Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 8 of 26
Found at i:1383329 original size:40 final size:42
Alignment explanation
Indices: 1383284--1383363 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 42
1383274 ATGTAAATAT
1383284 AAATA-TAAGATATAATT-T-TTTATAAATTTATAA-AAATAAA
1 AAATATTAA-ATATAATTATATTTA-AAATTTATAATAAATAAA
*
1383324 AAATATTAAATATAATTATATTTAATATTTATAATAAATA
1 AAATATTAAATATAATTATATTTAAAATTTATAATAAATA
1383364 TTTAATCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
40 13 0.37
41 13 0.37
42 9 0.26
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (42 bp):
AAATATTAAATATAATTATATTTAAAATTTATAATAAATAAA
Found at i:1386701 original size:38 final size:38
Alignment explanation
Indices: 1386648--1386738 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 38
1386638 AATAGCAGTA
* *
1386648 TCAATCCACGGAAATCAAATATGCAGTTGGGT-GCTATG
1 TCAATCCACGAAAATCAAATATG-AGTTGAGTGGCTATG
1386686 TCAATCCACGAAAATCAAATATGAGTTGAGTGGCTATG
1 TCAATCCACGAAAATCAAATATGAGTTGAGTGGCTATG
* *
1386724 TCAAACCACAAAAAT
1 TCAATCCACGAAAAT
1386739 GTAAATAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
37 7 0.15
38 41 0.85
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (38 bp):
TCAATCCACGAAAATCAAATATGAGTTGAGTGGCTATG
Found at i:1391463 original size:39 final size:39
Alignment explanation
Indices: 1391395--1391475 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
1391385 ATGGCAGTGT
* * *
1391395 CAATTCACGGAAATCAAATATGCAGTTGGGTGGCTATGC
1 CAATCCACGAAAATCAAATATGCAATTGGGTGGCTATGC
1391434 CAATCCACGAAAATCAAATATGCAATTGGGTGGCTATGC
1 CAATCCACGAAAATCAAATATGCAATTGGGTGGCTATGC
1391473 CAA
1 CAA
1391476 ATCACAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (39 bp):
CAATCCACGAAAATCAAATATGCAATTGGGTGGCTATGC
Found at i:1391486 original size:39 final size:39
Alignment explanation
Indices: 1391405--1391486 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
1391395 CAATTCACGG
* *
1391405 AAATCAAATATGCAGTTGGGTGGCTATGCCAATCCACGA
1 AAATCAAATATGCAATTGGGTGGCTATGCCAATCCACAA
1391444 AAATCAAATATGCAATTGGGTGGCTATGCCAAAT-CACAA
1 AAATCAAATATGCAATTGGGTGGCTATGCC-AATCCACAA
1391483 AAAT
1 AAAT
1391487 GTAAATAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
39 37 0.93
40 3 0.08
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (39 bp):
AAATCAAATATGCAATTGGGTGGCTATGCCAATCCACAA
Found at i:1392448 original size:2 final size:2
Alignment explanation
Indices: 1392441--1392476 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1392431 TTTGATAGGG
1392441 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
1392477 TCCTTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1396148 original size:2 final size:2
Alignment explanation
Indices: 1396141--1396167 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1396131 GTTCTTGGAT
1396141 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1396168 GAAGGGGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1399645 original size:22 final size:21
Alignment explanation
Indices: 1399611--1399676 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
1399601 TATATTAAAA
1399611 ATAAAA-A-TTAAATTAAATTT
1 ATAAAATATTTAAATT-AATTT
*
1399631 ATAAAATATTTAAATTTA-TT
1 ATAAAATATTTAAATTAATTT
* *
1399651 ATTAAAATATTTTAACTCAATTT
1 A-TAAAATA-TTTAAATTAATTT
1399674 ATA
1 ATA
1399677 TTATTATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 9 0.24
21 9 0.24
22 16 0.43
23 3 0.08
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAAATATTTAAATTAATTT
Found at i:1400073 original size:26 final size:27
Alignment explanation
Indices: 1400042--1400109 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 27
1400032 TTTATATCCA
1400042 ATTTATAT-ATTTTATAAATATTT-TAT
1 ATTTATATAATTTTA-AAATATTTATAT
1400068 ATTTATATAAATTTTAAAATATTTATAT
1 ATTTATAT-AATTTTAAAATATTTATAT
*
1400096 ATTAATATAATTTT
1 ATTTATATAATTTT
1400110 TACGTTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
26 8 0.21
27 14 0.37
28 16 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTTATATAATTTTAAAATATTTATAT
Found at i:1400076 original size:19 final size:19
Alignment explanation
Indices: 1400042--1400083 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1400032 TTTATATCCA
1400042 ATTTATATATTTTATAAAT
1 ATTTATATATTTTATAAAT
1400061 ATTT-TATATTTATATAAAT
1 ATTTATATATTT-TATAAAT
1400080 -TTTA
1 ATTTA
1400084 AAATATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTATATATTTTATAAAT
Found at i:1405158 original size:3 final size:3
Alignment explanation
Indices: 1405150--1405184 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1405140 CTCTTTTGTT
*
1405150 ATC ATC ATC ATC GTC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1405185 TATGAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:1406717 original size:6 final size:6
Alignment explanation
Indices: 1406708--1406766 Score: 84
Period size: 6 Copynumber: 10.0 Consensus size: 6
1406698 TATATATATA
* *
1406708 TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTG-G TGTGTG TGTGTG
1 TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG
*
1406755 TGTGTG TGTGCG
1 TGTGCG TGTGCG
1406767 CGCTTCATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
5 5 0.10
6 46 0.90
ACGTcount: A:0.00, C:0.10, G:0.51, T:0.39
Consensus pattern (6 bp):
TGTGCG
Found at i:1406749 original size:2 final size:2
Alignment explanation
Indices: 1406708--1406764 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
1406698 TATATATATA
* * * * *
1406708 TG TG CG TG TG CG TG TG CG TG TG CG TG TG CG TG TG -G TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1406749 TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG
1406765 CGCGCTTCAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.00, C:0.09, G:0.51, T:0.40
Consensus pattern (2 bp):
TG
Found at i:1407320 original size:14 final size:14
Alignment explanation
Indices: 1407293--1407335 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1407283 TTTTATCTCG
* *
1407293 TTTTATTTTTTTAA
1 TTTTATTATATTAA
*
1407307 TTTTTTTATATTAA
1 TTTTATTATATTAA
*
1407321 TTTTATTATTTTAA
1 TTTTATTATATTAA
1407335 T
1 T
1407336 ATAGATATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATTATATTAA
Found at i:1407376 original size:26 final size:25
Alignment explanation
Indices: 1407318--1407374 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
1407308 TTTTTTATAT
* *
1407318 TAATTTT-ATTATTTTAATATAGATA
1 TAATTTTAATTA-TTTAATAAAAATA
1407343 TAATTTTAATTATTTAATAAAAATA
1 TAATTTTAATTATTTAATAAAAATA
1407368 TAATTTT
1 TAATTTT
1407375 TATTTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TAATTTTAATTATTTAATAAAAATA
Found at i:1407389 original size:14 final size:15
Alignment explanation
Indices: 1407365--1407429 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
1407355 TTTAATAAAA
1407365 ATATAATTTTTATTT
1 ATATAATTTTTATTT
1407380 ATAT-ATTTTTATTT
1 ATATAATTTTTATTT
* * *
1407394 AATTTAAATTTAATTT
1 -ATATAATTTTTATTT
1407410 -T-TAATTATTTATTTT
1 ATATAATT-TTTA-TTT
1407425 ATATA
1 ATATA
1407430 TACATATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
13 4 0.10
14 14 0.36
15 10 0.26
16 9 0.23
17 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATATAATTTTTATTT
Found at i:1407408 original size:36 final size:36
Alignment explanation
Indices: 1407352--1407424 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
1407342 ATAATTTTAA
*
1407352 TTATTTAATAAAAATATAATTTTTATTTATATATTT
1 TTATTTAATAAAAATATAATTTTTAATTATATATTT
** * *
1407388 TTATTTAATTTAAATTTAATTTTTAATTATTTATTT
1 TTATTTAATAAAAATATAATTTTTAATTATATATTT
1407424 T
1 T
1407425 ATATATACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (36 bp):
TTATTTAATAAAAATATAATTTTTAATTATATATTT
Found at i:1407565 original size:21 final size:21
Alignment explanation
Indices: 1407541--1407591 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1407531 AATTTTATCG
* * *
1407541 TTATATTAATTAATCTTATTA
1 TTATAATAACTAATCTTACTA
*
1407562 TTATAATAACTCATCTTACTA
1 TTATAATAACTAATCTTACTA
*
1407583 TTATTATAA
1 TTATAATAA
1407592 TTTTTAATCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATAATAACTAATCTTACTA
Found at i:1409393 original size:2 final size:2
Alignment explanation
Indices: 1409388--1409419 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1409378 CTCTCTGATG
1409388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1409420 ATTTGCAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1414616 original size:12 final size:12
Alignment explanation
Indices: 1414598--1414627 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1414588 ATGCATTTGC
1414598 AATCATAATTTA
1 AATCATAATTTA
*
1414610 GATCATAATTTA
1 AATCATAATTTA
1414622 AATCAT
1 AATCAT
1414628 GTAGGCAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (12 bp):
AATCATAATTTA
Found at i:1415222 original size:11 final size:10
Alignment explanation
Indices: 1415192--1415336 Score: 60
Period size: 10 Copynumber: 15.1 Consensus size: 10
1415182 ATCGTATTCG
1415192 TATATTTTAA
1 TATATTTTAA
1415202 TATATTTTAA
1 TATATTTTAA
*
1415212 TTATTTTTTAA
1 -TATATTTTAA
*
1415223 -A-ATTAT-A
1 TATATTTTAA
*
1415230 TAAATTTTAA
1 TATATTTTAA
* *
1415240 TATGTTAATAA
1 TATATT-TTAA
* *
1415251 TTTATATT-A
1 TATATTTTAA
1415260 TATATTTTAA
1 TATATTTTAA
*
1415270 CATA-TTT-A
1 TATATTTTAA
*
1415278 TATATTTTTA
1 TATATTTTAA
1415288 TCATA-TTT-A
1 T-ATATTTTAA
*
1415297 T-TATTTTTA
1 TATATTTTAA
* *
1415306 T-TA-TGTAT
1 TATATTTTAA
1415314 TATATTTTATA
1 TATATTTTA-A
1415325 TAATATTTTAA
1 T-ATATTTTAA
1415336 T
1 T
1415337 TTTTTTAAGT
Statistics
Matches: 100, Mismatches: 20, Indels: 29
0.67 0.13 0.19
Matches are distributed among these distances:
7 3 0.03
8 14 0.14
9 26 0.26
10 28 0.28
11 21 0.21
12 8 0.08
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (10 bp):
TATATTTTAA
Found at i:1415280 original size:18 final size:18
Alignment explanation
Indices: 1415257--1415303 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
1415247 ATAATTTATA
1415257 TTATATATTTTAACATAT
1 TTATATATTTTAACATAT
*
1415275 TTATATATTTTTATCATAT
1 TTATATA-TTTTAACATAT
1415294 TTAT-TATTTT
1 TTATATATTTT
1415304 TATTATGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 9 0.33
19 14 0.52
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATATATTTTAACATAT
Found at i:1415292 original size:19 final size:19
Alignment explanation
Indices: 1415257--1415340 Score: 81
Period size: 18 Copynumber: 4.6 Consensus size: 19
1415247 ATAATTTATA
*
1415257 TTATATA-TTTTAACATAT
1 TTATATATTTTTATCATAT
1415275 TTATATATTTTTATCATAT
1 TTATATATTTTTATCATAT
1415294 TTAT-TATTTTTAT--TAT
1 TTATATATTTTTATCATAT
* *
1415310 GTATTATATTTTATATAATAT
1 TTA-TATATTTT-TATCATAT
1415331 TT-TA-ATTTTT
1 TTATATATTTTT
1415341 TTAAGTTGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
16 5 0.09
17 2 0.04
18 27 0.47
19 19 0.33
21 4 0.07
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.64
Consensus pattern (19 bp):
TTATATATTTTTATCATAT
Found at i:1415304 original size:18 final size:18
Alignment explanation
Indices: 1415264--1415323 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
1415254 ATATTATATA
*
1415264 TTTTAACATATTTATATAT
1 TTTTATCATATTTAT-TAT
1415283 TTTTATCATATTTATTAT
1 TTTTATCATATTTATTAT
*
1415301 TTTTAT--TATGTATTAT
1 TTTTATCATATTTATTAT
1415317 ATTTTAT
1 -TTTTAT
1415324 ATAATATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.24
17 6 0.16
18 9 0.24
19 14 0.37
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTATCATATTTATTAT
Found at i:1417528 original size:15 final size:14
Alignment explanation
Indices: 1417504--1417538 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1417494 TTTTATAGAC
1417504 ATGATAATATTAAAT
1 ATGATAATA-TAAAT
*
1417519 ATGATTATATAAAT
1 ATGATAATATAAAT
1417533 ATGATA
1 ATGATA
1417539 TAAAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (14 bp):
ATGATAATATAAAT
Found at i:1417533 original size:14 final size:14
Alignment explanation
Indices: 1417504--1417546 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1417494 TTTTATAGAC
*
1417504 ATGATAATATTAAAT
1 ATGATTATA-TAAAT
1417519 ATGATTATATAAAT
1 ATGATTATATAAAT
*
1417533 ATGA-TATAAAAAT
1 ATGATTATATAAAT
1417546 A
1 A
1417547 ATTAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 9 0.35
14 9 0.35
15 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
ATGATTATATAAAT
Found at i:1417576 original size:22 final size:20
Alignment explanation
Indices: 1417524--1417578 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
1417514 TAAATATGAT
1417524 TATATAAATATGATATAAAAA
1 TATA-AAATATGATATAAAAA
*
1417545 TAATTAAAATATGATATGACAAA
1 T-A-TAAAATATGATAT-AAAAA
1417568 TATACAAATAT
1 TATA-AAATAT
1417579 TTTAAAATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 3 0.10
22 19 0.66
23 7 0.24
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (20 bp):
TATAAAATATGATATAAAAA
Found at i:1417616 original size:32 final size:30
Alignment explanation
Indices: 1417580--1417657 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 30
1417570 TACAAATATT
*
1417580 TTAAAATCTATATAATATAAATTATTAACATA
1 TTAAAATCTATATAATAT-AATT-GTAACATA
1417612 TTAAAATCTATATAA-AT-ATTGTAACATA
1 TTAAAATCTATATAATATAATTGTAACATA
1417640 --AAAATCTATATAAATATA
1 TTAAAATCTATAT-AATATA
1417658 GAATATCTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
26 11 0.26
27 2 0.05
28 9 0.21
29 3 0.07
31 2 0.05
32 15 0.36
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.38
Consensus pattern (30 bp):
TTAAAATCTATATAATATAATTGTAACATA
Found at i:1417643 original size:26 final size:28
Alignment explanation
Indices: 1417581--1417656 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 28
1417571 ACAAATATTT
*
1417581 TAAAATCTATATAATATAAATTATTAACATA
1 TAAAATCTATATAA-AT--ATTAGTAACATA
1417612 TTAAAATCTATATAAATATT-GTAACATA
1 -TAAAATCTATATAAATATTAGTAACATA
1417640 -AAAATCTATATAAATAT
1 TAAAATCTATATAAATAT
1417657 AGAATATCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
26 17 0.40
28 7 0.16
29 3 0.07
31 2 0.05
32 14 0.33
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (28 bp):
TAAAATCTATATAAATATTAGTAACATA
Found at i:1420011 original size:13 final size:13
Alignment explanation
Indices: 1419993--1420018 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1419983 TACAAGGGAG
1419993 ACTATTCTAGAAA
1 ACTATTCTAGAAA
1420006 ACTATTCTAGAAA
1 ACTATTCTAGAAA
1420019 TAAAAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
ACTATTCTAGAAA
Found at i:1423153 original size:8 final size:9
Alignment explanation
Indices: 1423135--1423185 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
1423125 ATATTTGATA
1423135 TAATATATT
1 TAATATATT
1423144 TAAT-TATT
1 TAATATATT
* *
1423152 TAAAATTTT
1 TAATATATT
*
1423161 TTATATATT
1 TAATATATT
1423170 TAA-ATATAT
1 TAATATAT-T
1423179 TAATATA
1 TAATATA
1423186 CGTTAAACAC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
8 11 0.33
9 19 0.58
10 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATATATT
Found at i:1423674 original size:18 final size:18
Alignment explanation
Indices: 1423641--1423705 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
1423631 TTAATGTATT
1423641 ATATAATTATATAAATTTTA
1 ATAT-ATTA-ATAAATTTTA
*
1423661 ATATATTAATAAATTAT-
1 ATATATTAATAAATTTTA
1423678 AT-TA-T-ATAAATTTTA
1 ATATATTAATAAATTTTA
*
1423693 ATATATTCATAAA
1 ATATATTAATAAA
1423706 ATCATTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 8 0.21
15 3 0.08
16 4 0.10
17 3 0.08
18 13 0.33
19 4 0.10
20 4 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATATTAATAAATTTTA
Found at i:1424012 original size:8 final size:8
Alignment explanation
Indices: 1423996--1424036 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
1423986 ATTTAACTTG
*
1423996 AAATTTTT
1 AAATATTT
1424004 AAATATTT
1 AAATATTT
1424012 AAAATATTT
1 -AAATATTT
1424021 AAATA--T
1 AAATATTT
1424027 AAATATTT
1 AAATATTT
1424035 AA
1 AA
1424037 TAAAAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
6 6 0.21
8 15 0.52
9 8 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATATTT
Found at i:1424986 original size:9 final size:10
Alignment explanation
Indices: 1424959--1425064 Score: 69
Period size: 10 Copynumber: 10.8 Consensus size: 10
1424949 TATCGTGTTC
1424959 ATATATTTTA
1 ATATATTTTA
1424969 ATATATTTTA
1 ATATATTTTA
1424979 AT-TATTTTTA
1 ATATA-TTTTA
* * *
1424989 AAATAATAT-
1 ATATATTTTA
* *
1424998 ATAAATTTTG
1 ATATATTTTA
*
1425008 ATATATTAATA
1 ATATATT-TTA
* *
1425019 ATTTATATT-
1 ATATATTTTA
1425028 ATATATTTTA
1 ATATATTTTA
1425038 ATAT-TTTT-
1 ATATATTTTA
*
1425046 ATATATTTTT
1 ATATATTTTA
1425056 ATCATATTT
1 AT-ATATTT
1425065 ATATTATTTT
Statistics
Matches: 73, Mismatches: 15, Indels: 15
0.71 0.15 0.15
Matches are distributed among these distances:
8 4 0.05
9 22 0.30
10 33 0.45
11 14 0.19
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (10 bp):
ATATATTTTA
Found at i:1425062 original size:11 final size:10
Alignment explanation
Indices: 1425026--1425075 Score: 61
Period size: 9 Copynumber: 5.2 Consensus size: 10
1425016 ATAATTTATA
1425026 TTATATA-TT
1 TTATATATTT
1425035 TTA-ATATTT
1 TTATATATTT
1425044 TTATATATTT
1 TTATATATTT
1425054 TTATCATATTT
1 TTAT-ATATTT
*
1425065 ATAT-TATTT
1 TTATATATTT
1425074 TT
1 TT
1425076 TATTATGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 3 0.08
9 14 0.39
10 10 0.28
11 9 0.25
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATATATTT
Found at i:1425076 original size:21 final size:21
Alignment explanation
Indices: 1425019--1425078 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
1425009 TATATTAATA
1425019 ATTTATATTATATATTTTA-AT
1 ATTTATATTATAT-TTTTATAT
*
1425040 ATTTTTA-TATATTTTTATCAT
1 ATTTATATTATATTTTTAT-AT
1425061 ATTTATATTAT-TTTTTAT
1 ATTTATATTATATTTTTAT
1425079 TATGTATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 5 0.15
20 5 0.15
21 21 0.62
22 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTATATTATATTTTTATAT
Found at i:1425081 original size:10 final size:11
Alignment explanation
Indices: 1425019--1425081 Score: 62
Period size: 10 Copynumber: 6.0 Consensus size: 11
1425009 TATATTAATA
*
1425019 ATTTATATTAT
1 ATTTTTATTAT
1425030 ATATTTTA--AT
1 AT-TTTTATTAT
1425040 ATTTTTA-TAT
1 ATTTTTATTAT
*
1425050 ATTTTTATCAT
1 ATTTTTATTAT
*
1425061 ATTTATATTAT
1 ATTTTTATTAT
1425072 -TTTTTATTAT
1 ATTTTTATTAT
1425082 GTATTAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
9 5 0.11
10 22 0.50
11 13 0.30
12 4 0.09
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTTATTAT
Found at i:1425103 original size:40 final size:43
Alignment explanation
Indices: 1425009--1425104 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 43
1424999 TAAATTTTGA
*
1425009 TATATTAATAATTTATATTATATATTTTAATATTTTTATATATTT
1 TATA-TAAT-ATTTATATTATATATTTTAATATTATTATATATTT
* *
1425054 T-TATCATATTTATATTAT-T-TTTTATTATGTATTA-A-ATTT
1 TATATAATATTTATATTATATATTTTAATAT-TATTATATATTT
1425093 TATATAATATTT
1 TATATAATATTT
1425105 TAAATATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
39 5 0.11
40 18 0.40
41 5 0.11
42 11 0.24
43 3 0.07
44 2 0.04
45 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (43 bp):
TATATAATATTTATATTATATATTTTAATATTATTATATATTT
Found at i:1426047 original size:22 final size:21
Alignment explanation
Indices: 1426013--1426055 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
1426003 ATTTACAAAA
*
1426013 AAAGATTAAAATCTTTTTAATT
1 AAAGATTAAAATC-ATTTAATT
**
1426035 AAAGATTCTAATCATTTAATT
1 AAAGATTAAAATCATTTAATT
1426056 TATATTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (21 bp):
AAAGATTAAAATCATTTAATT
Found at i:1428192 original size:6 final size:6
Alignment explanation
Indices: 1428181--1428252 Score: 64
Period size: 6 Copynumber: 12.5 Consensus size: 6
1428171 TATTTATTAA
* *
1428181 ATAAAT ATAAAT AT-AAT TTAAATT ATTAAAT AT--AT AAAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAA-T A-TAAAT ATAAAT ATAAAT ATAAAT
*
1428228 ATAAAT AT-AAT ATATAT -TAAAT ATA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATA
1428253 TTATAATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
4 3 0.06
5 13 0.25
6 30 0.57
7 3 0.06
8 4 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATAAAT
Found at i:1428242 original size:29 final size:30
Alignment explanation
Indices: 1428174--1428279 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 30
1428164 ATTTTTTTAT
* * *
1428174 TTATTAAATA-AATATAAATATAATTTAAA
1 TTATTAAATATATTAAAAATATAATATAAA
1428203 TTATTAAATATA-TAAAAATATAAATATAAA
1 TTATTAAATATATTAAAAATAT-AATATAAA
* * *
1428233 -TA-TAATATATATTAAATATATTATAATAAT
1 TTATTAA-ATATATTAAAAATATAAT-ATAAA
1428263 TATATTAAAATATATTA
1 T-TATT-AAATATATTA
1428280 TATCATATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
28 3 0.05
29 27 0.43
30 20 0.32
32 2 0.03
33 9 0.14
34 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TTATTAAATATATTAAAAATATAATATAAA
Found at i:1428266 original size:14 final size:14
Alignment explanation
Indices: 1428249--1428298 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
1428239 ATATATTAAA
1428249 TATATTATAATAAT
1 TATATTATAATAAT
*
1428263 TATATTAAAATATAT
1 TATATTATAATA-AT
* * *
1428278 TATATCATATTTAT
1 TATATTATAATAAT
1428292 TATATTA
1 TATATTA
1428299 ATTTTTATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATTATAATAAT
Found at i:1428299 original size:29 final size:24
Alignment explanation
Indices: 1428234--1428281 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1428224 AAATATAAAT
1428234 ATAATATATATT-AAATATATTATA
1 ATAAT-TATATTAAAATATATTATA
1428258 ATAATTATATTAAAATATATTATA
1 ATAATTATATTAAAATATATTATA
1428282 TCATATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAATTATATTAAAATATATTATA
Found at i:1430459 original size:23 final size:25
Alignment explanation
Indices: 1430417--1430467 Score: 88
Period size: 23 Copynumber: 2.1 Consensus size: 25
1430407 CGTGTACGTA
1430417 AATATTAAATTAATTAAATAAATAT
1 AATATTAAATTAATTAAATAAATAT
1430442 AATA-TAAATT-ATTAAATAAATAT
1 AATATTAAATTAATTAAATAAATAT
1430465 AAT
1 AAT
1430468 TTTTATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 16 0.62
24 6 0.23
25 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AATATTAAATTAATTAAATAAATAT
Found at i:1430483 original size:16 final size:17
Alignment explanation
Indices: 1430462--1430510 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
1430452 ATTAAATAAA
*
1430462 TATAATTTTTA-TATTT
1 TATAATTTTTATTATAT
*
1430478 TATAATATTTATTATAT
1 TATAATTTTTATTATAT
1430495 TAT-A-TTTTATT-TAT
1 TATAATTTTTATTATAT
1430509 TA
1 TA
1430511 AAAAAGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 5 0.17
15 6 0.21
16 11 0.38
17 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATAATTTTTATTATAT
Found at i:1430494 original size:19 final size:19
Alignment explanation
Indices: 1430466--1430510 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1430456 AATAAATATA
*
1430466 ATTT-TTATATTTTATAAT
1 ATTTATTATATTATATAAT
**
1430484 ATTTATTATATTATATTTT
1 ATTTATTATATTATATAAT
1430503 ATTTATTA
1 ATTTATTA
1430511 AAAAAGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTATTATATTATATAAT
Found at i:1433474 original size:27 final size:27
Alignment explanation
Indices: 1433444--1433526 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
1433434 GTAATATGTT
1433444 TTTATATTTTTATAAATTATATTTATA
1 TTTATATTTTTATAAATTATATTTATA
* * **
1433471 TTTA-ATATATTATATAATAATATAAAT-
1 TTTATAT-TTTTATA-AATTATATTTATA
* *
1433498 TTTAATATATTAATAAATTATATTATATA
1 TTT-ATATTTTTATAAATTATATT-TATA
1433527 AATTTTAATA
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
26 2 0.05
27 20 0.50
28 16 0.40
29 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTATATTTTTATAAATTATATTTATA
Found at i:1433515 original size:18 final size:17
Alignment explanation
Indices: 1433491--1433546 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
1433481 TATATAATAA
1433491 TATAAATTTTAATATAT
1 TATAAATTTTAATATAT
*
1433508 TAATAAATTAT-AT-TA-
1 T-ATAAATTTTAATATAT
*
1433523 TATAAATTTTAATAGAT
1 TATAAATTTTAATATAT
1433540 TCATAAA
1 T-ATAAA
1433547 ATTATTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 3 0.10
17 4 0.13
18 13 0.42
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
TATAAATTTTAATATAT
Found at i:1433525 original size:20 final size:20
Alignment explanation
Indices: 1433445--1433526 Score: 68
Period size: 20 Copynumber: 4.3 Consensus size: 20
1433435 TAATATGTTT
* *
1433445 TTATATTTTTATAAATTATA
1 TTATATATTAATAAATTATA
*
1433465 TT-TATATTTAATATATTATA
1 TTATATA-TTAATAAATTATA
*
1433485 -TA-ATAAT-ATAAATT-T-
1 TTATATATTAATAAATTATA
*
1433500 TAATATATTAATAAATTATA
1 TTATATATTAATAAATTATA
1433520 TTATATA
1 TTATATA
1433527 AATTTTAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
16 2 0.04
17 10 0.21
18 8 0.17
19 8 0.17
20 19 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATATATTAATAAATTATA
Found at i:1433531 original size:32 final size:34
Alignment explanation
Indices: 1433467--1433558 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 34
1433457 AAATTATATT
*
1433467 TATATTTAATATATTATATAATAATATAAATTTTAA
1 TATA-TTAATAAATTATAT-ATAATATAAATTTTAA
1433503 TATATTAATAAATTATAT-T-ATATAAATTTTAA
1 TATATTAATAAATTATATATAATATAAATTTTAA
* *
1433535 TAGATTCATAAAATTAT-T-TAATAT
1 TATATTAAT-AAATTATATATAATAT
1433559 TTTTTATTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
32 22 0.43
33 12 0.24
35 13 0.25
36 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (34 bp):
TATATTAATAAATTATATATAATATAAATTTTAA
Found at i:1437164 original size:23 final size:22
Alignment explanation
Indices: 1437118--1437164 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1437108 ACGATTATAT
*
1437118 AAATATAACATAAAAATAATTA
1 AAATATAACATAAAAATAAGTA
* *
1437140 AAATATGACATAACAAATACGTA
1 AAATATAACATAA-AAATAAGTA
1437163 AA
1 AA
1437165 TATTTCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.23
Consensus pattern (22 bp):
AAATATAACATAAAAATAAGTA
Found at i:1437549 original size:16 final size:17
Alignment explanation
Indices: 1437523--1437556 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1437513 GATAAAAATC
*
1437523 AAATAAAATTATTTTAA
1 AAATAAAATTATTATAA
1437540 AAAT-AAATTATTATAA
1 AAATAAAATTATTATAA
1437556 A
1 A
1437557 TAAAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAAAATTATTATAA
Found at i:1438596 original size:6 final size:6
Alignment explanation
Indices: 1438585--1438647 Score: 53
Period size: 6 Copynumber: 10.5 Consensus size: 6
1438575 AATTTATTAA
*
1438585 ATAAAT ATAAAT AT-AAT TTAAATT ATTAAAT ATGTAAA- A-AAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAA-T A-TAAAT A--TAAAT ATAAAT ATAAAT
1438634 ATAAAT AT-AAT ATA
1 ATAAAT ATAAAT ATA
1438648 CATTTTAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
4 3 0.06
5 10 0.21
6 22 0.47
7 4 0.09
8 8 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (6 bp):
ATAAAT
Found at i:1438665 original size:23 final size:22
Alignment explanation
Indices: 1438639--1438705 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 22
1438629 TAAATATAAA
1438639 TATAATATACATTTTAATTATAT
1 TATAATATACA-TTTAATTATAT
** *
1438662 TATAATACTGTATTTAAATATAT
1 TATAATA-TACATTTAATTATAT
1438685 TAT-AT-TACATTT-ATTATAT
1 TATAATATACATTTAATTATAT
1438704 TA
1 TA
1438706 ATTTTTGTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 8 0.22
20 5 0.14
22 2 0.05
23 20 0.54
24 2 0.05
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (22 bp):
TATAATATACATTTAATTATAT
Found at i:1438792 original size:14 final size:14
Alignment explanation
Indices: 1438773--1438803 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1438763 TAATAACTAT
*
1438773 CAAAATTCAATGTA
1 CAAAATTCAATATA
1438787 CAAAATTCAATATA
1 CAAAATTCAATATA
1438801 CAA
1 CAA
1438804 GCATGGCTAT
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:0.55, C:0.16, G:0.03, T:0.26
Consensus pattern (14 bp):
CAAAATTCAATATA
Found at i:1441322 original size:6 final size:6
Alignment explanation
Indices: 1441311--1441361 Score: 50
Period size: 6 Copynumber: 8.0 Consensus size: 6
1441301 AATTAATTAA
*
1441311 ATAAAT ATAAAT AT-AAT ATAAATT ATTAAAT ATAAAA ATAATAT ATTAAAT
1 ATAAAT ATAAAT ATAAAT ATAAA-T A-TAAAT ATAAAT ATAA-AT A-TAAAT
1441362 CATATTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 5 0.13
6 18 0.47
7 8 0.21
8 7 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATAAAT
Found at i:1441340 original size:19 final size:19
Alignment explanation
Indices: 1441296--1441361 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
1441286 TGTACGAATG
1441296 TATTAAAT-TAATTAAATA
1 TATTAAATATAATTAAATA
*
1441314 AATATAAATATAATATAAAT-
1 TAT-TAAATATAAT-TAAATA
**
1441334 TATTAAATATAAAAATAATA
1 TATTAAATATAATTA-AATA
1441354 TATTAAAT
1 TATTAAAT
1441362 CATATTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.08
19 17 0.44
20 14 0.36
21 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTAAATATAATTAAATA
Found at i:1441357 original size:20 final size:19
Alignment explanation
Indices: 1441296--1441361 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 19
1441286 TGTACGAATG
1441296 TATTAAAT-TAATTAAATAAA
1 TATTAAATATAA--AAATAAA
*
1441316 TA-TAAATAT-AATATAAA
1 TATTAAATATAAAAATAAA
1441333 TTATTAAATATAAAAATAATA
1 -TATTAAATATAAAAATAA-A
1441354 TATTAAAT
1 TATTAAAT
1441362 CATATTAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 6 0.15
18 2 0.05
19 13 0.33
20 17 0.44
21 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTAAATATAAAAATAAA
Found at i:1441919 original size:6 final size:7
Alignment explanation
Indices: 1441894--1441937 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
1441884 AAAAAGAAAG
*
1441894 ATTTCTA
1 ATTTTTA
1441901 ATTTTTA
1 ATTTTTA
1441908 ATTTTTA
1 ATTTTTA
1441915 ATTTTTA
1 ATTTTTA
*
1441922 ATTTTAA
1 ATTTTTA
1441929 ATTTATTA
1 ATTT-TTA
1441937 A
1 A
1441938 ATATTAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
7 30 0.91
8 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (7 bp):
ATTTTTA
Found at i:1444443 original size:18 final size:20
Alignment explanation
Indices: 1444387--1444444 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 20
1444377 TAAATTAAAT
1444387 TTATATTTAATGTATAATATAA
1 TTATA-TTAATGT-TAATATAA
* *
1444409 TTATATAAATTTTAATATAA
1 TTATATTAATGTTAATATAA
1444429 -TA-ATTAATGTTAATAT
1 TTATATTAATGTTAATAT
1444445 TATATAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 12 0.38
19 2 0.06
20 8 0.25
21 5 0.16
22 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTATATTAATGTTAATATAA
Found at i:1445481 original size:20 final size:20
Alignment explanation
Indices: 1445456--1445493 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1445446 AGAATTGAAG
1445456 AGGGATACAAGAGAGGGATA
1 AGGGATACAAGAGAGGGATA
**
1445476 AGGGATACTTGAGAGGGA
1 AGGGATACAAGAGAGGGA
1445494 GGAGGGAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.05, G:0.42, T:0.13
Consensus pattern (20 bp):
AGGGATACAAGAGAGGGATA
Found at i:1445499 original size:20 final size:20
Alignment explanation
Indices: 1445455--1445500 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1445445 AAGAATTGAA
*
1445455 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
1445475 AAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
1445495 GAGGGA
1 GAGGGA
1445501 GCCTCTATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.48, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:1445617 original size:28 final size:27
Alignment explanation
Indices: 1445582--1445647 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
1445572 AGCCTGCATA
1445582 TTTGACAAATACAAAGGA-AACCACCATT
1 TTTGACAAATACAAA--ATAACCACCATT
*
1445610 TTTGACAAACACAAAATAACCACCATT
1 TTTGACAAATACAAAATAACCACCATT
*
1445637 TTTTACAAATA
1 TTTGACAAATA
1445648 AATGGGTGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.56
28 14 0.41
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (27 bp):
TTTGACAAATACAAAATAACCACCATT
Found at i:1449799 original size:27 final size:28
Alignment explanation
Indices: 1449744--1449807 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
1449734 AGCCTCCATA
* *
1449744 TTTGATAAATACAAAAGAAACTACTATT
1 TTTGACAAACACAAAAGAAACTACTATT
*
1449772 TTTGACAAACACAAAA-TAACTACTATT
1 TTTGACAAACACAAAAGAAACTACTATT
*
1449799 TTTTACAAA
1 TTTGACAAA
1449808 TAAATAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 18 0.56
28 14 0.44
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (28 bp):
TTTGACAAACACAAAAGAAACTACTATT
Found at i:1450130 original size:3 final size:3
Alignment explanation
Indices: 1450122--1450146 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1450112 AAGAGAAAAA
1450122 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1450147 TTTAGAATTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1452003 original size:22 final size:22
Alignment explanation
Indices: 1451978--1452019 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1451968 GCTAAATATC
1451978 ATATT-TAATAGAAATTATTATT
1 ATATTATAA-AGAAATTATTATT
*
1452000 ATATTATAAATAAATTATTA
1 ATATTATAAAGAAATTATTA
1452020 ACTAACTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATTATAAAGAAATTATTATT
Found at i:1452217 original size:18 final size:18
Alignment explanation
Indices: 1452176--1452219 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1452166 TAAAATTAAT
*
1452176 TAATTTTATATATTTTTA
1 TAATTTTATATATTTTGA
*
1452194 TAATTTTATTTATGTTTGA
1 TAATTTTATATAT-TTTGA
1452213 T-ATTTTA
1 TAATTTTA
1452220 ATAATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TAATTTTATATATTTTGA
Found at i:1457428 original size:20 final size:21
Alignment explanation
Indices: 1457383--1457429 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1457373 AAAATAATTA
1457383 TTTTAATAATTATTTATAAAT
1 TTTTAATAATTATTTATAAAT
*
1457404 TTTTAAT-ATATATTTAT-ATT
1 TTTTAATAAT-TATTTATAAAT
1457424 TTTTAA
1 TTTTAA
1457430 AAAAGATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAATAATTATTTATAAAT
Found at i:1457826 original size:22 final size:21
Alignment explanation
Indices: 1457791--1457860 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
1457781 AATGATAATG
1457791 AAAATAAATTATTTTTTAAAAT
1 AAAATAAA-TATTTTTTAAAAT
** * *
1457813 AAAATTTATAATTTATAAATAT
1 AAAATAAATATTTTTTAAA-AT
1457835 AAAATAAATATTTTTTAAAAT
1 AAAATAAATATTTTTTAAAAT
*
1457856 TAAAT
1 AAAAT
1457861 CTAATTTAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
21 15 0.39
22 23 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATAAATATTTTTTAAAAT
Found at i:1457877 original size:43 final size:42
Alignment explanation
Indices: 1457791--1457885 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 42
1457781 AATGATAATG
1457791 AAAATAAATTATTTTTTAAAATAAAATTTATAATTTATAAATAT
1 AAAATAAA-TATTTTTTAAAATAAAA-TTATAATTTATAAATAT
* * *
1457835 AAAATAAATATTTTTTAAAATTAAA-TCTAATTTAAGTGAATAT
1 AAAATAAATATTTTTTAAAATAAAATTATAATTT-A-TAAATAT
1457878 AAAA-AAAT
1 AAAATAAAT
1457886 TACTAAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
41 7 0.15
42 5 0.11
43 26 0.57
44 8 0.17
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (42 bp):
AAAATAAATATTTTTTAAAATAAAATTATAATTTATAAATAT
Found at i:1458347 original size:20 final size:20
Alignment explanation
Indices: 1458305--1458347 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1458295 AAGTCGGATT
* * **
1458305 ATTCAGATTTATATGATTTA
1 ATTCAAATTGATATGATACA
1458325 ATTCAAATTGATATGATACA
1 ATTCAAATTGATATGATACA
1458345 ATT
1 ATT
1458348 TGAATTTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (20 bp):
ATTCAAATTGATATGATACA
Found at i:1458543 original size:12 final size:12
Alignment explanation
Indices: 1458523--1458561 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1458513 ACTTAGAAAG
*
1458523 TATGCATATATA
1 TATGTATATATA
1458535 TATGTATATATA
1 TATGTATATATA
*
1458547 TATGTATGTATA
1 TATGTATATATA
1458559 TAT
1 TAT
1458562 TCAAATTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (12 bp):
TATGTATATATA
Found at i:1465406 original size:39 final size:40
Alignment explanation
Indices: 1465348--1465449 Score: 129
Period size: 39 Copynumber: 2.6 Consensus size: 40
1465338 TCGAGGATAA
* *
1465348 CCTTGAGTTGGTGGTGGGTATC-GAC-CAGGTGGTGAATGG
1 CCTTGAGTTGGTGGAGGGTATCTGACTC-GGTGGCGAATGG
** *
1465387 GGTTGAGTTGGTGGAGGGTA-CTGACTCGGTGGCGGATGG
1 CCTTGAGTTGGTGGAGGGTATCTGACTCGGTGGCGAATGG
1465426 CCTTGAGTTGGTGGAGGGTATCTG
1 CCTTGAGTTGGTGGAGGGTATCTG
1465450 GATGGTGGAT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
38 1 0.02
39 48 0.91
40 4 0.08
ACGTcount: A:0.14, C:0.12, G:0.46, T:0.28
Consensus pattern (40 bp):
CCTTGAGTTGGTGGAGGGTATCTGACTCGGTGGCGAATGG
Found at i:1465494 original size:18 final size:18
Alignment explanation
Indices: 1465420--1465497 Score: 52
Period size: 18 Copynumber: 4.2 Consensus size: 18
1465410 ACTCGGTGGC
1465420 GGATGGCCTTGAGTTGGT
1 GGATGGCCTTGAGTTGGT
* ** *
1465438 GGAGGGTATCTG-GATGGT
1 GGATGGCCT-TGAGTTGGT
*
1465456 GGAT-GCCTTTGAGAGGGTGGT
1 GGATGGCC-TT--GA-GTTGGT
1465477 GGATGGCCTTGAGTTGGT
1 GGATGGCCTTGAGTTGGT
1465495 GGA
1 GGA
1465498 GGGTATCTAG
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
17 2 0.05
18 23 0.52
19 5 0.11
21 11 0.25
22 3 0.07
ACGTcount: A:0.14, C:0.09, G:0.47, T:0.29
Consensus pattern (18 bp):
GGATGGCCTTGAGTTGGT
Found at i:1465519 original size:39 final size:39
Alignment explanation
Indices: 1465471--1466102 Score: 217
Period size: 39 Copynumber: 16.1 Consensus size: 39
1465461 CCTTTGAGAG
*
1465471 GGTGGTGGATGGCCTTGAGTTGGTGGAGGGTATCTAGAT
1 GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAGAT
* ** * ***
1465510 GGTGTTGGAT-GCCTTTGAGTGGGTGGCCACGGAAATGTCCTT
1 GGTGGTGGATGGCC-TTGAGTGGGTGG--A-GGGTATCTAGAT
* * * *
1465552 GGTGGTGGATGACCTTGAGTTGGTGGCGGGTAT-T-GCCTT
1 GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAG--AT
** * *
1465591 GGTGGTGGATAACCTTGAGTGGGTGGTGTGTATCTAGAT
1 GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAGAT
* * * *
1465630 GGTGGTGGATGGCCTTGAGTGGGTGGCGAGTGT-T-GCCTT
1 GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAG--AT
* * ** * * * * *
1465669 GGAGGTGAATGAACATGAGTGGGCGGTGGGCAT-T-GCCTT
1 GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAG--AT
* * * * * * *
1465708 CGTGGTGGATGACCATGTA-TGAGTGGCGAGTAT-T-GCCT
1 GGTGGTGGATGGCCTTG-AGTGGGTGGAGGGTATCTAG-AT
* * * *
1465746 AGGTGGTTGATCAG-CTTGAGTGGGTGGTGTGTATCTAGAT
1 -GGTGGTGGAT-GGCCTTGAGTGGGTGGAGGGTATCTAGAT
* * *
1465786 GGTGGTGGATGGCCTTGAGTGGGTGGCGAGTAT-T-GCCTT
1 GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAG--AT
* * * * * * *
1465825 GGAGGTGCATGACCATAAGTGGGTGGTGGGTAT-T-GCCTT
1 GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAG--AT
* * * * *
1465864 GGTGGCGGATGACCATGAGTGGGTGGCGGGTAT-T-GCCT
1 GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAG-AT
* * * * *
1465902 AGGTGGTGGATGACCTCGAGTGGGTGGTGTGCATCTAGAT
1 -GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAGAT
* * *
1465942 GGTGGTGGATGGCCTTGAGTGGGTGGCGAGTAT-T-GCCTT
1 GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAG--AT
* * * * * *
1465981 GGAGGTGGATGACCATGAGTGGGTGGTGGGTACCTAGTT
1 GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAGAT
* *
1466020 GGTGGTGGATGGCCTTGAGTGGGTGGCGGGTA-CT-GCCT
1 GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAG-AT
* * * * *
1466058 AGGAGGAGAATGACCTTGAGTGGGTGGAGGGTATCTAGAC
1 -GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAGAT
1466098 GGTGG
1 GGTGG
1466103 CATGTACCTT
Statistics
Matches: 457, Mismatches: 105, Indels: 62
0.73 0.17 0.10
Matches are distributed among these distances:
37 4 0.01
38 16 0.04
39 394 0.86
40 9 0.02
41 6 0.01
42 26 0.06
43 2 0.00
ACGTcount: A:0.15, C:0.12, G:0.44, T:0.29
Consensus pattern (39 bp):
GGTGGTGGATGGCCTTGAGTGGGTGGAGGGTATCTAGAT
Found at i:1465574 original size:21 final size:21
Alignment explanation
Indices: 1465550--1465655 Score: 64
Period size: 21 Copynumber: 5.3 Consensus size: 21
1465540 GGAAATGTCC
1465550 TTGGTGGTGGATGACCTTGAG
1 TTGGTGGTGGATGACCTTGAG
* * **
1465571 TTGGTGGCGGGT-A--TTGCC
1 TTGGTGGTGGATGACCTTGAG
*
1465589 TTGGTGGTGGATAACCTTGAG
1 TTGGTGGTGGATGACCTTGAG
* *
1465610 TGGGTGGT-G-TGTATC-T-AG
1 TTGGTGGTGGATG-ACCTTGAG
* *
1465628 ATGGTGGTGGATGGCCTTGAG
1 TTGGTGGTGGATGACCTTGAG
*
1465649 TGGGTGG
1 TTGGTGG
1465656 CGAGTGTTGC
Statistics
Matches: 60, Mismatches: 17, Indels: 16
0.65 0.18 0.17
Matches are distributed among these distances:
18 21 0.35
19 5 0.08
20 7 0.12
21 27 0.45
ACGTcount: A:0.12, C:0.09, G:0.45, T:0.33
Consensus pattern (21 bp):
TTGGTGGTGGATGACCTTGAG
Found at i:1465666 original size:78 final size:78
Alignment explanation
Indices: 1465551--1466102 Score: 610
Period size: 78 Copynumber: 7.1 Consensus size: 78
1465541 GAAATGTCCT
* * * * *
1465551 TGGTGGTGGATGACCTTGAGTTGGTGGCGGGTATTGCCTTGGTGGTGGATAACCTTGAGTGGGTG
1 TGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGGATGACCTTGAGTGGGTG
*
1465616 GTGTGTATCTAGA
66 GTGGGTATCTAGA
* * * * *
1465629 TGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTGTTGCCTTGGAGGTGAATGAACATGAGTGGGCG
1 TGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGGATGACCTTGAGTGGGTG
* *
1465694 GTGGGCAT-T-GCCT
66 GTGGGTATCTAG--A
* * * * * * * * *
1465707 TCGTGGTGGATGACCATGTA-TGAGTGGCGAGTATTGCCTAGGTGGTTGATCAGCTTGAGTGGGT
1 TGGTGGTGGATGGCCTTG-AGTGGGTGGCGAGTATTGCCTTGGAGGTGGATGACCTTGAGTGGGT
*
1465771 GGTGTGTATCTAGA
65 GGTGGGTATCTAGA
* * *
1465785 TGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGCATGACCATAAGTGGGTG
1 TGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGGATGACCTTGAGTGGGTG
*
1465850 GTGGGTAT-T-GCCT
66 GTGGGTATCTAG--A
* * * * * * *
1465863 TGGTGGCGGATGACCATGAGTGGGTGGCGGGTATTGCCTAGGTGGTGGATGACCTCGAGTGGGTG
1 TGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGGATGACCTTGAGTGGGTG
* *
1465928 GTGTGCATCTAGA
66 GTGGGTATCTAGA
*
1465941 TGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGGATGACCATGAGTGGGTG
1 TGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGGATGACCTTGAGTGGGTG
* *
1466006 GTGGGTACCTAGT
66 GTGGGTATCTAGA
* * * * *
1466019 TGGTGGTGGATGGCCTTGAGTGGGTGGCGGGTACTGCCTAGGAGGAGAATGACCTTGAGTGGGTG
1 TGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGGATGACCTTGAGTGGGTG
*
1466084 GAGGGTATCTAGA
66 GTGGGTATCTAGA
*
1466097 CGGTGG
1 TGGTGG
1466103 CATGTACCTT
Statistics
Matches: 386, Mismatches: 78, Indels: 20
0.80 0.16 0.04
Matches are distributed among these distances:
76 2 0.01
77 3 0.01
78 376 0.97
79 3 0.01
80 2 0.01
ACGTcount: A:0.15, C:0.12, G:0.44, T:0.28
Consensus pattern (78 bp):
TGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGGATGACCTTGAGTGGGTG
GTGGGTATCTAGA
Found at i:1465927 original size:21 final size:20
Alignment explanation
Indices: 1465903--1465967 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
1465893 GTATTGCCTA
1465903 GGTGGTGGATGACCTCGAGTG
1 GGTGGTGGATG-CCTCGAGTG
* *
1465924 GGTGGT-G-TGCATCTAGAT-
1 GGTGGTGGATGCCTCGAG-TG
*
1465942 GGTGGTGGATGGCCTTGAGTG
1 GGTGGTGGAT-GCCTCGAGTG
1465963 GGTGG
1 GGTGG
1465968 CGAGTATTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
18 11 0.32
19 4 0.12
20 3 0.09
21 16 0.47
ACGTcount: A:0.12, C:0.11, G:0.49, T:0.28
Consensus pattern (20 bp):
GGTGGTGGATGCCTCGAGTG
Found at i:1466008 original size:21 final size:20
Alignment explanation
Indices: 1465984--1466045 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
1465974 TTGCCTTGGA
1465984 GGTGGATGACCATGAGTGGGT
1 GGTGGATGACC-TGAGTGGGT
* *
1466005 GGTGGGT-ACCT-AGTTGGT
1 GGTGGATGACCTGAGTGGGT
*
1466023 GGTGGATGGCCTTGAGTGGGT
1 GGTGGATGACC-TGAGTGGGT
1466044 GG
1 GG
1466046 CGGGTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
18 12 0.36
19 3 0.09
20 4 0.12
21 14 0.42
ACGTcount: A:0.13, C:0.10, G:0.50, T:0.27
Consensus pattern (20 bp):
GGTGGATGACCTGAGTGGGT
Found at i:1466116 original size:156 final size:156
Alignment explanation
Indices: 1465549--1466102 Score: 774
Period size: 156 Copynumber: 3.6 Consensus size: 156
1465539 CGGAAATGTC
* * * *
1465549 CTTGGTGGTGGATGACCTTGAGTTGGTGGCGGGTATTGCCTTGGTGGTGGATAACCTTGAGTGGG
1 CTTGGTGGTGGATGACCATGAGTGGGTGGCGGGTATTGCCTAGGTGGTGGATGACCTTGAGTGGG
*
1465614 TGGTGTGTATCTAGATGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTGTTGCCTTGGAGGTGAAT
66 TGGTGTGTATCTAGATGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGAAT
* * *
1465679 GAACATGAGTGGGCGGTGGGCA-TTG
131 GACCATGAGTGGGTGGTGGGTACTTG
* * * * * *
1465704 CCTTCGTGGTGGATGACCATGTA-TGAGTGGCGAGTATTGCCTAGGTGGTTGATCAGCTTGAGTG
1 -CTTGGTGGTGGATGACCATG-AGTGGGTGGCGGGTATTGCCTAGGTGGTGGATGACCTTGAGTG
*
1465768 GGTGGTGTGTATCTAGATGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGC
64 GGTGGTGTGTATCTAGATGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGA
*
1465833 ATGACCATAAGTGGGTGGTGGGTA-TTG
129 ATGACCATGAGTGGGTGGTGGGTACTTG
* *
1465860 CCTTGGTGGCGGATGACCATGAGTGGGTGGCGGGTATTGCCTAGGTGGTGGATGACCTCGAGTGG
1 -CTTGGTGGTGGATGACCATGAGTGGGTGGCGGGTATTGCCTAGGTGGTGGATGACCTTGAGTGG
* *
1465925 GTGGTGTGCATCTAGATGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGGA
65 GTGGTGTGTATCTAGATGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGAA
*
1465990 TGACCATGAGTGGGTGGTGGGTACCTAG
130 TGACCATGAGTGGGTGGTGGGTA-CTTG
* * * * * *
1466018 -TTGGTGGTGGATGGCCTTGAGTGGGTGGCGGGTACTGCCTAGGAGGAGAATGACCTTGAGTGGG
1 CTTGGTGGTGGATGACCATGAGTGGGTGGCGGGTATTGCCTAGGTGGTGGATGACCTTGAGTGGG
* * *
1466082 TGGAGGGTATCTAGACGGTGG
66 TGGTGTGTATCTAGATGGTGG
1466103 CATGTACCTT
Statistics
Matches: 355, Mismatches: 39, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
155 1 0.00
156 351 0.99
157 1 0.00
158 2 0.01
ACGTcount: A:0.15, C:0.12, G:0.44, T:0.29
Consensus pattern (156 bp):
CTTGGTGGTGGATGACCATGAGTGGGTGGCGGGTATTGCCTAGGTGGTGGATGACCTTGAGTGGG
TGGTGTGTATCTAGATGGTGGTGGATGGCCTTGAGTGGGTGGCGAGTATTGCCTTGGAGGTGAAT
GACCATGAGTGGGTGGTGGGTACTTG
Found at i:1467739 original size:11 final size:11
Alignment explanation
Indices: 1467706--1467740 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1467696 AAATGATTTT
*
1467706 TTAATTTTTAA
1 TTAATTTTAAA
1467717 TTAAATTTTAAA
1 TT-AATTTTAAA
1467729 TTAATTTTAAA
1 TTAATTTTAAA
1467740 T
1 T
1467741 CGATTCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTAATTTTAAA
Found at i:1474252 original size:33 final size:34
Alignment explanation
Indices: 1474185--1474252 Score: 79
Period size: 33 Copynumber: 2.0 Consensus size: 34
1474175 TATAAATATT
*
1474185 AATATATAAAAAATTTAATATTTTATTATGTTTA
1 AATATATAAAAAATTTAATATTTAATTATGTTTA
*
1474219 AATA-ATAAAATATGTTAAT-TTTAATT-TGATTTA
1 AATATATAAAAAAT-TTAATATTTAATTATG-TTTA
1474252 A
1 A
1474253 TTTAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 2 0.07
33 19 0.63
34 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (34 bp):
AATATATAAAAAATTTAATATTTAATTATGTTTA
Found at i:1474570 original size:21 final size:21
Alignment explanation
Indices: 1474546--1474595 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1474536 TAACATGTTG
1474546 AATTTAAAT-ATCATAATACTT
1 AATTTAAATAATCATAA-ACTT
*
1474567 AATTTGAATAATCATAAACTT
1 AATTTAAATAATCATAAACTT
1474588 AA-TTAAAT
1 AATTTAAAT
1474596 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 14 0.54
22 7 0.27
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (21 bp):
AATTTAAATAATCATAAACTT
Found at i:1474762 original size:41 final size:40
Alignment explanation
Indices: 1474707--1474787 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 40
1474697 AAATTAAATT
**
1474707 AAGTAAATTTATTT-ATCTCAAATTGAA-TTTAAATTTTAA
1 AAGTAAATTTATTTAAT-TCAAATCAAATTTTAAATTTTAA
1474746 AAGTAAAATTTAATTTAATTCAAATCAAATTTTAAATTTTAA
1 AAGT-AAATTT-ATTTAATTCAAATCAAATTTTAAATTTTAA
1474788 TTTTTAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
39 4 0.11
40 6 0.17
41 12 0.33
42 14 0.39
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (40 bp):
AAGTAAATTTATTTAATTCAAATCAAATTTTAAATTTTAA
Found at i:1483104 original size:19 final size:18
Alignment explanation
Indices: 1483080--1483149 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 18
1483070 AAAATTTTAT
1483080 TATTTGTATATTTAAATTA
1 TATTTGTATATTT-AATTA
* *
1483099 TATTTGTATATTTTATTT
1 TATTTGTATATTTAATTA
1483117 TATTGTGATTATATTTAA-TA
1 TATT-TG--TATATTTAATTA
1483137 TATTT-TATATTTA
1 TATTTGTATATTTA
1483150 TATATTTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
16 8 0.18
18 7 0.16
19 16 0.36
20 5 0.11
21 8 0.18
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TATTTGTATATTTAATTA
Found at i:1483118 original size:40 final size:37
Alignment explanation
Indices: 1483073--1483148 Score: 91
Period size: 40 Copynumber: 2.0 Consensus size: 37
1483063 TTAAATAAAA
*
1483073 ATTTTATTAT-TTGTATATTTAAATTATATTTGTATATTTT
1 ATTTTATTATGAT-TATATTT-AA-TATATTT-TATATTTT
*
1483113 ATTTTATTGTGATTATATTTAATATATTTTATATTT
1 ATTTTATTATGATTATATTTAATATATTTTATATTT
1483149 ATATATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 7 0.21
38 7 0.21
39 2 0.06
40 16 0.48
41 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (37 bp):
ATTTTATTATGATTATATTTAATATATTTTATATTTT
Found at i:1483152 original size:15 final size:15
Alignment explanation
Indices: 1483096--1483157 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
1483086 TATATTTAAA
*
1483096 TTATATTTGTATATT
1 TTATATTTATATATT
* *
1483111 TTAT-TTTAT-TGTGA
1 TTATATTTATATAT-T
1483125 TTATATTTAATATATT
1 TTATATTT-ATATATT
1483141 TTATATTTATATATT
1 TTATATTTATATATT
1483156 TT
1 TT
1483158 TGATATATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
13 2 0.05
14 8 0.21
15 16 0.42
16 10 0.26
17 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (15 bp):
TTATATTTATATATT
Found at i:1490875 original size:33 final size:32
Alignment explanation
Indices: 1490798--1490882 Score: 84
Period size: 33 Copynumber: 2.6 Consensus size: 32
1490788 AATATATTTT
* *
1490798 TATTATATTTTGATACATTTATAATTTGTATTA
1 TATTATATTTT-AAATATTTATAATTTGTATTA
*
1490831 TA-TAAATTTTTAAATATTTATATATTTGT-TTAA
1 TATTATA-TTTTAAATATTTATA-ATTTGTATT-A
*
1490864 TATTATATTTTAATTATTT
1 TATTATATTTTAAATATTT
1490883 TTTTATCATA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
32 14 0.33
33 26 0.60
34 3 0.07
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (32 bp):
TATTATATTTTAAATATTTATAATTTGTATTA
Found at i:1496203 original size:79 final size:81
Alignment explanation
Indices: 1496067--1496221 Score: 199
Period size: 79 Copynumber: 1.9 Consensus size: 81
1496057 CATATATGTA
* *
1496067 AACAAATAAAATTTTTTATTCTTTTCATATATCACAAAAAATATTAAATTAACTTTATTTACTAG
1 AACAAATAAAATTTTTAATTCTTTTCATATATCACAAAAAATATTAAATTAAATTTATTTACTAG
1496132 ATTACTATAAAATATC
66 ATTACTATAAAATATC
* * * * * *
1496148 AACAAATAAAA-TTTTAA-T-TTTTCTATCTCTCATAAAAAATGTTAAGTTAAATTTATTTATTA
1 AACAAATAAAATTTTTAATTCTTTTC-ATATATCACAAAAAATATTAAATTAAATTTATTTACTA
*
1496210 GATTGCTATAAA
65 GATTACTATAAA
1496222 CTATATGTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
78 5 0.08
79 43 0.67
80 5 0.08
81 11 0.17
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.43
Consensus pattern (81 bp):
AACAAATAAAATTTTTAATTCTTTTCATATATCACAAAAAATATTAAATTAAATTTATTTACTAG
ATTACTATAAAATATC
Found at i:1496490 original size:17 final size:18
Alignment explanation
Indices: 1496460--1496495 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1496450 TATCGAAACT
*
1496460 ATTTATTATTTAAACTTA
1 ATTTATTATTTAAAATTA
1496478 ATTTATT-TTTAAAATTA
1 ATTTATTATTTAAAATTA
1496495 A
1 A
1496496 AAATGAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTATTATTTAAAATTA
Found at i:1501790 original size:14 final size:14
Alignment explanation
Indices: 1501771--1501804 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1501761 ATATATATTT
1501771 AATATAAATATAAA
1 AATATAAATATAAA
* *
1501785 AATATAATTTTAAA
1 AATATAAATATAAA
1501799 AATATA
1 AATATA
1501805 TAAAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATATAAATATAAA
Found at i:1501813 original size:20 final size:20
Alignment explanation
Indices: 1501776--1501829 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1501766 TATTTAATAT
*
1501776 AAATATAAAAATATAATTTTAA
1 AAATATATAAA-A-AATTTTAA
1501798 AAATATATAAAAAATTTTAA
1 AAATATATAAAAAATTTTAA
*
1501818 AAAAAT-TAAAAA
1 AAATATATAAAAA
1501830 TATTCACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 6 0.20
20 13 0.43
21 1 0.03
22 10 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATATATAAAAAATTTTAA
Found at i:1511171 original size:27 final size:30
Alignment explanation
Indices: 1511123--1511186 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 30
1511113 GTATTTAGTT
*
1511123 TAATTTATTTATTTAAATATTTTAAAATATA
1 TAATTTA-ATATTTAAATATTTTAAAATATA
*
1511154 -AATTTAATATTT-AA-ATTTTAATATATA
1 TAATTTAATATTTAAATATTTTAAAATATA
1511181 TAATTT
1 TAATTT
1511187 TTTTTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 12 0.40
28 7 0.23
29 5 0.17
30 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TAATTTAATATTTAAATATTTTAAAATATA
Found at i:1511173 original size:14 final size:14
Alignment explanation
Indices: 1511141--1511187 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
1511131 TTATTTAAAT
*
1511141 ATTTTAAAATATAA
1 ATTTTAATATATAA
*
1511155 A-TTTAATATTTAA
1 ATTTTAATATATAA
1511168 ATTTTAATATATATA
1 ATTTTAATATATA-A
1511183 ATTTT
1 ATTTT
1511188 TTTTATTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 11 0.39
14 11 0.39
15 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTTAATATATAA
Found at i:1511441 original size:13 final size:12
Alignment explanation
Indices: 1511425--1511485 Score: 58
Period size: 13 Copynumber: 5.2 Consensus size: 12
1511415 AATGATAATC
1511425 AAAATATATATAA
1 AAAATATAT-TAA
*
1511438 AAAAT-TATTAT
1 AAAATATATTAA
1511449 AAAAT-T-TTAA
1 AAAATATATTAA
1511459 AAAA-ATATTTAA
1 AAAATATA-TTAA
1511471 ATAAATATATTAA
1 A-AAATATATTAA
1511484 AA
1 AA
1511486 TAAAACAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
10 8 0.20
11 8 0.20
12 9 0.22
13 13 0.32
14 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAATATATTAA
Found at i:1511486 original size:14 final size:13
Alignment explanation
Indices: 1511450--1511489 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
1511440 AATTATTATA
1511450 AAAT-TTTAAAA-
1 AAATATTTAAAAT
1511461 AAATATTT-AAAT
1 AAATATTTAAAAT
1511473 AAATATATTAAAAT
1 AAATAT-TTAAAAT
1511487 AAA
1 AAA
1511490 ACAAACAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.28
12 9 0.36
13 2 0.08
14 7 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATATTTAAAAT
Found at i:1524809 original size:9 final size:9
Alignment explanation
Indices: 1524797--1524866 Score: 54
Period size: 9 Copynumber: 7.8 Consensus size: 9
1524787 AAATTTTTAA
1524797 AAATTAATT
1 AAATTAATT
*
1524806 AAATTAAAT
1 AAATTAATT
* *
1524815 AAATTTATA
1 AAATTAATT
1524824 AAATTAATT
1 AAATTAATT
*
1524833 AAAAATAATT
1 -AAATTAATT
*
1524843 TAA--AATT
1 AAATTAATT
*
1524850 AAAATAATTT
1 AAATTAA-TT
1524860 AAATTAA
1 AAATTAA
1524867 AATTTATAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
7 6 0.13
9 25 0.53
10 16 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
AAATTAATT
Found at i:1524863 original size:15 final size:16
Alignment explanation
Indices: 1524829--1524869 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
1524819 TTATAAAATT
1524829 AATTAAAAATAATTTAA
1 AATT-AAAATAATTTAA
1524846 AATTAAAATAATTT-A
1 AATTAAAATAATTTAA
1524861 AATTAAAAT
1 AATTAAAAT
1524870 TTATAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 10 0.42
16 10 0.42
17 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTAAAATAATTTAA
Found at i:1525046 original size:17 final size:18
Alignment explanation
Indices: 1525006--1525047 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1524996 TTTTATGTAA
*
1525006 ATTAAATAAAATATATTT
1 ATTAATTAAAATATATTT
*
1525024 A-AAATTAAAATA-ATTT
1 ATTAATTAAAATATATTT
1525040 ATTAATTA
1 ATTAATTA
1525048 TTCATTATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 5 0.25
17 14 0.70
18 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAATTAAAATATATTT
Found at i:1525097 original size:18 final size:19
Alignment explanation
Indices: 1525074--1525130 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 19
1525064 AAATTAATAA
1525074 TTAATAAAAT-AAATATTT
1 TTAATAAAATAAAATATTT
*
1525092 TTAAT-AATTAAAATAATTT
1 TTAATAAAATAAAAT-ATTT
*
1525111 TAAAATAAAATAAAATATTT
1 T-TAATAAAATAAAATATTT
1525131 ATATTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.09
18 9 0.28
19 5 0.16
20 7 0.22
21 8 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAATAAAATAAAATATTT
Found at i:1525837 original size:26 final size:27
Alignment explanation
Indices: 1525794--1525844 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
1525784 TGTTTAAATT
1525794 TTAAATAATATTAAATATAAATTTATA
1 TTAAATAATATTAAATATAAATTTATA
* *
1525821 TTAAA-AATTTTAAATATAATTTTA
1 TTAAATAATATTAAATATAAATTTA
1525845 AAATATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAATAATATTAAATATAAATTTATA
Found at i:1526704 original size:2 final size:2
Alignment explanation
Indices: 1526691--1526725 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1526681 ACGTGTGCAA
*
1526691 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1526726 ATTAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1527238 original size:16 final size:17
Alignment explanation
Indices: 1527219--1527250 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1527209 TGTTTGAATA
1527219 TATTATTT-ATTATTTT
1 TATTATTTAATTATTTT
1527235 TATTATTTAATTATTT
1 TATTATTTAATTATTT
1527251 AAAGGAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTATTTAATTATTTT
Found at i:1527592 original size:22 final size:22
Alignment explanation
Indices: 1527566--1527642 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
1527556 AGATTGAGCT
1527566 TATAATTATATTTAAATTATTA
1 TATAATTATATTTAAATTATTA
* *
1527588 TATAATTTTATATAAATT-TTA
1 TATAATTATATTTAAATTATTA
1527609 -ATATATTAATAATTTAAATTA-TA
1 TATA-ATT-AT-ATTTAAATTATTA
*
1527632 TATATTTATAT
1 TATAATTATAT
1527643 ATTTATAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
20 3 0.07
21 8 0.18
22 19 0.42
23 12 0.27
24 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATAATTATATTTAAATTATTA
Found at i:1527955 original size:2 final size:2
Alignment explanation
Indices: 1527948--1527976 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1527938 GAAATTACAC
1527948 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1527977 GATTTCGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1528137 original size:22 final size:21
Alignment explanation
Indices: 1528112--1528174 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
1528102 AATAACAAAT
*
1528112 ATAATATTAAAATATTATATAA
1 ATAATATTAAAATATT-TAAAA
* *
1528134 ATAAAATATAATATATTTAAAA
1 ATAATAT-TAAAATATTTAAAA
*
1528156 ATAAGTATTACAATATTTA
1 ATAA-TATTAAAATATTTA
1528175 TTATATATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 23 0.70
23 10 0.30
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
ATAATATTAAAATATTTAAAA
Found at i:1528154 original size:16 final size:16
Alignment explanation
Indices: 1528117--1528159 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1528107 CAAATATAAT
*
1528117 ATTAAAATATTATATA
1 ATTAAAATATAATATA
*
1528133 AATAAAATATAATATA
1 ATTAAAATATAATATA
*
1528149 TTTAAAA-ATAA
1 ATTAAAATATAA
1528160 GTATTACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTAAAATATAATATA
Found at i:1528844 original size:25 final size:25
Alignment explanation
Indices: 1528811--1528858 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1528801 TTTTTAATTT
* *
1528811 TTAATTTTTTATGTATATATAAAAA
1 TTAAATTTTAATGTATATATAAAAA
* *
1528836 TTAAATTTTAATTTATATTTAAA
1 TTAAATTTTAATGTATATATAAA
1528859 TATAAATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TTAAATTTTAATGTATATATAAAAA
Found at i:1528874 original size:31 final size:31
Alignment explanation
Indices: 1528804--1528877 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 31
1528794 TTAATTATTT
* *
1528804 TTAATTTTTAATTTTTTATGTATATATAAAAA
1 TTAA-TTTTAATTTTATATGTAAATATAAAAA
*
1528836 TTAAATTTTAA-TTTATATTTAAATATAAATAA
1 TT-AATTTTAATTTTATATGTAAATATAAA-AA
1528868 TTAATTTTAA
1 TTAATTTTAA
1528878 AAGTAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 23 0.62
32 12 0.32
33 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
TTAATTTTAATTTTATATGTAAATATAAAAA
Found at i:1528918 original size:18 final size:18
Alignment explanation
Indices: 1528895--1528936 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1528885 ATATATTAAT
* *
1528895 TAAATTATTTTTATAAAA
1 TAAATTAATTTAATAAAA
*
1528913 TAAATTAATTTAATCAAA
1 TAAATTAATTTAATAAAA
1528931 TAAATT
1 TAAATT
1528937 TAAATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTAATAAAA
Found at i:1529353 original size:29 final size:31
Alignment explanation
Indices: 1529304--1529364 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
1529294 ATTTATTTAT
*
1529304 TTTAATTTTAAATATATAAAAA-TAAAAATA
1 TTTAATTTTAAATATAAAAAAATTAAAAATA
1529334 TTTAA-TTT-AATAATAAAAAAATTAAAAATA
1 TTTAATTTTAAAT-ATAAAAAAATTAAAAATA
1529364 T
1 T
1529365 CTTTCTTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 3 0.11
29 11 0.39
30 14 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
TTTAATTTTAAATATAAAAAAATTAAAAATA
Found at i:1534276 original size:2 final size:2
Alignment explanation
Indices: 1534269--1534293 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1534259 AAGATACAAT
1534269 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1534294 TGGTTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1535300 original size:18 final size:16
Alignment explanation
Indices: 1535280--1535312 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
1535270 TTTTTTTTAA
1535280 AAAAAATTTAAATATAT
1 AAAAAA-TTAAATATAT
1535297 AAAAAATTAAATATAT
1 AAAAAATTAAATATAT
1535313 TTATATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAAATTAAATATAT
Found at i:1535341 original size:17 final size:17
Alignment explanation
Indices: 1535303--1535342 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1535293 ATATAAAAAA
1535303 TTAA-ATATATTTATAT
1 TTAATATATATTTATAT
**
1535319 AAAATATATATTTATAT
1 TTAATATATATTTATAT
1535336 TTAATAT
1 TTAATAT
1535343 TTACGTCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATATATTTATAT
Found at i:1536449 original size:13 final size:14
Alignment explanation
Indices: 1536431--1536459 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1536421 TATGTTTGAC
1536431 ATAAATATA-AAAA
1 ATAAATATATAAAA
1536444 ATAAATATATAAAA
1 ATAAATATATAAAA
1536458 AT
1 AT
1536460 GACAGCAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAATATATAAAA
Found at i:1543743 original size:7 final size:7
Alignment explanation
Indices: 1543710--1543742 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
1543700 GAATGTTCCA
1543710 TTTTTTC
1 TTTTTTC
1543717 TTTTTTC
1 TTTTTTC
1543724 TTTTTTC
1 TTTTTTC
1543731 TTTTTT-
1 TTTTTTC
1543737 TTTTTT
1 TTTTTT
1543743 TAAGTTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
TTTTTTC
Found at i:1549410 original size:59 final size:57
Alignment explanation
Indices: 1549344--1549453 Score: 175
Period size: 59 Copynumber: 1.9 Consensus size: 57
1549334 CATATAAATA
*
1549344 TAAATATATCAAAGTGTTAAACATAATAAAAAAATTATATATACATATACATATATTAT
1 TAAATATATCAAAGTATTAAACATAAT-AAAAAA-TATATATACATATACATATATTAT
* *
1549403 TAAATATATCAAAGTATTAAACATAATAAAATATATATATATATATACATA
1 TAAATATATCAAAGTATTAAACATAATAAAAAATATATATACATATACATA
1549454 CATTTAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
57 17 0.35
58 5 0.10
59 26 0.54
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (57 bp):
TAAATATATCAAAGTATTAAACATAATAAAAAATATATATACATATACATATATTAT
Found at i:1551516 original size:2 final size:2
Alignment explanation
Indices: 1551509--1551551 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1551499 ACGGGTGTTT
1551509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1551551 T
1 T
1551552 CTCAGAGAGA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1551889 original size:20 final size:20
Alignment explanation
Indices: 1551864--1551926 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
1551854 TTTTCACACA
1551864 TAAAAAAATAAAATAAATAT
1 TAAAAAAATAAAATAAATAT
*
1551884 TAAAAAAATAATATAAATAT
1 TAAAAAAATAAAATAAATAT
* *
1551904 AAAAAAATATAAAATAATTAT
1 TAAAAAA-ATAAAATAAATAT
1551925 TA
1 TA
1551927 TTAACTAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 25 0.68
21 12 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAAAATAAAATAAATAT
Found at i:1551905 original size:11 final size:10
Alignment explanation
Indices: 1551863--1551916 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
1551853 TTTTTCACAC
*
1551863 ATAAAAAAAT
1 ATAAATAAAT
1551873 A-AAATAAAT
1 ATAAATAAAT
1551882 ATTAAA-AAA-
1 A-TAAATAAAT
1551891 ATAATATAAAT
1 ATAA-ATAAAT
*
1551902 ATAAAAAAAT
1 ATAAATAAAT
1551912 ATAAA
1 ATAAA
1551917 ATAATTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 3 0.08
9 10 0.27
10 17 0.46
11 7 0.19
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
ATAAATAAAT
Found at i:1552531 original size:14 final size:15
Alignment explanation
Indices: 1552509--1552540 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1552499 TTTCATCTAT
1552509 TTGATTTGATGGCAA
1 TTGATTTGATGGCAA
1552524 TTGA-TTGATGGCAA
1 TTGATTTGATGGCAA
1552538 TTG
1 TTG
1552541 GCGAATGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.25, C:0.06, G:0.28, T:0.41
Consensus pattern (15 bp):
TTGATTTGATGGCAA
Done.