Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold737
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: 8057
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Found at i:3013 original size:22 final size:22
Alignment explanation
Indices: 2971--3017 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
2961 TTTTTGTAAA
2971 AAGGATAAAGTGTTTAAAATGTT
1 AAGGATAAAGTG-TTAAAATGTT
2994 AAGGACTAAAGTG-TAAAATGTT
1 AAGGA-TAAAGTGTTAAAATGTT
3016 AA
1 AA
3018 AATATTAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 11 0.48
23 5 0.22
24 7 0.30
ACGTcount: A:0.47, C:0.02, G:0.21, T:0.30
Consensus pattern (22 bp):
AAGGATAAAGTGTTAAAATGTT
Found at i:4861 original size:51 final size:51
Alignment explanation
Indices: 4785--4979 Score: 225
Period size: 51 Copynumber: 3.8 Consensus size: 51
4775 CATGAGAACT
* * * **
4785 CATGTGTAGTACTATGTGTAGGCTACTATGAGTATAAGATAGTTATGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTATGGTCA
4836 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTT-TGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG-TTATGGTCA
* * * * *
4887 -AGTATGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GGTATTGGTCA
1 CA-TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTA-TGGTCA
* * *
4938 CGTGTGTAGTACTAAGTGTAGGCTACTATGTGTACCAAATAG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG
4980 CATTGATCAT
Statistics
Matches: 121, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
51 115 0.95
52 3 0.02
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (51 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTATGGTCA
Found at i:4965 original size:102 final size:102
Alignment explanation
Indices: 4789--4980 Score: 278
Period size: 102 Copynumber: 1.9 Consensus size: 102
4779 AGAACTCATG
* * *
4789 TGTAGTACTATGTGTAGGCTACTATGAGTATAAGATAGTTATGGTCACATGTGTAGTACTAAGTG
1 TGTAGTACTATGTGCAGGCTACTACGAGTACAAGATAGTTATGGTCACATGTGTAGTACTAAGTG
*
4854 CAGGCTACTATGTGTACCAGATAGCTTTGGTCAAGTA
66 CAGGCTACTATGTGTACCAAATAGCTTTGGTCAAGTA
* ** * *
4891 TGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GGTATTGGTCACGTGTGTAGTACTAAGT
1 TGTAGTACTATGTGCAGGCTACTACGAGTACAAGATAGTTA-TGGTCACATGTGTAGTACTAAGT
*
4955 GTAGGCTACTATGTGTACCAAATAGC
65 GCAGGCTACTATGTGTACCAAATAGC
4981 ATTGATCATA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 3 0.04
102 76 0.96
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (102 bp):
TGTAGTACTATGTGCAGGCTACTACGAGTACAAGATAGTTATGGTCACATGTGTAGTACTAAGTG
CAGGCTACTATGTGTACCAAATAGCTTTGGTCAAGTA
Found at i:5001 original size:51 final size:50
Alignment explanation
Indices: 4788--5007 Score: 183
Period size: 51 Copynumber: 4.3 Consensus size: 50
4778 GAGAACTCAT
* * * ** * *
4788 GTGTAGTACTATGTGTAGGCTACTATGAGTATAAGATAG-TTATGGTCACAT
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCAT-TGGTCA-AA
*
4839 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTTTGGTC-AA
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCATTGGTCAAA
* * * * * **
4888 GTATGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGTATTGGTCACGT
1 G--TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCATTGGTCA-AA
* * *
4941 GTGTAGTACTAAGTGTAGGCTACTATGTGTACCAAATAGCATTGATCATAA
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCATTGGTCA-AA
* * *
4992 GGGTGGTACTATGTGC
1 GTGTAGTACTAAGTGC
5008 GGAACCACCG
Statistics
Matches: 135, Mismatches: 29, Indels: 10
0.78 0.17 0.06
Matches are distributed among these distances:
49 2 0.01
51 130 0.96
52 2 0.01
53 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.32
Consensus pattern (50 bp):
GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCATTGGTCAAA
Found at i:7313 original size:39 final size:39
Alignment explanation
Indices: 7259--7375 Score: 189
Period size: 39 Copynumber: 3.0 Consensus size: 39
7249 ATTTTGATGG
*
7259 TAATCACATAACATTTAAGCATATATCACACTACACATA
1 TAATCACATAACATTTAAGCATATATCACAATACACATA
* *
7298 TAATCACATAACATTTAAGCAAATATCACAATACTCATA
1 TAATCACATAACATTTAAGCATATATCACAATACACATA
* *
7337 TAATCACATAACATTCAAGTATATATCACAATACACATA
1 TAATCACATAACATTTAAGCATATATCACAATACACATA
7376 ACATGTTTAT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 71 1.00
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (39 bp):
TAATCACATAACATTTAAGCATATATCACAATACACATA
Found at i:7365 original size:22 final size:22
Alignment explanation
Indices: 7261--7366 Score: 65
Period size: 22 Copynumber: 5.3 Consensus size: 22
7251 TTTGATGGTA
* *
7261 ATCACATAACATTTAAGCATAT
1 ATCACATAACATTCAAGTATAT
7283 ATCACACT-ACA--C-A-TATA-
1 ATCACA-TAACATTCAAGTATAT
* * *
7300 ATCACATAACATTTAAGCAAAT
1 ATCACATAACATTCAAGTATAT
7322 ATCACA-ATAC--TC-A-TATA-
1 ATCACATA-ACATTCAAGTATAT
7339 ATCACATAACATTCAAGTATAT
1 ATCACATAACATTCAAGTATAT
7361 ATCACA
1 ATCACA
7367 ATACACATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 28
0.63 0.08 0.29
Matches are distributed among these distances:
16 1 0.02
17 17 0.27
18 6 0.10
19 4 0.06
20 3 0.05
21 7 0.11
22 23 0.37
23 1 0.02
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.28
Consensus pattern (22 bp):
ATCACATAACATTCAAGTATAT
Done.