Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016349.1 Corchorus olitorius cultivar O-4 contig16382, 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: 85658
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:18327 original size:27 final size:27
Alignment explanation
Indices: 18289--18354 Score: 100
Period size: 25 Copynumber: 2.5 Consensus size: 27
18279 GTCATATTTT
*
18289 GAATATAACAATTTTTTTTTGGCACAA
1 GAATATGACAATTTTTTTTTGGCACAA
*
18316 GAATATGGCAA--TTTTTTTGGCACAA
1 GAATATGACAATTTTTTTTTGGCACAA
18341 GAATATGACAATTT
1 GAATATGACAATTT
18355 AATTATCACT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 24 0.71
27 10 0.29
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (27 bp):
GAATATGACAATTTTTTTTTGGCACAA
Found at i:27772 original size:2 final size:2
Alignment explanation
Indices: 27765--27800 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
27755 TTAGGTATGC
27765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27801 TTTAATCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28865 original size:13 final size:13
Alignment explanation
Indices: 28847--28871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28837 ATAAAGATAG
28847 AAAAATAAAAAAT
1 AAAAATAAAAAAT
28860 AAAAATAAAAAA
1 AAAAATAAAAAA
28872 GGAGAGGATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:56546 original size:52 final size:52
Alignment explanation
Indices: 56482--56587 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
56472 TTTTGATCAT
56482 ATGATCAACTTGTTCAACATTGAATATCTTATAGCAACATAACTAGCAATAA
1 ATGATCAACTTGTTCAACATTGAATATCTTATAGCAACATAACTAGCAATAA
56534 ATGATCAACTTGTTCAACATTGAATATCTTATAGCAACATAACTAGCAATAA
1 ATGATCAACTTGTTCAACATTGAATATCTTATAGCAACATAACTAGCAATAA
56586 AT
1 AT
56588 TCTTCCAGCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.31
Consensus pattern (52 bp):
ATGATCAACTTGTTCAACATTGAATATCTTATAGCAACATAACTAGCAATAA
Found at i:64095 original size:59 final size:58
Alignment explanation
Indices: 63999--64119 Score: 215
Period size: 59 Copynumber: 2.1 Consensus size: 58
63989 CAGAGATTAC
63999 AAATATCCGAAGGAATAGTCCCGCACCAGCTCAATCTTAGCTAGAATGCTAATACATT
1 AAATATCCGAAGGAATAGTCCCGCACCAGCTCAATCTTAGCTAGAATGCTAATACATT
* *
64057 AAATCATCCGGAGGAATAGTCCCGCACCAGCTCAATCTTAGCTAGAGTGCTAATACATT
1 AAAT-ATCCGAAGGAATAGTCCCGCACCAGCTCAATCTTAGCTAGAATGCTAATACATT
64116 AAAT
1 AAAT
64120 TGAAGCGTAC
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 4 0.07
59 56 0.93
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (58 bp):
AAATATCCGAAGGAATAGTCCCGCACCAGCTCAATCTTAGCTAGAATGCTAATACATT
Found at i:64204 original size:42 final size:42
Alignment explanation
Indices: 64157--64246 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
64147 GTCAAATCTC
*
64157 TAATTTCATTTATAACTATCAAACAAACCAAATACACAAAAT
1 TAATTTCATTTATAACTACCAAACAAACCAAATACACAAAAT
64199 TAATTTCATTTATAACTACCAAACAAACCAAATACACAAAAT
1 TAATTTCATTTATAACTACCAAACAAACCAAATACACAAAAT
64241 TAATTT
1 TAATTT
64247 ACAAATTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (42 bp):
TAATTTCATTTATAACTACCAAACAAACCAAATACACAAAAT
Found at i:67150 original size:7 final size:7
Alignment explanation
Indices: 67138--67169 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
67128 ATTAAGCCCA
67138 TTCTATT
1 TTCTATT
67145 TTCTATT
1 TTCTATT
67152 TTCTATT
1 TTCTATT
*
67159 TTCTATG
1 TTCTATT
67166 TTCT
1 TTCT
67170 TACTAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.12, C:0.16, G:0.03, T:0.69
Consensus pattern (7 bp):
TTCTATT
Found at i:79550 original size:20 final size:20
Alignment explanation
Indices: 79522--79566 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
79512 GTTCCGTTGT
*
79522 TTAATATCTAACGCAACGAC
1 TTAAGATCTAACGCAACGAC
79542 TTAAGATCTAACGCAACGAC
1 TTAAGATCTAACGCAACGAC
*
79562 CTAAG
1 TTAAG
79567 TGTCCGCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.22
Consensus pattern (20 bp):
TTAAGATCTAACGCAACGAC
Found at i:83258 original size:4 final size:4
Alignment explanation
Indices: 83249--83274 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
83239 TGTTAAACAA
83249 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
83275 CGAGTAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Done.