Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012066.1 Corchorus capsularis cultivar CVL-1 contig12087, 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: 14505
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:3245 original size:28 final size:29
Alignment explanation
Indices: 3186--3245 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
3176 CACGCCCCAA
3186 TGCAAGTAAGAGCCGCAAGAACGTATGCT
1 TGCAAGTAAGAGCCGCAAGAACGTATGCT
3215 TGCAAGTAAGAGCCGCAA-AACGTATGCT
1 TGCAAGTAAGAGCCGCAAGAACGTATGCT
3243 TGC
1 TGC
3246 TCTCTGCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (29 bp):
TGCAAGTAAGAGCCGCAAGAACGTATGCT
Found at i:6546 original size:76 final size:76
Alignment explanation
Indices: 6456--6607 Score: 286
Period size: 76 Copynumber: 2.0 Consensus size: 76
6446 TGTGTTTTTC
* *
6456 TTGGTTACTCAGATAACAAAAGTGTCTTCTTATGTCTAGATGTTGAGTCCTCCAAGATCATTGTG
1 TTGGTTACTCAGATAACAAAAGTGCCTTCTTATGTCTAGATGTTGAGTCCTCCAAGATCATTGTA
6521 TCTAGGCATGT
66 TCTAGGCATGT
6532 TTGGTTACTCAGATAACAAAAGTGCCTTCTTATGTCTAGATGTTGAGTCCTCCAAGATCATTGTA
1 TTGGTTACTCAGATAACAAAAGTGCCTTCTTATGTCTAGATGTTGAGTCCTCCAAGATCATTGTA
6597 TCTAGGCATGT
66 TCTAGGCATGT
6608 AGAGTTTGTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (76 bp):
TTGGTTACTCAGATAACAAAAGTGCCTTCTTATGTCTAGATGTTGAGTCCTCCAAGATCATTGTA
TCTAGGCATGT
Found at i:11867 original size:13 final size:13
Alignment explanation
Indices: 11849--11875 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11839 TATCCCCATG
11849 TTGGAAGCGCATA
1 TTGGAAGCGCATA
11862 TTGGAAGCGCATA
1 TTGGAAGCGCATA
11875 T
1 T
11876 GATGCTGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (13 bp):
TTGGAAGCGCATA
Found at i:11951 original size:22 final size:22
Alignment explanation
Indices: 11925--12000 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
11915 AGCGCATATG
11925 ATGCTGGCAGAGAGTATGAATA
1 ATGCTGGCAGAGAGTATGAATA
* * *
11947 ATGCTGTTGGAAGCGGAGCGTAT--ATG
1 ATGC---T-G--GCAGAGAGTATGAATA
11973 ATGCTGGCAGAGAGTATGAATA
1 ATGCTGGCAGAGAGTATGAATA
11995 ATGCTG
1 ATGCTG
12001 TTGGAAGCGC
Statistics
Matches: 40, Mismatches: 6, Indels: 16
0.65 0.10 0.26
Matches are distributed among these distances:
20 9 0.22
22 13 0.32
23 1 0.03
25 1 0.03
26 7 0.17
28 9 0.22
ACGTcount: A:0.30, C:0.11, G:0.34, T:0.25
Consensus pattern (22 bp):
ATGCTGGCAGAGAGTATGAATA
Found at i:12008 original size:48 final size:48
Alignment explanation
Indices: 11865--12009 Score: 254
Period size: 48 Copynumber: 3.0 Consensus size: 48
11855 GCGCATATTG
* *
11865 GAAGCGCATATGATGCTGGCAAAGAGTATGAATAATGCTGTTGGAAGA
1 GAAGCGCATATGATGCTGGCAGAGAGTATGAATAATGCTGTTGGAAGC
11913 GAAGCGCATATGATGCTGGCAGAGAGTATGAATAATGCTGTTGGAAGC
1 GAAGCGCATATGATGCTGGCAGAGAGTATGAATAATGCTGTTGGAAGC
* *
11961 GGAGCGTATATGATGCTGGCAGAGAGTATGAATAATGCTGTTGGAAGC
1 GAAGCGCATATGATGCTGGCAGAGAGTATGAATAATGCTGTTGGAAGC
12009 G
1 G
12010 CCACCACCAT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 93 1.00
ACGTcount: A:0.32, C:0.11, G:0.34, T:0.23
Consensus pattern (48 bp):
GAAGCGCATATGATGCTGGCAGAGAGTATGAATAATGCTGTTGGAAGC
Found at i:12178 original size:15 final size:15
Alignment explanation
Indices: 12141--12180 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
12131 TTGTTGGAAG
*
12141 GTTGGAAACGCCACT
1 GTTGGAAGCGCCACT
*
12156 GTTGGAAGCGCCATT
1 GTTGGAAGCGCCACT
12171 GTTGGAAGCG
1 GTTGGAAGCG
12181 TCAGCGCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.23
Consensus pattern (15 bp):
GTTGGAAGCGCCACT
Found at i:12587 original size:115 final size:116
Alignment explanation
Indices: 12375--12598 Score: 355
Period size: 115 Copynumber: 1.9 Consensus size: 116
12365 GATGGAAGAA
* **
12375 AATATTTTCTTTGAGGTGCAACCCAAGTTTAAAGTGCAACACTTAGGAAATACTCTCTGAGATGC
1 AATATTTTCTTTGAGGTGCAACCCAAGTTTAAAGTGCAACACTCAGGAAATACTCTCCAAGATGC
12440 AACCAAAACTCTAAGGTGCAACACTTCTTGCAATTTTTTTTTTTGCAGGAT
66 AACCAAAACTCTAAGGTGCAACACTTCTTGCAATTTTTTTTTTTGCAGGAT
* *
12491 AATATTTTC-TTGAGGTGCGACCCAAGTTTAAAGTGCAACACTCAGGAAATA-TTTCCCAAGATG
1 AATATTTTCTTTGAGGTGCAACCCAAGTTTAAAGTGCAACACTCAGGAAATACTCT-CCAAGATG
*
12554 CAACTAAAACTCTAAGGTGCAACAC-TCTTTGCAATTTTTTTTTTT
65 CAACCAAAACTCTAAGGTGCAACACTTC-TTGCAATTTTTTTTTTT
12599 AGCTCCAGAG
Statistics
Matches: 100, Mismatches: 6, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
114 4 0.04
115 87 0.87
116 9 0.09
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (116 bp):
AATATTTTCTTTGAGGTGCAACCCAAGTTTAAAGTGCAACACTCAGGAAATACTCTCCAAGATGC
AACCAAAACTCTAAGGTGCAACACTTCTTGCAATTTTTTTTTTTGCAGGAT
Done.