Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 121 of 163
Found at i:33419448 original size:13 final size:13
Alignment explanation
Indices: 33419417--33419469 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
33419407 TTTCTTTATT
*
33419417 TTATTT-TTATTA
1 TTATTTATTAATA
* *
33419429 ATATTTATTAATG
1 TTATTTATTAATA
*
33419442 TTATTTATTACTA
1 TTATTTATTAATA
*
33419455 TTATTTATTATTA
1 TTATTTATTAATA
33419468 TT
1 TT
33419470 GTTGTTATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
12 5 0.15
13 28 0.85
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (13 bp):
TTATTTATTAATA
Found at i:33419465 original size:3 final size:3
Alignment explanation
Indices: 33419412--33419485 Score: 51
Period size: 3 Copynumber: 24.0 Consensus size: 3
33419402 CTCACTTTCT
* * * * *
33419412 TTA TT- TTA TTT TTA TTA ATA TTTA TTA ATG TTA TTTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA
* *
33419458 TTTA TTA TTA TTG TTG TTA TTA TTA TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA
33419486 ATTGTTTTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
2 2 0.04
3 45 0.82
4 8 0.15
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:33420143 original size:17 final size:18
Alignment explanation
Indices: 33420121--33420160 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
33420111 AAATTTATAC
33420121 TTAAATTTATA-ATAAAT
1 TTAAATTTATACATAAAT
*
33420138 TTAAATTTATACTTAAAT
1 TTAAATTTATACATAAAT
33420156 TTAAA
1 TTAAA
33420161 ATAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATTTATACATAAAT
Found at i:33420143 original size:29 final size:29
Alignment explanation
Indices: 33420110--33420170 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
33420100 TTAATTTAAA
*
33420110 TAAATTTATACTTAAATTTATAATAAATT
1 TAAATTTATACTTAAATTTAAAATAAATT
33420139 TAAATTTATACTTAAATTTAAAATAAATT
1 TAAATTTATACTTAAATTTAAAATAAATT
33420168 TAA
1 TAA
33420171 CTTTTGTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAATTTATACTTAAATTTAAAATAAATT
Found at i:33420158 original size:12 final size:11
Alignment explanation
Indices: 33420102--33420140 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
33420092 TAGACTTTTT
33420102 AATTTA-AATA
1 AATTTATAATA
*
33420112 AATTTATACTTA
1 AATTTATA-ATA
33420124 AATTTATAATA
1 AATTTATAATA
33420135 AATTTA
1 AATTTA
33420141 AATTTATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 6 0.24
11 9 0.36
12 10 0.40
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTTATAATA
Found at i:33420165 original size:23 final size:23
Alignment explanation
Indices: 33420102--33420173 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 23
33420092 TAGACTTTTT
33420102 AATTT-AAATAAATTTATACTTA
1 AATTTAAAATAAATTTATACTTA
33420124 AATTTATAATAAATTTAAATTTATACTTA
1 AA-TT-T-A-AAA--TAAATTTATACTTA
33420153 AATTTAAAATAAATTTA-ACTT
1 AATTTAAAATAAATTTATACTT
33420174 TTGTTAGGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
22 6 0.14
23 10 0.23
24 1 0.02
25 3 0.07
26 1 0.02
27 4 0.09
28 2 0.05
29 16 0.37
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTTAAAATAAATTTATACTTA
Found at i:33420307 original size:2 final size:2
Alignment explanation
Indices: 33420300--33420324 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33420290 CCTTGTAATA
33420300 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
33420325 ATTAGATTTC
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:33423044 original size:14 final size:15
Alignment explanation
Indices: 33423019--33423047 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
33423009 ATTTTTTTTG
33423019 CTTTTCGTCTTGTTT
1 CTTTTCGTCTTGTTT
33423034 CTTTT-GTCTTGTTT
1 CTTTTCGTCTTGTTT
33423048 TCTTCTGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.17, G:0.14, T:0.69
Consensus pattern (15 bp):
CTTTTCGTCTTGTTT
Found at i:33423049 original size:15 final size:16
Alignment explanation
Indices: 33423014--33423051 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
33423004 TGTTTATTTT
33423014 TTTTGCTTTTCGTCTTG
1 TTTT-CTTTTCGTCTTG
33423031 -TTTCTTTT-GTCTTG
1 TTTTCTTTTCGTCTTG
33423045 TTTTCTT
1 TTTTCTT
33423052 CTGTTCTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
15 11 0.55
16 3 0.15
ACGTcount: A:0.00, C:0.16, G:0.13, T:0.71
Consensus pattern (16 bp):
TTTTCTTTTCGTCTTG
Found at i:33423285 original size:26 final size:26
Alignment explanation
Indices: 33423238--33423287 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
33423228 GGCTTGGGTG
**
33423238 TGTAATTGGACATTGATTTTTTTTTT
1 TGTAATTGGACATTGACCTTTTTTTT
33423264 TGTAATTGGAC-TTGGACCTTTTTT
1 TGTAATTGGACATT-GACCTTTTTT
33423288 ATGAAATGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.56
Consensus pattern (26 bp):
TGTAATTGGACATTGACCTTTTTTTT
Found at i:33423328 original size:16 final size:17
Alignment explanation
Indices: 33423297--33423337 Score: 66
Period size: 16 Copynumber: 2.4 Consensus size: 17
33423287 TATGAAATGG
33423297 ATTTTTATTTTGTGTTTT
1 ATTTTT-TTTTGTGTTTT
33423315 ATTTTTTTTT-TGTTTT
1 ATTTTTTTTTGTGTTTT
33423331 ATTTTTT
1 ATTTTTT
33423338 CACGGACCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 13 0.57
17 4 0.17
18 6 0.26
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (17 bp):
ATTTTTTTTTGTGTTTT
Found at i:33424042 original size:28 final size:30
Alignment explanation
Indices: 33424022--33424077 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
33424012 ATTTTATCAT
33424022 AATGAAAATAAAAA-A-TAAATTCATTTATA
1 AATGAAAATAAAAATATTAAATT-ATTTATA
33424051 AATGAAAATAAAAATATTAAATTATTT
1 AATGAAAATAAAAATATTAAATTATTT
33424078 CTCGAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
29 14 0.56
30 5 0.20
31 6 0.24
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (30 bp):
AATGAAAATAAAAATATTAAATTATTTATA
Found at i:33424462 original size:13 final size:12
Alignment explanation
Indices: 33424424--33424463 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
33424414 TTTCTACTTA
33424424 AAAATAAATAA-
1 AAAATAAATAAT
*
33424435 AAAATAAATACT
1 AAAATAAATAAT
33424447 AAAATAACATAAT
1 AAAATAA-ATAAT
33424460 AAAA
1 AAAA
33424464 CAACAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 7 0.28
13 8 0.32
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:33428182 original size:16 final size:14
Alignment explanation
Indices: 33428139--33428187 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
33428129 TTGTTTCAAT
**
33428139 GAAAATGATTTCCG
1 GAAAATGATTTTTG
33428153 GAAAATGATTTTTG
1 GAAAATGATTTTTG
33428167 GAAAATGACTTTTTTG
1 GAAAATGA--TTTTTG
33428183 GAAAA
1 GAAAA
33428188 GCTAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 20 0.65
16 11 0.35
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (14 bp):
GAAAATGATTTTTG
Found at i:33428397 original size:21 final size:20
Alignment explanation
Indices: 33428355--33428414 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
33428345 AGCTTATTTA
* **
33428355 TATTTTAATTAATCATGTTT
1 TATTTTAATTAATCTTAATT
33428375 TAGTTTTAATTAATCTTAATT
1 TA-TTTTAATTAATCTTAATT
* *
33428396 TA-CTTAATTAAGCTTAATT
1 TATTTTAATTAATCTTAATT
33428415 GTTAATTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 15 0.44
20 2 0.06
21 17 0.50
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
TATTTTAATTAATCTTAATT
Found at i:33429183 original size:24 final size:25
Alignment explanation
Indices: 33429155--33429204 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
33429145 TTTTTCCCTC
*
33429155 TTTTTGGAGAAGG-TTTCTTTTTGT
1 TTTTTGGAGAAGGATTTCTTTCTGT
33429179 TTTTTGGAGAAGGATTTCTTTCTGT
1 TTTTTGGAGAAGGATTTCTTTCTGT
33429204 T
1 T
33429205 ATTCATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.14, C:0.06, G:0.24, T:0.56
Consensus pattern (25 bp):
TTTTTGGAGAAGGATTTCTTTCTGT
Found at i:33435076 original size:33 final size:33
Alignment explanation
Indices: 33435013--33435105 Score: 114
Period size: 34 Copynumber: 2.8 Consensus size: 33
33435003 GCCCTAAATT
* * * *
33435013 ACTAAAATCCAAAACTCACTTAACCTTAACCCAA
1 ACTAAAA-CCCAAACCCATTTAACCCTAACCCAA
*
33435047 ACTAAAACCCAAACCCATTTAACCCTAACCTAA
1 ACTAAAACCCAAACCCATTTAACCCTAACCCAA
*
33435080 ACTAAAAACCCAAACCCTTTTAACCC
1 ACT-AAAACCCAAACCCATTTAACCC
33435106 AAGCCCGAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 24 0.46
34 28 0.54
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.19
Consensus pattern (33 bp):
ACTAAAACCCAAACCCATTTAACCCTAACCCAA
Found at i:33435094 original size:34 final size:34
Alignment explanation
Indices: 33435013--33435105 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 34
33435003 GCCCTAAATT
* * * * *
33435013 ACTAAAATCCAAAACTCACTTAACCTTAACCCAA
1 ACTAAAAACCCAAACCCATTTAACCCTAACCCAA
*
33435047 ACT-AAAACCCAAACCCATTTAACCCTAACCTAA
1 ACTAAAAACCCAAACCCATTTAACCCTAACCCAA
*
33435080 ACTAAAAACCCAAACCCTTTTAACCC
1 ACTAAAAACCCAAACCCATTTAACCC
33435106 AAGCCCGAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 27 0.53
34 24 0.47
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.19
Consensus pattern (34 bp):
ACTAAAAACCCAAACCCATTTAACCCTAACCCAA
Found at i:33435221 original size:23 final size:24
Alignment explanation
Indices: 33435191--33435241 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
33435181 CGTTGACCGA
*
33435191 ATCGAATCGAATCGTTGACT-TTG
1 ATCGAATCGAATAGTTGACTGTTG
33435214 ATCGAATCGAATAGTTGACTGTTG
1 ATCGAATCGAATAGTTGACTGTTG
33435238 ATCG
1 ATCG
33435242 TTGATTGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (24 bp):
ATCGAATCGAATAGTTGACTGTTG
Found at i:33435784 original size:26 final size:26
Alignment explanation
Indices: 33435755--33435806 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
33435745 GATGACACTG
*
33435755 TATTATGATGTTAAT-GTGATGATTGA
1 TATTATGATGTAAATGGT-ATGATTGA
*
33435781 TATTATGTTGTAAATGGTATGATTGA
1 TATTATGATGTAAATGGTATGATTGA
33435807 GTTTGAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (26 bp):
TATTATGATGTAAATGGTATGATTGA
Found at i:33435938 original size:6 final size:6
Alignment explanation
Indices: 33435927--33435966 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
33435917 AGTAATTTCA
* *
33435927 TGAGAT TGAGAT TGAGTT TGAGTT TGAGTT TGAGTT TGAG
1 TGAGTT TGAGTT TGAGTT TGAGTT TGAGTT TGAGTT TGAG
33435967 ATTAATACTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (6 bp):
TGAGTT
Found at i:33436346 original size:13 final size:12
Alignment explanation
Indices: 33436324--33436361 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
33436314 TATTTATATT
33436324 TTCTTTATTTTA
1 TTCTTTATTTTA
33436336 TTCTATTATTTTA
1 TTCT-TTATTTTA
33436349 TT-TTTATATTTA
1 TTCTTTAT-TTTA
33436361 T
1 T
33436362 AAGCTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.17
12 10 0.42
13 10 0.42
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (12 bp):
TTCTTTATTTTA
Found at i:33436497 original size:2 final size:2
Alignment explanation
Indices: 33436490--33436569 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
33436480 ATTATAAACA
33436490 AT AT AT AT AT AT AT 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 AT AT AT AT
33436532 AT AT AT AT AT 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 AT AT
33436570 TTGTGTTTTG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33438863 original size:23 final size:22
Alignment explanation
Indices: 33438821--33438863 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
33438811 AAACTAACTC
*
33438821 GTGTCTAATTTTCACGAACACA
1 GTGTCTAATTTTCACAAACACA
33438843 GTGTCCTAACTTTTCA-AAACA
1 GTGT-CTAA-TTTTCACAAACA
33438864 TGCATCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 8 0.44
24 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (22 bp):
GTGTCTAATTTTCACAAACACA
Found at i:33448909 original size:6 final size:6
Alignment explanation
Indices: 33448895--33448941 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
33448885 GAGAGTTCTC
* * * *
33448895 AAAAGG AAAAAG AAAATG AAAAAC AAGAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
33448942 CAAGAAGATA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:33448927 original size:24 final size:24
Alignment explanation
Indices: 33448900--33448949 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
33448890 TTCTCAAAAG
*
33448900 GAAAAAGAAAATGAAAAACAAGAA
1 GAAAAAGAAAAAGAAAAACAAGAA
33448924 GAAAAAGAAAAAGAAAAACAAGAA
1 GAAAAAGAAAAAGAAAAACAAGAA
33448948 GA
1 GA
33448950 TACCCATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAACAAGAA
Found at i:33448949 original size:12 final size:12
Alignment explanation
Indices: 33448912--33448949 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
33448902 AAAAGAAAAT
33448912 GAAAAACAAGAA
1 GAAAAACAAGAA
* *
33448924 GAAAAAGAAAAA
1 GAAAAACAAGAA
33448936 GAAAAACAAGAA
1 GAAAAACAAGAA
33448948 GA
1 GA
33448950 TACCCATACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.00
Consensus pattern (12 bp):
GAAAAACAAGAA
Found at i:33452712 original size:23 final size:23
Alignment explanation
Indices: 33452663--33452713 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
33452653 TTATTATTAT
* *
33452663 TTTGTAACTCTCCTGCCATTATA
1 TTTGTAACTCTCCAGCCAGTATA
* *
33452686 TTTGTAACTCTCCAGCTAGTATG
1 TTTGTAACTCTCCAGCCAGTATA
33452709 TTTGT
1 TTTGT
33452714 TTTAATTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.45
Consensus pattern (23 bp):
TTTGTAACTCTCCAGCCAGTATA
Found at i:33455205 original size:33 final size:34
Alignment explanation
Indices: 33455163--33455232 Score: 124
Period size: 33 Copynumber: 2.1 Consensus size: 34
33455153 GTCATCGACA
33455163 TAGTACTGTTCGGCAACTG-ATCTCAAATGAAGT
1 TAGTACTGTTCGGCAACTGTATCTCAAATGAAGT
33455196 TAGTACTGTTCGGCAACTGTTATCTCAAATGAAGT
1 TAGTACTGTTCGGCAACTG-TATCTCAAATGAAGT
33455231 TA
1 TA
33455233 TCTCTATAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 19 0.54
35 16 0.46
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (34 bp):
TAGTACTGTTCGGCAACTGTATCTCAAATGAAGT
Found at i:33459539 original size:14 final size:14
Alignment explanation
Indices: 33459520--33459549 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33459510 TTATTTTTAC
33459520 TTGGATACTTTCAT
1 TTGGATACTTTCAT
*
33459534 TTGGATACTTTTAT
1 TTGGATACTTTCAT
33459548 TT
1 TT
33459550 TTACTTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (14 bp):
TTGGATACTTTCAT
Found at i:33460638 original size:21 final size:21
Alignment explanation
Indices: 33460614--33460678 Score: 66
Period size: 19 Copynumber: 3.3 Consensus size: 21
33460604 ACCAAAATTG
33460614 GTATACTCTCTCATATTTTTT
1 GTATACTCTCTCATATTTTTT
* * *
33460635 GTATA--CTCTCAGATATTTC
1 GTATACTCTCTCATATTTTTT
*
33460654 G-ATATTCTCTCAT-TTTTTT
1 GTATACTCTCTCATATTTTTT
33460673 GTATAC
1 GTATAC
33460679 CTTGTAAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
18 3 0.09
19 17 0.50
20 9 0.26
21 5 0.15
ACGTcount: A:0.22, C:0.18, G:0.08, T:0.52
Consensus pattern (21 bp):
GTATACTCTCTCATATTTTTT
Found at i:33461261 original size:19 final size:19
Alignment explanation
Indices: 33461234--33461325 Score: 53
Period size: 20 Copynumber: 4.7 Consensus size: 19
33461224 TTGATACATC
*
33461234 TCATCTTTTTGGTATATCT
1 TCATATTTTTGGTATATCT
** *
33461253 TCATATTTTTTGGTATCCCC
1 TCATA-TTTTTGGTATATCT
33461273 TCATGATTTCTT-GTA-ATCT
1 TCAT-ATTT-TTGGTATATCT
* * * *
33461292 GCACATTTTCTAGTATTTCT
1 TCATATTTT-TGGTATATCT
*
33461312 TTATATTTTTGGTA
1 TCATATTTTTGGTA
33461326 CTCCACAAAT
Statistics
Matches: 53, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
17 1 0.02
18 5 0.09
19 14 0.26
20 30 0.57
21 3 0.06
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.54
Consensus pattern (19 bp):
TCATATTTTTGGTATATCT
Found at i:33461801 original size:15 final size:15
Alignment explanation
Indices: 33461781--33461817 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
33461771 ACAATTGTTG
33461781 TACAAGGTATTTAAT
1 TACAAGGTATTTAAT
33461796 TACAAGGTATTTAAT
1 TACAAGGTATTTAAT
33461811 TACAAGG
1 TACAAGG
33461818 AAATTCTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (15 bp):
TACAAGGTATTTAAT
Found at i:33462801 original size:27 final size:27
Alignment explanation
Indices: 33462743--33462808 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
33462733 ATCCAAAGAT
* *
33462743 TGCCACAAAGGCTTCCATTTCGTGATC
1 TGCCACAAATGCTTCCATTTCATGATC
* *
33462770 TGCCACATATGCTTCCATTTCATAGTTC
1 TGCCACAAATGCTTCCATTTCAT-GATC
33462798 -GCCACAAATGC
1 TGCCACAAATGC
33462809 AGTCTTTGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 30 0.91
28 3 0.09
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (27 bp):
TGCCACAAATGCTTCCATTTCATGATC
Found at i:33471298 original size:19 final size:16
Alignment explanation
Indices: 33471256--33471306 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
33471246 TTTAACAATT
33471256 AAAAAATAATTATAAA
1 AAAAAATAATTATAAA
*
33471272 AAAGAATAATTATATTAA
1 AAAAAATAATTATA--AA
33471290 AAATAAATAA-TATAAA
1 AAA-AAATAATTATAAA
33471306 A
1 A
33471307 TATTCAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 16 0.53
18 9 0.30
19 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (16 bp):
AAAAAATAATTATAAA
Found at i:33471842 original size:18 final size:19
Alignment explanation
Indices: 33471814--33471872 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
33471804 TAATATATAT
*
33471814 TTATTATATATATTATAAA
1 TTATTAAATATATTATAAA
*
33471833 TTA-TAAATATATTTTAAA
1 TTATTAAATATATTATAAA
* * *
33471851 TAATTAAAAATATAATAAA
1 TTATTAAATATATTATAAA
33471870 TTA
1 TTA
33471873 ATTTTTTTGA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATTAAATATATTATAAA
Found at i:33475273 original size:24 final size:24
Alignment explanation
Indices: 33475257--33475307 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
33475247 AGTTTGACTT
33475257 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
33475281 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
33475305 AAA
1 AAA
33475308 GATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:33486457 original size:68 final size:69
Alignment explanation
Indices: 33486385--33486523 Score: 253
Period size: 70 Copynumber: 2.0 Consensus size: 69
33486375 GATTAAAAAA
*
33486385 ACTATTTTAAAAAATAATTAGAGATTGCCC-TTTTTTCAAATTTAGGGGAATATGTCAATTTTGG
1 ACTATTTTAAAAAATAATTAGAGATTGCCCTTTTTTTCAAATTGAGGGGAATATGTCAATTTTGG
33486449 ATAG
66 ATAG
33486453 ACTATTTTAAAAAATAATTAGAGATTGCCCTTTTTTTTCAAATTGAGGGGAATATGTCAATTTTG
1 ACTATTTTAAAAAATAATTAGAGATTGCCC-TTTTTTTCAAATTGAGGGGAATATGTCAATTTTG
33486518 GATAG
65 GATAG
33486523 A
1 A
33486524 GAAACAAAAA
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 30 0.44
70 38 0.56
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.40
Consensus pattern (69 bp):
ACTATTTTAAAAAATAATTAGAGATTGCCCTTTTTTTCAAATTGAGGGGAATATGTCAATTTTGG
ATAG
Found at i:33492666 original size:28 final size:29
Alignment explanation
Indices: 33492633--33492691 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
33492623 TTGAAAAATA
*
33492633 TTAATTTTTTATAACT-TTTTATA-GATTT
1 TTAATTTTTTA-AAATATTTTATATGATTT
33492661 TTAATTTTTTAAAATATTTTATATGATTT
1 TTAATTTTTTAAAATATTTTATATGATTT
33492690 TT
1 TT
33492692 TTAAAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 3 0.11
28 18 0.64
29 7 0.25
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (29 bp):
TTAATTTTTTAAAATATTTTATATGATTT
Found at i:33493176 original size:11 final size:11
Alignment explanation
Indices: 33493162--33493199 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
33493152 TGTTTTGCTA
33493162 TTATTTTATTG
1 TTATTTTATTG
*
33493173 TTATTTTATTA
1 TTATTTTATTG
33493184 TTATTTTATTG
1 TTATTTTATTG
33493195 TTATT
1 TTATT
33493200 GTTTGGATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (11 bp):
TTATTTTATTG
Found at i:33494426 original size:3 final size:3
Alignment explanation
Indices: 33494418--33494457 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
33494408 ACCCCTGTCA
33494418 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
33494458 ACCTTTTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:33502571 original size:27 final size:27
Alignment explanation
Indices: 33502541--33502599 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
33502531 TTCCGGAGTG
* *
33502541 GTCAGACGATAGATATCATACGGGTTA
1 GTCAGACCATAGATATAATACGGGTTA
* * * *
33502568 GTCAGGCCATGGATGTAATACGGGTTG
1 GTCAGACCATAGATATAATACGGGTTA
33502595 GTCAG
1 GTCAG
33502600 GTCAGGAGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.25
Consensus pattern (27 bp):
GTCAGACCATAGATATAATACGGGTTA
Found at i:33503560 original size:30 final size:30
Alignment explanation
Indices: 33503524--33503705 Score: 174
Period size: 30 Copynumber: 6.1 Consensus size: 30
33503514 TAAAATTATT
*
33503524 TTTGACCCCTAAAGTTTTTAAAAATTCAAA
1 TTTGACCCCTAAAGTTTTCAAAAATTCAAA
*
33503554 TTTGACCTCC-GAA-TTTTCTAAAAATTCAAA
1 TTTGACC-CCTAAAGTTTTC-AAAAATTCAAA
* * * *
33503584 TTTCA-TCCTCAAA-TTTCCAAAAATTTAAA
1 TTTGACCCCT-AAAGTTTTCAAAAATTCAAA
* *
33503613 TTTAATCCCTAAAGTTTTCAAAAATTCAAA
1 TTTGACCCCTAAAGTTTTCAAAAATTCAAA
* * *
33503643 TTTGACCCCTAAAATTTCCAAAAATTTAAA
1 TTTGACCCCTAAAGTTTTCAAAAATTCAAA
* * * *
33503673 TTTAACCCTTAAAGTTTTTAAAAATTAAAA
1 TTTGACCCCTAAAGTTTTCAAAAATTCAAA
33503703 TTT
1 TTT
33503706 AACCTCGTTT
Statistics
Matches: 124, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.02
29 21 0.17
30 99 0.80
31 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.38
Consensus pattern (30 bp):
TTTGACCCCTAAAGTTTTCAAAAATTCAAA
Found at i:33503630 original size:89 final size:90
Alignment explanation
Indices: 33503530--33503707 Score: 234
Period size: 89 Copynumber: 2.0 Consensus size: 90
33503520 TATTTTTGAC
* * * * * *
33503530 CCCTAAAGTTTTTAAAAATTCAAATTTGACCTCC-GAATTTTCTAAAAATTCAAATTTCATCCTC
1 CCCTAAAGTTTTCAAAAATTCAAATTTGACC-CCTAAAATTTCCAAAAATTCAAATTTAACCCTC
*
33503594 AAA-TTTCCAAAAATTTAAATTTAAT
65 AAAGTTTCCAAAAATTAAAATTTAAT
* *
33503619 CCCTAAAGTTTTCAAAAATTCAAATTTGACCCCTAAAATTTCCAAAAATTTAAATTTAACCCTTA
1 CCCTAAAGTTTTCAAAAATTCAAATTTGACCCCTAAAATTTCCAAAAATTCAAATTTAACCCTCA
**
33503684 AAGTTTTTAAAAATTAAAATTTAA
66 AAGTTTCCAAAAATTAAAATTTAA
33503708 CCTCGTTTTA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
88 2 0.03
89 56 0.74
90 18 0.24
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (90 bp):
CCCTAAAGTTTTCAAAAATTCAAATTTGACCCCTAAAATTTCCAAAAATTCAAATTTAACCCTCA
AAGTTTCCAAAAATTAAAATTTAAT
Found at i:33503667 original size:60 final size:59
Alignment explanation
Indices: 33503524--33503705 Score: 206
Period size: 60 Copynumber: 3.1 Consensus size: 59
33503514 TAAAATTATT
* ** * * **
33503524 TTTGACCCCTAAAGTTTTTAAAAATTCAAATTTGACCTCCGAA-TTTTCTAAAAATTCAAA
1 TTTGACCCCTAAAATTTCCAAAAATTTAAATTTAACC-CTAAAGTTTTC-AAAAATTCAAA
* * *
33503584 TTTCA-TCCTCAAATTTCCAAAAATTTAAATTTAATCCCTAAAGTTTTCAAAAATTCAAA
1 TTTGACCCCTAAAATTTCCAAAAATTTAAATTTAA-CCCTAAAGTTTTCAAAAATTCAAA
* *
33503643 TTTGACCCCTAAAATTTCCAAAAATTTAAATTTAACCCTTAAAGTTTTTAAAAATTAAAA
1 TTTGACCCCTAAAATTTCCAAAAATTTAAATTTAACCC-TAAAGTTTTCAAAAATTCAAA
33503703 TTT
1 TTT
33503706 AACCTCGTTT
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
59 43 0.42
60 60 0.58
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.38
Consensus pattern (59 bp):
TTTGACCCCTAAAATTTCCAAAAATTTAAATTTAACCCTAAAGTTTTCAAAAATTCAAA
Found at i:33508699 original size:29 final size:29
Alignment explanation
Indices: 33508657--33508714 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
33508647 TACAAGAAGC
*
33508657 TTTATAAAAGTTTATATGATGCCCGAGTA
1 TTTACAAAAGTTTATATGATGCCCGAGTA
33508686 TTTACAAAAGTTTATATGATGCCCGAGTA
1 TTTACAAAAGTTTATATGATGCCCGAGTA
33508715 GTATCCCCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (29 bp):
TTTACAAAAGTTTATATGATGCCCGAGTA
Found at i:33515547 original size:50 final size:50
Alignment explanation
Indices: 33515420--33515553 Score: 196
Period size: 50 Copynumber: 2.7 Consensus size: 50
33515410 ATCTTTTACC
* * * * *
33515420 CCTAAAGCTATGGAGGTGCAGATTGAAACCGCAATGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCACAATGGCAAATCTCATACA
* *
33515470 CCTAAAGCTGTAGAGGGGCAGAATGAAGCCACAATGGCAAATCTCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCACAATGGCAAATCTCATACA
*
33515520 CCTAAAGCTGTAGAGGGGCAGATTGAAGTCACAA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCACAA
33515554 GGATGAATCT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.19
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGGCAGATTGAAGCCACAATGGCAAATCTCATACA
Found at i:33515658 original size:40 final size:40
Alignment explanation
Indices: 33515605--33515899 Score: 280
Period size: 40 Copynumber: 7.4 Consensus size: 40
33515595 AGTTACAACC
* *
33515605 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
* * ** *
33515645 CCCAATGTTTTACCCCGATCATG-GGACAGATTGAA-AGCAA
1 TCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGA-CAA
*
33515685 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
* **
33515725 TCAAATCTTTTACCCCGATCATG-GGGCAGATTG-AGAGCAA
1 TCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGA-CAA
* * *
33515765 TCCTATCTTTTACCCTAA-CTAGAGGGTAGATTGAAGACCA
1 TCCAATCTTTTACCCTAATC-AGAGGGCAGATTGAAGACAA
* * * * *
33515805 TTCGATCTCTTA-CCTCGATCATG-GGGCAGATTGAAGACTA
1 TCCAATCTTTTACCCT-AATCA-GAGGGCAGATTGAAGACAA
* * *
33515845 TCCAATCTATTACCTTAATCAGAGGACAGATTGAAGACAA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
33515885 TCCAATCTTTTACCC
1 TCCAATCTTTTACCC
33515900 CTAAAGTTAT
Statistics
Matches: 203, Mismatches: 38, Indels: 28
0.75 0.14 0.10
Matches are distributed among these distances:
39 11 0.05
40 182 0.90
41 10 0.05
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (40 bp):
TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
Found at i:33515738 original size:80 final size:80
Alignment explanation
Indices: 33515605--33515900 Score: 405
Period size: 80 Copynumber: 3.7 Consensus size: 80
33515595 AGTTACAACC
* * *
33515605 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAACCCAATGTTTTACCCCGATCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATGGG
*
33515670 ACAGATTGAAAGCAA
66 GCAGATTGAAAGCAA
*
33515685 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCAAATCTTTTACCCCGATCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATGGG
*
33515750 GCAGATTGAGAGCAA
66 GCAGATTGAAAGCAA
* * * * * * * *
33515765 TCCTATCTTTTACCCTAACTAGAGGGTAGATTGAAGACCATTCGATCTCTTACCTCGATCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATGGG
*
33515830 GCAGATTG-AAGACTA
66 GCAGATTGAAAG-CAA
* * * *
33515845 TCCAATCTATTACCTTAATCAGAGGACAGATTGAAGACAATCCAATCTTTTACCCC
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCC
33515901 TAAAGTTATA
Statistics
Matches: 186, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
79 2 0.01
80 184 0.99
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (80 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATGGG
GCAGATTGAAAGCAA
Found at i:33516432 original size:15 final size:16
Alignment explanation
Indices: 33516406--33516435 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33516396 CCAAATTTTA
33516406 TTATTTTATTTATTAT
1 TTATTTTATTTATTAT
33516422 TTATTTT-TTTATTA
1 TTATTTTATTTATTA
33516436 AATAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTTATTTATTAT
Found at i:33517017 original size:2 final size:2
Alignment explanation
Indices: 33517010--33517079 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
33517000 TTTCATGTAT
33517010 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33517052 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
33517080 CTTTTACATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33517722 original size:30 final size:29
Alignment explanation
Indices: 33517692--33517876 Score: 201
Period size: 30 Copynumber: 6.2 Consensus size: 29
33517682 TTATTTTTTG
* * *
33517692 ACCCCTAAAGTTTTTAAAAATTTAAATTTG
1 ACCCCTAAA-TTTTCAAAAATTCAAATTTA
* * *
33517722 ACCTCTAAATTTTCTAAAAATTTAAATTTC
1 ACCCCTAAATTTTC-AAAAATTCAAATTTA
*
33517752 ACCCCCAAATTTTCCAAAAATTCAAATTTA
1 ACCCCTAAATTTT-CAAAAATTCAAATTTA
* *
33517782 ATCCCC-ATAGTTTTCAAAAATTCAAATTTG
1 A-CCCCTA-AATTTTCAAAAATTCAAATTTA
*
33517812 ACCCCTTAAATTTCCAAAAATTCAAATTTA
1 ACCCC-TAAATTTTCAAAAATTCAAATTTA
*
33517842 ACCCCTAAAGTTTTTAAAAATTCAAATTTA
1 ACCCCTAAA-TTTTCAAAAATTCAAATTTA
33517872 ACCCC
1 ACCCC
33517877 GTTTTTATGT
Statistics
Matches: 134, Mismatches: 14, Indels: 14
0.83 0.09 0.09
Matches are distributed among these distances:
29 12 0.09
30 111 0.83
31 11 0.08
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.36
Consensus pattern (29 bp):
ACCCCTAAATTTTCAAAAATTCAAATTTA
Found at i:33517891 original size:90 final size:90
Alignment explanation
Indices: 33517700--33517876 Score: 243
Period size: 90 Copynumber: 2.0 Consensus size: 90
33517690 TGACCCCTAA
* * * * *
33517700 AGTTTTTAAAAATTTAAATTTGACCTCTAAATTTTCTAAAAATTTAAATTTCACCCCCAAATTTT
1 AGTTTTTAAAAATTCAAATTTGACCCCTAAATTTTCCAAAAATTCAAATTTAACCCCCAAATTTT
33517765 CCAAAAATTCAAATTTAATCCCCAT
66 CCAAAAATTCAAATTTAATCCCCAT
* *
33517790 AGTTTTCAAAAATTCAAATTTGACCCCTTAAA-TTTCCAAAAATTCAAATTTAACCCCTAAAGTT
1 AGTTTTTAAAAATTCAAATTTGACCCC-TAAATTTTCCAAAAATTCAAATTTAACCCCCAAA-TT
*
33517854 TT-TAAAAATTCAAATTTAA-CCCC
64 TTCCAAAAATTCAAATTTAATCCCC
33517877 GTTTTTATGT
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
89 4 0.05
90 65 0.84
91 8 0.10
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.37
Consensus pattern (90 bp):
AGTTTTTAAAAATTCAAATTTGACCCCTAAATTTTCCAAAAATTCAAATTTAACCCCCAAATTTT
CCAAAAATTCAAATTTAATCCCCAT
Found at i:33520878 original size:27 final size:27
Alignment explanation
Indices: 33520843--33520953 Score: 116
Period size: 27 Copynumber: 4.1 Consensus size: 27
33520833 CTTAAATAGG
* *
33520843 CACTGGTGCCGCCTA-TCTATATGGCAC
1 CACTGGTGCCGCCTACCCAATA-GGCAC
* *
33520870 CACTAGTGCCACCTACCCAATAGGCAC
1 CACTGGTGCCGCCTACCCAATAGGCAC
* * *
33520897 CACTGGTGTCGCCTACCCCATAAGCAC
1 CACTGGTGCCGCCTACCCAATAGGCAC
* * *
33520924 CATTGGTGCCACCTACCCCATAGGCAC
1 CACTGGTGCCGCCTACCCAATAGGCAC
33520951 CAC
1 CAC
33520954 CCAAAATTTT
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
27 65 0.94
28 4 0.06
ACGTcount: A:0.23, C:0.40, G:0.18, T:0.19
Consensus pattern (27 bp):
CACTGGTGCCGCCTACCCAATAGGCAC
Found at i:33521464 original size:18 final size:18
Alignment explanation
Indices: 33521438--33521472 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33521428 CCAAATTTAT
*
33521438 CTTGGTCTTGATCTTGAG
1 CTTGATCTTGATCTTGAG
*
33521456 CTTGATCTTGATGTTGA
1 CTTGATCTTGATCTTGA
33521473 TAGACATCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.26, T:0.46
Consensus pattern (18 bp):
CTTGATCTTGATCTTGAG
Found at i:33525412 original size:60 final size:57
Alignment explanation
Indices: 33525296--33525415 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 57
33525286 TAATTTATTC
* *
33525296 TTTATGCAAAAAAATAAACATACTTAAAATAACAAAAAAACCTAAATAACATCAACT
1 TTTATGCAAAAAAATAAACATACTTAAAACAACAAAAAAACCTAAATAACACCAACT
* ****
33525353 TTTATGCAAGAAAATGAAACATACTTAAAAGCAACATAAAATGTTTAAATAACACCAACT
1 TTTATGCAAAAAAAT-AAACATACTTAAAA-CAACA-AAAAAACCTAAATAACACCAACT
33525413 TTT
1 TTT
33525416 CTAATGATTC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 14 0.26
58 14 0.26
59 4 0.08
60 21 0.40
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (57 bp):
TTTATGCAAAAAAATAAACATACTTAAAACAACAAAAAAACCTAAATAACACCAACT
Found at i:33527157 original size:15 final size:15
Alignment explanation
Indices: 33527108--33527154 Score: 78
Period size: 15 Copynumber: 3.1 Consensus size: 15
33527098 TCTTTTAACG
33527108 TTATCTTTTAAATATT
1 TTATC-TTTAAATATT
33527124 TTATCTTTAAATATT
1 TTATCTTTAAATATT
33527139 TTATCTTTAAA-ATT
1 TTATCTTTAAATATT
33527153 TT
1 TT
33527155 TATTTATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.16
15 21 0.68
16 5 0.16
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATCTTTAAATATT
Found at i:33528545 original size:105 final size:103
Alignment explanation
Indices: 33528409--33528789 Score: 379
Period size: 113 Copynumber: 3.6 Consensus size: 103
33528399 TTGAAGTTCT
* * *
33528409 AGATATCGTTGACACAATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACATATAGTATATTGG
1 AGATATTGTTGACACAATGAGAAAGCAAGGCATTAAGCCTGATGTTGTCACATATAGCATATTGG
* *
33528474 TTAATGCATATTGCAAGAAGGGTATGATTTCTAAAGCTGA
66 TTGATGCATATTGCAAGAAGGG-ATG-TTTCTAAAGCTAA
** * *
33528514 AGATATTGTTGACAGTATGAGAAAGCTAGGCATTAAGCCTGATGTTGTCACATATAACATATTGG
1 AGATATTGTTGACACAATGAGAAAGCAAGGCATTAAGCCTGATGTTGTCACATATAGCATATTGG
* *
33528579 TTGATGCGCATTGCAAGGTTGCAAGGAGGGAATTGTTTCTAAAGTTAA
66 TTGAT--GCA-T---A--TTGCAAGAAGGG-A-TGTTTCTAAAGCTAA
* * * * * *
33528627 AGATATTGTTGACACAATGAGAAAGCAAGGTATTGAGCCTGACGTTATCACGTATAGCATATTGA
1 AGATATTGTTGACACAATGAGAAAGCAAGGCATTAAGCCTGATGTTGTCACATATAGCATATTGG
* * * *
33528692 TTGATGCACATTACAAGAAGGAGATGGTTT-TGAAGC-ACT
66 TTGATGCATATTGCAAGAAGG-GAT-GTTTCTAAAGCTA-A
* * * * *
33528731 AGATATTGTTGACACAATGAGAAAGCAAAGCATCAAGACTAATGTTGTCACATACAGCA
1 AGATATTGTTGACACAATGAGAAAGCAAGGCATTAAGCCTGATGTTGTCACATATAGCA
33528790 CTCTTATGCA
Statistics
Matches: 226, Mismatches: 38, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
103 1 0.00
104 54 0.24
105 76 0.34
106 1 0.00
107 4 0.02
108 1 0.00
111 4 0.02
113 83 0.37
114 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (103 bp):
AGATATTGTTGACACAATGAGAAAGCAAGGCATTAAGCCTGATGTTGTCACATATAGCATATTGG
TTGATGCATATTGCAAGAAGGGATGTTTCTAAAGCTAA
Found at i:33531292 original size:2 final size:2
Alignment explanation
Indices: 33531285--33531310 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33531275 CATATTTATG
33531285 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
33531311 TCAACCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33534104 original size:105 final size:105
Alignment explanation
Indices: 33533920--33534142 Score: 279
Period size: 105 Copynumber: 2.1 Consensus size: 105
33533910 TCTCTTGATA
* * * * *
33533920 TTGTCACTTATAATATATTGATAGATGCACATTGCAAGCAGAGGATGATTTCTGAAGCTGTAGAT
1 TTGTCACATATAACATATTGATAGATGCACATTGCAAGCAGAGGATGATTTCTAAAGCCGAAGAT
* *
33533985 ACTGTTAATGCAATGAGAAAGCAAGGCATTGAACCTAATG
66 ACTGCTAATACAATGAGAAAGCAAGGCATTGAACCTAATG
* * * *
33534025 TTGTCACATATAGCATATTGGTTGATGCACATTGCAA--AGAGGGAATGGTTTCTAAAGCCGAAG
1 TTGTCACATATAACATATTGATAGATGCACATTGCAAGCAGA-GG-ATGATTTCTAAAGCCGAAG
* * * *
33534088 ATATTGCTGATACAATGAGAAAGCAAGGCATTGAGCCTGATG
64 ATACTGCTAATACAATGAGAAAGCAAGGCATTGAACCTAATG
33534130 TTGTCACATATAA
1 TTGTCACATATAA
33534143 TGCATTAATA
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
103 3 0.03
104 2 0.02
105 95 0.95
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (105 bp):
TTGTCACATATAACATATTGATAGATGCACATTGCAAGCAGAGGATGATTTCTAAAGCCGAAGAT
ACTGCTAATACAATGAGAAAGCAAGGCATTGAACCTAATG
Found at i:33540001 original size:19 final size:19
Alignment explanation
Indices: 33539948--33540001 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
33539938 AAGACCTAAG
*
33539948 AAAATTATATAAAA-TGTAA
1 AAAATTATA-AAAATTATAA
**
33539967 AAAA-TATAAATTTTATAA
1 AAAATTATAAAAATTATAA
33539985 AAAATTATAAAAATTAT
1 AAAATTATAAAAATTAT
33540002 CGTACCAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 2 0.07
18 12 0.43
19 14 0.50
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAATTATAAAAATTATAA
Found at i:33540192 original size:19 final size:20
Alignment explanation
Indices: 33540156--33540193 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
33540146 TTAAAAAGAT
33540156 TTTTTGATGCATTTTATAAC
1 TTTTTGATGCATTTTATAAC
33540176 TTTTT-ATG-ATTTCTATAA
1 TTTTTGATGCATTT-TATAA
33540194 AATTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (20 bp):
TTTTTGATGCATTTTATAAC
Found at i:33541123 original size:22 final size:21
Alignment explanation
Indices: 33541098--33541156 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
33541088 AATAAAAATG
33541098 AAAATGTTTAAAAATGTTATTA-
1 AAAATGTTTAAAAAT-TTA-TAC
*
33541120 AAAAAGTTTAAAAATTTATAC
1 AAAATGTTTAAAAATTTATAC
*
33541141 AAAATTTTTAGAAAAT
1 AAAATGTTTA-AAAAT
33541157 AAAAGAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 2 0.06
21 11 0.34
22 19 0.59
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (21 bp):
AAAATGTTTAAAAATTTATAC
Found at i:33541264 original size:28 final size:28
Alignment explanation
Indices: 33541207--33541264 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
33541197 AATATTACTA
* ***
33541207 TTAATTTTTTTTAAATACTTATATCTAT
1 TTAATTTTTTATAAATACTTATAAAAAT
33541235 TTAATTTTTTATAAATAC-TATTAAAAAT
1 TTAATTTTTTATAAATACTTA-TAAAAAT
33541263 TT
1 TT
33541265 TAAAAACAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (28 bp):
TTAATTTTTTATAAATACTTATAAAAAT
Found at i:33541544 original size:15 final size:15
Alignment explanation
Indices: 33541497--33541544 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
33541487 AAAATATTAG
* *
33541497 AAATATTTTATTTTA
1 AAATATTTTAATATA
*
33541512 AAATATAATTTAAAATA
1 AAATAT--TTTAATATA
33541529 AAATATTTTAATATA
1 AAATATTTTAATATA
33541544 A
1 A
33541545 TTTAATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 15 0.56
17 12 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATTTTAATATA
Found at i:33541561 original size:41 final size:41
Alignment explanation
Indices: 33541482--33541562 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
33541472 GAAAAATATA
* * *
33541482 AAAATAAAATATTAGAAATATTTTATTTTAAAATATAATTT
1 AAAATAAAATATTAGAAATAATTTAATATAAAATATAATTT
**
33541523 AAAATAAAATATTTTAATATAATTTAATATAAAA-ATAATT
1 AAAATAAAATATTAGAA-ATAATTTAATATAAAATATAATT
33541563 ATATTAGGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 21 0.62
42 13 0.38
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (41 bp):
AAAATAAAATATTAGAAATAATTTAATATAAAATATAATTT
Found at i:33541602 original size:16 final size:16
Alignment explanation
Indices: 33541581--33541666 Score: 54
Period size: 16 Copynumber: 5.6 Consensus size: 16
33541571 AATGTTATTA
33541581 AATTATATTTAATAAT
1 AATTATATTTAATAAT
*
33541597 AATTATA-TTAAAATAT
1 AATTATATTTAATA-AT
* * *
33541613 AATTA-AATTATTTAT
1 AATTATATTTAATAAT
** * *
33541628 TTTTAT-TTTTATTA-
1 AATTATATTTAATAAT
33541642 AATTATATTTAATAAT
1 AATTATATTTAATAAT
*
33541658 AATTCTATT
1 AATTATATT
33541667 ATATTTAATA
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
14 4 0.08
15 22 0.43
16 25 0.49
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTATATTTAATAAT
Found at i:33541606 original size:21 final size:21
Alignment explanation
Indices: 33541577--33541677 Score: 82
Period size: 21 Copynumber: 4.9 Consensus size: 21
33541567 TAGGAATGTT
*
33541577 ATTAAATTATATTTAATAATA
1 ATTATATTATATTTAATAATA
* * *
33541598 ATTATATTAAAATATAATTA-A
1 ATTATATT-ATATTTAATAATA
* ** *
33541619 ATTAT-TTAT-TTTTATTTTT
1 ATTATATTATATTTAATAATA
*
33541638 ATTAAATTATATTTAATAATA
1 ATTATATTATATTTAATAATA
*
33541659 ATTCTATTATATTTAATAA
1 ATTATATTATATTTAATAA
33541678 CAATAATAAT
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
18 5 0.08
19 5 0.08
20 6 0.10
21 36 0.60
22 8 0.13
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTATATTATATTTAATAATA
Found at i:33542563 original size:17 final size:17
Alignment explanation
Indices: 33542541--33542575 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
33542531 CAGAGTATGC
* *
33542541 ATGAAGGTACATCGTTG
1 ATGAAGGAACATCATTG
33542558 ATGAAGGAACATCATTG
1 ATGAAGGAACATCATTG
33542575 A
1 A
33542576 AAACCCTTCA
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:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (17 bp):
ATGAAGGAACATCATTG
Found at i:33546556 original size:320 final size:320
Alignment explanation
Indices: 33545972--33546614 Score: 1223
Period size: 320 Copynumber: 2.0 Consensus size: 320
33545962 GGTTATGCAT
* *
33545972 TAAAACACGACAACACACACACCAATTCTAATCTTTACAAGCATAATAAGCCTAAGCATTAAAGT
1 TAAAACACCACAACACACACACCAATTCTAATCTTTACAAGCATAATAAGCCTAAGCAATAAAGT
33546037 TGTAATTCAAGCATTTACACAATCCAAGTAGTAAGATTTCAACATCTTTGGTTTCATATAAAAAG
66 TGTAATTCAAGCATTTACACAATCCAAGTAGTAAGATTTCAACATCTTTGGTTTCATATAAAAAG
33546102 TTAATAACATTCTAGTACATGCCATAAGACCAAGTGATGCAAAATCTACCGACAACTCCGCGACA
131 TTAATAACATTCTAGTACATGCCATAAGACCAAGTGATGCAAAATCTACCGACAACTCCGCGACA
33546167 GTATGATTTCAAGTGAGGTTGGTGGTCTGATCTTCAGTCAGCAAAAACGATCTACAAAACAAAAA
196 GTATGATTTCAAGTGAGGTTGGTGGTCTGATCTTCAGTCAGCAAAAACGATCTACAAAACAAAAA
*
33546232 TAATAACTTTGGTAAGCTTTATAGCTTAGTAAGTTCGATAGTTAAGAAATACCACTATGG
261 TAATAACTTTGGTAAGCTTTATAGCTTAGTAAGTTCGATAGTTAAGAAATACCAATATGG
33546292 TAAAACACCACAACACACACACCAATTCTAATCTTTACAAGCATAATAAGCCTAAGCAATAAAGT
1 TAAAACACCACAACACACACACCAATTCTAATCTTTACAAGCATAATAAGCCTAAGCAATAAAGT
33546357 TGTAATTCAAGCATTTACACAATCCAAGTAGTAAGATTTCAACATCTTTGGTTTCATATAAAAAG
66 TGTAATTCAAGCATTTACACAATCCAAGTAGTAAGATTTCAACATCTTTGGTTTCATATAAAAAG
33546422 TTAATAACATTCTAGTACATGCCATAAGACCAAGTGATGCAAAATCTACCGACAACTCCGCGACA
131 TTAATAACATTCTAGTACATGCCATAAGACCAAGTGATGCAAAATCTACCGACAACTCCGCGACA
* * * *
33546487 GTGTGATTTCAGGTGAGGTTGGTGGTCTGATCTTCAGTCGGCAAAAACGATCTACAAAACAACAA
196 GTATGATTTCAAGTGAGGTTGGTGGTCTGATCTTCAGTCAGCAAAAACGATCTACAAAACAAAAA
33546552 TAATAACTTTGGTAAGCTTTATAGCTTAGTAAGTTCGATAGTTAAGAAATACCAATATGG
261 TAATAACTTTGGTAAGCTTTATAGCTTAGTAAGTTCGATAGTTAAGAAATACCAATATGG
33546612 TAA
1 TAA
33546615 TAGCAACAAT
Statistics
Matches: 316, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
320 316 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (320 bp):
TAAAACACCACAACACACACACCAATTCTAATCTTTACAAGCATAATAAGCCTAAGCAATAAAGT
TGTAATTCAAGCATTTACACAATCCAAGTAGTAAGATTTCAACATCTTTGGTTTCATATAAAAAG
TTAATAACATTCTAGTACATGCCATAAGACCAAGTGATGCAAAATCTACCGACAACTCCGCGACA
GTATGATTTCAAGTGAGGTTGGTGGTCTGATCTTCAGTCAGCAAAAACGATCTACAAAACAAAAA
TAATAACTTTGGTAAGCTTTATAGCTTAGTAAGTTCGATAGTTAAGAAATACCAATATGG
Found at i:33558341 original size:17 final size:17
Alignment explanation
Indices: 33558321--33558368 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
33558311 TCTTTTTTCA
*
33558321 ATTTTAATAATTTTTAC
1 ATTTTAATAATTTTAAC
* *
33558338 ATTTTAAAACATTTTAAT
1 ATTTTAATA-ATTTTAAC
33558356 ATTTTAATAATTT
1 ATTTTAATAATTT
33558369 ATCTATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATAATTTTAAC
Found at i:33585951 original size:12 final size:12
Alignment explanation
Indices: 33585934--33585964 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
33585924 ACTCTATACT
*
33585934 ACCAACATGTAA
1 ACCAACATCTAA
33585946 ACCAACATCTAA
1 ACCAACATCTAA
33585958 ACCAACA
1 ACCAACA
33585965 ATATTTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.32, G:0.03, T:0.13
Consensus pattern (12 bp):
ACCAACATCTAA
Found at i:33586135 original size:11 final size:11
Alignment explanation
Indices: 33586119--33586145 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
33586109 TTATATATCG
33586119 ATTTATTAAAT
1 ATTTATTAAAT
33586130 ATTTATTAAAT
1 ATTTATTAAAT
33586141 ATTTA
1 ATTTA
33586146 AATAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTATTAAAT
Found at i:33587742 original size:25 final size:25
Alignment explanation
Indices: 33587714--33587761 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
33587704 ACCTAAAACA
33587714 AAAAACCTAAAACTA-AAACTAAAT
1 AAAAACCTAAAACTACAAACTAAAT
*
33587738 AAAAACCTAAAACTACTAACTAAA
1 AAAAACCTAAAACTACAAACTAAA
33587762 ACCCTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.17
Consensus pattern (25 bp):
AAAAACCTAAAACTACAAACTAAAT
Found at i:33587761 original size:21 final size:22
Alignment explanation
Indices: 33587714--33587770 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 22
33587704 ACCTAAAACA
33587714 AAAAACCTAAAACTAAAACTAAAT
1 AAAAACCTAAAACT--AACTAAAT
*
33587738 AAAAACCTAAAACT-ACTAACT
1 AAAAACCTAAAACTAACTAAAT
*
33587759 AAAACCCTAAAA
1 AAAAACCTAAAA
33587771 TGACTTGGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 17 0.55
24 14 0.45
ACGTcount: A:0.63, C:0.21, G:0.00, T:0.16
Consensus pattern (22 bp):
AAAAACCTAAAACTAACTAAAT
Found at i:33589823 original size:110 final size:110
Alignment explanation
Indices: 33589627--33589840 Score: 311
Period size: 110 Copynumber: 1.9 Consensus size: 110
33589617 TAAAGAACAC
* * * * *
33589627 TTATCGATTTTAAAATAGGATGTTCTATTACTTAGGTTCAAAGAAAAACCATACCTAATACGTTA
1 TTATCGATTTTAAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAACAATACCCAACACGTTA
* *
33589692 GGGTACAATTTCTCGAGTTCCCTAAAATAAAAGAACATTAAATAT
66 GGGCACAATTTCTCGAATTCCCTAAAATAAAAGAACATTAAATAT
* * * * *
33589737 TTATCGATTTTTAAATAGGATATTCAATTATTTAGGTTTAAAGAAAAATAATACCCAGCACGTTA
1 TTATCGATTTTAAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAACAATACCCAACACGTTA
*
33589802 GGGCACAATTTCTCGAATTCCCTAAAATAAAATAACATT
66 GGGCACAATTTCTCGAATTCCCTAAAATAAAAGAACATT
33589841 GTCTTGATTT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 91 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (110 bp):
TTATCGATTTTAAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAACAATACCCAACACGTTA
GGGCACAATTTCTCGAATTCCCTAAAATAAAAGAACATTAAATAT
Found at i:33590162 original size:2 final size:2
Alignment explanation
Indices: 33590155--33590216 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
33590145 GGATAAATGA
33590155 AT AT AT AT AT AT AT 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 AT AT AT AT
33590197 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
33590217 TATTTAATTC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33590375 original size:5 final size:5
Alignment explanation
Indices: 33590365--33590394 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
33590355 AGTAAACATG
33590365 AAAAT AAAAT AAAAT AAAAT AAATAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAA-AT AAAA
33590395 AAGGTTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:33590385 original size:15 final size:16
Alignment explanation
Indices: 33590346--33590394 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 16
33590336 ATGGAATATG
33590346 AAATAAATGAGTAAACATGA
1 AAATAAAT-A-TAAA-AT-A
33590366 AAATAAA-ATAAAATA
1 AAATAAATATAAAATA
33590381 AAATAAATATAAAA
1 AAATAAATATAAAA
33590395 AAGGTTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 8 0.29
16 8 0.29
17 4 0.14
18 1 0.04
20 7 0.25
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.20
Consensus pattern (16 bp):
AAATAAATATAAAATA
Found at i:33593114 original size:29 final size:28
Alignment explanation
Indices: 33593082--33593159 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
33593072 AAATTTTAGG
* *
33593082 AAATTACATTATGACCCCGAAACTTTCAA
1 AAATTACATT-TAACCCCGAAACTCTCAA
* * *
33593111 AAATTACCATTTTACCCCCAAACTCTCCA
1 AAATTA-CATTTAACCCCGAAACTCTCAA
*
33593140 AAATTCCATTTTAACCCCGA
1 AAATTACA-TTTAACCCCGA
33593160 TTTCATCAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.05
29 34 0.85
30 4 0.10
ACGTcount: A:0.37, C:0.31, G:0.04, T:0.28
Consensus pattern (28 bp):
AAATTACATTTAACCCCGAAACTCTCAA
Found at i:33593191 original size:57 final size:58
Alignment explanation
Indices: 33593110--33593354 Score: 343
Period size: 57 Copynumber: 4.2 Consensus size: 58
33593100 GAAACTTTCA
*
33593110 AAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCA-TTTTAACCCCGATTTCATC
1 AAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * * * *
33593167 AAAATTACCATTTTACCTCTAAACTTTCCAAAATTCTATTTTTGACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
33593225 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTC-ATTTTCACC
1 -AAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCCCGA-TTTCACC
* * *
33593284 AAAATTATCATTTTACCCCCGAACTCTCAAAAATTCCA-TTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCCCGATTTCACC
33593341 AAAATTACCATTTT
1 AAAATTACCATTTT
33593355 GCCTCCGAGT
Statistics
Matches: 167, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
57 63 0.38
58 54 0.32
59 50 0.30
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:33593362 original size:29 final size:28
Alignment explanation
Indices: 33593110--33593354 Score: 157
Period size: 29 Copynumber: 8.5 Consensus size: 28
33593100 GAAACTTTCA
* ** *
33593110 AAAATTACCATTTTACCCCCAAACTCTCC
1 AAAATTACCATTTTA-CCCCGATTTCACC
*
33593139 AAAATT-CCATTTTAACCCCGATTTCATC
1 AAAATTACCATTTT-ACCCCGATTTCACC
**
33593167 AAAATTACCATTTTACCTCTAAACTTT--CC
1 AAAATTACCATTTTACC-C-CGA-TTTCACC
*
33593196 AAAATT-CTATTTTTGACCCCGATTTCACC
1 AAAATTACCA-TTTT-ACCCCGATTTCACC
33593225 AAAAATTACCATTTTACCCCCGAACTTT--CC
1 -AAAATTACCATTTTA-CCCCG-A-TTTCACC
*
33593255 AAAATT-CCATTTTTAACCTC-ATTTTCACC
1 AAAATTACCA-TTTT-ACCCCGA-TTTCACC
* ** * *
33593284 AAAATTATCATTTTACCCCCGAACTCTCA
1 AAAATTACCATTTTA-CCCCGATTTCACC
33593313 AAAATT-CCATTTTAACCCCGATTTCACC
1 AAAATTACCATTTT-ACCCCGATTTCACC
33593341 AAAATTACCATTTT
1 AAAATTACCATTTT
33593355 GCCTCCGAGT
Statistics
Matches: 168, Mismatches: 25, Indels: 46
0.70 0.10 0.19
Matches are distributed among these distances:
27 7 0.04
28 52 0.31
29 75 0.45
30 25 0.15
31 6 0.04
32 3 0.02
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCGATTTCACC
Found at i:33600905 original size:14 final size:14
Alignment explanation
Indices: 33600886--33600917 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
33600876 ATAGAAATCT
33600886 TTTGTAAAAGGGCA
1 TTTGTAAAAGGGCA
33600900 TTTGTAAAAGGGCA
1 TTTGTAAAAGGGCA
33600914 TTTG
1 TTTG
33600918 AGTTTTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.34
Consensus pattern (14 bp):
TTTGTAAAAGGGCA
Found at i:33605813 original size:76 final size:76
Alignment explanation
Indices: 33605429--33606019 Score: 900
Period size: 76 Copynumber: 7.8 Consensus size: 76
33605419 ATCAGACCGC
* * * *
33605429 AGCAAGATCATTCCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
*
33605494 ATTGAAGTAAA
66 ATTGAAGTAAG
* *
33605505 AGCAAGATTTTTTCCTATCCGCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
33605569 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * *
33605580 AGCGAGATCTTTTCCTATTCGCTTGAAATTGAAGTAGAG-TGGATAACACGTATTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
33605644 ATTGAAGTAAG
66 ATTGAAGTAAG
*
33605655 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
*
33605719 ATTGAAGTAAA
66 ATTGAAGTAAG
*
33605730 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAATAAGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
33605795 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * * * * *
33605806 AGCAAGATCGTTGCCCATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
33605871 ATTGAAGTAAG
66 ATTGAAGTAAG
* * *
33605882 AGCAAGATCATTTCATATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
33605947 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * * *
33605958 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCT
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCT
33606020 CTGAAGAGTA
Statistics
Matches: 478, Mismatches: 36, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
75 216 0.45
76 262 0.55
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (76 bp):
AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
ATTGAAGTAAG
Found at i:33605985 original size:38 final size:37
Alignment explanation
Indices: 33605490--33605994 Score: 230
Period size: 38 Copynumber: 13.4 Consensus size: 37
33605480 TCTTTATCTC
* ** *
33605490 TGAAATTGAAGTAAAAGCAAGATTTTTTCCTATCCGCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTT-CTATCCTCT
* * *
33605528 TGAAATTGAAGTAGAGTGGATA-ACACGTCTT-TAT-CTC-
1 TGAAATTGAAGTA-AGAGCA-AGA-TCGT-TTCTATCCTCT
* * * *
33605565 TGAAATTGAAGTAAGAGCGAGATCTTTTCCTATTCGCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTT-CTATCCTCT
* * *
33605603 TGAAATTGAAGTAGAGTGGATA-ACACGTATT-TAT-CTC-
1 TGAAATTGAAGTA-AGAGCA-AGA-TCGT-TTCTATCCTCT
* *
33605640 TGAAATTGAAGTAAGAGCAAGATCTTTTCCTATCCGCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTT-CTATCCTCT
* * *
33605678 TGAAATTGAAGTAGAGTGGATA-ACACGTCTT-TAT-CTC-
1 TGAAATTGAAGTA-AGAGCA-AGA-TCGT-TTCTATCCTCT
* * *
33605715 TGAAATTGAAGTAAAAGCAAGATCTTTTCCTATCCGCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTT-CTATCCTCT
* * *
33605753 TGAAATTGAAGTAGAGTTGGATA-ATAAGTCTT-TAT-CTC-
1 TGAAATTGAAGTA-AG-AGCA-AGAT-CGT-TTCTATCCTCT
* *
33605791 TGAAATTGAAGTAAGAGCAAGATCGTTGCCCATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCGTT-TCTATCCTCT
* *
33605829 TGAAATTGAAGTAA-AGCTGGATATCAAGTCTT-TAT-CTC-
1 TGAAATTGAAGTAAGAGC--AAGATC--GT-TTCTATCCTCT
*
33605867 TGAAATTGAAGTAAGAGCAAGATCATTTCATATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTTC-TATCCTCT
***
33605905 TGAAATTGAAGT-AGAGTTGGATAACAAGTCTT-TAT-CTC-
1 TGAAATTGAAGTAAGAGCAAGAT--C--GT-TTCTATCCTCT
*
33605943 TGAAATTGAAGTAAGAGCAAGATCGTTTCCCATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCGTTT-CTATCCTCT
33605981 TGAAATTGAAGTAA
1 TGAAATTGAAGTAA
33605995 AGTTGGATAG
Statistics
Matches: 349, Mismatches: 61, Indels: 114
0.67 0.12 0.22
Matches are distributed among these distances:
34 11 0.03
35 15 0.04
36 33 0.09
37 71 0.20
38 137 0.39
39 46 0.13
40 20 0.06
41 11 0.03
42 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (37 bp):
TGAAATTGAAGTAAGAGCAAGATCGTTTCTATCCTCT
Found at i:33606326 original size:6 final size:6
Alignment explanation
Indices: 33606288--33606381 Score: 63
Period size: 6 Copynumber: 15.8 Consensus size: 6
33606278 GGCTTGGGCT
* **
33606288 TTTAAA GTTTAAA -TTAAT TTTAAA TTT-GT TTTAAA TTTAAA TTT--A
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
33606333 TCTTAAA TTTAAA TTTACTTA TTTAAA TTT-AT TTTAGA TTTAAA TTTAA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
33606382 TCAAATTCAA
Statistics
Matches: 67, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
4 2 0.03
5 13 0.19
6 39 0.58
7 8 0.12
8 5 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:33606326 original size:17 final size:17
Alignment explanation
Indices: 33606301--33606380 Score: 94
Period size: 17 Copynumber: 4.9 Consensus size: 17
33606291 AAAGTTTAAA
* * *
33606301 TTAATTTTAAATTTGTT
1 TTAAATTTAAATTTATC
33606318 TTAAATTTAAATTTATC
1 TTAAATTTAAATTTATC
33606335 TTAAATTTAAATTTA-C
1 TTAAATTTAAATTTATC
*
33606351 TT--ATTTAAATTTATT
1 TTAAATTTAAATTTATC
*
33606366 TTAGATTTAAATTTA
1 TTAAATTTAAATTTA
33606381 ATCAAATTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
14 11 0.20
15 2 0.04
16 3 0.05
17 40 0.71
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TTAAATTTAAATTTATC
Found at i:33606329 original size:28 final size:29
Alignment explanation
Indices: 33606287--33606342 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
33606277 GGGCTTGGGC
*
33606287 TTTTAAAGTTTAAATTAATTTTAAATTTG
1 TTTTAAAGTTTAAATTAATCTTAAATTTG
*
33606316 TTTTAAA-TTTAAATTTATCTTAAATTT
1 TTTTAAAGTTTAAATTAATCTTAAATTT
33606343 AAATTTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (29 bp):
TTTTAAAGTTTAAATTAATCTTAAATTTG
Found at i:33606360 original size:31 final size:31
Alignment explanation
Indices: 33606322--33606380 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
33606312 TTTGTTTTAA
33606322 ATTTAAATTTATCTTAAATTTAAATTTACTT
1 ATTTAAATTTATCTTAAATTTAAATTTACTT
* *
33606353 ATTTAAATTTATTTTAGATTTAAATTTA
1 ATTTAAATTTATCTTAAATTTAAATTTA
33606381 ATCAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (31 bp):
ATTTAAATTTATCTTAAATTTAAATTTACTT
Found at i:33606373 original size:11 final size:11
Alignment explanation
Indices: 33606295--33606374 Score: 52
Period size: 11 Copynumber: 6.9 Consensus size: 11
33606285 GCTTTTAAAG
*
33606295 TTTAAATTAAT
1 TTTAAATTTAT
*
33606306 TTTAAATTTGT
1 TTTAAATTTAT
*
33606317 TTTAAATTTAAA
1 TTTAAATTT-AT
** * *
33606329 TTTATCTTAAA
1 TTTAAATTTAT
33606340 TTTAAATTTACTT
1 TTTAAATTTA--T
33606353 ATTTAAATTTAT
1 -TTTAAATTTAT
*
33606365 TTTAGATTTA
1 TTTAAATTTA
33606375 AATTTAATCA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
11 36 0.68
12 7 0.13
14 10 0.19
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:33607581 original size:7 final size:7
Alignment explanation
Indices: 33607569--33607597 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
33607559 TTTTAAAGGA
33607569 AATAAAG
1 AATAAAG
33607576 AATAAAG
1 AATAAAG
33607583 AATAAAG
1 AATAAAG
33607590 AA-AAAG
1 AATAAAG
33607596 AA
1 AA
33607598 GAAAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (7 bp):
AATAAAG
Found at i:33608496 original size:117 final size:118
Alignment explanation
Indices: 33608346--33608596 Score: 382
Period size: 117 Copynumber: 2.1 Consensus size: 118
33608336 CCTAAAACTT
* * *
33608346 CCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACC-CTGATTTCATC-AA
1 CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCTC-AATTTCACCAAA
* * * *
33608409 AATTACCATTTTACCTCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
65 AATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCGATTTCA
* *
33608463 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCAATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCTCAATTTCACCAAAA
*
33608528 ATTACCATTTTACCCCCAAACTCTCAAAAATTTCATTTTTAACCCCGATTTCA
66 ATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCGATTTCA
33608581 CC-AAAATTACCATTTT
1 CCAAAAATTACCATTTT
33608597 GCCTCCGAGT
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
117 68 0.56
118 54 0.44
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (118 bp):
CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCTCAATTTCACCAAAA
ATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTTTAACCCCGATTTCA
Found at i:33608499 original size:59 final size:59
Alignment explanation
Indices: 33608346--33608596 Score: 382
Period size: 59 Copynumber: 4.3 Consensus size: 59
33608336 CCTAAAACTT
*
33608346 CCAAAAATTACCATTTTACCCCTAAACTCTCCAAAATTCCATTTTTAACC-CTGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCTC-GATTTCA
* * *
33608405 TC-AAAATTACCATTTTACCTCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCA
* * *
33608463 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCA
* * *
33608522 CCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTTCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCA
33608581 CC-AAAATTACCATTTT
1 CCAAAAATTACCATTTT
33608597 GCCTCCGAGT
Statistics
Matches: 176, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
58 66 0.38
59 110 0.62
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTCCATTTTTAACCTCGATTTCA
Found at i:33608586 original size:29 final size:29
Alignment explanation
Indices: 33608376--33608596 Score: 161
Period size: 29 Copynumber: 7.5 Consensus size: 29
33608366 CCTAAACTCT
*
33608376 CCAAAATTCCATTTTTAACCCTGATTTCA
1 CCAAAATTCCATTTTTAACCCCGATTTCA
* *
33608405 TCAAAATTACCA-TTTT-ACCTCCAAACTTT--
1 CCAAAATT-CCATTTTTAACC-CC-GA-TTTCA
*
33608434 CCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAATTCCATTTTTAACCCCGATTTCA
*
33608463 CCAAAAATTACCA-TTTTACCCCCGAACTTT--
1 CC-AAAATT-CCATTTTTAACCCCG-A-TTTCA
* *
33608493 CCAAAATTCCATTTTTAACCTCAATTTCA
1 CCAAAATTCCATTTTTAACCCCGATTTCA
* * ** *
33608522 CCAAAAATTACCA-TTTTACCCCCAAACTCT
1 CC-AAAATT-CCATTTTTAACCCCGATTTCA
* *
33608552 CAAAAATTTCATTTTTAACCCCGATTTCA
1 CCAAAATTCCATTTTTAACCCCGATTTCA
33608581 CCAAAATTACCATTTT
1 CCAAAATT-CCATTTT
33608597 GCCTCCGAGT
Statistics
Matches: 148, Mismatches: 25, Indels: 37
0.70 0.12 0.18
Matches are distributed among these distances:
27 6 0.04
28 13 0.09
29 67 0.45
30 49 0.33
31 10 0.07
32 3 0.02
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (29 bp):
CCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:33608604 original size:29 final size:29
Alignment explanation
Indices: 33608349--33608604 Score: 133
Period size: 29 Copynumber: 8.8 Consensus size: 29
33608339 AAAACTTCCA
* ** *
33608349 AAAATTACCATTTTACC-CCTAAACTCTCC
1 AAAATTACCATTTTACCTCC-GATTTCACC
* *
33608378 AAAATT-CCATTTTTAACC-CTGATTTCATC
1 AAAATTACCA-TTTT-ACCTCCGATTTCACC
*
33608407 AAAATTACCATTTTACCTCCAAACTTT--CC
1 AAAATTACCATTTTACCTCC-GA-TTTCACC
33608436 AAAATT-CCATTTTTAACCT-CGATTTCACC
1 AAAATTACCA-TTTT-ACCTCCGATTTCACC
*
33608465 AAAAATTACCATTTTACCCCCGAACTTT--CC
1 -AAAATTACCATTTTACCTCCG-A-TTTCACC
*
33608495 AAAATT-CCATTTTTAACCT-CAATTTCACC
1 AAAATTACCA-TTTT-ACCTCCGATTTCACC
* * ** * *
33608524 AAAAATTACCATTTTACCCCCAAACTCTCA
1 -AAAATTACCATTTTACCTCCGATTTCACC
*
33608554 AAAATT-TCATTTTTAACC-CCGATTTCACC
1 AAAATTACCA-TTTT-ACCTCCGATTTCACC
*
33608583 AAAATTACCATTTTGCCTCCGA
1 AAAATTACCATTTTACCTCCGA
33608605 GTATCCAAAA
Statistics
Matches: 175, Mismatches: 26, Indels: 52
0.69 0.10 0.21
Matches are distributed among these distances:
27 6 0.03
28 18 0.10
29 88 0.50
30 50 0.29
31 10 0.06
32 3 0.02
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTACCTCCGATTTCACC
Found at i:33608630 original size:58 final size:58
Alignment explanation
Indices: 33608346--33608636 Score: 318
Period size: 59 Copynumber: 5.0 Consensus size: 58
33608336 CCTAAAACTT
* * *
33608346 CCAAAAATTACCATTTTACC-CCTAAACTCTCCAAAATTCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCTCC--GACTATCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
33608405 TC-AAAATTACCATTTTACCTCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCTCC-GACTATCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
33608463 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCAATTTCA
1 CCAAAAATTACCATTTTACCTCCG-ACTATCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
33608522 CCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTTCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCTCC-GACTATCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
33608581 CC-AAAATTACCATTTTGCCTCCGAGTATCCAAAAGTCCCGTTTTCAACCCCGATTT
1 CCAAAAATTACCATTTTACCTCCGACTATCCAAAA-TTCCATTTTTAACCCCGATTT
33608637 TATCGTTTCT
Statistics
Matches: 203, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
57 8 0.04
58 86 0.42
59 109 0.54
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCTCCGACTATCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:33609995 original size:12 final size:12
Alignment explanation
Indices: 33609967--33609999 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
33609957 TGCTTTAAAC
33609967 TTCTTG-ATTTT
1 TTCTTGTATTTT
33609978 TT-TTGTATTTT
1 TTCTTGTATTTT
33609989 TTCTTGTATTT
1 TTCTTGTATTT
33610000 CTCTGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 3 0.15
11 9 0.45
12 8 0.40
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (12 bp):
TTCTTGTATTTT
Found at i:33612233 original size:2 final size:2
Alignment explanation
Indices: 33612221--33612276 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
33612211 TGAGACTATT
33612221 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
33612262 TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA T
33612277 GTGTGAAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33628318 original size:25 final size:24
Alignment explanation
Indices: 33628289--33628345 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
33628279 GTCTGCAATT
*
33628289 TTTTTTTCTATCTGTAATTTTTCTG
1 TTTTTTTCT-TCTGTAATTTTTCTA
33628314 TTTTTTTC-TCTGTAATTTTTCTA
1 TTTTTTTCTTCTGTAATTTTTCTA
*
33628337 TTTCTTTCT
1 TTTTTTTCT
33628346 CTATTTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 21 0.72
25 8 0.28
ACGTcount: A:0.11, C:0.14, G:0.05, T:0.70
Consensus pattern (24 bp):
TTTTTTTCTTCTGTAATTTTTCTA
Found at i:33628367 original size:15 final size:13
Alignment explanation
Indices: 33628333--33628443 Score: 64
Period size: 13 Copynumber: 9.4 Consensus size: 13
33628323 CTGTAATTTT
33628333 TCTA-TTTCTTTC
1 TCTATTTTCTTTC
33628345 TCTATTTTCTTTC
1 TCTATTTTCTTTC
*
33628358 TCTATATT-TTT-
1 TCTATTTTCTTTC
*
33628369 T-T-GTTTCTTTC
1 TCTATTTTCTTTC
**
33628380 TCTATGAT-TTT-
1 TCTATTTTCTTTC
33628391 TCTA-TTTCTTTC
1 TCTATTTTCTTTC
* **
33628403 TCTGTAAT-TTT-
1 TCTATTTTCTTTC
*
33628414 TC-AGTTTCTTTC
1 TCTATTTTCTTTC
*
33628426 TCTGTTTTCTTTC
1 TCTATTTTCTTTC
33628439 TCTAT
1 TCTAT
33628444 AATTTTTTTG
Statistics
Matches: 70, Mismatches: 18, Indels: 21
0.64 0.17 0.19
Matches are distributed among these distances:
9 2 0.03
10 6 0.09
11 14 0.20
12 19 0.27
13 29 0.41
ACGTcount: A:0.10, C:0.19, G:0.05, T:0.67
Consensus pattern (13 bp):
TCTATTTTCTTTC
Found at i:33628368 original size:58 final size:57
Alignment explanation
Indices: 33628292--33628405 Score: 165
Period size: 58 Copynumber: 2.0 Consensus size: 57
33628282 TGCAATTTTT
* * *
33628292 TTTTCTATCTGTAATTTTTCTGTTTTTTTCTCTGTAATTTTTCTATTTCTTTCTCTA
1 TTTTCTATCTCTAATTTTTCTGTTTCTTTCTCTATAATTTTTCTATTTCTTTCTCTA
* * *
33628349 TTTTCTTTCTCTATATTTTTTTGTTTCTTTCTCTATGATTTTTCTATTTCTTTCTCT
1 TTTTCTATCTCTA-ATTTTTCTGTTTCTTTCTCTATAATTTTTCTATTTCTTTCTCT
33628406 GTAATTTTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 11 0.22
58 39 0.78
ACGTcount: A:0.11, C:0.17, G:0.04, T:0.68
Consensus pattern (57 bp):
TTTTCTATCTCTAATTTTTCTGTTTCTTTCTCTATAATTTTTCTATTTCTTTCTCTA
Found at i:33628376 original size:22 final size:23
Alignment explanation
Indices: 33628350--33628428 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 23
33628340 CTTTCTCTAT
*
33628350 TTTCTTTCTCTAT-ATTTTTTTG
1 TTTCTTTCTCTATAATTTTTCTG
* *
33628372 TTTCTTTCTCTATGATTTTTCTA
1 TTTCTTTCTCTATAATTTTTCTG
* *
33628395 TTTCTTTCTCTGTAATTTTTCAG
1 TTTCTTTCTCTATAATTTTTCTG
33628418 TTTCTTTCTCT
1 TTTCTTTCTCT
33628429 GTTTTCTTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
22 13 0.26
23 37 0.74
ACGTcount: A:0.10, C:0.18, G:0.05, T:0.67
Consensus pattern (23 bp):
TTTCTTTCTCTATAATTTTTCTG
Found at i:33628376 original size:35 final size:35
Alignment explanation
Indices: 33628314--33628393 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
33628304 AATTTTTCTG
*
33628314 TTTTTTTCTCTGTAATTTTTCTATTTCTTTCTCTA
1 TTTTTTTCTCTATAATTTTTCTATTTCTTTCTCTA
* *
33628349 TTTTCTTTCTCTAT-ATTTTTTTGTTTCTTTCTCTA
1 TTTT-TTTCTCTATAATTTTTCTATTTCTTTCTCTA
*
33628384 TGATTTTTCT
1 T-TTTTTTCT
33628394 ATTTCTTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 29 0.74
36 10 0.26
ACGTcount: A:0.10, C:0.16, G:0.04, T:0.70
Consensus pattern (35 bp):
TTTTTTTCTCTATAATTTTTCTATTTCTTTCTCTA
Found at i:33628405 original size:81 final size:82
Alignment explanation
Indices: 33628305--33628462 Score: 266
Period size: 81 Copynumber: 1.9 Consensus size: 82
33628295 TCTATCTGTA
* *
33628305 ATTTTTCTGTTTTTTTCTCTGTAATTTTTCTA-TTTCTTTCTCTATTTTCTTTCTCTAT-ATTTT
1 ATTTTTCTATTTCTTTCTCTGTAATTTTTC-AGTTTCTTTCTCTATTTTCTTTCTCTATAATTTT
33628368 TTTGTTTCTTTCTCTATG
65 TTTGTTTCTTTCTCTATG
*
33628386 ATTTTTCTATTTCTTTCTCTGTAATTTTTCAGTTTCTTTCTCTGTTTTCTTTCTCTATAATTTTT
1 ATTTTTCTATTTCTTTCTCTGTAATTTTTCAGTTTCTTTCTCTATTTTCTTTCTCTATAATTTTT
33628451 TTGTTTCTTTCT
66 TTGTTTCTTTCT
33628463 GTCAGACTAG
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
80 1 0.01
81 53 0.74
82 18 0.25
ACGTcount: A:0.10, C:0.16, G:0.05, T:0.68
Consensus pattern (82 bp):
ATTTTTCTATTTCTTTCTCTGTAATTTTTCAGTTTCTTTCTCTATTTTCTTTCTCTATAATTTTT
TTGTTTCTTTCTCTATG
Found at i:33628432 original size:58 final size:58
Alignment explanation
Indices: 33628305--33628462 Score: 165
Period size: 58 Copynumber: 2.7 Consensus size: 58
33628295 TCTATCTGTA
* * * * *
33628305 ATTTTTCTGTTTTTTTCTCTGTAATTTTTCTATTTCTTTCTCTATTTTCTTTCTCTAT
1 ATTTCTCTGTTTCTTTCTCTATAATTTTTCTATTTCTTTCTCTATATTCTTTCACTAT
* * * * * *
33628363 ATTTTTTTGTTTCTTTCTCTATGATTTTTCTATTTCTTTCTCTGTAATT-TTTCAGTTT
1 ATTTCTCTGTTTCTTTCTCTATAATTTTTCTATTTCTTTCTCTAT-ATTCTTTCACTAT
* * *
33628421 CTTTCTCTGTTTTCTTTCTCTATAATTTTTTTGTTTCTTTCT
1 ATTTCTCTG-TTTCTTTCTCTATAATTTTTCTATTTCTTTCT
33628463 GTCAGACTAG
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
58 52 0.63
59 31 0.37
ACGTcount: A:0.10, C:0.16, G:0.05, T:0.68
Consensus pattern (58 bp):
ATTTCTCTGTTTCTTTCTCTATAATTTTTCTATTTCTTTCTCTATATTCTTTCACTAT
Found at i:33629684 original size:21 final size:22
Alignment explanation
Indices: 33629646--33629700 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
33629636 AAAGAGACAT
* **
33629646 GTATTGATAGATATCTTAA-AA
1 GTATTGATACATGCCTTAACAA
*
33629667 GTATTGATACATGCCTTAACTA
1 GTATTGATACATGCCTTAACAA
33629689 -TATTGATACATG
1 GTATTGATACATG
33629701 GGTGTCAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (22 bp):
GTATTGATACATGCCTTAACAA
Found at i:33639584 original size:17 final size:17
Alignment explanation
Indices: 33639553--33639599 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
33639543 AAAATCTTCA
* *
33639553 TTGAAA-CCTTAAAATT
1 TTGAAATCCCTAAAATG
33639569 TTGAAATCCCTAAAATG
1 TTGAAATCCCTAAAATG
*
33639586 TTAAAATCCCTAAA
1 TTGAAATCCCTAAA
33639600 TCATTAGCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (17 bp):
TTGAAATCCCTAAAATG
Found at i:33639655 original size:16 final size:16
Alignment explanation
Indices: 33639626--33639669 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
33639616 ATCTTCTTTG
33639626 AATCCCTAAAATATTAA
1 AATCCCT-AAATATTAA
*
33639643 AATCCCTAAATATTGA
1 AATCCCTAAATATTAA
*
33639659 AATCCATAAAT
1 AATCCCTAAAT
33639670 CGTTGAATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (16 bp):
AATCCCTAAATATTAA
Found at i:33640797 original size:51 final size:51
Alignment explanation
Indices: 33640725--33640837 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 51
33640715 GTGAAGTTGC
* * *
33640725 TGCTGATTTTGCAATAGCAGATGGAGAGGATAATGTTGTTGATGAATATGA
1 TGCTAATTTTGCAACAGCAGATGGAGAGGATAATGTTGCTGATGAATATGA
* * * *
33640776 TGCTAATTTTGCAACATCAGATGGAGTGGATACTGTTGCTGATGAATATGC
1 TGCTAATTTTGCAACAGCAGATGGAGAGGATAATGTTGCTGATGAATATGA
*
33640827 TGTTAATTTTG
1 TGCTAATTTTG
33640838 ATGATAAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.28, C:0.09, G:0.27, T:0.36
Consensus pattern (51 bp):
TGCTAATTTTGCAACAGCAGATGGAGAGGATAATGTTGCTGATGAATATGA
Found at i:33644132 original size:24 final size:24
Alignment explanation
Indices: 33644100--33644146 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
33644090 ACACGAATCG
*
33644100 AGAATGGTTAGCTCTTATGAGCCC
1 AGAATGGTTAGCTCATATGAGCCC
33644124 AGAATGGTTAGCTCATATGAGCC
1 AGAATGGTTAGCTCATATGAGCC
33644147 TAGACAGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (24 bp):
AGAATGGTTAGCTCATATGAGCCC
Found at i:33647526 original size:15 final size:15
Alignment explanation
Indices: 33647503--33647537 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
33647493 TTTTTGGAAT
*
33647503 GATTAGGGACTTCAC
1 GATTTGGGACTTCAC
*
33647518 GATTTGGGATTTCAC
1 GATTTGGGACTTCAC
33647533 GATTT
1 GATTT
33647538 TGTTCTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (15 bp):
GATTTGGGACTTCAC
Found at i:33658482 original size:29 final size:27
Alignment explanation
Indices: 33658436--33658492 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 27
33658426 GACAATAATA
33658436 ATTTAAAAAAATTAAAATATAAATATT
1 ATTTAAAAAAATTAAAATATAAATATT
33658463 ATTTAAAAATTAATTAAAATATAAATATT
1 ATTTAAAAA--AATTAAAATATAAATATT
33658492 A
1 A
33658493 AATCATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 9 0.32
29 19 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
ATTTAAAAAAATTAAAATATAAATATT
Found at i:33658706 original size:30 final size:30
Alignment explanation
Indices: 33658662--33658740 Score: 142
Period size: 30 Copynumber: 2.7 Consensus size: 30
33658652 TGAGTAATAA
*
33658662 TATACAT-GAATTTTGATTTTGTGTAATTT
1 TATACATAAAATTTTGATTTTGTGTAATTT
33658691 TATACATAAAATTTTGATTTTGTGTAATTT
1 TATACATAAAATTTTGATTTTGTGTAATTT
33658721 TATACATAAAATTTTGATTT
1 TATACATAAAATTTTGATTT
33658741 GATCAAATTC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 7 0.15
30 41 0.85
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (30 bp):
TATACATAAAATTTTGATTTTGTGTAATTT
Found at i:33658952 original size:29 final size:30
Alignment explanation
Indices: 33658898--33658954 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
33658888 TTTGAGCCAC
* * *
33658898 AATTAGAATTTCATATGTATAATTACATGA
1 AATTAAAATTTCATATATACAATTACATGA
33658928 AATTAAAATTT-ATATATACAATTACAT
1 AATTAAAATTTCATATATACAATTACAT
33658955 ATTAAATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (30 bp):
AATTAAAATTTCATATATACAATTACATGA
Found at i:33658979 original size:29 final size:27
Alignment explanation
Indices: 33658912--33658979 Score: 64
Period size: 31 Copynumber: 2.4 Consensus size: 27
33658902 AGAATTTCAT
* *
33658912 ATGTATAATTACATGAAATTAAAATTT
1 ATGTATAATTACATGAAATCAAAATTC
* *
33658939 ATATATACAATTACATATTAAATCAAAATTC
1 ATGTAT--AATTAC--ATGAAATCAAAATTC
33658970 ATGTATAATT
1 ATGTATAATT
33658980 TTAAGATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
27 5 0.16
29 10 0.31
31 17 0.53
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (27 bp):
ATGTATAATTACATGAAATCAAAATTC
Found at i:33661190 original size:63 final size:65
Alignment explanation
Indices: 33661117--33661248 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 65
33661107 ATTGTGTAGC
** *
33661117 CTGGTTCATCTGGTGACAAAGATTTGTATATTTCTATAGATGAAACCAAG-TTTTG-TTGAATGT
1 CTGGTTCATCTAATGACAAAGATTTGTATATTTCAATAGATGAAACCAAGTTTTTGTTTGAATGT
* * * * *
33661180 CTGGTTCATCTAATGACAAAGATTTTTATGTTTCAATTGATGAAACTAAGTTTTTGTTTGAATTT
1 CTGGTTCATCTAATGACAAAGATTTGTATATTTCAATAGATGAAACCAAGTTTTTGTTTGAATGT
33661245 CTGG
1 CTGG
33661249 ATTGTAGCAG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
63 43 0.73
64 5 0.08
65 11 0.19
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (65 bp):
CTGGTTCATCTAATGACAAAGATTTGTATATTTCAATAGATGAAACCAAGTTTTTGTTTGAATGT
Found at i:33670100 original size:32 final size:33
Alignment explanation
Indices: 33670007--33670107 Score: 105
Period size: 35 Copynumber: 3.0 Consensus size: 33
33669997 ATCCAAATAA
* * * *
33670007 ACAGCAAAACATTTCAAATATGAAAGTAAAAGCC
1 ACAGCAAAACATTACAAACATGCAAGTAACAG-C
** *
33670041 AACAGCAAAACATTGTAAACATGCAAGTAGCAGC
1 -ACAGCAAAACATTACAAACATGCAAGTAACAGC
*
33670075 ACAGGAAAACATTACAAA-ATGCAAGTAACAGC
1 ACAGCAAAACATTACAAACATGCAAGTAACAGC
33670107 A
1 A
33670108 AATGGGTAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
32 14 0.25
33 15 0.27
34 1 0.02
35 26 0.46
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.15
Consensus pattern (33 bp):
ACAGCAAAACATTACAAACATGCAAGTAACAGC
Found at i:33673878 original size:3 final size:3
Alignment explanation
Indices: 33673870--33673899 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
33673860 GGAATGCAGA
33673870 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33673900 TTGTTAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:33677183 original size:3 final size:3
Alignment explanation
Indices: 33677175--33677202 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
33677165 TTTTCTAGTT
33677175 GAG GAG GAG GAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG G
33677203 TACCTGCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:33679756 original size:28 final size:30
Alignment explanation
Indices: 33679694--33679760 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
33679684 TTTTCTCATT
* *
33679694 TTGGTACCTAAACATTTTTTTTTGTTATAA
1 TTGGTACCTAAACATATTTTTTTCTTATAA
* *
33679724 ATGGTACCTAAAC-TATTTTTTTCTTA-AG
1 TTGGTACCTAAACATATTTTTTTCTTATAA
33679752 TTGGTACCT
1 TTGGTACCT
33679761 TTGTGGTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 9 0.28
29 11 0.34
30 12 0.38
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.49
Consensus pattern (30 bp):
TTGGTACCTAAACATATTTTTTTCTTATAA
Done.