Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012108.1 Corchorus olitorius cultivar O-4 contig12141, 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: 8360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2743 original size:27 final size:27
Alignment explanation
Indices: 2707--2768 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
2697 ACCAAAAAGA
*
2707 TTTT-TTTATTTATTT-ACTATTTATAT
1 TTTTATTTATTAATTTAACTA-TTATAT
*
2733 TTTTATTTATTAATTTAACTATTATCT
1 TTTTATTTATTAATTTAACTATTATAT
*
2760 ATTTATTTA
1 TTTTATTTA
2769 CTATTTATCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 4 0.13
27 23 0.74
28 4 0.13
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTATTTATTAATTTAACTATTATAT
Found at i:2757 original size:19 final size:18
Alignment explanation
Indices: 2735--2824 Score: 54
Period size: 19 Copynumber: 4.4 Consensus size: 18
2725 ATTTATATTT
*
2735 TTATTTATTAATTTAACTA
1 TTATCTATTAATTT-ACTA
*
2754 TTATCTATTTATTTACTA
1 TTATCTATTAATTTACTA
2772 TTTATCCTTTTATTTATTAATTTAGCTA
1 -TTAT-C---TA--T-T-AATTTA-CTA
*
2800 TTATCTATTTATTTACTA
1 TTATCTATTAATTTACTA
2818 TTATCTA
1 TTATCTA
2825 CTTTTTTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 21
0.70 0.05 0.26
Matches are distributed among these distances:
18 14 0.25
19 21 0.37
20 2 0.04
21 1 0.02
23 4 0.07
25 1 0.02
26 2 0.04
27 9 0.16
28 3 0.05
ACGTcount: A:0.29, C:0.10, G:0.01, T:0.60
Consensus pattern (18 bp):
TTATCTATTAATTTACTA
Found at i:2783 original size:46 final size:46
Alignment explanation
Indices: 2713--2834 Score: 190
Period size: 46 Copynumber: 2.6 Consensus size: 46
2703 AAGATTTTTT
*
2713 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
1 TATTTATTTACTATTTATACTTTTATTTATTAATTTAACTATTATC
* *
2759 TATTTATTTACTATTTATCCTTTTATTTATTAATTTAGCTATTATC
1 TATTTATTTACTATTTATACTTTTATTTATTAATTTAACTATTATC
* *
2805 TATTTATTTACTATTATCTACTTTTTTTTA
1 TATTTATTTACTATT-TATACTTTTATTTA
2835 CCTACCTATT
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 58 0.84
47 11 0.16
ACGTcount: A:0.27, C:0.09, G:0.01, T:0.63
Consensus pattern (46 bp):
TATTTATTTACTATTTATACTTTTATTTATTAATTTAACTATTATC
Found at i:2803 original size:27 final size:27
Alignment explanation
Indices: 2717--2814 Score: 80
Period size: 27 Copynumber: 3.7 Consensus size: 27
2707 TTTTTTTATT
* *
2717 TATTTA-CTATTTATATT-TTTATTTAT
1 TATTTATCTATTTAT-TTATTAATTTAC
* * *
2743 TAATTTAACTA-TTATCTATTTATTTAC
1 T-ATTTATCTATTTATTTATTAATTTAC
2770 TATTTATCCT-TTTATTTATTAATTTAGC
1 TATTTAT-CTATTTATTTATTAATTTA-C
2798 TA-TTATCTATTTATTTA
1 TATTTATCTATTTATTTA
2815 CTATTATCTA
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
26 9 0.15
27 45 0.75
28 6 0.10
ACGTcount: A:0.29, C:0.08, G:0.01, T:0.62
Consensus pattern (27 bp):
TATTTATCTATTTATTTATTAATTTAC
Found at i:3805 original size:198 final size:198
Alignment explanation
Indices: 3467--3864 Score: 778
Period size: 198 Copynumber: 2.0 Consensus size: 198
3457 ACAATTCTAG
3467 ATGATTAAGGGGGATAGTATTTATTATAACATTTATGTGAAAGGAAAGGATAATTACAAAAAAGG
1 ATGATTAAGGGGGATAGTATTTATTATAACATTTATGTGAAAGGAAAGGATAATTACAAAAAAGG
3532 GCTTAAGGGCAAGAACTGGTTAGAAACTAACCTAGGGTCTTCTGAGTAATTTGGCAAGTGAGAAA
66 GCTTAAGGGCAAGAACTGGTTAGAAACTAACCTAGGGTCTTCTGAGTAATTTGGCAAGTGAGAAA
3597 AGACATAAAAGGACAAAAAAAGTTCAAATAGAGCCTCCTCATCGATCCTCAAAAGGGGCCTTTGG
131 AGACATAAAAGGACAAAAAAAGTTCAAATAGAGCCTCCTCATCGATCCTCAAAAGGGGCCTTTGG
3662 TAA
196 TAA
3665 ATGATTAAGGGGGATAGTATTTATTATAACATTTATGTGAAAGGAAAGGATAATTACAAAAAAGG
1 ATGATTAAGGGGGATAGTATTTATTATAACATTTATGTGAAAGGAAAGGATAATTACAAAAAAGG
3730 GCTTAAGGGCAAGAACTGGTTAGAAACTAACCTAGGGTCTTCTGAGTAATTTGGCAAGTGAGAAA
66 GCTTAAGGGCAAGAACTGGTTAGAAACTAACCTAGGGTCTTCTGAGTAATTTGGCAAGTGAGAAA
* *
3795 AGACATAAAAGGACAAAAAAAGTTCAAATGGAGCCTCCTCATCGATCTTCAAAAGGGGCCTTTGG
131 AGACATAAAAGGACAAAAAAAGTTCAAATAGAGCCTCCTCATCGATCCTCAAAAGGGGCCTTTGG
3860 TAA
196 TAA
3863 AT
1 AT
3865 TCCCTGGGTC
Statistics
Matches: 198, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
198 198 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (198 bp):
ATGATTAAGGGGGATAGTATTTATTATAACATTTATGTGAAAGGAAAGGATAATTACAAAAAAGG
GCTTAAGGGCAAGAACTGGTTAGAAACTAACCTAGGGTCTTCTGAGTAATTTGGCAAGTGAGAAA
AGACATAAAAGGACAAAAAAAGTTCAAATAGAGCCTCCTCATCGATCCTCAAAAGGGGCCTTTGG
TAA
Found at i:6770 original size:18 final size:18
Alignment explanation
Indices: 6743--6777 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6733 TATTTCTAGA
*
6743 TTTGGGGTCTTGCTAAAG
1 TTTGGAGTCTTGCTAAAG
*
6761 TTTGGAGTCTTGGTAAA
1 TTTGGAGTCTTGCTAAA
6778 ATTTTGGGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.09, G:0.31, T:0.40
Consensus pattern (18 bp):
TTTGGAGTCTTGCTAAAG
Found at i:7727 original size:11 final size:11
Alignment explanation
Indices: 7711--7745 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
7701 TTTTTCTGTT
7711 TTTTGTTTTTG
1 TTTTGTTTTTG
*
7722 TTTTGTTTTCG
1 TTTTGTTTTTG
7733 TTTTGTTTTTG
1 TTTTGTTTTTG
7744 TT
1 TT
7746 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Done.