Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007882.1 Corchorus capsularis cultivar CVL-1 contig07903, 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: 10152
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:734 original size:21 final size:22
Alignment explanation
Indices: 689--737 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
679 CAAAATTGGT
*
689 AATCA-AGAGTTTTCAAGATTT
1 AATCAGAGAGTTTTCAAGATTA
710 AATCAGAG-GTTTTCAA-ATTCA
1 AATCAGAGAGTTTTCAAGATT-A
731 AATCAGA
1 AATCAGA
738 CTTAGTGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 20 0.80
22 2 0.08
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (22 bp):
AATCAGAGAGTTTTCAAGATTA
Found at i:4917 original size:1 final size:1
Alignment explanation
Indices: 4911--4947 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
4901 ACCAAAAGTG
4911 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4948 CAGAAGAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6247 original size:32 final size:32
Alignment explanation
Indices: 6206--6376 Score: 254
Period size: 32 Copynumber: 5.3 Consensus size: 32
6196 AATTTGGTTT
6206 AGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
1 AGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
*
6238 AGCCGCCCCATGAGGACGGCCTGCCGTGGCGA
1 AGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
* *
6270 AGCCGCCCCATGATGGCGGTCTGCCGTGGCGA
1 AGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
*
6302 AGCCGCCCCATGAGGGCGGCCTGCCATGGCGA
1 AGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
* * *
6334 AGCCGCCCTAGTG-GGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCA-TGAGGGCGGCCTG-CCGTGGCGA
6367 AGCCGCCCCA
1 AGCCGCCCCA
6377 GTGGGGAGGC
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
32 108 0.85
33 19 0.15
ACGTcount: A:0.14, C:0.37, G:0.37, T:0.11
Consensus pattern (32 bp):
AGCCGCCCCATGAGGGCGGCCTGCCGTGGCGA
Found at i:6413 original size:17 final size:16
Alignment explanation
Indices: 6352--6479 Score: 68
Period size: 16 Copynumber: 7.8 Consensus size: 16
6342 TAGTGGGGCG
*
6352 GCCTGCCCA-TGGTGAA
1 GCCTCCCCAGTGGTG-A
* *
6368 GCCGCCCCAGTGGGGA
1 GCCTCCCCAGTGGTGA
*
6384 GGCTCCGCC-GTGGTTGA
1 GCCTCC-CCAGTGG-TGA
6401 GCCTCCCCAGTGG-GAA
1 GCCTCCCCAGTGGTG-A
*
6417 GGCTCCGCC-GTGGTTGA
1 GCCTCC-CCAGTGG-TGA
* *
6434 GCCTCCCTAGTGGGGA
1 GCCTCCCCAGTGGTGA
*
6450 GGCTCCGCC-GTGGTTGA
1 GCCTCC-CCAGTGG-TGA
*
6467 GCCTCCCTAGTGG
1 GCCTCCCCAGTGG
6480 GGAGGCTCCG
Statistics
Matches: 84, Mismatches: 16, Indels: 23
0.68 0.13 0.19
Matches are distributed among these distances:
15 1 0.01
16 41 0.49
17 41 0.49
18 1 0.01
ACGTcount: A:0.11, C:0.33, G:0.38, T:0.19
Consensus pattern (16 bp):
GCCTCCCCAGTGGTGA
Found at i:6495 original size:16 final size:16
Alignment explanation
Indices: 6377--6495 Score: 73
Period size: 16 Copynumber: 7.2 Consensus size: 16
6367 AGCCGCCCCA
6377 GTGGGGAGGCTCCGCC
1 GTGGGGAGGCTCCGCC
* *
6393 GTGGTTGAGCCTCC-CC
1 GTGG-GGAGGCTCCGCC
*
6409 AGTGGGAAGGCTCCGCC
1 -GTGGGGAGGCTCCGCC
* * *
6426 GTGGTTGAGCCTCC-CTA
1 GTGG-GGAGGCTCCGC-C
6443 GTGGGGAGGCTCCGCC
1 GTGGGGAGGCTCCGCC
* * *
6459 GTGGTTGAGCCTCC-CTA
1 GTGG-GGAGGCTCCGC-C
*
6476 GTGGGGAGGCTCCGTC
1 GTGGGGAGGCTCCGCC
6492 GTGG
1 GTGG
6496 CTGAGCCGTC
Statistics
Matches: 75, Mismatches: 19, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
16 40 0.53
17 35 0.47
ACGTcount: A:0.09, C:0.29, G:0.41, T:0.20
Consensus pattern (16 bp):
GTGGGGAGGCTCCGCC
Found at i:6514 original size:33 final size:33
Alignment explanation
Indices: 6367--6516 Score: 221
Period size: 33 Copynumber: 4.5 Consensus size: 33
6357 CCCATGGTGA
* *
6367 AGCCGCCCCAGTGGGGAGGCTCCGCCGTGGTTG
1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
* *
6400 AGCCTCCCCAGTGGGAAGGCTCCGCCGTGGTTG
1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
6433 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
* *
6466 AGCCTCCCTAGTGGGGAGGCTCCGTCGTGGCTG
1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
*
6499 AGCCGT-CCTAATGGGGAG
1 AGCC-TCCCTAGTGGGGAG
6517 ACTCAGTGTA
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
33 108 0.99
34 1 0.01
ACGTcount: A:0.11, C:0.31, G:0.39, T:0.19
Consensus pattern (33 bp):
AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
Done.