Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016376.1 Corchorus olitorius cultivar O-4 contig16409, 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: 27800
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:136 original size:41 final size:41
Alignment explanation
Indices: 1--540 Score: 724
Period size: 41 Copynumber: 13.3 Consensus size: 41
* *
1 TTATTTAAATGTTTGGAGAGACAGCTCTCATCGATCAC-TT
1 TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
* *
41 TTAATTAAATGTTTGGAGAGAGAGCTCTCATCGGTCA-TTT
1 TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
* *
81 TTAATTAAATGTTTGGAGAGATAGCTCTCATCGGTCACGTT
1 TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
122 TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
1 TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
*
163 TTATTTAAATGTTTGGAGAGACAGCTCTCATCGGTCAC-TT
1 TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
* * *
203 TTAATTAAATGTTTGGAGAAATAGCTCTCATCGGTCACGTT
1 TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
* *
244 TTATTTAAATGTTTAGAGAGACAGCTCTCATCGGTCACTTAT
1 TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTT-T
*
286 TTAATTT-ATTGTTTGGAGAGATAGCTCTCATCGGTCAC--T
1 TT-ATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
* * ** *
325 TT-TTTAATTGTTTTGAGAGGCAGCTCTCATTGGTCACTTTTT
1 TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCAC--TTT
*
367 TTAATTAAATGTTTGGAGAGATAGCTCTCATCGGTCAC-TT
1 TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
* *
407 TAAATTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
1 TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
* *
448 TTATTTAAATGTTTGGAGAGACAGCTCTCATCAGTCACTTT
1 TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
* * *
489 TTATTTAAATGTTTGGAGAAACT-GCTCTCATCAGTCAGTTT
1 TTATTTAAATGTTTGGAGAGA-TAGCTCTCATCGGTCACTTT
530 TT-TTT-AATGTT
1 TTATTTAAATGTT
541 GGTGACTTTT
Statistics
Matches: 450, Mismatches: 37, Indels: 27
0.88 0.07 0.05
Matches are distributed among these distances:
37 3 0.01
38 27 0.06
39 9 0.02
40 151 0.34
41 193 0.43
42 34 0.08
43 33 0.07
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (41 bp):
TTATTTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTT
Found at i:149 original size:81 final size:82
Alignment explanation
Indices: 1--540 Score: 749
Period size: 81 Copynumber: 6.7 Consensus size: 82
* * *
1 TTATTTAAATGTTTGGAGAGACAGCTCTCATCGATCAC-TTTTAATTAAATGTTTGGAGAGAGAG
1 TTATTTAAATGTTTGGAGAGACAGCTCTCATCGGTCACTTTTTATTTAAATGTTTGGAGAGATAG
65 CTCTCATCGGTCA-TTT
66 CTCTCATCGGTCACTTT
* * *
81 TTAATTAAATGTTTGGAGAGATAGCTCTCATCGGTCACGTTTTATTTAAATGTTTGGAGAGATAG
1 TTATTTAAATGTTTGGAGAGACAGCTCTCATCGGTCACTTTTTATTTAAATGTTTGGAGAGATAG
146 CTCTCATCGGTCACTTT
66 CTCTCATCGGTCACTTT
* *
163 TTATTTAAATGTTTGGAGAGACAGCTCTCATCGGTCAC-TTTTAATTAAATGTTTGGAGAAATAG
1 TTATTTAAATGTTTGGAGAGACAGCTCTCATCGGTCACTTTTTATTTAAATGTTTGGAGAGATAG
*
227 CTCTCATCGGTCACGTT
66 CTCTCATCGGTCACTTT
* *
244 TTATTTAAATGTTTAGAGAGACAGCTCTCATCGGTCACTTATTTAATTT-ATTGTTTGGAGAGAT
1 TTATTTAAATGTTTGGAGAGACAGCTCTCATCGGTCACTT-TTT-ATTTAAATGTTTGGAGAGAT
308 AGCTCTCATCGGTCAC--T
64 AGCTCTCATCGGTCACTTT
* * * * *
325 TT-TTTAATTGTTTTGAGAGGCAGCTCTCATTGGTCACTTTTTTTAATTAAATGTTTGGAGAGAT
1 TTATTTAAATGTTTGGAGAGACAGCTCTCATCGGTCAC--TTTTTATTTAAATGTTTGGAGAGAT
389 AGCTCTCATCGGTCAC-TT
64 AGCTCTCATCGGTCACTTT
* * * *
407 TAAATTAAATGTTTGGAGAGATAGCTCTCATCGGTCACTTTTTATTTAAATGTTTGGAGAGACAG
1 TTATTTAAATGTTTGGAGAGACAGCTCTCATCGGTCACTTTTTATTTAAATGTTTGGAGAGATAG
*
472 CTCTCATCAGTCACTTT
66 CTCTCATCGGTCACTTT
* * * *
489 TTATTTAAATGTTTGGAGAAACTGCTCTCATCAGTCAGTTTTT-TTT-AATGTT
1 TTATTTAAATGTTTGGAGAGACAGCTCTCATCGGTCACTTTTTATTTAAATGTT
541 GGTGACTTTT
Statistics
Matches: 412, Mismatches: 37, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
80 75 0.18
81 191 0.46
82 82 0.20
83 61 0.15
84 3 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (82 bp):
TTATTTAAATGTTTGGAGAGACAGCTCTCATCGGTCACTTTTTATTTAAATGTTTGGAGAGATAG
CTCTCATCGGTCACTTT
Found at i:596 original size:38 final size:38
Alignment explanation
Indices: 545--620 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
535 AATGTTGGTG
* *
545 ACTTTTTTAATTGTTTGGAGAGATATCTCTCACCGGTC
1 ACTTTTTTAATTGTTTGGAGAGACATCTCCCACCGGTC
* *
583 ACTTTTTTAATTGTTTGGGGAGACATCTCCCATCGGTC
1 ACTTTTTTAATTGTTTGGAGAGACATCTCCCACCGGTC
621 TCCTAATTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (38 bp):
ACTTTTTTAATTGTTTGGAGAGACATCTCCCACCGGTC
Found at i:641 original size:50 final size:50
Alignment explanation
Indices: 585--842 Score: 385
Period size: 50 Copynumber: 5.1 Consensus size: 50
575 CACCGGTCAC
*
585 TTTTTTA-ATTGTTTGGGGAGACATCTCCCATCGGTCTCCTAATTACTAAA
1 TTTTTTAGA-TGTTTGGGGAGACAGCTCCCATCGGTCTCCTAATTACTAAA
* *
635 TTTTTTAGATGTTTGGAGAGACAGCTCCCATCGGTTTCCTAATTACTAAA
1 TTTTTTAGATGTTTGGGGAGACAGCTCCCATCGGTCTCCTAATTACTAAA
* *
685 TTTTTTATATGTTTAGGGAGACAGCTCCCATCGGTCTCCTAATTACTAAA
1 TTTTTTAGATGTTTGGGGAGACAGCTCCCATCGGTCTCCTAATTACTAAA
*
735 TTTTTTAGATGTTTGGGGAGACAGCTCCCAT-GATCTCCTAATTACTAAAA
1 TTTTTTAGATGTTTGGGGAGACAGCTCCCATCGGTCTCCTAATTACT-AAA
* ** *
785 TTTTTTAGATGTTTGGAGAGATGGCTCTCATCGGTCTCCTAATTACTAAA
1 TTTTTTAGATGTTTGGGGAGACAGCTCCCATCGGTCTCCTAATTACTAAA
835 CTTTTTTA
1 -TTTTTTA
843 AACATTTGAG
Statistics
Matches: 189, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
49 14 0.07
50 153 0.81
51 22 0.12
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (50 bp):
TTTTTTAGATGTTTGGGGAGACAGCTCCCATCGGTCTCCTAATTACTAAA
Found at i:1051 original size:2 final size:2
Alignment explanation
Indices: 1046--1083 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1036 AAAAAAAAAA
*
1046 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1084 GGAGGGTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10731 original size:2 final size:2
Alignment explanation
Indices: 10724--10748 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10714 CAGTGTATTG
10724 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10749 TATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12006 original size:31 final size:32
Alignment explanation
Indices: 11964--12039 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
11954 CTTTATCGAT
*
11964 TGGACTCAATTGATC-CAATCTTATGAGTAGA
1 TGGACTAAATTGATCTCAATCTTATGAGTAGA
* * *
11995 TGGATTAAATTGA-CTCAATCTTGTGAGTATA
1 TGGACTAAATTGATCTCAATCTTATGAGTAGA
12026 TGGACTAAATTGAT
1 TGGACTAAATTGAT
12040 TGATTTTTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 1 0.03
31 37 0.97
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.36
Consensus pattern (32 bp):
TGGACTAAATTGATCTCAATCTTATGAGTAGA
Found at i:23795 original size:3 final size:3
Alignment explanation
Indices: 23787--23815 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
23777 AACTAAAAGC
23787 TCT TCT TCT TCT TCT TC- TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
23816 CACACTGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:27659 original size:43 final size:43
Alignment explanation
Indices: 27598--27691 Score: 179
Period size: 43 Copynumber: 2.2 Consensus size: 43
27588 GCTGATCACA
27598 ATCCAAAATTGGACTTGACGATTTTGATTCTATATTGCTTCCG
1 ATCCAAAATTGGACTTGACGATTTTGATTCTATATTGCTTCCG
27641 ATCCAAAATTGGACTTGACGATTTTGATTCTATATTGCTTCCG
1 ATCCAAAATTGGACTTGACGATTTTGATTCTATATTGCTTCCG
27684 ATTCCAAA
1 A-TCCAAA
27692 TACAAAGAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 44 0.88
44 6 0.12
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (43 bp):
ATCCAAAATTGGACTTGACGATTTTGATTCTATATTGCTTCCG
Done.