Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2473
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: 66056
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4346 original size:19 final size:19
Alignment explanation
Indices: 4322--4360 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
4312 CACTCATTCA
4322 TCATGGTAAAGAAGGCTTG
1 TCATGGTAAAGAAGGCTTG
4341 TCATGGTAAAGAAGGCTTG
1 TCATGGTAAAGAAGGCTTG
4360 T
1 T
4361 TTAGCCCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (19 bp):
TCATGGTAAAGAAGGCTTG
Found at i:6207 original size:28 final size:28
Alignment explanation
Indices: 6144--6241 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
6134 ATATTAAGTC
*
6144 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
6171 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
6199 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
6228 CGCACACTTAGTGC
1 CGCACACTTAGTGC
6242 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:8924 original size:15 final size:15
Alignment explanation
Indices: 8901--8930 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8891 TTTAGTAGTT
8901 TATAAACAAAAAAAA
1 TATAAACAAAAAAAA
*
8916 TATATACAAAAAAAA
1 TATAAACAAAAAAAA
8931 CTACTTTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
TATAAACAAAAAAAA
Found at i:11097 original size:12 final size:12
Alignment explanation
Indices: 11078--11111 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11068 AAAAAGAAAA
11078 GAGTGAAAAGGT
1 GAGTGAAAAGGT
* *
11090 GTGTGAAAAAGT
1 GAGTGAAAAGGT
11102 GAGTGAAAAG
1 GAGTGAAAAG
11112 AAACGAGGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (12 bp):
GAGTGAAAAGGT
Found at i:12512 original size:4 final size:4
Alignment explanation
Indices: 12503--12530 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
12493 AAGTTTTATT
12503 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
12531 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:19536 original size:33 final size:33
Alignment explanation
Indices: 19498--19560 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
19488 GATTACTCAC
19498 TTCACTCG-TTTCTTTTACAAACTCTCTTTCTTT
1 TTCACTCGATTTCTTTT-CAAACTCTCTTTCTTT
* *
19531 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAACTCTCTTTC
19561 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 19 0.70
34 8 0.30
ACGTcount: A:0.14, C:0.27, G:0.05, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAACTCTCTTTCTTT
Found at i:19587 original size:21 final size:21
Alignment explanation
Indices: 19558--19613 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
19548 CAAGCTCTCT
*
19558 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
19579 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
19600 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
19614 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:19606 original size:14 final size:14
Alignment explanation
Indices: 19557--19613 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
19547 TCAAGCTCTC
19557 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
19570 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
19584 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
19598 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
19612 TT
1 TT
19614 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:19641 original size:18 final size:18
Alignment explanation
Indices: 19620--19678 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
19610 TTTTCTCTCA
19620 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
19638 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
19656 CTTCTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
19674 GTTTT
1 CTTTT
19679 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:19695 original size:6 final size:6
Alignment explanation
Indices: 19575--19682 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
19565 TCTTTTTTCG
* * * **
19575 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
19626 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
19674 -GTTTT CTTT
1 CTTTTT CTTT
19683 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 27, Indels: 6
0.69 0.26 0.06
Matches are distributed among these distances:
5 4 0.06
6 56 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:20557 original size:12 final size:12
Alignment explanation
Indices: 20541--20578 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
20531 TTTTTGCTCG
20541 ATTTTTTTTTCA
1 ATTTTTTTTTCA
* *
20553 CTTTTTTTTTGA
1 ATTTTTTTTTCA
20565 ATTTTTTTTTCA
1 ATTTTTTTTTCA
20577 AT
1 AT
20579 CAAAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.74
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:20557 original size:24 final size:24
Alignment explanation
Indices: 20530--20576 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
20520 TCTTTTCTTT
20530 TTTTTTGCTCG-ATTTTTTTTTCAC
1 TTTTTT-CTCGAATTTTTTTTTCAC
* *
20554 TTTTTTTTTGAATTTTTTTTTCA
1 TTTTTTCTCGAATTTTTTTTTCA
20577 ATCAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (24 bp):
TTTTTTCTCGAATTTTTTTTTCAC
Found at i:20561 original size:30 final size:30
Alignment explanation
Indices: 20497--20562 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
20487 TTAAACTTGA
*
20497 TTTTTTTTTGCTCACCTTTTTTTTCTTTTC
1 TTTTTTTTTGCTCACCTTTTTTTTCCTTTC
*
20527 TTTTTTTTTGCTCGA-TTTTTTTTTCACTTT-
1 TTTTTTTTTGCTC-ACCTTTTTTTTC-CTTTC
20557 TTTTTT
1 TTTTTT
20563 GAATTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.76
Consensus pattern (30 bp):
TTTTTTTTTGCTCACCTTTTTTTTCCTTTC
Found at i:20598 original size:13 final size:13
Alignment explanation
Indices: 20528--20604 Score: 52
Period size: 13 Copynumber: 5.6 Consensus size: 13
20518 TTTCTTTTCT
20528 TTTTTTTTGCTCG-A
1 TTTTTTTT--TCGAA
*
20542 TTTTTTTTTC-AC
1 TTTTTTTTTCGAA
20554 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
*
20566 TTTTTTTTTCAATCAAAA
1 -TTTTTTTT---TC-GAA
20584 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
20597 TTTTTTTT
1 TTTTTTTT
20605 GATTTTTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
12 12 0.24
13 18 0.35
14 10 0.20
16 1 0.02
17 8 0.16
18 2 0.04
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:21944 original size:11 final size:10
Alignment explanation
Indices: 21930--21967 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
21920 ACTTTTCACT
21930 TTTTTTTGTTC
1 TTTTTTT-TTC
*
21941 TTTTTTTTAC
1 TTTTTTTTTC
21951 TTTTTTTTTC
1 TTTTTTTTTC
21961 TTTTTTT
1 TTTTTTT
21968 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:21975 original size:23 final size:21
Alignment explanation
Indices: 21922--21983 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 21
21912 CTCACAAGAC
21922 TTTTCACTTTTTTTTGTTCTTTT
1 TTTTCAC-TTTTTTT-TTCTTTT
21945 TTTT-ACTTTTTTTTTCTTTT
1 TTTTCACTTTTTTTTTCTTTT
21965 TTTGCTCACTTCTTTTTTT
1 TTT--TCACTT-TTTTTTT
21984 TTGAATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 10 0.29
21 7 0.20
22 3 0.09
23 8 0.23
24 7 0.20
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTTCACTTTTTTTTTCTTTT
Found at i:23537 original size:20 final size:20
Alignment explanation
Indices: 23514--23560 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
23504 AGGTTAAGAT
*
23514 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
23534 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
23554 TGAGCTG
1 TGAGCTG
23561 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:25198 original size:10 final size:10
Alignment explanation
Indices: 25185--25219 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
25175 AAGCTCGGTT
25185 GAGCTCAAAC
1 GAGCTCAAAC
*
25195 GAGCTGAAAC
1 GAGCTCAAAC
*
25205 GAGCTTAAAC
1 GAGCTCAAAC
25215 GAGCT
1 GAGCT
25220 GAGTTGAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:25228 original size:20 final size:20
Alignment explanation
Indices: 25182--25229 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
25172 AGTAAGCTCG
25182 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
25202 AACGAGCTTAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
25222 GTTGAGCT
1 GTTGAGCT
25230 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:28392 original size:13 final size:13
Alignment explanation
Indices: 28376--28406 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28366 AAAAATAATA
28376 ATAAAATGTTTTC
1 ATAAAATGTTTTC
*
28389 ATAAGATGTTTTC
1 ATAAAATGTTTTC
28402 ATAAA
1 ATAAA
28407 GGGTGGCTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (13 bp):
ATAAAATGTTTTC
Found at i:31339 original size:23 final size:22
Alignment explanation
Indices: 31287--31339 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
31277 TCCACGTCTT
*
31287 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
31309 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
31332 TTTCTTTT
1 TTTCTTTT
31340 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:36137 original size:15 final size:14
Alignment explanation
Indices: 36104--36143 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
36094 ATAGAAATAT
*
36104 CAAAAGAAAAAGAG
1 CAAAAGAAAAAGAA
*
36118 CAAAATAAAAAGAA
1 CAAAAGAAAAAGAA
36132 CGAAAAGAAAAA
1 C-AAAAGAAAAA
36144 TAGTGGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.75, C:0.07, G:0.15, T:0.03
Consensus pattern (14 bp):
CAAAAGAAAAAGAA
Found at i:37888 original size:18 final size:18
Alignment explanation
Indices: 37855--37889 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37845 TTGCTACTGG
*
37855 TTTTAATGTGCCAATTTT
1 TTTTAATGAGCCAATTTT
*
37873 TTTTAATGAGCTAATTT
1 TTTTAATGAGCCAATTT
37890 AATGTGCTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTTAATGAGCCAATTTT
Found at i:38739 original size:19 final size:19
Alignment explanation
Indices: 38715--38754 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
38705 AGCTCCCATG
38715 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
38734 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
38753 TA
1 TA
38755 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:41312 original size:27 final size:26
Alignment explanation
Indices: 41281--41339 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
41271 AATACATAGT
*
41281 TTTAATATGTCTATTTTA-GGACATCAA
1 TTTAATATGTCTATCTTAGGGACA--AA
*
41308 TTTAATGTGTCTATCTTAGGGACAAA
1 TTTAATATGTCTATCTTAGGGACAAA
41334 TTTAAT
1 TTTAAT
41340 CAGCTACTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.28
27 16 0.55
28 5 0.17
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (26 bp):
TTTAATATGTCTATCTTAGGGACAAA
Found at i:44458 original size:20 final size:20
Alignment explanation
Indices: 44435--44481 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
44425 GGGTTAAGAT
*
44435 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
44455 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
44475 TGAGCTG
1 TGAGCTG
44482 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:47325 original size:12 final size:11
Alignment explanation
Indices: 47310--47351 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
47300 GACTTTTCAC
47310 TTCTTTTTTTT
1 TTCTTTTTTTT
47321 GTTCTTTTTTTT
1 -TTCTTTTTTTT
*
47333 TAC--TTTTTT
1 TTCTTTTTTTT
47342 TTCTTTTTTT
1 TTCTTTTTTT
47352 GCTCACTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 8 0.31
11 7 0.27
12 11 0.42
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:47328 original size:11 final size:10
Alignment explanation
Indices: 47314--47351 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
47304 TTTCACTTCT
47314 TTTTTTTGTTC
1 TTTTTTT-TTC
47325 TTTTTTTTTAC
1 TTTTTTTTT-C
47336 -TTTTTTTTC
1 TTTTTTTTTC
47345 TTTTTTT
1 TTTTTTT
47352 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 1 0.04
10 16 0.64
11 8 0.32
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:47359 original size:22 final size:20
Alignment explanation
Indices: 47315--47386 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 20
47305 TTCACTTCTT
*
47315 TTTTTTGTTCTTTTTTTTTAC
1 TTTTTT-TTCTTTTTTTTCAC
47336 TTTTTTTTCTTTTTTTGCTCAC
1 TTTTTTTTCTTTTTTT--TCAC
* *
47358 TTCTTTTTT-TTTTAATTTCAA
1 TT-TTTTTTCTTTT-TTTTCAC
47379 TTTTTTTT
1 TTTTTTTT
47387 GTGATACTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
20 16 0.36
21 11 0.25
22 9 0.20
23 8 0.18
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTTTTTCTTTTTTTTCAC
Found at i:48923 original size:20 final size:20
Alignment explanation
Indices: 48900--48946 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
48890 GGGTTAAGAT
*
48900 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
48920 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
48940 TGAGCTG
1 TGAGCTG
48947 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:54840 original size:10 final size:10
Alignment explanation
Indices: 54827--54872 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
54817 AGCTCCGTCT
*
54827 AGCTCAATTC
1 AGCTCATTTC
*
54837 AGCTCATTTG
1 AGCTCATTTC
54847 AGCTCATTTC
1 AGCTCATTTC
* *
54857 AGCTCGTTTG
1 AGCTCATTTC
54867 AGCTCA
1 AGCTCA
54873 CCAAGCTTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (10 bp):
AGCTCATTTC
Found at i:54850 original size:20 final size:20
Alignment explanation
Indices: 54827--54872 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
54817 AGCTCCGTCT
54827 AGCTCAATTCAGCTCATTTG
1 AGCTCAATTCAGCTCATTTG
* *
54847 AGCTCATTTCAGCTCGTTTG
1 AGCTCAATTCAGCTCATTTG
54867 AGCTCA
1 AGCTCA
54873 CCAAGCTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (20 bp):
AGCTCAATTCAGCTCATTTG
Found at i:56626 original size:12 final size:12
Alignment explanation
Indices: 56611--56641 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
56601 TTCTTTTTGC
56611 TTTTCAAAGGCT
1 TTTTCAAAGGCT
56623 TTTTCAAAGGCT
1 TTTTCAAAGGCT
56635 TTTTCAA
1 TTTTCAA
56642 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:56698 original size:5 final size:5
Alignment explanation
Indices: 56688--56744 Score: 59
Period size: 5 Copynumber: 12.0 Consensus size: 5
56678 CCTCTTGCTC
* *
56688 TCTTT TCTTT T-TTAT T-TTT TCTTT TC-TT TC-TT GCTTT TTTTT TCTTT
1 TCTTT TCTTT TCTT-T TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT
56735 TCTTT TCTTT
1 TCTTT TCTTT
56745 GTTTTCTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
4 11 0.24
5 34 0.76
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:56749 original size:14 final size:13
Alignment explanation
Indices: 56688--56751 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 13
56678 CCTCTTGCTC
56688 TCTTTTCTTTTTT
1 TCTTTTCTTTTTT
*
56701 ATTTTTTCTTTTCTT
1 -TCTTTTCTTTT-TT
56716 TCTTGCTT-TTTTTT
1 TCTT--TTCTTTTTT
56730 TCTTTTCTTTTCTT
1 TCTTTTCTTTT-TT
*
56744 TGTTTTCT
1 TCTTTTCT
56752 CTTTACAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
12 2 0.05
13 4 0.10
14 28 0.67
15 6 0.14
16 2 0.05
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.80
Consensus pattern (13 bp):
TCTTTTCTTTTTT
Found at i:56749 original size:19 final size:19
Alignment explanation
Indices: 56688--56751 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
56678 CCTCTTGCTC
56688 TCTTTTCTTTT-TTATTTTT
1 TCTTTTCTTTTCTT-TTTTT
56707 TCTTTTCTTTCTTGCTTTTTTTT
1 TCTTTTC-TT-TT-C-TTTTTTT
*
56730 TCTTTTCTTTTCTTTGTTT
1 TCTTTTCTTTTCTTTTTTT
56749 TCT
1 TCT
56752 CTTTACAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 16 0.41
20 3 0.08
21 4 0.10
22 2 0.05
23 12 0.31
24 2 0.05
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.80
Consensus pattern (19 bp):
TCTTTTCTTTTCTTTTTTT
Found at i:57672 original size:13 final size:13
Alignment explanation
Indices: 57654--57723 Score: 72
Period size: 13 Copynumber: 5.5 Consensus size: 13
57644 AAAAAAAAAA
57654 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
57667 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
**
57680 TTTTTTTTCAAAT
1 TTTTTTTTTGAAT
* * * *
57693 TTCTCTTCT-ATT
1 TTTTTTTTTGAAT
57705 TTTTTTTTTG-AT
1 TTTTTTTTTGAAT
57717 TTTTTTT
1 TTTTTTT
57724 CAATTACAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
12 16 0.36
13 29 0.64
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Done.