Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008113.1 Kokia drynarioides strain JFW-HI SEQ_122771, 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: 3444
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26
Found at i:620 original size:17 final size:17
Alignment explanation
Indices: 593--632 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
583 CATGCCATCA
593 AAAAGAAAAAAAAAAAG
1 AAAAGAAAAAAAAAAAG
* * *
610 AGAAGAGAAAAAAGAAG
1 AAAAGAAAAAAAAAAAG
627 AAAAGA
1 AAAAGA
633 TGGGTCAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAAG
Found at i:1612 original size:12 final size:12
Alignment explanation
Indices: 1597--1631 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1587 AAAGAAAATT
1597 AAAAAAGAGAAA
1 AAAAAAGAGAAA
*
1609 AAAAAAGGGAAA
1 AAAAAAGAGAAA
1621 AAGAAAAGAGA
1 AA-AAAAGAGA
1632 GGTCGAGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAAAGAGAAA
Found at i:2672 original size:50 final size:50
Alignment explanation
Indices: 2603--3229 Score: 287
Period size: 50 Copynumber: 12.7 Consensus size: 50
2593 GTATCATTAA
* * * * *
2603 ATGTGATAGG-AAAGGTTGAGGCCGTAATGGCGAACCTGGTATCTTAGAAT
1 ATGTGAT-GGAAAAGATTGAGGCCGTAACGGCGAACCTGGTACCATAGAAG
* * *
2653 ATGTGATGGAAAAGATTGAGGCCTTAACGGTGAATCTGGTACCAT-GAA-
1 ATGTGATGGAAAAGATTGAGGCCGTAACGGCGAACCTGGTACCATAGAAG
* * * * ** * *
2701 ATGTGATGGGAAATATTGAGGTCGCAATTGCGAACCCGATACCAT-GAAG
1 ATGTGATGGAAAAGATTGAGGCCGTAACGGCGAACCTGGTACCATAGAAG
* * * * * * * * *
2750 ATTTAAAGGGAAAAGGTTAAGGCTGTAACGGTGAACCAGGTACCTTAGAAG
1 ATGT-GATGGAAAAGATTGAGGCCGTAACGGCGAACCTGGTACCATAGAAG
* * * * *
2801 AGGTGATGGAAAGGATTGAGGTCGCAACGGCGAATCC-GGTACCAT-GATG
1 ATGTGATGGAAAAGATTGAGGCCGTAACGGCGAA-CCTGGTACCATAGAAG
* * * * * * *
2850 ATGCGATGGGAAATG-TTGAGGCCGTAATGGCAAACCCGATTCCATA-AAG
1 ATGTGAT-GGAAAAGATTGAGGCCGTAACGGCGAACCTGGTACCATAGAAG
* * * ** * * *
2899 ATTTGAAGGGAAAGATTGAGGCCACAACGGCGAACCTCGTACCTTAAAAG
1 ATGTGATGGAAAAGATTGAGGCCGTAACGGCGAACCTGGTACCATAGAAG
* * * * * *
2949 ATGTGATGGGAAAGATTAAGGCCGCAACGGTGAA-TTCGATACCAT-GAA-
1 ATGTGATGGAAAAGATTGAGGCCGTAACGGCGAACCT-GGTACCATAGAAG
* * * * * *
2997 ATGTGATGGGAAAGGTTGAGACCGTAATGACGAA-CTCGATACCAT-GAAG
1 ATGTGATGGAAAAGATTGAGGCCGTAACGGCGAACCT-GGTACCATAGAAG
* * * * * ** * *** *
3046 ATTTAAAGGGAAAGGTTGAGGCCACAACGGCAAACCCAATACCTTAGAAG
1 ATGTGATGGAAAAGATTGAGGCCGTAACGGCGAACCTGGTACCATAGAAG
* * * ** *
3096 ATGTGATGGGAAGGATTGAGGCCGCAACGGTAAATCTGGTACCAT-GAAG
1 ATGTGATGGAAAAGATTGAGGCCGTAACGGCGAACCTGGTACCATAGAAG
* * * * * * **
3145 ATGCGATTGAAAA-AGTTGAGGCAGCAATGGCAAACCCAGTACCAT-GAAG
1 ATGTGATGGAAAAGA-TTGAGGCCGTAACGGCGAACCTGGTACCATAGAAG
* * * * *
3194 ATTTGAAGGGAAAGGTTGAGGCCGTAATGGCGAACC
1 ATGTGATGGAAAAGATTGAGGCCGTAACGGCGAACC
3230 CGACACCTTA
Statistics
Matches: 429, Mismatches: 132, Indels: 33
0.72 0.22 0.06
Matches are distributed among these distances:
48 85 0.20
49 166 0.39
50 170 0.40
51 8 0.02
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (50 bp):
ATGTGATGGAAAAGATTGAGGCCGTAACGGCGAACCTGGTACCATAGAAG
Found at i:2910 original size:49 final size:49
Alignment explanation
Indices: 2549--3319 Score: 390
Period size: 49 Copynumber: 15.7 Consensus size: 49
2539 CCGAGGAAAT
* * * * * * * * *
2549 ATGAAGATTTGAAGGGAAAGGCTAAGGCCGCAACGACGAATCCGGTATC
1 ATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
* * * * * * * *
2598 ATTAA-ATGTGATAGGAAAGGTTGAGGCCGTAATGGCGAACCTGGTATC
1 ATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
* * * * ** ** * * *
2646 TTAGAATATGTGATGGAAAAGATTGAGGCCTTAACGGTGAATCTGGTACC
1 AT-GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
** * ** *
2696 ATGAA-ATGTGATGGGAAATATTGAGGTCGCAATTGCGAACCCGATACC
1 ATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
* * * * * * ** * *
2744 ATGAAGATTTAAAGGGAAAAGGTTAAGGCTGTAACGGTGAACCAGGTACC
1 ATGAAGATGTGATGGG-AAAGGTTGAGGCCGCAACGGCAAACCCGATACC
* * * * * *
2794 TTAGAAGAGGTGAT-GGAAAGGATTGAGGTCGCAACGGCGAATCCGGTACC
1 AT-GAAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGCAAACCCGATACC
* * * * * *
2844 ATGATGATGCGATGGGAAATGTTGAGGCCGTAATGGCAAACCCGATTCC
1 ATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
* * * * * *
2893 ATAAAGATTTGAAGGGAAAGATTGAGGCCACAACGGCGAACCTCG-TACC
1 ATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACC-CGATACC
* * * * ** **
2942 TTAAAAGATGTGATGGGAAAGATTAAGGCCGCAACGGTGAATTCGATACC
1 AT-GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
* * * * * *
2992 ATGAA-ATGTGATGGGAAAGGTTGAGACCGTAATGACGAACTCGATACC
1 ATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
* * * * *
3040 ATGAAGATTTAAAGGGAAAGGTTGAGGCCACAACGGCAAACCCAATACC
1 ATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
* * * * *
3089 TTAGAAGATGTGATGGG-AAGGATTGAGGCCGCAACGGTAAATCTGGTACC
1 AT-GAAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGCAAACCCGATACC
* * * * * *
3139 ATGAAGATGCGATTGAAAAAGTTGAGGCAGCAATGGCAAACCC-AGTACC
1 ATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGA-TACC
* * * * * *
3188 ATGAAGATTTGAAGGGAAAGGTTGAGGCCGTAATGGCGAACCCGACACC
1 ATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
* * ** * * *** * * *
3237 TTAAAAGATG-GATGACAATGATTGAGGCCGCAATAACGAATCTGATACC
1 AT-GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
*
3286 ATGAA-ATATGATGGGAAAGGTTGAGGCCGCAACG
1 ATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACG
3320 ACGAGTCTTA
Statistics
Matches: 538, Mismatches: 166, Indels: 37
0.73 0.22 0.05
Matches are distributed among these distances:
47 2 0.00
48 132 0.25
49 225 0.42
50 172 0.32
51 7 0.01
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (49 bp):
ATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCCGATACC
Found at i:2928 original size:148 final size:147
Alignment explanation
Indices: 2611--3317 Score: 695
Period size: 148 Copynumber: 4.8 Consensus size: 147
2601 AAATGTGATA
** * * * * *
2611 GGAAAGGTTGAGGCCGTAATGGCGAACCTGGTATCTTAGAATATGTGATGGAAAAGATTGAGGCC
1 GGAAAGGTTGAGGCCACAACGGCGAACCAGGTACCTTAGAAGATGTGATGGAAAGGATTGAGGCC
** * * * * * *
2676 TTAACGGTGAATCTGGTACCATGAAATGTGATGGGAAATATTGAGGTCGCAATTGCGAACCCGAT
66 GCAACGGTGAATCCGGTACCATGAAATGCGATGGGAAATGTTGAGGCCGCAATGGCAAACCCGAT
2741 ACCATGAAGATTTAAAG
131 ACCATGAAGATTTAAAG
* *** * * *
2758 GGAAAAGGTTAAGGCTGTAACGGTGAACCAGGTACCTTAGAAGAGGTGATGGAAAGGATTGAGGT
1 GG-AAAGGTTGAGGCCACAACGGCGAACCAGGTACCTTAGAAGATGTGATGGAAAGGATTGAGGC
* * *
2823 CGCAACGGCGAATCCGGTACCATGATGATGCGATGGGAAATGTTGAGGCCGTAATGGCAAACCCG
65 CGCAACGGTGAATCCGGTACCATGA-AATGCGATGGGAAATGTTGAGGCCGCAATGGCAAACCCG
* * *
2888 ATTCCATAAAGATTTGAAG
129 ATACCATGAAGATTTAAAG
* ** * *
2907 GGAAAGATTGAGGCCACAACGGCGAACCTCGTACCTTAAAAGATGTGATGGGAAA-GATTAAGGC
1 GGAAAGGTTGAGGCCACAACGGCGAACCAGGTACCTTAGAAGATGTGAT-GGAAAGGATTGAGGC
* * * * * * * * *
2971 CGCAACGGTGAATTCGATACCATGAAATGTGATGGGAAAGGTTGAGACCGTAATGACGAACTCGA
65 CGCAACGGTGAATCCGGTACCATGAAATGCGATGGGAAATGTTGAGGCCGCAATGGCAAACCCGA
3036 TACCATGAAGATTTAAAG
130 TACCATGAAGATTTAAAG
* * *
3054 GGAAAGGTTGAGGCCACAACGGCAAACCCA-ATACCTTAGAAGATGTGATGGGAAGGATTGAGGC
1 GGAAAGGTTGAGGCCACAACGGCGAA-CCAGGTACCTTAGAAGATGTGATGGAAAGGATTGAGGC
* * * * * *
3118 CGCAACGGTAAATCTGGTACCATGAAGATGCGATTGAAAAAGTTGAGGCAGCAATGGCAAACCC-
65 CGCAACGGTGAATCCGGTACCATGAA-ATGCGATGGGAAATGTTGAGGCCGCAATGGCAAACCCG
*
3182 AGTACCATGAAGATTTGAAG
129 A-TACCATGAAGATTTAAAG
** * * ** * *
3202 GGAAAGGTTGAGGCCGTAATGGCGAACCCGACACCTTAAAAGATG-GAT-GACAATGATTGAGGC
1 GGAAAGGTTGAGGCCACAACGGCGAACCAGGTACCTTAGAAGATGTGATGGA-AAGGATTGAGGC
**** * * ** *
3265 CGCAATAACGAATCTGATACCATGAAATATGATGGGAAAGGTTGAGGCCGCAA
65 CGCAACGGTGAATCCGGTACCATGAAATGCGATGGGAAATGTTGAGGCCGCAA
3318 CGACGAGTCT
Statistics
Matches: 459, Mismatches: 92, Indels: 19
0.81 0.16 0.03
Matches are distributed among these distances:
146 26 0.06
147 158 0.34
148 220 0.48
149 55 0.12
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (147 bp):
GGAAAGGTTGAGGCCACAACGGCGAACCAGGTACCTTAGAAGATGTGATGGAAAGGATTGAGGCC
GCAACGGTGAATCCGGTACCATGAAATGCGATGGGAAATGTTGAGGCCGCAATGGCAAACCCGAT
ACCATGAAGATTTAAAG
Found at i:3198 original size:295 final size:296
Alignment explanation
Indices: 2611--3317 Score: 872
Period size: 295 Copynumber: 2.4 Consensus size: 296
2601 AAATGTGATA
* * * *
2611 GGAAAGGTTGAGGCCGTAATGGCGAACCTGGTATCTTAGAATATGTGATGGAAAAGATTGAGGCC
1 GGAAAGGTTGAGGCCGTAATGGCGAACCTCGTACCTTAAAAGATGTGATGGAAAAGATTGAGGCC
** * ** **
2676 TTAACGGTGAATCTGGTACCATGAAATGTGATGGGAAATATTGAGGTCGCAATTGCGAACCCGAT
66 GCAACGGTGAATCTGATACCATGAAATGTGATGGGAAAGGTTGAGACCGCAATTGCGAACCCGAT
*** ** *
2741 ACCATGAAGATTTAAAGGGAAAAGGTTAAGGCTGTAACGGTGAACCAGGTACCTTAGAAGAGGTG
131 ACCATGAAGATTTAAAGGGAAAAGGTTAAGGCCACAACGGCAAACCAGATACCTTAGAAGAGGTG
* * * * *
2806 ATGGAAAGGATTGAGGTCGCAACGGCGAATCCGGTACCATGATGATGCGATGGGAAATGTTGAGG
196 ATGGAAAGGATTGAGGCCGCAACGGCAAATCCGGTACCATGAAGATGCGATGGAAAAAGTTGAGG
* * *
2871 CCGTAATGGCAAACCCGATTCCATAAAGATTTGAAG
261 CAGCAATGGCAAACCCGATACCATAAAGATTTGAAG
* ** * * *
2907 GGAAAGATTGAGGCCACAACGGCGAACCTCGTACCTTAAAAGATGTGATGGGAAAGATTAAGGCC
1 GGAAAGGTTGAGGCCGTAATGGCGAACCTCGTACCTTAAAAGATGTGATGGAAAAGATTGAGGCC
* *
2972 GCAACGGTGAAT-TCGATACCATGAAATGTGATGGGAAAGGTTGAGACCGTAA-TGACGAACTCG
66 GCAACGGTGAATCT-GATACCATGAAATGTGATGGGAAAGGTTGAGACCGCAATTG-CGAACCCG
* *
3035 ATACCATGAAGATTTAAAGGG-AAAGGTTGAGGCCACAACGGCAAACCCA-ATACCTTAGAAGAT
129 ATACCATGAAGATTTAAAGGGAAAAGGTTAAGGCCACAACGGCAAA-CCAGATACCTTAGAAGAG
* * * *
3098 GTGATGGGAAGGATTGAGGCCGCAACGGTAAATCTGGTACCATGAAGATGCGATTGAAAAAGTTG
193 GTGATGGAAAGGATTGAGGCCGCAACGGCAAATCCGGTACCATGAAGATGCGATGGAAAAAGTTG
*
3163 AGGCAGCAATGGCAAACCC-AGTACCATGAAGATTTGAAG
258 AGGCAGCAATGGCAAACCCGA-TACCATAAAGATTTGAAG
* *
3202 GGAAAGGTTGAGGCCGTAATGGCGAACC-CGACACCTTAAAAGATG-GAT-GACAATGATTGAGG
1 GGAAAGGTTGAGGCCGTAATGGCGAACCTCG-TACCTTAAAAGATGTGATGGA-AAAGATTGAGG
**** * *
3264 CCGCAATAACGAATCTGATACCATGAAATATGATGGGAAAGGTTGAGGCCGCAA
64 CCGCAACGGTGAATCTGATACCATGAAATGTGATGGGAAAGGTTGAGACCGCAA
3318 CGACGAGTCT
Statistics
Matches: 349, Mismatches: 55, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
293 1 0.00
294 60 0.17
295 160 0.46
296 128 0.37
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (296 bp):
GGAAAGGTTGAGGCCGTAATGGCGAACCTCGTACCTTAAAAGATGTGATGGAAAAGATTGAGGCC
GCAACGGTGAATCTGATACCATGAAATGTGATGGGAAAGGTTGAGACCGCAATTGCGAACCCGAT
ACCATGAAGATTTAAAGGGAAAAGGTTAAGGCCACAACGGCAAACCAGATACCTTAGAAGAGGTG
ATGGAAAGGATTGAGGCCGCAACGGCAAATCCGGTACCATGAAGATGCGATGGAAAAAGTTGAGG
CAGCAATGGCAAACCCGATACCATAAAGATTTGAAG
Done.