Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008690.1 Corchorus capsularis cultivar CVL-1 contig08711, 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: 24797
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:8517 original size:19 final size:18
Alignment explanation
Indices: 8493--8528 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8483 TGAAGATTTC
8493 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
8512 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
8529 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:13369 original size:52 final size:52
Alignment explanation
Indices: 13271--13370 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
13261 GTGTATGGTC
* *
13271 AATCCCATTTGTGCGAGTAGGAGTATGTTGGACTTGGACTGTCCATAATGGG
1 AATCCCATTTGTGCGAGTAGGAGTATGTTGGACTTGGACCGCCCATAATGGG
* *
13323 AATCCCATTTGTGCGAGTGGGAGTATGTTGGACTTGGGCCGCCCATAA
1 AATCCCATTTGTGCGAGTAGGAGTATGTTGGACTTGGACCGCCCATAA
13371 CGACCAGGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (52 bp):
AATCCCATTTGTGCGAGTAGGAGTATGTTGGACTTGGACCGCCCATAATGGG
Found at i:20565 original size:180 final size:180
Alignment explanation
Indices: 20263--20759 Score: 994
Period size: 180 Copynumber: 2.8 Consensus size: 180
20253 ATGGAAAGGG
20263 AAAGCCTATTGTACTTTGGAGTGCATTGTATATTCAAGATTTCCCTTTGGTATGTTGTATTTTTA
1 AAAGCCTATTGTACTTTGGAGTGCATTGTATATTCAAGATTTCCCTTTGGTATGTTGTATTTTTA
20328 TCTAGACCTTTTTATTTACTGGAGTATTATTTTGGTATTGTGACAATGGGCTATCAATTTGGCTG
66 TCTAGACCTTTTTATTTACTGGAGTATTATTTTGGTATTGTGACAATGGGCTATCAATTTGGCTG
20393 CTGCTTTGGAGTGCATTGTATATTCAAGATTTGGAGTACAATAGGCTATC
131 CTGCTTTGGAGTGCATTGTATATTCAAGATTTGGAGTACAATAGGCTATC
20443 AAAGCCTATTGTACTTTGGAGTGCATTGTATATTCAAGATTTCCCTTTGGTATGTTGTATTTTTA
1 AAAGCCTATTGTACTTTGGAGTGCATTGTATATTCAAGATTTCCCTTTGGTATGTTGTATTTTTA
20508 TCTAGACCTTTTTATTTACTGGAGTATTATTTTGGTATTGTGACAATGGGCTATCAATTTGGCTG
66 TCTAGACCTTTTTATTTACTGGAGTATTATTTTGGTATTGTGACAATGGGCTATCAATTTGGCTG
20573 CTGCTTTGGAGTGCATTGTATATTCAAGATTTGGAGTACAATAGGCTATC
131 CTGCTTTGGAGTGCATTGTATATTCAAGATTTGGAGTACAATAGGCTATC
20623 AAAGCCTATTGTACTTTGGAGTGCATTGTATATTCAAGATTTCCCTTTGGTATGTTGTATTTTTA
1 AAAGCCTATTGTACTTTGGAGTGCATTGTATATTCAAGATTTCCCTTTGGTATGTTGTATTTTTA
20688 TCTAGACCTTTTTATTTACTGGAGTATTATTTTGGTATTGTGACAATGGGCTATCAATTTGGCTG
66 TCTAGACCTTTTTATTTACTGGAGTATTATTTTGGTATTGTGACAATGGGCTATCAATTTGGCTG
20753 CTGCTTT
131 CTGCTTT
20760 CCCACTCTAT
Statistics
Matches: 317, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 317 1.00
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.44
Consensus pattern (180 bp):
AAAGCCTATTGTACTTTGGAGTGCATTGTATATTCAAGATTTCCCTTTGGTATGTTGTATTTTTA
TCTAGACCTTTTTATTTACTGGAGTATTATTTTGGTATTGTGACAATGGGCTATCAATTTGGCTG
CTGCTTTGGAGTGCATTGTATATTCAAGATTTGGAGTACAATAGGCTATC
Found at i:24250 original size:29 final size:29
Alignment explanation
Indices: 24208--24265 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
24198 CCAACAAGGT
24208 AATTAGTTGAACTCCCAACTAATTAATCA
1 AATTAGTTGAACTCCCAACTAATTAATCA
*
24237 AATTAGTTGAACTCCCCACTAATTAATCA
1 AATTAGTTGAACTCCCAACTAATTAATCA
24266 TTGAAATCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (29 bp):
AATTAGTTGAACTCCCAACTAATTAATCA
Done.