Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024516.1 Corchorus olitorius cultivar O-4 contig24549, 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: 9460
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:865 original size:31 final size:31
Alignment explanation
Indices: 830--971 Score: 185
Period size: 31 Copynumber: 4.6 Consensus size: 31
820 GGTGTTCGAC
*
830 GTGGCATGCCACGTGTACCAAAAAGCGACAT
1 GTGGCACGCCACGTGTACCAAAAAGCGACAT
*
861 GTGGCACGCCACGTGTACCAAAAAGCGACAC
1 GTGGCACGCCACGTGTACCAAAAAGCGACAT
* *
892 GTGGCACACCACGTGTACCAAAAAGTGACAT
1 GTGGCACGCCACGTGTACCAAAAAGCGACAT
** * * *
923 GTGGCACGCCATATGTACCAAAACGTGACAC
1 GTGGCACGCCACGTGTACCAAAAAGCGACAT
* *
954 GTGTCACGCCATGTGTAC
1 GTGGCACGCCACGTGTAC
972 ATTTGTCCAC
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 99 1.00
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (31 bp):
GTGGCACGCCACGTGTACCAAAAAGCGACAT
Found at i:925 original size:62 final size:62
Alignment explanation
Indices: 828--971 Score: 207
Period size: 62 Copynumber: 2.3 Consensus size: 62
818 ACGGTGTTCG
* *
828 ACGTGGCATGCCACGTGTACCAAAAAGCGACATGTGGCACGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGACATGTGGCACGCCACATGTACCAAAAAGCGAC
* * * * *
890 ACGTGGCACACCACGTGTACCAAAAAGTGACATGTGGCACGCCATATGTACCAAAACGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGACATGTGGCACGCCACATGTACCAAAAAGCGAC
* *
952 ACGTGTCACGCCATGTGTAC
1 ACGTGGCACGCCACGTGTAC
972 ATTTGTCCAC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.16
Consensus pattern (62 bp):
ACGTGGCACGCCACGTGTACCAAAAAGCGACATGTGGCACGCCACATGTACCAAAAAGCGAC
Found at i:1938 original size:31 final size:31
Alignment explanation
Indices: 1903--1968 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1893 TCTTTCTAAC
* *
1903 AACAGAATTTACTTAATTAAAGAATCTATAA
1 AACAGAATTTACCTAATTAAAGAATCTACAA
1934 AACAGAATTTACCTAATTAAAGAATCTACAA
1 AACAGAATTTACCTAATTAAAGAATCTACAA
1965 AACA
1 AACA
1969 ATTGGGGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.27
Consensus pattern (31 bp):
AACAGAATTTACCTAATTAAAGAATCTACAA
Found at i:4834 original size:131 final size:131
Alignment explanation
Indices: 4572--5006 Score: 617
Period size: 132 Copynumber: 3.3 Consensus size: 131
4562 ACAAAGGACT
* * * * * *
4572 AATATATTAA-AAACGACTAATATGAGTTGTTGCGAATAA-AATAGGATTTCGCTGCGAC-TACA
1 AATATATTAAGCAACGACTAATATAAGTCGTTGCGAA-AAGAGTAAGATTTCGCAGCGACTTA-A
4634 TTTGTCGCTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAATCAATTT
64 TTTGT-GCTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAATCAATTT
4699 GTAA
128 GTAA
* * * *
4703 AATATATTAAGCAACGACTATTGTTAGTCGTTGCGAAATGAGTAAGATTTCGCAGCGACTTAATT
1 AATATATTAAGCAACGACTAATATAAGTCGTTGCGAAAAGAGTAAGATTTCGCAGCGACTTAATT
4768 TGTGGCTTCAAAAGTAATTATGTTTTTT-TAGCGACTTTCAAGGTCGCTGCGAAAATCAATTTGT
66 TGT-GCTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAATCAATTTGT
4832 AA
130 AA
* * * * *
4834 AATATATTAAGCAACGACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTTCGCAACGACTGAATC
1 AATATATTAAGCAACGACTAATATAAGTCGTTGCGAAAAGAGTAAGATTTCGCAGCGACTTAATT
* * * * *
4899 TGTCCTTTCAAAAGTAATCATATTTTTTGTAGCGACTTTCAATGTCGCTTCGAAAATCAATTTGT
66 TGTGC-TTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAATCAATTTGT
4964 AA
130 AA
4966 AATATATTAAGCAACGACTAATATAAGTCGTTGCGAAAAGA
1 AATATATTAAGCAACGACTAATATAAGTCGTTGCGAAAAGA
5007 CTATGAATTC
Statistics
Matches: 273, Mismatches: 26, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
130 1 0.00
131 128 0.47
132 142 0.52
133 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (131 bp):
AATATATTAAGCAACGACTAATATAAGTCGTTGCGAAAAGAGTAAGATTTCGCAGCGACTTAATT
TGTGCTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAATCAATTTGTA
A
Found at i:5077 original size:132 final size:130
Alignment explanation
Indices: 4666--5067 Score: 382
Period size: 131 Copynumber: 3.1 Consensus size: 130
4656 TGTTTTTTGT
* *****
4666 AGCGACTTTCAAGGTCGCTGCGAAAATCAATTTGTAAAATATATTAAGCAACGACTATTGTTAGT
1 AGCGACTTTCAATGTCGCTGCGAAAATCAATTTGTAAAATATATTAAGCAACGACTAACAAAAGT
* * * * * ** * * * * *
4731 CGTTGCGAAATGAGTAAGATTTCGCAGCGACTTAATTTGTGGC-TTCAAAAGTAATTATGTTTTT
66 CGTTGCGAAAAGACTAAGAATTCGCAACGACTGAATAAGT-CCTTTAAAAAGTAATCA-ATTTTA
**
4795 TT
129 GC
*
4797 AGCGACTTTCAAGGTCGCTGCGAAAATCAATTTGTAAAATATATTAAGCAACGACTAACAAAAGT
1 AGCGACTTTCAATGTCGCTGCGAAAATCAATTTGTAAAATATATTAAGCAACGACTAACAAAAGT
* * ** * *
4862 CGTTGCGAAAAGAGTAAGATTTCGCAACGACTGAATCTGTCCTTTCAAAAGTAATCATATTTTTT
66 CGTTGCGAAAAGACTAAGAATTCGCAACGACTGAATAAGTCCTTTAAAAAGTAATCA-A-TTTTA
*
4927 GT
129 GC
* * *
4929 AGCGACTTTCAATGTCGCTTCGAAAATCAATTTGTAAAATATATTAAGCAACGACTAATATAAGT
1 AGCGACTTTCAATGTCGCTGCGAAAATCAATTTGTAAAATATATTAAGCAACGACTAACAAAAGT
* ** *
4994 CGTTGCGAAAAGACTATGAATTCGCAATTACT-AATAAAGTCGTTGTAAAAAGGGTAA-C-A-TT
66 CGTTGCGAAAAGACTAAGAATTCGCAACGACTGAAT-AAGTCCTT-TAAAAA--GTAATCAATTT
5055 TAGC
127 TAGC
5059 AGCGACTTT
1 AGCGACTTT
5068 GTTTTTGTCG
Statistics
Matches: 237, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
130 14 0.06
131 113 0.48
132 100 0.42
133 5 0.02
134 1 0.00
135 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (130 bp):
AGCGACTTTCAATGTCGCTGCGAAAATCAATTTGTAAAATATATTAAGCAACGACTAACAAAAGT
CGTTGCGAAAAGACTAAGAATTCGCAACGACTGAATAAGTCCTTTAAAAAGTAATCAATTTTAGC
Found at i:5627 original size:26 final size:28
Alignment explanation
Indices: 5580--5634 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
5570 AACATAAATG
5580 ATTACAAACGAAAATAATCACTTTACAT
1 ATTACAAACGAAAATAATCACTTTACAT
*
5608 ATTACAAA-G-AACTAATCACTTTACAT
1 ATTACAAACGAAAATAATCACTTTACAT
5634 A
1 A
5635 GATAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 17 0.65
27 1 0.04
28 8 0.31
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (28 bp):
ATTACAAACGAAAATAATCACTTTACAT
Found at i:6078 original size:3 final size:3
Alignment explanation
Indices: 6070--6131 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
6060 AATTTATTTC
6070 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6118 ATT -TT ATT A-T ATT A
1 ATT ATT ATT ATT ATT A
6132 AGCATAAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.07
3 53 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:7521 original size:33 final size:33
Alignment explanation
Indices: 7479--7544 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
7469 ACATAAAGGG
* *
7479 CATGCAATTTGAAAAGGA-GGGAACACCATTAAT
1 CATGCAATTT-AAAAAGATAGGAACACCATTAAT
*
7512 CATGCAATTTAAAAAGATAGGAACACTATTAAT
1 CATGCAATTTAAAAAGATAGGAACACCATTAAT
7545 TGAAGTTAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 6 0.21
33 23 0.79
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (33 bp):
CATGCAATTTAAAAAGATAGGAACACCATTAAT
Found at i:7838 original size:2 final size:2
Alignment explanation
Indices: 7831--7857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7821 ATGAAATGTG
7831 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7858 GTTTCTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.