Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013788.1 Corchorus capsularis cultivar CVL-1 contig13809, 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: 27868
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:936 original size:12 final size:12
Alignment explanation
Indices: 919--943 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
909 CATCAACTGC
919 ATAAACTTAATT
1 ATAAACTTAATT
931 ATAAACTTAATT
1 ATAAACTTAATT
943 A
1 A
944 AGAGATCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAAACTTAATT
Found at i:1513 original size:16 final size:16
Alignment explanation
Indices: 1494--1546 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1484 GACCCGGAAT
1494 CCGAATGACTCGAAAC
1 CCGAATGACTCGAAAC
* * *
1510 CCGAATAACCCG-AGC
1 CCGAATGACTCGAAAC
1525 CC-AGATGACTCGAAAC
1 CCGA-ATGACTCGAAAC
1541 CCGAAT
1 CCGAAT
1547 AACCCAAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
14 1 0.04
15 10 0.36
16 16 0.57
17 1 0.04
ACGTcount: A:0.36, C:0.34, G:0.19, T:0.11
Consensus pattern (16 bp):
CCGAATGACTCGAAAC
Found at i:1872 original size:12 final size:11
Alignment explanation
Indices: 1857--1891 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
1847 ATTTTTCATG
1857 TTATTATTATAT
1 TTATTATT-TAT
1869 TTATTATTTAT
1 TTATTATTTAT
1880 TTATTTATTTAT
1 TTA-TTATTTAT
1892 GTCTTTTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTAT
Found at i:7504 original size:32 final size:33
Alignment explanation
Indices: 7468--7541 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
7458 TCACTATACA
7468 GTGAGGCGTCTCTT-GGGAAGCCTCACCGTACG
1 GTGAGGCGTCTCTTGGGGAAGCCTCACCGTACG
* *
7500 GTGAGGCGTCTCTTGGGGACGCCTCCCCGTACG
1 GTGAGGCGTCTCTTGGGGAAGCCTCACCGTACG
7533 GTGAGGCGT
1 GTGAGGCGT
7542 AGGGCTGTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 14 0.36
33 25 0.64
ACGTcount: A:0.12, C:0.28, G:0.38, T:0.22
Consensus pattern (33 bp):
GTGAGGCGTCTCTTGGGGAAGCCTCACCGTACG
Found at i:8362 original size:57 final size:57
Alignment explanation
Indices: 8299--8513 Score: 351
Period size: 57 Copynumber: 3.8 Consensus size: 57
8289 ACTTCAGTAA
8299 TCAAAAATCAGAATTCAGAAACCAAGATCAGAAGCAAATC-GAAAATCAACATAAAGT
1 TCAAAAATCAGAATTCAGAAACCAAGATCAGAAGCAAATCAG-AAATCAACATAAAGT
* * *
8356 TCAAAAATCAGAATTCAAAAACCAAGACCAGAATCAAATCAGAAATCAACATAAAGT
1 TCAAAAATCAGAATTCAGAAACCAAGATCAGAAGCAAATCAGAAATCAACATAAAGT
* *
8413 TCAAAAATCAGAATTCAGAAACCAAGATCAGAAGCAAATAAGAAATCAACATAAATT
1 TCAAAAATCAGAATTCAGAAACCAAGATCAGAAGCAAATCAGAAATCAACATAAAGT
* *
8470 TCAAAAATCAAAATTCAGAAACCAAGATCAGAATCAAATCAGAA
1 TCAAAAATCAGAATTCAGAAACCAAGATCAGAAGCAAATCAGAA
8514 GCAAATCAGA
Statistics
Matches: 146, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
57 145 0.99
58 1 0.01
ACGTcount: A:0.56, C:0.18, G:0.10, T:0.16
Consensus pattern (57 bp):
TCAAAAATCAGAATTCAGAAACCAAGATCAGAAGCAAATCAGAAATCAACATAAAGT
Found at i:8373 original size:26 final size:26
Alignment explanation
Indices: 8344--8429 Score: 75
Period size: 26 Copynumber: 3.1 Consensus size: 26
8334 AAATCGAAAA
8344 TCAACATAAAGTTCAAAAATCAGAAT
1 TCAACATAAAGTTCAAAAATCAGAAT
* ** *
8370 TCAA-AAACCAAGACCAGAATCAAATCAGAAA
1 TCAACATA--AAGTTC--AA--AAATCAGAAT
8401 TCAACATAAAGTTCAAAAATCAGAAT
1 TCAACATAAAGTTCAAAAATCAGAAT
8427 TCA
1 TCA
8430 GAAACCAAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 2 0.04
26 16 0.36
27 4 0.09
28 2 0.04
29 2 0.04
30 4 0.09
31 13 0.29
32 2 0.04
ACGTcount: A:0.55, C:0.19, G:0.08, T:0.19
Consensus pattern (26 bp):
TCAACATAAAGTTCAAAAATCAGAAT
Found at i:8512 original size:11 final size:11
Alignment explanation
Indices: 8496--8529 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
8486 AGAAACCAAG
8496 ATCAGAATCAA
1 ATCAGAATCAA
*
8507 ATCAGAAGCAA
1 ATCAGAATCAA
8518 ATCAGAAATCAA
1 ATCAG-AATCAA
8530 CAGAAGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.15
Consensus pattern (11 bp):
ATCAGAATCAA
Found at i:12768 original size:33 final size:33
Alignment explanation
Indices: 12725--12855 Score: 181
Period size: 33 Copynumber: 4.0 Consensus size: 33
12715 GAAGCAATTG
* *
12725 ATACGGGGAGGCGTCCCCAGGAGACGCGTCACC
1 ATACGAGGAGGCGTCCCCAGGAGACGCCTCACC
*
12758 ATACGAGGAGGCATCCCCAGGAGACGCCTCACC
1 ATACGAGGAGGCGTCCCCAGGAGACGCCTCACC
* * * *
12791 ATACGGGGAGGCGTCCCTAGGAGGCGCCGCACC
1 ATACGAGGAGGCGTCCCCAGGAGACGCCTCACC
* *
12824 ATACGAGGAGGCGTCCCTAGGAGGCGCCTCAC
1 ATACGAGGAGGCGTCCCCAGGAGACGCCTCAC
12856 TGTATGGTTA
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.22, C:0.34, G:0.34, T:0.10
Consensus pattern (33 bp):
ATACGAGGAGGCGTCCCCAGGAGACGCCTCACC
Found at i:12869 original size:66 final size:66
Alignment explanation
Indices: 12725--12855 Score: 201
Period size: 66 Copynumber: 2.0 Consensus size: 66
12715 GAAGCAATTG
12725 ATACGGGGAGGCGTCCCCAGGAGACGCGTCACCATACGAGGAGGCATCCCCAGGAGACGCCTCAC
1 ATACGGGGAGGCGTCCCCAGGAGACGCGTCACCATACGAGGAGGCATCCCCAGGAGACGCCTCAC
12790 C
66 C
* * * * *
12791 ATACGGGGAGGCGTCCCTAGGAGGCGCCG-CACCATACGAGGAGGCGTCCCTAGGAGGCGCCTCA
1 ATACGGGGAGGCGTCCCCAGGAGACG-CGTCACCATACGAGGAGGCATCCCCAGGAGACGCCTCA
12855 C
65 C
12856 TGTATGGTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 57 0.97
67 2 0.03
ACGTcount: A:0.22, C:0.34, G:0.34, T:0.10
Consensus pattern (66 bp):
ATACGGGGAGGCGTCCCCAGGAGACGCGTCACCATACGAGGAGGCATCCCCAGGAGACGCCTCAC
C
Found at i:19386 original size:24 final size:24
Alignment explanation
Indices: 19326--19372 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
19316 CTCCTCCTAA
19326 AAATTAAAATATATAAGTATATAC
1 AAATTAAAATATATAAGTATATAC
19350 AAATTAAAATATATAAGTATATA
1 AAATTAAAATATATAAGTATATA
19373 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (24 bp):
AAATTAAAATATATAAGTATATAC
Found at i:20015 original size:6 final size:6
Alignment explanation
Indices: 20006--20041 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
19996 TAAATCGTCT
20006 TTTTTC TTTTTC -TTTTC -TTTTC TTTTTC TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
20042 GTAAGGATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:20028 original size:16 final size:16
Alignment explanation
Indices: 20007--20037 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
19997 AAATCGTCTT
20007 TTTTCTTTTTCTTTTC
1 TTTTCTTTTTCTTTTC
20023 TTTTCTTTTTCTTTT
1 TTTTCTTTTTCTTTT
20038 TCTTGTAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTC
Found at i:24056 original size:36 final size:38
Alignment explanation
Indices: 24008--24078 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 38
23998 GGTCGTTTTT
*
24008 TGAAGAATTAGAGTGCTTAGT-AAATCTGGATCGTCTG
1 TGAAGAATTAGAGTGCTTAGTAAAATCTGAATCGTCTG
24045 TGAAG-ATTAGAGTGCTTAGTAAAATCTGAATCGT
1 TGAAGAATTAGAGTGCTTAGTAAAATCTGAATCGT
24079 TGTTGGATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 15 0.47
37 17 0.53
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.32
Consensus pattern (38 bp):
TGAAGAATTAGAGTGCTTAGTAAAATCTGAATCGTCTG
Found at i:26450 original size:30 final size:30
Alignment explanation
Indices: 26414--26477 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
26404 GTAGCACCCC
* *
26414 CTTTTGCCGC-AGAACTCACTTTGCGAAACA
1 CTTTTGCCGCAAG-ACTCACTTTACCAAACA
* *
26444 CTTTTGCTGCAAGACTCGCTTTACCAAACA
1 CTTTTGCCGCAAGACTCACTTTACCAAACA
26474 CTTT
1 CTTT
26478 ACAACAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31
Consensus pattern (30 bp):
CTTTTGCCGCAAGACTCACTTTACCAAACA
Done.