Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1694
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, 835
Length: 1393
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Found at i:114 original size:43 final size:43
Alignment explanation
Indices: 47--394 Score: 423
Period size: 43 Copynumber: 8.3 Consensus size: 43
37 AGATTCTGTT
* * *
47 TTTAGCGGCGTTTGTGATAAAAAGCGCCGCTAAAGGTTTTAGTC
1 TTTAGCGGCGTTTGTGGT-AAAAGCGCCGCTAAAGGTCTTGGTC
*
91 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTAGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
*
134 TTTAGCGGCGTTTGTGGTATAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
*
177 TTTAGCGGCGTTTTTAGG-AAAAGCGCCGCTAAAGGTCTTGG--
1 TTTAGCGGCGTTTGT-GGTAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
218 --T-----CGTTTGTGGAAAAAACGCCGCTAAAGGACCTGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
*
254 TTTAGCGGCG-TTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
296 TTTAGCAGCGTTTGTGGTATATGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
339 TTTAGTGGCGTTCGTGGGAGAAGCGCCGCTAAAGGTCCTT-GTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGT-CTTGGTC
382 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
395 TTAGAAAAAA
Statistics
Matches: 265, Mismatches: 26, Indels: 27
0.83 0.08 0.08
Matches are distributed among these distances:
33 2 0.01
34 26 0.10
38 1 0.00
39 1 0.00
42 37 0.14
43 176 0.66
44 22 0.08
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:241 original size:77 final size:76
Alignment explanation
Indices: 142--295 Score: 236
Period size: 77 Copynumber: 2.0 Consensus size: 76
132 TCTTTAGCGG
* * * * * *
142 CGTTTGTGGTATAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTTTAGGAAAAGCGCCGCT
1 CGTTTGTGGAAAAAACGCCGCTAAAGGACCTGGTCTTTAGCGGCG-TTGTAGGAAAAGCGCCGCT
207 AAAGGTCTTGGT
65 AAAGGTCTTGGT
*
219 CGTTTGTGGAAAAAACGCCGCTAAAGGACCTGGTCTTTAGCGGCGTTGTGGGAAAAGCGCCGCTA
1 CGTTTGTGGAAAAAACGCCGCTAAAGGACCTGGTCTTTAGCGGCGTTGTAGGAAAAGCGCCGCTA
284 AAGGTCTTGGT
66 AAGGTCTTGGT
295 C
1 C
296 TTTAGCAGCG
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
76 30 0.43
77 40 0.57
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.27
Consensus pattern (76 bp):
CGTTTGTGGAAAAAACGCCGCTAAAGGACCTGGTCTTTAGCGGCGTTGTAGGAAAAGCGCCGCTA
AAGGTCTTGGT
Found at i:269 original size:42 final size:43
Alignment explanation
Indices: 219--417 Score: 220
Period size: 43 Copynumber: 4.6 Consensus size: 43
209 AGGTCTTGGT
* *
219 CGTTTGTGGAAAAAACGCCGCTAAAGGACCTGGTCTTTAGCGG
1 CGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGG
* * *
262 CG-TTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCAG
1 CGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGG
* * * * *
304 CGTTTGTGGTATATGCGCCGCTAAAGGTCTTGGTCTTTAGTGG
1 CGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGG
* * * *
347 CGTTCGTGGGAGAAGCGCCGCTAAAGGTCCTTGTCTTTAGCGG
1 CGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGG
* * *
390 CGTTTTTAGAAAAAAAACGCCGCTAAAG
1 CGTTTGT-G-GAAAAAGCGCCGCTAAAG
418 TTAGCGACGC
Statistics
Matches: 130, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
42 37 0.28
43 78 0.60
44 1 0.01
45 14 0.11
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.27
Consensus pattern (43 bp):
CGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGG
Found at i:322 original size:119 final size:120
Alignment explanation
Indices: 99--346 Score: 358
Period size: 119 Copynumber: 2.1 Consensus size: 120
89 TCTTTAGCGG
* * * * * *
99 CGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTAGTCTTTAGCGGCGTTTGTGGTATAAGCGCCGCT
1 CGTTTGTGGAAAAAACGCCGCTAAAGGACCTAGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
* *
164 AAAGGTCTTGGTCTTTAGCGGCGTTTTTAGGAAAAGCGCCGCTAAAGGTCTTGGT
66 AAAGGTCTTGGTCTTTAGCAGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCTTGGT
*
219 CGTTTGTGGAAAAAACGCCGCTAAAGGACCTGGTCTTTAGCGGCG-TTGTGGGAAAAGCGCCGCT
1 CGTTTGTGGAAAAAACGCCGCTAAAGGACCTAGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
* *
283 AAAGGTCTTGGTCTTTAGCAGCGTTTGT-GGTATATGCGCCGCTAAAGGTCTTGGT
66 AAAGGTCTTGGTCTTTAGCAGCGTTTGTAGG-AAAAGCGCCGCTAAAGGTCTTGGT
338 C-TTTAGTGG
1 CGTTT-GTGG
347 CGTTCGTGGG
Statistics
Matches: 115, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
118 5 0.04
119 70 0.61
120 40 0.35
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (120 bp):
CGTTTGTGGAAAAAACGCCGCTAAAGGACCTAGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
AAAGGTCTTGGTCTTTAGCAGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCTTGGT
Found at i:339 original size:162 final size:164
Alignment explanation
Indices: 55--375 Score: 495
Period size: 162 Copynumber: 2.0 Consensus size: 164
45 TTTTTAGCGG
*** *
55 CGTTTGTGATAAAAAGCGCCGCTAAAGGTTTTAGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGC
1 CGTTTGTGATAAAAAGCGCCGCTAAAGGACCTAGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
*
120 TAAAGGTCTTAGTCTTTAGCGGCGTTTGTGGTATAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGG
66 TAAAGGTCTTAGTCTTTAGCAGCGTTTGTGGTATAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGG
**
185 CGTTTTTAGGAAAAGCGCCGCTAAAGGTCTTGGT
131 CGTTCGTAGGAAAAGCGCCGCTAAAGGTCTTGGT
*
219 CGTTTGTGGA-AAAAA-CGCCGCTAAAGGACCTGGTCTTTAGCGGCG-TTGTGGGAAAAGCGCCG
1 CGTTTGT-GATAAAAAGCGCCGCTAAAGGACCTAGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCG
* * *
281 CTAAAGGTCTTGGTCTTTAGCAGCGTTTGTGGTATATGCGCCGCTAAAGGTCTTGGTCTTTAGTG
65 CTAAAGGTCTTAGTCTTTAGCAGCGTTTGTGGTATAAGCGCCGCTAAAGGTCTTGGTCTTTAGCG
* *
346 GCGTTCGTGGGAGAAGCGCCGCTAAAGGTC
130 GCGTTCGTAGGAAAAGCGCCGCTAAAGGTC
376 CTTGTCTTTA
Statistics
Matches: 143, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
162 103 0.72
163 26 0.18
164 12 0.08
165 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (164 bp):
CGTTTGTGATAAAAAGCGCCGCTAAAGGACCTAGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
TAAAGGTCTTAGTCTTTAGCAGCGTTTGTGGTATAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGG
CGTTCGTAGGAAAAGCGCCGCTAAAGGTCTTGGT
Found at i:1278 original size:15 final size:15
Alignment explanation
Indices: 1258--1289 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1248 GACCAAAGAC
1258 GATTGTTGGTAGTAG
1 GATTGTTGGTAGTAG
1273 GATTGTTGGTAGTAG
1 GATTGTTGGTAGTAG
1288 GA
1 GA
1290 AATAGGTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.38
Consensus pattern (15 bp):
GATTGTTGGTAGTAG
Found at i:1370 original size:28 final size:27
Alignment explanation
Indices: 1334--1393 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
1324 TATAAAAAAA
*
1334 TTACCAAAATGT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAA--TTTTTTTAT
*
1362 TTACTAAAATATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
1389 TTACC
1 TTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.46
28 10 0.36
29 5 0.18
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Done.