Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1873
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: 38543
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:3747 original size:67 final size:64
Alignment explanation
Indices: 3629--3784 Score: 179
Period size: 67 Copynumber: 2.4 Consensus size: 64
3619 AGACATTATG
* * * * * * *
3629 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGATAAGAGAGTTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGAGGACACCATGTAGACAAGAGAGCTACGAGATAA
* *
3693 ATGTAGCTAGGTCGCATGCGTGGTTCTAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-AGGACACCATGTAGACAAGAGAGCTACGAGAT
3758 AA
63 AA
* *
3760 AT-TGGCTAGGTCACATGGGTGGTAC
1 ATGTAGCTAGGTCGCATGGGTGGTAC
3785 CGAATGTTCA
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 25 0.33
66 21 0.28
67 30 0.39
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGAGGACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:9292 original size:12 final size:11
Alignment explanation
Indices: 9275--9318 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
9265 TTTAAAGAAT
9275 TTTTATTTTTTA
1 TTTTA-TTTTTA
9287 TTTTATTTTTA
1 TTTTATTTTTA
*
9298 TTTTCACTTTTA
1 TTTT-ATTTTTA
9310 TCTTTATTT
1 T-TTTATTT
9319 ATCTTCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 10 0.36
12 15 0.54
13 3 0.11
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:9308 original size:18 final size:17
Alignment explanation
Indices: 9273--9318 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
9263 TGTTTAAAGA
*
9273 ATTTTTATTTTTTATTTT
1 ATTTTTA-TTTTCATTTT
9291 ATTTTTATTTTCACTTTT
1 ATTTTTATTTTCA-TTTT
*
9309 ATCTTTATTT
1 ATTTTTATTT
9319 ATCTTCTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTTATTTTCATTTT
Found at i:9345 original size:25 final size:26
Alignment explanation
Indices: 9316--9369 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
9306 TTTATCTTTA
9316 TTTATCTTC-TTTAAGTACT-TTTCAT
1 TTTATCTTCATTTAA-TACTATTTCAT
*
9341 TTTATTTTCATTTAATACTATTTCAT
1 TTTATCTTCATTTAATACTATTTCAT
9367 TTT
1 TTT
9370 TAGGTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.22, C:0.13, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTATCTTCATTTAATACTATTTCAT
Found at i:12866 original size:25 final size:25
Alignment explanation
Indices: 12838--12905 Score: 108
Period size: 21 Copynumber: 2.9 Consensus size: 25
12828 AAAGGTAAGG
12838 TGGGAAACCCAAACAAACTAGGTCT
1 TGGGAAACCCAAACAAACTAGGTCT
12863 TGGGAAA-CC---CAAACTAGGTCT
1 TGGGAAACCCAAACAAACTAGGTCT
12884 TGGGAAACCCAAACAAACTAGG
1 TGGGAAACCCAAACAAACTAGG
12906 ATGAGTATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
21 19 0.49
22 2 0.05
24 2 0.05
25 16 0.41
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (25 bp):
TGGGAAACCCAAACAAACTAGGTCT
Found at i:14879 original size:20 final size:20
Alignment explanation
Indices: 14854--14897 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
14844 TTTATTTTAA
*
14854 ATTTTAT-TCTTTATTTCTTT
1 ATTTTATATCTTTATATC-TT
14874 ATTTTATATCTTTATATCTT
1 ATTTTATATCTTTATATCTT
14894 ATTT
1 ATTT
14898 ATTATTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTATATCTTTATATCTT
Found at i:14902 original size:27 final size:27
Alignment explanation
Indices: 14845--14907 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
14835 TTTCTTTATT
* *
14845 TTATTTTAAATTTTATTCTTTATTTCT
1 TTATTTTATATTTTATTCTTTATTTCA
14872 TTATTTTATATCTTTATATC-TTATTT-A
1 TTATTTTATAT-TTTAT-TCTTTATTTCA
14899 TTATTTTAT
1 TTATTTTAT
14908 TTTCAGCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 19 0.59
28 11 0.34
29 2 0.06
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (27 bp):
TTATTTTATATTTTATTCTTTATTTCA
Found at i:15147 original size:14 final size:15
Alignment explanation
Indices: 15128--15156 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
15118 TTATGTGTCC
15128 ATTGTTCTTT-TTCT
1 ATTGTTCTTTATTCT
15142 ATTGTTCTTTATTCT
1 ATTGTTCTTTATTCT
15157 TAGCTTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.69
Consensus pattern (15 bp):
ATTGTTCTTTATTCT
Found at i:21227 original size:21 final size:21
Alignment explanation
Indices: 21201--21241 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21191 TGGGTGGATC
* *
21201 AGCTCTTATGAGCTTCTGTTA
1 AGCTCTCACGAGCTTCTGTTA
21222 AGCTCTCACGAGCTTCTGTT
1 AGCTCTCACGAGCTTCTGTT
21242 GGCATGTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (21 bp):
AGCTCTCACGAGCTTCTGTTA
Found at i:26073 original size:28 final size:28
Alignment explanation
Indices: 26009--26186 Score: 277
Period size: 28 Copynumber: 6.4 Consensus size: 28
25999 AGATTGGCGT
* * * *
26009 TAAGTGTGCGGGTTTAAATTGTACAGCAC
1 TAAGTGTGCGAGTTT-GATTATATAGCAC
26038 TAAGTGTGCGAGTTTGATTATATAGCAC
1 TAAGTGTGCGAGTTTGATTATATAGCAC
26066 TAAGTGTGCGAGTTTGATTATATAGCAC
1 TAAGTGTGCGAGTTTGATTATATAGCAC
*
26094 TAAGTGTGCGAGTTTGATTATGTAGCAC
1 TAAGTGTGCGAGTTTGATTATATAGCAC
26122 TAAGTGTGCGAGTTTGATTATATAGCAC
1 TAAGTGTGCGAGTTTGATTATATAGCAC
*
26150 TATGTGTGCGAG-TTGATTATATAGCAC
1 TAAGTGTGCGAGTTTGATTATATAGCAC
*
26177 TGAGTGTGCG
1 TAAGTGTGCG
26187 GACTTAATAT
Statistics
Matches: 140, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
27 23 0.16
28 103 0.74
29 14 0.10
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (28 bp):
TAAGTGTGCGAGTTTGATTATATAGCAC
Found at i:35716 original size:27 final size:27
Alignment explanation
Indices: 35682--35859 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
35672 TTAATTGTAC
35682 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
35709 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35735 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
35763 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
35791 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35818 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
35845 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35860 GACTTAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:35796 original size:82 final size:81
Alignment explanation
Indices: 35683--35838 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
35673 TAATTGTACA
* *
35683 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
35747 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
35764 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
35829 TGCGAGTTGA
65 TGCGAATTGA
35839 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:35850 original size:82 final size:81
Alignment explanation
Indices: 35679--35859 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
35669 GGATTAATTG
* *
35679 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
35744 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
35760 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
35824 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
35842 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35860 GACTTAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.