Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015244.1 Corchorus olitorius cultivar O-4 contig15277, 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: 8965
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Found at i:4332 original size:50 final size:50
Alignment explanation
Indices: 4272--4420 Score: 217
Period size: 50 Copynumber: 3.0 Consensus size: 50
4262 GTTTTACAAT
*
4272 AAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAGA
1 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGA
* * * *
4322 AAAATCGCTTTCCATTGGTGAGTTCAAGATCAAAATTTGCTTTTCAAAGT
1 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGA
* * * *
4372 AAGATTGCATTCCATTTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
4421 GACATTGAAG
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 87 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (50 bp):
AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGA
Found at i:4787 original size:25 final size:27
Alignment explanation
Indices: 4739--4823 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 27
4729 TCAGCATGAA
4739 CAAGAAAGC-AA-ATTC-AAGGACAAA-T
1 CAAGAAAGCAAAGATTCGAA-G-CAAAGT
4764 CAAGAAGAGCAAAGA-T-GAAGCAAAGT
1 CAAGAA-AGCAAAGATTCGAAGCAAAGT
4790 CAAGAAAGCAAAGATTCGAAGCAACAGT
1 CAAGAAAGCAAAGATTCGAAGCAA-AGT
*
4818 CCAGAA
1 CAAGAA
4824 GTTTCAATCA
Statistics
Matches: 51, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
25 18 0.35
26 12 0.24
27 12 0.24
28 9 0.18
ACGTcount: A:0.53, C:0.16, G:0.21, T:0.09
Consensus pattern (27 bp):
CAAGAAAGCAAAGATTCGAAGCAAAGT
Found at i:4802 original size:14 final size:14
Alignment explanation
Indices: 4739--4802 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
4729 TCAGCATGAA
*
4739 CAAGAAAGCAAATT
1 CAAGAAAGCAAAGT
*
4753 CAAG-GA-CAAA-T
1 CAAGAAAGCAAAGT
4764 CAAGAAGAGCAAAG-
1 CAAGAA-AGCAAAGT
*
4778 -ATG-AAGCAAAGT
1 CAAGAAAGCAAAGT
4790 CAAGAAAGCAAAG
1 CAAGAAAGCAAAG
4803 ATTCGAAGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
11 12 0.31
12 5 0.13
13 6 0.15
14 16 0.41
ACGTcount: A:0.56, C:0.14, G:0.22, T:0.08
Consensus pattern (14 bp):
CAAGAAAGCAAAGT
Found at i:5081 original size:50 final size:50
Alignment explanation
Indices: 5022--5356 Score: 499
Period size: 50 Copynumber: 6.7 Consensus size: 50
5012 CGAAGGTTTT
* * * * *
5022 GGCTTTTCCATAAGTCAAACTCGTTTCCATACAAGTCGATTATCAGCATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* * *
5072 GGCTTTTCCACAAGCTAAACTCGTTTCCATACGAGTCGATTATCAATATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* * *
5122 GTCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAATATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
*
5172 GGCTTTTCCACAAGCCAAACTTGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
5222 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* *
5272 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* * **
5322 GGCTTTTTCATAAGCCATAGTTCGTTTCCATACGA
1 GGCTTTTCCACAAGCCA-AACTCGTTTCCATACGA
5357 TACATTACCA
Statistics
Matches: 266, Mismatches: 18, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
50 251 0.94
51 15 0.06
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.31
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
Found at i:5643 original size:35 final size:35
Alignment explanation
Indices: 5372--5642 Score: 366
Period size: 35 Copynumber: 7.8 Consensus size: 35
5362 TACCATCTTC
5372 TCAGATGACTCGGTGTAGCATCTTCAAAGATGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGATGAAT
* * **
5407 T-AGATGACTCGATGTAGCATCTTCAAAAATGACC
1 TCAGATGACTCGGTGTAGCATCTTCAAAGATGAAT
* *
5441 TCAGATGATTCGGTGTAGCATCTTCAAAGACGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGATGAAT
* *
5476 TCAGATGACTCGGTGTAGCACCTTCAAACATGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGATGAAT
* * * *
5511 TTAGAAGACTCGGTGTAACATCTTCAAAG-TTATAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGATGA-AT
*
5546 TCAGATGACTCGGTGTAGCATCTTCAAAGATAAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGATGAAT
* *
5581 TTAGATGACTCGGTGTAGCATCTTCAATGATGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGATGAAT
* *
5616 TCAAATGACTCGGTGTAGCATTTTCAA
1 TCAGATGACTCGGTGTAGCATCTTCAA
5643 TATGAACTAG
Statistics
Matches: 203, Mismatches: 30, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
34 32 0.16
35 169 0.83
36 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (35 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGATGAAT
Found at i:5969 original size:29 final size:29
Alignment explanation
Indices: 5897--5970 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 29
5887 GGGTCACTTA
5897 AGGGGGCATTTTGGTCATTCTGCATATCC
1 AGGGGGCATTTTGGTCATTCTGCATATCC
* *
5926 A-GGGGCATTTTGGTCATTTTGCATATCT
1 AGGGGGCATTTTGGTCATTCTGCATATCC
5954 AGGGGGCATTTTGGTCA
1 AGGGGGCATTTTGGTCA
5971 GTTCAAGTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 26 0.62
29 16 0.38
ACGTcount: A:0.18, C:0.16, G:0.30, T:0.36
Consensus pattern (29 bp):
AGGGGGCATTTTGGTCATTCTGCATATCC
Done.