Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003916.1 Kokia drynarioides strain JFW-HI SEQ_116986, 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, 815
Length: 1359
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Found at i:465 original size:214 final size:213
Alignment explanation
Indices: 17--1359 Score: 978
Period size: 214 Copynumber: 6.3 Consensus size: 213
7 TTTTGTAAAG
*
17 AACTTTTGGTCTTTGGATTAAAAACTTATTTATGTGAGAATTGTTTCT-T-TTGGTTCTTGGCCG
1 AACTTTTGGACTTTGGATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCG
* * *
80 AACTTCCGAGCTTGTCAAACTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAATATTCAAGA
66 AACTTCCAAACTTGTCAAACTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGA
* ** * * * *
145 CGATCGATTCCTTCGAGCAATTTTCCAAACATTCCAACCTTGGAAAAAAAGCACCATTTGGTCCA
131 CGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATCCTTGG-GAAATAGCATCATTTGGTCC-
* * * * *
210 AAATAGTTTGCCCTTTTGTA
194 AAATAATCTGTCATTTCGTA
**** * * **
230 AA---AAAAAATTCAGTCTTAAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGC
1 AACTTTTGGACTT-TGGATT-AAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGC
* * * * *
292 TGAACTTCTAAACTTTTCTATCTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAA
64 CGAACTTCCAAACTTGTCAAACTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAA
* * * * * *
357 GACGATCCATTTCTTGGAGCAATTTTTTGAACATTCGATTCTTGGGAAATTGCATCATTTGGTCC
129 GACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATCCTTGGGAAATAGCATCATTTGGTCC
*
422 AAATAATCTGTTATTTCGTA
194 AAATAATCTGTCATTTCGTA
* * *
442 AACTTTTGGACTTTGGATTAAAAACTTATTTATGTGAGAATTATTTCTCTCTTGGTTCTTAGTCG
1 AACTTTTGGACTTTGGATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCG
* * *
507 AACTTCCAAACTTGTCAAACTTTTAT-TAGTT-ATTT-TAACTTTGGTTCCTTAAAGTGTTCAAG
66 AACTTCCAAACTTGTCAAACTTTT-TCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAG
* * *** *
569 ACGATCCATTCCTTCTAGCAATTTTCTGAACATTCCATGCTCAAGAAATCA-CATCATTAGGTCC
130 ACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATCCTTGGGAAAT-AGCATCATTTGGTCC
* *
633 GAAT-AGCTTGTCATTTCGTAAA
194 AAATAATC-TGTCATTTCGT--A
* * * * * * * *
655 CAACTTTTGGTCTTTGAATTAAAGACTTATTTACGTGAAAATTGTCTCTCTCCTGGTTCATGGCC
1 -AACTTTTGGACTTTGGATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCC
* ** * * *
720 GAACATCTGAACATGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAG
65 GAACTTCCAAACTTGTCAAACTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAG
* ** * * * * * ***
785 ACAATCCATTCCTTCGAGCAATTTTCTGAGTATTCCATGCTCGAGAAATCGTATCATTTCCACCA
130 ACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATCCTTGGGAAATAGCATCATTTGGTCCA
* * * * *
850 AGTAATTTTTTATTTTGTAAA
195 AATAATCTGTCATTTCGT--A
* *** * ** * * **
871 CAACTATTACTCTTTGAATT--AAACTTATTTATGTGAGAACAGTTTTTCTCTTGGTTGTTGGTT
1 -AACTTTTGGACTTTGGATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCC
* * * * *** *
934 GAACTTCCAAGCCTT-CCAAACTTTTTCGAGTTCTATTATAGCTTCATTTCCTTACAGTATTCAA
65 GAACTTCCAA-ACTTGTCAAACTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAA
* * *
998 AACGATCCATTCCTTCGAAC-A-TTTCATG--C--T-CA------GGAAATCGCATCATTTGGTC
129 GACGATCCATTCCTTCGAGCAATTTTC-TGAACATTCCATCCTTGGGAAATAGCATCATTTGGTC
* * *
1050 CAAATAGTTTGTCATTTTGTAAA
193 CAAATAATCTGTCATTTCGT--A
* * * * * * * **
1073 CAACTTTTGG-TTTTAGAATTAAAAACTTATTTACGTAATAATGGTTTCTCCCTTGGTTCTTTAC
1 -AACTTTTGGACTTT-GGATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGC
** * * * * * * * **
1137 TAAACTTTCGAACTTGCCAAACTTTTACGAGTTATTTTAAAACCTCAGTTCCTTAAAGTATTCAA
64 CGAACTTCCAAACTTGTCAAACTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAA
* * * ** * * * **
1202 GACAATTCATTCTTTCGAGCAATTTTCCAAACATTCCATGCTCGGGAAAGT-GCATAATTTTTTC
129 GACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATCCTTGGGAAA-TAGCATCATTTGGTC
* * * * *
1266 CAAATATTTTATCCTTTTGTTAA
193 CAAATAATCTGTCATTTCG-T-A
** * * *
1289 TAACTTTTGGTGTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTAGTTCTTGGTC
1 -AACTTTTGGACTTTGGATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCC
1354 GAACTT
65 GAACTT
Statistics
Matches: 889, Mismatches: 201, Indels: 77
0.76 0.17 0.07
Matches are distributed among these distances:
201 3 0.00
202 46 0.05
203 3 0.00
204 95 0.11
205 1 0.00
206 4 0.00
207 1 0.00
208 2 0.00
209 2 0.00
210 6 0.01
211 94 0.11
212 52 0.06
213 89 0.10
214 282 0.32
215 8 0.01
216 195 0.22
217 6 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (213 bp):
AACTTTTGGACTTTGGATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCG
AACTTCCAAACTTGTCAAACTTTTTCGAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGA
CGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATCCTTGGGAAATAGCATCATTTGGTCCAA
ATAATCTGTCATTTCGTA
Found at i:1307 original size:418 final size:419
Alignment explanation
Indices: 596--1359 Score: 957
Period size: 418 Copynumber: 1.8 Consensus size: 419
586 GCAATTTTCT
*
596 GAACATTCCATGCTCAAGAAATCACATCATTAGGTCCGAATAGCTTGTCATTTCGTAAACAACTT
1 GAACATTCCATGCTCAAGAAATCACATCATTAGGTCCAAATAGCTTGTCATTTCGTAAACAACTT
* * * *
661 TTGGTCTTTGAATTAAAGACTTATTTACGTGAAAATTGTCTCTCTCCTGGTTCATGGCCGAACAT
66 TTGGTCTTTGAATTAAAAACTTATTTACGTGAAAATGGTCTCTCTCCTGGTTCATGACCAAACAT
* * * * **
726 CTGAACATGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACAATC
131 CTGAACATGCCAAACTTTTACAAGTTATTTTAAAACCTCAGTTCCTTAAAGTATTCAAGACAATC
** ** * * *
791 CATTCCTTCGAGCAATTTTCTGAGTATTCCATGCTCGAGAAATCGTATCATTTCCACCAAGTAAT
196 CATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATAATTTCCACCAAATAAT
* *
856 TTTTTATTTTGTAAACAACTATTACTCTTTGAATT-AAACTTATTTATGTGAGAACAGTTTTTCT
261 TTTTCATTTTGTAAACAACTATTACTCTTTGAATTAAAACTTATTTATGTGAGAACAGTTTCTCT
* * *
920 CTTGGTTGTTGGTTGAACTTCCAAGCCTTCCAAACTTTTTCGAGTTCTATTATAGCTTCATTTCC
326 CTTAGTTCTTGGTCGAACTTCCAAGCCTTCCAAACTTTTTCGAGTTCTATTATAGCTTCATTTCC
985 TTACAGTATTCAAAACGATCCATTCCTTC
391 TTACAGTATTCAAAACGATCCATTCCTTC
* * * * * *
1014 GAACATTTCATGCTCAGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTT
1 GAACATTCCATGCTCAAGAAATCACATCATTAGGTCCAAATAGCTTGTCATTTCGTAAACAACTT
* * * *
1079 TTGGT-TTTAGAATTAAAAACTTATTTACGT-AATAATGGTTTCTC-CCTTGGTTCTTTACTAAA
66 TTGGTCTTT-GAATTAAAAACTTATTTACGTGAA-AATGGTCTCTCTCC-TGGTTCATGACCAAA
* * *
1141 C-TTTCGAACTTGCCAAACTTTTACGAGTTATTTTAAAACCTCAGTTCCTTAAAGTATTCAAGAC
128 CATCT-GAACATGCCAAACTTTTACAAGTTATTTTAAAACCTCAGTTCCTTAAAGTATTCAAGAC
* * * ***
1205 AATTCATTCTTTCGAGCAATTTTCCAAACATTCCATGCTCGGGAAAGT-GCATAATTTTTTCCAA
192 AATCCATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCGAGAAA-TCGCATAATTTCCACCAA
* * * * ** * **
1269 AT-ATTTTATCCTTTTGTTAATAACTTTTGGTGTTTGAATTAAAAACTTATTTATGTGAGAATTG
256 ATAATTTT-TCATTTTGTAAACAACTATTACTCTTTGAATT-AAAACTTATTTATGTGAGAACAG
1333 TTTCTCTCTTAGTTCTTGGTCGAACTT
319 TTTCTCTCTTAGTTCTTGGTCGAACTT
Statistics
Matches: 287, Mismatches: 51, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
417 14 0.05
418 229 0.80
419 1 0.00
420 43 0.15
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (419 bp):
GAACATTCCATGCTCAAGAAATCACATCATTAGGTCCAAATAGCTTGTCATTTCGTAAACAACTT
TTGGTCTTTGAATTAAAAACTTATTTACGTGAAAATGGTCTCTCTCCTGGTTCATGACCAAACAT
CTGAACATGCCAAACTTTTACAAGTTATTTTAAAACCTCAGTTCCTTAAAGTATTCAAGACAATC
CATTCCTTCGAGCAATTTTCCAAACATTCCATGCTCGAGAAATCGCATAATTTCCACCAAATAAT
TTTTCATTTTGTAAACAACTATTACTCTTTGAATTAAAACTTATTTATGTGAGAACAGTTTCTCT
CTTAGTTCTTGGTCGAACTTCCAAGCCTTCCAAACTTTTTCGAGTTCTATTATAGCTTCATTTCC
TTACAGTATTCAAAACGATCCATTCCTTC
Done.