Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold518
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: 30739
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3137 original size:17 final size:18
Alignment explanation
Indices: 3111--3158 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
3101 AAATCTAAAT
* *
3111 ACGAGGAAGCAACTGT-A
1 ACGAGTAAGCAACTATGA
*
3128 ACGAGTAAGCAATTATGA
1 ACGAGTAAGCAACTATGA
3146 ACGAGTAATGCAA
1 ACGAGTAA-GCAA
3159 TTTAGCTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 13 0.50
18 9 0.35
19 4 0.15
ACGTcount: A:0.44, C:0.15, G:0.25, T:0.17
Consensus pattern (18 bp):
ACGAGTAAGCAACTATGA
Found at i:3730 original size:42 final size:41
Alignment explanation
Indices: 3671--3749 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
3661 CGCACCAATG
3671 GAATGCCTTCGGGACTTAACAC-CGGATTTTAATAACTCGTAC
1 GAATGCCTTCGGGACTTAAC-CTCGGA-TTTAATAACTCGTAC
3713 GAATGCCTTCGGGACTTAACCTCGGATTTAATAACTC
1 GAATGCCTTCGGGACTTAACCTCGGATTTAATAACTC
3750 CGCAAAAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
41 12 0.33
42 24 0.67
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (41 bp):
GAATGCCTTCGGGACTTAACCTCGGATTTAATAACTCGTAC
Found at i:8649 original size:40 final size:40
Alignment explanation
Indices: 8566--8907 Score: 467
Period size: 40 Copynumber: 8.6 Consensus size: 40
8556 TTGAATGCTG
* * * * * *
8566 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
8606 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
8646 TCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
8685 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
8725 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
8765 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
8805 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
8845 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
8884 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
8908 TGAACGAGGA
Statistics
Matches: 278, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
39 70 0.25
40 200 0.72
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:8824 original size:120 final size:119
Alignment explanation
Indices: 8566--8907 Score: 474
Period size: 119 Copynumber: 2.9 Consensus size: 119
8556 TTGAATGCTG
* * * * * * * *
8566 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGAT-CCGAAGGCCT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGG-CA
*
8629 TTGTGCGAGATACTAAATCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTATTAAA
63 TTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
8685 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT-
*
8750 GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
65 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
8805 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTG
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTG
* * * *
8870 TGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
66 TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
8908 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 18, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
118 4 0.02
119 103 0.51
120 94 0.47
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTG
TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:14931 original size:48 final size:48
Alignment explanation
Indices: 14840--14946 Score: 139
Period size: 48 Copynumber: 2.2 Consensus size: 48
14830 TTGTCTTTTC
*
14840 TTTCTTTTTCAATTTTTCTTCTTTTCCTCACACTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTTTCTTCTTTT-CTCACACCTTTGTTCAATCTCAA
*
14889 TTTCTTTTTCGATTTCTT-TCTCTTTT-TCACATCCTTT-TTCAATCTCAA
1 TTTCTTTTTCAATTT-TTCT-TCTTTTCTCACA-CCTTTGTTCAATCTCAA
14937 TTTCTTTTTC
1 TTTCTTTTTC
14947 CATGACACTC
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
48 26 0.49
49 19 0.36
50 8 0.15
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (48 bp):
TTTCTTTTTCAATTTTTCTTCTTTTCTCACACCTTTGTTCAATCTCAA
Found at i:16047 original size:23 final size:24
Alignment explanation
Indices: 15992--16046 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
15982 TTTAACTTGA
* *
15992 TTTTTTTTGCTCACTTTTTTTTCT
1 TTTTTTTTGCTCAATTTTTTTACT
16016 TTTTTTTTGCTCAATTTTTTTACT
1 TTTTTTTTGCTCAATTTTTTTACT
16040 TTTTTTT
1 TTTTTTT
16047 GAATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTTTTTTGCTCAATTTTTTTACT
Found at i:16066 original size:12 final size:13
Alignment explanation
Indices: 16039--16066 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16029 ATTTTTTTAC
16039 TTTTTTTTGAATT
1 TTTTTTTTGAATT
16052 TTTTTTTTGAATT
1 TTTTTTTTGAATT
16065 TT
1 TT
16067 GATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:17153 original size:20 final size:20
Alignment explanation
Indices: 17130--17183 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
17120 AGTTTTTCCC
*
17130 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
17150 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
17170 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
17184 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:17165 original size:30 final size:30
Alignment explanation
Indices: 17130--17203 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
17120 AGTTTTTCCC
17130 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
17160 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
17190 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
17204 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:17193 original size:20 final size:20
Alignment explanation
Indices: 17130--17194 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
17120 AGTTTTTCCC
* * * *
17130 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
17150 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
17169 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
17190 AGCTC
1 AGCTC
17195 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:18836 original size:10 final size:11
Alignment explanation
Indices: 18814--18838 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18804 AAAAAAATTG
18814 AAATTCAAAAA
1 AAATTCAAAAA
18825 AAATTCAAAAA
1 AAATTCAAAAA
18836 AAA
1 AAA
18839 AGTGAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:18860 original size:26 final size:27
Alignment explanation
Indices: 18831--18906 Score: 70
Period size: 29 Copynumber: 2.9 Consensus size: 27
18821 AAAAAAATTC
18831 AAAAAAAAAGTGAAAAAAA-TCG-GCAA
1 AAAAAAAAAGTGAAAAAAAGT-GAGCAA
*
18857 AAAAAGAAA--GAAAAAAAGTGAGCAA
1 AAAAAAAAAGTGAAAAAAAGTGAGCAA
* *
18882 AAAAAATCAAGTTAAAAAAAAGTGA
1 AAAAAA-AAAG-TGAAAAAAAGTGA
18907 AAAGTCTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 9 0.22
25 10 0.25
26 10 0.25
29 11 0.28
ACGTcount: A:0.70, C:0.05, G:0.16, T:0.09
Consensus pattern (27 bp):
AAAAAAAAAGTGAAAAAAAGTGAGCAA
Found at i:19933 original size:21 final size:22
Alignment explanation
Indices: 19907--19948 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
19897 AAAGAGATTG
*
19907 AAAAAGAAATTG-AAAGAAAAC
1 AAAAAGAAAATGAAAAGAAAAC
19928 AAAAAGAAAATGAAAAGAAAA
1 AAAAAGAAAATGAAAAGAAAA
19949 AGAAATTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.07
Consensus pattern (22 bp):
AAAAAGAAAATGAAAAGAAAAC
Found at i:19942 original size:6 final size:6
Alignment explanation
Indices: 19919--20022 Score: 59
Period size: 6 Copynumber: 17.2 Consensus size: 6
19909 AAAGAAATTG
* * ** *
19919 AAAG-A AAACAA AAAGAA AATG-A AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
19965 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
20016 AAAGAA A
1 AAAGAA A
20023 TTGAGAATGA
Statistics
Matches: 70, Mismatches: 24, Indels: 9
0.68 0.23 0.09
Matches are distributed among these distances:
5 7 0.10
6 52 0.74
7 7 0.10
8 4 0.06
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (6 bp):
AAAGAA
Found at i:19961 original size:18 final size:17
Alignment explanation
Indices: 19922--19978 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
19912 GAAATTGAAA
* *
19922 GAAAACAAAAAGAAAAT
1 GAAAAGAAAAAGAAATT
19939 GAAAAGAAAAAGAAATT
1 GAAAAGAAAAAGAAATT
*
19956 GCAAAAGAAAAAGAAATC
1 G-AAAAGAAAAAGAAATT
19974 GAAAA
1 GAAAA
19979 AGTGAGAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 20 0.56
18 16 0.44
ACGTcount: A:0.72, C:0.05, G:0.16, T:0.07
Consensus pattern (17 bp):
GAAAAGAAAAAGAAATT
Found at i:19980 original size:18 final size:16
Alignment explanation
Indices: 19908--19978 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 16
19898 AAGAGATTGA
**
19908 AAAAGAAATTGAAA-G
1 AAAAGAAAAAGAAATG
*
19923 AAAACAAAAAGAAAATG
1 AAAAGAAAAAG-AAATG
19940 AAAAGAAAAAGAAATTG
1 AAAAGAAAAAGAAA-TG
19957 CAAAAGAAAAAGAAATCG
1 -AAAAGAAAAAGAAAT-G
19975 AAAA
1 AAAA
19979 AGTGAGAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
15 8 0.17
16 6 0.13
17 18 0.38
18 15 0.32
ACGTcount: A:0.72, C:0.04, G:0.15, T:0.08
Consensus pattern (16 bp):
AAAAGAAAAAGAAATG
Found at i:20016 original size:27 final size:27
Alignment explanation
Indices: 19986--20070 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
19976 AAAAGTGAGA
*
19986 GAAAAAGAAAATGAAGAA-AAGAAAATT
1 GAAAAAGAAAATG-AGAAGAAAAAAATT
*
20013 GAAAAAGAAATTGAGAATGAAAAAAATT
1 GAAAAAGAAAATGAGAA-GAAAAAAATT
* *
20041 G-AAAAGAAAAAGCGAA-AAAAGAAATT
1 GAAAAAGAAAATGAGAAGAAAA-AAATT
20067 GAAA
1 GAAA
20071 GAGAGCTTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
25 4 0.08
26 10 0.20
27 26 0.53
28 9 0.18
ACGTcount: A:0.68, C:0.01, G:0.19, T:0.12
Consensus pattern (27 bp):
GAAAAAGAAAATGAGAAGAAAAAAATT
Found at i:20034 original size:12 final size:12
Alignment explanation
Indices: 19897--20026 Score: 54
Period size: 12 Copynumber: 10.9 Consensus size: 12
19887 AGAAAAGGAG
*
19897 AAAGAGATTGAA
1 AAAGAAATTGAA
19909 AAAGAAATTG--
1 AAAGAAATTGAA
**
19919 AAAGAAA-ACAA
1 AAAGAAATTGAA
*
19930 AAAGAAAATG-A
1 AAAGAAATTGAA
**
19941 AAAGAAAAAGAA
1 AAAGAAATTGAA
** *
19953 ATTGCAAA-AGAA
1 AAAG-AAATTGAA
*
19965 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
19977 AAAGTGAGAGAA
1 AAAGAAATTGAA
*
19989 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
20003 AAAGAAAATTGAA
1 AAAG-AAATTGAA
20016 AAAGAAATTGA
1 AAAGAAATTGA
20027 GAATGAAAAA
Statistics
Matches: 89, Mismatches: 20, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
10 7 0.08
11 20 0.22
12 42 0.47
13 9 0.10
14 6 0.07
15 5 0.06
ACGTcount: A:0.68, C:0.02, G:0.19, T:0.11
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:20104 original size:33 final size:33
Alignment explanation
Indices: 20067--20129 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
20057 AAAAGAAATT
20067 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
20100 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
20130 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Done.