Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017152.1 Corchorus olitorius cultivar O-4 contig17185, 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: 18544
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Found at i:6074 original size:96 final size:94
Alignment explanation
Indices: 5925--6112 Score: 340
Period size: 94 Copynumber: 2.0 Consensus size: 94
5915 AGTAGTATAC
5925 ACTATCAATGCACTCTATAATGACACACCATCCATGTGTAAATTAAAAAAAAAAAAGCTAAAGTC
1 ACTATCAATGCACTCTATAATGACACACCATCCATGTGTAAATT--AAAAAAAAAAGCTAAAGTC
5990 ATTGATATTAAATACTATTAAATTATTATCT
64 ATTGATATTAAATACTATTAAATTATTATCT
* *
6021 ACTATCAATGCACTCTATAATGACACACCATCCATGTGTAAATTAAAAAAAAAATCTAAAGTCCT
1 ACTATCAATGCACTCTATAATGACACACCATCCATGTGTAAATTAAAAAAAAAAGCTAAAGTCAT
6086 TGATATTAAATACTATTAAATTATTAT
66 TGATATTAAATACTATTAAATTATTAT
6113 AGATATTATT
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
94 46 0.51
96 44 0.49
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (94 bp):
ACTATCAATGCACTCTATAATGACACACCATCCATGTGTAAATTAAAAAAAAAAGCTAAAGTCAT
TGATATTAAATACTATTAAATTATTATCT
Found at i:6483 original size:16 final size:16
Alignment explanation
Indices: 6462--6493 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6452 TCTATCTATA
6462 CTAATTATAATGCGAG
1 CTAATTATAATGCGAG
6478 CTAATTATAATGCGAG
1 CTAATTATAATGCGAG
6494 AACCTAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
CTAATTATAATGCGAG
Found at i:6553 original size:49 final size:49
Alignment explanation
Indices: 6478--6573 Score: 165
Period size: 49 Copynumber: 2.0 Consensus size: 49
6468 ATAATGCGAG
*
6478 CTAATTATAATGCGAGAACCTAAGTTTGTCTCACGAGTTGATTCGGAAA
1 CTAATTATAATGCGAGAACCTAAGTTTGTCTCACGAGTTGACTCGGAAA
* *
6527 CTAATTATAATGTGAGAACCTGAGTTTGTCTCACGAGTTGACTCGGA
1 CTAATTATAATGCGAGAACCTAAGTTTGTCTCACGAGTTGACTCGGA
6574 GACAAACTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (49 bp):
CTAATTATAATGCGAGAACCTAAGTTTGTCTCACGAGTTGACTCGGAAA
Found at i:8690 original size:44 final size:42
Alignment explanation
Indices: 8642--8764 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 42
8632 TAACCTCATG
*
8642 ATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATACT
1 ATGAAATTTTGATAATCTCCCTATGAAATTTTGATCTA-A-ACT
*
8686 ATGAAATTTTGATAA-C-CCTCTTATGAAATTTTGAAAACTAAACT
1 ATGAAATTTTGATAATCTCC-C-TATGAAATTTTG--ATCTAAACT
* * *
8730 ATGAAATTTCGATAATCTTCATATGAAATTTTGAT
1 ATGAAATTTTGATAATCTCCCTATGAAATTTTGAT
8765 ATCTTCCATG
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
42 3 0.04
43 2 0.03
44 55 0.82
45 2 0.03
46 5 0.07
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (42 bp):
ATGAAATTTTGATAATCTCCCTATGAAATTTTGATCTAAACT
Found at i:8710 original size:22 final size:21
Alignment explanation
Indices: 8601--8765 Score: 84
Period size: 22 Copynumber: 7.5 Consensus size: 21
8591 TTGATACTAC
**
8601 AAATTTTGATAACTTTCCTATG
1 AAATTTTGATAACCAT-CTATG
** *
8623 ATTTTTTTATAACC-TCATGATG
1 AAATTTTGATAACCATC-T-ATG
* *
8645 AAATTTTGTTAATCTC-CCTATG
1 AAATTTTGATAA-C-CATCTATG
*
8667 AAATTTTGATCTA-CATACTATG
1 AAATTTTGAT-AACCAT-CTATG
*
8689 AAATTTTGATAACCCTCTTATG
1 AAATTTTGATAACCATC-TATG
* * *
8711 AAATTTTGAAAACTAAACTATG
1 AAATTTTGATAAC-CATCTATG
* * *
8733 AAATTTCGATAATCTTCATATG
1 AAATTTTGATAACCATC-TATG
8755 AAATTTTGATA
1 AAATTTTGATA
8766 TCTTCCATGA
Statistics
Matches: 107, Mismatches: 25, Indels: 22
0.69 0.16 0.14
Matches are distributed among these distances:
20 2 0.02
21 5 0.05
22 94 0.88
23 4 0.04
24 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.42
Consensus pattern (21 bp):
AAATTTTGATAACCATCTATG
Found at i:9362 original size:131 final size:131
Alignment explanation
Indices: 9128--9368 Score: 437
Period size: 131 Copynumber: 1.8 Consensus size: 131
9118 AGCTTTGGAA
*
9128 AAACTATTGATTTTGTCTCATTTCGGCCAAATAGGCCCATTAGACTCGTTTGAGTCCATGAAGTC
1 AAACTATTGATTTTGTCTCATTTCGGCCAAATAAGCCCATTAGACTCGTTTGAGTCCATGAAGTC
*
9193 CATATTGCCAAATCAAATGTCTTGAAGTCTCAATCTGATATTCTTGCTCGTTTGAGTCCATGAGA
66 CAAATTGCCAAATCAAATGTCTTGAAGTCTCAATCTGATATTCTTGCTCGTTTGAGTCCATGAGA
9258 C
131 C
*
9259 AAACTATTGATTTTGTCTCATTTCGGCCAAATAAGCCCATTAGGCTCGTTTGAGTCCATGAAGTC
1 AAACTATTGATTTTGTCTCATTTCGGCCAAATAAGCCCATTAGACTCGTTTGAGTCCATGAAGTC
* *
9324 CAAATTGCCAAGTCAGATGTCTTGAAGTCTCAATCTGATATTCTT
66 CAAATTGCCAAATCAAATGTCTTGAAGTCTCAATCTGATATTCTT
9369 AGACCCAATT
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 105 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (131 bp):
AAACTATTGATTTTGTCTCATTTCGGCCAAATAAGCCCATTAGACTCGTTTGAGTCCATGAAGTC
CAAATTGCCAAATCAAATGTCTTGAAGTCTCAATCTGATATTCTTGCTCGTTTGAGTCCATGAGA
C
Found at i:12300 original size:30 final size:29
Alignment explanation
Indices: 12259--12378 Score: 116
Period size: 29 Copynumber: 4.1 Consensus size: 29
12249 TGAACGGCTT
* *
12259 CGTCTTGGACATTGGCACATGAACGACGAA
1 CGTCCTGGACATTGCCACATGAAC-ACGAA
*
12289 CGTCCTGGACATTGCCAAATGAACACGAA
1 CGTCCTGGACATTGCCACATGAACACGAA
* * * **
12318 CGCCCTGGACATTACCATC-GGAACACGTT
1 CGTCCTGGACATTGCCA-CATGAACACGAA
* *
12347 CGTCCTGGACTTTGCCACAGGAACGACGAA
1 CGTCCTGGACATTGCCACATGAAC-ACGAA
12377 CG
1 CG
12379 CTAGGATCTT
Statistics
Matches: 73, Mismatches: 14, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
28 1 0.01
29 46 0.63
30 26 0.36
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.18
Consensus pattern (29 bp):
CGTCCTGGACATTGCCACATGAACACGAA
Found at i:18365 original size:13 final size:13
Alignment explanation
Indices: 18323--18367 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
18313 TCATGCACCC
*
18323 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
18337 AAAACCATTT-AT
1 AAAACAATTTAAT
18349 AAAACAATTTAAT
1 AAAACAATTTAAT
18362 AAAACA
1 AAAACA
18368 GTAATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 8 0.30
14 9 0.33
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAACAATTTAAT
Done.