Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016794.1 Corchorus olitorius cultivar O-4 contig16827, 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: 11960
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:2789 original size:13 final size:14
Alignment explanation
Indices: 2763--2793 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2753 GCATTTTCAG
2763 TATTTTTTGTTGTT
1 TATTTTTTGTTGTT
2777 TATTTTTTG-TGTT
1 TATTTTTTGTTGTT
2790 TATT
1 TATT
2794 GCTTAACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.10, C:0.00, G:0.13, T:0.77
Consensus pattern (14 bp):
TATTTTTTGTTGTT
Found at i:6506 original size:13 final size:13
Alignment explanation
Indices: 6490--6516 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6480 TTTTCAAAAA
6490 AAAAATGGTTTTC
1 AAAAATGGTTTTC
6503 AAAAATGGTTTTC
1 AAAAATGGTTTTC
6516 A
1 A
6517 CGAGGATACT
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:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
AAAAATGGTTTTC
Found at i:7834 original size:31 final size:30
Alignment explanation
Indices: 7789--7846 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
7779 GTGTTTGGCT
*
7789 TAATGTGTCTCGTGTCCGAATCGTGTCGGG
1 TAATGTGTCTCGTGTCAGAATCGTGTCGGG
* *
7819 TAATCGTGTTTCGTGTCATAATCGTGTC
1 TAAT-GTGTCTCGTGTCAGAATCGTGTC
7847 AGGATACGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.38
Consensus pattern (30 bp):
TAATGTGTCTCGTGTCAGAATCGTGTCGGG
Found at i:8539 original size:35 final size:35
Alignment explanation
Indices: 8490--8827 Score: 291
Period size: 35 Copynumber: 9.5 Consensus size: 35
8480 TCAGATGCTG
* * *
8490 AATTTATTTTAATTGATCCAGGGCGATCTTTATTC
1 AATTTATTTCAATTGACCCAGGGCGATCTTTCTTC
* * * *
8525 AGTTTATTTCAATTGATCCAGGGCGGTCCTTCTTC
1 AATTTATTTCAATTGACCCAGGGCGATCTTTCTTC
* ** * *
8560 AATTTATTCCGGTTGACCCAGGGC-AGTCCTTCTCC
1 AATTTATTTCAATTGACCCAGGGCGA-TCTTTCTTC
* * *
8595 AATTTATTTCAGTTGATCCAGGGTGATCTTTCTTC
1 AATTTATTTCAATTGACCCAGGGCGATCTTTCTTC
*** * * * *
8630 AAAACATTTCAGTCGACCCAGGGCGGTCCTTCTTC
1 AATTTATTTCAATTGACCCAGGGCGATCTTTCTTC
** * *
8665 AATTTATTTCAGCTGACCCAGGGTGGTCTTTCTTC
1 AATTTATTTCAATTGACCCAGGGCGATCTTTCTTC
* * * *
8700 AGTTCATTTCAATTGACCCAGGGCGGTCTTTTCGTC
1 AATTTATTTCAATTGACCCAGGGCGATC-TTTCTTC
*
8736 AATTTACTTTTAATTGACCCAGGGCGATCTTTTCTTC
1 AATTTA-TTTCAATTGACCCAGGGCGATC-TTTCTTC
* * *
8773 AATTTATTTCAATGGATCCAGGGCGATCTTTTCTGC
1 AATTTATTTCAATTGACCCAGGGCGATC-TTTCTTC
* *
8809 AGTTTATTTTCAGTTGACC
1 AATTTA-TTTCAATTGACC
8828 GCAAATTGGT
Statistics
Matches: 246, Mismatches: 52, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
35 162 0.66
36 42 0.17
37 42 0.17
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.39
Consensus pattern (35 bp):
AATTTATTTCAATTGACCCAGGGCGATCTTTCTTC
Found at i:9424 original size:30 final size:30
Alignment explanation
Indices: 9378--10166 Score: 873
Period size: 30 Copynumber: 25.8 Consensus size: 30
9368 TCAGTTCACT
*
9378 TTGATGATCATTGCTTTATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
*
9408 TTGAGGATCTTTGCTTTATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
9438 TTGAGGATCATTGCTTTATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
*
9468 TTGAGGATCGTTGCTTTATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
* * *
9498 TTGAGGATCGTTGCATCATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
* * *
9528 TTAAGGATCATTGCATCATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
* *
9558 TTGAGGATCATTGCGTCATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
9588 TTGAGGATCATTGCTTTATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
* * *
9618 TTGAGGATCATTGCATCATTTTAATCCTAG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
* *
9648 TTGAGGATCTTTGCTTTA-ATTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
9677 TTGAGGATCATTGCTTTATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
*
9707 TTGAGGATCGTTGCTTTATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
* *
9737 TTGAGGATCATTGCATCATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
* * * *
9767 TTGACGATCATTGCATCATTTAAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
* *
9797 TTGAGGATCGTTGCTTTATTTTAATCCTGA
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
9827 TTGAGGATCATTGCTTTATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
** * *
9857 TTGAGGAT-ATTTGCTCCATTTCAATCTTGG
1 TTGAGGATCA-TTGCTTTATTTTAATCCTGG
* *
9887 TTGAGGATCGTTGCTTTATTTTAGTCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
*
9917 TTGAGGATCGTTGCTTTATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
* * * *
9947 TTGAGGATCGTTGCTTTCTTTCAATCCTTG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
* * * *
9977 TTTAGGATCTTTACTTTATCTATTTCAATCCTCG
1 TTGAGGATCATTGCTTTA--T-TTT-AATCCTGG
* * * * *
10011 TTTAGTACCGTTAGTTGGTTTCATTTTGATCCTGG
1 TTGAGGA---TCA-TTGCTTT-ATTTTAATCCTGG
* * **
10046 TTTAGGATCATTGCTTCATAAGTTAATCTTAGTTGTGG
1 TTGAGGATCATTGCTT--T-A--T--T-TTAATCCTGG
* * *
10084 TTGAGGATGATTG-TTTCATTTTAATCTTGA
1 TTGAGGATCATTGCTTT-ATTTTAATCCTGG
* *
10114 TTTAGGATCATTGCTTCATTTTAATCCTGG
1 TTGAGGATCATTGCTTTATTTTAATCCTGG
* * *
10144 TTTAGGATCATTACTTTAGTTTA
1 TTGAGGATCATTGCTTTATTTTA
10167 TTTGAATCTT
Statistics
Matches: 653, Mismatches: 86, Indels: 40
0.84 0.11 0.05
Matches are distributed among these distances:
29 27 0.04
30 551 0.84
31 8 0.01
32 3 0.00
33 5 0.01
34 13 0.02
35 15 0.02
36 3 0.00
37 5 0.01
38 22 0.03
39 1 0.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.46
Consensus pattern (30 bp):
TTGAGGATCATTGCTTTATTTTAATCCTGG
Found at i:10865 original size:15 final size:15
Alignment explanation
Indices: 10841--10870 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10831 TATTCCATGA
10841 TTGATCTCAATTAAT
1 TTGATCTCAATTAAT
*
10856 TTGATTTCAATTAAT
1 TTGATCTCAATTAAT
10871 AGATTGGCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (15 bp):
TTGATCTCAATTAAT
Done.