Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 115 of 120
Found at i:34679371 original size:18 final size:18
Alignment explanation
Indices: 34679336--34679376 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
34679326 TTTTCGATAG
34679336 TAAATTAAACAATAAAAT
1 TAAATTAAACAATAAAAT
*
34679354 TAAACTTAAAGAAT-AAAT
1 TAAA-TTAAACAATAAAAT
34679372 TAAAT
1 TAAAT
34679377 ATTAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 12 0.57
19 8 0.38
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAATTAAACAATAAAAT
Found at i:34679381 original size:19 final size:19
Alignment explanation
Indices: 34679337--34679382 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
34679327 TTTCGATAGT
34679337 AAATTAAACAATAAAATTA
1 AAATTAAACAATAAAATTA
* *
34679356 AACTTAAAGAAT-AAATTA
1 AAATTAAACAATAAAATTA
34679374 AATATTAAA
1 AA-ATTAAA
34679383 ATTAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AAATTAAACAATAAAATTA
Found at i:34691553 original size:14 final size:15
Alignment explanation
Indices: 34691518--34691557 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
34691508 TATTTATAAT
*
34691518 ATTTATG-AATT-CG
1 ATTTATGAAATTGAG
34691531 ATTTATGAAATTGAG
1 ATTTATGAAATTGAG
34691546 ATTT-TGAAATTG
1 ATTTATGAAATTG
34691558 TATTTTTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 7 0.29
14 12 0.50
15 5 0.21
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (15 bp):
ATTTATGAAATTGAG
Found at i:34693367 original size:6 final size:6
Alignment explanation
Indices: 34693351--34693445 Score: 87
Period size: 6 Copynumber: 17.0 Consensus size: 6
34693341 TTTTGTTTAT
* * * * *
34693351 TTTAAA ATTAAT TTTAAA TTT-TA TTTAAA TTTAAA TTT-AT TTTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
34693397 TTTAAA TTT--A TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA -TTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
34693440 TTTAAA
1 TTTAAA
34693446 AATGATATTA
Statistics
Matches: 71, Mismatches: 11, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
4 6 0.08
5 16 0.23
6 49 0.69
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:34693378 original size:17 final size:16
Alignment explanation
Indices: 34693358--34693445 Score: 96
Period size: 17 Copynumber: 5.7 Consensus size: 16
34693348 TATTTTAAAA
*
34693358 TTAATTTTAAATTTTAT
1 TTAAATTTAAA-TTTAT
34693375 TTAAATTTAAATTTATT
1 TTAAATTTAAATTTA-T
*
34693392 TTAAGTTTAAATTTAT
1 TTAAATTTAAATTTAT
34693408 TTAAATTT--A--T-T
1 TTAAATTTAAATTTAT
*
34693419 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAT
34693435 TTAAATTTAAA
1 TTAAATTTAAA
34693446 AATGATATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
11 9 0.15
12 1 0.02
13 1 0.02
14 1 0.02
15 1 0.02
16 23 0.38
17 25 0.41
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:34693409 original size:27 final size:27
Alignment explanation
Indices: 34693346--34693443 Score: 117
Period size: 27 Copynumber: 3.5 Consensus size: 27
34693336 TTGGATTTTG
* *
34693346 TTTATTTTAAAATTAATTTTAAATTT-TA
1 TTTA-TTT-AAATTTATTTTAAATTTAAA
*
34693374 TTTAAATTTAAATTTATTTTAAGTTTAAA
1 TTT--ATTTAAATTTATTTTAAATTTAAA
34693403 TTTATTTAAATTTATTTTAAATTTAAA
1 TTTATTTAAATTTATTTTAAATTTAAA
*
34693430 TTTAATTAAATTTA
1 TTTATTTAAATTTA
34693444 AAAATGATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
27 36 0.58
28 18 0.29
29 7 0.11
30 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (27 bp):
TTTATTTAAATTTATTTTAAATTTAAA
Found at i:34693427 original size:11 final size:11
Alignment explanation
Indices: 34693346--34693427 Score: 71
Period size: 11 Copynumber: 7.4 Consensus size: 11
34693336 TTGGATTTTG
34693346 TTTATTTTAAAA
1 TTTATTTT-AAA
*
34693358 TTAATTTTAAA
1 TTTATTTTAAA
34693369 TTT-TATTTAAA
1 TTTAT-TTTAAA
* *
34693380 TTTAAATTT-AT
1 TTT-ATTTTAAA
*
34693391 TTTAAGTTTAAA
1 TTT-ATTTTAAA
34693403 TTTA-TTTAAA
1 TTTATTTTAAA
34693413 TTTATTTTAAA
1 TTTATTTTAAA
34693424 TTTA
1 TTTA
34693428 AATTTAATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
10 11 0.19
11 34 0.58
12 14 0.24
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (11 bp):
TTTATTTTAAA
Found at i:34694498 original size:15 final size:15
Alignment explanation
Indices: 34694464--34694498 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
34694454 TTTTCGAAAT
34694464 GTTT-CCAGATCTGG
1 GTTTCCCAGATCTGG
34694478 GTTTTCCCAGATCTGG
1 G-TTTCCCAGATCTGG
34694494 GTTTC
1 GTTTC
34694499 GAAAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 7 0.37
16 11 0.58
ACGTcount: A:0.11, C:0.23, G:0.26, T:0.40
Consensus pattern (15 bp):
GTTTCCCAGATCTGG
Found at i:34695416 original size:30 final size:30
Alignment explanation
Indices: 34695360--34695723 Score: 453
Period size: 30 Copynumber: 12.1 Consensus size: 30
34695350 TTGTAAGTCC
* * *
34695360 CTTTGTCCAGAAATTATATTTAGACCCCGAAA
1 CTTT-TCCA-AAATTACATTTTGACCCCAAAA
*
34695392 CTTTTCCAAAATTACATTTTGACCCCAACA
1 CTTTTCCAAAATTACATTTTGACCCCAAAA
***
34695422 CTTTTCCAAAATTACATTTTGACCTTGAAA
1 CTTTTCCAAAATTACATTTTGACCCCAAAA
* *
34695452 CTTTTCCAAAATTACATATTAACCCCAAAA
1 CTTTTCCAAAATTACATTTTGACCCCAAAA
*
34695482 CTTTTCCATAATTACATTTTGACCCCAAAA
1 CTTTTCCAAAATTACATTTTGACCCCAAAA
* * * *
34695512 TTTTTCCAAAATTATATTTTGACCACGAAA
1 CTTTTCCAAAATTACATTTTGACCCCAAAA
34695542 CTTTTCCAAAATTACATTTTGACCCCAAAA
1 CTTTTCCAAAATTACATTTTGACCCCAAAA
* * *
34695572 CTTTTCCAAAATTACGTATTGTCCCCAAAA
1 CTTTTCCAAAATTACATTTTGACCCCAAAA
* *
34695602 CTTTTCCATAATTACATTTTGACCCCGAAA
1 CTTTTCCAAAATTACATTTTGACCCCAAAA
*
34695632 CTTTTCCAAAATTGCATTTTGACCCCAAAA
1 CTTTTCCAAAATTACATTTTGACCCCAAAA
* * * *
34695662 ATTTTCTAAAATTATATTTTGACCCCGAAA
1 CTTTTCCAAAATTACATTTTGACCCCAAAA
* *
34695692 C-TTTCAAAAATTACCATTTT-ACCCCCAAA
1 CTTTTCCAAAATTA-CATTTTGACCCCAAAA
34695721 CTT
1 CTT
34695724 CCCTAAATCC
Statistics
Matches: 285, Mismatches: 45, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
29 20 0.07
30 257 0.90
31 4 0.01
32 4 0.01
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (30 bp):
CTTTTCCAAAATTACATTTTGACCCCAAAA
Found at i:34695759 original size:59 final size:58
Alignment explanation
Indices: 34695696--34695892 Score: 198
Period size: 59 Copynumber: 3.4 Consensus size: 58
34695686 CCGAAACTTT
* * *
34695696 CAAAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCTTTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
* * * * * * * ** * **
34695755 CAAAACTTACCGTTTTGCCTCCGAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTGC
1 CAAAAATTACCATTTTACCCCCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
* * *
34695814 CAAAATTTACCATTTTATTCCCCAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA-
1 CAAAAATTACCATTTTA-CCCCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
34695872 CAAAAATTACCATTTTACCCC
1 CAAAAATTACCATTTTACCCC
34695893 TAAAAACCCA
Statistics
Matches: 105, Mismatches: 32, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
57 3 0.03
58 16 0.15
59 75 0.71
60 11 0.10
ACGTcount: A:0.28, C:0.30, G:0.05, T:0.37
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
Found at i:34699102 original size:9 final size:9
Alignment explanation
Indices: 34699088--34699112 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
34699078 ATATTTATAG
34699088 ATATAAATA
1 ATATAAATA
34699097 ATATAAATA
1 ATATAAATA
34699106 ATATAAA
1 ATATAAA
34699113 ACTTTACTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATATAAATA
Found at i:34699777 original size:16 final size:16
Alignment explanation
Indices: 34699756--34699786 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34699746 ATAATATTTT
*
34699756 TTTGTTATATTAAAAG
1 TTTGTTATAATAAAAG
34699772 TTTGTTATAATAAAA
1 TTTGTTATAATAAAA
34699787 AGCTTCAAAG
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:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTGTTATAATAAAAG
Found at i:34700859 original size:19 final size:17
Alignment explanation
Indices: 34700835--34700870 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
34700825 ATACATTAAA
34700835 AAATATATATATATATACT
1 AAATATATA-ATAT-TACT
34700854 AAATATATAATATTACT
1 AAATATATAATATTACT
34700871 TTAATGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 4 0.24
19 9 0.53
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATATAATATTACT
Found at i:34701560 original size:13 final size:13
Alignment explanation
Indices: 34701542--34701576 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
34701532 TTTGAGCACT
*
34701542 TGTGTGTGCTAGG
1 TGTGTGTGCAAGG
34701555 TGTGTGTGCAAGG
1 TGTGTGTGCAAGG
34701568 TGTGTGTGC
1 TGTGTGTGC
34701577 GTTGTCAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.09, C:0.09, G:0.46, T:0.37
Consensus pattern (13 bp):
TGTGTGTGCAAGG
Found at i:34702209 original size:17 final size:17
Alignment explanation
Indices: 34702183--34702215 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
34702173 TATAATACCT
*
34702183 TATATTTATATTATATA
1 TATATATATATTATATA
34702200 TATATATATATTATAT
1 TATATATATATTATAT
34702216 TGTGTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATATATATTATATA
Found at i:34705318 original size:24 final size:24
Alignment explanation
Indices: 34705281--34705336 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
34705271 GATAAAAGAT
34705281 AAATATATTAATTTGAAATTTTT-TA
1 AAATA-ATTAATTT-AAATTTTTATA
* *
34705306 AAATAATTTATTTTAATTTTTAATA
1 AAATAATTAATTTAAATTTTT-ATA
34705331 AAATAA
1 AAATAA
34705337 GATCAGCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.26
24 7 0.26
25 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
AAATAATTAATTTAAATTTTTATA
Found at i:34709396 original size:20 final size:22
Alignment explanation
Indices: 34709357--34709397 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
34709347 TTTTAATAAA
*
34709357 AAATATAAAATTATTAAATATT
1 AAATATAAAATTAATAAATATT
34709379 AAAT-TAAAA-TAATAAATAT
1 AAATATAAAATTAATAAATAT
34709398 ATGTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 5 0.28
22 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATATAAAATTAATAAATATT
Found at i:34711636 original size:14 final size:14
Alignment explanation
Indices: 34711617--34711653 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
34711607 TGCTACAATT
34711617 TTACTATTTTGTTA
1 TTACTATTTTGTTA
*
34711631 TTACTATTTTGTTG
1 TTACTATTTTGTTA
*
34711645 TTATTATTT
1 TTACTATTT
34711654 AGATACGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.08, T:0.68
Consensus pattern (14 bp):
TTACTATTTTGTTA
Found at i:34711858 original size:12 final size:12
Alignment explanation
Indices: 34711841--34711866 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34711831 TTAATTTTTT
34711841 ATATAAAAAATA
1 ATATAAAAAATA
34711853 ATATAAAAAATA
1 ATATAAAAAATA
34711865 AT
1 AT
34711867 TTGGGCGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
ATATAAAAAATA
Found at i:34712701 original size:13 final size:13
Alignment explanation
Indices: 34712660--34712702 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
34712650 TAATAATTAT
*
34712660 TAAAAATTTAGAA
1 TAAAAATTTAAAA
34712673 TAAAATATTATAAAA
1 TAAAA-ATT-TAAAA
*
34712688 TAAAAAATTAAAA
1 TAAAAATTTAAAA
34712701 TA
1 TA
34712703 TCCAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 12 0.46
14 5 0.19
15 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (13 bp):
TAAAAATTTAAAA
Found at i:34721741 original size:10 final size:9
Alignment explanation
Indices: 34721726--34721811 Score: 50
Period size: 10 Copynumber: 9.2 Consensus size: 9
34721716 TTTTACGAAA
34721726 TTTATATTT
1 TTTATATTT
34721735 CTTTATATTT
1 -TTTATATTT
34721745 TTTATAATTT
1 TTTAT-ATTT
* *
34721755 TCTTACGACTT
1 T-TTA-TATTT
* **
34721766 TATA-AAAT
1 TTTATATTT
34721774 TTTATATTT
1 TTTATATTT
*
34721783 TTATAGATTT
1 TT-TATATTT
*
34721793 TATATATTT
1 TTTATATTT
34721802 TTT-TATTT
1 TTTATATTT
34721810 TT
1 TT
34721812 AATAAATTTG
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
8 12 0.20
9 17 0.29
10 23 0.39
11 7 0.12
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTATATTT
Found at i:34721746 original size:38 final size:37
Alignment explanation
Indices: 34721703--34721793 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 37
34721693 TGGTATGATA
* **
34721703 ATTTTTATAATTTTTTTACGAAATTTAT-ATTTCTTTAT
1 ATTTTTATAATTTTCTTACG-AATTTATAAAAT-TTTAT
*
34721741 ATTTTTTATAATTTTCTTACGACTTTATAAAATTTTAT
1 A-TTTTTATAATTTTCTTACGAATTTATAAAATTTTAT
34721779 ATTTTTATAGATTTT
1 ATTTTTATA-ATTTT
34721794 ATATATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
37 8 0.17
38 18 0.39
39 20 0.43
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (37 bp):
ATTTTTATAATTTTCTTACGAATTTATAAAATTTTAT
Found at i:34721803 original size:27 final size:28
Alignment explanation
Indices: 34721735--34721812 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
34721725 ATTTATATTT
34721735 CTTTATAT-TTTTTATAATTTTCT-TACGA
1 CTTTATATATTTTTAT-ATTTT-TATACGA
* *
34721763 CTTTATAAAATTTTATATTTTTATA-GA
1 CTTTATATATTTTTATATTTTTATACGA
* *
34721790 TTTTATATATTTTTTTATTTTTA
1 CTTTATATATTTTTATATTTTTA
34721813 ATAAATTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
27 22 0.52
28 14 0.33
29 6 0.14
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (28 bp):
CTTTATATATTTTTATATTTTTATACGA
Found at i:34733434 original size:17 final size:17
Alignment explanation
Indices: 34733395--34733431 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
34733385 TGTCAAGAAG
34733395 AAAAC-AGAAAGAAACA
1 AAAACAAGAAAGAAACA
34733411 AAAACAAGAAAGAAAGCA
1 AAAACAAGAAAGAAA-CA
34733429 AAA
1 AAA
34733432 CAAATATAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 9 0.47
18 5 0.26
ACGTcount: A:0.76, C:0.11, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAACAAGAAAGAAACA
Found at i:34734589 original size:44 final size:45
Alignment explanation
Indices: 34734538--34734627 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
34734528 CATTGCATGT
*
34734538 CGACACCCCCTATTTC-AAAAAAATTTATATTTTTGGGTGTCGGC
1 CGACACCCCCTATTTCAAAAAAAAATTATATTTTTGGGTGTCGGC
*
34734582 CGACACCCCCTATTTCAAAAAAAAATTATATTTTTGGGTGTTGGC
1 CGACACCCCCTATTTCAAAAAAAAATTATATTTTTGGGTGTCGGC
34734627 C
1 C
34734628 ATTGCATGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 16 0.37
45 27 0.63
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (45 bp):
CGACACCCCCTATTTCAAAAAAAAATTATATTTTTGGGTGTCGGC
Found at i:34772912 original size:14 final size:14
Alignment explanation
Indices: 34772893--34772924 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
34772883 TAGATTTGTG
34772893 AATTCGATCGATTA
1 AATTCGATCGATTA
*
34772907 AATTCGATCGATTT
1 AATTCGATCGATTA
34772921 AATT
1 AATT
34772925 AATTGAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (14 bp):
AATTCGATCGATTA
Found at i:34786468 original size:23 final size:23
Alignment explanation
Indices: 34786441--34786502 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
34786431 TAAAATGATG
34786441 AAATTATAATTTAATTATAATAA
1 AAATTATAATTTAATTATAATAA
* * * *
34786464 AAATTGTATTTTTATTATTATAA
1 AAATTATAATTTAATTATAATAA
34786487 AAATTATAATTTAATT
1 AAATTATAATTTAATT
34786503 TCGACCCCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AAATTATAATTTAATTATAATAA
Found at i:34789223 original size:20 final size:20
Alignment explanation
Indices: 34789187--34789224 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34789177 CCATATAAGG
*
34789187 AAAAATGTTTTTGAAAAGCC
1 AAAAATGTTTTTCAAAAGCC
34789207 AAAAAT-TTCTTTCAAAAG
1 AAAAATGTT-TTTCAAAAG
34789225 TTGTTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (20 bp):
AAAAATGTTTTTCAAAAGCC
Found at i:34803974 original size:26 final size:29
Alignment explanation
Indices: 34803945--34803999 Score: 89
Period size: 26 Copynumber: 2.0 Consensus size: 29
34803935 CTCGAAAGGT
34803945 AAGCTTTTTCATTG-CGGTT-TCT-ATGA
1 AAGCTTTTTCATTGTCGGTTATCTGATGA
34803971 AAGCTTTTTCATTGTCGGTTATCTGATGA
1 AAGCTTTTTCATTGTCGGTTATCTGATGA
34804000 TCTGGTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 14 0.54
27 5 0.19
28 3 0.12
29 4 0.15
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (29 bp):
AAGCTTTTTCATTGTCGGTTATCTGATGA
Found at i:34805273 original size:22 final size:24
Alignment explanation
Indices: 34805248--34805303 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
34805238 CTTTTACAGC
*
34805248 ATTTTGGTAA-TCTTTTTTA-ATA
1 ATTTTGATAACTCTTTTTTATATA
*
34805270 ATTTTGATAACTTTTTTTTATATA
1 ATTTTGATAACTCTTTTTTATATA
*
34805294 ATTTCGATAA
1 ATTTTGATAA
34805304 TAATTAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 9 0.31
23 8 0.28
24 12 0.41
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (24 bp):
ATTTTGATAACTCTTTTTTATATA
Found at i:34805512 original size:31 final size:32
Alignment explanation
Indices: 34805472--34805535 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 32
34805462 GTATATTAGC
*
34805472 AGAGAAATTAAA-TTCTAATTTTTATATTT-TTA
1 AGAGAAATTAAAGTAC-AA-TTTTATATTTATTA
34805504 AGAG-AATTAAAGTACAATTTTATATTTATTA
1 AGAGAAATTAAAGTACAATTTTATATTTATTA
34805535 A
1 A
34805536 TTTAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 10 0.34
31 13 0.45
32 6 0.21
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (32 bp):
AGAGAAATTAAAGTACAATTTTATATTTATTA
Found at i:34806280 original size:27 final size:25
Alignment explanation
Indices: 34806250--34806312 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
34806240 GTATGAGAGG
34806250 ATTTTCTTATTTAATATTAATATAATT
1 ATTTT-TTATTTAATATTAA-ATAATT
*
34806277 A-TTTTTATTTAATATTAAATTATT
1 ATTTTTTATTTAATATTAAATAATT
34806301 ATTATTATTATT
1 ATT-TT-TTATT
34806313 ATAGTTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 6 0.19
25 15 0.47
26 5 0.16
27 6 0.19
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTTTTATTTAATATTAAATAATT
Found at i:34806286 original size:25 final size:24
Alignment explanation
Indices: 34806256--34806309 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
34806246 GAGGATTTTC
*
34806256 TTATTTAATATTAATATAATTATTT
1 TTATTTAATATTAA-ATAATTATTA
*
34806281 TTATTTAATATTAAATTATTATTA
1 TTATTTAATATTAAATAATTATTA
34806305 TTATT
1 TTATT
34806310 ATTATAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATTTAATATTAAATAATTATTA
Found at i:34806297 original size:21 final size:19
Alignment explanation
Indices: 34806266--34806306 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
34806256 TTATTTAATA
*
34806266 TTAATATAATTATTTTTAT
1 TTAATATAATTATTATTAT
34806285 TTAATATTAAATTATTATTAT
1 TTAATA-T-AATTATTATTAT
34806306 T
1 T
34806307 ATTATTATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAATATAATTATTATTAT
Found at i:34823135 original size:9 final size:9
Alignment explanation
Indices: 34823118--34823151 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
34823108 ATAAAATAAA
*
34823118 CTAAACTTC
1 CTAACCTTC
34823127 CTAACCTTC
1 CTAACCTTC
*
34823136 CTAAGCTTC
1 CTAACCTTC
34823145 CTAACCT
1 CTAACCT
34823152 CCAAACTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.26, C:0.38, G:0.03, T:0.32
Consensus pattern (9 bp):
CTAACCTTC
Found at i:34826251 original size:14 final size:15
Alignment explanation
Indices: 34826216--34826264 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
34826206 ACTTTAAATT
34826216 TTAAAA-AATATAAA
1 TTAAAATAATATAAA
34826230 TCTAAAAATAAT-TAAA
1 T-T-AAAATAATATAAA
*
34826246 TTAAAAT-ATATGAA
1 TTAAAATAATATAAA
34826260 TTAAA
1 TTAAA
34826265 TTCATAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
13 2 0.07
14 14 0.47
15 2 0.07
16 9 0.30
17 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
TTAAAATAATATAAA
Found at i:34827489 original size:2 final size:2
Alignment explanation
Indices: 34827482--34827524 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
34827472 AGAGGATGGA
34827482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34827524 A
1 A
34827525 GAAAGAGATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34831215 original size:26 final size:26
Alignment explanation
Indices: 34831179--34831231 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
34831169 TTGTAGCTCA
34831179 ACGGTTTCTTTCTTGCACAGTTGTGT
1 ACGGTTTCTTTCTTGCACAGTTGTGT
34831205 ACGGTTTCTTTCTTGCACAGTTGTGT
1 ACGGTTTCTTTCTTGCACAGTTGTGT
34831231 A
1 A
34831232 TTATATTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (26 bp):
ACGGTTTCTTTCTTGCACAGTTGTGT
Found at i:34837108 original size:3 final size:3
Alignment explanation
Indices: 34837100--34837126 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
34837090 TATACTTAAA
34837100 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
34837127 CAAAACGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:34837724 original size:15 final size:15
Alignment explanation
Indices: 34837704--34837735 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
34837694 TATTCATGTA
34837704 ATATGCTGCAAATGG
1 ATATGCTGCAAATGG
*
34837719 ATATGCTGCACATGG
1 ATATGCTGCAAATGG
34837734 AT
1 AT
34837736 CCCATGGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (15 bp):
ATATGCTGCAAATGG
Found at i:34839608 original size:220 final size:221
Alignment explanation
Indices: 34839369--34839808 Score: 828
Period size: 220 Copynumber: 2.0 Consensus size: 221
34839359 ATATTAAAAA
34839369 AATGAAAAAAAAAATGTTTAGCTTATCTTTACTCCATCGATTTCAGAATTTGAGCCTATACTTGT
1 AATGAAAAAAAAAATGTTTAGCTTATCTTTACTCCATCGATTTCAGAATTTGAGCCTATACTTGT
* *
34839434 CAATCCAATGATATGGACATCAAGAAATTAAATATCAAGAACCTTTAAAGCATCAATCCACAATC
66 CAATCCAATGACATGGACATCAAGAAATTAAATATCAAGAACCTTTAAAGCATCAAGCCACAATC
34839499 AAAGGCCAGTTCTTTAAAAACAAAATCATCCCCAAACAATTAACAAGAAGTTCACTTTCTTCTAG
131 AAAGGCCAGTTCTTTAAAAACAAAATCATCCCCAAACAATTAACAAGAAGTTCACTTTCTTCTAG
34839564 ATATATGCATTATCCCCATTAGCAAG
196 ATATATGCATTATCCCCATTAGCAAG
*
34839590 AATG-AAAAAAAAATGTTTAGCTTATCTTTACTCCATCGATTTCGGAATTTGAGCCTATACTTGT
1 AATGAAAAAAAAAATGTTTAGCTTATCTTTACTCCATCGATTTCAGAATTTGAGCCTATACTTGT
34839654 CAATCCAATGACATGGACATCAAGAAATTAAATATCAAGAACCTTTAAAGCATCAAGCCACAATC
66 CAATCCAATGACATGGACATCAAGAAATTAAATATCAAGAACCTTTAAAGCATCAAGCCACAATC
* *
34839719 AAAGGCCAGTTCTTTAAAAACAAAATCATCTCCAAACAATTAACAAGAAGTTCACTTTCTTTTAG
131 AAAGGCCAGTTCTTTAAAAACAAAATCATCCCCAAACAATTAACAAGAAGTTCACTTTCTTCTAG
34839784 ATATATGCATTATCCCCATTAGCAA
196 ATATATGCATTATCCCCATTAGCAA
34839809 AAGATAAAAA
Statistics
Matches: 214, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
220 210 0.98
221 4 0.02
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (221 bp):
AATGAAAAAAAAAATGTTTAGCTTATCTTTACTCCATCGATTTCAGAATTTGAGCCTATACTTGT
CAATCCAATGACATGGACATCAAGAAATTAAATATCAAGAACCTTTAAAGCATCAAGCCACAATC
AAAGGCCAGTTCTTTAAAAACAAAATCATCCCCAAACAATTAACAAGAAGTTCACTTTCTTCTAG
ATATATGCATTATCCCCATTAGCAAG
Found at i:34844533 original size:6 final size:6
Alignment explanation
Indices: 34844522--34844549 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
34844512 CGATTCACTC
34844522 CTTCCT CTTCCT CTTCCT CTTCCT CTTC
1 CTTCCT CTTCCT CTTCCT CTTCCT CTTC
34844550 ATCCTCTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
CTTCCT
Found at i:34844597 original size:27 final size:27
Alignment explanation
Indices: 34844522--34844604 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
34844512 CGATTCACTC
* * * *
34844522 CTTCCTCTTCCTCTTCCTCTTCCTCTT
1 CTTCCTCCTCCTCCTCTTCTTCTTCTT
* * *
34844549 CATCCTCTAACTCGTCCACTTCTTCTTCTT
1 CTTCCTC---CTCCTCCTCTTCTTCTTCTT
*
34844579 CTTCCTCCTCCTCCTCTTCTCCTTCT
1 CTTCCTCCTCCTCCTCTTCTTCTTCT
34844605 GAATTATCAT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
27 22 0.52
30 20 0.48
ACGTcount: A:0.05, C:0.47, G:0.01, T:0.47
Consensus pattern (27 bp):
CTTCCTCCTCCTCCTCTTCTTCTTCTT
Found at i:34845495 original size:6 final size:6
Alignment explanation
Indices: 34845484--34845514 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
34845474 CGTCGTTTCG
34845484 CTGGCC CTGGCC CTGGCC CTGGCC C-GGCC CT
1 CTGGCC CTGGCC CTGGCC CTGGCC CTGGCC CT
34845515 CCTTTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.00, C:0.52, G:0.32, T:0.16
Consensus pattern (6 bp):
CTGGCC
Found at i:34847332 original size:15 final size:15
Alignment explanation
Indices: 34847312--34847363 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
34847302 ACTACAAAAC
34847312 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
34847327 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
34847346 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
34847361 ATT
1 ATT
34847364 AATATTGGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:34852426 original size:23 final size:23
Alignment explanation
Indices: 34852383--34852427 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34852373 AAAAAAATTC
**
34852383 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
34852406 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
34852428 ATTCGAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:34854975 original size:21 final size:22
Alignment explanation
Indices: 34854929--34854973 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
34854919 GGTATCCAGC
34854929 GAAAA-ATAAAATAAAACAAAA
1 GAAAAGATAAAATAAAACAAAA
34854950 G-AAAGATAAAA-AAAA-AAAA
1 GAAAAGATAAAATAAAACAAAA
34854969 GAAAA
1 GAAAA
34854974 AGGAGAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.82, C:0.02, G:0.09, T:0.07
Consensus pattern (22 bp):
GAAAAGATAAAATAAAACAAAA
Found at i:34855502 original size:16 final size:18
Alignment explanation
Indices: 34855469--34855505 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
34855459 TATTGTGATG
*
34855469 TATATTATTTTATTTTTA
1 TATATTATTTTATGTTTA
34855487 TATATTA-TTTA-GTTTA
1 TATATTATTTTATGTTTA
34855503 TAT
1 TAT
34855506 CATATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 4 0.22
18 7 0.39
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TATATTATTTTATGTTTA
Found at i:34859985 original size:24 final size:24
Alignment explanation
Indices: 34859957--34860015 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
34859947 TAGAGTAATA
*
34859957 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
* * *
34859981 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAT
*
34860005 AGAATTTAACT
1 AGAGTTTAACT
34860016 GAAAGATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAT
Found at i:34860018 original size:24 final size:24
Alignment explanation
Indices: 34859969--34860019 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
34859959 AGTTTGACTC
* * *
34859969 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAATTTAACTG
34859993 AAACAAATAAACAGAATTTAACTG
1 AAACAAATAAACAGAATTTAACTG
34860017 AAA
1 AAA
34860020 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAACTG
Found at i:34861930 original size:3 final size:3
Alignment explanation
Indices: 34861922--34861956 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
34861912 ATATTTATCT
34861922 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
34861957 TTTAAAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:34862365 original size:21 final size:21
Alignment explanation
Indices: 34862322--34862365 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
34862312 AAAAAGTTAA
*
34862322 AAAATATAAAATAATAATTTT
1 AAAATATAAAATAATAATATT
*
34862343 AAAATCTAAAATAATTAA-ATT
1 AAAATATAAAATAA-TAATATT
34862364 AA
1 AA
34862366 CAATTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATATAAAATAATAATATT
Found at i:34863138 original size:15 final size:14
Alignment explanation
Indices: 34863107--34863155 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 14
34863097 TTTTGTTATT
*
34863107 AAATTATTA-TAAA
1 AAATTAATATTAAA
*
34863120 AAATTAATAGTTTAA
1 AAATTAATA-TTAAA
*
34863135 AAATTTATATTAAA
1 AAATTAATATTAAA
34863149 AAATTAA
1 AAATTAA
34863156 GAAAAACTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 8 0.28
14 10 0.34
15 11 0.38
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
AAATTAATATTAAA
Found at i:34864623 original size:15 final size:16
Alignment explanation
Indices: 34864603--34864632 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34864593 GCCGTTGTTC
34864603 GAAGAGAAA-AAGAGA
1 GAAGAGAAACAAGAGA
34864618 GAAGAGAAACAAGAG
1 GAAGAGAAACAAGAG
34864633 CTGAGATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (16 bp):
GAAGAGAAACAAGAGA
Found at i:34866502 original size:19 final size:18
Alignment explanation
Indices: 34866458--34866506 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
34866448 CCTTGAAAAT
*
34866458 TAAAAATATAAAATTTTA
1 TAAAATTATAAAATTTTA
* *
34866476 -AAAGTTATATAATTTTTA
1 TAAAATTATA-AAATTTTA
34866494 TAAAATTATAAAA
1 TAAAATTATAAAA
34866507 AAGTAACATA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
17 7 0.29
18 9 0.38
19 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TAAAATTATAAAATTTTA
Found at i:34866578 original size:25 final size:25
Alignment explanation
Indices: 34866550--34866602 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
34866540 TCATTTTTAT
34866550 TTAT-TTTTCATTTTCTT-TATAAGCA
1 TTATATTTTCA-TTTCTTATA-AAGCA
*
34866575 TTATATTTTTATTTCTTATAAAGCA
1 TTATATTTTCATTTCTTATAAAGCA
34866600 TTA
1 TTA
34866603 AAAGAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.58
Consensus pattern (25 bp):
TTATATTTTCATTTCTTATAAAGCA
Found at i:34870569 original size:15 final size:16
Alignment explanation
Indices: 34870543--34870572 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34870533 CTTGGTAGGG
34870543 AAGAAAAGTGAGAGGA
1 AAGAAAAGTGAGAGGA
34870559 AAGAAAA-TGAGAGG
1 AAGAAAAGTGAGAGG
34870573 GTGATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.07
Consensus pattern (16 bp):
AAGAAAAGTGAGAGGA
Found at i:34883302 original size:4 final size:4
Alignment explanation
Indices: 34883286--34883320 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
34883276 GACATCATTA
* *
34883286 TATG TATG CATG TATG TATT TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
34883321 TCCCTGACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.03, G:0.20, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:34890438 original size:18 final size:19
Alignment explanation
Indices: 34890417--34890466 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
34890407 TAAAAATTTA
34890417 ATTATTAAATATAAT-TAG
1 ATTATTAAATATAATATAG
* *
34890435 ATTATTTAATA-AATATAT
1 ATTATTAAATATAATATAG
34890453 ATT-TTAAATTATAA
1 ATTATTAAA-TATAA
34890467 AAAATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 7 0.27
18 17 0.65
19 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATTATTAAATATAATATAG
Found at i:34891290 original size:23 final size:23
Alignment explanation
Indices: 34891242--34891291 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
34891232 CAATGATATT
34891242 TTTAAAAATCTAATGATAATAAA
1 TTTAAAAATCTAATGATAATAAA
*
34891265 TTTAAATAT-TAA-GATAAATAATA
1 TTTAAAAATCTAATGAT-AATAA-A
34891288 TTTA
1 TTTA
34891292 TTTTTGTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 3 0.12
22 8 0.33
23 13 0.54
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
TTTAAAAATCTAATGATAATAAA
Found at i:34894668 original size:93 final size:93
Alignment explanation
Indices: 34894481--34894672 Score: 255
Period size: 93 Copynumber: 2.1 Consensus size: 93
34894471 CATGAAACTG
* ** * *
34894481 AAAGAAAATTTCTTTAGTGGTTCGGCCGAGAAATATGCTGGTGTGTTATATGGTCTTGGTGTTGA
1 AAAGAAAAGTTCTTTAGTGGTTCGAACGAGAAATATGCTGGTGTGTTATATGGCCTTGGTGTTCA
34894546 GAATGGACAGAATACTCTCTAATAAATC
66 GAATGGACAGAATACTCTCTAATAAATC
* *
34894574 AAAGAAAAGTTCTTTAGTTGG-TCGAATGAGAAATATGCTGGTTTGTTATATGGCCTTGGTTGTT
1 AAAGAAAAGTTCTTTAG-TGGTTCGAACGAGAAATATGCTGGTGTGTTATATGGCCTTGG-TGTT
* *
34894638 CAGAATTGACAGAATACT-TCTTAA-ATATC
64 CAGAATGGACAGAATACTCTC-TAATAAATC
34894667 AAAGAA
1 AAAGAA
34894673 TTATGAAATA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
93 61 0.70
94 26 0.30
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (93 bp):
AAAGAAAAGTTCTTTAGTGGTTCGAACGAGAAATATGCTGGTGTGTTATATGGCCTTGGTGTTCA
GAATGGACAGAATACTCTCTAATAAATC
Found at i:34923498 original size:4 final size:4
Alignment explanation
Indices: 34923489--34923514 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
34923479 TTGGTACCCA
34923489 AGAT AGAT AGAT AGAT AGAT AGAT AG
1 AGAT AGAT AGAT AGAT AGAT AGAT AG
34923515 GAGAGATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (4 bp):
AGAT
Found at i:34930545 original size:14 final size:14
Alignment explanation
Indices: 34930523--34930566 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
34930513 AGAAATCAAT
*
34930523 AATATAATATATAA
1 AATAAAATATATAA
* *
34930537 AATAAAATAAATAG
1 AATAAAATATATAA
34930551 AATAAAATATTATAA
1 AATAAAATA-TATAA
34930566 A
1 A
34930567 CTAGAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
AATAAAATATATAA
Found at i:34930579 original size:19 final size:19
Alignment explanation
Indices: 34930533--34930579 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
34930523 AATATAATAT
**
34930533 ATAAAATAAAATAAATAGA
1 ATAAAATATTATAAATAGA
34930552 ATAAAATATTATAAACTAGA
1 ATAAAATATTATAAA-TAGA
34930572 A-AAAATAT
1 ATAAAATAT
34930580 CTATTCGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
ATAAAATATTATAAATAGA
Found at i:34937341 original size:71 final size:71
Alignment explanation
Indices: 34937225--34937366 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
34937215 GCAAACAAAA
34937225 CCAAATTTGGCTTCAGATTTGTGCTTGCTCAATCATATACTAATTATGGAAATCAGAGCCCTAAC
1 CCAAATTTGGCTTCAGATTTGTGCTTGCTCAATCATATACTAATTATGGAAATCAGAGCCCTAAC
34937290 TATAAC
66 TATAAC
34937296 CCAAATTTGGCTTCAGATTTGTGCTTGCTCAATCATATACTAATTATGGAAATCAGAGCCCTAAC
1 CCAAATTTGGCTTCAGATTTGTGCTTGCTCAATCATATACTAATTATGGAAATCAGAGCCCTAAC
34937361 TATAAC
66 TATAAC
34937367 TCTATGCCCT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (71 bp):
CCAAATTTGGCTTCAGATTTGTGCTTGCTCAATCATATACTAATTATGGAAATCAGAGCCCTAAC
TATAAC
Found at i:34953284 original size:22 final size:21
Alignment explanation
Indices: 34953256--34953342 Score: 76
Period size: 22 Copynumber: 4.2 Consensus size: 21
34953246 TATATTGTTA
34953256 TTTTGGTGTTGTTTTTTTACTG
1 TTTTGGTGTTG-TTTTTTACTG
* *
34953278 TTTTGGTTATTGTTTTTTGCTG
1 TTTTGG-TGTTGTTTTTTACTG
* *
34953300 TTTT--TG-TGTTTTTTGCTTT
1 TTTTGGTGTTGTTTTTTAC-TG
34953319 TTTTGGTG-T-TTTTTTACTG
1 TTTTGGTGTTGTTTTTTACTG
34953338 TTTTG
1 TTTTG
34953343 ATTGTTATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
18 10 0.18
19 12 0.22
20 7 0.13
21 3 0.05
22 19 0.35
23 4 0.07
ACGTcount: A:0.03, C:0.05, G:0.21, T:0.71
Consensus pattern (21 bp):
TTTTGGTGTTGTTTTTTACTG
Found at i:34953311 original size:18 final size:19
Alignment explanation
Indices: 34953288--34953332 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
34953278 TTTTGGTTAT
34953288 TGTTTTTTGCTGTTTTT-G
1 TGTTTTTTGCTGTTTTTGG
*
34953306 TGTTTTTTGCTTTTTTTGG
1 TGTTTTTTGCTGTTTTTGG
34953325 TGTTTTTT
1 TGTTTTTT
34953333 TACTGTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.00, C:0.04, G:0.20, T:0.76
Consensus pattern (19 bp):
TGTTTTTTGCTGTTTTTGG
Found at i:34953322 original size:19 final size:18
Alignment explanation
Indices: 34953288--34953342 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
34953278 TTTTGGTTAT
*
34953288 TGTTTTTTGCTGTTTTTG
1 TGTTTTTTGCTGTTTTGG
*
34953306 TGTTTTTTGCTTTTTTTGG
1 TGTTTTTTGC-TGTTTTGG
*
34953325 TGTTTTTTTACTGTTTTG
1 TG-TTTTTTGCTGTTTTG
34953343 ATTGTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 10 0.32
19 14 0.45
20 7 0.23
ACGTcount: A:0.02, C:0.05, G:0.20, T:0.73
Consensus pattern (18 bp):
TGTTTTTTGCTGTTTTGG
Found at i:34953362 original size:23 final size:21
Alignment explanation
Indices: 34953336--34953385 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
34953326 GTTTTTTTAC
*
34953336 TGTTTTGATTGTTATTTTCGTGT
1 TGTTTTGACTGTTATTTT--TGT
*
34953359 TGTTTTTACTGTTATTTTTGT
1 TGTTTTGACTGTTATTTTTGT
34953380 TGTTTT
1 TGTTTT
34953386 TAATGTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.36
23 16 0.64
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (21 bp):
TGTTTTGACTGTTATTTTTGT
Found at i:34953486 original size:78 final size:77
Alignment explanation
Indices: 34953335--34953479 Score: 172
Period size: 78 Copynumber: 1.9 Consensus size: 77
34953325 TGTTTTTTTA
** *
34953335 CTGTTTTGATTGTTATTTTCGTGTTGTTTTTACTGTTATTTTTGTTGTTTTTAATGTTGTTTACT
1 CTGTTTTGATTGTTATTTTC-TGTTGTTTGGACTGTTATTTTTGTTGTTTTTAATATTGTTTACT
34953400 GTTATTTTTGCTG
65 GTTATTTTTGCTG
*
34953413 CTGTTTTGGA-TGTTATTTT-TGTTGTTTGGA-TGTTATTTTT-TATGCGTTTTTACTATTGTTT
1 CTGTTTT-GATTGTTATTTTCTGTTGTTTGGACTGTTATTTTTGT-T--GTTTTTAATATTGTTT
34953474 CACTGT
62 -ACTGT
34953480 CTTTTTTAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
74 1 0.02
75 11 0.19
76 9 0.16
77 14 0.24
78 21 0.36
79 2 0.03
ACGTcount: A:0.11, C:0.07, G:0.19, T:0.63
Consensus pattern (77 bp):
CTGTTTTGATTGTTATTTTCTGTTGTTTGGACTGTTATTTTTGTTGTTTTTAATATTGTTTACTG
TTATTTTTGCTG
Found at i:34953586 original size:15 final size:15
Alignment explanation
Indices: 34953568--34953597 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34953558 AATATAAAAA
34953568 AAATTAATTTATTTT
1 AAATTAATTTATTTT
34953583 AAATTAATTTATTTT
1 AAATTAATTTATTTT
34953598 TTAATATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AAATTAATTTATTTT
Found at i:34954412 original size:24 final size:23
Alignment explanation
Indices: 34954364--34954419 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
34954354 TTAAGATGAC
34954364 TATATAAAAATTTCGAAATAAAAA
1 TATATAAAAATTTC-AAATAAAAA
*
34954388 TATATAAAAATATT-AAATATTAAA
1 TATATAAAAAT-TTCAAATA-AAAA
34954412 TAT-TAAAA
1 TATATAAAA
34954420 TAATATGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 10 0.34
24 17 0.59
25 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
TATATAAAAATTTCAAATAAAAA
Found at i:34958474 original size:22 final size:23
Alignment explanation
Indices: 34958428--34958476 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
34958418 AAATTCATAA
*
34958428 AATATTATTTACTTCTATTTTTTTT
1 AATATTATTTACTTCTA--TATTTT
34958453 AATATTATTTACTTCTA-ATTTT
1 AATATTATTTACTTCTATATTTT
34958475 AA
1 AA
34958477 ATGGATTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
25 17 0.74
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (23 bp):
AATATTATTTACTTCTATATTTT
Found at i:34969110 original size:20 final size:20
Alignment explanation
Indices: 34969080--34969133 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
34969070 TTCTCAAAAT
* *
34969080 TTTTGAAAATTTTAGTTATAC
1 TTTT-AAAATTTTAATTAAAC
34969101 TTTTAAAATTTTAATTAAAC
1 TTTTAAAATTTTAATTAAAC
*
34969121 TTCTAAAAGTTTT
1 TTTTAAAA-TTTT
34969134 GAAAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTAAAATTTTAATTAAAC
Found at i:34970090 original size:21 final size:21
Alignment explanation
Indices: 34970066--34970111 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
34970056 AATTCTTTTC
* *
34970066 ATTTAAAAATATAATTTATAT
1 ATTTAAAAATAAAATTTAAAT
**
34970087 ATTTTTAAATAAAATTTAAAT
1 ATTTAAAAATAAAATTTAAAT
34970108 ATTT
1 ATTT
34970112 TATTAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTAAAAATAAAATTTAAAT
Found at i:34970122 original size:21 final size:21
Alignment explanation
Indices: 34970072--34970112 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
34970062 TTTCATTTAA
* *
34970072 AAATATAATTTATATATTTTT
1 AAATAAAATTTAAATATTTTT
34970093 AAATAAAATTTAAATATTTT
1 AAATAAAATTTAAATATTTT
34970113 ATTAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATAAAATTTAAATATTTTT
Found at i:34979887 original size:34 final size:34
Alignment explanation
Indices: 34979848--34979915 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
34979838 AACAGATATC
*
34979848 ATTTTGACGTATAGAAATCAATGGATGGAAATTT
1 ATTTTGACGTACAGAAATCAATGGATGGAAATTT
* *
34979882 ATTTTGACGTGCAGAGATCAATGGATGGAAATTT
1 ATTTTGACGTACAGAAATCAATGGATGGAAATTT
34979916 TAACGGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.34
Consensus pattern (34 bp):
ATTTTGACGTACAGAAATCAATGGATGGAAATTT
Found at i:34999509 original size:25 final size:25
Alignment explanation
Indices: 34999469--34999518 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
34999459 TGATTCTTTC
*
34999469 TTCATCATTCCTAAAACTATTTACA
1 TTCATCATTCCTAAAACTATATACA
*
34999494 TTCATCATT-CTCAAAATTATATACA
1 TTCATCATTCCT-AAAACTATATACA
34999519 GGCAAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (25 bp):
TTCATCATTCCTAAAACTATATACA
Found at i:35002084 original size:94 final size:94
Alignment explanation
Indices: 35001923--35002103 Score: 299
Period size: 94 Copynumber: 1.9 Consensus size: 94
35001913 TTAGCCTGAG
* *
35001923 TGCTTCCTCTTTCATTGCCTCTGCATGCTTTCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
1 TGCTTCCTCTTTCATTGCCTCTGCACGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
35001988 CCACTCTTGCAGTAGGTACTTTGTTCTCA
66 CCACTCTTGCAGTAGGTACTTTGTTCTCA
* * **
35002017 TGCTTCCTCTTTCATTGCCTCTGCGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGTTGGTGATA
1 TGCTTCCTCTTTCATTGCCTCTGCACGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
*
35002082 CCATTCTTGCAGTAGGTACTTT
66 CCACTCTTGCAGTAGGTACTTT
35002104 TTTTCTCAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 80 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (94 bp):
TGCTTCCTCTTTCATTGCCTCTGCACGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
CCACTCTTGCAGTAGGTACTTTGTTCTCA
Found at i:35008202 original size:19 final size:20
Alignment explanation
Indices: 35008180--35008233 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
35008170 ATTATTAAAT
*
35008180 AAAATATTAATTTTAA-TTA
1 AAAATATTAATTATAATTTA
* *
35008199 AAAATATAAAATATAATTTA
1 AAAATATTAATTATAATTTA
35008219 AAAATAATTAATTAT
1 AAAAT-ATTAATTAT
35008234 TGATTGACAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 13 0.46
20 8 0.29
21 7 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATATTAATTATAATTTA
Found at i:35012468 original size:12 final size:12
Alignment explanation
Indices: 35012451--35012534 Score: 52
Period size: 12 Copynumber: 7.3 Consensus size: 12
35012441 ATAACATCCA
35012451 AACAACAAAAAT
1 AACAACAAAAAT
* *
35012463 AACAACCAAAAC
1 AACAACAAAAAT
* **
35012475 AGCAGTAAAAAT
1 AACAACAAAAAT
35012487 AACAAC---AA-
1 AACAACAAAAAT
*
35012495 AACAACATTAAA-
1 AACAACA-AAAAT
*
35012507 AACAACAAAAAC
1 AACAACAAAAAT
*
35012519 AGCAACAAAAAT
1 AACAACAAAAAT
35012531 AACA
1 AACA
35012535 GTAAAAACAA
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
8 6 0.11
9 2 0.04
11 3 0.06
12 42 0.79
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:35012485 original size:24 final size:23
Alignment explanation
Indices: 35012437--35012534 Score: 82
Period size: 20 Copynumber: 4.4 Consensus size: 23
35012427 AAAACGTATA
* *
35012437 AAAAATAACATCC-AAACA--AC
1 AAAAATAACAACCAAAACAGCAT
35012457 AAAAATAACAACCAAAACAGCAGT
1 AAAAATAACAACCAAAACAGCA-T
*
35012481 AAAAATAACAA-CAAAACAACAT
1 AAAAATAACAACCAAAACAGCAT
* * *
35012503 -TAAA-AACAACAAAAACAGCAAC
1 AAAAATAACAACCAAAACAGC-AT
35012525 AAAAATAACA
1 AAAAATAACA
35012535 GTAAAAACAA
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
20 17 0.27
21 15 0.24
22 2 0.03
23 13 0.21
24 15 0.24
ACGTcount: A:0.68, C:0.20, G:0.03, T:0.08
Consensus pattern (23 bp):
AAAAATAACAACCAAAACAGCAT
Found at i:35012490 original size:44 final size:45
Alignment explanation
Indices: 35012437--35012566 Score: 138
Period size: 44 Copynumber: 2.9 Consensus size: 45
35012427 AAAACGTATA
* **
35012437 AAAAATAACATCCAAACAACA-AAAATAACAACCAAAACAGCAGT
1 AAAAATAACATCAAAACAACACAAAATAACAACCAAAACAGCAAC
* ** *
35012481 AAAAATAACAACAAAACAACATTAAA-AACAACAAAAACAGCAAC
1 AAAAATAACATCAAAACAACACAAAATAACAACCAAAACAGCAAC
* * *
35012525 AAAAATAACAGTAAAAACAACACGAAAATAGCAATCAAAACA
1 AAAAATAACA-TCAAAACAACAC-AAAATAACAACCAAAACA
35012567 ATAAAAAATC
Statistics
Matches: 69, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
44 44 0.64
45 12 0.17
46 3 0.04
47 10 0.14
ACGTcount: A:0.67, C:0.20, G:0.05, T:0.08
Consensus pattern (45 bp):
AAAAATAACATCAAAACAACACAAAATAACAACCAAAACAGCAAC
Found at i:35012545 original size:33 final size:34
Alignment explanation
Indices: 35012489--35012564 Score: 93
Period size: 33 Copynumber: 2.2 Consensus size: 34
35012479 GTAAAAATAA
*
35012489 CAAC-AAAACAACATTAAAAACAACA-AAAACAG
1 CAACAAAAACAACAGTAAAAACAACACAAAACAG
* *
35012521 CAACAAAAATAACAGTAAAAACAACACGAAAATAG
1 CAACAAAAACAACAGTAAAAACAACAC-AAAACAG
35012556 CAATCAAAA
1 CAA-CAAAA
35012565 CAATAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 4 0.11
33 19 0.51
35 9 0.24
36 5 0.14
ACGTcount: A:0.67, C:0.20, G:0.05, T:0.08
Consensus pattern (34 bp):
CAACAAAAACAACAGTAAAAACAACACAAAACAG
Found at i:35012565 original size:56 final size:56
Alignment explanation
Indices: 35012450--35012573 Score: 133
Period size: 56 Copynumber: 2.2 Consensus size: 56
35012440 AATAACATCC
* * * * *
35012450 AAACAACAAAAATAACAACCAAAACAGCAGTAAAAATAACAACAAAACAACATTAA
1 AAACAACAAAAACAACAACAAAAACAACAGTAAAAACAACAACAAAACAACAATAA
* * * * *
35012506 AAACAACAAAAACAGCAACAAAAATAACAGTAAAAACAAC-ACGAAAATAGCAATCA
1 AAACAACAAAAACAACAACAAAAACAACAGTAAAAACAACAAC-AAAACAACAATAA
*
35012562 AAACAATAAAAA
1 AAACAACAAAAA
35012574 ATCATCAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
55 2 0.04
56 54 0.96
ACGTcount: A:0.69, C:0.19, G:0.05, T:0.08
Consensus pattern (56 bp):
AAACAACAAAAACAACAACAAAAACAACAGTAAAAACAACAACAAAACAACAATAA
Found at i:35016270 original size:7 final size:8
Alignment explanation
Indices: 35016258--35016290 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
35016248 CATATATTGA
35016258 TTAAA-AT
1 TTAAATAT
35016265 TTAAA-AT
1 TTAAATAT
35016272 TTAAATAT
1 TTAAATAT
35016280 TTAAATAT
1 TTAAATAT
35016288 TTA
1 TTA
35016291 TCTAAGTCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 12 0.48
8 13 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TTAAATAT
Found at i:35016283 original size:15 final size:15
Alignment explanation
Indices: 35016258--35016290 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
35016248 CATATATTGA
35016258 TTAAAATTTAAA-AT
1 TTAAAATTTAAATAT
35016272 TTAAATATTTAAATAT
1 TTAAA-ATTTAAATAT
35016288 TTA
1 TTA
35016291 TCTAAGTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAAATTTAAATAT
Found at i:35024793 original size:3 final size:3
Alignment explanation
Indices: 35024785--35024823 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
35024775 TAGTTTTGAA
35024785 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CCTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CT
35024824 CTTGGCTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:35027470 original size:10 final size:10
Alignment explanation
Indices: 35027455--35027495 Score: 82
Period size: 10 Copynumber: 4.1 Consensus size: 10
35027445 CAAGCAGTGG
35027455 ATGAAAGAGA
1 ATGAAAGAGA
35027465 ATGAAAGAGA
1 ATGAAAGAGA
35027475 ATGAAAGAGA
1 ATGAAAGAGA
35027485 ATGAAAGAGA
1 ATGAAAGAGA
35027495 A
1 A
35027496 ATATAGTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.29, T:0.10
Consensus pattern (10 bp):
ATGAAAGAGA
Found at i:35030565 original size:20 final size:19
Alignment explanation
Indices: 35030514--35030566 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
35030504 ACTATAATGC
35030514 ATATTAATAACTATAAATAA
1 ATATTAATAA-TATAAATAA
* *
35030534 ATTATTACATAATATAATTAT
1 A-TATTA-ATAATATAAATAA
35030555 ATATTATATAAT
1 ATATTA-ATAAT
35030567 TATTAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 11 0.39
21 13 0.46
22 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATTAATAATATAAATAA
Found at i:35030568 original size:28 final size:28
Alignment explanation
Indices: 35030537--35030596 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
35030527 TAAATAAATT
** *
35030537 ATTACATAATATAATTATATAT-TATATA
1 ATTA-ATAATATAACAATACATGTATATA
*
35030565 ATTATTAATATAACAATACATGTATATA
1 ATTAATAATATAACAATACATGTATATA
35030593 ATTA
1 ATTA
35030597 GTCATACATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (28 bp):
ATTAATAATATAACAATACATGTATATA
Found at i:35037345 original size:31 final size:31
Alignment explanation
Indices: 35037310--35037377 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
35037300 TGATTATTAA
35037310 ACTATT-CAAAAGTTTTCATTTAAATCACTAG
1 ACTATTCCAAAA-TTTTCATTTAAATCACTAG
* *
35037341 ACTATTCCAAAATTTTTATTTAAGTCACTAG
1 ACTATTCCAAAATTTTCATTTAAATCACTAG
*
35037372 GCTATT
1 ACTATT
35037378 ATGTTTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (31 bp):
ACTATTCCAAAATTTTCATTTAAATCACTAG
Found at i:35038862 original size:2 final size:2
Alignment explanation
Indices: 35038855--35038887 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35038845 GAAGACTTTA
35038855 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
35038888 TGTTAACTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:35041246 original size:21 final size:22
Alignment explanation
Indices: 35041199--35041255 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
35041189 AACAGTACAG
**
35041199 ATTTCTACCGATACCTGTACTA
1 ATTTCTACCGATACAAGTACTA
35041221 A-TTCTACCGATACAAGTA-TA
1 ATTTCTACCGATACAAGTACTA
*
35041241 ATTTCTATCGATACA
1 ATTTCTACCGATACA
35041256 TGTCATGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.10
21 27 0.87
22 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (22 bp):
ATTTCTACCGATACAAGTACTA
Found at i:35042075 original size:51 final size:51
Alignment explanation
Indices: 35042012--35042179 Score: 203
Period size: 51 Copynumber: 3.3 Consensus size: 51
35042002 CCGTATAGGA
* * * * * * *
35042012 ATTCATATACTCATAATGACACTGAGTCGTTGGACCCTTAATTCATCATGG
1 ATTCATTTACTCACAATGACACTTAGTCATCGGACCCTTAATTCATAAAGG
*
35042063 ATTCATTTACTCACAATGATACTTAGTCATCGGA-CCTGTAATTCATAAAGG
1 ATTCATTTACTCACAATGACACTTAGTCATCGGACCCT-TAATTCATAAAGG
* * * * *
35042114 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAAG
1 ATTCATTTACTCACAATGACACTTAGTCATCGGACCCTTAATTCATAAAGG
35042165 ATTCATTTACTCACA
1 ATTCATTTACTCACA
35042180 GACTTTTAAT
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
50 3 0.03
51 95 0.95
52 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (51 bp):
ATTCATTTACTCACAATGACACTTAGTCATCGGACCCTTAATTCATAAAGG
Found at i:35042253 original size:85 final size:85
Alignment explanation
Indices: 35042108--35042263 Score: 294
Period size: 85 Copynumber: 1.8 Consensus size: 85
35042098 CTGTAATTCA
35042108 TAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAAGATTCATTT
1 TAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAAGATTCATTT
35042173 ACTCACAGACTTTTAATCCG
66 ACTCACAGACTTTTAATCCG
* *
35042193 TAAAGGATTCATTTACTCACGATGACTCTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTT
1 TAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAAGATTCATTT
35042258 ACTCAC
66 ACTCAC
35042264 GATGACACTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 69 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (85 bp):
TAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAAGATTCATTT
ACTCACAGACTTTTAATCCG
Found at i:35048383 original size:15 final size:16
Alignment explanation
Indices: 35048354--35048383 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35048344 ATTAAATTAG
35048354 AATACAAATTTATCAT
1 AATACAAATTTATCAT
35048370 AATACAAA-TTATCA
1 AATACAAATTTATCA
35048384 AGATTTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (16 bp):
AATACAAATTTATCAT
Found at i:35055913 original size:56 final size:56
Alignment explanation
Indices: 35055711--35055914 Score: 227
Period size: 55 Copynumber: 3.6 Consensus size: 56
35055701 TTGTCAACCT
* * *
35055711 ATGACCGACACCTTCTTTTTCAGATAAAAAAATATTTGTTT-AGGTGTCGCCCATGCC
1 ATGACCGACACC-CCTTTTTCAGATAAAAAATTATTTTTTTGA-GTGTCGCCCATGCC
* ** *
35055768 ATGATCGACACATCTTTTTCAGATAAAAAA-TA-TTTTTTGGGTGTCGCCCATGCC
1 ATGACCGACACCCCTTTTTCAGATAAAAAATTATTTTTTTGAGTGTCGCCCATGCC
** * * *
35055822 ATGATTGATATCCCCTTTTTCAAATAAAAAATTATTTTTTTGAGTGTCTCCCAT-CC
1 ATGACCGACA-CCCCTTTTTCAGATAAAAAATTATTTTTTTGAGTGTCGCCCATGCC
*
35055878 ATGGCCGACACCCCTTTTTCAGATAAAAAATTTATTT
1 ATGACCGACACCCCTTTTTCAGATAAAAAA-TTATTT
35055915 AATAAAGAGA
Statistics
Matches: 126, Mismatches: 16, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
54 27 0.21
55 38 0.30
56 34 0.27
57 27 0.21
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (56 bp):
ATGACCGACACCCCTTTTTCAGATAAAAAATTATTTTTTTGAGTGTCGCCCATGCC
Found at i:35057670 original size:2 final size:2
Alignment explanation
Indices: 35057663--35057687 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35057653 ACCACCATCC
35057663 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
35057688 AAGAATAGTA
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:35073491 original size:23 final size:24
Alignment explanation
Indices: 35073449--35073496 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
35073439 TATTTTAGTT
35073449 AAAAAAATATAAGTACTTAATTGA
1 AAAAAAATATAAGTACTTAATTGA
35073473 AAAAAAAT-TCAAGTA-TTAATTGA
1 AAAAAAATAT-AAGTACTTAATTGA
35073496 A
1 A
35073497 TATTGAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.29
Consensus pattern (24 bp):
AAAAAAATATAAGTACTTAATTGA
Found at i:35074250 original size:18 final size:19
Alignment explanation
Indices: 35074223--35074263 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
35074213 CATTTTCTTT
35074223 CTTTTATTTT-TCTTATTTC
1 CTTTTATTTTCTCTTA-TTC
*
35074242 CTTTT-TTTTCTGTTATTC
1 CTTTTATTTTCTCTTATTC
35074260 CTTT
1 CTTT
35074264 GTTCTTCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.73
Consensus pattern (19 bp):
CTTTTATTTTCTCTTATTC
Found at i:35074297 original size:19 final size:19
Alignment explanation
Indices: 35074262--35074298 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
35074252 TGTTATTCCT
35074262 TTGTTCTTCCTTCTTTCTC
1 TTGTTCTTCCTTCTTTCTC
35074281 TTGTTGCTTCCTT-TTTCT
1 TTGTT-CTTCCTTCTTTCT
35074299 TTTTTGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.00, C:0.27, G:0.08, T:0.65
Consensus pattern (19 bp):
TTGTTCTTCCTTCTTTCTC
Found at i:35082589 original size:2 final size:2
Alignment explanation
Indices: 35082582--35082622 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35082572 TCTTCATTTA
35082582 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
35082623 TAGGCACATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:35087109 original size:20 final size:20
Alignment explanation
Indices: 35087084--35087123 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
35087074 TTGATAATTA
35087084 TTTTTACATTCAACTTAAAT
1 TTTTTACATTCAACTTAAAT
* * *
35087104 TTTTTATATTTAAGTTAAAT
1 TTTTTACATTCAACTTAAAT
35087124 CTTAGATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTTACATTCAACTTAAAT
Found at i:35087110 original size:26 final size:26
Alignment explanation
Indices: 35087080--35087156 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
35087070 TAACTTGATA
35087080 ATTATTTTTACATTCAACTTAAATTT
1 ATTATTTTTACATTCAACTTAAATTT
* * * * *
35087106 TTTATATTTA-AGTTAAATCTTAGA-TA
1 ATTATTTTTACA-TTCAA-CTTAAATTT
35087132 ATTATTTTTACATTCAA-TTAAATTT
1 ATTATTTTTACATTCAACTTAAATTT
35087157 GACGACCAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 9
0.66 0.18 0.16
Matches are distributed among these distances:
24 4 0.11
25 2 0.05
26 25 0.68
27 6 0.16
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (26 bp):
ATTATTTTTACATTCAACTTAAATTT
Found at i:35093088 original size:14 final size:14
Alignment explanation
Indices: 35093039--35093090 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
35093029 AAAACTTAAT
35093039 AAAATTAAAATTTTA
1 AAAATT-AAATTTTA
* * *
35093054 AAAATAAAAGTATA
1 AAAATTAAATTTTA
35093068 AAAATTAAATTTTA
1 AAAATTAAATTTTA
*
35093082 AATATTAAA
1 AAAATTAAA
35093091 AAATTACATA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 25 0.83
15 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
AAAATTAAATTTTA
Found at i:35093976 original size:19 final size:19
Alignment explanation
Indices: 35093952--35093994 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
35093942 ATAAATGGAA
*
35093952 AAATTTTAAAATTATATAT
1 AAATTTTAAAATAATATAT
* *
35093971 AAATTTTAATATAATGTAT
1 AAATTTTAAAATAATATAT
35093990 AAATT
1 AAATT
35093995 AATATATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
AAATTTTAAAATAATATAT
Found at i:35094291 original size:29 final size:30
Alignment explanation
Indices: 35094259--35094317 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
35094249 TCACAAATAA
* *
35094259 AATT-ACATAAAATCAAAGTTCATGTATAC
1 AATTAACATAAAACCAAAATTCATGTATAC
*
35094288 AATTACACATTAAACCAAAATTCATGTATA
1 AATTA-ACATAAAACCAAAATTCATGTATA
35094318 GTTTTGAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
31 21 0.84
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (30 bp):
AATTAACATAAAACCAAAATTCATGTATAC
Found at i:35102305 original size:39 final size:39
Alignment explanation
Indices: 35102262--35102412 Score: 223
Period size: 39 Copynumber: 3.9 Consensus size: 39
35102252 AAATGCCTGT
* * *
35102262 GGGCCAGATGAGTTCCATATATCCTCAGCAAATGCCAAC
1 GGGCCAGATGGGTTCAATGTATCCTCAGCAAATGCCAAC
* *
35102301 GGGCCAGATGGGTTCAATGTATCCTCAGCAAGTGCC-AG
1 GGGCCAGATGGGTTCAATGTATCCTCAGCAAATGCCAAC
*
35102339 GGGCCCAGATGGGTTCAATGTATCCTCAGCAAATGCCAGC
1 GGG-CCAGATGGGTTCAATGTATCCTCAGCAAATGCCAAC
*
35102379 TGGCCAGATGGGTTCAATGTATCCTCAGCAAATG
1 GGGCCAGATGGGTTCAATGTATCCTCAGCAAATG
35102413 TATGGCAATC
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
38 4 0.04
39 95 0.94
40 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.22
Consensus pattern (39 bp):
GGGCCAGATGGGTTCAATGTATCCTCAGCAAATGCCAAC
Found at i:35110230 original size:37 final size:37
Alignment explanation
Indices: 35110177--35110252 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
35110167 TCCATCACCA
*
35110177 CTCTCACATATGGTCTATGATTTAATCATAATTATGT
1 CTCTCACATATAGTCTATGATTTAATCATAATTATGT
* *
35110214 CTCTCTCATATAGTCTATGATTTAATCATAATTGTGT
1 CTCTCACATATAGTCTATGATTTAATCATAATTATGT
35110251 CT
1 CT
35110253 AAGTGTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.45
Consensus pattern (37 bp):
CTCTCACATATAGTCTATGATTTAATCATAATTATGT
Found at i:35110242 original size:20 final size:20
Alignment explanation
Indices: 35110183--35110243 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
35110173 ACCACTCTCA
*
35110183 CATATGGTCTATGATTTAAT
1 CATATAGTCTATGATTTAAT
*
35110203 CATA-A-T-TATG-TCTCT-CT
1 CATATAGTCTATGAT-T-TAAT
35110220 CATATAGTCTATGATTTAAT
1 CATATAGTCTATGATTTAAT
35110240 CATA
1 CATA
35110244 ATTGTGTCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 14
0.65 0.06 0.29
Matches are distributed among these distances:
16 1 0.03
17 10 0.32
18 3 0.10
19 2 0.06
20 14 0.45
21 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
CATATAGTCTATGATTTAAT
Found at i:35110630 original size:63 final size:63
Alignment explanation
Indices: 35110531--35110657 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
35110521 TAACAAAGTG
35110531 ATAATTGATTGAAACTTTGGGGGTAAATAATGCATAACCCTATTATATATTAACTATAAATTT
1 ATAATTGATTGAAACTTTGGGGGTAAATAATGCATAACCCTATTATATATTAACTATAAATTT
*
35110594 ATAATTGATTGAAATTTTGGGGGTAAATAATGCATAACCCTATTATATATTAACTATAAATTT
1 ATAATTGATTGAAACTTTGGGGGTAAATAATGCATAACCCTATTATATATTAACTATAAATTT
35110657 A
1 A
35110658 ATTTTTGTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.39
Consensus pattern (63 bp):
ATAATTGATTGAAACTTTGGGGGTAAATAATGCATAACCCTATTATATATTAACTATAAATTT
Found at i:35111780 original size:27 final size:24
Alignment explanation
Indices: 35111720--35111780 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 24
35111710 GAGTAAATTC
35111720 TTCAATATTATTTTTTTTTTAAAA
1 TTCAATATTATTTTTTTTTTAAAA
35111744 -TCTAATATTATTTTTTTATTTACAAAA
1 TTC-AATATTATTTTTTT-TTT--AAAA
*
35111771 TTCAAAATTA
1 TTCAATATTA
35111781 ATACCTTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.06
24 14 0.45
25 3 0.10
27 10 0.32
28 2 0.06
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (24 bp):
TTCAATATTATTTTTTTTTTAAAA
Found at i:35114075 original size:17 final size:17
Alignment explanation
Indices: 35114053--35114086 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35114043 CTTTATATAT
*
35114053 ATATATATAGAGGATAC
1 ATATATAGAGAGGATAC
35114070 ATATATAGAGAGGATAC
1 ATATATAGAGAGGATAC
35114087 TGTATAGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (17 bp):
ATATATAGAGAGGATAC
Found at i:35121424 original size:30 final size:30
Alignment explanation
Indices: 35121390--35121450 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
35121380 ACTTTCAGAT
35121390 AAACTATATCCTTGCTTTTGAGCCAGAAAC
1 AAACTATATCCTTGCTTTTGAGCCAGAAAC
35121420 AAACTATATCCTTGCTTTTGAGCCAGAAAC
1 AAACTATATCCTTGCTTTTGAGCCAGAAAC
35121450 A
1 A
35121451 TTCCCTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (30 bp):
AAACTATATCCTTGCTTTTGAGCCAGAAAC
Found at i:35126849 original size:21 final size:21
Alignment explanation
Indices: 35126809--35126854 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
35126799 AAATGTGAAA
**
35126809 AAAAACTTGTAAAATTTATTTT
1 AAAAACTTGTAAAAAGTA-TTT
35126831 AAAAA-TTGTAAAAAGTATTT
1 AAAAACTTGTAAAAAGTATTT
35126851 AAAA
1 AAAA
35126855 TATTAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 10 0.45
22 5 0.23
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (21 bp):
AAAAACTTGTAAAAAGTATTT
Found at i:35129704 original size:42 final size:41
Alignment explanation
Indices: 35129625--35129704 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 41
35129615 GGGAAATCAT
*
35129625 AAATATTTACAAAACAATATCTAACATAAAAATATTTTCAG
1 AAATATTTACAAAACAATATCTAACATAAAAAAATTTTCAG
*
35129666 AAATATTTTCAAATACAATAT-TAA-ATAATTAAAAATTTT
1 AAATATTTACAAA-ACAATATCTAACATAA--AAAAATTTT
35129705 AAAAGAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 4 0.12
41 15 0.44
42 15 0.44
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (41 bp):
AAATATTTACAAAACAATATCTAACATAAAAAAATTTTCAG
Found at i:35133914 original size:19 final size:19
Alignment explanation
Indices: 35133890--35133937 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
35133880 CAATATCTTA
35133890 AAATTAAAATATAAG-GACT
1 AAATTAAAATA-AAGAGACT
* *
35133909 AAATTATAATAGAGAGACT
1 AAATTAAAATAAAGAGACT
35133928 AAATCTAAAA
1 AAAT-TAAAA
35133938 AAGTGCATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 18 0.75
20 4 0.17
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.25
Consensus pattern (19 bp):
AAATTAAAATAAAGAGACT
Found at i:35135436 original size:53 final size:53
Alignment explanation
Indices: 35135349--35135499 Score: 227
Period size: 53 Copynumber: 2.9 Consensus size: 53
35135339 ATTACATAGG
* * * *
35135349 TTATGGATATGGTTACATTGTTACCATGTGTTGTTATCAATGCTCATGACAGC
1 TTATGGATATAGTTACACTGTTACTATGTATTGTTATCAATGCTCATGACAGC
* *
35135402 TTATTGATATAGTTACACTGTTACTATGTATTGTTATCAAT--TCATGGCAGC
1 TTATGGATATAGTTACACTGTTACTATGTATTGTTATCAATGCTCATGACAGC
35135453 TTATGGATATAGTTACACTGTTA-TATGTATTGTTATCAATGCTCATG
1 TTATGGATATAGTTACACTGTTACTATGTATTGTTATCAATGCTCATG
35135500 GCATATCTAA
Statistics
Matches: 89, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
50 17 0.19
51 31 0.35
52 5 0.06
53 36 0.40
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (53 bp):
TTATGGATATAGTTACACTGTTACTATGTATTGTTATCAATGCTCATGACAGC
Found at i:35136504 original size:149 final size:149
Alignment explanation
Indices: 35136231--35136530 Score: 449
Period size: 149 Copynumber: 2.0 Consensus size: 149
35136221 GGGATTACAG
* **
35136231 TTATAAATTGAGGTAAACTTATTGCAAGATTTGATATCTATAAATGGTTTCTGCAGATACATAGT
1 TTATAAATTGAGGGAAACTTATTGCAAGATTTGATATCTATAAATGACTTCTGCAGATACATAGT
* * *
35136296 TTTTTGAGCACTACTTTCACACTTGCTAGTTGCTATATGCAGTGCATTAACGGTAATGTTGGAAG
66 TCTTTGAGCACTACCTTCAAACTTGCTAGTTGCTATATGCAGTGCATTAACGGTAATGTTGGAAG
*
35136361 TCTTCCTCGTAAATTCCCT
131 TCTTCCTCATAAATTCCCT
* * **
35136380 TTATAATTTGAGGGAAATTTATTGCAAGATTTGATATCTATAAATGACTTCTGCAGATGTATAGT
1 TTATAAATTGAGGGAAACTTATTGCAAGATTTGATATCTATAAATGACTTCTGCAGATACATAGT
* * * *
35136445 TCTTTGAGCACTCCCTTCAAACTTGCTAGTTGCTATATG-TGTGGCATTAATGGTCATGTTGGAA
66 TCTTTGAGCACTACCTTCAAACTTGCTAGTTGCTATATGCAGT-GCATTAACGGTAATGTTGGAA
35136509 GTCTTCCTCATAAATTCCCT
130 GTCTTCCTCATAAATTCCCT
35136529 TT
1 TT
35136531 GATTTAAATG
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
148 2 0.01
149 133 0.99
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (149 bp):
TTATAAATTGAGGGAAACTTATTGCAAGATTTGATATCTATAAATGACTTCTGCAGATACATAGT
TCTTTGAGCACTACCTTCAAACTTGCTAGTTGCTATATGCAGTGCATTAACGGTAATGTTGGAAG
TCTTCCTCATAAATTCCCT
Done.