Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold795
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: 15455
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:985 original size:34 final size:33
Alignment explanation
Indices: 921--986 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
911 TTAAAGATGT
* *
921 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
954 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
987 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:2990 original size:16 final size:16
Alignment explanation
Indices: 2969--3000 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2959 CATTCTGCAT
2969 TTAAACAACAACAGCA
1 TTAAACAACAACAGCA
*
2985 TTAAACAACAGCAGCA
1 TTAAACAACAACAGCA
3001 AAACACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.25, G:0.09, T:0.12
Consensus pattern (16 bp):
TTAAACAACAACAGCA
Found at i:6492 original size:24 final size:23
Alignment explanation
Indices: 6438--6515 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
6428 GGATAATTGA
**
6438 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
6461 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
6485 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
6506 GAAATAGTAT
1 GAAATGGTAT
6516 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:6500 original size:21 final size:21
Alignment explanation
Indices: 6474--6540 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
6464 TTGGTATTTG
6474 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
6495 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
6516 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
6539 GG
1 GG
6541 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:10756 original size:15 final size:15
Alignment explanation
Indices: 10736--10845 Score: 53
Period size: 17 Copynumber: 6.9 Consensus size: 15
10726 TTTTCACTCA
10736 CTTTTTCTTTTTCTT
1 CTTTTTCTTTTTCTT
*
10751 CTTTTTCTTTTATCGCT
1 CTTTTTCTTTT-TC-TT
* *
10768 CTCTTTTCATTCTCTT
1 CT-TTTTCTTTTTCTT
**
10784 -TTTTTGAATTTTCTTT
1 CTTTTT-CTTTTTC-TT
*
10800 TTTTTTCATTTTTCTT
1 CTTTTTC-TTTTTCTT
* * *
10816 TTCTTTTGTATTTTCGT
1 CT-TTTTCT-TTTTCTT
10833 C-TTTTCTTTTTCT
1 CTTTTTCTTTTTCT
10846 CTCATTTGAT
Statistics
Matches: 73, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
14 9 0.12
15 22 0.30
16 10 0.14
17 25 0.34
18 7 0.10
ACGTcount: A:0.05, C:0.18, G:0.04, T:0.73
Consensus pattern (15 bp):
CTTTTTCTTTTTCTT
Found at i:10802 original size:17 final size:17
Alignment explanation
Indices: 10777--10830 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
10767 TCTCTTTTCA
*
10777 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
10794 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
10811 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
10828 TTC
1 TTC
10831 GTCTTTTCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:10812 original size:12 final size:11
Alignment explanation
Indices: 10792--10842 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
10782 TTTTTTTGAA
10792 TTTTCTTTTT-
1 TTTTCTTTTTC
10802 TTTTCATTTTTC
1 TTTTC-TTTTTC
*
10814 TTTTCTTTTGTA
1 TTTTCTTTT-TC
10826 TTTTCGTCTTTTC
1 TTTTC-T-TTTTC
10839 TTTT
1 TTTT
10843 TCTCTCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
10 5 0.15
11 9 0.26
12 11 0.32
13 6 0.18
14 3 0.09
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.78
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:13059 original size:14 final size:13
Alignment explanation
Indices: 13040--13087 Score: 87
Period size: 13 Copynumber: 3.6 Consensus size: 13
13030 CCGTATGCAA
13040 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
13053 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
13066 TTTTTTTTTCGAAT
1 TTTTTTTTTC-AAT
13080 TTTTTTTT
1 TTTTTTTT
13088 ACGCACCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 23 0.68
14 11 0.32
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:13420 original size:21 final size:21
Alignment explanation
Indices: 13396--13462 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
13386 TTGGTTTGTG
13396 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
13417 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
13438 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
13461 GG
1 GG
13463 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Done.