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 112 of 147
Found at i:20149166 original size:20 final size:20
Alignment explanation
Indices: 20149141--20149193 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
20149131 AATAGGATCA
20149141 AGTTGGTTTTAGGGGTTAGG
1 AGTTGGTTTTAGGGGTTAGG
*
20149161 AGTTGGTTTTAGAGGTTAGG
1 AGTTGGTTTTAGGGGTTAGG
20149181 AGTTGG-TTTAGGG
1 AGTTGGTTTTAGGG
20149194 TCTAAGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (20 bp):
AGTTGGTTTTAGGGGTTAGG
Found at i:20149248 original size:26 final size:25
Alignment explanation
Indices: 20149183--20149248 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 25
20149173 AGGTTAGGAG
* * *
20149183 TTGGTTTAGGGTCTAAGTTAAGGTT
1 TTGGTTTAAGGTTTAAGTTAAAGTT
*
20149208 TTGGTTTTAGAGTTTAAGCTTAAAGTT
1 TTGGTTTAAG-GTTTAAG-TTAAAGTT
20149235 TTGGTTTAAGGTTT
1 TTGGTTTAAGGTTT
20149249 GGTTTGAGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 8 0.24
26 10 0.29
27 16 0.47
ACGTcount: A:0.21, C:0.03, G:0.27, T:0.48
Consensus pattern (25 bp):
TTGGTTTAAGGTTTAAGTTAAAGTT
Found at i:20149356 original size:13 final size:13
Alignment explanation
Indices: 20149325--20149359 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
20149315 GGGTCTAAGG
* *
20149325 TTAGGATTTGGAA
1 TTAGGGTTTGAAA
20149338 TTAGGGTTTGAAA
1 TTAGGGTTTGAAA
20149351 TTAGGGTTT
1 TTAGGGTTT
20149360 TTGATAACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (13 bp):
TTAGGGTTTGAAA
Found at i:20154814 original size:150 final size:150
Alignment explanation
Indices: 20154543--20154844 Score: 489
Period size: 150 Copynumber: 2.0 Consensus size: 150
20154533 CTTCTTTAAG
* * * *
20154543 TTGTTACATAATGGTTATGATCTATAAGACAAGAATTGATTTATAAGATTTTTTTTTGAAGAGTT
1 TTGTTACATAATGGGTATGATCTAGAAGACAAGAATTGATTTATAAGAGTTCTTTTTGAAGAGTT
* *
20154608 CTACTTGTATTCAACTTTAAGAAGCTTTCTTAGTTAAAAAGTTTTATTCCAATAAAAAATGTGT-
66 CTACTTGTATTCAACTTCAAAAAGCTTTCTTAGTTAAAAAGTTTTATTCCAATAAAAAATGTGTC
20154672 ATAACCAATTGAAGTCCAAGC
131 A-AACCAATTGAAGTCCAAGC
*
20154693 TTGTTACATGATGGGTATGATCTAGAAGACAAGAATTGATTTATAAGAGTTCTTTTTGAAGAGTT
1 TTGTTACATAATGGGTATGATCTAGAAGACAAGAATTGATTTATAAGAGTTCTTTTTGAAGAGTT
* * *
20154758 CTATTTGTATTCAACTTCAAAAAGCTTTCTTGGTTAAAGAGTTTTATTCCAATAAAAAATGTGTC
66 CTACTTGTATTCAACTTCAAAAAGCTTTCTTAGTTAAAAAGTTTTATTCCAATAAAAAATGTGTC
*
20154823 AAGCCAATTGAAGTCCAAGC
131 AAACCAATTGAAGTCCAAGC
20154843 TT
1 TT
20154845 TCACTGAATG
Statistics
Matches: 140, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
150 139 0.99
151 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (150 bp):
TTGTTACATAATGGGTATGATCTAGAAGACAAGAATTGATTTATAAGAGTTCTTTTTGAAGAGTT
CTACTTGTATTCAACTTCAAAAAGCTTTCTTAGTTAAAAAGTTTTATTCCAATAAAAAATGTGTC
AAACCAATTGAAGTCCAAGC
Found at i:20162082 original size:3 final size:3
Alignment explanation
Indices: 20162074--20162116 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
20162064 TGGCCGGACC
20162074 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
20162117 TTTTTGTCGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:20162634 original size:2 final size:2
Alignment explanation
Indices: 20162627--20162657 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20162617 TTCGACTTAG
20162627 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20162658 GTCTTTCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20162885 original size:2 final size:2
Alignment explanation
Indices: 20162880--20162904 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20162870 CATTTGTGTG
20162880 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20162905 GCTTTTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20169119 original size:15 final size:15
Alignment explanation
Indices: 20169096--20169126 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20169086 TACTATAGAG
20169096 ACTTAGGCAGACTGA
1 ACTTAGGCAGACTGA
*
20169111 ACTTGGGCAGACTGA
1 ACTTAGGCAGACTGA
20169126 A
1 A
20169127 AAGGTCGCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.19
Consensus pattern (15 bp):
ACTTAGGCAGACTGA
Found at i:20175100 original size:17 final size:18
Alignment explanation
Indices: 20175073--20175108 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
20175063 TAAGATTATG
20175073 ATAAGATAAAATAAAATT
1 ATAAGATAAAATAAAATT
*
20175091 ATAA-ATAAAATTAAATT
1 ATAAGATAAAATAAAATT
20175108 A
1 A
20175109 AATAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
ATAAGATAAAATAAAATT
Found at i:20175541 original size:2 final size:2
Alignment explanation
Indices: 20175534--20175569 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20175524 GATATTTCTT
20175534 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20175570 AAAGGGGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20178089 original size:2 final size:2
Alignment explanation
Indices: 20178076--20178110 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
20178066 AAAGCTTCTT
20178076 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20178111 TCTCGTTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20179475 original size:2 final size:2
Alignment explanation
Indices: 20179468--20179493 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20179458 TGCCCTCAAG
20179468 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
20179494 TGAAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20192890 original size:23 final size:23
Alignment explanation
Indices: 20192864--20192909 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
20192854 TATCTGATAG
**
20192864 TGCTATTGGGTGGATAATTATTC
1 TGCTATTGAATGGATAATTATTC
20192887 TGCTATTGAATGGATAATTATTC
1 TGCTATTGAATGGATAATTATTC
20192910 AATAATCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (23 bp):
TGCTATTGAATGGATAATTATTC
Found at i:20194201 original size:2 final size:2
Alignment explanation
Indices: 20194194--20194227 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20194184 ATTAGTGTTT
20194194 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
20194228 ACAGTAGGAA
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:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:20198606 original size:1 final size:1
Alignment explanation
Indices: 20198600--20198632 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
20198590 AAAGGCTTGC
20198600 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20198633 CAAATAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:20199869 original size:16 final size:16
Alignment explanation
Indices: 20199839--20199888 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
20199829 TAATTAATCA
20199839 TTTTTATTAATATTTTAT
1 TTTTTATT-A-ATTTTAT
20199857 TTTTTATTAATTTTAT
1 TTTTTATTAATTTTAT
* *
20199873 ATATTATTAATTTTAT
1 TTTTTATTAATTTTAT
20199889 AATTATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 21 0.70
17 1 0.03
18 8 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTATTAATTTTAT
Found at i:20199902 original size:18 final size:16
Alignment explanation
Indices: 20199850--20199895 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
20199840 TTTTATTAAT
* *
20199850 ATTTTATTTTTTATTA
1 ATTTTATATATTATTA
20199866 ATTTTATATATTATTA
1 ATTTTATATATTATTA
20199882 ATTTTATA-ATTATT
1 ATTTTATATATTATT
20199896 TTTAATTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 6 0.21
16 22 0.79
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTATATATTATTA
Found at i:20199925 original size:83 final size:84
Alignment explanation
Indices: 20199771--20199926 Score: 187
Period size: 85 Copynumber: 1.9 Consensus size: 84
20199761 AATGTAAATT
*
20199771 TTTTTTATTAATTTTACATATATACATTTTTTATTAATTATTTTTTATCATAGTCAAATAATTAA
1 TTTTTTATTAATTTTACATATATACA-TTTTTATTAATTATTTTTAATCATAGTCAAATAATTAA
*
20199836 TCATTTTTATTAATATTTTA
65 TAATTTTTATTAATATTTTA
* * *
20199856 TTTTTTATTAATTTTATATATTATTA-A-TTTTA-TAATTATTTTTAATTATGATGTCAATTAA-
1 TTTTTTATTAATTTTACATA-TA-TACATTTTTATTAATTATTTTTAATCAT-A-GTCAAATAAT
20199917 TAA-AATTTTT
62 TAATAATTTTT
20199927 TGTTAGATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
83 21 0.34
84 9 0.15
85 27 0.44
86 3 0.05
87 2 0.03
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (84 bp):
TTTTTTATTAATTTTACATATATACATTTTTATTAATTATTTTTAATCATAGTCAAATAATTAAT
AATTTTTATTAATATTTTA
Found at i:20200274 original size:17 final size:17
Alignment explanation
Indices: 20200239--20200282 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
20200229 CAATTCATAA
*
20200239 TAATT-TAAAA-TAATT
1 TAATTATAAAATTAATC
20200254 TAATTATAAAATTAATC
1 TAATTATAAAATTAATC
20200271 TAATTATAAAAT
1 TAATTATAAAAT
20200283 CGAATTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 5 0.19
16 5 0.19
17 16 0.62
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATTATAAAATTAATC
Found at i:20201217 original size:19 final size:19
Alignment explanation
Indices: 20201161--20201219 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
20201151 TTAATTTTAT
20201161 ATCT-TAATTTTAGTATATA
1 ATCTATAATTTTA-TATATA
* *
20201180 AACGTAAAATTTT-TATATA
1 ATC-TATAATTTTATATATA
*
20201199 ATCTATAATTTTATTTATA
1 ATCTATAATTTTATATATA
20201218 AT
1 AT
20201220 ATTTTAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 8 0.25
19 17 0.53
20 1 0.03
21 6 0.19
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
ATCTATAATTTTATATATA
Found at i:20203217 original size:151 final size:149
Alignment explanation
Indices: 20203024--20203294 Score: 380
Period size: 150 Copynumber: 1.8 Consensus size: 149
20203014 TCTAAAAATA
* * * * * *
20203024 TTAAAAATAAATGACTTAAATGCCCTATAAATTTTAAGAAATAACAAATTTACCTTTAAATTTTT
1 TTAAAAATAAATAACATAAATACCCTATAAATTTTAAAAAATAACAAATTTACATTTAAATTTCT
* *
20203089 AGCATTTTTTATTTATTTAATAAAGATTATTTTTCATTAAATGTATAACTTTTATTAGTTAATTA
66 AGCA-TTTTTATTTATTTAATAAAGATTATTTGTCATTAAATATATAACTTTTATTAGTTAATTA
20203154 TTTAAATTAAAATATAAGTG
130 TTTAAATTAAAATATAAGTG
* ** * *
20203174 TTAAAAATTAATAACATAAATACCCTTATAAATTTTAAAAAATAATGAATTTATATTTCAATTTC
1 TTAAAAATAAATAACATAAATACCC-TATAAATTTTAAAAAATAACAAATTTACATTTAAATTTC
* * *
20203239 TAGCATTTTTATTTATTTAATAAATATTATTTGTCATTAAATATGTAGCTTTTATT
65 TAGCATTTTTATTTATTTAATAAAGATTATTTGTCATTAAATATATAACTTTTATT
20203295 TATTTAAATT
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
150 67 0.64
151 37 0.36
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (149 bp):
TTAAAAATAAATAACATAAATACCCTATAAATTTTAAAAAATAACAAATTTACATTTAAATTTCT
AGCATTTTTATTTATTTAATAAAGATTATTTGTCATTAAATATATAACTTTTATTAGTTAATTAT
TTAAATTAAAATATAAGTG
Found at i:20203952 original size:57 final size:57
Alignment explanation
Indices: 20203884--20203996 Score: 226
Period size: 57 Copynumber: 2.0 Consensus size: 57
20203874 ATATATATTT
20203884 ATATGTTTAATGATTGTAATTGCGTCTTAACATTACAATGCCTAAATGAATATTTAA
1 ATATGTTTAATGATTGTAATTGCGTCTTAACATTACAATGCCTAAATGAATATTTAA
20203941 ATATGTTTAATGATTGTAATTGCGTCTTAACATTACAATGCCTAAATGAATATTTA
1 ATATGTTTAATGATTGTAATTGCGTCTTAACATTACAATGCCTAAATGAATATTTA
20203997 CTTTATGAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (57 bp):
ATATGTTTAATGATTGTAATTGCGTCTTAACATTACAATGCCTAAATGAATATTTAA
Found at i:20206358 original size:22 final size:21
Alignment explanation
Indices: 20206324--20206365 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
20206314 CTTATAGCAA
* *
20206324 TTGATATATGAGCTTAAACAT
1 TTGATATAAGAGCATAAACAT
20206345 TTGATATAAAGAGCATAAACA
1 TTGATAT-AAGAGCATAAACA
20206366 AAAAGAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (21 bp):
TTGATATAAGAGCATAAACAT
Found at i:20209466 original size:22 final size:22
Alignment explanation
Indices: 20209441--20209490 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
20209431 AGTTTAGGCA
* *
20209441 AAATTAGTAATAACTTTATATT
1 AAATTAATAATAACTGTATATT
* *
20209463 AAATCAATGATAACTGTATATT
1 AAATTAATAATAACTGTATATT
20209485 AAATTA
1 AAATTA
20209491 TGGATAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (22 bp):
AAATTAATAATAACTGTATATT
Found at i:20209509 original size:22 final size:22
Alignment explanation
Indices: 20209494--20209747 Score: 106
Period size: 22 Copynumber: 11.7 Consensus size: 22
20209484 TAAATTATGG
20209494 ATAATTTAATAGTAAATAAATA
1 ATAATTTAATAGTAAATAAATA
* *
20209516 ATAATTTAGTAGTAAATAATTA
1 ATAATTTAATAGTAAATAAATA
*
20209538 ATAAGATAGTT-ATATGCCAATATAACATA
1 AT-A-AT--TTAATA-G-TAA-ATAA-ATA
*
20209567 ATAA--TAA-A-TATAT-AATA
1 ATAATTTAATAGTAAATAAATA
* *
20209584 AT-A--TAGTCGTAAATAACA-A
1 ATAATTTAATAGTAAATAA-ATA
*
20209603 ATAATTTAATAGTAAAT-ATTA
1 ATAATTTAATAGTAAATAAATA
*
20209624 ATAGA--TAATTA-TAAATACATA
1 ATA-ATTTAA-TAGTAAATAAATA
* ** * **
20209645 ATAATATAGCAGTAAATTAAGG
1 ATAATTTAATAGTAAATAAATA
* *
20209667 ATAATTTAATA-AAAATAAGTA
1 ATAATTTAATAGTAAATAAATA
* * *
20209688 ATAACTTAATAGTAAATTAATG
1 ATAATTTAATAGTAAATAAATA
* * *
20209710 ATAAATTAGTAGTAAATTAATA
1 ATAATTTAATAGTAAATAAATA
20209732 ATAATTTAATAGTAAA
1 ATAATTTAATAGTAAA
20209748 CAAGATTCAA
Statistics
Matches: 169, Mismatches: 39, Indels: 48
0.66 0.15 0.19
Matches are distributed among these distances:
16 3 0.02
17 5 0.03
18 5 0.03
19 6 0.04
20 12 0.07
21 28 0.17
22 87 0.51
23 3 0.02
24 3 0.02
25 2 0.01
26 3 0.02
27 3 0.02
28 5 0.03
29 4 0.02
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (22 bp):
ATAATTTAATAGTAAATAAATA
Found at i:20209690 original size:64 final size:64
Alignment explanation
Indices: 20209564--20209690 Score: 152
Period size: 64 Copynumber: 2.0 Consensus size: 64
20209554 CCAATATAAC
* * *
20209564 ATAATAATAAATATATAATAATATAGTCGTAAATAACAAATAATTTAATAGTAAATATTAATAG
1 ATAATAATAAATACATAATAATATAGTCGTAAATAACAAATAATTTAATAGAAAATAGTAATAG
* **
20209628 ATAATTATAAATACATAATAATATAG-CAGTAAATTAA-GGATAATTTAATA-AAAATAAGTAAT
1 ATAATAATAAATACATAATAATATAGTC-GTAAA-TAACAAATAATTTAATAGAAAAT-AGTAAT
20209690 A
63 A
20209691 ACTTAATAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
63 5 0.09
64 46 0.85
65 3 0.06
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (64 bp):
ATAATAATAAATACATAATAATATAGTCGTAAATAACAAATAATTTAATAGAAAATAGTAATAG
Found at i:20209730 original size:33 final size:33
Alignment explanation
Indices: 20209657--20209741 Score: 82
Period size: 33 Copynumber: 2.6 Consensus size: 33
20209647 AATATAGCAG
** * *
20209657 TAAATTAAGGATAATTTAAT-AAAAATAAGTAA
1 TAAATTAATAATAAATTAATGATAAATAAGTAA
* * * *
20209689 TAACTTAATAGTAAATTAATGATAAATTAGTAG
1 TAAATTAATAATAAATTAATGATAAATAAGTAA
*
20209722 TAAATTAATAATAATTTAAT
1 TAAATTAATAATAAATTAAT
20209742 AGTAAACAAG
Statistics
Matches: 41, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
32 15 0.37
33 26 0.63
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.36
Consensus pattern (33 bp):
TAAATTAATAATAAATTAATGATAAATAAGTAA
Found at i:20210089 original size:22 final size:22
Alignment explanation
Indices: 20210064--20210399 Score: 104
Period size: 22 Copynumber: 15.3 Consensus size: 22
20210054 TAAATCATAA
20210064 ATAACTTAATAATAAATTAATG
1 ATAACTTAATAATAAATTAATG
* * * *
20210086 ATAATTTAGTAGTAAA-TAATTT
1 ATAACTTAATAATAAATTAA-TG
* *
20210108 AGAACTTAGTAGTAATTAA-TAATTG
1 ATAACTTA--A-TAATAAATTAA-TG
* *
20210133 A-AAATTAA-AAGTAAATCAAT-
1 ATAACTTAATAA-TAAATTAATG
* * *
20210153 AGAACTTAATAAT-AATCATTG
1 ATAACTTAATAATAAATTAATG
* * * * *
20210174 ATAAATTGATAATTAATCAATA
1 ATAACTTAATAATAAATTAATG
* *
20210196 ATAATTTAATATAGTAAATTAGTG
1 ATAACTTAATA-A-TAAATTAATG
* * *
20210220 ATAACTTAATAGTATATTAATA
1 ATAACTTAATAATAAATTAATG
* * *
20210242 ATAATTTAATAGTTAA-TAATTG
1 ATAACTTAATAATAAATTAA-TG
* * *
20210264 ATAACTTAGTAGTAAATTAATA
1 ATAACTTAATAATAAATTAATG
* *
20210286 ATAA-TATAATAGTAAA-TACATA
1 ATAACT-TAATAATAAATTA-ATG
* * * *
20210308 ACAACTTAATAGTAAATCAATT
1 ATAACTTAATAATAAATTAATG
* ** *
20210330 ATAACATAACT-ATAAATGCATA
1 ATAACTTAA-TAATAAATTAATG
* * * *
20210352 ATAGCATAGTAGTAAATTAATG
1 ATAACTTAATAATAAATTAATG
20210374 ATAACTTAATAA-AAA--AATG
1 ATAACTTAATAATAAATTAATG
20210393 ATAACTT
1 ATAACTT
20210400 GATGGTTAAT
Statistics
Matches: 235, Mismatches: 59, Indels: 43
0.70 0.18 0.13
Matches are distributed among these distances:
19 11 0.05
20 9 0.04
21 34 0.14
22 142 0.60
23 7 0.03
24 21 0.09
25 11 0.05
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (22 bp):
ATAACTTAATAATAAATTAATG
Found at i:20210432 original size:22 final size:22
Alignment explanation
Indices: 20210137--20210750 Score: 197
Period size: 22 Copynumber: 28.1 Consensus size: 22
20210127 TAATTGAAAA
* * *
20210137 TTAAAAGTAAATCAAT-AGAAC
1 TTAATAGTAAATCAATGATAAT
* * *
20210158 TTAATAAT-AATCATTGATAAA
1 TTAATAGTAAATCAATGATAAT
* * * *
20210179 TTGATAATTAATCAATAATAAT
1 TTAATAGTAAATCAATGATAAT
* * *
20210201 TTAATATAGTAAATTAGTGATAAC
1 TT-A-ATAGTAAATCAATGATAAT
* * *
20210225 TTAATAGTATATTAATAATAAT
1 TTAATAGTAAATCAATGATAAT
* *
20210247 TTAATAGTTAAT-AATTGATAAC
1 TTAATAGTAAATCAA-TGATAAT
* * *
20210269 TTAGTAGTAAATTAATAATAAT
1 TTAATAGTAAATCAATGATAAT
* * * *
20210291 ATAATAGTAAAT-ACATAACAAC
1 TTAATAGTAAATCA-ATGATAAT
* *
20210313 TTAATAGTAAATCAATTATAAC
1 TTAATAGTAAATCAATGATAAT
* * **
20210335 ATAACTA-TAAATGC-ATAATAGC
1 TTAA-TAGTAAAT-CAATGATAAT
* * * *
20210357 ATAGTAGTAAATTAATGATAAC
1 TTAATAGTAAATCAATGATAAT
* *
20210379 TTAATA--AAA-AAATGATAAC
1 TTAATAGTAAATCAATGATAAT
* * * *
20210398 TTGATGGTTAATCATTGATAAT
1 TTAATAGTAAATCAATGATAAT
*
20210420 TTAATAGTAAATCAATGAAAAT
1 TTAATAGTAAATCAATGATAAT
* *
20210442 TTAGTAGTAAATAACAA--ATAGCT
1 TTAATAGTAAAT--CAATGATA-AT
*** ** *
20210465 TT-ATAGTAAATTTGTTTTAGT
1 TTAATAGTAAATCAATGATAAT
* * *
20210486 TTAATAGTAAATAAATTATAAAC
1 TTAATAGTAAATCAATGAT-AAT
* * * *
20210509 TTAGTAGTAAAT-TATAAATAAC
1 TTAATAGTAAATCAAT-GATAAT
* *
20210531 TTAAGAATAAATCAATGATAAT
1 TTAATAGTAAATCAATGATAAT
* * * *
20210553 TTAGTAGTTAAT-AACT-AAAAC
1 TTAATAGTAAATCAA-TGATAAT
*
20210574 TCAATAGTAAATCAATGATAAT
1 TTAATAGTAAATCAATGATAAT
* * * *
20210596 ATAGTTA-CAAATGC-ATAATAAT
1 TTA-ATAGTAAAT-CAATGATAAT
*
20210618 ATAA-AGTAAATC-ATGATAAT
1 TTAATAGTAAATCAATGATAAT
* *
20210638 TTAATAGTAAATTATTGATAAT
1 TTAATAGTAAATCAATGATAAT
* * * * *
20210660 TTAGTAGTAAATTACTAATAAA
1 TTAATAGTAAATCAATGATAAT
* * * *
20210682 GTCATAGTAAATCATTGATAAC
1 TTAATAGTAAATCAATGATAAT
* *
20210704 TTAGTTGTAAATCAATGATAAT
1 TTAATAGTAAATCAATGATAAT
* *
20210726 TTAGTTA-TAAATTAATGATAAT
1 TTA-ATAGTAAATCAATGATAAT
20210748 TTA
1 TTA
20210751 GTTGTATATT
Statistics
Matches: 438, Mismatches: 122, Indels: 65
0.70 0.20 0.10
Matches are distributed among these distances:
19 13 0.03
20 21 0.05
21 52 0.12
22 304 0.69
23 30 0.07
24 18 0.04
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (22 bp):
TTAATAGTAAATCAATGATAAT
Found at i:20210790 original size:22 final size:22
Alignment explanation
Indices: 20210760--20210889 Score: 95
Period size: 22 Copynumber: 6.0 Consensus size: 22
20210750 AGTTGTATAT
* * *
20210760 TAGTTAATTATTAACAACTTCA
1 TAGTAAATTATTAATAACTTAA
* *
20210782 TAGTAAATTAGTAATAACTTTA
1 TAGTAAATTATTAATAACTTAA
*
20210804 TAATAAATTATCT-ATAACTTAA
1 TAGTAAATTAT-TAATAACTTAA
* * **
20210826 TAGTAAATTATCAAT-ATTTTG
1 TAGTAAATTATTAATAACTTAA
* *
20210847 TAGTAAATTGTTTATAACTTAA
1 TAGTAAATTATTAATAACTTAA
* *
20210869 AAGTAAATCATCT-ATAACTTA
1 TAGTAAATTAT-TAATAACTTA
20210890 GTGATAAATT
Statistics
Matches: 83, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
21 15 0.18
22 66 0.80
23 2 0.02
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (22 bp):
TAGTAAATTATTAATAACTTAA
Found at i:20210867 original size:43 final size:44
Alignment explanation
Indices: 20210775--20210876 Score: 118
Period size: 43 Copynumber: 2.3 Consensus size: 44
20210765 AATTATTAAC
*
20210775 AACTTCATAGTAAATTAGTAATAACTTTATAATAAATTATCTAT
1 AACTTAATAGTAAATTAGTAATAACTTTATAATAAATTATCTAT
* * * * *
20210819 AACTTAATAGTAAATTA-TCAAT-ATTTTGTAGTAAATTGTTTAT
1 AACTTAATAGTAAATTAGT-AATAACTTTATAATAAATTATCTAT
*
20210862 AACTTAAAAGTAAAT
1 AACTTAATAGTAAAT
20210877 CATCTATAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 31 0.62
44 19 0.38
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (44 bp):
AACTTAATAGTAAATTAGTAATAACTTTATAATAAATTATCTAT
Found at i:20211450 original size:22 final size:22
Alignment explanation
Indices: 20211404--20211578 Score: 109
Period size: 22 Copynumber: 8.0 Consensus size: 22
20211394 AGTAGTAAAT
* * *
20211404 TAGTTAATCATTGATAATTTTA
1 TAGTAAATCATTGATAACTTAA
*
20211426 TAGTAAATCATTGATAACTTCA
1 TAGTAAATCATTGATAACTTAA
* * *
20211448 TAGAAAATTAGTT-ATAACTTTA
1 TAGTAAATCA-TTGATAACTTAA
* * * ** *
20211470 TAATTAATTATCAATAACTTAG
1 TAGTAAATCATTGATAACTTAA
* * * *
20211492 CAATAAATCATTCATAATTTAA
1 TAGTAAATCATTGATAACTTAA
*
20211514 TAGTAAATCATTGATAATTTAA
1 TAGTAAATCATTGATAACTTAA
* ** * *
20211536 TAATAAATCACGGATAACATAG
1 TAGTAAATCATTGATAACTTAA
* *
20211558 TAATAAATCAGTGATAACTTA
1 TAGTAAATCATTGATAACTTA
20211579 GTCGTCAATT
Statistics
Matches: 120, Mismatches: 31, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
21 1 0.01
22 117 0.98
23 2 0.02
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (22 bp):
TAGTAAATCATTGATAACTTAA
Found at i:20211790 original size:21 final size:22
Alignment explanation
Indices: 20211762--20211867 Score: 81
Period size: 22 Copynumber: 4.9 Consensus size: 22
20211752 AAATCAGTAA
20211762 TAATAATAAATTAATGATAGCT
1 TAATAATAAATTAATGATAGCT
* **
20211784 T-ATAATAAATCAATTTTAGCT
1 TAATAATAAATTAATGATAGCT
* * *
20211805 TAATAGTAAAGT-ATAGATAACT
1 TAATAATAAATTAAT-GATAGCT
* * **
20211827 TAATAATAAATTATTCATATTT
1 TAATAATAAATTAATGATAGCT
* *
20211849 TAATAGTAAATTAGTGATA
1 TAATAATAAATTAATGATA
20211868 TAACTTAGTA
Statistics
Matches: 63, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
21 20 0.32
22 42 0.67
23 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (22 bp):
TAATAATAAATTAATGATAGCT
Found at i:20219211 original size:33 final size:33
Alignment explanation
Indices: 20219172--20219257 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
20219162 ATTAATACTA
*
20219172 GAACTAAAGCCTACTTGAAAATTAAGCCGTTAT
1 GAACTAAAGCCTACTTGAAAATTAAGCCATTAT
** * *
20219205 GAACTAAAATCTACTTGACAATTAAGCCATTGT
1 GAACTAAAGCCTACTTGAAAATTAAGCCATTAT
*
20219238 GAACTAAAGCGTACTTGAAA
1 GAACTAAAGCCTACTTGAAA
20219258 TACTAGAAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (33 bp):
GAACTAAAGCCTACTTGAAAATTAAGCCATTAT
Found at i:20221547 original size:3 final size:3
Alignment explanation
Indices: 20221539--20221571 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
20221529 TTACAATTAC
20221539 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20221572 TTATAAGACT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20231063 original size:14 final size:14
Alignment explanation
Indices: 20231044--20231076 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
20231034 GGTTTAATGG
20231044 TATTAAAATGTAAT
1 TATTAAAATGTAAT
*
20231058 TATTAAAATTTAAT
1 TATTAAAATGTAAT
20231072 TATTA
1 TATTA
20231077 TGTTATTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TATTAAAATGTAAT
Found at i:20237160 original size:13 final size:13
Alignment explanation
Indices: 20237142--20237166 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20237132 TAGATTGGAT
20237142 ATGTAAAACATAC
1 ATGTAAAACATAC
20237155 ATGTAAAACATA
1 ATGTAAAACATA
20237167 GGCCCATTTA
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:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (13 bp):
ATGTAAAACATAC
Found at i:20249793 original size:17 final size:17
Alignment explanation
Indices: 20249763--20249821 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
20249753 AATGATTGTA
20249763 GGAGATT-TGTGATTTCG
1 GGAGATTATG-GATTTCG
* *
20249780 GGATATTATGGATTTCA
1 GGAGATTATGGATTTCG
* *
20249797 AGAGATTATGGATTTTG
1 GGAGATTATGGATTTCG
20249814 GGAGATTA
1 GGAGATTA
20249822 GAGATTTCAC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 32 0.94
18 2 0.06
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.39
Consensus pattern (17 bp):
GGAGATTATGGATTTCG
Found at i:20249811 original size:34 final size:34
Alignment explanation
Indices: 20249764--20249830 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
20249754 ATGATTGTAG
*
20249764 GAGATTTGTGATTTCGGGATATTATG-GATTTCAA
1 GAGATTTGTGATTTCGGGAGATTA-GAGATTTCAA
*
20249798 GAGATTATG-GATTTTGGGAGATTAGAGATTTCA
1 GAGATT-TGTGATTTCGGGAGATTAGAGATTTCA
20249831 CATTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 1 0.03
34 26 0.90
35 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.28, T:0.39
Consensus pattern (34 bp):
GAGATTTGTGATTTCGGGAGATTAGAGATTTCAA
Found at i:20257433 original size:25 final size:26
Alignment explanation
Indices: 20257399--20257449 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
20257389 TGGGTTAGGG
*
20257399 ATATTTTATA-TAATTTTCACAAATC
1 ATATATTATATTAATTTTCACAAATC
* *
20257424 ATATATTATATTCATTTTCATAAATC
1 ATATATTATATTAATTTTCACAAATC
20257450 TACCTGCTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATATTATATTAATTTTCACAAATC
Found at i:20257746 original size:88 final size:90
Alignment explanation
Indices: 20257634--20257806 Score: 287
Period size: 88 Copynumber: 1.9 Consensus size: 90
20257624 TTGATGTTCT
*
20257634 TTATTTATTTATGCTTTATCTTATTTTCCATATTTTATTTAATTTATGATCTATTTTAATTATTC
1 TTATTTATTTATGCGTTATCTTATTTTCCATATTTTATTTAATTTATGATCTATTTTAATTATTC
*
20257699 TATTAACTACTATGAATTATTCACA
66 TATTAACTACAATGAATTATTCACA
* *
20257724 TTATTTATTT-TG-GTTATCTTATTTTCCATGTTTTATTTAGTTTATGATCTATTTTAATTATTC
1 TTATTTATTTATGCGTTATCTTATTTTCCATATTTTATTTAATTTATGATCTATTTTAATTATTC
*
20257787 TATTAACTGCAATGAATTAT
66 TATTAACTACAATGAATTAT
20257807 GATTGTAATC
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
88 66 0.85
89 2 0.03
90 10 0.13
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (90 bp):
TTATTTATTTATGCGTTATCTTATTTTCCATATTTTATTTAATTTATGATCTATTTTAATTATTC
TATTAACTACAATGAATTATTCACA
Found at i:20259316 original size:2 final size:2
Alignment explanation
Indices: 20259311--20259371 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
20259301 ACACATATAA
20259311 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
20259353 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
20259372 AGTTTGACTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20260418 original size:18 final size:20
Alignment explanation
Indices: 20260395--20260436 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
20260385 AAATTTCAAA
*
20260395 AATCAAT-AAATTGAA-TCG
1 AATCAATAAAATTCAATTCG
20260413 AATCAATAAAATTCAATTCG
1 AATCAATAAAATTCAATTCG
20260433 AATC
1 AATC
20260437 GAATCAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 7 0.33
20 7 0.33
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (20 bp):
AATCAATAAAATTCAATTCG
Found at i:20263563 original size:12 final size:11
Alignment explanation
Indices: 20263526--20263567 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
20263516 GAGATCAACT
*
20263526 AAAA-AAAATC
1 AAAATAAAATA
*
20263536 AAAATAGAATA
1 AAAATAAAATA
20263547 AAAATAAAATAA
1 AAAATAAAAT-A
20263559 AAAATAAAA
1 AAAATAAAA
20263568 AACTAACAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 4 0.15
11 13 0.48
12 10 0.37
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:20263569 original size:20 final size:20
Alignment explanation
Indices: 20263546--20263583 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20263536 AAAATAGAAT
20263546 AAAAATAA-AATAAAAAATAA
1 AAAAATAACAA-AAAAAATAA
*
20263566 AAAACTAACAAAAAAAAT
1 AAAAATAACAAAAAAAAT
20263584 TAATTGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAAATAACAAAAAAAATAA
Found at i:20266620 original size:20 final size:20
Alignment explanation
Indices: 20266595--20266634 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20266585 CAATTCCCAC
20266595 ATGAGAAAGCTAGGGACTAG
1 ATGAGAAAGCTAGGGACTAG
20266615 ATGAGAAAGCTAGGGACTAG
1 ATGAGAAAGCTAGGGACTAG
20266635 GTGATAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.35, T:0.15
Consensus pattern (20 bp):
ATGAGAAAGCTAGGGACTAG
Found at i:20269132 original size:23 final size:23
Alignment explanation
Indices: 20269106--20269179 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
20269096 TAAAACCAGA
20269106 AAAAT-AATTAAAAAACTAAAAAT
1 AAAATAAATTAAAAAA-TAAAAAT
* **
20269129 AAAATGAGCTAAAAAAT-AAAAT
1 AAAATAAATTAAAAAATAAAAAT
* *
20269151 AAAATAAAATCAAAATATAAAAAT
1 AAAAT-AAATTAAAAAATAAAAAT
20269175 AAAAT
1 AAAAT
20269180 GGAAAAAGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
22 10 0.24
23 13 0.32
24 18 0.44
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.20
Consensus pattern (23 bp):
AAAATAAATTAAAAAATAAAAAT
Found at i:20270011 original size:3 final size:3
Alignment explanation
Indices: 20270003--20270096 Score: 67
Period size: 3 Copynumber: 32.3 Consensus size: 3
20269993 AAGAAAGAAA
* *
20270003 AAT AAT AAT AAT AAT AAC AA- AAT AAT AAT AAT AAT AAT -AT GAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
20270048 AAT ACCAT -AT AAT -AT ACT AAT AAT ATAT AAA AAT -AT ATAT AAT -AT
1 AAT A--AT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT
20270093 AAT A
1 AAT A
20270097 TAAAACTTAG
Statistics
Matches: 75, Mismatches: 5, Indels: 22
0.74 0.05 0.22
Matches are distributed among these distances:
2 14 0.19
3 53 0.71
4 6 0.08
5 2 0.03
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20270026 original size:20 final size:20
Alignment explanation
Indices: 20270001--20270039 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
20269991 AAAAGAAAGA
20270001 AAAATAATAATAATAATAAC
1 AAAATAATAATAATAATAAC
20270021 AAAATAATAATAATAATAA
1 AAAATAATAATAATAATAA
20270040 TATGATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAATAATAATAATAAC
Found at i:20270051 original size:10 final size:9
Alignment explanation
Indices: 20270027--20270099 Score: 58
Period size: 10 Copynumber: 7.4 Consensus size: 9
20270017 TAACAAAATA
20270027 ATAATA-AT
1 ATAATATAT
20270035 AATAATATGAT
1 -ATAATAT-AT
*
20270046 ATAATACCAT
1 ATAATA-TAT
20270056 ATAATATACT
1 ATAATATA-T
20270066 AATAATATAT
1 -ATAATATAT
*
20270076 AAAAATATAT
1 -ATAATATAT
20270086 ATAATATAAT
1 ATAATAT-AT
20270096 ATAA
1 ATAA
20270100 AACTTAGTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
9 13 0.24
10 31 0.57
11 10 0.19
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (9 bp):
ATAATATAT
Found at i:20270097 original size:22 final size:23
Alignment explanation
Indices: 20270059--20270101 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
20270049 ATACCATATA
20270059 ATATACTAATAATATATAAAAAT
1 ATATACTAATAATATATAAAAAT
20270082 ATATA-TAAT-ATAATATAAAA
1 ATATACTAATAAT-ATATAAAA
20270102 CTTAGTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.11
22 12 0.63
23 5 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
ATATACTAATAATATATAAAAAT
Found at i:20270452 original size:118 final size:116
Alignment explanation
Indices: 20270330--20270677 Score: 328
Period size: 117 Copynumber: 2.9 Consensus size: 116
20270320 TTATTTGGAG
* * *
20270330 TAAGCTAAGATCGAATGATCGGGACGAAACTGCGAGTCTAAAAAAAAATGACCAAGACCAAGTCG
1 TAAGCTAAGATCGAATGACCGGGACGAAACTGCGAGTCTAAAAAAAAGTGA-CAGGACCAAGTCG
* *
20270395 AGGTTAAAAATGACTGACTGGGACGAAATCATGAGTCAGGAAATGATCTAGAA
65 AGGTTAAAAATGACTGACT-GGATGAAACCATGAGTCAGGAAATGATCTAGAA
* * * * * *
20270448 TAAGCTAAGATCAAATGACCAGGATGAACCTGCGAGTCTAAAAATAAAGTGACAGGATCAAGTGG
1 TAAGCTAAGATCGAATGACCGGGACGAAACTGCGAGTCTAAAAA-AAAGTGACAGGACCAAGTCG
* * * * *
20270513 AGG-TCAAAAT-AGCTGATCAT-GATAAAACCACGAGTCAGGAAATGATCTTGAT
65 AGGTTAAAAATGA-CTGA-C-TGGATGAAACCATGAGTCAGGAAATGATCTAGAA
* * * *
20270565 TAAGCCAAGATTGAATGACCGGGACGAAA-T-CGTAAGTCTAAGGATAAAGTGAACAGGACCAAG
1 TAAGCTAAGATCGAATGACCGGGACGAAACTGCG--AGTCTAA-AAAAAAGTG-ACAGGACCAAG
** * * * *
20270628 TTAAGGTTAAAAATGGCTGACTAGGATGAAACCGTGAGTTAAGAAATGAT
62 TCGAGGTTAAAAATGACTGACT-GGATGAAACCATGAGTCAGGAAATGAT
20270678 TTAAATGGAA
Statistics
Matches: 184, Mismatches: 34, Indels: 23
0.76 0.14 0.10
Matches are distributed among these distances:
115 2 0.01
116 2 0.01
117 73 0.40
118 69 0.38
119 38 0.21
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (116 bp):
TAAGCTAAGATCGAATGACCGGGACGAAACTGCGAGTCTAAAAAAAAGTGACAGGACCAAGTCGA
GGTTAAAAATGACTGACTGGATGAAACCATGAGTCAGGAAATGATCTAGAA
Found at i:20271685 original size:11 final size:11
Alignment explanation
Indices: 20271658--20271723 Score: 66
Period size: 11 Copynumber: 6.1 Consensus size: 11
20271648 CTTTTTCCTC
20271658 CTTTTTT-TCTT
1 CTTTTTTGT-TT
20271669 CATTTTTTGTTT
1 C-TTTTTTGTTT
20271681 CTTTTTTGTTT
1 CTTTTTTGTTT
20271692 -TTTTTTGTTT
1 CTTTTTTGTTT
* *
20271702 TTTTTTTTTTT
1 CTTTTTTGTTT
*
20271713 GTTTTTT-TTT
1 CTTTTTTGTTT
20271723 C
1 C
20271724 ACAACTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
10 13 0.27
11 26 0.53
12 9 0.18
13 1 0.02
ACGTcount: A:0.02, C:0.08, G:0.06, T:0.85
Consensus pattern (11 bp):
CTTTTTTGTTT
Found at i:20271722 original size:10 final size:10
Alignment explanation
Indices: 20271671--20271722 Score: 72
Period size: 10 Copynumber: 5.2 Consensus size: 10
20271661 TTTTTCTTCA
20271671 TTTTTTGTTT
1 TTTTTTGTTT
20271681 CTTTTTTGTTT
1 -TTTTTTGTTT
20271692 TTTTTTGTTT
1 TTTTTTGTTT
20271702 TTTTTT-TTT
1 TTTTTTGTTT
20271711 TTGTTTT-TTT
1 TT-TTTTGTTT
20271721 TT
1 TT
20271723 CACAACTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
9 5 0.12
10 25 0.62
11 10 0.25
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:20271742 original size:1 final size:1
Alignment explanation
Indices: 20271671--20271722 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
20271661 TTTTTCTTCA
* * * * *
20271671 TTTTTTGTTTCTTTTTTGTTTTTTTTTGTTTTTTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20271723 CACAACTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:20274964 original size:35 final size:35
Alignment explanation
Indices: 20274906--20274982 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
20274896 ATATACATAC
*
20274906 AATAAATAAATAATTGAACAAGTATAAGCAATGAA
1 AATAAATAAATAAATGAACAAGTATAAGCAATGAA
* * *
20274941 AATAAATAAATAAAT-AATTAAGTATAAGTAATTAA
1 AATAAATAAATAAATGAA-CAAGTATAAGCAATGAA
*
20274976 AAAAAAT
1 AATAAAT
20274983 CTTAAATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 34 0.94
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.26
Consensus pattern (35 bp):
AATAAATAAATAAATGAACAAGTATAAGCAATGAA
Found at i:20276102 original size:17 final size:15
Alignment explanation
Indices: 20276071--20276108 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
20276061 CCAACAAAAT
20276071 AATAAAA-GACTAAA
1 AATAAAATGACTAAA
20276085 AATAAAATGAGCTAAA
1 AATAAAATGA-CTAAA
20276101 AATAAAAT
1 AATAAAAT
20276109 CAAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 7 0.32
15 2 0.09
16 13 0.59
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.18
Consensus pattern (15 bp):
AATAAAATGACTAAA
Found at i:20276974 original size:3 final size:3
Alignment explanation
Indices: 20276968--20277068 Score: 97
Period size: 3 Copynumber: 34.3 Consensus size: 3
20276958 ATTATATCAA
20276968 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
20277015 GAT -AT AAT ACCAT -AT AAT -AT ACT AAT AAT ATAT AAA AAT -AT ATAT
1 AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT
20277060 AAT -AT AAT A
1 AAT AAT AAT A
20277069 TAAAACTCGA
Statistics
Matches: 84, Mismatches: 4, Indels: 20
0.78 0.04 0.19
Matches are distributed among these distances:
2 12 0.14
3 64 0.76
4 6 0.07
5 2 0.02
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:20277023 original size:10 final size:9
Alignment explanation
Indices: 20276955--20277071 Score: 66
Period size: 9 Copynumber: 12.4 Consensus size: 9
20276945 AAGAAAAAAA
20276955 ATAAT-TAT
1 ATAATATAT
*
20276963 ATCAAAATA-
1 AT-AATATAT
20276972 ATAATA-AT
1 ATAATATAT
20276980 AATAATA-AT
1 -ATAATATAT
20276989 AATAATA-AT
1 -ATAATATAT
20276998 AATAATA-AT
1 -ATAATATAT
20277007 AATAATATGAT
1 -ATAATAT-AT
*
20277018 ATAATACCAT
1 ATAATA-TAT
20277028 ATAATATACT
1 ATAATATA-T
20277038 AATAATATAT
1 -ATAATATAT
*
20277048 AAAAATATAT
1 -ATAATATAT
20277058 ATAATATAAT
1 ATAATAT-AT
20277068 ATAA
1 ATAA
20277072 AACTCGATCT
Statistics
Matches: 93, Mismatches: 6, Indels: 18
0.79 0.05 0.15
Matches are distributed among these distances:
7 1 0.01
8 5 0.05
9 44 0.47
10 33 0.35
11 10 0.11
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (9 bp):
ATAATATAT
Found at i:20277581 original size:21 final size:21
Alignment explanation
Indices: 20277555--20277601 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
20277545 CTAAGCCACT
20277555 ATATCTTTTAGGTTACGATCC
1 ATATCTTTTAGGTTACGATCC
*
20277576 ATATCTTTTAGGTTACGATCT
1 ATATCTTTTAGGTTACGATCC
20277597 ATATC
1 ATATC
20277602 AGACCAAGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.45
Consensus pattern (21 bp):
ATATCTTTTAGGTTACGATCC
Found at i:20285878 original size:60 final size:60
Alignment explanation
Indices: 20285809--20285995 Score: 182
Period size: 60 Copynumber: 3.1 Consensus size: 60
20285799 CAGTCATTCG
* *
20285809 TTCTAATCTCGACTCGATTCAGATCATTTTTTTAACCTGTGATTCAATCATGGTCACTCA
1 TTCTGATCTCGACTCGATTCAGATCATTTTTTTAACCTGTGATTCAATCCTGGTCACTCA
* * * * * *
20285869 TTCTGATCTCGACTTGATCCAGATCATTTTTCTAACCTGT-AGTTTAACCCTCGTCACTTC-
1 TTCTGATCTCGACTCGATTCAGATCATTTTTTTAACCTGTGA-TTCAATCCTGGTCAC-TCA
* * * * * * *
20285929 TTTTGATCTC-ATATCGGTTCAGATCATTTTTTTGACCAGTGGTTCAATCCTGGTCATTCA
1 TTCTGATCTCGA-CTCGATTCAGATCATTTTTTTAACCTGTGATTCAATCCTGGTCACTCA
*
20285989 TTTTGAT
1 TTCTGAT
20285996 TTCAGCTAAG
Statistics
Matches: 101, Mismatches: 21, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
59 4 0.04
60 95 0.94
61 2 0.02
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.42
Consensus pattern (60 bp):
TTCTGATCTCGACTCGATTCAGATCATTTTTTTAACCTGTGATTCAATCCTGGTCACTCA
Found at i:20286012 original size:60 final size:59
Alignment explanation
Indices: 20285828--20286017 Score: 168
Period size: 60 Copynumber: 3.2 Consensus size: 59
20285818 CGACTCGATT
* * * * *
20285828 CAGATCATTTTTTTAACCTGTGATTCAATCATGGTCACTCATTCTGATCTC-GACTTGATC
1 CAGATCATTTTTTTAACCTGTGGTTCAATCCTGGTCATTCATTTTGATCTCAG-CTAG-TC
* * * * * ** * *
20285888 CAGATCATTTTTCTAACCTGTAGTTTAACCCTCGTCACTTC-TTTTGATCTCATATCGGTT
1 CAGATCATTTTTTTAACCTGTGGTTCAATCCTGGTCA-TTCATTTTGATCTCAGCT-AGTC
* * *
20285948 CAGATCATTTTTTTGACCAGTGGTTCAATCCTGGTCATTCATTTTGATTTCAGCTAAGTC
1 CAGATCATTTTTTTAACCTGTGGTTCAATCCTGGTCATTCATTTTGATCTCAGCT-AGTC
20286008 CAGATCATTT
1 CAGATCATTT
20286018 AAATTATTAG
Statistics
Matches: 100, Mismatches: 26, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
59 3 0.03
60 94 0.94
61 3 0.03
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (59 bp):
CAGATCATTTTTTTAACCTGTGGTTCAATCCTGGTCATTCATTTTGATCTCAGCTAGTC
Found at i:20286202 original size:3 final size:3
Alignment explanation
Indices: 20286194--20286234 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
20286184 GATCAACTAT
20286194 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20286235 GTTGTTGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20286239 original size:3 final size:3
Alignment explanation
Indices: 20286233--20286282 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
20286223 ATTATTATTA
20286233 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
20286281 TT
1 TT
20286283 ATTATTATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:20286566 original size:15 final size:15
Alignment explanation
Indices: 20286546--20286629 Score: 64
Period size: 15 Copynumber: 5.7 Consensus size: 15
20286536 AGGAAATATC
20286546 TTTGGGTTTAAAGTT
1 TTTGGGTTTAAAGTT
*
20286561 TTTGGGTTTAAAATT
1 TTTGGGTTTAAAGTT
* **
20286576 TATGGGTTTTGA-TAT
1 TTTGGGTTTAAAGT-T
* *
20286591 TCTGGGTTTAAAG-C
1 TTTGGGTTTAAAGTT
* *
20286605 TCTGGGTTTGAAGTT
1 TTTGGGTTTAAAGTT
*
20286620 TTTGGATTTA
1 TTTGGGTTTA
20286630 GGTTTGAATT
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
14 13 0.25
15 40 0.75
ACGTcount: A:0.20, C:0.04, G:0.26, T:0.50
Consensus pattern (15 bp):
TTTGGGTTTAAAGTT
Found at i:20289309 original size:5 final size:5
Alignment explanation
Indices: 20289299--20289325 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
20289289 ATAAGATTAT
20289299 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
20289326 TAATAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:20289628 original size:27 final size:26
Alignment explanation
Indices: 20289590--20289653 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
20289580 ATAAAATAAG
*
20289590 ATAATATTATTTGATCTACTATGATAT-
1 ATAATATTATTTGATCT--TATCATATC
*
20289617 ATAATATTATTTTTATCTTATCATATC
1 ATAATATTA-TTTGATCTTATCATATC
20289644 ATAATATTAT
1 ATAATATTAT
20289654 ATACCAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 8 0.24
27 18 0.55
28 7 0.21
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.52
Consensus pattern (26 bp):
ATAATATTATTTGATCTTATCATATC
Found at i:20292369 original size:21 final size:22
Alignment explanation
Indices: 20292339--20292383 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
20292329 ATCGACAAAA
20292339 ATTATAATATAATTATTT-TTAT
1 ATTATAATAT-ATTATTTGTTAT
*
20292361 ATTAT-ATATATTTTTTGTTAT
1 ATTATAATATATTATTTGTTAT
20292382 AT
1 AT
20292384 CAAAAAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 10 0.48
22 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTATAATATATTATTTGTTAT
Found at i:20293888 original size:23 final size:21
Alignment explanation
Indices: 20293838--20293892 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
20293828 ATACTGTCAA
*
20293838 TAAATTAAAT-AATATTATTT
1 TAAAATAAATAAATATTATTT
*
20293858 TATTAATAAATAAATATTAATTTT
1 TA-AAATAAATAAATATT-A-TTT
20293882 TAAAATAAATA
1 TAAAATAAATA
20293893 TATAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.07
21 6 0.21
22 6 0.21
23 9 0.32
24 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAATAAATAAATATTATTT
Found at i:20293998 original size:31 final size:31
Alignment explanation
Indices: 20293929--20294001 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
20293919 AATTTACTCT
* * *
20293929 TTAATAAAATGATATTATCTTATTCATTTTA
1 TTAATAAGATGACATTATCCTATTCATTTTA
*
20293960 TTAATAAGATGACATTGTCCTATTCATTTTA
1 TTAATAAGATGACATTATCCTATTCATTTTA
20293991 TTAATAAGATG
1 TTAATAAGATG
20294002 GAATCAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (31 bp):
TTAATAAGATGACATTATCCTATTCATTTTA
Found at i:20294499 original size:21 final size:23
Alignment explanation
Indices: 20294473--20294521 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
20294463 TTCTTTTATG
20294473 AAAAAATCGT-AAT-ATAAATAT
1 AAAAAATCGTAAATCATAAATAT
*
20294494 AAAAAATTGTAAATCATAAATAT
1 AAAAAATCGTAAATCATAAATAT
*
20294517 TAAAA
1 AAAAA
20294522 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
AAAAAATCGTAAATCATAAATAT
Found at i:20294533 original size:21 final size:23
Alignment explanation
Indices: 20294473--20294535 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 23
20294463 TTCTTTTATG
*
20294473 AAAAAATCGT-AA-TATAAATAT
1 AAAAAATTGTAAATTATAAATAT
*
20294494 AAAAAATTGTAAATCATAAATAT
1 AAAAAATTGTAAATTATAAATAT
*
20294517 -TAAAATT-TAAATTATAAAT
1 AAAAAATTGTAAATTATAAAT
20294536 TTATATGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 20 0.56
22 8 0.22
23 8 0.22
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (23 bp):
AAAAAATTGTAAATTATAAATAT
Found at i:20298382 original size:25 final size:26
Alignment explanation
Indices: 20298333--20298382 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
20298323 GGGAAAGAGA
* *
20298333 AAAATATGAAGAAAAGATAGAAAAAG
1 AAAATATGAAGAAAAGAAAAAAAAAG
20298359 AAAA-ATGAAGAAAAGAAAAAAAAA
1 AAAATATGAAGAAAAGAAAAAAAAA
20298383 TTTATAGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (26 bp):
AAAATATGAAGAAAAGAAAAAAAAAG
Found at i:20299886 original size:43 final size:43
Alignment explanation
Indices: 20299777--20299972 Score: 166
Period size: 43 Copynumber: 4.5 Consensus size: 43
20299767 TACCTTTTTT
* * **
20299777 TTTTAGATTTTTCAAAGTTTCAAAGCTTTTGGTGAAAAGG-GC-
1 TTTTAGATTTTTCAAAGTTTCAAAGCCTTTGATG-AGGGGAGCA
* * *
20299819 TTTGT-CA-TTTTCAAAGTTTTAAAGCCTTTGGTGAGGGGAGCA
1 TTT-TAGATTTTTCAAAGTTTCAAAGCCTTTGATGAGGGGAGCA
* * * *
20299861 TTTTAGATTTTCCAAAGTTTCAAAGCCTTTAATAAGGGTAGCA
1 TTTTAGATTTTTCAAAGTTTCAAAGCCTTTGATGAGGGGAGCA
** *
20299904 TTTTAGATTTTTTTTTCAAAGTTTCAAAGTTTTTGATGGGGGGAGCA
1 TTTTAGA----TTTTTCAAAGTTTCAAAGCCTTTGATGAGGGGAGCA
* *
20299951 TTTTAAATTTTTAAAAGTTTCA
1 TTTTAGATTTTTCAAAGTTTCA
20299973 GTGCCTTTAT
Statistics
Matches: 124, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
40 3 0.02
41 27 0.22
42 8 0.06
43 51 0.41
47 35 0.28
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (43 bp):
TTTTAGATTTTTCAAAGTTTCAAAGCCTTTGATGAGGGGAGCA
Found at i:20299951 original size:47 final size:47
Alignment explanation
Indices: 20299868--20299962 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 47
20299858 GCATTTTAGA
* *
20299868 TTTTCCAAAGTTTCAAAGCCTTTAATAAGGGTAGCATTTTAGATTTT
1 TTTTCCAAAGTTTCAAAGCCTTTAATAAGGGGAGCATTTTAAATTTT
* ** * **
20299915 TTTTTCAAAGTTTCAAAGTTTTTGATGGGGGGAGCATTTTAAATTTT
1 TTTTCCAAAGTTTCAAAGCCTTTAATAAGGGGAGCATTTTAAATTTT
20299962 T
1 T
20299963 AAAAGTTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (47 bp):
TTTTCCAAAGTTTCAAAGCCTTTAATAAGGGGAGCATTTTAAATTTT
Found at i:20300166 original size:43 final size:42
Alignment explanation
Indices: 20300109--20300211 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 42
20300099 GAGCTCTTTC
* *
20300109 ATTTTCAAAGTTTCAAAAACTC-AGTCGACGGGGAGCATTTTAA
1 ATTTTCAAAGTTTCAAAAACTCTAAT-GA-AGGGAGCATTTTAA
* ** *
20300152 ATTTTAAAAGTTTCAAAGCCTCTAATGAAGGGAGCATTTTAG
1 ATTTTCAAAGTTTCAAAAACTCTAATGAAGGGAGCATTTTAA
20300194 ATTTTCCAAAGTTTCAAA
1 ATTTT-CAAAGTTTCAAA
20300212 GTTTTAAAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
42 17 0.33
43 32 0.63
44 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (42 bp):
ATTTTCAAAGTTTCAAAAACTCTAATGAAGGGAGCATTTTAA
Found at i:20300266 original size:41 final size:42
Alignment explanation
Indices: 20300209--20300378 Score: 159
Period size: 44 Copynumber: 4.0 Consensus size: 42
20300199 CCAAAGTTTC
*
20300209 AAAGTTTTAAAGCCTCTGGTTG-GGGGAGCA-TTTAGATTTTA
1 AAAGTTTGAAAGCCTCT-GTTGAGGGGAGCATTTTAGATTTTA
* *
20300250 AAAGTTTGAAAGCCTCTAG-TGATGGGAGCATTTTAAATTTTCA
1 AAAGTTTGAAAGCCTCT-GTTGAGGGGAGCATTTTAGATTTT-A
* * *
20300293 AAAGTTTCAAAGCTTCTGTTGAAGAGGAGCATTTTAGATTTTTA
1 AAAGTTTGAAAGCCTCTGTTG-AGGGGAGCATTTTAGA-TTTTA
* * * *
20300337 AAAG-TTGCAAAGCCTTTGTTGATGGGGACCCTTTTCGATTTT
1 AAAGTTTG-AAAGCCTCTGTTGA-GGGGAGCATTTTAGATTTT
20300379 TCTTAACTCG
Statistics
Matches: 105, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
40 2 0.02
41 24 0.23
42 10 0.10
43 25 0.24
44 40 0.38
45 4 0.04
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (42 bp):
AAAGTTTGAAAGCCTCTGTTGAGGGGAGCATTTTAGATTTTA
Found at i:20302053 original size:13 final size:13
Alignment explanation
Indices: 20302035--20302068 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
20302025 TAATAACAAT
20302035 AATAAAATACTAA
1 AATAAAATACTAA
20302048 AATAAAA-ACTAA
1 AATAAAATACTAA
*
20302060 AAGAAAATA
1 AATAAAATA
20302069 AAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (13 bp):
AATAAAATACTAA
Found at i:20302066 original size:25 final size:25
Alignment explanation
Indices: 20302021--20302068 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
20302011 GAAATAAAAG
* *
20302021 AAAATAATAACAATAATAAAATACT
1 AAAATAAAAACAATAAGAAAATACT
20302046 AAAATAAAAACTAA-AAGAAAATA
1 AAAATAAAAAC-AATAAGAAAATA
20302069 AAAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (25 bp):
AAAATAAAAACAATAAGAAAATACT
Found at i:20302293 original size:17 final size:17
Alignment explanation
Indices: 20302245--20302296 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
20302235 TCTATTTATC
*
20302245 AATATTAAACTATTAAT
1 AATATTAAAATATTAAT
* *
20302262 AATAATAGAAA-ATTATT
1 AATATTA-AAATATTAAT
*
20302279 GATATTAAAATATTAAT
1 AATATTAAAATATTAAT
20302296 A
1 A
20302297 TTAGTTTCAT
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
16 3 0.12
17 21 0.81
18 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (17 bp):
AATATTAAAATATTAAT
Found at i:20302344 original size:20 final size:22
Alignment explanation
Indices: 20302316--20302355 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20302306 TATTGAAAAA
20302316 AATACAAAAAGA-AAAAAAATT
1 AATACAAAAAGACAAAAAAATT
20302337 AATA-AAAAAGACAAAAAAA
1 AATACAAAAAGACAAAAAAA
20302356 ACAATGGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.10
Consensus pattern (22 bp):
AATACAAAAAGACAAAAAAATT
Found at i:20302475 original size:14 final size:12
Alignment explanation
Indices: 20302442--20302482 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
20302432 TTGTGACCTA
20302442 ACCAGACTAGCC
1 ACCAGACTAGCC
20302454 ACCAGACTAGTCCC
1 ACCAGACTAG--CC
*
20302468 ATCAGACTAGCC
1 ACCAGACTAGCC
20302480 ACC
1 ACC
20302483 CTTTCATCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 14 0.56
14 11 0.44
ACGTcount: A:0.32, C:0.41, G:0.15, T:0.12
Consensus pattern (12 bp):
ACCAGACTAGCC
Found at i:20302987 original size:25 final size:24
Alignment explanation
Indices: 20302959--20303008 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
20302949 CCCAGCTTTC
* *
20302959 AAACACCCCATGAAACCCTTCACCT
1 AAACACCCCA-CAAAACCTTCACCT
*
20302984 AAACATCCCACAAAACCTTCACCT
1 AAACACCCCACAAAACCTTCACCT
20303008 A
1 A
20303009 CTAGAAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.40, C:0.42, G:0.02, T:0.16
Consensus pattern (24 bp):
AAACACCCCACAAAACCTTCACCT
Found at i:20303831 original size:16 final size:16
Alignment explanation
Indices: 20303810--20303840 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20303800 GTTTTATAAT
20303810 AATAATAATAATTAAC
1 AATAATAATAATTAAC
*
20303826 AATAATAATGATTAA
1 AATAATAATAATTAA
20303841 ATGACAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (16 bp):
AATAATAATAATTAAC
Found at i:20304227 original size:7 final size:7
Alignment explanation
Indices: 20304215--20304292 Score: 54
Period size: 7 Copynumber: 10.9 Consensus size: 7
20304205 AACCGAAACC
20304215 CCAAAAT
1 CCAAAAT
20304222 CCAAAAT
1 CCAAAAT
**
20304229 CACAAACC
1 C-CAAAAT
20304237 CCAAAAT
1 CCAAAAT
20304244 CCAAAAT
1 CCAAAAT
*
20304251 -CACAAAC
1 CCA-AAAT
20304258 CCTAAAAT
1 CC-AAAAT
20304266 CCAAAA-
1 CCAAAAT
20304272 CCTTAAAAT
1 CC--AAAAT
*
20304281 TC-AAAT
1 CCAAAAT
20304287 CCAAAA
1 CCAAAA
20304293 ATCCCAAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
6 9 0.16
7 29 0.53
8 15 0.27
9 2 0.04
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.14
Consensus pattern (7 bp):
CCAAAAT
Found at i:20304238 original size:22 final size:22
Alignment explanation
Indices: 20304210--20304271 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
20304200 CTTTAAACCG
20304210 AAACCCCAAAATCCAAAATCAC
1 AAACCCCAAAATCCAAAATCAC
20304232 AAACCCCAAAATCCAAAATCAC
1 AAACCCCAAAATCCAAAATCAC
*
20304254 AAACCCTAAAATCCAAAA
1 AAACCCCAAAATCCAAAA
20304272 CCTTAAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.56, C:0.34, G:0.00, T:0.10
Consensus pattern (22 bp):
AAACCCCAAAATCCAAAATCAC
Found at i:20304256 original size:15 final size:14
Alignment explanation
Indices: 20304215--20304292 Score: 54
Period size: 15 Copynumber: 5.4 Consensus size: 14
20304205 AACCGAAACC
20304215 CCAAAATCCAAAAT
1 CCAAAATCCAAAAT
**
20304229 CACAAACCCCAAAAT
1 C-CAAAATCCAAAAT
*
20304244 CCAAAAT-CACAAAC
1 CCAAAATCCA-AAAT
20304258 CCTAAAATCCAAAA-
1 CC-AAAATCCAAAAT
*
20304272 CCTTAAAATTC-AAAT
1 CC--AAAATCCAAAAT
20304287 CCAAAA
1 CCAAAA
20304293 ATCCCAAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
13 6 0.12
14 15 0.29
15 29 0.56
16 2 0.04
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.14
Consensus pattern (14 bp):
CCAAAATCCAAAAT
Found at i:20311300 original size:19 final size:20
Alignment explanation
Indices: 20311278--20311319 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
20311268 AATCCAAAAC
20311278 AAAAAAAAAGA-AAAAAAGA
1 AAAAAAAAAGAGAAAAAAGA
*
20311297 AAAAAAAAAGAGAAAAGAGA
1 AAAAAAAAAGAGAAAAAAGA
20311317 AAA
1 AAA
20311320 CATGTACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAGAAAAAAGA
Found at i:20312524 original size:15 final size:15
Alignment explanation
Indices: 20312504--20312532 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20312494 ACAAGAAAAA
20312504 CATTTGCATTTGCAT
1 CATTTGCATTTGCAT
20312519 CATTTGCATTTGCA
1 CATTTGCATTTGCA
20312533 CTTGTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (15 bp):
CATTTGCATTTGCAT
Found at i:20313182 original size:22 final size:22
Alignment explanation
Indices: 20313157--20313199 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20313147 GGACGTGATT
*
20313157 TTTAAGACCTCCGAGCATAATC
1 TTTAAGACCTCCAAGCATAATC
20313179 TTTAAGACCTCCAAGCATAAT
1 TTTAAGACCTCCAAGCATAAT
20313200 TTCGATTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.28
Consensus pattern (22 bp):
TTTAAGACCTCCAAGCATAATC
Found at i:20313303 original size:88 final size:88
Alignment explanation
Indices: 20313177--20313342 Score: 224
Period size: 88 Copynumber: 1.9 Consensus size: 88
20313167 CCGAGCATAA
* * * * * *
20313177 TCTTTAAGACCTCCAAGCATAATTTCGATTCATGGTGTTGTCCTGATCAATTTTTAATTTTTTGA
1 TCTTTAAGACCTCCAAGAAAAATTTCGATTCACGGTGTTATCCTAATCAATTTTTAATTTTTCGA
20313242 CTTGCGGTATTATTTCGGTCAAT
66 CTTGCGGTATTATTTCGGTCAAT
* * * *
20313265 TCTTTAAGACCTCCGAGAAAAATTTTGATTTACGGTGTTATCCTAATCAATTTTTTATTTTTCGA
1 TCTTTAAGACCTCCAAGAAAAATTTCGATTCACGGTGTTATCCTAATCAATTTTTAATTTTTCGA
* *
20313330 CTTGTGGTGTTAT
66 CTTGCGGTATTAT
20313343 CCCAATCGAT
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
88 66 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (88 bp):
TCTTTAAGACCTCCAAGAAAAATTTCGATTCACGGTGTTATCCTAATCAATTTTTAATTTTTCGA
CTTGCGGTATTATTTCGGTCAAT
Found at i:20313355 original size:88 final size:88
Alignment explanation
Indices: 20313177--20313365 Score: 207
Period size: 88 Copynumber: 2.1 Consensus size: 88
20313167 CCGAGCATAA
* * * * * *
20313177 TCTTTAAGACCTCCAAGCATAATTTCGATTCATGGTGTTGTCCTGATCAATTTTTAATTTTTTGA
1 TCTTTAAGACCTCCAAGAAAAATTTCGATTCACGGTGTTATCCTAATCAATTTTTAATTTTTCGA
** **
20313242 CTTGCGGTATTATTTCGGTCAAT
66 CTTGCGGTATTATCCCAATCAAT
* * * *
20313265 TCTTTAAGACCTCCGAGAAAAATTTTGATTTACGGTGTTATCCTAATCAATTTTTTATTTTTCGA
1 TCTTTAAGACCTCCAAGAAAAATTTCGATTCACGGTGTTATCCTAATCAATTTTTAATTTTTCGA
* * *
20313330 CTTGTGGTGTTATCCCAATCGAT
66 CTTGCGGTATTATCCCAATCAAT
* *
20313353 TCTATAAAACCTC
1 TCTTTAAGACCTC
20313366 TTAGCATAAT
Statistics
Matches: 82, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
88 82 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (88 bp):
TCTTTAAGACCTCCAAGAAAAATTTCGATTCACGGTGTTATCCTAATCAATTTTTAATTTTTCGA
CTTGCGGTATTATCCCAATCAAT
Found at i:20315858 original size:22 final size:22
Alignment explanation
Indices: 20315805--20315887 Score: 114
Period size: 22 Copynumber: 3.8 Consensus size: 22
20315795 TTTTAAATCG
*
20315805 AAACCCTAAAATCCAAAATCTC
1 AAACCCTAAAATCCAAAATCCC
*
20315827 -AACCCCAAAATCCAAAATCCC
1 AAACCCTAAAATCCAAAATCCC
*
20315848 AAACCATAAAATCCAAAATCCC
1 AAACCCTAAAATCCAAAATCCC
* *
20315870 GAACCCTAAAATTCAAAA
1 AAACCCTAAAATCCAAAA
20315888 CCTTAAAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
21 19 0.36
22 34 0.64
ACGTcount: A:0.52, C:0.33, G:0.01, T:0.14
Consensus pattern (22 bp):
AAACCCTAAAATCCAAAATCCC
Found at i:20315889 original size:15 final size:15
Alignment explanation
Indices: 20315871--20315901 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20315861 CAAAATCCCG
20315871 AACCCTAAAATTCAA
1 AACCCTAAAATTCAA
*
20315886 AACCTTAAAATTCAA
1 AACCCTAAAATTCAA
20315901 A
1 A
20315902 TCCAAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (15 bp):
AACCCTAAAATTCAA
Found at i:20317644 original size:2 final size:2
Alignment explanation
Indices: 20317637--20317667 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20317627 GATTTAGCAA
20317637 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 A
20317668 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20317672 original size:2 final size:2
Alignment explanation
Indices: 20317667--20317691 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20317657 ATATATATAT
20317667 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
20317692 AGAAAGATAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20318715 original size:24 final size:24
Alignment explanation
Indices: 20318688--20318735 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
20318678 GGTAAATAAG
* *
20318688 ATTGATTCTTTTTTATGTTGCCTT
1 ATTGATTCTTTCTTACGTTGCCTT
20318712 ATTGATTCTTTCTTACGTTGCCTT
1 ATTGATTCTTTCTTACGTTGCCTT
20318736 TTACACCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.17, G:0.12, T:0.58
Consensus pattern (24 bp):
ATTGATTCTTTCTTACGTTGCCTT
Found at i:20320856 original size:47 final size:47
Alignment explanation
Indices: 20320787--20320884 Score: 160
Period size: 47 Copynumber: 2.1 Consensus size: 47
20320777 GATTATAGAA
* * * *
20320787 CATCCTCATTTAAGATTTCTATTTAGTTATGCATTTTAATTTTTAAT
1 CATCCTCATTTAAAATTTCTATTTAGTTATACATTTTAATCTTTAAC
20320834 CATCCTCATTTAAAATTTCTATTTAGTTATACATTTTAATCTTTAAC
1 CATCCTCATTTAAAATTTCTATTTAGTTATACATTTTAATCTTTAAC
20320881 CATC
1 CATC
20320885 ACATTCAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.30, C:0.16, G:0.04, T:0.50
Consensus pattern (47 bp):
CATCCTCATTTAAAATTTCTATTTAGTTATACATTTTAATCTTTAAC
Found at i:20321278 original size:18 final size:18
Alignment explanation
Indices: 20321257--20321295 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
20321247 TTTATATAAT
20321257 ATAAATACATAAATTATC
1 ATAAATACATAAATTATC
20321275 ATAAATACATAAATTATC
1 ATAAATACATAAATTATC
20321293 ATA
1 ATA
20321296 TCTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAATACATAAATTATC
Found at i:20321279 original size:10 final size:10
Alignment explanation
Indices: 20321264--20321295 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20321254 AATATAAATA
20321264 CATAAATTAT
1 CATAAATTAT
20321274 CATAAA-TA-
1 CATAAATTAT
20321282 CATAAATTAT
1 CATAAATTAT
20321292 CATA
1 CATA
20321296 TCTAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.30
9 4 0.20
10 10 0.50
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (10 bp):
CATAAATTAT
Found at i:20325747 original size:128 final size:126
Alignment explanation
Indices: 20325535--20326009 Score: 370
Period size: 128 Copynumber: 3.7 Consensus size: 126
20325525 ACAACAACAA
* * * * * *
20325535 AAAAGTTATTACGAAAATTTTTATAACATTTGTAATGATAAAATATTAATATTACAAAAACTTGT
1 AAAAGTTGTTACAAAAATTTTTATCACATTTGTAATGATAAAAAATTATTATTAC-AAAACTTAT
* ** * **
20325600 TTCATAAGCAA-AGATTTTTCAATGTTGTTGCTTAATTTATTAATTTATTTTTTAAAAATGACA-
65 TTTATTTGCAATA-ATTTTTCAATGTAGTT-CTTAATTTATT-ATTTAAATTTTAAAAATGACAT
* * * *
20325663 AAAAGTTGTTACAAAAATTTTTATCATATTTGTAATGATAAAATATTATTGTTACACAAGCTTAT
1 AAAAGTTGTTACAAAAATTTTTATCACATTTGTAATGATAAAAAATTATTATTACA-AAACTTAT
* * * * * * *
20325728 TTTATTTGCAATAAGTTTTCAATGTCGTTATTAA-ATAGCTTTTTTAAAAATTTTATACAATTAC
65 TTTATTTGCAATAATTTTTCAATGTAGTTCTTAATTTA--TTATTT--AAATTTTA-AAAATGAC
20325792 AT
125 AT
* * * * *
20325794 AAAAATTGTTACGAAAATTTTTATCACATTTATAATGTTAAAAAATTATTGTTGA-AAAACTTAT
1 AAAAGTTGTTACAAAAATTTTTATCACATTTGTAATGATAAAAAATTATTATT-ACAAAACTTAT
* ** * * ** *
20325858 TTTAGTTGCAATGTTTTTTCATTGTAATTACTTAATTTATTTATAAAAATATTAAAAA-G-CAAT
65 TTTATTTGCAATAATTTTTCAATGTAGTT-CTTAATTTA-TTATTTAAATTTTAAAAATGAC-AT
* * * *
20325921 GCAAAAGTTGTTACAAAAATGTTTATCATATTTGTAATGATAAAAAAATTATTATTGCGAGAACT
1 --AAAAGTTGTTACAAAAATTTTTATCACATTTGTAATGAT-AAAAAATTATTATTAC-AAAACT
20325986 TATTTTATTTGCAA-AGATTTTTCA
62 TATTTTATTTGCAATA-ATTTTTCA
20326010 TTATCGTTAA
Statistics
Matches: 274, Mismatches: 55, Indels: 33
0.76 0.15 0.09
Matches are distributed among these distances:
126 3 0.01
127 10 0.04
128 82 0.30
129 47 0.17
130 49 0.18
131 80 0.29
132 3 0.01
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.43
Consensus pattern (126 bp):
AAAAGTTGTTACAAAAATTTTTATCACATTTGTAATGATAAAAAATTATTATTACAAAACTTATT
TTATTTGCAATAATTTTTCAATGTAGTTCTTAATTTATTATTTAAATTTTAAAAATGACAT
Found at i:20330562 original size:18 final size:17
Alignment explanation
Indices: 20330533--20330567 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
20330523 ACACTTTGAT
*
20330533 TTATTTTTTATTTTTTA
1 TTATTTTTTATTGTTTA
20330550 TTATTTTTATATTGTTTA
1 TTATTTTT-TATTGTTTA
20330568 AATAAATATT
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:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (17 bp):
TTATTTTTTATTGTTTA
Found at i:20330975 original size:23 final size:23
Alignment explanation
Indices: 20330958--20331015 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 23
20330948 TATCATTATA
20330958 AAAAAT-AACATAAAATCAAAAT
1 AAAAATCAACATAAAATCAAAAT
20330980 AAAAATCAACATAAAAT--AAAT
1 AAAAATCAACATAAAATCAAAAT
*
20331001 -AAAATCAAAATAAAA
1 AAAAATCAACATAAAA
20331016 AAAAAAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 14 0.41
21 4 0.12
22 6 0.18
23 10 0.29
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (23 bp):
AAAAATCAACATAAAATCAAAAT
Found at i:20330981 original size:11 final size:11
Alignment explanation
Indices: 20330967--20331015 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
20330957 AAAAAATAAC
20330967 ATAAAATCAAA
1 ATAAAATCAAA
*
20330978 ATAAAAATCAAC
1 AT-AAAATCAAA
20330990 ATAAAAT--AA
1 ATAAAATCAAA
20330999 ATAAAATCAAA
1 ATAAAATCAAA
20331010 ATAAAA
1 ATAAAA
20331016 AAAAAAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 8 0.24
11 15 0.45
12 10 0.30
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.18
Consensus pattern (11 bp):
ATAAAATCAAA
Found at i:20330983 original size:5 final size:5
Alignment explanation
Indices: 20330959--20331019 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
20330949 ATCATTATAA
* *
20330959 AAAAT AACAT AAAAT CAAAAT AAAAAT CAACAT AAAAT -AAAT AAAAT
1 AAAAT AAAAT AAAAT -AAAAT -AAAAT -AAAAT AAAAT AAAAT AAAAT
20331006 CAAAAT AAAA- AAAA
1 -AAAAT AAAAT AAAA
20331020 AAGAAAAGAG
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
4 8 0.17
5 20 0.43
6 19 0.40
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:20331963 original size:3 final size:3
Alignment explanation
Indices: 20331957--20332031 Score: 114
Period size: 3 Copynumber: 25.0 Consensus size: 3
20331947 AATGAAAAAA
* * *
20331957 AAT AAT AGT AGT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
20332005 AAT AGT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
20332032 TTTATTTAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20332624 original size:34 final size:34
Alignment explanation
Indices: 20332347--20332646 Score: 157
Period size: 34 Copynumber: 8.8 Consensus size: 34
20332337 AAGGCTTATT
*
20332347 TGACCAGAGGCTATGAAACTTTAAAAGAAAGCTCCTC
1 TGACCAGAGGCTATGAAACTTTAAATG---GCTCCTC
* * * *
20332384 TAACTAGAAG-TAATGAAACTTTAAATAGCTCCTC
1 TGACCAGAGGCT-ATGAAACTTTAAATGGCTCCTC
* * * * * *** *
20332418 TGACCAAAAGCTCTTAAA-ATTAAAAAACTCTTC
1 TGACCAGAGGCTATGAAACTTTAAATGGCTCCTC
20332451 TGACCAGAGGCTATGAAACTCTT-AATGGCTCCTC
1 TGACCAGAGGCTATGAAACT-TTAAATGGCTCCTC
* * * *
20332485 TGACCAGAGGCAATGACACTTTAAA-GAAAGCTCATT
1 TGACCAGAGGCTATGAAACTTTAAATG---GCTCCTC
* * * * * * *
20332521 TAACCAAAAG-TAATAAAATTTTAAATAGCTTCTC
1 TGACCAGAGGCT-ATGAAACTTTAAATGGCTCCTC
* * * * * *
20332555 TGACCAAAAGCTCTTAAAATTAAAAAT---TCCTC
1 TGACCAGAGGCTATGAAACTT-TAAATGGCTCCTC
20332587 TGACCAGAGGCTATGAAACTTTAAATGGCTCCTC
1 TGACCAGAGGCTATGAAACTTTAAATGGCTCCTC
* *
20332621 TGACTAGAGGCAATGAAACTTTAAAT
1 TGACCAGAGGCTATGAAACTTTAAAT
20332647 TTAAAAGTTT
Statistics
Matches: 196, Mismatches: 52, Indels: 33
0.70 0.19 0.12
Matches are distributed among these distances:
31 4 0.02
32 20 0.10
33 28 0.14
34 93 0.47
35 8 0.04
36 23 0.12
37 20 0.10
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (34 bp):
TGACCAGAGGCTATGAAACTTTAAATGGCTCCTC
Found at i:20332642 original size:136 final size:137
Alignment explanation
Indices: 20332347--20332645 Score: 458
Period size: 136 Copynumber: 2.2 Consensus size: 137
20332337 AAGGCTTATT
* * * * *
20332347 TGACCAGAGGCTATGAAACTTTAAAAGAAAGCTCCTCTAACTAGAAGTAATGAAACTTTAAATAG
1 TGACCAGAGGCAATGAAACTTT-AAAGAAAGCTCATCTAACCAAAAGTAATAAAACTTTAAATAG
*
20332412 CTCCTCTGACCAAAAGCTCTTAAAATTAAAAAACTCTTCTGACCAGAGGCTATGAAACTCTTAAT
65 CTCCTCTGACCAAAAGCTCTTAAAATTAAAAAACTCCTCTGACCAGAGGCTATGAAACTCTTAAT
20332477 GGCTCCTC
130 GGCTCCTC
* * *
20332485 TGACCAGAGGCAATGACACTTTAAAGAAAGCTCATTTAACCAAAAGTAATAAAATTTTAAATAGC
1 TGACCAGAGGCAATGAAACTTTAAAGAAAGCTCATCTAACCAAAAGTAATAAAACTTTAAATAGC
* *
20332550 TTCTCTGACCAAAAGCTCTTAAAATT-AAAAATTCCTCTGACCAGAGGCTATGAAACT-TTAAAT
66 TCCTCTGACCAAAAGCTCTTAAAATTAAAAAACTCCTCTGACCAGAGGCTATGAAACTCTT-AAT
20332613 GGCTCCTC
130 GGCTCCTC
*
20332621 TGACTAGAGGCAATGAAACTTTAAA
1 TGACCAGAGGCAATGAAACTTTAAA
20332646 TTTAAAAGTT
Statistics
Matches: 147, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
135 2 0.01
136 63 0.43
137 62 0.42
138 20 0.14
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (137 bp):
TGACCAGAGGCAATGAAACTTTAAAGAAAGCTCATCTAACCAAAAGTAATAAAACTTTAAATAGC
TCCTCTGACCAAAAGCTCTTAAAATTAAAAAACTCCTCTGACCAGAGGCTATGAAACTCTTAATG
GCTCCTC
Found at i:20332852 original size:17 final size:17
Alignment explanation
Indices: 20332830--20332875 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
20332820 AATGATGATC
20332830 ATGATGCAAATACACTT
1 ATGATGCAAATACACTT
*
20332847 ATGATGCAAATGCACTT
1 ATGATGCAAATACACTT
20332864 ATGATGCAAATA
1 ATGATGCAAATA
20332876 AAGAGATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (17 bp):
ATGATGCAAATACACTT
Found at i:20340677 original size:13 final size:13
Alignment explanation
Indices: 20340659--20340686 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20340649 GTACATTTGG
20340659 TTCCATCATATTT
1 TTCCATCATATTT
20340672 TTCCATCATATTT
1 TTCCATCATATTT
20340685 TT
1 TT
20340687 TAAATTTTAA
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:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (13 bp):
TTCCATCATATTT
Found at i:20344128 original size:15 final size:15
Alignment explanation
Indices: 20344110--20344149 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
20344100 AAATAAAATT
20344110 AACAATATAATTAGC
1 AACAATATAATTAGC
20344125 AACAATATAATTAGC
1 AACAATATAATTAGC
20344140 AACAATATAA
1 AACAATATAA
20344150 AACAAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.25
Consensus pattern (15 bp):
AACAATATAATTAGC
Found at i:20345517 original size:3 final size:3
Alignment explanation
Indices: 20345509--20345537 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20345499 AACATTAAAT
20345509 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
20345538 TCATCATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:20348800 original size:21 final size:20
Alignment explanation
Indices: 20348770--20348826 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
20348760 TCCCTTTAAA
20348770 AGGGGATCGATCCCTTACCT-T
1 AGGGGATCGATCCCTTA--TGT
* *
20348791 AGGTGATCGATCCTTTATGT
1 AGGGGATCGATCCCTTATGT
20348811 AGGGGATCGATCCCTT
1 AGGGGATCGATCCCTT
20348827 TTTTAGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 15 0.48
21 15 0.48
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (20 bp):
AGGGGATCGATCCCTTATGT
Found at i:20357132 original size:41 final size:41
Alignment explanation
Indices: 20357086--20357167 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
20357076 TGCCTTACCC
*
20357086 GATCGATCCCTTACT-TTAGGGGATCGATCT-GTTTTTTAGGT
1 GATCGATCCCTTA-TGTGAGGGGATCGAT-TAGTTTTTTAGGT
*
20357127 GATCGATCCCTTATGTGGGGGGATCGATTAGTTTTTTAGGT
1 GATCGATCCCTTATGTGAGGGGATCGATTAGTTTTTTAGGT
20357168 TTCAACACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 2 0.05
41 35 0.95
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (41 bp):
GATCGATCCCTTATGTGAGGGGATCGATTAGTTTTTTAGGT
Found at i:20357266 original size:20 final size:20
Alignment explanation
Indices: 20357202--20357266 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
20357192 TTGAACAACT
*
20357202 GATCGATCCCTTTAAG-AGGG
1 GATCGATCCC-TTATGTAGGG
* *
20357222 GATCGATCCTTTACCT-TAGGT
1 GATCGATCCCTTA--TGTAGGG
20357243 GATCGATCCCTTATGTAGGG
1 GATCGATCCCTTATGTAGGG
20357263 GATC
1 GATC
20357267 AATCTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 4 0.11
20 17 0.47
21 15 0.42
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (20 bp):
GATCGATCCCTTATGTAGGG
Found at i:20361735 original size:17 final size:17
Alignment explanation
Indices: 20361715--20361750 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20361705 TTTTGCCTTC
* *
20361715 TTGAATTTATTTATTTG
1 TTGAATATATTAATTTG
20361732 TTGAATATATTAATTTG
1 TTGAATATATTAATTTG
20361749 TT
1 TT
20361751 ATTTAGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (17 bp):
TTGAATATATTAATTTG
Found at i:20361953 original size:43 final size:43
Alignment explanation
Indices: 20361892--20361979 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
20361882 TATAGAAGGT
* *
20361892 TGTTGTGAATAACATTATATTAGAATATATTTCATAAAGATAA
1 TGTTGTGAATAACATTATATTAGAATATATATCAAAAAGATAA
* *
20361935 TGTTGTGAATAATATTATATTAGAATGTATATCAAAAAGATAA
1 TGTTGTGAATAACATTATATTAGAATATATATCAAAAAGATAA
20361978 TG
1 TG
20361980 ATCTTAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.39
Consensus pattern (43 bp):
TGTTGTGAATAACATTATATTAGAATATATATCAAAAAGATAA
Found at i:20361989 original size:43 final size:43
Alignment explanation
Indices: 20361897--20361994 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
20361887 AAGGTTGTTG
* * * * *
20361897 TGAATAACATTATATTAGAATATATTTCATAAAGATAATGTTG
1 TGAATAATATTATATTAGAATATATATCAAAAAGATAATGATC
*
20361940 TGAATAATATTATATTAGAATGTATATCAAAAAGATAATGATC
1 TGAATAATATTATATTAGAATATATATCAAAAAGATAATGATC
*
20361983 TTAATAAT-TTAT
1 TGAATAATATTAT
20361995 GGTTAAGATT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 4 0.08
43 44 0.92
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (43 bp):
TGAATAATATTATATTAGAATATATATCAAAAAGATAATGATC
Found at i:20362707 original size:19 final size:19
Alignment explanation
Indices: 20362683--20362719 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20362673 GGAAATGATT
20362683 AATTATAACATTCTTTTTC
1 AATTATAACATTCTTTTTC
*
20362702 AATTATAACTTTCTTTTT
1 AATTATAACATTCTTTTT
20362720 ATAAAATAAC
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:0.30, C:0.14, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTATAACATTCTTTTTC
Found at i:20363275 original size:51 final size:51
Alignment explanation
Indices: 20363212--20363309 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
20363202 TCAACCGTAA
* * *
20363212 TTGAGAGCTTTTTGGGATTTAATTCCATAATCAATTCACATTAAAATGATG
1 TTGAGAGATTTTTGAGATTTAATTCCAGAATCAATTCACATTAAAATGATG
* **
20363263 TTGAGAGATTTTTTAGATTTAATTTTAGAATCAATTCACATTAAAAT
1 TTGAGAGATTTTTGAGATTTAATTCCAGAATCAATTCACATTAAAAT
20363310 TAAAATCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (51 bp):
TTGAGAGATTTTTGAGATTTAATTCCAGAATCAATTCACATTAAAATGATG
Done.