Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012449.1 Corchorus capsularis cultivar CVL-1 contig12470, 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: 28349
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4984 original size:107 final size:108
Alignment explanation
Indices: 4798--5042 Score: 397
Period size: 107 Copynumber: 2.3 Consensus size: 108
4788 AGTTTAGCCT
* **
4798 TAATTTCACTAAGTTTAGTCCCAAAATAAAATTTTATTTTTATTTTAAGGGTAAATTTTAAAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
4863 AATAATTTAATGTTATAGGGTTTTAGAAATAAAATACA-A-AAC
65 AATAATTTAATGTTATAGGGTTTTAGAAATAAAATACATATAAC
*
4905 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* *
4970 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATATATATAAC
65 AATAATTTAATGTTATAGGGTTTTAGAAATAAAATACATATAAC
5014 TAA-TTCACTAAGTTTAGCCCAAATTAAAA
1 TAATTTCACTAAGTTTAGCCCAAATTAAAA
5043 ATAAAATTTT
Statistics
Matches: 129, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
107 108 0.84
108 15 0.12
109 6 0.05
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.41
Consensus pattern (108 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATTTAATGTTATAGGGTTTTAGAAATAAAATACATATAAC
Found at i:24429 original size:21 final size:19
Alignment explanation
Indices: 24382--24440 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
24372 CTATTTAACA
24382 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
*
24401 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--T
*
24422 ATTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
24441 TAGAACAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.51
21 17 0.49
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAT
Found at i:28077 original size:15 final size:16
Alignment explanation
Indices: 28057--28119 Score: 76
Period size: 15 Copynumber: 4.0 Consensus size: 16
28047 GTGAATTCTT
*
28057 TTTCC-TTCGTTCCTA
1 TTTCCTTTCCTTCCTA
*
28072 TTTCCTTTCCCTTGCTA
1 TTTCCTTT-CCTTCCTA
*
28089 TTTCCTTTCCTTTCTA
1 TTTCCTTTCCTTCCTA
28105 TTT-CTTTCCTTCCTA
1 TTTCCTTTCCTTCCTA
28120 CCAAACAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
15 16 0.38
16 12 0.29
17 14 0.33
ACGTcount: A:0.06, C:0.33, G:0.03, T:0.57
Consensus pattern (16 bp):
TTTCCTTTCCTTCCTA
Found at i:28091 original size:17 final size:17
Alignment explanation
Indices: 28069--28113 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
28059 TCCTTCGTTC
28069 CTATTTCCTTTCCCTTG
1 CTATTTCCTTTCCCTTG
*
28086 CTATTTCCTTT-CCTTT
1 CTATTTCCTTTCCCTTG
28102 CTATTT-CTTTCC
1 CTATTTCCTTTCC
28114 TTCCTACCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.15
16 11 0.42
17 11 0.42
ACGTcount: A:0.07, C:0.33, G:0.02, T:0.58
Consensus pattern (17 bp):
CTATTTCCTTTCCCTTG
Found at i:28105 original size:16 final size:16
Alignment explanation
Indices: 28069--28115 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
28059 TCCTTCGTTC
28069 CTATTTCCTTTCCCTTG
1 CTATTTCCTTT-CCTTG
*
28086 CTATTTCCTTTCCTTT
1 CTATTTCCTTTCCTTG
28102 CTATTT-CTTTCCTT
1 CTATTTCCTTTCCTT
28116 CCTACCAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.28
16 10 0.34
17 11 0.38
ACGTcount: A:0.06, C:0.32, G:0.02, T:0.60
Consensus pattern (16 bp):
CTATTTCCTTTCCTTG
Done.