Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023823.1 Corchorus olitorius cultivar O-4 contig23856, 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: 20604
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Found at i:1017 original size:14 final size:14
Alignment explanation
Indices: 992--1030 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
982 AATTTGTCAT
992 GAGAAA-TAAAAAA
1 GAGAAATTAAAAAA
*
1005 GATAAATTAAAAAA
1 GAGAAATTAAAAAA
*
1019 GAGAAATGAAAA
1 GAGAAATTAAAA
1031 TTTGTTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (14 bp):
GAGAAATTAAAAAA
Found at i:12778 original size:43 final size:41
Alignment explanation
Indices: 12705--13232 Score: 396
Period size: 42 Copynumber: 13.0 Consensus size: 41
12695 CAAGTTTTCA
* *
12705 AAGTATTTTTCAAAGAT-TTCAATTCAGGGAAAGATCCCA-CC
1 AAGT-TTTTTCAAAG-TCTTTAATTTAGGGAAAGATCCCATCC
*
12746 AGAGTATTTTTCAAAGTTTTTCAATTTAGGGAAAGATCCCA-CC
1 A-AGT-TTTTTCAAAGTCTTT-AATTTAGGGAAAGATCCCATCC
* * * *
12789 AAAGCATTTTTCAAAGTTTTTCAATTTAGGAAAAGATCTCATCCC
1 -AAG-TTTTTTCAAAGTCTTT-AATTTAGGGAAAGATCCCAT-CC
12834 GAAG-TTTTTCAGAAGT-TTTAATTTAGGGAAAGATCCCATCC
1 -AAGTTTTTTCA-AAGTCTTTAATTTAGGGAAAGATCCCATCC
* * *
12875 -AG--TCTTCAAAGTTTTTAATTTAGGGAAAGATCCCAT-T
1 AAGTTTTTTCAAAGTCTTTAATTTAGGGAAAGATCCCATCC
* * * *
12912 AAG--CTTTC-AAGAT-TTCTAA-TT-GGAAAAGGTCCCAT-T
1 AAGTTTTTTCAAAG-TCTT-TAATTTAGGGAAAGATCCCATCC
*
12948 AAGTTTGTTT--AAGTCTTTAGTTTAGGGAAAGATCCCATCC
1 AAGTTT-TTTCAAAGTCTTTAATTTAGGGAAAGATCCCATCC
*
12988 -AGTTTCTTTTTAAAGTCTTTAATTTAGGGAAAGATCCCATCC
1 AAG-TT-TTTTCAAAGTCTTTAATTTAGGGAAAGATCCCATCC
*
13030 -AGTTTCTTTTTAAAGTCTTTAATTTAGGGAAAGATCCCATCC
1 AAG-TT-TTTTCAAAGTCTTTAATTTAGGGAAAGATCCCATCC
* *
13072 -AGTTTCTTTTTAAAGTCTTTAATTTA-GGAAAGGATCCCATTC
1 AAG-TT-TTTTCAAAGTCTTTAATTTAGGGAAA-GATCCCATCC
* *
13114 -AG-TTTTTCAGAAG-CTTTAATTCAGGGAAAGATCCCATTC
1 AAGTTTTTTCA-AAGTCTTTAATTTAGGGAAAGATCCCATCC
*
13153 -AGTTTTCTTCGAAG-CTTTAATTTAGGGAAAGATCCCAT-C
1 AAGTTTT-TTCAAAGTCTTTAATTTAGGGAAAGATCCCATCC
*
13192 TAGTCTTTTTTCAAAGT-TTTCAA-TTAGGGGAAAGATCCCAT
1 AAG--TTTTTTCAAAGTCTTT-AATTTA-GGGAAAGATCCCAT
13233 TAAAGATTTT
Statistics
Matches: 427, Mismatches: 26, Indels: 67
0.82 0.05 0.13
Matches are distributed among these distances:
36 16 0.04
37 14 0.03
38 44 0.10
39 46 0.11
40 45 0.11
41 25 0.06
42 162 0.38
43 65 0.15
44 5 0.01
45 5 0.01
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (41 bp):
AAGTTTTTTCAAAGTCTTTAATTTAGGGAAAGATCCCATCC
Found at i:12800 original size:85 final size:85
Alignment explanation
Indices: 12703--12871 Score: 220
Period size: 85 Copynumber: 2.0 Consensus size: 85
12693 ATCAAGTTTT
* *
12703 CAAAGTATTTTTCAAAG-ATTTCAATTCAGGGAAAGATCCCA-CCAG-AGTATTTTTCA-AAGTT
1 CAAAGCATTTTTCAAAGTATTTCAATTCAGGAAAAGATCCCATCCAGAAG--TTTTTCAGAAG-T
12764 TTTCAATTTAGGGAAAGATCCCAC
63 TTT-AATTTAGGGAAAGATCCCAC
* * * *
12788 CAAAGCATTTTTCAAAGTTTTTCAATTTAGGAAAAGATCTCATCCCGAAGTTTTTCAGAAGTTTT
1 CAAAGCATTTTTCAAAGTATTTCAATTCAGGAAAAGATCCCATCCAGAAGTTTTTCAGAAGTTTT
12853 AATTTAGGGAAAGATCCCA
66 AATTTAGGGAAAGATCCCA
12872 TCCAGTCTTC
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
85 35 0.47
86 31 0.42
87 6 0.08
88 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (85 bp):
CAAAGCATTTTTCAAAGTATTTCAATTCAGGAAAAGATCCCATCCAGAAGTTTTTCAGAAGTTTT
AATTTAGGGAAAGATCCCAC
Found at i:13046 original size:84 final size:82
Alignment explanation
Indices: 12710--13232 Score: 410
Period size: 81 Copynumber: 6.4 Consensus size: 82
12700 TTTCAAAGTA
* * ** * *
12710 TTTTTCAAAGAT-TTCAATTCAGGGAAAGATCCCA-CCAGAGTATTTTTCAAAGTTTTTCAATTT
1 TTTTTCAAAG-TCTTTAATTTAGGGAAAGATCCCATCCAGTTTCTTTTT-AAAGTCTTT-AATTT
*
12773 AGGGAAAGATCCCA-CCAAAGCA
63 AGGGAAAGATCCCATCC--AG-T
* * * * ** *
12795 TTTTTCAAAGTTTTTCAATTTAGGAAAAGATCTCATCCCGAAGT-TTTTCAGAAGT-TTTAATTT
1 TTTTTCAAAGTCTTT-AATTTAGGGAAAGATCCCATCCAG-TTTCTTTTTA-AAGTCTTTAATTT
12858 AGGGAAAGATCCCATCCAG-
63 AGGGAAAGATCCCATCCAGT
* * ** *
12877 -TCTTCAAAGTTTTTAATTTAGGGAAAGATCCCATTAAG---C--TTTCAAGAT-TTCTAA-TT-
1 TTTTTCAAAGTCTTTAATTTAGGGAAAGATCCCATCCAGTTTCTTTTTAAAG-TCTT-TAATTTA
* * **
12933 GGAAAAGGTCCCATTAAGT
64 GGGAAAGATCCCATCCAGT
*
12952 TTGTTT--AAGTCTTTAGTTTAGGGAAAGATCCCATCCAGTTTCTTTTTAAAGTCTTTAATTTAG
1 TT-TTTCAAAGTCTTTAATTTAGGGAAAGATCCCATCCAGTTTCTTTTTAAAGTCTTTAATTTAG
13015 GGAAAGATCCCATCCAGTT
65 GGAAAGATCCCATCCAG-T
*
13034 TCTTTTTAAAGTCTTTAATTTAGGGAAAGATCCCATCCAGTTTCTTTTTAAAGTCTTTAATTTA-
1 T-TTTTCAAAGTCTTTAATTTAGGGAAAGATCCCATCCAGTTTCTTTTTAAAGTCTTTAATTTAG
*
13098 GGAAAGGATCCCATTCAG-
65 GGAAA-GATCCCATCCAGT
* * * **
13116 TTTTTCAGAAG-CTTTAATTCAGGGAAAGATCCCATTCAGTTT-TCTTCGAAG-CTTTAATTTAG
1 TTTTTCA-AAGTCTTTAATTTAGGGAAAGATCCCATCCAGTTTCTTTTTAAAGTCTTTAATTTAG
*
13178 GGAAAGATCCCATCTAGTCT
65 GGAAAGATCCCATCCAG--T
13198 TTTTTCAAAGT-TTTCAA-TTAGGGGAAAGATCCCAT
1 TTTTTCAAAGTCTTT-AATTTA-GGGAAAGATCCCAT
13233 TAAAGATTTT
Statistics
Matches: 366, Mismatches: 39, Indels: 69
0.77 0.08 0.15
Matches are distributed among these distances:
74 17 0.05
75 35 0.10
76 4 0.01
77 2 0.01
78 1 0.00
79 24 0.07
80 40 0.11
81 69 0.19
82 32 0.09
83 6 0.02
84 69 0.19
85 31 0.08
86 22 0.06
87 11 0.03
88 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (82 bp):
TTTTTCAAAGTCTTTAATTTAGGGAAAGATCCCATCCAGTTTCTTTTTAAAGTCTTTAATTTAGG
GAAAGATCCCATCCAGT
Found at i:13208 original size:121 final size:125
Alignment explanation
Indices: 12711--13233 Score: 370
Period size: 123 Copynumber: 4.3 Consensus size: 125
12701 TTCAAAGTAT
* * * * *
12711 TTTTCAAAGAT-TTCAATTCAGGGAAAGATCCCA-CCAGAGTAT-TTTTCAAAGTTTTTCAATTT
1 TTTTCAAAG-TCTTTAATTTAGGGAAAGATCCCATTC--AGT-TCTTTTCAAAGTCTTT-AATTC
* * * * *
12773 AGGGAAAGATCCCA-CCAAAGCATT-T-TTCAAAGTTTTTCAATTTAGGAAAAGATCTCATCCCG
61 AGGGAAAGATCCCATCC--AG-TTTCTCTTCAAAGTCTTT-AATTTAGGGAAAGATCCCATCCAG
**
12835 AAGT-
122 -TTTC
* * *
12839 TTTTCAGAAGT-TTTAATTTAGGGAAAGATCCCATCCAG-TC--TTCAAAGTTTTTAATTTAGGG
1 TTTTCA-AAGTCTTTAATTTAGGGAAAGATCCCATTCAGTTCTTTTCAAAGTCTTTAATTCAGGG
** * * **
12900 AAAGATCCCATTAAG---CT-TTC-AAGAT-TTCTAA-TT-GGAAAAGGTCCCATTAAGTTT-
65 AAAGATCCCATCCAGTTTCTCTTCAAAG-TCTT-TAATTTAGGGAAAGATCCCATCCAGTTTC
* * * * *
12954 GTTT--AAGTCTTTAGTTTAGGGAAAGATCCCATCCAGTTTCTTTTTAAAGTCTTTAATTTAGGG
1 TTTTCAAAGTCTTTAATTTAGGGAAAGATCCCATTCAG-TTCTTTTCAAAGTCTTTAATTCAGGG
* *
13017 AAAGATCCCATCCAGTTTCTTTTTAAAGTCTTTAATTTAGGGAAAGATCCCATCCAGTTTC
65 AAAGATCCCATCCAGTTTCTCTTCAAAGTCTTTAATTTAGGGAAAGATCCCATCCAGTTTC
*
13078 TTTTTAAAGTCTTTAATTTA-GGAAAGGATCCCATTCAG-T-TTTTCAGAAG-CTTTAATTCAGG
1 TTTTCAAAGTCTTTAATTTAGGGAAA-GATCCCATTCAGTTCTTTTCA-AAGTCTTTAATTCAGG
* * *
13139 GAAAGATCCCATTCAGTTT-TCTTCGAAG-CTTTAATTTAGGGAAAGATCCCATCTAGTCTT-
64 GAAAGATCCCATCCAGTTTCTCTTCAAAGTCTTTAATTTAGGGAAAGATCCCATCCAGT-TTC
13199 TTTTCAAAGT-TTTCAA-TTAGGGGAAAGATCCCATT
1 TTTTCAAAGTCTTT-AATTTA-GGGAAAGATCCCATT
13234 AAAGATTTTA
Statistics
Matches: 333, Mismatches: 33, Indels: 65
0.77 0.08 0.15
Matches are distributed among these distances:
112 4 0.01
113 26 0.08
115 6 0.02
116 13 0.04
117 34 0.10
118 7 0.02
119 6 0.02
120 8 0.02
121 54 0.16
122 22 0.07
123 70 0.21
124 19 0.06
125 6 0.02
126 24 0.07
127 2 0.01
128 27 0.08
129 5 0.02
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (125 bp):
TTTTCAAAGTCTTTAATTTAGGGAAAGATCCCATTCAGTTCTTTTCAAAGTCTTTAATTCAGGGA
AAGATCCCATCCAGTTTCTCTTCAAAGTCTTTAATTTAGGGAAAGATCCCATCCAGTTTC
Found at i:14161 original size:2 final size:2
Alignment explanation
Indices: 14156--14188 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14146 TTATTTTTTC
14156 TA TA TA TA 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 TA TA TA TA T
14189 CTTGCTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18627 original size:37 final size:38
Alignment explanation
Indices: 18559--18637 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 38
18549 TTAGAGTTGC
*
18559 CATTTAAGTAAACCTACTTAGGTCTACGTTTAGAATCT
1 CATTTAAGGAAACCTACTTAGGTCTACGTTTAGAATCT
* *
18597 CATTTAAGGAAACCT-GTTAGGTCTATGTTTAGAATCT
1 CATTTAAGGAAACCTACTTAGGTCTACGTTTAGAATCT
18634 CATT
1 CATT
18638 AGAATTTCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 24 0.63
38 14 0.37
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (38 bp):
CATTTAAGGAAACCTACTTAGGTCTACGTTTAGAATCT
Found at i:18784 original size:39 final size:39
Alignment explanation
Indices: 18694--18786 Score: 150
Period size: 39 Copynumber: 2.4 Consensus size: 39
18684 TCGTTTGATT
* *
18694 AAACCTACTTAGATCCTTGTTTAGAATTTTCGTTTAAGC
1 AAACCTACTTAGGTCCTTGTTTAGAATTTCCGTTTAAGC
*
18733 AAACCTGCTTAGGTCCTTGTTTAGAATTTCCGTTTAAGC
1 AAACCTACTTAGGTCCTTGTTTAGAATTTCCGTTTAAGC
*
18772 AAACCCACTTAGGTC
1 AAACCTACTTAGGTC
18787 TCTGTTCCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (39 bp):
AAACCTACTTAGGTCCTTGTTTAGAATTTCCGTTTAAGC
Found at i:19195 original size:38 final size:39
Alignment explanation
Indices: 18791--19282 Score: 245
Period size: 39 Copynumber: 12.9 Consensus size: 39
18781 TAGGTCTCTG
* * *
18791 TTCCGTTTAAGTAAACCTGTTTAGGACTTCTGCTTT-GAG-
1 TTCCATTTAAGTAAACCTGCTTAGGTC-TCTG-TTTAGAGT
* *
18830 TT-CATTTGAGTAAACCTGCTTAGGTCT-TCGTTTATAAGT
1 TTCCATTTAAGTAAACCTGCTTAGGTCTCT-GTTTA-GAGT
* * *
18869 TT-CGTTTAA-TCAAACCCGCTTAGGT-TCTTGTTTAGAAT
1 TTCCATTTAAGT-AAACCTGCTTAGGTCTC-TGTTTAGAGT
* ** * * * * *
18907 TCCCGCTTAAGTGAACTTGCTTAAGTCTATGCTTAGA-T
1 TTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGAGT
* * * * *
18945 TTTCGTTCAA-TCAAACCTGCTTAGGTC-CATTTTTATAGT
1 TTCCATTTAAGT-AAACCTGCTTAGGTCTC-TGTTTAGAGT
* * * * * * * *
18984 CTCGC-CTT-AGAAAAATCTGATCATGTCTCTGCTTAGAG-
1 TTC-CATTTAAG-TAAACCTGCTTAGGTCTCTGTTTAGAGT
* *
19022 TTCCATTTAAGAAAACCTGCTTAGGATCTCTGTCTAGAGT
1 TTCCATTTAAGTAAACCTGCTTAGG-TCTCTGTTTAGAGT
* * * * * *
19062 TT-CGTTTAAGGAAACCTGCTTAGGTATTTATTTAAAG-
1 TTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGAGT
* *
19099 TTCCAATT--G--AATCTGCTTAGGTCTCTGTTTAGAGT
1 TTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGAGT
* * * *
19134 TTCCAGTTAAGTAAACCTACTTAGGTCTCCGTTTAGAAT
1 TTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGAGT
** * *
19173 TT-CATTCGAGTAAACTTGCTTAGGTCTCTGCTTAGAGT
1 TTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGAGT
* * * **
19211 TGCCATTTGAG-AAAGCTTGCTTAGGAATC-GTTTAGAGT
1 TTCCATTTAAGTAAA-CCTGCTTAGGTCTCTGTTTAGAGT
*
19249 TTCCATTTAAGTAAACCTACTTAGGTCTCTGTTT
1 TTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTT
19283 CGAACTTCCG
Statistics
Matches: 335, Mismatches: 87, Indels: 62
0.69 0.18 0.13
Matches are distributed among these distances:
34 20 0.06
35 7 0.02
36 5 0.01
37 7 0.02
38 136 0.41
39 153 0.46
40 7 0.02
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (39 bp):
TTCCATTTAAGTAAACCTGCTTAGGTCTCTGTTTAGAGT
Found at i:19262 original size:77 final size:77
Alignment explanation
Indices: 19111--19279 Score: 189
Period size: 77 Copynumber: 2.2 Consensus size: 77
19101 CCAATTGAAT
* * **
19111 CTGCTTAGGTCTCTGTTTAGAGTTTCCAGTTAAGTAAACCTACTTAGGTCTCCGTTTAGAATTTC
1 CTGCTTAGGTCTCTGCTTAGAGTTGCCAGTTAAGTAAACCTACTTAGGAATCCGTTTAGAATTTC
*
19176 ATTCGAGTAAAC
66 ATTCAAGTAAAC
* * * * * *
19188 TTGCTTAGGTCTCTGCTTAGAGTTGCCATTTGAG-AAAGCTTGCTTAGGAAT-CGTTTAGAGTTT
1 CTGCTTAGGTCTCTGCTTAGAGTTGCCAGTTAAGTAAA-CCTACTTAGGAATCCGTTTAGAATTT
*
19251 CCATTTAAGTAAAC
65 -CATTCAAGTAAAC
*
19265 CTACTTAGGTCTCTG
1 CTGCTTAGGTCTCTG
19280 TTTCGAACTT
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
76 14 0.18
77 62 0.82
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (77 bp):
CTGCTTAGGTCTCTGCTTAGAGTTGCCAGTTAAGTAAACCTACTTAGGAATCCGTTTAGAATTTC
ATTCAAGTAAAC
Found at i:19341 original size:64 final size:64
Alignment explanation
Indices: 19240--19360 Score: 143
Period size: 64 Copynumber: 1.9 Consensus size: 64
19230 CTTAGGAATC
* * * *
19240 GTTTAGAGTTTCCATTTAAGTAAACCTACTTAGGTCTCTGTTTCGAACTTCCGTTTAGGTCTCT
1 GTTTAGAGTTTCCATTCAAGTAAACCTACTTAAGTCTCTATTTAGAACTTCCGTTTAGGTCTCT
* * * ** * *
19304 GTTTAGAGTTTTCGTTCAAGTTAACCTGTTTAAGTCTCTATTTAGAATTTTCGTTTA
1 GTTTAGAGTTTCCATTCAAGTAAACCTACTTAAGTCTCTATTTAGAACTTCCGTTTA
19361 AGTGAACATG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
64 46 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (64 bp):
GTTTAGAGTTTCCATTCAAGTAAACCTACTTAAGTCTCTATTTAGAACTTCCGTTTAGGTCTCT
Found at i:19348 original size:39 final size:39
Alignment explanation
Indices: 19292--19393 Score: 134
Period size: 39 Copynumber: 2.6 Consensus size: 39
19282 TCGAACTTCC
* * *
19292 GTTTAGGTCTCTGTTTAGAGTTTTCGTTCAAGTTAACCT
1 GTTTAGGTCTCTATTTAGAGTTTTCGTTCAAGTGAACAT
* * *
19331 GTTTAAGTCTCTATTTAGAATTTTCGTTTAAGTGAACAT
1 GTTTAGGTCTCTATTTAGAGTTTTCGTTCAAGTGAACAT
19370 GTTTAGGTCTCTGA-TTAGAGTTTT
1 GTTTAGGTCTCT-ATTTAGAGTTTT
19394 GTTAAGAAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
39 53 0.98
40 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.47
Consensus pattern (39 bp):
GTTTAGGTCTCTATTTAGAGTTTTCGTTCAAGTGAACAT
Done.