Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019504.1 Corchorus olitorius cultivar O-4 contig19537, 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: 26712
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Found at i:4027 original size:54 final size:54
Alignment explanation
Indices: 3963--4107 Score: 191
Period size: 54 Copynumber: 2.7 Consensus size: 54
3953 GTACAGGTGT
* * *
3963 TTAAAATGACCCAATGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAACAGATC
1 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAACAGATC
***
4017 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAGTTGATC
1 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAACAGATC
* * * *
4071 TTAAGTTGACCTAGTGCGGTCATTTCAAAGAAGTTTT
1 TTAAGATGACCCAGTGTGGTC-TTTCATAGAAGTTTT
4108 TATGATCAGA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 66 0.82
55 14 0.17
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (54 bp):
TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAACAGATC
Found at i:4132 original size:35 final size:34
Alignment explanation
Indices: 4090--4893 Score: 891
Period size: 35 Copynumber: 22.5 Consensus size: 34
4080 CCTAGTGCGG
4090 TCATTTCAAAGAAGTTTTTATGATCAGAGTTGATC
1 TCATTTC-AAGAAGTTTTTATGATCAGAGTTGATC
* *
4125 TCGTTTCAAGAAGTTTTCGTATGATCAGAGTTAATC
1 TCATTTCAAGAAGTTTT--TATGATCAGAGTTGATC
*
4161 TCATTTCAATAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTTATGATCAGAGTTGATC
*
4196 TCATTTCAATAAGTTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG--TTTTTATGATCAGAGTTGATC
*
4232 TCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTTATGATCAGAGTTGATC
* *
4267 TCATTTCCAAGAAGTTTTCGATGATTAGAGTTGATC
1 TCATTT-CAAGAAGTTTT-TATGATCAGAGTTGATC
*
4303 TCATTTCAATAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTTATGATCAGAGTTGATC
* *
4338 TCATTTCCATAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTTATGATCAGAGTTGATC
* *
4373 TCCTTTGAAGAAGTTTTCGT-TGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTT--TATGATCAGAGTTGATC
* * *
4408 CCGTTTCAAGAAGTTTTTTATGATCAAAGTTGATC
1 TCATTTCAAGAAG-TTTTTATGATCAGAGTTGATC
*
4443 TCATTTCCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTT-CAAGAAGTTTT-TATGATCAGAGTTGATC
*
4479 TCATTTCAATAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTTATGATCAGAGTTGATC
* *
4514 TCATTTCCATAAGCTTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG---TTTTTATGATCAGAGTTGATC
*
4551 TCCTTTCAAGAAGTTTTCGT-TGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTT--TATGATCAGAGTTGATC
*
4586 TCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTTATGATCAGAGTTGATC
* *
4621 TCCTTTCAAGAAGTTTTCGT-TGAACAGAGTTGATC
1 TCATTTCAAGAAGTTTT--TATGATCAGAGTTGATC
* *
4656 TCCTTTCAAGAAGTTTTCGT-TGATCAGAGTTAATC
1 TCATTTCAAGAAGTTTT--TATGATCAGAGTTGATC
* *
4691 TCGTTTCAAGAAGTTTTTTATGATCAGAGTTAATC
1 TCATTTCAAGAAG-TTTTTATGATCAGAGTTGATC
* *
4726 TCCTTTCAAGAAGTTTTCGT-TGATCAGAGATGATC
1 TCATTTCAAGAAGTTTT--TATGATCAGAGTTGATC
4761 TCATTTCAAGAAGTGTTTTTTTTTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAA--G---------TTTTTATGATCAGAGTTGATC
*
4806 TCATTTCAAGAAGTTTTTTATGATTAGAGTTGATC
1 TCATTTCAAGAAG-TTTTTATGATCAGAGTTGATC
*
4841 TCGTTTCAAGAAGTTTTCGT-TGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTT--TATGATCAGAGTTGATC
4876 TCATTTCAAGAAGTTTTT
1 TCATTTCAAGAAGTTTTT
4894 TTTATGATCA
Statistics
Matches: 682, Mismatches: 47, Indels: 82
0.84 0.06 0.10
Matches are distributed among these distances:
33 1 0.00
34 33 0.05
35 438 0.64
36 141 0.21
37 37 0.05
43 1 0.00
44 1 0.00
45 26 0.04
46 4 0.01
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (34 bp):
TCATTTCAAGAAGTTTTTATGATCAGAGTTGATC
Found at i:4180 original size:71 final size:71
Alignment explanation
Indices: 4090--4903 Score: 1004
Period size: 70 Copynumber: 11.4 Consensus size: 71
4080 CCTAGTGCGG
* *
4090 TCATTTCAAAGAAG-TTTTTATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGTATGATCAGA
1 TCATTTC-AAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGA
*
4154 GTTAATC
65 GTTGATC
* * *
4161 TCATTTCAATAAGTTTTTTATGATCAGAGTTGATCTCATTTCAATAAGTTTTTTTATGATCAGAG
1 TCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAG
4226 TTGATC
66 TTGATC
* * *
4232 TCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCCAAGAAGTTTTC-GATGATTAGA
1 TCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTT-CAAGAAGTTTTCTTATGATCAGA
4296 GTTGATC
65 GTTGATC
* * *
4303 TCATTTCAATAAGTTTTTTATGATCAGAGTTGATCTCATTTCCATAAGTTTT-TTATGATCAGAG
1 TCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAG
4367 TTGATC
66 TTGATC
* * * * * *
4373 TCCTTTGAAGAAGTTTTCGT-TGATCAGAGTTGATCCCGTTTCAAGAAGTTTT-TTATGATCAAA
1 TCATTTCAAGAAGTTTT-TTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGA
4436 GTTGATC
65 GTTGATC
** *
4443 TCATTTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAATAAGTTTT-TTATGATCAGA
1 TCATTT-CAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGA
4507 GTTGATC
65 GTTGATC
* * * *
4514 TCATTTCCATAAGCTTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGT-TGATCAG
1 TCATTTCAAGAAG--TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAG
4578 AGTTGATC
64 AGTTGATC
* * * *
4586 TCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGT-TGAACAGAG
1 TCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAG
4650 TTGATC
66 TTGATC
* * * *
4656 TCCTTTCAAGAAGTTTTCGT-TGATCAGAGTTAATCTCGTTTCAAGAAGTTTT-TTATGATCAGA
1 TCATTTCAAGAAGTTTT-TTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGA
*
4719 GTTAATC
65 GTTGATC
* * * *
4726 TCCTTTCAAGAAGTTTTCGT-TGATCAGAGATGATCTCATTTCAAGAAGTGTTTTTTTTTTTTTT
1 TCATTTCAAGAAGTTTT-TTATGATCAGAGTTGATCTCATTTCAAGAA--G-------TTTTCTT
4790 ATGATCAGAGTTGATC
56 ATGATCAGAGTTGATC
* * *
4806 TCATTTCAAGAAGTTTTTTATGATTAGAGTTGATCTCGTTTCAAGAAGTTTTCGT-TGATCAGAG
1 TCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAG
4870 TTGATC
66 TTGATC
4876 TCATTTCAAGAAGTTTTTTTTATGATCA
1 TCATTTCAAGAAG--TTTTTTATGATCA
4904 TTGGGTTTTA
Statistics
Matches: 654, Mismatches: 65, Indels: 47
0.85 0.08 0.06
Matches are distributed among these distances:
69 1 0.00
70 285 0.44
71 221 0.34
72 83 0.13
73 1 0.00
78 1 0.00
79 5 0.01
80 57 0.09
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (71 bp):
TCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCTTATGATCAGAG
TTGATC
Found at i:4604 original size:283 final size:281
Alignment explanation
Indices: 4093--4903 Score: 1171
Period size: 283 Copynumber: 2.8 Consensus size: 281
4083 AGTGCGGTCA
*
4093 TTTCAAAGAAGTTTT--TATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGTATGATCAGAGT
1 TTTC-AAGAAGTTTTCGT-TGATCAGAGTTGATCTCGTTTCAAGAAGTTTT-TTATGATCAGAGT
* **
4156 TAATCTCATTTCAATAAGTTTTTTATGATCAGAGTTGATCTCATTTCAATAAGTTTTTTTATGAT
63 TAATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAATAAGTTTTTTTATGAT
*
4221 CAGAGTTGATCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCCAAGAAGTTTTC
128 CAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTT-CAAGAAGTTTTC
* * * * *
4286 GATGATTAGAGTTGATCTCATTTCAATAAGTTTTTTATGATCAGAGTTGATCTCATTTCCATAAG
192 GTTGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
* *
4351 TTTT-TTATGATCAGAGTTGATCTCC
257 TTTTCGT-TGAACAGAGTTGATCTCC
* * * *
4376 TTTGAAGAAGTTTTCGTTGATCAGAGTTGATCCCGTTTCAAGAAGTTTTTTATGATCAAAGTTGA
1 TTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTAA
4441 TCTCATTTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAATAAG-TTTTTTATGATCA
66 TCTCATTT-CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAATAAGTTTTTTTATGATCA
* * *
4505 GAGTTGATCTCATTTCCATAAGCTTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCG
130 GAGTTGATCTCATTTCAAGAAG--TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCG
* *
4570 TTGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGT
193 TTGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGT
4635 TTTCGTTGAACAGAGTTGATCTCC
258 TTTCGTTGAACAGAGTTGATCTCC
*
4659 TTTCAAGAAGTTTTCGTTGATCAGAGTTAATCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTAA
1 TTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTAA
* * * *
4724 TCTCCTTTCAAGAAGTTTTCGTTGATCAGAGATGATCTCATTTCAAGAAGTGTTTTTTTTTTTTT
66 TCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAATAA--G-------TTTTTT
* *
4789 TATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATTAGAGTTGATCTCGTTTCAAGAAG
122 TATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAG
4854 TTTTCGTTGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTTATGATCA
187 TTTTCGTTGATCAGAGTTGATCTCATTTCAAGAAG--TTTTTTATGATCA
4904 TTGGGTTTTA
Statistics
Matches: 475, Mismatches: 35, Indels: 27
0.88 0.07 0.05
Matches are distributed among these distances:
282 101 0.21
283 231 0.49
284 30 0.06
290 67 0.14
292 46 0.10
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.43
Consensus pattern (281 bp):
TTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTAA
TCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAATAAGTTTTTTTATGATCAG
AGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
ATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTT
CGTTGAACAGAGTTGATCTCC
Found at i:4813 original size:80 final size:80
Alignment explanation
Indices: 4704--4854 Score: 232
Period size: 80 Copynumber: 1.9 Consensus size: 80
4694 TTTCAAGAAG
*
4704 TTTTTTATGATCAGAGTTAATCTCCTTTCAAGAAGTTTTCGT-TGATCAGAGATGATCTCATTTC
1 TTTTTTATGATCAGAGTTAATCTCATTTCAAGAAGTTTT-GTATGATCAGAGATGATCTCATTTC
4768 AAGAAGTGTTTTTTTT
65 AAGAAGTGTTTTTTTT
* * * * *
4784 TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATTAGAGTTGATCTCGTTTCA
1 TTTTTTATGATCAGAGTTAATCTCATTTCAAGAAGTTTTGTATGATCAGAGATGATCTCATTTCA
4849 AGAAGT
66 AGAAGT
4855 TTTCGTTGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
79 1 0.02
80 63 0.98
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (80 bp):
TTTTTTATGATCAGAGTTAATCTCATTTCAAGAAGTTTTGTATGATCAGAGATGATCTCATTTCA
AGAAGTGTTTTTTTT
Found at i:4840 original size:45 final size:44
Alignment explanation
Indices: 4744--4840 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 44
4734 AGAAGTTTTC
* ***
4744 GTTGATCAGAGATGATCTCATTTCAAGAAGTGTTTTTTTTTTTT
1 GTTGATCAGAGATGATCTCATTTCAAGAAGTGTTTTTTATTAGA
* *
4788 TTATGATCAGAGTTGATCTCATTTCAAGAAGT-TTTTTATGATTAGA
1 GT-TGATCAGAGATGATCTCATTTCAAGAAGTGTTTTT-T-ATTAGA
4834 GTTGATC
1 GTTGATC
4841 TCGTTTCAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
44 6 0.14
45 34 0.79
46 3 0.07
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.46
Consensus pattern (44 bp):
GTTGATCAGAGATGATCTCATTTCAAGAAGTGTTTTTTATTAGA
Found at i:4878 original size:115 final size:114
Alignment explanation
Indices: 4676--4896 Score: 379
Period size: 115 Copynumber: 1.9 Consensus size: 114
4666 AAGTTTTCGT
*
4676 TGATCAGAGTTAATCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTAATCTCCTTTCAAGAAGTT
1 TGATCAGAGTTAATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTAATCTCCTTTCAAGAAGTT
4741 TTCGTTGATCAGAGATGATCTCATTTCAAGAAGTGTTTTTTTTTTTTTTA
66 TTCGTTGATCAGAGATGATCTCATTTCAAGAAGT-TTTTTTTTTTTTTTA
* * * *
4791 TGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATTAGAGTTGATCTCGTTTCAAGAAGTT
1 TGATCAGAGTTAATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTAATCTCCTTTCAAGAAGTT
*
4856 TTCGTTGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTT
66 TTCGTTGATCAGAGATGATCTCATTTCAAGAAGTTTTTTTT
4897 ATGATCATTG
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
114 7 0.07
115 93 0.93
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.45
Consensus pattern (114 bp):
TGATCAGAGTTAATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTAATCTCCTTTCAAGAAGTT
TTCGTTGATCAGAGATGATCTCATTTCAAGAAGTTTTTTTTTTTTTTTA
Found at i:14736 original size:33 final size:30
Alignment explanation
Indices: 14679--14738 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 30
14669 TTTTAAAATA
14679 AAAATAAAAAACTAATTATAAATAATATAT
1 AAAATAAAAAACTAATTATAAATAATATAT
14709 AAAATAAAAATAACTAATTTATAAATAATA
1 AAAAT-AAAA-AACTAA-TTATAAATAATA
14739 ACTAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 5 0.19
31 4 0.15
32 6 0.22
33 12 0.44
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (30 bp):
AAAATAAAAAACTAATTATAAATAATATAT
Found at i:14738 original size:18 final size:17
Alignment explanation
Indices: 14688--14747 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
14678 AAAAATAAAA
14688 AACTAATTATAAATAAT
1 AACTAATTATAAATAAT
*
14705 ATA-TAA-AATAAA-AAT
1 A-ACTAATTATAAATAAT
14720 AACTAATTTATAAATAAT
1 AACTAA-TTATAAATAAT
14738 AACTAATTAT
1 AACTAATTAT
14748 TAATTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 1 0.03
15 7 0.19
16 5 0.14
17 13 0.36
18 10 0.28
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (17 bp):
AACTAATTATAAATAAT
Found at i:18375 original size:51 final size:50
Alignment explanation
Indices: 18274--18375 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
18264 GTTCTTCATA
* **
18274 TTTTTCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
18324 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
18375 T
1 T
18376 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 6 0.13
51 38 0.84
52 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Done.