Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008583.1 Corchorus capsularis cultivar CVL-1 contig08604, 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: 24637
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3117 original size:31 final size:32
Alignment explanation
Indices: 3059--3121 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
3049 CTTCTAATTA
*
3059 AAATATTTTATCTTTGTTTTTTCTTGAATTTG
1 AAATATTTTATCTTCGTTTTTTCTTGAATTTG
3091 AAATATTTTATCTTCGTTTTTT-TTGAATTTG
1 AAATATTTTATCTTCGTTTTTTCTTGAATTTG
3122 GATGATTACC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.22, C:0.06, G:0.10, T:0.62
Consensus pattern (32 bp):
AAATATTTTATCTTCGTTTTTTCTTGAATTTG
Found at i:4469 original size:183 final size:181
Alignment explanation
Indices: 4154--4517 Score: 629
Period size: 183 Copynumber: 2.0 Consensus size: 181
4144 GTATAGATAG
*
4154 ATAAAAGTACGAGTTTTGTGAAACTTTTGAATCGAACATTATACCCTTATTTTTTTGAATATATC
1 ATAAAAGTACGAGTTTTGTGAAACTTTTGAAACGAACATTATACCCTTATTTTTTTGAATATATC
* * *
4219 TCTTAAATGTCCTTGCTTAAACTATTGTAGTTTTATTCTACTAAAAACTCTATTTTTATTTAATT
66 TCTTAAATGCCCTTGCTTAAACTATCGTAGTTTTATTCTACTAAAAACTCTATTTTTATTCAATT
4284 ATTAAATCTAATTTCTTTATAATTTCTTTATTTTTACCATTTTTTACTATTTT
131 ATTAAATCTAATTTCTTTATAATTTCTTTATTTTTACCA--TTTTACTATTTT
* * *
4337 ATAAAATTACGAGTTTTGTGAAACTTTTGAAACGACCATTATACTCTTATTTTTTTGAATATATC
1 ATAAAAGTACGAGTTTTGTGAAACTTTTGAAACGAACATTATACCCTTATTTTTTTGAATATATC
* *
4402 TCTTAAATGCCCTTGCTTAAGCTATCGTAGTTTTATTGTACTAAAAACTCTATTTTTATTCAATT
66 TCTTAAATGCCCTTGCTTAAACTATCGTAGTTTTATTCTACTAAAAACTCTATTTTTATTCAATT
4467 ATTAAATCTAATTTCTTTATAATTTCTTTATTTTTACCATTTTACTATTTT
131 ATTAAATCTAATTTCTTTATAATTTCTTTATTTTTACCATTTTACTATTTT
4518 CAATAAAAAT
Statistics
Matches: 172, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
181 12 0.07
183 160 0.93
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (181 bp):
ATAAAAGTACGAGTTTTGTGAAACTTTTGAAACGAACATTATACCCTTATTTTTTTGAATATATC
TCTTAAATGCCCTTGCTTAAACTATCGTAGTTTTATTCTACTAAAAACTCTATTTTTATTCAATT
ATTAAATCTAATTTCTTTATAATTTCTTTATTTTTACCATTTTACTATTTT
Found at i:6137 original size:65 final size:66
Alignment explanation
Indices: 6007--6139 Score: 178
Period size: 69 Copynumber: 2.0 Consensus size: 66
5997 AATCAACCTT
** * *
6007 TACACAGTTTTTTTTCTTCTTCCTTCCTCTTCCTCTCCCCATTGTTAATTTAGCCATGAACACAA
1 TACACAGTTTTCCTTCTTCTCCCTTCCTCTTCCTCTCCCCATTG---ATTTAGCCAAGAACACAA
6072 TATC
63 TATC
* *
6076 TACACAGTTTTCCTTCTTCTCCCTTCCTCTTTCTCTTCCCATTG-TTTAGCCAAGAACACAATAT
1 TACACAGTTTTCCTTCTTCTCCCTTCCTCTTCCTCTCCCCATTGATTTAGCCAAGAACACAATAT
6140 ATAGTATTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
65 19 0.33
69 39 0.67
ACGTcount: A:0.20, C:0.32, G:0.06, T:0.42
Consensus pattern (66 bp):
TACACAGTTTTCCTTCTTCTCCCTTCCTCTTCCTCTCCCCATTGATTTAGCCAAGAACACAATAT
C
Found at i:6213 original size:26 final size:26
Alignment explanation
Indices: 6177--6228 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6167 ACATATCTAT
6177 GCACTTTGGGAGATTGATTAGAAGAC
1 GCACTTTGGGAGATTGATTAGAAGAC
6203 GCACTTTGGGAGATTGATTAGAAGAC
1 GCACTTTGGGAGATTGATTAGAAGAC
6229 CTTGGAGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (26 bp):
GCACTTTGGGAGATTGATTAGAAGAC
Found at i:15664 original size:11 final size:10
Alignment explanation
Indices: 15646--15679 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
15636 GAAGTTCGTG
15646 TTTTGAAGAT
1 TTTTGAAGAT
15656 TTCTTGAAGAT
1 TT-TTGAAGAT
15667 ATTTTGAAGAT
1 -TTTTGAAGAT
15678 TT
1 TT
15680 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:17483 original size:41 final size:43
Alignment explanation
Indices: 17421--17506 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 43
17411 GTCGATAAAA
*
17421 AAAATAAATAATTTTTCTTTTCCGTTTTT-CTTTTT-TTTTTT
1 AAAATAAATAATTTTTATTTTCCGTTTTTGCTTTTTATTTTTT
*
17462 AAAA-AAATATATTTTTATTTTCTGTTTTTGCTTTTTAATTTTTT
1 AAAATAAATA-ATTTTTATTTTCCGTTTTTGCTTTTT-ATTTTTT
17506 A
1 A
17507 TTTAAGAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
40 5 0.13
41 21 0.54
42 6 0.15
44 7 0.18
ACGTcount: A:0.26, C:0.07, G:0.03, T:0.64
Consensus pattern (43 bp):
AAAATAAATAATTTTTATTTTCCGTTTTTGCTTTTTATTTTTT
Found at i:20777 original size:33 final size:33
Alignment explanation
Indices: 20711--20779 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
20701 GACCATTCGA
* ** *
20711 GCCACCTGCCCGGATGAGCCCAGCCTTTGCCGC
1 GCCACATGCCCGGATGAGCCCAGCCACTACCGC
20744 GCCACATGCCCGGATGAG-CCAGGCCACTACCGC
1 GCCACATGCCCGGATGAGCCCA-GCCACTACCGC
20777 GCC
1 GCC
20780 TCTTGCTCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.16, C:0.45, G:0.28, T:0.12
Consensus pattern (33 bp):
GCCACATGCCCGGATGAGCCCAGCCACTACCGC
Found at i:22003 original size:19 final size:19
Alignment explanation
Indices: 21979--22016 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21969 GGTAGTTAAA
21979 AAAAAAAAATCTTTTTCAT
1 AAAAAAAAATCTTTTTCAT
* *
21998 AAAAAACAATGTTTTTCAT
1 AAAAAAAAATCTTTTTCAT
22017 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (19 bp):
AAAAAAAAATCTTTTTCAT
Found at i:22885 original size:11 final size:10
Alignment explanation
Indices: 22867--22900 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
22857 GAAGTTCGTG
22867 TTTTGAAGAT
1 TTTTGAAGAT
22877 TTCTTGAAGAT
1 TT-TTGAAGAT
22888 ATTTTGAAGAT
1 -TTTTGAAGAT
22899 TT
1 TT
22901 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:24590 original size:35 final size:33
Alignment explanation
Indices: 24530--24607 Score: 111
Period size: 35 Copynumber: 2.3 Consensus size: 33
24520 AATATGCTCT
*
24530 AAAAAGTTTTTGTTTTTCCGTTTTTTCTAAAAA
1 AAAAAGTTTTTGTTTTTCCGATTTTTCTAAAAA
* *
24563 AAAAAGTTTTTCCTTTTTTGCGATTTTTCTAAAAA
1 AAAAAGTTTTT--GTTTTTCCGATTTTTCTAAAAA
24598 AAAAAGTTTT
1 AAAAAGTTTT
24608 GCGATTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 11 0.28
35 29 0.73
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (33 bp):
AAAAAGTTTTTGTTTTTCCGATTTTTCTAAAAA
Done.