Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014641.1 Corchorus olitorius cultivar O-4 contig14674, 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: 8630
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Found at i:2346 original size:40 final size:40
Alignment explanation
Indices: 2239--2611 Score: 577
Period size: 40 Copynumber: 9.2 Consensus size: 40
2229 TTACGCAGCC
*
2239 ATTCACATTTAACTTTCCCAATTGACATTGAACTTGCCTT
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT
*
2279 GATTCACATTCAACTTTCCCAATTGACATTAAACTTGCCTT
1 -ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT
* *
2320 AATTCACA-TCCACTTTTCCAATTGACATTGAACTTGCCTT
1 -ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT
* *
2360 ATTCACATTCAACATTCCCAATTGACATTGACCTTGCCTT
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT
* *
2400 ATTCACATTCAAATTTCCCAAATGACATTGAACTTGCCTT
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT
*
2440 GATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTT
1 -ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT
*
2481 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTT
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT
* *
2521 ATTCACATTCAATTTTCCCAATTCACATTGAACTTGCCTT
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT
*
2561 AATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTT
1 -ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT
2602 AATTCACATT
1 -ATTCACATT
2612 GGCCCTCAAT
Statistics
Matches: 310, Mismatches: 19, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
39 7 0.02
40 172 0.55
41 131 0.42
ACGTcount: A:0.29, C:0.28, G:0.06, T:0.37
Consensus pattern (40 bp):
ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT
Found at i:2349 original size:81 final size:80
Alignment explanation
Indices: 2239--2611 Score: 577
Period size: 81 Copynumber: 4.6 Consensus size: 80
2229 TTACGCAGCC
* *
2239 ATTCACATTTAACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATTCAACTTTCCCAATTG
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT-ATTCACATTCAACTTTCCCAATTC
*
2304 ACATTAAACTTGCCTT
65 ACATTGAACTTGCCTT
* * * *
2320 AATTCACA-TCCACTTTTCCAATTGACATTGAACTTGCCTTATTCACATTCAACATTCCCAATTG
1 -ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTTATTCACATTCAACTTTCCCAATTC
*
2384 ACATTGACCTTGCCTT
65 ACATTGAACTTGCCTT
* *
2400 ATTCACATTCAAATTTCCCAAATGACATTGAACTTGCCTTGATTCACATTCAACTTTCCCAATTC
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT-ATTCACATTCAACTTTCCCAATTC
2465 ACATTGAACTTGCCTT
65 ACATTGAACTTGCCTT
* *
2481 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTATTCACATTCAATTTTCCCAATTCA
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTTATTCACATTCAACTTTCCCAATTCA
2546 CATTGAACTTGCCTT
66 CATTGAACTTGCCTT
*
2561 AATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTAATTCACATT
1 -ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT-ATTCACATT
2612 GGCCCTCAAT
Statistics
Matches: 270, Mismatches: 17, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
79 7 0.03
80 104 0.39
81 143 0.53
82 16 0.06
ACGTcount: A:0.29, C:0.28, G:0.06, T:0.37
Consensus pattern (80 bp):
ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTTATTCACATTCAACTTTCCCAATTCA
CATTGAACTTGCCTT
Found at i:2469 original size:121 final size:121
Alignment explanation
Indices: 2239--2611 Score: 604
Period size: 121 Copynumber: 3.1 Consensus size: 121
2229 TTACGCAGCC
* *
2239 ATTCACATTTAACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATTCAACTTTCCCAATTG
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTT-ATTCACATTCAAATTTCCCAATTG
* * * *
2304 ACATTAAACTTGCCTTAATTCACA-TCCACTTTTCCAATTGACATTGAACTTGCCTT
65 ACATTGAACTTGCCTTAATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTT
* * *
2360 ATTCACATTCAACATTCCCAATTGACATTGACCTTGCCTTATTCACATTCAAATTTCCCAAATGA
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTTATTCACATTCAAATTTCCCAATTGA
*
2425 CATTGAACTTGCCTTGATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTT
66 CATTGAACTTGCCTTAATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTT
* * *
2481 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTATTCACATTCAATTTTCCCAATTCA
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTTATTCACATTCAAATTTCCCAATTGA
2546 CATTGAACTTGCCTTAATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTT
66 CATTGAACTTGCCTTAATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTT
2602 AATTCACATT
1 -ATTCACATT
2612 GGCCCTCAAT
Statistics
Matches: 233, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
120 44 0.19
121 180 0.77
122 9 0.04
ACGTcount: A:0.29, C:0.28, G:0.06, T:0.37
Consensus pattern (121 bp):
ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTTATTCACATTCAAATTTCCCAATTGA
CATTGAACTTGCCTTAATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTT
Found at i:2511 original size:161 final size:162
Alignment explanation
Indices: 2239--2611 Score: 597
Period size: 161 Copynumber: 2.3 Consensus size: 162
2229 TTACGCAGCC
* *
2239 ATTCACATTTAACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATTCAACTTTCCCAATTG
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATTCAACTTTCCCAATTC
* * *
2304 ACATTAAACTTGCCTTAATTCACATCCACTTTTCCAATTGACATTGAACTTGCCTTATTCACATT
66 ACATTAAACTTGCCTTAATTCACATCAACTTTCCCAATTCACATTGAACTTGCCTTATTCACATT
* *
2369 CAACATTCCCAATTGACATTGACCTTGCCTT-
131 CAACATTCCCAATTCACATTGAACTTGCCTTA
* *
2400 ATTCACATTCAAATTTCCCAAATGACATTGAACTTGCCTTGATTCACATTCAACTTTCCCAATTC
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATTCAACTTTCCCAATTC
*
2465 ACATTGAACTTGCCTT-ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTATTCACAT
66 ACATTAAACTTGCCTTAATTCACA-TCAACTTTCCCAATTCACATTGAACTTGCCTTATTCACAT
**
2529 TCAATTTTCCCAATTCACATTGAACTTGCCTTA
130 TCAACATTCCCAATTCACATTGAACTTGCCTTA
* *
2562 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTAATTCACATT
1 ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATT
2612 GGCCCTCAAT
Statistics
Matches: 194, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
160 7 0.04
161 141 0.73
162 46 0.24
ACGTcount: A:0.29, C:0.28, G:0.06, T:0.37
Consensus pattern (162 bp):
ATTCACATTCAACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATTCAACTTTCCCAATTC
ACATTAAACTTGCCTTAATTCACATCAACTTTCCCAATTCACATTGAACTTGCCTTATTCACATT
CAACATTCCCAATTCACATTGAACTTGCCTTA
Found at i:6237 original size:10 final size:10
Alignment explanation
Indices: 6217--6245 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
6207 TACAATGAAC
6217 TGCCA-AAAA
1 TGCCACAAAA
6226 TGCCACAAAA
1 TGCCACAAAA
6236 TGCCACAAAA
1 TGCCACAAAA
6246 ATTATCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.52, C:0.28, G:0.10, T:0.10
Consensus pattern (10 bp):
TGCCACAAAA
Done.