Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003611.1 Corchorus capsularis cultivar CVL-1 contig03619, 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, 631
Length: 1053
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.45
Found at i:105 original size:22 final size:20
Alignment explanation
Indices: 80--424 Score: 159
Period size: 22 Copynumber: 15.4 Consensus size: 20
70 CTTATTATTC
80 TTTACTTTGTACTGATTACTAT
1 TTTACTTT-TACTGATTACT-T
* **
102 TTTACTCTTGTTGATTACCTT
1 TTTACTTTTACTGATTA-CTT
* * *
123 CTTACTTTTTAGTGATTACCAT
1 TTTAC-TTTTACTGATTA-CTT
145 TTTACTCTTTTACTGATTACTATTT
1 TTTA--CTTTTACTGATTAC---TT
*
170 TCTGCTCCTTTTTTACTGATTACTCT
1 T-T--TAC--TTTTACTGATTACT-T
*
196 TTTAGTTTTTACTGATTACCTT
1 TTTA-CTTTTACTGATTA-CTT
*
218 TTTGCGTTTTACTGATTATCTT
1 TTTAC-TTTTACTGATTA-CTT
*
240 TTTACTTCTTGCTGATTAGCTT
1 TTTACTT-TTACTGATTA-CTT
*
262 TTTACTCTTTACTGATCACCTT
1 TTTACT-TTTACTGATTA-CTT
* * *
284 TTTACTCTTACTGATTTCCT
1 TTTACTTTTACTGATTACTT
*
304 TTTACTTCTTACTTATTACTTTTTTTT
1 TTTACTT-TTACTGATTAC------TT
* *
331 TTTACTCTTACTGATTACTA
1 TTTACTTTTACTGATTACTT
*
351 TTTACTTTTTACTGACTACTAT
1 TTTAC-TTTTACTGATTACT-T
* **
373 TTTACTCTTGTTGATTACCTT
1 TTTACTTTTACTGATTA-CTT
* *
394 CTTACTTTTTGCTGATTACTAT
1 TTTAC-TTTTACTGATTACT-T
416 TTTACTTTT
1 TTTACTTTT
425 TTACTGTGGA
Statistics
Matches: 248, Mismatches: 45, Indels: 61
0.70 0.13 0.17
Matches are distributed among these distances:
20 14 0.06
21 62 0.25
22 117 0.47
23 15 0.06
24 1 0.00
25 4 0.02
26 14 0.06
27 7 0.03
28 14 0.06
ACGTcount: A:0.17, C:0.19, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTACTTTTACTGATTACTT
Found at i:139 original size:43 final size:43
Alignment explanation
Indices: 81--421 Score: 226
Period size: 43 Copynumber: 7.6 Consensus size: 43
71 TTATTATTCT
*
81 TTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCTTC
1 TTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCTTC
* * * *
124 TTACTTTTTAGTGATTACCATTTTACTCTTTTACTGATTACTATTTTC
1 TTACTTTTTACTGATTACTATTTTACTCTTGT--TGATTAC---CTTC
* * * * *
172 TGCTCCTTTTTTACTGATTACTCTTTTAGT-TTTTACTGATTACCTTT
1 T--TAC-TTTTTACTGATTACTATTTTACTCTTGT--TGATTACCTTC
* * * * *
219 TTGCGTTTTACTGATTATCT-TTTTACTTCTTGCTGATTAGCTTT
1 TTACTTTTTACTGATTA-CTATTTTAC-TCTTGTTGATTACCTTC
* * ** *
263 TTACTCTTTACTGATCACCT-TTTTACTCTTACTGATTTCCTT-
1 TTACTTTTTACTGATTA-CTATTTTACTCTTGTTGATTACCTTC
* * * **
305 TTACTTCTTACTTATTACTTTTTTTTTTTACTCTTACTGATTA-CTAT-
1 TTACTTTTTACTGATTAC-----TATTTTACTCTTGTTGATTACCT-TC
*
352 TTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCTTC
1 TTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCTTC
*
395 TTACTTTTTGCTGATTACTATTTTACT
1 TTACTTTTTACTGATTACTATTTTACT
422 TTTTTACTGT
Statistics
Matches: 239, Mismatches: 39, Indels: 40
0.75 0.12 0.13
Matches are distributed among these distances:
41 1 0.00
42 31 0.13
43 68 0.28
44 48 0.20
45 12 0.05
46 5 0.02
47 36 0.15
48 4 0.02
50 15 0.06
51 19 0.08
ACGTcount: A:0.18, C:0.19, G:0.07, T:0.56
Consensus pattern (43 bp):
TTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCTTC
Found at i:164 original size:15 final size:15
Alignment explanation
Indices: 146--199 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
136 GATTACCATT
146 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
161 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
174 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
189 TTACTCTTTTA
1 TTACTCTTTTA
200 GTTTTTACTG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 7 0.23
14 6 0.20
15 17 0.57
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:364 original size:21 final size:22
Alignment explanation
Indices: 330--430 Score: 95
Period size: 21 Copynumber: 4.7 Consensus size: 22
320 TACTTTTTTT
*
330 TTTTAC-TCTTACTGATTACTA
1 TTTTACTTTTTACTGATTACTA
*
351 -TTTACTTTTTACTGACTACTA
1 TTTTACTTTTTACTGATTACTA
*
372 TTTTACTCTTGT--TGATTACCT-
1 TTTTACT-TTTTACTGATTA-CTA
* *
393 TCTTACTTTTTGCTGATTACTA
1 TTTTACTTTTTACTGATTACTA
415 TTTTACTTTTTTACTG
1 TTTTAC-TTTTTACTG
431 TGGAAACCCC
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
20 8 0.12
21 26 0.41
22 19 0.30
23 11 0.17
ACGTcount: A:0.19, C:0.18, G:0.07, T:0.56
Consensus pattern (22 bp):
TTTTACTTTTTACTGATTACTA
Done.