Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015260.1 Corchorus olitorius cultivar O-4 contig15293, 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: 76808
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:826 original size:2 final size:2
Alignment explanation
Indices: 819--853 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
809 TTCATTTGGC
819 AT AT AT AT 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
854 GGCTTAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6774 original size:31 final size:30
Alignment explanation
Indices: 6703--6774 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
6693 TGAACTGTCG
*
6703 TTTTGCACCC-CACTTTTTTATTTTGATCA
1 TTTTGCACCCTCACTGTTTTATTTTGATCA
* * *
6732 TATCGCACCCTCA-TGTTTTATTTTGGGTGCA
1 TTTTGCACCCTCACTGTTTTATTTT-GAT-CA
6763 TTTTGCACCCTC
1 TTTTGCACCCTC
6775 TGTGACGGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 18 0.53
30 4 0.12
31 12 0.35
ACGTcount: A:0.15, C:0.26, G:0.12, T:0.46
Consensus pattern (30 bp):
TTTTGCACCCTCACTGTTTTATTTTGATCA
Found at i:12771 original size:20 final size:20
Alignment explanation
Indices: 12743--12782 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12733 AAACCAAATT
12743 CACCATGATAGAGAACTCGA
1 CACCATGATAGAGAACTCGA
*
12763 CACCTTGATAGAGAACTCGA
1 CACCATGATAGAGAACTCGA
12783 ATTCACTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (20 bp):
CACCATGATAGAGAACTCGA
Found at i:30086 original size:23 final size:23
Alignment explanation
Indices: 30060--30123 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
30050 CTGTTTTTTG
*
30060 TCATCATCTGATATATTGTTAGT
1 TCATCATCTGATAAATTGTTAGT
* *
30083 TCATAATCTGATACATTGTTAGT
1 TCATCATCTGATAAATTGTTAGT
30106 TCATCATCTGATAAATTG
1 TCATCATCTGATAAATTG
30124 CAATGGTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (23 bp):
TCATCATCTGATAAATTGTTAGT
Found at i:47705 original size:30 final size:30
Alignment explanation
Indices: 47671--47730 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
47661 CAACACACAA
47671 AAACTTACAGGAGAAAGATCACTGACAAAG
1 AAACTTACAGGAGAAAGATCACTGACAAAG
47701 AAACTTACAGGAGAAAGATCACTGACAAAG
1 AAACTTACAGGAGAAAGATCACTGACAAAG
47731 TCAATATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (30 bp):
AAACTTACAGGAGAAAGATCACTGACAAAG
Found at i:53823 original size:28 final size:28
Alignment explanation
Indices: 53791--53847 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
53781 AAGAAGGCCG
53791 ATCCATGCTGATACTAGAAGAATCCACT
1 ATCCATGCTGATACTAGAAGAATCCACT
53819 ATCCATGCTGATACTAGAAGAATCCACT
1 ATCCATGCTGATACTAGAAGAATCCACT
53847 A
1 A
53848 CAGAATTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (28 bp):
ATCCATGCTGATACTAGAAGAATCCACT
Found at i:56654 original size:18 final size:19
Alignment explanation
Indices: 56613--56655 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
56603 ATGAAGGGAA
56613 AAGAAAACTAAAAACTAGT
1 AAGAAAACTAAAAACTAGT
56632 AAGAAAACTAAAAACTAGT
1 AAGAAAACTAAAAACTAGT
56651 -AGAAA
1 AAGAAA
56656 GCCCAAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.65, C:0.09, G:0.12, T:0.14
Consensus pattern (19 bp):
AAGAAAACTAAAAACTAGT
Found at i:64343 original size:216 final size:216
Alignment explanation
Indices: 63802--64343 Score: 703
Period size: 216 Copynumber: 2.5 Consensus size: 216
63792 TTGGGGATAC
* ***
63802 TTTTGGGTATATAAGAAAAAATGTGAATCTCTAAAGAATTTGGGGATGATGCATATGATTATACA
1 TTTTGGGTATAT-A-AAAAAATGTCAATCTCTAAAGAATTTGGGGATGATGCATATGATTATTTG
* * * * * *
63867 TGGATGATGAGAAATTATTTAGGTATAAAATATATCAGTTTGGGGATGCTGAATTTTGCATTTTA
64 GGGATGATGAGAATTTATTTGGGTATAAAGTATATCACTTT--GGATACTGAATTTTGCATTTTA
* * *
63932 TTTAATTACTATATGACACTAAATTCATATGGATGGGGTTTATTCAATTAATTAGGATGAAAATA
127 TTTAATTACTAGATGACACTAAATTCATATAGACGGGGTTTATTCAATTAATTAGGATGAAAATA
* *
63997 TGGATTAAACCTCGTTTAAAGCCAA
192 TGGATTAAACATCGTTTAAAACCAA
64022 TTTTGGGTATATAAAAAAATGTCAATCTCTAAAGAATTTGGGGATGATGCATATGATTATTTGGG
1 TTTTGGGTATATAAAAAAATGTCAATCTCTAAAGAATTTGGGGATGATGCATATGATTATTTGGG
* ** * * * *
64087 AATGATGAGAATGGATTTGGGTATAAAGCATATCACTTTGGATACTGAATTTTGCGTTTTGTTTC
66 GATGATGAGAATTTATTTGGGTATAAAGTATATCACTTTGGATACTGAATTTTGCATTTTATTTA
* * **
64152 ATTATTAGATGACACTAAATTCATATAGACGTGGTTTATTCAATTAATTAGGATGATGATATGGA
131 ATTACTAGATGACACTAAATTCATATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGA
64217 TTAAAACAT-GTTTAAAACCAA
196 TT-AAACATCGTTTAAAACCAA
* * * *
64238 TTTTGGGTATATAAAAAATTGTTAATCTTTAAA-AACTTTGGGGATTG-TGCTTATGATTATTTG
1 TTTTGGGTATATAAAAAAATGTCAATCTCTAAAGAA-TTTGGGGA-TGATGCATATGATTATTTG
* * *
64301 GGGATGATGAGAATTTATTTGGGTATAACGTAAATAACTTTGG
64 GGGATGATGAGAATTTATTTGGGTATAAAGTATATCACTTTGG
64344 GGATACTGGA
Statistics
Matches: 282, Mismatches: 37, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
215 2 0.01
216 182 0.65
217 7 0.02
218 78 0.28
219 1 0.00
220 12 0.04
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (216 bp):
TTTTGGGTATATAAAAAAATGTCAATCTCTAAAGAATTTGGGGATGATGCATATGATTATTTGGG
GATGATGAGAATTTATTTGGGTATAAAGTATATCACTTTGGATACTGAATTTTGCATTTTATTTA
ATTACTAGATGACACTAAATTCATATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGA
TTAAACATCGTTTAAAACCAA
Found at i:64683 original size:21 final size:20
Alignment explanation
Indices: 64659--64704 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
64649 AAAAAAATAC
64659 AAAATAAAAAAGTCAAAGAAA
1 AAAATAAAAAA-TCAAAGAAA
* * *
64680 AAAATAATAAATCGAATAAA
1 AAAATAAAAAATCAAAGAAA
64700 AAAAT
1 AAAAT
64705 GTAGATGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (20 bp):
AAAATAAAAAATCAAAGAAA
Found at i:70041 original size:13 final size:13
Alignment explanation
Indices: 70020--70049 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
70010 CATAGACATC
70020 TATAATTTTTCAT
1 TATAATTTTTCAT
*
70033 TATAGTTTTTCAT
1 TATAATTTTTCAT
70046 TATA
1 TATA
70050 TATTAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (13 bp):
TATAATTTTTCAT
Done.