Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold866
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: 16193
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:5184 original size:20 final size:20
Alignment explanation
Indices: 5146--5185 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
5136 TTTTAAATTT
5146 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
5167 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
5186 TATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:10267 original size:24 final size:24
Alignment explanation
Indices: 10238--10288 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
10228 TGGACATGTT
10238 AAAAATGCATG-AAACATAATAAAA
1 AAAAATGC-TGAAAACATAATAAAA
10262 AAAAATGCTGAAAACATAATAAAA
1 AAAAATGCTGAAAACATAATAAAA
10286 AAA
1 AAA
10289 TGTATGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.16
Consensus pattern (24 bp):
AAAAATGCTGAAAACATAATAAAA
Found at i:11968 original size:28 final size:28
Alignment explanation
Indices: 11866--13744 Score: 1731
Period size: 28 Copynumber: 66.5 Consensus size: 28
11856 CACTGACACG
** *
11866 TGTGGGCTTTGAATAGAGTGTTACTAACT
1 TGTGGGCTTTGAA-AGAGTGCCACTGACT
* *
11895 TGCGTGGGCTTTTAAAAGGGTGCCACTGACT
1 T--GTGGGC-TTTGAAAGAGTGCCACTGACT
11926 TGCGTGGGCTTTGAAAGAGTGCCACTGACT
1 T--GTGGGCTTTGAAAGAGTGCCACTGACT
* *
11956 CGTGGGCTTTGAAAGAATGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* *
11984 CGTGGGCTTTTGAAAAGGTTGCATGCCACTTGACT
1 TGTGGGC-TTTG-AAA-G-AG--TGCCAC-TGACT
* * *
12019 GCGTGCGGCTTT-AAAGGGTGCCACTAACT
1 -TGTG-GGCTTTGAAAGAGTGCCACTGACT
12048 TGCGTGGGCTTTGAAA-AGGATGCCACTGACT
1 T--GTGGGCTTTGAAAGA-G-TGCCACTGACT
12079 TGT-GGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
** *
12106 CATGGGCTTTGAAAG-GTTGCCACTAACT
1 TGTGGGCTTTGAAAGAG-TGCCACTGACT
* *
12134 CGTGGGC-TTGAAAGGGTGCCACT-ACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
12160 TGT-GGCTTTAAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAA-GAGTGCCACTGAC-T
* *
12189 GTGTGGGCTTTGAAA-TGTGCCACCGACT
1 -TGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
12217 TGTGGGCTTTAAAAAAGTGCCACTAAAT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
12245 TGTGGGCTTCGCAAGGGTGCCACTGGCT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
12273 TGTGTGCTTCGAAAGGGTTGCCACTGAC-
1 TGTGGGCTTTGAAAGAG-TGCCACTGACT
* * *
12301 TGTGGGCTCTAAAAGGAGTG-CAAT-ACTT
1 TGTGGGCTTTGAAA-GAGTGCCACTGAC-T
* *
12329 GTGTGGGCTTTAAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
12358 TGTGGGCTTTGAAATAGTACCACTGAAT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
12386 TGTGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
12414 TGTGGGCTTCGAAAGGGTG-CACTAACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
12441 TGTGGGCTTCGAACGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* *
12469 TGTGGGCTCTAAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAA-GAGTGCCACTGAC-T
*
12499 GTGTGGGCTTTGAAAGTGTGCCACTGACT
1 -TGTGGGCTTTGAAAGAGTGCCACTGACT
12528 TGT-GGCTTTGAAAGAGTGCCACTGA--
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* * * * *
12553 -ATGGGATTCGCAAGGGTGCCA-TGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
12579 TGTGGGCTTCGAAAGGGTGGCCACTAACT
1 TGTGGGCTTTGAAAGAGT-GCCACTGACT
*
12608 TGTGGGCTTTG-AAGAGTGCCA-TGA-A
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
12633 TATGGGCTTCGCAAGGGTTGCCACTGACT
1 TGTGGGCTTTGAAAGAG-TGCCACTGACT
* * *
12662 TGTGGGCTTCGAAAGGGTGCCA-TATACT
1 TGTGGGCTTTGAAAGAGTGCCACT-GACT
* *
12690 TATGGG-TTTGAAAG-GTGCCACTGAAT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
12716 TATGGGCTTCGCAAGGGTGCCAC-GACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
12743 TGTGAGCTTTGAAAGAGTGCCA-TGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* *
12770 CGTGGGCTTTGAAA-AGGTGCCATTGGACT
1 TGTGGGCTTTGAAAGA-GTGCCACT-GACT
*
12799 CGTGGGCTTTGAAAG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
12826 TGCGTGGGCTTT-AAATGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAA-GAGTGCCACTGAC-T
*
12857 GTGTGGGCTTTGAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGAGTGCCACTGACT
*
12886 TG-GGGCTTTG-AA-AGTGCCACTGAAT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* *
12911 TGTGGGCTTCGCAAG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
12938 TGTGGGCTTCGAAAGGGGTGCCACTAAACT
1 TGTGGGCTTTGAAA-GAGTGCCACT-GACT
*
12968 TGT-GGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
12995 TATGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* *
13023 TGTGGGC-TTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
13050 TGTGGGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
13078 TATGGGCTTCGCAAGGGTGCCACTGA-T
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
13105 TGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
13133 CGTGGGCTTTGAAA-AGGTTGCCACTGACT
1 TGTGGGCTTTGAAAGA-G-TGCCACTGACT
*
13162 CGTGGGCTTTGAAAG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
13189 TGCGTGGGCTTTTAAAAGGAGTGCCACTGACTT
1 T--GTGGGC-TTTGAAA-GAGTGCCACTGAC-T
*
13222 GTGTGGGCTTTGAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
13251 TATGGGCTTTAAAAGAGTGCCACTAAAT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
** * * *
13279 TGTGGGCTCCGCAAGGGTTGCCATTGACT
1 TGTGGGCTTTGAAAGAG-TGCCACTGACT
* *
13308 TGTGGGCTTCG-AAGCGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* *
13335 TGTGGGCTCTAAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAA-GAGTGCCACTGACT
* *
13364 TGTGTGGCTTTGAAAGGGTGCCATTGACT
1 TGTG-GGCTTTGAAAGAGTGCCACTGACT
*
13393 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
13421 TGTGGGCTTTGAAAAGAGTGCCACTGAAT
1 TGTGGGCTTTG-AAAGAGTGCCACTGACT
* * *
13450 TGTGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* *
13478 TGTGGGCTTCGAAAG-GTGTCCACTAACT
1 TGTGGGCTTTGAAAGAGTG-CCACTGACT
13506 TGTGGGCTTTGAAAG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
13533 TTTGGGCTTTGAAAGAGTGCCACTGA-T
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* *
13560 TGTGGGCTTTGCAAGGGTGCCA-TGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* *
13587 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
13615 TGT-GGCTTTGAAATG-GTGCCACTGACT
1 TGTGGGCTTTGAAA-GAGTGCCACTGACT
* * *
13642 TGTGGGCTTTAAAAGATTGCCACTGATT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
13670 TGTGGGCTTTGAAAAGAGTGCCACTGTCT
1 TGTGGGCTTTG-AAAGAGTGCCACTGACT
13699 TGTGGGCTTTGAAAGGAGTGTGCCACTGACT
1 TGTGGGCTTTGAAA-GA--GTGCCACTGACT
13730 TGTGGGCTTTGAAAG
1 TGTGGGCTTTGAAAG
13745 GGATGAACAT
Statistics
Matches: 1552, Mismatches: 198, Indels: 199
0.80 0.10 0.10
Matches are distributed among these distances:
24 4 0.00
25 39 0.03
26 45 0.03
27 388 0.25
28 532 0.34
29 280 0.18
30 118 0.08
31 95 0.06
32 24 0.02
33 2 0.00
34 10 0.01
35 5 0.00
36 7 0.00
37 3 0.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGAGTGCCACTGACT
Found at i:14978 original size:9 final size:8
Alignment explanation
Indices: 14966--15012 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
14956 TTTTTGCTAT
14966 TTTTTCTTG
1 TTTTT-TTG
14975 TTTTTTTG
1 TTTTTTTG
14983 TTTTTTT-
1 TTTTTTTG
*
14990 TGTTTGTT-
1 T-TTTTTTG
14998 TTTTTTTG
1 TTTTTTTG
15006 TTTTTTT
1 TTTTTTT
15013 TGGTGTAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 6 0.18
8 23 0.68
9 5 0.15
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:14978 original size:10 final size:10
Alignment explanation
Indices: 14954--15013 Score: 68
Period size: 10 Copynumber: 5.6 Consensus size: 10
14944 CCTTTTTCTC
14954 TTTTTTTGCTAT
1 TTTTTTTG-T-T
14966 TTTTTCTTGTT
1 TTTTT-TTGTT
14977 TTTTTGTT-TT
1 TTTTT-TTGTT
14987 TTTTGTTTGTT
1 TTTT-TTTGTT
14998 TTTTTTTGTT
1 TTTTTTTGTT
15008 TTTTTT
1 TTTTTT
15014 GGTGTAAAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 20 0.45
11 15 0.34
12 6 0.14
13 3 0.07
ACGTcount: A:0.02, C:0.03, G:0.10, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:15009 original size:21 final size:21
Alignment explanation
Indices: 14954--15012 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 21
14944 CCTTTTTCTC
14954 TTTTTTTGCTATTTTTTCTTGTT
1 TTTTTTTG-T-TTTTTTCTTGTT
14977 TTTTTGTT-TTTTTTGT-TTGTT
1 TTTTT-TTGTTTTTT-TCTTGTT
14998 TTTTTTTGTTTTTTT
1 TTTTTTTGTTTTTTT
15013 TGGTGTAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
20 3 0.09
21 21 0.64
22 2 0.06
23 5 0.15
24 2 0.06
ACGTcount: A:0.02, C:0.03, G:0.10, T:0.85
Consensus pattern (21 bp):
TTTTTTTGTTTTTTTCTTGTT
Found at i:15014 original size:9 final size:9
Alignment explanation
Indices: 14965--15013 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
14955 TTTTTTGCTA
14965 TTTTTTCTTG
1 TTTTTT-TTG
14975 -TTTTTTTG
1 TTTTTTTTG
14983 TTTTTTTTG
1 TTTTTTTTG
14992 TTTGTTTTT-
1 TTT-TTTTTG
15001 TTTTGTTTT-
1 TTTT-TTTTG
15010 TTTT
1 TTTT
15014 GGTGTAAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
8 4 0.11
9 27 0.75
10 5 0.14
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (9 bp):
TTTTTTTTG
Done.