Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1129
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: 15278
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:2225 original size:78 final size:79
Alignment explanation
Indices: 2078--2228 Score: 295
Period size: 78 Copynumber: 1.9 Consensus size: 79
2068 AAATAACTGT
2078 TTTGGTAATTTTTAATCAAGAAATGAACTTGGCAAAATGGTTAAGGGTTGTTTTTCATTATGGGT
1 TTTGGTAATTTTTAATCAAGAAATGAACTTGGCAAAATGGTTAAGGGTTGTTTTTCATTATGGGT
2143 GGCCTGGGATTCTG
66 GGCCTGGGATTCTG
2157 TTTGGTAATTTTTAATCAAGAAATGAACTTGGC-AAATGGTTAAGGGTTGTTTTTCATTATGGGT
1 TTTGGTAATTTTTAATCAAGAAATGAACTTGGCAAAATGGTTAAGGGTTGTTTTTCATTATGGGT
2221 GGCCTGGG
66 GGCCTGGG
2229 TTCAAATCCA
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 39 0.54
79 33 0.46
ACGTcount: A:0.25, C:0.09, G:0.27, T:0.39
Consensus pattern (79 bp):
TTTGGTAATTTTTAATCAAGAAATGAACTTGGCAAAATGGTTAAGGGTTGTTTTTCATTATGGGT
GGCCTGGGATTCTG
Found at i:2276 original size:11 final size:11
Alignment explanation
Indices: 2260--2300 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
2250 CTTTCATATT
2260 TTTTTTCTTTC
1 TTTTTTCTTTC
2271 TTTTTTCTTCATC
1 TTTTTTCTT--TC
*
2284 TTCTTTCTTTC
1 TTTTTTCTTTC
2295 TTTTTT
1 TTTTTT
2301 ACCTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:2314 original size:24 final size:22
Alignment explanation
Indices: 2260--2314 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
2250 CTTTCATATT
**
2260 TTTTTTCTTTCTTTTTTCTTCA
1 TTTTTTCTTTCTTTTTTCTAAA
2282 TCTTCTTTCTTTCTTTTTTACCTAAA
1 T-TT-TTTCTTTCTTTTTT--CTAAA
2308 TTTTTTC
1 TTTTTTC
2315 AACCCATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 2 0.07
24 18 0.67
25 2 0.07
26 4 0.15
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTCTTTCTTTTTTCTAAA
Found at i:2681 original size:23 final size:22
Alignment explanation
Indices: 2655--2699 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2645 CCACTCAATC
2655 GGAAAACCCACTTTGGTTTTTTT
1 GGAAAACCC-CTTTGGTTTTTTT
* **
2678 GGAAAGCCCCTTTTTTTTTTTT
1 GGAAAACCCCTTTGGTTTTTTT
2700 TCGATCCCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (22 bp):
GGAAAACCCCTTTGGTTTTTTT
Found at i:8575 original size:97 final size:97
Alignment explanation
Indices: 8409--8647 Score: 370
Period size: 97 Copynumber: 2.5 Consensus size: 97
8399 TGAAAAATGG
* *
8409 GGTTGGAGTATCCCCTCGGAAGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAGAA
1 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTAAGAA
8474 TAAGATTTAAACTTTGATGTGTTTAAAAGCAA
66 TAAGATTTAAACTTTGATGTGTTTAAAAGCAA
*
8506 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCTCGATGATGACAATTTAAGTAAGAA
1 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTAAGAA
***
8571 TAAGATTTAAACTTTGATGTGTTTAAAAGTGG
66 TAAGATTTAAACTTTGATGTGTTTAAAAGCAA
* * * * * *
8603 GGTTAGAGTATCCTCTCGAAGGAATAGGGTTGGAGTATCACCGAT
1 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGAT
8648 AAATAAAATT
Statistics
Matches: 129, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 129 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (97 bp):
GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTAAGAA
TAAGATTTAAACTTTGATGTGTTTAAAAGCAA
Found at i:10722 original size:34 final size:34
Alignment explanation
Indices: 10642--10751 Score: 105
Period size: 34 Copynumber: 3.2 Consensus size: 34
10632 TTTTCCTGTT
* * * ***
10642 TCTTTACAGCTCCATGCTGCTGTTTGATGCTTAT
1 TCTTTGCAGCTCCAAGCTGCTGTTAGATGCTGCC
* *
10676 TGCTTTGTAGCTCCAAGCTGCTGTTCGATGCTGCC
1 T-CTTTGCAGCTCCAAGCTGCTGTTAGATGCTGCC
* *
10711 TCTTTGCAGCTCCATA-CTGCTATTAGGTGCTGCC
1 TCTTTGCAGCTCCA-AGCTGCTGTTAGATGCTGCC
10745 TCTTTGC
1 TCTTTGC
10752 TGGAGCTATT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 35 0.56
35 28 0.44
ACGTcount: A:0.13, C:0.27, G:0.21, T:0.39
Consensus pattern (34 bp):
TCTTTGCAGCTCCAAGCTGCTGTTAGATGCTGCC
Found at i:15020 original size:20 final size:20
Alignment explanation
Indices: 14983--15021 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
14973 ACAATTTGTA
*
14983 TTGATACAATAGGTAATGTT
1 TTGATACAATAAGTAATGTT
15003 TTGATAC-ATAAGTGAATGT
1 TTGATACAATAAGT-AATGT
15022 ATCGATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGATACAATAAGTAATGTT
Found at i:15139 original size:40 final size:40
Alignment explanation
Indices: 15076--15151 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
15066 TCTAGAAAAG
* *
15076 AAATGTATCGATACATAAGTAAATGTATCGATACATAAGT
1 AAATGTATCGACACATAAGTAAATGTATCAATACATAAGT
*** *
15116 AAATGTATCGACACATGCTTAAATGTGTCAATACAT
1 AAATGTATCGACACATAAGTAAATGTATCAATACAT
15152 TTCTCATGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (40 bp):
AAATGTATCGACACATAAGTAAATGTATCAATACATAAGT
Found at i:15141 original size:20 final size:20
Alignment explanation
Indices: 15076--15131 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
15066 TCTAGAAAAG
15076 AAATGTATCGATACATAAGT
1 AAATGTATCGATACATAAGT
15096 AAATGTATCGATACATAAGT
1 AAATGTATCGATACATAAGT
*
15116 AAATGTATCGACACAT
1 AAATGTATCGATACAT
15132 GCTTAAATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (20 bp):
AAATGTATCGATACATAAGT
Done.