Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021817.1 Corchorus olitorius cultivar O-4 contig21850, 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: 14947
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:6619 original size:32 final size:32
Alignment explanation
Indices: 6576--6667 Score: 123
Period size: 31 Copynumber: 2.9 Consensus size: 32
6566 TTGCGCATCA
*
6576 CTTTTTGGTACATGTGGCGTGCCACGTTTTCG
1 CTTTTTGGTACATGTGGCGTGCCACGTTGTCG
* * *
6608 CTTTTTAGTACATGTGGTGTGCCAC-ATGTCG
1 CTTTTTGGTACATGTGGCGTGCCACGTTGTCG
* *
6639 CTTTTTGGTATACGTGGCGTGCCACGTTG
1 CTTTTTGGTACATGTGGCGTGCCACGTTG
6668 GATACCATGA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 25 0.50
32 25 0.50
ACGTcount: A:0.12, C:0.21, G:0.28, T:0.39
Consensus pattern (32 bp):
CTTTTTGGTACATGTGGCGTGCCACGTTGTCG
Found at i:10178 original size:2 final size:2
Alignment explanation
Indices: 10166--10201 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
10156 CCCAAACAAC
10166 AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10202 CTAGTTAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11706 original size:57 final size:58
Alignment explanation
Indices: 11637--11750 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 58
11627 ATTAATAAAA
*
11637 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAGACGTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCT
* * *
11694 TATCAAGTGACATGTTTTTTTATTAGATGCCTAAAAAAGACGTTTTAGGACCGAGGC
1 TATCAAGTGACATGTTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGC
11751 ATGATGCTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 14 0.27
58 38 0.73
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (58 bp):
TATCAAGTGACATGTTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCT
Found at i:13064 original size:36 final size:36
Alignment explanation
Indices: 13017--13086 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
13007 TTCAATAACC
* *
13017 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
13053 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
13087 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:13942 original size:197 final size:202
Alignment explanation
Indices: 13603--14008 Score: 628
Period size: 197 Copynumber: 2.0 Consensus size: 202
13593 GCTTAATAAC
* * *
13603 TTTATCAATGTTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAAAGGTGAATATTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
13668 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTGGTTGA-T
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTTGATT
* *
13732 --TTATTAAATTAAATTAGATCAATGTCAAACAAAA-TTTCAAAATTATAAAAGATATTAAAGAT
131 GATTATAAAATTAAATTAGATCAATGTCAAAAAAAAGTTTCAAAATTATAAAAGATATT-AAGAT
13794 CCGATTAA
195 CCGATTAA
13802 TTTATCAAAGGTGAATATTA-TAA-TTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAAAGGTGAATATTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
13865 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAG-TGG
66 GATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTTGA
*
13929 TTGATTTATTAAATTAAATTAGATCAATGTCAAAAAAAAGTTTCAAAATTATAAAAGATATTAAG
129 TTGA-TTATAAAATTAAATTAGATCAATGTCAAAAAAAAGTTTCAAAATTATAAAAGATATTAAG
*
13994 ATCCGATTTA
193 ATCCGATTAA
14004 TTTAT
1 TTTAT
14009 TATTAAGGAA
Statistics
Matches: 191, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
197 65 0.34
198 6 0.03
199 48 0.25
202 50 0.26
203 22 0.12
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (202 bp):
TTTATCAAAGGTGAATATTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTTGATT
GATTATAAAATTAAATTAGATCAATGTCAAAAAAAAGTTTCAAAATTATAAAAGATATTAAGATC
CGATTAA
Found at i:14171 original size:39 final size:40
Alignment explanation
Indices: 14117--14197 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
14107 ATACCTAAGA
*
14117 ATTTAATTAATGTAAGTACTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTACTTCAGTTATTATATATATTAC
* *
14156 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTACTTCAGTTATTATATATATTAC
14196 AT
1 AT
14198 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTACTTCAGTTATTATATATATTAC
Done.