Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023282.1 Corchorus olitorius cultivar O-4 contig23315, 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: 3180
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Found at i:695 original size:11 final size:10
Alignment explanation
Indices: 670--694 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
660 AAAAGGAGCT
670 AAAAAGAAAA
1 AAAAAGAAAA
680 AAAAAGAAAA
1 AAAAAGAAAA
690 AAAAA
1 AAAAA
695 AAACTGGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:737 original size:38 final size:38
Alignment explanation
Indices: 686--773 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
676 AAAAAAAAAG
*
686 AAAAAAAAAAAAC-TGGACCTAAAATAGAAAGAGGT-AA
1 AAAAAAAAAAAACTTGG-CCTAAAACAGAAAGAGGTCAA
* *
723 AAAAAAACAAAAACTTGGCCTAAAACAGAGAGAGGTCAG
1 AAAAAAA-AAAAACTTGGCCTAAAACAGAAAGAGGTCAA
*
762 AAAAAAAGAAAA
1 AAAAAAAAAAAA
774 TAAATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
37 7 0.16
38 26 0.59
39 11 0.25
ACGTcount: A:0.64, C:0.10, G:0.17, T:0.09
Consensus pattern (38 bp):
AAAAAAAAAAAACTTGGCCTAAAACAGAAAGAGGTCAA
Found at i:1753 original size:58 final size:58
Alignment explanation
Indices: 1601--1800 Score: 328
Period size: 58 Copynumber: 3.3 Consensus size: 58
1591 CAGTTTAAAA
1601 CAAAATCTCATCTTGTTTTTTAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATT
1 CAAAATCTCATCTTGTTTTTTAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATT
1659 CAAAATCTCATCTTGTTTTTCTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATT
1 CAAAATCTCATCTTG---TT-TTTT--AATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATT
* *
1723 CAAAATCTTACCTTGTTTTTTAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATT
1 CAAAATCTCATCTTGTTTTTTAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATT
1781 CAAAATCTCATCTTGTTTTT
1 CAAAATCTCATCTTGTTTTT
1801 GGATGATCAC
Statistics
Matches: 132, Mismatches: 4, Indels: 12
0.89 0.03 0.08
Matches are distributed among these distances:
58 70 0.53
60 4 0.03
61 4 0.03
62 4 0.03
64 50 0.38
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (58 bp):
CAAAATCTCATCTTGTTTTTTAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATT
Found at i:2414 original size:59 final size:58
Alignment explanation
Indices: 2225--2520 Score: 432
Period size: 57 Copynumber: 5.0 Consensus size: 58
2215 ACCTTTTATC
* **
2225 TAGAGAGTTTTCAATTCAAAATCTTACCTTGTTTTTTAATCCTGTTCGAGGTCTCTGT
1 TAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGT
* *
2283 TAGAGAGTTTTCAATTCAAAATCTCATCTTGTTTTCTTTTAAAATCTTGTTCGAGGTCTCTGT
1 TAGAGAGTTTTCAATTCAAAATCTTATCTTG-----TTTTAAAATCCTGTTCGAGGTCTCTGT
* *
2346 TAGAGAGTTTTCAATTCAAAATCTAACCTTGTTTCTAAAATCCTGTTCGAGGTCTCTGT
1 TAGAGAGTTTTCAATTCAAAATCTTATCTTGTTT-TAAAATCCTGTTCGAGGTCTCTGT
*
2405 TAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTT-TAATCCTGTTCGAGGTCTCTGT
1 TAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGT
* * *
2462 TAGAGAGTTTTCAATTCAAAATCTTATCTTGTCTTAAACTCCTGGTCGAGGTCTCTGT
1 TAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGT
2520 T
1 T
2521 TGAATCACAT
Statistics
Matches: 216, Mismatches: 15, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
57 55 0.25
58 53 0.25
59 55 0.25
63 53 0.25
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (58 bp):
TAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGT
Found at i:2773 original size:29 final size:29
Alignment explanation
Indices: 2740--3025 Score: 369
Period size: 29 Copynumber: 9.9 Consensus size: 29
2730 TTCGCACGCT
*
2740 CAGGGGAATTTTGGTCATTTTTGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * *
2769 CAGGGGCATTTTGGTCATTTTCGCACATT
1 CAGGGGCATTTTGGTCATTTTTGCATATC
2798 CAGGGGCATTTTGGTCATTTTTGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* *
2827 CATGGGCATTTTGGTCATTTTTGCACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
*
2856 CAGGGGCATTTTGGTCATTTTTGCATATA
1 CAGGGGCATTTTGGTCATTTTTGCATATC
*
2885 C-GGGGCATTTTGGTCATTTTTGCATATA
1 CAGGGGCATTTTGGTCATTTTTGCATATC
2913 C-GGGGCATTTTGGTCATTTTTGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * *
2941 CGGGGGCATTTTGGTCATTTTTACACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * * * * * *
2970 TAGGGGCATTTCGATCATCTTTACACATT
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * *
2999 CTGGGGTAGTTTGGTCATTTTTGCATA
1 CAGGGGCATTTTGGTCATTTTTGCATA
3026 CTCTAGGTTC
Statistics
Matches: 226, Mismatches: 30, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
28 55 0.24
29 171 0.76
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.41
Consensus pattern (29 bp):
CAGGGGCATTTTGGTCATTTTTGCATATC
Found at i:3012 original size:143 final size:144
Alignment explanation
Indices: 2742--3025 Score: 399
Period size: 143 Copynumber: 2.0 Consensus size: 144
2732 CGCACGCTCA
* *
2742 GGGGAATTTTGGTCATTTTTGCATATCCAGGGGCATTTTGGTCATTTTCGCACATTCAGGGGCAT
1 GGGGAATTTTGGTCATTTTTGCATATACAGGGGCATTTTGGTCATTTTCGCACATCCAGGGGCAT
* * * * * * * *
2807 TTTGGTCATTTTTGCATATCCATGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTGGTC
66 TTTGGTCATTTTTACACATCCAGGGGCATTTCGATCATCTTTACACATCCAGGGGCAGTTTGGTC
2872 ATTTTTGCATATAC
131 ATTTTTGCATATAC
* * * *
2886 GGGGCATTTTGGTCATTTTTGCATATAC-GGGGCATTTTGGTCATTTTTGCATATCCGGGGGCAT
1 GGGGAATTTTGGTCATTTTTGCATATACAGGGGCATTTTGGTCATTTTCGCACATCCAGGGGCAT
* * * *
2950 TTTGGTCATTTTTACACATCTAGGGGCATTTCGATCATCTTTACACATTCTGGGGTAGTTTGGTC
66 TTTGGTCATTTTTACACATCCAGGGGCATTTCGATCATCTTTACACATCCAGGGGCAGTTTGGTC
3015 ATTTTTGCATA
131 ATTTTTGCATA
3026 CTCTAGGTTC
Statistics
Matches: 122, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
143 96 0.79
144 26 0.21
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.41
Consensus pattern (144 bp):
GGGGAATTTTGGTCATTTTTGCATATACAGGGGCATTTTGGTCATTTTCGCACATCCAGGGGCAT
TTTGGTCATTTTTACACATCCAGGGGCATTTCGATCATCTTTACACATCCAGGGGCAGTTTGGTC
ATTTTTGCATATAC
Done.