Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: evm.model.Ga01G0877
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, 266
Length: 444
ACGTcount: A:0.16, C:0.09, G:0.50, T:0.25
Found at i:120 original size:24 final size:24
Alignment explanation
Indices: 91--147 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
81 ATTAGGAGGA
* * *
91 GGAGGTGGTGGAGGGTTTGGTGGT
1 GGAGGTGGAGGAGGGCTAGGTGGT
115 GGAGGTGGAGGAGGGCTAGGTGGT
1 GGAGGTGGAGGAGGGCTAGGTGGT
*
139 GGAGCTGGA
1 GGAGGTGGA
148 TTTGGTGGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.14, C:0.04, G:0.61, T:0.21
Consensus pattern (24 bp):
GGAGGTGGAGGAGGGCTAGGTGGT
Found at i:183 original size:18 final size:18
Alignment explanation
Indices: 162--200 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
152 GTGGGGGCGC
* *
162 TGGTGCTGGTGGTGGCCT
1 TGGTGCAGGTGGTGGACT
*
180 TGGTGGAGGTGGTGGACT
1 TGGTGCAGGTGGTGGACT
198 TGG
1 TGG
201 AGGAGGAGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.10, G:0.54, T:0.31
Consensus pattern (18 bp):
TGGTGCAGGTGGTGGACT
Found at i:205 original size:18 final size:18
Alignment explanation
Indices: 169--212 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
159 CGCTGGTGCT
* *
169 GGTGGTGGCCTTGGTGGA
1 GGTGGTGGACTTGGAGGA
187 GGTGGTGGACTTGGAGGA
1 GGTGGTGGACTTGGAGGA
*
205 GGAGGTGG
1 GGTGGTGG
213 TGGAGGGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.07, G:0.59, T:0.23
Consensus pattern (18 bp):
GGTGGTGGACTTGGAGGA
Found at i:244 original size:18 final size:20
Alignment explanation
Indices: 202--256 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 20
192 TGGACTTGGA
*
202 GGAGGAGGTGGTGGAGGGTTC
1 GGAGGAGGTGGTGG-TGGTTC
223 GGAGGAGGTGGTGGTGG-T-
1 GGAGGAGGTGGTGGTGGTTC
*
241 GGAGTAGGTGGTGGTG
1 GGAGGAGGTGGTGGTG
257 CTGGTGGTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 15 0.47
19 1 0.03
20 2 0.06
21 14 0.44
ACGTcount: A:0.13, C:0.02, G:0.64, T:0.22
Consensus pattern (20 bp):
GGAGGAGGTGGTGGTGGTTC
Found at i:278 original size:24 final size:24
Alignment explanation
Indices: 181--275 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 24
171 TGGTGGCCTT
* **
181 GGTGGAGGTGGTGGACTTGGAGGA
1 GGTGGTGGTGGTGGGTTTGGAGGA
* * *
205 GGAGGTGGTGGAGGGTTCGGAGGA
1 GGTGGTGGTGGTGGGTTTGGAGGA
* * *
229 GGTGGTGGTGGTGGAG-TAGGTGGT
1 GGTGGTGGTGGTGG-GTTTGGAGGA
*
253 GGTGCTGGTGGTGGGTTTGGAGG
1 GGTGGTGGTGGTGGGTTTGGAGG
276 TGGGGCAGGA
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
23 1 0.02
24 53 0.96
25 1 0.02
ACGTcount: A:0.12, C:0.03, G:0.61, T:0.24
Consensus pattern (24 bp):
GGTGGTGGTGGTGGGTTTGGAGGA
Found at i:321 original size:18 final size:18
Alignment explanation
Indices: 283--340 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
273 AGGTGGGGCA
* *
283 GGAGCAGGAGCTGGAGGT
1 GGAGCTGGAGGTGGAGGT
* *
301 GGA-CTAGGTGGTGGTGGT
1 GGAGCT-GGAGGTGGAGGT
319 GGAGCTGGAGGTGGAGGT
1 GGAGCTGGAGGTGGAGGT
337 GGAG
1 GGAG
341 GCGGCTTCGG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
17 1 0.03
18 29 0.91
19 2 0.06
ACGTcount: A:0.17, C:0.07, G:0.59, T:0.17
Consensus pattern (18 bp):
GGAGCTGGAGGTGGAGGT
Found at i:331 original size:15 final size:15
Alignment explanation
Indices: 288--335 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
278 GGGCAGGAGC
288 AGGAGCTGGAGGTGG
1 AGGAGCTGGAGGTGG
** * *
303 ACTAGGTGGTGGTGG
1 AGGAGCTGGAGGTGG
*
318 TGGAGCTGGAGGTGG
1 AGGAGCTGGAGGTGG
333 AGG
1 AGG
336 TGGAGGCGGC
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.17, C:0.06, G:0.58, T:0.19
Consensus pattern (15 bp):
AGGAGCTGGAGGTGG
Found at i:394 original size:30 final size:30
Alignment explanation
Indices: 349--428 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 30
339 AGGCGGCTTC
* *
349 GGTGGAGGAGGTGGGTTTGGCGGTGGAGCT
1 GGTGCAGGTGGTGGGTTTGGCGGTGGAGCT
* *
379 GGTGCAGGTGGTGGGTTCGGTGGTGGAGCT
1 GGTGCAGGTGGTGGGTTTGGCGGTGGAGCT
* *
409 GGTGCAGGTAGTGGGCTTGG
1 GGTGCAGGTGGTGGGTTTGG
429 AGGAGGACTG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.09, C:0.09, G:0.57, T:0.25
Consensus pattern (30 bp):
GGTGCAGGTGGTGGGTTTGGCGGTGGAGCT
Done.