Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold706
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: 9239
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Found at i:1868 original size:128 final size:127
Alignment explanation
Indices: 1640--2166 Score: 835
Period size: 128 Copynumber: 4.1 Consensus size: 127
1630 AGATAGGATT
* *
1640 TGTAATTTCCAACCTATT-CAACTGCTGACCAGGGAGATAAGAC-TAGCGGCTTAAATCTGCTTC
1 TGTAATTTCCAACCTATTGC-ACTGCTGACCAGGGAGATAGGACTTA-TGGCTTAAATCTGCTTC
*
1703 CTTACTCTTGAAGATAAGATTTCTCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATC
64 CTTACTCTTGAAGATAAGATTTC-CGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATC
* * * * *
1768 TGTAATTTCTAACCTACTACACTGCAGACCAGGGAGATAGGACTTATGGCTTAAATCTGCTTCCC
1 TGTAATTTCCAACCTATTGCACTGCTGACCAGGGAGATAGGACTTATGGCTTAAATCTGCTTCCT
*
1833 TACTCTTGAAGATAAGATTTACCGTCTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAGATC
66 TACTCTTGAAGATAAGATTT-CCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATC
* *
1896 TGTAATTTCCAACCTATTGCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATTTGCTTCCT
1 TGTAATTTCCAACCTATTGCACTGCTGACCAGGGAGATAGGACTTATGGCTTAAATCTGCTTCCT
1961 TACTCTTGAAGATAAGATTCTCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATC
66 TACTCTTGAAGATAAGATT-TCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATC
*
2024 TGTAATTTCCAACCTATTGCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCT
1 TGTAATTTCCAACCTATTGCACTGCTGACCAGGGAGATAGGACTTATGGCTTAAATCTGCTTCCT
2089 TACTCTTGAAGATAAGA-TTCGTCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATC
66 TACTCTTGAAGATAAGATTTC--CGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATC
* * *
2152 TATATTTTTCAACCT
1 TGTAATTTCCAACCT
2167 GCTCCGCTGT
Statistics
Matches: 373, Mismatches: 20, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
126 2 0.01
127 1 0.00
128 365 0.98
129 5 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (127 bp):
TGTAATTTCCAACCTATTGCACTGCTGACCAGGGAGATAGGACTTATGGCTTAAATCTGCTTCCT
TACTCTTGAAGATAAGATTTCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATC
Found at i:2252 original size:88 final size:88
Alignment explanation
Indices: 2157--3042 Score: 1189
Period size: 88 Copynumber: 10.1 Consensus size: 88
2147 AGATCTATAT
* * * *
2157 TTTTCAACCTGCTCCGCTGTAACCCAGGGAGGTAAGGCTGGGGTCTTCGATCTGCTTAACTGTCA
1 TTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCA
2222 GTACAGGAAGGCAAGATCTGCTA
66 GTACAGGAAGGCAAGATCTGCTA
* * * * * * * * *
2245 TCTTCAACCTGCTCCACTGCAATCCAGGGAGGTAAGGCTAGTGTCTTCGATTTGTTTCGCTGTCG
1 TTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCA
2310 GTGA-AGGAAGGCAAGATCTGCTA
66 GT-ACAGGAAGGCAAGATCTGCTA
* *
2333 TTTTCAACCTGCTCCGCTGCAACCTAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCACTGTCA
1 TTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCA
* *
2398 GTGCAGGAAGGCAAGATTTGCTA
66 GTACAGGAAGGCAAGATCTGCTA
* * * * * *
2421 TTTTCAACCTGTTCCGCTGCAACCCATGGAGGCAAGACTGGTGTCTTCGATCAGCTTCGCTGTCG
1 TTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCA
* *
2486 GTGCAGGAAGGCAAGATTTGCTA
66 GTACAGGAAGGCAAGATCTGCTA
* ** * * * **
2509 TTTTTAACCTGCTCCGCTGCAACTTAGGGAGGCAAGTCTGCTGTCTTCGATCTGCTTCGCTGTTG
1 TTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCA
*
2574 GTGCAGGAAGGCAAGATCTGCTA
66 GTACAGGAAGGCAAGATCTGCTA
* * * *
2597 TTTTTAACCTGCTCTGCTGCAACCCAGGGAGGCAAGTCTGGTGTCTTCGATCTGCTTAACTGTCA
1 TTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCA
2662 GTACAGGAAGGCAAGATCTGCTA
66 GTACAGGAAGGCAAGATCTGCTA
* * * * ** ** *
2685 TCTTCAACCTGCTCCACTGCAATCTAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTTGCCATCG
1 TTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCA
* *
2750 GTGCAGGAAGGCAAGATATGCTA
66 GTACAGGAAGGCAAGATCTGCTA
* *
2773 TTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGTCTGGTGTCTTCGATCTGCTTAACTGTCA
1 TTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCA
2838 GTACAGGAAGGCAAGATCTGCTA
66 GTACAGGAAGGCAAGATCTGCTA
* *
2861 TTTTCAACCTGCTCCGCTGCAACCCAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTAACTGTCA
1 TTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCA
* *
2926 GTACAGGAAGACAAGATCTGTTA
66 GTACAGGAAGGCAAGATCTGCTA
* * * * *
2949 TTTTCAACCTGCTCCACTGCAATCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGTCG
1 TTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCA
* *
3014 GTGCAGGAAGGCAAGATCTGTTA
66 GTACAGGAAGGCAAGATCTGCTA
*
3037 TCTTCA
1 TTTTCA
3043 CTGATCTGTT
Statistics
Matches: 705, Mismatches: 91, Indels: 4
0.88 0.11 0.00
Matches are distributed among these distances:
88 704 1.00
89 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (88 bp):
TTTTCAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCA
GTACAGGAAGGCAAGATCTGCTA
Found at i:2609 original size:45 final size:45
Alignment explanation
Indices: 2300--2609 Score: 136
Period size: 44 Copynumber: 7.0 Consensus size: 45
2290 TTCGATTTGT
* * *
2300 TTCGCTGTCGGTGAAGGAAGGCAAGATCTGCTATTTTCAACCTGC
1 TTCGCTGTAGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* * ** * * * * * * *
2345 TCCGCTGCA--ACCTAGGGAGGCAAG-GCTGGTGTCTTTGATCTGC
1 TTCGCTGTAGGTGC-AGGAAGGCAAGATCTGCTATTTTTAACCTGC
* * *
2388 TTCACTGTCA-GTGCAGGAAGGCAAGATTTGCTATTTTCAACCTG-
1 TTCGCTGT-AGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *** * * * ** * *
2432 TTCCGCTGCA-ACCCATGG-AGGCAAGA-CTGGTGTCTTCGATCAGC
1 TT-CGCTGTAGGTGCA-GGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
2476 TTCGCTGTCGGTGCAGGAAGGCAAGATTTGCTATTTTTAACCTGC
1 TTCGCTGTAGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* * ** * * * * ** *
2521 TCCGCTGCAACT-TAGGGAGGCAAG-TCTGCTGTCTTCGATCTGC
1 TTCGCTGTAGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
2564 TTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 TTCGCTGTAGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
2609 T
1 T
2610 CTGCTGCAAC
Statistics
Matches: 175, Mismatches: 78, Indels: 24
0.63 0.28 0.09
Matches are distributed among these distances:
43 54 0.31
44 66 0.38
45 55 0.31
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (45 bp):
TTCGCTGTAGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
Found at i:5270 original size:6 final size:6
Alignment explanation
Indices: 5246--5304 Score: 64
Period size: 6 Copynumber: 9.7 Consensus size: 6
5236 CATTTTCATT
* * ** *
5246 TTTTGA CTTTGA CTTTGA TTTTGA TTTTTCT TTTTGC TTTTGA TTTTGA
1 TTTTGA TTTTGA TTTTGA TTTTGA -TTTTGA TTTTGA TTTTGA TTTTGA
5295 TTTTGA TTTT
1 TTTTGA TTTT
5305 TCTTCCTCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
6 41 0.91
7 4 0.09
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.68
Consensus pattern (6 bp):
TTTTGA
Found at i:5273 original size:25 final size:25
Alignment explanation
Indices: 5245--5298 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
5235 TCATTTTCAT
*
5245 TTTTTGACTTTGAC-TTTGATTTTGA
1 TTTTTCACTTTG-CTTTTGATTTTGA
**
5270 TTTTTCTTTTTGCTTTTGATTTTGA
1 TTTTTCACTTTGCTTTTGATTTTGA
5295 TTTT
1 TTTT
5299 GATTTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.11, C:0.07, G:0.13, T:0.69
Consensus pattern (25 bp):
TTTTTCACTTTGCTTTTGATTTTGA
Found at i:5288 original size:31 final size:31
Alignment explanation
Indices: 5245--5308 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
5235 TCATTTTCAT
5245 TTTTTGACTTTGACTTTGATTTTGATTTTTC
1 TTTTTGACTTTGACTTTGATTTTGATTTTTC
*
5276 TTTTTG-CTTTTGATTTTGATTTTGATTTTTC
1 TTTTTGAC-TTTGACTTTGATTTTGATTTTTC
5307 TT
1 TT
5309 CCTCCTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.11, C:0.08, G:0.12, T:0.69
Consensus pattern (31 bp):
TTTTTGACTTTGACTTTGATTTTGATTTTTC
Found at i:5325 original size:31 final size:31
Alignment explanation
Indices: 5253--5317 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
5243 ATTTTTTGAC
* ** *
5253 TTTGACTTTGATTTTGATTTTTCTTTTTGCT
1 TTTGATTTTGATTTTGATTTTTCTTCCTCCT
5284 TTTGATTTTGATTTTGATTTTTCTTCCTCCT
1 TTTGATTTTGATTTTGATTTTTCTTCCTCCT
5315 TTT
1 TTT
5318 TTTTTTGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.09, C:0.12, G:0.11, T:0.68
Consensus pattern (31 bp):
TTTGATTTTGATTTTGATTTTTCTTCCTCCT
Done.