Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017137.1 Corchorus olitorius cultivar O-4 contig17170, 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: 29782
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:12 original size:2 final size:2
Alignment explanation
Indices: 6--40 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 GTACG
6 TA TA TA TA 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 TA TA TA TA T
41 TACTCCTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5829 original size:31 final size:30
Alignment explanation
Indices: 5791--5867 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
5781 TTAGGCTAAG
*
5791 GGGGCAAAACGTCCCAAAATTAAAATTCAAT
1 GGGGCAAAACGT-CCAAAATCAAAATTCAAT
*
5822 GGGGCAAAATGTCCAAAATCAAAATTC-A-
1 GGGGCAAAACGTCCAAAATCAAAATTCAAT
*
5850 GAGGACAAAACGTCCAAA
1 G-GGGCAAAACGTCCAAA
5868 CGCTACAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.02
29 15 0.37
30 14 0.34
31 11 0.27
ACGTcount: A:0.47, C:0.19, G:0.18, T:0.16
Consensus pattern (30 bp):
GGGGCAAAACGTCCAAAATCAAAATTCAAT
Found at i:5840 original size:30 final size:31
Alignment explanation
Indices: 5791--5849 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
5781 TTAGGCTAAG
*
5791 GGGGCAAAACGTCCCAAAATTAAAATTCAAT
1 GGGGCAAAACGTCCCAAAATCAAAATTCAAT
*
5822 GGGGCAAAATGT-CCAAAATCAAAATTCA
1 GGGGCAAAACGTCCCAAAATCAAAATTCA
5850 GAGGACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.19
Consensus pattern (31 bp):
GGGGCAAAACGTCCCAAAATCAAAATTCAAT
Found at i:25761 original size:31 final size:30
Alignment explanation
Indices: 25653--25759 Score: 110
Period size: 31 Copynumber: 3.5 Consensus size: 30
25643 AAAGGCTAAT
*
25653 TGCTCAAATAAGGGCCCAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCCAATGTTTG-CAAAA
* * **
25684 TGCTCAAATAAGGGCCCAATCTTT-TAATT
1 TGCTCAAATAAGGGCCCAATGTTTGCAAAA
*
25713 TGGC-CAAATAAGGGCCTAATGTTTGACAAAA
1 T-GCTCAAATAAGGGCCCAATGTTTG-CAAAA
*
25744 TACTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
25760 TAGCATGAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
29 21 0.34
30 3 0.05
31 37 0.61
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCCAATGTTTGCAAAA
Found at i:25866 original size:29 final size:29
Alignment explanation
Indices: 25829--25930 Score: 107
Period size: 29 Copynumber: 3.4 Consensus size: 29
25819 TTATAACGTT
25829 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
** * * *
25858 AGGCCCTTATTTGAG-CATTTTCGATAACATT
1 AGGCCCTTATTTG-GCCAAATT--AAAAGATC
*
25889 AGGCCCTTATGTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
*
25918 AGACCCTTATTTG
1 AGGCCCTTATTTG
25931 AGCATTTTAG
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
29 33 0.59
30 2 0.04
31 21 0.38
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:25891 original size:60 final size:60
Alignment explanation
Indices: 25797--25961 Score: 233
Period size: 60 Copynumber: 2.8 Consensus size: 60
25787 AAACTTACGC
** **
25797 CAGGCCCTTAAATGAGCATTTTTTATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTAGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* * *
25857 CAGGCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATGTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTAGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* *
25917 CAGACCCTTATTTGAGCATTTTAGCA-AATGTTAGGCCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTAG-ATAACGTTAGGCCCTTATTTG
25962 AGCAATTAGT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 92 0.99
61 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTAGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:25896 original size:31 final size:29
Alignment explanation
Indices: 25798--25965 Score: 90
Period size: 31 Copynumber: 5.6 Consensus size: 29
25788 AACTTACGCC
** *
25798 AGGCCCTTAAATGAGCATTTTTTATAACGTT
1 AGGCCCTTATTTGAGCA--TTTTATAACATT
** * * *
25829 AGGCCCTTATTTG-GCCAAATTAAAAGATC
1 AGGCCCTTATTTGAG-CATTTTATAACATT
25858 AGGCCCTTATTTGAGCATTTTCGATAACATT
1 AGGCCCTTATTTGAGCATTTT--ATAACATT
* ** * * *
25889 AGGCCCTTATGTG-GCCAAATTAAAAGATC
1 AGGCCCTTATTTGAG-CATTTTATAACATT
* *
25918 AGACCCTTATTTGAGCATTTTAGCAA-ATGTT
1 AGGCCCTTATTTGAGCATTTTA-TAACA--TT
25949 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
25966 ATTAGTCCGA
Statistics
Matches: 102, Mismatches: 26, Indels: 18
0.70 0.18 0.12
Matches are distributed among these distances:
29 45 0.44
30 6 0.06
31 51 0.50
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (29 bp):
AGGCCCTTATTTGAGCATTTTATAACATT
Found at i:28219 original size:58 final size:58
Alignment explanation
Indices: 28109--28224 Score: 144
Period size: 58 Copynumber: 2.0 Consensus size: 58
28099 ATTAATCAAA
*
28109 TATCAAGTGACATGTTCTTTATTAGATGCAAAAAAAAAAGACGTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGC-AAAAAAAAAGACGTTTTAGGACCAAGGCT
* * ** * *
28168 TATCGAGTGACATGTTTTTTTATTAGATGC-CTAAAAAGGACGTTTTAGGACCGAGGC
1 TATCAAGTGACATG-TTCTTTATTAGATGCAAAAAAAAAGACGTTTTAGGACCAAGGC
28225 ATGATGCTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 22 0.45
59 13 0.27
60 14 0.29
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCAAAAAAAAAGACGTTTTAGGACCAAGGCT
Found at i:29546 original size:36 final size:34
Alignment explanation
Indices: 29489--29560 Score: 99
Period size: 36 Copynumber: 2.1 Consensus size: 34
29479 ATTCAATAAC
* *
29489 CTTATATCTTTTGTGTATTTTGGTTATCATATTT
1 CTTATATATTTTGTGTATTTTGATTATCATATTT
*
29523 CTTATACTATTTTTTGTAATTTTGATTATCATATTT
1 CTTATA-TATTTTGTGT-ATTTTGATTATCATATTT
29559 CT
1 CT
29561 CCAAAATCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 6 0.18
35 8 0.24
36 19 0.58
ACGTcount: A:0.21, C:0.10, G:0.08, T:0.61
Consensus pattern (34 bp):
CTTATATATTTTGTGTATTTTGATTATCATATTT
Done.