Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015713.1 Corchorus olitorius cultivar O-4 contig15746, 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: 16102
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:522 original size:20 final size:20
Alignment explanation
Indices: 482--523 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
472 TATTATGTGA
**
482 TATTATAAATTGAAATGAAT
1 TATTATAAATTGAAAAAAAT
502 TATTATAAATTGAAAAAAAT
1 TATTATAAATTGAAAAAAAT
522 TA
1 TA
524 AATAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (20 bp):
TATTATAAATTGAAAAAAAT
Found at i:2342 original size:20 final size:20
Alignment explanation
Indices: 2313--2350 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2303 TATTCTGGGA
2313 TTTTTATGGATGTTTATGTC
1 TTTTTATGGATGTTTATGTC
* *
2333 TTTTTTTGGATTTTTATG
1 TTTTTATGGATGTTTATG
2351 GAATATACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.03, G:0.18, T:0.66
Consensus pattern (20 bp):
TTTTTATGGATGTTTATGTC
Found at i:2346 original size:10 final size:10
Alignment explanation
Indices: 2310--2352 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
2300 TTATATTCTG
2310 GGATTTTTAT
1 GGATTTTTAT
*
2320 GGATGTTTAT
1 GGATTTTTAT
** *
2330 GTCTTTTTTT
1 GGATTTTTAT
2340 GGATTTTTAT
1 GGATTTTTAT
2350 GGA
1 GGA
2353 ATATACTAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.23, T:0.58
Consensus pattern (10 bp):
GGATTTTTAT
Found at i:3388 original size:24 final size:24
Alignment explanation
Indices: 3356--3438 Score: 166
Period size: 24 Copynumber: 3.5 Consensus size: 24
3346 TGACGATGAG
3356 CTACGGCCACGCCCAGTGGAGGTA
1 CTACGGCCACGCCCAGTGGAGGTA
3380 CTACGGCCACGCCCAGTGGAGGTA
1 CTACGGCCACGCCCAGTGGAGGTA
3404 CTACGGCCACGCCCAGTGGAGGTA
1 CTACGGCCACGCCCAGTGGAGGTA
3428 CTACGGCCACG
1 CTACGGCCACG
3439 ACCCCTCTCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.20, C:0.35, G:0.33, T:0.12
Consensus pattern (24 bp):
CTACGGCCACGCCCAGTGGAGGTA
Found at i:4346 original size:22 final size:22
Alignment explanation
Indices: 4333--4385 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 22
4323 ATGAATATAT
4333 TAATAAATATAAATATAAATAA
1 TAATAAATATAAATATAAATAA
4355 TAATAAATATTACAACTATTAAATAA
1 TAATAAATA-TA-AA-TA-TAAATAA
4381 TAATA
1 TAATA
4386 CCACCTGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.33
23 2 0.07
24 2 0.07
25 2 0.07
26 12 0.44
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (22 bp):
TAATAAATATAAATATAAATAA
Found at i:4348 original size:16 final size:16
Alignment explanation
Indices: 4315--4366 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
4305 CACCTGCGGC
4315 AATAATAAATGAATATATT
1 AATAAT-AAT-AA-ATATT
*
4334 AATAA-ATATAAATATA
1 AATAATA-ATAAATATT
4350 AATAATAATAAATATT
1 AATAATAATAAATATT
4366 A
1 A
4367 CAACTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 18 0.62
17 4 0.14
18 2 0.07
19 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AATAATAATAAATATT
Found at i:5696 original size:33 final size:33
Alignment explanation
Indices: 5659--5792 Score: 160
Period size: 33 Copynumber: 3.8 Consensus size: 33
5649 GTGGCTATGA
*
5659 CCATGCCGTCCACCGAGGGCGCCATGGCCAAGT
1 CCATGCCGCCCACCGAGGGCGCCATGGCCAAGT
* *
5692 CCATGCCGCCCACCGAGGGCGCCATGGCGGCGTGGCTATGA
1 CCATGCCGCCCACCGAGGGCGCCAT---GGC----C-AAGT
*
5733 CCATGCCGTCCACCGAGGGCGCCATGGCCAAGT
1 CCATGCCGCCCACCGAGGGCGCCATGGCCAAGT
5766 CCATGCCGCCCACCGAGGGCGCCATGG
1 CCATGCCGCCCACCGAGGGCGCCATGG
5793 ACATAACCAC
Statistics
Matches: 86, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
33 52 0.60
34 1 0.01
36 3 0.03
38 3 0.03
40 1 0.01
41 26 0.30
ACGTcount: A:0.16, C:0.40, G:0.33, T:0.11
Consensus pattern (33 bp):
CCATGCCGCCCACCGAGGGCGCCATGGCCAAGT
Found at i:5764 original size:74 final size:74
Alignment explanation
Indices: 5643--5792 Score: 300
Period size: 74 Copynumber: 2.0 Consensus size: 74
5633 GCCCTCACAG
5643 GGCGGCGTGGCTATGACCATGCCGTCCACCGAGGGCGCCATGGCCAAGTCCATGCCGCCCACCGA
1 GGCGGCGTGGCTATGACCATGCCGTCCACCGAGGGCGCCATGGCCAAGTCCATGCCGCCCACCGA
5708 GGGCGCCAT
66 GGGCGCCAT
5717 GGCGGCGTGGCTATGACCATGCCGTCCACCGAGGGCGCCATGGCCAAGTCCATGCCGCCCACCGA
1 GGCGGCGTGGCTATGACCATGCCGTCCACCGAGGGCGCCATGGCCAAGTCCATGCCGCCCACCGA
5782 GGGCGCCAT
66 GGGCGCCAT
5791 GG
1 GG
5793 ACATAACCAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.16, C:0.37, G:0.35, T:0.12
Consensus pattern (74 bp):
GGCGGCGTGGCTATGACCATGCCGTCCACCGAGGGCGCCATGGCCAAGTCCATGCCGCCCACCGA
GGGCGCCAT
Found at i:5807 original size:33 final size:33
Alignment explanation
Indices: 5731--5809 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
5721 GCGTGGCTAT
* *
5731 GACCATGCCGTCCACCGAGGGCGCCATGGCCAA
1 GACCATGCCGCCCACCGAGGGCGCCATGGACAA
*
5764 GTCCATGCCGCCCACCGAGGGCGCCATGGACATA
1 GACCATGCCGCCCACCGAGGGCGCCATGGACA-A
*
5798 -ACCACGCCGCCC
1 GACCATGCCGCCC
5810 TAGTAGGGCG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 39 0.98
34 1 0.03
ACGTcount: A:0.20, C:0.43, G:0.28, T:0.09
Consensus pattern (33 bp):
GACCATGCCGCCCACCGAGGGCGCCATGGACAA
Found at i:6069 original size:11 final size:11
Alignment explanation
Indices: 6053--6077 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6043 GCAAAACCCT
6053 AAAAGAAAAGA
1 AAAAGAAAAGA
6064 AAAAGAAAAGA
1 AAAAGAAAAGA
6075 AAA
1 AAA
6078 GGGCACGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:7625 original size:31 final size:31
Alignment explanation
Indices: 7590--7652 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
7580 AGGGACACTT
7590 GGGCTAGACATTCCAAAAGCGGACTATGCTC
1 GGGCTAGACATTCCAAAAGCGGACTATGCTC
7621 GGGCTAGACATTCCAAAAGCGGACTATGCTC
1 GGGCTAGACATTCCAAAAGCGGACTATGCTC
7652 G
1 G
7653 CAATGTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (31 bp):
GGGCTAGACATTCCAAAAGCGGACTATGCTC
Found at i:12937 original size:32 final size:32
Alignment explanation
Indices: 12896--12960 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
12886 CGATTGTCGA
12896 TCTATCTAATATTGTATAATTTTCGGTCCACT
1 TCTATCTAATATTGTATAATTTTCGGTCCACT
12928 TCTATCTAATATTGTATAATTTTCGGTCCACT
1 TCTATCTAATATTGTATAATTTTCGGTCCACT
12960 T
1 T
12961 GTCCGATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (32 bp):
TCTATCTAATATTGTATAATTTTCGGTCCACT
Found at i:14157 original size:6 final size:6
Alignment explanation
Indices: 14142--14176 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
14132 GAGCCAATTC
*
14142 CATTTG CATTTT CATTTT CATTTT CATTTT CATTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT CATTT
14177 GTTTTTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.03, T:0.63
Consensus pattern (6 bp):
CATTTT
Found at i:14408 original size:39 final size:39
Alignment explanation
Indices: 14189--14411 Score: 155
Period size: 39 Copynumber: 5.6 Consensus size: 39
14179 TTTTTTTCTT
* * * *
14189 CATCTCCAATCAAGGCTGCGGCATTTTCA-ATTGACTTTC
1 CATCTCCAATCAAGGCTGAGGCATTTTCATTTTCA-TTTG
* * * *
14228 CATCTGATCCAATCGAGGCTGTGGCATTTTCCGTTGT-ATTTG
1 CATC---TCCAATCAAGGCTGAGGCATTTT-CATTTTCATTTG
* * * *
14270 CATTTCCAA-CTAAGGCTGTGGCATTTTCCTTTGTACTATTAG
1 CATCTCCAATC-AAGGCTGAGGCATTTTCATTT-T-C-ATTTG
* ** * *
14312 CATCTCCAATCAAGGCTGAGGGAAATTCATTTTTAATTG
1 CATCTCCAATCAAGGCTGAGGCATTTTCATTTTCATTTG
* *
14351 CATCTTCAATCAAGGCTGAGACATTTTCATTTTCATTTG
1 CATCTCCAATCAAGGCTGAGGCATTTTCATTTTCATTTG
* *
14390 CATTTTCAATCAAGGCTGAGGC
1 CATCTCCAATCAAGGCTGAGGC
14412 TGATCCTACC
Statistics
Matches: 144, Mismatches: 29, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
38 4 0.03
39 80 0.56
41 1 0.01
42 55 0.38
43 3 0.02
44 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (39 bp):
CATCTCCAATCAAGGCTGAGGCATTTTCATTTTCATTTG
Found at i:14988 original size:2 final size:2
Alignment explanation
Indices: 14981--15015 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
14971 TCTTTTTAGG
*
14981 TA TA TA TA TA TA TA TA TA TA TC TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
15016 AGTCTAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15287 original size:39 final size:40
Alignment explanation
Indices: 15231--15311 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
15221 TTTAATTCCT
15231 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* * *
15271 ATGTAATA-CTATAATAACTGAAATACTTATATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
15310 AT
1 AT
15312 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:15301 original size:18 final size:18
Alignment explanation
Indices: 15241--15301 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 18
15231 ATGTAATATA
*
15241 TATAATAACTAAAATACT
1 TATAATAACTGAAATACT
* *
15259 TACATTAATTAAATGTAATAC-
1 T--A-TAA-TAACTGAAATACT
15280 TATAATAACTGAAATACT
1 TATAATAACTGAAATACT
15298 TATA
1 TATA
15302 TTAATTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 10 0.30
18 8 0.24
19 1 0.03
20 1 0.03
21 4 0.12
22 9 0.27
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (18 bp):
TATAATAACTGAAATACT
Found at i:15338 original size:25 final size:24
Alignment explanation
Indices: 15302--15348 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
15292 AATACTTATA
15302 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
15326 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
15349 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Done.