Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011383.1 Corchorus capsularis cultivar CVL-1 contig11404, 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: 5016
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Found at i:2065 original size:48 final size:48
Alignment explanation
Indices: 1988--2421 Score: 412
Period size: 49 Copynumber: 8.9 Consensus size: 48
1978 CTTTTTAGTC
* * * **
1988 TTTACTTGCTATTTCCTAAAACGTCCTTCCCGGACGGAAGGCACTGCT
1 TTTACTTGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
*
2036 TTTA-TCTGCTATTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
1 TTTACT-TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
* ** *
2084 TTTACTTGCTTTTTTTCCAAAACGCCCTTCCTAGACGGAAGGCGCTTAT
1 TTTACTTGC-TTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
* * **
2133 TTTACTTGCTTTTTCCCAAAATGCCTTTCCTAGACGGAAGGCACTTAT
1 TTTACTTGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
* * * *
2181 CTTTACTCGCTTTTTCCCTAAACGCCCTTCCCAGACGGAAGGCACTTGTT
1 -TTTACTTGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTT-AT
* ** *
2231 TTTA-TCTG-TTATTTCCCAAAATGCCCTTCCTAGACGGAAGCCACTTAT
1 TTTACT-TGCTT-TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
* * * * *
2279 TTTCGCTTGCTTTTTTCCTAAAATGCCCTTCCCGGACGGAAAGCACTAAT
1 TTT-ACTTGC-TTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
* * * * *
2329 CTTTACCTG-TTTTGTCTCGAAACGCCCCTCCCGGACGGAAGGCACTAATT
1 -TTTACTTGCTTTT-TCCCAAAACGCCCTTCCCGGACGGAAGGCACTTA-T
* *
2379 TTTACTTG--TTTACCCTAAAACGCCCTTCCCGGATGGAAGGCAC
1 TTTACTTGCTTTTTCCC-AAAACGCCCTTCCCGGACGGAAGGCAC
2422 CATTCTCTTA
Statistics
Matches: 325, Mismatches: 46, Indels: 30
0.81 0.11 0.07
Matches are distributed among these distances:
47 3 0.01
48 122 0.38
49 158 0.49
50 37 0.11
51 5 0.02
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (48 bp):
TTTACTTGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTAT
Found at i:2121 original size:97 final size:97
Alignment explanation
Indices: 1988--2421 Score: 432
Period size: 97 Copynumber: 4.5 Consensus size: 97
1978 CTTTTTAGTC
* * * *
1988 TTTACTTGC-TATTTCCTAAAACGTCCTTCCCGGACGGAAGGCACTGCTTTTATCTGCTATTTCC
1 TTTACTTGCTTTTTTCCTAAAACGCCCTTCCCAGACGGAAGGCACTGATTTTATCTGCTATTTCC
*
2052 CAAAACGCCCTTCCCGGACGGAAGGCACTTAT
66 CAAAACGCCCTTCCCAGACGGAAGGCACTTAT
* * * *
2084 TTTACTTGCTTTTTTTCC-AAAACGCCCTTCCTAGACGGAAGGCGCTTATTTTA-CTTGCTTTTT
1 TTTACTTGC-TTTTTTCCTAAAACGCCCTTCCCAGACGGAAGGCACTGATTTTATC-TGCTATTT
* * *
2147 CCCAAAATGCCTTTCCTAGACGGAAGGCACTTAT
64 CCCAAAACGCCCTTCCCAGACGGAAGGCACTTAT
* * * *
2181 CTTTACTCGCTTTTTCCCT-AAACGCCCTTCCCAGACGGAAGGCACTTGTTTTTATCTGTTATTT
1 -TTTACTTGCTTTTTTCCTAAAACGCCCTTCCCAGACGGAAGGCAC-TGATTTTATCTGCTATTT
* * *
2245 CCCAAAATGCCCTTCCTAGACGGAAGCCACTTAT
64 CCCAAAACGCCCTTCCCAGACGGAAGGCACTTAT
* * * * * * *
2279 TTTCGCTTGCTTTTTTCCTAAAATGCCCTTCCCGGACGGAAAGCACTAATCTTTACCTG-TTTTG
1 TTT-ACTTGCTTTTTTCCTAAAACGCCCTTCCCAGACGGAAGGCACTGAT-TTTATCTGCTATT-
* * * * *
2343 TCTCGAAACGCCCCTCCCGGACGGAAGGCACTAATT
63 TCCCAAAACGCCCTTCCCAGACGGAAGGCACTTA-T
** * *
2379 TTTACTTG--TTTACCCTAAAACGCCCTTCCCGGATGGAAGGCAC
1 TTTACTTGCTTTTTTCCTAAAACGCCCTTCCCAGACGGAAGGCAC
2422 CATTCTCTTA
Statistics
Matches: 280, Mismatches: 46, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
96 10 0.04
97 130 0.46
98 75 0.27
99 61 0.22
100 4 0.01
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (97 bp):
TTTACTTGCTTTTTTCCTAAAACGCCCTTCCCAGACGGAAGGCACTGATTTTATCTGCTATTTCC
CAAAACGCCCTTCCCAGACGGAAGGCACTTAT
Done.