Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2130
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: 26318
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:7735 original size:5 final size:5
Alignment explanation
Indices: 7725--7822 Score: 74
Period size: 6 Copynumber: 18.2 Consensus size: 5
7715 TATGTCTTTC
* *
7725 AAAAT AAAAT AATAAT AAAATT GAAAT GAAAAT AAAAAT CAAAAGA AAAAT
1 AAAAT AAAAT AA-AAT AAAA-T AAAAT -AAAAT -AAAAT -AAAA-T AAAAT
*
7776 AAAAAT AAAAT -AAAG AAAAT AAAAAT AAGAAT -AAAT AAAAT AAAAT
1 -AAAAT AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAAT AAAAT
7822 A
1 A
7823 GGAGGATTCA
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
4 6 0.08
5 31 0.41
6 39 0.51
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:7792 original size:21 final size:20
Alignment explanation
Indices: 7730--7820 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
7720 CTTTCAAAAT
*
7730 AAAATAATAATAAAATTGAAATG
1 AAAATAAAAATAAAA-T-AAA-G
* *
7753 AAAATAAAAATCAAA-AGA-
1 AAAATAAAAATAAAATAAAG
7771 AAAATAAAAATAAAATAAAG
1 AAAATAAAAATAAAATAAAG
*
7791 AAAATAAAAATAAGAATAAAT
1 AAAATAAAAATAA-AATAAAG
7812 AAAATAAAA
1 AAAATAAAA
7821 TAGGAGGATT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
18 14 0.24
19 2 0.03
20 15 0.25
21 15 0.25
23 13 0.22
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAATAAAAATAAAATAAAG
Found at i:7801 original size:26 final size:25
Alignment explanation
Indices: 7748--7814 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 25
7738 AATAAAATTG
* **
7748 AAATGAAAATAAA-AATCAAAAGAA
1 AAATAAAAATAAATAAAGAAAAGAA
*
7772 AAATAAAAATAAAATAAAGAAAATAA
1 AAATAAAAAT-AAATAAAGAAAAGAA
*
7798 AAATAAGAATAAATAAA
1 AAATAAAAATAAATAAA
7815 ATAAAATAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 9 0.25
25 10 0.28
26 17 0.47
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (25 bp):
AAATAAAAATAAATAAAGAAAAGAA
Found at i:7806 original size:35 final size:37
Alignment explanation
Indices: 7730--7822 Score: 111
Period size: 35 Copynumber: 2.5 Consensus size: 37
7720 CTTTCAAAAT
*
7730 AAAATAATAATAAAATTGAAATGAAAATAAAAATCAAAAGA
1 AAAATAAAAATAAAA-T-AAATGAAAATAAAAAT--AAAGA
7771 AAAATAAAAATAAAATAAA-GAAAATAAAAAT-AAGA
1 AAAATAAAAATAAAATAAATGAAAATAAAAATAAAGA
7806 ATAAAT-AAAATAAAATA
1 A-AAATAAAAATAAAATA
7823 GGAGGATTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
35 16 0.32
36 4 0.08
38 12 0.24
39 3 0.06
40 1 0.02
41 14 0.28
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.18
Consensus pattern (37 bp):
AAAATAAAAATAAAATAAATGAAAATAAAAATAAAGA
Found at i:16056 original size:28 final size:28
Alignment explanation
Indices: 16025--16082 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
16015 ACTTATGGAT
16025 TATTTTGAGATATTATTGATAGGGATTA
1 TATTTTGAGATATTATTGATAGGGATTA
16053 TATTTTGAGATATTATTGATAGGGATTA
1 TATTTTGAGATATTATTGATAGGGATTA
16081 TA
1 TA
16083 AATTGAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.47
Consensus pattern (28 bp):
TATTTTGAGATATTATTGATAGGGATTA
Found at i:16088 original size:28 final size:28
Alignment explanation
Indices: 16029--16090 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
16019 ATGGATTATT
**
16029 TTGAGATATTATTGATAGGGATTATATT
1 TTGAGATATTATTGATAGGGATTATAAA
16057 TTGAGATATTATTGATAGGGATTATAAA
1 TTGAGATATTATTGATAGGGATTATAAA
16085 TTGAGA
1 TTGAGA
16091 AGAATTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (28 bp):
TTGAGATATTATTGATAGGGATTATAAA
Found at i:21691 original size:25 final size:25
Alignment explanation
Indices: 21657--21706 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
21647 GGCAGGGGAG
21657 CCTGAAATCACTCTGACTCTGTCTC
1 CCTGAAATCACTCTGACTCTGTCTC
21682 CCTGAAATCACTCTGACTCTGTCTC
1 CCTGAAATCACTCTGACTCTGTCTC
21707 ACAAAAGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.36, G:0.12, T:0.32
Consensus pattern (25 bp):
CCTGAAATCACTCTGACTCTGTCTC
Found at i:23718 original size:27 final size:28
Alignment explanation
Indices: 23688--23830 Score: 98
Period size: 27 Copynumber: 5.3 Consensus size: 28
23678 CAGTCCTGGT
* *
23688 GGACCTTCT-ATATAGGATAGTCCTAAC
1 GGACCTTCTCACATAAGATAGTCCTAAC
23715 GGACCTT-TCACATAAGATAGTCCTAAC
1 GGACCTTCTCACATAAGATAGTCCTAAC
* * * * *
23742 GAACCTTC-CACATAATATAGTCTTGAT
1 GGACCTTCTCACATAAGATAGTCCTAAC
* * ** * *
23769 GGACCCTC-CACATATGATAGTATTGAT
1 GGACCTTCTCACATAAGATAGTCCTAAC
* * *
23796 GGACCTTC-CATACATGATAGTCCTAAC
1 GGACCTTCTCACATAAGATAGTCCTAAC
*
23823 AGACCTTC
1 GGACCTTC
23831 CACTTATATG
Statistics
Matches: 94, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
26 1 0.01
27 93 0.99
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (28 bp):
GGACCTTCTCACATAAGATAGTCCTAAC
Found at i:26073 original size:13 final size:13
Alignment explanation
Indices: 26051--26083 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
26041 AAGGTTTTTT
26051 TTAT-TAAACTAA
1 TTATCTAAACTAA
26063 TTATCTAAACTAA
1 TTATCTAAACTAA
*
26076 TTAACTAA
1 TTATCTAA
26084 TTTAGTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Done.