Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019513.1 Corchorus olitorius cultivar O-4 contig19546, 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: 41313
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3591 original size:36 final size:35
Alignment explanation
Indices: 3551--3641 Score: 148
Period size: 36 Copynumber: 2.6 Consensus size: 35
3541 CCCAAGCTTA
3551 GCCTAGGCGCTTGGGCCGCGCTGGCCCGCGCGCCTG
1 GCCTAGGCGCTTGGGCCGCGCTGGCCCG-GCGCCTG
*
3587 GCCTAGGCGCTTGGGCCGCGCTGGCCTGGCGCCTG
1 GCCTAGGCGCTTGGGCCGCGCTGGCCCGGCGCCTG
*
3622 GCCTA-GCGTTTGGGCCGCGC
1 GCCTAGGCGCTTGGGCCGCGC
3642 CAGGCAGGCC
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
34 14 0.26
35 12 0.23
36 27 0.51
ACGTcount: A:0.03, C:0.38, G:0.42, T:0.16
Consensus pattern (35 bp):
GCCTAGGCGCTTGGGCCGCGCTGGCCCGGCGCCTG
Found at i:9281 original size:46 final size:46
Alignment explanation
Indices: 9210--9305 Score: 183
Period size: 46 Copynumber: 2.1 Consensus size: 46
9200 GTCGTAAAAG
*
9210 AAACATTGAGAATGTCAAATGTGTTGGTGTGGCTCCCCCGTGTTGC
1 AAACATTGAGAATGTCAAATATGTTGGTGTGGCTCCCCCGTGTTGC
9256 AAACATTGAGAATGTCAAATATGTTGGTGTGGCTCCCCCGTGTTGC
1 AAACATTGAGAATGTCAAATATGTTGGTGTGGCTCCCCCGTGTTGC
9302 AAAC
1 AAAC
9306 GATGACTGCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (46 bp):
AAACATTGAGAATGTCAAATATGTTGGTGTGGCTCCCCCGTGTTGC
Found at i:11830 original size:15 final size:15
Alignment explanation
Indices: 11782--11831 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
11772 TGCTAGGGTG
*
11782 AATGGTGCAAACAAC
1 AATGGTGCGAACAAC
*
11797 AATGGTGCGAATAAC
1 AATGGTGCGAACAAC
* *
11812 AATGGTGTGAACAAT
1 AATGGTGCGAACAAC
11827 AATGG
1 AATGG
11832 AAAGGGTGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20
Consensus pattern (15 bp):
AATGGTGCGAACAAC
Found at i:17949 original size:17 final size:19
Alignment explanation
Indices: 17921--17956 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
17911 CGGCCTAGTC
17921 CCTGATTTAAAT-CAATTT
1 CCTGATTTAAATGCAATTT
17939 CCTGA-TTAAATGCAATTT
1 CCTGATTTAAATGCAATTT
17957 GGTCCCTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (19 bp):
CCTGATTTAAATGCAATTT
Found at i:18590 original size:24 final size:24
Alignment explanation
Indices: 18541--18619 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 24
18531 AATTTGAAGA
*
18541 AAAAAATGAAAAA-G-AAGAAAAG-
1 AAAAAATGAAAAATGTAA-AAATGT
18563 AAAAAATGAAAAATGTAAAAATGT
1 AAAAAATGAAAAATGTAAAAATGT
*
18587 -AAAAATCAGAAAAT-TAAAAGATGT
1 AAAAAATGA-AAAATGTAAAA-ATGT
18611 AATAAAATG
1 AA-AAAATG
18620 TGTTTTCAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
22 13 0.28
23 17 0.36
24 11 0.23
25 1 0.02
26 5 0.11
ACGTcount: A:0.68, C:0.01, G:0.14, T:0.16
Consensus pattern (24 bp):
AAAAAATGAAAAATGTAAAAATGT
Found at i:24473 original size:13 final size:13
Alignment explanation
Indices: 24455--24481 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24445 ATGGATGCTT
24455 TATACATTGATTG
1 TATACATTGATTG
24468 TATACATTGATTG
1 TATACATTGATTG
24481 T
1 T
24482 GAGGGAGTTT
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:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TATACATTGATTG
Found at i:26960 original size:163 final size:163
Alignment explanation
Indices: 26682--26988 Score: 472
Period size: 163 Copynumber: 1.9 Consensus size: 163
26672 CAGAAGCATG
* *
26682 GATTTCCAAAGCACATACCATTTAAATGGTTCATAGACAAAACAGGAGTAAACAAAATATAGCTT
1 GATTTCCAAAGCACAAACCATTTAAATGGTTCATAAACAAAACAGGAGTAAACAAAATATAGCTT
* ** *
26747 CTAACGACAAAGAGAAAACCTCTTCAGAAGCTTCAAACTGAGACAGAATCTGAGAAGCAAGATAA
66 CTAACGACAAAGACAAAACCTCAGCAGAAGCTTCAAACTGAGACAGAATCTCAGAAGCAAGATAA
*
26812 TGAGTAAGAGTTTTAGAGGTACAAAAAAACATA
131 AGAGTAAGAGTTTTAGAGGTACAAAAAAACATA
* *
26845 GATTTCCAAAGCACAAAGCATTTAAATGGTTCATAAACAAAACAGGGGTAAACAAAATGA-AGCT
1 GATTTCCAAAGCACAAACCATTTAAATGGTTCATAAACAAAACAGGAGTAAACAAAAT-ATAGCT
* * * * *
26909 TCTAAGGATAAAGACAAAACCTGAGCAGAAGCTTCAACCTGAGATAGAATCTCAGAAGCAAGATA
65 TCTAACGACAAAGACAAAACCTCAGCAGAAGCTTCAAACTGAGACAGAATCTCAGAAGCAAGATA
26974 AAGAGTAAGAGTTTT
130 AAGAGTAAGAGTTTT
26989 GGAGATCAAT
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
163 128 0.99
164 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.21
Consensus pattern (163 bp):
GATTTCCAAAGCACAAACCATTTAAATGGTTCATAAACAAAACAGGAGTAAACAAAATATAGCTT
CTAACGACAAAGACAAAACCTCAGCAGAAGCTTCAAACTGAGACAGAATCTCAGAAGCAAGATAA
AGAGTAAGAGTTTTAGAGGTACAAAAAAACATA
Found at i:31016 original size:13 final size:13
Alignment explanation
Indices: 30998--31024 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30988 TACTAATTGG
30998 GCTGGTAGAAATA
1 GCTGGTAGAAATA
31011 GCTGGTAGAAATA
1 GCTGGTAGAAATA
31024 G
1 G
31025 AATTTGCATT
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:0.37, C:0.07, G:0.33, T:0.22
Consensus pattern (13 bp):
GCTGGTAGAAATA
Found at i:32042 original size:8 final size:8
Alignment explanation
Indices: 32027--32067 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
32017 TTCAAAAATG
32027 AAAAAACA
1 AAAAAACA
*
32035 AAACAACA
1 AAAAAACA
*
32043 AAACAAAAA
1 AAA-AAACA
32052 AAAAAACA
1 AAAAAACA
32060 AAAAAACA
1 AAAAAACA
32068 GAGCATGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 22 0.79
9 6 0.21
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:32052 original size:20 final size:20
Alignment explanation
Indices: 32027--32067 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
32017 TTCAAAAATG
* *
32027 AAAAAACAAAACAACAAAAC
1 AAAAAAAAAAACAAAAAAAC
32047 AAAAAAAAAAACAAAAAAAC
1 AAAAAAAAAAACAAAAAAAC
32067 A
1 A
32068 GAGCATGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAACAAAAAAAC
Found at i:35768 original size:14 final size:13
Alignment explanation
Indices: 35749--35786 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
35739 ATTTTGTCAT
35749 GAGAAATAGAAAAA
1 GAGAAAT-GAAAAA
*
35763 GAGAAAT-TAAAA
1 GAGAAATGAAAAA
35775 GAGAAATGAAAA
1 GAGAAATGAAAA
35787 TTTGTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 11 0.52
13 3 0.14
14 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (13 bp):
GAGAAATGAAAAA
Found at i:36964 original size:13 final size:13
Alignment explanation
Indices: 36946--36970 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36936 CTCTTCATCC
36946 CTTTTCCATGTGA
1 CTTTTCCATGTGA
36959 CTTTTCCATGTG
1 CTTTTCCATGTG
36971 GGATATTGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.16, T:0.48
Consensus pattern (13 bp):
CTTTTCCATGTGA
Done.