Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2308
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: 47061
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1522 original size:12 final size:12
Alignment explanation
Indices: 1501--1548 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
1491 ATTGTAGTTT
1501 CTCGAAAAAAAA
1 CTCGAAAAAAAA
1513 CTC--AAAAAAA
1 CTCGAAAAAAAA
*
1523 TTCGAAAAAAAA
1 CTCGAAAAAAAA
*
1535 TTCGAAAAAAAA
1 CTCGAAAAAAAA
1547 CT
1 CT
1549 AGTTTCCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 9 0.28
12 23 0.72
ACGTcount: A:0.65, C:0.15, G:0.06, T:0.15
Consensus pattern (12 bp):
CTCGAAAAAAAA
Found at i:1530 original size:22 final size:23
Alignment explanation
Indices: 1502--1545 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1492 TTGTAGTTTC
1502 TCGAAAAAAAACTC-AAAAAAAT
1 TCGAAAAAAAACTCGAAAAAAAT
*
1524 TCGAAAAAAAATTCGAAAAAAA
1 TCGAAAAAAAACTCGAAAAAAA
1546 ACTAGTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.68, C:0.11, G:0.07, T:0.14
Consensus pattern (23 bp):
TCGAAAAAAAACTCGAAAAAAAT
Found at i:1604 original size:12 final size:12
Alignment explanation
Indices: 1587--1633 Score: 69
Period size: 13 Copynumber: 3.8 Consensus size: 12
1577 TATCAAGTTG
1587 TGAAAAAAAATT
1 TGAAAAAAAATT
1599 TGAAAAAAAAATT
1 TG-AAAAAAAATT
1612 GTGAAAAAAAA-T
1 -TGAAAAAAAATT
1624 TGAAAAAAAA
1 TGAAAAAAAA
1634 GAGAGCTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.30
12 3 0.09
13 18 0.55
14 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (12 bp):
TGAAAAAAAATT
Found at i:1613 original size:26 final size:25
Alignment explanation
Indices: 1584--1633 Score: 91
Period size: 26 Copynumber: 2.0 Consensus size: 25
1574 GGATATCAAG
1584 TTGTGAAAAAAAATTTGAAAAAAAAA
1 TTGTGAAAAAAAA-TTGAAAAAAAAA
1610 TTGTGAAAAAAAATTGAAAAAAAA
1 TTGTGAAAAAAAATTGAAAAAAAA
1634 GAGAGCTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (25 bp):
TTGTGAAAAAAAATTGAAAAAAAAA
Found at i:5817 original size:12 final size:11
Alignment explanation
Indices: 5781--5820 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
5771 TAGTTTCTCG
*
5781 AAAAAAACTCA
1 AAAAAAATTCA
5792 AAAAAAATTCA
1 AAAAAAATTCA
5803 AAAAAAATTCGA
1 AAAAAAATTC-A
5815 AAAAAA
1 AAAAAA
5821 CTAGTTTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 20 0.74
12 7 0.26
ACGTcount: A:0.75, C:0.10, G:0.03, T:0.12
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:5882 original size:14 final size:13
Alignment explanation
Indices: 5863--5908 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
5853 TCAAGTTGTG
5863 AAAAAAAATTTGA
1 AAAAAAAATTTGA
5876 AAAAAAAATTGTGA
1 AAAAAAAATT-TGA
5890 AAAAAAAA-TTGA
1 AAAAAAAATTTGA
5902 AAAAAAA
1 AAAAAAA
5909 GAGAGCTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.31
13 11 0.34
14 11 0.34
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTTGA
Found at i:5887 original size:26 final size:26
Alignment explanation
Indices: 5858--5908 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
5848 GGATATCAAG
*
5858 TTGTGAAAAAAAATTTGAAAAAAAAA
1 TTGTGAAAAAAAAATTGAAAAAAAAA
5884 TTGTGAAAAAAAAATTGAAAAAAAA
1 TTGTGAAAAAAAAATTGAAAAAAAA
5909 GAGAGCTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.22
Consensus pattern (26 bp):
TTGTGAAAAAAAAATTGAAAAAAAAA
Found at i:18835 original size:20 final size:20
Alignment explanation
Indices: 18788--18835 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
18778 AGTAAGCTCG
18788 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
18808 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
18828 GTTGAGCT
1 GTTGAGCT
18836 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:23258 original size:20 final size:20
Alignment explanation
Indices: 23211--23258 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
23201 AGTAAGCTCG
23211 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
23231 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
23251 GTTGAGCT
1 GTTGAGCT
23259 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:24927 original size:11 final size:12
Alignment explanation
Indices: 24897--24928 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
24887 TTTCACTCTT
24897 CTCTTTTTCAAA
1 CTCTTTTTCAAA
24909 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
24921 TTCTTTTT
1 CTCTTTTT
24929 TCGCTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:24940 original size:27 final size:27
Alignment explanation
Indices: 24910--24971 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
24900 TTTTTCAAAC
*
24910 TCTTTTTCAAATTCTT-TTTTC-GCTTTT
1 TCTTTTTC-AATT-TTCTTTTCTGCATTT
*
24937 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATTTTCTTTTCTGCATTT
24964 TCTTTTTC
1 TCTTTTTC
24972 TCTCTCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 9 0.29
27 20 0.65
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATTTTCTTTTCTGCATTT
Found at i:24963 original size:14 final size:14
Alignment explanation
Indices: 24912--24970 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
24902 TTTCAAACTC
*
24912 TTTTTCAA-ATTCT
1 TTTTTCAATTTTCT
**
24925 TTTTTCGCTTTT-T
1 TTTTTCAATTTTCT
24938 CTTTTTCAATTTTCT
1 -TTTTTCAATTTTCT
24953 TTTCTTC-ATTTTCT
1 TTT-TTCAATTTTCT
24967 TTTT
1 TTTT
24971 CTCTCTCTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 8 0.22
14 25 0.68
15 4 0.11
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTCAATTTTCT
Found at i:26102 original size:15 final size:15
Alignment explanation
Indices: 26084--26134 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
26074 TTTAACTTGA
26084 TTTTTTTTTGCTCAC
1 TTTTTTTTTGCTCAC
**
26099 TTTTTTTTT-CTTTC
1 TTTTTTTTTGCTCAC
26113 TTTTTTTTTGCTCGA-
1 TTTTTTTTTGCTC-AC
26128 TTTTTTT
1 TTTTTTT
26135 CACTTCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.04, C:0.14, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTTTTTTTGCTCAC
Found at i:26116 original size:29 final size:30
Alignment explanation
Indices: 26065--26134 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
26055 GCAAGACTTT
26065 TCACTTTTTTTTAACTTGATTTTTTTTTGC
1 TCACTTTTTTTTAACTTGATTTTTTTTTGC
* **
26095 TCACTTTTTTTT-TCTTTCTTTTTTTTTGC
1 TCACTTTTTTTTAACTTGATTTTTTTTTGC
26124 TCGA-TTTTTTT
1 TC-ACTTTTTTT
26135 CACTTCTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.64
30 13 0.36
ACGTcount: A:0.09, C:0.14, G:0.06, T:0.71
Consensus pattern (30 bp):
TCACTTTTTTTTAACTTGATTTTTTTTTGC
Found at i:26145 original size:29 final size:28
Alignment explanation
Indices: 26065--26146 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 28
26055 GCAAGACTTT
*
26065 TCACTTTTTTTTAACTTGATTTTTTTTTGC
1 TCAC-TTTTTTTAACTT-TTTTTTTTTTGC
**
26095 TCACTTTTTTTTTCTTTCTTTTTTTTTGC
1 TCACTTTTTTTAACTTT-TTTTTTTTTGC
* *
26124 TCGA-TTTTTTTCACTTCTTTTTT
1 TC-ACTTTTTTTAACTTTTTTTTT
26147 GAATTTTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
28 6 0.14
29 33 0.75
30 5 0.11
ACGTcount: A:0.09, C:0.16, G:0.05, T:0.71
Consensus pattern (28 bp):
TCACTTTTTTTAACTTTTTTTTTTTTGC
Found at i:30613 original size:30 final size:30
Alignment explanation
Indices: 30579--30675 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
30569 AGCTCACTCC
*
30579 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
30609 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
30639 TAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
30669 TAGCTCA
1 TAGCTCA
30676 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 48 0.91
31 5 0.09
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:32401 original size:12 final size:12
Alignment explanation
Indices: 32384--32412 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
32374 TATACAAGTC
32384 AAAAAAATTCAA
1 AAAAAAATTCAA
32396 AAAAAAATTCAA
1 AAAAAAATTCAA
32408 AAAAA
1 AAAAA
32413 TTTCGAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:32421 original size:11 final size:11
Alignment explanation
Indices: 32384--32426 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
32374 TATACAAGTC
32384 AAAAAAATTCAA
1 AAAAAAATTC-A
32396 AAAAAAATTCA
1 AAAAAAATTCA
*
32407 AAAAAATTTCGA
1 AAAAAAATTC-A
32419 AAAGAAAA
1 AAA-AAAA
32427 AAAAATCTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 10 0.37
12 14 0.52
13 3 0.11
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:32443 original size:17 final size:19
Alignment explanation
Indices: 32406--32443 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
32396 AAAAAAATTC
*
32406 AAAAAAATTTCGAAAAGAA
1 AAAAAAATCTCGAAAAGAA
32425 AAAAAAATCT-GAAAA-AA
1 AAAAAAATCTCGAAAAGAA
32442 AA
1 AA
32444 TGTGTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
19 9 0.50
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (19 bp):
AAAAAAATCTCGAAAAGAA
Found at i:33379 original size:21 final size:20
Alignment explanation
Indices: 33345--33412 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
33335 ACATTCTTGT
33345 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
33366 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
33387 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
33408 AAAGA
1 AAAGA
33413 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:33380 original size:6 final size:5
Alignment explanation
Indices: 33356--33412 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
33346 AAGAGAAAAC
*
33356 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
33403 AAAGA AAAGA
1 AAAGA AAAGA
33413 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:33387 original size:15 final size:14
Alignment explanation
Indices: 33356--33412 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
33346 AAGAGAAAAC
33356 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
33372 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
33387 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
33403 AAAGAAAAGA
1 AAAGAAAAGA
33413 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:33489 original size:12 final size:12
Alignment explanation
Indices: 33481--33505 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33471 TTTGAAAAGC
33481 AAAAAGAAAATG
1 AAAAAGAAAATG
33493 AAAAAGAAAATG
1 AAAAAGAAAATG
33505 A
1 A
33506 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:33502 original size:18 final size:18
Alignment explanation
Indices: 33475--33530 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
33465 AAAGCCTTTG
33475 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
33494 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
33512 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
33529 AA
1 AA
33531 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:33515 original size:30 final size:31
Alignment explanation
Indices: 33481--33562 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
33471 TTTGAAAAGC
*
33481 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
33511 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
33541 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
33563 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:36696 original size:30 final size:31
Alignment explanation
Indices: 36662--36758 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
36652 AGCTCACTCC
*
36662 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
36692 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
36722 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
36752 TAGCTCA
1 TAGCTCA
36759 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:42332 original size:33 final size:33
Alignment explanation
Indices: 42294--42356 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
42284 GATTACTCAC
42294 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
42327 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
42357 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:42383 original size:21 final size:21
Alignment explanation
Indices: 42354--42409 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
42344 CAAGCTCTCT
*
42354 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
42375 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
42396 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
42410 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:42402 original size:14 final size:14
Alignment explanation
Indices: 42353--42409 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
42343 TCAAGCTCTC
42353 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
42366 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
42380 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
42394 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
42408 TT
1 TT
42410 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:42446 original size:18 final size:17
Alignment explanation
Indices: 42423--42484 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 17
42413 TCACTTTTTG
42423 ATTTCTTTTTCTTTTGCA
1 ATTTCTTTTTCTTTT-CA
42441 ATTTCTTTTTCTTTTTC-
1 ATTTCTTTTTC-TTTTCA
*
42458 -TTTTTGTTTTC-TTTCA
1 ATTTCT-TTTTCTTTTCA
42474 ATTTCTTTTTC
1 ATTTCTTTTTC
42485 AATCTCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 4 0.11
16 9 0.24
17 9 0.24
18 12 0.32
19 4 0.11
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.73
Consensus pattern (17 bp):
ATTTCTTTTTCTTTTCA
Found at i:42484 original size:6 final size:6
Alignment explanation
Indices: 42371--42471 Score: 62
Period size: 6 Copynumber: 16.7 Consensus size: 6
42361 TCTTTTTTCG
* * * **
42371 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
42422 -GATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CTTTTT -GTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
42468 CTTT
1 CTTT
42472 CAATTTCTTT
Statistics
Matches: 68, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
5 7 0.10
6 49 0.72
7 9 0.13
8 3 0.04
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:42484 original size:12 final size:12
Alignment explanation
Indices: 42430--42494 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 12
42420 TTGATTTCTT
*
42430 TTTCTTTTGCAA
1 TTTCTTTTTCAA
**
42442 TTTCTTTTTCTT
1 TTTCTTTTTCAA
*
42454 TTTCTTTTT--G
1 TTTCTTTTTCAA
*
42464 TTT-TCTTTCAA
1 TTTCTTTTTCAA
42475 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
42487 TCTCTTTT
1 TTTCTTTT
42495 CCTTTTCTCG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
9 4 0.10
10 3 0.07
11 3 0.07
12 32 0.76
ACGTcount: A:0.09, C:0.17, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:43524 original size:28 final size:28
Alignment explanation
Indices: 43465--43525 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
43455 TTAAACTTGA
*
43465 TTTTTTTTGCTCACCTTTTTTTCTTTTCT
1 TTTTTTTTGCTCA-CTTTTTTTCCTTTCT
43494 TTTTTTTTGCTCGA-TTTTTTTCACTTT-T
1 TTTTTTTTGCTC-ACTTTTTTTC-CTTTCT
43522 TTTT
1 TTTT
43526 GAATTTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 13 0.45
29 15 0.52
30 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (28 bp):
TTTTTTTTGCTCACTTTTTTTCCTTTCT
Done.