Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011962.1 Corchorus capsularis cultivar CVL-1 contig11983, 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, 1000
Length: 30294
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:30 original size:7 final size:7
Alignment explanation
Indices: 1--481 Score: 800
Period size: 7 Copynumber: 71.1 Consensus size: 7
1 AACCCT-
1 AACCCTA
7 AACCCT-
1 AACCCTA
13 AA-CCT-
1 AACCCTA
18 AACCCTA
1 AACCCTA
25 AACCCTA
1 AACCCTA
32 AACCCTA
1 AACCCTA
39 AACCCT-
1 AACCCTA
45 AACCCTA
1 AACCCTA
52 AACCCTA
1 AACCCTA
59 AACCCTA
1 AACCCTA
66 AACCCT-
1 AACCCTA
72 AACCCT-
1 AACCCTA
78 AACCCTA
1 AACCCTA
85 AACCCTA
1 AACCCTA
92 AACCCTA
1 AACCCTA
99 AACCCTA
1 AACCCTA
106 AACCCTA
1 AACCCTA
113 AACCCTA
1 AACCCTA
120 AACCCTA
1 AACCCTA
127 AACCCT-
1 AACCCTA
133 AACCCTA
1 AACCCTA
140 AACCCT-
1 AACCCTA
146 AACCCT-
1 AACCCTA
152 AACCCTA
1 AACCCTA
159 AACCCTA
1 AACCCTA
166 AACCCT-
1 AACCCTA
172 AACCCTA
1 AACCCTA
179 AACCCTA
1 AACCCTA
186 AACCCTA
1 AACCCTA
193 AACCCT-
1 AACCCTA
199 AACCCTA
1 AACCCTA
206 AACCCTA
1 AACCCTA
213 AACCCTA
1 AACCCTA
220 AACCCTA
1 AACCCTA
227 AACCCTA
1 AACCCTA
234 AACCCTA
1 AACCCTA
241 AACCCT-
1 AACCCTA
247 AACCCTA
1 AACCCTA
254 AACCCTA
1 AACCCTA
261 AACCCTA
1 AACCCTA
268 AACCCTA
1 AACCCTA
275 AACCCT-
1 AACCCTA
281 AACCCTA
1 AACCCTA
288 AACCCTA
1 AACCCTA
295 AACCCTA
1 AACCCTA
302 AACCCTA
1 AACCCTA
309 AACCCTA
1 AACCCTA
316 AACCCTA
1 AACCCTA
323 AACCCTA
1 AACCCTA
330 AACCCCTA
1 AA-CCCTA
338 AACCCTA
1 AACCCTA
345 AACCCTA
1 AACCCTA
352 AACCCTA
1 AACCCTA
359 AACCCTA
1 AACCCTA
*
366 ACCCCTA
1 AACCCTA
373 AACCCTA
1 AACCCTA
380 AACCCT-
1 AACCCTA
386 AACCCTA
1 AACCCTA
393 AACCCTA
1 AACCCTA
400 AACCCTA
1 AACCCTA
407 AACCCT-
1 AACCCTA
413 AACCCTA
1 AACCCTA
420 AACCCTA
1 AACCCTA
427 AACCCTA
1 AACCCTA
434 AACCCT-
1 AACCCTA
440 AACCCTA
1 AACCCTA
*
447 AATCCTA
1 AACCCTA
*
454 AACCATA
1 AACCCTA
461 AACCCT-
1 AACCCTA
467 AACCCTA
1 AACCCTA
474 AACCCTA
1 AACCCTA
481 A
1 A
482 TAGGTCTAAA
Statistics
Matches: 454, Mismatches: 6, Indels: 29
0.93 0.01 0.06
Matches are distributed among these distances:
5 5 0.01
6 95 0.21
7 347 0.76
8 7 0.02
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (7 bp):
AACCCTA
Found at i:49 original size:27 final size:27
Alignment explanation
Indices: 1--481 Score: 764
Period size: 27 Copynumber: 18.3 Consensus size: 27
1 AACCCT-AACCCT-AA-CCTAACCCTA
1 AACCCTAAACCCTAAACCCTAACCCTA
25 AACCCTAAACCCTAAACCCTAACCCTA
1 AACCCTAAACCCTAAACCCTAACCCTA
52 AACCCTAAACCCTAAACCCTAACCCT-
1 AACCCTAAACCCTAAACCCTAACCCTA
78 AACCCTAAACCCT--A----AACCCTA
1 AACCCTAAACCCTAAACCCTAACCCTA
99 AACCCTAAACCCTAAACCCTAAACCCTA
1 AACCCTAAACCCTAAACCCT-AACCCTA
127 AACCCT-AACCCTAAACCCTAACCCT-
1 AACCCTAAACCCTAAACCCTAACCCTA
152 AACCCTAAACCCTAAACCCTAACCCTA
1 AACCCTAAACCCTAAACCCTAACCCTA
179 AACCCTAAACCCTAAACCCTAACCCTA
1 AACCCTAAACCCTAAACCCTAACCCTA
206 AACCCTAAACCCTAAACCCTAAACCCTA
1 AACCCTAAACCCTAAACCCT-AACCCTA
234 AACCCTAAACCCT-AACCCTAAACCCTA
1 AACCCTAAACCCTAAACCCT-AACCCTA
261 AACCCTAAACCCTAAACCCTAACCCTA
1 AACCCTAAACCCTAAACCCTAACCCTA
288 AACCCTAAACCCTAAACCCTAAACCCTA
1 AACCCTAAACCCTAAACCCT-AACCCTA
316 AACCCTAAACCCTAAA--C---CCCTA
1 AACCCTAAACCCTAAACCCTAACCCTA
338 AACCCTAAACCCTAAACCCTAAACCCTA
1 AACCCTAAACCCTAAACCCT-AACCCTA
*
366 ACCCCTAAACCCTAAACCCTAACCCTA
1 AACCCTAAACCCTAAACCCTAACCCTA
393 AACCCTAAACCCTAAACCCTAACCCTA
1 AACCCTAAACCCTAAACCCTAACCCTA
420 AACCCTAAACCCTAAACCCTAACCCTA
1 AACCCTAAACCCTAAACCCTAACCCTA
* *
447 AATCCTAAACCATAAACCCTAACCCTA
1 AACCCTAAACCCTAAACCCTAACCCTA
474 AACCCTAA
1 AACCCTAA
482 TAGGTCTAAA
Statistics
Matches: 430, Mismatches: 5, Indels: 41
0.90 0.01 0.09
Matches are distributed among these distances:
20 6 0.01
21 13 0.03
22 21 0.05
23 1 0.00
24 8 0.02
25 12 0.03
26 41 0.10
27 242 0.56
28 86 0.20
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (27 bp):
AACCCTAAACCCTAAACCCTAACCCTA
Found at i:7700 original size:2 final size:2
Alignment explanation
Indices: 7693--7720 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7683 AAATGAAATA
7693 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7721 CATAGCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9063 original size:3 final size:3
Alignment explanation
Indices: 9057--9081 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9047 AAGAAGGAAA
9057 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
9082 GTAACCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19519 original size:2 final size:2
Alignment explanation
Indices: 19512--19548 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19502 TCAAAAGCTT
19512 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19549 TTGTTTGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22370 original size:2 final size:2
Alignment explanation
Indices: 22365--22391 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22355 TATATATATA
22365 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
22392 CTAGACACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:30260 original size:2 final size:2
Alignment explanation
Indices: 30248--30294 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
30238 TGTCTATCAA
30248 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30291 AT AT
1 AT AT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.