Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020367.1 Corchorus olitorius cultivar O-4 contig20400, 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, 965
Length: 1609
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Found at i:98 original size:35 final size:35
Alignment explanation
Indices: 3--231 Score: 323
Period size: 35 Copynumber: 6.5 Consensus size: 35
1 GT
* * *
3 ATGATCAGAGTTGTTCTCCTTTCAAGTAAGTTTTTT
1 ATGATCAGAGTTGATCTCATTTCAAG-AAGTTTTTG
* *
39 ATGATCAGAGTTGTTCTTCCTTTCAAGAAGTTTTTG
1 ATGATCAGAGTTGATC-TCATTTCAAGAAGTTTTTG
*
75 ATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTG
1 ATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTG
*
110 ATTATCAGAGTTGATCTCATTTCAAGAAGTTTTTG
1 ATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTG
*
145 ATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTT
1 ATGATCAGAGTTGATCTCATTTCAAGAAG-TTTTTG
* **
181 ATGATCAGAGTTGATCTCATTCCAAGAAGTTTTCA
1 ATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTG
*
216 ATGGTCAGAGTTGATC
1 ATGATCAGAGTTGATC
232 CCAAAAGATC
Statistics
Matches: 180, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
35 98 0.54
36 72 0.40
37 10 0.06
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.41
Consensus pattern (35 bp):
ATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTG
Found at i:192 original size:106 final size:107
Alignment explanation
Indices: 3--231 Score: 327
Period size: 106 Copynumber: 2.1 Consensus size: 107
1 GT
* * * * *
3 ATGATCAGAGTTGTTCTCCTTTCAAGTAAGTTTTTTATGATCAGAGTTGTTCTTCCTTTCAAGAA
1 ATGATCAGAGTTGATCTCATTTCAAGTAAGTTTTTGATGATCAGAGTTGATCTTCATTTCAAGAA
* * **
68 GTTTTTGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTG
66 GTTTTTGATGATCAGAGTTGATCTCATTCCAAGAAGTTTTCA
*
110 ATTATCAGAGTTGATCTCATTTCAAG-AAGTTTTTGATGATCAGAGTTGATC-TCATTTCAAGAA
1 ATGATCAGAGTTGATCTCATTTCAAGTAAGTTTTTGATGATCAGAGTTGATCTTCATTTCAAGAA
*
173 GTTTTTTTATGATCAGAGTTGATCTCATTCCAAGAAGTTTTCA
66 G-TTTTTGATGATCAGAGTTGATCTCATTCCAAGAAGTTTTCA
*
216 ATGGTCAGAGTTGATC
1 ATGATCAGAGTTGATC
232 CCAAAAGATC
Statistics
Matches: 108, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
105 12 0.11
106 73 0.68
107 23 0.21
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.41
Consensus pattern (107 bp):
ATGATCAGAGTTGATCTCATTTCAAGTAAGTTTTTGATGATCAGAGTTGATCTTCATTTCAAGAA
GTTTTTGATGATCAGAGTTGATCTCATTCCAAGAAGTTTTCA
Found at i:313 original size:54 final size:54
Alignment explanation
Indices: 197--744 Score: 385
Period size: 54 Copynumber: 10.2 Consensus size: 54
187 AGAGTTGATC
* *
197 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGAT-CCCAAAAGATCCAGTGGGG
1 TCATTCCAAGAAGTTTTTAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * *
250 TCATTCCAAGAAGTTTTTAATGGTCAGAATTGATCCCCAAAAGGTCCAGTGTGG
1 TCATTCCAAGAAGTTTTTAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * *
304 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCGCC-AAAGATCCAATGCGG
1 TCATTCCAAGAAGTTTTTAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * * * *
357 TCATTCCAAGAAG-TTTT-ATGATCAGAGTTGATCCTCAGATGATCCCGTGCGG
1 TCATTCCAAGAAGTTTTTAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * * * *
409 TCATTCCAAGAAGTTTTTGATGATCAGAGTTGATCTCCAGATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTTAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * * * ** * *
463 TCCTTCCAAAAAGTTTTCGAA-GTTCAGAGTTGATGTCCAGATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTT-TAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * * * * * * * * *
517 TTC-TTCCTAGAAGTTTTCAAAGATCAAAGTTGATCTCCAGATGATCCGGTGCTG
1 -TCATTCCAAGAAGTTTTTAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* * * * ** * * * **
571 TCATTTCAAGAAATTTTCGAA-GATCAGAGTTGATCTTCAGATGATCCGGTATGG
1 TCATTCCAAGAAGTTTT-TAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* ** * * * * * *
625 TCGTTTTAAGAAGTTTTCGAA-GATCAGAGTTGATCTCCAGATGATCCAGTGTGG
1 TCATTCCAAGAAGTTTT-TAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
* *** * * ** **
679 TCGTT-CAAGAAGTTTCCGATGATCAGAGTTGATCTCCAATTTGATCCAGTATGG
1 TCATTCCAAGAAGTTTTTAATGGTCAGAGTTGATCCCCAA-AAGATCCAGTGCGG
*
733 TCACTCCAAGAA
1 TCATTCCAAGAA
745 AGGTTTTCGT
Statistics
Matches: 424, Mismatches: 59, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
51 16 0.04
52 28 0.07
53 92 0.22
54 277 0.65
55 11 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (54 bp):
TCATTCCAAGAAGTTTTTAATGGTCAGAGTTGATCCCCAAAAGATCCAGTGCGG
Found at i:529 original size:108 final size:108
Alignment explanation
Indices: 197--744 Score: 567
Period size: 108 Copynumber: 5.1 Consensus size: 108
187 AGAGTTGATC
* * * *
197 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC-CCAAAAGATCCAGTGGGGTCATTCCAAGA
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCATTCCAAGA
* * * * * * * *
261 AGTTTT-TAATGGTCAGAATTGATCCCCAAAAGGTCCAGTGTGG
66 AGTTTTCGAA-GATCAGAGTTGATCTCCAGATGATCCAGTGCGG
* * * *
304 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCGCCA-AAGATCCAATGCGGTCATTCCAAGA
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCATTCCAAGA
* *
368 AGTTTT--ATGATCAGAGTTGATC-CTCAGATGATCCCGTGCGG
66 AGTTTTCGAAGATCAGAGTTGATCTC-CAGATGATCCAGTGCGG
** * *
409 TCATTCCAAGAAGTTTTTGATGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCCTTCCAAAA
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCATTCCAAGA
* *
474 AGTTTTCGAAGTTCAGAGTTGATGTCCAGATGATCCAGTGCGG
66 AGTTTTCGAAGATCAGAGTTGATCTCCAGATGATCCAGTGCGG
* * * * * *
517 TTC-TTCCTAGAAGTTTTCAAAGATCAAAGTTGATCTCCAGATGATCCGGTGCTGTCATTTCAAG
1 -TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCATTCCAAG
* * * **
581 AAATTTTCGAAGATCAGAGTTGATCTTCAGATGATCCGGTATGG
65 AAGTTTTCGAAGATCAGAGTTGATCTCCAGATGATCCAGTGCGG
* ** * *
625 TCGTTTTAAGAAGTTTTCGAA-GATCAGAGTTGATCTCCAGATGATCCAGTGTGGTCGTT-CAAG
1 TCATTCCAAGAAGTTTTC-AATGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCATTCCAAG
* * **
688 AAGTTTCCGATGATCAGAGTTGATCTCCA-ATTTGATCCAGTATGG
65 AAGTTTTCGAAGATCAGAGTTGATCTCCAGA--TGATCCAGTGCGG
*
733 TCACTCCAAGAA
1 TCATTCCAAGAA
745 AGGTTTTCGT
Statistics
Matches: 374, Mismatches: 56, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
104 1 0.00
105 59 0.16
106 29 0.08
107 95 0.25
108 185 0.49
109 5 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (108 bp):
TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCATTCCAAGA
AGTTTTCGAAGATCAGAGTTGATCTCCAGATGATCCAGTGCGG
Found at i:605 original size:162 final size:160
Alignment explanation
Indices: 197--744 Score: 572
Period size: 162 Copynumber: 3.4 Consensus size: 160
187 AGAGTTGATC
* * * *
197 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCCAAAAGATCCAGTGGGGTCATTCCAAGAA
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAA
* * * * * * *
262 GTTTTTAATGGTCAGAATTGATCCCCAAAAGGTCCAGTGTGGTCATTCCAAGAAGTTTTC-AATG
66 GTTTTGAA-GATCAGAGTTGATCTCCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCGAA-G
* * *
326 GTCAGAGTTGATCG-CCA-AAGATCCAATGCGG
129 ATCAGAGTTGAT-GTCCAGATGATCCAGTGCGG
*
357 TCATTCCAAGAAGTTTT--ATGATCAGAGTTGATCCTCAGATGATCCCGTGCGGTCATTCCAAGA
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCC-CAGATGATCCAGTGCGGTCATTCCAAGA
* * * *
420 AGTTTTTGATGATCAGAGTTGATCTCCAGATGATCCAGTGCGGTCCTTCCAAAAAGTTTTCGAAG
65 AG-TTTTGAAGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCGAAG
*
485 TTCAGAGTTGATGTCCAGATGATCCAGTGCGG
129 ATCAGAGTTGATGTCCAGATGATCCAGTGCGG
* * * * * *
517 TTC-TTCCTAGAAGTTTTCAAAGATCAAAGTTGATCTCCAGATGATCCGGTGCTGTCATTTCAAG
1 -TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTCCAAG
* * * * * **
581 AAATTTTCGAAGATCAGAGTTGATCTTCAGATGATCCGGTATGGTCGTTTTAAGAAGTTTTCGAA
64 AAGTTTT-GAAGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCGAA
* *
646 GATCAGAGTTGATCTCCAGATGATCCAGTGTGG
128 GATCAGAGTTGATGTCCAGATGATCCAGTGCGG
* * * ** *
679 TCGTT-CAAGAAGTTTCCGATGATCAGAGTTGATCTCCA-ATTTGATCCAGTATGGTCACTCCAA
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC-CCAGA--TGATCCAGTGCGGTCATTCCAA
742 GAA
63 GAA
745 AGGTTTTCGT
Statistics
Matches: 326, Mismatches: 49, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
158 17 0.05
159 83 0.25
160 50 0.15
161 36 0.11
162 139 0.43
163 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (160 bp):
TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAA
GTTTTGAAGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCGAAGAT
CAGAGTTGATGTCCAGATGATCCAGTGCGG
Done.