Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008817.1 Corchorus capsularis cultivar CVL-1 contig08838, 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: 7873
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Found at i:4060 original size:36 final size:35
Alignment explanation
Indices: 4013--4131 Score: 131
Period size: 36 Copynumber: 3.4 Consensus size: 35
4003 CTCTTTTTAG
* *
4013 ATTAAATTCTTTATTGATTTCACTTAATTACCTTGA
1 ATTAAGTTCTTTATTGATCTCACTTAATTACC-TGA
4049 ATTAAGTTCTTTA-T--TCT-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGATCTCACTTAATTA-CCTGA
* *
4081 ATTAAG-CCTTTTATTGACCTCACTTAATTACACTGA
1 ATTAAGTTC-TTTATTGATCTCACTTAATTAC-CTGA
4117 ATTAAGTTCTTTATT
1 ATTAAGTTCTTTATT
4132 TTACTTAATT
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
31 1 0.01
32 22 0.31
33 5 0.07
35 4 0.06
36 37 0.53
37 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (35 bp):
ATTAAGTTCTTTATTGATCTCACTTAATTACCTGA
Found at i:4075 original size:32 final size:32
Alignment explanation
Indices: 4034--4146 Score: 122
Period size: 32 Copynumber: 3.4 Consensus size: 32
4024 TATTGATTTC
4034 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
* *
4066 ACTTAATTACCCTGAATTAAG-CCTTTTATTGACCT
1 ACTTAATTACCTTGAATTAAGTTC-TTTATT---CT
*
4101 CACTTAATTACAC-TGAATTAAGTTCTTTATTTT
1 -ACTTAATTAC-CTTGAATTAAGTTCTTTATTCT
*
4134 ACTTAATTTCCTT
1 ACTTAATTACCTT
4147 TCCTGAAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
31 2 0.03
32 36 0.53
33 1 0.01
35 2 0.03
36 25 0.37
37 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (32 bp):
ACTTAATTACCTTGAATTAAGTTCTTTATTCT
Found at i:4225 original size:71 final size:70
Alignment explanation
Indices: 4168--4415 Score: 214
Period size: 71 Copynumber: 3.5 Consensus size: 70
4158 AGCTTGTGTC
* * **
4168 TTTTTACTTAATTTCATTGAAATTAAGCCAGTCTTCCCTTTACCTAGTTTCCTTGAAACGAAGCC
1 TTTTTACTTAATTTCATTGAAATTAAGCCAATCTT-CCTTTACCTAATTTCCTTGAAATTAAGCC
4233 AATTCT
65 AATTCT
* ** *
4239 TTTTTACTTAATTTCCTTGAAATTAAGCCAATCTTGTTTTACTTAATTTCCTTGAAATTAAGCC-
1 TTTTTACTTAATTTCATTGAAATTAAGCCAATCTTCCTTTACCTAATTTCCTTGAAATTAAGCCA
*
4303 AGTCTT
66 ATTC-T
* ** * * * * *
4309 TTCTTTACCTAGCTTCCTTGAAACTAAGCCGATCTAT-CTTTACTTAATTTCTTTGAAATTAAGC
1 TT-TTTACTTAATTTCATTGAAATTAAGCCAATCT-TCCTTTACCTAATTTCCTTGAAATTAAGC
*
4373 C-AGTCT
64 CAATTCT
* * * * *
4379 ATTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTT
1 -TT-TTTACTTAATTTCATTGAAATTAAGCCAATCTT
4416 TTATCAGTCT
Statistics
Matches: 154, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
69 3 0.02
70 28 0.18
71 122 0.79
72 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (70 bp):
TTTTTACTTAATTTCATTGAAATTAAGCCAATCTTCCTTTACCTAATTTCCTTGAAATTAAGCCA
ATTCT
Found at i:4254 original size:35 final size:34
Alignment explanation
Indices: 4130--4417 Score: 254
Period size: 35 Copynumber: 8.1 Consensus size: 34
4120 AAGTTCTTTA
** *
4130 TTTTACTTAATTTCCTTTCCTGAAATTAAGCTTGTGTCT
1 TTTTACTTAATTTCC--T--TGAAATTAAGCCAGTCT-T
*
4169 TTTTACTTAATTTCATTGAAATTAAGCCAGTCTT
1 TTTTACTTAATTTCCTTGAAATTAAGCCAGTCTT
* * * ** *
4203 CCCTTTACCTAGTTTCCTTGAAACGAAGCCAATTCTT
1 --TTTTACTTAATTTCCTTGAAATTAAGCC-AGTCTT
*
4240 TTTTACTTAATTTCCTTGAAATTAAGCCAATCTT
1 TTTTACTTAATTTCCTTGAAATTAAGCCAGTCTT
4274 GTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTT
1 -TTTTACTTAATTTCCTTGAAATTAAGCCAGTC-TT
* ** *
4310 TCTTTACCTAGCTTCCTTGAAACTAAGCC-GATCTAT
1 T-TTTACTTAATTTCCTTGAAATTAAGCCAG-TCT-T
* *
4346 CTTTACTTAATTTCTTTGAAATTAAGCCAGTCTAT
1 TTTTACTTAATTTCCTTGAAATTAAGCCAGTCT-T
* * *
4381 TCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTT
1 T-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTT
4416 TT
1 TT
4418 ATCAGTCTAA
Statistics
Matches: 206, Mismatches: 33, Indels: 25
0.78 0.12 0.09
Matches are distributed among these distances:
34 7 0.03
35 100 0.49
36 79 0.38
37 6 0.03
39 14 0.07
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (34 bp):
TTTTACTTAATTTCCTTGAAATTAAGCCAGTCTT
Found at i:4280 original size:106 final size:106
Alignment explanation
Indices: 4168--4415 Score: 347
Period size: 106 Copynumber: 2.3 Consensus size: 106
4158 AGCTTGTGTC
* *
4168 TTTTTACTTAATTTCATTGAAATTAAGCCAGTCTTCCCTTTACCTAGTTTCCTTGAAACGAAGCC
1 TTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTCCCTTTACCTAGCTTCCTTGAAACGAAGCC
*
4233 AATTCT-TTTTTACTTAATTTCCTTGAAATTAAGCCAATCT-
66 AA-TCTATCTTTACTTAATTTCCTTGAAATTAAGCCAATCTA
** *
4273 TGTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGCTTCCTTGAAACTAAGC
1 T-TTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTCCCTTTACCTAGCTTCCTTGAAACGAAGC
* * *
4338 CGATCTATCTTTACTTAATTTCTTTGAAATTAAGCCAGTCTA
65 CAATCTATCTTTACTTAATTTCCTTGAAATTAAGCCAATCTA
* * *
4380 TTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTT
1 TT-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTT
4416 TTATCAGTCT
Statistics
Matches: 127, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
105 4 0.03
106 92 0.72
107 31 0.24
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (106 bp):
TTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTCCCTTTACCTAGCTTCCTTGAAACGAAGCC
AATCTATCTTTACTTAATTTCCTTGAAATTAAGCCAATCTA
Found at i:4425 original size:11 final size:11
Alignment explanation
Indices: 4409--4541 Score: 56
Period size: 11 Copynumber: 11.6 Consensus size: 11
4399 GAAACTAAGC
4409 CAGTCTTTTAT
1 CAGTCTTTTAT
** *
4420 CAGTCTAATCT
1 CAGTCTTTTAT
*
4431 CAGTCTTCTAT
1 CAGTCTTTTAT
*
4442 CAATCTGATTTAATAT
1 CAGTC---TTT--TAT
*
4458 CAGTCTTGTAT
1 CAGTCTTTTAT
*
4469 CAGTCTAATT-T
1 CAGTCT-TTTAT
**
4480 CAGTCTAATAT
1 CAGTCTTTTAT
* *
4491 TAGTCTTTTTT
1 CAGTCTTTTAT
*
4502 CAGTCTAATT-T
1 CAGTCT-TTTAT
*
4513 CAGTCTTTTGT
1 CAGTCTTTTAT
4524 CAGTCTTCTT-T
1 CAGTCTT-TTAT
4535 CAGTCTT
1 CAGTCTT
4542 CTTTTGCCTA
Statistics
Matches: 92, Mismatches: 20, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
10 4 0.04
11 72 0.78
12 5 0.05
13 2 0.02
14 2 0.02
16 7 0.08
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48
Consensus pattern (11 bp):
CAGTCTTTTAT
Found at i:4434 original size:22 final size:22
Alignment explanation
Indices: 4409--4485 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
4399 GAAACTAAGC
*
4409 CAGTCTTTTATCAGTCTAATCT
1 CAGTCTTTTATCAGTCTAATAT
* *
4431 CAGTCTTCTATCAATCTGATTTAATAT
1 CAGTCTT-T-T--ATCAG-TCTAATAT
* *
4458 CAGTCTTGTATCAGTCTAATTT
1 CAGTCTTTTATCAGTCTAATAT
4480 CAGTCT
1 CAGTCT
4486 AATATTAGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
22 19 0.44
23 5 0.12
24 1 0.02
25 1 0.02
26 4 0.09
27 13 0.30
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (22 bp):
CAGTCTTTTATCAGTCTAATAT
Found at i:4463 original size:27 final size:27
Alignment explanation
Indices: 4425--4479 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
4415 TTTATCAGTC
* *
4425 TAATCTCAGTCTTCTATCAATCTGATT
1 TAATATCAGTCTTCTATCAATCTAATT
* *
4452 TAATATCAGTCTTGTATCAGTCTAATT
1 TAATATCAGTCTTCTATCAATCTAATT
4479 T
1 T
4480 CAGTCTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (27 bp):
TAATATCAGTCTTCTATCAATCTAATT
Found at i:4495 original size:22 final size:22
Alignment explanation
Indices: 4452--4518 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
4442 CAATCTGATT
* ** *
4452 TAATATCAGTCTTGTATCAGTC
1 TAATTTCAGTCTAATATTAGTC
4474 TAATTTCAGTCTAATATTAGTC
1 TAATTTCAGTCTAATATTAGTC
**
4496 TTTTTTCAGTCTAAT-TTCAGTC
1 TAATTTCAGTCTAATATT-AGTC
4518 T
1 T
4519 TTTGTCAGTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 2 0.05
22 36 0.95
ACGTcount: A:0.25, C:0.16, G:0.10, T:0.48
Consensus pattern (22 bp):
TAATTTCAGTCTAATATTAGTC
Found at i:4519 original size:22 final size:22
Alignment explanation
Indices: 4468--4546 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
4458 CAGTCTTGTA
**
4468 TCAGTCTAATTTCAGTCTAATAT
1 TCAGTCTTTTTTCAGTCTAAT-T
4491 T-AGTCTTTTTTCAGTCTAATT
1 TCAGTCTTTTTTCAGTCTAATT
* **
4512 TCAGTCTTTTGTCAGTCTTCTT
1 TCAGTCTTTTTTCAGTCTAATT
4534 TCAGTCTTCTTTT
1 TCAGTCTT-TTTT
4547 GCCTAATTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.04
22 42 0.88
23 4 0.08
ACGTcount: A:0.18, C:0.19, G:0.10, T:0.53
Consensus pattern (22 bp):
TCAGTCTTTTTTCAGTCTAATT
Found at i:4529 original size:33 final size:33
Alignment explanation
Indices: 4452--4540 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
4442 CAATCTGATT
* *
4452 TAATATCAGTCTTGTATCAGTCTAATTTCAGTC
1 TAATATCAGTCTTCTTTCAGTCTAATTTCAGTC
* *
4485 TAATATTAGTCTTTTTTCAGTCTAATTTCAGTC
1 TAATATCAGTCTTCTTTCAGTCTAATTTCAGTC
** *
4518 TTTTGTCAGTCTTCTTTCAGTCT
1 TAATATCAGTCTTCTTTCAGTCT
4541 TCTTTTGCCT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.49
Consensus pattern (33 bp):
TAATATCAGTCTTCTTTCAGTCTAATTTCAGTC
Found at i:4542 original size:11 final size:11
Alignment explanation
Indices: 4492--4545 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
4482 GTCTAATATT
*
4492 AGTCTTTTTTC
1 AGTCTTCTTTC
**
4503 AGTCTAATTTC
1 AGTCTTCTTTC
4514 AGTCTT-TTGTC
1 AGTCTTCTT-TC
4525 AGTCTTCTTTC
1 AGTCTTCTTTC
4536 AGTCTTCTTT
1 AGTCTTCTTT
4546 TGCCTAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 2 0.05
11 34 0.89
12 2 0.05
ACGTcount: A:0.13, C:0.20, G:0.11, T:0.56
Consensus pattern (11 bp):
AGTCTTCTTTC
Done.