Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015929.1 Corchorus capsularis cultivar CVL-1 contig15950, 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: 21469
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:469 original size:12 final size:13
Alignment explanation
Indices: 444--477 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
434 ATAATTATTG
444 TTTGCTTTATTAA
1 TTTGCTTTATTAA
457 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
469 TCTGCTTTA
1 TTTGCTTTA
478 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:485 original size:6 final size:6
Alignment explanation
Indices: 474--500 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
464 TATAATCTGC
474 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
501 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:4381 original size:10 final size:10
Alignment explanation
Indices: 4366--4429 Score: 58
Period size: 10 Copynumber: 6.0 Consensus size: 10
4356 ACATCACCGC
4366 GCCATGCCCG
1 GCCATGCCCG
*
4376 GCCATGTCCG
1 GCCATGCCCG
4386 CGCCATGCCCG
1 -GCCATGCCCG
*
4397 GCCATGTCCG
1 GCCATGCCCG
4407 CGCC-TCCAGCCCG
1 -GCCAT---GCCCG
4420 GCCATGCCCG
1 GCCATGCCCG
4430 ACCAATGCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 24 0.55
11 12 0.27
12 3 0.07
13 5 0.11
ACGTcount: A:0.09, C:0.50, G:0.28, T:0.12
Consensus pattern (10 bp):
GCCATGCCCG
Found at i:4392 original size:11 final size:11
Alignment explanation
Indices: 4362--4410 Score: 66
Period size: 10 Copynumber: 4.6 Consensus size: 11
4352 CGAGACATCA
4362 CCGCGCCATGC
1 CCGCGCCATGC
*
4373 CCG-GCCATGT
1 CCGCGCCATGC
4383 CCGCGCCATGC
1 CCGCGCCATGC
*
4394 CCG-GCCATGT
1 CCGCGCCATGC
4404 CCGCGCC
1 CCGCGCC
4411 TCCAGCCCGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 18 0.55
11 15 0.45
ACGTcount: A:0.08, C:0.51, G:0.29, T:0.12
Consensus pattern (11 bp):
CCGCGCCATGC
Found at i:4425 original size:23 final size:21
Alignment explanation
Indices: 4362--4410 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
4352 CGAGACATCA
4362 CCGCGCCATGCCCGGCCATGT
1 CCGCGCCATGCCCGGCCATGT
4383 CCGCGCCATGCCCGGCCATGT
1 CCGCGCCATGCCCGGCCATGT
4404 CCGCGCC
1 CCGCGCC
4411 TCCAGCCCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.08, C:0.51, G:0.29, T:0.12
Consensus pattern (21 bp):
CCGCGCCATGCCCGGCCATGT
Found at i:7631 original size:12 final size:13
Alignment explanation
Indices: 7606--7639 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
7596 ATAATTATTG
7606 TTTGCTTTATTAA
1 TTTGCTTTATTAA
7619 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
7631 TCTGCTTTA
1 TTTGCTTTA
7640 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:7647 original size:6 final size:6
Alignment explanation
Indices: 7636--7662 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7626 TATAATCTGC
7636 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
7663 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:19334 original size:6 final size:6
Alignment explanation
Indices: 19323--19348 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19313 AGATGCTGAG
19323 CCTACA CCTACA CCTACA CCTACA CC
1 CCTACA CCTACA CCTACA CCTACA CC
19349 ATCTCAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (6 bp):
CCTACA
Found at i:20189 original size:3 final size:3
Alignment explanation
Indices: 20175--20204 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
20165 ATTATTTACC
*
20175 ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20205 TAGTACCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:20385 original size:23 final size:23
Alignment explanation
Indices: 20355--20406 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
20345 TTTATCATCA
20355 ATCTCATCATAAACCAATTAGAT
1 ATCTCATCATAAACCAATTAGAT
20378 ATCTCATCATAAACCAATTAGAT
1 ATCTCATCATAAACCAATTAGAT
20401 ATCTCA
1 ATCTCA
20407 ATATTATGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.23, G:0.04, T:0.31
Consensus pattern (23 bp):
ATCTCATCATAAACCAATTAGAT
Found at i:21278 original size:25 final size:24
Alignment explanation
Indices: 21250--21301 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
21240 TTCAAACCCT
*
21250 AAACTTAATTTCTAACAACTTCTTC
1 AAACTTAATTTCTAACAA-ATCTTC
* *
21275 AAACTTCATTTTTAACAAATCTTC
1 AAACTTAATTTCTAACAAATCTTC
21299 AAA
1 AAA
21302 TTCATTTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (24 bp):
AAACTTAATTTCTAACAAATCTTC
Found at i:21347 original size:26 final size:26
Alignment explanation
Indices: 21318--21385 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
21308 TTCCTTCATT
21318 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
21344 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
21370 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
21386 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Done.