Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012220.1 Corchorus olitorius cultivar O-4 contig12253, 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: 17665
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:508 original size:21 final size:21
Alignment explanation
Indices: 484--600 Score: 182
Period size: 21 Copynumber: 5.6 Consensus size: 21
474 CTTAGGCAAT
* *
484 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
505 TCCAATGATCTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
526 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
547 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
568 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAACTTGGAACCTT-C
589 TCCAATGAACTT
1 TCCAATGAACTT
601 CTAGCATCTT
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 3 0.03
21 87 0.97
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (21 bp):
TCCAATGAACTTGGAACCTTC
Found at i:5577 original size:21 final size:21
Alignment explanation
Indices: 5515--5570 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
5505 GAGGCTACAG
5515 AAGAGACAGATACAGAAATGA
1 AAGAGACAGATACAGAAATGA
*
5536 AAGAGACAGATTCAGAAATGA
1 AAGAGACAGATACAGAAATGA
* *
5557 CAGAGAAAGATACA
1 AAGAGACAGATACA
5571 TGAATGATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.55, C:0.11, G:0.23, T:0.11
Consensus pattern (21 bp):
AAGAGACAGATACAGAAATGA
Found at i:6364 original size:30 final size:30
Alignment explanation
Indices: 6328--6384 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
6318 CAAGAGCAAC
6328 AATGATGCGCCCAAGG-CTTATCATGGAGGG
1 AATGATGCG-CCAAGGACTTATCATGGAGGG
6358 AATGATGCGCCAAGGACTTATCATGGA
1 AATGATGCGCCAAGGACTTATCATGGA
6385 CTTGAAGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (30 bp):
AATGATGCGCCAAGGACTTATCATGGAGGG
Found at i:9360 original size:12 final size:12
Alignment explanation
Indices: 9343--9374 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
9333 TGTTAGCTAC
9343 TAAGAGTGAGAT
1 TAAGAGTGAGAT
9355 TAAGAGTGAGAT
1 TAAGAGTGAGAT
9367 TAAGAGTG
1 TAAGAGTG
9375 CTTTGCATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.34, T:0.25
Consensus pattern (12 bp):
TAAGAGTGAGAT
Found at i:9726 original size:29 final size:31
Alignment explanation
Indices: 9677--9739 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
9667 TCTTCAAAGG
*
9677 GGAGGGGATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGATGCGCCCAAGGACTTATCAT
*
9707 GGAGGGAATGATG-GGCCAAGGACTTATCAT
1 GGAGGGAATGATGCGCCCAAGGACTTATCAT
9737 GGA
1 GGA
9740 CTTGAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.27, C:0.16, G:0.38, T:0.19
Consensus pattern (31 bp):
GGAGGGAATGATGCGCCCAAGGACTTATCAT
Found at i:9806 original size:18 final size:19
Alignment explanation
Indices: 9783--9820 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
9773 GTGCATGGGT
*
9783 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
9801 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
9820 T
1 T
9821 AACACTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:11339 original size:19 final size:18
Alignment explanation
Indices: 11315--11361 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
11305 GTCCATCGTT
*
11315 ATCTCCATGGTCTCCATGC
1 ATCTCCAT-GCCTCCATGC
11334 ATCTCCATGCCTCCATGC
1 ATCTCCATGCCTCCATGC
*
11352 AGC-CCATGCC
1 ATCTCCATGCC
11362 CATCCTTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 7 0.27
18 11 0.42
19 8 0.31
ACGTcount: A:0.17, C:0.43, G:0.15, T:0.26
Consensus pattern (18 bp):
ATCTCCATGCCTCCATGC
Found at i:15781 original size:16 final size:16
Alignment explanation
Indices: 15756--15797 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
15746 TAAATAAAAT
*
15756 ATTCTCTCTCTCTCAA
1 ATTCCCTCTCTCTCAA
* *
15772 ATTCCTTCTCTCTCCA
1 ATTCCCTCTCTCTCAA
15788 ATTCCCTCTC
1 ATTCCCTCTC
15798 AACTTTTCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTCCCTCTCTCTCAA
Found at i:16025 original size:21 final size:21
Alignment explanation
Indices: 15999--16110 Score: 156
Period size: 21 Copynumber: 5.4 Consensus size: 21
15989 TGCTAGAAGT
15999 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
16020 TCATTGGAG-AAGCTACAAGC
1 TCATTGGAGCAAGTTCCAAGC
16040 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
16061 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
16082 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
16103 TCATTGGA
1 TCATTGGA
16111 AATGCCTAAG
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
20 19 0.24
21 61 0.76
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:16044 original size:41 final size:42
Alignment explanation
Indices: 15990--16110 Score: 165
Period size: 41 Copynumber: 2.9 Consensus size: 42
15980 GCTTGAAGAT
*
15990 GCTAGAAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAG-AA
1 GCTACAAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGCAA
* *
16031 GCTACAAGCTCATTGGAGCAAGTTCCAAGCTCATTGGAGCAG
1 GCTACAAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGCAA
* * *
16073 GTTCCAAGTTCATTGGAG-AAGGTTTCAAGCTCATTGGA
1 GCTACAAGTTCATTGGAGCAA-GTTCCAAGCTCATTGGA
16111 AATGCCTAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
41 39 0.55
42 32 0.45
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (42 bp):
GCTACAAGTTCATTGGAGCAAGTTCCAAGCTCATTGGAGCAA
Done.