Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012449.1 Corchorus olitorius cultivar O-4 contig12482, 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: 6175
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Found at i:288 original size:31 final size:31
Alignment explanation
Indices: 251--332 Score: 139
Period size: 31 Copynumber: 2.6 Consensus size: 31
241 GCCCTAATTG
*
251 ATTATATCCTTAATTGCTTGAAATCGAAAAAG
1 ATTATATCCTTAATTGCTTGAAATC-AAAAAC
283 A-TATATCCTTAATTGCTTGAAATCAAAAAC
1 ATTATATCCTTAATTGCTTGAAATCAAAAAC
313 ATTATATCCTTAATTGCTTG
1 ATTATATCCTTAATTGCTTG
333 TTTTGTAACG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
30 6 0.12
31 41 0.85
32 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (31 bp):
ATTATATCCTTAATTGCTTGAAATCAAAAAC
Found at i:2718 original size:12 final size:13
Alignment explanation
Indices: 2700--2731 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
2690 GACTTTTAGT
2700 AGTTAATTAAGTG
1 AGTTAATTAAGTG
2713 -GTTAATTAAGTG
1 AGTTAATTAAGTG
2725 AGTTAAT
1 AGTTAAT
2732 GGCCGGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
AGTTAATTAAGTG
Found at i:3856 original size:23 final size:21
Alignment explanation
Indices: 3818--3874 Score: 96
Period size: 23 Copynumber: 2.6 Consensus size: 21
3808 TAAAAAAATA
3818 TTTTTTAAAAAAATATATAAT
1 TTTTTTAAAAAAATATATAAT
3839 TTTTTTAAAAATATATATATAAT
1 TTTTTTAAAAA-A-ATATATAAT
3862 TTTTTTAAAAAAA
1 TTTTTTAAAAAAA
3875 AATTTGGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 12 0.35
22 2 0.06
23 20 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTTTAAAAAAATATATAAT
Found at i:4028 original size:17 final size:17
Alignment explanation
Indices: 4006--4044 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
3996 AAATATTTCA
4006 TTTTTCTTCTTTTCT-TT
1 TTTTTCTT-TTTTCTATT
4023 TTTTTCTTTTTTCTATT
1 TTTTTCTTTTTTCTATT
4040 TTTTT
1 TTTTT
4045 AAATCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTCTTTTTTCTATT
Found at i:4385 original size:23 final size:23
Alignment explanation
Indices: 4357--4400 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
4347 TAAAATGCAC
4357 CAAAACAGTCACCACTAACCCAT
1 CAAAACAGTCACCACTAACCCAT
4380 CAAAACAGTCACCACTAACCC
1 CAAAACAGTCACCACTAACCC
4401 TCTTCCTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.41, G:0.05, T:0.11
Consensus pattern (23 bp):
CAAAACAGTCACCACTAACCCAT
Found at i:5087 original size:75 final size:75
Alignment explanation
Indices: 5003--5177 Score: 174
Period size: 75 Copynumber: 2.3 Consensus size: 75
4993 GATGCTCAAA
* * *
5003 ATTTAAATTCGAATCAGAAACCTGATAAAGTGAATCAGCTTCAAG-TTGTTG-CAAATCATCATC
1 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATT-TTGCCAAA-CACCATC
*
5066 AGAAAACTTAGT
64 AGAAAACTCAGT
* ** * * * * *
5078 ATTTGAATTCAAAAGAGGAATCTGGTCAAGTGAATCAACTTCAAGATTTTGCCTAACACCATCAG
1 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATTTTGCCAAACACCATCAG
* *
5143 CAAACTCATT
66 AAAACTCAGT
* *
5153 ATTTGAATTCGAATTAGCAACCTGA
1 ATTTGAATTCGAATCAGAAACCTGA
5178 GAAGGAGCAT
Statistics
Matches: 78, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
75 73 0.94
76 5 0.06
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (75 bp):
ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATTTTGCCAAACACCATCAG
AAAACTCAGT
Done.