Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009339.1 Kokia drynarioides strain JFW-HI SEQ_124046, 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: 3861
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Found at i:717 original size:216 final size:215
Alignment explanation
Indices: 1--3861 Score: 3961
Period size: 216 Copynumber: 18.0 Consensus size: 215
* * *
1 GTCTATTGGTCCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTACAACTTCGG
1 GTCTATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGG
* * * * *
66 TTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGTAATTTCCCGAACATTCCATGCTCGAGGA
66 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCTGAACATTCCATGCTCGAGAA
** * * * *
131 ATCGCATCATTTGGTGTAAATAGTTTCTAATTTTGTAAACAAATTTTTGTCTTTGAGTTAAAAAC
131 ATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAAC-ACTTTTTGTCTTTGAATTAAAAAC
**
196 TTATTTACGTGAGAATTGTTT
195 TTATTTTGGTGAGAATTGTTT
* * **
217 GTCTCA-TGGTTCTTGGTTGAACTTCCGAACTTGTCAAAGTTTTACGAGTTCTTGAATAACTTAG
1 GTCT-ATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAG
* ** *
281 GTTCCTTAAAGCATTCAAGACGATCCACACCTTCGAGCAATTTT-TCGAACATTCCATGCTCGAG
65 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCT-GAACATTCCATGCTCGAG
* * * *
345 AAATCGCATCATTTGGTCCAATTAGTTTGTCA-TTTGTAAATAGCTTTTTGTATTTAAATTAAAA
129 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACA-CTTTTTGTCTTTGAATTAAAA
* * *
409 ACTTATTGTGATGAGAATAGTTT
193 ACTTATTTTGGTGAGAATTGTTT
* * *
432 GTCT-TTCGGTTCTTGGACGAACATCCGAACTGGT-AAACCTTTTACGAGTTCTTTTATAACTTA
1 GTCTATT-GGTTCTTGGTCGAACTTCCGAACTTGTCAAA-CTTTTACGAGTTCTTTTATAACTTA
* * * * *
495 GGTTCCTTAAAGTATTCAAAACGATGCATTCCTTTGAGAAATTTTCTGAACATTCCATTCTCGGG
64 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCTGAACATTCCATGCTCGAG
* * * * *
560 AAATCGTATCATTTGGTCAAAATAATTTGTCATTTTGTAAAACACTTTTTATGTTTGAATTAAAA
129 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGT-AAACACTTTTTGTCTTTGAATTAAAA
* *
625 ACTTATTTTGGTAATAATTGTTT
193 ACTTATTTTGGTGAGAATTGTTT
* * * * *
648 GTCTATTAGTCCTTGGTCAAACTTCTGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGG
1 GTCTATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGG
* *
713 TTCCTTAAAGTATTCAAGACGATCCACTCCTTCGAGCAATTTT-TCGAACATTCCATGCTCGAGA
66 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCT-GAACATTCCATGCTCGAGA
* * **
777 AATCGCATCATTTGGTACAAATAGTTTGTCATTTTGTAAATAGCTTTTTGTAATTGAATTAAAAA
130 AATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACA-CTTTTTGTCTTTGAATTAAAAA
* * *
842 CTTATTGTGATGAGAATAGTTT
194 CTTATTTTGGTGAGAATTGTTT
** * * * *
864 GTCT-TTCGGTTCTTGGAAGAACATCCGAACTGGTAAAACTTTTACGAGTTCTTTTATAAATTAG
1 GTCTATT-GGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAG
* * * * * ** * *
928 GTTTCTTAAAGTATTCAAAACAATACATTCCTTCGGGAAATTTT-TGGAATGTTCCATTCTCGGG
65 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCT-GAACATTCCATGCTCGAG
* *
992 AAATCGCATCATTTGGTCCGAATAGTTTCTCATTTTGTAAAACACTTTTTGTCTTTGAATTAAAA
129 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGT-AAACACTTTTTGTCTTTGAATTAAAA
1057 ACTTATTTTGGTGAGAATTGTTT
193 ACTTATTTTGGTGAGAATTGTTT
* * * *
1080 GTCTATTGGTCCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACAAGTTCTTTTACAACTTCGG
1 GTCTATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGG
* * * * *
1145 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGTAATTTCCCGAACATTCCATGCTCAAGGA
66 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCTGAACATTCCATGCTCGAGAA
* ** * * ** ** * *
1210 ATCACATCATTTGGTGTAAATAGTTTCTAATTTTGTAAACAAAATTTAATTTTTGAGTTAAAAAC
131 ATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAAC-ACTTTTTGTCTTTGAATTAAAAAC
**
1275 TTATTTACGTGAGAATTGTTT
195 TTATTTTGGTGAGAATTGTTT
* * **
1296 GTCTCA-TGGTTCTTGGTTGAACTTCCGAACTTGTCAAAGTTTTACGAGTTCTTGAATAACTTAG
1 GTCT-ATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAG
** * *
1360 GTTCCTTAAA-TCATTCAAGACGATCCACACCTTTGAGCAATTTT-TCGAACATTCCATGCTCGA
65 GTTCCTTAAAGT-ATTCAAGACGATCCATTCCTTCGAGAAATTTTCT-GAACATTCCATGCTCGA
* * *
1423 GAAATCGCATCATTTGGTCCAATTAGTTTGTCATTTTGTAAACAGC-TTTTGTATTTAAATTAAA
128 GAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACA-CTTTTTGTCTTTGAATTAAA
* * *
1487 AACTTATTGTGATGAGAATAGTTT
192 AACTTATTTTGGTGAGAATTGTTT
* * * * *
1511 GTCT-TTCGGTTCTTGGACGAACATCCGAACTGGTAAAACTTTTACGAGTTCTTTTATAACTTAA
1 GTCTATT-GGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAG
* * * * * * * * *
1575 GTTCCTTAAAGTATTCAAAACAATGCATTCCTTTGGGAAATTTTTTGAACGTTCCATTCTCGGGA
65 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCTGAACATTCCATGCTCGAGA
1640 AATCGCATCATTTGGTCCAAATA----G-----TT-T--ACACTTTTTGTCTTTGAATTAAAAAC
130 AATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACACTTTTTGTCTTTGAATTAAAAAC
*
1693 TAATATTTTGGTGAGAATTTTTT
195 T--TATTTTGGTGAGAATTGTTT
* * * *
1716 GTCTATTGATCCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTACAACTTCGG
1 GTCTATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGG
* * * ** *
1781 TTCCTTAAAGTATTCAAGACGATCCATTCCTTTGAGGAATTTCCCAAACATTTCATGCTCGAGAA
66 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCTGAACATTCCATGCTCGAGAA
* * *
1846 ATCGCATCAATTGGTCTAAATAGTTTGTCATTTTGTAAACAAGTTTTTGTCTTT-AAGTTAAAAA
131 ATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAAC-ACTTTTTGTCTTTGAA-TTAAAAA
**
1910 CTTATTTACGTGAGAATTGTTT
194 CTTATTTTGGTGAGAATTGTTT
* * ** * **
1932 GTCTCA-TGGTTCTTGCTCGAACGTCAAAACTTGTCAAAATTTTACGAGTTCTTGAATAACTTAG
1 GTCT-ATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAG
* * * * * * * *
1996 GTTCCTTTAGGTACTCAAGACGAACCATTCCTTCGAGCAATTTT-TCGAAAATAT-AAAGCTCGA
65 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCT-GAACAT-TCCATGCTCGA
* * * *
2059 GAAATCACATCATTTGGACCAATTAGTTTGTCATTTTGTAAAGAACTTTTTGTCTTTGAATT-AA
128 GAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAA-CACTTTTTGTCTTTGAATTAAA
* *
2123 AACTAATTTAGGTGAGAATTGTTT
192 AACTTATTTTGGTGAGAATTGTTT
* ** * * *
2147 GTCTCTTGGTTCTTGCACGAACATCCGAACTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGG
1 GTCTATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGG
* * * *
2212 TTCCTTAAAGTATTCAAAACGATGCATTCCTTCGAGAAATTTTCTTAACATTCCATTCTCGAGAA
66 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCTGAACATTCCATGCTCGAGAA
* * * *
2277 ATCGTATCATTTGGTCAAAATAGTTTATCATTTTGT-AACACTTTTTATCTTTGAATTAAAAACT
131 ATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACACTTTTTGTCTTTGAATTAAAAACT
2341 TATTTTGGTGAGAATTGTTT
196 TATTTTGGTGAGAATTGTTT
* * * * * * ** * * *
2361 GTCAATTGGTCCTTGGCCAAACCTCTGAACTCCTCAAACTTTTACGACTTCTTTTATAACTTTGA
1 GTCTATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGG
* ** * *
2426 TTCCTCAAAGTATTCAAGACGATCCATTCCTTCGAGGTA-TTTCTCGAACATTCCACGCTTGAGA
66 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCT-GAACATTCCATGCTCGAGA
* * * *
2490 AATCGCATGAATTGGTCCAAATAGTTTGTCA-TTT-TATA-A-------TCTTTGAGTTAAAAAC
130 AATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACACTTTTTGTCTTTGAATTAAAAAC
** * *
2545 TTATTTACGTGAGGATTATTT
195 TTATTTTGGTGAGAATTGTTT
* * * * * * **
2566 GCCTCA-TGGATCTTGGCCGAACTTCCAAACTTGTCAAAGTTTTATGAGTTCTTGAATAACTTAG
1 GTCT-ATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAG
* **
2630 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGTAATTTTCT-AAGCATTCCACACTCGAG
65 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCTGAA-CATTCCATGCTCGAG
*
2694 AAATCGCATCATTTGGCCAATTGGTCCAAATAACTTAGGTTTGTCATTTTGTAAACAAGTTTTTG
129 AAATCGCATCA--T------TTGGTCC--A-AA--TA-GTTTGTCATTTTGTAAAC-ACTTTTTG
* **
2759 TCTTTGAGTTAAAAACTTATTTACGTGAGAATTGTTT
179 TCTTTGAATTAAAAACTTATTTTGGTGAGAATTGTTT
** * * *
2796 GTCTCA-TGGTTCTTGGTCGAACTTCAAAACTTGTCAAAATTTTACAAGTTCTTTAATAACTTAG
1 GTCT-ATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAG
* * * * * * ** * *
2860 GTTTCTTAAGGTATTCAAGACGATCCATTCCCTCGAGCAATTTTTTGAAAATTTAAAGTTCGAGA
65 GTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCTGAACATTCCATGCTCGAGA
* * * * *
2925 AATCGCATCATTTGGACCGATTAGTTTGTCATTTTGTAAAGAACTTTTTGTCTTCGAATT-AAAA
130 AATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAA-CACTTTTTGTCTTTGAATTAAAAA
* *
2989 CATATTTAGGTGAGAATTGTTT
194 CTTATTTTGGTGAGAATTGTTT
* * * ** * *
3011 GTCTCTTGGTTCTTGGACGAACATCCGAACCGGTAAAACTTTTATGAGTTCTTTTATAACTTAGG
1 GTCTATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGG
* ** * * * * * *
3076 TTCCTTAAATTATTCAA-ACTGATGTATTTCTTCGAGAAATTTTTTGAACATTTCATTCTTGGGA
66 TTCCTTAAAGTATTCAAGAC-GATCCATTCCTTCGAGAAATTTTCTGAACATTCCATGCTCGAGA
* ** * * *
3140 AATCGTATCATTTGGTAAAAATAGTTTGTCATTTTCTAAAACACATTTTATCTTTGAATTAAAAA
130 AATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGT-AAACACTTTTTGTCTTTGAATTAAAAA
*
3205 CTTATTTTGGGGAGAATTGTTT
194 CTTATTTTGGTGAGAATTGTTT
* * * *
3227 GTCTATTGGTCCTTGGTC--A------AACTTCTCAAACTTTTACGACTTCTTTTATAACTTCGG
1 GTCTATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGG
* * * * * * *
3284 TTCCTTAAAGTATTCAAGATGATCCCTTACTTTGAGGAATTTCCCGAACATTCCATGCTCGAGAA
66 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCTGAACATTCCATGCTCGAGAA
* * * *
3349 ATCACATCATTTGGTCTAAGTAGTTTCTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAAC
131 ATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAAC-ACTTTTTGTCTTTGAATTAAAAAC
*
3414 TTATTTAT-GTGGGAATTGTTT
195 TTATTT-TGGTGAGAATTGTTT
* * * * * ** * *
3435 GCCTCA-TGGTCCTTGG-CTGAACTTCCGAACTTGTCAAAGTTTTATGAGTTATTGAATGACATA
1 GTCT-ATTGGTTCTTGGTC-GAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTA
* * * *
3498 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTCCGGGCAATTTTTTGAACATTCCATGCTCGAG
64 GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCTGAACATTCCATGCTCGAG
* ** * * * * *
3563 AAATTGCATTGTTTAGTCCAATTAGTTTGTCTTTTTGTAAACAACTTTTTGTATTTGAATTAGAA
129 AAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAAC-ACTTTTTGTCTTTGAATTAAAA
*
3628 ACTTATTTTGGTGAGAATTATTT
193 ACTTATTTTGGTGAGAATTGTTT
* * ** * * *
3651 GTCTCTAGGTTCTTGGAGGAACATCCGAACTGGTAAAACTTTTACGAGTTCTTTTATAACTTAGG
1 GTCTATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGG
* * * * * *
3716 TACCTTAAAGTATTCAAAATGATGCATTCCTTCGAGAAATTTT-TCGAACATTCCATTCTCGGGA
66 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCT-GAACATTCCATGCTCGAGA
* * *
3780 AATCGTATCATTTGGTCAAAATAGTTTGTCATTTTGTAAAACACTTTTTATCTTTGAATTAAAAA
130 AATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGT-AAACACTTTTTGTCTTTGAATTAAAAA
*
3845 CTTATTTTGGTAAGAAT
194 CTTATTTTGGTGAGAAT
Statistics
Matches: 2995, Mismatches: 543, Indels: 214
0.80 0.14 0.06
Matches are distributed among these distances:
202 1 0.00
203 23 0.01
204 2 0.00
205 279 0.09
206 10 0.00
207 5 0.00
208 160 0.05
209 4 0.00
210 1 0.00
211 1 0.00
212 2 0.00
213 33 0.01
214 164 0.05
215 672 0.22
216 1407 0.47
217 31 0.01
218 23 0.01
219 9 0.00
220 3 0.00
221 3 0.00
222 6 0.00
223 1 0.00
228 1 0.00
230 152 0.05
231 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (215 bp):
GTCTATTGGTTCTTGGTCGAACTTCCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTAGG
TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGAAATTTTCTGAACATTCCATGCTCGAGAA
ATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACACTTTTTGTCTTTGAATTAAAAACT
TATTTTGGTGAGAATTGTTT
Done.