Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008300.1 Corchorus olitorius cultivar O-4 contig08327, 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, 636
Length: 1060
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:29 original size:21 final size:21
Alignment explanation
Indices: 1--503 Score: 602
Period size: 21 Copynumber: 23.9 Consensus size: 21
*
1 GGGGTTTGACTCTCAAAATTT
1 GGGGTTTGACTATCAAAATTT
* *
22 GCGGTTTGACTATCAAATTTT
1 GGGGTTTGACTATCAAAATTT
*
43 GGGGTTTGACTATCAAATTTT
1 GGGGTTTGACTATCAAAATTT
*
64 GGGGTTTGACTCTCAAAATTT
1 GGGGTTTGACTATCAAAATTT
* *
85 GCGGTTTGACTATCAAACTTT
1 GGGGTTTGACTATCAAAATTT
*
106 GGGGTTTGACTATCAAATTTT
1 GGGGTTTGACTATCAAAATTT
* * *
127 GGGGTTTTACTACCAAACTTT
1 GGGGTTTGACTATCAAAATTT
*
148 GGGG-TTGACTAT-AGAATTTT
1 GGGGTTTGACTATCA-AAATTT
*
168 GGGGTTTGACTTTCAAAATTT
1 GGGGTTTGACTATCAAAATTT
*
189 GGGGGTTTGACTATCAAATTTT
1 -GGGGTTTGACTATCAAAATTT
* *
211 GGGGTTCGACTTTCAAAATTT
1 GGGGTTTGACTATCAAAATTT
* *
232 GCGGTTTGACTATCAAATTTT
1 GGGGTTTGACTATCAAAATTT
* * *
253 GGGGTTTTACTACCAAACTTT
1 GGGGTTTGACTATCAAAATTT
274 GGGGTTTGACTAT-AAAATTTT
1 GGGGTTTGACTATCAAAA-TTT
*
295 GGGGTTTGACTTTCAAAATTT
1 GGGGTTTGACTATCAAAATTT
*
316 GGGGTTTGACTATCAAATTTT
1 GGGGTTTGACTATCAAAATTT
* *
337 GGGGTTTGACTACCAAACTTT
1 GGGGTTTGACTATCAAAATTT
* *
358 GGGGTTTGACTACCAAACTTT
1 GGGGTTTGACTATCAAAATTT
*
379 GGGGTTTGACTATCAAAGTTTT
1 GGGGTTTGACTATCAAA-ATTT
*
401 AGGGG-TTGACTATCAAACTTTT
1 -GGGGTTTGACTATCAAA-ATTT
*
423 GGGGTTTGACTATCAAACTTT
1 GGGGTTTGACTATCAAAATTT
*
444 GGGGTTTGA-TAGTTAAAATTT
1 GGGGTTTGACTA-TCAAAATTT
* *
465 GGGGTTTAATTATCAAAATTT
1 GGGGTTTGACTATCAAAATTT
*
486 GGGGGTTGACTATCAAAA
1 GGGGTTTGACTATCAAAA
504 CATCATTGTA
Statistics
Matches: 420, Mismatches: 51, Indels: 22
0.85 0.10 0.04
Matches are distributed among these distances:
19 1 0.00
20 20 0.05
21 338 0.80
22 57 0.14
23 4 0.01
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (21 bp):
GGGGTTTGACTATCAAAATTT
Found at i:597 original size:53 final size:53
Alignment explanation
Indices: 540--661 Score: 181
Period size: 53 Copynumber: 2.3 Consensus size: 53
530 CAAAAGGATG
*
540 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTATACATGC
* * * * *
593 ATGGTTAAACCCCAAAATTTAATATTCAAACCATATAACATCATTATACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTATACATGC
*
646 ATGGTCAAATCCCAAA
1 ATGGTCAAACCCCAAA
662 GGATGATGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 61 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (53 bp):
ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTATACATGC
Found at i:683 original size:74 final size:73
Alignment explanation
Indices: 593--734 Score: 185
Period size: 74 Copynumber: 1.9 Consensus size: 73
583 TTGTACATGC
* * * * * * *
593 ATGGTTAAACCCCAAAATTTAATATTCAAACCATATAACATCATTATACATGCATGGTCAAATCC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACA-AACACCATTATACATGCATAGTCAAACCC
658 CAAAGGATG
65 CAAAGGATG
* * *
667 ATGGTCAATCCCCAAAATTCAATAGTCAAACCACAATCACCATTGTACATGCATAGTCAAACCCC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAACACCATTATACATGCATAGTCAAACCCC
732 AAA
66 AAA
735 ATTCAATAGT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
73 28 0.48
74 30 0.52
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.24
Consensus pattern (73 bp):
ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAACACCATTATACATGCATAGTCAAACCCC
AAAGGATG
Found at i:747 original size:73 final size:73
Alignment explanation
Indices: 599--757 Score: 169
Period size: 73 Copynumber: 2.2 Consensus size: 73
589 ATGCATGGTT
* * * * * *
599 AAACCCCAAAATTTAATATTCAAACCATATAACATCATTATACATGCATGGTCAAATCCCAAAGG
1 AAACCCCAAAATTCAATAGTCAAACCACATAACACCATTATACATGCATAGTCAAACCCCAAA-G
* *
664 ATGATGGTC
65 ATAATAGTC
* * *
673 AATCCCCAAAATTCAATAGTCAAACCACA-ATCACCATTGTACATGCATAGTCAAACCCCAAA-A
1 AAACCCCAAAATTCAATAGTCAAACCACATAACACCATTATACATGCATAGTCAAACCCCAAAGA
736 TTCAATAGTC
66 -T-AATAGTC
*
746 AAACCACAAAAT
1 AAACCCCAAAAT
758 ATCATTGTAC
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
71 1 0.01
72 1 0.01
73 43 0.61
74 25 0.36
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.23
Consensus pattern (73 bp):
AAACCCCAAAATTCAATAGTCAAACCACATAACACCATTATACATGCATAGTCAAACCCCAAAGA
TAATAGTC
Found at i:772 original size:126 final size:127
Alignment explanation
Indices: 499--825 Score: 458
Period size: 126 Copynumber: 2.6 Consensus size: 127
489 GGTTGACTAT
* *
499 CAAAACATCATTGTACATGTATAGTCAAAACCAAAAGGATGATGGTCAAACCCCAAAATTCAATA
1 CAAAACATCATTGTACATGCATAGTCAAAACCCAAAGGATGATGGTCAAACCCCAAAATTCAATA
* * * * *
564 GTCAAACCACAAAACATCATTGTACATGCATGGTTAAACCCCAAAATTTAATATTCAAACCA
66 GTCAAACCACAAAACACCATTGTACATGCATAGTCAAACCCCAAAATTCAATAGTCAAACCA
* * * * * *
626 TATAACATCATTATACATGCATGGTCAAATCCCAAAGGATGATGGTCAATCCCCAAAATTCAATA
1 CAAAACATCATTGTACATGCATAGTCAAAACCCAAAGGATGATGGTCAAACCCCAAAATTCAATA
*
691 GTCAAACCAC-AATCACCATTGTACATGCATAGTCAAACCCCAAAATTCAATAGTCAAACCA
66 GTCAAACCACAAAACACCATTGTACATGCATAGTCAAACCCCAAAATTCAATAGTCAAACCA
* * * * * *
752 CAAAATATCATTGTACATGCATAGTCAAACCCCAAAAGATGATGTTCAAACCCCAACATTCGATA
1 CAAAACATCATTGTACATGCATAGTCAAAACCCAAAGGATGATGGTCAAACCCCAAAATTCAATA
*
817 ATCAAACCA
66 GTCAAACCA
826 TGAAAAACAT
Statistics
Matches: 174, Mismatches: 26, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
126 107 0.61
127 67 0.39
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.23
Consensus pattern (127 bp):
CAAAACATCATTGTACATGCATAGTCAAAACCCAAAGGATGATGGTCAAACCCCAAAATTCAATA
GTCAAACCACAAAACACCATTGTACATGCATAGTCAAACCCCAAAATTCAATAGTCAAACCA
Found at i:786 original size:53 final size:52
Alignment explanation
Indices: 670--788 Score: 195
Period size: 52 Copynumber: 2.3 Consensus size: 52
660 AAGGATGATG
*
670 GTCAATCCCCAAAATTCAATAGTCAAACCACAATCACCATTGTACATGCATA
1 GTCAAACCCCAAAATTCAATAGTCAAACCACAATCACCATTGTACATGCATA
*
722 GTCAAACCCCAAAATTCAATAGTCAAACCACAAAAT-ATCATTGTACATGCATA
1 GTCAAACCCCAAAATTCAATAGTCAAACCAC--AATCACCATTGTACATGCATA
775 GTCAAACCCCAAAA
1 GTCAAACCCCAAAA
789 GATGATGTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
52 30 0.48
53 30 0.48
54 3 0.05
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.21
Consensus pattern (52 bp):
GTCAAACCCCAAAATTCAATAGTCAAACCACAATCACCATTGTACATGCATA
Done.