Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021231.1 Corchorus olitorius cultivar O-4 contig21264, 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: 24724
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Found at i:2759 original size:20 final size:21
Alignment explanation
Indices: 2722--2764 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
2712 ATCTCACACA
2722 AAGATTATCAAAAATCATAGG
1 AAGATTATCAAAAATCATAGG
*
2743 AAGATTA-CAAAATTCATAGG
1 AAGATTATCAAAAATCATAGG
2763 AA
1 AA
2765 AATTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (21 bp):
AAGATTATCAAAAATCATAGG
Found at i:2838 original size:21 final size:21
Alignment explanation
Indices: 2812--2887 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
2802 CTTATGAAGT
* *
2812 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTAATAGGTAA
* **
2833 TTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTAATA-GGTAA
2855 TTATCAAAATTTAATAGGTAA
1 TTATCAAAATTTAATAGGTAA
2876 TTATCAAAATTT
1 TTATCAAAATTT
2888 CATAAAAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 29 0.62
22 18 0.38
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (21 bp):
TTATCAAAATTTAATAGGTAA
Found at i:2859 original size:43 final size:43
Alignment explanation
Indices: 2768--2891 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 43
2758 ATAGGAAAAT
* * * * * *
2768 TTATTAAAATTTTATAGTTAGGTTATCAAAGTTTCTTATGAAGT
1 TTATCAAAATTTTATAGGTA-ATTATCAAAATTTCATATGAAGG
* **
2812 TTATCACAATTTTATAGGTAATTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTTATAGGTAATTATCAAAATTTCATATGAAGG
*
2855 TTATCAAAATTTAATAGGTAATTATCAAAATTTCATA
1 TTATCAAAATTTTATAGGTAATTATCAAAATTTCATA
2892 AAAATATTCA
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
43 52 0.75
44 17 0.25
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (43 bp):
TTATCAAAATTTTATAGGTAATTATCAAAATTTCATATGAAGG
Found at i:5127 original size:14 final size:15
Alignment explanation
Indices: 5110--5139 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5100 GTTTTTGACA
5110 TGTGTTTTTGT-TAT
1 TGTGTTTTTGTCTAT
5124 TGTGTTTTTGTCTAT
1 TGTGTTTTTGTCTAT
5139 T
1 T
5140 TGCCCCTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.07, C:0.03, G:0.20, T:0.70
Consensus pattern (15 bp):
TGTGTTTTTGTCTAT
Found at i:8224 original size:19 final size:18
Alignment explanation
Indices: 8200--8238 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
8190 AATTAGCTTA
8200 TTTAAAAAGTGCCTTCAGT
1 TTTAAAAA-TGCCTTCAGT
* *
8219 TTTAAACATGGCTTCAGT
1 TTTAAAAATGCCTTCAGT
8237 TT
1 TT
8239 AGTGGCTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (18 bp):
TTTAAAAATGCCTTCAGT
Found at i:11830 original size:14 final size:14
Alignment explanation
Indices: 11811--11837 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11801 AATCAGAGGA
11811 GGTGGGGGGGGGGG
1 GGTGGGGGGGGGGG
11825 GGTGGGGGGGGGG
1 GGTGGGGGGGGGG
11838 AATAATCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.93, T:0.07
Consensus pattern (14 bp):
GGTGGGGGGGGGGG
Found at i:12218 original size:16 final size:16
Alignment explanation
Indices: 12197--12229 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12187 ATATTTCAAT
12197 TTTAAAAAATAAATGG
1 TTTAAAAAATAAATGG
*
12213 TTTAAAATATAAATGG
1 TTTAAAAAATAAATGG
12229 T
1 T
12230 CAAAAATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (16 bp):
TTTAAAAAATAAATGG
Found at i:12385 original size:33 final size:33
Alignment explanation
Indices: 12348--12416 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
12338 TCTATGGTTT
12348 ATACCGATAAAATTATGGTGGAATTGTTTAAGA
1 ATACCGATAAAATTATGGTGGAATTGTTTAAGA
12381 ATACCGATAAAATTATGGTGGAATTGTTTAAGA
1 ATACCGATAAAATTATGGTGGAATTGTTTAAGA
12414 ATA
1 ATA
12417 GATTTGATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (33 bp):
ATACCGATAAAATTATGGTGGAATTGTTTAAGA
Done.