Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018625.1 Corchorus olitorius cultivar O-4 contig18658, 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: 31775
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1949 original size:22 final size:22
Alignment explanation
Indices: 1919--1961 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1909 GCTTCACTAA
1919 CCTAAGGTTAAT-TATCAGTTAG
1 CCTAAGGTTAATCTAT-AGTTAG
*
1941 CCTATGGTTAATCTATAGTTA
1 CCTAAGGTTAATCTATAGTTA
1962 CATGTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (22 bp):
CCTAAGGTTAATCTATAGTTAG
Found at i:11103 original size:24 final size:24
Alignment explanation
Indices: 11075--11194 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
11065 GAATTTTTGC
*
11075 CATGACCATTATGTGGCCGTTTCT
1 CATGACCACTATGTGGCCGTTTCT
* * **
11099 CATGACCACCATGTGGTCGAATCT
1 CATGACCACTATGTGGCCGTTTCT
* ** *
11123 CACGACCACTATGTGGCCGAATCC
1 CATGACCACTATGTGGCCGTTTCT
*
11147 CACGACCACTATGTGGCCGTTTCT
1 CATGACCACTATGTGGCCGTTTCT
*
11171 CATGACCACTATGTGGTCGTTTCT
1 CATGACCACTATGTGGCCGTTTCT
11195 ATTTTCCTCC
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 82 1.00
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (24 bp):
CATGACCACTATGTGGCCGTTTCT
Found at i:14718 original size:24 final size:24
Alignment explanation
Indices: 14685--14770 Score: 127
Period size: 24 Copynumber: 3.6 Consensus size: 24
14675 ATTTTTGTCG
** *
14685 CGACCACTATGTGGCCGTTTCTCA
1 CGACCACTATGTGGCCGAATCCCA
* *
14709 TGACCACTATGTGGCTGAATCCCA
1 CGACCACTATGTGGCCGAATCCCA
14733 CGACCACTATGTGGCCGAATCCCA
1 CGACCACTATGTGGCCGAATCCCA
14757 CGACCACTATGTGG
1 CGACCACTATGTGG
14771 TTGTTTCCAT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.23
Consensus pattern (24 bp):
CGACCACTATGTGGCCGAATCCCA
Found at i:16774 original size:4 final size:4
Alignment explanation
Indices: 16765--16790 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
16755 TTTCAATCAC
16765 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
16791 TCCTTTGGTA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:21716 original size:54 final size:53
Alignment explanation
Indices: 21169--21704 Score: 494
Period size: 54 Copynumber: 10.0 Consensus size: 53
21159 GTGTTCAAAG
* * * *
21169 TGATCCAGTGCGGTCCTTCTAAGAAGTTTTCAATGATGAAAGTTCATC-CTCAGA
1 TGATCCAGTGCGGTCGTTC-AAGAAGTTTTCAATGATCAGAGTTGATCTC-CAGA
* * * *
21223 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATTAGAATTGATC-CTTAGA
1 TGATCCAGTGCGGTCGTT-CAAGAAGTTTTCAATGATCAGAGTTGATCTC-CAGA
* *
21277 TGATCTAGTGCGGTCAGTGCAAGAAGTTTTCAATGATCAGAGTTGATC-CTCAGA
1 TGATCCAGTGCGGTC-GTTCAAGAAGTTTTCAATGATCAGAGTTGATCTC-CAGA
* ** * * * * * *
21331 TGATCTAGTGCAATCATTCCAAGATGTTCTCAATTATCAGAGTTGATC-CTTATA
1 TGATCCAGTGCGGTCGTT-CAAGAAGTTTTCAATGATCAGAGTTGATCTC-CAGA
* * * *
21385 TGATCCAGTGCGGTCATTCCGAGAAGTTTTCGAA-GTTCAGAGTTGATGTCCAGA
1 TGATCCAGTGCGGTCGTT-CAAGAAGTTTTC-AATGATCAGAGTTGATCTCCAGA
* * * * *
21439 TGATCCAGTGCAGTCCTTCTGAGAAGTTTTTGAA-GATCAGAGTTGATCTCAAGA
1 TGATCCAGTGCGGTCGTTC-AAGAAG-TTTTCAATGATCAGAGTTGATCTCCAGA
* *
21493 TGATCCGGTGCGGTCGTTTCGAGAAGTTTTCGAA-GATCAGAGTTGATCTCCAGA
1 TGATCCAGTGCGGTCG-TTCAAGAAGTTTTC-AATGATCAGAGTTGATCTCCAGA
* * *
21547 TGATCCGGTGCGGTCGTTTAAGAAGTTTTCGAA-GATCAGAGTTGATCTTCAGA
1 TGATCCAGTGCGGTCGTTCAAGAAGTTTTC-AATGATCAGAGTTGATCTCCAGA
* * * * * *
21600 TGATCCGGTGTGATCGTTTCAATAAGTTTTCAAAGATCAGAGTTGATCTCCAGT
1 TGATCCAGTGCGGTCG-TTCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAGA
* * *
21654 TTATCCAGTGTGATCGTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCCA
1 TGATCCAGTGCGGTCGTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCCA
21705 ATTTGATCCA
Statistics
Matches: 415, Mismatches: 56, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
53 89 0.21
54 314 0.76
55 12 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (53 bp):
TGATCCAGTGCGGTCGTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAGA
Found at i:23098 original size:4 final size:4
Alignment explanation
Indices: 23079--23313 Score: 78
Period size: 4 Copynumber: 58.2 Consensus size: 4
23069 ACTTATTTAC
* ** * *
23079 TATT TATCT T-TT TATT TATT AATT TAAC TA-T TATC TATT TATT TA-C
1 TATT TAT-T TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
* ** *
23125 TATT TATCT T-TT TATT TATT AATT TAAC TA-T TATC TATT TATT TACTAT
1 TATT TAT-T TATT TATT TATT TATT TATT TATT TATT TATT TATT TA-T-T
* * ** ** * *
23174 TATC TACT T-TT T-TT TACC TACC TATT TATC TAAT TATCT ATATT CCTATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT-T -TATT --TATT
* * * *
23224 TATCT T-TT TATT TATC TATT ATTTT TACTT AATT T-TC TATT TATT TATT
1 TAT-T TATT TATT TATT TATT -TATT TA-TT TATT TATT TATT TATT TATT
*
23273 TATT TATT TATT TATT TATC TA-T TACTT T-TT TATTT TATT T
1 TATT TATT TATT TATT TATT TATT TA-TT TATT TA-TT TATT T
23314 TAATATTTTT
Statistics
Matches: 170, Mismatches: 39, Indels: 44
0.67 0.15 0.17
Matches are distributed among these distances:
3 24 0.14
4 114 0.67
5 22 0.13
6 10 0.06
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (4 bp):
TATT
Found at i:23103 original size:27 final size:27
Alignment explanation
Indices: 23073--23169 Score: 97
Period size: 27 Copynumber: 3.9 Consensus size: 27
23063 TTATCTACTT
23073 ATTT-ACTATTTATCTTTTTATTTATTA
1 ATTTAACTA-TTATCTTTTTATTTATTA
23100 ATTTAACTATTATC----TA--T-TT-
1 ATTTAACTATTATCTTTTTATTTATTA
23119 ATTT-ACTATTTATCTTTTTATTTATTA
1 ATTTAACTA-TTATCTTTTTATTTATTA
*
23146 ATTTAACTATTATCTATTTATTTA
1 ATTTAACTATTATCTTTTTATTTA
23170 CTATTATCTA
Statistics
Matches: 58, Mismatches: 1, Indels: 22
0.72 0.01 0.27
Matches are distributed among these distances:
18 4 0.07
19 9 0.16
20 2 0.03
21 1 0.02
23 4 0.07
25 1 0.02
26 2 0.03
27 27 0.47
28 8 0.14
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTTAACTATTATCTTTTTATTTATTA
Found at i:23124 original size:46 final size:47
Alignment explanation
Indices: 23057--23291 Score: 232
Period size: 46 Copynumber: 4.9 Consensus size: 47
23047 GGTTTTTTTA
*
23057 TAACTATTATCTACTTATTTACTATTTATCTTTTTATTTATTA-ATT
1 TAACTATTATCTATTTATTTACTATTTATCTTTTTATTTATTATATT
23103 TAACTATTATCTATTTATTTACTATTTATCTTTTTATTTATTA-ATT
1 TAACTATTATCTATTTATTTACTATTTATCTTTTTATTTATTATATT
* *
23149 TAACTATTATCTATTTATTTACTA-TTATCTACTTTTTTTTACCTACCTATT
1 TAACTATTATCTATTTATTTACTATTTATCT--TTTTATTTA-TTA--TATT
* *
23200 TATCTAATTATCTA--TA-TTCCTATTTATCTTTTTATTTATCTATTATTT
1 TAACT-ATTATCTATTTATTTACTATTTATCTTTTTATTTAT-TA-TA-TT
* * *
23248 TTACTTAATTTTCTATTTATTTATTTATTTAT-TTATTTATTTAT
1 TAAC-T-ATTATCTATTTATTTA-CTATTTATCTT-TTTATTTAT
23292 CTATTACTTT
Statistics
Matches: 160, Mismatches: 13, Indels: 25
0.81 0.07 0.13
Matches are distributed among these distances:
45 6 0.04
46 69 0.43
47 10 0.06
48 16 0.10
49 14 0.09
50 8 0.05
51 9 0.06
52 12 0.08
53 16 0.10
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (47 bp):
TAACTATTATCTATTTATTTACTATTTATCTTTTTATTTATTATATT
Found at i:23296 original size:12 final size:12
Alignment explanation
Indices: 23079--23291 Score: 103
Period size: 12 Copynumber: 18.2 Consensus size: 12
23069 ACTTATTTAC
*
23079 TATTTATCTTTT
1 TATTTATCTATT
23091 TATTTAT-TAATT
1 TATTTATCT-ATT
23103 TAACTATTATCTATT
1 T-A-T-TTATCTATT
23118 TATTTA-CTATT
1 TATTTATCTATT
*
23129 TATCTT-TTTATT
1 TAT-TTATCTATT
* * **
23141 TATTAATTTAAC
1 TATTTATCTATT
23153 TA-TTATCTATT
1 TATTTATCTATT
23164 TATTTA-CTA-T
1 TATTTATCTATT
*
23174 TATCTA-CT-TT
1 TATTTATCTATT
* * **
23184 TTTTTACCTACC
1 TATTTATCTATT
*
23196 TATTTATCTAAT
1 TATTTATCTATT
*
23208 TATCTA--TATT
1 TATTTATCTATT
*
23218 CCTATTTATCTTTT
1 --TATTTATCTATT
23232 TATTTATCTA-T
1 TATTTATCTATT
23243 TATTT-T-TACTT
1 TATTTATCTA-TT
*
23254 AATTT-TCTATT
1 TATTTATCTATT
*
23265 TATTTATTTATT
1 TATTTATCTATT
*
23277 TATTTATTTATT
1 TATTTATCTATT
23289 TAT
1 TAT
23292 CTATTACTTT
Statistics
Matches: 155, Mismatches: 26, Indels: 40
0.70 0.12 0.18
Matches are distributed among these distances:
9 2 0.01
10 17 0.11
11 40 0.26
12 80 0.52
13 2 0.01
14 5 0.03
15 8 0.05
16 1 0.01
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (12 bp):
TATTTATCTATT
Done.