Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 29 of 199
Found at i:12128337 original size:6 final size:6
Alignment explanation
Indices: 12128328--12128374 Score: 71
Period size: 6 Copynumber: 8.0 Consensus size: 6
12128318 TAGATATAAA
12128328 AAATAT AAATAT AAATAT AAATA- AAATA- ATAATAT AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT A-AATAT AAATAT AAATAT
12128375 TTATAATGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 6 0.15
6 32 0.82
7 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:12128338 original size:29 final size:31
Alignment explanation
Indices: 12128305--12128380 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 31
12128295 GCTTTTAAAA
* *
12128305 AAATATATATTTATAGATATAA-AA-AATAT
1 AAATATATATTTATAAATAAAATAATAATAT
*
12128334 AAATATA-A-ATATAAATAAAATAATAATAT
1 AAATATATATTTATAAATAAAATAATAATAT
12128363 AAATATAAATATTTATAA
1 AAATAT--ATATTTATAA
12128381 TGAATATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 9 0.24
28 3 0.08
29 18 0.49
31 1 0.03
32 1 0.03
33 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (31 bp):
AAATATATATTTATAAATAAAATAATAATAT
Found at i:12128353 original size:23 final size:23
Alignment explanation
Indices: 12128327--12128373 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
12128317 ATAGATATAA
12128327 AAAAT-ATAAATATAAATATAAAT
1 AAAATAAT-AATATAAATATAAAT
12128350 AAAATAATAATATAAATATAAAT
1 AAAATAATAATATAAATATAAAT
12128373 A
1 A
12128374 TTTATAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAATAATAATATAAATATAAAT
Found at i:12134783 original size:35 final size:35
Alignment explanation
Indices: 12134737--12134806 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
12134727 CTCCTCGCTT
12134737 GTGACACTAGTTTGATTGACTTGGCATTTAATAGA
1 GTGACACTAGTTTGATTGACTTGGCATTTAATAGA
12134772 GTGACACTAGTTTGATTGACTTGGCATTTAATAGA
1 GTGACACTAGTTTGATTGACTTGGCATTTAATAGA
12134807 TAATTAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (35 bp):
GTGACACTAGTTTGATTGACTTGGCATTTAATAGA
Found at i:12135932 original size:6 final size:6
Alignment explanation
Indices: 12135921--12135968 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
12135911 AAAAAATTGG
12135921 ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA
1 ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA
12135969 GTAAATCCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATTTGA
Found at i:12136221 original size:18 final size:18
Alignment explanation
Indices: 12136198--12136232 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12136188 CCAATTATCG
*
12136198 ATTCAACCGGTTCGATCA
1 ATTCAACCAGTTCGATCA
*
12136216 ATTCAATCAGTTCGATC
1 ATTCAACCAGTTCGATC
12136233 GAATAAATTA
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:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (18 bp):
ATTCAACCAGTTCGATCA
Found at i:12143346 original size:3 final size:3
Alignment explanation
Indices: 12143338--12143368 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12143328 GATAGGAAAG
12143338 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12143369 TAAGATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12153095 original size:25 final size:25
Alignment explanation
Indices: 12153043--12153091 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
12153033 ACATGGAAGG
12153043 TAATTAAAATCACCATGATAAAAGC
1 TAATTAAAATCACCATGATAAAAGC
12153068 TAATT-AAAT-ACCAT-AGTAAAAGC
1 TAATTAAAATCACCATGA-TAAAAGC
12153091 T
1 T
12153092 CTAAACCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 1 0.04
23 13 0.57
24 4 0.17
25 5 0.22
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (25 bp):
TAATTAAAATCACCATGATAAAAGC
Found at i:12156799 original size:19 final size:18
Alignment explanation
Indices: 12156759--12156804 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
12156749 AAGTTTGATA
* *
12156759 TTTTTAAAATTTTAATAT
1 TTTTTAAAATTCTAATAC
*
12156777 TTTTTAAGAATTCTAATGC
1 TTTTTAA-AATTCTAATAC
12156796 TTTTTAAAA
1 TTTTTAAAA
12156805 AAAATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (18 bp):
TTTTTAAAATTCTAATAC
Found at i:12156923 original size:16 final size:16
Alignment explanation
Indices: 12156899--12156941 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
12156889 AAAATTTTAA
12156899 TATTATTTTTAATGTT
1 TATTATTTTTAATGTT
* *
12156915 TATTTTTTTTAATTTT
1 TATTATTTTTAATGTT
*
12156931 TAATATTTTTA
1 TATTATTTTTA
12156942 TGAAAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TATTATTTTTAATGTT
Found at i:12164091 original size:18 final size:18
Alignment explanation
Indices: 12164051--12164093 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
12164041 CAAAAGCCCA
* *
12164051 AGCTTTTTCCCAGTATTG
1 AGCTTGTTCCCAGTATAG
12164069 AGCTTGTTCCCAGTACTAG
1 AGCTTGTTCCCAGTA-TAG
12164088 -GCTTGT
1 AGCTTGT
12164094 GATTTTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (18 bp):
AGCTTGTTCCCAGTATAG
Found at i:12169637 original size:30 final size:29
Alignment explanation
Indices: 12169603--12169663 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
12169593 GTGATTTGTG
* *
12169603 AAAATTGAATCAAATTAAAATTTCATATAT
1 AAAATTGAATAAAATCAAAATTT-ATATAT
* *
12169633 AAAATTGTATAAAATCAAAATTTATGTAT
1 AAAATTGAATAAAATCAAAATTTATATAT
12169662 AA
1 AA
12169664 CATTACATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAATTGAATAAAATCAAAATTTATATAT
Found at i:12178000 original size:5 final size:5
Alignment explanation
Indices: 12177963--12177996 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
12177953 CCTTTTAAAC
* *
12177963 AACAA AACAA AACAA AACAA AACAG AACAG AACA
1 AACAA AACAA AACAA AACAA AACAA AACAA AACA
12177997 GAACTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.74, C:0.21, G:0.06, T:0.00
Consensus pattern (5 bp):
AACAA
Found at i:12182666 original size:124 final size:123
Alignment explanation
Indices: 12182428--12182673 Score: 320
Period size: 124 Copynumber: 2.0 Consensus size: 123
12182418 CAAAGAATCA
*
12182428 AGAACCAAGCTTCATTGAGTGATTGGAAAGAGAATCTGAGAAACCTTTAAAGTTCTCTTCTTTCT
1 AGAACCAAGCTTCATTGAGTGATTGAAAAGAGAATCTGAGAAACCTTTAAAGTTCTCTTCTTTCT
* * * * * *
12182493 GTAGGTCAGTAATAAGGCATGAATCCAGATAACATAGTATTGACATTGAATTTGTCTCG
66 GTAGCTAAGCAATAAGACATGAATCCAGATAACATAATATCGACATTGAA-TTGTCTCG
*
12182552 AGAACCAAGCTTCATTGAGTGATTGTAAAAG-GCATCTGAGAAACCTTTAAAGTTTCTCTT-TTG
1 AGAACCAAGCTTCATTGAGTGATTG-AAAAGAGAATCTGAGAAACCTTTAAAG-TTCTCTTCTT-
* * *
12182615 T-TGTTGCTAAGCAATAAGATATGAATCCAGAT-ACTATAATATCGACCTTGAATTGTCTC
63 TCTGTAGCTAAGCAATAAGACATGAATCCAGATAAC-ATAATATCGACATTGAATTGTCTC
12182674 AATTTCTAGA
Statistics
Matches: 107, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
123 9 0.08
124 86 0.80
125 12 0.11
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (123 bp):
AGAACCAAGCTTCATTGAGTGATTGAAAAGAGAATCTGAGAAACCTTTAAAGTTCTCTTCTTTCT
GTAGCTAAGCAATAAGACATGAATCCAGATAACATAATATCGACATTGAATTGTCTCG
Found at i:12197868 original size:2 final size:2
Alignment explanation
Indices: 12197861--12197895 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12197851 ATCACTATTT
12197861 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12197896 TTTAAAAAAA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:12199582 original size:25 final size:25
Alignment explanation
Indices: 12199534--12199582 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
12199524 CATCTTTTCA
* **
12199534 TTAACTATTTAAGTGTTGGTGATAG
1 TTAACTATTTAAATGTTGACGATAG
*
12199559 TTAATTATTTAAATGTTGACGATA
1 TTAACTATTTAAATGTTGACGATA
12199583 AAAATATAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (25 bp):
TTAACTATTTAAATGTTGACGATAG
Found at i:12208965 original size:21 final size:21
Alignment explanation
Indices: 12208941--12208980 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12208931 AATAGACATG
12208941 AATG-ATATAAAAAAATAAAAA
1 AATGAATAT-AAAAAATAAAAA
*
12208962 AATGAATATTAAAAATAAA
1 AATGAATATAAAAAATAAA
12208981 GATCCGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (21 bp):
AATGAATATAAAAAATAAAAA
Found at i:12223103 original size:22 final size:23
Alignment explanation
Indices: 12223059--12223104 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
12223049 TTGAACCGAT
*
12223059 TTTTCTATTTTTTTAAATATTTA
1 TTTTCTATTTTTATAAATATTTA
* *
12223082 TTTT-TATTTTTATGAATTTTTA
1 TTTTCTATTTTTATAAATATTTA
12223104 T
1 T
12223105 ATAATTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTCTATTTTTATAAATATTTA
Found at i:12229061 original size:5 final size:5
Alignment explanation
Indices: 12229051--12229088 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
12229041 CATTCTGTGA
12229051 AGCAC AGCAC AGCAC AGCAC AGCAC AGCAC AGCAC AGC
1 AGCAC AGCAC AGCAC AGCAC AGCAC AGCAC AGCAC AGC
12229089 CAAGGCATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.39, C:0.39, G:0.21, T:0.00
Consensus pattern (5 bp):
AGCAC
Found at i:12235495 original size:3 final size:3
Alignment explanation
Indices: 12235489--12235513 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12235479 CCTTCTTCTT
12235489 CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC C
12235514 AATCGGGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:12238253 original size:21 final size:22
Alignment explanation
Indices: 12238228--12238282 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
12238218 ATCTTAATTC
12238228 TAATAAATTTAAAAAATACAT-A
1 TAATAAATTTAAAAAAT-CATAA
* *
12238250 -AAT-ATTTTAAAAAATTATAA
1 TAATAAATTTAAAAAATCATAA
12238270 TAATAAATTTAAA
1 TAATAAATTTAAA
12238283 TTTTATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.07
20 12 0.44
21 6 0.22
22 7 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TAATAAATTTAAAAAATCATAA
Found at i:12238325 original size:25 final size:24
Alignment explanation
Indices: 12238295--12238343 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
12238285 TTATCAAAAT
**
12238295 TTATATAAATATTAAATAAATATAA
1 TTATATAAATACAAAATAAA-ATAA
*
12238320 TTATATTAATACAAAATAAAATAA
1 TTATATAAATACAAAATAAAATAA
12238344 GAATCCCCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
TTATATAAATACAAAATAAAATAA
Found at i:12240678 original size:15 final size:15
Alignment explanation
Indices: 12240658--12240691 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12240648 TATTCGAGTC
12240658 ATATATTT-TTTAATT
1 ATATATTTGTTT-ATT
12240673 ATATATTTGTTTATT
1 ATATATTTGTTTATT
12240688 ATAT
1 ATAT
12240692 TATAAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
ATATATTTGTTTATT
Found at i:12255780 original size:31 final size:31
Alignment explanation
Indices: 12255712--12255780 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
12255702 TTTTAAAATT
* * * *
12255712 TATATAATTGAATTAAAATTAAAATTTCATA
1 TATATATTTGAATCAAAATCAAAATATCATA
*
12255743 TATATATTTGAATCATAATCAAAATATCATA
1 TATATATTTGAATCAAAATCAAAATATCATA
12255774 TATATAT
1 TATATAT
12255781 ATATATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (31 bp):
TATATATTTGAATCAAAATCAAAATATCATA
Found at i:12256114 original size:22 final size:23
Alignment explanation
Indices: 12256061--12256116 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
12256051 CCCGTTTTTA
* * *
12256061 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
12256084 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
12256106 ATTAAAATTAA
1 ATTAAAATTAA
12256117 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:12256129 original size:16 final size:16
Alignment explanation
Indices: 12256092--12256131 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12256082 TTAATAAAAT
* *
12256092 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
12256108 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
12256124 TAAAATTA
1 TAAAATTA
12256132 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:12256210 original size:59 final size:59
Alignment explanation
Indices: 12256142--12256311 Score: 313
Period size: 59 Copynumber: 2.9 Consensus size: 59
12256132 TCAAATTATT
* *
12256142 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAACTTATCA
12256201 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAACTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAACTTATCA
*
12256260 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
12256312 ACAAACTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 108 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAACTTATCA
Found at i:12266937 original size:29 final size:29
Alignment explanation
Indices: 12266873--12266946 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
12266863 ACTACCAAAA
*
12266873 TAGTCACTTTTGTTTGACTCAAGTTACATTT
1 TAGTCACTTATGTTTGA--CAAGTTACATTT
*
12266904 TAGTCACTTATGTTTGA-AATGTTACGTTT
1 TAGTCACTTATGTTTGACAA-GTTACATTT
12266933 TAGTCACTTATGTT
1 TAGTCACTTATGTT
12266947 ATCATGTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 22 0.55
31 16 0.40
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.49
Consensus pattern (29 bp):
TAGTCACTTATGTTTGACAAGTTACATTT
Found at i:12266968 original size:31 final size:29
Alignment explanation
Indices: 12266898--12266971 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
12266888 GACTCAAGTT
* *
12266898 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
12266927 ACGTTTTAGTCACTTATGTTATCATGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
12266958 ACATTTTAGTCACT
1 ACATTTTAGTCACT
12266972 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:12268359 original size:31 final size:31
Alignment explanation
Indices: 12268324--12268400 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
12268314 AAAAAAACTA
*
12268324 AATAATCCAATAACTTAAATAAAAATTTTCG
1 AATAATTCAATAACTTAAATAAAAATTTTCG
** * * *
12268355 AATAATTTTATTACTTAAATAAAACTTTTCT
1 AATAATTCAATAACTTAAATAAAAATTTTCG
*
12268386 ACTAATTCAATAACT
1 AATAATTCAATAACT
12268401 ATTTTATAAC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (31 bp):
AATAATTCAATAACTTAAATAAAAATTTTCG
Found at i:12270116 original size:105 final size:105
Alignment explanation
Indices: 12269998--12270193 Score: 302
Period size: 105 Copynumber: 1.9 Consensus size: 105
12269988 TCATTTTTTA
* * * * *
12269998 TGATAACTTATATTCAAATTTATAAAAGTCAATTAACAATGTTATTAATTGAACTTTAATTTTTA
1 TGATAACTCATATTCAAATTTATAAAAGCCAATTAACAATGTTATCAATTAAACTTTAATTTGTA
*
12270063 ACCAATAGAGGAACTAAATTCTTAAAGTTAAAAGTTAAAT
66 ACAAATAGAGGAACTAAATTCTTAAAGTTAAAAGTTAAAT
*
12270103 TGATAACTCATATTCAAATTTATAGAAGCCAATTAACAATGTTATCAATTAAACTTTAATTTGTA
1 TGATAACTCATATTCAAATTTATAAAAGCCAATTAACAATGTTATCAATTAAACTTTAATTTGTA
* * *
12270168 ACAAATAGAGGGATTAAGTTCTTAAA
66 ACAAATAGAGGAACTAAATTCTTAAA
12270194 ACTATAAGCA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 81 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (105 bp):
TGATAACTCATATTCAAATTTATAAAAGCCAATTAACAATGTTATCAATTAAACTTTAATTTGTA
ACAAATAGAGGAACTAAATTCTTAAAGTTAAAAGTTAAAT
Found at i:12280502 original size:6 final size:6
Alignment explanation
Indices: 12280493--12280523 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
12280483 AGCACCAGAA
*
12280493 GCTGAT GCTGAT GCTGAT GCTGAT GCCGAT G
1 GCTGAT GCTGAT GCTGAT GCTGAT GCTGAT G
12280524 AACCCTCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.19, G:0.35, T:0.29
Consensus pattern (6 bp):
GCTGAT
Found at i:12282675 original size:3 final size:3
Alignment explanation
Indices: 12282667--12282699 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
12282657 GGTCAGCGTT
12282667 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
12282700 CTGTTTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:12287149 original size:24 final size:24
Alignment explanation
Indices: 12287117--12287171 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
12287107 TTCAGTGCAT
12287117 CCCGTTAATTGCTCTTCGGAGCTA
1 CCCGTTAATTGCTCTTCGGAGCTA
*
12287141 CCCGTTAATTGCTCTTTGGAGCTA
1 CCCGTTAATTGCTCTTCGGAGCTA
*
12287165 CCGGTTA
1 CCCGTTA
12287172 TAGGCTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.35
Consensus pattern (24 bp):
CCCGTTAATTGCTCTTCGGAGCTA
Found at i:12287178 original size:24 final size:25
Alignment explanation
Indices: 12287117--12287199 Score: 91
Period size: 24 Copynumber: 3.4 Consensus size: 25
12287107 TTCAGTGCAT
* *
12287117 CCCGTTA-ATTGCTCTTCGGAGCTA
1 CCCGTTATATGGCTCTTTGGAGCTA
*
12287141 CCCGTTA-ATTGCTCTTTGGAGCTA
1 CCCGTTATATGGCTCTTTGGAGCTA
* *
12287165 CCGGTTATA-GGCTCTTTGTGAGCTT
1 CCCGTTATATGGCTCTTTG-GAGCTA
12287190 CCCGTTATAT
1 CCCGTTATAT
12287200 TTCCCGAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
24 37 0.73
25 14 0.27
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (25 bp):
CCCGTTATATGGCTCTTTGGAGCTA
Found at i:12287244 original size:24 final size:24
Alignment explanation
Indices: 12287210--12287269 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
12287200 TTCCCGAATA
12287210 AGCTTCCCGTTACAAGGCTCAATG
1 AGCTTCCCGTTACAAGGCTCAATG
*
12287234 AGCTTCTCGTTACAAGGCTCAATG
1 AGCTTCCCGTTACAAGGCTCAATG
*
12287258 ACCTTCCCGTTA
1 AGCTTCCCGTTA
12287270 TAATGTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.28
Consensus pattern (24 bp):
AGCTTCCCGTTACAAGGCTCAATG
Found at i:12289570 original size:41 final size:41
Alignment explanation
Indices: 12289520--12289818 Score: 481
Period size: 41 Copynumber: 7.3 Consensus size: 41
12289510 AATTCATCAT
*
12289520 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * *
12289561 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
12289602 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
12289643 ATTCAGATCACCGGCGCTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * *
12289684 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
12289725 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* *
12289766 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
12289807 ATTCATATCACC
1 ATTCAGATCACC
12289819 AATTCCAAAC
Statistics
Matches: 238, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 238 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:12289744 original size:123 final size:123
Alignment explanation
Indices: 12289520--12289818 Score: 553
Period size: 123 Copynumber: 2.4 Consensus size: 123
12289510 AATTCATCAT
*
12289520 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCT
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCT
12289585 GCTAGGTTTATAACCTGATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
66 GCTAGGTTTATAACCTGATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
12289643 ATTCAGATCACCGGCGCTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCT
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCT
12289708 GCTAGGTTTATAACCTGATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
66 GCTAGGTTTATAACCTGATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * *
12289766 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCATATCACC
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACC
12289819 AATTCCAAAC
Statistics
Matches: 170, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 170 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (123 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCT
GCTAGGTTTATAACCTGATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:12290054 original size:19 final size:19
Alignment explanation
Indices: 12290030--12290066 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12290020 TTGTTCGATC
*
12290030 CACACATATATATATATTA
1 CACACATATACATATATTA
12290049 CACACATATACATATATT
1 CACACATATACATATATT
12290067 CGCACATTAA
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:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (19 bp):
CACACATATACATATATTA
Found at i:12291627 original size:5 final size:5
Alignment explanation
Indices: 12291612--12291651 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
12291602 TTTTTATGTT
* *
12291612 TTATA -TATA TTATA TTATA TTGTA TTGTA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA T
12291652 AAGTAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:12293501 original size:46 final size:46
Alignment explanation
Indices: 12293427--12293565 Score: 215
Period size: 46 Copynumber: 3.0 Consensus size: 46
12293417 ACAAGGCTAT
* *
12293427 AACTCATTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
12293473 AACTCAGTATGGTTTTCTTTACTAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* * *
12293519 AACTCAGTATGGCTTTCTTCACTGGAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
12293565 A
1 A
12293566 CCTTGCCATG
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 84 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:12294096 original size:46 final size:46
Alignment explanation
Indices: 12294040--12294151 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 46
12294030 CCATGGAAAC
**
12294040 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAGTCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
*
12294086 TTGTGCAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
*
12294132 TTGTGAAAAGCAGGTATGGT
1 TTGTGAAAAGTAGGTATGGT
12294152 AAAATAACAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:12294568 original size:46 final size:46
Alignment explanation
Indices: 12294500--12294593 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
12294490 ACAATGCTAT
* * *
12294500 AACTCAATATGGTTTCCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAATATGATTTCCTTCACTGAAACACCATACCTACATTTCAC
* *
12294546 AACTCAGTATGATTTTCTTCACTGAAACACCATACCTACATTTCAC
1 AACTCAATATGATTTCCTTCACTGAAACACCATACCTACATTTCAC
12294592 AA
1 AA
12294594 TTTTCCATGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (46 bp):
AACTCAATATGATTTCCTTCACTGAAACACCATACCTACATTTCAC
Found at i:12297123 original size:37 final size:37
Alignment explanation
Indices: 12297079--12297170 Score: 175
Period size: 37 Copynumber: 2.5 Consensus size: 37
12297069 CACTTGTCCC
12297079 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
*
12297116 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
12297153 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
12297171 TAAAGCTATC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (37 bp):
TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
Found at i:12297201 original size:46 final size:46
Alignment explanation
Indices: 12297134--12297500 Score: 437
Period size: 46 Copynumber: 7.6 Consensus size: 46
12297124 TAAGTGTAGC
** **
12297134 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
12297180 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
12297226 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
12297278 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
12297330 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
12297376 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
12297422 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
12297474 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
12297501 AGTACTCAAA
Statistics
Matches: 290, Mismatches: 18, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
46 154 0.53
48 1 0.00
49 1 0.00
50 2 0.01
51 3 0.01
52 129 0.44
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:12297253 original size:52 final size:52
Alignment explanation
Indices: 12297177--12297494 Score: 426
Period size: 52 Copynumber: 6.3 Consensus size: 52
12297167 TAGCTAAAGC
* *
12297177 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
12297230 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * *
12297282 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
12297334 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
12297380 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
12297426 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
12297478 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
12297495 ATCAGAAGTA
Statistics
Matches: 239, Mismatches: 16, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
46 84 0.35
47 2 0.01
48 2 0.01
52 133 0.56
53 18 0.08
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:12297442 original size:196 final size:196
Alignment explanation
Indices: 12297134--12297486 Score: 598
Period size: 196 Copynumber: 1.8 Consensus size: 196
12297124 TAAGTGTAGC
** * * * *
12297134 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCACT
*
12297199 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
* *
12297264 GTAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
131 GTAGCCAAAGCTACCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
12297329 T
196 T
*
12297330 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTATCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCACT
*
12297395 TGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
*
12297460 GTAGCTAAAGCTACCACTTATCACTTT
131 GTAGCCAAAGCTACCACTTATCACTTT
12297487 ATCACTTGAT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
196 145 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (196 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATCACT
TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
GTAGCCAAAGCTACCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTA
T
Found at i:12297489 original size:98 final size:97
Alignment explanation
Indices: 12297151--12297500 Score: 494
Period size: 98 Copynumber: 3.6 Consensus size: 97
12297141 CACTTTGTTT
* * *
12297151 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAG
1 CTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTGATCAGATAAGTATAG
12297216 CCGAAGCTATCACTTATCACTTTTCACTTGTCA
66 CCGAAGCTATCACTTATCAC-TTTCACTTGTCA
*
12297249 CTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAA
1 CTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTT--A----TCACTTGATCAGATAA
* *
12297314 GTGTAGCTGAAGCTATCACTTATCAC--T---TTGTCA
60 GTATAGCCGAAGCTATCACTTATCACTTTCACTTGTCA
* *
12297347 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTATCACTTGATCAGATAAGTATAG
1 CTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTGATCAGATAAGTATAG
*
12297412 CCGAAGCTATTACTTATCACTTTCCACTTGTCA
66 CCGAAGCTATCACTTATCACTTT-CACTTGTCA
* *
12297445 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGA
1 CTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTGATCAGA
12297501 AGTACTCAAA
Statistics
Matches: 226, Mismatches: 14, Indels: 24
0.86 0.05 0.09
Matches are distributed among these distances:
92 39 0.17
94 1 0.00
96 1 0.00
98 145 0.64
101 1 0.00
104 39 0.17
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (97 bp):
CTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTATCACTTGATCAGATAAGTATAG
CCGAAGCTATCACTTATCACTTTCACTTGTCA
Found at i:12301258 original size:28 final size:29
Alignment explanation
Indices: 12301199--12301258 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
12301189 GAATTGAAAA
*
12301199 TTTTAATTTTTTTATATTATTTGGTAAGT
1 TTTTAATTTTTTTATATTATTTGGAAAGT
*
12301228 TTTTAATTTTTTTA-ATTATTT-GAAATT
1 TTTTAATTTTTTTATATTATTTGGAAAGT
12301255 TTTT
1 TTTT
12301259 CCAAAGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 8 0.28
28 7 0.24
29 14 0.48
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (29 bp):
TTTTAATTTTTTTATATTATTTGGAAAGT
Found at i:12302045 original size:18 final size:19
Alignment explanation
Indices: 12302018--12302053 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12302008 TTTTTATCTT
*
12302018 ATATTATAATTTTGTTATA
1 ATATTATAATTTTATTATA
12302037 ATATT-TAATTTTATTAT
1 ATATTATAATTTTATTAT
12302054 CAGCATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
ATATTATAATTTTATTATA
Found at i:12316279 original size:28 final size:27
Alignment explanation
Indices: 12316236--12316290 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
12316226 TCCGAATTTC
*
12316236 AAATCCGAAGCTTAAACTCTAAATCTT
1 AAATCCGAACCTTAAACTCTAAATCTT
* *
12316263 AAATCTCGAACCTTAAATTTTAAATCTT
1 AAATC-CGAACCTTAAACTCTAAATCTT
12316291 GAATGGATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (27 bp):
AAATCCGAACCTTAAACTCTAAATCTT
Found at i:12316503 original size:19 final size:20
Alignment explanation
Indices: 12316463--12316501 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12316453 ATTTTTATTT
12316463 ATATATAATTCACTTTATAA
1 ATATATAATTCACTTTATAA
*
12316483 ATATAT-ATTTACTTT-TAA
1 ATATATAATTCACTTTATAA
12316501 A
1 A
12316502 ATTCTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATATAATTCACTTTATAA
Found at i:12324060 original size:9 final size:9
Alignment explanation
Indices: 12324048--12324131 Score: 57
Period size: 9 Copynumber: 9.1 Consensus size: 9
12324038 AAATATATTT
12324048 ATTTTTTAA
1 ATTTTTTAA
*
12324057 ATTTTTTTA
1 ATTTTTTAA
12324066 A--TTTTAA
1 ATTTTTTAA
12324073 ATATTTTTAAA
1 AT-TTTTT-AA
*
12324084 ATACTTTTAAA
1 AT--TTTTTAA
*
12324095 ATTTTTTTA
1 ATTTTTTAA
*
12324104 ATTTTTTTA
1 ATTTTTTAA
*
12324113 A-TTTTAAA
1 ATTTTTTAA
12324121 ATATTTTTAA
1 AT-TTTTTAA
12324131 A
1 A
12324132 ATAATTTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
7 6 0.10
8 6 0.10
9 24 0.41
10 11 0.19
11 8 0.14
12 4 0.07
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:12324072 original size:16 final size:16
Alignment explanation
Indices: 12324037--12324082 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
12324027 CCCGATATAA
* *
12324037 TAAATATATTTATTTTT
1 TAAATATTTTTA-ATTT
*
12324054 TAAATTTTTTTAATTT
1 TAAATATTTTTAATTT
12324070 TAAATATTTTTAA
1 TAAATATTTTTAA
12324083 AATACTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAAATATTTTTAATTT
Found at i:12324094 original size:37 final size:36
Alignment explanation
Indices: 12324051--12324131 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 36
12324041 TATATTTATT
*
12324051 TTTTAAATTTTTTTAATTTTAAATATTTTTAAAATAC
1 TTTTAAATTTTTTTAATTTT-AATAATTTTAAAATAC
** *
12324088 TTTTAAAATTTTTTTAATTTTTTTAATTTTAAAATAT
1 TTTT-AAATTTTTTTAATTTTAATAATTTTAAAATAC
12324125 TTTTAAA
1 TTTTAAA
12324132 ATAATTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
36 3 0.08
37 20 0.51
38 16 0.41
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (36 bp):
TTTTAAATTTTTTTAATTTTAATAATTTTAAAATAC
Found at i:12324140 original size:12 final size:11
Alignment explanation
Indices: 12324067--12324140 Score: 56
Period size: 11 Copynumber: 7.4 Consensus size: 11
12324057 ATTTTTTTAA
12324067 TTTT-AAATAT
1 TTTTAAAATAT
*
12324077 TTTTAAAATAC
1 TTTTAAAATAT
12324088 TTTTAAAAT-T
1 TTTTAAAATAT
*
12324098 TTTT-TAAT-T
1 TTTTAAAATAT
*
12324107 TTTT----TAA
1 TTTTAAAATAT
12324114 TTTTAAAATAT
1 TTTTAAAATAT
12324125 TTTTAAAATAAT
1 TTTTAAAAT-AT
12324137 TTTT
1 TTTT
12324141 TAGTATTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
6 1 0.02
7 4 0.08
9 8 0.15
10 8 0.15
11 25 0.48
12 6 0.12
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:12326642 original size:37 final size:38
Alignment explanation
Indices: 12326601--12326691 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 38
12326591 ACACATGAAT
* *
12326601 TTGAACTATTGATTTTTGTTTTGC-TGCATATAAGTTG
1 TTGAACTATTGATTTTTGGTATGCATGCATATAAGTTG
* * *
12326638 TTGAATTGTTGATTTTTGGTATGCAATGTATATAAGTTG
1 TTGAACTATTGATTTTTGGTATGC-ATGCATATAAGTTG
* *
12326677 TTAAACTAGTGATTT
1 TTGAACTATTGATTT
12326692 AATAAGTTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
37 20 0.47
39 23 0.53
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.49
Consensus pattern (38 bp):
TTGAACTATTGATTTTTGGTATGCATGCATATAAGTTG
Found at i:12337486 original size:20 final size:20
Alignment explanation
Indices: 12337444--12337492 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
12337434 CTGCTGCCTC
*
12337444 TGTCCCTTCCACCATGGTGT
1 TGTCCCTTCCACCATGGTAT
*
12337464 TGTCCTTTCCACCA-GGCTAT
1 TGTCCCTTCCACCATGG-TAT
12337484 TGTCCCTTC
1 TGTCCCTTC
12337493 AATGGGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.10, C:0.37, G:0.16, T:0.37
Consensus pattern (20 bp):
TGTCCCTTCCACCATGGTAT
Found at i:12337571 original size:4 final size:4
Alignment explanation
Indices: 12337557--12337611 Score: 58
Period size: 4 Copynumber: 13.0 Consensus size: 4
12337547 TGTATCAACT
*
12337557 AGAA A-AA AGAA AGAAA AGAA AGAA AGGAGA AGAA GAGGA AGAA AGAA
1 AGAA AGAA AGAA AG-AA AGAA AGAA A-GA-A AGAA -AGAA AGAA AGAA
12337604 AGAA AGAA
1 AGAA AGAA
12337612 GGTAATGTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
3 3 0.07
4 28 0.64
5 11 0.25
6 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:12337575 original size:9 final size:9
Alignment explanation
Indices: 12337561--12337608 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
12337551 TCAACTAGAA
12337561 AAAAGAAAG
1 AAAAGAAAG
12337570 AAAAGAAAG
1 AAAAGAAAG
*
12337579 AAAGGAGAAG
1 AAAAGA-AAG
* *
12337589 AAGAGGAAG
1 AAAAGAAAG
12337598 -AAAGAAAG
1 AAAAGAAAG
12337606 AAA
1 AAA
12337609 GAAGGTAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
8 6 0.19
9 19 0.61
10 6 0.19
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:12338362 original size:38 final size:38
Alignment explanation
Indices: 12338312--12338396 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
12338302 TAACTGACTC
* *
12338312 TTTTA-ATC-ATATAATTGATGTTAACTTATTTAATTT
1 TTTTATATCAATATAATTGATATTAACTCATTTAATTT
* *
12338348 TTTTATATCAATATAGTTGTTATTAACTCATTTAATTT
1 TTTTATATCAATATAATTGATATTAACTCATTTAATTT
12338386 TTTTATATCAA
1 TTTTATATCAA
12338397 CTTTGGGGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 5 0.12
37 3 0.07
38 35 0.81
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (38 bp):
TTTTATATCAATATAATTGATATTAACTCATTTAATTT
Found at i:12338603 original size:55 final size:56
Alignment explanation
Indices: 12338504--12338647 Score: 160
Period size: 55 Copynumber: 2.7 Consensus size: 56
12338494 TACCTATTTG
* * *
12338504 ACAGGCGCCAATCAATTTTTTATATTAAAAAA-A-A---TTAATTGCGCCTACCTA
1 ACAGACGCGAATCAATTTTTTATATTAAAAAATATATTTTTAATCGCGCCTACCTA
* * * *
12338555 ATAGACGCGACTCAA-TTTTTATATTAAAAAATATATTTTTAATCGCGCCTATCTG
1 ACAGACGCGAATCAATTTTTTATATTAAAAAATATATTTTTAATCGCGCCTACCTA
*
12338610 ACAGGCGCGAATCAATTTTTTATATT--AAAATATATTTT
1 ACAGACGCGAATCAATTTTTTATATTAAAAAATATATTTT
12338648 GTTGTTTAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
50 16 0.21
51 12 0.16
52 1 0.01
54 12 0.16
55 26 0.34
56 10 0.13
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (56 bp):
ACAGACGCGAATCAATTTTTTATATTAAAAAATATATTTTTAATCGCGCCTACCTA
Found at i:12338929 original size:16 final size:16
Alignment explanation
Indices: 12338908--12338952 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
12338898 AACTCATTTA
*
12338908 ATTTTTTATATAATGT
1 ATTTTTTATATAATAT
12338924 ATTTTTTATATAATAT
1 ATTTTTTATATAATAT
*
12338940 A-ATTTTATATAAT
1 ATTTTTTATATAAT
12338953 TTTTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTTTTATATAATAT
Found at i:12338962 original size:16 final size:15
Alignment explanation
Indices: 12338909--12338963 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
12338899 ACTCATTTAA
*
12338909 TTTTTTATATAATGTA
1 TTTTTTATATAAT-TT
*
12338925 TTTTTTATATAATAT
1 TTTTTTATATAATTT
**
12338940 AATTTTATATAATTT
1 TTTTTTATATAATTT
12338955 TTTATTTAT
1 TTT-TTTAT
12338964 TGAACAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
15 13 0.42
16 18 0.58
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTTTTATATAATTT
Found at i:12342064 original size:11 final size:11
Alignment explanation
Indices: 12342048--12342073 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12342038 TAGAAGAGAC
12342048 GAAACAGGGGA
1 GAAACAGGGGA
12342059 GAAACAGGGGA
1 GAAACAGGGGA
12342070 GAAA
1 GAAA
12342074 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:12342308 original size:18 final size:18
Alignment explanation
Indices: 12342285--12342327 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
12342275 ATGTGAGGTA
12342285 AGTATTAATATTAGTATT
1 AGTATTAATATTAGTATT
*
12342303 AGTATTATTATTAGTATT
1 AGTATTAATATTAGTATT
*
12342321 ATTATTA
1 AGTATTA
12342328 TTATGAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
AGTATTAATATTAGTATT
Found at i:12342313 original size:3 final size:3
Alignment explanation
Indices: 12342287--12342331 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
12342277 GTGAGGTAAG
* * * *
12342287 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12342332 GAGTGGGAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:12342526 original size:24 final size:24
Alignment explanation
Indices: 12342472--12342543 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
12342462 TGTGTGAAGT
*
12342472 TGTGAAATAATTATTG-ATTG-AAA
1 TGTGAAA-AATGATTGAATTGAAAA
*
12342495 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTGAATTGAAAA
12342520 TGTGAAAAATTGTAATTGAATTGA
1 TGTGAAAAA-TG--ATTGAATTGA
12342544 GAATATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.22
24 14 0.35
25 7 0.17
27 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (24 bp):
TGTGAAAAATGATTGAATTGAAAA
Found at i:12342746 original size:37 final size:39
Alignment explanation
Indices: 12342687--12342782 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
12342677 CGGATAGATT
* * * *
12342687 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
12342724 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
12342763 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
12342783 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:12349280 original size:11 final size:11
Alignment explanation
Indices: 12349264--12349289 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12349254 TAGAAGAGAC
12349264 GAAACAGGGGA
1 GAAACAGGGGA
12349275 GAAACAGGGGA
1 GAAACAGGGGA
12349286 GAAA
1 GAAA
12349290 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:12349524 original size:18 final size:18
Alignment explanation
Indices: 12349501--12349543 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
12349491 ATGTGAGGTA
12349501 AGTATTAATATTAGTATT
1 AGTATTAATATTAGTATT
*
12349519 AGTATTATTATTAGTATT
1 AGTATTAATATTAGTATT
*
12349537 ATTATTA
1 AGTATTA
12349544 TTATGAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
AGTATTAATATTAGTATT
Found at i:12349529 original size:3 final size:3
Alignment explanation
Indices: 12349503--12349547 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
12349493 GTGAGGTAAG
* * * *
12349503 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12349548 GAGTGGGAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:12349742 original size:24 final size:24
Alignment explanation
Indices: 12349688--12349759 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
12349678 TGTGTGAAGT
*
12349688 TGTGAAATAATTATTG-ATTG-AAA
1 TGTGAAA-AATGATTGAATTGAAAA
*
12349711 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTGAATTGAAAA
12349736 TGTGAAAAATTGTAATTGAATTGA
1 TGTGAAAAA-TG--ATTGAATTGA
12349760 GAATATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.22
24 14 0.35
25 7 0.17
27 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (24 bp):
TGTGAAAAATGATTGAATTGAAAA
Found at i:12367586 original size:31 final size:31
Alignment explanation
Indices: 12367551--12367617 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
12367541 AAAAAAACTT
*
12367551 AATAGCCCAGTGAATTAAATAAAAACTTTTG
1 AATAGCCCAGTGAATTAAATAAAAACTTTCG
** * *
12367582 AATAGTTCAGTGACTTAAATGAAAACTTTCG
1 AATAGCCCAGTGAATTAAATAAAAACTTTCG
12367613 AATAG
1 AATAG
12367618 ATCAGTGACC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (31 bp):
AATAGCCCAGTGAATTAAATAAAAACTTTCG
Found at i:12367623 original size:31 final size:31
Alignment explanation
Indices: 12367558--12367626 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
12367548 CTTAATAGCC
* * *
12367558 CAGTGAATTAAATAAAAACTTTTGAATAGTT
1 CAGTGACTTAAATAAAAACTTTCGAATAGAT
*
12367589 CAGTGACTTAAATGAAAACTTTCGAATAGAT
1 CAGTGACTTAAATAAAAACTTTCGAATAGAT
12367620 CAGTGAC
1 CAGTGAC
12367627 CAAATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAACTTTCGAATAGAT
Found at i:12381822 original size:27 final size:26
Alignment explanation
Indices: 12381792--12381849 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 26
12381782 TTTTTTAAAA
12381792 AATTT-ATTAACTTTTTATATTTTTGTG
1 AATTTAATTAA-TTTTTAT-TTTTTGTG
12381819 AATTTTGAATTAATTTTTATTTTTTGTG
1 AA-TTT-AATTAATTTTTATTTTTTGTG
12381847 AAT
1 AAT
12381850 ATTTTCATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
27 3 0.11
28 13 0.46
29 7 0.25
30 5 0.18
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.62
Consensus pattern (26 bp):
AATTTAATTAATTTTTATTTTTTGTG
Found at i:12382228 original size:6 final size:6
Alignment explanation
Indices: 12382217--12382241 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12382207 AATTAATTAA
12382217 TTATGG TTATGG TTATGG TTATGG T
1 TTATGG TTATGG TTATGG TTATGG T
12382242 GGAGGGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TTATGG
Found at i:12384260 original size:3 final size:3
Alignment explanation
Indices: 12384252--12384303 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
12384242 GCATACTTCC
* * * *
12384252 TAA TAA TAA TAA TAA TAA TAA TGA TAA TGA TGA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12384300 TAA T
1 TAA T
12384304 GTGTTCCTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12392374 original size:92 final size:94
Alignment explanation
Indices: 12392260--12392430 Score: 240
Period size: 95 Copynumber: 1.8 Consensus size: 94
12392250 TCTTTTTATA
* * * * * *
12392260 AACATACTCGGTGCCATTCAC-G-ACTAC-AAAGAATGAACTATTCTTCATTTTAAATTCAATGC
1 AACACACTCGGTCCCATTCACAGTACGACAAAAGAACGAACTATTCTT-AATATAAATTCAATGC
12392322 AAACGCAACGCATCTTCAGGAGATTCATAG
65 AAACGCAACGCATCTTCAGGAGATTCATAG
*
12392352 AACACACTCGGTCCCATTCACGAGTACGACAAAAGAACGAATTATTCTTAATATAAATTCAATGC
1 AACACACTCGGTCCCATTCAC-AGTACGACAAAAGAACGAACTATTCTTAATATAAATTCAATGC
12392417 AAACGCAACGCATC
65 AAACGCAACGCATC
12392431 ATCATCAGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
92 19 0.28
94 1 0.01
95 32 0.47
96 16 0.24
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (94 bp):
AACACACTCGGTCCCATTCACAGTACGACAAAAGAACGAACTATTCTTAATATAAATTCAATGCA
AACGCAACGCATCTTCAGGAGATTCATAG
Found at i:12393601 original size:13 final size:13
Alignment explanation
Indices: 12393585--12393609 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12393575 CTATTTTTTT
12393585 AAAAATATTTTAA
1 AAAAATATTTTAA
12393598 AAAAATATTTTA
1 AAAAATATTTTA
12393610 GTTCTTTATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAATATTTTAA
Found at i:12396854 original size:24 final size:24
Alignment explanation
Indices: 12396827--12396873 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
12396817 TGGTGTGGCA
*
12396827 ACAGGAGTTGATGATGAAGCAGCT
1 ACAGGAGTTGATGATGAAACAGCT
12396851 ACAGGAGTTGATGATGAAACAGC
1 ACAGGAGTTGATGATGAAACAGC
12396874 ATCAGATGGT
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:0.36, C:0.13, G:0.32, T:0.19
Consensus pattern (24 bp):
ACAGGAGTTGATGATGAAACAGCT
Found at i:12406700 original size:21 final size:21
Alignment explanation
Indices: 12406661--12406701 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12406651 CCACAAGAAA
* * *
12406661 CCTCTTTATAAATATATTTCT
1 CCTCTTTAAAAAGAGATTTCT
12406682 CCTCTTTAAAAAGAGATTTC
1 CCTCTTTAAAAAGAGATTTC
12406702 ATAGGGAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.44
Consensus pattern (21 bp):
CCTCTTTAAAAAGAGATTTCT
Found at i:12412012 original size:29 final size:30
Alignment explanation
Indices: 12411964--12412022 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
12411954 AAATTAGATC
* *
12411964 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAATTCCATATATAAAATTGCACA
*
12411994 AAATC-AAATTCCATATATACAATTGCACA
1 AAATCAAAATTCCATATATAAAATTGCACA
12412023 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATCAAAATTCCATATATAAAATTGCACA
Found at i:12414290 original size:19 final size:18
Alignment explanation
Indices: 12414248--12414290 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
12414238 ATATAAAAAG
* *
12414248 AAATTAAAAATTTATTGT
1 AAATTAAAAATATATTAT
12414266 AGAATTAAAAATATATATAT
1 A-AATTAAAAATATAT-TAT
12414286 AAATT
1 AAATT
12414291 TCGAGTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 17 0.81
20 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
AAATTAAAAATATATTAT
Found at i:12414910 original size:4 final size:4
Alignment explanation
Indices: 12414903--12414946 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
12414893 TATATATATC
*
12414903 TATG TATG TATG TATG TATG TACG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12414947 ACTGCCCTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:12415714 original size:18 final size:18
Alignment explanation
Indices: 12415691--12415730 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12415681 CAATTCATCG
*
12415691 ATATAAA-TCTATAGATAT
1 ATATAAATTCAATA-ATAT
12415709 ATATAAATTCAATAATAT
1 ATATAAATTCAATAATAT
12415727 ATAT
1 ATAT
12415731 CCAAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (18 bp):
ATATAAATTCAATAATAT
Found at i:12419188 original size:24 final size:24
Alignment explanation
Indices: 12419136--12419190 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
12419126 AAGCTCATAT
* * *
12419136 GAGCCAATAACGGGTAGCTCCGAA
1 GAGCCATTAACGAGAAGCTCCGAA
*
12419160 GAGCCATTAACGAGAAGCTCCGGA
1 GAGCCATTAACGAGAAGCTCCGAA
*
12419184 TAGCCAT
1 GAGCCAT
12419191 ATATTGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (24 bp):
GAGCCATTAACGAGAAGCTCCGAA
Found at i:12419749 original size:21 final size:20
Alignment explanation
Indices: 12419725--12419766 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
12419715 AAATTTAGCA
*
12419725 CAATTGAATACAATTCATATT
1 CAATTCAATACAATTCA-ATT
*
12419746 CAATTCAATTCAATTCAATT
1 CAATTCAATACAATTCAATT
12419766 C
1 C
12419767 CTAGGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (20 bp):
CAATTCAATACAATTCAATT
Found at i:12419753 original size:5 final size:5
Alignment explanation
Indices: 12419725--12419766 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
12419715 AAATTTAGCA
* *
12419725 CAATT GAATA CAATT CATATT CAATT CAATT CAATT CAATT C
1 CAATT CAATT CAATT CA-ATT CAATT CAATT CAATT CAATT C
12419767 CTAGGAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (5 bp):
CAATT
Found at i:12425897 original size:9 final size:9
Alignment explanation
Indices: 12425883--12426017 Score: 56
Period size: 9 Copynumber: 14.1 Consensus size: 9
12425873 GCCCATTTTT
12425883 ATTTTAAAA
1 ATTTTAAAA
12425892 ATTTTAAAAA
1 ATTTT-AAAA
**
12425902 ATTAAAAAA
1 ATTTTAAAA
* *
12425911 AATTAAAAA
1 ATTTTAAAA
*
12425920 ATATTTTAAA
1 AT-TTTAAAA
**
12425930 ATTAAAAAA
1 ATTTTAAAA
**
12425939 ATTAAAAAA
1 ATTTTAAAA
12425948 GTATTTTAAAA
1 --ATTTTAAAA
*
12425959 ATATTTTAAA
1 AT-TTTAAAA
*
12425969 A-TTAAAAA
1 ATTTTAAAA
* *
12425977 AATTAAAAA
1 ATTTTAAAA
12425986 ATTATGTAAAAA
1 ATT-T-T-AAAA
*
12425998 ATATTTTAAA
1 AT-TTTAAAA
12426008 ATTTTAAAA
1 ATTTTAAAA
12426017 A
1 A
12426018 ATAAATATAT
Statistics
Matches: 97, Mismatches: 19, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
8 6 0.06
9 48 0.49
10 27 0.28
11 8 0.08
12 7 0.07
13 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:12425903 original size:10 final size:10
Alignment explanation
Indices: 12425883--12426019 Score: 64
Period size: 10 Copynumber: 14.2 Consensus size: 10
12425873 GCCCATTTTT
12425883 ATTTT-AAAA
1 ATTTTAAAAA
12425892 ATTTTAAAAA
1 ATTTTAAAAA
12425902 A--TTAAAAA
1 ATTTTAAAAA
**
12425910 AAATTAAAAA
1 ATTTTAAAAA
*
12425920 ATATTT-TAAA
1 AT-TTTAAAAA
12425930 A--TTAAAAA
1 ATTTTAAAAA
* *
12425938 AATTAAAAAA
1 ATTTTAAAAA
12425948 GTATTTTAAAAA
1 --ATTTTAAAAA
12425960 TATTTT--AAA
1 -ATTTTAAAAA
12425969 A--TTAAAAA
1 ATTTTAAAAA
*
12425977 A-ATTAAAAA
1 ATTTTAAAAA
12425986 ATTATGTAAAAA
1 ATT-T-TAAAAA
*
12425998 ATATTT-TAAA
1 AT-TTTAAAAA
12426008 ATTTTAAAAA
1 ATTTTAAAAA
12426018 AT
1 AT
12426020 AAATATATTT
Statistics
Matches: 101, Mismatches: 10, Indels: 33
0.70 0.07 0.23
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 17 0.17
9 19 0.19
10 33 0.33
11 10 0.10
12 17 0.17
13 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:12425926 original size:39 final size:38
Alignment explanation
Indices: 12425882--12426019 Score: 179
Period size: 39 Copynumber: 3.5 Consensus size: 38
12425872 GGCCCATTTT
*
12425882 TATTTTAAAAATTTTAAAAAATTAAAAAA-AATTAAAAAA
1 TATTTT-AAAA-TTAAAAAAATTAAAAAATAATTAAAAAA
* *
12425921 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAA-TAATTAAAAAA
*
12425960 TATTTTAAAATTAAAAAAATTAAAAAATTATGTAAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAATAAT-TAAAAAA
*
12425999 TATTTTAAAATTTTAAAAAAT
1 TATTTTAAAA-TTAAAAAAAT
12426020 AAATATATTT
Statistics
Matches: 88, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
37 16 0.18
38 6 0.07
39 57 0.65
40 9 0.10
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (38 bp):
TATTTTAAAATTAAAAAAATTAAAAAATAATTAAAAAA
Found at i:12425936 original size:27 final size:29
Alignment explanation
Indices: 12425899--12425958 Score: 106
Period size: 28 Copynumber: 2.1 Consensus size: 29
12425889 AAAATTTTAA
12425899 AAAATTAAAAAAAATTAAAAAA-TATTTT
1 AAAATTAAAAAAAATTAAAAAAGTATTTT
12425927 AAAATT-AAAAAAATTAAAAAAGTATTTT
1 AAAATTAAAAAAAATTAAAAAAGTATTTT
12425955 AAAA
1 AAAA
12425959 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAATTAAAAAAAATTAAAAAAGTATTTT
Found at i:12429976 original size:18 final size:19
Alignment explanation
Indices: 12429932--12429976 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
12429922 CTTTGACTAA
12429932 TAAAATT-ATATATAAATT
1 TAAAATTAATATATAAATT
* *
12429950 TTAATTTAATATAT-AATT
1 TAAAATTAATATATAAATT
12429968 TAAAATTAA
1 TAAAATTAA
12429977 ATCAGTGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAATTAATATATAAATT
Found at i:12430522 original size:26 final size:27
Alignment explanation
Indices: 12430465--12430522 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
12430455 GTATAGGGGT
* * **
12430465 ATGGTGCCTATTTGATAGGCGGCACTG
1 ATGGTGCCTATCTGATAGGCGACACCA
*
12430492 GTGGTG-CTATCTGATAGGCGACACCA
1 ATGGTGCCTATCTGATAGGCGACACCA
12430518 ATGGT
1 ATGGT
12430523 ATTTTCCTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.28
Consensus pattern (27 bp):
ATGGTGCCTATCTGATAGGCGACACCA
Found at i:12431757 original size:17 final size:18
Alignment explanation
Indices: 12431731--12431764 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12431721 TTTGTCACAA
12431731 TTTATAATTAT-ATATTT
1 TTTATAATTATAATATTT
*
12431748 TTTATCATTATAATATT
1 TTTATAATTATAATATT
12431765 AAAGGAGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATAATTATAATATTT
Found at i:12435756 original size:25 final size:24
Alignment explanation
Indices: 12435709--12435758 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
12435699 ATTTATAATT
** *
12435709 TATAAAAATTAAATTAAACTAAAA
1 TATAAAAATTAAACAAAAATAAAA
12435733 TATATAAAATTAAACAAAAATAAAA
1 TATA-AAAATTAAACAAAAATAAAA
12435758 T
1 T
12435759 TAATATACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (24 bp):
TATAAAAATTAAACAAAAATAAAA
Found at i:12436802 original size:2 final size:2
Alignment explanation
Indices: 12436795--12436823 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12436785 TTAGTCGGTT
12436795 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12436824 AAACCCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12444696 original size:41 final size:41
Alignment explanation
Indices: 12444609--12444738 Score: 145
Period size: 41 Copynumber: 3.2 Consensus size: 41
12444599 GTTTTTGAGG
* * * *
12444609 CTTTAGCGGCGTTTTTAGAAAAGCGACGCTAATGCTCTGGG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
* * *
12444650 ATTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCCCAGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
* * * *
12444691 CTTTAGCGACGCTTCTGG-GTAAGCGCCGCTAATACTCTGGT
1 CTTTAGCGGCGTTTTTGGAG-AAGCGCCGCTAATGCTCTGGT
12444732 CTTTAGC
1 CTTTAGC
12444739 AATGCTCGGG
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 1 0.01
41 73 0.99
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.29
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
Found at i:12449713 original size:24 final size:22
Alignment explanation
Indices: 12449685--12449728 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
12449675 AATTTAAAAA
12449685 ATAAAACATAATATAATATTTATC
1 ATAAAA-ATAA-ATAATATTTATC
*
12449709 ATAAAAATAAATATTATTTA
1 ATAAAAATAAATAATATTTA
12449729 ACTAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAAAAATAAATAATATTTATC
Found at i:12450578 original size:50 final size:50
Alignment explanation
Indices: 12450506--12450949 Score: 531
Period size: 50 Copynumber: 8.7 Consensus size: 50
12450496 ACATGCCAAA
** *
12450506 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGT-CTCGGTGCCCAT
* * * * *
12450557 GCCAT-TCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
12450606 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
* *
12450656 GCCATGTCCCAGACATGGTCTTACA-GGGACCTCTCATGATCTTAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--G-TC-T-CGG-TGCCCAT
*
12450711 GCTATGTCCCAGACAT-GTCTTACAT-GGACCTCTCCGTCTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT-CGTCTCGGTGCCCAT
* * * *
12450760 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
*
12450810 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTTGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
* * *
12450860 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--G-TC-T-CGG-TGCCCAT
*
12450916 GCCATGTCCCAGACATGGTCTT-CATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
12450950 TTACCCAAAT
Statistics
Matches: 342, Mismatches: 33, Indels: 32
0.84 0.08 0.08
Matches are distributed among these distances:
48 1 0.00
49 48 0.14
50 188 0.55
51 15 0.04
52 5 0.01
53 4 0.01
54 19 0.06
55 34 0.10
56 28 0.08
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
Found at i:12450672 original size:100 final size:104
Alignment explanation
Indices: 12450498--12450949 Score: 635
Period size: 100 Copynumber: 4.4 Consensus size: 104
12450488 TGATAATAAC
* ** *
12450498 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GGTGCCCATGCCAT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGT-CTCGGTGCCCATGCCAT
* *
12450562 -TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
64 GTCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
12450599 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
12450663 CCCAGACATGGTCTTACA-GGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
12450703 ATGCCAATGCTATGTCCCAGACAT-GTCTTACAT-GGACCTCTCCGTCTCGGTGCCCATGCCATG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT-CGTCTCGGTGCCCATGCCATG
*
12450766 TCCCAGACATGGTCTTACAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
*
12450803 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTTGGTGCCCATGCCATGT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
12450867 CCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
12450908 ATGCCAATGCCATGTCCCAGACATGGTCTT-CATGGGATCTCT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
12450950 TTACCCAAAT
Statistics
Matches: 318, Mismatches: 15, Indels: 32
0.87 0.04 0.09
Matches are distributed among these distances:
98 1 0.00
99 51 0.16
100 115 0.36
101 9 0.03
102 6 0.02
103 12 0.04
104 52 0.16
105 44 0.14
106 28 0.09
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (104 bp):
ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:12450849 original size:204 final size:205
Alignment explanation
Indices: 12450498--12450942 Score: 756
Period size: 204 Copynumber: 2.2 Consensus size: 205
12450488 TGATAATAAC
* **
12450498 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGACCTTCTCGTGATGGTGCCCATGCCATT
*
12450563 CCCAGACATGGTCTTATAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTT
65 CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTT
12450628 ACATGGGACCTCTCGTCTCGGTGCCCATGCCATGTCCCAGACATGGTCTTACA-GGGACCTCTCA
130 ACATGGGACCTCTCGTCTCGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCA
12450692 TGATCTTAAGG
195 TGATCTTAAGG
* *
12450703 ATGCCAATGCTATGTCCCAGACAT-GTCTTACATGGACC-TCTCCGT-CTCGGTGCCCATGCCAT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGACCTTCT-CGTGAT-GGTGCCCATGCCAT
12450765 GTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTC
64 -TCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTC
*
12450830 TTACATGGGACCTCTCGTCTTGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
128 TTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
12450895 CATGATCTTAAGG
193 CATGATCTTAAGG
12450908 ATGCCAATGCCATGTCCCAGACATGGTCTT-CATGG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGG
12450943 GATCTCTTTA
Statistics
Matches: 227, Mismatches: 8, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
202 4 0.02
203 20 0.09
204 126 0.56
205 72 0.32
206 5 0.02
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (205 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGACCTTCTCGTGATGGTGCCCATGCCATTC
CCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTA
CATGGGACCTCTCGTCTCGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT
GATCTTAAGG
Found at i:12456516 original size:13 final size:13
Alignment explanation
Indices: 12456498--12456523 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12456488 TTTCCAGAAA
12456498 TTATGAATTTATT
1 TTATGAATTTATT
12456511 TTATGAATTTATT
1 TTATGAATTTATT
12456524 GATGATGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:12459353 original size:29 final size:30
Alignment explanation
Indices: 12459294--12459351 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
12459284 TCCGAGCCTT
*
12459294 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
12459324 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
12459352 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:12459580 original size:13 final size:13
Alignment explanation
Indices: 12459562--12459593 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12459552 TTTCCAGCAA
12459562 TTATGAATTTATT
1 TTATGAATTTATT
12459575 TTATGAATTTATT
1 TTATGAATTTATT
*
12459588 TGATGA
1 TTATGA
12459594 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:12459846 original size:50 final size:51
Alignment explanation
Indices: 12459688--12459935 Score: 272
Period size: 50 Copynumber: 4.8 Consensus size: 51
12459678 ATTTGGGTAA
* *
12459688 AGAGATCCCATGTAAGACCATGTTCT-GGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATG-TCTGGGACATGGCATTGGCA-CC----GATCACG
* * *
12459744 AGAGGTCCCCTGTAAGACCATGTCT-GGACATGGCATGGGCACCGA-GACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCACG
* * *
12459793 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA-GATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCACG
* * *
12459843 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCACG
** *
12459893 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
12459936 TGTTATTATC
Statistics
Matches: 168, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
49 27 0.16
50 67 0.40
51 34 0.20
54 2 0.01
55 18 0.11
56 20 0.12
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (51 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCACG
Found at i:12459881 original size:105 final size:102
Alignment explanation
Indices: 12459688--12459936 Score: 337
Period size: 101 Copynumber: 2.4 Consensus size: 102
12459678 ATTTGGGTAA
12459688 AGAGATCCCATGTAAGACCATGTTCT-GGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCC
1 AGAGATCCCATGTAAGACCATG-TCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCC
* *
12459752 CCTGTAAGACCATGTCTGGACATGGCATGGGCACCGA-GACG
62 CCTATAAGACCATGTCTGGACATGGCATGGGCACC-ATCACG
* * *
12459793 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
12459855 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCT-GGACATGGCATGGGCACCATCACG
* *
12459893 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
12459937 GTTATTATCA
Statistics
Matches: 131, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
99 28 0.21
100 25 0.19
101 37 0.28
104 5 0.04
105 36 0.27
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (102 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGACATGGCATGGGCACCATCACG
Found at i:12464140 original size:13 final size:13
Alignment explanation
Indices: 12464122--12464153 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12464112 TTTCCAGCAA
12464122 TTATGAATTTATT
1 TTATGAATTTATT
12464135 TTATGAATTTATT
1 TTATGAATTTATT
*
12464148 TGATGA
1 TTATGA
12464154 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:12464361 original size:50 final size:50
Alignment explanation
Indices: 12464248--12464445 Score: 261
Period size: 50 Copynumber: 3.8 Consensus size: 50
12464238 ATTTGGGTAA
* *
12464248 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--G
* *
12464304 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* *
12464354 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * *
12464404 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
12464446 TGTTATTATC
Statistics
Matches: 131, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
50 86 0.66
52 1 0.01
53 3 0.02
55 2 0.02
56 39 0.30
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:12464447 original size:106 final size:103
Alignment explanation
Indices: 12464248--12464438 Score: 298
Period size: 106 Copynumber: 1.9 Consensus size: 103
12464238 ATTTGGGTAA
12464248 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
*
12464313 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
12464354 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
12464416 TAAGACCATGTCTGGGACATGGC
66 TAAGACCATGTCTGGGACATGGC
12464439 TTTGGCATGT
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
100 37 0.46
101 2 0.02
105 2 0.02
106 40 0.49
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:12468113 original size:18 final size:18
Alignment explanation
Indices: 12468092--12468176 Score: 116
Period size: 18 Copynumber: 4.7 Consensus size: 18
12468082 TTTACGGTAT
12468092 TATTCACGTATACGGCAC
1 TATTCACGTATACGGCAC
* * *
12468110 TATTCACATATACAGTAC
1 TATTCACGTATACGGCAC
*
12468128 TATTTACGTATACGGCAC
1 TATTCACGTATACGGCAC
*
12468146 TATTCACGTATACGGTAC
1 TATTCACGTATACGGCAC
*
12468164 TGTTCACGTATAC
1 TATTCACGTATAC
12468177 AGTAGTTGGG
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (18 bp):
TATTCACGTATACGGCAC
Found at i:12468144 original size:36 final size:36
Alignment explanation
Indices: 12468092--12468176 Score: 134
Period size: 36 Copynumber: 2.4 Consensus size: 36
12468082 TTTACGGTAT
12468092 TATTCACGTATACGGCACTATTCACATATACAGTAC
1 TATTCACGTATACGGCACTATTCACATATACAGTAC
* * *
12468128 TATTTACGTATACGGCACTATTCACGTATACGGTAC
1 TATTCACGTATACGGCACTATTCACATATACAGTAC
*
12468164 TGTTCACGTATAC
1 TATTCACGTATAC
12468177 AGTAGTTGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (36 bp):
TATTCACGTATACGGCACTATTCACATATACAGTAC
Found at i:12482729 original size:22 final size:21
Alignment explanation
Indices: 12482704--12482747 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
12482694 ATAATAATTT
12482704 TATTT-ATATTTTAAATTGTAAA
1 TATTTAAT-TTTTAAATT-TAAA
12482726 TATTTAATTTTTAAATTTAAA
1 TATTTAATTTTTAAATTTAAA
12482747 T
1 T
12482748 TTATGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 14 0.67
23 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TATTTAATTTTTAAATTTAAA
Found at i:12483845 original size:20 final size:21
Alignment explanation
Indices: 12483822--12483880 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
12483812 AACTATTCAA
12483822 ATAA-TATTTTTTGAATAGTT
1 ATAATTATTTTTTGAATAGTT
*
12483842 ATAATTCTTTTTTGAATAGTT
1 ATAATTATTTTTTGAATAGTT
*
12483863 ATAATTATTATTT-AATAG
1 ATAATTATTTTTTGAATAG
12483881 GTGTCTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 26 0.74
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (21 bp):
ATAATTATTTTTTGAATAGTT
Found at i:12486145 original size:18 final size:18
Alignment explanation
Indices: 12486107--12486142 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12486097 TTATTATTTT
*
12486107 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
12486125 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
12486143 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:12502092 original size:41 final size:41
Alignment explanation
Indices: 12501980--12502077 Score: 187
Period size: 41 Copynumber: 2.4 Consensus size: 41
12501970 TCGGATTTAT
12501980 TGCCGGTGAACTGAATCAGGCTATAGGCCTAGCAGGCTAAG
1 TGCCGGTGAACTGAATCAGGCTATAGGCCTAGCAGGCTAAG
12502021 TGCCGGTGAACTGAATCAGGCTATAGGCCTAGCAGGCTAAG
1 TGCCGGTGAACTGAATCAGGCTATAGGCCTAGCAGGCTAAG
*
12502062 TGCCGGTGAACGGAAT
1 TGCCGGTGAACTGAAT
12502078 TAAACTATAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.27, C:0.21, G:0.33, T:0.19
Consensus pattern (41 bp):
TGCCGGTGAACTGAATCAGGCTATAGGCCTAGCAGGCTAAG
Found at i:12502106 original size:41 final size:41
Alignment explanation
Indices: 12501980--12502092 Score: 145
Period size: 41 Copynumber: 2.8 Consensus size: 41
12501970 TCGGATTTAT
* ** *
12501980 TGCCGGTGAACTGAATCAGGCTATAGGCCTAGCAGGCTAAG
1 TGCCGGTGAACGGAATCAAACTATAAGCCTAGCAGGCTAAG
* ** *
12502021 TGCCGGTGAACTGAATCAGGCTATAGGCCTAGCAGGCTAAG
1 TGCCGGTGAACGGAATCAAACTATAAGCCTAGCAGGCTAAG
*
12502062 TGCCGGTGAACGGAATTAAACTATAAGCCTA
1 TGCCGGTGAACGGAATCAAACTATAAGCCTA
12502093 TTAGGTGAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.20
Consensus pattern (41 bp):
TGCCGGTGAACGGAATCAAACTATAAGCCTAGCAGGCTAAG
Found at i:12505358 original size:19 final size:19
Alignment explanation
Indices: 12505334--12505371 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12505324 GAAAAGACTT
12505334 CTTTCGTCTACCAATCATA
1 CTTTCGTCTACCAATCATA
12505353 CTTTCGTCTACCAATCATA
1 CTTTCGTCTACCAATCATA
12505372 TTAGAGAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.05, T:0.37
Consensus pattern (19 bp):
CTTTCGTCTACCAATCATA
Found at i:12509185 original size:20 final size:20
Alignment explanation
Indices: 12509160--12509199 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12509150 CAAACATGAC
*
12509160 ATAGGTAATTACGATGTAAT
1 ATAGGTAATTACGATATAAT
12509180 ATAGGTAATTACGATATAAT
1 ATAGGTAATTACGATATAAT
12509200 TACACTCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.35
Consensus pattern (20 bp):
ATAGGTAATTACGATATAAT
Done.