Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006251.1 Corchorus capsularis cultivar CVL-1 contig06270, 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: 23408
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Found at i:3767 original size:22 final size:22
Alignment explanation
Indices: 3739--3780 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3729 GCGGCTAGAC
* *
3739 TATTTTTTTTTAAAATAATAAT
1 TATTTTTTTTAAAAAAAATAAT
3761 TATTTTTTTTAAAAAAAATA
1 TATTTTTTTTAAAAAAAATA
3781 GCCTAGCTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTTTTTAAAAAAAATAAT
Found at i:5307 original size:25 final size:25
Alignment explanation
Indices: 5279--5394 Score: 169
Period size: 25 Copynumber: 4.6 Consensus size: 25
5269 CACTAATGTT
* **
5279 CTTGCGTTTGGCAAACGAGCCTACA
1 CTTGCGTTTAGCAAACGAGCCTATG
*
5304 CTTGCGTTTAGCAAACGATCCTATG
1 CTTGCGTTTAGCAAACGAGCCTATG
* *
5329 CTTGCGTTCAGCAAACGAGCCTGTG
1 CTTGCGTTTAGCAAACGAGCCTATG
*
5354 CTTGCGTTTAGCAAACGAGCCTGTG
1 CTTGCGTTTAGCAAACGAGCCTATG
5379 CTTGCGTTTAGCAAAC
1 CTTGCGTTTAGCAAAC
5395 ACATAGGCTG
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 83 1.00
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (25 bp):
CTTGCGTTTAGCAAACGAGCCTATG
Found at i:5976 original size:13 final size:13
Alignment explanation
Indices: 5958--5983 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5948 ACATTACGTT
5958 CCAAAGCCTTTAA
1 CCAAAGCCTTTAA
5971 CCAAAGCCTTTAA
1 CCAAAGCCTTTAA
5984 GAAATTCGGC
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:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
CCAAAGCCTTTAA
Found at i:7458 original size:320 final size:320
Alignment explanation
Indices: 6876--7515 Score: 1280
Period size: 320 Copynumber: 2.0 Consensus size: 320
6866 AGTAGCTATC
6876 TTACCTTCAAAACTCAAACCATGATCAGAAGTAAGAGTTTCTGGGATACCAAAGCGATAGATAAG
1 TTACCTTCAAAACTCAAACCATGATCAGAAGTAAGAGTTTCTGGGATACCAAAGCGATAGATAAG
6941 GTCTTGTTCTATGAAGTTTTTAACATCGGTATGGGTGGTAGATTTCATAGCTCTAGCTTCCACCC
66 GTCTTGTTCTATGAAGTTTTTAACATCGGTATGGGTGGTAGATTTCATAGCTCTAGCTTCCACCC
7006 ACTTGGTAAAATAGTCTGTAGCGACGATGATAAAAACACCACCTCTGGCCGGCGGGTGTAGTTTC
131 ACTTGGTAAAATAGTCTGTAGCGACGATGATAAAAACACCACCTCTGGCCGGCGGGTGTAGTTTC
7071 CCAATTAAATCTATGGCCCGGCCTCGAAAAGGCCATGGTTTGATGATGGAGTGTAAATCAACTGA
196 CCAATTAAATCTATGGCCCGGCCTCGAAAAGGCCATGGTTTGATGATGGAGTGTAAATCAACTGA
7136 TGGAGTTCTTTTAATAGGGCCATAATTTTTACACTCTTGACATCCTTTTGCGAACTCCAT
261 TGGAGTTCTTTTAATAGGGCCATAATTTTTACACTCTTGACATCCTTTTGCGAACTCCAT
7196 TTACCTTCAAAACTCAAACCATGATCAGAAGTAAGAGTTTCTGGGATACCAAAGCGATAGATAAG
1 TTACCTTCAAAACTCAAACCATGATCAGAAGTAAGAGTTTCTGGGATACCAAAGCGATAGATAAG
7261 GTCTTGTTCTATGAAGTTTTTAACATCGGTATGGGTGGTAGATTTCATAGCTCTAGCTTCCACCC
66 GTCTTGTTCTATGAAGTTTTTAACATCGGTATGGGTGGTAGATTTCATAGCTCTAGCTTCCACCC
7326 ACTTGGTAAAATAGTCTGTAGCGACGATGATAAAAACACCACCTCTGGCCGGCGGGTGTAGTTTC
131 ACTTGGTAAAATAGTCTGTAGCGACGATGATAAAAACACCACCTCTGGCCGGCGGGTGTAGTTTC
7391 CCAATTAAATCTATGGCCCGGCCTCGAAAAGGCCATGGTTTGATGATGGAGTGTAAATCAACTGA
196 CCAATTAAATCTATGGCCCGGCCTCGAAAAGGCCATGGTTTGATGATGGAGTGTAAATCAACTGA
7456 TGGAGTTCTTTTAATAGGGCCATAATTTTTACACTCTTGACATCCTTTTGCGAACTCCAT
261 TGGAGTTCTTTTAATAGGGCCATAATTTTTACACTCTTGACATCCTTTTGCGAACTCCAT
7516 ACAATCTTTC
Statistics
Matches: 320, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
320 320 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (320 bp):
TTACCTTCAAAACTCAAACCATGATCAGAAGTAAGAGTTTCTGGGATACCAAAGCGATAGATAAG
GTCTTGTTCTATGAAGTTTTTAACATCGGTATGGGTGGTAGATTTCATAGCTCTAGCTTCCACCC
ACTTGGTAAAATAGTCTGTAGCGACGATGATAAAAACACCACCTCTGGCCGGCGGGTGTAGTTTC
CCAATTAAATCTATGGCCCGGCCTCGAAAAGGCCATGGTTTGATGATGGAGTGTAAATCAACTGA
TGGAGTTCTTTTAATAGGGCCATAATTTTTACACTCTTGACATCCTTTTGCGAACTCCAT
Found at i:10140 original size:15 final size:15
Alignment explanation
Indices: 10117--10152 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
10107 TTCTCTACAG
*
10117 CTTCCTTCAAAGCTT
1 CTTCTTTCAAAGCTT
10132 CTTCTTTCAAAGCTT
1 CTTCTTTCAAAGCTT
10147 CTTCTT
1 CTTCTT
10153 CGATTTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.31, G:0.06, T:0.47
Consensus pattern (15 bp):
CTTCTTTCAAAGCTT
Found at i:15734 original size:25 final size:25
Alignment explanation
Indices: 15706--15821 Score: 187
Period size: 25 Copynumber: 4.6 Consensus size: 25
15696 CGCTCATGTT
* **
15706 CTTGCGTTTGGCAAACGAGCCTACG
1 CTTGCGTTTAGCAAACGAGCCTGTG
*
15731 CTTGCGTTTAGCAAACGAGCTTGTG
1 CTTGCGTTTAGCAAACGAGCCTGTG
*
15756 CTTGCGTTAAGCAAACGAGCCTGTG
1 CTTGCGTTTAGCAAACGAGCCTGTG
15781 CTTGCGTTTAGCAAACGAGCCTGTG
1 CTTGCGTTTAGCAAACGAGCCTGTG
15806 CTTGCGTTTAGCAAAC
1 CTTGCGTTTAGCAAAC
15822 ACATAGGCTG
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 84 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.28
Consensus pattern (25 bp):
CTTGCGTTTAGCAAACGAGCCTGTG
Found at i:17502 original size:18 final size:20
Alignment explanation
Indices: 17466--17507 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
17456 ACTACGTGAG
17466 TATATATATGAAGATAAAAT
1 TATATATATGAAGATAAAAT
* *
17486 TATATATATGAAAAAAAAAT
1 TATATATATGAAGATAAAAT
17506 TA
1 TA
17508 GAAAGGTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (20 bp):
TATATATATGAAGATAAAAT
Found at i:17760 original size:2 final size:2
Alignment explanation
Indices: 17753--17779 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17743 CTCAAACCGT
17753 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
17780 CCAAATACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18730 original size:82 final size:82
Alignment explanation
Indices: 18593--18814 Score: 374
Period size: 82 Copynumber: 2.7 Consensus size: 82
18583 ACCTTGTTAA
*
18593 TTGTCATTTGTCACTGTGCCATTAAAACGAAAATTGATAATTAT-TGAATCCAAATTCATTCCTA
1 TTGTCAATTGTCACTGTGCCATTAAAACGAAAATTGATAATT-TGTGAATCCAAATTCATTCCTA
*
18657 ACTACTTATTCAAATACC
65 ACTACTTATCCAAATACC
*
18675 TTGTCAATTGTCACTGTGCCATTAAAACGAAAACTGATAATTTGTGAATCCAAATTCATTCCTAA
1 TTGTCAATTGTCACTGTGCCATTAAAACGAAAATTGATAATTTGTGAATCCAAATTCATTCCTAA
18740 CTACTTATCCAAATACC
66 CTACTTATCCAAATACC
* * *
18757 TTGTCAATTATCACTGTGCCATTAAAACGAAAATTGATGATTAGTGAATCCAAATTCA
1 TTGTCAATTGTCACTGTGCCATTAAAACGAAAATTGATAATTTGTGAATCCAAATTCA
18815 ATTGGGAACA
Statistics
Matches: 132, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
81 1 0.01
82 131 0.99
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (82 bp):
TTGTCAATTGTCACTGTGCCATTAAAACGAAAATTGATAATTTGTGAATCCAAATTCATTCCTAA
CTACTTATCCAAATACC
Found at i:21856 original size:16 final size:16
Alignment explanation
Indices: 21835--21865 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21825 ATCCGTGAAG
21835 CCTTTGCGTACAAATT
1 CCTTTGCGTACAAATT
*
21851 CCTTTGCGTGCAAAT
1 CCTTTGCGTACAAAT
21866 CCGTCAAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (16 bp):
CCTTTGCGTACAAATT
Found at i:22041 original size:27 final size:27
Alignment explanation
Indices: 22011--22090 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
22001 GCATTAGGGT
* *
22011 CACCCAAGGGTATTTTGGTCATTTTTG
1 CACCCAGGGGCATTTTGGTCATTTTTG
22038 CACCCAGGGGCATTTTGGTCATTTTTG
1 CACCCAGGGGCATTTTGGTCATTTTTG
* *
22065 TACTCAGGGGCATTTTAGG-CATTTTT
1 CACCCAGGGGCATTTT-GGTCATTTTT
22091 AGGTTCACCT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 46 0.96
28 2 0.04
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (27 bp):
CACCCAGGGGCATTTTGGTCATTTTTG
Found at i:22361 original size:95 final size:95
Alignment explanation
Indices: 22218--22410 Score: 377
Period size: 95 Copynumber: 2.0 Consensus size: 95
22208 AATTTAGTTT
22218 TGTTGCACTTTAATCATATAGCTTAATCACTTTTAGTAATAGATTTGGTTTTCGATTGCGATTCC
1 TGTTGCACTTTAATCATATAGCTTAATCACTTTTAGTAATAGATTTGGTTTTCGATTGCGATTCC
22283 CATTGTGATTTTCATATTCATTTTTAAGTA
66 CATTGTGATTTTCATATTCATTTTTAAGTA
*
22313 TGTTGCACTTTAATCATATAGTTTAATCACTTTTAGTAATAGATTTGGTTTTCGATTGCGATTCC
1 TGTTGCACTTTAATCATATAGCTTAATCACTTTTAGTAATAGATTTGGTTTTCGATTGCGATTCC
22378 CATTGTGATTTTCATATTCATTTTTAAGTA
66 CATTGTGATTTTCATATTCATTTTTAAGTA
22408 TGT
1 TGT
22411 CCTATCTACC
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 97 1.00
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (95 bp):
TGTTGCACTTTAATCATATAGCTTAATCACTTTTAGTAATAGATTTGGTTTTCGATTGCGATTCC
CATTGTGATTTTCATATTCATTTTTAAGTA
Done.