Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007458.1 Corchorus capsularis cultivar CVL-1 contig07479, 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: 35051
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:17470 original size:12 final size:12
Alignment explanation
Indices: 17453--17478 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17443 AAATGTTGAC
17453 GTAACTTAACTT
1 GTAACTTAACTT
17465 GTAACTTAACTT
1 GTAACTTAACTT
17477 GT
1 GT
17479 TGGATGTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (12 bp):
GTAACTTAACTT
Found at i:19999 original size:23 final size:23
Alignment explanation
Indices: 19973--20095 Score: 114
Period size: 23 Copynumber: 5.5 Consensus size: 23
19963 AACGTCCTAA
*
19973 CTATGAAATTTTAATAAACTTTC
1 CTATGAAATTTTAATAAACCTTC
19996 CTATGAAATTTTAATAAACCTTC
1 CTATGAAATTTTAATAAACCTTC
*
20019 CTATGAAATTTTGAT-AACC-TC
1 CTATGAAATTTTAATAAACCTTC
* **
20040 ATTATGATTTTTTAAT-AACC-TC
1 -CTATGAAATTTTAATAAACCTTC
** *
20062 CTTATGAAATTTTGTTAAATC-TC
1 C-TATGAAATTTTAATAAACCTTC
20085 CTAT-AAATTTT
1 CTATGAAATTTT
20096 TTGATACCAT
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
21 9 0.11
22 34 0.40
23 42 0.49
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.45
Consensus pattern (23 bp):
CTATGAAATTTTAATAAACCTTC
Found at i:20095 original size:45 final size:46
Alignment explanation
Indices: 19973--20097 Score: 118
Period size: 45 Copynumber: 2.8 Consensus size: 46
19963 AACGTCCTAA
* *
19973 CTATGAAATTTTAATAAACTTTCCTATGAAA--TTTTAATAAACCTTC
1 CTATGAAATTTTGATAAA-TCTCCTAT-AAATTTTTTAATAAACCTTC
* * *
20019 CTATGAAATTTTGAT-AACCTCAT-TATGATTTTTTAAT-AACC-TC
1 CTATGAAATTTTGATAAATCTCCTATA-AATTTTTTAATAAACCTTC
*
20062 CTTATGAAATTTTGTTAAATCTCCTATAAATTTTTT
1 C-TATGAAATTTTGATAAATCTCCTATAAATTTTTT
20098 GATACCATAG
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
42 1 0.02
43 5 0.08
44 20 0.31
45 22 0.34
46 16 0.25
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (46 bp):
CTATGAAATTTTGATAAATCTCCTATAAATTTTTTAATAAACCTTC
Found at i:22848 original size:2 final size:2
Alignment explanation
Indices: 22843--22892 Score: 61
Period size: 2 Copynumber: 26.0 Consensus size: 2
22833 ATCTAAAATA
*
22843 AT AT AT AT AT AT AT AT AT AT AGT AG A- AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
22884 -T AT AT AT AT
1 AT AT AT AT AT
22893 CAACCCTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
1 3 0.07
2 38 0.88
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23337 original size:45 final size:45
Alignment explanation
Indices: 23273--23363 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
23263 CTTTAATTTG
*
23273 GTTCTTCGGTGCCGACTGCCTGCTTCCTTTCTTGGGTTGAGCTGA
1 GTTCTTCGGTGCCGACTGCCTGCTCCCTTTCTTGGGTTGAGCTGA
* *
23318 GTTCTTCGGTTCCGACTGCCTTCTCCCTTTCTTGGGTTGAGCTGA
1 GTTCTTCGGTGCCGACTGCCTGCTCCCTTTCTTGGGTTGAGCTGA
23363 G
1 G
23364 GCGGTCGATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.07, C:0.27, G:0.27, T:0.38
Consensus pattern (45 bp):
GTTCTTCGGTGCCGACTGCCTGCTCCCTTTCTTGGGTTGAGCTGA
Found at i:30853 original size:129 final size:130
Alignment explanation
Indices: 30618--30857 Score: 335
Period size: 129 Copynumber: 1.9 Consensus size: 130
30608 GGATTTTCTC
* * * *
30618 TTTTTATGATAAAATATCATGTATGTTTCTTTTTTCTATGCCAAGTTTCTAACTCGATAATTGTC
1 TTTTTATGATAAAATATCATGCATGTTCCTTTTTTCTATGCCAAATTCCTAACTCGATAATTGTC
*
30683 CAAAAATTTTTCAAATCCCGTACAGAGACATAAGCCCGCGGCGAAGTGTGCGACTAGATTGACTG
66 CAAAAATTTTTCAAATCCCGTACAGAGACACAAGCCCGCGGCGAAGTGTGCGACTAGATTGACTG
* *
30748 TTTTTAT-AGTAAAATATTATGCATGTTCCTTTTTTC-ATGCCAAATTCCTAATTC-AGTAATTG
1 TTTTTATGA-TAAAATATCATGCATGTTCCTTTTTTCTATGCCAAATTCCTAACTCGA-TAATTG
* * *
30810 TCCAACAATTTTTCAAATTCCC-TATAGAGACACAAGCCTGCGGCGAAG
64 TCCAAAAATTTTTCAAA-TCCCGTACAGAGACACAAGCCCGCGGCGAAG
30858 CGCGGGCCAA
Statistics
Matches: 97, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
128 1 0.01
129 61 0.63
130 35 0.36
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (130 bp):
TTTTTATGATAAAATATCATGCATGTTCCTTTTTTCTATGCCAAATTCCTAACTCGATAATTGTC
CAAAAATTTTTCAAATCCCGTACAGAGACACAAGCCCGCGGCGAAGTGTGCGACTAGATTGACTG
Found at i:31209 original size:34 final size:32
Alignment explanation
Indices: 31171--31241 Score: 108
Period size: 31 Copynumber: 2.2 Consensus size: 32
31161 TATTGAAGGC
31171 ATTTGTTCATAAGTGAACAATTATGAAGAGACTT
1 ATTTGTTC-TAA-TGAACAATTATGAAGAGACTT
*
31205 ATTTG-TCTTATGAACAATTATGAAGAGACTT
1 ATTTGTTCTAATGAACAATTATGAAGAGACTT
31236 ATTTGT
1 ATTTGT
31242 CTATAAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
31 26 0.74
32 2 0.06
33 2 0.06
34 5 0.14
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.39
Consensus pattern (32 bp):
ATTTGTTCTAATGAACAATTATGAAGAGACTT
Found at i:31220 original size:31 final size:31
Alignment explanation
Indices: 31184--31243 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
31174 TGTTCATAAG
31184 TGAACAATTATGAAGAGACTTATTTGTCTTA
1 TGAACAATTATGAAGAGACTTATTTGTCTTA
31215 TGAACAATTATGAAGAGACTTATTTGTCT
1 TGAACAATTATGAAGAGACTTATTTGTCT
31244 ATAAAATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (31 bp):
TGAACAATTATGAAGAGACTTATTTGTCTTA
Found at i:31322 original size:37 final size:37
Alignment explanation
Indices: 31272--31342 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
31262 ATATAATTAT
* *
31272 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
31309 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
31343 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:32055 original size:19 final size:19
Alignment explanation
Indices: 32031--32069 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
32021 TGTTCAGCCC
32031 AGTAATTGGATGCGACACA
1 AGTAATTGGATGCGACACA
32050 AGTAATTGGATGCGACACA
1 AGTAATTGGATGCGACACA
32069 A
1 A
32070 TAGTCATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (19 bp):
AGTAATTGGATGCGACACA
Found at i:32587 original size:31 final size:32
Alignment explanation
Indices: 32549--32610 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
32539 TGGGGGTGTC
32549 TTGGTTTCTTAAAGAAAC-AAAGAGATATATG
1 TTGGTTTCTTAAAGAAACAAAAGAGATATATG
* *
32580 TTGGTTTCTTAGAGAAACAAAAGAGTTATAT
1 TTGGTTTCTTAAAGAAACAAAAGAGATATAT
32611 CACTATGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.34
Consensus pattern (32 bp):
TTGGTTTCTTAAAGAAACAAAAGAGATATATG
Done.