Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 14 of 24
Found at i:2844603 original size:22 final size:22
Alignment explanation
Indices: 2844578--2844626 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2844568 TTGAGTTTTT
2844578 TAATATTTTTAAATATTTCA-TA
1 TAATATTTTTAAAT-TTTCAGTA
*
2844600 TAATTTTTTTAAATTTTCAGTA
1 TAATATTTTTAAATTTTCAGTA
2844622 -AATAT
1 TAATAT
2844627 GAATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (22 bp):
TAATATTTTTAAATTTTCAGTA
Found at i:2847598 original size:22 final size:21
Alignment explanation
Indices: 2847558--2847606 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
2847548 TGTAATATTT
*
2847558 TTATATTTTAATATATTATAA
1 TTATATTTAAATATATTATAA
* *
2847579 TTATATTTAAAATATTTTATAT
1 TTATATTT-AAATATATTATAA
2847601 TTATAT
1 TTATAT
2847607 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATATTTAAATATATTATAA
Found at i:2847616 original size:18 final size:18
Alignment explanation
Indices: 2847579--2847661 Score: 70
Period size: 18 Copynumber: 4.8 Consensus size: 18
2847569 TATATTATAA
*
2847579 TTATATTTA-A-AATATT
1 TTATATTTATATAATTTT
2847595 TTATATTTATATAATTTT
1 TTATATTTATATAATTTT
2847613 TTATATATTA-ATAA-TTT
1 TTATAT-TTATATAATTTT
*
2847630 TTATA-ATATA-AATTTT
1 TTATATTTATATAATTTT
**
2847646 AAAATATTTATATAAT
1 -TTATATTTATATAAT
2847662 CGTAAATTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
15 4 0.07
16 13 0.24
17 12 0.22
18 19 0.35
19 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATATTTATATAATTTT
Found at i:2847621 original size:20 final size:18
Alignment explanation
Indices: 2847550--2847631 Score: 71
Period size: 18 Copynumber: 4.4 Consensus size: 18
2847540 ATTAGTTATG
*
2847550 TAATATTTTTATATTTTAA
1 TAAT-TTTTTATATATTAA
*
2847569 TATATTATAATTATAT-TTAA
1 TA-ATT-T-TTTATATATTAA
*
2847589 -AATATTTTATAT-TTATA
1 TAATTTTTTATATATTA-A
2847606 TAATTTTTTATATATTAA
1 TAATTTTTTATATATTAA
2847624 TAATTTTT
1 TAATTTTT
2847632 ATAATATAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
16 9 0.17
17 2 0.04
18 22 0.42
19 7 0.13
20 7 0.13
21 6 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TAATTTTTTATATATTAA
Found at i:2850002 original size:12 final size:12
Alignment explanation
Indices: 2849987--2850039 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
2849977 GATAATTTTA
2849987 TATTTATAATAT
1 TATTTATAATAT
*
2849999 TA-TTAAAATAT
1 TATTTATAATAT
* *
2850010 TAATTTATATTAA
1 T-ATTTATAATAT
2850023 TATTTATAATAT
1 TATTTATAATAT
2850035 TATTT
1 TATTT
2850040 TTATTATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 9 0.27
12 17 0.52
13 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTTATAATAT
Found at i:2850026 original size:24 final size:24
Alignment explanation
Indices: 2849987--2850045 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
2849977 GATAATTTTA
* *
2849987 TATTTATAATATTA-TTAAAATAT
1 TATTTATATTAATATTTAAAATAT
*
2850010 TAATTTATATTAATATTTATAATAT
1 T-ATTTATATTAATATTTAAAATAT
*
2850035 TATTTTTATTA
1 TATTTATATTA
2850046 TTAAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 1 0.03
24 20 0.67
25 9 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TATTTATATTAATATTTAAAATAT
Found at i:2850047 original size:12 final size:12
Alignment explanation
Indices: 2849987--2850048 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
2849977 GATAATTTTA
*
2849987 TATTTATAATAT
1 TATTTATATTAT
* *
2849999 TA-TTAAAATAT
1 TATTTATATTAT
*
2850010 TAATTTATATTAA
1 T-ATTTATATTAT
*
2850023 TATTTATAATAT
1 TATTTATATTAT
*
2850035 TATTTTTATTAT
1 TATTTATATTAT
2850047 TA
1 TA
2850049 AATAATAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 9 0.22
12 24 0.60
13 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTTATATTAT
Found at i:2850335 original size:2 final size:2
Alignment explanation
Indices: 2850328--2850367 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2850318 AGACTGATGT
2850328 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2850368 ATTACCCCTG
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):
GA
Found at i:2852622 original size:6 final size:6
Alignment explanation
Indices: 2852611--2852635 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2852601 CAGTACACAA
2852611 GGTGAT GGTGAT GGTGAT GGTGAT G
1 GGTGAT GGTGAT GGTGAT GGTGAT G
2852636 ATGGTGTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTGAT
Found at i:2857899 original size:67 final size:67
Alignment explanation
Indices: 2857789--2857914 Score: 234
Period size: 67 Copynumber: 1.9 Consensus size: 67
2857779 TTATACACTC
* *
2857789 TTCGAATAAGAATCTATTTTTTGAAAGATCCTGGCTTTTGTGCTTTGGTAAGTCTTCGAAAGGAC
1 TTCGAATAAGAATCTATTTTTTGAAAAATCCTGGCTTTCGTGCTTTGGTAAGTCTTCGAAAGGAC
2857854 TT
66 TT
2857856 TTCGAATAAGAATCTATTTTTTGAAAAATCCTGGCTTTCGTGCTTTGGTAAGTCTTCGA
1 TTCGAATAAGAATCTATTTTTTGAAAAATCCTGGCTTTCGTGCTTTGGTAAGTCTTCGA
2857915 GATCCTTTCG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (67 bp):
TTCGAATAAGAATCTATTTTTTGAAAAATCCTGGCTTTCGTGCTTTGGTAAGTCTTCGAAAGGAC
TT
Found at i:2858054 original size:18 final size:18
Alignment explanation
Indices: 2858031--2858081 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
2858021 AATTCTTTTC
2858031 TTTCTATTATATTAGTAT
1 TTTCTATTATATTAGTAT
*
2858049 TTTCTATTTTATT--TA-
1 TTTCTATTATATTAGTAT
*
2858064 TTT-TATTCTATTAGTAT
1 TTTCTATTATATTAGTAT
2858081 T
1 T
2858082 AGATTAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 8 0.29
15 3 0.11
16 4 0.14
17 1 0.04
18 12 0.43
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTCTATTATATTAGTAT
Found at i:2858083 original size:6 final size:6
Alignment explanation
Indices: 2858072--2858111 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
2858062 TATTTTATTC
*
2858072 TATTAG TATTAG -ATTAG TATTA- TATT-C TATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG T
2858112 TAGTGATCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
5 13 0.43
6 17 0.57
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (6 bp):
TATTAG
Found at i:2858092 original size:27 final size:26
Alignment explanation
Indices: 2858062--2858115 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 26
2858052 CTATTTTATT
*
2858062 TATTTTATTCTATTAGTATTAGATTAG
1 TATTATATTCTATTAGTATTAG-TTAG
2858089 TATTATATTCTATTAGTATTAGTTAG
1 TATTATATTCTATTAGTATTAGTTAG
2858115 T
1 T
2858116 GATCCCGGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.56
Consensus pattern (26 bp):
TATTATATTCTATTAGTATTAGTTAG
Found at i:2873507 original size:29 final size:29
Alignment explanation
Indices: 2873437--2873516 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
2873427 AATATGTAAC
* *
2873437 TTTTTATTAATGTATTATTT-TTGTATATAA
1 TTTTTATTAAT-TA-TATTTATTATACATAA
** *
2873467 TTTTTAAAAATTATATTTATTATACATGA
1 TTTTTATTAATTATATTTATTATACATAA
* *
2873496 TTTTTATTAATTTTTTTTATT
1 TTTTTATTAATTATATTTATT
2873517 TTTATACGTA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 5 0.12
29 26 0.65
30 9 0.22
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (29 bp):
TTTTTATTAATTATATTTATTATACATAA
Found at i:2873945 original size:24 final size:22
Alignment explanation
Indices: 2873910--2873967 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
2873900 AAAAAATATT
2873910 AAAAA-ATA-TTTTTATATTAA
1 AAAAATATATTTTTTATATTAA
* *
2873930 TAAATTATATATTTTTATAATTAA
1 AAAAATATAT-TTTTTAT-ATTAA
2873954 AAAAATATATTTTT
1 AAAAATATATTTTT
2873968 ATTATATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.10
21 3 0.10
23 11 0.37
24 13 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAAAATATATTTTTTATATTAA
Found at i:2873961 original size:22 final size:22
Alignment explanation
Indices: 2873909--2873969 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
2873899 TAAAAAATAT
2873909 TAAAAA-ATATTTTTATATTAA
1 TAAAAATATATTTTTATATTAA
*
2873930 TAAATTATATATTTTTATAATTAA
1 TAAA-AATATATTTTTAT-ATTAA
2873954 -AAAAATATATTTTTAT
1 TAAAAATATATTTTTAT
2873970 TATATAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 4 0.11
22 13 0.37
23 13 0.37
24 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAAAATATATTTTTATATTAA
Found at i:2878862 original size:2 final size:2
Alignment explanation
Indices: 2878855--2878879 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2878845 TTTCCTTTTA
2878855 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
2878880 ATGATCACAC
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:2888927 original size:20 final size:20
Alignment explanation
Indices: 2888902--2888940 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2888892 ATTAAATATA
2888902 AATTTATAATA-ATTTAAATT
1 AATTTA-AATATATTTAAATT
*
2888922 AATTTAATTATATTTAAAT
1 AATTTAAATATATTTAAAT
2888941 AATATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTAAATATATTTAAATT
Found at i:2888951 original size:30 final size:30
Alignment explanation
Indices: 2888903--2888998 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 30
2888893 TTAAATATAA
*
2888903 ATTTATAATAAT-TTAAATTAATTTAATTAT
1 ATTTA-AATAATATAAAATTAATTTAATTAT
2888933 ATTTAAATAATATAAAATTAAATTT--TTAT
1 ATTTAAATAATATAAAATT-AATTTAATTAT
2888962 ATTTTAAATAATA-AATAATT--TTTAAATTAT
1 A-TTTAAATAATATAA-AATTAATTT-AATTAT
2888992 A-TTAAAT
1 ATTTAAAT
2888999 CAAATCTGAA
Statistics
Matches: 58, Mismatches: 1, Indels: 16
0.77 0.01 0.21
Matches are distributed among these distances:
27 3 0.05
28 6 0.10
29 13 0.22
30 31 0.53
31 5 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTAAATAATATAAAATTAATTTAATTAT
Found at i:2889439 original size:20 final size:18
Alignment explanation
Indices: 2889414--2889466 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
2889404 AGTTAAATCA
2889414 AATTTAAGATTTAATTTTAT
1 AATTTAA-ATTTAATTTT-T
*
2889434 AATTTAATTTTTAAATTTTT
1 AATTTAA-ATTT-AATTTTT
2889454 -ATTTAAATTTAAT
1 AATTTAAATTTAAT
2889467 ATAAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.10
18 3 0.10
19 6 0.21
20 11 0.38
21 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
AATTTAAATTTAATTTTT
Found at i:2889450 original size:13 final size:13
Alignment explanation
Indices: 2889416--2889466 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
2889406 TTAAATCAAA
2889416 TTTAAGATTTAA-T
1 TTTAA-ATTTAATT
2889429 TTTATAATTTAATT
1 TTTA-AATTTAATT
2889443 TTTAAATTT--TT
1 TTTAAATTTAATT
2889454 ATTTAAATTTAAT
1 -TTTAAATTTAAT
2889467 ATAAAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.06
12 9 0.27
13 15 0.45
14 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TTTAAATTTAATT
Found at i:2890162 original size:20 final size:20
Alignment explanation
Indices: 2890138--2890189 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
2890128 TTATATCATT
2890138 TAAAATATATTTAAAAATAAA
1 TAAAATATATTTAAAAA-AAA
*
2890159 AAAAAT-TATTTAAAAAAAA
1 TAAAATATATTTAAAAAAAA
2890178 TTAAAATATATT
1 -TAAAATATATT
2890190 CTAGTTGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 15 0.56
21 9 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAATATATTTAAAAAAAA
Found at i:2890420 original size:2 final size:2
Alignment explanation
Indices: 2890403--2890436 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2890393 CAAATGAAAC
* *
2890403 TA TA TA TG TA TG 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
2890437 GGAGAATGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2891438 original size:19 final size:18
Alignment explanation
Indices: 2891391--2891440 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
2891381 AAATAAAAAA
*
2891391 TATTATATTATTCATGTT
1 TATTATATTATTCATATT
* *
2891409 TAAATAAATTATATCATATT
1 T-ATTATATTAT-TCATATT
2891429 TATTATATTATT
1 TATTATATTATT
2891441 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 2 0.08
19 16 0.64
20 7 0.28
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
TATTATATTATTCATATT
Found at i:2892243 original size:2 final size:2
Alignment explanation
Indices: 2892236--2892273 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2892226 TTTATTTCTC
2892236 AT AT AT AT A- AT -T 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
2892274 TGGTCCTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2896692 original size:2 final size:2
Alignment explanation
Indices: 2896685--2896714 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2896675 GACTAATGTG
2896685 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
2896715 GAAACATTAC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2902066 original size:17 final size:17
Alignment explanation
Indices: 2902042--2902078 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 17
2902032 ATATAATTTT
2902042 TAAAAAAATTTAAATATA
1 TAAAAAAA-TTAAATATA
2902060 TAAAAAAATTAAATATA
1 TAAAAAAATTAAATATA
2902077 TA
1 TA
2902079 TTTTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAAAATTAAATATA
Found at i:2902079 original size:19 final size:18
Alignment explanation
Indices: 2902042--2902078 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2902032 ATATAATTTT
*
2902042 TAAAAAAATTTAAATATA
1 TAAAAAAATTAAAATATA
2902060 TAAAAAAATT-AAATATA
1 TAAAAAAATTAAAATATA
2902077 TA
1 TA
2902079 TTTTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAAAATTAAAATATA
Found at i:2902107 original size:17 final size:17
Alignment explanation
Indices: 2902049--2902107 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
2902039 TTTTAAAAAA
* *
2902049 ATTTAAATATATAAAAA
1 ATTTAAATATATAATAT
* * *
2902066 AATTAAATATATATTTTT
1 ATTTAAATATATA-ATAT
2902084 ATATTAAATATATAATAT
1 AT-TTAAATATATAATAT
2902102 ATTTAA
1 ATTTAA
2902108 TTTTCAAACC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 16 0.50
18 5 0.16
19 11 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTAAATATATAATAT
Found at i:2903008 original size:20 final size:19
Alignment explanation
Indices: 2902954--2903008 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2902944 AAATCGATTT
*
2902954 AATTTAATAAAAAATTTTA
1 AATTTAATAAAAAATTATA
*
2902973 AATTTAATTACAAAATTATA
1 AATTTAA-TAAAAAATTATA
*
2902993 AATATTAATATAAAAT
1 AAT-TTAATAAAAAAT
2903009 ATATTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.23
20 20 0.65
21 4 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTTAATAAAAAATTATA
Found at i:2908503 original size:30 final size:29
Alignment explanation
Indices: 2908469--2908542 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
2908459 TGGATTAAAT
**
2908469 TTTAAATTAATTTAAAAAT-TTATTGTATTA
1 TTTAAATTAATAAAAAAATATT-TT-TATTA
*
2908499 TTTAAAATAATAAAAAAATATTTTTATTA
1 TTTAAATTAATAAAAAAATATTTTTATTA
2908528 TTTAAATTAAATAAA
1 TTTAAATT-AATAAA
2908543 TTTGAATTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 12 0.32
30 24 0.63
31 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
TTTAAATTAATAAAAAAATATTTTTATTA
Found at i:2908514 original size:28 final size:30
Alignment explanation
Indices: 2908482--2908542 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
2908472 AAATTAATTT
*
2908482 AAAAATTTATTGTATTATTTAAAAT-AATAA
1 AAAAATAT-TTGTATTATTTAAAATAAATAA
* *
2908512 AAAAATATTTTTATTATTTAAATTAAATAA
1 AAAAATATTTGTATTATTTAAAATAAATAA
2908542 A
1 A
2908543 TTTGAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
AAAAATATTTGTATTATTTAAAATAAATAA
Found at i:2909179 original size:2 final size:2
Alignment explanation
Indices: 2909174--2909203 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2909164 TTGTAAAAAA
*
2909174 AT AT AT AT TT 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
2909204 TTACATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2916380 original size:17 final size:15
Alignment explanation
Indices: 2916347--2916377 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2916337 TATTTTTTTT
2916347 ATTTTTTAAATTAAA
1 ATTTTTTAAATTAAA
*
2916362 ATTTTTTATATTAAA
1 ATTTTTTAAATTAAA
2916377 A
1 A
2916378 AATATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTTTAAATTAAA
Found at i:2916380 original size:23 final size:24
Alignment explanation
Indices: 2916354--2916409 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
2916344 TTTATTTTTT
* *
2916354 AAATTAAAAT-TTTTTATATTAAA
1 AAATTAAAATATTTATATACTAAA
2916377 AAA-TATAAATATTTATATACTAAA
1 AAATTA-AAATATTTATATACTAAA
*
2916401 AATTTAAAA
1 AAATTAAAA
2916410 GAATAAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 2 0.07
23 7 0.26
24 16 0.59
25 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
AAATTAAAATATTTATATACTAAA
Found at i:2917080 original size:34 final size:33
Alignment explanation
Indices: 2917011--2917084 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 33
2917001 ATTTTTTAAA
2917011 AAATTT-AAAAAATATATTATATTTTAATAATT
1 AAATTTAAAAAAATATATTATATTTTAATAATT
*
2917043 AAATTTAAATAAAATA-ATTTTATTATTAAATAA-T
1 AAATTTAAA-AAAATATATTATATT-TT-AATAATT
2917077 AAATTTAA
1 AAATTTAA
2917085 TCGATCTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
32 6 0.16
33 9 0.24
34 17 0.46
35 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AAATTTAAAAAAATATATTATATTTTAATAATT
Found at i:2918651 original size:2 final size:2
Alignment explanation
Indices: 2918644--2918680 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2918634 CAACTGGTAC
2918644 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
2918681 ACTCTTTTCA
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:2922851 original size:2 final size:2
Alignment explanation
Indices: 2922844--2922882 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2922834 TGCATGAAAA
* * *
2922844 AG AG AG AG AC AC AA 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 AG AG AG AG A
2922883 AGAAACTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.54, C:0.05, G:0.41, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2924709 original size:20 final size:19
Alignment explanation
Indices: 2924679--2924743 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 19
2924669 CAATAATTTA
2924679 TAAATAAATATTCAAAAAAAT
1 TAAA-AAATATT-AAAAAAAT
*
2924700 TAAAAAATATTAATTAAAAAA
1 TAAAAAATATTAA--AAAAAT
*
2924721 T-ATAAATATTAAAAAAAAT
1 TAAAAAATATT-AAAAAAAT
2924740 TAAA
1 TAAA
2924744 TATATAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
19 8 0.22
20 16 0.44
21 12 0.33
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAAAATATTAAAAAAAT
Found at i:2924731 original size:16 final size:16
Alignment explanation
Indices: 2924698--2924746 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 16
2924688 ATTCAAAAAA
*
2924698 ATTAAAAAATAT-TA-
1 ATTAAAAAATATAAAT
2924712 ATTAAAAAATATAAAT
1 ATTAAAAAATATAAAT
*
2924728 ATTAAAAAAAATTAAAT
1 ATTAAAAAATA-TAAAT
2924745 AT
1 AT
2924747 ATAATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 12 0.40
15 1 0.03
16 10 0.33
17 7 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTAAAAAATATAAAT
Found at i:2924766 original size:26 final size:26
Alignment explanation
Indices: 2924704--2924766 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
2924694 AAAAATTAAA
2924704 AAATATTAATTAAAAAATATAAATATT
1 AAATA-TAATTAAAAAATATAAATATT
* * * *
2924731 AAAAAAAATT-AAATATATAATATTTT
1 AAATATAATTAAAAAATATAA-ATATT
2924757 AAATATAATT
1 AAATATAATT
2924767 TACTGTTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 9 0.31
26 16 0.55
27 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATATAATTAAAAAATATAAATATT
Found at i:2925641 original size:18 final size:20
Alignment explanation
Indices: 2925604--2925642 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2925594 GTGCAAGTTG
2925604 GGTGCGGGAAGCACGTGAGA
1 GGTGCGGGAAGCACGTGAGA
2925624 GGTGCGGGAA-CA-GTGAGA
1 GGTGCGGGAAGCACGTGAGA
2925642 G
1 G
2925643 CTGATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 10 0.53
ACGTcount: A:0.26, C:0.13, G:0.51, T:0.10
Consensus pattern (20 bp):
GGTGCGGGAAGCACGTGAGA
Found at i:2927238 original size:24 final size:24
Alignment explanation
Indices: 2927211--2927272 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
2927201 CATAAAAAAA
* *
2927211 ATTATAAATGATAATTTTAAA-ATT
1 ATTATAAATTATAA-TTAAAATATT
2927235 ATTA-AATATTATAATTAAAATATT
1 ATTATAA-ATTATAATTAAAATATT
*
2927259 ATTATTAATTATAA
1 ATTATAAATTATAA
2927273 AAAATTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 7 0.22
24 24 0.75
25 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTATAAATTATAATTAAAATATT
Found at i:2927407 original size:25 final size:26
Alignment explanation
Indices: 2927374--2927425 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
2927364 TTATAAAATT
* *
2927374 AAAAATTATATCATTAATAT-ATTAA
1 AAAAATTATATAATTAAAATAATTAA
2927399 AAAAATTATATAATTAAAATAATTAA
1 AAAAATTATATAATTAAAATAATTAA
2927425 A
1 A
2927426 TATTAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAAATTATATAATTAAAATAATTAA
Found at i:2927414 original size:17 final size:16
Alignment explanation
Indices: 2927390--2927432 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
2927380 TATATCATTA
2927390 ATATATTAAAAAAATT
1 ATATATTAAAAAAATT
*
2927406 ATATAATTAAAATAATT
1 ATAT-ATTAAAAAAATT
*
2927423 AAATATTAAA
1 ATATATTAAA
2927433 TAACTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATATTAAAAAAATT
Found at i:2928158 original size:21 final size:19
Alignment explanation
Indices: 2928116--2928159 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
2928106 ATTTATTAAA
* *
2928116 ATTTAAAATTCTATATTAT
1 ATTTAAAATTCGATACTAT
2928135 ATTTAAAATTACGATAACTAT
1 ATTTAAAATT-CGAT-ACTAT
2928156 ATTT
1 ATTT
2928160 TTTATAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 8 0.38
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (19 bp):
ATTTAAAATTCGATACTAT
Found at i:2928335 original size:16 final size:16
Alignment explanation
Indices: 2928309--2928346 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2928299 TAATTAATTT
2928309 ATATAATTATTTTAAAA
1 ATAT-ATTATTTTAAAA
*
2928326 ATATATTATTTTATAA
1 ATATATTATTTTAAAA
2928342 ATATA
1 ATATA
2928347 AAATTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATATTATTTTAAAA
Found at i:2928352 original size:16 final size:16
Alignment explanation
Indices: 2928317--2928355 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2928307 TTATATAATT
**
2928317 ATTTTAAAAATATATT
1 ATTTTAAAAATATAAA
*
2928333 ATTTTATAAATATAAA
1 ATTTTAAAAATATAAA
2928349 ATTTTAA
1 ATTTTAA
2928356 TTTTAATATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTTAAAAATATAAA
Found at i:2928993 original size:2 final size:2
Alignment explanation
Indices: 2928986--2929012 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2928976 GCCCAATACC
2928986 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 A
2929013 CAGTGCTGGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2935944 original size:3 final size:3
Alignment explanation
Indices: 2935936--2935978 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
2935926 CGTATTGTTT
* * *
2935936 TTA TTA TTA TTA TTA TTA TTT TTA TTAA TTT TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
2935979 GTGCTTTTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2936578 original size:20 final size:21
Alignment explanation
Indices: 2936553--2936602 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
2936543 TTACGAAAAT
*
2936553 AATTTATATTAATAT-ATTAA
1 AATTTATATTAATATAAATAA
*
2936573 AATTTAT-GTAATATAAATAA
1 AATTTATATTAATATAAATAA
*
2936593 AATTAATATT
1 AATTTATATT
2936603 TTATATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.25
20 17 0.71
21 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
AATTTATATTAATATAAATAA
Found at i:2942371 original size:2 final size:2
Alignment explanation
Indices: 2942366--2942390 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2942356 TGTATTTTTT
2942366 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
2942391 TTGTTTAGTA
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:2943326 original size:2 final size:2
Alignment explanation
Indices: 2943321--2943361 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2943311 AAAAAGTGTG
*
2943321 TA TA TA TA TA TA TA -A AA 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
2943362 AATAAATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2943688 original size:2 final size:2
Alignment explanation
Indices: 2943681--2943723 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2943671 TGTAGAATTT
2943681 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
2943723 T
1 T
2943724 CAGTTCAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2945791 original size:17 final size:16
Alignment explanation
Indices: 2945769--2945812 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
2945759 TTAGAGATGC
2945769 AATTATATTTTTATTTT
1 AATTATATTTTTA-TTT
2945786 AATTATATTATTTATTT
1 AATTATATT-TTTATTT
*
2945803 ATTTATATTT
1 AATTATATTT
2945813 AATTCGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 1 0.04
17 20 0.80
18 4 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTATATTTTTATTT
Found at i:2949020 original size:37 final size:38
Alignment explanation
Indices: 2948951--2949024 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
2948941 CTAGAGCTGA
2948951 AAGCAAATAGAAACAATCAAAAGTTAACAAAATGGGCG
1 AAGCAAATAGAAACAATCAAAAGTTAACAAAATGGGCG
* *
2948989 AAGCAAATAGAAA-AATGATAAGTTAACAAAATGGGC
1 AAGCAAATAGAAACAATCAAAAGTTAACAAAATGGGC
2949025 TAAAGAGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 21 0.62
38 13 0.38
ACGTcount: A:0.55, C:0.11, G:0.19, T:0.15
Consensus pattern (38 bp):
AAGCAAATAGAAACAATCAAAAGTTAACAAAATGGGCG
Found at i:2951245 original size:24 final size:24
Alignment explanation
Indices: 2951217--2951266 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2951207 AAGAGCTATC
2951217 ATTAAACAAATATCAGATTTAAAT
1 ATTAAACAAATATCAGATTTAAAT
2951241 ATTAAACAAATATCAGATTTAAAT
1 ATTAAACAAATATCAGATTTAAAT
2951265 AT
1 AT
2951267 AAGTGTACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (24 bp):
ATTAAACAAATATCAGATTTAAAT
Found at i:2953114 original size:24 final size:25
Alignment explanation
Indices: 2953087--2953134 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2953077 CAAGTGTTCA
2953087 ATTGT-GATAAAAAAGTAATATGAG
1 ATTGTGGATAAAAAAGTAATATGAG
* *
2953111 ATTGTGGTTAAATAAGTAATATGA
1 ATTGTGGATAAAAAAGTAATATGA
2953135 TTTTAAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (25 bp):
ATTGTGGATAAAAAAGTAATATGAG
Found at i:2960509 original size:7 final size:7
Alignment explanation
Indices: 2960479--2960522 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
2960469 TTTTAAAAAG
2960479 TAATATT
1 TAATATT
2960486 TAATAAATT
1 TAAT--ATT
2960495 TAA-A-T
1 TAATATT
2960500 TAATATT
1 TAATATT
2960507 TAATATT
1 TAATATT
2960514 TAATATT
1 TAATATT
2960521 TA
1 TA
2960523 TAACTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.12
6 2 0.06
7 21 0.64
9 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAATATT
Found at i:2961127 original size:33 final size:33
Alignment explanation
Indices: 2961085--2961151 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
2961075 ATAAAAGGAG
* *
2961085 ACTGGAGGCATCTTACTAACTCTTGTAGGTTGC
1 ACTGGAGGCATCTCACTAACTCTTGTAGCTTGC
*
2961118 ACTGGAGGCATCTCACTGACTCTTGTAGCTTGC
1 ACTGGAGGCATCTCACTAACTCTTGTAGCTTGC
2961151 A
1 A
2961152 GTAGCCAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (33 bp):
ACTGGAGGCATCTCACTAACTCTTGTAGCTTGC
Found at i:2961673 original size:2 final size:2
Alignment explanation
Indices: 2961666--2961694 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2961656 AAAACGAGGA
2961666 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
2961695 GGTTTAACAT
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:2966070 original size:22 final size:22
Alignment explanation
Indices: 2966044--2966090 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2966034 TTTCGATTTA
*
2966044 AATATTAACA-AATAAATAATAT
1 AATA-TAACATAATAAAAAATAT
*
2966066 AATATAATATAATAAAAAATAT
1 AATATAACATAATAAAAAATAT
2966088 AAT
1 AAT
2966091 TATATCTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AATATAACATAATAAAAAATAT
Found at i:2967178 original size:2 final size:2
Alignment explanation
Indices: 2967168--2967202 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2967158 ATATAACAAA
2967168 AT AT A- 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
2967203 GAAGAGACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2967534 original size:22 final size:21
Alignment explanation
Indices: 2967504--2967561 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
2967494 ATTTTATATT
* *
2967504 TATAATTATATTTAAAATATCA
1 TATATTTATA-TTAAAATATAA
* *
2967526 TATATTTATA-TAAATTTTAA
1 TATATTTATATTAAAATATAA
2967546 TATATTTATATATAAA
1 TATATTTATAT-TAAA
2967562 TTATTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 17 0.57
22 13 0.43
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATTTATATTAAAATATAA
Found at i:2967891 original size:101 final size:104
Alignment explanation
Indices: 2967719--2967925 Score: 312
Period size: 101 Copynumber: 2.0 Consensus size: 104
2967709 CGAAAATGAG
* * **
2967719 GAGTAAGCAAATCATCTTACTAAAGCTCGTTCAGTAAATTTTAATGTTTAGAAAAAAAAAGTAAT
1 GAGTAAGCAAATCATCTTACGAAAGCTCGTTAAGTAAATTTTAATGTTTAGAAAAAAAAACAAAT
2967784 --AAAAT-AATAAATAAAAGGGCCCCATAAAATCAATTC
66 AAAAAATAAATAAATAAAAGGGCCCCATAAAATCAATTC
* *
2967820 GAGTAAGCAAATCATCTTACGAAATCTCGTTAAGTATATTTTAATGTTTAGAAAAAAAAACAAAT
1 GAGTAAGCAAATCATCTTACGAAAGCTCGTTAAGTAAATTTTAATGTTTAGAAAAAAAAACAAA-
*
2967885 GTAATAAATAAATAAATAAAAGGGCCCCATAAAATCAATTC
65 -TAAAAAATAAATAAATAAAAGGGCCCCATAAAATCAATTC
2967926 TCTCTTCTCT
Statistics
Matches: 94, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
101 58 0.62
103 1 0.01
105 4 0.04
106 31 0.33
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.27
Consensus pattern (104 bp):
GAGTAAGCAAATCATCTTACGAAAGCTCGTTAAGTAAATTTTAATGTTTAGAAAAAAAAACAAAT
AAAAAATAAATAAATAAAAGGGCCCCATAAAATCAATTC
Found at i:2971912 original size:3 final size:3
Alignment explanation
Indices: 2971904--2971940 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2971894 ATATATGTAT
*
2971904 TTA TTA TTA TTA TTA TTA TTA TTA TGA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2971941 TTGAGTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2974090 original size:34 final size:34
Alignment explanation
Indices: 2974044--2974261 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
2974034 GTAAAAACCA
*
2974044 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2974078 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
2974112 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
2974146 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2974179 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
2974213 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2974246 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2974262 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2974158 original size:68 final size:67
Alignment explanation
Indices: 2974042--2974261 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
2974032 TGGTAAAAAC
* * *
2974042 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
2974107 AT
66 AT
* * *
2974109 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
2974174 AAT
65 AAT
* * * * * *
2974177 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
2974242 AT
66 AT
2974244 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
2974262 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:2978354 original size:19 final size:19
Alignment explanation
Indices: 2978327--2978389 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2978317 TCACGTGTAC
* *
2978327 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
2978346 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
2978365 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
2978384 AGTACC
1 AGTACC
2978390 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:2978740 original size:34 final size:34
Alignment explanation
Indices: 2978694--2978876 Score: 246
Period size: 34 Copynumber: 5.4 Consensus size: 34
2978684 GTAAAAACCA
*
2978694 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2978728 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
2978762 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
2978796 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2978829 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
2978863 CCATTTAATCAACA
1 CCATTTAATCAACA
2978877 TTTTGTACTT
Statistics
Matches: 132, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
33 26 0.20
34 104 0.79
35 2 0.02
ACGTcount: A:0.39, C:0.28, G:0.08, T:0.24
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2978870 original size:101 final size:102
Alignment explanation
Indices: 2978694--2978876 Score: 323
Period size: 101 Copynumber: 1.8 Consensus size: 102
2978684 GTAAAAACCA
* *
2978694 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAAT
2978759 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
66 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
* *
2978796 CCATTTAATCAACAATGGTAAGCTACCAAATCT-CCATTTAGTCAACAATGGCAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAAT
2978860 CACCCATTTAATCAACA
66 CACCCATTTAATCAACA
2978877 TTTTGTACTT
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 46 0.60
102 31 0.40
ACGTcount: A:0.39, C:0.28, G:0.08, T:0.24
Consensus pattern (102 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAAT
CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
Found at i:2982754 original size:6 final size:6
Alignment explanation
Indices: 2982743--2982773 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2982733 CATCTTAGCT
2982743 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
2982774 AAAAGAGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.35, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:2988849 original size:27 final size:26
Alignment explanation
Indices: 2988793--2988853 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
2988783 GTGATATTAT
*
2988793 TTAATTTTTTAAATATTATATTTAAG
1 TTAATTTTTTAAATATTATAATTAAG
**
2988819 TTAAATTTTTTATTTATTATTAATTAA-
1 TT-AATTTTTTAAATATTA-TAATTAAG
2988846 TTAATTTT
1 TTAATTTT
2988854 AAATAAGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 8 0.27
27 16 0.53
28 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TTAATTTTTTAAATATTATAATTAAG
Found at i:2990787 original size:3 final size:3
Alignment explanation
Indices: 2990779--2990825 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
2990769 GCTAGATGGC
* *
2990779 TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT AAT AAT TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT
2990826 ATTTTGTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2992493 original size:12 final size:12
Alignment explanation
Indices: 2992462--2992495 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2992452 ATCATATATC
*
2992462 ATAATAACTATG
1 ATAATAATTATG
2992474 ATAA-AATTATG
1 ATAATAATTATG
2992485 ATAATAATTAT
1 ATAATAATTAT
2992496 TATGTCTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (12 bp):
ATAATAATTATG
Found at i:2994427 original size:27 final size:27
Alignment explanation
Indices: 2994387--2994562 Score: 95
Period size: 27 Copynumber: 6.5 Consensus size: 27
2994377 TATATATCTA
2994387 ATAATATTAAATATTAT-TATATAAAT
1 ATAATATTAAATATTATATATATAAAT
*
2994413 ATAATATTAACATA-TATATATATATAT
1 ATAATATTAA-ATATTATATATATAAAT
* * *
2994440 ATAATAATAAAATATAATATA-ACAAA-
1 ATAAT-ATTAAATATTATATATATAAAT
*
2994466 ATATATTTTAAA-ATTAATATAATATAAATT
1 ATA-ATATTAAATATT-ATAT-ATATAAA-T
*
2994496 CTTAATCTATTAAA-A-T-T-TATATAAAT
1 -ATAA--TATTAAATATTATATATATAAAT
* *
2994522 ATAATA-TAATATAATTAAAATATATTAAT
1 ATAATATTAA-AT-ATT-ATATATATAAAT
2994551 ATAATA-TAAATA
1 ATAATATTAAATA
2994563 GATAAACTAG
Statistics
Matches: 116, Mismatches: 14, Indels: 39
0.69 0.08 0.23
Matches are distributed among these distances:
22 3 0.03
23 3 0.03
25 6 0.05
26 26 0.22
27 33 0.28
28 16 0.14
29 18 0.16
30 1 0.01
31 3 0.03
32 7 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
ATAATATTAAATATTATATATATAAAT
Found at i:2994461 original size:15 final size:15
Alignment explanation
Indices: 2994443--2994568 Score: 70
Period size: 15 Copynumber: 8.5 Consensus size: 15
2994433 TATATATATA
2994443 ATAATAAAATATAAT
1 ATAATAAAATATAAT
*
2994458 ATAACAAAATAT-AT
1 ATAATAAAATATAAT
*
2994472 -T-TTAAAAT-TAAT
1 ATAATAAAATATAAT
*
2994484 ATAATATAAATTCTTAAT
1 ATAATA-AAA-T-ATAAT
* * *
2994502 CTATTAAAAT-TTAT
1 ATAATAAAATATAAT
*
2994516 ATAAATATAATATAAT
1 AT-AATAAAATATAAT
2994532 ATAATTAAAATAT-AT
1 ATAA-TAAAATATAAT
*
2994547 -TAATATAATATAA-
1 ATAATAAAATATAAT
2994560 ATAGATAAA
1 ATA-ATAAA
2994569 CTAGTAAATA
Statistics
Matches: 84, Mismatches: 14, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
11 1 0.01
12 7 0.08
13 9 0.11
14 14 0.17
15 28 0.33
16 14 0.17
17 3 0.04
18 8 0.10
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (15 bp):
ATAATAAAATATAAT
Found at i:2994532 original size:10 final size:10
Alignment explanation
Indices: 2994514--2994559 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
2994504 ATTAAAATTT
2994514 ATATAAATATA
1 ATAT-AATATA
2994525 ATATAATATA
1 ATATAATATA
*
2994535 AT-TAAAAT-
1 ATATAATATA
2994543 ATATTAATATA
1 ATA-TAATATA
2994554 ATATAA
1 ATATAA
2994560 ATAGATAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
8 2 0.07
9 5 0.17
10 16 0.53
11 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATAATATA
Found at i:2994985 original size:13 final size:13
Alignment explanation
Indices: 2994967--2994991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2994957 ATAATTAAAT
2994967 TTATTTTTATATA
1 TTATTTTTATATA
2994980 TTATTTTTATAT
1 TTATTTTTATAT
2994992 TCATTATATT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTTTATATA
Found at i:2995003 original size:15 final size:14
Alignment explanation
Indices: 2994967--2995014 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
2994957 ATAATTAAAT
*
2994967 TTATTTTTATA-TA
1 TTATATTTATATTA
*
2994980 TTATTTTTATATTCA
1 TTATATTTATATT-A
*
2994995 TTATATTTATTTTA
1 TTATATTTATATTA
2995009 TTATAT
1 TTATAT
2995015 ATAAAATTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 11 0.35
14 8 0.26
15 12 0.39
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATATTTATATTA
Found at i:2995014 original size:34 final size:33
Alignment explanation
Indices: 2994942--2995016 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
2994932 TATTTTTATA
2994942 ATATATTATGTTAATATAATTAAATTTATTTTT
1 ATATATTATGTTAATATAATTAAATTTATTTTT
* * * *
2994975 ATATATTATTTTTATATTCATTATATTTATTTTATT
1 ATATATTATGTTAATA-TAATTAAATTTA-TTT-TT
2995011 ATATAT
1 ATATAT
2995017 AAAATTACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 14 0.40
34 10 0.29
35 3 0.09
36 8 0.23
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (33 bp):
ATATATTATGTTAATATAATTAAATTTATTTTT
Found at i:2999056 original size:25 final size:24
Alignment explanation
Indices: 2999010--2999057 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2999000 TAAAATATCG
* *
2999010 TAAAAAGTTATATTTTTTATTAAT
1 TAAAAAGTTATATTTATAATTAAT
*
2999034 TAAAAAGTTATCTCTTATAATTAA
1 TAAAAAGTTATAT-TTATAATTAA
2999058 GAGTGTGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (24 bp):
TAAAAAGTTATATTTATAATTAAT
Found at i:3003532 original size:23 final size:25
Alignment explanation
Indices: 3003501--3003548 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
3003491 TACAAGTTAA
*
3003501 AAATTTAATTA-AAATAT-TATATT
1 AAATATAATTATAAATATATATATT
*
3003524 AAATATAATTATATATATATATATT
1 AAATATAATTATAAATATATATATT
3003549 GGAACCTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 5 0.24
25 6 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATATAATTATAAATATATATATT
Found at i:3004720 original size:2 final size:2
Alignment explanation
Indices: 3004708--3004745 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3004698 TGGTATACAC
*
3004708 AT AT TT 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
3004746 GTGGATTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3006654 original size:16 final size:16
Alignment explanation
Indices: 3006629--3006662 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3006619 TATGATTGTT
3006629 AAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAC
* *
3006645 AAAAACAAAACAAAAC
1 AAAAAAAAAAAAAAAC
3006661 AA
1 AA
3006663 GACAGAAGAC
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:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAC
Found at i:3008221 original size:33 final size:33
Alignment explanation
Indices: 3008184--3008257 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
3008174 TATGACAACA
3008184 ATAATATAAAAATAAAAATATATTAAAATTTAT
1 ATAATATAAAAATAAAAATATATTAAAATTTAT
* ** *
3008217 ATAATAT-AAATTATTATTATATTAAAATTTAT
1 ATAATATAAAAATAAAAATATATTAAAATTTAT
3008249 ATAAATATA
1 AT-AATATA
3008258 TTATTTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 23 0.66
33 12 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
ATAATATAAAAATAAAAATATATTAAAATTTAT
Found at i:3008223 original size:17 final size:17
Alignment explanation
Indices: 3008203--3008252 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
3008193 AAATAAAAAT
3008203 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
*
3008220 ATA-T-AAA-TTATTATT
1 ATATTAAAATTTA-TATA
3008235 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
3008252 A
1 A
3008253 ATATATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.11
15 9 0.33
16 2 0.07
17 10 0.37
18 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:3008243 original size:32 final size:31
Alignment explanation
Indices: 3008202--3008262 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 31
3008192 AAAATAAAAA
3008202 TATATTAAAATTTATATAATATAAATTATTAT
1 TATATTAAAATTTATATAA-ATAAATTATTAT
*
3008234 TATATTAAAATTTATATAAATATATTATT
1 TATATTAAAATTTATATAAATAAATTATT
3008263 TTAAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 9 0.32
32 19 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TATATTAAAATTTATATAAATAAATTATTAT
Found at i:3008528 original size:4 final size:4
Alignment explanation
Indices: 3008519--3008543 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3008509 AACTATGTAA
3008519 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
3008544 CTCTCCGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:3008753 original size:15 final size:15
Alignment explanation
Indices: 3008729--3008769 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
3008719 AATATAATAT
3008729 AAAAAT-AATAATTA
1 AAAAATAAATAATTA
*
3008743 AAAAATAAATACTTA
1 AAAAATAAATAATTA
*
3008758 AAAAATATATAA
1 AAAAATAAATAA
3008770 ATATATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAATAAATAATTA
Found at i:3009810 original size:2 final size:2
Alignment explanation
Indices: 3009803--3009842 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3009793 GGGAGACATG
3009803 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3009843 GAAAAGGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3015476 original size:219 final size:219
Alignment explanation
Indices: 3015097--3015522 Score: 852
Period size: 219 Copynumber: 1.9 Consensus size: 219
3015087 TATTATGCAA
3015097 CTTCATCTAAAGATAATTAGATGTTTTTGAATTTTGATTAGGACTATTTGGGTAAGACTTATGTC
1 CTTCATCTAAAGATAATTAGATGTTTTTGAATTTTGATTAGGACTATTTGGGTAAGACTTATGTC
3015162 AAGATCTTTTGTTGTTCTGTGTTATTTTTTGTGTCCATTGGTAATAAGGTGTAGGTGATACAATA
66 AAGATCTTTTGTTGTTCTGTGTTATTTTTTGTGTCCATTGGTAATAAGGTGTAGGTGATACAATA
3015227 TCAAATCCTTAATCCCTCTCGTTCTAGGTTTAGGATGCAATTCATCCAGTAGAACCTTAAACCTC
131 TCAAATCCTTAATCCCTCTCGTTCTAGGTTTAGGATGCAATTCATCCAGTAGAACCTTAAACCTC
3015292 ATTGCAGATTATTTGTTGATCTTT
196 ATTGCAGATTATTTGTTGATCTTT
3015316 CTTCATCTAAAGATAATTAGATGTTTTTGAATTTTGATTAGGACTATTTGGGTAAGACTTATGTC
1 CTTCATCTAAAGATAATTAGATGTTTTTGAATTTTGATTAGGACTATTTGGGTAAGACTTATGTC
3015381 AAGATCTTTTGTTGTTCTGTGTTATTTTTTGTGTCCATTGGTAATAAGGTGTAGGTGATACAATA
66 AAGATCTTTTGTTGTTCTGTGTTATTTTTTGTGTCCATTGGTAATAAGGTGTAGGTGATACAATA
3015446 TCAAATCCTTAATCCCTCTCGTTCTAGGTTTAGGATGCAATTCATCCAGTAGAACCTTAAACCTC
131 TCAAATCCTTAATCCCTCTCGTTCTAGGTTTAGGATGCAATTCATCCAGTAGAACCTTAAACCTC
3015511 ATTGCAGATTAT
196 ATTGCAGATTAT
3015523 AAATTCGAGA
Statistics
Matches: 207, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
219 207 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (219 bp):
CTTCATCTAAAGATAATTAGATGTTTTTGAATTTTGATTAGGACTATTTGGGTAAGACTTATGTC
AAGATCTTTTGTTGTTCTGTGTTATTTTTTGTGTCCATTGGTAATAAGGTGTAGGTGATACAATA
TCAAATCCTTAATCCCTCTCGTTCTAGGTTTAGGATGCAATTCATCCAGTAGAACCTTAAACCTC
ATTGCAGATTATTTGTTGATCTTT
Found at i:3016826 original size:1 final size:1
Alignment explanation
Indices: 3016815--3016845 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
3016805 CCAGCTCTTG
*
3016815 CCCCCCTCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
3016846 TTTCAATGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:3020267 original size:15 final size:14
Alignment explanation
Indices: 3020240--3020274 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
3020230 TGGCTGAAGC
3020240 TCTTCCTTCTCTTCA
1 TCTT-CTTCTCTTCA
3020255 TCTTCTTCTTCTTCA
1 TCTTCTTC-TCTTCA
3020270 TCTTC
1 TCTTC
3020275 CTTGCCATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.06, C:0.37, G:0.00, T:0.57
Consensus pattern (14 bp):
TCTTCTTCTCTTCA
Found at i:3021560 original size:20 final size:20
Alignment explanation
Indices: 3021537--3021590 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
3021527 TTTTAAATAA
3021537 AATTTTTATTAATTAAAAAT
1 AATTTTTATTAATTAAAAAT
* *
3021557 AA-TTTAATTTATTTAAAAAT
1 AATTTTTA-TTAATTAAAAAT
* *
3021577 AATATTTAATAATT
1 AATTTTTATTAATT
3021591 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
19 4 0.15
20 19 0.73
21 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTTTATTAATTAAAAAT
Found at i:3021831 original size:24 final size:25
Alignment explanation
Indices: 3021795--3021858 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 25
3021785 AAGTTTTGAA
* *
3021795 AATATTAAAAATTATTTTTAAAT-T
1 AATATTTATAATTATTTTTAAATAT
**
3021819 AATATTTATAATTAAATTTAAATAT
1 AATATTTATAATTATTTTTAAATAT
*
3021844 AAT-TTTGT-ATTATTT
1 AATATTTATAATTATTT
3021859 AAATAGTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 5 0.16
24 23 0.72
25 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
AATATTTATAATTATTTTTAAATAT
Found at i:3023130 original size:22 final size:21
Alignment explanation
Indices: 3023105--3023151 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
3023095 TTTAGTTATG
*
3023105 ATAATATTCAATTAAATAATTT
1 ATAATATTCAATCAAAT-ATTT
*
3023127 ATAA-ATTTAATCAAATATTT
1 ATAATATTCAATCAAATATTT
*
3023147 TTAAT
1 ATAAT
3023152 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 7 0.33
21 10 0.48
22 4 0.19
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAATATTCAATCAAATATTT
Found at i:3023259 original size:12 final size:12
Alignment explanation
Indices: 3023236--3023273 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3023226 TAAAATTAAA
*
3023236 TAATTAAAATTT
1 TAATTTAAATTT
*
3023248 TATTTTAAA-TT
1 TAATTTAAATTT
3023259 TAATTTAAATTT
1 TAATTTAAATTT
3023271 TAA
1 TAA
3023274 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATTTAAATTT
Found at i:3028755 original size:12 final size:12
Alignment explanation
Indices: 3028738--3028762 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3028728 ACCCACATTA
3028738 TGCTTCAGATAG
1 TGCTTCAGATAG
3028750 TGCTTCAGATAG
1 TGCTTCAGATAG
3028762 T
1 T
3028763 TTTTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TGCTTCAGATAG
Found at i:3029097 original size:17 final size:17
Alignment explanation
Indices: 3029070--3029114 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
3029060 AATAAAATTT
3029070 AAAAAGCAAAAAAAAAAA
1 AAAAAG-AAAAAAAAAAA
* *
3029088 AAAAAGAAAAACAAGAA
1 AAAAAGAAAAAAAAAAA
*
3029105 AGAAAGAAAA
1 AAAAAGAAAA
3029115 GAGCATGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAA
Found at i:3032645 original size:36 final size:37
Alignment explanation
Indices: 3032599--3032672 Score: 141
Period size: 36 Copynumber: 2.0 Consensus size: 37
3032589 TACTGCTGAA
3032599 AAGTAAGTTAGTGAATTGATTCTC-TTTTTGATAGAT
1 AAGTAAGTTAGTGAATTGATTCTCTTTTTTGATAGAT
3032635 AAGTAAGTTAGTGAATTGATTCTCTTTTTTGATAGAT
1 AAGTAAGTTAGTGAATTGATTCTCTTTTTTGATAGAT
3032672 A
1 A
3032673 CTTATACATC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 24 0.65
37 13 0.35
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (37 bp):
AAGTAAGTTAGTGAATTGATTCTCTTTTTTGATAGAT
Found at i:3041739 original size:6 final size:6
Alignment explanation
Indices: 3041728--3041773 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
3041718 GGCTGGCATT
3041728 GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAG
1 GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAG
3041774 GGCCAACGCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (6 bp):
GGAGTA
Found at i:3042281 original size:18 final size:19
Alignment explanation
Indices: 3042246--3042282 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3042236 TTTAAACATC
3042246 TTTATAATTTTATTAAATA
1 TTTATAATTTTATTAAATA
*
3042265 TTTATTATTTT-TTAAATA
1 TTTATAATTTTATTAAATA
3042283 ATCAATCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATAATTTTATTAAATA
Found at i:3048737 original size:13 final size:13
Alignment explanation
Indices: 3048719--3048788 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 13
3048709 ATAAATATAT
3048719 AAAATTTTTAAAA
1 AAAATTTTTAAAA
**
3048732 AAAATTAATAAAA
1 AAAATTTTTAAAA
*
3048745 GAAATATTTTT-AAT
1 -AAA-ATTTTTAAAA
** *
3048759 CTAATTTTAAAAA
1 AAAATTTTTAAAA
*
3048772 AAAAATTTTAAAA
1 AAAATTTTTAAAA
3048785 AAAA
1 AAAA
3048789 GCCGTCAATT
Statistics
Matches: 41, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
12 5 0.12
13 27 0.66
14 5 0.12
15 4 0.10
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (13 bp):
AAAATTTTTAAAA
Found at i:3048780 original size:14 final size:14
Alignment explanation
Indices: 3048761--3048788 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3048751 TTTTTAATCT
3048761 AATTTTAAAAAAAA
1 AATTTTAAAAAAAA
3048775 AATTTTAAAAAAAA
1 AATTTTAAAAAAAA
3048789 GCCGTCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATTTTAAAAAAAA
Found at i:3048808 original size:19 final size:20
Alignment explanation
Indices: 3048784--3048824 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3048774 AAATTTTAAA
*
3048784 AAAAAGCCGTCA-ATTTTTT
1 AAAAAGCCATCATATTTTTT
*
3048803 AAAAAGCTATCATATTTTTT
1 AAAAAGCCATCATATTTTTT
3048823 AA
1 AA
3048825 CATAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (20 bp):
AAAAAGCCATCATATTTTTT
Found at i:3053334 original size:14 final size:14
Alignment explanation
Indices: 3053312--3053344 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3053302 ATTTAAATTA
*
3053312 TTTAAATTTATTTT
1 TTTAGATTTATTTT
3053326 TTTAGATTTATTTT
1 TTTAGATTTATTTT
3053340 TTTAG
1 TTTAG
3053345 TAAAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (14 bp):
TTTAGATTTATTTT
Found at i:3055401 original size:36 final size:36
Alignment explanation
Indices: 3055354--3055425 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3055344 TTTTTTTGTG
3055354 CCTTAAATATGACTTTTCAAGGACCCTCATGAGAAA
1 CCTTAAATATGACTTTTCAAGGACCCTCATGAGAAA
3055390 CCTTAAATATGACTTTTCAAGGACCCTCATGAGAAA
1 CCTTAAATATGACTTTTCAAGGACCCTCATGAGAAA
3055426 ATTTAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (36 bp):
CCTTAAATATGACTTTTCAAGGACCCTCATGAGAAA
Found at i:3057652 original size:3 final size:3
Alignment explanation
Indices: 3057646--3057683 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3057636 CTACTATCCT
*
3057646 TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3057684 TTTTAATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3059373 original size:23 final size:24
Alignment explanation
Indices: 3059324--3059373 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
3059314 AAAAAATCAT
*
3059324 AATATTATAAATAAATATATTAAA
1 AATATTATAAATAAATATAATAAA
* *
3059348 AATATTA-AAATTAATATAATATA
1 AATATTATAAATAAATATAATAAA
3059371 AAT
1 AAT
3059374 GATTGATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AATATTATAAATAAATATAATAAA
Found at i:3059469 original size:23 final size:21
Alignment explanation
Indices: 3059395--3059469 Score: 53
Period size: 23 Copynumber: 3.4 Consensus size: 21
3059385 TAAAATTTAT
**
3059395 ATAAAATATATAATAT-TTTAA
1 ATAAAAT-TATAATATAAATAA
*
3059416 ATATAATTATAATATAAATAAA
1 ATAAAATTATAATATAAAT-AA
*
3059438 ATATAAATTACTATATATATATAA
1 ATA-AAATTA-TA-ATATAAATAA
*
3059462 ATAGAATT
1 ATAAAATT
3059470 TGAACTTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 8 0.19
21 7 0.16
22 5 0.12
23 9 0.21
24 7 0.16
25 7 0.16
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (21 bp):
ATAAAATTATAATATAAATAA
Found at i:3059717 original size:18 final size:18
Alignment explanation
Indices: 3059676--3059717 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3059666 TATAATTAAA
3059676 TTTAAATAAAATAATATT
1 TTTAAATAAAATAATATT
3059694 TATTAAAT-AAATAATAATT
1 T-TTAAATAAAATAAT-ATT
3059713 TTTAA
1 TTTAA
3059718 TTTTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTAAATAAAATAATATT
Found at i:3061434 original size:25 final size:25
Alignment explanation
Indices: 3061406--3061465 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
3061396 ATTAATTAAA
3061406 ATTTTTAATGAA-ATGATATT-ATTTT
1 ATTTTTAAT-AATAT-ATATTAATTTT
3061431 ATTTATTAATAATATATATTAATTTT
1 ATTT-TTAATAATATATATTAATTTT
*
3061457 TTTTTTAAT
1 ATTTTTAAT
3061466 TAAAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 16 0.52
26 15 0.48
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (25 bp):
ATTTTTAATAATATATATTAATTTT
Found at i:3065285 original size:3 final size:3
Alignment explanation
Indices: 3065277--3065318 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
3065267 TTTTTATTCC
*
3065277 TTA TTA TTA TTA ATA TT- TTGGA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT--A TTA TTA TTA TTA TTA TTA TT
3065319 TTTTTATGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
5 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3065293 original size:25 final size:24
Alignment explanation
Indices: 3065265--3065325 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
3065255 CCTTCTCATT
*
3065265 TATTTTTATTCCTTATTATTATTAA
1 TATTTTTATT-ATTATTATTATTAA
* *
3065290 TATTTTGGATTATTATTATTATTAT
1 TATTTT-TATTATTATTATTATTAA
3065315 TATTTTT-TTAT
1 TATTTTTATTAT
3065326 GAGGTCATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 4 0.13
25 24 0.77
26 3 0.10
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (24 bp):
TATTTTTATTATTATTATTATTAA
Found at i:3066056 original size:2 final size:2
Alignment explanation
Indices: 3066051--3066078 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3066041 ACACACACAC
3066051 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
3066079 TATGAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3066237 original size:16 final size:16
Alignment explanation
Indices: 3066216--3066246 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3066206 GAAAGCTAAT
3066216 ATACATACATATATAC
1 ATACATACATATATAC
3066232 ATACATACATATATA
1 ATACATACATATATA
3066247 TATATATATA
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (16 bp):
ATACATACATATATAC
Found at i:3066256 original size:8 final size:8
Alignment explanation
Indices: 3066220--3066254 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
3066210 GCTAATATAC
3066220 ATACATAT
1 ATACATAT
*
3066228 ATACATAC
1 ATACATAT
3066236 ATACATAT
1 ATACATAT
*
3066244 ATATATAT
1 ATACATAT
3066252 ATA
1 ATA
3066255 TAAGAAAACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
ATACATAT
Found at i:3066256 original size:12 final size:12
Alignment explanation
Indices: 3066214--3066254 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3066204 GAGAAAGCTA
3066214 ATATACATACAT
1 ATATACATACAT
3066226 ATATACATACAT
1 ATATACATACAT
* * *
3066238 ACATATATATAT
1 ATATACATACAT
3066250 ATATA
1 ATATA
3066255 TAAGAAAACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATACATACAT
Found at i:3067167 original size:2 final size:2
Alignment explanation
Indices: 3067155--3067191 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
3067145 TCTCATTACC
3067155 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
3067192 CCAAATATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Done.