Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008434.1 Corchorus capsularis cultivar CVL-1 contig08455, 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: 21942
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:5589 original size:33 final size:35
Alignment explanation
Indices: 5533--5597 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
5523 AAGAATTCCG
*
5533 CAAAAATAAAAGATAGAAAAGAGATAATTTGATGC
1 CAAAAATAAAAGAAAGAAAAGAGATAATTTGATGC
5568 CAAAAA-AAAA-AAAGAAAAGAGATAATTTGA
1 CAAAAATAAAAGAAAGAAAAGAGATAATTTGA
5598 GGAGAAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 19 0.66
34 4 0.14
35 6 0.21
ACGTcount: A:0.63, C:0.05, G:0.15, T:0.17
Consensus pattern (35 bp):
CAAAAATAAAAGAAAGAAAAGAGATAATTTGATGC
Found at i:12196 original size:63 final size:63
Alignment explanation
Indices: 12119--12250 Score: 255
Period size: 63 Copynumber: 2.1 Consensus size: 63
12109 TAATTTAAAC
12119 ACTAAAAATTAAAGAATTAAATTATATATTTATTGTATTATAATTATATTAAGCAAACTTTAA
1 ACTAAAAATTAAAGAATTAAATTATATATTTATTGTATTATAATTATATTAAGCAAACTTTAA
12182 ACTAAAAATTAAAGAATTAAATTATATATTTATTGTATTATAATTATATTAAGCAAACTTTAA
1 ACTAAAAATTAAAGAATTAAATTATATATTTATTGTATTATAATTATATTAAGCAAACTTTAA
*
12245 ATTAAA
1 ACTAAA
12251 TAGTAAATAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (63 bp):
ACTAAAAATTAAAGAATTAAATTATATATTTATTGTATTATAATTATATTAAGCAAACTTTAA
Found at i:13169 original size:22 final size:21
Alignment explanation
Indices: 13135--13530 Score: 111
Period size: 22 Copynumber: 17.6 Consensus size: 21
13125 CTAATCCCTG
*
13135 TGAAACTTTGATACCCACACTA
1 TGAAA-TTTGATAACCACACTA
13157 TGAAATTTCGATAACCATC-CTA
1 TGAAATTT-GATAACCA-CACTA
* *
13179 TTAAATTTTGATTACCACACTA
1 TGAAA-TTTGATAACCACACTA
13201 TGAAACTTTGATAACCACACTA
1 TGAAA-TTTGATAACCACACTA
* * *
13223 TAAAATAGTGATAACCTCTAC-A
1 TGAAAT-TTGATAACCAC-ACTA
* **
13245 TGAAATTAATTTTGCTAACTTCACTA
1 TG--A--AA-TTTGATAACCACACTA
* *
13271 TAAAATTTTGATAACCACAATAA
1 TGAAA-TTTGATAACCACACT-A
* ****
13294 TTGTGAAAAGGTTGATTTGGTACACTA
1 ---TG-AAA-TTTGA-TAACCACACTA
*
13321 TGAAATTTGGATAACCATACTA
1 TGAAATTT-GATAACCACACTA
* *
13343 TGAAATTTTGATAACCTCCCTA
1 TGAAA-TTTGATAACCACACTA
* ** *
13365 -GGAATGTTGATAACTTCCCTA
1 TGAAAT-TTGATAACCACACTA
* * * *
13386 TAGAATTTTGTTAATCTCACTA
1 T-GAAATTTGATAACCACACTA
*
13408 TGAAATTTTGATAAGCACAAC-A
1 TGAAA-TTTGATAACCAC-ACTA
* * **
13430 TCAAATTTTGATTACC-TTCTA
1 TGAAA-TTTGATAACCACACTA
* *
13451 TGAAATTTTTG-TGACCACATTA
1 TGAAA--TTTGATAACCACACTA
* * *
13473 TGAAATTTGGATAATCATATTA
1 TGAAATTT-GATAACCACACTA
**
13495 TGAAATTTTGATAGTCACACTA
1 TGAAA-TTTGATAACCACACTA
13517 TGAAATTTTGATAA
1 TGAAA-TTTGATAA
13531 TCTGCAAAGT
Statistics
Matches: 279, Mismatches: 64, Indels: 62
0.69 0.16 0.15
Matches are distributed among these distances:
20 5 0.02
21 35 0.13
22 183 0.66
23 23 0.08
24 4 0.01
25 2 0.01
26 13 0.05
27 9 0.03
28 5 0.02
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (21 bp):
TGAAATTTGATAACCACACTA
Found at i:14007 original size:31 final size:31
Alignment explanation
Indices: 13962--14036 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
13952 TTTAGTAATG
* *
13962 ACAATTTAGAAATATGTTTTAAAAAAAAGGGT
1 ACAATTGA-AAATATATTTTAAAAAAAAGGGT
*
13994 ACAATTGAAAATATATTTTAAAAATAAGGGT
1 ACAATTGAAAATATATTTTAAAAAAAAGGGT
14025 ACAATTGGAAAA
1 ACAATT-GAAAA
14037 CATAAAGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
31 27 0.69
32 12 0.31
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.29
Consensus pattern (31 bp):
ACAATTGAAAATATATTTTAAAAAAAAGGGT
Found at i:14763 original size:21 final size:21
Alignment explanation
Indices: 14737--14801 Score: 130
Period size: 21 Copynumber: 3.1 Consensus size: 21
14727 TTGTCTTTTC
14737 AATTTTGTTTAGGTTCATAAT
1 AATTTTGTTTAGGTTCATAAT
14758 AATTTTGTTTAGGTTCATAAT
1 AATTTTGTTTAGGTTCATAAT
14779 AATTTTGTTTAGGTTCATAAT
1 AATTTTGTTTAGGTTCATAAT
14800 AA
1 AA
14802 AGAAATAGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.51
Consensus pattern (21 bp):
AATTTTGTTTAGGTTCATAAT
Done.