Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011295.1 Corchorus olitorius cultivar O-4 contig11328, 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: 2902
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.24
Found at i:100 original size:26 final size:26
Alignment explanation
Indices: 59--112 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
49 AAGCTAGTAA
*
59 TGAAGTACGAAAGACCAAAGTGCCCC
1 TGAAGTACGAAAGACCAAAATGCCCC
85 TGAAGTAC-AAATGACCAAAATGCCCC
1 TGAAGTACGAAA-GACCAAAATGCCCC
111 TG
1 TG
113 GACTTTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (26 bp):
TGAAGTACGAAAGACCAAAATGCCCC
Found at i:561 original size:25 final size:25
Alignment explanation
Indices: 523--573 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
513 ACTATGGACC
* *
523 AACATTGGACTTCCCACAATGACTT
1 AACATCGGACTTCCCAAAATGACTT
*
548 AACATCGGATTTCCCAAAATGACTT
1 AACATCGGACTTCCCAAAATGACTT
573 A
1 A
574 GTATTGAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (25 bp):
AACATCGGACTTCCCAAAATGACTT
Found at i:987 original size:27 final size:27
Alignment explanation
Indices: 910--963 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
900 AAATCAAAAG
*
910 TGAACCTA-AAATGACCAAAATGCCCC
1 TGAACATACAAATGACCAAAATGCCCC
936 TGAACATACAAATGACCAAAATGCCCC
1 TGAACATACAAATGACCAAAATGCCCC
963 T
1 T
964 AGGTGTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.43, C:0.30, G:0.11, T:0.17
Consensus pattern (27 bp):
TGAACATACAAATGACCAAAATGCCCC
Found at i:1497 original size:30 final size:30
Alignment explanation
Indices: 1461--2181 Score: 1016
Period size: 30 Copynumber: 24.0 Consensus size: 30
1451 AACTAAAGTG
1461 ATGATCCT-AAACCAGGATTAAAATGAAGCA
1 ATGATCCTCAAA-CAGGATTAAAATGAAGCA
* *
1491 ATGATCCTCAAACAGGATTAAAATGACGCG
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
* * *
1521 ATGATCCTCAAACAGGATTAGAATAAAGCT
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
* * *
1551 ATGATCCTCAACCAGGATTTAAATGAGGCA
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
* *
1581 ATGATCCTCAAACAGGATTTAAATGAGGCA
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
* *
1611 ATGATCCTCAAACAGGATTAGAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
*
1641 AGGATCCTCAAACAGGATTAAAATGAAGCA
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
1671 ATGATCCTCAAACAGGATTAAAATGAAGCA
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
*
1701 ATGATCCTCAAACGGGATTAAAATGAAGCA
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
* *
1731 ATGATCCTCAAACAGGATTAAAATGACGCG
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
1761 ATGATCCTCAAACAGGATTAAAATGAAGCA
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
1791 ATGATCCTCAAACAGGATTAAAATGAAGCA
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
* * *
1821 ATGATTCTCAAACAGGATTAAAATGACGCG
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
* * *
1851 ATGATCCTCAAACAGGATTAGAATAAAGCT
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
* *
1881 ATGATCCTC-AACTAGGATTTAAATGAGGCA
1 ATGATCCTCAAAC-AGGATTAAAATGAAGCA
*
1911 ATGATCCTCAAACAGGA-TATAAATGACGCA
1 ATGATCCTCAAACAGGATTA-AAATGAAGCA
*
1941 ATGATCCTCAAACAGGATTAGAAATAAAGCA
1 ATGATCCTCAAACAGGATTA-AAATGAAGCA
* *
1972 AGGATCCTCAAACAGGATTAAAATGAAGCT
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
* *
2002 ATGATCCTCAACCAGGATTAAACATAAAGCA
1 ATGATCCTCAAACAGGATTAAA-ATGAAGCA
*
2033 ATGATCCTCAAACAGGATTAAAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
* *
2063 ATGATCCTCAAACAGGATTAACATGGAGCA
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
* **
2093 ATGATCCTCAAACAGGATTTAAATGACTCA
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
* * *
2123 ATGATCCTCAAATAGGATTAGAATAAAGCA
1 ATGATCCTCAAACAGGATTAAAATGAAGCA
*
2153 ATGATCCTCAAACAGGATTAAAATAAAGC
1 ATGATCCTCAAACAGGATTAAAATGAAGC
2182 TGATAAAGCA
Statistics
Matches: 616, Mismatches: 69, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
29 4 0.01
30 550 0.89
31 62 0.10
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (30 bp):
ATGATCCTCAAACAGGATTAAAATGAAGCA
Found at i:2507 original size:35 final size:35
Alignment explanation
Indices: 2443--2894 Score: 442
Period size: 36 Copynumber: 13.0 Consensus size: 35
2433 CATTTTGCAG
* *
2443 TCAATTGAAATAAACTGCAGAGAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGA-AAGATCGCCCTGGA
* * * *
2479 TCTACTGAAGTAAACTGAGGATAGATCG-CC----
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
2509 T----TGAAATAAACTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* *
2541 TCAATTGAAATAAACTGATAAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGA-AGAAAGATCGCCCTGGA
* *
2577 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
2612 TCAACTGAAATAAACTGAAGAAAGGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAA-GATCGCCCTGGA
* * *
2648 TCAATTGAAATAAACTGAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* *
2683 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
2718 TCAACTGAAATAAACTGAAGAAAGGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAA-GATCGCCCTGGA
*
2754 TCAA-TTAATATAAACTGAAGAAAGGATCGCCCTGGA
1 TCAACTGAA-ATAAACTGAAGAAA-GATCGCCCTGGA
** * * *
2790 TCAAACT-AAATAAACTGAA-ATGGGACCACCCTGGC
1 TC-AACTGAAATAAACTGAAGA-AAGATCGCCCTGGA
* * * * * * *
2825 TCAATTGAAATGAATTTAATAAGGAATCGCCCTGAA
1 TCAACTGAAATAAACTGAAGAAAG-ATCGCCCTGGA
* * * *
2861 TCAACTGAAGTGAATTGAAGAAAGACCGCCCTGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGG
2895 GTCAGCTG
Statistics
Matches: 352, Mismatches: 44, Indels: 41
0.81 0.10 0.09
Matches are distributed among these distances:
26 13 0.04
27 7 0.02
28 2 0.01
30 1 0.00
32 1 0.00
34 5 0.01
35 144 0.41
36 173 0.49
37 5 0.01
38 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (35 bp):
TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
Found at i:2626 original size:71 final size:70
Alignment explanation
Indices: 2510--2898 Score: 453
Period size: 71 Copynumber: 5.5 Consensus size: 70
2500 TAGATCGCCT
* * * *
2510 TGAAATAAACTGAAGAAAAGATCGCCCTGGATCAATTGAAATAAACTGATAAAAAGATCGCCCTG
1 TGAAATAAACTGAAG-AAAGACCGCCCTGGGTCAACTGAAATAAACTGA-AAAAGGATCGCCCTG
2575 GATCAAC
64 GATCAAC
2582 TGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGGATCGCCCTGG
1 TGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAA-AAAGGATCGCCCTGG
*
2647 ATCAAT
65 ATCAAC
*
2653 TGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAA-GACCGCCCTGG
1 TGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAA-AAAGGATCGCCCTGG
*
2717 GTCAAC
65 ATCAAC
* * *
2723 TGAAATAAACTGAAGAAAGGATCGCCCTGGATCAA-TTAATATAAACTGAAGAAAGGATCGCCCT
1 TGAAATAAACTGAAGAAA-GACCGCCCTGGGTCAACTGAA-ATAAACTGAA-AAAGGATCGCCCT
2787 GGATCAAAC
63 GGATC-AAC
** * * * * * * *
2796 T-AAATAAACTGAA-ATGGGACCACCCTGGCTCAATTGAAATGAATTTAATAAGGAATCGCCCTG
1 TGAAATAAACTGAAGA-AAGACCGCCCTGGGTCAACTGAAATAAACTGAAAAAGG-ATCGCCCTG
*
2859 AATCAAC
64 GATCAAC
* * *
2866 TGAAGTGAATTGAAGAAAGACCGCCCTGGGTCA
1 TGAAATAAACTGAAGAAAGACCGCCCTGGGTCA
2899 GCTG
Statistics
Matches: 276, Mismatches: 31, Indels: 21
0.84 0.09 0.06
Matches are distributed among these distances:
70 44 0.16
71 185 0.67
72 43 0.16
73 4 0.01
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.19
Consensus pattern (70 bp):
TGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAAAAGGATCGCCCTGGA
TCAAC
Done.