Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001413.1 Corchorus capsularis cultivar CVL-1 contig01413, whole genome shotgun sequence
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, 763
Length: 1272
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:254 original size:25 final size:25
Alignment explanation
Indices: 209--358 Score: 79
Period size: 23 Copynumber: 6.2 Consensus size: 25
199 ATTTTTTANA
*
209 TTATATA-TATAT-TTTAATTTTTT
1 TTATATATTATATATATAATTTTTT
*
232 ATT-T-TATTATTTATATAATTTTTT
1 -TTATATATTATATATATAATTTTTT
** *
256 TTATATATTATATATAT-A-TAATA
1 TTATATATTATATATATAATTTTTT
* *
279 TTATA-A-TATA-ATATTATATTTTA
1 TTATATATTATATATATAAT-TTTTT
* *
302 ATATATTATTATATTTATATATATATTTAT
1 TTATA-TATTATA--TATATA-AT-TTTTT
332 TTATATA-TATATATAT-ATTTTTT
1 TTATATATTATATATATAATTTTTT
355 TTAT
1 TTAT
359 TTTTTGTATA
Statistics
Matches: 98, Mismatches: 14, Indels: 29
0.70 0.10 0.21
Matches are distributed among these distances:
20 4 0.04
21 5 0.05
22 3 0.03
23 29 0.30
24 16 0.16
25 12 0.12
26 9 0.09
28 4 0.04
29 6 0.06
30 10 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTATATATTATATATATAATTTTTT
Found at i:257 original size:21 final size:24
Alignment explanation
Indices: 228--271 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
218 TATTTTAATT
228 TTTTATTTTAT-TATT-TATATAA
1 TTTTATTTTATATATTATATATAA
250 TTTT-TTTTATATATTATATATA
1 TTTTATTTTATATATTATATATA
272 TATAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 8 0.40
23 6 0.30
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTATTTTATATATTATATATAA
Found at i:262 original size:2 final size:2
Alignment explanation
Indices: 257--349 Score: 80
Period size: 2 Copynumber: 51.5 Consensus size: 2
247 TAATTTTTTT
257 TA TA TA T- TA TA TA TA TA TA -A TA T- TA TA -A TA TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
293 TA TA T- TT TA -A TA TA T- TA T- TA TA TT TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
331 TT TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
350 TTTTTTTATT
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
1 10 0.14
2 64 0.86
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:314 original size:8 final size:8
Alignment explanation
Indices: 230--350 Score: 51
Period size: 8 Copynumber: 15.2 Consensus size: 8
220 TTTTAATTTT
*
230 TTATTTTA
1 TTATTATA
238 TTATTTATA
1 TTA-TTATA
*
247 TAATT-T-
1 TTATTATA
*
253 TTTTTATA
1 TTATTATA
261 -TATTATA
1 TTATTATA
268 -TATATATA
1 TTAT-TATA
*
276 ATATTATA
1 TTATTATA
* *
284 ATATAATA
1 TTATTATA
*
292 TTA-TATT
1 TTATTATA
*
299 TTAATATA
1 TTATTATA
307 TTATTATA
1 TTATTATA
315 TT-TATATA
1 TTAT-TATA
323 TATATT-TA
1 T-TATTATA
331 TT-TATATA
1 TTAT-TATA
339 TATATATATA
1 T-TAT-TATA
349 TT
1 TT
351 TTTTTTATTT
Statistics
Matches: 89, Mismatches: 11, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
6 4 0.04
7 19 0.21
8 45 0.51
9 13 0.15
10 8 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTATTATA
Found at i:343 original size:18 final size:18
Alignment explanation
Indices: 209--351 Score: 78
Period size: 18 Copynumber: 8.1 Consensus size: 18
199 ATTTTTTANA
209 TTATATATATAT-TTTAAT
1 TTATATATATATATTT-AT
* *
227 TT-TTTAT-TTTA-TTAT
1 TTATATATATATATTTAT
242 TTATATA-AT-T-TTT-T
1 TTATATATATATATTTAT
256 TTATATATTATATATATATAAT
1 TTATATA-TATATAT-T-T-AT
278 ATTATA-ATATAATATTATAT
1 -TTATATATAT-ATATT-TAT
298 TT-TA-ATATAT-TATTAT
1 TTATATATATATAT-TTAT
314 ATT-TATATATATATTTAT
1 -TTATATATATATATTTAT
*
332 TTATATATATATATATAT
1 TTATATATATATATTTAT
350 TT
1 TT
352 TTTTTATTTT
Statistics
Matches: 102, Mismatches: 4, Indels: 38
0.71 0.03 0.26
Matches are distributed among these distances:
14 8 0.08
15 7 0.07
16 14 0.14
17 14 0.14
18 35 0.34
19 4 0.04
20 3 0.03
21 6 0.06
22 6 0.06
23 5 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATATATATATTTAT
Done.