Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015103.1 Corchorus olitorius cultivar O-4 contig15136, 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: 2314
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Found at i:162 original size:50 final size:48
Alignment explanation
Indices: 77--220 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 48
67 GGAAGGTCCT
* * *
77 TATCTTCATTTCCAAAAAATGCCCCTTCTCGGTCGGAAGATCCCAGTTTTC
1 TATC-TCA-TTCC-AAAAATGCCCCTTCCCAGTCGGAAGGTCCCAGTTTTC
* **
128 GATATCTCATTCCAAAAATGTCCCTTCCCAGTCGGAAGGTCCTTGTTTTC
1 --TATCTCATTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCCCAGTTTTC
*
178 -A--T--TTCCAAAAATGCCCCTTCCTAGTCGGAAGGTCCCAGTTTTC
1 TATCTCATTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCCCAGTTTTC
221 CTTCGATAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
43 37 0.46
45 1 0.01
47 1 0.01
50 31 0.38
51 4 0.05
52 3 0.04
53 4 0.05
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (48 bp):
TATCTCATTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCCCAGTTTTC
Found at i:216 original size:93 final size:94
Alignment explanation
Indices: 40--220 Score: 258
Period size: 94 Copynumber: 1.9 Consensus size: 94
30 TCTTTGTTTT
* ** *
40 TCATTCCCAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATCTTCATTTCCAAAAAATGCCCCTTC
1 TCATTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCCTTATCTTCATTTCCAAAAAATGCCCCTTC
*
105 TCGGTCGGAAGATCCCAGTTTTCGATATC
66 TCAGTCGGAAGATCCCAGTTTTCGATATC
* * *
134 TCATTCCAAAAATGTCCCTTCCCAGTCGGAAGGTCCTTGTTTTCATTTCC-AAAAATGCCCCTTC
1 TCATTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCCTTATCTTCATTTCCAAAAAATGCCCCTTC
*
198 -CTAGTCGGAAGGTCCCAGTTTTC
66 TC-AGTCGGAAGATCCCAGTTTTC
221 CTTCGATAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
92 1 0.01
93 33 0.43
94 43 0.56
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (94 bp):
TCATTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCCTTATCTTCATTTCCAAAAAATGCCCCTTC
TCAGTCGGAAGATCCCAGTTTTCGATATC
Found at i:289 original size:41 final size:41
Alignment explanation
Indices: 228--345 Score: 159
Period size: 41 Copynumber: 2.9 Consensus size: 41
218 TTCCTTCGAT
* *
228 AATTCCTAGTTTGCCATTCCTCATCGGAAGGTGTTGTTTTA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTTA
*
269 AATTCCCAGTTTGCCCTTCCTCATAGGAAGGTGTTG-TTTA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTTA
* * *
309 AATTCCCAATTTG-CCTTTCTCGGTCGGAAGGTGTTGT
1 AATTCCCAGTTTGCCCTTCCTC-ATCGGAAGGTGTTGT
346 CATCATTATT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 7 0.10
40 28 0.41
41 33 0.49
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTTA
Found at i:419 original size:48 final size:48
Alignment explanation
Indices: 318--597 Score: 399
Period size: 48 Copynumber: 5.9 Consensus size: 48
308 AAATTCCCAA
* * * *
318 TTTGCCTTTCTCGGTCGGAAGGTGTTGTCATC---A--TTATTCTCGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCCGT
*
361 TTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCCAT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCCGT
* *
409 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCCGT
* *
457 TTTGCCCTTCCCAGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCCGT
* *
505 TTTGCCCTTCCCGGTCGGAAGGTGTTTTCTTCGATATTTTATTCCCGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCCGT
* * *
553 TTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCAATATTTCATTCC
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCC
598 TGTCTTCAAT
Statistics
Matches: 211, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
43 29 0.14
46 1 0.00
48 181 0.86
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (48 bp):
TTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCCGT
Done.