Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003898.1 Corchorus capsularis cultivar CVL-1 contig03906, 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: 2123
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Found at i:221 original size:7 final size:7
Alignment explanation
Indices: 211--247 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
201 TTCGAAAAAA
211 AAAAATC
1 AAAAATC
218 AAAAATAC
1 AAAAAT-C
226 AAAAATC
1 AAAAATC
233 AAAAATC
1 AAAAATC
240 AAAAATC
1 AAAAATC
247 A
1 A
248 GGAAAAATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.73, C:0.14, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATC
Found at i:229 original size:15 final size:15
Alignment explanation
Indices: 171--247 Score: 70
Period size: 15 Copynumber: 5.1 Consensus size: 15
161 AGAAGTCAAG
*
171 AAAAATACAATCAAATA
1 AAAAATACAA--AAATC
* *
188 AAAAACATAAAAATTC
1 AAAAATACAAAAA-TC
204 GAAAAA-A-AAAAATC
1 -AAAAATACAAAAATC
218 AAAAATACAAAAATC
1 AAAAATACAAAAATC
233 AAAAAT-CAAAAATC
1 AAAAATACAAAAATC
247 A
1 A
248 GGAAAAATGC
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
13 5 0.09
14 12 0.23
15 21 0.40
16 2 0.04
17 13 0.25
ACGTcount: A:0.73, C:0.12, G:0.01, T:0.14
Consensus pattern (15 bp):
AAAAATACAAAAATC
Found at i:230 original size:22 final size:22
Alignment explanation
Indices: 171--245 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
161 AGAAGTCAAG
171 AAAAATACAATCAAATAAAAAACAT-
1 AAAAATACAA--AAA-AAAAAA-ATC
* *
196 AAAAATTCGAAAAAAAAAAATC
1 AAAAATACAAAAAAAAAAAATC
**
218 AAAAATACAAAAATCAAAAATC
1 AAAAATACAAAAAAAAAAAATC
240 AAAAAT
1 AAAAAT
246 CAGGAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.05
22 30 0.70
23 3 0.07
25 8 0.19
ACGTcount: A:0.73, C:0.11, G:0.01, T:0.15
Consensus pattern (22 bp):
AAAAATACAAAAAAAAAAAATC
Found at i:734 original size:20 final size:20
Alignment explanation
Indices: 690--744 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
680 TATAATTAAG
*
690 TAATAGATAACTAAAAAAAA
1 TAATAGATAAATAAAAAAAA
*
710 TAATAGATAAAT-AAAAAGA
1 TAATAGATAAATAAAAAAAA
*
729 TAAATAGATATATAAA
1 T-AATAGATAAATAAA
745 CAAATGGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.23
20 21 0.70
21 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (20 bp):
TAATAGATAAATAAAAAAAA
Found at i:743 original size:24 final size:23
Alignment explanation
Indices: 690--772 Score: 66
Period size: 24 Copynumber: 3.7 Consensus size: 23
680 TATAATTAAG
*
690 TAATAGAT-AACTAAAA-A-AAA
1 TAATAGATAAACAAAAAGATAAA
*
710 TAATAGATAAATAAAAAGATAAA
1 TAATAGATAAACAAAAAGATAAA
* **
733 TAGATATATAAACAAATGGATAAA
1 TA-ATAGATAAACAAAAAGATAAA
757 TAAGTATG-TAAACAAA
1 TAA-TA-GATAAACAAA
773 TATATATATA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 8 0.16
21 6 0.12
22 1 0.02
23 6 0.12
24 29 0.58
ACGTcount: A:0.64, C:0.04, G:0.10, T:0.23
Consensus pattern (23 bp):
TAATAGATAAACAAAAAGATAAA
Found at i:773 original size:24 final size:24
Alignment explanation
Indices: 727--773 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
717 TAAATAAAAA
727 GATAAATAGATATATAAACAAATG
1 GATAAATAGATATATAAACAAATG
*
751 GATAAATA-AGTATGTAAACAAAT
1 GATAAATAGA-TATATAAACAAAT
774 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (24 bp):
GATAAATAGATATATAAACAAATG
Found at i:880 original size:17 final size:17
Alignment explanation
Indices: 858--907 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
848 AGATAGATAA
858 ATAATAGTATTAAATAG
1 ATAATAGTATTAAATAG
*
875 ATAATAGTACTAAATAG
1 ATAATAGTATTAAATAG
*
892 ATAATAATATTAAATA
1 ATAATAGTATTAAATA
908 ATTATTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (17 bp):
ATAATAGTATTAAATAG
Found at i:995 original size:22 final size:21
Alignment explanation
Indices: 967--1009 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
957 AACTAAGTAG
* *
967 ATAGATAGATAGATAATAATAA
1 ATAGATAAATAAATAA-AATAA
989 ATAGATAAATAAATAAAATAA
1 ATAGATAAATAAATAAAATAA
1010 TTTAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (21 bp):
ATAGATAAATAAATAAAATAA
Found at i:1720 original size:29 final size:27
Alignment explanation
Indices: 1666--1720 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1656 ATTTTTTTTT
*
1666 CTTACTCTTTTTACTAATTACTCTTTC
1 CTTACTCTTTTTACTAATTACACTTTC
* *
1693 CTTACTCTCTTTTATTGATTACCACTTT
1 CTTACTCT-TTTTACTAATTA-CACTTT
1721 TTACTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 8 0.35
28 10 0.43
29 5 0.22
ACGTcount: A:0.18, C:0.25, G:0.02, T:0.55
Consensus pattern (27 bp):
CTTACTCTTTTTACTAATTACACTTTC
Found at i:1819 original size:21 final size:21
Alignment explanation
Indices: 1795--1843 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1785 ACATATTACT
1795 ATTTTACTCTTACTAATAACC
1 ATTTTACTCTTACTAATAACC
* * *
1816 ATTTTGCTCTTACTAATTACT
1 ATTTTACTCTTACTAATAACC
1837 ATTTTAC
1 ATTTTAC
1844 CTTTTATTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTTTACTCTTACTAATAACC
Found at i:1887 original size:52 final size:51
Alignment explanation
Indices: 1816--1918 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 51
1806 ACTAATAACC
* * * * *
1816 ATTTTGCTCTTACTAATTA-CTATTTTACCTTTTATTGGTTACTTTTTTACT
1 ATTTTACTCTTACTAATTACCT-TCTTACCTTTTACTGATTACTATTTTACT
* *
1867 ATTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGATTACTATTTTACT
1 ATTTTACTC-TTACTAATTACCTTCTTACCTTTTACTGATTACTATTTTACT
1919 CTTTACTGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
51 8 0.19
52 33 0.77
53 2 0.05
ACGTcount: A:0.20, C:0.17, G:0.05, T:0.57
Consensus pattern (51 bp):
ATTTTACTCTTACTAATTACCTTCTTACCTTTTACTGATTACTATTTTACT
Found at i:1895 original size:22 final size:21
Alignment explanation
Indices: 1868--2065 Score: 201
Period size: 21 Copynumber: 9.3 Consensus size: 21
1858 TTTTTTACTA
1868 TTTTACTCTTTACTGATTACC
1 TTTTACTCTTTACTGATTACC
* *
1889 TTCTTACTTTTTACTGATTACTA
1 TT-TTACTCTTTACTGATTAC-C
1912 TTTTACTCTTTACTGATTACC
1 TTTTACTCTTTACTGATTACC
1933 ATTTTACTC-TTACTGATTACC
1 -TTTTACTCTTTACTGATTACC
1954 TTTTACTCTTTACTGATTACC
1 TTTTACTCTTTACTGATTACC
*
1975 ATTTTGCTCTCTT--TGATTACC
1 -TTTTACTCT-TTACTGATTACC
* *
1996 ATTTTGCTC-TTACTGATTACTA
1 -TTTTACTCTTTACTGATTAC-C
*
2018 TTTTAC-CTTTTACTGATTATC
1 TTTTACTC-TTTACTGATTACC
* * *
2039 -ATTACTTTTTATTGATTACC
1 TTTTACTCTTTACTGATTACC
2059 TTTTACT
1 TTTTACT
2066 ATTTCATTCT
Statistics
Matches: 150, Mismatches: 14, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.01
20 24 0.16
21 60 0.40
22 60 0.40
23 4 0.03
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTTACTCTTTACTGATTACC
Found at i:1896 original size:30 final size:31
Alignment explanation
Indices: 1832--1903 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
1822 CTCTTACTAA
* * * *
1832 TTACTATTTTAC-CTTTTATTGGTTACTTTT
1 TTACTATTTTACTCTTTTACTGATTACCTTC
1862 TTACTATTTTACTC-TTTACTGATTACCTTC
1 TTACTATTTTACTCTTTTACTGATTACCTTC
1892 TTACT-TTTTACT
1 TTACTATTTTACT
1904 GATTACTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 7 0.19
30 29 0.78
31 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.04, T:0.60
Consensus pattern (31 bp):
TTACTATTTTACTCTTTTACTGATTACCTTC
Found at i:1947 original size:21 final size:21
Alignment explanation
Indices: 1862--2065 Score: 195
Period size: 22 Copynumber: 9.6 Consensus size: 21
1852 GGTTACTTTT
*
1862 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTC-TTACTGA
*
1884 TTACC-TTCTTACTTTTTACTGA
1 TTACCATT-TTAC-TCTTACTGA
*
1906 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTC-TTACTGA
1928 TTACCATTTTACTCTTACTGA
1 TTACCATTTTACTCTTACTGA
1949 TTACC-TTTTACTCTTTACTGA
1 TTACCATTTTACTC-TTACTGA
* *
1970 TTACCATTTTGCTCTCT-TTGA
1 TTACCATTTTACTCT-TACTGA
*
1991 TTACCATTTTGCTCTTACTGA
1 TTACCATTTTACTCTTACTGA
* *
2012 TTACTATTTTACCTTTTACTGA
1 TTACCATTTTA-CTCTTACTGA
* * *
2034 TTATCA--TTACTTTTTATTGA
1 TTACCATTTTAC-TCTTACTGA
2054 TTACC-TTTTACT
1 TTACCATTTTACT
2066 ATTTCATTCT
Statistics
Matches: 155, Mismatches: 15, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.01
20 25 0.16
21 62 0.40
22 64 0.41
23 3 0.02
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (21 bp):
TTACCATTTTACTCTTACTGA
Found at i:2065 original size:49 final size:51
Alignment explanation
Indices: 2012--2113 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 51
2002 CTCTTACTGA
* *
2012 TTACTATTTTAC-CTTTTACTGATTAT-CATTACTTTTTATTGATTA-CCTT
1 TTACTATTTCACTC-TTTACTGATTATCCATTACTTTTTACTGATTACCCTT
* *
2061 TTACTATTTCATTCTTTACTGATTATCCTTTACTTTTTACTGATTACCCTT
1 TTACTATTTCACTCTTTACTGATTATCCATTACTTTTTACTGATTACCCTT
2112 TT
1 TT
2114 CTCTTTACCA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
49 22 0.48
50 18 0.39
51 6 0.13
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.57
Consensus pattern (51 bp):
TTACTATTTCACTCTTTACTGATTATCCATTACTTTTTACTGATTACCCTT
Found at i:2099 original size:21 final size:21
Alignment explanation
Indices: 2073--2121 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2063 ACTATTTCAT
*
2073 TCTTTACTGATTATCCTTTAC
1 TCTTTACTGATTACCCTTTAC
* *
2094 TTTTTACTGATTACCCTTTTC
1 TCTTTACTGATTACCCTTTAC
2115 TCTTTAC
1 TCTTTAC
2122 CA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.16, C:0.24, G:0.04, T:0.55
Consensus pattern (21 bp):
TCTTTACTGATTACCCTTTAC
Done.