Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000560.1 Corchorus capsularis cultivar CVL-1 contig00560, 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: 2397
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Found at i:1703 original size:22 final size:21
Alignment explanation
Indices: 1652--2211 Score: 167
Period size: 22 Copynumber: 25.7 Consensus size: 21
1642 ATGATCCCAT
*
1652 TATGAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTAC
*
1673 TATGAAATTTTGATAACGGTAC
1 TATGAAATTTTGATAAC-CTAC
* ** * **
1695 TATGGAATTTCAAGAATCCTTT
1 TATGAAATTTTGATAA-CCTAC
* * * *
1717 TATAAAATTTTTA-AACTTTC
1 TATGAAATTTTGATAACCTAC
* *
1737 TTATGAAATTTTGTTAACCTCCC
1 -TATGAAATTTTGATAACCT-AC
* * *
1760 TAAGGAATTTTGA-ATACCTCAA
1 TATGAAATTTTGATA-ACCT-AC
* *
1782 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCT-AC
* *
1804 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC--TAC
* * * *
1827 TATGAGATGTTGACAACCTCC
1 TATGAAATTTTGATAACCTAC
* *
1848 ATATGATATATTGATAACC-AC
1 -TATGAAATTTTGATAACCTAC
* * * * *
1869 TTTATAAAAATTTAAAAACCTCC
1 --TATGAAATTTTGATAACCTAC
1892 ATATG-AATTGTTAGTAATAA--TAC
1 -TATGAAATT-TT-G--ATAACCTAC
* *
1915 TTTCAAATTTTGATAATCAC-AC
1 TATGAAATTTTGATAA-C-CTAC
* * *
1937 TATAAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCT-AC
* *
1959 TATGAAATTTTGATAAATCTTTC
1 TATGAAATTTTGAT-AA-CCTAC
* * *
1982 TATAAAATTTTAATAAACCTCTC
1 TATGAAATTTTGAT-AACCT-AC
* * * *
2005 TATAAAAGTTTGATAACTTTC
1 TATGAAATTTTGATAACCTAC
*
2026 TTATGAAATCTTGATAA-CTAC
1 -TATGAAATTTTGATAACCTAC
* *
2047 ----AAATTTTGATAAGCTCCC
1 TATGAAATTTTGATAACCT-AC
** *
2065 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCT-AC
* * * *
2087 TATGAAAATTTGTTAATCTCCC
1 TATGAAATTTTGATAACCT-AC
* * *
2109 CATGAAATTTTGATCTACATAC
1 TATGAAATTTTGAT-AACCTAC
2131 TATGAAATTTTGATAACCCT-C
1 TATGAAATTTTGATAA-CCTAC
2152 TTATGAAATTTTGATAA-CTAAAC
1 -TATGAAATTTTGATAACCT--AC
* *
2175 TATGAAAATTTGATAACCTTC
1 TATGAAATTTTGATAACCTAC
2196 ATATGAAATTTTGATA
1 -TATGAAATTTTGATA
2212 TCCTCACTGA
Statistics
Matches: 392, Mismatches: 106, Indels: 81
0.68 0.18 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
19 4 0.01
20 6 0.02
21 44 0.11
22 257 0.66
23 62 0.16
24 2 0.01
25 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTAC
Found at i:1986 original size:45 final size:46
Alignment explanation
Indices: 1919--2020 Score: 118
Period size: 46 Copynumber: 2.3 Consensus size: 46
1909 TAATACTTTC
* *
1919 AAATTTTGAT-AATCACACTATAAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCACACTATAAAATTGTAATAAACCTCGCTATA
*** * *
1963 AAATTTTGATAAATCTTTCTATAAAATTTTAATAAACCTCTCTATA
1 AAATTTTGATAAATCACACTATAAAATTGTAATAAACCTCGCTATA
*
2009 AAAGTTTGATAA
1 AAATTTTGATAA
2021 CTTTCTTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 10 0.21
45 17 0.35
46 21 0.44
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (46 bp):
AAATTTTGATAAATCACACTATAAAATTGTAATAAACCTCGCTATA
Found at i:2265 original size:20 final size:19
Alignment explanation
Indices: 2202--2268 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
2192 CTTCATATGA
2202 AATTTTGATATCC-TCACTG
1 AATTTTGATATCCTTC-CTG
*
2221 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCTTCCTG
*
2240 AATTTTGGTATCCTTCCTG
1 AATTTTGATATCCTTCCTG
2259 AAATTTTGAT
1 -AATTTTGAT
2269 TACTCCATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 33 0.79
20 9 0.21
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (19 bp):
AATTTTGATATCCTTCCTG
Done.