Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016191.1 Corchorus capsularis cultivar CVL-1 contig16212, 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: 31012
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--41 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
42 TATTCTTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2133 original size:41 final size:41
Alignment explanation
Indices: 2088--2180 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
2078 TCCTCCATTG
* * *
2088 TTGAAGGATATTTAAGAATATTTTTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAAAATATATTTTTTAAAGGATTTACTT
* *
2129 TTGAAGGATATTTAAAAATGTATTTTTTAAAGGTTTTACTT
1 TTGAAGGATATTTAAAAATATATTTTTTAAAGGATTTACTT
2170 TTGAAGGATAT
1 TTGAAGGATAT
2181 ATTATGATGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.48
Consensus pattern (41 bp):
TTGAAGGATATTTAAAAATATATTTTTTAAAGGATTTACTT
Found at i:3363 original size:14 final size:14
Alignment explanation
Indices: 3344--3378 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3334 AAAAAAGTAC
*
3344 TCATAATATTGTTT
1 TCATAAAATTGTTT
3358 TCATAAAATTGTTT
1 TCATAAAATTGTTT
3372 TCATAAA
1 TCATAAA
3379 GTACTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (14 bp):
TCATAAAATTGTTT
Found at i:4731 original size:65 final size:64
Alignment explanation
Indices: 4624--4747 Score: 178
Period size: 65 Copynumber: 1.9 Consensus size: 64
4614 TTAATTTATC
* *
4624 TTTTTTTTTTACCCCATTCGGGTATCCAGAGCTTTGCTCTGACTACAATCCGGATTCAACCCATG
1 TTTTTCTTTTACCCCATTC--GTATCCAAAGCTTTGCTCTGACT--AATCCGGATTCAACCCATG
4689 TTG
62 TTG
*
4692 TTTTTCTTTTACCCCATTC-TATCCAAAGCTTTGCTCTGACTAATTCGGATTCAACC
1 TTTTTCTTTTACCCCATTCGTATCCAAAGCTTTGCTCTGACTAATCCGGATTCAACC
4748 TGTGTCGTGC
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
63 14 0.26
65 21 0.40
68 18 0.34
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (64 bp):
TTTTTCTTTTACCCCATTCGTATCCAAAGCTTTGCTCTGACTAATCCGGATTCAACCCATGTTG
Found at i:9830 original size:49 final size:49
Alignment explanation
Indices: 9773--9871 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
9763 CATAATATAT
9773 AATGCCTTACGAAATGAGAAATTATTAGATGAGACCGACTCCTCATGTC
1 AATGCCTTACGAAATGAGAAATTATTAGATGAGACCGACTCCTCATGTC
9822 AATGCCTTACGAAATGAGAAATTATTAGATGAGACCGACTCCTCATGTC
1 AATGCCTTACGAAATGAGAAATTATTAGATGAGACCGACTCCTCATGTC
9871 A
1 A
9872 TCTAAGATCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (49 bp):
AATGCCTTACGAAATGAGAAATTATTAGATGAGACCGACTCCTCATGTC
Found at i:11968 original size:17 final size:17
Alignment explanation
Indices: 11946--11978 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11936 TCCCCTCTGT
11946 TTTCATCTTCATATCTA
1 TTTCATCTTCATATCTA
11963 TTTCATCTTCATATCT
1 TTTCATCTTCATATCT
11979 CTTTTCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTCATCTTCATATCTA
Found at i:11988 original size:17 final size:17
Alignment explanation
Indices: 11945--11988 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
11935 TTCCCCTCTG
11945 TTTTCATCTTCATATCT
1 TTTTCATCTTCATATCT
*
11962 ATTTCATCTTCATATCT
1 TTTTCATCTTCATATCT
11979 CTTTTC-TCTT
1 -TTTTCATCTT
11989 TCTTCTCCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.16, C:0.25, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTCATCTTCATATCT
Found at i:24848 original size:28 final size:28
Alignment explanation
Indices: 24782--24865 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 28
24772 ACTTTTTGCT
*
24782 CCATGAACTTCAATTTTGGACATTTTTC
1 CCATGAACTTCAATTTTGGACATTTTAC
* * *
24810 CCTCTGAACTTCAATTTTGTATATTTTAC
1 CC-ATGAACTTCAATTTTGGACATTTTAC
* *
24839 CCATAAACTTCAATTTAGGGACATTTT
1 CCATGAACTTCAATTT-TGGACATTTT
24866 GCCCCTCAGC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
28 14 0.31
29 31 0.69
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (28 bp):
CCATGAACTTCAATTTTGGACATTTTAC
Done.