Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 6 of 135
Found at i:2386299 original size:23 final size:23
Alignment explanation
Indices: 2386265--2386308 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2386255 AATTTATGTA
2386265 CTTTTTAATTTT-AAGATTTTATT
1 CTTTTTAATTTTCAA-ATTTTATT
*
2386288 CTTTTTACTTTTCAAATTTTA
1 CTTTTTAATTTTCAAATTTTA
2386309 AAATTTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (23 bp):
CTTTTTAATTTTCAAATTTTATT
Found at i:2391680 original size:15 final size:15
Alignment explanation
Indices: 2391660--2391694 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2391650 AGAACATGAC
* *
2391660 GACGACGATGAGGAT
1 GACGACGACGACGAT
2391675 GACGACGACGACGAT
1 GACGACGACGACGAT
2391690 GACGA
1 GACGA
2391695 TGATAAGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.37, T:0.09
Consensus pattern (15 bp):
GACGACGACGACGAT
Found at i:2391681 original size:21 final size:21
Alignment explanation
Indices: 2391657--2391697 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2391647 GAAAGAACAT
*
2391657 GACGACGACGATGAGGATGAC
1 GACGACGACGATGACGATGAC
2391678 GACGACGACGATGACGATGA
1 GACGACGACGATGACGATGA
2391698 TAAGGAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.37, T:0.10
Consensus pattern (21 bp):
GACGACGACGATGACGATGAC
Found at i:2414747 original size:10 final size:11
Alignment explanation
Indices: 2414725--2414756 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
2414715 TAATGGTAAC
2414725 ATTTT-ATATA
1 ATTTTGATATA
2414735 ATTTTGATA-A
1 ATTTTGATATA
2414745 ATTTTGATATA
1 ATTTTGATATA
2414756 A
1 A
2414757 AACTTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (11 bp):
ATTTTGATATA
Found at i:2428626 original size:22 final size:22
Alignment explanation
Indices: 2428585--2428626 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2428575 TTTATCGTTG
*
2428585 TAAAAAAAATACACTAATATCT
1 TAAAAAAAATAAACTAATATCT
* *
2428607 TAAAAAATATAAACTCATAT
1 TAAAAAAAATAAACTAATAT
2428627 TACTCATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAAAAATAAACTAATATCT
Found at i:2446551 original size:18 final size:18
Alignment explanation
Indices: 2446528--2446562 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2446518 AATTGAATTT
2446528 TTTTTTTC-ATTCTTTAAG
1 TTTTTTTCTATT-TTTAAG
2446546 TTTTTTTCTATTTTTAA
1 TTTTTTTCTATTTTTAA
2446563 AATAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTTTTCTATTTTTAAG
Found at i:2449363 original size:24 final size:24
Alignment explanation
Indices: 2449336--2449395 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
2449326 ATAACCAAAA
*
2449336 CAACAACAAA-AACAACAAAAATAG
1 CAACAA-AAATAACAACAAAAACAG
* *
2449360 CAACAAAAATAGCAATAAAAACAG
1 CAACAAAAATAACAACAAAAACAG
2449384 CAACAAAAATAA
1 CAACAAAAATAA
2449396 TAGCATCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.70, C:0.18, G:0.05, T:0.07
Consensus pattern (24 bp):
CAACAAAAATAACAACAAAAACAG
Found at i:2449379 original size:11 final size:12
Alignment explanation
Indices: 2449348--2449394 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
2449338 ACAACAAAAA
2449348 CAACAAAAATAG
1 CAACAAAAATAG
2449360 CAACAAAAATAG
1 CAACAAAAATAG
* *
2449372 CAATAAAAACAG
1 CAACAAAAATAG
2449384 CAACAAAAATA
1 CAACAAAAATA
2449395 ATAGCATCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.68, C:0.17, G:0.06, T:0.09
Consensus pattern (12 bp):
CAACAAAAATAG
Found at i:2449413 original size:21 final size:20
Alignment explanation
Indices: 2449385--2449427 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
2449375 TAAAAACAGC
* * *
2449385 AACAAAAATAATAGCATCAA
1 AACAAAAAAAATAACACCAA
2449405 AACATAAAAAAATAACACCAA
1 AACA-AAAAAAATAACACCAA
2449426 AA
1 AA
2449428 TAGCAACTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.70, C:0.16, G:0.02, T:0.12
Consensus pattern (20 bp):
AACAAAAAAAATAACACCAA
Found at i:2449458 original size:36 final size:35
Alignment explanation
Indices: 2449346--2449485 Score: 101
Period size: 36 Copynumber: 4.0 Consensus size: 35
2449336 CAACAACAAA
* *
2449346 AACAACA--AAAATAGCAACAAAAATAGCAATAAAAAC
1 AACAACACCAAAATAGCAAC-AAAACAG-TA-AAAAAC
* ** *
2449382 AGCAACAAAAATAATAGCATCAAAACA-T-AAAAA-
1 AACAACACCAA-AATAGCAACAAAACAGTAAAAAAC
*
2449415 AATAACACCAAAATAGCAACTAAAACAGTAAAAAAC
1 AACAACACCAAAATAGCAAC-AAAACAGTAAAAAAC
* * *
2449451 AACAACACCGAAACAGTAACCAAAACAGTAAAAAA
1 AACAACACCAAAATAGCAA-CAAAACAGTAAAAAA
2449486 TAGCATCAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
32 8 0.10
33 13 0.16
34 6 0.07
35 5 0.06
36 35 0.42
37 1 0.01
38 7 0.08
39 8 0.10
ACGTcount: A:0.66, C:0.19, G:0.06, T:0.09
Consensus pattern (35 bp):
AACAACACCAAAATAGCAACAAAACAGTAAAAAAC
Found at i:2467796 original size:14 final size:14
Alignment explanation
Indices: 2467779--2467809 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2467769 TTAATTTTTT
*
2467779 AAATTTAAAGTTAA
1 AAATTTAAAATTAA
2467793 AAATTTAAAATTAA
1 AAATTTAAAATTAA
2467807 AAA
1 AAA
2467810 AACTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
AAATTTAAAATTAA
Found at i:2467816 original size:23 final size:23
Alignment explanation
Indices: 2467790--2467839 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
2467780 AATTTAAAGT
*
2467790 TAAAAATTTAAAATTAAAAAAAC
1 TAAAAATTTAAAAATAAAAAAAC
** *
2467813 TAAATTTTTAAAAATAAAATAAC
1 TAAAAATTTAAAAATAAAAAAAC
2467836 TAAA
1 TAAA
2467840 TACTAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAAATTTAAAAATAAAAAAAC
Found at i:2467840 original size:23 final size:23
Alignment explanation
Indices: 2467796--2467840 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2467786 AAGTTAAAAA
*
2467796 TTTAAAATTAAAAAAACTAAATT
1 TTTAAAAATAAAAAAACTAAATT
*
2467819 TTTAAAAATAAAATAACTAAAT
1 TTTAAAAATAAAAAAACTAAAT
2467841 ACTAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
TTTAAAAATAAAAAAACTAAATT
Found at i:2485323 original size:6 final size:6
Alignment explanation
Indices: 2485314--2485361 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
2485304 TGAGCCTGAG
2485314 CCTGTC CCTGTC CCTGTC CCTGTC CCTGTC CCTGTC CCTGTC CCTGTC
1 CCTGTC CCTGTC CCTGTC CCTGTC CCTGTC CCTGTC CCTGTC CCTGTC
2485362 TCCGCCCTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.17, T:0.33
Consensus pattern (6 bp):
CCTGTC
Found at i:2488281 original size:108 final size:108
Alignment explanation
Indices: 2488075--2488311 Score: 309
Period size: 108 Copynumber: 2.2 Consensus size: 108
2488065 GATGACACAA
* ** * *
2488075 AAAGTCCTCAGAAGAGAAGCCATGATGCAACCATGAGTAGTCCTCAACGTATAAACCATCATGAA
1 AAAGTCCTCAAAAGAGAAGCCATGATGCAAAAATGAGTAGTCCTCAACATATAAACCATAATGAA
* *
2488140 GATACACAAAAACCTCAAGATATAAGCTGGAATGGAGATACAC
66 GATACACAAAAACCTCAAGATATAAGCTAGAATGAAGATACAC
*
2488183 AAAGTCCTCAAAAGAGAGGCCATGATGCAAAAATGAGTAGTCCTCAACATATAAATCC-TAATGA
1 AAAGTCCTCAAAAGAGAAGCCATGATGCAAAAATGAGTAGTCCTCAACATATAAA-CCATAATGA
* * *
2488247 AGATGCACAAAAAGCTCGAA-ATATAA-ATCAGAATGAAGATACAC
65 AGATACACAAAAACCTC-AAGATATAAGCT-AGAATGAAGATACAC
* *
2488291 AGAGTCCTCAAAAGATAAGCC
1 AAAGTCCTCAAAAGAGAAGCC
2488312 GCAATGAAAA
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
107 1 0.01
108 107 0.96
109 4 0.04
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.18
Consensus pattern (108 bp):
AAAGTCCTCAAAAGAGAAGCCATGATGCAAAAATGAGTAGTCCTCAACATATAAACCATAATGAA
GATACACAAAAACCTCAAGATATAAGCTAGAATGAAGATACAC
Found at i:2491321 original size:13 final size:13
Alignment explanation
Indices: 2491302--2491336 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2491292 GACAATCTAA
*
2491302 AATAAAACAATTT
1 AATAAAAAAATTT
*
2491315 GATAAAAAAATTT
1 AATAAAAAAATTT
2491328 AATAAAAAA
1 AATAAAAAA
2491337 TAATAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (13 bp):
AATAAAAAAATTT
Found at i:2501121 original size:23 final size:24
Alignment explanation
Indices: 2501095--2501140 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2501085 TAATGTGCTG
* *
2501095 AAACGCATT-ATATTATGTAAAAC
1 AAACCCATTAATACTATGTAAAAC
2501118 AAACCCATTAATACTATGTAAAA
1 AAACCCATTAATACTATGTAAAA
2501141 TCTCTCAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (24 bp):
AAACCCATTAATACTATGTAAAAC
Found at i:2502660 original size:3 final size:3
Alignment explanation
Indices: 2502643--2502704 Score: 58
Period size: 3 Copynumber: 21.7 Consensus size: 3
2502633 GATATAATTT
* * * *
2502643 AAG AAG -AG AAA AAG AAG AA- AAG AAG AAA AAG AAG AGG AAG AGG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
2502689 -AG GAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AA
2502705 TGAAAAGAGA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
2 6 0.13
3 41 0.87
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2503333 original size:30 final size:31
Alignment explanation
Indices: 2503268--2503335 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
2503258 ATTATTAATC
*
2503268 AGTGACTGTTTTATCACTTTTTGATAATGTT
1 AGTGACTGTTTTATCACTTTTTCATAATGTT
* *
2503299 AGTGACTGTTTTATTATTTTTTCA-AA-GTT
1 AGTGACTGTTTTATCACTTTTTCATAATGTT
2503328 AAGTGACT
1 -AGTGACT
2503336 AAAATAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 9 0.27
31 21 0.64
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (31 bp):
AGTGACTGTTTTATCACTTTTTCATAATGTT
Found at i:2511587 original size:9 final size:9
Alignment explanation
Indices: 2511569--2511602 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2511559 AGGCTATCCG
*
2511569 TAATATAAA
1 TAATAAAAA
*
2511578 TAATGAAAA
1 TAATAAAAA
2511587 TAATAAAAA
1 TAATAAAAA
2511596 TAATAAA
1 TAATAAA
2511603 TAAAAAAAAG
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:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (9 bp):
TAATAAAAA
Found at i:2511596 original size:18 final size:16
Alignment explanation
Indices: 2511569--2511610 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
2511559 AGGCTATCCG
*
2511569 TAATATAAATAATGAAAA
1 TAATAAAAATAAT--AAA
2511587 TAATAAAAATAATAAA
1 TAATAAAAATAATAAA
2511603 TAA-AAAAA
1 TAATAAAAA
2511611 AGGGAGACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
18 12 0.52
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
TAATAAAAATAATAAA
Found at i:2514219 original size:3 final size:3
Alignment explanation
Indices: 2514202--2514251 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
2514192 TTCACCAGCT
2514202 TTC TT- TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2514247 TTC TT
1 TTC TT
2514252 ATCTTATTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:2515353 original size:3 final size:3
Alignment explanation
Indices: 2515345--2515369 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2515335 CATAAATCAT
2515345 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
2515370 CTAATTCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2518053 original size:15 final size:15
Alignment explanation
Indices: 2518009--2518053 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
2517999 ATCAGGAGGT
2518009 TGATGAAGATGACGA
1 TGATGAAGATGACGA
* **
2518024 TGAGGAAGACAACGA
1 TGATGAAGATGACGA
*
2518039 TGATGATGATGACGA
1 TGATGAAGATGACGA
2518054 AGAATTGGAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.33, T:0.18
Consensus pattern (15 bp):
TGATGAAGATGACGA
Found at i:2522668 original size:6 final size:6
Alignment explanation
Indices: 2522635--2522665 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2522625 CTCCTTCCTT
*
2522635 TTTTCC TTTTCC TTTTCC TTTTCC TATTCC T
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC T
2522666 ATTATTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTTCC
Found at i:2531368 original size:5 final size:5
Alignment explanation
Indices: 2531358--2531383 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2531348 TTGTTGTGTC
2531358 TGCAT TGCAT TGCAT TGCAT TGCAT T
1 TGCAT TGCAT TGCAT TGCAT TGCAT T
2531384 TTTATTTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TGCAT
Found at i:2533196 original size:39 final size:39
Alignment explanation
Indices: 2533141--2533216 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
2533131 ATTAATATTT
*
2533141 ATCTTTGTACATACTGGGGATTAATTGATTTGTAACTTC
1 ATCTTTGTACATACTGGGGATTAACTGATTTGTAACTTC
*
2533180 ATCTTTGTACGA-ACTGGGGATTAGCTGATTTGTAACT
1 ATCTTTGTAC-ATACTGGGGATTAACTGATTTGTAACT
2533217 ACATAGGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 33 0.97
40 1 0.03
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (39 bp):
ATCTTTGTACATACTGGGGATTAACTGATTTGTAACTTC
Found at i:2533317 original size:3 final size:3
Alignment explanation
Indices: 2533309--2533352 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2533299 CTTATCACAA
*
2533309 AAG AAG AAG AAG GAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2533353 AGACAACACG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2542678 original size:29 final size:29
Alignment explanation
Indices: 2542636--2542695 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
2542626 TATGTATACA
*
2542636 TATACGAACTCCCTTGACCTCAAATCATG
1 TATACGAACTCCCTTGACCCCAAATCATG
2542665 TATACGAACTCCCTTGACCCCAAATCATG
1 TATACGAACTCCCTTGACCCCAAATCATG
2542694 TA
1 TA
2542696 AAGCCCATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.32, G:0.10, T:0.27
Consensus pattern (29 bp):
TATACGAACTCCCTTGACCCCAAATCATG
Found at i:2542962 original size:72 final size:72
Alignment explanation
Indices: 2542845--2542999 Score: 276
Period size: 72 Copynumber: 2.2 Consensus size: 72
2542835 GTGTTGATTG
*
2542845 GCCAAAAGCAGGGCTAGACCCAAAGCTGAAAGAAGGAGTAGAAGATGATCCAAAAGTAGGAGTGT
1 GCCAAAAGCAGGGCTAGACCCAAAGCTCAAAGAAGGAGTAGAAGATGATCCAAAAGTAGGAGTGT
*
2542910 TGGAAAT
66 TGGAAAC
2542917 GCCAAAAGCAGGGCTAGACCCAAAGC-CAAATGAAGGAGTAGAAGATGATCCAAAAGTAGGAGTG
1 GCCAAAAGCAGGGCTAGACCCAAAGCTCAAA-GAAGGAGTAGAAGATGATCCAAAAGTAGGAGTG
2542981 TTGGAAAC
65 TTGGAAAC
2542989 GCCAAAAGCAG
1 GCCAAAAGCAG
2543000 AACTTGGCAC
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
71 3 0.04
72 77 0.96
ACGTcount: A:0.42, C:0.16, G:0.30, T:0.12
Consensus pattern (72 bp):
GCCAAAAGCAGGGCTAGACCCAAAGCTCAAAGAAGGAGTAGAAGATGATCCAAAAGTAGGAGTGT
TGGAAAC
Found at i:2543060 original size:45 final size:45
Alignment explanation
Indices: 2542960--2543069 Score: 121
Period size: 45 Copynumber: 2.4 Consensus size: 45
2542950 AGGAGTAGAA
* * *
2542960 GATGATCCAAAAGTAGGAGTGTTGGAAACGCCAAAAGCAGAACTT
1 GATGCTCCAAAAGCAGGAGTCTTGGAAACGCCAAAAGCAGAACTT
*** * * ** *
2543005 GGCACACCAAAAACAGGAGTCTTGGAAGTGCCAAAAGCAGAATTT
1 GATGCTCCAAAAGCAGGAGTCTTGGAAACGCCAAAAGCAGAACTT
2543050 GATGCTCCAAAAGCAGGAGT
1 GATGCTCCAAAAGCAGGAGT
2543070 GCCAGAAGTC
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.16
Consensus pattern (45 bp):
GATGCTCCAAAAGCAGGAGTCTTGGAAACGCCAAAAGCAGAACTT
Found at i:2543248 original size:24 final size:24
Alignment explanation
Indices: 2543190--2543248 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
2543180 TTCCAGTTGA
2543190 ACCGAAGGCAGGAGTGCCTGTGAC
1 ACCGAAGGCAGGAGTGCCTGTGAC
* *
2543214 ACCAAAAGCAGGAGTG-CT-TGCAGC
1 ACCGAAGGCAGGAGTGCCTGTG-A-C
2543238 ACCGAAGGCAG
1 ACCGAAGGCAG
2543249 AAGTACTGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 3 0.10
24 24 0.83
ACGTcount: A:0.31, C:0.25, G:0.34, T:0.10
Consensus pattern (24 bp):
ACCGAAGGCAGGAGTGCCTGTGAC
Found at i:2549415 original size:29 final size:29
Alignment explanation
Indices: 2549374--2549445 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
2549364 TGAATCAAAT
* *
2549374 TAAAATTTTATGTATAAAATCACACA-AAA
1 TAAAAGTTCATGTAT-AAATCACACATAAA
* * *
2549403 TCAAAGTTCATGTATGAATTACACATTAAA
1 TAAAAGTTCATGTATAAATCACACA-TAAA
2549433 TAAAAGTTCATGT
1 TAAAAGTTCATGT
2549446 TTAATTTTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
28 8 0.23
29 12 0.34
30 15 0.43
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.33
Consensus pattern (29 bp):
TAAAAGTTCATGTATAAATCACACATAAA
Found at i:2555132 original size:21 final size:20
Alignment explanation
Indices: 2555102--2555140 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
2555092 AGGCATAGAT
2555102 TCCAACTTCAATTCTACGTA
1 TCCAACTTCAATTCTACGTA
2555122 TCCAAGCTTCAATTCTACG
1 TCCAA-CTTCAATTCTACG
2555141 CATCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (20 bp):
TCCAACTTCAATTCTACGTA
Found at i:2562811 original size:27 final size:29
Alignment explanation
Indices: 2562760--2562819 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 29
2562750 GATTCTTTTT
2562760 AAGCTGGTAACTAAAATTTTGTTTTTGTCAC
1 AAGCTGGTAACTAAAA--TTGTTTTTGTCAC
2562791 AAGCTGGTAACTAAAA-T-TTTTTGTCAC
1 AAGCTGGTAACTAAAATTGTTTTTGTCAC
2562818 AA
1 AA
2562820 CTGCTATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 12 0.41
28 1 0.03
31 16 0.55
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (29 bp):
AAGCTGGTAACTAAAATTGTTTTTGTCAC
Found at i:2568069 original size:354 final size:342
Alignment explanation
Indices: 2567286--2568194 Score: 1188
Period size: 344 Copynumber: 2.6 Consensus size: 342
2567276 CTTTTTTGTT
* * *
2567286 TGCAGGTCAAAGAAGCTGAAGCTGCAGAACAGACTTCTAGCTCTGATGAGTCAGAGATGAATATT
1 TGCAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAGTCAGAGAAGAATATT
* *
2567351 GTAAATCAAGGCACTGCTCCAAGAAGAATACACTTGCAAACGAAACTTTCTACTGGGGCAATGAA
66 GTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGCAAAC--AACTTTCTACTGGGCCAATGAA
* ** * *
2567416 GGGTTCTGCAGGTTGTGTCAATGGTGAGAACATGACTAA-TCCTGGCCTCGTTGAAGAAGAAGTT
129 AGGTTCTGCAGGCCGTGTCGATGGTGGGAACATGAC-AAGTCCTGGCCTCGTTGAAGAAGAAGTT
*
2567480 CAGTCTGCTCTTACTGAGGTAGAGTTACCAGGAAAAGCTAATTTTGAGCACTGTTGATATCTTGT
193 CAGTCTGCTCTAACTGAGGTAGAGTTACCAGGAAAAGCTAATTTTGAGCACTGTTGATATCTTGT
**
2567545 TTATCTTACTGCCAAAGGCCAAGTTATAATATTAGTACACTGAAATACATTTCTCAAGGTGAACA
258 TTATCTTACTGCCAAAGGCCAAAATATAATATTAGTACACTGAAATACATTTCTCAAGGTGAACA
*
2567610 ATATCTTCCAATACTTTGAA
323 ATATCTTCCAATACTTTAAA
* * *
2567630 TGCAGGTCACAGAAGCTGAAGCTGCTGGACTGACTTCTAGCTCGGATGAGTCAGAGAAGAATATT
1 TGCAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAGTCAGAGAAGAATATT
** *
2567695 GTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGCAAACTAGACTTTCTACCAGACCAATGAA
66 GTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGCAAAC-A-ACTTTCTACTGGGCCAATGAA
* * *
2567760 AGGTTCTGCAGGCGGTGTCGATGGTGGGAGCATGGCAAGTCCTGGCCTCGTTGAAGAAGAAGTTC
129 AGGTTCTGCAGGCCGTGTCGATGGTGGGAACATGACAAGTCCTGGCCTCGTTGAAGAAGAAGTTC
* * *
2567825 AATCTGCTCTAACCGAGGTAGAGTTACCAGGAAAAAGCTAATTTTGAGCGCTGTTGATGCA-CTG
194 AGTCTGCTCTAACTGAGGTAGAGTTACCAGG-AAAAGCTAATTTTGAGCACTGTTGAT--ATCT-
* * ** * * *
2567889 TTTATCATACTCCTTTTCTTTTGCTGAAGG-TAAAATATAATGTTAGT-CACTGAATTACATTTC
255 TGT-T--TA-T-C-TTAC---TGCCAAAGGCCAAAATATAATATTAGTACACTGAAATACATTTC
* *
2567952 TCGAA-GTGAGCAATTTCTTCCAATACTTTAAA
311 TC-AAGGTGAACAATATCTTCCAATACTTTAAA
2567984 TGCAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAGTCAGAGAAGAATATT
1 TGCAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAGTCAGAGAAGAATATT
* * * * * * *
2568049 GTAAACCAAGCCATTGCTCCAAGAAGAATATGTTTG---A-AACTTTCTTCTGGGCCGATGAAAG
66 GTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGCAAACAACTTTCTACTGGGCCAATGAAAG
* *
2568110 GTTCTGCAGGCCGTGTCGATGGTGGGAACATGACAAGTCCTGGCCTCGGTAAAGAAGAAGTTCAG
131 GTTCTGCAGGCCGTGTCGATGGTGGGAACATGACAAGTCCTGGCCTCGTTGAAGAAGAAGTTCAG
2568175 TCTGCTCTAACTGAGGTAGA
196 TCTGCTCTAACTGAGGTAGA
2568195 TGAACTAGGA
Statistics
Matches: 494, Mismatches: 55, Indels: 28
0.86 0.10 0.05
Matches are distributed among these distances:
343 3 0.01
344 199 0.40
345 25 0.05
346 2 0.00
347 3 0.01
348 97 0.20
349 1 0.00
350 2 0.00
351 2 0.00
352 1 0.00
353 3 0.01
354 134 0.27
355 15 0.03
356 7 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (342 bp):
TGCAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAGTCAGAGAAGAATATT
GTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGCAAACAACTTTCTACTGGGCCAATGAAAG
GTTCTGCAGGCCGTGTCGATGGTGGGAACATGACAAGTCCTGGCCTCGTTGAAGAAGAAGTTCAG
TCTGCTCTAACTGAGGTAGAGTTACCAGGAAAAGCTAATTTTGAGCACTGTTGATATCTTGTTTA
TCTTACTGCCAAAGGCCAAAATATAATATTAGTACACTGAAATACATTTCTCAAGGTGAACAATA
TCTTCCAATACTTTAAA
Found at i:2583696 original size:17 final size:17
Alignment explanation
Indices: 2583674--2583706 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2583664 AATAATCATT
2583674 CTTATTTATTAAACATC
1 CTTATTTATTAAACATC
2583691 CTTATTTATTAAACAT
1 CTTATTTATTAAACAT
2583707 GTAATAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
CTTATTTATTAAACATC
Found at i:2585600 original size:21 final size:23
Alignment explanation
Indices: 2585571--2585613 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
2585561 CTAGTTTTAT
2585571 TATAGTTTTC-TTCTTT-TTGTA
1 TATAGTTTTCATTCTTTATTGTA
*
2585592 TATATTTTTCATTCTTTATTGT
1 TATAGTTTTCATTCTTTATTGT
2585614 CGTCATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 6 0.32
23 4 0.21
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.67
Consensus pattern (23 bp):
TATAGTTTTCATTCTTTATTGTA
Found at i:2592805 original size:6 final size:6
Alignment explanation
Indices: 2592794--2592847 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
2592784 TGTAGTCCTT
* *
2592794 TTTTTC TTTTTC TTTTT- TTTTT- TTTTTA ATTTTC TTTTCTC TTTTT-
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT-TC TTTTTC
2592840 TTTTTC TT
1 TTTTTC TT
2592848 AATATATTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
5 15 0.36
6 21 0.50
7 6 0.14
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:2592820 original size:22 final size:24
Alignment explanation
Indices: 2592792--2592847 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 24
2592782 AGTGTAGTCC
2592792 TTTTTTTCTTTTTCTTTT-T-TTT
1 TTTTTTTCTTTTTCTTTTCTCTTT
**
2592814 TTTTTTTAATTTTCTTTTCTCTTT
1 TTTTTTTCTTTTTCTTTTCTCTTT
2592838 TTTTTTTCTT
1 TTTTTTTCTT
2592848 AATATATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 16 0.57
23 1 0.04
24 11 0.39
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.86
Consensus pattern (24 bp):
TTTTTTTCTTTTTCTTTTCTCTTT
Found at i:2592838 original size:27 final size:28
Alignment explanation
Indices: 2592795--2592850 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
2592785 GTAGTCCTTT
* *
2592795 TTTTCTTTTTCTTTTTTTTTTTTTTTAA
1 TTTTCTTTTTCTCTTTTTTTTTTCTTAA
2592823 TTTTC-TTTTCTCTTTTTTTTTTCTTAA
1 TTTTCTTTTTCTCTTTTTTTTTTCTTAA
2592850 T
1 T
2592851 ATATTCTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (28 bp):
TTTTCTTTTTCTCTTTTTTTTTTCTTAA
Found at i:2599243 original size:2 final size:2
Alignment explanation
Indices: 2599236--2599265 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2599226 TTTGGTGGGG
2599236 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2599266 AGAAAACCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2603811 original size:2 final size:2
Alignment explanation
Indices: 2603804--2603845 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
2603794 GTTAGGCTCC
*
2603804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A
2603846 CTTGATGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2608385 original size:17 final size:17
Alignment explanation
Indices: 2608363--2608397 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2608353 TGCTCTGTTC
2608363 AATGGATTGTTTCCGTT
1 AATGGATTGTTTCCGTT
2608380 AATGGATTGTTTCCGTT
1 AATGGATTGTTTCCGTT
2608397 A
1 A
2608398 GTAAAAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.46
Consensus pattern (17 bp):
AATGGATTGTTTCCGTT
Found at i:2617749 original size:14 final size:14
Alignment explanation
Indices: 2617730--2617768 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2617720 AAATATAGTA
2617730 AAATATTAAAAAAT
1 AAATATTAAAAAAT
*
2617744 AAATATTTAAAAAT
1 AAATATTAAAAAAT
*
2617758 ATATATTAAAA
1 AAATATTAAAA
2617769 TATTTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATTAAAAAAT
Found at i:2627277 original size:23 final size:24
Alignment explanation
Indices: 2627235--2627284 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
2627225 TATTTGGGTT
2627235 AAGACTAAAATTTGAAAATT-AAA
1 AAGACTAAAATTTGAAAATTCAAA
*
2627258 AAGACTAAAA-TTGATCAATTCAAA
1 AAGACTAAAATTTGA-AAATTCAAA
2627282 AAG
1 AAG
2627285 TACATAGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 14 0.58
24 6 0.25
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.24
Consensus pattern (24 bp):
AAGACTAAAATTTGAAAATTCAAA
Found at i:2632102 original size:16 final size:16
Alignment explanation
Indices: 2632047--2632108 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
2632037 GTCATTATTG
*
2632047 TTTTAAAATAATAAAA
1 TTTTAAATTAATAAAA
* **
2632063 TTTT-AATT-TTAATT
1 TTTTAAATTAATAAAA
*
2632077 TTTTATAATTTATAAAA
1 TTTTA-AATTAATAAAA
2632094 TTTTAAATTAATAAA
1 TTTTAAATTAATAAA
2632109 GTTAAAATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
14 7 0.20
15 3 0.09
16 17 0.49
17 8 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAATTAATAAAA
Found at i:2635936 original size:17 final size:16
Alignment explanation
Indices: 2635898--2635934 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2635888 ATTATGTTTG
*
2635898 AAAAATGGACTTTGAT
1 AAAAATGAACTTTGAT
2635914 AAAAATGAACTTTGAT
1 AAAAATGAACTTTGAT
2635930 AAAAA
1 AAAAA
2635935 ATTAGACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (16 bp):
AAAAATGAACTTTGAT
Found at i:2637571 original size:5 final size:5
Alignment explanation
Indices: 2637561--2637589 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2637551 TAACCCCCTT
2637561 TTCTG TTCTG TTCTG TTCTG TTCTG TTCT
1 TTCTG TTCTG TTCTG TTCTG TTCTG TTCT
2637590 TTGTTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.17, T:0.62
Consensus pattern (5 bp):
TTCTG
Found at i:2642058 original size:17 final size:17
Alignment explanation
Indices: 2642032--2642064 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2642022 AACACTACTT
2642032 AAGAAATAATA-ATAAA
1 AAGAAATAATATATAAA
2642048 AAGATAATAATATATAA
1 AAGA-AATAATATATAA
2642065 TCAGTAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (17 bp):
AAGAAATAATATATAAA
Found at i:2644758 original size:2 final size:2
Alignment explanation
Indices: 2644751--2644776 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2644741 TACATTCTCA
2644751 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
2644777 GCTCACCTTC
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:2646724 original size:5 final size:6
Alignment explanation
Indices: 2646706--2646730 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2646696 TTCTTCTCTG
2646706 TTGTTT TTGTTT TTGTTT TTGTTT T
1 TTGTTT TTGTTT TTGTTT TTGTTT T
2646731 CCTTTCTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTGTTT
Found at i:2647156 original size:16 final size:15
Alignment explanation
Indices: 2647135--2647172 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2647125 AATGGAATGA
2647135 AAATAAATATTTAATT
1 AAATAAA-ATTTAATT
2647151 AAAT-AAATTTAATT
1 AAATAAAATTTAATT
*
2647165 AATTAAAA
1 AAATAAAA
2647173 ATTTTAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 11 0.55
15 5 0.25
16 4 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATAAAATTTAATT
Found at i:2647248 original size:20 final size:20
Alignment explanation
Indices: 2647223--2647261 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2647213 TTTCACATGT
*
2647223 CTCTCTTCTTCATCTTCTTC
1 CTCTCTTCTCCATCTTCTTC
2647243 CTCTCTTCTCCATCTTCTT
1 CTCTCTTCTCCATCTTCTT
2647262 TTTCTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (20 bp):
CTCTCTTCTCCATCTTCTTC
Found at i:2647475 original size:113 final size:113
Alignment explanation
Indices: 2647272--2647502 Score: 381
Period size: 113 Copynumber: 2.0 Consensus size: 113
2647262 TTTCTTCTTC
* *
2647272 TCTTTTGATTCCAATATATTTAGTTACAAATTTGTCTCAAAGCTTGAATCTTTAAAATTCATTAA
1 TCTTTTGATTCCAATATATTTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACTCATTAA
* * *
2647337 CCAAAAGATTCAATATATTTTGTTCCAATATCTTCTTCCCGTTAAGTT
66 CCAAAAGATTCAATATATTTGGTTCCAATATCTTCTTCCCATTAAATT
* *
2647385 TCTTTTGATTCCAATATATTTAGTTACAAATCTGTTTCAAATCTTGAATCTTTAAAACTCATTAA
1 TCTTTTGATTCCAATATATTTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACTCATTAA
* *
2647450 CCAAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCTATTAAATT
66 CCAAAAGATTCAATATATTTGGTTCCAATATCTTCTTCCCATTAAATT
2647498 TCTTT
1 TCTTT
2647503 GAGTTAATGG
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (113 bp):
TCTTTTGATTCCAATATATTTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACTCATTAA
CCAAAAGATTCAATATATTTGGTTCCAATATCTTCTTCCCATTAAATT
Found at i:2654419 original size:87 final size:87
Alignment explanation
Indices: 2654283--2654519 Score: 221
Period size: 87 Copynumber: 2.7 Consensus size: 87
2654273 AAGTATCTTG
* * ** * * *
2654283 AAAATTAAATAAGAATAAACAAAAATTATTATAATTATTCAAGAAAATAAAAAAAATTATTGTAG
1 AAAATGAAATAA-AATAAATACTAATAATTATAATTATTCGA-AAAATAAAAAAAATTATTGCAG
* * * * * *
2654348 CACTAGATTTAAATTTAAGTGTCTCG
64 CACCAAATTCAAACTT-AGTG-CCCA
* *
2654374 AAAATGAAATAAAAT-AA-A-TAATCATTATAATTATTCCGAAAAATAAAAAAAA-TATTGCATC
1 AAAATGAAATAAAATAAATACTAATAATTATAATTATT-CGAAAAATAAAAAAAATTATTGCAGC
2654435 ACCAAATTCAAACTTAGTGCCCA
65 ACCAAATTCAAACTTAGTGCCCA
* *
2654458 AAAATGAAATAAAATAAATACTAATAATTATAATTCTTTCGGAAAATAAAAAAGATATTATT
1 AAAATGAAATAAAATAAATACTAATAATTATAATT-ATTCGAAAAATAAAAAA-A-ATTATT
2654520 CTAACATTAG
Statistics
Matches: 123, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
84 17 0.14
85 6 0.05
86 19 0.15
87 54 0.44
88 6 0.05
89 3 0.02
90 7 0.06
91 11 0.09
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (87 bp):
AAAATGAAATAAAATAAATACTAATAATTATAATTATTCGAAAAATAAAAAAAATTATTGCAGCA
CCAAATTCAAACTTAGTGCCCA
Found at i:2657541 original size:49 final size:49
Alignment explanation
Indices: 2657469--2657567 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
2657459 TTATCAAATA
2657469 ATCAATTTAATTTTAATTATAAACCATTTAATAAATATATTTGTAAGAT
1 ATCAATTTAATTTTAATTATAAACCATTTAATAAATATATTTGTAAGAT
2657518 ATCAATTTAATTTTAATTATAAACCATTTAATAAATATATTTGTAAGAT
1 ATCAATTTAATTTTAATTATAAACCATTTAATAAATATATTTGTAAGAT
2657567 A
1 A
2657568 AGAAAGGATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (49 bp):
ATCAATTTAATTTTAATTATAAACCATTTAATAAATATATTTGTAAGAT
Found at i:2660186 original size:4 final size:4
Alignment explanation
Indices: 2660172--2660217 Score: 56
Period size: 4 Copynumber: 11.0 Consensus size: 4
2660162 GACTGGCATA
* *
2660172 GTAT ATAT GTAT GTAT GTAT GTAT GTAT GACTAT GTAT ATAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G--TAT GTAT GTAT GTAT
2660218 ATGAATGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 32 0.89
6 4 0.11
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:2660225 original size:18 final size:18
Alignment explanation
Indices: 2660175--2660227 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 18
2660165 TGGCATAGTA
* *
2660175 TATATGTATGTATGTATG
1 TATATGAATGTATATATG
2660193 TATGTATGACTATGTATATATG
1 TA--TATGA--ATGTATATATG
2660215 TATATGAATGTAT
1 TATATGAATGTAT
2660228 TTGCATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 8 0.28
20 9 0.31
22 12 0.41
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (18 bp):
TATATGAATGTATATATG
Found at i:2661611 original size:38 final size:38
Alignment explanation
Indices: 2661556--2661628 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
2661546 ATAATGTTTG
* * *
2661556 TAATTTTTTGTGTAAAAGATAATTTCTGAAACTCCTTT
1 TAATTTTATGTGGAAAAGATAATTTCTAAAACTCCTTT
2661594 TAATTTTATGTGGAAAAGATAATTTCTAAAACTCC
1 TAATTTTATGTGGAAAAGATAATTTCTAAAACTCC
2661629 ATGTTTGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (38 bp):
TAATTTTATGTGGAAAAGATAATTTCTAAAACTCCTTT
Found at i:2662318 original size:29 final size:28
Alignment explanation
Indices: 2662249--2662321 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
2662239 CAATTAGAGT
* *
2662249 TTCATGTGTATAATTGCACAAAATTAAAT
1 TTCAT-TGTATAATTGCACAAAATCAAAG
*
2662278 TTCATTTATATAATTGCACATTAAATCAAAG
1 TTCA-TTGTATAATTGCACA--AAATCAAAG
2662309 TTCA-TGTATAATT
1 TTCATTGTATAATT
2662322 TTAAGATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 25 0.68
30 1 0.03
31 11 0.30
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (28 bp):
TTCATTGTATAATTGCACAAAATCAAAG
Found at i:2677129 original size:43 final size:43
Alignment explanation
Indices: 2677059--2677140 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
2677049 TTATGAGGAA
** * * *
2677059 AAATGCCTCTAAAGAACATGGTTTTTAGCGGCGCTTTCCTCAC
1 AAATGCCTCTAAAGAACATAATCTTTAGCGACACTTTCCTCAC
2677102 AAATGCCGT-TAAAGAACATAATCTTTAGCGACACTTTCC
1 AAATGCC-TCTAAAGAACATAATCTTTAGCGACACTTTCC
2677141 CATAAACGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 32 0.97
44 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (43 bp):
AAATGCCTCTAAAGAACATAATCTTTAGCGACACTTTCCTCAC
Found at i:2684190 original size:31 final size:31
Alignment explanation
Indices: 2684155--2684220 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
2684145 CATGTAACGA
*
2684155 AAAAAGTTATAATTT-AGTCACTGAACTATCC
1 AAAAA-TTATAATTTAAGTCACTAAACTATCC
* * *
2684186 AAAAATTTTCATTTAAGTCACTAAACTATTC
1 AAAAATTATAATTTAAGTCACTAAACTATCC
2684217 AAAA
1 AAAA
2684221 GCTTTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.33
Consensus pattern (31 bp):
AAAAATTATAATTTAAGTCACTAAACTATCC
Found at i:2694156 original size:17 final size:16
Alignment explanation
Indices: 2694127--2694167 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
2694117 AGAGATTAAT
2694127 TTATTTTTATATAAAA
1 TTATTTTTATATAAAA
*
2694143 TTATTTGTTTTATAAAA
1 TTATTT-TTATATAAAA
*
2694160 TAATTTTT
1 TTATTTTT
2694168 TGTGCAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTATTTTTATATAAAA
Found at i:2694164 original size:20 final size:19
Alignment explanation
Indices: 2694131--2694170 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2694121 ATTAATTTAT
*
2694131 TTTTATATAAAATTATTTG
1 TTTTATAAAAAATTATTTG
*
2694150 TTTTATAAAATAATTTTTTG
1 TTTTATAAAA-AATTATTTG
2694170 T
1 T
2694171 GCAATCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTATAAAAAATTATTTG
Found at i:2694211 original size:21 final size:21
Alignment explanation
Indices: 2694177--2694216 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2694167 TTGTGCAATC
2694177 AATTTATTATTTATATAAATTA
1 AATTTATTATTTATA-AAATTA
*
2694199 AATTTCTT-TTTATAAAAT
1 AATTTATTATTTATAAAAT
2694217 AGTTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTTATTATTTATAAAATTA
Found at i:2699724 original size:30 final size:32
Alignment explanation
Indices: 2699690--2699754 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
2699680 AGCCACTCAA
*
2699690 TTTAGCCATTTACATTTT-AATTA-TTTTTAT
1 TTTAGCCATTCACATTTTAAATTATTTTTTAT
** *
2699720 TTTAGTTATTCACGTTTTAAATTATTTTTTAT
1 TTTAGCCATTCACATTTTAAATTATTTTTTAT
2699752 TTT
1 TTT
2699755 GATCACTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 14 0.48
31 5 0.17
32 10 0.34
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.63
Consensus pattern (32 bp):
TTTAGCCATTCACATTTTAAATTATTTTTTAT
Found at i:2709939 original size:29 final size:29
Alignment explanation
Indices: 2709902--2709958 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2709892 AATTTTGTAT
2709902 AAAAATATA-TTCATAATATTTTAATAAAC
1 AAAAATATATTTCATAA-ATTTTAATAAAC
* * *
2709931 AAAAGTATATTTTATAAATTTTATTAAA
1 AAAAATATATTTCATAAATTTTAATAAA
2709959 TATGCAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (29 bp):
AAAAATATATTTCATAAATTTTAATAAAC
Found at i:2712161 original size:18 final size:19
Alignment explanation
Indices: 2712138--2712180 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
2712128 AAAAATATAT
* *
2712138 TAATTATGATT-ATGATTA
1 TAATTATAATTCATGAATA
2712156 TAATTATAATTCATGAATA
1 TAATTATAATTCATGAATA
2712175 -AATTAT
1 TAATTAT
2712181 TTTTTACGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (19 bp):
TAATTATAATTCATGAATA
Found at i:2713427 original size:18 final size:20
Alignment explanation
Indices: 2713389--2713428 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2713379 GTAATTGGAA
*
2713389 TTTACCGCTAAACTATTAAT
1 TTTACCACTAAACTATTAAT
2713409 TTTACCACT-AACT-TTAAT
1 TTTACCACTAAACTATTAAT
2713427 TT
1 TT
2713429 CTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (20 bp):
TTTACCACTAAACTATTAAT
Found at i:2715175 original size:34 final size:34
Alignment explanation
Indices: 2715137--2715201 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
2715127 GGTATAATTT
* *
2715137 ATGCTAATTAGAGTTTT-TTATTATAAGGATTTTA
1 ATGCTAATTAGA-TTTTAGTATAATAAGGATTTTA
*
2715171 ATGCTAATTGGATTTTAGTATAATAAGGATT
1 ATGCTAATTAGATTTTAGTATAATAAGGATT
2715202 ATTTATAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 4 0.15
34 23 0.85
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (34 bp):
ATGCTAATTAGATTTTAGTATAATAAGGATTTTA
Found at i:2718608 original size:15 final size:15
Alignment explanation
Indices: 2718588--2718617 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2718578 ATGTACCGAC
2718588 CATCCTCAACCTCAT
1 CATCCTCAACCTCAT
*
2718603 CATCCTCTACCTCAT
1 CATCCTCAACCTCAT
2718618 ACACTGCCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (15 bp):
CATCCTCAACCTCAT
Found at i:2720945 original size:18 final size:18
Alignment explanation
Indices: 2720915--2720967 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2720905 TTGGAAATCA
*
2720915 AGAAACAAA-AAGAAGCTG
1 AGAAA-AAAGAAGAAGCAG
2720933 AGAAAAAAGAAGAAG-AG
1 AGAAAAAAGAAGAAGCAG
*
2720950 AGAAAGAAGAAAGAAGCA
1 AGAAAAAAG-AAGAAGCA
2720968 ACAGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 12 0.40
18 17 0.57
19 1 0.03
ACGTcount: A:0.66, C:0.06, G:0.26, T:0.02
Consensus pattern (18 bp):
AGAAAAAAGAAGAAGCAG
Found at i:2727519 original size:3 final size:3
Alignment explanation
Indices: 2727511--2727548 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2727501 CACTCAATAA
2727511 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2727549 AAGTGGTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2734343 original size:11 final size:11
Alignment explanation
Indices: 2734327--2734352 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2734317 TTAAAATCGA
2734327 TATTAATTTAT
1 TATTAATTTAT
2734338 TATTAATTTAT
1 TATTAATTTAT
2734349 TATT
1 TATT
2734353 TTTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTAATTTAT
Found at i:2740161 original size:31 final size:31
Alignment explanation
Indices: 2740121--2740180 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2740111 TTTAATTCGA
2740121 TTAAATTTAATTATTGTACTTTTCGAATTAG
1 TTAAATTTAATTATTGTACTTTTCGAATTAG
* * *
2740152 TTAATTTTAATTATTGTATTTTTTGAATT
1 TTAAATTTAATTATTGTACTTTTCGAATT
2740181 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.58
Consensus pattern (31 bp):
TTAAATTTAATTATTGTACTTTTCGAATTAG
Found at i:2743185 original size:22 final size:24
Alignment explanation
Indices: 2743145--2743205 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 24
2743135 TAAACGGAAC
* *
2743145 AAACAGAGAGTACCGAAGTACT-G
1 AAACAGAGAGCACAGAAGTACTGG
* *
2743168 -AACAGAGAGCACATAAGTGCTGG
1 AAACAGAGAGCACAGAAGTACTGG
2743191 ACAACAGAGAGCACA
1 A-AACAGAGAGCACA
2743206 CAAAGTGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 17 0.55
23 1 0.03
25 13 0.42
ACGTcount: A:0.44, C:0.20, G:0.26, T:0.10
Consensus pattern (24 bp):
AAACAGAGAGCACAGAAGTACTGG
Found at i:2743219 original size:23 final size:23
Alignment explanation
Indices: 2743145--2743335 Score: 96
Period size: 23 Copynumber: 8.5 Consensus size: 23
2743135 TAAACGGAAC
* * *
2743145 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
2743167 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
2743189 GGACAACAGAGAGCACACAAAGTGCT
1 --A-AACAGAGAGCACACAAAGTGCT
* *
2743215 AAACAAAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
* *
2743235 --AC--TGAGCACCCAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
2743254 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
2743277 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
* * *
2743302 AAACAAAGAGCACACACAGTGAT
1 AAACAGAGAGCACACAAAGTGCT
*
2743325 AATCAGAGAGC
1 AAACAGAGAGC
2743336 GCGCTAGTGT
Statistics
Matches: 126, Mismatches: 27, Indels: 31
0.68 0.15 0.17
Matches are distributed among these distances:
16 9 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.02
22 18 0.14
23 53 0.42
24 3 0.02
25 28 0.22
26 8 0.06
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:2743224 original size:25 final size:25
Alignment explanation
Indices: 2743168--2743232 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
2743158 CGAAGTACTG
* **
2743168 AACAGAGAGCACATAAGTGCTGGAC
1 AACAGAGAGCACAAAAGTGCTAAAC
2743193 AACAGAGAGCACACAAAGTGCTAAAC
1 AACAGAGAGCACA-AAAGTGCTAAAC
2743219 AA-AGAGTA-CACAAA
1 AACAGAG-AGCACAAA
2743233 GTACTGAGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 2 0.06
25 21 0.60
26 12 0.34
ACGTcount: A:0.49, C:0.20, G:0.22, T:0.09
Consensus pattern (25 bp):
AACAGAGAGCACAAAAGTGCTAAAC
Found at i:2758880 original size:17 final size:18
Alignment explanation
Indices: 2758850--2758887 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
2758840 GTGTTATGAA
*
2758850 AAAACTATCCACAAATGC
1 AAAACTATCCACAAAAGC
2758868 AAAACTA-CCACAAAAGC
1 AAAACTATCCACAAAAGC
2758885 AAA
1 AAA
2758888 CGAAAACGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.58, C:0.26, G:0.05, T:0.11
Consensus pattern (18 bp):
AAAACTATCCACAAAAGC
Found at i:2761678 original size:23 final size:23
Alignment explanation
Indices: 2761605--2761796 Score: 127
Period size: 23 Copynumber: 8.6 Consensus size: 23
2761595 TATACGGAAC
* * *
2761605 AAACAAAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
2761627 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
2761648 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
2761674 AAACAGAGAGTATACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
* *
2761694 --AC--TGAGCACACAAGGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
2761713 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
2761736 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
2761759 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
2761784 AAACAGAGAGCAC
1 AAACAGAGAGCAC
2761797 GCTAGTGTTC
Statistics
Matches: 134, Mismatches: 20, Indels: 31
0.72 0.11 0.17
Matches are distributed among these distances:
16 8 0.06
18 3 0.02
19 1 0.01
20 1 0.01
21 18 0.13
23 63 0.47
24 2 0.01
25 30 0.22
26 8 0.06
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:2761791 original size:48 final size:46
Alignment explanation
Indices: 2761697--2761796 Score: 139
Period size: 48 Copynumber: 2.1 Consensus size: 46
2761687 ACAAAGTACT
* *
2761697 GAGCACACAAGGTGCTAATCAGAGAGCACACGAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAAACAGA
*
2761743 GAGCACACAAAGTGCTAATAACAGAGAGCACGA-GACGTGCTAAACAGA
1 GAGCACACAAAGTGCTAAT--CAGAGAGCAC-ACGAAGTGCTAAACAGA
2761791 GAGCAC
1 GAGCAC
2761797 GCTAGTGTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
46 18 0.38
48 29 0.60
49 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.26, T:0.11
Consensus pattern (46 bp):
GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAAACAGA
Found at i:2765103 original size:18 final size:18
Alignment explanation
Indices: 2765076--2765111 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2765066 ATCATTTTAC
2765076 TCAATATCAT-AAAATAA
1 TCAATATCATCAAAATAA
2765093 TCAAGTATCATCAAAATAA
1 TCAA-TATCATCAAAATAA
2765112 CATTTATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 6 0.35
19 7 0.41
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.28
Consensus pattern (18 bp):
TCAATATCATCAAAATAA
Found at i:2765919 original size:6 final size:6
Alignment explanation
Indices: 2765900--2765938 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
2765890 ACAGTTCATA
* *
2765900 TCACTT TCAATT TCATTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
2765939 ATTTTGATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (6 bp):
TCACTT
Found at i:2765925 original size:12 final size:12
Alignment explanation
Indices: 2765904--2765943 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2765894 TTCATATCAC
*
2765904 TTTCAATTTCAT
1 TTTCACTTTCAT
*
2765916 TTTCACTTTCAC
1 TTTCACTTTCAT
2765928 TTTCACTTTCAAT
1 TTTCACTTTC-AT
2765941 TTT
1 TTT
2765944 GATCACAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTCACTTTCAT
Found at i:2766115 original size:22 final size:22
Alignment explanation
Indices: 2766089--2766134 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2766079 TAAACATATA
2766089 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
2766111 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
2766133 AT
1 AT
2766135 CACATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATTTCACATATACATTGTTC
Found at i:2766139 original size:18 final size:20
Alignment explanation
Indices: 2766093--2766142 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
2766083 CATATAATAT
2766093 TTCACATATACATTGTTCATA
1 TTCACATATACATTGTTCA-A
2766114 TTTCACATATACATTGTTC-A
1 -TTCACATATACATTGTTCAA
2766134 -TCACATATA
1 TTCACATATA
2766143 TATCATCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.32
20 1 0.04
22 18 0.64
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (20 bp):
TTCACATATACATTGTTCAA
Found at i:2771685 original size:23 final size:22
Alignment explanation
Indices: 2771648--2771712 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 22
2771638 ACAAAGTACT
2771648 GAGCACACAAGGTGCTAATCAAA
1 GAGCACACAA-GTGCTAATCAAA
* *
2771671 TAGCACACGAAGTGCTAATCAGA
1 GAGCACAC-AAGTGCTAATCAAA
2771694 GAGCACACACAGTGCTAAT
1 GAGCACACA-AGTGCTAAT
2771713 AACAGAGAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.92
24 2 0.05
ACGTcount: A:0.40, C:0.23, G:0.22, T:0.15
Consensus pattern (22 bp):
GAGCACACAAGTGCTAATCAAA
Found at i:2771739 original size:23 final size:23
Alignment explanation
Indices: 2771648--2771744 Score: 83
Period size: 23 Copynumber: 4.1 Consensus size: 23
2771638 ACAAAGTACT
* *
2771648 GAGCACACA-AGGTGCTAATCAAA
1 GAGCACACACA-GTGCTAAACAGA
* *
2771671 TAGCACACGA-AGTGCTAATCAGA
1 GAGCACAC-ACAGTGCTAAACAGA
2771694 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACACAGTGCT-A-AACAGA
*
2771719 GAGCACGAGAC-GTGCTAAACAGA
1 GAGCAC-ACACAGTGCTAAACAGA
2771742 GAG
1 GAG
2771745 TGCGCTAGTG
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
22 1 0.02
23 40 0.62
24 4 0.06
25 16 0.25
26 3 0.05
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (23 bp):
GAGCACACACAGTGCTAAACAGA
Found at i:2774913 original size:21 final size:19
Alignment explanation
Indices: 2774873--2774915 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
2774863 ATTTGATTTT
2774873 TGTTTAGAATAAGATGAAA
1 TGTTTAGAATAAGATGAAA
2774892 TGTTTAAGAATTAAGTAT-AAA
1 TGTTT-AGAA-TAAG-ATGAAA
2774913 TGT
1 TGT
2774916 AGAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 10 0.48
22 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (19 bp):
TGTTTAGAATAAGATGAAA
Found at i:2775038 original size:15 final size:15
Alignment explanation
Indices: 2775015--2775050 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2775005 ATAACTTAAA
*
2775015 TTCAGCACTTAAATT
1 TTCAACACTTAAATT
*
2775030 TTCAACACTTAATTT
1 TTCAACACTTAAATT
2775045 TTCAAC
1 TTCAAC
2775051 TTATCAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (15 bp):
TTCAACACTTAAATT
Found at i:2775756 original size:13 final size:15
Alignment explanation
Indices: 2775720--2775762 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
2775710 CGAGAATAGG
2775720 TTTTTAATTAATAAA
1 TTTTTAATTAATAAA
2775735 TTTAATTAATTAA-AAA
1 TTT--TTAATTAATAAA
*
2775751 TTTTAAATTAAT
1 TTTTTAATTAAT
2775763 TACACATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 7 0.29
15 3 0.12
16 6 0.25
17 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTTAATTAATAAA
Found at i:2777774 original size:20 final size:20
Alignment explanation
Indices: 2777749--2777788 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2777739 TCATTTTTAG
*
2777749 ATAAATAAAAGAAACTAAAA
1 ATAAATAAAAAAAACTAAAA
2777769 ATAAATAAAAAAAACTAAAA
1 ATAAATAAAAAAAACTAAAA
2777789 TAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.15
Consensus pattern (20 bp):
ATAAATAAAAAAAACTAAAA
Found at i:2780329 original size:25 final size:24
Alignment explanation
Indices: 2780296--2780348 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
2780286 GTTTAATAAA
*
2780296 TTTAGATTTCGATTTTTTATATTTTT
1 TTTAGATTT-GATTTTTTA-ATTATT
2780322 TTTA-ATTTGATTTTTTAATTATT
1 TTTAGATTTGATTTTTTAATTATT
2780345 TTTA
1 TTTA
2780349 TTTGACTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 9 0.35
24 9 0.35
25 4 0.15
26 4 0.15
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.70
Consensus pattern (24 bp):
TTTAGATTTGATTTTTTAATTATT
Found at i:2780333 original size:24 final size:23
Alignment explanation
Indices: 2780296--2780353 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 23
2780286 GTTTAATAAA
*
2780296 TTTAGATTTCGATTTTTTATATTTTT
1 TTTA-ATTT-GATTTTTTA-ATTATT
2780322 TTTAATTTGATTTTTTAATTATT
1 TTTAATTTGATTTTTTAATTATT
2780345 TTT-ATTTGA
1 TTTAATTTGA
2780354 CTATTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 6 0.19
23 8 0.26
24 9 0.29
25 4 0.13
26 4 0.13
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (23 bp):
TTTAATTTGATTTTTTAATTATT
Found at i:2785577 original size:17 final size:17
Alignment explanation
Indices: 2785557--2785604 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
2785547 TTATTAATGT
2785557 TAAATTTTTTATTGAAA
1 TAAATTTTTTATTGAAA
* * *
2785574 TAAAATTTTAATGTTAAA
1 TAAATTTTTTAT-TGAAA
*
2785592 TAAATTTATTATT
1 TAAATTTTTTATT
2785605 TTTTAACTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TAAATTTTTTATTGAAA
Found at i:2791721 original size:18 final size:18
Alignment explanation
Indices: 2791681--2791715 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2791671 CGGATGTTTG
*
2791681 CGTGGCGGTGGAGGGAGA
1 CGTGGCGATGGAGGGAGA
2791699 CGTGGCGATGG-GGGAGA
1 CGTGGCGATGGAGGGAGA
2791716 GGGTGGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.17, C:0.11, G:0.60, T:0.11
Consensus pattern (18 bp):
CGTGGCGATGGAGGGAGA
Found at i:2805113 original size:15 final size:15
Alignment explanation
Indices: 2805095--2805135 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2805085 TTTGTATTAT
2805095 TTATTTTTAATATAA
1 TTATTTTTAATATAA
*
2805110 TTATTTTT-TTATAA
1 TTATTTTTAATATAA
2805124 TTACTTTTTAAT
1 TTA-TTTTTAAT
2805136 TTTTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 8 0.36
15 13 0.59
16 1 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTTTTAATATAA
Found at i:2805114 original size:19 final size:18
Alignment explanation
Indices: 2805090--2805141 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
2805080 ATATTTTTGT
2805090 ATTATTTATTTTTAATATA
1 ATTATTTATTTTTAAT-TA
2805109 ATTATTT-TTTTATAATTA
1 ATTATTTATTTT-TAATTA
*
2805127 CTT-TTTAATTTTTAA
1 ATTATTT-ATTTTTAA
2805142 AATTTCATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.10
18 11 0.38
19 15 0.52
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTATTTATTTTTAATTA
Found at i:2805117 original size:30 final size:29
Alignment explanation
Indices: 2805077--2805135 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
2805067 AATAATATCC
*
2805077 ATAATATTTTTGTATTATTTA-TTTTTAAT
1 ATAATATTTTTGTA-TAATTACTTTTTAAT
*
2805106 ATAATTATTTTTTTATAATTACTTTTTAAT
1 ATAA-TATTTTTGTATAATTACTTTTTAAT
2805136 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (29 bp):
ATAATATTTTTGTATAATTACTTTTTAAT
Found at i:2822993 original size:10 final size:10
Alignment explanation
Indices: 2822972--2823013 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
2822962 TGCTAATAAG
2822972 TTTTAT-ATT
1 TTTTATAATT
*
2822981 TTTTATCATT
1 TTTTATAATT
*
2822991 TTTAATAATT
1 TTTTATAATT
2823001 TTTATATAATT
1 TTT-TATAATT
2823012 TT
1 TT
2823014 GTATTGAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 6 0.21
10 14 0.50
11 8 0.29
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:2823366 original size:29 final size:30
Alignment explanation
Indices: 2823309--2823388 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
2823299 ATCTTAAAAT
* *
2823309 TATACATAAATTATAATTTAATATATAATTA
1 TATATATAAATTTTAATTT-ATATATAATTA
* *
2823340 TATATATAAATTTTAATTT-TATGTAATTT
1 TATATATAAATTTTAATTTATATATAATTA
*
2823369 TATATATGAAATTTTGATTT
1 TATATAT-AAATTTTAATTT
2823389 GATCAAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 15 0.35
30 11 0.26
31 17 0.40
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
TATATATAAATTTTAATTTATATATAATTA
Found at i:2823398 original size:30 final size:29
Alignment explanation
Indices: 2823308--2823399 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 29
2823298 AATCTTAAAA
* * * *
2823308 TTATACATAAATTATAATTTAATATATAATT
1 TTATATATAAATTTTAATTTGAT-CA-AATT
* * **
2823339 ATATATATAAATTTTAATTTTATGTAATT
1 TTATATATAAATTTTAATTTGATCAAATT
*
2823368 TTATATATGAAATTTTGATTTGATCAAATT
1 TTATATAT-AAATTTTAATTTGATCAAATT
2823398 TT
1 TT
2823400 TGTAAATTAT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 11 0.22
30 19 0.39
31 19 0.39
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (29 bp):
TTATATATAAATTTTAATTTGATCAAATT
Found at i:2823489 original size:29 final size:30
Alignment explanation
Indices: 2823437--2823514 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
2823427 TAGCATAATT
* * * *
2823437 TTATATTTATATATTACAATAATAAA-TAA
1 TTATATTTATTTAATATAAAAATAAATTAA
*
2823466 TTATATTTATTTAATATAAAAATAAATTGA
1 TTATATTTATTTAATATAAAAATAAATTAA
2823496 TGTAT-TTTATTTAAATATA
1 T-TATATTTATTT-AATATA
2823515 TATGATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 22 0.54
30 10 0.24
31 9 0.22
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (30 bp):
TTATATTTATTTAATATAAAAATAAATTAA
Found at i:2823607 original size:29 final size:30
Alignment explanation
Indices: 2823575--2823638 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
2823565 AAATTTCACA
* * *
2823575 TATATAATTGC-ACTAAATTAAAATTCATG
1 TATACAATTGCAACTAAATCAAAACTCATG
*
2823604 TATACAATTGCATATTAAATCAAAACTCATG
1 TATACAATTGCA-ACTAAATCAAAACTCATG
2823635 TATA
1 TATA
2823639 ATTTTGAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 10 0.34
31 19 0.66
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (30 bp):
TATACAATTGCAACTAAATCAAAACTCATG
Found at i:2824198 original size:17 final size:17
Alignment explanation
Indices: 2824173--2824210 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2824163 TGAACTAATC
2824173 TTTTCTATTTT-TAAAAT
1 TTTTCTATTTTAT-AAAT
*
2824190 TTTTTTATTTTATAAAT
1 TTTTCTATTTTATAAAT
2824207 TTTT
1 TTTT
2824211 AATAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCTATTTTATAAAT
Found at i:2824316 original size:2 final size:2
Alignment explanation
Indices: 2824309--2824333 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2824299 AAATAAATAA
2824309 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
2824334 AAGAAAAATT
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:2828788 original size:27 final size:27
Alignment explanation
Indices: 2828755--2828807 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2828745 TCAGCAAGTT
*
2828755 TCAGCTTGCTTT-TTGTTTCGGATTTCC
1 TCAGCTTGCTTTGTTG-CTCGGATTTCC
*
2828782 TCAGCTTTCTTTGTTGCTCGGATTTC
1 TCAGCTTGCTTTGTTGCTCGGATTTC
2828808 AACTCCCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.08, C:0.23, G:0.19, T:0.51
Consensus pattern (27 bp):
TCAGCTTGCTTTGTTGCTCGGATTTCC
Found at i:2865097 original size:16 final size:15
Alignment explanation
Indices: 2865075--2865120 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2865065 TTTGATCAAG
2865075 GATTTAACTTAATAC
1 GATTTAACTTAATAC
* *
2865090 GATGTTAACTAAACAC
1 GAT-TTAACTTAATAC
*
2865106 GGTTTAACTTAATAC
1 GATTTAACTTAATAC
2865121 TACAGGTCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (15 bp):
GATTTAACTTAATAC
Found at i:2874836 original size:20 final size:20
Alignment explanation
Indices: 2874811--2874849 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2874801 AGCCTCGTTG
* *
2874811 ATCTATTAATCACTCAAATA
1 ATCTATCAATCAATCAAATA
2874831 ATCTATCAATCAATCAAAT
1 ATCTATCAATCAATCAAAT
2874850 GTTTGACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ATCTATCAATCAATCAAATA
Found at i:2889274 original size:23 final size:23
Alignment explanation
Indices: 2889244--2889287 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
2889234 AATATGCTAA
2889244 TGTGATTACATAGTAGTATCTAG
1 TGTGATTACATAGTAGTATCTAG
2889267 TGTGATTACATAGTAGTATCT
1 TGTGATTACATAGTAGTATCT
2889288 GTTCATACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (23 bp):
TGTGATTACATAGTAGTATCTAG
Found at i:2897485 original size:15 final size:15
Alignment explanation
Indices: 2897465--2897497 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2897455 CAAAAAATTT
*
2897465 AAATATCAATTTAAA
1 AAATATCAAATTAAA
2897480 AAATATCAAATTAAA
1 AAATATCAAATTAAA
2897495 AAA
1 AAA
2897498 ATGGTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATATCAAATTAAA
Found at i:2897491 original size:16 final size:16
Alignment explanation
Indices: 2897465--2897509 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2897455 CAAAAAATTT
2897465 AAATATC-AATTTAAA
1 AAATATCAAATTTAAA
*
2897480 AAATATCAAATTAAAA
1 AAATATCAAATTTAAA
*
2897496 AAATGGTCAAATTT
1 AAAT-ATCAAATTT
2897510 GAGTATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 7 0.28
16 11 0.44
17 7 0.28
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (16 bp):
AAATATCAAATTTAAA
Found at i:2900690 original size:21 final size:20
Alignment explanation
Indices: 2900666--2900704 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2900656 TATAATATGA
2900666 TATAAAAAAAACTAAACACAC
1 TATAAAAAAAA-TAAACACAC
**
2900687 TATACTAAAAATAAACAC
1 TATAAAAAAAATAAACAC
2900705 CAGGAGCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (20 bp):
TATAAAAAAAATAAACACAC
Found at i:2903255 original size:15 final size:15
Alignment explanation
Indices: 2903235--2903265 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2903225 GTAAGTTATG
2903235 AATTTTGATATTTTT
1 AATTTTGATATTTTT
*
2903250 AATTTTTATATTTTT
1 AATTTTGATATTTTT
2903265 A
1 A
2903266 GAAATTAAAA
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:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
AATTTTGATATTTTT
Found at i:2912349 original size:3 final size:3
Alignment explanation
Indices: 2912341--2912390 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2912331 GATTTTTTGT
2912341 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2912389 TT
1 TT
2912391 TTGTTCGGTT
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:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2913728 original size:16 final size:15
Alignment explanation
Indices: 2913684--2913732 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
2913674 TGAGTATGTC
*
2913684 TTTGTATAAATGATT
1 TTTGTATAAATAATT
*
2913699 TGTGTAATTAAATAATAT
1 TTTGT-A-TAAATAAT-T
2913717 TTTGTATAAATAATT
1 TTTGTATAAATAATT
2913732 T
1 T
2913733 AAAAAAAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 8 0.29
18 5 0.18
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (15 bp):
TTTGTATAAATAATT
Found at i:2914611 original size:2 final size:2
Alignment explanation
Indices: 2914604--2914685 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
2914594 GTATTATCTG
2914604 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2914646 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2914686 GCTTACTTTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2915450 original size:38 final size:38
Alignment explanation
Indices: 2915396--2915486 Score: 166
Period size: 38 Copynumber: 2.4 Consensus size: 38
2915386 AGTTATGAAC
2915396 GTAGCTTTTCCCTTTTGTGTATCTGTTATTTGTGAAGA
1 GTAGCTTTTCCCTTTTGTGTATCTGTTATTTGTGAAGA
*
2915434 GTGGCTTTTCCCTTTTGTGTATCTGTTATTTGTGAAGA
1 GTAGCTTTTCCCTTTTGTGTATCTGTTATTTGTGAAGA
2915472 GTAGCTTTT-CCTTTT
1 GTAGCTTTTCCCTTTT
2915487 ACACACTCAC
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 6 0.12
38 45 0.88
ACGTcount: A:0.13, C:0.14, G:0.21, T:0.52
Consensus pattern (38 bp):
GTAGCTTTTCCCTTTTGTGTATCTGTTATTTGTGAAGA
Found at i:2923679 original size:16 final size:16
Alignment explanation
Indices: 2923658--2923712 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
2923648 AGCTTAATTT
2923658 AATAATATATATAAAA
1 AATAATATATATAAAA
* * **
2923674 AATAATA-ACACAATTT
1 AATAATATATATAA-AA
2923690 AATAATATATATAAAA
1 AATAATATATATAAAA
2923706 AATAATA
1 AATAATA
2923713 ACACAATTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
15 4 0.14
16 21 0.72
17 4 0.14
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAATATATATAAAA
Done.