Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005051.1 Corchorus capsularis cultivar CVL-1 contig05069, 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: 23733
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2124 original size:13 final size:12
Alignment explanation
Indices: 2101--2140 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
2091 TTAATACAGG
2101 TATCGACGGATA
1 TATCGACGGATA
2113 TATCGAACGGATA
1 TATCG-ACGGATA
*
2126 TATCGATGGATA
1 TATCGACGGATA
2138 TAT
1 TAT
2141 TGAGGTATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 14 0.54
13 12 0.46
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:2322 original size:13 final size:13
Alignment explanation
Indices: 2304--2329 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2294 TAGGCATTAT
2304 TTTATATTTTTTA
1 TTTATATTTTTTA
2317 TTTATATTTTTTA
1 TTTATATTTTTTA
2330 CTGCGAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATATTTTTTA
Found at i:3596 original size:10 final size:10
Alignment explanation
Indices: 3581--3608 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3571 AATTTAATAT
3581 GGATATTTAC
1 GGATATTTAC
3591 GGATATTTAC
1 GGATATTTAC
3601 GGATATTT
1 GGATATTT
3609 CGAGATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (10 bp):
GGATATTTAC
Found at i:3734 original size:12 final size:12
Alignment explanation
Indices: 3717--3755 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3707 GTACAGATAT
3717 CGGATATATCGA
1 CGGATATATCGA
3729 CGGATATATCGA
1 CGGATATATCGA
3741 --G--ATATCGA
1 CGGATATATCGA
3749 CGGATAT
1 CGGATAT
3756 TTAATTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
10 2 0.09
12 14 0.61
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:12430 original size:29 final size:30
Alignment explanation
Indices: 12396--12453 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
12386 TAATTAACTT
12396 TTTGTAACTAACTTATGAACTAAC-ATGAC
1 TTTGTAACTAACTTATGAACTAACTATGAC
*
12425 TTTGTAACTATCTTATGAACTAACTATGA
1 TTTGTAACTAACTTATGAACTAACTATGA
12454 ACTCTAACGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (30 bp):
TTTGTAACTAACTTATGAACTAACTATGAC
Found at i:12461 original size:29 final size:28
Alignment explanation
Indices: 12400--12461 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
12390 TAACTTTTTG
*
12400 TAACTAACTTATGAACTAACATGACTTTG
1 TAACTAACTTATGAACTAACATGAC-TTC
*
12429 TAACTATCTTATGAACTAACTATGAAC-TC
1 TAACTAACTTATGAACTAAC-ATG-ACTTC
12458 TAAC
1 TAAC
12462 GGAGCTGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 24 0.83
30 3 0.10
31 2 0.07
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (28 bp):
TAACTAACTTATGAACTAACATGACTTC
Found at i:12487 original size:16 final size:16
Alignment explanation
Indices: 12466--12497 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12456 TCTAACGGAG
12466 CTGGTTGCATAATAAA
1 CTGGTTGCATAATAAA
12482 CTGGTTGCATAATAAA
1 CTGGTTGCATAATAAA
12498 AGGTTAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
CTGGTTGCATAATAAA
Found at i:20728 original size:31 final size:31
Alignment explanation
Indices: 20687--20877 Score: 94
Period size: 31 Copynumber: 6.5 Consensus size: 31
20677 TTTGTGCGTA
* * *
20687 TGGCATGCCACGTGTCGCTTTTTGGTACATG
1 TGGCATGCCACGTATCACTTTTTGATACATG
*
20718 TGGCGTGCCACGTATCACTTTTTGATACA--
1 TGGCATGCCACGTATCACTTTTTGATACATG
* ** *
20747 T-G-A---CA--TGTCACTTTTTGGCACACG
1 TGGCATGCCACGTATCACTTTTTGATACATG
* * * * *
20771 TGACGTGCCACGTGTCACTTTTTGATCCACG
1 TGGCATGCCACGTATCACTTTTTGATACATG
** * * *
20802 TGGTGTGCCACGTGTCACTTTTTGATCCACG
1 TGGCATGCCACGTATCACTTTTTGATACATG
** * * * * *
20833 TGGTGTGCCTCGTGTTACTTTTTTATCCATG
1 TGGCATGCCACGTATCACTTTTTGATACATG
20864 TGGCATGCCACGTA
1 TGGCATGCCACGTA
20878 GAACACCGTG
Statistics
Matches: 128, Mismatches: 23, Indels: 18
0.76 0.14 0.11
Matches are distributed among these distances:
22 14 0.11
24 3 0.02
28 1 0.01
29 3 0.02
31 107 0.84
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.36
Consensus pattern (31 bp):
TGGCATGCCACGTATCACTTTTTGATACATG
Found at i:20853 original size:62 final size:62
Alignment explanation
Indices: 20752--20876 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 62
20742 ATACATGACA
**
20752 TGTCACTTTTTGGCACACGTGACGTGCCACGTGTCACTTTTTGATCCACGTGGTGTGCCACG
1 TGTCACTTTTTGGCACACGTGACGTGCCACGTGTCACTTTTTGATCCACGTGGCATGCCACG
* ** * * * *
20814 TGTCACTTTTTGATC-CACGTGGTGTGCCTCGTGTTACTTTTTTATCCATGTGGCATGCCACG
1 TGTCACTTTTTG-GCACACGTGACGTGCCACGTGTCACTTTTTGATCCACGTGGCATGCCACG
20876 T
1 T
20877 AGAACACCGT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 52 0.98
63 1 0.02
ACGTcount: A:0.14, C:0.26, G:0.24, T:0.37
Consensus pattern (62 bp):
TGTCACTTTTTGGCACACGTGACGTGCCACGTGTCACTTTTTGATCCACGTGGCATGCCACG
Found at i:21158 original size:7 final size:7
Alignment explanation
Indices: 21146--21186 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
21136 CCAACCATAC
21146 ATTTTTT
1 ATTTTTT
21153 ATTTTTT
1 ATTTTTT
**
21160 ATTTACT
1 ATTTTTT
21167 -TTTTTT
1 ATTTTTT
21173 ATTTTTT
1 ATTTTTT
21180 ATTTTTT
1 ATTTTTT
21187 GCAATACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 4 0.14
7 25 0.86
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (7 bp):
ATTTTTT
Found at i:22730 original size:2 final size:2
Alignment explanation
Indices: 22723--22754 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
22713 CTCCACTAAT
22723 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22755 TTAGAATTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.