Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015560.1 Corchorus capsularis cultivar CVL-1 contig15581, 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: 17861
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Found at i:111 original size:34 final size:33
Alignment explanation
Indices: 39--145 Score: 153
Period size: 34 Copynumber: 3.2 Consensus size: 33
29 AATATAGCCG
*** *
39 AGCCGCCCCAGTGGGGCGGCCTATTCATAGTGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
72 AGCCGCCCCAGTGGGGCGGCCTGCCCAATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCC-ATGGTGA
*
106 AGCCGCCCAAGTGGGGCGGCCTGCCCATGGT-A
1 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
138 AGCCGCCC
1 AGCCGCCC
146 TCTTGGGGCG
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
32 9 0.13
33 28 0.41
34 31 0.46
ACGTcount: A:0.16, C:0.36, G:0.36, T:0.13
Consensus pattern (33 bp):
AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
Found at i:5616 original size:14 final size:15
Alignment explanation
Indices: 5599--5627 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5589 TTATCTTTTA
5599 ATTATTA-TTTTATT
1 ATTATTACTTTTATT
5613 ATTATTACTTTTATT
1 ATTATTACTTTTATT
5628 TAATTTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTATTACTTTTATT
Found at i:5758 original size:86 final size:83
Alignment explanation
Indices: 5651--5944 Score: 401
Period size: 86 Copynumber: 3.6 Consensus size: 83
5641 ATTTCCTTTT
* *
5651 ATATCTTCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATCATTCAATCTTT
1 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATCATTCTAT-TTT
5716 AATATTTATTTGTTTCTTAAA
65 -ATATTTATTT-TTTCTTAAA
*
5737 ATATCTCCTAAATCTTCCACAATTTGGCAAGATTTAGAAAATATTCTCA--A-C-TT-TATTATT
1 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATCATTCTATT-TT
5797 AT-TTTA---TTTCTTAAA
65 ATATTTATTTTTTCTTAAA
* *
5812 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGGAAATATTCTCATTATTAATTCTATTTT
1 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTA-TCATTCTATTTT
5877 -TAATTTATTTATTTTCTTAAA
65 AT-ATTTA-TT-TTTTCTTAAA
5898 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCT
1 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCT
5945 ATCATTATTT
Statistics
Matches: 187, Mismatches: 7, Indels: 28
0.84 0.03 0.13
Matches are distributed among these distances:
75 56 0.30
77 1 0.01
79 5 0.03
80 7 0.04
81 12 0.06
82 2 0.01
83 1 0.01
84 1 0.01
86 102 0.55
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (83 bp):
ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATCATTCTATTTTA
TATTTATTTTTTCTTAAA
Found at i:5837 original size:161 final size:161
Alignment explanation
Indices: 5651--5944 Score: 493
Period size: 161 Copynumber: 1.8 Consensus size: 161
5641 ATTTCCTTTT
* *
5651 ATATCTTCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTA-TCATTCAATCTT
1 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTAATTCAAT-TT
*
5715 TAATATTTATTT-GTTTCTTAAAATATCTCCTAAATCTTCCACAATTTGGCAAGATTTAGAAAAT
65 TAA-ATTTATTTAGTTTCTTAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAAT
5779 ATTCTCAACTTTATTATTATTTTATTTCTTAAA
129 ATTCTCAACTTTATTATTATTTTATTTCTTAAA
* *
5812 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGGAAATATTCTCATTATTAATTCTATTTT
1 ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTAATTCAATTTT
* *
5877 TAATTTATTTATTTTCTTAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATAT
66 AAATTTATTTAGTTTCTTAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATAT
5942 TCT
131 TCT
5945 ATCATTATTT
Statistics
Matches: 124, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
160 8 0.06
161 109 0.88
162 7 0.06
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (161 bp):
ATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTAATTCAATTTT
AAATTTATTTAGTTTCTTAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATAT
TCTCAACTTTATTATTATTTTATTTCTTAAA
Found at i:6687 original size:16 final size:16
Alignment explanation
Indices: 6666--6702 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6656 TAACGCCTCT
6666 TGTCTCTCCGTCTATC
1 TGTCTCTCCGTCTATC
* *
6682 TGTCTCTCTGTCTATT
1 TGTCTCTCCGTCTATC
6698 TGTCT
1 TGTCT
6703 ATGCCAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.05, C:0.30, G:0.14, T:0.51
Consensus pattern (16 bp):
TGTCTCTCCGTCTATC
Found at i:7206 original size:35 final size:35
Alignment explanation
Indices: 7179--8053 Score: 721
Period size: 35 Copynumber: 25.2 Consensus size: 35
7169 AAATTTCTTG
* *
7179 AAATGAGATCACCTTTGATCGTTGGAAACTACTGA
1 AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
*
7214 AAATGTGATCAACTCTGATCGTTGGAAACTACTGA
1 AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
* *
7249 AAATGCGATCAACTCTGATCGTTGGAAAATACTGA
1 AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
*
7284 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
1 AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
*
7319 AAAT---A-CAACTCTGATCGTTGGGAACTACTGA
1 AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
* *
7350 AAATGCGATCAACTCTGATCGTTGGGAACTACTGA
1 AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
*
7385 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
1 AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
*
7420 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
1 AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
* *
7455 AAATGCGATCAACTCTGATCGTTGGAAACTTCTGA
1 AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
* *
7490 AAATGTGATCAACTCTGATCGTTGGAAAATACTGA
1 AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
* *
7525 AAATGTGATCAACTCTGATCGTTGGAAAATACTGA
1 AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
* *
7560 AAATGCGATCAACTCTGATCGTTGGAAAATACTGA
1 AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
* * * *
7595 AAATGAGATCAATTCTGA-CCTCTGAAAACTTCTTG-
1 AAATGAGATCAACTCTGATCGT-TGGAAACTAC-TGA
* * *
7630 AAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG-
1 AAATGAGATCAACTCTGATCGT-TGGAAACTAC-TGA
* * * *
7665 GAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG-
1 AAATGAGATCAACTCTGATCGT-TGGAAACTAC-TGA
* * * *
7700 GAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG-
1 AAATGAGATCAACTCTGATCGT-TGGAAACTAC-TGA
* * * *
7735 GAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG-
1 AAATGAGATCAACTCTGATCGT-TGGAAACTAC-TGA
* * * *
7770 GAATGAGATCAACTCTGA-CCTCTGAAAACTCCTTG-
1 AAATGAGATCAACTCTGATCGT-TGGAAACTAC-TGA
* * * *
7805 GAATGAGATCAACTCTGA-CCTCTGAAAACTCCTTG-
1 AAATGAGATCAACTCTGATCGT-TGGAAACTAC-TGA
* * * *
7840 GAATGAGATCAACTCTGA-CCTCTGAAAACTCCTTG-
1 AAATGAGATCAACTCTGATCGT-TGGAAACTAC-TGA
* * * *
7875 GAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG-
1 AAATGAGATCAACTCTGATCGT-TGGAAACTAC-TGA
* * *
7910 GAATGAGATCAACTCTGA-CCTCTGGAAACTTCTTG-
1 AAATGAGATCAACTCTGATCGT-TGGAAACTAC-TGA
* * *
7945 AAATGAGATCAACTCTGA-CCTCTGCAAACTTCTTG-
1 AAATGAGATCAACTCTGATCGT-TGGAAACTAC-TGA
* * * *
7980 GAATGAGATCAACTCTGA-CCTCTGAAAACTTCTG-
1 AAATGAGATCAACTCTGATCGT-TGGAAACTACTGA
* * *
8014 -AATGAGATCAACTCTGA-CCTCTGAAAACTTCTGA
1 AAATGAGATCAACTCTGATCGT-TGGAAACTACTGA
8048 AAATGA
1 AAATGA
8054 CCGCACTGGA
Statistics
Matches: 804, Mismatches: 28, Indels: 16
0.95 0.03 0.02
Matches are distributed among these distances:
31 29 0.04
32 1 0.00
33 33 0.04
34 5 0.01
35 734 0.91
36 2 0.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (35 bp):
AAATGAGATCAACTCTGATCGTTGGAAACTACTGA
Found at i:7670 original size:70 final size:70
Alignment explanation
Indices: 7596--8045 Score: 814
Period size: 70 Copynumber: 6.5 Consensus size: 70
7586 AAATACTGAA
* *
7596 AATGAGATCAATTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTT
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTT
7661 CTTGG
66 CTTGG
7666 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTT
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTT
7731 CTTGG
66 CTTGG
*
7736 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTC
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTT
7801 CTTGG
66 CTTGG
* *
7806 AATGAGATCAACTCTGACCTCTGAAAACTCCTTGGAATGAGATCAACTCTGACCTCTGAAAACTC
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTT
7871 CTTGG
66 CTTGG
*
7876 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGGAAACTT
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTT
*
7941 CTTGA
66 CTTGG
*
7946 AATGAGATCAACTCTGACCTCTGCAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTT
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTT
8011 C-T-G
66 CTTGG
8014 AATGAGATCAACTCTGACCTCTGAAAACTTCT
1 AATGAGATCAACTCTGACCTCTGAAAACTTCT
8046 GAAAATGACC
Statistics
Matches: 368, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
68 31 0.08
69 1 0.00
70 336 0.91
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (70 bp):
AATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTT
CTTGG
Found at i:17742 original size:14 final size:15
Alignment explanation
Indices: 17725--17753 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17715 TTATCTTTTA
17725 ATTATTA-TTTTATT
1 ATTATTACTTTTATT
17739 ATTATTACTTTTATT
1 ATTATTACTTTTATT
17754 TAATTTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTATTACTTTTATT
Done.