Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023874.1 Corchorus olitorius cultivar O-4 contig23907, 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: 5564
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:779 original size:20 final size:20
Alignment explanation
Indices: 754--803 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
744 ATACGAACTC
*
754 AATATTATTGAAATATCCTT
1 AATATTATTGAAAAATCCTT
* *
774 AATATTAATAAAAAATCCTT
1 AATATTATTGAAAAATCCTT
794 AATATTATTG
1 AATATTATTG
804 TAATTTATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (20 bp):
AATATTATTGAAAAATCCTT
Found at i:1346 original size:7 final size:7
Alignment explanation
Indices: 1319--1378 Score: 102
Period size: 7 Copynumber: 8.3 Consensus size: 7
1309 CATGGCTATA
1319 TATCTTAC
1 TATC-TAC
1327 TATCTATC
1 TATCTA-C
1335 TATCTAC
1 TATCTAC
1342 TATCTAC
1 TATCTAC
1349 TATCTAC
1 TATCTAC
1356 TATCTAC
1 TATCTAC
1363 TATCTAC
1 TATCTAC
1370 TATCTAC
1 TATCTAC
1377 TA
1 TA
1379 CTATATAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
7 40 0.78
8 11 0.22
ACGTcount: A:0.28, C:0.27, G:0.00, T:0.45
Consensus pattern (7 bp):
TATCTAC
Found at i:1493 original size:19 final size:20
Alignment explanation
Indices: 1469--1510 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1459 ATAAATATTC
*
1469 TTTTTA-GTCATTTAACTTT
1 TTTTTAGGTCATTCAACTTT
*
1488 TTTTTAGGTGATTCAACTTT
1 TTTTTAGGTCATTCAACTTT
1508 TTT
1 TTT
1511 ATTAATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.62
Consensus pattern (20 bp):
TTTTTAGGTCATTCAACTTT
Found at i:1645 original size:15 final size:16
Alignment explanation
Indices: 1620--1649 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1610 AATAATTATT
1620 TTTAGATTATAATATA
1 TTTAGATTATAATATA
1636 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
1650 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:1879 original size:19 final size:20
Alignment explanation
Indices: 1855--1896 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1845 ATAAATATTC
*
1855 TTTTTA-GTCATTTAACTTT
1 TTTTTAGGTCATTCAACTTT
*
1874 TTTTTAGGTGATTCAACTTT
1 TTTTTAGGTCATTCAACTTT
1894 TTT
1 TTT
1897 ATTAATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.62
Consensus pattern (20 bp):
TTTTTAGGTCATTCAACTTT
Found at i:2031 original size:15 final size:16
Alignment explanation
Indices: 2006--2035 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1996 AATAATTATT
2006 TTTAGATTATAATATA
1 TTTAGATTATAATATA
2022 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
2036 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:5271 original size:215 final size:212
Alignment explanation
Indices: 4861--5289 Score: 610
Period size: 212 Copynumber: 2.0 Consensus size: 212
4851 TTTTGGTGCC
* * * *
4861 AAGACTCCTTGAAATATCTATATTCATTTAATAAAAAACTAGACACATTGTATTTAAGGATTTGT
1 AAGACTCCTTGAAATATCTATATTCATCTAATAAAAAACTAGACACATTGAATTTAACGATTTGG
* * **
4926 TTTTACGAGCATTTGAATCTTATTTCGATTTATTTAGAAATTCTGAAAAAAATATGAAAAACGAT
66 TTTTACGAGCATTTGAATCTTATTTCGATTTAATTACAAATAATGAAAAAAATATGAAAAACGAT
*
4991 ATCAAAAACGTTAAAAGCCCTCCAATCTTTTTGGCAATAAATTATATATATTTTATGATTATTTT
131 ATCAAAAACGTTAAAAGCCCTCCAATCTTTTTGGCAATAAATTATATATATTTTATGAGTATTTT
* *
5056 ATCCAAATATTGAGGAA
196 ATCCAAAAATTAAGGAA
* * *
5073 AAGACTCCTTGAAATATCTATATTGATCTAAT-AAAAACTTAGCCACCTTGAATTTAACGATTTG
1 AAGACTCCTTGAAATATCTATATTCATCTAATAAAAAAC-TAGACACATTGAATTTAACGATTTG
*
5137 GTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTACAAATGAATGCAGAAAAAATATGAAAAA
65 GTTTTACGAGCATTTGAATCTTATTTCGATTTAATTACAAAT-AATG-A-AAAAAATATGAAAAA
* * * ***
5202 CGATATTAAAAGCG-TAAAGAGTCCTCCAATCTTTTTGGTGTTAAATTATATATATTTTATGAGT
127 CGATATCAAAAACGTTAAA-AGCCCTCCAATCTTTTTGGCAATAAATTATATATATTTTATGAGT
5266 ATTTTATCCAAAAATTAAGGAA
191 ATTTTATCCAAAAATTAAGGAA
5288 AA
1 AA
5290 ATCGCTTTTT
Statistics
Matches: 191, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
211 6 0.03
212 89 0.47
213 2 0.01
214 5 0.03
215 89 0.47
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (212 bp):
AAGACTCCTTGAAATATCTATATTCATCTAATAAAAAACTAGACACATTGAATTTAACGATTTGG
TTTTACGAGCATTTGAATCTTATTTCGATTTAATTACAAATAATGAAAAAAATATGAAAAACGAT
ATCAAAAACGTTAAAAGCCCTCCAATCTTTTTGGCAATAAATTATATATATTTTATGAGTATTTT
ATCCAAAAATTAAGGAA
Done.