Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009379.1 Corchorus capsularis cultivar CVL-1 contig09400, 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: 18808
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 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 T
36 TAATGTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7983 original size:1 final size:1
Alignment explanation
Indices: 7977--8016 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
7967 AAACAAGAGG
7977 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8017 GAACTTCCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12086 original size:12 final size:12
Alignment explanation
Indices: 12064--12097 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12054 CAAAAGAGAG
12064 GAAAAATAAAAAC
1 GAAAAA-AAAAAC
*
12077 GAAAAAAAAAAT
1 GAAAAAAAAAAC
12089 GAAAAAAAA
1 GAAAAAAAA
12098 GAGAGAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.82, C:0.03, G:0.09, T:0.06
Consensus pattern (12 bp):
GAAAAAAAAAAC
Found at i:12909 original size:12 final size:13
Alignment explanation
Indices: 12891--12923 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
12881 GTGGGTTTAG
12891 TAGTTTGTTTATT
1 TAGTTTGTTTATT
*
12904 TA-TTTGTTTGTT
1 TAGTTTGTTTATT
12916 TAGTTTGT
1 TAGTTTGT
12924 AATTAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.70
Consensus pattern (13 bp):
TAGTTTGTTTATT
Found at i:13595 original size:50 final size:51
Alignment explanation
Indices: 13540--13635 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 51
13530 TTTGATTTGA
* *
13540 TTTGATTTGCTTCAAGGGTC-AAATGACTTGATCTTGAATTGATGAGGGAG
1 TTTGATTTGATTCAAGGGTCTAAATGACTTGATCTCGAATTGATGAGGGAG
* **
13590 TTTGATTTGATTCGAGGGTCTTGATGACTTGATCTCGAATTGATGA
1 TTTGATTTGATTCAAGGGTCTAAATGACTTGATCTCGAATTGATGA
13636 TAATTTGACT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 18 0.45
51 22 0.55
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (51 bp):
TTTGATTTGATTCAAGGGTCTAAATGACTTGATCTCGAATTGATGAGGGAG
Found at i:14804 original size:67 final size:66
Alignment explanation
Indices: 14696--14916 Score: 325
Period size: 67 Copynumber: 3.2 Consensus size: 66
14686 AGTTCATTCA
* *
14696 CTTTTTTTTTTTTTGTGCTCTAAGTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGA
1 CTTTTTTTTTCTTT-TGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGA
14761 GC
65 GC
*
14763 CTTTTTTTTTCTTTTGCTTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCTA
1 CTTTTTTTTTCTTTTGC-TCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGC-G
14828 AGC
64 AGC
*
14831 CTTTTTTTTTTTCTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTATCAACTTAGC
1 C--TTTTTTTTTC-TTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGC
*
14896 GTAGT
63 G-AGC
*
14901 CTTTTTTTTTTTTTTG
1 CTTTTTTTTTCTTTTG
14917 GGTTTACTAA
Statistics
Matches: 141, Mismatches: 7, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
66 3 0.02
67 62 0.44
68 13 0.09
70 57 0.40
71 6 0.04
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (66 bp):
CTTTTTTTTTCTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAG
C
Found at i:14877 original size:70 final size:69
Alignment explanation
Indices: 14697--14912 Score: 332
Period size: 70 Copynumber: 3.1 Consensus size: 69
14687 GTTCATTCAC
* * *
14697 TTTTTTTTTT-TTTGTGCTCTAAGTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGA
1 TTTTTTTTTTCTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCTA
14761 GCC-
66 GCCT
14764 -TTTTTTTTTC-TTTTGCTTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCT
1 TTTTTTTTTTCTTTTTGC-TCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCT
14827 AAGCCT
65 -AGCCT
*
14833 TTTTTTTTTTCTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTATCAACTTAGCGT
1 TTTTTTTTTTCTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGC-T
*
14898 AGTCT
65 AGCCT
14903 TTTTTTTTTT
1 TTTTTTTTTT
14913 TTTGGGTTTA
Statistics
Matches: 137, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
66 14 0.10
67 44 0.32
68 4 0.03
70 68 0.50
71 7 0.05
ACGTcount: A:0.15, C:0.21, G:0.14, T:0.50
Consensus pattern (69 bp):
TTTTTTTTTTCTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCTA
GCCT
Done.