Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011883.1 Corchorus olitorius cultivar O-4 contig11916, 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: 17834
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Found at i:8114 original size:68 final size:68
Alignment explanation
Indices: 7998--8198 Score: 332
Period size: 68 Copynumber: 3.0 Consensus size: 68
7988 CTTACATACC
*
7998 AGCTAAGAAGAGAGATGAAGATTAAAAAAGATGAAGATGCAAAATGAAGTGAGAAGAGAGAAAGT
1 AGCTAAGAAGAGAGATGAAGATTAAAAAAGATGAAGATGCAAAGTGAAGTGAGAAGAGAGAAAGT
8063 CAA
66 CAA
* * * *
8066 ATCTAGGAAGAGAGATGAAGTTTAAAAAAGATGAAGATGCAAAGTGAAGTGAAAAGAGAGAAAGT
1 AGCTAAGAAGAGAGATGAAGATTAAAAAAGATGAAGATGCAAAGTGAAGTGAGAAGAGAGAAAGT
8131 CAA
66 CAA
*
8134 AGCTAAGAAGAGAGATGAAGATTCAAAAAGATG-AGAATGCAAAGTGAAGTGAGAAGAGAGAAAG
1 AGCTAAGAAGAGAGATGAAGATTAAAAAAGATGAAG-ATGCAAAGTGAAGTGAGAAGAGAGAAAG
8198 T
65 T
8199 GTAGCTCAGA
Statistics
Matches: 122, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
67 2 0.02
68 120 0.98
ACGTcount: A:0.52, C:0.04, G:0.29, T:0.14
Consensus pattern (68 bp):
AGCTAAGAAGAGAGATGAAGATTAAAAAAGATGAAGATGCAAAGTGAAGTGAGAAGAGAGAAAGT
CAA
Found at i:11099 original size:137 final size:137
Alignment explanation
Indices: 10851--11112 Score: 398
Period size: 137 Copynumber: 1.9 Consensus size: 137
10841 CTTGCAGCGT
* * *
10851 TTGAAAAATCTCGATGAGAAGAATCAGATGGTCAGGGAGGTGTGAAAACCAAACAATCGGAAAAT
1 TTGAAAAATCTCGACGAGAAGAATCAGATGGTCAGGGAGATGAGAAAACCAAACAATCGGAAAAT
* * * *
10916 TACAGATGTCGAGTCAAATTTAAAACTTTGACTAGAAGGTGCGGTCTTATTCGGCGTCGATTCTA
66 TACAGATCTCAAGTCAAATTTAAAACTTTAACTAGAAGATGCGGTCTTATTCGGCGTCGATTCTA
10981 GCAGCAA
131 GCAGCAA
* * *
10988 TTGAAAGATCTCGACGAGAAGAATCGGATGGTCAGGGAGATGAGAAAACCAAACAATCGGAAGAT
1 TTGAAAAATCTCGACGAGAAGAATCAGATGGTCAGGGAGATGAGAAAACCAAACAATCGGAAAAT
* * * *
11053 TTCAGATCTCAAGTCAAATTTAAAACTTTAACTGGAAGATGTGGTCTTATTCGGTGTCGA
66 TACAGATCTCAAGTCAAATTTAAAACTTTAACTAGAAGATGCGGTCTTATTCGGCGTCGA
11113 AACGAGCTGA
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
137 111 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (137 bp):
TTGAAAAATCTCGACGAGAAGAATCAGATGGTCAGGGAGATGAGAAAACCAAACAATCGGAAAAT
TACAGATCTCAAGTCAAATTTAAAACTTTAACTAGAAGATGCGGTCTTATTCGGCGTCGATTCTA
GCAGCAA
Found at i:14070 original size:51 final size:51
Alignment explanation
Indices: 13973--14070 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
13963 TTCATACTTT
* **
13973 TCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGTTTCTC
1 TCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTTCTC
*
14024 TCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TCTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGTT
14071 CTTCATTCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 2 0.05
51 38 0.93
52 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (51 bp):
TCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTTCTC
Found at i:16729 original size:203 final size:201
Alignment explanation
Indices: 16485--16893 Score: 748
Period size: 203 Copynumber: 2.0 Consensus size: 201
16475 TTTCTTAATA
16485 ATAAATAAATTCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATTCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
16550 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATATTTCTATATATATAATAGT
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTT-T-TATATATAATAAT
16615 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATAATAACATT
129 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATAATAACATT
16680 CACCATTG
194 CACCATTG
16688 ATAAATAAA-TCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
1 ATAAATAAATTCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
*
16752 TAATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTGGTATAGTTTTATATATAATAATA
65 TAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTTTATATATAATAATA
*
16817 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
130 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATAATAACATTC
16882 ACCATTG
195 ACCATTG
16889 ATAAA
1 ATAAA
16894 GTTATTAAGC
Statistics
Matches: 201, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
201 89 0.44
202 8 0.04
203 104 0.52
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (201 bp):
ATAAATAAATTCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTTTATATATAATAATAA
TGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATAATAACATTCA
CCATTG
Found at i:17453 original size:36 final size:36
Alignment explanation
Indices: 17406--17475 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
17396 GAGATTTTGG
* *
17406 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
17442 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
17476 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.