Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2446
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: 60194
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3805 original size:13 final size:15
Alignment explanation
Indices: 3787--3820 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3777 CAAGTTTGTG
*
3787 AAAAAAATT-TTGAA
1 AAAAAAATTGTAGAA
3801 AAAAAAATTGTAGAA
1 AAAAAAATTGTAGAA
3816 AAAAA
1 AAAAA
3821 GAGAGCTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (15 bp):
AAAAAAATTGTAGAA
Found at i:4936 original size:16 final size:18
Alignment explanation
Indices: 4894--4938 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4884 CAAAGAGATT
4894 GTGGAAAAAGAAAGAGAA
1 GTGGAAAAAGAAAGAGAA
* *
4912 GTTGAAAAAGAAA-CG-A
1 GTGGAAAAAGAAAGAGAA
4928 GTGGAAAAAGA
1 GTGGAAAAAGA
4939 TGAAAGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
17 1 0.04
18 12 0.50
ACGTcount: A:0.58, C:0.02, G:0.31, T:0.09
Consensus pattern (18 bp):
GTGGAAAAAGAAAGAGAA
Found at i:7069 original size:22 final size:21
Alignment explanation
Indices: 7035--7077 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
7025 GGGCTGTTAA
*
7035 AAAAGGAGCTTAAAGATCATT
1 AAAAGGAGCTTAAAGAGCATT
*
7056 AAAAGGAGTTTTAAAGAGCATT
1 AAAAGGAG-CTTAAAGAGCATT
7078 TTATGCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (21 bp):
AAAAGGAGCTTAAAGAGCATT
Found at i:7836 original size:11 final size:11
Alignment explanation
Indices: 7822--7863 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
7812 AAAAAATTTG
7822 AAAAAAAATCA
1 AAAAAAAATCA
7833 AAAAAAAATCA
1 AAAAAAAATCA
*
7844 AAAAAATTAATTA
1 AAAAAA--AATCA
7857 AAAAAAA
1 AAAAAAA
7864 TTGTATACGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 18 0.64
13 10 0.36
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:24350 original size:16 final size:16
Alignment explanation
Indices: 24329--24370 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
24319 TAGCTTCTTC
24329 TTTTTTTTCACGAAAT
1 TTTTTTTTCACGAAAT
*
24345 TTTTTTTTCACGAATT
1 TTTTTTTTCACGAAAT
24361 TTTTTTTTCA
1 TTTTTTTTCA
24371 ACTTGATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTTTTTCACGAAAT
Found at i:24435 original size:20 final size:20
Alignment explanation
Indices: 24410--24447 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
24400 GGAAACCAAA
24410 TTTTTTTTCAATTTTTTTTT
1 TTTTTTTTCAATTTTTTTTT
*
24430 TTTTTTTTGAATTTTTTT
1 TTTTTTTTCAATTTTTTT
24448 GAAGAAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.84
Consensus pattern (20 bp):
TTTTTTTTCAATTTTTTTTT
Found at i:27010 original size:13 final size:13
Alignment explanation
Indices: 26994--27023 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
26984 TTTAAACAAA
*
26994 TTAATTAACTTAT
1 TTAATTAACTAAT
27007 TTAATTAACTAAT
1 TTAATTAACTAAT
27020 TTAA
1 TTAA
27024 CTGATGTGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:42976 original size:6 final size:6
Alignment explanation
Indices: 42965--42998 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
42955 AATTTTTTTC
* *
42965 TCAATA TCAATA TCAATA TCAATC TCAATC TCAA
1 TCAATA TCAATA TCAATA TCAATA TCAATA TCAA
42999 ATTCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (6 bp):
TCAATA
Found at i:43021 original size:25 final size:25
Alignment explanation
Indices: 42987--43040 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
42977 TCAATATCAA
*
42987 TCTCAATCTCAAATTCTTTTTTTTT
1 TCTCAATCTCAAATTCTTTTTTTCT
* **
43012 TCTCACTCTCATTTTCTTTTTTTCT
1 TCTCAATCTCAAATTCTTTTTTTCT
43037 TCTC
1 TCTC
43041 TCAATTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (25 bp):
TCTCAATCTCAAATTCTTTTTTTCT
Found at i:43041 original size:21 final size:22
Alignment explanation
Indices: 43006--43048 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
42996 CAAATTCTTT
*
43006 TTTTTTTCTCACTCTCATTTTC
1 TTTTTTTCTCACTCTCAATTTC
*
43028 TTTTTTTCT-TCTCTCAATTTC
1 TTTTTTTCTCACTCTCAATTTC
43049 ATTCAAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTTTTCTCACTCTCAATTTC
Found at i:43881 original size:26 final size:28
Alignment explanation
Indices: 43851--43914 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
43841 TTTCAATCAC
43851 TCTTTTTTTTTCAATTT-G-A-TTTTTTT
1 TCTTTTTTTTT-AATTTCGAATTTTTTTT
43877 TCTTTTTTTTTAATTTCGAATTTTTTTT
1 TCTTTTTTTTTAATTTCGAATTTTTTTT
43905 TCTTTTTTTT
1 TCTTTTTTTT
43915 CTTCAATACT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
25 5 0.14
26 12 0.34
27 1 0.03
28 17 0.49
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (28 bp):
TCTTTTTTTTTAATTTCGAATTTTTTTT
Found at i:43978 original size:12 final size:12
Alignment explanation
Indices: 43961--44002 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
43951 ATACAACTTT
43961 TTTTTTTTTGAA
1 TTTTTTTTTGAA
43973 TTTTTTTTTGAA
1 TTTTTTTTTGAA
43985 TTTTTTTTT--A
1 TTTTTTTTTGAA
43995 TTTTTTTT
1 TTTTTTTT
44003 ACATACCGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 9 0.30
12 21 0.70
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:44312 original size:24 final size:23
Alignment explanation
Indices: 44258--44335 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
44248 GGATAATTAA
**
44258 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
44281 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
44305 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
44326 GAAATAGTAT
1 GAAATGGTAT
44336 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:44320 original size:21 final size:21
Alignment explanation
Indices: 44294--44355 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
44284 TTGGTATTTG
44294 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
44315 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
44336 GGTATTTGGTACGAATTGGT
1 GG-AATTGGTACGAAATGGT
44356 TATGTTCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 21 0.62
22 13 0.38
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:45690 original size:30 final size:30
Alignment explanation
Indices: 45656--45755 Score: 78
Period size: 30 Copynumber: 3.2 Consensus size: 30
45646 TAAACTAAAA
45656 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
45686 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
45716 TGAGCTAAGGTTTTAGCTCGTGTGAGCTAAA-T
1 TGAGCTAA-GCTTTAGCTC--GTGAGCTAAAGT
45748 ATGAGCTA
1 -TGAGCTA
45756 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
29 1 0.02
30 27 0.53
31 8 0.16
32 1 0.02
33 14 0.27
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:49816 original size:12 final size:12
Alignment explanation
Indices: 49799--49850 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 12
49789 TATTGGATTA
49799 AAAAAAAAATCG
1 AAAAAAAAATCG
*
49811 -AAAAAAATTC-
1 AAAAAAAAATCG
*
49821 AAAAAAAAGT-G
1 AAAAAAAAATCG
*
49832 AAAAAAAAATTG
1 AAAAAAAAATCG
49844 AAAAAAA
1 AAAAAAA
49851 GAGAAGAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 26 0.76
12 8 0.24
ACGTcount: A:0.77, C:0.04, G:0.08, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATCG
Found at i:52366 original size:66 final size:66
Alignment explanation
Indices: 52260--52392 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
52250 TTGTGTTCAA
52260 TAAGTAGTGGTGAGGAGTTTATTTGCTTGATCGATGAACGGATTAAGTTGAATGTGTCCACATGT
1 TAAGTAGTGGTGAGGAGTTTATTTGCTTGATCGATGAACGGATTAAGTTGAATGTGTCCACATGT
52325 C
66 C
52326 TAAGTAGTGGTGAGGAGTTTATTTGCTTGATCGATGAACGGATTAAGTTGAATGTGTCCACATGT
1 TAAGTAGTGGTGAGGAGTTTATTTGCTTGATCGATGAACGGATTAAGTTGAATGTGTCCACATGT
52391 C
66 C
52392 T
1 T
52393 CTTGAAAATT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.35
Consensus pattern (66 bp):
TAAGTAGTGGTGAGGAGTTTATTTGCTTGATCGATGAACGGATTAAGTTGAATGTGTCCACATGT
C
Found at i:53570 original size:12 final size:13
Alignment explanation
Indices: 53548--53576 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
53538 AAGTTTTATT
53548 TTTATTTTATTTA
1 TTTATTTTATTTA
53561 TTTA-TTTATTTA
1 TTTATTTTATTTA
53573 TTTA
1 TTTA
53577 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:55969 original size:13 final size:12
Alignment explanation
Indices: 55936--55991 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
55926 AGGAATGTGA
*
55936 AAAAAGAAATTG
1 AAAAAGAAGTTG
55948 AAAAAGAAGTTG
1 AAAAAGAAGTTG
*
55960 AAGAAAGAAG-AG
1 AA-AAAGAAGTTG
*
55972 AAAATG-AGTTAG
1 AAAAAGAAGTT-G
55984 AAAAAGAA
1 AAAAAGAA
55992 ACAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 22 0.63
13 8 0.23
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.12
Consensus pattern (12 bp):
AAAAAGAAGTTG
Done.