Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015623.1 Corchorus olitorius cultivar O-4 contig15656, 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: 13502
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:138 original size:2 final size:2
Alignment explanation
Indices: 131--197 Score: 55
Period size: 2 Copynumber: 33.5 Consensus size: 2
121 CTTTCCAAAA
* * * ** * *
131 AT AT AT AT AT AT AT AT AT AT AT AT GAC AT AA AC GG GT -T AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
173 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
198 ATTGATGGAG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
1 1 0.02
2 52 0.96
3 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2817 original size:35 final size:35
Alignment explanation
Indices: 2766--2836 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
2756 AAGGAACAAT
2766 CATATATACTGCCTCTGGATTTTGATTCTGATTGG
1 CATATATACTGCCTCTGGATTTTGATTCTGATTGG
*
2801 CATATATACTGTCTCTGGATTTTGATTCTGATTGG
1 CATATATACTGCCTCTGGATTTTGATTCTGATTGG
2836 C
1 C
2837 TAGTGTTCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.44
Consensus pattern (35 bp):
CATATATACTGCCTCTGGATTTTGATTCTGATTGG
Found at i:10477 original size:19 final size:21
Alignment explanation
Indices: 10437--10479 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
10427 AGTTTTTAAG
*
10437 TAAAAATGTAATATATATAAA
1 TAAAAATATAATATATATAAA
10458 TAAAAATATAATAT-TA-AAA
1 TAAAAATATAATATATATAAA
10477 TAA
1 TAA
10480 TTAATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 13 0.62
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
TAAAAATATAATATATATAAA
Found at i:10682 original size:18 final size:18
Alignment explanation
Indices: 10659--10706 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
10649 CTAGGATTTA
*
10659 TTTTTAAAGGATATGTAT
1 TTTTTAAAGGATATGTAG
10677 TTTTTAAAGGAT-T-TAG
1 TTTTTAAAGGATATGTAG
10693 TTTTT-AAGGATATG
1 TTTTTAAAGGATATG
10707 ATATATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.22
16 8 0.30
17 1 0.04
18 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (18 bp):
TTTTTAAAGGATATGTAG
Found at i:10701 original size:15 final size:15
Alignment explanation
Indices: 10651--10703 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 15
10641 TTGCATCCCT
10651 AGGATTTATTTTTAA
1 AGGATTTATTTTTAA
10666 AGGATATGTATTTTTTAA
1 AGGAT-T-TA-TTTTTAA
10684 AGGATTTAGTTTTT-A
1 AGGATTTA-TTTTTAA
10699 AGGAT
1 AGGAT
10704 ATGATATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 11 0.32
16 8 0.24
17 3 0.09
18 12 0.35
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (15 bp):
AGGATTTATTTTTAA
Found at i:12486 original size:11 final size:12
Alignment explanation
Indices: 12462--12495 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
12452 ACATCTAATT
12462 AACTAAACTCAA
1 AACTAAACTCAA
12474 AACTAAA-TCAA
1 AACTAAACTCAA
12485 AACTAAACTCA
1 AACTAAACTCA
12496 TCCAAGAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.18
Consensus pattern (12 bp):
AACTAAACTCAA
Found at i:12818 original size:29 final size:30
Alignment explanation
Indices: 12759--12837 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
12749 GCTAAATATC
*
12759 CAAAA-AATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA
*
12789 CAAAATAATTCCTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGGA
* *
12818 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
12838 CAAAAATGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 24 0.56
30 5 0.12
31 14 0.33
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.42
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGGA
Found at i:13029 original size:31 final size:31
Alignment explanation
Indices: 12986--13073 Score: 133
Period size: 31 Copynumber: 2.9 Consensus size: 31
12976 ACTAATATGT
*
12986 CCAAA-AAAAACATAAGGGATTTTTTTGTCT
1 CCAAAGAAAAACATAAGGGATTTTTTTGTCC
**
13016 TTAAAGAAAAACATAAGGGATTTTTTTGTCC
1 CCAAAGAAAAACATAAGGGATTTTTTTGTCC
*
13047 CCAAAGAAAAGCATAAGGGATTTTTTT
1 CCAAAGAAAAACATAAGGGATTTTTTT
13074 AGTATTTAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 3 0.06
31 48 0.94
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (31 bp):
CCAAAGAAAAACATAAGGGATTTTTTTGTCC
Found at i:13391 original size:155 final size:152
Alignment explanation
Indices: 13220--13499 Score: 402
Period size: 155 Copynumber: 1.8 Consensus size: 152
13210 TAATTCCCTA
* * **
13220 AAAATGTAAAATTAAAATAGTTATAAAAATATT-GAATTTAATTAAATAAAAATAGAATTTTTGG
1 AAAATGTAAAAATAAAATAGTTATAAAAATATTAG-ATTTAATTAAATAAAAATAGAATTCTTAA
* *
13284 T-GAAATAAAACTGTAAAAGTTTAAATAATGTCATTTAAGAAATATATTTTAAAAAAATTCTAAT
65 TAG-AATAAAACTGTAAAAGTTTAAACAATGACATTTAAGAAATATA-TTT-AAAAAATTCTAAT
13348 ATATCTAACTTTTTAATTAAATTAGT
127 ATATCTAACTTTTTAATTAAATTAGT
* * *
13374 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTGATTAAATAAAAATAGAGTTCTTAA
1 AAAAT-GTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAATTCTTAA
* *
13439 TAGAGTAAAATTGTAAAAGTTTAAACAATGACATTTAAGAAATATATTTAAAAAATTCTAA
65 TAGAATAAAACTGTAAAAGTTTAAACAATGACATTTAAGAAATATATTTAAAAAATTCTAA
13500 ATA
Statistics
Matches: 112, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
153 12 0.11
154 8 0.07
155 90 0.80
156 2 0.02
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (152 bp):
AAAATGTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAATTCTTAAT
AGAATAAAACTGTAAAAGTTTAAACAATGACATTTAAGAAATATATTTAAAAAATTCTAATATAT
CTAACTTTTTAATTAAATTAGT
Done.