Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016156.1 Corchorus capsularis cultivar CVL-1 contig16177, 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: 11628
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:542 original size:12 final size:12
Alignment explanation
Indices: 509--544 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
499 CTATCTCTAG
*
509 ACTTTACAGCAT
1 ACTTTACAGTAT
521 ACTTTACAGTAT
1 ACTTTACAGTAT
533 ACTTTACAGTAT
1 ACTTTACAGTAT
545 GCTTGACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.39
Consensus pattern (12 bp):
ACTTTACAGTAT
Found at i:4286 original size:19 final size:19
Alignment explanation
Indices: 4262--4299 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4252 TCTCTGACCT
4262 TCCAACTACCTCTCCATTC
1 TCCAACTACCTCTCCATTC
*
4281 TCCAACTGCCTCTCCATTC
1 TCCAACTACCTCTCCATTC
4300 CTTGGTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.47, G:0.03, T:0.32
Consensus pattern (19 bp):
TCCAACTACCTCTCCATTC
Found at i:7481 original size:21 final size:21
Alignment explanation
Indices: 7455--7499 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
7445 TTTTTCTGGA
*
7455 TTGCTAAACACTGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
7476 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
7497 TTG
1 TTG
7500 ACGCTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:7767 original size:32 final size:31
Alignment explanation
Indices: 7713--7863 Score: 122
Period size: 32 Copynumber: 4.7 Consensus size: 31
7703 TACCGTGGCG
* * *
7713 AAGCCGCCTCACTTGGGAGGCTTCGCCACGGC
1 AAGCCGCCCCA-TGGGGCGGCTTCGCCACGGC
* * **
7745 AAGCCGCCCCATGAGGGCGGCTTCCCCATGAA
1 AAGCCGCCCCATG-GGGCGGCTTCGCCACGGC
* *
7777 AAGGCCGCCCCACTGGGGCGGCTTAGCCAGGGC
1 AA-GCCGCCCCA-TGGGGCGGCTTCGCCACGGC
* **
7810 AGGCCGTCCCGGTGGGGCGGCTTCGCCACGGC
1 AAGCCG-CCCCATGGGGCGGCTTCGCCACGGC
* *
7842 AGGCCGCCCCGGTGGGGCGGCT
1 AAGCCGCCCC-ATGGGGCGGCT
7864 CGGCTATTTT
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
31 4 0.04
32 64 0.67
33 26 0.27
34 2 0.02
ACGTcount: A:0.13, C:0.37, G:0.38, T:0.12
Consensus pattern (31 bp):
AAGCCGCCCCATGGGGCGGCTTCGCCACGGC
Found at i:8126 original size:33 final size:33
Alignment explanation
Indices: 8029--8187 Score: 200
Period size: 33 Copynumber: 4.9 Consensus size: 33
8019 AAAAAGCCTT
* * *
8029 GCCGCCCTAGTGGGGCGGCT-AGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* *
8061 GCCGTCCTAGT-GGGACGGCT-AGTCGTGGCAGA
1 GCCGTCCTAGTGGGGA-GGCTCCGCCGTGGCAGA
8093 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
** * *
8126 GCCGTATTAGTGGGGAGGCTCCGTCGTGGCCGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
8159 GCCGTCCTAGTGGGGAGGCTCCG-CGTGGC
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGC
8188 TAAGGGCAAA
Statistics
Matches: 113, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
31 3 0.03
32 46 0.41
33 64 0.57
ACGTcount: A:0.12, C:0.28, G:0.43, T:0.17
Consensus pattern (33 bp):
GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
Found at i:9230 original size:19 final size:19
Alignment explanation
Indices: 9198--9242 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
9188 TTTCTTCCTT
*
9198 CTTCTT-CTTCTTCTCGAG
1 CTTCTTCCTTATTCTCGAG
9216 CTTCTTCCTTATTCTCGAG
1 CTTCTTCCTTATTCTCGAG
9235 CTTCTTCC
1 CTTCTTCC
9243 ATCTTCTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.07, C:0.36, G:0.09, T:0.49
Consensus pattern (19 bp):
CTTCTTCCTTATTCTCGAG
Found at i:9249 original size:19 final size:19
Alignment explanation
Indices: 9206--9250 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
9196 TTCTTCTTCT
*
9206 TCTTCTCGAGCTTCTTCCT
1 TCTTCTCGAGCTTCTTCCA
*
9225 TATTCTCGAGCTTCTTCCA
1 TCTTCTCGAGCTTCTTCCA
9244 TCTTCTC
1 TCTTCTC
9251 ATTATGCCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.36, G:0.09, T:0.47
Consensus pattern (19 bp):
TCTTCTCGAGCTTCTTCCA
Found at i:10746 original size:16 final size:17
Alignment explanation
Indices: 10716--10781 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
10706 GTGGCCACAC
10716 TTTTTTAATTGACTTAA-
1 TTTTTTAATT-ACTTAAT
10733 TTTTTTAATTACTTAAT
1 TTTTTTAATTACTTAAT
**
10750 TTTTTTAATT-CGGAAAT
1 TTTTTTAATTAC-TTAAT
10767 TTTTTTAATTACTTA
1 TTTTTTAATTACTTA
10782 TTAATTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
16 7 0.17
17 34 0.81
18 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.61
Consensus pattern (17 bp):
TTTTTTAATTACTTAAT
Found at i:10771 original size:34 final size:35
Alignment explanation
Indices: 10733--10803 Score: 101
Period size: 34 Copynumber: 2.0 Consensus size: 35
10723 ATTGACTTAA
10733 TTTTTTAATTACTTAATT-TTTTT-AATTCGGAAAT
1 TTTTTTAATTACTT-ATTATTTTTGAATTCGGAAAT
*
10767 TTTTTTAATTACTTATTAATTTTTGAATTCTGAAAT
1 TTTTTTAATTACTTATT-ATTTTTGAATTCGGAAAT
10803 T
1 T
10804 CCATGTGGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 3 0.09
34 14 0.42
35 5 0.15
36 11 0.33
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.59
Consensus pattern (35 bp):
TTTTTTAATTACTTATTATTTTTGAATTCGGAAAT
Done.