Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010955.1 Corchorus capsularis cultivar CVL-1 contig10976, 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: 7247
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:5301 original size:21 final size:21
Alignment explanation
Indices: 5261--5301 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5251 TTCTTTTTAT
** *
5261 TAAGTTTAGCCTTAATTTAAC
1 TAAGTTTAGCCCCAAATTAAC
5282 TAAGTTTAGCCCCAAATTAA
1 TAAGTTTAGCCCCAAATTAA
5302 AATTTTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (21 bp):
TAAGTTTAGCCCCAAATTAAC
Found at i:5445 original size:107 final size:107
Alignment explanation
Indices: 5273--5536 Score: 424
Period size: 107 Copynumber: 2.5 Consensus size: 107
5263 AGTTTAGCCT
* *
5273 TAATTTAACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
5338 AATAATTTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAATTTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
*
5380 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * *
5445 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 AATAATTTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
* ** *
5487 TAA-TTCACTAAGTTTAG-CCCAAATCAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
5537 TAGAAAAATT
Statistics
Matches: 147, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
105 29 0.20
106 14 0.10
107 104 0.71
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (107 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATTTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:6266 original size:217 final size:216
Alignment explanation
Indices: 5771--6403 Score: 671
Period size: 217 Copynumber: 2.9 Consensus size: 216
5761 TTTATTATCA
* ** *
5771 TCATATATTAAAACGACGTTTTCGAAAAATATTGTTATAAATGTCGTTAAAGTTTATCTTAAAGC
1 TCATATATTAAAACGACGTTTTCGAAAAATGTTGTTATAAATGTCGAAAAAGTATATCTTAAAGC
* * * *** * * * *
5836 GACGTTTGTTAAAAAATATTGTATGCCCGAGCGAAGTTTGAGAAAAAAACGTCTTTACAAACATC
66 GACGTTTGTTAAAAAATGTCGCATGATTGAACGACGTTTGAG--AAAAACGTCTCTACAAACGTC
** * * * * ** *
5901 ACAAAAGTGTAACCGAGAGCGACGTTATTTAAAAACATCACTCAATTTTGAAAAAGAGTCGCAAG
129 ACAAAAGCATAAACAAGAGCGACATTATTAAAAAACATCACTCAATTAAGAAAAAGACTCGCAAG
* * *
5966 GTGCTGCGACGTTTATTAAAATG
194 GTACTACGACATTTATTAAAATG
* * * * * *
5989 TCATATACTAATACGACGTTTTTGAAAAACGTTGTTATAAATGTCGAAAAAGTCTATCTTAAAAC
1 TCATATATTAAAACGACGTTTTCGAAAAATGTTGTTATAAATGTCGAAAAAGTATATCTTAAAGC
* * * *
6054 GGCGTTCGTTAAAAAATGTCGCATGTTTGAACGACGTTTGAGAAAAATGTCTCTACAAACGTCAC
66 GACGTTTGTTAAAAAATGTCGCATGATTGAACGACGTTTGAGAAAAACGTCTCTACAAACGTCAC
* ** * *
6119 AAAAGCATAAACAATAGCGACATTATTAAAAAATGTCACTTAATTAAGAAAGAGTACTCGCAAGG
131 AAAAGCATAAACAAGAGCGACATTATTAAAAAACATCACTCAATTAAGAAAAAG-ACTCGCAAGG
6184 TACTACGACATTTATTAAAATG
195 TACTACGACATTTATTAAAATG
* * *
6206 TCATATATTAAAACGACATTTCCGAAAAATGTTGTTATAAATGTCGGAAAAGTATATCTTAAAGC
1 TCATATATTAAAACGACGTTTTCGAAAAATGTTGTTATAAATGTCGAAAAAGTATATCTTAAAGC
* * * * * **
6271 GACGTTTGTTAAAAAATGTCGCATGATTAAACAACTTTTGA-ATAAAACATCTCTACAAATGTTG
66 GACGTTTGTTAAAAAATGTCGCATGATTGAACGACGTTTGAGA-AAAACGTCTCTACAAACGTCA
* ** * * *
6335 CAAAAGCATAAACAAGAGTGATGTTA-TAAGAAAACGTCACTCAATTTATAAAATAG--TCGCAA
130 CAAAAGCATAAACAAGAGCGACATTATTAA-AAAACATCACTCAATTAAGAAAA-AGACTCGCAA
6397 GGTACTA
193 GGTACTA
6404 TCACTTTTGA
Statistics
Matches: 343, Mismatches: 68, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
215 13 0.04
216 65 0.19
217 175 0.51
218 90 0.26
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.29
Consensus pattern (216 bp):
TCATATATTAAAACGACGTTTTCGAAAAATGTTGTTATAAATGTCGAAAAAGTATATCTTAAAGC
GACGTTTGTTAAAAAATGTCGCATGATTGAACGACGTTTGAGAAAAACGTCTCTACAAACGTCAC
AAAAGCATAAACAAGAGCGACATTATTAAAAAACATCACTCAATTAAGAAAAAGACTCGCAAGGT
ACTACGACATTTATTAAAATG
Found at i:6684 original size:11 final size:11
Alignment explanation
Indices: 6668--6692 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6658 TTTATATCTT
6668 TTTGATTTTGA
1 TTTGATTTTGA
6679 TTTGATTTTGA
1 TTTGATTTTGA
6690 TTT
1 TTT
6693 CTTTTAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTGATTTTGA
Done.