Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014728.1 Kokia drynarioides strain JFW-HI SEQ_129767, 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: 3039
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Found at i:393 original size:221 final size:221
Alignment explanation
Indices: 8--3039 Score: 3716
Period size: 221 Copynumber: 13.3 Consensus size: 221
1 CTATTGC
*
8 AAAAGGGACACAAATGACGTTGTGTCACTGTTTCATTCAA-TCATTTTCCATTGAAGAAGAGAAA
1 AAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATTCA-TTTCCATTGAAGAAGAGAAA
* * * * **
72 GGATTGTATGAAATAGGGATTTTATCCCTTTCCAATTGTTTTATGCCACATCAACAATTTCATTT
65 GGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCC
* * *
137 TGAATTTCAAGATTTTAATTTTAATTT-TATTTTTTCAGGATGAAAATATTGAAATTAAGATTGA
130 TGAATTTCAGGATTTTAATTTTAATTTGT-TTTTTTCAGGATGAAAATGTTGAAATTAAGAATGA
* * *
201 AAATACTGATGTGGCATAAAACTAATGG
194 AAATACTGATGTGGCGTAAAACTATTAG
* *
229 AAAAGGGACACAAATGACATGGTGTCA-TGGTTTCATTCAATTCATTTCCATTGAAGAGGAGAAA
1 AAAAGGGACACAAATGACGTGGTGTCACT-GTTTCATTCAATTCATTTCCATTGAAGAAGAGAAA
*
293 GGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCC
65 GGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCC
* * *
358 TGTATTTCAGGATTTTGATTTTAATTTGTTTTTTTCAGGATGAAAAAGTTGAAATTAAGAATGAA
130 TGAATTTCAGGATTTTAATTTTAATTTGTTTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAA
* *
423 AATACTGATATGGTGTAAAACTATTAG
195 AATACTGATGTGGCGTAAAACTATTAG
* *
450 AAAAGGGGCACAAATGACGTTGTGTCACTGTTTCATTCAATCGTTTTCCATTTCATTCAATCCTT
1 AAAAGGGACACAAATGACGTGGTGTCACTG--T--TTC-A-----TT-CA----ATTC-A----T
* * * * ** * *
515 TTCCATTAAAGAAGAGAAAGGGTGGTATGAAGTAGGGATATTATCCCTTTCCGATAGTTTTTTGC
46 TTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGC
* * *
580 CACACCAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGTTTCTTTTCAGGATGTAA
111 CACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGTTT-TTTTCAGGATGAAA
* * *
645 ATGTTGAAATTAAGAATGAAAATACTGATGTAGCGAAAAATTATT-G
175 ATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAG
* *
691 AAAAAGGGACACAAATGGCGTGGTTTCACTGTTTTATTCATCCTTTTCCATTTTATTAAATCATT
1 -AAAAGGGACACAAATGACGTGGTGTCACTG---T-TTCA-----TT-CA----A-T---TCA-T
* * *
756 TTCCATTGAAGAAGAGAAAGGATTGTATGAAACAAGGATATTATCCCTTTCCAATAGTTTTACGC
46 TTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGC
* * * * *
821 CACATAAACAATTTCATCCTAAATTTCTGGATTTTAATTTTAATTTGATTTTCTCAGGATGAAAA
111 CACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGTTTTTTTCAGGATGAAAA
* * *
886 TGTTGACATTAAGAATGAAAATACTGATGTGGCGTAAAACCAATAG
176 TGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAG
*
932 AAAAGGGACACAAAATGACGTGGTGTCATTGTTTCATTCAA-TCATTTTCCATTGAAGAAGAGAA
1 AAAAGGGACAC-AAATGACGTGGTGTCACTGTTTCATTCAATTCA-TTTCCATTGAAGAAGAGAA
*
996 AGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATC
64 AGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATC
* *
1061 CTAAATTTCAGGATTTTAATTTTAATTTGATTTTTTT-AGGATGAAAATGATGAAATTAAGAATG
129 CTGAATTTCAGGATTTTAATTTTAATTTG-TTTTTTTCAGGATGAAAATGTTGAAATTAAGAATG
*
1125 AAAATACTGATATGGCGTAAAACTATTAG
193 AAAATACTGATGTGGCGTAAAACTATTAG
* * * ** * *
1154 AAAAGGGACATAGATGATGTCATGTCACTGTTTCATTCAATTCTTTTCCGTTGAAGAAGAGAAAG
1 AAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATTCATTTCCATTGAAGAAGAGAAAG
* * *
1219 GATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTAAGTCACACCAACAATTTCATCCT
66 GATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCT
* * * *
1284 GTATTTCAGGATTTTAATTTTAATTTGATTTTTTCAGGATGGAAATGTTGAAATTAATAATGAAA
131 GAATTTCAGGATTTTAATTTTAATTTGTTTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAA
*
1349 ATACTGATATGGCGTAAAACTATTAG
196 ATACTGATGTGGCGTAAAACTATTAG
* *
1375 AAAAGGGACACAACTGACGTGGTGTCACTGTTTCATTCAATTCTTTTCCATTGAAGAAGAGAAAG
1 AAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATTCATTTCCATTGAAGAAGAGAAAG
*
1440 GATTGTATAAAACAGGGATATTATCCCTGTCCAATAGTTTTATGCCACATCAACAATTTCATCCT
66 GATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCT
* * * * *
1505 AAATTTCAGGATTTTAATTTTAATTTGATTTTCTCAAGATGAAAATGTTGACATTAAGAATGAAA
131 GAATTTCAGGATTTTAATTTTAATTTGTTTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAA
* *
1570 ATACTGATGTGGCGTAAAACCAATAG
196 ATACTGATGTGGCGTAAAACTATTAG
*
1596 AAAAGGGACACAAAATGACGTGGTGTCACTGTTTTATTCAA-TCATTTTCCATTGAAGAAGAGAA
1 AAAAGGGACAC-AAATGACGTGGTGTCACTGTTTCATTCAATTCA-TTTCCATTGAAGAAGAGAA
*
1660 AGGATTGTATGAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATC
64 AGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATC
* * *
1725 CTG-ATTTTAGGATTTTAATTTTATTTTGATTTTTTT-AGGATGAAAATGATGAAATTAAGAATG
129 CTGAATTTCAGGATTTTAATTTTAATTTG-TTTTTTTCAGGATGAAAATGTTGAAATTAAGAATG
* *
1788 AAAATATTGATTTGGCGTAAAACTATTAG
193 AAAATACTGATGTGGCGTAAAACTATTAG
* * * * * * *
1817 AAAAGGGACATAGATGACGTCGTGTCACTGTTTCATTCAATTCTTTTCCGTCGAAGAAGAGGAAG
1 AAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATTCATTTCCATTGAAGAAGAGAAAG
*
1882 GATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACACCAACAATTTCATCCT
66 GATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCT
* * *
1947 GTATTTCAGGATTTTAATTTTAATTTG-ATTTTTCAGGATAAAAATGTTGAAATTAAGAATGAAA
131 GAATTTCAGGATTTTAATTTTAATTTGTTTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAA
* *
2011 ATACTGATATGGCGTAAAACCATTAG
196 ATACTGATGTGGCGTAAAACTATTAG
* *
2037 AGAAGGGACACAACTGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCATTTCATTCAATCCTT
1 AAAAGGGACACAAATGACGTGGTGTCACTG--T--TTC-A-----TT-CA----ATTC-A----T
* * * * ** * *
2102 TTCCATTAAAGAAGAGAAAGGGTGGTATGAAGTAGGGATATTTTCCCTTTCCGATAGTTTTATGC
46 TTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGC
* * * *
2167 CACACCAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGCTTCTTTTCAGGATGTAA
111 CACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTG-TTTTTTTCAGGATGAAA
* * *
2232 ATGTCGAAATTAAGAATGAAAATACTGATGTAGCGTAAAATTATT-G
175 ATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAG
*
2278 AAAAAGGGACACAAATGACGTGGTTTCACTGTTTTATTCAATCCTTTTCCATTTTATTAAATCAT
1 -AAAAGGGACACAAATGACGTGGTGTCACTG---T-TTC-A-----TT-CA----A-T---TCA-
* *
2343 TTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAAGGATATTATCCCTTTCCAATAGTTTTATG
45 TTTCCATTGAAGAAGAGAAAGGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATG
* ** * * *
2408 CCACATGAACAATTTCATTTTCAATTTCAAGATTTTAATTTTAATTT-TAATTTTTCAGGATGAA
110 CCACATCAACAATTTCATCCTGAATTTCAGGATTTTAATTTTAATTTGT-TTTTTTCAGGATGAA
* *
2472 AATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGG
174 AATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTAG
* * * * *
2520 AAAAGGGACACAAAATGACGTGCTGTCACTATTTCATTCAATCCTTTTCCATTGAAGAGGAGAAA
1 AAAAGGGACAC-AAATGACGTGGTGTCACTGTTTCATTCAATTCATTTCCATTGAAGAAGAGAAA
* * * *
2585 GGATTGTATAAAACAGTGATATTATCCCTTTCTAATAGTTTTATGCCACACCAACAGTTTCATCC
65 GGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCC
* * *
2650 TGAATTTCAGGATTTGAATTTTAATTTGATTTTTTCAGGATGAAAATGATGAAATTAAGAATGAA
130 TGAATTTCAGGATTTTAATTTTAATTTGTTTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAA
*
2715 AATACTGATCTGGCGTAAAACTATTAG
195 AATACTGATGTGGCGTAAAACTATTAG
* *
2742 AAAAGGGGCACAAATGACGTTGTGTCACTGTTTCATTCAA-TCATTTTCCATTGAAGAAGAGAAA
1 AAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATTCA-TTTCCATTGAAGAAGAGAAA
* * **
2806 GGATTGTATGAAACAGGGATATTATCCCTTTCCAATTGTTTTATGCCACATCAACAATTTCATTT
65 GGATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCC
* *
2871 TGAATTTCAGGATTTTAATTTTAATTT-TATTTTTTCAGGATGAAAATATTGAAATTAAGATTGA
130 TGAATTTCAGGATTTTAATTTTAATTTGT-TTTTTTCAGGATGAAAATGTTGAAATTAAGAATGA
* * *
2935 AAATACTGATGTGGCATAAAACTAATGG
194 AAATACTGATGTGGCGTAAAACTATTAG
* *
2963 AAAAGGGACACAAATGACGTGGTGTCACGGTTTCATTCAATTCATTTCCATTGAAGAGGAGAAAG
1 AAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATTCATTTCCATTGAAGAAGAGAAAG
3028 GATTGTATAAAA
66 GATTGTATAAAA
Statistics
Matches: 2469, Mismatches: 265, Indels: 154
0.85 0.09 0.05
Matches are distributed among these distances:
219 5 0.00
220 192 0.08
221 972 0.39
222 468 0.19
223 7 0.00
224 3 0.00
225 4 0.00
226 2 0.00
227 2 0.00
230 2 0.00
231 8 0.00
232 6 0.00
235 4 0.00
236 4 0.00
237 6 0.00
238 4 0.00
239 1 0.00
240 163 0.07
241 304 0.12
242 299 0.12
243 7 0.00
244 1 0.00
245 3 0.00
246 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (221 bp):
AAAAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATTCATTTCCATTGAAGAAGAGAAAG
GATTGTATAAAACAGGGATATTATCCCTTTCCAATAGTTTTATGCCACATCAACAATTTCATCCT
GAATTTCAGGATTTTAATTTTAATTTGTTTTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAA
ATACTGATGTGGCGTAAAACTATTAG
Found at i:505 original size:20 final size:20
Alignment explanation
Indices: 480--521 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
470 TGTGTCACTG
*
480 TTTCATTCAATCGTTTTCCA
1 TTTCATTCAATCCTTTTCCA
500 TTTCATTCAATCCTTTTCCA
1 TTTCATTCAATCCTTTTCCA
520 TT
1 TT
522 AAAGAAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTCATTCAATCCTTTTCCA
Found at i:2092 original size:20 final size:20
Alignment explanation
Indices: 2067--2108 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2057 GGTGTCACTG
2067 TTTCATTCAATCCTTTTCCA
1 TTTCATTCAATCCTTTTCCA
2087 TTTCATTCAATCCTTTTCCA
1 TTTCATTCAATCCTTTTCCA
2107 TT
1 TT
2109 AAAGAAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.29, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTCATTCAATCCTTTTCCA
Found at i:2334 original size:20 final size:20
Alignment explanation
Indices: 2309--2350 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2299 GGTTTCACTG
* *
2309 TTTTATTCAATCCTTTTCCA
1 TTTTATTAAATCATTTTCCA
2329 TTTTATTAAATCATTTTCCA
1 TTTTATTAAATCATTTTCCA
2349 TT
1 TT
2351 GAAGAAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.19, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATTAAATCATTTTCCA
Found at i:2348 original size:242 final size:239
Alignment explanation
Indices: 1847--3014 Score: 1417
Period size: 242 Copynumber: 5.0 Consensus size: 239
1837 CGTGTCACTG
* * * *
1847 TTTCATTCAATTC-TTTTCCGTCGAAGAAGAGGAAGGATTGTATAAAACAGGGATATTATCCCTT
1 TTTCATTCAA-TCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTT
* *
1911 TCCAATAGTTTTATGCCACACCAACAATTTCATCCTGTATTTCAGGATTTTAATTTTAATTTGA-
65 TCCAATAGTTTTATGCCACACCAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGAT
* * * *
1975 TTTTTCAGGATAAAAATGTTGAAATTAAGAATGAAAATACTGATATGGCGTAAAACCATT-AGAG
130 TTTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGA-AA
*
2039 AAGGGACACAACTGACGTGGTGTCACTGTTTCATTCAATCCTTTTCCA
194 AAGGGACACAAATGACGTGGTGTCACTGTTTCATTCAAT-C-TTTCCA
* * * * ** *
2087 TTTCATTCAATCCTTTTCCATTAAAGAAGAGAAAGGGTGGTATGAAGTAGGGATATTTTCCCTTT
1 TTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTT
* *
2152 CCGATAGTTTTATGCCACACCAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGCTT
66 CCAATAGTTTTATGCCACACCAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGATT
* * * *
2217 CTTTTCAGGATGTAAATGTCGAAATTAAGAATGAAAATACTGATGTAGCGTAAAATTATTGAAAA
131 -TTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGAAAA
* *
2282 AGGGACACAAATGACGTGGTTTCACTGTTTTATTCAATCCTTTTCCA
195 AGGGACACAAATGACGTGGTGTCACTGTTTCATTCAAT-C-TTTCCA
* * *
2329 TTTTATTAAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAAGGATATTATCCCTTT
1 TTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTT
** * * * * *
2394 CCAATAGTTTTATGCCACATGAACAATTTCATTTTCAATTTCAAGATTTTAATTTTAATTTTAAT
66 CCAATAGTTTTATGCCACACCAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGATT
* *
2459 TTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTAATGGAAAA
131 TTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGAAAAA
2524 GGGACACAAAATGAC---GTG---CTG------TC-A-C--T--A
196 GGGACAC-AAATGACGTGGTGTCACTGTTTCATTCAATCTTTCCA
* * * *
2551 TTTCATTCAATCCTTTTCCATTGAAGAGGAGAAAGGATTGTATAAAACAGTGATATTATCCCTTT
1 TTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTT
* * * *
2616 CTAATAGTTTTATGCCACACCAACAGTTTCATCCTGAATTTCAGGATTTGAATTTTAATTTGATT
66 CCAATAGTTTTATGCCACACCAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGATT
* *
2681 TTTTCAGGATGAAAATGATGAAATTAAGAATGAAAATACTGATCTGGCGTAAAACTATT-AGAAA
131 TTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGA-AAA
* *
2745 AGGGGCACAAATGACGT--TG----TG------TC-A-C--T--G
195 AGGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCTTTCCA
2772 TTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTT
1 TTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTT
* * * *
2837 CCAATTGTTTTATGCCACATCAACAATTTCATTTTGAATTTCAGGATTTTAATTTTAATTTTATT
66 CCAATAGTTTTATGCCACACCAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGATT
* * * * *
2902 TTTTCAGGATGAAAATATTGAAATTAAGATTGAAAATACTGATGTGGCATAAAACTAATGGAAAA
131 TTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGAAAAA
*
2967 GGGACACAAATGACGTGGTGTCACGGTTTCATTCAATTCATTTCCA
196 GGGACACAAATGACGTGGTGTCACTGTTTCATTCAA-TC-TTTCCA
3013 TT
1 TT
3015 GAAGAGGAGA
Statistics
Matches: 802, Mismatches: 97, Indels: 57
0.84 0.10 0.06
Matches are distributed among these distances:
221 204 0.25
222 181 0.23
223 2 0.00
224 1 0.00
227 2 0.00
229 1 0.00
230 2 0.00
233 2 0.00
234 1 0.00
236 4 0.00
239 5 0.01
240 111 0.14
241 69 0.09
242 216 0.27
243 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (239 bp):
TTTCATTCAATCATTTTCCATTGAAGAAGAGAAAGGATTGTATGAAACAGGGATATTATCCCTTT
CCAATAGTTTTATGCCACACCAACAATTTCATCTTGAATTTCAGGATTTTAATTTTAATTTGATT
TTTTCAGGATGAAAATGTTGAAATTAAGAATGAAAATACTGATGTGGCGTAAAACTATTGAAAAA
GGGACACAAATGACGTGGTGTCACTGTTTCATTCAATCTTTCCA
Done.