Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 14 of 19
Found at i:2991726 original size:2 final size:2
Alignment explanation
Indices: 2991719--2991764 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2991709 AATGGTACTA
2991719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2991761 AT AT
1 AT AT
2991765 TCTTTCAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2992520 original size:11 final size:12
Alignment explanation
Indices: 2992505--2992533 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2992495 TCCAATTGTG
2992505 CGTCAACTGTAT
1 CGTCAACTGTAT
2992517 -GTCAACTGTAT
1 CGTCAACTGTAT
2992528 CGTCAA
1 CGTCAA
2992534 TTTTAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (12 bp):
CGTCAACTGTAT
Found at i:2992548 original size:13 final size:13
Alignment explanation
Indices: 2992530--2992581 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
2992520 AACTGTATCG
*
2992530 TCAATTTTAAAAT
1 TCAATTTGAAAAT
*
2992543 TCAATTTGAAATAG
1 TCAATTTGAAA-AT
*
2992557 TAAATATT-AAAAT
1 TCAAT-TTGAAAAT
2992570 TCAATTTGAAAA
1 TCAATTTGAAAA
2992582 AAATTATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 2 0.06
13 19 0.61
14 8 0.26
15 2 0.06
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (13 bp):
TCAATTTGAAAAT
Found at i:2995254 original size:1 final size:1
Alignment explanation
Indices: 2995248--2995747 Score: 766
Period size: 1 Copynumber: 500.0 Consensus size: 1
2995238 GTGTTTCACG
*
2995248 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* *
2995313 CCCCCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* * *
2995378 CCCCCCCCCCCCCCCTCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* **
2995443 CCCTCCCCCCCCCCCCCATCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* *** *
2995508 CCTCCCCCCCCCCTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCTCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
** * *
2995573 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTTCTCCCCCCCCGCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
*** * * * *
2995638 CCCCCCCCCTTTCTCCCCCCCCCCTCCCCCCCCCCCCCCCCCCTCCCCCTCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
*
2995703 CCCCCCCCCCCCCCCCCCCCCCCCCTCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2995748 AAACGAAACT
Statistics
Matches: 458, Mismatches: 41, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 458 1.00
ACGTcount: A:0.01, C:0.95, G:0.00, T:0.04
Consensus pattern (1 bp):
C
Found at i:2996618 original size:12 final size:12
Alignment explanation
Indices: 2996601--2996632 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2996591 TTCAACAAAG
2996601 GCTGCCAACTGT
1 GCTGCCAACTGT
2996613 GCTGCCAACTGT
1 GCTGCCAACTGT
*
2996625 GCCGCCAA
1 GCTGCCAA
2996633 TTTTGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.38, G:0.25, T:0.19
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:2996649 original size:12 final size:12
Alignment explanation
Indices: 2996634--2996679 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
2996624 TGCCGCCAAT
2996634 TTTGAAATTCAA
1 TTTGAAATTCAA
*
2996646 TTTGAAATAGTAAA
1 TTTGAAAT--TCAA
2996660 TGTTGAAATTCAA
1 T-TTGAAATTCAA
2996673 TTTGAAA
1 TTTGAAA
2996680 CAGTGAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (12 bp):
TTTGAAATTCAA
Found at i:2998232 original size:2 final size:2
Alignment explanation
Indices: 2998225--2998249 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2998215 GATTTGACTC
2998225 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
2998250 GTTGTATATT
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:2999468 original size:24 final size:22
Alignment explanation
Indices: 2999441--2999490 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2999431 TTAAATTCAG
* *
2999441 ATTTAAATTTGATTTGATTTATTT
1 ATTTAAATATGA-TT-AATTATTT
2999465 ATTTAAATATGATTAATTATTT
1 ATTTAAATATGATTAATTATTT
2999487 ATTT
1 ATTT
2999491 TATCTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 2 0.08
24 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (22 bp):
ATTTAAATATGATTAATTATTT
Found at i:2999521 original size:17 final size:17
Alignment explanation
Indices: 2999476--2999521 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
2999466 TTTAAATATG
2999476 ATTAATTATTTATTTTAT
1 ATTAA-TATTTATTTTAT
* *
2999494 -CTAAAATTTATTTTAT
1 ATTAATATTTATTTTAT
2999510 ATTAATATTTAT
1 ATTAATATTTAT
2999522 ATATTTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTAATATTTATTTTAT
Found at i:2999526 original size:21 final size:21
Alignment explanation
Indices: 2999502--2999541 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2999492 ATCTAAAATT
2999502 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
2999523 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
2999542 AATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:2999764 original size:25 final size:25
Alignment explanation
Indices: 2999728--2999782 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
2999718 ATTTTATATT
2999728 TATATATCTTTTTCAAAAAAT-ATAA
1 TATATATCTTTTT-AAAAAATGATAA
*
2999753 TATATATTTTTTTAAAAAATGATAA
1 TATATATCTTTTTAAAAAATGATAA
*
2999778 AATAT
1 TATAT
2999783 GTTTAAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (25 bp):
TATATATCTTTTTAAAAAATGATAA
Found at i:3002901 original size:23 final size:23
Alignment explanation
Indices: 3002866--3002914 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
3002856 TATGCTATTT
*
3002866 TTTATGTTGTTA-TATATTTGTTA
1 TTTATGTTATTATTATATTT-TTA
* *
3002889 TTTATTTTATTATTTTATTTTTA
1 TTTATGTTATTATTATATTTTTA
3002912 TTT
1 TTT
3002915 TAAAAAGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.73
Consensus pattern (23 bp):
TTTATGTTATTATTATATTTTTA
Found at i:3002902 original size:19 final size:20
Alignment explanation
Indices: 3002875--3002916 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
3002865 TTTTATGTTG
3002875 TTATATATTTGT-TATTTATT
1 TTATATATTT-TATATTTATT
*
3002895 TTAT-TATTTTATTTTTATT
1 TTATATATTTTATATTTATT
3002914 TTA
1 TTA
3002917 AAAAGGATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.75
20 4 0.20
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (20 bp):
TTATATATTTTATATTTATT
Found at i:3004101 original size:16 final size:18
Alignment explanation
Indices: 3004060--3004108 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 18
3004050 ATATCCTGTG
*
3004060 TTTATAAAATTTTAATAT
1 TTTATATAATTTTAATAT
*
3004078 ATTA-ATAA-TTTAAT-T
1 TTTATATAATTTTAATAT
3004093 TTTATATAAATTTTAA
1 TTTATAT-AATTTTAA
3004109 AATATTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 5 0.20
18 8 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTATATAATTTTAATAT
Found at i:3013964 original size:20 final size:20
Alignment explanation
Indices: 3013919--3013967 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3013909 TTTTATTAAG
*
3013919 ATTTAATCATAAATATATAAT
1 ATTTAAT-ATAAAAATATAAT
3013940 A-TTAATATAAAAATA-AATT
1 ATTTAATATAAAAATATAA-T
3013959 ATTTAATAT
1 ATTTAATAT
3013968 TTTAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 10 0.40
20 12 0.48
21 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTTAATATAAAAATATAAT
Found at i:3014441 original size:16 final size:16
Alignment explanation
Indices: 3014393--3014442 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 16
3014383 ATAATTTTAC
3014393 ATATTTTTA-C-AATA
1 ATATTTTTATCAAATA
* * *
3014407 AAATTTTAATAATAATA
1 ATATTTTTATCA-AATA
3014424 ATATTTTTATCAAATA
1 ATATTTTTATCAAATA
3014440 ATA
1 ATA
3014443 ATTTAAATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 7 0.26
16 7 0.26
17 13 0.48
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTTTTATCAAATA
Found at i:3014747 original size:4 final size:4
Alignment explanation
Indices: 3014738--3014765 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3014728 AATTAAGAAA
3014738 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
3014766 CAATAAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:3015201 original size:20 final size:19
Alignment explanation
Indices: 3015176--3015217 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3015166 AGTTTTAAAA
*
3015176 TATATTAAAATATTATTTTT
1 TATATTAAAATA-TATTTAT
*
3015196 TATATTAATATATATTTAT
1 TATATTAAAATATATTTAT
3015215 TAT
1 TAT
3015218 TAATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATTAAAATATATTTAT
Found at i:3022354 original size:2 final size:2
Alignment explanation
Indices: 3022347--3022371 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3022337 ATTAGGTTAT
3022347 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
3022372 GCATTGAAAA
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:3023752 original size:41 final size:41
Alignment explanation
Indices: 3023706--3023798 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 41
3023696 AATTTTACGA
3023706 ATAAAATTAATAAAAT-TATACA-TATATTTTAATATATTATTT
1 ATAAAATTAATAAAATATATA-ATTATATTTTAAT-T-TTATTT
* * *
3023748 -TAAAAATAAATAAAATATATAATTTTTTTTTAATTTTATTT
1 AT-AAAATTAATAAAATATATAATTATATTTTAATTTTATTT
3023789 ATAAAATTAA
1 ATAAAATTAA
3023799 AACTTTATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
41 14 0.33
42 16 0.37
43 13 0.30
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (41 bp):
ATAAAATTAATAAAATATATAATTATATTTTAATTTTATTT
Found at i:3028177 original size:14 final size:15
Alignment explanation
Indices: 3028150--3028178 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3028140 TTAAAATTTA
3028150 AATTTTAAATATAAT
1 AATTTTAAATATAAT
3028165 AATTTTAAA-ATAAT
1 AATTTTAAATATAAT
3028179 TAAGTACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTAAATATAAT
Found at i:3028679 original size:15 final size:15
Alignment explanation
Indices: 3028633--3028682 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
3028623 AATGAAAAAG
3028633 TATTTTAATTTTTGTA
1 TATTTTAATTTTT-TA
* * *
3028649 T-TATTAA-ATTTAA
1 TATTTTAATTTTTTA
3028662 TATTTTAATTTTTTA
1 TATTTTAATTTTTTA
3028677 TATTTT
1 TATTTT
3028683 TGAAATTGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
13 2 0.08
14 8 0.31
15 15 0.58
16 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
TATTTTAATTTTTTA
Found at i:3030410 original size:2 final size:2
Alignment explanation
Indices: 3030403--3030451 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3030393 CTTTCTGTTT
3030403 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
3030445 TA TA TA T
1 TA TA TA T
3030452 CAATAGAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3034232 original size:2 final size:2
Alignment explanation
Indices: 3034225--3034275 Score: 66
Period size: 2 Copynumber: 24.5 Consensus size: 2
3034215 TTCATATGAA
* *
3034225 AT AT AT AT AT AT AT AT AC AGT GAA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT AT
3034269 AT AT AT A
1 AT AT AT A
3034276 CACACACACA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 42 0.98
4 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3034582 original size:2 final size:2
Alignment explanation
Indices: 3034575--3034608 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3034565 AATAAGCAAA
* *
3034575 AT AT AT AT AC AA 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
3034609 GTAGATAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3035304 original size:2 final size:2
Alignment explanation
Indices: 3035297--3035330 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3035287 TAACTCCAAG
3035297 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
3035331 AATAAGTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3036380 original size:25 final size:28
Alignment explanation
Indices: 3036341--3036396 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
3036331 ATTATTCATG
*
3036341 TAAAAATTTATAAAA-AAATT-TAATTT
1 TAAAAATTTAAAAAATAAATTATAATTT
*
3036367 TAAAAA-TTAAAAAATAAATTATACTTT
1 TAAAAATTTAAAAAATAAATTATAATTT
3036394 TAA
1 TAA
3036397 TCACTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 7 0.27
26 11 0.42
27 8 0.31
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
TAAAAATTTAAAAAATAAATTATAATTT
Found at i:3036882 original size:2 final size:2
Alignment explanation
Indices: 3036875--3036915 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3036865 CGATCGATCT
3036875 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3036916 GTGACAGAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3047189 original size:2 final size:2
Alignment explanation
Indices: 3047184--3047223 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3047174 TAAAAAACTA
3047184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3047224 GCATGTCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3047663 original size:30 final size:30
Alignment explanation
Indices: 3047583--3047663 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
3047573 AAATAATATC
*
3047583 AATTTAATTAATGAAATAAATAAAAAAATA
1 AATTAAATTAATGAAATAAATAAAAAAATA
* * * * *
3047613 AATTCAATTGATGTATTAAATAAAAATA-A
1 AATTAAATTAATGAAATAAATAAAAAAATA
*
3047642 AATATAAATTAATAAAATAAAT
1 AAT-TAAATTAATGAAATAAAT
3047664 TAAAGCATAT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (30 bp):
AATTAAATTAATGAAATAAATAAAAAAATA
Found at i:3047924 original size:21 final size:21
Alignment explanation
Indices: 3047856--3047924 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
3047846 ATATAACCGT
**
3047856 TTATTTTATTTTTAAAAA-AAA
1 TTATTTTA-TTTTAAAAATTTA
* *
3047877 TTATTTTTATATT-AATATTTA
1 TTA-TTTTATTTTAAAAATTTA
3047898 TATATTTTATTTTAAAAATTTA
1 T-TATTTTATTTTAAAAATTTA
3047920 TTATT
1 TTATT
3047925 AAATAACAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
20 3 0.08
21 20 0.53
22 15 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTTTATTTTAAAAATTTA
Found at i:3048253 original size:2 final size:2
Alignment explanation
Indices: 3048241--3048286 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3048231 ACGTGCGTGC
*
3048241 AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3048283 AT AT
1 AT AT
3048287 TAAACTGATC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3048731 original size:2 final size:2
Alignment explanation
Indices: 3048724--3048760 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3048714 GTATACATAC
3048724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3048761 AATCCTTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3049241 original size:2 final size:2
Alignment explanation
Indices: 3049236--3049271 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3049226 GTGTATGTAT
*
3049236 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3049272 CTTACTGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3054871 original size:17 final size:17
Alignment explanation
Indices: 3054849--3054898 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
3054839 AGAAAATATG
3054849 AATATAAATATTTACT-A
1 AATATAAATATTTA-TAA
*
3054866 AATATAAATATAATATAA
1 AATATAAATAT-TTATAA
3054884 AATATAACATATTTA
1 AATATAA-ATATTTA
3054899 AATATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 12 0.43
18 12 0.43
19 4 0.14
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (17 bp):
AATATAAATATTTATAA
Found at i:3055347 original size:14 final size:13
Alignment explanation
Indices: 3055316--3055363 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
3055306 ATTATTTAAA
3055316 ATATTTTAAAAAT
1 ATATTTTAAAAAT
*
3055329 GTATTTTAAAAATT
1 ATATTTTAAAAA-T
**
3055343 ATATTTATAATTAT
1 ATATTT-TAAAAAT
3055357 ATATTTT
1 ATATTTT
3055364 TATAATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 12 0.41
14 13 0.45
15 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
ATATTTTAAAAAT
Found at i:3055349 original size:13 final size:13
Alignment explanation
Indices: 3055298--3055358 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
3055288 AACTTAAAAA
*
3055298 TAAAATTTATTATT
1 TAAAAATTA-TATT
3055312 T-AAAA-TAT-TT
1 TAAAAATTATATT
3055322 TAAAAATGTAT-TT
1 TAAAAAT-TATATT
3055335 TAAAAATTATATT
1 TAAAAATTATATT
*
3055348 T-ATAATTATAT
1 TAAAAATTATAT
3055359 ATTTTTATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
10 3 0.07
11 5 0.12
12 14 0.34
13 18 0.44
14 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
TAAAAATTATATT
Found at i:3063193 original size:12 final size:12
Alignment explanation
Indices: 3063176--3063203 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3063166 AAACCTCATA
3063176 TATTTCTAAATT
1 TATTTCTAAATT
3063188 TATTTCTAAATT
1 TATTTCTAAATT
3063200 TATT
1 TATT
3063204 GGTGTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTTCTAAATT
Found at i:3069200 original size:3 final size:3
Alignment explanation
Indices: 3069192--3069238 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
3069182 TTGTCTTGTG
* * *
3069192 ATT ATT ATT ATT ATT ATT ATT ATT GTT GTT GTT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3069239 GATGATGATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3081141 original size:12 final size:11
Alignment explanation
Indices: 3081124--3081195 Score: 62
Period size: 12 Copynumber: 6.6 Consensus size: 11
3081114 GATCGATTTA
3081124 ATTTAAATTATT
1 ATTTAAA-TATT
*
3081136 ATTTAAATATA
1 ATTTAAATATT
3081147 ATTATAAATATT
1 ATT-TAAATATT
3081159 AATTTAAA-A--
1 -ATTTAAATATT
* *
3081168 ATATAAATAAT
1 ATTTAAATATT
3081179 -TTTAAATATT
1 ATTTAAATATT
3081189 ATTTAAA
1 ATTTAAA
3081196 ACAATAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
8 6 0.12
9 1 0.02
10 8 0.16
11 13 0.27
12 18 0.37
13 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTTAAATATT
Found at i:3081179 original size:30 final size:32
Alignment explanation
Indices: 3081139--3081223 Score: 106
Period size: 30 Copynumber: 2.8 Consensus size: 32
3081129 AATTATTATT
* *
3081139 TAAATATAATTATAAATATTAATTT-AAA-AA
1 TAAAAATAATTTTAAATATTAATTTAAAACAA
*
3081169 TATAAATAATTTTAAATATT-ATTTAAAACAA
1 TAAAAATAATTTTAAATATTAATTTAAAACAA
3081200 TAAAAATAAATTTTAAA-ATTAATT
1 TAAAAAT-AATTTTAAATATTAATT
3081224 AGTAAGACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 4 0.09
30 20 0.43
31 11 0.23
32 12 0.26
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
TAAAAATAATTTTAAATATTAATTTAAAACAA
Found at i:3082160 original size:17 final size:18
Alignment explanation
Indices: 3082138--3082207 Score: 67
Period size: 17 Copynumber: 4.1 Consensus size: 18
3082128 TATTAAAATT
3082138 ATATAAA-TATAAATATA
1 ATATAAATTATAAATATA
*
3082155 ATATAAATTATTACATATA
1 ATATAAATTA-TAAATATA
* * *
3082174 TTA-AAATTTTAAACATA
1 ATATAAATTATAAATATA
3082191 ATAT-AA-TATAAATATA
1 ATATAAATTATAAATATA
3082207 A
1 A
3082208 AAAATATTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
16 9 0.21
17 17 0.40
18 7 0.17
19 9 0.21
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAATTATAAATATA
Found at i:3082255 original size:24 final size:23
Alignment explanation
Indices: 3082209--3082255 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
3082199 TAAATATAAA
*
3082209 AAATATTATATTTATTATTTTTT
1 AAATATTATATTTATTATATTTT
3082232 AAATA-TATATTTATATTATATTTT
1 AAATATTATA-TT-TATTATATTTT
3082256 TATGTCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 7 0.33
24 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
AAATATTATATTTATTATATTTT
Found at i:3082500 original size:3 final size:3
Alignment explanation
Indices: 3082492--3082517 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3082482 TAAGCTTAAA
3082492 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3082518 AAACAAAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3085806 original size:14 final size:14
Alignment explanation
Indices: 3085785--3085821 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
3085775 AATATAAAAA
3085785 AATATTTTTT-AA-
1 AATATTTTTTAAAT
3085797 AATATTTTTTAAAT
1 AATATTTTTTAAAT
3085811 AATATTTTTTA
1 AATATTTTTTA
3085822 GCTAATCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATATTTTTTAAAT
Found at i:3085810 original size:11 final size:12
Alignment explanation
Indices: 3085783--3085821 Score: 60
Period size: 12 Copynumber: 3.1 Consensus size: 12
3085773 ATAATATAAA
3085783 AAAATATTTTTT
1 AAAATATTTTTT
3085795 AAAATATTTTTT
1 AAAATATTTTTT
3085807 AAATAATATTTTTT
1 -AA-AATATTTTTT
3085821 A
1 A
3085822 GCTAATCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.48
13 3 0.12
14 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAAATATTTTTT
Found at i:3085887 original size:24 final size:26
Alignment explanation
Indices: 3085842--3085914 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
3085832 ATTTAGTACT
* *
3085842 TAAAAACATCAATAGATCTAATAATG-
1 TAAAAAAAT-AATAGATATAATAATGA
3085868 TAAAAAAATAA-AGATATAAT-ATGA
1 TAAAAAAATAATAGATATAATAATGA
* *
3085892 TTAAAAAATTAATAAATATAATA
1 -TAAAAAAATAATAGATATAATA
3085915 TAAAATATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 3 0.08
24 8 0.21
25 12 0.31
26 16 0.41
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (26 bp):
TAAAAAAATAATAGATATAATAATGA
Found at i:3085930 original size:18 final size:18
Alignment explanation
Indices: 3085909--3086024 Score: 54
Period size: 16 Copynumber: 6.6 Consensus size: 18
3085899 ATTAATAAAT
3085909 ATAATATAAAATATAATA
1 ATAATATAAAATATAATA
*
3085927 ATAA-ATTAAAAT-TTAT-
1 ATAATA-TAAAATATAATA
*
3085943 ATAATATAAATTATTAATA
1 ATAATATAAAATA-TAATA
3085962 TATTAATTTATATAAATATAA-A
1 -A-TAA--TATA-AAATATAATA
*
3085984 AT--T-TTAAATA-AATA
1 ATAATATAAAATATAATA
*
3085998 ATAATAT-AAATAAAAT-
1 ATAATATAAAATATAATA
3086014 ATAAATATAAA
1 AT-AATATAAA
3086025 GATTGCAAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 34
0.66 0.04 0.30
Matches are distributed among these distances:
13 2 0.03
14 8 0.11
15 1 0.01
16 18 0.24
17 14 0.18
18 15 0.20
20 2 0.03
21 4 0.05
22 1 0.01
23 7 0.09
24 4 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATATAAAATATAATA
Found at i:3085933 original size:32 final size:32
Alignment explanation
Indices: 3085897--3086017 Score: 103
Period size: 32 Copynumber: 3.9 Consensus size: 32
3085887 TATGATTAAA
3085897 AAATTAATAAATATAATATAAAATATAATAAT
1 AAATTAATAAATATAATATAAAATATAATAAT
*
3085929 AAATTAA-AATTTATATAATAT-AAAT-TATTAAT
1 AAATTAATAA---ATATAATATAAAATATAATAAT
* ** * *
3085961 ATATTAATTTATATAAATATAAAATTTTA-AAT
1 AAATTAATAAATAT-AATATAAAATATAATAAT
3085993 AAA-TAAT-AATATAA-ATAAAATATAA
1 AAATTAATAAATATAATATAAAATATAA
3086018 ATATAAAGAT
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
28 9 0.12
29 2 0.03
30 8 0.11
31 11 0.15
32 28 0.39
33 5 0.07
34 9 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
AAATTAATAAATATAATATAAAATATAATAAT
Found at i:3085982 original size:6 final size:6
Alignment explanation
Indices: 3085903--3086024 Score: 57
Period size: 6 Copynumber: 20.8 Consensus size: 6
3085893 TAAAAAATTA
**
3085903 ATAAAT AT-AAT ATAAA- ATATAAT AATAAAT -TAAA- ATTTAT AT-AAT
1 ATAAAT ATAAAT ATAAAT ATA-AAT -ATAAAT ATAAAT ATAAAT ATAAAT
* * * *
3085948 ATAAATT ATTAATAT ATTAAT -T-TAT ATAAAT ATAAAAT TTTAA- ATAAAT
1 ATAAA-T A-TAA-AT ATAAAT ATAAAT ATAAAT AT-AAAT ATAAAT ATAAAT
3085997 A-ATAAT ATAAAT A-AAAT ATAAAT ATAAA
1 ATA-AAT ATAAAT ATAAAT ATAAAT ATAAA
3086025 GATTGCAAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 34
0.67 0.08 0.26
Matches are distributed among these distances:
4 2 0.02
5 29 0.33
6 36 0.40
7 13 0.15
8 8 0.09
9 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATAAAT
Found at i:3086014 original size:11 final size:12
Alignment explanation
Indices: 3085991--3086020 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
3085981 AAAATTTTAA
3085991 ATAAATAATAAT
1 ATAAATAATAAT
3086003 ATAAATAA-AAT
1 ATAAATAATAAT
3086014 ATAAATA
1 ATAAATA
3086021 TAAAGATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAAATAATAAT
Found at i:3086699 original size:22 final size:22
Alignment explanation
Indices: 3086652--3086695 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3086642 ATTAAAAAAA
* *
3086652 TATTTATGTTATTTATTAATTT
1 TATTTATGATATTTATAAATTT
3086674 TATTTATGATATTTA-AAATTT
1 TATTTATGATATTTATAAATTT
3086695 T
1 T
3086696 TATTGAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
TATTTATGATATTTATAAATTT
Found at i:3087326 original size:21 final size:22
Alignment explanation
Indices: 3087275--3087331 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
3087265 AATTATAACT
*
3087275 TTTTAAAAAACTACTCATTTAC
1 TTTTAAAAAACTATTCATTTAC
*
3087297 ATTT-AAAAACTATTCATTTA-
1 TTTTAAAAAACTATTCATTTAC
*
3087317 TTTTAAAAAATTATT
1 TTTTAAAAAACTATT
3087332 GTTTTTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTTAAAAAACTATTCATTTAC
Found at i:3094769 original size:16 final size:15
Alignment explanation
Indices: 3094748--3094791 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
3094738 GATATGAAAA
3094748 TTTTAAATTATAATT
1 TTTTAAATTATAATT
*
3094763 TTGTTAAATT-TTATT
1 TT-TTAAATTATAATT
3094778 TTTTAAA-TATAATT
1 TTTTAAATTATAATT
3094792 AAATAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 1 0.04
14 9 0.36
15 8 0.32
16 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TTTTAAATTATAATT
Found at i:3096776 original size:65 final size:64
Alignment explanation
Indices: 3096686--3096823 Score: 222
Period size: 65 Copynumber: 2.1 Consensus size: 64
3096676 TGTCGAGGTT
* *
3096686 TCCATATTTAGCATTGCTGAAGACCAAAAAGTGATCTGCAACTCGAAGATATCCTGTGCCCTTGA
1 TCCATATTTAGCATTGCCGAAGACCAAAAAGTGATCTGCAACTCG-AGATATCCTGAGCCCTTGA
* * *
3096751 TCCTTATTTAGCATTGCCGAGGACCAAAAAGTGATCTGCAACTCGAGATATCCTGAGCTCTTGA
1 TCCATATTTAGCATTGCCGAAGACCAAAAAGTGATCTGCAACTCGAGATATCCTGAGCCCTTGA
3096815 TCCATATTT
1 TCCATATTT
3096824 GAGCTGGAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 25 0.37
65 42 0.63
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (64 bp):
TCCATATTTAGCATTGCCGAAGACCAAAAAGTGATCTGCAACTCGAGATATCCTGAGCCCTTGA
Found at i:3101921 original size:6 final size:6
Alignment explanation
Indices: 3101893--3101936 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
3101883 ATAAAACCCT
*
3101893 AAAGAC AAAAGAC AGAA-AC AAAGAC AAAGAC AAAGAC AGAGAC A
1 AAAGAC -AAAGAC A-AAGAC AAAGAC AAAGAC AAAGAC AAAGAC A
3101937 CAAGGATAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
5 2 0.06
6 24 0.71
7 8 0.24
ACGTcount: A:0.66, C:0.16, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAC
Found at i:3101935 original size:18 final size:18
Alignment explanation
Indices: 3101893--3101950 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
3101883 ATAAAACCCT
*
3101893 AAAGACAAAAGACAGAAAC
1 AAAGAC-AAAGACAGAGAC
*
3101912 AAAGACAAAGACAAAGAC
1 AAAGACAAAGACAGAGAC
* *
3101930 AGAGACACAAGGATAGAGAC
1 AAAGACA-AA-GACAGAGAC
3101950 A
1 A
3101951 GCGTATATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 16 0.50
19 8 0.25
20 8 0.25
ACGTcount: A:0.62, C:0.16, G:0.21, T:0.02
Consensus pattern (18 bp):
AAAGACAAAGACAGAGAC
Found at i:3108243 original size:19 final size:19
Alignment explanation
Indices: 3108198--3108245 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
3108188 CATTAATTTA
3108198 ATTAAAA-ATTATAAAAAT
1 ATTAAAATATTATAAAAAT
3108216 ATTTAAAAATATTATAATAAAT
1 A-TT-AAAATATTATAA-AAAT
3108238 A-TAAAATA
1 ATTAAAATA
3108246 AAATAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 1 0.04
19 8 0.31
20 5 0.19
21 7 0.27
22 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAAATATTATAAAAAT
Found at i:3108540 original size:2 final size:2
Alignment explanation
Indices: 3108533--3108564 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3108523 TTTCATTTAG
3108533 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
3108565 CAAAAGCTTG
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):
AT
Found at i:3110782 original size:2 final size:2
Alignment explanation
Indices: 3110775--3110811 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3110765 GGTTTTATTT
3110775 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3110812 GCTTCCTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3114507 original size:20 final size:19
Alignment explanation
Indices: 3114470--3114506 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3114460 AAAAAGAAAG
3114470 TAAATTTATTTTAAAAAAC
1 TAAATTTATTTTAAAAAAC
3114489 TAAATTTATTTTAAAAAA
1 TAAATTTATTTTAAAAAA
3114507 AATTTCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATTTATTTTAAAAAAC
Found at i:3114973 original size:22 final size:23
Alignment explanation
Indices: 3114948--3114997 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
3114938 TTTATTATTT
3114948 AATATAAATATTTTCAATA-CA-A
1 AATATAAATATTTT-AATAGCATA
**
3114970 AATATTGATATTTTAATAGCATA
1 AATATAAATATTTTAATAGCATA
3114993 AATAT
1 AATAT
3114998 TTTTAACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 14 0.58
23 6 0.25
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (23 bp):
AATATAAATATTTTAATAGCATA
Found at i:3114998 original size:23 final size:22
Alignment explanation
Indices: 3114955--3114998 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3114945 TTTAATATAA
3114955 ATATTTTCAATACAAAATATTG
1 ATATTTTCAATACAAAATATTG
3114977 ATATTTT-AATAGCATAAATATT
1 ATATTTTCAATA-CA-AAATATT
3114999 TTTAACGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 9 0.45
23 7 0.35
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (22 bp):
ATATTTTCAATACAAAATATTG
Found at i:3120067 original size:16 final size:16
Alignment explanation
Indices: 3120048--3120081 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3120038 ATATATTTAA
3120048 ATATAAATATAAATAT
1 ATATAAATATAAATAT
* *
3120064 ATATATATTTAAATAT
1 ATATAAATATAAATAT
3120080 AT
1 AT
3120082 GAAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAAATATAAATAT
Found at i:3120552 original size:2 final size:2
Alignment explanation
Indices: 3120545--3120581 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3120535 CAAAATCCTT
*
3120545 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3120582 GGTTATTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3121585 original size:13 final size:13
Alignment explanation
Indices: 3121567--3121591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3121557 TCTCTCTCTC
3121567 TATATATATATAA
1 TATATATATATAA
3121580 TATATATATATA
1 TATATATATATA
3121592 TATTAAATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:3122697 original size:2 final size:2
Alignment explanation
Indices: 3122690--3122718 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3122680 TTTTCTATTC
3122690 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
3122719 AAAAGTAACA
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:3125215 original size:2 final size:2
Alignment explanation
Indices: 3125208--3125238 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3125198 ATTCAAAGAC
3125208 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3125239 AGAAGTGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3126319 original size:2 final size:2
Alignment explanation
Indices: 3126314--3126353 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3126304 ATATATATAT
3126314 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3126354 GAAGGGGAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3127298 original size:23 final size:22
Alignment explanation
Indices: 3127272--3127346 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
3127262 CTTAAGAGTT
** *
3127272 TATTTAATTATTTTTAAAAATTA
1 TATTTAATTAAATTT-AAAATAA
3127295 TATTTAA-TAAATTTAAAATAA
1 TATTTAATTAAATTTAAAATAA
*
3127316 TATTTAA-TAAACTATT-TAATAA
1 TATTTAATTAAA-T-TTAAAATAA
3127338 TATTTAATT
1 TATTTAATT
3127347 GCTGATGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
21 17 0.38
22 18 0.40
23 10 0.22
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTTAATTAAATTTAAAATAA
Found at i:3127309 original size:22 final size:21
Alignment explanation
Indices: 3127288--3127345 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
3127278 ATTATTTTTA
*
3127288 AAAATTATATTTAATAAATTT
1 AAAATAATATTTAATAAATTT
3127309 AAAATAATATTTAATAAACTATT
1 AAAATAATATTTAATAAA-T-TT
*
3127332 -TAATAATATTTAAT
1 AAAATAATATTTAAT
3127346 TGCTGATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 17 0.52
22 14 0.42
23 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATAATATTTAATAAATTT
Found at i:3127341 original size:10 final size:10
Alignment explanation
Indices: 3127294--3127345 Score: 61
Period size: 10 Copynumber: 4.9 Consensus size: 10
3127284 TTTAAAAATT
3127294 ATATTTAATA
1 ATATTTAATA
3127304 A-ATTTAAAATA
1 ATATTT--AATA
3127315 ATATTTAATAA
1 ATATTTAAT-A
3127326 ACTATTTAATA
1 A-TATTTAATA
3127337 ATATTTAAT
1 ATATTTAAT
3127346 TGCTGATGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
11 9 0.24
12 12 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (10 bp):
ATATTTAATA
Found at i:3127670 original size:2 final size:2
Alignment explanation
Indices: 3127663--3127707 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3127653 TTCAGTGGCT
3127663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3127704 TA TA
1 TA TA
3127708 GTATTAGCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3127712 original size:8 final size:7
Alignment explanation
Indices: 3127662--3127713 Score: 56
Period size: 8 Copynumber: 7.4 Consensus size: 7
3127652 GTTCAGTGGC
3127662 TTATATA
1 TTATATA
3127669 -TATATA
1 TTATATA
3127675 -TATATA
1 TTATATA
3127681 -TATATA
1 TTATATA
3127687 TATATATA
1 T-TATATA
3127695 TATATATA
1 T-TATATA
3127703 TTATAGTA
1 TTATA-TA
3127711 TTA
1 TTA
3127714 GCACACGAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
6 18 0.43
7 4 0.10
8 20 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (7 bp):
TTATATA
Found at i:3129773 original size:51 final size:51
Alignment explanation
Indices: 3129678--3129775 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
3129668 CTTTTTCATT
* ** *
3129678 CTTAGAATGTTCAAAGTTCAAAGGCACTGAAACTCTGGATGGAGATTGACC
1 CTTAGAATCTTCAAAGTTCAAAGGCACTGAAACTCTAAAAGGAGATTGACC
* *
3129729 CTTAGAATCTTCCAAA-TTCACAGGCACTGAATCTCTAAAAGGAGATT
1 CTTAGAATCTT-CAAAGTTCAAAGGCACTGAAACTCTAAAAGGAGATT
3129776 TACAAGCCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
51 36 0.90
52 4 0.10
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (51 bp):
CTTAGAATCTTCAAAGTTCAAAGGCACTGAAACTCTAAAAGGAGATTGACC
Found at i:3132659 original size:22 final size:21
Alignment explanation
Indices: 3132616--3132666 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3132606 TCATTGTATG
*
3132616 TATTT-TTTTAATCATATTTT
1 TATTTATTTTAATCATATGTT
*
3132636 TATTTATTTTAATTATATCGTT
1 TATTTATTTTAATCATAT-GTT
*
3132658 TATATATTT
1 TATTTATTT
3132667 ATATGTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 5 0.19
21 11 0.42
22 10 0.38
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTTATTTTAATCATATGTT
Found at i:3133582 original size:26 final size:30
Alignment explanation
Indices: 3133546--3133599 Score: 80
Period size: 27 Copynumber: 1.9 Consensus size: 30
3133536 TAAATATTTA
3133546 TTTTAATTAATAT-ATT-TATTA-ATAAAT
1 TTTTAATTAATATAATTATATTATATAAAT
3133573 TTTTAA-TAATATAATTATATTATATAA
1 TTTTAATTAATATAATTATATTATATAA
3133600 TTTAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 6 0.25
27 9 0.38
28 5 0.21
29 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTTAATTAATATAATTATATTATATAAAT
Found at i:3134648 original size:25 final size:26
Alignment explanation
Indices: 3134619--3134673 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
3134609 ATTTATAATT
*
3134619 TTTAAAATATTT-AAATTTAAATTTA
1 TTTAAAATATTTGAAATTAAAATTTA
** *
3134644 TTTAATTTATTTGATATTAAAATTTA
1 TTTAAAATATTTGAAATTAAAATTTA
3134670 TTTA
1 TTTA
3134674 TTATTCAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTAAAATATTTGAAATTAAAATTTA
Found at i:3142879 original size:4 final size:4
Alignment explanation
Indices: 3142870--3142898 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
3142860 CACGCAATAA
3142870 TTTC TTTC TTTC TTTC TTTC TTT- TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
3142899 GGAAAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:3143737 original size:21 final size:21
Alignment explanation
Indices: 3143708--3143757 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3143698 ATTACTCGAG
*
3143708 TTTATTTTAAATA-TATTTAAA
1 TTTAATTTAAATATTATTT-AA
*
3143729 TTTAATTTAATTATTATTTAA
1 TTTAATTTAAATATTATTTAA
*
3143750 TTAAATTT
1 TTTAATTT
3143758 TATATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAATTTAAATATTATTTAA
Found at i:3143981 original size:11 final size:11
Alignment explanation
Indices: 3143967--3144000 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3143957 TTTAAAATAC
3143967 TTTTAATTTAA
1 TTTTAATTTAA
*
3143978 TTTTAAATTAAA
1 TTTT-AATTTAA
3143990 TTTTAATTTAA
1 TTTTAATTTAA
3144001 AATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:3143996 original size:18 final size:18
Alignment explanation
Indices: 3143973--3144008 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3143963 ATACTTTTAA
* *
3143973 TTTAATTTTAAATTAAAT
1 TTTAATTTAAAATAAAAT
3143991 TTTAATTTAAAATAAAAT
1 TTTAATTTAAAATAAAAT
3144009 AGATGAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAATTTAAAATAAAAT
Found at i:3143997 original size:23 final size:24
Alignment explanation
Indices: 3143937--3144000 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
3143927 TTTATTAAAT
*
3143937 AATTAAA-TTTAATTAAATAATTTA
1 AATTAAATTTTAATTTAAT-ATTTA
* *
3143961 AAAT-ACTTTTAATTTAAT-TTTA
1 AATTAAATTTTAATTTAATATTTA
3143983 AATTAAATTTTAATTTAA
1 AATTAAATTTTAATTTAA
3144001 AATAAAATAG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
22 7 0.21
23 13 0.39
24 13 0.39
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTAAATTTTAATTTAATATTTA
Found at i:3149210 original size:18 final size:17
Alignment explanation
Indices: 3149196--3149244 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
3149186 TAATTAATTT
3149196 ATATAATTATTTTAAATA
1 ATATAA-TATTTTAAATA
3149214 ATATAATA-TTT-AATA
1 ATATAATATTTTAAATA
*
3149229 ATTTTAA-ATTTTAAAT
1 A-TATAATATTTTAAAT
3149245 TTTCGTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 6 0.22
16 10 0.37
17 5 0.19
18 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATAATATTTTAAATA
Found at i:3152283 original size:2 final size:2
Alignment explanation
Indices: 3152278--3152317 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
3152268 TTTTTTACTT
* *
3152278 TA TA TA TA TA TA TA TA TA TA TG TG 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
3152318 AATAGTGACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3153707 original size:13 final size:13
Alignment explanation
Indices: 3153691--3153720 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3153681 ATTTTTTTTA
3153691 AATATTTATATTT
1 AATATTTATATTT
*
3153704 AATATTTATGTTT
1 AATATTTATATTT
3153717 AATA
1 AATA
3153721 AATATTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:3156425 original size:2 final size:2
Alignment explanation
Indices: 3156418--3156444 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3156408 TTTTAACTAC
3156418 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3156445 TGCCATCTTG
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3161516 original size:9 final size:9
Alignment explanation
Indices: 3161493--3161522 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3161483 CATCTCATCT
3161493 TTTTATTTA
1 TTTTATTTA
3161502 -TTTATTTA
1 TTTTATTTA
3161510 TTTTATTTA
1 TTTTATTTA
3161519 TTTT
1 TTTT
3161523 TCTGTTGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTATTTA
Found at i:3165953 original size:2 final size:2
Alignment explanation
Indices: 3165946--3165977 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3165936 GAAGGTCCCT
3165946 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3165978 ATTCCTTTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3171325 original size:23 final size:23
Alignment explanation
Indices: 3171292--3171347 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
3171282 ATATTATTGG
3171292 TTAAATT-TTTATTATTAA-TAAA
1 TTAAATTATTTA-TATTAATTAAA
*
3171314 TTAAATTATTTATATTAATTACA
1 TTAAATTATTTATATTAATTAAA
3171337 TTAAA-TATTTA
1 TTAAATTATTTA
3171348 ACAAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 19 0.61
23 12 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAAATTATTTATATTAATTAAA
Found at i:3171486 original size:30 final size:30
Alignment explanation
Indices: 3171459--3171518 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3171449 TTATAATTAC
3171459 TTAATAAAATAAATTAAATAACTTAATTTA
1 TTAATAAAATAAATTAAATAACTTAATTTA
* *
3171489 TTACTAAAATAAATTCAATAA-TATAATTTA
1 TTAATAAAATAAATTAAATAACT-TAATTTA
3171519 ATAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (30 bp):
TTAATAAAATAAATTAAATAACTTAATTTA
Found at i:3175941 original size:17 final size:16
Alignment explanation
Indices: 3175917--3175964 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
3175907 TATTTTATAA
3175917 AAAATTTTAATATATT
1 AAAATTTTAATATATT
*
3175933 AATAATTTTTATCATA-T
1 AA-AATTTTAAT-ATATT
3175950 AAAA-TTTAATATATT
1 AAAATTTTAATATATT
3175965 TTTATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 3 0.11
15 6 0.22
16 4 0.15
17 11 0.41
18 3 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
AAAATTTTAATATATT
Found at i:3176946 original size:24 final size:24
Alignment explanation
Indices: 3176918--3176969 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3176908 ATTTTATATA
* *
3176918 TTAATAAATTATTTTATATAAATT
1 TTAATAAATTAATTTATATAAATC
* *
3176942 TTAATATATTAATTTATTTAAATC
1 TTAATAAATTAATTTATATAAATC
3176966 TTAA
1 TTAA
3176970 ATTTTTGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAATAAATTAATTTATATAAATC
Found at i:3182006 original size:2 final size:2
Alignment explanation
Indices: 3181961--3181994 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3181951 TTTAGCCAGT
3181961 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
3181995 ATGGGATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3182181 original size:22 final size:22
Alignment explanation
Indices: 3182131--3182198 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
3182121 AAATTATATC
* *
3182131 ATTAAATTAAATATATATTTT-TT
1 ATTAAA-TAATTAT-TATTTTAAT
3182154 ATTAAATAATTATTATTTTAAT
1 ATTAAATAATTATTATTTTAAT
3182176 ATTAAAT--TTA-TATATTTAAT
1 ATTAAATAATTATTAT-TTTAAT
3182196 ATT
1 ATT
3182199 TAATTTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 3 0.07
20 12 0.29
21 6 0.15
22 14 0.34
23 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTAAATAATTATTATTTTAAT
Found at i:3182186 original size:20 final size:19
Alignment explanation
Indices: 3182132--3182213 Score: 80
Period size: 20 Copynumber: 4.3 Consensus size: 19
3182122 AATTATATCA
*
3182132 TTAA-ATTAAATATATATT
1 TTAATATTAAATTTATATT
*
3182150 TT-TTATTAAATAATTATTATT
1 TTAATATTAAAT--TTA-TATT
3182171 TTAATATTAAATTTATATAT
1 TTAATATTAAATTTATAT-T
*
3182191 TTAATATTTAATTTAT-TT
1 TTAATATTAAATTTATATT
3182209 TTAAT
1 TTAAT
3182214 TAAATAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
18 15 0.28
19 4 0.07
20 21 0.39
21 6 0.11
22 8 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAATATTAAATTTATATT
Found at i:3182208 original size:24 final size:24
Alignment explanation
Indices: 3182181--3182227 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3182171 TTAATATTAA
*
3182181 ATTTATATATTTAAT-ATTTAATTT
1 ATTTATA-ATTAAATAATTTAATTT
*
3182205 ATTTTTAATTAAATAATTTAATT
1 ATTTATAATTAAATAATTTAATT
3182228 CAAGGTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTATAATTAAATAATTTAATTT
Found at i:3185074 original size:15 final size:16
Alignment explanation
Indices: 3185056--3185093 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3185046 AAAATTTAAA
3185056 TTATTT-TAAAATTTT
1 TTATTTATAAAATTTT
**
3185071 TTATTTATATTATTTT
1 TTATTTATAAAATTTT
3185087 TTATTTA
1 TTATTTA
3185094 AATTATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTATAAAATTTT
Found at i:3185087 original size:16 final size:16
Alignment explanation
Indices: 3185066--3185101 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
3185056 TTATTTTAAA
*
3185066 ATTTTTTATTTATATT
1 ATTTTTTATTTAAATT
3185082 ATTTTTTATTTAAATT
1 ATTTTTTATTTAAATT
3185098 ATTT
1 ATTT
3185102 AATTTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTTATTTAAATT
Found at i:3185103 original size:9 final size:9
Alignment explanation
Indices: 3185087--3185138 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
3185077 ATATTATTTT
3185087 TTATTTAAA
1 TTATTTAAA
3185096 TTATTT-AA
1 TTATTTAAA
*
3185104 TTTTTTAAA
1 TTATTTAAA
3185113 --ATTTAAA
1 TTATTTAAA
3185120 TTTATTTTAAA
1 -TTA-TTTAAA
3185131 TTATTTAA
1 TTATTTAA
3185139 TAAAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
7 6 0.17
8 7 0.19
9 13 0.36
10 4 0.11
11 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTATTTAAA
Found at i:3185117 original size:40 final size:40
Alignment explanation
Indices: 3185049--3185127 Score: 92
Period size: 40 Copynumber: 1.9 Consensus size: 40
3185039 AATTAAAAAA
*
3185049 ATTTAAATTATTTTAAAATTTTTTATTTATA-TTATTTTTT
1 ATTTAAATTATTTT-AAATTTTTTATTTAAATTTATTTTTT
3185089 ATTTAAATTA-TTT-AATTTTTTAAAATTTAAATTTATTTT
1 ATTTAAATTATTTTAAATTTTTT---ATTTAAATTTATTTT
3185128 AAATTATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
37 8 0.24
39 3 0.09
40 16 0.47
41 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (40 bp):
ATTTAAATTATTTTAAATTTTTTATTTAAATTTATTTTTT
Found at i:3187123 original size:15 final size:15
Alignment explanation
Indices: 3187099--3187128 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3187089 CAATTCGTCA
3187099 TCATCATCATCATCT
1 TCATCATCATCATCT
*
3187114 TCATCCTCATCATCT
1 TCATCATCATCATCT
3187129 AATTCGTCTA
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:0.37, G:0.00, T:0.40
Consensus pattern (15 bp):
TCATCATCATCATCT
Found at i:3190627 original size:3 final size:3
Alignment explanation
Indices: 3190619--3190646 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3190609 ATGAAGATCT
3190619 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3190647 CATCAATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3191235 original size:26 final size:24
Alignment explanation
Indices: 3191197--3191264 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 24
3191187 TGGACAGAAT
3191197 AAAAAAGAGAAAGAGA-GGAAAAGA
1 AAAAAAGAGAAAGAGATGGAAAA-A
*
3191221 AAAAAAGAAGCAAAGAGATTGAAAAA
1 AAAAAAG-AG-AAAGAGATGGAAAAA
*
3191247 AAAAAGAGAGAAAAAGAT
1 AAAAA-AGAGAAAGAGAT
3191265 AAAAAATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 7 0.18
25 9 0.24
26 15 0.39
27 7 0.18
ACGTcount: A:0.71, C:0.01, G:0.24, T:0.04
Consensus pattern (24 bp):
AAAAAAGAGAAAGAGATGGAAAAA
Found at i:3191303 original size:3 final size:3
Alignment explanation
Indices: 3191297--3191323 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3191287 TTATAAGGAG
3191297 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
3191324 TAAGAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:3191333 original size:2 final size:2
Alignment explanation
Indices: 3191326--3191355 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3191316 ATGATGATTA
3191326 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3191356 TAAAAATAAT
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):
AG
Found at i:3191613 original size:20 final size:19
Alignment explanation
Indices: 3191586--3191625 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3191576 TACTTATAAG
* *
3191586 ATTAAATAATTTTTTATTT
1 ATTAAATAATATTATATTT
3191605 ATTATAATAATATTATATTT
1 ATTA-AATAATATTATATTT
3191625 A
1 A
3191626 ATACAACACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTAAATAATATTATATTT
Found at i:3191814 original size:2 final size:2
Alignment explanation
Indices: 3191807--3191839 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3191797 CAACTCTCAA
3191807 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3191840 ATTTCTTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3192520 original size:3 final size:3
Alignment explanation
Indices: 3192512--3192539 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3192502 ATTGGGTTCT
3192512 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3192540 GAATCCTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3194797 original size:17 final size:19
Alignment explanation
Indices: 3194759--3194799 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
3194749 TATATTACGT
3194759 AATTA-TAAATATAATATA
1 AATTATTAAATATAATATA
3194777 AATTATTAAATAT-AT-TA
1 AATTATTAAATATAATATA
3194794 AATTAT
1 AATTAT
3194800 ATTTAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 7 0.32
19 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTATTAAATATAATATA
Found at i:3195412 original size:2 final size:2
Alignment explanation
Indices: 3195407--3195431 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3195397 TCTGGCACAC
3195407 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
3195432 AAACATAGCT
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:3202836 original size:2 final size:2
Alignment explanation
Indices: 3202829--3202867 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3202819 TATTTATTAG
3202829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3202868 AATAATGTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3204558 original size:15 final size:15
Alignment explanation
Indices: 3204518--3204558 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
3204508 TTATAAAAAA
*
3204518 TAATTTTAAAATATT
1 TAATTTTAAAAAATT
*
3204533 T-A-TTTACAAAATT
1 TAATTTTAAAAAATT
3204546 TAATTTTAAAAAA
1 TAATTTTAAAAAA
3204559 AAATTCACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
13 10 0.48
14 2 0.10
15 9 0.43
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TAATTTTAAAAAATT
Found at i:3204905 original size:2 final size:2
Alignment explanation
Indices: 3204898--3204929 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3204888 ATATTAGTAC
3204898 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
3204930 GAATAAATCA
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):
AT
Found at i:3205466 original size:21 final size:21
Alignment explanation
Indices: 3205440--3205480 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3205430 TTAATTATAT
*
3205440 ATTTAATAAATTAT-TATTAAA
1 ATTTAA-AAATAATATATTAAA
3205461 ATTTAAAAATAATATATTAA
1 ATTTAAAAATAATATATTAA
3205481 TTTATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTAAAAATAATATATTAAA
Found at i:3205484 original size:19 final size:18
Alignment explanation
Indices: 3205422--3205484 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 18
3205412 TTTAAATATT
3205422 TTTAAAAATTAATTA-TATA
1 TTTAAAAA-TAATTATTA-A
*
3205441 TTTAATAAATTATTATTAAAA
1 TTTAA-AAATAATTATT--AA
3205462 TTTAAAAATAATATATTAA
1 TTTAAAAATAAT-TATTAA
3205481 TTTA
1 TTTA
3205485 TTTTTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 16 0.43
20 10 0.27
21 10 0.27
22 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAAAAATAATTATTAA
Found at i:3205484 original size:40 final size:41
Alignment explanation
Indices: 3205395--3205484 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 41
3205385 ATGAACGTGG
*
3205395 ATTAA-TTAAAAATTATTTTTAAATATTTTTAAAAATTAATT
1 ATTAATTTAAAAATTATTATTAAATA-TTTTAAAAATTAATT
3205436 A-TATATTTAATAAATTATTATTAAA-A-TTTAAAAA-TAATAT
1 ATTA-ATTTAA-AAATTATTATTAAATATTTTAAAAATTAAT-T
3205476 ATTAATTTA
1 ATTAATTTA
3205485 TTTTTTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
39 4 0.09
40 17 0.40
41 4 0.09
42 5 0.12
43 13 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (41 bp):
ATTAATTTAAAAATTATTATTAAATATTTTAAAAATTAATT
Found at i:3208115 original size:4 final size:4
Alignment explanation
Indices: 3208106--3208140 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
3208096 ACGCGTGCCT
**
3208106 TTTA TTTA TTTA TTTA TTTA TGGA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3208141 TGAGAGAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:3208459 original size:27 final size:28
Alignment explanation
Indices: 3208398--3208462 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
3208388 TTTTTTGAGG
*
3208398 ATTAGTATTATATTTATATATTTAAATTT
1 ATTA-TATTATATTTATATATTAAAATTT
3208427 AATTATATTATATTTATAT-TTAAAATATT
1 -ATTATATTATATTTATATATTAAAAT-TT
3208456 -TTATATT
1 ATTATATT
3208463 TATAAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 7 0.21
28 6 0.18
29 16 0.48
30 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTATATTATATTTATATATTAAAATTT
Found at i:3213074 original size:31 final size:31
Alignment explanation
Indices: 3213027--3213106 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
3213017 ATCACCAAAC
* **
3213027 AAATCCAAATTAAATTTATTAATTATTAACT
1 AAATTCAAATTAAATTTATTAACCATTAACT
* *
3213058 AAATTCAATTTAAATTTATTAACCGTTAACT
1 AAATTCAAATTAAATTTATTAACCATTAACT
*
3213089 AAATTTAAATTAAATTTA
1 AAATTCAAATTAAATTTA
3213107 ATTTGATTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.42
Consensus pattern (31 bp):
AAATTCAAATTAAATTTATTAACCATTAACT
Done.