Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 128 of 147
Found at i:23076114 original size:18 final size:18
Alignment explanation
Indices: 23076091--23076152 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
23076081 TGCGAAATTG
*
23076091 TTTTTAATAAAGATTGTA
1 TTTTTAATAAAAATTGTA
* *
23076109 TTTTTATCTTGAAAACATTGTT
1 TTTTTA--AT-AAAA-ATTGTA
23076131 TTTTTAATAAAAATTGTA
1 TTTTTAATAAAAATTGTA
23076149 TTTT
1 TTTT
23076153 CTATCTTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
18 15 0.43
19 4 0.11
20 2 0.06
21 3 0.09
22 11 0.31
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (18 bp):
TTTTTAATAAAAATTGTA
Found at i:23076128 original size:22 final size:21
Alignment explanation
Indices: 23076103--23076164 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 21
23076093 TTTAATAAAG
23076103 ATTGTATTTTTATCTTGAAAA
1 ATTGTATTTTTATCTTGAAAA
**
23076124 CATTGT-TTTTT-TAAT-AAAA
1 -ATTGTATTTTTATCTTGAAAA
23076143 ATTGTATTTTCTATCTTAGAAA
1 ATTGTATTTT-TATCTT-GAAA
23076165 CATCGTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
18 5 0.16
19 8 0.26
20 3 0.10
21 7 0.23
22 5 0.16
23 3 0.10
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (21 bp):
ATTGTATTTTTATCTTGAAAA
Found at i:23076308 original size:112 final size:112
Alignment explanation
Indices: 23076103--23076324 Score: 261
Period size: 112 Copynumber: 2.0 Consensus size: 112
23076093 TTTAATAAAG
* * * * * *
23076103 ATTGTATTTTTATCTTGAAAACATTGTTTTTTTAATAAAAATTGTATTTTCTATCTTAGAAACAT
1 ATTGCATTTTTATCTTAAAAACATTGTCTTTTCAACAAAAATTGCATTTTCTATCTTAGAAACAT
* * * * *
23076168 CGTCTTTATTGAATTTTGAAAAATATTTTTTCATGCTTTTAACAACA
66 CGCCTCTATTAAATTTTAAAAAATATTTTTTCATACTTTTAACAACA
* * *
23076215 ATTGCATTTTTATCTTAAAAATATTGTCTTTTCAACAAAAATTGCATTTTTTATTTTA-AAA-A-
1 ATTGCATTTTTATCTTAAAAACATTGTCTTTTCAACAAAAATTGCATTTTCTATCTTAGAAACAT
*
23076277 CGCCATCTATTAAATTTTAAAAAATAAATTTTTTCATATTTTTAACAA
66 CGCC-TCTATTAAATTTTAAAAAAT--ATTTTTTCATACTTTTAACAA
23076325 AGATCACATT
Statistics
Matches: 92, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
109 3 0.03
110 18 0.20
111 3 0.03
112 68 0.74
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (112 bp):
ATTGCATTTTTATCTTAAAAACATTGTCTTTTCAACAAAAATTGCATTTTCTATCTTAGAAACAT
CGCCTCTATTAAATTTTAAAAAATATTTTTTCATACTTTTAACAACA
Found at i:23079433 original size:46 final size:46
Alignment explanation
Indices: 23079383--23079497 Score: 180
Period size: 46 Copynumber: 2.5 Consensus size: 46
23079373 CATGCAAAAA
* *
23079383 AAATTATCATTCAATAATAATATAACAATACAATAATATAATATAT
1 AAATTATCATGCAATAATAATATAACAAAACAATAATATAATATAT
* *
23079429 AAATTATCATGCACTAACAATATAACAAAACAATAATATAATATAT
1 AAATTATCATGCAATAATAATATAACAAAACAATAATATAATATAT
23079475 AAATTATCATGCAAT--TAATATAA
1 AAATTATCATGCAATAATAATATAA
23079498 GTTATCATGA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 7 0.11
46 56 0.89
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (46 bp):
AAATTATCATGCAATAATAATATAACAAAACAATAATATAATATAT
Found at i:23079649 original size:25 final size:23
Alignment explanation
Indices: 23079605--23079675 Score: 63
Period size: 25 Copynumber: 2.9 Consensus size: 23
23079595 ACTTACACAG
* *
23079605 AAAAATAAAAATATGAAAAACA-C
1 AAAAATAAAAATA-AAAAAAAATC
23079628 AAAAATAAGAAATAAAATAAAAATC
1 AAAAATAA-AAATAAAA-AAAAATC
*
23079653 AAAACTAAAAATTAAAAGAAAAA
1 AAAAATAAAAA-TAAAA-AAAAA
23079676 AGAAAAGCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 10 0.25
24 12 0.30
25 18 0.45
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (23 bp):
AAAAATAAAAATAAAAAAAAATC
Found at i:23079661 original size:13 final size:12
Alignment explanation
Indices: 23079629--23079675 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
23079619 GAAAAACACA
23079629 AAAATAAGAAAT-
1 AAAATAA-AAATC
23079641 AAAATAAAAATC
1 AAAATAAAAATC
*
23079653 AAAACTAAAAATT
1 AAAA-TAAAAATC
*
23079666 AAAAGAAAAA
1 AAAATAAAAA
23079676 AGAAAAGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 4 0.13
12 16 0.52
13 11 0.35
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAATAAAAATC
Found at i:23079840 original size:2 final size:2
Alignment explanation
Indices: 23079833--23079863 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
23079823 GCTTTAGTTT
*
23079833 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
23079864 AGCATAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:23080716 original size:23 final size:24
Alignment explanation
Indices: 23080669--23080719 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
23080659 ACTTTTGACA
*
23080669 TTTTTTTTTAACTTTCGATTCTTT
1 TTTTTTTTTAACTTTCGAGTCTTT
* *
23080693 TTTTTTTTTAATTTTTGAGT-TTT
1 TTTTTTTTTAACTTTCGAGTCTTT
23080716 TTTT
1 TTTT
23080720 AAAAATAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (24 bp):
TTTTTTTTTAACTTTCGAGTCTTT
Found at i:23081007 original size:19 final size:19
Alignment explanation
Indices: 23080983--23081019 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
23080973 CTTGATAAAG
23080983 CAATTATTTGCAAACATAC
1 CAATTATTTGCAAACATAC
23081002 CAATTATTTGCAAACATA
1 CAATTATTTGCAAACATA
23081020 TGTCTACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.32
Consensus pattern (19 bp):
CAATTATTTGCAAACATAC
Found at i:23082102 original size:14 final size:14
Alignment explanation
Indices: 23082083--23082109 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23082073 TATTGTTGTG
23082083 TGTTTTATATTTTA
1 TGTTTTATATTTTA
23082097 TGTTTTATATTTT
1 TGTTTTATATTTT
23082110 TAAAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (14 bp):
TGTTTTATATTTTA
Found at i:23082306 original size:26 final size:26
Alignment explanation
Indices: 23082270--23082349 Score: 99
Period size: 26 Copynumber: 3.0 Consensus size: 26
23082260 AATATAATAA
*
23082270 TATTAATATAATTTTATTTATTTATT
1 TATTAATATAATATTATTTATTTATT
*
23082296 TATTAATATAATATTATTTAGTAATATAT
1 TATTAATATAATATTATTTA-T-TTAT-T
*
23082325 TATTTAT-TAATATTATTTATTTATT
1 TATTAATATAATATTATTTATTTATT
23082350 AACATAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
25 1 0.02
26 22 0.47
27 2 0.04
28 15 0.32
29 7 0.15
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (26 bp):
TATTAATATAATATTATTTATTTATT
Found at i:23082322 original size:13 final size:13
Alignment explanation
Indices: 23082304--23082343 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
23082294 TTTATTAATA
23082304 TAATATTATTTAG
1 TAATATTATTTAG
*
23082317 TAATATATTATTTAT
1 T-A-ATATTATTTAG
23082332 TAATATTATTTA
1 TAATATTATTTA
23082344 TTTATTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.46
14 2 0.08
15 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
TAATATTATTTAG
Found at i:23082324 original size:15 final size:15
Alignment explanation
Indices: 23082270--23082384 Score: 103
Period size: 15 Copynumber: 7.5 Consensus size: 15
23082260 AATATAATAA
*
23082270 TATTAATATAAT-TT
1 TATTAATATATTATT
23082284 TATT--TAT-TTATT
1 TATTAATATATTATT
23082296 TATTAATATAATATTATT
1 TATT-A-AT-ATATTATT
*
23082314 TAGTAATATATTATT
1 TATTAATATATTATT
23082329 TATTAATATTATTTATT
1 TATTAATA-TA-TTATT
* *
23082346 TATTAACATAATATT
1 TATTAATATATTATT
*
23082361 TATTAATATAATATT
1 TATTAATATATTATT
23082376 TATATAATA
1 TAT-TAATA
23082385 AAAATATTAT
Statistics
Matches: 85, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
11 1 0.01
12 9 0.11
14 4 0.05
15 36 0.42
16 12 0.14
17 15 0.18
18 8 0.09
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (15 bp):
TATTAATATATTATT
Found at i:23082343 original size:50 final size:51
Alignment explanation
Indices: 23082287--23082409 Score: 146
Period size: 50 Copynumber: 2.4 Consensus size: 51
23082277 ATAATTTTAT
*
23082287 TTATTTATTTATTAATATAATATTATTTAGTAATATATTATTTAT-TAAT-A
1 TTATTTATTTATTAATATAATA-TATTTAGTAATATAATATTTATATAATAA
* *
23082337 TTATTTATTTATTAACAT-A-ATATTTATTAATATAATATTTATATAATAA
1 TTATTTATTTATTAATATAATATATTTAGTAATATAATATTTATATAATAA
**
23082386 AAATATTATTTCATTAATATAATA
1 TTAT-TTATTT-ATTAATATAATA
23082410 ATTGTAGCGT
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
47 20 0.33
48 5 0.08
49 4 0.07
50 23 0.38
51 7 0.11
52 1 0.02
53 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.54
Consensus pattern (51 bp):
TTATTTATTTATTAATATAATATATTTAGTAATATAATATTTATATAATAA
Found at i:23082361 original size:32 final size:32
Alignment explanation
Indices: 23082291--23082405 Score: 122
Period size: 32 Copynumber: 3.4 Consensus size: 32
23082281 TTTTATTTAT
* * *
23082291 TTATTTATTAATATAATATTATTTAGTAATATA
1 TTATTTATTAATATTAT-TTATTTATTAAAATA
*
23082324 TTATTTATTAATATTATTTATTTATTAACATA
1 TTATTTATTAATATTATTTATTTATTAAAATA
* * *
23082356 ATATTTATTAATATAATATTTATATAATAAAAATA
1 TTATTTATTAATAT--TATTTAT-TTATTAAAATA
23082391 TTATTTCATTAATAT
1 TTATTT-ATTAATAT
23082406 AATAATTGTA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
32 26 0.37
33 16 0.23
34 7 0.10
35 13 0.19
36 8 0.11
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (32 bp):
TTATTTATTAATATTATTTATTTATTAAAATA
Found at i:23082492 original size:22 final size:23
Alignment explanation
Indices: 23082462--23082504 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
23082452 ATGGGGGCAA
23082462 CTAATATATAT-AATATTAAATAT
1 CTAATATATATAAATA-TAAATAT
23082485 CTAA-ATATATAAATATAAAT
1 CTAATATATATAAATATAAAT
23082505 TAACTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (23 bp):
CTAATATATATAAATATAAATAT
Found at i:23085683 original size:18 final size:19
Alignment explanation
Indices: 23085649--23085684 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
23085639 ATATATAAAG
*
23085649 TTTTTTTGAAAGCAAATTT
1 TTTTTTTGAAAGAAAATTT
23085668 TTTTTTTGAAA-AAAATT
1 TTTTTTTGAAAGAAAATT
23085685 CGAGTTCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (19 bp):
TTTTTTTGAAAGAAAATTT
Found at i:23086936 original size:7 final size:7
Alignment explanation
Indices: 23086924--23086961 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
23086914 CTTGAGTTTC
23086924 TTTATTT
1 TTTATTT
23086931 TTTA-TT
1 TTTATTT
23086937 TTTATTT
1 TTTATTT
*
23086944 GTTTATAT
1 -TTTATTT
23086952 TTTATTT
1 TTTATTT
23086959 TTT
1 TTT
23086962 CAAATCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 6 0.22
7 15 0.56
8 6 0.22
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (7 bp):
TTTATTT
Found at i:23089327 original size:27 final size:24
Alignment explanation
Indices: 23089296--23089357 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 24
23089286 TTTAGAAATC
23089296 TTTATTTTATTAAATTCATATATTATT
1 TTTATTTTATTAAA-TC--ATATTATT
*
23089323 TTTATTATAATTTTAAATCATATTATT
1 TTTATT-T--TATTAAATCATATTATT
23089350 TTTATTTT
1 TTTATTTT
23089358 TTATATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
24 1 0.03
26 1 0.03
27 20 0.65
28 1 0.03
29 2 0.06
30 6 0.19
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTATTTTATTAAATCATATTATT
Found at i:23091567 original size:12 final size:13
Alignment explanation
Indices: 23091542--23091566 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23091532 TTTTAACCAT
23091542 TATTTTATAAAAA
1 TATTTTATAAAAA
23091555 TATTTTATAAAA
1 TATTTTATAAAA
23091567 TTAAAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTTTATAAAAA
Found at i:23092977 original size:2 final size:2
Alignment explanation
Indices: 23092970--23093003 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
23092960 AGGCCTTCAC
23092970 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
23093004 TCCCCCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:23095745 original size:19 final size:20
Alignment explanation
Indices: 23095716--23095753 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
23095706 AATCATATCA
*
23095716 TTTTTTATATATTTTTCATC
1 TTTTTTATATATTTATCATC
23095736 TTTTTT-TATATTTATCAT
1 TTTTTTATATATTTATCAT
23095754 TGTATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTTATATATTTATCATC
Found at i:23096525 original size:21 final size:22
Alignment explanation
Indices: 23096501--23096542 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
23096491 AATCGAGTTT
23096501 GAAT-ATTT-TAATATTTAATTC
1 GAATAATTTATAAT-TTTAATTC
23096522 GAATAATTTATAATTTTAATT
1 GAATAATTTATAATTTTAATT
23096543 AAATTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
GAATAATTTATAATTTTAATTC
Found at i:23102774 original size:18 final size:18
Alignment explanation
Indices: 23102753--23102798 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
23102743 CGATTTGACA
23102753 TTTAATAAAACTTATCAT
1 TTTAATAAAACTTATCAT
23102771 TTTAATAAAACTTATCAT
1 TTTAATAAAACTTATCAT
*
23102789 TTTAAGAAAA
1 TTTAATAAAA
23102799 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (18 bp):
TTTAATAAAACTTATCAT
Found at i:23103712 original size:7 final size:7
Alignment explanation
Indices: 23103689--23103735 Score: 67
Period size: 7 Copynumber: 6.4 Consensus size: 7
23103679 ATTTTTATTG
*
23103689 TTTTTTA
1 TTTTATA
23103696 TTTTATTA
1 TTTTA-TA
23103704 TTTTATA
1 TTTTATA
23103711 TTTTATA
1 TTTTATA
23103718 TTTTATA
1 TTTTATA
23103725 TTTTATTA
1 TTTTA-TA
23103733 TTT
1 TTT
23103736 ATTAATGCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
7 25 0.68
8 12 0.32
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTATA
Found at i:23103737 original size:14 final size:15
Alignment explanation
Indices: 23103681--23103735 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
23103671 TTTTCATCAT
* *
23103681 TTTTATTGTTTTTTA
1 TTTTATTATTTTATA
23103696 TTTTATTATTTTATA
1 TTTTATTATTTTATA
23103711 TTTTA-TATTTTATA
1 TTTTATTATTTTATA
23103725 TTTTATTATTT
1 TTTTATTATTT
23103736 ATTAATGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.38
15 23 0.62
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTATTATTTTATA
Found at i:23103859 original size:6 final size:6
Alignment explanation
Indices: 23103848--23103897 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
23103838 ATCCTTGAAA
*
23103848 ATTTTT ATTTTTT ATTTTT A-TTAT ATTTTT ATTTTT ATTATTAT ATTTTT
1 ATTTTT A-TTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT-TT-T ATTTTT
23103898 TATATATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 4 0.11
6 20 0.53
7 10 0.26
8 4 0.11
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:23103876 original size:11 final size:11
Alignment explanation
Indices: 23103860--23103908 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
23103850 TTTTATTTTT
23103860 TATTTTTATTA
1 TATTTTTATTA
23103871 TATTTTTATT-
1 TATTTTTATTA
*
23103881 T-TTATTATTA
1 TATTTTTATTA
23103891 TATTTTT-TATA
1 TATTTTTAT-TA
23103902 TATTTTT
1 TATTTTT
23103909 TATACCTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 7 0.21
10 3 0.09
11 23 0.70
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TATTTTTATTA
Found at i:23103878 original size:17 final size:16
Alignment explanation
Indices: 23103852--23103911 Score: 77
Period size: 17 Copynumber: 3.7 Consensus size: 16
23103842 TTGAAAATTT
23103852 TTATTTTTTATTTTTA
1 TTATTTTTTATTTTTA
23103868 TTATATTTTTATTTTTA
1 TTAT-TTTTTATTTTTA
* *
23103885 TTATTATAT-TTTTTA
1 TTATTTTTTATTTTTA
23103900 TATATTTTTTAT
1 T-TATTTTTTAT
23103912 ACCTATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 7 0.19
16 13 0.35
17 17 0.46
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTTTTATTTTTA
Found at i:23103890 original size:20 final size:18
Alignment explanation
Indices: 23103853--23103900 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 18
23103843 TGAAAATTTT
23103853 TATTTTTTATTTTTATTA
1 TATTTTTTATTTTTATTA
*
23103871 TATTTTTATTTTTATTATTA
1 TATTTTT-TATTT-TTATTA
23103891 TATTTTTTAT
1 TATTTTTTAT
23103901 ATATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 7 0.27
19 6 0.23
20 13 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTTTTTATTTTTATTA
Found at i:23103904 original size:31 final size:30
Alignment explanation
Indices: 23103848--23103908 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
23103838 ATCCTTGAAA
*
23103848 ATTTTTATTTTTTATTTTTATTATATTTTT
1 ATTTTTATTTTATATTTTTATTATATTTTT
23103878 ATTTTTATTATTATATTTTT-TATATATTTTT
1 ATTTTTATT-TTATATTTTTAT-TATATTTTT
23103909 TATACCTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (30 bp):
ATTTTTATTTTATATTTTTATTATATTTTT
Found at i:23105469 original size:19 final size:19
Alignment explanation
Indices: 23105405--23105475 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
23105395 ATTAATGACA
* *
23105405 ATTAAATTTGGGCTTCAAT
1 ATTAAATTTGAGCTTCAAC
*
23105424 ATTAAATTTGAGCTTCAGC
1 ATTAAATTTGAGCTTCAAC
* * *
23105443 TTTGAATTTGAGCTTTAAC
1 ATTAAATTTGAGCTTCAAC
*
23105462 ATTAAATTTAAGCT
1 ATTAAATTTGAGCT
23105476 GTTAGATCCA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.42
Consensus pattern (19 bp):
ATTAAATTTGAGCTTCAAC
Found at i:23112163 original size:21 final size:21
Alignment explanation
Indices: 23112137--23112181 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
23112127 ATAATAAAAT
*
23112137 ATAAGTATTAAAA-CCAAATAA
1 ATAAGTA-TAAAATACAAATAA
23112158 ATAAGTATAAAATACAAATAA
1 ATAAGTATAAAATACAAATAA
23112179 ATA
1 ATA
23112182 TTAAGTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.24
Consensus pattern (21 bp):
ATAAGTATAAAATACAAATAA
Found at i:23114802 original size:17 final size:18
Alignment explanation
Indices: 23114777--23114814 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
23114767 AAATCTAGAT
*
23114777 ATCACA-TTTTTCTTAAA
1 ATCACATTTTTTCTCAAA
*
23114794 ATCATATTTTTTCTCAAA
1 ATCACATTTTTTCTCAAA
23114812 ATC
1 ATC
23114815 TAAAATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47
Consensus pattern (18 bp):
ATCACATTTTTTCTCAAA
Found at i:23115745 original size:21 final size:21
Alignment explanation
Indices: 23115698--23115745 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
23115688 TATTATTTTT
*
23115698 TAAA-ATAATTTTATTAAAAT
1 TAAATATAATTTTATTAAAAA
23115718 TAAATATAATTTT-TTAAAAA
1 TAAATATAATTTTATTAAAAA
23115738 TAATATAT
1 TAA-ATAT
23115746 GAATCATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAATATAATTTTATTAAAAA
Found at i:23115929 original size:7 final size:7
Alignment explanation
Indices: 23115917--23115954 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
23115907 AAAAATTATT
23115917 TATTTTA
1 TATTTTA
23115924 TATTTTA
1 TATTTTA
*
23115931 T-TATTA
1 TATTTTA
*
23115937 TTTTTTA
1 TATTTTA
23115944 TATTTTA
1 TATTTTA
23115951 TATT
1 TATT
23115955 ATTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TATTTTA
Found at i:23115954 original size:19 final size:20
Alignment explanation
Indices: 23115919--23115957 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
23115909 AAATTATTTA
23115919 TTTTATATTTTATTATTATT
1 TTTTATATTTTATTATTATT
23115939 TTTTATATTTTA-TATTATT
1 TTTTATATTTTATTATTATT
23115958 AAAATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATATTTTATTATTATT
Found at i:23115958 original size:22 final size:20
Alignment explanation
Indices: 23115911--23115956 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
23115901 AATTTTAAAA
23115911 ATTATT-TATTTTATATTTT
1 ATTATTATATTTTATATTTT
*
23115930 ATTATTATTTTTTATATTTT
1 ATTATTATATTTTATATTTT
23115950 A-TATTAT
1 ATTATTAT
23115957 TAAAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTATTATATTTTATATTTT
Found at i:23117805 original size:16 final size:16
Alignment explanation
Indices: 23117786--23117832 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
23117776 GTACGAGTAT
23117786 ATAAAATTATAATAAA
1 ATAAAATTATAATAAA
* *
23117802 ATAATATTATAATTAAT
1 ATAAAATTATAA-TAAA
*
23117819 ATTAAATTA-AATAA
1 ATAAAATTATAATAA
23117833 TATTATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 3 0.12
16 13 0.50
17 10 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAAATTATAATAAA
Found at i:23117884 original size:12 final size:12
Alignment explanation
Indices: 23117869--23117898 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
23117859 ATATTAAAAT
23117869 AAATTTTTTTTA
1 AAATTTTTTTTA
23117881 AAATTTTTTTTA
1 AAATTTTTTTTA
*
23117893 TAATTT
1 AAATTT
23117899 AAATTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
AAATTTTTTTTA
Found at i:23118517 original size:16 final size:15
Alignment explanation
Indices: 23118496--23118533 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
23118486 GGATAACATG
23118496 ATAATTATTTTATATT
1 ATAATTA-TTTATATT
23118512 ATAATTGATTTATATT
1 ATAATT-ATTTATATT
23118528 -TAATTA
1 ATAATTA
23118534 AAAGGGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.05
15 5 0.24
16 14 0.67
17 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
ATAATTATTTATATT
Found at i:23119032 original size:28 final size:27
Alignment explanation
Indices: 23119000--23119077 Score: 113
Period size: 28 Copynumber: 2.9 Consensus size: 27
23118990 TTTTTTACTT
23119000 TAAAATAATTGAATCATCTTATATTAAA
1 TAAAATAATTGAATCATCTTATATT-AA
23119028 TAAAATAATTGAATCATCTTATATTAA
1 TAAAATAATTGAATCATCTTATATTAA
* *
23119055 TAAAAAAATT-AATTATCATTATA
1 TAAAATAATTGAATCATC-TTATA
23119078 ATTTTATTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 6 0.13
27 16 0.34
28 25 0.53
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (27 bp):
TAAAATAATTGAATCATCTTATATTAA
Found at i:23119641 original size:2 final size:2
Alignment explanation
Indices: 23119629--23119664 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
23119619 CATGTTCTTT
*
23119629 TA TA GA 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
23119665 CATACATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:23121098 original size:15 final size:15
Alignment explanation
Indices: 23121078--23121111 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
23121068 CATTCGATTA
23121078 ATTTAAAATTAAATG
1 ATTTAAAATTAAATG
*
23121093 ATTT-AAATTAAATT
1 ATTTAAAATTAAATG
23121107 ATTTA
1 ATTTA
23121112 TTTTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
ATTTAAAATTAAATG
Found at i:23121161 original size:15 final size:15
Alignment explanation
Indices: 23121144--23121172 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
23121134 TTTCATTTTA
23121144 AAAATTAA-TTAATC
1 AAAATTAATTTAATC
23121158 AAAATTAATTTAATC
1 AAAATTAATTTAATC
23121173 TGTTAGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTAATTTAATC
Found at i:23121713 original size:34 final size:35
Alignment explanation
Indices: 23121674--23121756 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 35
23121664 ATTAATTAAA
*
23121674 AATTAAATTTATTTTAA-AATTATTTTCAA-TAATTG
1 AATTAAATTTATTTTAATAA-T-TTATCAATTAATTG
* *
23121709 -ATTAAAATTAATTTAATAATTTATCAATTAATTG
1 AATTAAATTTATTTTAATAATTTATCAATTAATTG
*
23121743 AATTAAATTAATTT
1 AATTAAATTTATTT
23121757 GATTGATTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
33 6 0.15
34 21 0.54
35 12 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (35 bp):
AATTAAATTTATTTTAATAATTTATCAATTAATTG
Found at i:23121729 original size:22 final size:23
Alignment explanation
Indices: 23121687--23121729 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
23121677 TAAATTTATT
*
23121687 TTAAAATTATTTTCAATAATTGA
1 TTAAAATTAATTTCAATAATTGA
23121710 TTAAAATTAATTT-AATAATT
1 TTAAAATTAATTTCAATAATT
23121730 TATCAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAAAATTAATTTCAATAATTGA
Found at i:23125156 original size:21 final size:21
Alignment explanation
Indices: 23125130--23125174 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
23125120 ATAATAAAAT
*
23125130 ATAAGTATTAAAA-CCAAATAA
1 ATAAGTA-TAAAATACAAATAA
23125151 ATAAGTATAAAATACAAATAA
1 ATAAGTATAAAATACAAATAA
23125172 ATA
1 ATA
23125175 TTAAGTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.24
Consensus pattern (21 bp):
ATAAGTATAAAATACAAATAA
Found at i:23127406 original size:24 final size:25
Alignment explanation
Indices: 23127367--23127416 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
23127357 AAAAATGCCT
*
23127367 TAAATAATTTTTTATG-T-TTTTTA
1 TAAATAATTATTTATGATATTTTTA
23127390 TAAATAGATTATTTATGATATTTTTA
1 TAAATA-ATTATTTATGATATTTTTA
23127416 T
1 T
23127417 TGAAAAATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 9 0.39
25 1 0.04
26 7 0.30
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (25 bp):
TAAATAATTATTTATGATATTTTTA
Found at i:23127781 original size:17 final size:18
Alignment explanation
Indices: 23127756--23127793 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
23127746 AAATCTAGAT
*
23127756 ATCACA-TTTTTCTTAAA
1 ATCACATTTTTTCTCAAA
*
23127773 ATCATATTTTTTCTCAAA
1 ATCACATTTTTTCTCAAA
23127791 ATC
1 ATC
23127794 TAAAATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47
Consensus pattern (18 bp):
ATCACATTTTTTCTCAAA
Found at i:23130746 original size:5 final size:5
Alignment explanation
Indices: 23130726--23130760 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
23130716 GTACGAGTAT
*
23130726 ATAAA ATTATA ATAAA ATAAA ATAAA ATAAA ATAA
1 ATAAA A-TAAA ATAAA ATAAA ATAAA ATAAA ATAA
23130761 TATTATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
ATAAA
Found at i:23130788 original size:15 final size:15
Alignment explanation
Indices: 23130726--23130792 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 15
23130716 GTACGAGTAT
*
23130726 ATAAAATTATAATAAA
1 ATAATATTA-AATAAA
* *
23130742 ATAAAATAAAATAAA
1 ATAATATTAAATAAA
23130757 ATAATATT--AT-AA
1 ATAATATTAAATAAA
* *
23130769 TTAATATTAAATTAA
1 ATAATATTAAATAAA
23130784 ATAATATTA
1 ATAATATTA
23130793 TATTTGTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
12 9 0.21
13 2 0.05
14 2 0.05
15 22 0.51
16 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAATATTAAATAAA
Found at i:23131477 original size:16 final size:15
Alignment explanation
Indices: 23131456--23131493 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
23131446 TAATAACATG
23131456 ATAATTATTTTATATT
1 ATAATTA-TTTATATT
23131472 ATAATTGATTTATATT
1 ATAATT-ATTTATATT
23131488 -TAATTA
1 ATAATTA
23131494 AAAGGGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.05
15 5 0.24
16 14 0.67
17 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
ATAATTATTTATATT
Found at i:23131994 original size:28 final size:27
Alignment explanation
Indices: 23131962--23132039 Score: 113
Period size: 28 Copynumber: 2.9 Consensus size: 27
23131952 TTTTTTACTT
23131962 TAAAATAATTGAATCATCTTATATTAAA
1 TAAAATAATTGAATCATCTTATATT-AA
23131990 TAAAATAATTGAATCATCTTATATTAA
1 TAAAATAATTGAATCATCTTATATTAA
* *
23132017 TAAAAAAATT-AATTATCATTATA
1 TAAAATAATTGAATCATC-TTATA
23132040 ATTTTATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 6 0.13
27 16 0.34
28 25 0.53
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (27 bp):
TAAAATAATTGAATCATCTTATATTAA
Found at i:23133562 original size:14 final size:14
Alignment explanation
Indices: 23133543--23133589 Score: 76
Period size: 14 Copynumber: 3.3 Consensus size: 14
23133533 TTCGATTATT
23133543 TTTAAATTAAATTA
1 TTTAAATTAAATTA
23133557 TTTAAAATTAAATTA
1 TTT-AAATTAAATTA
*
23133572 ATTAAATTAAATTA
1 TTTAAATTAAATTA
23133586 TTTA
1 TTTA
23133590 TTTTTATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTAAATTAAATTA
Found at i:23133576 original size:4 final size:5
Alignment explanation
Indices: 23133544--23133585 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
23133534 TCGATTATTT
*
23133544 TTAAA TTAAA TT-AT TTAAAA TTAAA TT-AA TTAAA TTAAA TTA
1 TTAAA TTAAA TTAAA TT-AAA TTAAA TTAAA TTAAA TTAAA TTA
23133586 TTTATTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 7 0.22
5 22 0.69
6 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
TTAAA
Found at i:23133619 original size:27 final size:27
Alignment explanation
Indices: 23133568--23133620 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
23133558 TTAAAATTAA
*
23133568 ATTAATTAAATTAAATTATTTATTTTT
1 ATTAATTAAATTAAATTATTCATTTTT
*
23133595 ATTAATTGAATTAAAATT-TTCATTTT
1 ATTAATTAAATT-AAATTATTCATTTT
23133621 AAAAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
ATTAATTAAATTAAATTATTCATTTTT
Found at i:23133639 original size:15 final size:15
Alignment explanation
Indices: 23133622--23133650 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
23133612 TTTCATTTTA
23133622 AAAATTAA-TTAATC
1 AAAATTAATTTAATC
23133636 AAAATTAATTTAATC
1 AAAATTAATTTAATC
23133651 TGTTAGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTAATTTAATC
Found at i:23133868 original size:25 final size:26
Alignment explanation
Indices: 23133829--23133879 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
23133819 AATTATTTTA
* *
23133829 TTTTATTTTTATTAACTGAATTAATT
1 TTTTAATTTTATTAAATGAATTAATT
*
23133855 TTTTAATTTT-TTAAATTAATTAATT
1 TTTTAATTTTATTAAATGAATTAATT
23133880 GAAATTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTAATTTTATTAAATGAATTAATT
Found at i:23143146 original size:2 final size:2
Alignment explanation
Indices: 23143141--23143179 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
23143131 TTGTGTGTGC
23143141 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
23143180 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23143184 original size:2 final size:2
Alignment explanation
Indices: 23143179--23143220 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
23143169 ATATATATAT
23143179 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
23143221 TATGCGTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:23145192 original size:18 final size:17
Alignment explanation
Indices: 23145163--23145197 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
23145153 TTAAATGAAT
*
23145163 TTTTTTATATTATACTA
1 TTTTTTATATTAGACTA
23145180 TTTTTTATAATTAGACTA
1 TTTTTTAT-ATTAGACTA
23145198 AAAAAGTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTTTTATATTAGACTA
Found at i:23145440 original size:151 final size:152
Alignment explanation
Indices: 23145080--23145498 Score: 410
Period size: 152 Copynumber: 2.8 Consensus size: 152
23145070 TTAATAATTT
* * ** * * *
23145080 TAAAATTTTAATTTTAAAAATGTT-AAAGTGAT-TTTCTAAAATATCTTTAGTAAAATTTTTTAT
1 TAAAATTTTAATTCTAAAAATATTAAAAGTGATCGAT-T-AAATACCATTAAT-AAATTTTTTAT
* *
23145143 AAATTTTAATTTAAATGA-ATTTTTTTA-TATTATACTATTTTTTATAATTAGACTAAAAAAGTG
63 AAATTTTAATTTAAATGATTTTTTTTTATTATTAAACT-TTTTTTATAATTAGACTAAAAAAGTG
* *
23145206 CTAAAAGTGATTAACTAAACACTTAA
127 CTAAAAGTAATTAACAAAACACTTAA
* * *
23145232 TAAAATTTTAATTCTAAAAATATTAAAAGTGATTGATTAAATGCCATTAATAAA-TTTTTACAAA
1 TAAAATTTTAATTCTAAAAATATTAAAAGTGATCGATTAAATACCATTAATAAATTTTTTATAAA
*
23145296 TTTTAATTTAAATGATTTTGTTTTTATTATTAAACTTTTTTTATAATTAGACT-AAAAAGTGTTA
66 TTTTAATTTAAATGATTTT-TTTTTATTATTAAACTTTTTTTATAATTAGACTAAAAAAGTGCTA
* *
23145360 AAATTAATTGACAAAA-ATGCCTTTAA
130 AAAGTAATTAACAAAACA---C-TTAA
* ** * * *
23145386 TTAAATTTTAATT-TAAAAA-A-TGCAAGTTATCGATTAAAATACCATTAGT-GATTTTTTATAA
1 TAAAATTTTAATTCTAAAAATATTAAAAGTGATCGATT-AAATACCATTAATAAATTTTTTATAA
* * * * *
23145447 ATTTTAATATAAATAATTTTTTTTTATTATTAGACATTGTTTTATAAGTAGA
65 ATTTTAATTTAAATGATTTTTTTTTATTATTAAAC-TTTTTTTATAATTAGA
23145499 ATGCTTTTTC
Statistics
Matches: 225, Mismatches: 30, Indels: 24
0.81 0.11 0.09
Matches are distributed among these distances:
150 25 0.11
151 53 0.24
152 106 0.47
153 24 0.11
154 17 0.08
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (152 bp):
TAAAATTTTAATTCTAAAAATATTAAAAGTGATCGATTAAATACCATTAATAAATTTTTTATAAA
TTTTAATTTAAATGATTTTTTTTTATTATTAAACTTTTTTTATAATTAGACTAAAAAAGTGCTAA
AAGTAATTAACAAAACACTTAA
Found at i:23145528 original size:6 final size:6
Alignment explanation
Indices: 23145514--23145546 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
23145504 TTTTCACATC
*
23145514 AAATGA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
23145547 GAGATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:23148940 original size:24 final size:24
Alignment explanation
Indices: 23148896--23148941 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
23148886 CTCAGTAATT
*
23148896 TATTAAGTAGACATAATATATTCA
1 TATTAAGTAGACACAATATATTCA
*
23148920 TATTAAGTATA-ACAATAATATT
1 TATTAAGTAGACACAAT-ATATT
23148942 AAACCAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (24 bp):
TATTAAGTAGACACAATATATTCA
Found at i:23149519 original size:21 final size:21
Alignment explanation
Indices: 23149495--23149564 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
23149485 TAAAAAGAAA
23149495 AAAATTACTTAATACATAAAT
1 AAAATTACTTAATACATAAAT
* *
23149516 AAAATTACTT-AT-GA-AGA-
1 AAAATTACTTAATACATAAAT
23149533 AAAATTACTTAATACATAAAT
1 AAAATTACTTAATACATAAAT
23149554 AAAATTACTTA
1 AAAATTACTTA
23149565 TGAAGAAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
17 10 0.24
18 4 0.10
19 2 0.05
20 4 0.10
21 21 0.51
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAATTACTTAATACATAAAT
Found at i:23149538 original size:17 final size:17
Alignment explanation
Indices: 23149516--23149572 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
23149506 ATACATAAAT
23149516 AAAATTACTTATGAAGA
1 AAAATTACTTATGAAGA
* *
23149533 AAAATTACTTAATACATAAA
1 AAAATTACTT-AT-GA-AGA
23149553 TAAAATTACTTATGAAGA
1 -AAAATTACTTATGAAGA
23149571 AA
1 AA
23149573 CAAAATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 12 0.38
18 4 0.12
19 2 0.06
20 4 0.12
21 10 0.31
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (17 bp):
AAAATTACTTATGAAGA
Found at i:23149539 original size:38 final size:38
Alignment explanation
Indices: 23149494--23149572 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
23149484 TTAAAAAGAA
23149494 AAAAATTACTTAATACATAAATAAAATTACTTATGAAG
1 AAAAATTACTTAATACATAAATAAAATTACTTATGAAG
23149532 AAAAATTACTTAATACATAAATAAAATTACTTATGAAG
1 AAAAATTACTTAATACATAAATAAAATTACTTATGAAG
23149570 AAA
1 AAA
23149573 CAAAATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (38 bp):
AAAAATTACTTAATACATAAATAAAATTACTTATGAAG
Found at i:23152015 original size:22 final size:23
Alignment explanation
Indices: 23151954--23152015 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 23
23151944 ATACTTCATA
**
23151954 TAAAAACACCATTCAGCAATGTGC
1 TAAAAACACCATTCAGCAA-GACC
* *
23151978 TAAGACACACCCTTCAGCAA-ACC
1 TAA-AAACACCATTCAGCAAGACC
23152001 TAAAAACACCATTCA
1 TAAAAACACCATTCA
23152016 ACATATGATT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 10 0.32
23 4 0.13
24 3 0.10
25 14 0.45
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.18
Consensus pattern (23 bp):
TAAAAACACCATTCAGCAAGACC
Found at i:23155459 original size:92 final size:92
Alignment explanation
Indices: 23155302--23155483 Score: 346
Period size: 92 Copynumber: 2.0 Consensus size: 92
23155292 CCTCACAAAG
*
23155302 GTTGGGTGTTTGCTAAGTTGAAGTAAACAAAGGTATAGACAAGAGAATGATGAATGAACAACAAA
1 GTTGGGTGTTTGCTAAGTTGAAGTAAACAAAGGTATAGACAAAAGAATGATGAATGAACAACAAA
*
23155367 ATAGTTTGGATACAATAAATGCAAAAA
66 ATAGTTTGGATACAATAAATACAAAAA
23155394 GTTGGGTGTTTGCTAAGTTGAAGTAAACAAAGGTATAGACAAAAGAATGATGAATGAACAACAAA
1 GTTGGGTGTTTGCTAAGTTGAAGTAAACAAAGGTATAGACAAAAGAATGATGAATGAACAACAAA
23155459 ATAGTTTGGATACAATAAATACAAA
66 ATAGTTTGGATACAATAAATACAAA
23155484 GATATAGACT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.24
Consensus pattern (92 bp):
GTTGGGTGTTTGCTAAGTTGAAGTAAACAAAGGTATAGACAAAAGAATGATGAATGAACAACAAA
ATAGTTTGGATACAATAAATACAAAAA
Found at i:23163580 original size:220 final size:220
Alignment explanation
Indices: 23163151--23163557 Score: 568
Period size: 220 Copynumber: 1.9 Consensus size: 220
23163141 ATGTAACGGT
* * * * * * * *
23163151 TATAGTGAAGGCATTTTATAGTAGATGGCGTCTTTAATAATTTTTAAAATTTTTTGAGGGAAAAT
1 TATAGTGAAGGCATTTTACAGTAGAAGACGCCTTTAATAATGTCTAAAATTTTTAGAAGGAAAAT
*
23163216 ATTGAAGGCATCTGTTATTAACAAATGCCTTCAGTGATGGATTACTAAGTGTAAAGGTATATTGA
66 ATTGAAGGCATCTGTTATTAACAAATGCCTTCAGTAATGGATTACTAAGTGTAAAGGTATATTGA
* * *
23163281 AGGTATTTTTTGAATAAACACCTTCTATAACCATCGTGGAGTATTGAAGGCGTTTTATAATAAAA
131 AGGCATTTTTTGAATAAACACCTTCTATAACAATCGTGGAGTATTGAAGGCGATTTATAATAAAA
*
23163346 GATGCCTTTAATAATCCCATCGAGG
196 GACGCCTTTAATAATCCCATCGAGG
* * *
23163371 TATATTGAAGGTATTTTACAGTAGAAGACGCCTTTAATAATGTCTAAAATTTTTAGAAGGAAACT
1 TATAGTGAAGGCATTTTACAGTAGAAGACGCCTTTAATAATGTCTAAAATTTTTAGAAGGAAAAT
* * *
23163436 ACTT-AAGGCATCTGTTATTAACAAATGCCTTCCGTAATGGATTACTAAGTTTAAGGGTATATTG
66 A-TTGAAGGCATCTGTTATTAACAAATGCCTTCAGTAATGGATTACTAAGTGTAAAGGTATATTG
* * *
23163500 AAGTGCA-TTTTTGAATAAACGCTTTCTATAACAATCGTGGTA-TATTGAAGGTGATTTA
130 AAG-GCATTTTTTGAATAAACACCTTCTATAACAATCGTGG-AGTATTGAAGGCGATTTA
23163558 CTGTAGAAGA
Statistics
Matches: 163, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
220 158 0.97
221 5 0.03
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (220 bp):
TATAGTGAAGGCATTTTACAGTAGAAGACGCCTTTAATAATGTCTAAAATTTTTAGAAGGAAAAT
ATTGAAGGCATCTGTTATTAACAAATGCCTTCAGTAATGGATTACTAAGTGTAAAGGTATATTGA
AGGCATTTTTTGAATAAACACCTTCTATAACAATCGTGGAGTATTGAAGGCGATTTATAATAAAA
GACGCCTTTAATAATCCCATCGAGG
Found at i:23165301 original size:22 final size:22
Alignment explanation
Indices: 23165269--23165320 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
23165259 TTCGGTCATT
*
23165269 CCTTAGGCACCTACGTTTTATC
1 CCTTAGCCACCTACGTTTTATC
23165291 CCTTAGCCACCTACGTTTTATC
1 CCTTAGCCACCTACGTTTTATC
23165313 CCTTAGCC
1 CCTTAGCC
23165321 TTTCTTGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.37, G:0.12, T:0.35
Consensus pattern (22 bp):
CCTTAGCCACCTACGTTTTATC
Found at i:23165651 original size:93 final size:93
Alignment explanation
Indices: 23165492--23165675 Score: 341
Period size: 93 Copynumber: 2.0 Consensus size: 93
23165482 CCTCACAAAG
*
23165492 GTTGGGTGTTTGCTAAGTTGAAGTAAACAAAGGTATAAACAAGAGAATGATGAATGAACAACAAA
1 GTTGGGTGTTTGCTAAGTTGAAGTAAACAAAGGTATAAACAAAAGAATGATGAATGAACAACAAA
*
23165557 AATAGTTTGGATACAATAAATGCAAAAA
66 AATAGTTTGGATACAATAAATACAAAAA
*
23165585 GTTGGGTGTTTGCTAAGTTGAAGTAAACAAAGGTATAGACAAAAGAATGATGAATGAACAACAAA
1 GTTGGGTGTTTGCTAAGTTGAAGTAAACAAAGGTATAAACAAAAGAATGATGAATGAACAACAAA
23165650 AATAGTTTGGATACAATAAATACAAA
66 AATAGTTTGGATACAATAAATACAAA
23165676 GATATAGACT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (93 bp):
GTTGGGTGTTTGCTAAGTTGAAGTAAACAAAGGTATAAACAAAAGAATGATGAATGAACAACAAA
AATAGTTTGGATACAATAAATACAAAAA
Found at i:23173773 original size:22 final size:22
Alignment explanation
Indices: 23173748--23174037 Score: 97
Period size: 22 Copynumber: 13.4 Consensus size: 22
23173738 AAAAAACAAG
* *
23173748 TGATAACTTAATAGTTAATTAT
1 TGATAACTTAATAGTAAATTAA
* * *
23173770 TGATAATTTAATAATAAATCAA
1 TGATAACTTAATAGTAAATTAA
* *
23173792 TGACAACTTAATAGTAAATTAG
1 TGATAACTTAATAGTAAATTAA
* *
23173814 TGATAATTTAATAATAAATTAA
1 TGATAACTTAATAGTAAATTAA
* * *
23173836 T-TTAAGTTTAGTAGTAAA-TAA
1 TGATAA-CTTAATAGTAAATTAA
* *
23173857 TTGATAAATTTAGTAGTAAATCATAA
1 -TGAT-AACTTAATAGTAAAT--TAA
* *
23173883 --AT-ACTTAGTAGTAAATCAA
1 TGATAACTTAATAGTAAATTAA
* * * * * *
23173902 TAATAATTTAATAATTAATCAT
1 TGATAACTTAATAGTAAATTAA
* * * * *
23173924 TGAAAATTTAAAAGGAAATAAA
1 TGATAACTTAATAGTAAATTAA
*
23173946 T-ATAACATAGTAATAGTTAATT-A
1 TGATAAC-T--TAATAGTAAATTAA
*
23173969 TCAATAACTTAATAG----TTAA
1 T-GATAACTTAATAGTAAATTAA
23173988 --ATAACTTAATAGTAAATT-A
1 TGATAACTTAATAGTAAATTAA
* * *
23174007 TGAATAATTTAATA-TAAAATAG
1 TG-ATAACTTAATAGTAAATTAA
23174029 TGATAACTT
1 TGATAACTT
23174038 GATAATGAAT
Statistics
Matches: 201, Mismatches: 43, Indels: 49
0.69 0.15 0.17
Matches are distributed among these distances:
16 12 0.06
18 2 0.01
19 4 0.02
20 2 0.01
21 35 0.17
22 110 0.55
23 17 0.08
24 11 0.05
25 5 0.02
26 3 0.01
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (22 bp):
TGATAACTTAATAGTAAATTAA
Found at i:23173832 original size:44 final size:45
Alignment explanation
Indices: 23173715--23173922 Score: 151
Period size: 44 Copynumber: 4.7 Consensus size: 45
23173705 AATAACATAT
*** * *
23173715 TAGTAAATTAATGATTGGTTAATAA-AAAACAAGTGATAACTTAA
1 TAGTAAATTAATGATAATTTAATAATAAATCAAGTGACAACTTAA
* *
23173759 TAGTTAATTATTGATAATTTAATAATAAATCAA-TGACAACTTAA
1 TAGTAAATTAATGATAATTTAATAATAAATCAAGTGACAACTTAA
* * * * ** *
23173803 TAGTAAATTAGTGATAATTTAATAATAAATTAATTTA-AGTTTAG
1 TAGTAAATTAATGATAATTTAATAATAAATCAAGTGACAACTTAA
* * * *
23173847 TAGTAAA-TAATTGATAAATTTAGTAGTAAATC-A-T-AAATACTTAG
1 TAGTAAATTAA-TGAT-AATTTAATAATAAATCAAGTGACA-ACTTAA
* * *
23173891 TAGTAAATCAATAATAATTTAATAATTAATCA
1 TAGTAAATTAATGATAATTTAATAATAAATCA
23173923 TTGAAAATTT
Statistics
Matches: 131, Mismatches: 25, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
42 1 0.01
43 17 0.13
44 90 0.69
45 23 0.18
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.38
Consensus pattern (45 bp):
TAGTAAATTAATGATAATTTAATAATAAATCAAGTGACAACTTAA
Found at i:23173869 original size:23 final size:23
Alignment explanation
Indices: 23173803--23173877 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
23173793 GACAACTTAA
* * *
23173803 TAGTAAATTAGTGAT-AATTTAA
1 TAGTAAATAATTGATAAATTTAG
* *
23173825 TAATAAATTAATT--TAAGTTTAG
1 TAGTAAA-TAATTGATAAATTTAG
23173847 TAGTAAATAATTGATAAATTTAG
1 TAGTAAATAATTGATAAATTTAG
23173870 TAGTAAAT
1 TAGTAAAT
23173878 CATAAATACT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
21 6 0.14
22 17 0.40
23 19 0.45
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (23 bp):
TAGTAAATAATTGATAAATTTAG
Found at i:23173992 original size:16 final size:15
Alignment explanation
Indices: 23173971--23174004 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
23173961 GTTAATTATC
23173971 AATAACTTAATAGTTA
1 AATAACTTAATAG-TA
23173987 AATAACTTAATAGTA
1 AATAACTTAATAGTA
23174002 AAT
1 AAT
23174005 TATGAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
AATAACTTAATAGTA
Found at i:23174242 original size:22 final size:22
Alignment explanation
Indices: 23174045--23174244 Score: 77
Period size: 22 Copynumber: 9.1 Consensus size: 22
23174035 CTTGATAATG
*
23174045 AATC-ATGATTAATTTAGTAATA
1 AATCAATGA-TAATTTAGTAGTA
* *
23174067 AATCTATGATAATTTTGTA-TA
1 AATCAATGATAATTTAGTAGTA
* * *
23174088 AAT-AATTAAAAATTAAGTAGTA
1 AATCAA-TGATAATTTAGTAGTA
** * *
23174110 AATCAATGATAACATAATAATA
1 AATCAATGATAATTTAGTAGTA
* * * *
23174132 AATGC-ATAATAATATAATAGTC
1 AAT-CAATGATAATTTAGTAGTA
***
23174154 AATTGCTGATAATTTAG-ATGTA
1 AATCAATGATAATTTAGTA-GTA
*** *
23174176 AATTTTTGATAATTTAGTAATA
1 AATCAATGATAATTTAGTAGTA
* * *** * *
23174198 AATCACTAATAGCATAATTGTA
1 AATCAATGATAATTTAGTAGTA
23174220 AATCAATGATAATTTAGTAGTA
1 AATCAATGATAATTTAGTAGTA
23174242 AAT
1 AAT
23174245 TAGTTAATCA
Statistics
Matches: 127, Mismatches: 43, Indels: 16
0.68 0.23 0.09
Matches are distributed among these distances:
20 1 0.01
21 15 0.12
22 103 0.81
23 8 0.06
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.38
Consensus pattern (22 bp):
AATCAATGATAATTTAGTAGTA
Found at i:23174254 original size:30 final size:30
Alignment explanation
Indices: 23174220--23174276 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
23174210 CATAATTGTA
23174220 AATCAATGATAA-TTTAGTAGTAAATTAGTT
1 AATCAATGATAACTTT-GTAGTAAATTAGTT
*
23174250 AATCACTGATAACTTTGTAGTAAATTA
1 AATCAATGATAACTTTGTAGTAAATTA
23174277 TCGATAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (30 bp):
AATCAATGATAACTTTGTAGTAAATTAGTT
Found at i:23174375 original size:21 final size:22
Alignment explanation
Indices: 23174322--23174400 Score: 101
Period size: 22 Copynumber: 3.6 Consensus size: 22
23174312 ACCAAATCAC
23174322 TTAGTAGTAAATCA-TCA-ACAA
1 TTAGTAGTAAATCATTCATA-AA
* *
23174343 TTTAGTAGTAAATTATTCATAAC
1 -TTAGTAGTAAATCATTCATAAA
23174366 TTAG-AGTAAATCATTCATAAA
1 TTAGTAGTAAATCATTCATAAA
23174387 TTAGTAGTAAATCA
1 TTAGTAGTAAATCA
23174401 ATATTAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
21 19 0.38
22 26 0.52
23 4 0.08
24 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.35
Consensus pattern (22 bp):
TTAGTAGTAAATCATTCATAAA
Found at i:23174412 original size:22 final size:22
Alignment explanation
Indices: 23174322--23174421 Score: 98
Period size: 22 Copynumber: 4.6 Consensus size: 22
23174312 ACCAAATCAC
*
23174322 TTAGTAGTAAATC-ATCAACAAT
1 TTAGTAGTAAATCAATC-ATAAT
* * *
23174344 TTAGTAGTAAATTATTCATAAC
1 TTAGTAGTAAATCAATCATAAT
* *
23174366 TTAG-AGTAAATCATTCATAAA
1 TTAGTAGTAAATCAATCATAAT
23174387 TTAGTAGTAAATCAAT-ATTAAT
1 TTAGTAGTAAATCAATCA-TAAT
*
23174409 TTAGTAATAAATC
1 TTAGTAGTAAATC
23174422 GTTTATAATT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
21 20 0.30
22 44 0.67
23 2 0.03
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (22 bp):
TTAGTAGTAAATCAATCATAAT
Found at i:23174931 original size:20 final size:21
Alignment explanation
Indices: 23174887--23174932 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
23174877 GAAAGTTACC
*
23174887 AAATTGTATCAAATGTTACTA
1 AAATTGTATCAAATATTACTA
* *
23174908 AAATTTTATCAAA-ATTATTA
1 AAATTGTATCAAATATTACTA
23174928 AAATT
1 AAATT
23174933 AAAATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (21 bp):
AAATTGTATCAAATATTACTA
Found at i:23175116 original size:2 final size:2
Alignment explanation
Indices: 23175111--23175160 Score: 75
Period size: 2 Copynumber: 25.0 Consensus size: 2
23175101 TGTGTGTGTG
*
23175111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA GA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
23175153 TA TA TA TA
1 TA TA TA TA
23175161 GAGAGAGAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:23175165 original size:2 final size:2
Alignment explanation
Indices: 23175160--23175206 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
23175150 ATATATATAT
23175160 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
23175202 AG AG A
1 AG AG A
23175207 ATAAGGATTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:23175251 original size:13 final size:13
Alignment explanation
Indices: 23175235--23175262 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
23175225 AATATAGGTG
23175235 TTATATATATATA
1 TTATATATATATA
23175248 TTATATATATATA
1 TTATATATATATA
23175261 TT
1 TT
23175263 TATTTATCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATATATATATA
Found at i:23176534 original size:29 final size:29
Alignment explanation
Indices: 23176463--23176534 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
23176453 GTACTCTTTA
* *
23176463 ATTTTTAAGAATTTAATTTCTCTAATATT
1 ATTTTTAAGAATTTAATCTCTATAATATT
**
23176492 ATTTAAAAGAATTTAATC-CTTATAATATT
1 ATTTTTAAGAATTTAATCTC-TATAATATT
*
23176521 ATTTTTAAGGATTT
1 ATTTTTAAGAATTT
23176535 TAGTTTAATC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
28 1 0.03
29 34 0.97
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.51
Consensus pattern (29 bp):
ATTTTTAAGAATTTAATCTCTATAATATT
Found at i:23176611 original size:30 final size:30
Alignment explanation
Indices: 23176564--23176643 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
23176554 GTATAGAGAT
23176564 TAAATTTCTTAAAAAATAATATTATAAGAAC
1 TAAATTTCTT-AAAAATAATATTATAAGAAC
*
23176595 TAAATTTCTTAAAAATAATATTATATGAAC
1 TAAATTTCTTAAAAATAATATTATAAGAAC
**
23176625 TAAA-TTCTTTTAAATAATA
1 TAAATTTCTTAAAAATAATA
23176644 CCATAAAGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 13 0.28
30 23 0.50
31 10 0.22
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (30 bp):
TAAATTTCTTAAAAATAATATTATAAGAAC
Found at i:23179374 original size:12 final size:13
Alignment explanation
Indices: 23179357--23179389 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
23179347 AACATTTAAC
23179357 AAATTTAAATT-T
1 AAATTTAAATTAT
23179369 AAATTTAAATTAT
1 AAATTTAAATTAT
23179382 AATATTTA
1 AA-ATTTA
23179390 TAATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 3 0.16
14 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATTTAAATTAT
Found at i:23185116 original size:19 final size:17
Alignment explanation
Indices: 23185088--23185136 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
23185078 GACTTAAAAC
23185088 TTTT-TTTTTTTTACTTT
1 TTTTCTTTTTTTTAC-TT
*
23185105 TTTATCTTTTTTTCACTT
1 TTT-TCTTTTTTTTACTT
23185123 TTTTCTTTTTTTTA
1 TTTTCTTTTTTTTA
23185137 AAGGCATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 13 0.46
18 6 0.21
19 9 0.32
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTTTTTACTT
Found at i:23185134 original size:8 final size:8
Alignment explanation
Indices: 23185088--23185134 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
23185078 GACTTAAAAC
23185088 TTTTTT-T
1 TTTTTTCT
*
23185095 TTTTTACT
1 TTTTTTCT
23185103 TTTTTATCT
1 TTTTT-TCT
*
23185112 TTTTTTCAC
1 TTTTTTC-T
23185121 TTTTTTCT
1 TTTTTTCT
23185129 TTTTTT
1 TTTTTT
23185135 TAAAGGCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
7 5 0.15
8 14 0.42
9 14 0.42
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTCT
Found at i:23187005 original size:4 final size:4
Alignment explanation
Indices: 23186998--23187049 Score: 52
Period size: 4 Copynumber: 13.2 Consensus size: 4
23186988 TGCATACATA
* * * * *
23186998 AATG AATG TATG AATG AACG AATA AATA AATG AATG AATG AATA AAT-
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
23187045 AATG A
1 AATG A
23187050 TAAAGCTCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 3 0.08
4 37 0.93
ACGTcount: A:0.56, C:0.02, G:0.17, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:23187032 original size:20 final size:20
Alignment explanation
Indices: 23187007--23187046 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
23186997 AAATGAATGT
23187007 ATGAATGAACGAATAAATAA
1 ATGAATGAACGAATAAATAA
*
23187027 ATGAATGAATGAATAAATAA
1 ATGAATGAACGAATAAATAA
23187047 TGATAAAGCT
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:0.60, C:0.03, G:0.15, T:0.23
Consensus pattern (20 bp):
ATGAATGAACGAATAAATAA
Found at i:23188796 original size:2 final size:2
Alignment explanation
Indices: 23188789--23188813 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23188779 ATATAATACA
23188789 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
23188814 GTGTCATAAT
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:23189387 original size:7 final size:7
Alignment explanation
Indices: 23189375--23189404 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
23189365 TTTACCATCC
23189375 AATAATT
1 AATAATT
23189382 AATAATT
1 AATAATT
23189389 AATAATT
1 AATAATT
23189396 AATAATT
1 AATAATT
23189403 AA
1 AA
23189405 ATTTTGTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AATAATT
Found at i:23189715 original size:19 final size:20
Alignment explanation
Indices: 23189693--23189737 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
23189683 AAATATGCAA
23189693 AAAAAATT-AAAA-TTAAATT
1 AAAAAATTAAAAAGTT-AATT
23189712 AAAAAATTAAAAAGTTAATT
1 AAAAAATTAAAAAGTTAATT
23189732 AAAAAA
1 AAAAAA
23189738 ATTAGCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.33
20 14 0.58
21 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAAATTAAAAAGTTAATT
Found at i:23189717 original size:21 final size:22
Alignment explanation
Indices: 23189691--23189738 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 22
23189681 CAAAATATGC
23189691 AAAAAAAATT-AAAA-TTAAATT
1 AAAAAAAATTAAAAAGTT-AATT
23189712 --AAAAAATTAAAAAGTTAATT
1 AAAAAAAATTAAAAAGTTAATT
23189732 AAAAAAA
1 AAAAAAA
23189739 TTAGCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 8 0.35
20 8 0.35
21 2 0.09
22 5 0.22
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAAAAAATTAAAAAGTTAATT
Found at i:23189750 original size:21 final size:20
Alignment explanation
Indices: 23189692--23189752 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
23189682 AAAATATGCA
*
23189692 AAAAAAATTAAAATTAAATT
1 AAAAAAATTAAAATTTAATT
*
23189712 -AAAAAATTAAAAAGTTAATT
1 AAAAAAATT-AAAATTTAATT
*
23189732 AAAAAAATTAGCAATTTAATT
1 AAAAAAATTA-AAATTTAATT
23189753 TGCTAAAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 8 0.24
20 10 0.29
21 16 0.47
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (20 bp):
AAAAAAATTAAAATTTAATT
Found at i:23190713 original size:13 final size:13
Alignment explanation
Indices: 23190695--23190721 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23190685 GCCGTTCTCC
23190695 TTAGCGTTATGTT
1 TTAGCGTTATGTT
23190708 TTAGCGTTATGTT
1 TTAGCGTTATGTT
23190721 T
1 T
23190722 GGATAAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.22, T:0.56
Consensus pattern (13 bp):
TTAGCGTTATGTT
Found at i:23191481 original size:2 final size:2
Alignment explanation
Indices: 23191474--23191498 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23191464 CATATCATTA
23191474 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
23191499 GGCCAATCTT
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:23193166 original size:31 final size:31
Alignment explanation
Indices: 23193128--23193190 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
23193118 TCATGGTACG
23193128 TGATAAA-GTCAGTATTTCCTTCCTTTCTACT
1 TGATAAAGGT-AGTATTTCCTTCCTTTCTACT
* *
23193159 TGATAAAGGTATTATTTCCTTCCTTTTTACT
1 TGATAAAGGTAGTATTTCCTTCCTTTCTACT
23193190 T
1 T
23193191 CTTAACCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.49
Consensus pattern (31 bp):
TGATAAAGGTAGTATTTCCTTCCTTTCTACT
Found at i:23199319 original size:10 final size:10
Alignment explanation
Indices: 23199304--23199333 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
23199294 ATTGAGTTTT
23199304 TATATTTTAA
1 TATATTTTAA
23199314 TATATTTTAA
1 TATATTTTAA
23199324 T-TATTTTAA
1 TATATTTTAA
23199333 T
1 T
23199334 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:23199330 original size:9 final size:9
Alignment explanation
Indices: 23199306--23199335 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
23199296 TGAGTTTTTA
23199306 TATTTTAAT
1 TATTTTAAT
23199315 ATATTTTAAT
1 -TATTTTAAT
23199325 TATTTTAAT
1 TATTTTAAT
23199334 TA
1 TA
23199336 ATAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:23200032 original size:27 final size:29
Alignment explanation
Indices: 23199980--23200038 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
23199970 TAAATACAAA
*
23199980 TAACACATATATATATGAATAGACATGAC
1 TAACACATATATACATGAATAGACATGAC
23200009 TAACACGA-ATATACATGAA-A-ACATGAC
1 TAACAC-ATATATACATGAATAGACATGAC
23200036 TAA
1 TAA
23200039 AATAATAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 10 0.36
28 1 0.04
29 16 0.57
30 1 0.04
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (29 bp):
TAACACATATATACATGAATAGACATGAC
Found at i:23202831 original size:20 final size:19
Alignment explanation
Indices: 23202785--23202831 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
23202775 TAACTTAATT
*
23202785 TTTATTTTTTAAAATTCTA
1 TTTATTTATTAAAATTCTA
23202804 TTTA-TTATTAAAATAT-TA
1 TTTATTTATTAAAAT-TCTA
23202822 TATTATTTAT
1 T-TTATTTAT
23202832 AAATCATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 12 0.50
19 8 0.33
20 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTTATTAAAATTCTA
Found at i:23205378 original size:53 final size:52
Alignment explanation
Indices: 23205320--23205422 Score: 136
Period size: 53 Copynumber: 2.0 Consensus size: 52
23205310 TAATCATTGG
*
23205320 TATAAATTTTG-GAATTGATTTTAGAATAAGAAAATTAGAATAAGACAGAGAAA
1 TATAAATTTTGAG-ATTGATTTTAGAATAA-AAAAATAGAATAAGACAGAGAAA
** * *
23205373 TATAAATTTTGAGATTGATTTTAGTGTAAAAAAATAGAATGAGATAGAGA
1 TATAAATTTTGAGATTGATTTTAGAATAAAAAAATAGAATAAGACAGAGA
23205423 TTATTTTGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
52 18 0.41
53 25 0.57
54 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.18, T:0.32
Consensus pattern (52 bp):
TATAAATTTTGAGATTGATTTTAGAATAAAAAAATAGAATAAGACAGAGAAA
Found at i:23209249 original size:5 final size:5
Alignment explanation
Indices: 23209239--23209335 Score: 59
Period size: 5 Copynumber: 19.8 Consensus size: 5
23209229 TTTCACCAAA
23209239 AAAAT AAAAT ATTAAAT -AAAT -AAAT -AAAT AATATTAT AAAAT -AAAT
1 AAAAT AAAAT A--AAAT AAAAT AAAAT AAAAT AA-A--AT AAAAT AAAAT
*
23209285 AAAA- CAAAT AAAAT --AAT AAAAT GAAAAT AAAAAT AAAAT -AAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT AAAAT AAAAT
23209332 AAAA
1 AAAA
23209336 GAAACAAAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 26
0.72 0.03 0.25
Matches are distributed among these distances:
3 3 0.04
4 25 0.33
5 28 0.37
6 11 0.14
7 5 0.07
8 4 0.05
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:23209293 original size:13 final size:13
Alignment explanation
Indices: 23209236--23209354 Score: 88
Period size: 13 Copynumber: 9.4 Consensus size: 13
23209226 TTATTTCACC
23209236 AAAAAAATAAAAT
1 AAAAAAATAAAAT
**
23209249 -ATTAAAT-AAAT
1 AAAAAAATAAAAT
* *
23209260 AAATAAATAATAT
1 AAAAAAATAAAAT
* *
23209273 TATAAAAT-AAAT
1 AAAAAAATAAAAT
23209285 AAAACAAATAAAAT
1 AAAA-AAATAAAAT
*
23209299 AATAAAATGAAAAT
1 AAAAAAAT-AAAAT
23209313 --AAAAATAAAAT
1 AAAAAAATAAAAT
*
23209324 AAAAAAATAAAAG
1 AAAAAAATAAAAT
*
23209337 AAACAAAA-AAAAG
1 AAA-AAAATAAAAT
23209350 AAAAA
1 AAAAA
23209355 CCACCACTAG
Statistics
Matches: 85, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
11 9 0.11
12 23 0.27
13 37 0.44
14 16 0.19
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:23209302 original size:17 final size:16
Alignment explanation
Indices: 23209276--23209347 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 16
23209266 ATAATATTAT
23209276 AAAATAAATAAAACAAA
1 AAAAT-AATAAAACAAA
*
23209293 TAAAATAATAAAATGAAA
1 -AAAATAATAAAA-CAAA
*
23209311 ATAAA-AATAAAATAAA
1 A-AAATAATAAAACAAA
*
23209327 AAAATAAAAGAAACAAA
1 AAAATAATA-AAACAAA
23209344 AAAA
1 AAAA
23209348 AGAAAAACCA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
15 3 0.07
16 7 0.15
17 25 0.54
18 11 0.24
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.14
Consensus pattern (16 bp):
AAAATAATAAAACAAA
Found at i:23209347 original size:30 final size:30
Alignment explanation
Indices: 23209290--23209347 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
23209280 TAAATAAAAC
* *
23209290 AAATAAAATAATAAAATGAAAATAAAAATA
1 AAATAAAAAAATAAAATGAAAAAAAAAATA
23209320 AAATAAAAAAATAAAA-GAAACAAAAAAA
1 AAATAAAAAAATAAAATGAAA-AAAAAAA
23209348 AGAAAAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.81, C:0.02, G:0.03, T:0.14
Consensus pattern (30 bp):
AAATAAAAAAATAAAATGAAAAAAAAAATA
Found at i:23209354 original size:8 final size:8
Alignment explanation
Indices: 23209236--23209347 Score: 66
Period size: 8 Copynumber: 13.9 Consensus size: 8
23209226 TTATTTCACC
23209236 AAAAAAAT
1 AAAAAAAT
* *
23209244 AAAATATT
1 AAAAAAAT
*
23209252 AAATAAAT
1 AAAAAAAT
*
23209260 AAATAAAT
1 AAAAAAAT
* **
23209268 AATATTAT
1 AAAAAAAT
23209276 AAAATAAAT
1 AAAA-AAAT
23209285 AAAACAAAT
1 AAAA-AAAT
*
23209294 AAAATAAT
1 AAAAAAAT
**
23209302 AAAATGA-
1 AAAAAAAT
*
23209309 AAATAAA-
1 AAAAAAAT
*
23209316 AATAAAAT
1 AAAAAAAT
23209324 AAAAAAAT
1 AAAAAAAT
*
23209332 AAAAGAAAC
1 AAAA-AAAT
23209341 AAAAAAA
1 AAAAAAA
23209348 AGAAAAACCA
Statistics
Matches: 79, Mismatches: 22, Indels: 6
0.74 0.21 0.06
Matches are distributed among these distances:
7 9 0.11
8 49 0.62
9 21 0.27
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (8 bp):
AAAAAAAT
Found at i:23209749 original size:9 final size:9
Alignment explanation
Indices: 23209737--23209795 Score: 82
Period size: 9 Copynumber: 6.1 Consensus size: 9
23209727 AAATTTTGAA
23209737 AAAATTTTC
1 AAAATTTTC
23209746 AAAATTTTC
1 AAAATTTTC
23209755 AAAATTTTTCC
1 AAAA-TTTT-C
23209766 AAAATTTTC
1 AAAATTTTC
23209775 AAAATTTTTCC
1 AAAA-TTTT-C
23209786 AAAATTTTC
1 AAAATTTTC
23209795 A
1 A
23209796 GATCACTCCT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
9 20 0.43
10 16 0.35
11 10 0.22
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATTTTC
Found at i:23209749 original size:10 final size:10
Alignment explanation
Indices: 23209724--23209795 Score: 83
Period size: 10 Copynumber: 7.2 Consensus size: 10
23209714 CCGGTGATCC
23209724 CAAAAATTTT
1 CAAAAATTTT
*
23209734 GAAAAAATTTT
1 -CAAAAATTTT
23209745 C-AAAATTTT
1 CAAAAATTTT
*
23209754 CAAAATTTTT
1 CAAAAATTTT
*
23209764 CCAAAATTTT
1 CAAAAATTTT
*
23209774 CAAAATTTTT
1 CAAAAATTTT
*
23209784 CCAAAATTTT
1 CAAAAATTTT
23209794 CA
1 CA
23209796 GATCACTCCT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
9 9 0.18
10 32 0.64
11 9 0.18
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.42
Consensus pattern (10 bp):
CAAAAATTTT
Found at i:23209751 original size:20 final size:20
Alignment explanation
Indices: 23209726--23209795 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
23209716 GGTGATCCCA
* *
23209726 AAAATTTTGAAAAAATTTT-C
1 AAAATTTT-CAAAATTTTTCC
23209746 AAAATTTTCAAAATTTTTCC
1 AAAATTTTCAAAATTTTTCC
23209766 AAAATTTTCAAAATTTTTCC
1 AAAATTTTCAAAATTTTTCC
23209786 AAAATTTTCA
1 AAAATTTTCA
23209796 GATCACTCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.17
20 39 0.83
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.43
Consensus pattern (20 bp):
AAAATTTTCAAAATTTTTCC
Found at i:23217594 original size:33 final size:33
Alignment explanation
Indices: 23217557--23217624 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
23217547 TTGACCTTTG
23217557 TTGTGAAATTAAAAATCCCATTATCAATCAAGC
1 TTGTGAAATTAAAAATCCCATTATCAATCAAGC
23217590 TTGTGAAATTAAAAATCCCATTATCAATCAAGC
1 TTGTGAAATTAAAAATCCCATTATCAATCAAGC
23217623 TT
1 TT
23217625 TCAAGCTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (33 bp):
TTGTGAAATTAAAAATCCCATTATCAATCAAGC
Found at i:23219370 original size:8 final size:8
Alignment explanation
Indices: 23219357--23219382 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
23219347 CATATGATAT
23219357 ATGAATGC
1 ATGAATGC
23219365 ATGAATGC
1 ATGAATGC
23219373 ATGAATGC
1 ATGAATGC
23219381 AT
1 AT
23219383 AGGATGTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (8 bp):
ATGAATGC
Found at i:23223409 original size:23 final size:23
Alignment explanation
Indices: 23223383--23223432 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
23223373 GTCATAAACT
23223383 AAAT-AAAACAAAAA-AAACTAATA
1 AAATGAAAACAAAAATAAA--AATA
*
23223406 AAATGAAAATAAAAATAAAAATA
1 AAATGAAAACAAAAATAAAAATA
23223429 AAAT
1 AAAT
23223433 CAAGAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 12 0.50
24 9 0.38
25 3 0.12
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (23 bp):
AAATGAAAACAAAAATAAAAATA
Found at i:23223414 original size:19 final size:20
Alignment explanation
Indices: 23223378--23223424 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
23223368 AGAATGTCAT
23223378 AAACTAAATAAAACAAAA-A
1 AAACTAAATAAAACAAAATA
*
23223397 AAACT-AATAAAATGAAAATA
1 AAACTAAATAAAA-CAAAATA
*
23223417 AAAATAAA
1 AAACTAAA
23223425 AATAAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 7 0.30
19 9 0.39
20 5 0.22
21 2 0.09
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (20 bp):
AAACTAAATAAAACAAAATA
Found at i:23223815 original size:19 final size:19
Alignment explanation
Indices: 23223782--23223824 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
23223772 TCAATGGTTG
*
23223782 AAAAATTCAAATGGTTGTTA
1 AAAAATTCAAATGGTCG-TA
*
23223802 AAAAATTC-ATTGGTCGTA
1 AAAAATTCAAATGGTCGTA
23223820 AAAAA
1 AAAAA
23223825 AACCAAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 6 0.29
20 8 0.38
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.30
Consensus pattern (19 bp):
AAAAATTCAAATGGTCGTA
Found at i:23223825 original size:19 final size:20
Alignment explanation
Indices: 23223782--23223825 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
23223772 TCAATGGTTG
* *
23223782 AAAAATTCAAATGGTTGTTA
1 AAAAATTCAAATGGTCGTAA
*
23223802 AAAAATTC-ATTGGTCGTAA
1 AAAAATTCAAATGGTCGTAA
23223821 AAAAA
1 AAAAA
23223826 ACCAAACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAAATTCAAATGGTCGTAA
Found at i:23224745 original size:41 final size:41
Alignment explanation
Indices: 23224675--23224868 Score: 158
Period size: 41 Copynumber: 4.7 Consensus size: 41
23224665 TGAAAATTTA
* ** * *
23224675 AAAAGGCTCATCTAACCAAAAACATTGAAACTTTAAAATTC
1 AAAAGGCTCATCTAACCAGAGGCAATGAAACTTTAGAATTC
* *
23224716 AAAAGGCTCATTTAACCAGAGGCAATGAAACTTTAGAATTT
1 AAAAGGCTCATCTAACCAGAGGCAATGAAACTTTAGAATTC
* * * * *
23224757 AAATA-GCTCTTGTAACTAAAAGGCAATGAAACTTTGGAA-TC
1 AAA-AGGCTCATCTAAC-CAGAGGCAATGAAACTTTAGAATTC
* * * * * * *
23224798 AAAAGGTTCCTCTAATCAGAGGTAATGAAAGTTTGGAATTT
1 AAAAGGCTCATCTAACCAGAGGCAATGAAACTTTAGAATTC
* * *
23224839 AAAAGGCTCATCTGACTAGAGGCAAAGAAA
1 AAAAGGCTCATCTAACCAGAGGCAATGAAA
23224869 ATTTTAATTT
Statistics
Matches: 120, Mismatches: 29, Indels: 8
0.76 0.18 0.05
Matches are distributed among these distances:
40 19 0.16
41 81 0.68
42 20 0.17
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (41 bp):
AAAAGGCTCATCTAACCAGAGGCAATGAAACTTTAGAATTC
Done.