Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 9 of 318
Found at i:3104281 original size:31 final size:32
Alignment explanation
Indices: 3104227--3104293 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
3104217 ATAGTAAAAA
3104227 TATAATTTCATAATTTTAATAGTTTATATTTT
1 TATAATTTCATAATTTTAATAGTTTATATTTT
* * *
3104259 TATAATTT-ATCATTTTATTAGTTTCTATTTT
1 TATAATTTCATAATTTTAATAGTTTATATTTT
3104290 TATA
1 TATA
3104294 TTTTTTAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 24 0.75
32 8 0.25
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.61
Consensus pattern (32 bp):
TATAATTTCATAATTTTAATAGTTTATATTTT
Found at i:3104339 original size:30 final size:31
Alignment explanation
Indices: 3104285--3104350 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
3104275 ATTAGTTTCT
** *
3104285 ATTTTTATATTTTTTAAGTGATTAAATTA-A
1 ATTTTTATATTTTTTAAAAGATTAAAATATA
3104315 ATTTTTAT-TTTTTTAAAAGAATTAAAATATA
1 ATTTTTATATTTTTTAAAAG-ATTAAAATATA
3104346 ATTTT
1 ATTTT
3104351 ATTATTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 9 0.29
30 16 0.52
31 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (31 bp):
ATTTTTATATTTTTTAAAAGATTAAAATATA
Found at i:3105371 original size:30 final size:30
Alignment explanation
Indices: 3105337--3105399 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
3105327 ACTTATTTTA
3105337 TTGTTAATTTTGTTATTATTTTA-AAGACAT
1 TTGTTAATTTTGTTATTATTTTAGAAG-CAT
3105367 TTGTTAATTTTGTTATTATTTTAGAAGCAT
1 TTGTTAATTTTGTTATTATTTTAGAAGCAT
3105397 TTG
1 TTG
3105400 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAAGCAT
Found at i:3105552 original size:12 final size:12
Alignment explanation
Indices: 3105522--3105554 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3105512 TATATATTTT
3105522 AAAATT-ATATA
1 AAAATTAATATA
3105533 AAAA-TAATATA
1 AAAATTAATATA
3105544 AAAATTAATAT
1 AAAATTAATAT
3105555 GATCGGGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:3108531 original size:19 final size:20
Alignment explanation
Indices: 3108494--3108531 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3108484 TTAAGTTAAA
*
3108494 TTTTATAATTTATCCTTTAT
1 TTTTATAATTTATACTTTAT
*
3108514 TTTTAT-ATTTATATTTTA
1 TTTTATAATTTATACTTTA
3108532 AGTAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATAATTTATACTTTAT
Found at i:3108799 original size:22 final size:22
Alignment explanation
Indices: 3108775--3108818 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3108765 GAATGAAAAT
*
3108775 AAAGAAAAATAAAAAGAAAGTTA
1 AAAG-AAAATAAAAAAAAAGTTA
*
3108798 AAAGAACATAAAAAAAAAGTT
1 AAAGAAAATAAAAAAAAAGTT
3108819 TAAATTACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.14
Consensus pattern (22 bp):
AAAGAAAATAAAAAAAAAGTTA
Found at i:3109004 original size:29 final size:29
Alignment explanation
Indices: 3108964--3109031 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
3108954 TGCAAAAACG
*
3108964 TAAGTGACTAAAATATAACATTTTAAATA
1 TAAGTGACTAAAACATAACATTTTAAATA
3108993 TAAGTGACTAAAACATAACATTTTAAATA
1 TAAGTGACTAAAACATAACATTTTAAATA
*
3109022 AAAGTGACTA
1 TAAGTGACTA
3109032 TTTTAATTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (29 bp):
TAAGTGACTAAAACATAACATTTTAAATA
Found at i:3110055 original size:48 final size:48
Alignment explanation
Indices: 3109972--3110071 Score: 139
Period size: 48 Copynumber: 2.1 Consensus size: 48
3109962 ATCGATACAT
* * * * *
3109972 CACCAACTCAACATATTTTTATTTCCCTACTAATTTTGTGAAAAGAGA
1 CACCAACTCAACATATCTTTATTTCCCTACCAATTTCGCGAAAAAAGA
3110020 CACCTAACT-AACATATCTTTATTTCCCTACCAATTTCGCGAAAAAAGA
1 CACC-AACTCAACATATCTTTATTTCCCTACCAATTTCGCGAAAAAAGA
3110068 CACC
1 CACC
3110072 CAATTAACGA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 42 0.91
49 4 0.09
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (48 bp):
CACCAACTCAACATATCTTTATTTCCCTACCAATTTCGCGAAAAAAGA
Found at i:3110868 original size:23 final size:22
Alignment explanation
Indices: 3110842--3110891 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
3110832 GAACATAAAG
3110842 TAAA-AAAATAATTAGTAAAAAAT
1 TAAATAAAA-AATTAG-AAAAAAT
*
3110865 TAAATATAAAATTAG-AAAAA-
1 TAAATAAAAAATTAGAAAAAAT
3110885 TAAATAA
1 TAAATAA
3110892 TAACTCTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 6 0.25
21 5 0.21
23 10 0.42
24 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (22 bp):
TAAATAAAAAATTAGAAAAAAT
Found at i:3110905 original size:21 final size:21
Alignment explanation
Indices: 3110880--3110926 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3110870 ATAAAATTAG
*
3110880 AAAAATAAATAATAA-CTCTTA
1 AAAAAAAAATAA-AAGCTCTTA
*
3110901 TAAAAAAAATAAAAGCTCTTA
1 AAAAAAAAATAAAAGCTCTTA
3110922 AAAAA
1 AAAAA
3110927 GCAAACTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (21 bp):
AAAAAAAAATAAAAGCTCTTA
Found at i:3118544 original size:15 final size:15
Alignment explanation
Indices: 3118524--3118554 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3118514 AATCAACCAG
3118524 CTTTTAGTTGAAAAA
1 CTTTTAGTTGAAAAA
3118539 CTTTTAGTTGAAAAA
1 CTTTTAGTTGAAAAA
3118554 C
1 C
3118555 ATGCTGCGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (15 bp):
CTTTTAGTTGAAAAA
Found at i:3135434 original size:21 final size:21
Alignment explanation
Indices: 3135410--3135449 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3135400 AGACGAGCAA
*
3135410 TACTCCACAACAGGTGGAGCG
1 TACTCCAAAACAGGTGGAGCG
3135431 TACTCCAAAACAGGTGGAG
1 TACTCCAAAACAGGTGGAG
3135450 TTTGAGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.25, G:0.28, T:0.15
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGCG
Found at i:3146469 original size:36 final size:36
Alignment explanation
Indices: 3146382--3146470 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
3146372 GGTCCTATAT
* * * * *
3146382 ATGGGGAAAGGCTTACGTGAGGTCCTGCTCCCATAC
1 ATGGGGGAAGGCTTATGGGAGGTCCTACTCCCACAC
3146418 ATGGGAGG-AGGCTTATGGGAGGTCCTACTCCCACAC
1 ATGGG-GGAAGGCTTATGGGAGGTCCTACTCCCACAC
3146454 ATGGGGGAAGGCTTATG
1 ATGGGGGAAGGCTTATG
3146471 AGAAGTGATA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
35 2 0.04
36 43 0.93
37 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.21
Consensus pattern (36 bp):
ATGGGGGAAGGCTTATGGGAGGTCCTACTCCCACAC
Found at i:3146514 original size:50 final size:45
Alignment explanation
Indices: 3146441--3146531 Score: 128
Period size: 50 Copynumber: 1.9 Consensus size: 45
3146431 TATGGGAGGT
3146441 CCTACTCCCACACATGGGGGAAGGCTTATGAGAAGTGATAATAATGAC
1 CCTACTCCCACACATGGGGGAAGGCTTAT-AGAAG-G-TAATAATGAC
*
3146489 CCTACTCCCAAACATATGGGGGAAGGCTTATAGAAGGTAATAA
1 CCTACTCCC--ACACATGGGGGAAGGCTTATAGAAGGTAATAA
3146532 AGGTTCTGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
47 6 0.15
48 10 0.25
49 5 0.12
50 19 0.47
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (45 bp):
CCTACTCCCACACATGGGGGAAGGCTTATAGAAGGTAATAATGAC
Found at i:3146735 original size:50 final size:50
Alignment explanation
Indices: 3146676--3146776 Score: 114
Period size: 50 Copynumber: 2.0 Consensus size: 50
3146666 TATGGTAACG
* * * *
3146676 ATGATCCTACA-CTCAAACGCATGGGGGGAGGCTTACGAAAAGTGGTAATA
1 ATGACCCTACACCT-AAACGCATGGGGCGAGACTTACGAAAAGTGATAATA
* * * *
3146726 ATGACCCTACTCCTAGATGCATGGGGCGAGACTTATGAAAAGTGATAATA
1 ATGACCCTACACCTAAACGCATGGGGCGAGACTTACGAAAAGTGATAATA
3146776 A
1 A
3146777 AGGCCATGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 40 0.95
51 2 0.05
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.22
Consensus pattern (50 bp):
ATGACCCTACACCTAAACGCATGGGGCGAGACTTACGAAAAGTGATAATA
Found at i:3149612 original size:5 final size:5
Alignment explanation
Indices: 3149594--3149624 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
3149584 TCTCTTTTAT
3149594 ATATA ATAATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA
3149625 CTTAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:3151574 original size:46 final size:47
Alignment explanation
Indices: 3151480--3151583 Score: 131
Period size: 46 Copynumber: 2.2 Consensus size: 47
3151470 CATAGTAAAA
*
3151480 CTATGGTCTTGCACATAGTCATATATCACACACTGAAGCCATAGCCCAG
1 CTATGGTCTT-CACATAGTCACATAT-ACACACTGAAGCCATAGCCCAG
* *
3151529 CTATGGTCTT-ACATAGATCACATAT-CACACTGATGCCATATCCCAG
1 CTATGGTCTTCACATAG-TCACATATACACACTGAAGCCATAGCCCAG
*
3151575 ATATGGTCT
1 CTATGGTCT
3151584 ATATTGAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
46 27 0.54
47 6 0.12
48 7 0.14
49 10 0.20
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (47 bp):
CTATGGTCTTCACATAGTCACATATACACACTGAAGCCATAGCCCAG
Found at i:3152646 original size:25 final size:25
Alignment explanation
Indices: 3152615--3152724 Score: 152
Period size: 25 Copynumber: 4.4 Consensus size: 25
3152605 ATAAATGTGC
*
3152615 TAATCAGAGAGCACTGACGTACTAA
1 TAATCAGAGAGCACTGACGTGCTAA
3152640 -ATATCAGAGAGCACTGGA-GTGCTAA
1 TA-ATCAGAGAGCACT-GACGTGCTAA
*
3152665 TAATCAGAGAGCACTGGCGTGCTAA
1 TAATCAGAGAGCACTGACGTGCTAA
* *
3152690 TATTCAGAGAGCACTGGCGTGCTAA
1 TAATCAGAGAGCACTGACGTGCTAA
3152715 TAATCAGAGA
1 TAATCAGAGA
3152725 ACATGCTGAG
Statistics
Matches: 77, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
24 2 0.03
25 72 0.94
26 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.21
Consensus pattern (25 bp):
TAATCAGAGAGCACTGACGTGCTAA
Found at i:3152678 original size:50 final size:50
Alignment explanation
Indices: 3152615--3152724 Score: 177
Period size: 50 Copynumber: 2.2 Consensus size: 50
3152605 ATAAATGTGC
3152615 TAATCAGAGAGCACTGACGTACTAA-ATATCAGAGAGCACTGGAGTGCTAA
1 TAATCAGAGAGCACTGACGTACTAATAT-TCAGAGAGCACTGGAGTGCTAA
* * *
3152665 TAATCAGAGAGCACTGGCGTGCTAATATTCAGAGAGCACTGGCGTGCTAA
1 TAATCAGAGAGCACTGACGTACTAATATTCAGAGAGCACTGGAGTGCTAA
3152715 TAATCAGAGA
1 TAATCAGAGA
3152725 ACATGCTGAG
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 54 0.96
51 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.21
Consensus pattern (50 bp):
TAATCAGAGAGCACTGACGTACTAATATTCAGAGAGCACTGGAGTGCTAA
Found at i:3159376 original size:41 final size:41
Alignment explanation
Indices: 3159210--3159365 Score: 226
Period size: 41 Copynumber: 3.8 Consensus size: 41
3159200 TTTATCGTTA
* * * *
3159210 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
3159251 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGTCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
3159292 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
3159333 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
3159366 AAGAGCCGGT
Statistics
Matches: 105, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 100 0.95
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:3159636 original size:33 final size:32
Alignment explanation
Indices: 3159580--3159643 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
3159570 ATAGATATGT
3159580 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
3159612 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
3159644 AAAATAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:3159660 original size:33 final size:33
Alignment explanation
Indices: 3159586--3159660 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
3159576 ATGTATATAT
* * *
3159586 ATATATGT-TGCATTCGGCATAGGTGGATATAT
1 ATATATGTATGCATTCGGCATAGGTGAAAATAA
* *
3159618 TTATGTGTATGCATTCGGCATAGGTGAAAATAA
1 ATATATGTATGCATTCGGCATAGGTGAAAATAA
*
3159651 ATGTATGTAT
1 ATATATGTAT
3159661 CTATGCATTC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (33 bp):
ATATATGTATGCATTCGGCATAGGTGAAAATAA
Found at i:3166536 original size:41 final size:41
Alignment explanation
Indices: 3166370--3166525 Score: 226
Period size: 41 Copynumber: 3.8 Consensus size: 41
3166360 TTTATCGTTA
* * * *
3166370 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
3166411 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGTCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
3166452 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
3166493 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
3166526 AAGAGCCGGT
Statistics
Matches: 105, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 100 0.95
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:3166794 original size:33 final size:32
Alignment explanation
Indices: 3166739--3166801 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
3166729 GATAGATATG
3166739 TATATATATATGTTGCATTCGGCATAGGTGGA
1 TATATATATATGTTGCATTCGGCATAGGTGGA
* *
3166771 TATATTTATGTGTATGCATTCGGCATAGGTG
1 TATATATATATGT-TGCATTCGGCATAGGTG
3166802 AAAATAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (32 bp):
TATATATATATGTTGCATTCGGCATAGGTGGA
Found at i:3166818 original size:33 final size:33
Alignment explanation
Indices: 3166744--3166818 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
3166734 ATATGTATAT
* * *
3166744 ATATATGT-TGCATTCGGCATAGGTGGATATAT
1 ATATATGTATGCATTCGGCATAGGTGAAAATAA
* *
3166776 TTATGTGTATGCATTCGGCATAGGTGAAAATAA
1 ATATATGTATGCATTCGGCATAGGTGAAAATAA
*
3166809 ATGTATGTAT
1 ATATATGTAT
3166819 CTATGCATTC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (33 bp):
ATATATGTATGCATTCGGCATAGGTGAAAATAA
Found at i:3168414 original size:32 final size:32
Alignment explanation
Indices: 3168378--3168441 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
3168368 CCCTCGCGAG
3168378 TTCCCTTTCTAACAATATTGTTATATGAACAT
1 TTCCCTTTCTAACAATATTGTTATATGAACAT
3168410 TTCCCTTTCTAACAATATTGTTATATGAACAT
1 TTCCCTTTCTAACAATATTGTTATATGAACAT
3168442 ACATATATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (32 bp):
TTCCCTTTCTAACAATATTGTTATATGAACAT
Found at i:3186023 original size:13 final size:13
Alignment explanation
Indices: 3186007--3186039 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3185997 TTTAATTAAA
*
3186007 TTAGTTAATTAGT
1 TTAGATAATTAGT
3186020 TTAGATAATTAGT
1 TTAGATAATTAGT
3186033 TTA-ATAA
1 TTAGATAA
3186040 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:3189212 original size:16 final size:16
Alignment explanation
Indices: 3189178--3189215 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3189168 AAAAGTTAAC
**
3189178 AAAATATATGATAGTA
1 AAAATATATGATACAA
3189194 AAAATATATGATACAA
1 AAAATATATGATACAA
3189210 AAAATA
1 AAAATA
3189216 CCTGACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (16 bp):
AAAATATATGATACAA
Found at i:3190961 original size:15 final size:14
Alignment explanation
Indices: 3190933--3190967 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
3190923 TTTATATATT
3190933 TTTTGTATTTTTTG
1 TTTTGTATTTTTTG
*
3190947 TTTTGTTTTTGTTTG
1 TTTTGTATTT-TTTG
3190962 TTTTGT
1 TTTTGT
3190968 GTTTACACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.80
Consensus pattern (14 bp):
TTTTGTATTTTTTG
Found at i:3191255 original size:44 final size:44
Alignment explanation
Indices: 3191186--3192202 Score: 1291
Period size: 44 Copynumber: 23.1 Consensus size: 44
3191176 CAGGAACACC
* * * * * *
3191186 AATCTGTTATTTTCGATCTGTTCTCTGCCAATACAGAGATGTCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * * * *
3191230 AATCTG-TCATCTTCAATTTGCTCTCTGTCAACACAGAGACGCCA
1 AATCTGCT-ATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* *
3191274 AATCTGCTATCTTCGATCTGCCCTCTGCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* *
3191318 AATCTG-TCATCTTCGATCTGCTCTCCGACAATACAGAGACACCA
1 AATCTGCT-ATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* *** *
3191362 AATCTACTATCTTCGATCTGCTCTCTAACGATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
*
3191406 AATCTACTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * * * *
3191450 AATCTGCTATCTTCGATCTGCCCTCTGACAATACAAAGATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * * *
3191494 AATCTGCTATCTTCGATCTGCCCTCTGACGATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
** * *
3191538 AATCAACTATCTTCTATCTGCTCTCCGCCAATATAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
3191582 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * *
3191626 AATCTACTATCTTCGATCTGCTCTTCGCCAACACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* *
3191670 AATCTGCTATCTTCGATCTCCTCTCCGCCAACACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
3191714 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * ****
3191758 AATCTACTATCTTCGATCTGCCCTCCAATGATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
** * *
3191802 AATCTATTATATTCGATCTGCTCTCCGCCACTACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * *
3191846 AATCTACTATCTTCGATCTGCTTTCCGCCAATACAGAGACACCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
*
3191890 AATCTGCTATCTTCGATCTGCTCTCCTCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
** * * * *
3191934 AATCTATTATATTCGATCTGCTCTCCGCCACTACAGATATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * * * * * *
3191978 GATTTGTTATCTTCGATCTACCCTCTGACAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* ** * *
3192022 AATCTGCTATCTTCGATCTGCCCTCCAACGATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* *
3192066 AGTCTGCTATCTTCGATCTACTCTCCGCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * *
3192110 AATCTGTTATCTTCGATTTGCTCTCCGCCACTACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * *
3192154 AATCTGCTATCTTCGATTTGCTCTCCGCTACTACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
3192198 AATCT
1 AATCT
3192203 ATCTGGTCTT
Statistics
Matches: 851, Mismatches: 118, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
43 2 0.00
44 847 1.00
45 2 0.00
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27
Consensus pattern (44 bp):
AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
Found at i:3192975 original size:132 final size:131
Alignment explanation
Indices: 3192435--3193322 Score: 1048
Period size: 132 Copynumber: 6.7 Consensus size: 131
3192425 GCTAGTACTT
* * * * *** * * *
3192435 GCTTAAATATGCTTCGCTGCATCTTCAAGAAGC-CAAGATTTATCGTCTTTGATTTGCCTCACTG
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTC-AGATTCGCCGTCTTCGATCTGCTTCACTG
* * * * *
3192499 CAACTTCA-GGAAGACGAGGTCTACAATCCTCAGCCTACTCCACTACAACTTTA-GAGAGCTAGG
65 CAACTTCAGGGAA-ACAAGATCTA-AAT-TTTAGCCTACTCCACTACAACCTTAGGA-AGCTAGG
3192562 ACT--T-
126 A-TGGTG
* * * * **
3192566 ACTTAAATCTGCTTTACTGCAACATCAGGAAGC-CTAGATTCGCCGTCTTCAATCTGCCCCACTG
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTC-AGATTCGCCGTCTTCGATCTGCTTCACTG
* *
3192630 CAA-TCTCAGGGAAACAAGATCTATAATCTTCAGCCTACTCCACTACAACCTTAGGGAGCTAGGA
65 CAACT-TCAGGGAAACAAGATCTA-AAT-TTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGA
3192694 ---T-
127 TGGTG
* * * **
3192695 GCTTAAATCTGCTTCGCTGCATCATCAGGAAGC-CTAGATTCGCCGTCTTCGATCTGCCCCACTG
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTC-AGATTCGCCGTCTTCGATCTGCTTCACTG
* *
3192759 CAA-TCTCAGGGAAACAAGATCTATAATCTTCAGCCTACTCCACTACAACCTTAGGAAGTTAGGA
65 CAACT-TCAGGGAAACAAGATCTA-AAT-TTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGA
3192823 TGGTG
127 TGGTG
* * *
3192828 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATTTGTTTCACTGT
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGC
*
3192893 AACTTCAGGAAAACAAGATCTGAAATTTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGATGG
66 AACTTCAGGGAAACAAGATCT-AAATTTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGATGG
3192958 TG
130 TG
* *
3192960 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCACCGTCTTCGATCTGTTTCACTGC
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGC
* * * * * *
3193025 AACTTCAGGAAAACAATATCTAAAATTTTAGCCTACTCTACTACAACTTTAGGGAGCTAGGTTGG
66 AACTTCAGGGAAACAAGATCT-AAATTTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGATGG
3193090 TG
130 TG
*
3193092 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGTTTCACTGC
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGC
* * * * *
3193157 AACTTCAGGGAAACGAGATCTGAAAATTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGG
66 AACTTCAGGGAAACAAGATCT-AAATTTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGATGG
3193222 TG
130 TG
* * *
3193224 GCTTAAATCTGCTTCACTGCAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTACTTCACTTC
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGC
*
3193289 AATTTCAGGGAAACAAGATCTAAAATTTTAGCCT
66 AACTTCAGGGAAACAAGATCT-AAATTTTAGCCT
3193323 CATAGGCCCA
Statistics
Matches: 684, Mismatches: 63, Indels: 19
0.89 0.08 0.02
Matches are distributed among these distances:
129 122 0.18
130 1 0.00
131 98 0.14
132 384 0.56
133 76 0.11
134 3 0.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (131 bp):
GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGC
AACTTCAGGGAAACAAGATCTAAATTTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGATGGT
G
Found at i:3193116 original size:43 final size:43
Alignment explanation
Indices: 3193068--3193263 Score: 124
Period size: 43 Copynumber: 4.5 Consensus size: 43
3193058 TACTCTACTA
*
3193068 CAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTG
1 CAACTTTAGGGAGCTAGATTGGTGGCTTAAATCTGCTTCACTG
* * ** * ** *
3193111 CAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGTTTCACTG
1 CAACTTTAGGGAGCT-AGATT-GGTGGCTTAAATCTGCTTCACTG
* * * **** * ** * * *
3193156 CAACTTCAGGGAAACGAGATCT-GAAAATTTAGCCTACTCCACTA
1 CAACTTTAGGG-AGCTAGAT-TGGTGGCTTAAATCTGCTTCACTG
*
3193200 CAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCTTCACTG
1 CAACTTTAGGGAGCTAGATTGGTGGCTTAAATCTGCTTCACTG
*
3193243 CAACTTTAGGAAGCTCAGATT
1 CAACTTTAGGGAGCT-AGATT
3193264 CGCCGTCTTC
Statistics
Matches: 106, Mismatches: 41, Indels: 11
0.67 0.26 0.07
Matches are distributed among these distances:
42 1 0.01
43 44 0.42
44 27 0.25
45 31 0.29
46 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (43 bp):
CAACTTTAGGGAGCTAGATTGGTGGCTTAAATCTGCTTCACTG
Found at i:3194638 original size:90 final size:91
Alignment explanation
Indices: 3194537--3194719 Score: 316
Period size: 90 Copynumber: 2.0 Consensus size: 91
3194527 TTTTTCTTTC
3194537 TTTCTTTCTTTCTCTT-TTTTTTATTTTTTATTTTATTATTTTTTGAAGATCTAAGAGTATCATT
1 TTTCTTTCTTTCT-TTCTTTTTTATTTTTTATTTTATTATTTTTTGAAGATCTAAGAGTATCATT
*
3194601 TGAGGGTTTTCGCTGTGGCCTTTC-CT
65 TGAGGGTTTTCGCCGTGGCCTTTCACT
* *
3194627 TTTCTTTCTTTCTTTCTTTTTTATTTTTTATTTTATTATTTTTTTAAGATCTCAGAGTATCATTT
1 TTTCTTTCTTTCTTTCTTTTTTATTTTTTATTTTATTATTTTTTGAAGATCTAAGAGTATCATTT
3194692 GAGGGTTTTCGCCGTGGCCTTTCACT
66 GAGGGTTTTCGCCGTGGCCTTTCACT
3194718 TT
1 TT
3194720 CCTTGAAGGA
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
89 2 0.02
90 82 0.93
91 4 0.05
ACGTcount: A:0.14, C:0.14, G:0.13, T:0.59
Consensus pattern (91 bp):
TTTCTTTCTTTCTTTCTTTTTTATTTTTTATTTTATTATTTTTTGAAGATCTAAGAGTATCATTT
GAGGGTTTTCGCCGTGGCCTTTCACT
Found at i:3195276 original size:15 final size:16
Alignment explanation
Indices: 3195256--3195286 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3195246 TCAGCAACCG
3195256 CTTCTC-TTTTTCTTT
1 CTTCTCTTTTTTCTTT
3195271 CTTCTCTTTTTTCTTT
1 CTTCTCTTTTTTCTTT
3195287 TCCTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
CTTCTCTTTTTTCTTT
Found at i:3195299 original size:12 final size:13
Alignment explanation
Indices: 3195257--3195299 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 13
3195247 CAGCAACCGC
3195257 TTCTCTTTTTCTTT
1 TTCTCTTTTT-TTT
3195271 CTTCTCTTTTTTCTT
1 -TTCTCTTTTTT-TT
3195286 TTC-CTTTTTTTT
1 TTCTCTTTTTTTT
3195298 TT
1 TT
3195300 GAAATTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.15
13 7 0.26
14 4 0.15
15 12 0.44
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTCTTTTTTTT
Found at i:3202956 original size:46 final size:46
Alignment explanation
Indices: 3202889--3203063 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
3202879 TGTAACCCGC
3202889 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
3202935 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
3202985 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
3203028 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
3203064 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 63 0.58
47 26 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:3203009 original size:93 final size:93
Alignment explanation
Indices: 3202897--3203067 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
3202887 GCCCATAAGT
** *
3202897 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3202962 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
3202990 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
3203055 CGAGTTCGGATGC
66 CGAGCTCGGATGC
3203068 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:3205212 original size:15 final size:15
Alignment explanation
Indices: 3205192--3205227 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
3205182 TTTATATATT
3205192 TTTTGTATTTT-TTTG
1 TTTTGT-TTTTGTTTG
3205207 TTTTGTTTTTGTTTG
1 TTTTGTTTTTGTTTG
3205222 TTTTGT
1 TTTTGT
3205228 GTTTACACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.81
Consensus pattern (15 bp):
TTTTGTTTTTGTTTG
Found at i:3205215 original size:11 final size:11
Alignment explanation
Indices: 3205191--3205231 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
3205181 CTTTATATAT
*
3205191 TTTTTGTATT-
1 TTTTTGTTTTG
3205201 TTTTTGTTTTG
1 TTTTTGTTTTG
3205212 TTTTTG-TTTG
1 TTTTTGTTTTG
3205222 TTTTGTGTTT
1 TTTT-TGTTT
3205232 ACACGGGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 17 0.63
11 8 0.30
12 2 0.07
ACGTcount: A:0.02, C:0.00, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTTGTTTTG
Found at i:3209157 original size:6 final size:6
Alignment explanation
Indices: 3209130--3209214 Score: 64
Period size: 6 Copynumber: 13.8 Consensus size: 6
3209120 TGAATCCTCC
* * * *
3209130 TATTTT TTTTATT TATTCT TATTTT TA-TTT TATTTAT TTTCTTT TCTTTT
1 TATTTT TATT-TT TATTTT TATTTT TATTTT TATTT-T TAT-TTT TATTTT
* * * *
3209180 TCTTTT GATTTT TATTTT TATTTT CATTTT CATTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTT
3209215 CAATTTTATT
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
5 5 0.08
6 47 0.72
7 11 0.17
8 2 0.03
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:3209162 original size:5 final size:5
Alignment explanation
Indices: 3209130--3209234 Score: 58
Period size: 6 Copynumber: 20.2 Consensus size: 5
3209120 TGAATCCTCC
* *
3209130 TATTT T-TTT TA-TT TATTCT TATTTT TATTT TA-TT TATTT TCTTT TCTTTT
1 TATTT TATTT TATTT TATT-T TA-TTT TATTT TATTT TATTT TATTT T-ATTT
* *
3209180 TCTTT TGATTTT TATTTT TATTT TCATTT TCATTT CAATTT TA--T TATTT
1 TATTT T-A-TTT TA-TTT TATTT T-ATTT T-ATTT -TATTT TATTT TATTT
3209229 TATTT T
1 TATTT T
3209235 GAAAGACATA
Statistics
Matches: 82, Mismatches: 6, Indels: 24
0.73 0.05 0.21
Matches are distributed among these distances:
3 3 0.04
4 12 0.15
5 30 0.37
6 31 0.38
7 6 0.07
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:3216180 original size:35 final size:35
Alignment explanation
Indices: 3216134--3216204 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
3216124 AATAACAAGA
3216134 AGAATATAAAATGAATACCAGAACATCTGGTACAT
1 AGAATATAAAATGAATACCAGAACATCTGGTACAT
3216169 AGAATATAAAATGAATACCAGAACATCTGGTACAT
1 AGAATATAAAATGAATACCAGAACATCTGGTACAT
3216204 A
1 A
3216205 CTCTTGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (35 bp):
AGAATATAAAATGAATACCAGAACATCTGGTACAT
Found at i:3222670 original size:50 final size:50
Alignment explanation
Indices: 3222616--3222826 Score: 121
Period size: 50 Copynumber: 4.2 Consensus size: 50
3222606 TACTAAATTA
3222616 ATAAAAAAATACTTAAATAATACATTTGAAACATTATGTACTAAAATAAT
1 ATAAAAAAATACTTAAATAATACATTTGAAACATTATGTACTAAAATAAT
** * * * * * *
3222666 ATAAAAATAAAATACAAAAATATTATATTTTAAAAATTA--AAATAAAA-AA-
1 AT--AAA-AAAATACTTAAATAATACATTTGAAACATTATGTACTAAAATAAT
** * ** * ** * * *
3222715 ATAAAAAAATA-GGAACA-AAGTGCCAAAAT-CAAGGTTATTTATTAAATTAAT
1 ATAAAAAAATACTTAA-ATAA-T-AC-ATTTGAAACATTATGTACTAAAATAAT
* *
3222766 ATTAAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAAT
1 ATAAAAAAATACTTAAATAATACATTTGAAACATTATGTACTAAAATAAT
3222816 ATAAAAAAATA
1 ATAAAAAAATA
3222827 AAATACGAAA
Statistics
Matches: 111, Mismatches: 36, Indels: 28
0.63 0.21 0.16
Matches are distributed among these distances:
45 3 0.03
46 8 0.07
47 8 0.07
48 2 0.02
49 9 0.08
50 32 0.29
51 17 0.15
52 7 0.06
53 25 0.23
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (50 bp):
ATAAAAAAATACTTAAATAATACATTTGAAACATTATGTACTAAAATAAT
Found at i:3223032 original size:148 final size:151
Alignment explanation
Indices: 3222522--3223095 Score: 813
Period size: 148 Copynumber: 3.8 Consensus size: 151
3222512 TTTATTTTTT
* * * * *
3222522 AATAAAATAAG-AAATAATATATTTTAAAAAATAAAATCTGAAAATTTAAAAAATACAAATTAAA
1 AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAA-TAAAAAAATACAAA-CAAA
* *
3222586 GGGCCAAAATCAGGGTTATTTACTAAATTAATA--AAAAAATACTTAAATAATACATTTGAAACA
64 GGGCCAAAATCAAGGTTATTTACTAAATTAATATTAAAAAACACTTAAATAATACATTTGAAACA
3222649 TTATGTACTAAAATAATAT-AAA
129 TTATGTACTAAAATAATATAAAA
* * * *** ** *
3222671 AATAAAATACAAAAATATTATATTTTAAAAATTAAAATAAAAAAATAAAAAAATAGGAACAAAGT
1 AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATAAAAAAATACAAACAAAGG
*
3222736 GCCAAAATCAAGGTTATTTATTAAATTAATATTAAAAAACACTTAAATAATACATTTGAAACATT
66 GCCAAAATCAAGGTTATTTACTAAATTAATATTAAAAAACACTTAAATAATACATTTGAAACATT
3222801 ATGTACTAAAATAATATAAAAA
131 ATGTACTAAAATAATAT-AAAA
*
3222823 AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATAAAAAAATATAAACAAAAG
1 AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATAAAAAAATACAAAC-AAAG
* *
3222888 GGCCAAAATCAAGGTTATTTACTAAATT-A-A-TAAAAAA-ACTTAAATAATACACTTGAAATAT
65 GGCCAAAATCAAGGTTATTTACTAAATTAATATTAAAAAACACTTAAATAATACATTTGAAACAT
3222949 TATGTACTAAAATAATATAAAA
130 TATGTACTAAAATAATATAAAA
* * * *
3222971 AATAAAATATGAAAATAGTATATTTTAAAAATTAAAATCCGAAAATAAAAAAATACGAACAAAGT
1 AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATAAAAAAATACAAACAAAGG
* * *
3223036 GCCAAAATCAAGATTATTTATTAAATTAATATTAAAAAACACTTAAATAATATATTTGAA
66 GCCAAAATCAAGGTTATTTACTAAATTAATATTAAAAAACACTTAAATAATACATTTGAA
3223096 TCCATTCTCG
Statistics
Matches: 379, Mismatches: 36, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
147 29 0.08
148 94 0.25
149 61 0.16
150 90 0.24
151 19 0.05
152 56 0.15
153 30 0.08
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (151 bp):
AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATAAAAAAATACAAACAAAGG
GCCAAAATCAAGGTTATTTACTAAATTAATATTAAAAAACACTTAAATAATACATTTGAAACATT
ATGTACTAAAATAATATAAAA
Found at i:3223065 original size:300 final size:301
Alignment explanation
Indices: 3222522--3223095 Score: 938
Period size: 300 Copynumber: 1.9 Consensus size: 301
3222512 TTTATTTTTT
* * **
3222522 AATAAAATAAGAAATAATATATTTTAAAAAATAAAATCTGAAAATTTAAAAAATACAAATTAAAG
1 AATAAAATAAGAAATAATATATTTTAAAAAATAAAATCCGAAAATTAAAAAAATACAAACAAAAG
* *
3222587 GGCCAAAATCAGGGTTATTTACTAAATTAATAAAAAAATACTTAAATAATACATTTGAAACATTA
66 GGCCAAAATCAAGGTTATTTACTAAATTAATAAAAAAATACTTAAATAATACACTTGAAACATTA
*
3222652 TGTACTAAAATAATATAAAAATAAAATACAAAAATATTATATTTTAAAAATTAAAATAAAAAAAT
131 TGTACTAAAATAATATAAAAATAAAATACAAAAATAGTATATTTTAAAAATTAAAATAAAAAAAT
* *
3222717 AAAAAAATAGGAACAAAGTGCCAAAATCAAGGTTATTTATTAAATTAATATTAAAAAACACTTAA
196 AAAAAAATACGAACAAAGTGCCAAAATCAAGATTATTTATTAAATTAATATTAAAAAACACTTAA
3222782 ATAATACATTTGAAACATTATGTACTAAAATAATATAAAAA
261 ATAATACATTTGAAACATTATGTACTAAAATAATATAAAAA
* * *
3222823 AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAA-TAAAAAAATATAAACAAAA
1 AATAAAATAAG-AAATAATATATTTTAAAAAATAAAATCCGAAAATTAAAAAAATACAAACAAAA
*
3222887 GGGCCAAAATCAAGGTTATTTACTAAATTAAT-AAAAAA-ACTTAAATAATACACTTGAAATATT
65 GGGCCAAAATCAAGGTTATTTACTAAATTAATAAAAAAATACTTAAATAATACACTTGAAACATT
** ***
3222950 ATGTACTAAAATAATATAAAAAATAAAATATGAAAATAGTATATTTTAAAAATTAAAATCCGAAA
130 ATGTACTAAAATAATAT-AAAAATAAAATACAAAAATAGTATATTTTAAAAATTAAAATAAAAAA
3223015 ATAAAAAAATACGAACAAAGTGCCAAAATCAAGATTATTTATTAAATTAATATTAAAAAACACTT
194 ATAAAAAAATACGAACAAAGTGCCAAAATCAAGATTATTTATTAAATTAATATTAAAAAACACTT
*
3223080 AAATAATATATTTGAA
259 AAATAATACATTTGAA
3223096 TCCATTCTCG
Statistics
Matches: 252, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
299 40 0.16
300 125 0.50
301 56 0.22
302 31 0.12
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (301 bp):
AATAAAATAAGAAATAATATATTTTAAAAAATAAAATCCGAAAATTAAAAAAATACAAACAAAAG
GGCCAAAATCAAGGTTATTTACTAAATTAATAAAAAAATACTTAAATAATACACTTGAAACATTA
TGTACTAAAATAATATAAAAATAAAATACAAAAATAGTATATTTTAAAAATTAAAATAAAAAAAT
AAAAAAATACGAACAAAGTGCCAAAATCAAGATTATTTATTAAATTAATATTAAAAAACACTTAA
ATAATACATTTGAAACATTATGTACTAAAATAATATAAAAA
Found at i:3236743 original size:16 final size:17
Alignment explanation
Indices: 3236704--3236744 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
3236694 CAGCCAATTG
3236704 TAAATAATTTTTTTTAT
1 TAAATAATTTTTTTTAT
3236721 TAAAAATAATTTTTTTTA-
1 T--AAATAATTTTTTTTAT
3236739 TAAATA
1 TAAATA
3236745 TCACTTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 1 0.05
19 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATAATTTTTTTTAT
Found at i:3238863 original size:31 final size:30
Alignment explanation
Indices: 3238827--3238890 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
3238817 ACTTAACAAG
3238827 CAAATGCCTCTAAAATAATAACAAATAATAA
1 CAAATGCCTCTAAAATAATAACAAA-AATAA
* *
3238858 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAAATAA
3238888 CAA
1 CAA
3238891 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.23
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAAATAA
Found at i:3239867 original size:19 final size:18
Alignment explanation
Indices: 3239840--3239882 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3239830 AGTACCAAAA
*
3239840 AAAAATCAAAATAATTTTT
1 AAAAATCAAAAT-ATTTAT
* *
3239859 AAAATTCAACATATTTAT
1 AAAAATCAAAATATTTAT
3239877 AAAAAT
1 AAAAAT
3239883 TTTAAACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATCAAAATATTTAT
Found at i:3239932 original size:44 final size:44
Alignment explanation
Indices: 3239884--3239973 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
3239874 TATAAAAATT
3239884 TTAAACAAATCTAAAAAATACATAAAGAAAGTTCAATTTTTAAA
1 TTAAACAAATCTAAAAAATACATAAAGAAAGTTCAATTTTTAAA
3239928 TTAAACAAATCTAAAAAATACATAAAGAAAGTTCAATTTTTAAA
1 TTAAACAAATCTAAAAAATACATAAAGAAAGTTCAATTTTTAAA
3239972 TT
1 TT
3239974 TTTTTCTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (44 bp):
TTAAACAAATCTAAAAAATACATAAAGAAAGTTCAATTTTTAAA
Found at i:3241291 original size:23 final size:23
Alignment explanation
Indices: 3241209--3241295 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
3241199 CCTGATCAGT
*
3241209 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
3241231 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
3241251 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
3241274 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
3241296 TCGATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:3242298 original size:29 final size:30
Alignment explanation
Indices: 3242239--3242296 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3242229 TCCGAGCCTT
*
3242239 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
3242269 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
3242297 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:3242526 original size:13 final size:13
Alignment explanation
Indices: 3242508--3242539 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3242498 TTTCCAGCAA
3242508 TTATGAATTTATT
1 TTATGAATTTATT
3242521 TTATGAATTTATT
1 TTATGAATTTATT
*
3242534 TGATGA
1 TTATGA
3242540 TGATCCAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:3242747 original size:50 final size:50
Alignment explanation
Indices: 3242634--3242875 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
3242624 ATTTGGGTAA
* * *
3242634 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
3242690 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
3242740 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
3242790 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
3242840 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
3242876 TTTGGCAAGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:3242823 original size:100 final size:103
Alignment explanation
Indices: 3242634--3242882 Score: 362
Period size: 100 Copynumber: 2.4 Consensus size: 103
3242624 ATTTGGGTAA
3242634 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
3242699 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
3242740 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
3242802 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
3242840 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
3242883 AGTTATTATC
Statistics
Matches: 133, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:3247873 original size:18 final size:18
Alignment explanation
Indices: 3247850--3247884 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3247840 TAAATTACTT
3247850 TGATAATAAATTCTAATC
1 TGATAATAAATTCTAATC
3247868 TGATAATAAATTCTAAT
1 TGATAATAAATTCTAAT
3247885 TAATTAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (18 bp):
TGATAATAAATTCTAATC
Found at i:3247892 original size:18 final size:18
Alignment explanation
Indices: 3247852--3247888 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3247842 AATTACTTTG
*
3247852 ATAATAAATTCTAATCTG
1 ATAATAAATTCTAATCTA
3247870 ATAATAAATTCTAAT-TA
1 ATAATAAATTCTAATCTA
3247887 AT
1 AT
3247889 TAATTGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (18 bp):
ATAATAAATTCTAATCTA
Found at i:3249852 original size:3 final size:3
Alignment explanation
Indices: 3249844--3249884 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
3249834 ATTCAGATTA
*
3249844 CAC CAC CAC CAC CAC CGC C-C GCAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC -CAC CAC CAC CAC CAC CAC CA
3249885 GTCACTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
2 1 0.03
3 33 0.94
4 1 0.03
ACGTcount: A:0.29, C:0.66, G:0.05, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:3252096 original size:17 final size:17
Alignment explanation
Indices: 3252064--3252097 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3252054 TCTTCTTCTC
* *
3252064 CCTTTAATTTTGGGATT
1 CCTTTAATTATAGGATT
3252081 CCTTTAATTATAGGATT
1 CCTTTAATTATAGGATT
3252098 TTATGCAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (17 bp):
CCTTTAATTATAGGATT
Found at i:3252819 original size:11 final size:11
Alignment explanation
Indices: 3252803--3252827 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3252793 TTCTTTTTTT
3252803 AAAAAAAAAAG
1 AAAAAAAAAAG
3252814 AAAAAAAAAAG
1 AAAAAAAAAAG
3252825 AAA
1 AAA
3252828 GAGAGAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:3254388 original size:18 final size:19
Alignment explanation
Indices: 3254365--3254403 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3254355 TACAAATACA
*
3254365 AACATT-ACATAATTATTT
1 AACATTCACATAATGATTT
*
3254383 AACATTCACATCATGATTT
1 AACATTCACATAATGATTT
3254402 AA
1 AA
3254404 TCATATCGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (19 bp):
AACATTCACATAATGATTT
Found at i:3255095 original size:22 final size:22
Alignment explanation
Indices: 3255070--3255144 Score: 116
Period size: 22 Copynumber: 3.4 Consensus size: 22
3255060 GAGAGTACGG
* *
3255070 ATGTGCTAAACAGATAGCACAT
1 ATGTGCTAAACAAAGAGCACAT
3255092 ATGTGCTAAACAAAGAGCACAT
1 ATGTGCTAAACAAAGAGCACAT
3255114 ATGTGCTAAACAAAGAGCAC-T
1 ATGTGCTAAACAAAGAGCACAT
3255135 AATGTGCTAA
1 -ATGTGCTAA
3255145 TAATCAGAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 1 0.02
22 49 0.98
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (22 bp):
ATGTGCTAAACAAAGAGCACAT
Found at i:3255098 original size:44 final size:44
Alignment explanation
Indices: 3255034--3255144 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
3255024 TCAACTAATG
* * * * * * *
3255034 AACAGAGAGCACAGAAGTGCTATATAGAGAGTACGGATGTGCTA
1 AACAGAGAGCACATATGTGCTAAACAAAGAGCACAGATGTGCTA
* *
3255078 AACAGATAGCACATATGTGCTAAACAAAGAGCACATATGTGCTA
1 AACAGAGAGCACATATGTGCTAAACAAAGAGCACAGATGTGCTA
*
3255122 AACAAAGAGCAC-TAATGTGCTAA
1 AACAGAGAGCACAT-ATGTGCTAA
3255145 TAATCAGAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 1 0.02
44 54 0.98
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (44 bp):
AACAGAGAGCACATATGTGCTAAACAAAGAGCACAGATGTGCTA
Found at i:3256100 original size:5 final size:5
Alignment explanation
Indices: 3256090--3256122 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
3256080 TTGTTTGTTT
*
3256090 TATAA TATAA TATAA TATAA AATAA TAT-A TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA
3256123 CACTTAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:3264592 original size:48 final size:52
Alignment explanation
Indices: 3264472--3264662 Score: 151
Period size: 48 Copynumber: 3.7 Consensus size: 52
3264462 ATTAGGGTTT
* * * * * *
3264472 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAACTGGTAAGGTTTC-TAAGGC
1 AAGGCTACCATGTAAGACCATGTCAAGACATGGC-A-TTGTGA-G-CTCATAAGGC
** *
3264527 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATT-T-A-CT-ATAAGGC
1 AAGGCTACCATGTAAGACCATGTCAAGACATGGCATTGTGAGCTCATAAGGC
* * * *
3264575 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGCTACCATGTAAGACCATGTCAAGACATGGCATT-GTGAGCTCATAAGGC
* *
3264628 AAGGCTACCATGTAAGACAATGTCAAGATATGGCA
1 AAGGCTACCATGTAAGACCATGTCAAGACATGGCA
3264663 ATGGTAAGTT
Statistics
Matches: 111, Mismatches: 17, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
48 34 0.31
49 4 0.04
50 1 0.01
51 2 0.02
52 6 0.05
53 33 0.30
54 1 0.01
55 30 0.27
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (52 bp):
AAGGCTACCATGTAAGACCATGTCAAGACATGGCATTGTGAGCTCATAAGGC
Found at i:3264644 original size:53 final size:53
Alignment explanation
Indices: 3264472--3264719 Score: 205
Period size: 49 Copynumber: 4.8 Consensus size: 53
3264462 ATTAGGGTTT
* *
3264472 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAACTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-G-TTCATAAGGC
* * * *
3264527 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATT--T-A-CT-ATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* * *
3264575 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* * * * *
3264628 AAGGCTACCATGTAAGACAATGTCAAGATATGGCAATGGTAAGTT--TCAA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCAT-AAGGC
* * * *
3264677 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
3264720 GTACCCGCGT
Statistics
Matches: 159, Mismatches: 25, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
48 34 0.21
49 41 0.26
50 1 0.01
51 3 0.02
52 8 0.05
53 40 0.25
54 2 0.01
55 30 0.19
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:3264680 original size:101 final size:101
Alignment explanation
Indices: 3264472--3264721 Score: 276
Period size: 101 Copynumber: 2.4 Consensus size: 101
3264462 ATTAGGGTTT
*
3264472 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAACTGGTAAGGTTTCTAAGGCAAGGAAATCA
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAA-TGGTAAGGTTTCTAAGGCAAGGAAACCA
*
3264537 TGTAAGACCATGTCAAGACATGGCATTTACTATAAGGCA
65 TGTAAGACAATGTCAAGACATGGCA--TACTATAAGGCA
* * * **
3264576 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGA-G-TTCATAAGGCAAGGCTACCA
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATGGTAAGGTTTC-TAAGGCAAGGAAACCA
* * *
3264638 TGTAAGACAATGTCAAGATATGGCA-A-TGGTAAGTTTCAA
65 TGTAAGACAATGTCAAGACATGGCATACT-ATAAG--GC-A
* * *
3264677 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAGGT
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATGGTAAGGT
3264722 ACCCGCGTAT
Statistics
Matches: 122, Mismatches: 16, Indels: 16
0.79 0.10 0.10
Matches are distributed among these distances:
97 1 0.01
98 5 0.04
100 4 0.03
101 42 0.34
102 36 0.30
103 30 0.25
104 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (101 bp):
AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATGGTAAGGTTTCTAAGGCAAGGAAACCAT
GTAAGACAATGTCAAGACATGGCATACTATAAGGCA
Found at i:3264933 original size:16 final size:16
Alignment explanation
Indices: 3264912--3264942 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3264902 ATAAATTTGA
3264912 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
3264928 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
3264943 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:3269095 original size:21 final size:21
Alignment explanation
Indices: 3269071--3269111 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3269061 TTTCTCTTTC
3269071 AAATTTTATTTTTTTAATTAT
1 AAATTTTATTTTTTTAATTAT
3269092 AAATTTTATTTTTTTAATTA
1 AAATTTTATTTTTTTAATTA
3269112 CAAGAGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
AAATTTTATTTTTTTAATTAT
Found at i:3270278 original size:15 final size:15
Alignment explanation
Indices: 3270258--3270314 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
3270248 CGATGAATTT
3270258 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
3270273 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
3270288 ATTGAATTTATATTG
1 ATTGAATTTATATTG
3270303 ATTGAA-TTATAT
1 ATTGAATTTATAT
3270315 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:3270725 original size:23 final size:23
Alignment explanation
Indices: 3270699--3270773 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 23
3270689 AAGCACTTTA
3270699 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
3270722 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* * **
3270743 TGTGTTGT-TTT-AGGCACTTTA
1 TGTGTCGTATTTCAGGCACCTCG
3270764 TGTGTCGTAT
1 TGTGTCGTAT
3270774 ACTGATCAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 33 0.75
22 2 0.05
23 9 0.20
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:3273337 original size:6 final size:6
Alignment explanation
Indices: 3273298--3273325 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3273288 TTTATTTTAT
3273298 TTAATA TTAATA TTAATA TTAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAA
3273326 ATTTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:3274082 original size:16 final size:16
Alignment explanation
Indices: 3274061--3274093 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3274051 CATGTGGTAA
*
3274061 AAAAATTATAAAAAAT
1 AAAAATTAGAAAAAAT
3274077 AAAAATTAGAAAAAAT
1 AAAAATTAGAAAAAAT
3274093 A
1 A
3274094 TTTAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAAATTAGAAAAAAT
Found at i:3274135 original size:11 final size:10
Alignment explanation
Indices: 3274118--3274163 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
3274108 AAAATTAGGG
3274118 AAAAAATATA
1 AAAAAATATA
3274128 AAAGAAATATA
1 AAA-AAATATA
* *
3274139 AAAAATTGTA
1 AAAAAATATA
3274149 AAAAATATATA
1 AAAAA-ATATA
3274160 AAAA
1 AAAA
3274164 GACATCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 13 0.43
11 17 0.57
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (10 bp):
AAAAAATATA
Found at i:3274150 original size:21 final size:20
Alignment explanation
Indices: 3274118--3274163 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3274108 AAAATTAGGG
3274118 AAAAAATATAAAAGAA-ATAT
1 AAAAAATATAAAA-AATATAT
*
3274138 AAAAAATTGTAAAAAATATAT
1 AAAAAA-TATAAAAAATATAT
3274159 AAAAA
1 AAAAA
3274164 GACATCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAAAATATAAAAAATATAT
Found at i:3274532 original size:16 final size:17
Alignment explanation
Indices: 3274506--3274537 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3274496 TTTTTACAAC
3274506 TTTTTATTATTTTTTAT
1 TTTTTATTATTTTTTAT
3274523 TTTTTA-TATTTTTTA
1 TTTTTATTATTTTTTA
3274538 CCACATGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTATTATTTTTTAT
Found at i:3275571 original size:16 final size:17
Alignment explanation
Indices: 3275548--3275583 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3275538 GGAAATGAGA
*
3275548 ATTTTTAAATATTTAAT
1 ATTTTAAAATATTTAAT
3275565 ATTTTAAAAATATTTAAT
1 ATTTT-AAAATATTTAAT
3275583 A
1 A
3275584 ATTATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTAAAATATTTAAT
Found at i:3275831 original size:14 final size:13
Alignment explanation
Indices: 3275786--3275829 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 13
3275776 TTATATTAAT
3275786 AATATTAAAAATA
1 AATATTAAAAATA
3275799 AA-A-TAAAAATA
1 AATATTAAAAATA
*
3275810 ATATTTTAAAAATA
1 A-ATATTAAAAATA
3275824 AATATT
1 AATATT
3275830 TATTTTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 9 0.35
12 2 0.08
13 6 0.23
14 9 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AATATTAAAAATA
Found at i:3285095 original size:15 final size:15
Alignment explanation
Indices: 3285063--3285104 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
3285053 TTTTCCATAT
* *
3285063 TTAATTTCTCAACAC
1 TTAATTTTTCAGCAC
*
3285078 TTATTTTTTCAGCAC
1 TTAATTTTTCAGCAC
3285093 TTAATTTTTCAG
1 TTAATTTTTCAG
3285105 TTTATCAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.50
Consensus pattern (15 bp):
TTAATTTTTCAGCAC
Found at i:3287466 original size:18 final size:18
Alignment explanation
Indices: 3287443--3287480 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3287433 TATCTGAAAC
3287443 TTAATTTTGAATATGATA
1 TTAATTTTGAATATGATA
3287461 TTAATTTTGAATATGATA
1 TTAATTTTGAATATGATA
3287479 TT
1 TT
3287481 CCTATTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
TTAATTTTGAATATGATA
Found at i:3304468 original size:14 final size:12
Alignment explanation
Indices: 3304440--3304500 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 12
3304430 AATATACATA
3304440 AATTTTATATTT
1 AATTTTATATTT
3304452 AATTTATATATTTT
1 AATTT-TATA-TTT
*
3304466 AATTTCTA-ATAT
1 AATTT-TATATTT
*
3304478 AATTTTATCTTT
1 AATTTTATATTT
3304490 ATAGTTTTATA
1 A-A-TTTTATA
3304501 ATGTTATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
11 2 0.05
12 15 0.38
13 6 0.15
14 16 0.41
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (12 bp):
AATTTTATATTT
Found at i:3304470 original size:26 final size:26
Alignment explanation
Indices: 3304440--3304500 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
3304430 AATATACATA
*
3304440 AATTTTATATTTAATTTATATATTT-T
1 AATTTTATATATAATTT-TATATTTAT
*
3304466 AATTTCTA-ATATAATTTTATCTTTAT
1 AATTT-TATATATAATTTTATATTTAT
*
3304492 AGTTTTATA
1 AATTTTATA
3304501 ATGTTATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 8 0.28
26 19 0.66
27 2 0.07
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (26 bp):
AATTTTATATATAATTTTATATTTAT
Found at i:3311333 original size:38 final size:39
Alignment explanation
Indices: 3311249--3311383 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
3311239 ACCAATATGG
*
3311249 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
3311288 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
3311326 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
3311367 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
3311384 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:3316361 original size:103 final size:104
Alignment explanation
Indices: 3316117--3316382 Score: 426
Period size: 103 Copynumber: 2.6 Consensus size: 104
3316107 GTTGTACATA
** *
3316117 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
3316182 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* *
3316221 GAGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
3316286 CTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
3316324 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
3316383 TGTTGCAGGC
Statistics
Matches: 149, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:3337654 original size:17 final size:16
Alignment explanation
Indices: 3337622--3337652 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3337612 TACTTAAAGT
3337622 TTTAGTTATATTTTTG
1 TTTAGTTATATTTTTG
3337638 TTTAGTTATATTTTT
1 TTTAGTTATATTTTT
3337653 TGGTGCCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (16 bp):
TTTAGTTATATTTTTG
Found at i:3342074 original size:21 final size:22
Alignment explanation
Indices: 3342035--3342081 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3342025 TAGTAAGAAT
*
3342035 AAAAATGTTTTCTAAAATT-TA
1 AAAAATGTTTGCTAAAATTGTA
* *
3342056 AAAAATGTTTGGTATAATTGTA
1 AAAAATGTTTGCTAAAATTGTA
3342078 AAAA
1 AAAA
3342082 TAATAATGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (22 bp):
AAAAATGTTTGCTAAAATTGTA
Found at i:3345266 original size:21 final size:23
Alignment explanation
Indices: 3345215--3345266 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
3345205 GGGGGCCAAA
3345215 ATTAAATTATAACTTTTATAATAG
1 ATTAAA-TATAACTTTTATAATAG
*
3345239 -TAAAAATATAA-TTTT-TAATAG
1 AT-TAAATATAACTTTTATAATAG
3345260 ATTAAAT
1 ATTAAAT
3345267 CAAAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
21 10 0.42
22 5 0.21
23 6 0.25
24 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
ATTAAATATAACTTTTATAATAG
Found at i:3368340 original size:14 final size:14
Alignment explanation
Indices: 3368310--3368338 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3368300 TTTTTTAATA
3368310 TTATATTAATTTTT
1 TTATATTAATTTTT
3368324 TTATA-TAATTTTT
1 TTATATTAATTTTT
3368337 TT
1 TT
3368339 TAATATTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATATTAATTTTT
Found at i:3368771 original size:23 final size:22
Alignment explanation
Indices: 3368745--3368788 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3368735 CACTCGAAAT
3368745 CATTATA-AACTTAATTTTATATC
1 CATTATATAA-TT-ATTTTATATC
*
3368768 CATTTTATAATTATTTTATAT
1 CATTATATAATTATTTTATAT
3368789 ATTAGAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 8 0.42
24 2 0.11
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (22 bp):
CATTATATAATTATTTTATATC
Found at i:3369458 original size:20 final size:20
Alignment explanation
Indices: 3369435--3369472 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3369425 TAAATTTTCA
3369435 ATTTAATTATT-AAATTTAGT
1 ATTT-ATTATTAAAATTTAGT
*
3369455 ATTTTTTATTAAAATTTA
1 ATTTATTATTAAAATTTA
3369473 TCAACTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTTATTATTAAAATTTAGT
Found at i:3374890 original size:42 final size:42
Alignment explanation
Indices: 3374827--3374909 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
3374817 GCCTGAACCG
*
3374827 TGAAGGGTGGGTAAAAGCTAAGAAGCTCCTAAAATGGCCAAA
1 TGAAGGGTGGGTAAAAGCTAAGAAGCTCCCAAAATGGCCAAA
3374869 TGAAGGGTGGGTAGAAA-CTAAGAAGCTCCCAAAATGGCCAA
1 TGAAGGGTGGGTA-AAAGCTAAGAAGCTCCCAAAATGGCCAA
3374910 GTAAACCAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 36 0.92
43 3 0.08
ACGTcount: A:0.40, C:0.16, G:0.29, T:0.16
Consensus pattern (42 bp):
TGAAGGGTGGGTAAAAGCTAAGAAGCTCCCAAAATGGCCAAA
Found at i:3380552 original size:52 final size:52
Alignment explanation
Indices: 3380454--3380605 Score: 153
Period size: 52 Copynumber: 2.9 Consensus size: 52
3380444 CAGAAAAGAT
** * * *
3380454 GTGATATGTGCACCCGCATAAGACCATAGCTGGGCTATGGTATCGGTGCAAC
1 GTGATATGTGTTCCCGTATAAGACCATAACTGGGCTATGGCATCGGTGCAAC
* * ** *
3380506 GTGATATGTGTTCCCGTATAAGACCATAATTGGGCTATGGCGTCGGTGTGAT
1 GTGATATGTGTTCCCGTATAAGACCATAACTGGGCTATGGCATCGGTGCAAC
* * **
3380558 GTGATAATGTGATT-TCGTATAAGACCATATCTGGAATATGGCATCGGT
1 GTGAT-ATGTG-TTCCCGTATAAGACCATAACTGGGCTATGGCATCGGT
3380606 ATTATATGTG
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
52 47 0.57
53 33 0.40
54 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (52 bp):
GTGATATGTGTTCCCGTATAAGACCATAACTGGGCTATGGCATCGGTGCAAC
Found at i:3384354 original size:18 final size:18
Alignment explanation
Indices: 3384333--3384383 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
3384323 TAAAAGTCAG
*
3384333 TTATTCAGTAACGATAAA
1 TTATTCAGTAACAATAAA
* *
3384351 TTATTCAGTAATAATCAA
1 TTATTCAGTAACAATAAA
*
3384369 TTATTTAGTAACAAT
1 TTATTCAGTAACAAT
3384384 TTTTTTACGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (18 bp):
TTATTCAGTAACAATAAA
Found at i:3385667 original size:13 final size:13
Alignment explanation
Indices: 3385649--3385678 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3385639 TTTCTTTTCT
3385649 TTTCTTTTTCTCC
1 TTTCTTTTTCTCC
*
3385662 TTTCTTTTTTTCC
1 TTTCTTTTTCTCC
3385675 TTTC
1 TTTC
3385679 CCGTTTTGCT
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:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTCTTTTTCTCC
Found at i:3385896 original size:15 final size:16
Alignment explanation
Indices: 3385876--3385908 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3385866 TCTCAAATTG
*
3385876 TAATTAT-TTAATTAA
1 TAATTATCTTAATAAA
3385891 TAATTATCTTAATAAA
1 TAATTATCTTAATAAA
3385907 TA
1 TA
3385909 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTATCTTAATAAA
Found at i:3386105 original size:13 final size:13
Alignment explanation
Indices: 3386051--3386109 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
3386041 AATATCAATT
3386051 TAATAA-AAATAA
1 TAATAATAAATAA
*
3386063 TATTAATAAAT-A
1 TAATAATAAATAA
*
3386075 TAA-AATATAAAACCA
1 TAATAATA-AATA--A
3386090 TAATAATAAATAA
1 TAATAATAAATAA
3386103 TAATAAT
1 TAATAAT
3386110 TTAATATACA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
11 4 0.11
12 10 0.27
13 12 0.32
15 7 0.19
16 4 0.11
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:3390953 original size:21 final size:21
Alignment explanation
Indices: 3390927--3390993 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
3390917 CCTGATCAGT
*
3390927 ATACGACACATAAAGTGTCTG
1 ATACGACACATAAAGTGCCTG
** *
3390948 ATACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTG
3390969 AAATACGACACATAAAGTGCCTG
1 --ATACGACACATAAAGTGCCTG
3390992 AT
1 AT
3390994 CGATAAAGCC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 19 0.51
23 18 0.49
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.19
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:3390988 original size:23 final size:22
Alignment explanation
Indices: 3390927--3390992 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
3390917 CCTGATCAGT
*
3390927 ATACGACACATAAAGTGTCTG-
1 ATACGACACATAAAGTGCCTGA
** *
3390948 ATACGACACACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTG-A
3390971 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
3390993 TCGATAAAGC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.47
22 1 0.03
23 18 0.50
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTGA
Found at i:3391390 original size:15 final size:15
Alignment explanation
Indices: 3391365--3391418 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
3391355 TCATATATAT
3391365 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
3391381 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
3391396 AATAATTTCAATCAA
1 TATAAATTCAATCAA
3391411 TATAAATT
1 TATAAATT
3391419 TAATAAATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 30 0.88
16 4 0.12
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:3396371 original size:11 final size:11
Alignment explanation
Indices: 3396355--3396381 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3396345 TAGAAATTAG
3396355 TTTGTGAAACT
1 TTTGTGAAACT
3396366 TTTGTGAAACT
1 TTTGTGAAACT
3396377 TTTGT
1 TTTGT
3396382 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:3397915 original size:91 final size:91
Alignment explanation
Indices: 3397788--3397995 Score: 308
Period size: 91 Copynumber: 2.3 Consensus size: 91
3397778 TTGATTTTAG
* * *
3397788 TAAATTCATATAAGAACATTTTATCATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATTAAAAATTTTATGAAATTATATATCATTATTAAATTAT
* *
3397853 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATATTAATTATTTTAAATTATA
*
3397880 TAAATTCATATAAGAAAATTTATTATTAAAAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAAAATTTTATGAAATTATATATCATTATTAAATTATA
*
3397945 TGTAATATTTATTATTTTAAATTATA
66 TGTAATATTAATTATTTTAAATTATA
* * * *
3397971 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
3397996 GTTATAATTA
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 89 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATTAAAAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATATTAATTATTTTAAATTATA
Found at i:3397957 original size:27 final size:28
Alignment explanation
Indices: 3397897--3397970 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 28
3397887 ATATAAGAAA
* *
3397897 ATTTATTATTA-AAAATTTTATGAAATT
1 ATTTATTATTATTAAATTATATGAAATT
* *
3397924 ATATATTATTATTAAATTATATGTAA-T
1 ATTTATTATTATTAAATTATATGAAATT
3397951 ATTTATTATT-TTAAATTATA
1 ATTTATTATTATTAAATTATA
3397971 CAAATTCATA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 10 0.24
27 20 0.49
28 11 0.27
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (28 bp):
ATTTATTATTATTAAATTATATGAAATT
Found at i:3397962 original size:47 final size:47
Alignment explanation
Indices: 3397820--3397963 Score: 138
Period size: 47 Copynumber: 3.1 Consensus size: 47
3397810 ATCATTAAGA
*
3397820 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATTAATT
* * * **
3397867 A-TTT-T-AAATTGTATA-AATTCATATAAGA--AAATTTATTATTAAAA
1 ATTTTATGAAATTATATATAATT-AT-TAA-ATTATATTTAATATTAATT
* * *
3397911 ATTTTATGAAATTATATATTATTATTAAATTATATGTAATATTTATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATTAATT
3397958 ATTTTA
1 ATTTTA
3397964 AATTATACAA
Statistics
Matches: 74, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
43 3 0.04
44 24 0.32
45 8 0.11
46 8 0.11
47 28 0.38
48 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (47 bp):
ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATTAATT
Found at i:3397970 original size:44 final size:43
Alignment explanation
Indices: 3397828--3397970 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
3397818 GAATTTTATG
*
3397828 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATATTAATTATTTT
* ** * ** *
3397872 AAATTGTATAAATTCATATAAGAAAATT-TATTATTAAAAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAATATTAATTATT-TT
*
3397919 AAATTATATATTATTATTAAATTATATGTAATATTTATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATATTAATTATTTT
3397963 AAATTATA
1 AAATTATA
3397971 CAAATTCATA
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 10 0.14
46 9 0.12
47 15 0.20
48 3 0.04
49 6 0.08
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.50
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATATTAATTATTTT
Found at i:3398139 original size:120 final size:120
Alignment explanation
Indices: 3398011--3398303 Score: 457
Period size: 120 Copynumber: 2.4 Consensus size: 120
3398001 AATTATTTTA
* * *
3398011 AATTTTATTAAATCATATATTTTAATT-TAAATATATTTAATATTAATTAT-TTCAAGTTTTCT-
1 AATTTTATTAAATTATATATTTTAATTAT-AATATATTTAATAATAATTATGTT-AA-TTTTATA
*
3398073 TTTATAGTATCATATATTATGATTTGAATAAATTCATATAAGAATAATAATTATTAAG
63 TTTACAGTATCATATATTATGATTTGAATAAATTCATATAAGAATAATAATTATTAAG
*
3398131 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAGTTATGTTAATTTTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTTATATTT
* * *
3398196 ACAGTATCATATATTATGATTTGAGTAAATTCATGTAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAATAAATTCATATAAGAATAATAATTATTAAG
*
3398251 AATTTTATTAAATTATATAATTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
3398304 TAAATATGAT
Statistics
Matches: 160, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
119 5 0.03
120 152 0.95
121 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTTATATTT
ACAGTATCATATATTATGATTTGAATAAATTCATATAAGAATAATAATTATTAAG
Found at i:3398290 original size:15 final size:15
Alignment explanation
Indices: 3398256--3398297 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3398246 TTAAGAATTT
*
3398256 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3398270 -ATTTAATTATAATA
1 TATTTAATTATAATA
*
3398284 TATTTAATAATAAT
1 TATTTAATTATAAT
3398298 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 3 0.12
15 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:3398399 original size:155 final size:157
Alignment explanation
Indices: 3398240--3398554 Score: 571
Period size: 155 Copynumber: 2.0 Consensus size: 157
3398230 GTAAGAATAT
*
3398240 TAATTATTAAGAATTTTATTAAATTATATAATTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
*
3398305 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAAC-A
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
3398369 -AATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
*
3398395 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
3398460 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
3398525 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
3398552 TAA
1 TAA
3398555 GGGTATTCTA
Statistics
Matches: 153, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
155 125 0.82
156 1 0.01
157 27 0.18
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATAATTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:3398435 original size:18 final size:17
Alignment explanation
Indices: 3398407--3398441 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3398397 ATTATTAAGA
*
3398407 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3398424 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3398442 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3398690 original size:45 final size:44
Alignment explanation
Indices: 3398602--3398696 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 44
3398592 TTACACATCT
3398602 ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
*** *
3398646 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAGGA-TTACTATTACACCTCTATTCC
3398691 ATTACA
1 ATTACA
3398697 CCTCTAATCC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 20 0.43
45 26 0.57
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
Found at i:3398696 original size:16 final size:16
Alignment explanation
Indices: 3398677--3398728 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
3398667 GATTTGCTAT
* *
3398677 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
3398693 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3398709 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3398725 TACA
1 TACA
3398729 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:3399694 original size:22 final size:23
Alignment explanation
Indices: 3399669--3399714 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3399659 CAACCAAATC
*
3399669 AATTCA-ACATATTTTTAAGATA
1 AATTCATACATATTTATAAGATA
*
3399691 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3399714 A
1 A
3399715 CGTCATCACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3399720 original size:23 final size:23
Alignment explanation
Indices: 3399676--3399720 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3399666 ATCAATTCAA
* *
3399676 CATATTTTTAAGATAAATTCATG
1 CATATTTATAAGATAAAGTCATG
*
3399699 CATATTTATAAGATAACGTCAT
1 CATATTTATAAGATAAAGTCAT
3399721 CACATATCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (23 bp):
CATATTTATAAGATAAAGTCATG
Found at i:3402625 original size:42 final size:42
Alignment explanation
Indices: 3402562--3402688 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
3402552 CTTCGTTTTC
** * *
3402562 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
3402605 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
3402646 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
3402687 TC
1 TC
3402689 TCACTGATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.13
42 64 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:3402830 original size:31 final size:31
Alignment explanation
Indices: 3402795--3402943 Score: 235
Period size: 31 Copynumber: 4.8 Consensus size: 31
3402785 CTTGTCACTT
*
3402795 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
3402826 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
3402857 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
3402888 GTAGCAGAAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
3402919 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
3402944 TGTCATTTAT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 110 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:3403025 original size:50 final size:51
Alignment explanation
Indices: 3402919--3403047 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 51
3402909 CACTGATCAA
* * * *
3402919 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTATCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTATCATTGATCAGATAAAT
*
3402970 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAAT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTATCATTGATCAGATAAAT
*
3403020 GTAGCCAAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
3403048 TGCCATGGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 43 0.61
51 27 0.39
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTATCATTGATCAGATAAAT
Found at i:3406246 original size:41 final size:41
Alignment explanation
Indices: 3406200--3406300 Score: 184
Period size: 41 Copynumber: 2.5 Consensus size: 41
3406190 TATTCGGGAT
3406200 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTAAATCAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTAAATCAGGC
* *
3406241 TTATTGCCTAGCAAGCTTTGTGCCGGTGTATTATATCAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTAAATCAGGC
3406282 TTATTGCCTAGCAGGCTTT
1 TTATTGCCTAGCAGGCTTT
3406301 ATATGCCTGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.37
Consensus pattern (41 bp):
TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTAAATCAGGC
Found at i:3409550 original size:42 final size:41
Alignment explanation
Indices: 3409477--3409631 Score: 142
Period size: 42 Copynumber: 3.7 Consensus size: 41
3409467 CATAGTTCAA
*
3409477 CTATGGTCTTACACATCTTCACATAAT-GATGCCATTGCCCAG
1 CTATGGTCTTACACATATTCACAT-ATCGATGCCA-TGCCCAG
* *
3409519 CTATGGTCTTACACATATTCATATATCGATGCC---CCTAG
1 CTATGGTCTTACACATATTCACATATCGATGCCATGCCCAG
3409557 CTATGGTCTTACACGTAATCACATATCACATATCGATGCCATAGCCCAG
1 CTATGGTCTTACAC---AT---AT-TCACATATCGATGCCAT-GCCCAG
3409606 CTATGGTCTTACACGA-A-TCACATATC
1 CTATGGTCTTACAC-ATATTCACATATC
3409632 TCACTGATGC
Statistics
Matches: 95, Mismatches: 6, Indels: 25
0.75 0.05 0.20
Matches are distributed among these distances:
38 18 0.19
41 13 0.14
42 28 0.29
43 1 0.01
44 2 0.02
45 14 0.15
47 1 0.01
49 18 0.19
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (41 bp):
CTATGGTCTTACACATATTCACATATCGATGCCATGCCCAG
Found at i:3409773 original size:31 final size:31
Alignment explanation
Indices: 3409738--3409884 Score: 242
Period size: 31 Copynumber: 4.7 Consensus size: 31
3409728 CTTGTCACTT
*
3409738 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
3409769 GTAGCC-AGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
3409800 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
3409831 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
3409862 GTAGCCGAAGCTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
3409885 GTTGTCATTT
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
30 1 0.01
31 106 0.99
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:3414494 original size:23 final size:24
Alignment explanation
Indices: 3414456--3414500 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
3414446 GAGGATTTAT
3414456 AATATTCCGGGTGTGTTTGGGTTC
1 AATATTCCGGGTGTGTTTGGGTTC
*
3414480 AATATT-CTGGTGTGTTTGGGT
1 AATATTCCGGGTGTGTTTGGGT
3414501 GGAATCCGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.13, C:0.09, G:0.33, T:0.44
Consensus pattern (24 bp):
AATATTCCGGGTGTGTTTGGGTTC
Found at i:3415656 original size:11 final size:11
Alignment explanation
Indices: 3415640--3415665 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3415630 GGATATATAT
3415640 TTGGTTGTAAA
1 TTGGTTGTAAA
3415651 TTGGTTGTAAA
1 TTGGTTGTAAA
3415662 TTGG
1 TTGG
3415666 AAGTATCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (11 bp):
TTGGTTGTAAA
Found at i:3418358 original size:39 final size:39
Alignment explanation
Indices: 3418300--3418403 Score: 154
Period size: 39 Copynumber: 2.7 Consensus size: 39
3418290 TGGGGTTTCA
* * *
3418300 GTTTAGCTCTGATGAGCTTCAGTTAGCCTTCGGGCTTCC
1 GTTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTTCC
3418339 GTTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTTCC
1 GTTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTTCC
* * *
3418378 ATTTAGCACTTTTGTGTTTCAGTTAG
1 GTTTAGCACTTATGTGCTTCAGTTAG
3418404 ATTTCGGGTA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.40
Consensus pattern (39 bp):
GTTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTTCC
Done.