Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019828.1 Corchorus olitorius cultivar O-4 contig19861, 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: 11490
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:245 original size:130 final size:131
Alignment explanation
Indices: 98--341 Score: 409
Period size: 130 Copynumber: 1.9 Consensus size: 131
88 TTAAAATTTT
* * * *
98 TAATATATTTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATAAAATAGGTATAAGGATATT
1 TAATATATATAAATTTTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGATATT
163 AGATTTAATCAAATAAAAATAGAGTTTTTAGTTGAGT-AAACTATAAAAACATATTAAAAAAATT
66 AGATTTAATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACATATTAAAAAAATT
227 A
131 A
* * *
228 TAATATATATAAATTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATT
1 TAATATATATAAATTTTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGATATT
*
293 AGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
66 AGATTTAATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
342 GTCTAAACAA
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
130 94 0.90
131 11 0.10
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (131 bp):
TAATATATATAAATTTTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGATATT
AGATTTAATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACATATTAAAAAAATT
A
Found at i:574 original size:191 final size:191
Alignment explanation
Indices: 250--634 Score: 734
Period size: 191 Copynumber: 2.0 Consensus size: 191
240 ATTTTTTAAT
250 TAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
315 AGTTTTTAGTTGAGTAAAACTATAAAAGTCTAAACAATGGCATTTAAGAAATATATACGAAAAAT
66 AGTTTTTAGTTGAGTAAAACTATAAAAGTCTAAACAATGCCATTTAAGAAATATATACGAAAAAT
380 AAGGGTATAATGGGCGATTCAAAAGTCTTACAAGAGTATGTACTTTTTAATATAGTATAGA
131 AAGGGTATAATGGGCGATTCAAAAGTCTTACAAGAGTATGTACTTTTTAATATAGTATAGA
*
441 TAAAATAGTAAAATGGTGAAAATTAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
506 AGTTTTTAGTTGAGTAAAACTATAAAAGTCTAAACAATGCCATTTAAGAAATATATTCGAAAAAT
66 AGTTTTTAGTTGAGTAAAACTATAAAAGTCTAAACAATGCCATTTAAGAAATATATACGAAAAAT
*
571 AAGGGTATAATGGGCGATTCAAAAGTTTTACAAGAGTATGTACTTTTTAATATAGTATAGA
131 AAGGGTATAATGGGCGATTCAAAAGTCTTACAAGAGTATGTACTTTTTAATATAGTATAGA
632 TAA
1 TAA
635 CTTGGTTTGC
Statistics
Matches: 190, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
191 190 1.00
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (191 bp):
TAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGAGTAAAACTATAAAAGTCTAAACAATGCCATTTAAGAAATATATACGAAAAAT
AAGGGTATAATGGGCGATTCAAAAGTCTTACAAGAGTATGTACTTTTTAATATAGTATAGA
Found at i:5597 original size:286 final size:286
Alignment explanation
Indices: 5082--5650 Score: 1039
Period size: 286 Copynumber: 2.0 Consensus size: 286
5072 ATTTTTAACA
5082 AAGTAGTTCAACTTTGAATTTTATAGCCTACATAAGGGGTTGTACTAATATGGTCTACTGTGGGT
1 AAGTAGTTCAACTTTGAATTTTATAGCCTACATAAGGGGTTGTACTAATATGGTCTACTGTGGGT
* * *
5147 TTAAGCAATAACATAATGAAGAAAGGTCAATGGGGATGCAAATGATATAGTTGAATTAGTCATTA
66 TTAAGCAATAACATAATAAAAAAAGGTCAATGGGGATGCAAATGATATAGTTGAATTAGCCATTA
* *
5212 TAAGATTATCCTTGATAAATTAATGGTTCTACTAATTTATTTGAACCTATTAATACGACCGATGT
131 TAAGATTATCCTTGACAAATTAATGGCTCTACTAATTTATTTGAACCTATTAATACGACCGATGT
* *
5277 GATTAGATTTGTTGAATTTCTAATATATGGGTAAATTTATAATTATAATCAATTTAATTTTCACT
196 GATTAGATTCGTTGAATTTCTAATATAAGGGTAAATTTATAATTATAATCAATTTAATTTTCACT
5342 TTATTTTATGTAAAGTAATTAATACT
261 TTATTTTATGTAAAGTAATTAATACT
*
5368 AAGTAGTTCAACTTTGAATTTTATAGCTTACATAAGGGGTTGTACTAATATGGTCTACTGTGGGT
1 AAGTAGTTCAACTTTGAATTTTATAGCCTACATAAGGGGTTGTACTAATATGGTCTACTGTGGGT
5433 TTAAGCAATAACATAATAAAAAAAGGTCAATGGGGATGCAAATGATATAGTTGAATTAGCCATTA
66 TTAAGCAATAACATAATAAAAAAAGGTCAATGGGGATGCAAATGATATAGTTGAATTAGCCATTA
*
5498 TAAGATTATCCTTGACATATTAATGGCTCTACTAATTTATTTGAACCTATTAATACGACCGATGT
131 TAAGATTATCCTTGACAAATTAATGGCTCTACTAATTTATTTGAACCTATTAATACGACCGATGT
* *
5563 GATTAGATTCGTTGAATTTCTAATATAAGGGTAAATTTGTAATTATAATCCATTTAATTTTCACT
196 GATTAGATTCGTTGAATTTCTAATATAAGGGTAAATTTATAATTATAATCAATTTAATTTTCACT
5628 TTATTTTATGTAAAGTAATTAAT
261 TTATTTTATGTAAAGTAATTAAT
5651 GAAGATTAAT
Statistics
Matches: 272, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
286 272 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (286 bp):
AAGTAGTTCAACTTTGAATTTTATAGCCTACATAAGGGGTTGTACTAATATGGTCTACTGTGGGT
TTAAGCAATAACATAATAAAAAAAGGTCAATGGGGATGCAAATGATATAGTTGAATTAGCCATTA
TAAGATTATCCTTGACAAATTAATGGCTCTACTAATTTATTTGAACCTATTAATACGACCGATGT
GATTAGATTCGTTGAATTTCTAATATAAGGGTAAATTTATAATTATAATCAATTTAATTTTCACT
TTATTTTATGTAAAGTAATTAATACT
Found at i:6114 original size:26 final size:26
Alignment explanation
Indices: 6057--6108 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
6047 ATCAATTTCC
6057 AATAAAATTAATATTAGAAAAAATAA
1 AATAAAATTAATATTAGAAAAAATAA
6083 AATAAAA-TAAT-TTAAGAACAAAATAA
1 AATAAAATTAATATT-AGAA-AAAATAA
6109 GTTAAATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 2 0.08
25 8 0.33
26 14 0.58
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (26 bp):
AATAAAATTAATATTAGAAAAAATAA
Found at i:9296 original size:22 final size:22
Alignment explanation
Indices: 9268--9309 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
9258 AAGAGAATCG
9268 TCACAACCATAAATACATTGGC
1 TCACAACCATAAATACATTGGC
9290 TCACAACCATAAATACATTG
1 TCACAACCATAAATACATTG
9310 TCAAGACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (22 bp):
TCACAACCATAAATACATTGGC
Found at i:10263 original size:42 final size:42
Alignment explanation
Indices: 10204--10298 Score: 190
Period size: 42 Copynumber: 2.3 Consensus size: 42
10194 ACCAAATCAG
10204 ATGATTCCAAAGCTAAAAGAAATCTAACTCCTTAAACTAATA
1 ATGATTCCAAAGCTAAAAGAAATCTAACTCCTTAAACTAATA
10246 ATGATTCCAAAGCTAAAAGAAATCTAACTCCTTAAACTAATA
1 ATGATTCCAAAGCTAAAAGAAATCTAACTCCTTAAACTAATA
10288 ATGATTCCAAA
1 ATGATTCCAAA
10299 AAACCCCTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.26
Consensus pattern (42 bp):
ATGATTCCAAAGCTAAAAGAAATCTAACTCCTTAAACTAATA
Found at i:11294 original size:29 final size:31
Alignment explanation
Indices: 11262--11328 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
11252 ATGCAATTTG
11262 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
*
11291 GGATATAACGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
11322 GGATATA
1 GGATATA
11329 GTCCGTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Done.