Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000436.1 Kokia drynarioides strain JFW-HI SEQ_111272, 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, 694
Length: 1157
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.31
Found at i:238 original size:96 final size:97
Alignment explanation
Indices: 54--240 Score: 211
Period size: 96 Copynumber: 1.9 Consensus size: 97
44 CTTTTGCGAG
* ** * *
54 AAGGATATTTGATTATCTCGATTTGAAGAAATGTTGCACCTAGTAAGTTAATGCACAATATTTCG
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATATTTCG
* * *
119 AAATCGAAGATAAGAAAACATTGCCTCGATTA
66 AAACCCAAAATAAGAAAACATTGCCTCGATTA
* *
151 AAGG-TATTCGATTA-CTTCGATTTGAAGAAAAATTGCACCTAATGAGTTAAGGCGCAA-ATTTT
1 AAGGATATTCGATTATC-TCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATA-TTT
* *
213 CGGAACCCAAAATAA-AAGAATATTGCCT
64 CGAAACCCAAAATAAGAA-AACATTGCCT
241 TGATATTAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
95 4 0.05
96 67 0.89
97 4 0.05
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAATATTTCG
AAACCCAAAATAAGAAAACATTGCCTCGATTA
Found at i:564 original size:30 final size:29
Alignment explanation
Indices: 517--1076 Score: 369
Period size: 30 Copynumber: 19.1 Consensus size: 29
507 CAAAAATAGG
*
517 ATTTTGGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
** *
546 ATTTTTAAAAGATTCGA-GGTAAAAAATGG-G
1 ATTTTTGGAAG-TTCGAGGGT--AAAATGGTA
*
576 ATTTTTGGGAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
*
605 ATTTTTGGAAGGTTCG-GGGCTAAAAATGG-G
1 ATTTTTGGAA-GTTCGAGGG-T-AAAATGGTA
* *
635 ATTTTTGG-AGTTCGAGGGTAACATAGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
663 ATTTTTGGAAGATTCGA-GGTCAAAAAT-G-A
1 ATTTTTGGAAG-TTCGAGGGT--AAAATGGTA
*
692 GATTTTTGGAAGTT-TAGGGGTAAAATGGTA
1 -ATTTTTGGAAGTTCGA-GGGTAAAATGGTA
* *
722 ATTTTTAGAAAGTT-TAGGGCTAAAAAT-G-A
1 ATTTTT-GGAAGTTCGAGGG-T-AAAATGGTA
* * *
751 GATTTTTGGAAGTTTGGGGGTAAAATAGTA
1 -ATTTTTGGAAGTTCGAGGGTAAAATGGTA
*
781 A-TTTTGGAAGATTCG-GGGTCAAAAATGG-G
1 ATTTTTGGAAG-TTCGAGGGT--AAAATGGTA
* *
810 ATTTTTGGAAGTTTGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
** *
839 ATTTTTAAAATGTTCG-GGGCTAAAAATGG-G
1 ATTTTTGGAA-GTTCGAGGG-T-AAAATGGTA
* *
869 ATTTTTGGAAGTTTGAGGGTAAAATAGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
*
898 ATTTTTGGAAGATTCGA-GGTCAAAAATGG-G
1 ATTTTTGGAAG-TTCGAGGGT--AAAATGGTA
* *
928 ATTTTTGGAAGTTCGGGGGTAGAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* *
957 ATTTTTAGAATGTTCGAGGCTAAAAAT-G-A
1 ATTTTTGGAA-GTTCGAGGGT-AAAATGGTA
* *
986 GATTTTTAGAAGTTCGGGGGTAAAATGGTA
1 -ATTTTTGGAAGTTCGAGGGTAAAATGGTA
*
1016 ATTTTTAGAAGGTTCG-GGGCTAAAAAT-G-A
1 ATTTTTGGAA-GTTCGAGGG-T-AAAATGGTA
* *
1045 GATTTTTGGTAGTTCG-GAGGTAAAATGATA
1 -ATTTTTGGAAGTTCGAG-GGTAAAATGGTA
1075 AT
1 AT
1077 CATTCTGTTT
Statistics
Matches: 429, Mismatches: 48, Indels: 108
0.73 0.08 0.18
Matches are distributed among these distances:
27 5 0.01
28 74 0.17
29 143 0.33
30 162 0.38
31 45 0.10
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (29 bp):
ATTTTTGGAAGTTCGAGGGTAAAATGGTA
Found at i:578 original size:59 final size:59
Alignment explanation
Indices: 508--1076 Score: 647
Period size: 59 Copynumber: 9.7 Consensus size: 59
498 GTTCGGAATC
* * *
508 AAAAATAGGATTTTGGGAAGTTCGAGGGTAAAATGGTAATTTTTAAAAGATTCGAGG-T
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGGCT
* * * *
566 AAAAAATGGGATTTTTGGGAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGCT
1 -AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGGCT
* * *
626 AAAAATGGGATTTTTGG-AGTTCGAGGGTAACATAGTAATTTTTGGAAGATTCGAGG-T
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGGCT
* * * *
683 CAAAAATGAGATTTTTGGAAGTT-TAGGGGTAAAATGGTAATTTTTAGAAAGTTTAG-GGCT
1 -AAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTAG-AAGATTCGAGGCT
* * * * * *
743 AAAAATGAGATTTTTGGAAGTTTGGGGGTAAAATAGTAA-TTTTGGAAGATTCG-GGGT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGGCT
* * * *
800 CAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAAAATG-TTCGGGGCT
1 -AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAA-GATTCGAGGCT
* * *
860 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATAGTAATTTTTGGAAGATTCGAGG-T
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGGCT
* *
918 CAAAAATGGGATTTTTGGAAGTTCGGGGGTAGAATGGTAATTTTTAGAATG-TTCGAGGCT
1 -AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAA-GATTCGAGGCT
* * * * *
978 AAAAATGAGATTTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGCT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGGCT
* * *
1037 AAAAATGAGATTTTTGGTAGTTCG-GAGGTAAAATGATAAT
1 AAAAATGGGATTTTTGGAAGTTCGAG-GGTAAAATGGTAAT
1077 CATTCTGTTT
Statistics
Matches: 446, Mismatches: 47, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
57 10 0.02
58 98 0.22
59 324 0.73
60 14 0.03
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (59 bp):
AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGGCT
Found at i:962 original size:118 final size:118
Alignment explanation
Indices: 508--1076 Score: 759
Period size: 117 Copynumber: 4.8 Consensus size: 118
498 GTTCGGAATC
* * * ** *
508 AAAAATAGGATTTTGGGAAGTTCGAGGGTAAAATGGTAATTTTTAAAAGATTCGAGGTAAAAAAT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTGGAAGATTCGAGGTCAAAAAT
* * ** *
573 GGGATTTTTGGGAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGCT
66 GGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAAAATGTTCGGGGCT
*
626 AAAAATGGGATTTTTGG-AGTTCGAGGGTAACATAGTAATTTTTGGAAGATTCGAGGTCAAAAAT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTGGAAGATTCGAGGTCAAAAAT
* ** **
690 GAGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTAGAAA-GTTTAGGGCT
66 GGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTA-AAATGTTCGGGGCT
* * * *
743 AAAAATGAGATTTTTGGAAGTTTGGGGGTAAAATAGTAA-TTTTGGAAGATTCGGGGTCAAAAAT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTGGAAGATTCGAGGTCAAAAAT
*
807 GGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAAAATGTTCGGGGCT
66 GGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAAAATGTTCGGGGCT
*
860 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATAGTAATTTTTGGAAGATTCGAGGTCAAAAAT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTGGAAGATTCGAGGTCAAAAAT
* * *
925 GGGATTTTTGGAAGTTCGGGGGTAGAATGGTAATTTTTAGAATGTTCGAGGCT
66 GGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAAAATGTTCGGGGCT
* * * * * * *
978 AAAAATGAGATTTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCG-GGGCTAAAAA
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTGGAAGATTCGAGGTC-AAAAA
* * * *
1042 TGAGATTTTTGGTAGTTCGGAGGTAAAATGATAAT
65 TGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAAT
1077 CATTCTGTTT
Statistics
Matches: 401, Mismatches: 45, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
116 3 0.01
117 208 0.52
118 190 0.47
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (118 bp):
AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATAGTAATTTTTGGAAGATTCGAGGTCAAAAAT
GGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAAAATGTTCGGGGCT
Done.