Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014514.1 Corchorus olitorius cultivar O-4 contig14547, 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: 19613
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1730 original size:199 final size:199
Alignment explanation
Indices: 1362--2491 Score: 1752
Period size: 199 Copynumber: 5.6 Consensus size: 199
1352 ATAAGTTTAT
* * *
1362 TATAAGAAAAATTACACTACAATTCATC-GTCAGTGGAGTTTACCAGACTTCACGTGCGGGGTTT
1 TATAAGAAAAATT--A-TACAATACA-CAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTT
* * *
1426 AAGGGTTGACATATGTCCCCTTAGGAAATATGTATTAATATTAAATATTTAATTAGTTATGAAAT
62 AAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAAT
* *
1491 GGAGTATGTGTCAACTTCTTAATCTGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTAT
127 GG-GTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTAT
1556 AATAAT-CC
191 AATAATCCC
* *
1564 TATAAGAAAAATTATACAATACACTGTCAGTGGAGTTTAGCAGACTGCACGTGCGAGGTTTAAGG
1 TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
*
1629 GTTGACATGTGTCCCCTAAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGTGG
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATG-GG
1694 TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
130 TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
1759 ATCCC
195 ATCCC
1764 TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
1 TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
1829 GTTGACATGTGTCCCCTTAGGGAATACT-TATTAATATTAAATATATTTAATTAATTATGAAATG
66 GTTGACATGTGTCCCCTTAGGGAATA-TGTATTAATATT-AA-ATATTTAATTAATTATGAAAT-
1893 GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATA
127 GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATA
1958 ATAATCCC
192 ATAATCCC
* *
1966 TATAAGAAAAATTATACAATACACAGTTAGTGGAGTTTAGCAGACTGCACGTGTGGGGTTTAAGG
1 TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
2031 GTTGACATGTGTCCCCTTAGGGAATATGTCTTAATTAATATTAAATATTTAATTAATTATGAAAT
66 GTTGACATGTGTCCCCTTAGGGAATATG---T-ATTAATATTAAATATTTAATTAATTATGAAAT
* *
2096 GGGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGCATA
127 GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATA
2161 ATAATCCC
192 ATAATCCC
* * * *
2169 TATAAGAAAAATTATACAATACACCGTCAATGGAGTTTATCAGACTGCACGTGTGGGGTTTAAGG
1 TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
* * *
2234 GTTGGCATATGTCTCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGT
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGT
* * *
2299 ATGTGTCAACCTT-TTAACCCGTTTATGGAGTCCAAAATTTACACTTACAATGTATTGTATAATA
131 ATGTGTCAA-CTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
*
2363 AT-CA
195 ATCCC
* * ** *
2367 TATAAGAAAAATTATAGAATACA-ACGTCAGTAGAGTTTAGCAGACTGCACG-GACGATGTGTAA
1 TATAAGAAAAATTATACAATACACA-GTCAGTGGAGTTTAGCAGACTGCACGTG-CGGGGTTTAA
* * *
2430 GGGTTGACATGTGTCGCCTTAGGGAATATGTGTTAATATTTAATATTTAATTAATTATGAAA
64 GGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAA
2492 AAGCTCAGTT
Statistics
Matches: 869, Mismatches: 44, Indels: 34
0.92 0.05 0.04
Matches are distributed among these distances:
197 1 0.00
198 110 0.13
199 263 0.30
200 105 0.12
201 4 0.00
202 195 0.22
203 158 0.18
204 21 0.02
205 3 0.00
206 9 0.01
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (199 bp):
TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGT
ATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAA
TCCC
Found at i:2521 original size:16 final size:16
Alignment explanation
Indices: 2500--2530 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2490 AAAAGCTCAG
*
2500 TTAATAAGGTTACTAA
1 TTAATAAGATTACTAA
2516 TTAATAAGATTACTA
1 TTAATAAGATTACTA
2531 TACATGATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (16 bp):
TTAATAAGATTACTAA
Found at i:7860 original size:84 final size:84
Alignment explanation
Indices: 7719--7887 Score: 275
Period size: 84 Copynumber: 2.0 Consensus size: 84
7709 GTTTTTCTGA
* * * *
7719 AAGAAAACAACATGAAATCCATCCGGTCGAGGGGTTTTATGAGCCCCAATGTTTTTAATAGCTTG
1 AAGAAAACAACATGAAATCCATCCGGTCCAGGGGCTTTATGAGCCCCAATGCTTTTAATAGCCTG
*
7784 TTTAATCTCATCAACATGG
66 TTCAATCTCATCAACATGG
* *
7803 AAGAAAACAGCATGAAATCCATCCGGTCCAGGGGCTTTATGATCCCCAATGCTTTTAATAGCCTG
1 AAGAAAACAACATGAAATCCATCCGGTCCAGGGGCTTTATGAGCCCCAATGCTTTTAATAGCCTG
7868 TTCAATCTCATCAACATGG
66 TTCAATCTCATCAACATGG
7887 A
1 A
7888 GATCTCTACG
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (84 bp):
AAGAAAACAACATGAAATCCATCCGGTCCAGGGGCTTTATGAGCCCCAATGCTTTTAATAGCCTG
TTCAATCTCATCAACATGG
Found at i:19123 original size:2 final size:2
Alignment explanation
Indices: 19118--19164 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
19108 TCACTACAAG
* *
19118 CT CT CT CT CT CT CT CT CT AT CT CT CT CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19160 CT CT C
1 CT CT C
19165 CAATGTCCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Done.