Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005545.1 Corchorus capsularis cultivar CVL-1 contig05563, 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: 24198
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:3549 original size:166 final size:165
Alignment explanation
Indices: 3233--3581 Score: 486
Period size: 166 Copynumber: 2.1 Consensus size: 165
3223 TGAGTCATTT
* * *
3233 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATTCCCTCAAGAATCAAAAGTTATGACAT
1 GTCAATTGAGAAATGA-CAAAAAATTTAGTTATTTAATCCCCTCAAGAATCAAAAGGTATGACAT
* ** * *
3298 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTTG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAGATTAGTTCTCTAGCTCAAAAGCAAACCTTG
* *
3363 ACGGAGATCTTTTAGTAATTCCACTACTCTATTCAA
130 ACAGAGATCTTTTAGTAATTCCACTACTCTATTAAA
* *
3399 GTCCATTGAGAAATGACAAAAAATATTATTTATTTAATCCCCTCAAGAATCAAAAGGTA-GAACA
1 GTCAATTGAGAAATGACAAAAAAT-TTAGTTATTTAATCCCCTCAAGAATCAAAAGGTATG-ACA
* *
3463 TTTAAGTGATCTGCCACGTAGGAAAAGACGAAAAAGA-TAGTTCTCTAGCTCCAAAAGCAAACCT
64 TTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAGATTAGTTCTCTAGCT-CAAAAGCAAACCT
** * *
3527 TGGTAGAGATTTTTTTGTAATTCCACTACTCTATTAAA
128 TGACAGAGATCTTTTAGTAATTCCACTACTCTATTAAA
3565 GTCAATTGAGAAATGAC
1 GTCAATTGAGAAATGAC
3582 CAAGCAAGTC
Statistics
Matches: 161, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
165 21 0.13
166 140 0.87
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (165 bp):
GTCAATTGAGAAATGACAAAAAATTTAGTTATTTAATCCCCTCAAGAATCAAAAGGTATGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAGATTAGTTCTCTAGCTCAAAAGCAAACCTTGA
CAGAGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:3623 original size:66 final size:66
Alignment explanation
Indices: 3525--3650 Score: 216
Period size: 66 Copynumber: 1.9 Consensus size: 66
3515 AAAAGCAAAC
* * *
3525 CTTGGTAGAGATTTTTTTGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAGCAAG
1 CTTGGTAGAGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTAAGAAATGACCAAGCAAG
3590 T
66 T
*
3591 CTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTAAGAAATGACCAA
1 CTTGGTAGAGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTAAGAAATGACCAA
3651 AAAGTATAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (66 bp):
CTTGGTAGAGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTAAGAAATGACCAAGCAAG
T
Found at i:4761 original size:2 final size:2
Alignment explanation
Indices: 4754--4788 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4744 AATAGCTAAC
* *
4754 TA TA TA TA TA TA TA TA TA TA TA TA TC CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4789 CAATTTAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5338 original size:2 final size:2
Alignment explanation
Indices: 5331--5355 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5321 TTATGATACG
5331 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5356 GTTTACGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10064 original size:92 final size:92
Alignment explanation
Indices: 9942--10139 Score: 371
Period size: 92 Copynumber: 2.2 Consensus size: 92
9932 TGAATCTTAG
* *
9942 TTATCT-TGGTCTATGACCCTTTTGTTTGTTAAATTGTACTTATAGCATATACACACATTAGATT
1 TTATCTCTGGTTTGTGACCCTTTTGTTTGTTAAATTGTACTTATAGCATATACACACATTAGATT
10006 ATTACGTCCATTTATATTAATTTGTTA
66 ATTACGTCCATTTATATTAATTTGTTA
10033 TTATCTCTGGTTTGTGACCCTTTTGTTTGTTAAATTGTACTTATAGCATATACACACATTAGATT
1 TTATCTCTGGTTTGTGACCCTTTTGTTTGTTAAATTGTACTTATAGCATATACACACATTAGATT
10098 ATTACGTCCATTTATATTAATTTGTTA
66 ATTACGTCCATTTATATTAATTTGTTA
10125 TTATCTCTGGTTTGT
1 TTATCTCTGGTTTGT
10140 ATAGAATAAT
Statistics
Matches: 104, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
91 6 0.06
92 98 0.94
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.48
Consensus pattern (92 bp):
TTATCTCTGGTTTGTGACCCTTTTGTTTGTTAAATTGTACTTATAGCATATACACACATTAGATT
ATTACGTCCATTTATATTAATTTGTTA
Found at i:18325 original size:6 final size:6
Alignment explanation
Indices: 18315--18345 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
18305 TTGATGGTTG
*
18315 GTCCCG GTCCCA GTCCCA GTCCCA GTCCCA G
1 GTCCCA GTCCCA GTCCCA GTCCCA GTCCCA G
18346 ACAGGCAGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.13, C:0.48, G:0.23, T:0.16
Consensus pattern (6 bp):
GTCCCA
Found at i:18713 original size:6 final size:6
Alignment explanation
Indices: 18702--18726 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18692 ACAAGGCAAC
18702 AATGGG AATGGG AATGGG AATGGG A
1 AATGGG AATGGG AATGGG AATGGG A
18727 GAAGGGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.48, T:0.16
Consensus pattern (6 bp):
AATGGG
Found at i:22102 original size:39 final size:39
Alignment explanation
Indices: 22046--22125 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
22036 GATGATCATG
*
22046 CTTCAGGAACTAGTTCTCCCAAGGATAAACCAAAGCAGA
1 CTTCAGGAACTAGTTCTCCCAAGGAAAAACCAAAGCAGA
22085 CTTCAGGAACT-GATTCTCCCAAGGAAAAACCAAAGCAGA
1 CTTCAGGAACTAG-TTCTCCCAAGGAAAAACCAAAGCAGA
22124 CT
1 CT
22126 ATGTCAATTG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 1 0.03
39 38 0.97
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.17
Consensus pattern (39 bp):
CTTCAGGAACTAGTTCTCCCAAGGAAAAACCAAAGCAGA
Found at i:22960 original size:6 final size:6
Alignment explanation
Indices: 22951--22978 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
22941 TGGGGAGCCA
22951 GCTGGG GCTGGG GCTGGG GCTGGG GCTG
1 GCTGGG GCTGGG GCTGGG GCTGGG GCTG
22979 CAATTGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.64, T:0.18
Consensus pattern (6 bp):
GCTGGG
Found at i:23985 original size:6 final size:6
Alignment explanation
Indices: 23974--24009 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
23964 GAAAATATTA
*
23974 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTT TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
24010 AGAAATTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Done.