Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_5062
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: 12391
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Found at i:78 original size:40 final size:40
Alignment explanation
Indices: 2--377 Score: 542
Period size: 40 Copynumber: 9.4 Consensus size: 40
1 C
* * * * * *
2 TAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGAT
1 TAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGT
* * * *
42 TAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGT
1 TAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
82 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
1 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
122 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
1 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
*
162 TAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGT
1 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
*
202 TAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGT
1 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
242 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
1 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
*
282 TAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGT
1 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
* * * * *
322 TATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGC
1 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
*
361 TATGTCCCGAAGGCATT
1 TAAGTCCCGAAGGCATT
378 TGAACGAGGA
Statistics
Matches: 314, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.11
40 271 0.86
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
Found at i:2191 original size:48 final size:47
Alignment explanation
Indices: 2037--2322 Score: 328
Period size: 48 Copynumber: 6.1 Consensus size: 47
2027 TCACACCTAG
* * *
2037 GTGCCAATATCATGGCCTGAAGCCAAATCAATG-AAGCTCGAACCCAAA
1 GTGCTAATATCATGGCC-GAAGCCAAATCAATGTAA-CTCGCACCCGAA
* * *
2085 GTGCCAATATCATGGCTGAAGCCAAATC-A-GTAACTCACA-CCGAA
1 GTGCTAATATCATGGCCGAAGCCAAATCAATGTAACTCGCACCCGAA
* *
2129 GTGCTAATAGCATGGCTCGAAGCCAAATCAATGTAACTCGCACCCAAA
1 GTGCTAATATCATGGC-CGAAGCCAAATCAATGTAACTCGCACCCGAA
* * * * * *
2177 GTGCTAATATCATGGCCTAAACCAAATCGATGCAACTTGTACCCGAA
1 GTGCTAATATCATGGCCGAAGCCAAATCAATGTAACTCGCACCCGAA
* * *
2224 GTGCTAATATCAAAGCCCGAAGCCAAATCAAAGTAACTCGCACCCGAA
1 GTGCTAATATC-ATGGCCGAAGCCAAATCAATGTAACTCGCACCCGAA
* *
2272 GTGCTAATATCATGGCCCAAAGCCAAATCAATGTAACTCGCATCCGAA
1 GTGCTAATATCATGG-CCGAAGCCAAATCAATGTAACTCGCACCCGAA
2320 GTG
1 GTG
2323 AAGCCAAATC
Statistics
Matches: 200, Mismatches: 31, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
44 18 0.09
45 16 0.08
46 4 0.02
47 57 0.28
48 105 0.52
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (47 bp):
GTGCTAATATCATGGCCGAAGCCAAATCAATGTAACTCGCACCCGAA
Found at i:2260 original size:95 final size:94
Alignment explanation
Indices: 2027--2322 Score: 334
Period size: 92 Copynumber: 3.1 Consensus size: 94
2017 CTCAGAAGTC
* * * * * *
2027 TCACACCTAGGTGCCAATATCATGGCCTGAAGCCAAATCAATG-AAGCTCGAACCCAAAGTGCCA
1 TCACACCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA-CTCGCACCCAAAGTGCTA
*
2091 ATATCATGG-CTGAAGCCAAATCA-GTAAC-
65 ATATCATGGCCT-AAACCAAATCATGTAACT
* *
2119 TCACACCGAAGTGCTAATAGCATGGCTCGAAGCCAAATCAATGTAACTCGCACCCAAAGTGCTAA
1 TCACACCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCCAAAGTGCTAA
*
2184 TATCATGGCCTAAACCAAATCGATGCAACT
66 TATCATGGCCTAAACCAAATC-ATGTAACT
* ** * *
2214 TGTAC-CCGAAGTGCTAATATCAAAGCCCGAAGCCAAATCAAAGTAACTCGCACCCGAAGTGCTA
1 T-CACACCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCCAAAGTGCTA
*
2278 ATATCATGGCCCAAAGCCAAATCAATGTAAC-
65 ATATCATGGCCTAAA-CCAAATC-ATGTAACT
*
2309 TCGCATCCGAAGTG
1 TCACA-CCGAAGTG
2323 AAGCCAAATC
Statistics
Matches: 173, Mismatches: 22, Indels: 14
0.83 0.11 0.07
Matches are distributed among these distances:
92 71 0.41
93 5 0.03
94 5 0.03
95 69 0.40
96 23 0.13
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (94 bp):
TCACACCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAACTCGCACCCAAAGTGCTAA
TATCATGGCCTAAACCAAATCATGTAACT
Found at i:5167 original size:96 final size:96
Alignment explanation
Indices: 5009--5274 Score: 339
Period size: 96 Copynumber: 2.8 Consensus size: 96
4999 GGTGTCGATT
* * * *
5009 CCATGTTCCAAACATGGTCTTACA----C-CATATGTCAAGGCCGATGCCATGTCCCAGACATGG
1 CCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGACCGATGCCATGTCCCAGACATGG
*
5069 TCTTACACTAGCTCTCACGTA-AACTG-TGATG
66 TCTTACACTAGCTCT--CGTATAAATGCTGATG
* ** * *
5100 CCATGTTCCAAACATGGTCTTATATTGGCTCACATATCGAGGTCGATGCCATGTCCTATACATGG
1 CCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGACCGATGCCATGTCCCAGACATGG
**
5165 TCTTATGCTAGCTCTCGTATAAATGCTGATG
66 TCTTACACTAGCTCTCGTATAAATGCTGATG
*
5196 CCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGACCAATGCCATGTCCCAGACATGG
1 CCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGACCGATGCCATGTCCCAGACATGG
*
5261 TCTTACACTGGCTC
66 TCTTACACTAGCTC
5275 ACATATCCTT
Statistics
Matches: 149, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
91 23 0.15
94 4 0.03
95 5 0.03
96 117 0.79
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (96 bp):
CCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGACCGATGCCATGTCCCAGACATGG
TCTTACACTAGCTCTCGTATAAATGCTGATG
Found at i:5245 original size:48 final size:47
Alignment explanation
Indices: 4957--5281 Score: 193
Period size: 48 Copynumber: 6.9 Consensus size: 47
4947 AAAATGCAGT
* * *
4957 TGCCATG-TCTCAAACA-GGATCTTACACTGGTTCTCATATATCGGTGTCGA
1 TGCCATGTTC-CAAACATGG-TCTTACACTGG--CTCACATATC-GAGCCGA
* * * *
5007 TTCCATGTTCCAAACATGGTCTTACA----C-CATATGTCAAGGCCGA
1 TGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGA-GCCGA
* * * * * * *
5050 TGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACGTAAAC-TG-TGA
1 TGCCATGTTCCAAACATGGTCTTACACT-G-GCTCACAT-ATCGAGCCGA
* * *
5098 TGCCATGTTCCAAACATGGTCTTATATTGGCTCACATATCGAGGTCGA
1 TGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGA-GCCGA
* ** * * * ** *
5146 TGCCATG-TCCTATACATGGTCTTATGCTAGCTCTCGTATAAATGCTGA
1 TGCCATGTTCC-AAACATGGTCTTACACTGGCTCACATATCGA-GCCGA
* *
5194 TGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGACCAA
1 TGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGAG-CCGA
* *
5242 TGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATC
1 TGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATC
5282 CTTAGTATCA
Statistics
Matches: 210, Mismatches: 48, Indels: 36
0.71 0.16 0.12
Matches are distributed among these distances:
43 34 0.16
44 1 0.00
45 2 0.01
46 6 0.03
47 6 0.03
48 129 0.61
49 5 0.02
50 22 0.10
51 5 0.02
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (47 bp):
TGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGCCGA
Done.