Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017307.1 Corchorus olitorius cultivar O-4 contig17340, 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: 14747
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:3421 original size:263 final size:261
Alignment explanation
Indices: 2723--3660 Score: 1633
Period size: 262 Copynumber: 3.6 Consensus size: 261
2713 CGTTTCGACA
*
2723 CATATATCTCCATATTGTTGGTTGTCCATAGGGAAGAAAAAAAAATCATTTAGCAAATATTGGTT
1 CATATATCTCCATATTGTTGGCTGTCCATAGGGAAG--AAAAAAATCATTTAGCAAATATTGGTT
2788 ACATACTCAACTAAATTAAAAGAAAAAATAATTTGCTATAAAGACATAAAAGAGAAAGAAAACGC
64 ACATACTCAACTAAATTAAAAGAAAAAATAATTTGCTATAAAGACATAAAAGAGAAAGAAAACGC
* *
2853 TTTCATCAAAAGAAAAGAATGCCAAACCTTAAGTTTAGTCATGATCCAAAGCTTTTTGGAAATGA
129 TTTCATCAAAAGAAAAGGATGCCAAACCTTGAGTTTAGTCATGATCCAAAGCTTTTTGGAAATGA
*
2918 TCTAGCACCATTTTTGATGCTCAATTGAGTATATGGACAATTCTCTGGTTTCCGTAATTATGAGC
194 TCTAGCACCATTTTTGATGCTCAATTGAGTATATGGACAATTCTCTGGTTTCCGTAATTGTGAGC
2983 AAC
259 AAC
2986 CATATATCTCCATATTGTTGGCTGTCCATAGGGAAGAAAAAAATCATTTAGCAAATATTGGTTAC
1 CATATATCTCCATATTGTTGGCTGTCCATAGGGAAGAAAAAAATCATTTAGCAAATATTGGTTAC
*
3051 ATACTCAACTAAATTAACTAGAAAAAATAATTTGCTATAAAGACATAAAAGAGAAAGAAAACGCT
66 ATACTCAACTAAATTAA-AAGAAAAAATAATTTGCTATAAAGACATAAAAGAGAAAGAAAACGCT
3116 TTCATCAAAAGAAAAGGATGCCAAACCTTGAGTTTAGTCATGATCCAAAGCTTTTTGGAAATGAT
130 TTCATCAAAAGAAAAGGATGCCAAACCTTGAGTTTAGTCATGATCCAAAGCTTTTTGGAAATGAT
* * * *
3181 CTAGCACTATTTTTAATGCTCAATTGAGTATGTGGATAATTCTCTGGTTTCCGTAATTGTGAGCA
195 CTAGCACCATTTTTGATGCTCAATTGAGTATATGGACAATTCTCTGGTTTCCGTAATTGTGAGCA
3246 AC
260 AC
*
3248 CATATATCTCCATATTGTTGGTTGTCCATAGGGAAGAAGAAAAATCATTTAGCAAATATTGGTTA
1 CATATATCTCCATATTGTTGGCTGTCCATAGGGAAGAA-AAAAATCATTTAGCAAATATTGGTTA
*
3313 CATACTCAACTAAATTAACAGAAAAAAATAATTTGCTATAAAGACATAAAAGAGAAAGAAAACGC
65 CATACTCAACTAAATTAAAAG-AAAAAATAATTTGCTATAAAGACATAAAAGAGAAAGAAAACGC
3378 TTTCATCAAAAGAAAAGGATGCCAAACCTTGAGTTTAGTCATGATCCAAAGCTTTTTGGAAATGA
129 TTTCATCAAAAGAAAAGGATGCCAAACCTTGAGTTTAGTCATGATCCAAAGCTTTTTGGAAATGA
* * * *
3443 TCCAACACCATTTTTGATGCTCAATTGAGTATCTGGACAATTCTCTGGTTTCTGTAATTGTGAGC
194 TCTAGCACCATTTTTGATGCTCAATTGAGTATATGGACAATTCTCTGGTTTCCGTAATTGTGAGC
3508 AAC
259 AAC
** *
3511 CATATATCTCCATATTGTTGGCTGTCCATAGCAAAGAAAAAAAACATTTAGCAAATATTGGTTAC
1 CATATATCTCCATATTGTTGGCTGTCCATAGGGAAGAAAAAAATCATTTAGCAAATATTGGTTAC
* *
3576 ATACTCAACTAAATTAAAAGAAAAAATAATTTGCTATAAAGACATAAATGAGAAAAGAAAAGGCT
66 ATACTCAACTAAATTAAAAGAAAAAATAATTTGCTATAAAGACATAAAAGAG-AAAGAAAACGCT
*
3641 ATCATCAAAAGAAAAGGATG
130 TTCATCAAAAGAAAAGGATG
3661 TTTGGCAGAA
Statistics
Matches: 645, Mismatches: 26, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
261 77 0.12
262 285 0.44
263 283 0.44
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.29
Consensus pattern (261 bp):
CATATATCTCCATATTGTTGGCTGTCCATAGGGAAGAAAAAAATCATTTAGCAAATATTGGTTAC
ATACTCAACTAAATTAAAAGAAAAAATAATTTGCTATAAAGACATAAAAGAGAAAGAAAACGCTT
TCATCAAAAGAAAAGGATGCCAAACCTTGAGTTTAGTCATGATCCAAAGCTTTTTGGAAATGATC
TAGCACCATTTTTGATGCTCAATTGAGTATATGGACAATTCTCTGGTTTCCGTAATTGTGAGCAA
C
Found at i:5130 original size:2 final size:2
Alignment explanation
Indices: 5123--5158 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
5113 TTGTTTTCAT
5123 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
5159 GTCTATACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6319 original size:194 final size:192
Alignment explanation
Indices: 5961--6321 Score: 469
Period size: 195 Copynumber: 1.9 Consensus size: 192
5951 TTTGCACAAA
* *
5961 AACTTCTTAACCCGTTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATCCTATAAGAAAA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGAAAGTGTATTGTATCCTATAAGAAAA
* * ** * ** *
6026 TTTATATAATACACCGTCAGTGGAGTTTAGCCGACTGCACGTGTGGGGTTTAACTTTAAGGGTTG
66 ATTATACAATACACCGTCAGTCAAGTTTAGCAGACTGCACGTGTCAGG--T-ACTTTAAGGGTTC
* *
6091 ACATGTGTGCCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATGTGTC
128 ACATGTGTCCCCTAAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATGTGTC
* *
6156 AACTTCTTGACCCGCTTATGGAGTCCAAAATTTATACTGAAAGTGTATTGTATAATAATCCTATA
1 AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGAAAGTGTATTG-----T-ATCCTATA
* *
6221 AGAAAAATTATACAATAC-CCGTTAGTCAATTTTAGCAGACTGCACGTG-CAGG-A-TTTAAGGG
60 AGAAAAATTATACAATACACCGTCAGTCAAGTTTAGCAGACTGCACGTGTCAGGTACTTTAAGGG
6282 TTCACATGTGTCCCCTAAGGGAATATGTATTAATATTAAA
125 TTCACATGTGTCCCCTAAGGGAATATGTATTAATATTAAA
6322 CAAGTTGATC
Statistics
Matches: 144, Mismatches: 16, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
194 45 0.31
195 47 0.33
199 2 0.01
200 26 0.18
201 24 0.17
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (192 bp):
AACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGAAAGTGTATTGTATCCTATAAGAAAA
ATTATACAATACACCGTCAGTCAAGTTTAGCAGACTGCACGTGTCAGGTACTTTAAGGGTTCACA
TGTGTCCCCTAAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATGTGTC
Found at i:7629 original size:200 final size:200
Alignment explanation
Indices: 7209--8106 Score: 1191
Period size: 200 Copynumber: 4.5 Consensus size: 200
7199 ATTTAGTATA
* * * *
7209 TATATTTAATTAATTATGAAATGGGGTATGTGTCAACTTCATAACCCACTTATGAAGTCCAAAAT
1 TATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAAT
** * * * * ** *
7274 TTATGCTGGCAGTGTATTGTATAAT-AATCTTATAAAAAAACTTATGCAATACATTGTTAGTGGA
66 TTACACTGACAGTGTATTGTATAATAAATCCTATAAAAAAAATTATACAATACACCGTCAGTGGA
* * * *
7338 GTTTAACAGACTGCATGTGCGGGGTTTAAGGGTTGACATGTATCCCCTTAGGGAATATGTATTAA
131 GTTTAGCAGACTGCATGCGCAGGGCTTAAGGGTTGACATGTATCCCCTTAGGGAATATGTATTAA
**
7403 TATCA
196 TATTT
* *
7408 AATATTTAATTAATTATGAAAT-GTAGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAA
1 TATATTTAATTAATTATGAAATAG-GGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAA
*
7472 TTTACACTGACAGTGTATTGTATAATAATATCATATAAAAAAAATTATACAATACACCGTCAGTG
65 TTTACACTGACAGTGTATTGTATAATAA-ATCCTATAAAAAAAATTATACAATACACCGTCAGTG
* * *
7537 GAGTTTAGCAGACTGCATGCGCA-GGCTTAAGGATTGACATGTGTCCCCTTAGGGAATATGTACT
129 GAGTTTAGCAGACTGCATGCGCAGGGCTTAAGGGTTGACATGTATCCCCTTAGGGAATATGTATT
7601 AATATTT
194 AATATTT
*
7608 TATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTTCAAAAT
1 TATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAAT
* * * * * * *
7673 TTACACTAACAGTGTATTGTATAA-CAATCCTATCAAAATAAATTATATAACACACAGTCAGTGC
66 TTACACTGACAGTGTATTGTATAATAAATCCTAT-AAAAAAAATTATACAATACACCGTCAGTGG
* ** *
7737 AGTTTAGCATACTGCAAACGCAGGGCTTAAGGGTTGACATATATCCCCTTAGGGAATATGTATTA
130 AGTTTAGCAGACTGCATGCGCAGGGCTTAAGGGTTGACATGTATCCCCTTAGGGAATATGTATTA
7802 ATATTT
195 ATATTT
* *
7808 TATATTTAATTAATTATGAAATAGAGTATGTGTCAACTTCTTAACCCGCTTATGGAGTTCAAAAT
1 TATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAAT
*
7873 TTACACTGACAGTGTATTGTATAA-CAATCCTAT-AAAAAAATTATACAATACACCGTCAGTGGA
66 TTACACTGACAGTGTATTGTATAATAAATCCTATAAAAAAAATTATACAATACACCGTCAGTGGA
* * * ** *
7936 GTTTAGCAGACTGCACGTGCATGATTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAA
131 GTTTAGCAGACTGCATGCGCAGGGCTTAAGGGTTGACATGTATCCCCTTAGGGAATATGTATTAA
8001 TATCAAATAT
196 TAT----T-T
* * *
8011 TAATATCTAATTAATTATGAGATAGGGTATGTGTC-ACTTCTTAACCCGTTTATGGAGTCCAAAA
1 T-ATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAA
* * *
8075 TTTACATTGACGGTATATTGTATAAT-AATCCT
65 TTTACACTGACAGTGTATTGTATAATAAATCCT
8107 TATTATAAAG
Statistics
Matches: 621, Mismatches: 65, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
198 91 0.15
199 125 0.20
200 266 0.43
201 51 0.08
202 1 0.00
203 57 0.09
204 30 0.05
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (200 bp):
TATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAAT
TTACACTGACAGTGTATTGTATAATAAATCCTATAAAAAAAATTATACAATACACCGTCAGTGGA
GTTTAGCAGACTGCATGCGCAGGGCTTAAGGGTTGACATGTATCCCCTTAGGGAATATGTATTAA
TATTT
Found at i:8467 original size:16 final size:16
Alignment explanation
Indices: 8446--8477 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8436 TTCTACATAT
8446 AATAAAGATTTAGTAA
1 AATAAAGATTTAGTAA
*
8462 AATAAATATTTAGTAA
1 AATAAAGATTTAGTAA
8478 TATTTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (16 bp):
AATAAAGATTTAGTAA
Found at i:10088 original size:2 final size:2
Alignment explanation
Indices: 9987--10072 Score: 76
Period size: 2 Copynumber: 46.0 Consensus size: 2
9977 GACGTTTAGT
*
9987 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
10027 TA TA TA -A TA -A TA AA T- TA TA AA TG CA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10066 -A TA TA TA
1 TA TA TA TA
10073 ATTAAAAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
1 6 0.09
2 62 0.91
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Done.