Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1118
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: 54781
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:2126 original size:28 final size:27
Alignment explanation
Indices: 2059--2131 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
2049 CTTCACAATC
* *
2059 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
2086 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
2114 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
2132 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:2176 original size:51 final size:51
Alignment explanation
Indices: 2114--2284 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
2104 TTATTTCTGA
* * *
2114 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
2165 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
2218 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
2270 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2285 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:2303 original size:28 final size:28
Alignment explanation
Indices: 2267--2348 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
2257 ATTTTTCACA
*
2267 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
2295 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
2323 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
2349 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:8523 original size:122 final size:122
Alignment explanation
Indices: 8384--8629 Score: 492
Period size: 122 Copynumber: 2.0 Consensus size: 122
8374 GTAATTCGTA
8384 AAGATAAAAATATAGCATCAAGCATGAAAAATATCACCTACAGTAATAACAGCTTAAGTAAATAT
1 AAGATAAAAATATAGCATCAAGCATGAAAAATATCACCTACAGTAATAACAGCTTAAGTAAATAT
8449 TTTGACATTTTTTAGCTAAAAAATGGGCATGACAGAGTGGCTGATTGCTTCTCCTTC
66 TTTGACATTTTTTAGCTAAAAAATGGGCATGACAGAGTGGCTGATTGCTTCTCCTTC
8506 AAGATAAAAATATAGCATCAAGCATGAAAAATATCACCTACAGTAATAACAGCTTAAGTAAATAT
1 AAGATAAAAATATAGCATCAAGCATGAAAAATATCACCTACAGTAATAACAGCTTAAGTAAATAT
8571 TTTGACATTTTTTAGCTAAAAAATGGGCATGACAGAGTGGCTGATTGCTTCTCCTTC
66 TTTGACATTTTTTAGCTAAAAAATGGGCATGACAGAGTGGCTGATTGCTTCTCCTTC
8628 AA
1 AA
8630 CATAGGTGGC
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 124 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (122 bp):
AAGATAAAAATATAGCATCAAGCATGAAAAATATCACCTACAGTAATAACAGCTTAAGTAAATAT
TTTGACATTTTTTAGCTAAAAAATGGGCATGACAGAGTGGCTGATTGCTTCTCCTTC
Found at i:10560 original size:35 final size:34
Alignment explanation
Indices: 10480--10549 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 34
10470 TTTATTTGAT
10480 TTAAC-TCAAA-T-TAAAAAACTTATGTTTAAGA
1 TTAACATCAAATTATAAAAAACTTATGTTTAAGA
10511 TTAACATCAAATTAATAAAAAACTTATGTTTAAGA
1 TTAACATCAAATT-ATAAAAAACTTATGTTTAAGA
10546 TTAA
1 TTAA
10550 GGCTGTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
31 5 0.14
32 5 0.14
33 1 0.03
35 24 0.69
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.36
Consensus pattern (34 bp):
TTAACATCAAATTATAAAAAACTTATGTTTAAGA
Found at i:10910 original size:19 final size:19
Alignment explanation
Indices: 10882--10918 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
10872 AATTATAAAA
10882 AATTAATTA-TAAATTTTT
1 AATTAATTATTAAATTTTT
10900 AATTAAATTATTAAATTTT
1 AATT-AATTATTAAATTTT
10919 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATTAATTATTAAATTTTT
Found at i:11903 original size:21 final size:21
Alignment explanation
Indices: 11877--11918 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11867 AAAAATTATT
*
11877 TTTAT-ATTAATATTTATATAA
1 TTTATAATTAA-ATTTAAATAA
11898 TTTATAATTAAATTTAAATAA
1 TTTATAATTAAATTTAAATAA
11919 AAATACAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTATAATTAAATTTAAATAA
Found at i:12428 original size:19 final size:20
Alignment explanation
Indices: 12404--12442 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
12394 TACTTTTTTA
12404 AAAATACATT-TTACTCTTT
1 AAAATACATTATTACTCTTT
*
12423 AAAATATATTATTACTCTTT
1 AAAATACATTATTACTCTTT
12443 TACCCATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATACATTATTACTCTTT
Found at i:12560 original size:2 final size:2
Alignment explanation
Indices: 12553--12578 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12543 CATTAACATA
12553 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
12579 TATTTTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13548 original size:2 final size:2
Alignment explanation
Indices: 13541--13569 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13531 TTTGATGTGT
13541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13570 TTGTATTTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18529 original size:14 final size:16
Alignment explanation
Indices: 18488--18561 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 16
18478 ATGATTTTTC
*
18488 AATATAAATTTTAAAA
1 AATATATATTTTAAAA
18504 AATATATATTTTAAAA
1 AATATATATTTTAAAA
*
18520 AAT-T-TTTTTTAAAA
1 AATATATATTTTAAAA
* **
18534 AATATAGATTAAAAAA
1 AATATATATTTTAAAA
18550 AAT-TATTATTTT
1 AATATA-TATTTT
18562 GTAATAAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
14 12 0.26
15 4 0.09
16 30 0.65
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (16 bp):
AATATATATTTTAAAA
Found at i:18530 original size:30 final size:30
Alignment explanation
Indices: 18496--18553 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
18486 TCAATATAAA
* **
18496 TTTTAAAAAATATATATTTTAAAAAATTTT
1 TTTTAAAAAATATAGATTAAAAAAAATTTT
18526 TTTTAAAAAATATAGATTAAAAAAAATT
1 TTTTAAAAAATATAGATTAAAAAAAATT
18554 ATTATTTTGT
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:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
TTTTAAAAAATATAGATTAAAAAAAATTTT
Found at i:20588 original size:10 final size:11
Alignment explanation
Indices: 20573--20634 Score: 55
Period size: 10 Copynumber: 6.1 Consensus size: 11
20563 GTTTAAATTA
20573 AATTTT-TATT
1 AATTTTATATT
20583 AATTTTATATT
1 AATTTTATATT
*
20594 -ATTTTAAATT
1 AATTTTATATT
20604 --TTTTATATTT
1 AATTTTATA-TT
*
20614 AA-ATTA-ATT
1 AATTTTATATT
20623 AATTTTATATT
1 AATTTTATATT
20634 A
1 A
20635 TTAATTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
9 10 0.24
10 21 0.50
11 11 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
AATTTTATATT
Found at i:20627 original size:40 final size:36
Alignment explanation
Indices: 20580--20660 Score: 110
Period size: 40 Copynumber: 2.1 Consensus size: 36
20570 TTAAATTTTT
20580 ATTAATTTTATATTATTTTAAATTTTTTATATTTAAATT-A
1 ATTAATTTTATATTA--TT-AATTTTTTA-ATTT-AATTAA
20620 ATTAATTTTATATTATTAATTTTTTAATTTAATTAA
1 ATTAATTTTATATTATTAATTTTTTAATTTAATTAA
20656 ATTAA
1 ATTAA
20661 ATTAAAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 4 0.10
36 10 0.25
37 9 0.22
38 2 0.05
40 15 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (36 bp):
ATTAATTTTATATTATTAATTTTTTAATTTAATTAA
Found at i:20630 original size:21 final size:22
Alignment explanation
Indices: 20580--20665 Score: 62
Period size: 19 Copynumber: 4.2 Consensus size: 22
20570 TTAAATTTTT
**
20580 ATTAATTTTATA-TTATTTTAA
1 ATTAATTTTATATTTAAATTAA
20601 ATT--TTTTATATTTAAATT-A
1 ATTAATTTTATATTTAAATTAA
* *
20620 ATTAATTTTATATTATTAATT-T
1 ATTAATTTTATATT-TAAATTAA
*
20642 TTTAA-TTTA-A-TTAAATTAA
1 ATTAATTTTATATTTAAATTAA
20661 ATTAA
1 ATTAA
20666 AATAAATTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
18 5 0.10
19 16 0.31
20 6 0.12
21 16 0.31
22 9 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTAATTTTATATTTAAATTAA
Found at i:21114 original size:20 final size:20
Alignment explanation
Indices: 21091--21140 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
21081 AAAAGATTAC
* *
21091 ATTTTATTATTACAAATATA
1 ATTTTATTATTAAAAAAATA
21111 A-TTTACTTATTAAAAAAATA
1 ATTTTA-TTATTAAAAAAATA
21131 ATTATTATTA
1 ATT-TTATTA
21141 CATCAAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 4 0.16
20 14 0.56
21 4 0.16
22 3 0.12
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTTATTATTAAAAAAATA
Found at i:21441 original size:31 final size:30
Alignment explanation
Indices: 21392--21449 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
21382 AGTTAAAAGT
21392 AAATTTACAATTACACTTTAATTCAATTTTG
1 AAATTTACAATTACACTTTAATT-AATTTTG
* ** *
21423 AAATTTACTATTTTACTTTTATTAATT
1 AAATTTACAATTACACTTTAATTAATT
21450 AAATTTTATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 4 0.17
31 19 0.83
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (30 bp):
AAATTTACAATTACACTTTAATTAATTTTG
Found at i:21586 original size:18 final size:19
Alignment explanation
Indices: 21563--21602 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
21553 TTTATTTTAA
21563 TAATTAAAAATAAT-AAAT
1 TAATTAAAAATAATAAAAT
*
21581 TAATTAAAAATATTAAAAT
1 TAATTAAAAATAATAAAAT
21600 TAA
1 TAA
21603 AAAATTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAATTAAAAATAATAAAAT
Found at i:22781 original size:25 final size:26
Alignment explanation
Indices: 22752--22800 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
22742 TATTAAATTA
*
22752 TTAT-AAATTAAATTAAAAAATATTT
1 TTATAAAATAAAATTAAAAAATATTT
*
22777 TTATAAAATAAAATTTAAAAATAT
1 TTATAAAATAAAATTAAAAAATAT
22801 AATATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TTATAAAATAAAATTAAAAAATATTT
Found at i:22991 original size:20 final size:20
Alignment explanation
Indices: 22968--23007 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
22958 TTATTTTTAT
*
22968 ATATTATAAT-TTTATTTAAA
1 ATATTA-AATATTTATATAAA
22988 ATATTAAATATTTATATAAA
1 ATATTAAATATTTATATAAA
23008 TTATAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTAAATATTTATATAAA
Found at i:23024 original size:18 final size:18
Alignment explanation
Indices: 22959--23029 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
22949 TATATTTATT
* *
22959 TATTTTTATATATTATAA
1 TATTTATATAAATTATAA
* *
22977 T-TTTATTTAAAATATTAAA
1 TATTTATATAAATTA-T-AA
22996 TATTTATATAAATTATAA
1 TATTTATATAAATTATAA
*
23014 TATATTA-ATAATTTAT
1 TAT-TTATATAAATTAT
23030 TTATATAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
17 9 0.21
18 15 0.36
19 7 0.17
20 11 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTATATAAATTATAA
Found at i:23034 original size:31 final size:32
Alignment explanation
Indices: 22944--23073 Score: 97
Period size: 31 Copynumber: 4.0 Consensus size: 32
22934 TTAATGTATT
* * *
22944 TATATTATATTTATTTATTTTTATATATTATAA
1 TATATTA-ATATATTTATTTATATAAATTATAA
* *
22977 TTTTATTTAAAATATTAAATATTTATATAAATTATAA
1 -TATA-TTAATATATT---TATTTATATAAATTATAA
*
23014 TATATTAATA-ATTTATTTATATAAAATT-TGA
1 TATATTAATATATTTATTTATAT-AAATTATAA
* *
23045 TATATTTATATATTTATATA-AT-AATTATA
1 TATATTAATATATTTATTTATATAAATTATA
23074 TTATTTTTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
29 4 0.05
30 1 0.01
31 22 0.28
32 13 0.17
34 11 0.14
35 8 0.10
36 3 0.04
37 16 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (32 bp):
TATATTAATATATTTATTTATATAAATTATAA
Found at i:23057 original size:8 final size:8
Alignment explanation
Indices: 22949--23126 Score: 57
Period size: 8 Copynumber: 21.4 Consensus size: 8
22939 GTATTTATAT
22949 TATATTTA
1 TATATTTA
* *
22957 TTTATTTT
1 TATATTTA
22965 TATATATTA
1 TATAT-TTA
22974 TA-ATTT-
1 TATATTTA
*
22980 TAT-TTAA
1 TATATTTA
*
22987 AATA-TTA
1 TATATTTA
*
22994 AATATTTA
1 TATATTTA
*
23002 TATAAATTA
1 TAT-ATTTA
23011 TAATATATTA
1 T-ATAT-TTA
23021 -ATAATTTA
1 TAT-ATTTA
* *
23029 TTTATATA
1 TATATTTA
*
23037 -AAATTTGA
1 TATATTT-A
23045 TATATTTA
1 TATATTTA
23053 TATATTTA
1 TATATTTA
23061 TATAATAATTA
1 TAT-AT--TTA
23072 TATTATTT-
1 TA-TATTTA
*
23080 TTTATTTTA
1 TATA-TTTA
23089 TATTATATTA
1 TA-TAT-TTA
*
23099 TAATTATTTT
1 T-A-TATTTA
23109 TATA-TTA
1 TATATTTA
*
23116 TATAATTA
1 TATATTTA
23124 TAT
1 TAT
23127 TATATCGAAA
Statistics
Matches: 128, Mismatches: 20, Indels: 44
0.67 0.10 0.23
Matches are distributed among these distances:
6 4 0.03
7 21 0.16
8 51 0.40
9 25 0.20
10 14 0.11
11 12 0.09
12 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (8 bp):
TATATTTA
Found at i:23084 original size:51 final size:51
Alignment explanation
Indices: 22967--23084 Score: 125
Period size: 51 Copynumber: 2.3 Consensus size: 51
22957 TTTATTTTTA
* *
22967 TATATTATAATTTTATTTAAAATATTAAATATTTATATAAATTATAATATAT
1 TATATTAT-TTTTTATATAAAATATTAAATATTTATATAAATTATAATATAT
* * **
23019 TA-ATAATTTATTTATATAAAAT-TTGATATATTTATATATTTATATAATA-AT
1 TATATTATTT-TTTATATAAAATATT-AAATATTTATATAAAT-TATAATATAT
23070 TATATTATTTTTTAT
1 TATATTATTTTTTAT
23085 TTTATATTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
50 3 0.05
51 37 0.67
52 15 0.27
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (51 bp):
TATATTATTTTTTATATAAAATATTAAATATTTATATAAATTATAATATAT
Found at i:26473 original size:24 final size:23
Alignment explanation
Indices: 26390--26476 Score: 76
Period size: 22 Copynumber: 3.9 Consensus size: 23
26380 AATAGCTTGG
*
26390 TATATATAGTA-ATATATATAGCT
1 TATATATACTATATATATATA-CT
*
26413 T-TATTATTCTATATATATATA-T
1 TATA-TATACTATATATATATACT
* *
26435 TAGTATAAAGT-TATATATATACT
1 TA-TATATACTATATATATATACT
26458 TATATATACTA-ATATATAT
1 TATATATACTATATATATAT
26477 TCTATTTCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
22 28 0.55
23 12 0.24
24 11 0.22
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (23 bp):
TATATATACTATATATATATACT
Found at i:32336 original size:30 final size:32
Alignment explanation
Indices: 32295--32358 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 32
32285 GGTTGGAGAA
32295 GAAAAAAAAAAGAAGAA-AAA-A-GAAGATAT
1 GAAAAAAAAAAGAAGAAGAAAGACGAAGATAT
32324 GAAAAAACAAAAGAAGAAGAAAGACGAAGATAT
1 GAAAAAA-AAAAGAAGAAGAAAGACGAAGATAT
32357 GA
1 GA
32359 GGCTCTCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 7 0.23
30 10 0.32
31 3 0.10
32 1 0.03
33 10 0.32
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.06
Consensus pattern (32 bp):
GAAAAAAAAAAGAAGAAGAAAGACGAAGATAT
Found at i:32971 original size:42 final size:43
Alignment explanation
Indices: 32924--33038 Score: 151
Period size: 42 Copynumber: 2.7 Consensus size: 43
32914 GTATTTATCC
*
32924 ATATAAATGTCGTTAAAAGTTTAAATTTAACGGTGTTTACAA-
1 ATATAAATATCGTTAAAAGTTTAAATTTAACGGTGTTTACAAT
* ** *
32966 ATATAAAAATCGTTAAAAGTTTAAATTTATTGGTGTTTTCAAT
1 ATATAAATATCGTTAAAAGTTTAAATTTAACGGTGTTTACAAT
* * *
33009 TTACAAATATCGTTAAAAGTTTAAACTTAA
1 ATATAAATATCGTTAAAAGTTTAAATTTAA
33039 TAGCGTTTTC
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 37 0.60
43 25 0.40
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (43 bp):
ATATAAATATCGTTAAAAGTTTAAATTTAACGGTGTTTACAAT
Found at i:33047 original size:43 final size:43
Alignment explanation
Indices: 32928--33102 Score: 183
Period size: 43 Copynumber: 4.1 Consensus size: 43
32918 TTATCCATAT
* * * *
32928 AAATGTCGTTAAAAGTTTAAATTTAACGGTGTTTACAAATATA-
1 AAATATCGTTAAAAGTTTAAACTTAACGGTGTTTTC-AATTTAC
* **
32971 AAA-ATCGTTAAAAGTTTAAATTTATTGGTGTTTTCAATTTAC
1 AAATATCGTTAAAAGTTTAAACTTAACGGTGTTTTCAATTTAC
** *
33013 AAATATCGTTAAAAGTTTAAACTTAATAGCGTTTTCAATTTAC
1 AAATATCGTTAAAAGTTTAAACTTAACGGTGTTTTCAATTTAC
** ** * *
33056 AAATGCCACTAAAAGTGTAAACTTAGCGGTGTTTTCAATTTAC
1 AAATATCGTTAAAAGTTTAAACTTAACGGTGTTTTCAATTTAC
33099 AAAT
1 AAAT
33103 GTTAGCAAAC
Statistics
Matches: 112, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
41 5 0.04
42 31 0.28
43 76 0.68
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (43 bp):
AAATATCGTTAAAAGTTTAAACTTAACGGTGTTTTCAATTTAC
Found at i:35156 original size:20 final size:17
Alignment explanation
Indices: 35109--35169 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 17
35099 TAAATATTAA
35109 TATTTTAATTATATA--
1 TATTTTAATTATATATT
*
35124 AATTTTAA-TATAT-TT
1 TATTTTAATTATATATT
35139 TATATTTACATTATATATT
1 TAT-TTTA-ATTATATATT
35158 TATTTTAATTAT
1 TATTTTAATTAT
35170 TTTTATCTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 5 0.13
15 9 0.24
16 4 0.11
17 6 0.16
18 9 0.24
19 5 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTTAATTATATATT
Found at i:35511 original size:25 final size:24
Alignment explanation
Indices: 35463--35568 Score: 72
Period size: 25 Copynumber: 4.2 Consensus size: 24
35453 TAAATATTAA
**
35463 ATAAATATTATTTTTAAA-TTAAAT
1 ATAAAT-TTATTAATAAATTTAAAT
35487 ATAAATTTATTAATAATATTTAAAT
1 ATAAATTTATTAATAA-ATTTAAAT
* * *
35512 AATATATTTAATAAATAAATTCAAAT
1 -ATAAATTT-ATTAATAAATTTAAAT
* *
35538 TTCAAA-TAATTAAATAAATTTAAAT
1 AT-AAATTTATT-AATAAATTTAAAT
*
35563 TTAAAT
1 ATAAAT
35569 ATAGTAAATA
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
23 8 0.12
24 12 0.18
25 22 0.34
26 16 0.25
27 7 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAAATTTATTAATAAATTTAAAT
Found at i:35576 original size:25 final size:25
Alignment explanation
Indices: 35523--35578 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
35513 ATATATTTAA
*
35523 TAAATAAATTCAAATTTCAAATAAT
1 TAAATAAATTCAAATTTCAAATAAG
*
35548 TAAATAAATTTAAATTT-AAATATAG
1 TAAATAAATTCAAATTTCAAATA-AG
35573 TAAATA
1 TAAATA
35579 TCCCTTTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
TAAATAAATTCAAATTTCAAATAAG
Found at i:40134 original size:100 final size:99
Alignment explanation
Indices: 39948--40140 Score: 246
Period size: 100 Copynumber: 1.9 Consensus size: 99
39938 GTTATCGATA
* * * *
39948 ATGACAATTTGAGCAAAAAAGTAAGATTTAAATCTTGACAAGTTTAAAAATAGGGTTGGAGTATC
1 ATGACAATTTAAGCAAAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATAAGGTTAGAGTATC
*
40013 CCTTAAAAAGAATAGGATTGGAATATCCTCAATG
66 CCTCAAAAAGAATAGGATTGGAATATCCTCAATG
* * * *
40047 ATGACAATTTAAGCAAAAAAAATAAGATTTAAATTTTTATATGTTTAAAAATAAGGTTAGAGTAT
1 ATGACAATTTAAGC-AAAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATAAGGTTAGAGTAT
* *
40112 CCCCTCGAAAA-AATGAGG-TTGGAGTATCC
65 -CCCTCAAAAAGAAT-AGGATTGGAATATCC
40141 CCGATGAATA
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
99 13 0.16
100 56 0.70
101 11 0.14
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.30
Consensus pattern (99 bp):
ATGACAATTTAAGCAAAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATAAGGTTAGAGTATC
CCTCAAAAAGAATAGGATTGGAATATCCTCAATG
Found at i:42554 original size:52 final size:51
Alignment explanation
Indices: 42486--42615 Score: 138
Period size: 52 Copynumber: 2.5 Consensus size: 51
42476 GAACTAGATA
* * * *
42486 TATCAATACATTGAAGAATGTAT-TAATACATTTAG-GTCAAAAACTCAGAATC
1 TATC-ATACAATGAAGAATATATCGAA-ACATTT-GTGTCAAAAACCCAGAATC
*
42538 TATCGATACAATGAAGAATATATCGAAACATTTGTGTCAAAAACCCAGAATG
1 TATC-ATACAATGAAGAATATATCGAAACATTTGTGTCAAAAACCCAGAATC
* *
42590 TATTCATACAATGAAAAATTTATCGA
1 TA-TCATACAATGAAGAATATATCGA
42616 TAAATTTTCT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
51 1 0.01
52 62 0.93
53 4 0.06
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (51 bp):
TATCATACAATGAAGAATATATCGAAACATTTGTGTCAAAAACCCAGAATC
Found at i:42709 original size:20 final size:21
Alignment explanation
Indices: 42686--42731 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
42676 GCATGTGTTA
42686 ATACATTCAC-TTA-TGTATCG
1 ATACATT-ACTTTATTGTATCG
*
42706 ATACATTACTTTATTGTATTG
1 ATACATTACTTTATTGTATCG
42727 ATACA
1 ATACA
42732 AATTGTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 10 0.43
21 11 0.48
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (21 bp):
ATACATTACTTTATTGTATCG
Found at i:45976 original size:20 final size:20
Alignment explanation
Indices: 45951--46036 Score: 165
Period size: 20 Copynumber: 4.3 Consensus size: 20
45941 ATTTAACTGG
45951 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAGA
45971 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAGA
45991 ATGTAT-GATACATTGAAGA
1 ATGTATCGATACATTGAAGA
46010 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAGA
46030 ATGTATC
1 ATGTATC
46037 AATATATTTG
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
19 19 0.29
20 46 0.71
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAGA
Found at i:46002 original size:39 final size:40
Alignment explanation
Indices: 45951--46036 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 40
45941 ATTTAACTGG
45951 ATGTATCGATACATTGAAGAATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATTGAAGA
45991 ATGTAT-GATACATTGAAGAATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATTGAAGA
46030 ATGTATC
1 ATGTATC
46037 AATATATTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 39 0.87
40 6 0.13
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (40 bp):
ATGTATCGATACATTGAAGAATGTATCGATACATTGAAGA
Found at i:46153 original size:20 final size:21
Alignment explanation
Indices: 46114--46163 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
46104 ACAAGGTTTA
*
46114 GTATTGATACATTCACTTA-T
1 GTATTGATACATTAACTTATT
* *
46134 GTATCGATACATTAAGTTATT
1 GTATTGATACATTAACTTATT
46155 GTATTGATA
1 GTATTGATA
46164 AAAATTGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (21 bp):
GTATTGATACATTAACTTATT
Found at i:47503 original size:154 final size:154
Alignment explanation
Indices: 47142--47676 Score: 666
Period size: 154 Copynumber: 3.5 Consensus size: 154
47132 CTAGTGACCC
* * *
47142 TAAAGGACTAAAAAATAATCATAAATGAGATGAACCTATCCTAAATAG-ATACCTTTGGCATAAA
1 TAAAGGACTTAAAAATGATCATAAATGAGATGAACCTATCCTAAAT-GCACACCTTTGGCATAAA
* *** * * * ** *
47206 AGCATCCTAGCGGCAACCTAAGACTCAGTTCTAGGAAAATTATGAAAATGCTCCTAAGGTATA-C
65 AGCATCC-CGATACAACATAAGACTCAGTTTTAGAAAAATTACAAAAATGCCCCTAAGGTATACC
* *
47270 TTTCGACATTAAAATATCCCGGTAATCT
129 TTT-GACATTAAAGTAT-CCAGTAATCT
*
47298 TAAAGGACTTAAAAATGATCATAAATGAGATGAACCTATCCTAAATACACACCTTTGGCATAAAA
1 TAAAGGACTTAAAAATGATCATAAATGAGATGAACCTATCCTAAATGCACACCTTTGGCATAAAA
* *
47363 GCATCCCGATACAACATAAGACTCAGTTTTAAAAAAATTACAAAAATACCCCTAAGGTATACCTT
66 GCATCCCGATACAACATAAGACTCAGTTTTAGAAAAATTACAAAAATGCCCCTAAGGTATACCTT
47428 TGACATTAAAGTATCCAGTAATCT
131 TGACATTAAAGTATCCAGTAATCT
* *
47452 TAAAGGACTTAAAAATGATCATAAATGAGATAAACTTATCCTAAATGCACACCTTTGGCATAAAA
1 TAAAGGACTTAAAAATGATCATAAATGAGATGAACCTATCCTAAATGCACACCTTTGGCATAAAA
* * ** *
47517 GCATCCCGATGATAACTTAAGACTCAG-TTTAGAAAAATTACAAAAATGCCTTTAGGGTATACCT
66 GCATCCCGAT-ACAACATAAGACTCAGTTTTAGAAAAATTACAAAAATGCCCCTAAGGTATACCT
** * * *
47581 TCAACATGAAAGTA-CCTAGTAACCC
130 TTGACATTAAAGTATCC-AGTAATCT
* * * *
47606 CAAAAGACTTAAAAATGATCATAAATGAGATGAACCTA-CTCTAAATGCATACTTTTGGCATAAA
1 TAAAGGACTTAAAAATGATCATAAATGAGATGAACCTATC-CTAAATGCACACCTTTGGCATAAA
47670 AGCATCC
65 AGCATCC
47677 TGGTGACAAC
Statistics
Matches: 335, Mismatches: 39, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
153 3 0.01
154 193 0.58
155 69 0.21
156 70 0.21
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (154 bp):
TAAAGGACTTAAAAATGATCATAAATGAGATGAACCTATCCTAAATGCACACCTTTGGCATAAAA
GCATCCCGATACAACATAAGACTCAGTTTTAGAAAAATTACAAAAATGCCCCTAAGGTATACCTT
TGACATTAAAGTATCCAGTAATCT
Found at i:47819 original size:119 final size:119
Alignment explanation
Indices: 47580--47810 Score: 322
Period size: 119 Copynumber: 1.9 Consensus size: 119
47570 AGGGTATACC
* *
47580 TTCAACATGAAAGTACCTAGTAACCCCAAAAGACTTAAAAATGATCATAAATGAGATGAACCTAC
1 TTCAACATGAAAGTACCTAGTAACCCCAAAAGACTTAAAAAGGATCATAAATGAGATGAACCCAC
* ***
47645 TCTAAATGCATACTTTTGGCATAAAAGCATCCTGGTGACAACCTAAGGTATATT
66 TCTAAATGCATACTTTTAGCATAAAAGCATCCCAATGACAACCTAAGGTATATT
* * * * *
47699 TTCAACATTAAAGTACTTGGTAACGCTAAAAGACTTAAAAAGGATCATAAATGAGATGAACCCA-
1 TTCAACATGAAAGTACCTAGTAACCCCAAAAGACTTAAAAAGGATCATAAATGAGATGAACCCAC
*
47763 TCCTAAATGCACT-TTTTTAGCATAAAAGCATCCCAATGACAACCTAAG
66 T-CTAAATGCA-TACTTTTAGCATAAAAGCATCCCAATGACAACCTAAG
47811 ACTCATTTTA
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
118 1 0.01
119 96 0.98
120 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (119 bp):
TTCAACATGAAAGTACCTAGTAACCCCAAAAGACTTAAAAAGGATCATAAATGAGATGAACCCAC
TCTAAATGCATACTTTTAGCATAAAAGCATCCCAATGACAACCTAAGGTATATT
Found at i:48486 original size:165 final size:167
Alignment explanation
Indices: 47967--48661 Score: 775
Period size: 166 Copynumber: 4.2 Consensus size: 167
47957 AAAATTACAA
* * * *
47967 TTAAGTCCCTAAATTTTTAAAAATTTCATTTCATACCTAATAAAAAATCGAGAGGATACGAAAAG
1 TTAA-TCCCTAAACTTTTGAAAATTTCATTTCATACCTAATAGAAAATCGAGAGGATACAAAAAG
* * * *
48032 TTTTAAAAAATTTTTATACCCCTATAGAAA-GCCATAGGAATAACAGAAATCTTTAAAAATAACT
65 TTTTAAAAAATTTTTATACCCCTATA-AAAGGCCATAAGAATAATAGAAACCTTTAAAAATGACT
* * * *
48096 AAAATGATGATTTTTCCTCTAAAAAGTAAACTGTGC-AGT
129 AAAATGATGATTTTACCTCTAAAAACTAAAATTTGCTA-T
*** * ** * *
48135 TTAATATTTAAACTTTTGAAAATTTTATTTTGTACCTAAT-GAAAAATTGAGAGGATATGAAAAA
1 TTAATCCCTAAACTTTTGAAAATTTCATTTCATACCTAATAG-AAAATCGAGAGGATA-CAAAAA
** * * * *
48199 -TTTT-AAAAATTTTTATACCCCTACGAAAGACTATAGGAATAATAGAAACTTTTAAAAATGACT
64 GTTTTAAAAAATTTTTATACCCCTATAAAAGGCCATAAGAATAATAGAAACCTTTAAAAATGACT
* ** *
48262 AAAATGATGCTTTTATGTCTAAAAGCTAAAATTTGCTAT
129 AAAATGATGATTTTACCTCTAAAAACTAAAATTTGCTAT
*
48301 TTAATCCCTAAACTTTTGAAAATTTCATTTCATACCTAATAGAAAATTGAGAGGATACAAAAAGT
1 TTAATCCCTAAACTTTTGAAAATTTCATTTCATACCTAATAGAAAATCGAGAGGATACAAAAAGT
* * *
48366 TTT-AAAATTTTTTATACCCCTATAAAAGGCCATAAAAATAATAGAAACCTTTAGAAATGACTAA
66 TTTAAAAAATTTTTATACCCCTATAAAAGGCCATAAGAATAATAGAAACCTTTAAAAATGACTAA
* *
48430 AA-AATGATTTTACCTCTAAAAACTAAAAGTTGCTAT
131 AATGATGATTTTACCTCTAAAAACTAAAATTTGCTAT
* * ** * * *
48466 TTAATCCCTAAACTTTTGAAAATTTCATTTCGTACTCGACGA-AAAACCAAGAGGATACGAAAAG
1 TTAATCCCTAAACTTTTGAAAATTTCATTTCATAC-CTAATAGAAAATCGAGAGGATACAAAAAG
* * *
48530 TTTTGAAAAA-TTTTATA-CCCT-TAAGGAAGGCCA-AAGGGATAATAAAAACCTTTAAAAATGA
65 TTTTAAAAAATTTTTATACCCCTATAA--AAGGCCATAA-GAATAATAGAAACCTTTAAAAATGA
* *
48591 CTAAAATGATGATTTTAACTCTAAAAACTAAAATTTACTAT
127 CTAAAATGATGATTTTACCTCTAAAAACTAAAATTTGCTAT
*
48632 TTAATCCCTAAACTTTTCAAAATTTTCATT
1 TTAATCCCTAAACTTTTGAAAA-TTTCATT
48662 ATAGTACCTA
Statistics
Matches: 446, Mismatches: 68, Indels: 27
0.82 0.13 0.05
Matches are distributed among these distances:
163 3 0.01
164 6 0.01
165 133 0.30
166 241 0.54
167 55 0.12
168 8 0.02
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (167 bp):
TTAATCCCTAAACTTTTGAAAATTTCATTTCATACCTAATAGAAAATCGAGAGGATACAAAAAGT
TTTAAAAAATTTTTATACCCCTATAAAAGGCCATAAGAATAATAGAAACCTTTAAAAATGACTAA
AATGATGATTTTACCTCTAAAAACTAAAATTTGCTAT
Found at i:48586 original size:331 final size:333
Alignment explanation
Indices: 47967--48661 Score: 891
Period size: 331 Copynumber: 2.1 Consensus size: 333
47957 AAAATTACAA
* *
47967 TTAAGTCCCTAAATTTTTAAAAATTTCATTTCATACCTAATAAAAAATCGAGAGGATACGAAAAG
1 TTAA-TCCCTAAACTTTTAAAAATTTCATTTCATACCTAATAAAAAATCGAGAGGATACAAAAAG
** *
48032 TTTTAAAAAATTTTTATACCCCTATAGAAAGCCATAGGAATAACAGAAATCTTTAAAAATAACTA
65 TTTTAAAAAATTTTTATACCCCTATAGAAAGCCATAAAAATAACAGAAACCTTTAAAAATAACTA
* * * ** *
48097 AAATGATGATTTTTCCTCTAAAAAGTAAACTGTGCAGTTTAATATTTAAACTTTTGAAAATTTTA
130 AAATAATGATTTTACCTCTAAAAACTAAACTGTGCAGTTTAATACCTAAACTTTTGAAAATTTCA
* * *** * *
48162 TTTTGTACCTAATGAAAAATTGAGAGGATATGAAAAATTTTAAAAATTTTTATACCCCTACGAAA
195 TTTCGTACCTAACGAAAAACCAAGAGGATACGAAAAATTTTAAAAATTTTTATACCCCTAAGAAA
* * * * * ** *
48227 GACTATAGGAATAATAGAAACTTTTAAAAATGACTAAAATGATGCTTTTATGTCTAAAAGCTAAA
260 GACCAAAGGAATAATAAAAACCTTTAAAAATGACTAAAATGATGATTTTAACTCTAAAAACTAAA
*
48292 ATTTGCTAT
325 ATTTACTAT
* * *
48301 TTAATCCCTAAACTTTTGAAAATTTCATTTCATACCTAATAGAAAATTGAGAGGATACAAAAAGT
1 TTAATCCCTAAACTTTTAAAAATTTCATTTCATACCTAATAAAAAATCGAGAGGATACAAAAAGT
* * * *
48366 TTT-AAAATTTTTTATACCCCTATA-AAAGGCCATAAAAATAATAGAAACCTTTAGAAATGACTA
66 TTTAAAAAATTTTTATACCCCTATAGAAA-GCCATAAAAATAACAGAAACCTTTAAAAATAACTA
* *
48429 AAA-AATGATTTTACCTCTAAAAACTAAA-AGTTGCTA-TTTAATCCCTAAACTTTTGAAAATTT
130 AAATAATGATTTTACCTCTAAAAACTAAACTG-TGC-AGTTTAATACCTAAACTTTTGAAAATTT
* * *
48491 CATTTCGTA-CTCGACGAAAAACCAAGAGGATACGAAAAGTTTTGAAAAA-TTTTATACCCTTAA
193 CATTTCGTACCT-AACGAAAAACCAAGAGGATACGAAAAATTTT-AAAAATTTTTATACCCCTAA
* * *
48554 GGAAGGCCAAAGGGATAATAAAAACCTTTAAAAATGACTAAAATGATGATTTTAACTCTAAAAAC
256 GAAAGACCAAAGGAATAATAAAAACCTTTAAAAATGACTAAAATGATGATTTTAACTCTAAAAAC
48619 TAAAATTTACTAT
321 TAAAATTTACTAT
*
48632 TTAATCCCTAAACTTTTCAAAATTTTCATT
1 TTAATCCCTAAACTTTT-AAAAATTTCATT
48662 ATAGTACCTA
Statistics
Matches: 311, Mismatches: 44, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
330 3 0.01
331 177 0.57
332 68 0.22
333 59 0.19
334 4 0.01
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (333 bp):
TTAATCCCTAAACTTTTAAAAATTTCATTTCATACCTAATAAAAAATCGAGAGGATACAAAAAGT
TTTAAAAAATTTTTATACCCCTATAGAAAGCCATAAAAATAACAGAAACCTTTAAAAATAACTAA
AATAATGATTTTACCTCTAAAAACTAAACTGTGCAGTTTAATACCTAAACTTTTGAAAATTTCAT
TTCGTACCTAACGAAAAACCAAGAGGATACGAAAAATTTTAAAAATTTTTATACCCCTAAGAAAG
ACCAAAGGAATAATAAAAACCTTTAAAAATGACTAAAATGATGATTTTAACTCTAAAAACTAAAA
TTTACTAT
Found at i:48956 original size:19 final size:19
Alignment explanation
Indices: 48932--48987 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
48922 GATTCACGTT
48932 TTTTAGCCATAAAGCATAA
1 TTTTAGCCATAAAGCATAA
*
48951 TTTTAGCCAT---GC--AC
1 TTTTAGCCATAAAGCATAA
48965 TTTTAGCCATAAAGCATAA
1 TTTTAGCCATAAAGCATAA
48984 TTTT
1 TTTT
48988 TCATGTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 11 0.37
16 2 0.07
17 2 0.07
19 15 0.50
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (19 bp):
TTTTAGCCATAAAGCATAA
Found at i:49744 original size:16 final size:16
Alignment explanation
Indices: 49725--49758 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
49715 AAATATATAT
*
49725 ATTAAAAAAATTAAAA
1 ATTAAAAAAATAAAAA
*
49741 ATTAAAGAAATAAAAA
1 ATTAAAAAAATAAAAA
49757 AT
1 AT
49759 ATTCAAAAAA
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:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
ATTAAAAAAATAAAAA
Found at i:50428 original size:12 final size:12
Alignment explanation
Indices: 50411--50436 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
50401 AGCTCACGGC
50411 AAGGAGAAAAAA
1 AAGGAGAAAAAA
50423 AAGGAGAAAAAA
1 AAGGAGAAAAAA
50435 AA
1 AA
50437 CAGCAGCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGGAGAAAAAA
Found at i:50723 original size:46 final size:46
Alignment explanation
Indices: 50673--50766 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
50663 GATGATTAGA
50673 TTAATGGAAAATGCCAAATTTAGAGTAAAATATAGAGGTGTGATGC
1 TTAATGGAAAATGCCAAATTTAGAGTAAAATATAGAGGTGTGATGC
50719 TTAATGGAAAATGCCAAATTTAGAGTAAAATATAGAGGTGTGATGC
1 TTAATGGAAAATGCCAAATTTAGAGTAAAATATAGAGGTGTGATGC
50765 TT
1 TT
50767 GATTTTATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.30
Consensus pattern (46 bp):
TTAATGGAAAATGCCAAATTTAGAGTAAAATATAGAGGTGTGATGC
Done.