Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002489.1 Kokia drynarioides strain JFW-HI SEQ_114642, 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: 8117
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:60 original size:42 final size:42
Alignment explanation
Indices: 1--651 Score: 530
Period size: 42 Copynumber: 15.4 Consensus size: 42
* * * * *
1 GGTGAAGATTGGACGGGTGATGATGGTGAGTCAACTGTTAAG
1 GGTGAGGAGTGGACGGGTGATGGTGGTGAGTCTACTGTTGAG
** *
43 GGTGATAAGTGGACGGGTGGTGGTGGTGAGTCTACTGTTGAG
1 GGTGAGGAGTGGACGGGTGATGGTGGTGAGTCTACTGTTGAG
* ** * * *
85 GGTGATGAGTGGACTAGTGATGGTGGTGAGTGTACTTTTGAT
1 GGTGAGGAGTGGACGGGTGATGGTGGTGAGTCTACTGTTGAG
*
127 GGTGAGGAGTGGACGAGTGATGGTGGTGAGTCTACTGTTGAG
1 GGTGAGGAGTGGACGGGTGATGGTGGTGAGTCTACTGTTGAG
* * * *
169 GGTGAGGAGTGGATGGGTGGTAGTGGTGAGACTACTGTTGAG
1 GGTGAGGAGTGGACGGGTGATGGTGGTGAGTCTACTGTTGAG
* *
211 GGTGAGGAGTGGACAGGTGATGGTGGTGAGTCCACTAG-TGAG
1 GGTGAGGAGTGGACGGGTGATGGTGGTGAGTCTACT-GTTGAG
* * * * *
253 GGTGATGG-GTGGACGGGTGGTGATGATGAGTCCACTGTTG-N
1 GGTGA-GGAGTGGACGGGTGATGGTGGTGAGTCTACTGTTGAG
* * *
294 GGTGAAGAGTGGACGGGTGATGGTGATGAGTCTACAAG-TGAG
1 GGTGAGGAGTGGACGGGTGATGGTGGTGAGTCTAC-TGTTGAG
* * * *
336 GTTGAGGAGTGGACGAGTAGTGGTGGTGGTGGTGAGTCCACTTTTGAG
1 GGTGAGGAGTGGAC-----G-GGTGATGGTGGTGAGTCTACTGTTGAG
* * * * * *
384 GGTGAGGAGTGAACCGATGGTGGTGGTGAGTATA-TAATTGAG
1 GGTGAGGAGTGGACGGGTGATGGTGGTGAGTCTACT-GTTGAG
* * * * * * *
426 GTTGAAGAAG-GGACAGGTGATGATTGTGAGTCCACTCTTGAG
1 GGTG-AGGAGTGGACGGGTGATGGTGGTGAGTCTACTGTTGAG
*
468 GGTGAGGAATGGA----TGAGTGGTGGTGAGTCTACTGTTGAG
1 GGTGAGGAGTGGACGGGTGA-TGGTGGTGAGTCTACTGTTGAG
* ** * *
507 GGTAAGGAGTAAACGTGTGGTGGTGGTGGTGAGTCTACTATTGAG
1 GGTGAGGAGTGGAC--G-GGTGATGGTGGTGAGTCTACTGTTGAG
* * *
552 GGTGAGGAGTGGACGGGTGGTAGTGGTGAGTCTATTGTTGAG
1 GGTGAGGAGTGGACGGGTGATGGTGGTGAGTCTACTGTTGAG
* * * * * *
594 GGTAAAGAGTAGACGGGTGGTGGTGGTGAGTCCACTGTTAAG
1 GGTGAGGAGTGGACGGGTGATGGTGGTGAGTCTACTGTTGAG
* *
636 TGTGACGAGTGGACGG
1 GGTGAGGAGTGGACGG
652 ATGGGGTTTG
Statistics
Matches: 488, Mismatches: 96, Indels: 50
0.77 0.15 0.08
Matches are distributed among these distances:
38 3 0.01
39 27 0.06
40 1 0.00
41 36 0.07
42 344 0.70
43 9 0.02
45 32 0.07
46 2 0.00
47 1 0.00
48 33 0.07
ACGTcount: A:0.21, C:0.07, G:0.45, T:0.27
Consensus pattern (42 bp):
GGTGAGGAGTGGACGGGTGATGGTGGTGAGTCTACTGTTGAG
Found at i:241 original size:21 final size:21
Alignment explanation
Indices: 50--241 Score: 97
Period size: 21 Copynumber: 9.1 Consensus size: 21
40 AAGGGTGATA
* *
50 AGTGGACGGGTGGTGGTGGTG
1 AGTGGACTGGTGATGGTGGTG
** * * *
71 AGTCTACTGTTGAGGGTGATG
1 AGTGGACTGGTGATGGTGGTG
*
92 AGTGGACTAGTGATGGTGGTG
1 AGTGGACTGGTGATGGTGGTG
* **
113 AGTGTACTTTTGATGGTGAG-G
1 AGTGGACTGGTGATGGTG-GTG
134 AGTGGAC-GAGTGATGGTGGTG
1 AGTGGACTG-GTGATGGTGGTG
** * *
155 AGTCTACTGTTGAGGGTGAG-G
1 AGTGGACTGGTGATGGTG-GTG
* *
176 AGTGGA-TGGGTGGTAGTGGTG
1 AGTGGACT-GGTGATGGTGGTG
*** * *
197 AGACTACTGTTGAGGGTGAG-G
1 AGTGGACTGGTGATGGTG-GTG
*
218 AGTGGACAGGTGATGGTGGTG
1 AGTGGACTGGTGATGGTGGTG
239 AGT
1 AGT
242 CCACTAGTGA
Statistics
Matches: 119, Mismatches: 42, Indels: 20
0.66 0.23 0.11
Matches are distributed among these distances:
20 4 0.03
21 110 0.92
22 5 0.04
ACGTcount: A:0.18, C:0.06, G:0.48, T:0.28
Consensus pattern (21 bp):
AGTGGACTGGTGATGGTGGTG
Found at i:726 original size:42 final size:42
Alignment explanation
Indices: 680--793 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
670 TGGATGTTGT
* *
680 TGGTGAGTACACTG-TGGGGGT-TGAGGAGTGGACGAGTAGTGG
1 TGGTGAGTACACTGATAGGGGTGT-A-GAGTGGACGAGTAGTGA
* * *
722 TGGTGAGTCCACTGATAGGGGTGTAGAGTGGACGGGTGGTGA
1 TGGTGAGTACACTGATAGGGGTGTAGAGTGGACGAGTAGTGA
* * *
764 TGGTGAGTGCATTGATAGGGGTGGAGAGTG
1 TGGTGAGTACACTGATAGGGGTGTAGAGTG
794 TACAAATGGG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 54 0.87
43 7 0.11
44 1 0.02
ACGTcount: A:0.19, C:0.07, G:0.49, T:0.25
Consensus pattern (42 bp):
TGGTGAGTACACTGATAGGGGTGTAGAGTGGACGAGTAGTGA
Found at i:2528 original size:77 final size:77
Alignment explanation
Indices: 2440--2595 Score: 240
Period size: 77 Copynumber: 2.0 Consensus size: 77
2430 TTTACCAAAT
* * * * * * *
2440 ATAACTTGTATTTTCTATCTTTAGTTTGCAATAGGTTATATTATATTTTGGTCCTTATACTATAT
1 ATAACTTGTATTTTCTATATTTAATTTACAATAGGTTAAATTATATTGTGATCCTTATACTATAA
2505 CTAAAATTCATG
66 CTAAAATTCATG
*
2517 ATAACTTGTATTTTCTTTATTTAATTTACAATAGGTTAAATTATATTGTGATCCTTATACTATAA
1 ATAACTTGTATTTTCTATATTTAATTTACAATAGGTTAAATTATATTGTGATCCTTATACTATAA
2582 CTAAAATTCATG
66 CTAAAATTCATG
2594 AT
1 AT
2596 TTTGTTTTTA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (77 bp):
ATAACTTGTATTTTCTATATTTAATTTACAATAGGTTAAATTATATTGTGATCCTTATACTATAA
CTAAAATTCATG
Found at i:3913 original size:23 final size:22
Alignment explanation
Indices: 3883--3925 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
3873 GAAGTCAATT
3883 AAAATTTT-TATATAGTAATATTC
1 AAAATTTTAT-TATAG-AATATTC
3906 AAAATTTTATTATAGAATAT
1 AAAATTTTATTATAGAATAT
3926 CTATATAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 13 0.68
24 1 0.05
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
AAAATTTTATTATAGAATATTC
Found at i:3924 original size:22 final size:23
Alignment explanation
Indices: 3883--3925 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
3873 GAAGTCAATT
3883 AAAATTTTTATATAGTAATATTC
1 AAAATTTTTATATAGTAATATTC
3906 AAAA-TTTTATTATAG-AATAT
1 AAAATTTTTA-TATAGTAATAT
3926 CTATATAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (23 bp):
AAAATTTTTATATAGTAATATTC
Found at i:5454 original size:38 final size:38
Alignment explanation
Indices: 5410--5486 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
5400 TAGGAGATTG
5410 TATGTGGACTTAAATGGTTGAATGTGTAATGTTTTGGA
1 TATGTGGACTTAAATGGTTGAATGTGTAATGTTTTGGA
5448 TATGTGGACTTAAATGGTTGAATGTGTAATGTTTTGGA
1 TATGTGGACTTAAATGGTTGAATGTGTAATGTTTTGGA
5486 T
1 T
5487 GGTTTTTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.43
Consensus pattern (38 bp):
TATGTGGACTTAAATGGTTGAATGTGTAATGTTTTGGA
Done.