCATTTTATAATAAAAAGTGCCTTTGATAAACCCAAAAATTTTATAAAAGAAATTATTCA
9819599 AGGAATTGTTATTTGCAAACGCCTTCACTAATTATGTACAAAATTTAAAAAGAATTATTAAAGGC
259 AGGAATTGTTATTTGCAAACGCCTTCACTAATTATGTACAAAATTTAAAAAGAATTATTAAAGGC
* * *
9819664 ATTTTTCTTGAATATATACCTTCAATGAGTCTGAGTAAAATTTTTCTGGCAGTATATTGAAGGCG
324 ATTTTTCTTGAATATATACCTTCAATGAATCTGAGTAAAATTTGTCTGGCAGTATATTGAAGGCA
*
9819729 TTTTACAATAGAAGATGCCTTTAATAATCCCAACAAATTTAAAAAAAAAATTATTGAAACGTTTA
389 TTTTACAATAGAAGAAGCCTTTAATAATCCCAACAAATTTAAAAAAAAAATTATTGAAACGTTTA
* * *
9819794 TTATAAAAAAACACCTTCAATTTTTATGTAGATAATTTTAAAAAAATTATTGAAGGCGTTTGTCA
454 TTACAAAAAAACACCTTCAATTTTTATGTAAATAATTTTAAAAAAATTATTGAAGGCATTTGTCA
*
9819859 GTAGAAGATGCCTTTAATAATTCCAAAATTTTTTAGAAAAAAATTATTGAAGGTGTTTTGTTATT
519 GTAGAAGACGCCTTTAATAATTCCAAAATTTTTTAGAAAAAAATTATTGAAGGTGTTTTGTTATT
9819924 AACAAACGCCTTTAGTAATTATGTA
584 AACAAACGCCTTTAGTAATTATGTA
* *
9819949 CTAACAAATTTATTAAAGGCGTTTATCAT-CAAAAAATGCCTTTGATAATTCTTAAAAATTATAA
1 CTAACAAATTTATTAAAGGCGTTTATCATAAAAAAAATACCTTTGATAATTCTTAAAAATTATAA
*
9820013 AAAATATTTTGAGTAGAAAATCACCTTCACTAATAT-CCCGTGATAAAGGTGGAGGGAATTATTG
66 AAAATATTTTAAGTAGAAAATCACCTTCACTAATATCCCCGTGATAAAGGTGGAGGGAATTATTG
* *
9820077 ATGGCTTATTATGTAAAAAATGCCTTTAATAATTATGAACTTCAAAAGTTTAGAACAAATTATTA
131 ATGGCGTATTATGTAAAAAATGCCTTCAATAATTATGAACTTCAAAAGTTTAGAACAAATTATTA
*
9820142 AATGCATTTTATAATAAAAAGTGCC-TTGATATACCCAAAAATTTTATAAAAGAAATTATTCAAG
196 AATGCATTTTATAATAAAAAGTGCCTTTGATAAACCCAAAAATTTTATAAAAGAAATTATTCAAG
** * *
9820206 GCGTTGTTATTTGCAAACGCCTTCATTAATTATGTACAAAATTT-AAAAGAAATTATTAAAGGTA
261 GAATTGTTATTTGCAAACGCCTTCACTAATTATGTACAAAATTTAAAAAG-AATTATTAAAGGCA
* *
9820270 TTTTTCTTGAATATATGCCTTCAATGAATCTGAGTAAAATTTGTCTGGTAGTATATTGAAGGCAT
325 TTTTTCTTGAATATATACCTTCAATGAATCTGAGTAAAATTTGTCTGGCAGTATATTGAAGGCAT
* * * * *
9820335 TTTACAATAGAAGAAGCTTTTAATAATCTCAACATATTTTAAAAAAAAATTATT-AAAGGTATTT
390 TTTACAATAGAAGAAGCCTTTAATAATCCCAACAAATTTAAAAAAAAAATTATTGAAACG--TTT
* * * * *
9820399 ATTACCAAGAAACGCCTTCAATTTTTATGTAAATAA-TTTAAAAAAATTTATTGAAGGTATTTTT
453 ATTACAAAAAAACACCTTCAATTTTTATGTAAATAATTTTAAAAAAA-TTATTGAAGGCATTTGT
* *
9820463 CAGTAGAAGACGCCTTTAATAATTTCAAAATTTTTTAGAGAAAAATTATTGAAGGTGTTTTGTTA
517 CAGTAGAAGACGCCTTTAATAATTCCAAAATTTTTTAGAAAAAAATTATTGAAGGTGTTTTGTTA
9820528 TTAACAAACGCCTTTAGTAATTATGTA
582 TTAACAAACGCCTTTAGTAATTATGTA
9820555 CTAA
1 CTAA
9820559 ATTTCAAGGA
Statistics
Matches: 569, Mismatches: 37, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
604 9 0.02
605 210 0.37
606 254 0.45
607 68 0.12
610 28 0.05
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.36
Consensus pattern (608 bp):
CTAACAAATTTATTAAAGGCGTTTATCATAAAAAAAATACCTTTGATAATTCTTAAAAATTATAA
AAAATATTTTAAGTAGAAAATCACCTTCACTAATATCCCCGTGATAAAGGTGGAGGGAATTATTG
ATGGCGTATTATGTAAAAAATGCCTTCAATAATTATGAACTTCAAAAGTTTAGAACAAATTATTA
AATGCATTTTATAATAAAAAGTGCCTTTGATAAACCCAAAAATTTTATAAAAGAAATTATTCAAG
GAATTGTTATTTGCAAACGCCTTCACTAATTATGTACAAAATTTAAAAAGAATTATTAAAGGCAT
TTTTCTTGAATATATACCTTCAATGAATCTGAGTAAAATTTGTCTGGCAGTATATTGAAGGCATT
TTACAATAGAAGAAGCCTTTAATAATCCCAACAAATTTAAAAAAAAAATTATTGAAACGTTTATT
ACAAAAAAACACCTTCAATTTTTATGTAAATAATTTTAAAAAAATTATTGAAGGCATTTGTCAGT
AGAAGACGCCTTTAATAATTCCAAAATTTTTTAGAAAAAAATTATTGAAGGTGTTTTGTTATTAA
CAAACGCCTTTAGTAATTATGTA
Found at i:9827225 original size:99 final size:100
Alignment explanation
Indices: 9827100--9827279 Score: 227
Period size: 99 Copynumber: 1.8 Consensus size: 100
9827090 ATAAAAATAT
** * ** ** *
9827100 CACTAAATTAGTGACGTCTCAAAGATACAAATGCCGCTAATATAGAGGTATTTTTAGTTACAAAC
1 CACTAAATTAACGACATCTCAAAGATACAAACACCGCTAATATAGAGACATTTTCAGTTACAAAC
*
9827165 GCCAC-TAAAGCAACGATATTTTTCTTATAGACAC
66 GCCACAAAAAGCAACGATATTTTTCTTATAGACAC
* ** *
9827199 CACTAAATTAACGACATCTCAAAGATATAAACATTGCTAATATAGAGACGTTTTCAGTTACAAAC
1 CACTAAATTAACGACATCTCAAAGATACAAACACCGCTAATATAGAGACATTTTCAGTTACAAAC
*
9827264 GTCACAAAAAGCAACG
66 GCCACAAAAAGCAACG
9827280 GCGTTTCAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
99 57 0.86
100 9 0.14
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (100 bp):
CACTAAATTAACGACATCTCAAAGATACAAACACCGCTAATATAGAGACATTTTCAGTTACAAAC
GCCACAAAAAGCAACGATATTTTTCTTATAGACAC
Found at i:9844096 original size:21 final size:22
Alignment explanation
Indices: 9844058--9844109 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
9844048 TCCGAAATTA
9844058 ATAAAATATTATTTTTTTAAAT
1 ATAAAATATTATTTTTTTAAAT
9844080 ATAAAATATTA-TTTTTTAAAT
1 ATAAAATATTATTTTTTTAAAT
9844101 AT-AAATATT
1 ATAAAATATT
9844110 TAAAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 12 0.40
22 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAAAATATTATTTTTTTAAAT
Found at i:9844693 original size:23 final size:23
Alignment explanation
Indices: 9844666--9844718 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
9844656 TAATTTATAC
*
9844666 AATTATTTTAAGATATGATATTT
1 AATTATTTTAAGATATAATATTT
* * *
9844689 AATTAATTTAATATTTAATATTT
1 AATTATTTTAAGATATAATATTT
9844712 AA-TATTT
1 AATTATTT
9844719 AATATTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
AATTATTTTAAGATATAATATTT
Found at i:9844706 original size:7 final size:7
Alignment explanation
Indices: 9844683--9844725 Score: 68
Period size: 7 Copynumber: 5.9 Consensus size: 7
9844673 TTAAGATATG
9844683 ATATTTA
1 ATATTTA
9844690 ATTAATTTA
1 A-T-ATTTA
9844699 ATATTTA
1 ATATTTA
9844706 ATATTTA
1 ATATTTA
9844713 ATATTTA
1 ATATTTA
9844720 ATATTT
1 ATATTT
9844726 TTTATTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 26 0.76
8 2 0.06
9 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATATTTA
Found at i:9847499 original size:2 final size:2
Alignment explanation
Indices: 9847492--9847526 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9847482 AAAATTACAG
9847492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9847527 CAACACTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9848552 original size:14 final size:14
Alignment explanation
Indices: 9848517--9848544 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9848507 ATACCATGTC
9848517 TATCATAAGTGATG
1 TATCATAAGTGATG
9848531 TATCATAAGTGATG
1 TATCATAAGTGATG
9848545 ATAGATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
TATCATAAGTGATG
Found at i:9851707 original size:2 final size:2
Alignment explanation
Indices: 9851696--9851728 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
9851686 TGACGTAAGC
*
9851696 AT AT -T AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9851729 GAGTCTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:9854318 original size:29 final size:28
Alignment explanation
Indices: 9854268--9854323 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
9854258 TCAAATGTCT
*
9854268 ATATATGTTGTAAATTTGTAATATAATA
1 ATATATGTTGTAAATTTATAATATAATA
*
9854296 ATATATG-TGATATAATTTATAATTTAAT
1 ATATATGTTG-TA-AATTTATAATATAAT
9854324 TTTGATACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 9 0.38
29 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (28 bp):
ATATATGTTGTAAATTTATAATATAATA
Found at i:9861602 original size:22 final size:22
Alignment explanation
Indices: 9861563--9861611 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
9861553 GTTTGTCTTA
9861563 TTTATTTATTTATGTTT-AATCT
1 TTTATTTATTTATGTTTAAAT-T
*
9861585 TTTATTTATTT-GGTTTTAAATT
1 TTTATTTATTTATG-TTTAAATT
9861607 TTTAT
1 TTTAT
9861612 CATAAATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 1 0.04
22 20 0.83
23 3 0.12
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.69
Consensus pattern (22 bp):
TTTATTTATTTATGTTTAAATT
Found at i:9870762 original size:17 final size:17
Alignment explanation
Indices: 9870740--9870773 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
9870730 GAACGATATT
9870740 AACATGAAGTGCCATTA
1 AACATGAAGTGCCATTA
9870757 AACATGAAGTGCCATTA
1 AACATGAAGTGCCATTA
9870774 GGATAAATTC
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:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (17 bp):
AACATGAAGTGCCATTA
Found at i:9876688 original size:2 final size:2
Alignment explanation
Indices: 9876681--9876705 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9876671 AATCCGATAA
9876681 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
9876706 GCCTGGAAAA
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:9877588 original size:29 final size:28
Alignment explanation
Indices: 9877556--9877610 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
9877546 TTTAAAAATC
*
9877556 TTTTTAAAATGATCACTTAAATATTAATT
1 TTTTTAAAATAATCACTTAAAT-TTAATT
**
9877585 TTTTTAATTTAATCACTTAAATTTAA
1 TTTTTAAAATAATCACTTAAATTTAA
9877611 ATAAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTTTAAAATAATCACTTAAATTTAATT
Done.