Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024316.1 Corchorus olitorius cultivar O-4 contig24349, 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: 12042
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:87 original size:22 final size:22
Alignment explanation
Indices: 59--148 Score: 117
Period size: 22 Copynumber: 4.1 Consensus size: 22
49 CAAGCTAAGC
59 AGTAAAAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
*
81 AGTAAAAGAAAGAGTAATCCGA
1 AGTAAAAGAAAGAGTAATCAGA
** * *
103 AACAGAAGAAAGAGTAATCATA
1 AGTAAAAGAAAGAGTAATCAGA
* *
125 AGTGAAAGAAAGAGTAATTAGA
1 AGTAAAAGAAAGAGTAATCAGA
147 AG
1 AG
149 ATTAGAGTAA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.57, C:0.06, G:0.23, T:0.14
Consensus pattern (22 bp):
AGTAAAAGAAAGAGTAATCAGA
Found at i:1391 original size:6 final size:6
Alignment explanation
Indices: 1380--1412 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1370 TCCAAAAGCT
*
1380 TTTTTC TTTTTC TTTTTC TTTATC TTTTT- TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
1413 GTTTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:9142 original size:25 final size:25
Alignment explanation
Indices: 9091--9138 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
9081 ATTGGAGTAT
9091 TTATTTATCTTGTTTCTTAATTTTA
1 TTATTTATCTTGTTTCTTAATTTTA
* *
9116 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTTCTTAATTTT
9139 TATTGCTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (25 bp):
TTATTTATCTTGTTTCTTAATTTTA
Found at i:9590 original size:13 final size:13
Alignment explanation
Indices: 9572--9597 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9562 GTACTATTCA
9572 AATTCTTTGAGAT
1 AATTCTTTGAGAT
9585 AATTCTTTGAGAT
1 AATTCTTTGAGAT
9598 GATGGATAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
AATTCTTTGAGAT
Found at i:10360 original size:6 final size:6
Alignment explanation
Indices: 10349--10385 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
10339 TATTTCAAAT
10349 TTATAA TTATAA TTATAA TTTATAA TTATAA TATATA
1 TTATAA TTATAA TTATAA -TTATAA TTATAA T-TATA
10386 CTATATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 19 0.66
7 10 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTATAA
Found at i:10368 original size:19 final size:20
Alignment explanation
Indices: 10346--10385 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
10336 TTTTATTTCA
10346 AATTTATAATTATAAT-TAT
1 AATTTATAATTATAATATAT
10365 AATTTATAATTATAATATAT
1 AATTTATAATTATAATATAT
10385 A
1 A
10386 CTATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTATAATTATAATATAT
Found at i:10371 original size:13 final size:13
Alignment explanation
Indices: 10349--10385 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
10339 TATTTCAAAT
10349 TTATAA-TTATAA
1 TTATAATTTATAA
10361 TTATAATTTATAA
1 TTATAATTTATAA
*
10374 TTATAATATATA
1 TTATAATTTATA
10386 CTATATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTATAATTTATAA
Found at i:10395 original size:19 final size:18
Alignment explanation
Indices: 10349--10396 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
10339 TATTTCAAAT
10349 TTATAATTATAAT-TATAA
1 TTATAATTATAATATAT-A
10367 TTTATAATTATAATATATA
1 -TTATAATTATAATATATA
*
10386 CTATATATTAT
1 TTATA-ATTAT
10397 TTTTAGTGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.15
19 19 0.73
20 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATAATTATAATATATA
Found at i:11506 original size:12 final size:12
Alignment explanation
Indices: 11489--11516 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
11479 ACCTGGCAAT
11489 TCGTGTTTCGTG
1 TCGTGTTTCGTG
11501 TCGTGTTTCGTG
1 TCGTGTTTCGTG
11513 TCGT
1 TCGT
11517 ATAAACGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.32, T:0.50
Consensus pattern (12 bp):
TCGTGTTTCGTG
Done.