Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010068.1 Corchorus capsularis cultivar CVL-1 contig10089, 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: 12226
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:3647 original size:17 final size:17
Alignment explanation
Indices: 3625--3661 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3615 AATTAATCAC
3625 GTTGAATTTAGGTGAGT
1 GTTGAATTTAGGTGAGT
3642 GTTGAATTTAGGTGAGT
1 GTTGAATTTAGGTGAGT
3659 GTT
1 GTT
3662 TTTTATTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (17 bp):
GTTGAATTTAGGTGAGT
Found at i:8643 original size:16 final size:17
Alignment explanation
Indices: 8613--8646 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
8603 AGTAATTTAG
8613 TATTGAATGACTTGAAT
1 TATTGAATGACTTGAAT
*
8630 TATT-AATGATTTGAAT
1 TATTGAATGACTTGAAT
8646 T
1 T
8647 GATGCTCGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (17 bp):
TATTGAATGACTTGAAT
Found at i:10051 original size:59 final size:59
Alignment explanation
Indices: 9976--10094 Score: 202
Period size: 59 Copynumber: 2.0 Consensus size: 59
9966 GTTTTGATGG
* * * *
9976 AATCAATCAAGTAGGTCTACCGCAGGATCATGATTGAAGCATGATTACAGCGGGATCCA
1 AATCAATAAAGCAGGTCCACCGCAGGATCATGATTGAAGCATGATTACAGCGGAATCCA
10035 AATCAATAAAGCAGGTCCACCGCAGGATCATGATTGAAGCATGATTACAGCGGAATCCA
1 AATCAATAAAGCAGGTCCACCGCAGGATCATGATTGAAGCATGATTACAGCGGAATCCA
10094 A
1 A
10095 GATCGAAGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (59 bp):
AATCAATAAAGCAGGTCCACCGCAGGATCATGATTGAAGCATGATTACAGCGGAATCCA
Found at i:10289 original size:2 final size:2
Alignment explanation
Indices: 10282--10317 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10272 TTACTGCTGC
10282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10318 GTAACATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10361 original size:18 final size:18
Alignment explanation
Indices: 10338--10373 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10328 TCTGTTTATG
*
10338 AAACAAGTGAATGAAAAA
1 AAACAAGTGAAGGAAAAA
10356 AAACAAGTGAAGGAAAAA
1 AAACAAGTGAAGGAAAAA
10374 TGTAGTTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.67, C:0.06, G:0.19, T:0.08
Consensus pattern (18 bp):
AAACAAGTGAAGGAAAAA
Found at i:10841 original size:43 final size:42
Alignment explanation
Indices: 10758--11000 Score: 269
Period size: 43 Copynumber: 5.7 Consensus size: 42
10748 GTGACAGTAA
* * * *
10758 AGAACCTTCGAAAAGGGGAGGTTAGTTCCTACGAGTTGGCGTT
1 AGAACCTTCGAAAAAGGGAGGTTAGTTCCTGCGGGGTGGCG-T
10801 A-AACCTTCGAAAAAGGGAGGTTAGTTCCTGCGGAGGTGGCGT
1 AGAACCTTCGAAAAAGGGAGGTTAGTTCCTGCGG-GGTGGCGT
10843 AGAACCTTC-AAAAAGGGGAGGTTAGTTCCTGCGGGGGTGGCGT
1 AGAACCTTCGAAAAA-GGGAGGTTAGTTCCTGC-GGGGTGGCGT
* **
10886 AGAACCTTC-AAAAAGGGGAGGTTAGTTCTTGTAGGGTGGCGT
1 AGAACCTTCGAAAAA-GGGAGGTTAGTTCCTGCGGGGTGGCGT
* * *
10928 AGAACCTTCGAAAAGGGGATGTTAGTT-CTGACGGGGCGGCGT
1 AGAACCTTCGAAAAAGGGAGGTTAGTTCCTG-CGGGGTGGCGT
* * * *
10970 AAAAATCTTCGAAAAGGGGAGGTTTGTTCCT
1 -AGAACCTTCGAAAAAGGGAGGTTAGTTCCT
11001 AGCAGTCCTG
Statistics
Matches: 175, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
41 2 0.01
42 73 0.42
43 96 0.55
44 4 0.02
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (42 bp):
AGAACCTTCGAAAAAGGGAGGTTAGTTCCTGCGGGGTGGCGT
Found at i:10901 original size:85 final size:83
Alignment explanation
Indices: 10758--11005 Score: 293
Period size: 85 Copynumber: 2.9 Consensus size: 83
10748 GTGACAGTAA
* * *
10758 AGAACCTTCGAAAAGGGGAGGTTAGTTCCTACGAGTTGGCGTTAAACCTTCGAAAAAGGGAGGTT
1 AGAACCTTCGAAAAGGGGAGGTTAGTTCCTGCGGGGTGGCG-TAAACCTTCGAAAAAGGGAGGTT
*
10823 AGTTCCTGCGGAGGTGGCGT
65 AGTTCCTGCAG-GGTGGCGT
*
10843 AGAACCTTCAAAAAGGGGAGGTTAGTTCCTGCGGGGGTGGCGTAGAACCTTC-AAAAAGGGGAGG
1 AGAACCTTCGAAAAGGGGAGGTTAGTTCCTGC-GGGGTGGCGTA-AACCTTCGAAAAA-GGGAGG
* *
10907 TTAGTTCTTGTAGGGTGGCGT
63 TTAGTTCCTGCAGGGTGGCGT
* * * *
10928 AGAACCTTCGAAAAGGGGATGTTAGTT-CTGACGGGGCGGCGTAAAAATCTTCGAAAAGGGGAGG
1 AGAACCTTCGAAAAGGGGAGGTTAGTTCCTG-CGGGGTGGCGT--AAACCTTCGAAAAAGGGAGG
*
10992 TTTGTTCCTAGCAG
63 TTAGTTCCT-GCAG
11006 TCCTGCTGAG
Statistics
Matches: 140, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
84 12 0.09
85 90 0.64
86 38 0.27
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.23
Consensus pattern (83 bp):
AGAACCTTCGAAAAGGGGAGGTTAGTTCCTGCGGGGTGGCGTAAACCTTCGAAAAAGGGAGGTTA
GTTCCTGCAGGGTGGCGT
Found at i:11452 original size:79 final size:79
Alignment explanation
Indices: 11314--11473 Score: 243
Period size: 79 Copynumber: 2.0 Consensus size: 79
11304 ACAATGCCGG
*
11314 AATTTGAAATCATTAGTGTTCAAGTTGGGCGTTGCAAATCTTCACCCTCCAACTTGAGG-AGGGA
1 AATTTGAAATCATTAGTGTTCAAGTTGGGCGTTGCAAATCTTCACCCTCCAACTTGAGGAAGGCA
11378 GTGATGAAATCAAATC
66 -TGATGAAATC-AATC
* **
11394 AATTTG-AATCATTAGTGTTCAAGTTGGGCGTTGCGAATCTTCACGTTCCAACTTGAGGAAGGCA
1 AATTTGAAATCATTAGTGTTCAAGTTGGGCGTTGCAAATCTTCACCCTCCAACTTGAGGAAGGCA
*
11458 TGATGGAATCAATC
66 TGATGAAATCAATC
11472 AA
1 AA
11474 GCAGTTCTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
78 6 0.08
79 58 0.78
80 10 0.14
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (79 bp):
AATTTGAAATCATTAGTGTTCAAGTTGGGCGTTGCAAATCTTCACCCTCCAACTTGAGGAAGGCA
TGATGAAATCAATC
Found at i:11556 original size:59 final size:59
Alignment explanation
Indices: 11464--11641 Score: 320
Period size: 59 Copynumber: 3.0 Consensus size: 59
11454 GGCATGATGG
* *
11464 AATCAATCAAGCAGTTCTACCGCAGGATCATGATTGAAGCATGATTACAGCGGGATCCA
1 AATCAATAAAGCAGGTCTACCGCAGGATCATGATTGAAGCATGATTACAGCGGGATCCA
* *
11523 AATCAATAAAGCAGGTCCACCGCATGATCATGATTGAAGCATGATTACAGCGGGATCCA
1 AATCAATAAAGCAGGTCTACCGCAGGATCATGATTGAAGCATGATTACAGCGGGATCCA
11582 AATCAATAAAGCAGGTCTACCGCAGGATCATGATTGAAGCATGATTACAGCGGGATCCA
1 AATCAATAAAGCAGGTCTACCGCAGGATCATGATTGAAGCATGATTACAGCGGGATCCA
11641 A
1 A
11642 GATTGAAGCA
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 113 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (59 bp):
AATCAATAAAGCAGGTCTACCGCAGGATCATGATTGAAGCATGATTACAGCGGGATCCA
Found at i:11884 original size:18 final size:18
Alignment explanation
Indices: 11861--11896 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11851 TCTGTTTATG
*
11861 AAACAAGTGAATGAAAAA
1 AAACAAGTGAAGGAAAAA
11879 AAACAAGTGAAGGAAAAA
1 AAACAAGTGAAGGAAAAA
11897 TGTAATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.67, C:0.06, G:0.19, T:0.08
Consensus pattern (18 bp):
AAACAAGTGAAGGAAAAA
Done.