Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010212.1 Corchorus capsularis cultivar CVL-1 contig10233, 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: 19555
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--39 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 A
2 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40 AAGGAAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2301 original size:53 final size:53
Alignment explanation
Indices: 2218--2324 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
2208 TTGTTAGCAT
*
2218 TTCACAACAAAATTTGATTTCTTAAATGAATTTTCTTAAGAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAAATGAATTTTCTTAAAAGAATTTATAAAA
*
2271 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAAATGAATTTTCTTAAAAGAATTTATAAAA
2324 T
1 T
2325 AAAACAGCTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (53 bp):
TTCACAACAAAATTTGATTTCTTAAATGAATTTTCTTAAAAGAATTTATAAAA
Found at i:4336 original size:26 final size:26
Alignment explanation
Indices: 4307--4426 Score: 199
Period size: 26 Copynumber: 4.6 Consensus size: 26
4297 TACTTAGTTT
4307 ATTAGTTTATATTTAATTAGTATTTA
1 ATTAGTTTATATTTAATTAGTATTTA
4333 ATTAGTTTATGA-TTAATTAGTATTTA
1 ATTAGTTTAT-ATTTAATTAGTATTTA
4359 ATTAGTTTATATTTAATTAGTATTTA
1 ATTAGTTTATATTTAATTAGTATTTA
4385 ATTAGTTTATGA-TTAATTAGTATTTA
1 ATTAGTTTAT-ATTTAATTAGTATTTA
*
4411 ATTAGTTTATGTTTAA
1 ATTAGTTTATATTTAA
4427 AATGAAGGAA
Statistics
Matches: 89, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
25 1 0.01
26 86 0.97
27 2 0.02
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (26 bp):
ATTAGTTTATATTTAATTAGTATTTA
Found at i:4339 original size:52 final size:52
Alignment explanation
Indices: 4271--4426 Score: 210
Period size: 52 Copynumber: 3.0 Consensus size: 52
4261 TTAGTTTATG
* *
4271 ATTAGT-TTTAATTAGTTAATTA-AAATTACTTAGTTT-ATTAGTTTATATTTA
1 ATTAGTATTTAATTAGTTAATGATAAATTA-GTA-TTTAATTAGTTTATATTTA
* *
4322 ATTAGTATTTAATTAGTTTATGATTAATTAGTATTTAATTAGTTTATATTTA
1 ATTAGTATTTAATTAGTTAATGATAAATTAGTATTTAATTAGTTTATATTTA
* * *
4374 ATTAGTATTTAATTAGTTTATGATTAATTAGTATTTAATTAGTTTATGTTTA
1 ATTAGTATTTAATTAGTTAATGATAAATTAGTATTTAATTAGTTTATATTTA
4426 A
1 A
4427 AATGAAGGAA
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
51 9 0.09
52 83 0.86
53 5 0.05
ACGTcount: A:0.35, C:0.01, G:0.10, T:0.55
Consensus pattern (52 bp):
ATTAGTATTTAATTAGTTAATGATAAATTAGTATTTAATTAGTTTATATTTA
Found at i:4411 original size:11 final size:11
Alignment explanation
Indices: 4316--4416 Score: 94
Period size: 11 Copynumber: 8.1 Consensus size: 11
4306 TATTAGTTTA
4316 TATTTAATTAG
1 TATTTAATTAG
4327 TATTTAATTAG
1 TATTTAATTAG
4338 TTTATGATTAATTAG
1 --TAT--TTAATTAG
4353 TATTTAATTAG
1 TATTTAATTAG
4364 TTTATATTTAATTAG
1 ----TATTTAATTAG
4379 TATTTAATTAG
1 TATTTAATTAG
4390 TTTATGATTAATTAG
1 --TAT--TTAATTAG
4405 TATTTAATTAG
1 TATTTAATTAG
4416 T
1 T
4417 TTATGTTTAA
Statistics
Matches: 78, Mismatches: 0, Indels: 24
0.76 0.00 0.24
Matches are distributed among these distances:
11 39 0.50
13 12 0.15
15 27 0.35
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (11 bp):
TATTTAATTAG
Found at i:5059 original size:6 final size:6
Alignment explanation
Indices: 5028--5057 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5018 GGGTGGCTTC
5028 TGTTTT TGTTTT TGTTTT TGTTTT T-TTTT T
1 TGTTTT TGTTTT TGTTTT TGTTTT TGTTTT T
5058 TTCACACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TGTTTT
Found at i:7488 original size:19 final size:19
Alignment explanation
Indices: 7477--7513 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
7467 AATTTTTAAG
7477 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
7496 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
7514 ACAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:12192 original size:2 final size:2
Alignment explanation
Indices: 12185--12219 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
12175 TATAGTGGTG
*
12185 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12220 AATTTCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Done.