Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020688.1 Corchorus olitorius cultivar O-4 contig20721, 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: 13939
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Found at i:9330 original size:3 final size:3
Alignment explanation
Indices: 9322--9390 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
9312 CCTTTTAATA
9322 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9370 TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
9391 ATATATATAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9954 original size:292 final size:294
Alignment explanation
Indices: 9426--10016 Score: 906
Period size: 292 Copynumber: 2.0 Consensus size: 294
9416 TTTTTAGTGA
*
9426 CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGTCTCCTTTTGGCCTTTTTTTGG
1 CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGCCTTTTTTTGG
* * *
9491 TCTTTTCTCACTTTTCGGGTGACTAAAAGGCCCTTGATGAATATCCCCTTACTTTTCTTGCTGCC
66 TCTTTTATCACTTTTCGGGTGACTAAAAGGCCCTCGATGAATATCCCCTTACTTTTCCTGCTGCC
* *
9556 CTTTTTTTGTAATTTACTATTTTTGTATTAATGATTAAGTGTGTTTTAATTACGTATTAACTGTG
131 C-TTTTTTGTAATTTACTATTTTTATATTAATGATTAAGTGTGTTTTAATTACATATTAACTGTG
* *
9621 TGTGGATATTAGGATTTACCAGTTCAACTCCTCTACCGGAATTCCAAAGGA-T-TGTT-GCTATA
195 TATGGATATTAGGATTTACCAGTTCAACTCCTCTACCGGAATTCCAAAGGATTATATTAGCTATA
*
9683 AATGTATCTACCCGATTTCATTAATTTAACAATTG
260 AATGTATCTACCCGAGTTCATTAATTTAACAATTG
*
9718 CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGG-CTTTTTTTTG
1 CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGCCTTTTTTTGG
* *
9782 TCTTTTATCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTGTT
66 TCTTTTATCACTTTTCGGGTGACT-AAAAGGCCCTCGATGAATAT-C-CCCTTACTTTTCCTGCT
* * *
9847 GCCC-TTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATTTTAATTG
128 GCCCTTTTTTGTAATTTACTATTTTTATATTAATGATTAAGTGTGTTTTAATTACATATTAACTG
*
9911 TGTATGGATATTAGGATTTACC-GATTCAACTCCTCTGCCGGAATTCCAAAGGATTAATATTAGC
193 TGTATGGATATTAGGATTTACCAG-TTCAACTCCTCTACCGGAATTCCAAAGGATT-ATATTA--
* *
9975 GCTGTAAATGTGTCTACCCGAGTTCATTAATTTAACAATTG
254 GCTATAAATGTATCTACCCGAGTTCATTAATTTAACAATTG
10016 C
1 C
10017 AATCAAGAAT
Statistics
Matches: 271, Mismatches: 18, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
291 33 0.12
292 175 0.65
293 2 0.01
294 19 0.07
295 3 0.01
298 39 0.14
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (294 bp):
CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGCCTTTTTTTGG
TCTTTTATCACTTTTCGGGTGACTAAAAGGCCCTCGATGAATATCCCCTTACTTTTCCTGCTGCC
CTTTTTTGTAATTTACTATTTTTATATTAATGATTAAGTGTGTTTTAATTACATATTAACTGTGT
ATGGATATTAGGATTTACCAGTTCAACTCCTCTACCGGAATTCCAAAGGATTATATTAGCTATAA
ATGTATCTACCCGAGTTCATTAATTTAACAATTG
Found at i:11634 original size:10 final size:10
Alignment explanation
Indices: 11616--11647 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
11606 TTTATTCAAA
*
11616 ATCCGTAAAT
1 ATCCATAAAT
11626 ATCCATAAAT
1 ATCCATAAAT
11636 ATCCATAAAT
1 ATCCATAAAT
11646 AT
1 AT
11648 TCAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (10 bp):
ATCCATAAAT
Done.