Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023665.1 Corchorus olitorius cultivar O-4 contig23698, 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: 17277
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Found at i:388 original size:28 final size:27
Alignment explanation
Indices: 291--398 Score: 139
Period size: 27 Copynumber: 4.0 Consensus size: 27
281 TAAAAATGTG
*
291 CATG-AAATGACTAAAATGTCCCC-GGA
1 CATGCAAATGACCAAAATG-CCCCTGGA
* *
317 CGTGCAAATGACCAAAATACCCCTGGA
1 CATGCAAATGACCAAAATGCCCCTGGA
344 CATGCAAATGACCAAAATGCCCCTGGA
1 CATGCAAATGACCAAAATGCCCCTGGA
* *
371 CCTGAGAAATGACCAAAATGCCCCTGGA
1 CATG-CAAATGACCAAAATGCCCCTGGA
399 TGAGTGACCC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 7 0.10
27 43 0.60
28 22 0.31
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.16
Consensus pattern (27 bp):
CATGCAAATGACCAAAATGCCCCTGGA
Found at i:389 original size:55 final size:53
Alignment explanation
Indices: 291--398 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 53
281 TAAAAATGTG
* *
291 CATGAAATGACTAAAATGTCCCCGGACGTGCAAATGACCAAAATACCCCTGGA
1 CATGAAATGACCAAAATGTCCCCGGACCTGCAAATGACCAAAATACCCCTGGA
* *
344 CATGCAAATGACCAAAATG-CCCCTGGACCTGAGAAATGACCAAAATGCCCCTGGA
1 CATG-AAATGACCAAAATGTCCCC-GGACCTG-CAAATGACCAAAATACCCCTGGA
399 TGAGTGACCC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
53 8 0.17
54 19 0.40
55 21 0.44
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.16
Consensus pattern (53 bp):
CATGAAATGACCAAAATGTCCCCGGACCTGCAAATGACCAAAATACCCCTGGA
Found at i:8235 original size:3 final size:3
Alignment explanation
Indices: 8227--8251 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
8217 TTTAAATACA
8227 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
8252 AATAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:11671 original size:19 final size:18
Alignment explanation
Indices: 11643--11678 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11633 ACAGAAGATA
11643 CCAATCAGTAAACATCTT
1 CCAATCAGTAAACATCTT
*
11661 CCAACTCAGTAGACATCT
1 CCAA-TCAGTAAACATCT
11679 ATTCTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.36, C:0.31, G:0.08, T:0.25
Consensus pattern (18 bp):
CCAATCAGTAAACATCTT
Found at i:16172 original size:33 final size:33
Alignment explanation
Indices: 16127--16249 Score: 115
Period size: 33 Copynumber: 3.8 Consensus size: 33
16117 TCCAAAACAG
*
16127 AATTT-GTTTCATCACAAACAACACCTAAAATA
1 AATTTAGTGTCATCACAAACAACACCTAAAATA
* *
16159 AATTTAGTGTCATCACAAACAACACTTAAATTA
1 AATTTAGTGTCATCACAAACAACACCTAAAATA
** * * * *
16192 GGTTTAGTATCATCACTAACAACATCTAAAACA
1 AATTTAGTGTCATCACAAACAACACCTAAAATA
* **
16225 GATTTCA-TGTCATTGCAAACAACAC
1 AATTT-AGTGTCATCACAAACAACAC
16250 TCAAATTAGG
Statistics
Matches: 72, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
32 5 0.07
33 66 0.92
34 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.28
Consensus pattern (33 bp):
AATTTAGTGTCATCACAAACAACACCTAAAATA
Found at i:16214 original size:66 final size:66
Alignment explanation
Indices: 16135--16261 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 66
16125 AGAATTTGTT
* *
16135 TCATCACAAACAACACCTAAAATAAATTT-AGTGTCATCACAAACAACACTTAAATTAGGTTTAG
1 TCATCACAAACAACACCTAAAACAAATTTCA-TGTCATCACAAACAACACTCAAATTAGGTTTAG
16199 TA
65 TA
* * * **
16201 TCATCACTAACAACATCTAAAACAGATTTCATGTCATTGCAAACAACACTCAAATTAGGTT
1 TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATTAGGTT
16262 CAGAATTACT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
66 52 0.98
67 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (66 bp):
TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATTAGGTTTAGT
A
Found at i:16865 original size:15 final size:15
Alignment explanation
Indices: 16845--16876 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
16835 AAACTAAGTG
16845 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
16860 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
16875 GA
1 GA
16877 ACCCCCAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (15 bp):
GAGCTTGTTGATTTT
Done.