Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010774.1 Corchorus olitorius cultivar O-4 contig10806, 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: 9218
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Found at i:86 original size:39 final size:40
Alignment explanation
Indices: 43--123 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
33 ATACCTACGA
*
43 ATTTAATTAATGTAAATATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
* *
82 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
122 AT
1 AT
124 AGGAATTATA
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:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAATATTTCAGTTATTATATATATTAC
Found at i:1383 original size:25 final size:25
Alignment explanation
Indices: 1300--1369 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
1290 CAGCCTATGT
*
1300 GTTTTCCAAACGCAAGCATAGGTTC
1 GTTTTCCAAACGCAAGCACAGGTTC
1325 GTTTTCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGTTC
*
1350 ATTTTCCAAACGCAAGCACA
1 GTTTTCCAAACGCAAGCACA
1370 TGAGCGTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (25 bp):
GTTTTCCAAACGCAAGCACAGGTTC
Found at i:4479 original size:22 final size:22
Alignment explanation
Indices: 4435--4654 Score: 153
Period size: 22 Copynumber: 10.0 Consensus size: 22
4425 CACATTTTGC
*
4435 AAATTT-GATAACCT-AATATG
1 AAATTTCGATAACCTCACTATG
*
4455 AAATTTCGATAACCTCCCTATG
1 AAATTTCGATAACCTCACTATG
* *
4477 AAAATTCGATAACCACACTATG
1 AAATTTCGATAACCTCACTATG
* * *
4499 AAATTTGGGTAACCACACTATG
1 AAATTTCGATAACCTCACTATG
* * *
4521 AAATTTCGATAATCTCAGTGTG
1 AAATTTCGATAACCTCACTATG
* * *
4543 AAATTTTGATAATCTGC-CTATA
1 AAATTTCGATAACCT-CACTATG
** * *
4565 AAATTTTAATAATCACACTAAAT-
1 AAATTTCGATAACCTCACT--ATG
* * *
4588 AAAATT-GGTAACCGCACTATG
1 AAATTTCGATAACCTCACTATG
* * *
4609 AAAATTTTGATAACCACACCATG
1 -AAATTTCGATAACCTCACTATG
*
4632 AAATTTCGATAACCTCCCTATG
1 AAATTTCGATAACCTCACTATG
4654 A
1 A
4655 GAATGAAACT
Statistics
Matches: 158, Mismatches: 33, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
20 8 0.05
21 9 0.06
22 121 0.77
23 18 0.11
24 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.31
Consensus pattern (22 bp):
AAATTTCGATAACCTCACTATG
Found at i:4512 original size:44 final size:44
Alignment explanation
Indices: 4435--4654 Score: 173
Period size: 44 Copynumber: 5.0 Consensus size: 44
4425 CACATTTTGC
4435 AAATTTGATAACCTA-A-TATGAAATTTCGATAACCTCCCTATGA
1 AAATTTGATAACC-ACACTATGAAATTTCGATAACCTCCCTATGA
* * * * *
4478 AAATTCGATAACCACACTATGAAATTTGGGTAACCACACTATG-
1 AAATTTGATAACCACACTATGAAATTTCGATAACCTCCCTATGA
* * * * * * *
4521 AAATTTCGATAATCTCAGTGTGAAATTTTGATAATCTGCCTAT-A
1 AAATTT-GATAACCACACTATGAAATTTCGATAACCTCCCTATGA
* * * * * *
4565 AAATTTTAATAATCACACTAAAT-AAAATT-GGTAACCGCACTATGA
1 AAA-TTTGATAACCACACT--ATGAAATTTCGATAACCTCCCTATGA
*
4610 AAATTTTGATAACCACACCATGAAATTTCGATAACCTCCCTATGA
1 AAA-TTTGATAACCACACTATGAAATTTCGATAACCTCCCTATGA
4655 GAATGAAACT
Statistics
Matches: 134, Mismatches: 33, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
42 1 0.01
43 20 0.15
44 74 0.55
45 38 0.28
46 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.31
Consensus pattern (44 bp):
AAATTTGATAACCACACTATGAAATTTCGATAACCTCCCTATGA
Found at i:4715 original size:22 final size:22
Alignment explanation
Indices: 4690--4759 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
4680 TGTATTTTCG
*
4690 ATAATCTCTCCATAAAATTTTT
1 ATAACCTCTCCATAAAATTTTT
4712 ATAACCTC-CCTATAAAATTTTGT
1 ATAACCTCTCC-ATAAAATTTT-T
* * *
4735 -TAACCTCTCTAGAAAATTTTG
1 ATAACCTCTCCATAAAATTTTT
4756 ATAA
1 ATAA
4760 GCACAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 2 0.05
22 36 0.90
23 2 0.05
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (22 bp):
ATAACCTCTCCATAAAATTTTT
Found at i:4811 original size:22 final size:22
Alignment explanation
Indices: 4786--4847 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
4776 CCTCCCTCCC
*
4786 TATGAAATTTTGGTAACCTCTG
1 TATGAAATTTTGGTAACCTCTA
* *
4808 TATGAAATTTTGATAATCTCTA
1 TATGAAATTTTGGTAACCTCTA
4830 TATGAAATTTTGGTAACC
1 TATGAAATTTTGGTAACC
4848 ACACTACGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGGTAACCTCTA
Found at i:4837 original size:44 final size:44
Alignment explanation
Indices: 4786--4887 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 44
4776 CCTCCCTCCC
* ** *
4786 TATGAAATTTTGGTAACCTCTGTATGAAATTTTGATAATCTCTA
1 TATGAAATTTTGGTAACCACACTACGAAATTTTGATAATCTCTA
* * *
4830 TATGAAATTTTGGTAACCACACTACGATATTTTGATAATCTTTC
1 TATGAAATTTTGGTAACCACACTACGAAATTTTGATAATCTCTA
*
4874 TATGTAATTTTGGT
1 TATGAAATTTTGGT
4888 TTGATTGTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (44 bp):
TATGAAATTTTGGTAACCACACTACGAAATTTTGATAATCTCTA
Found at i:5625 original size:18 final size:19
Alignment explanation
Indices: 5578--5623 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
5568 ACAAAGTAAT
* *
5578 CAATGAAAAGTGAGTATGG
1 CAATAAAAATTGAGTATGG
5597 CAATAAAAATTGAGTATGG
1 CAATAAAAATTGAGTATGG
5616 CAATAAAA
1 CAATAAAA
5624 TTTTCAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.50, C:0.07, G:0.22, T:0.22
Consensus pattern (19 bp):
CAATAAAAATTGAGTATGG
Done.