Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012246.1 Kokia drynarioides strain JFW-HI SEQ_127247, 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: 1806
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Found at i:489 original size:216 final size:216
Alignment explanation
Indices: 1--1804 Score: 2041
Period size: 216 Copynumber: 8.4 Consensus size: 216
* * *
1 TGTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAAC
1 TGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAAC
* * *
66 TTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAA-TTTTCTGAAGATTCCATTAT
66 TTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTC-GAACATTCCATGAT
* * ** * * * *
130 CGAGAAATTGCATCATTTGGTAAAAATAGTTTGCCA-TTTGTAAATAAATTTTGGTCTTTGACTT
130 CGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATT
* *
194 AAAAACTTTTTTACATTG-CAAT
195 AAAAACTTTTTTAC-GTGAGAAT
* * * * * *
216 TCTTTCTCTCTTGGTTCTTGGACGAAGTTTCGAACTTGTCAAACATTTACTAGTTCTTTAACAAC
1 TGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAAC
* * * * * *
281 TTCGATCCCTGATAGTAGTCAAGATGATCCATTCCTTCGACCAATTTTTCGATCATTCCATGATC
66 TTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATC
* * *
346 AGGAAATCGTATCATTTGGTATAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTA
131 GGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTA
*
411 AAAACTTTTTTACGAGAGAAT
196 AAAACTTTTTTACGTGAGAAT
* * ** * *
432 TATTTCTCTCTTGGTTCTTGGATGAACTTTTGAACTGGTTAAACATTTACGAGTTCTTTTATAAC
1 TGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAAC
* * *
497 TTC-AGTTCTTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCT
66 TTCGA-TTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGAT
* *
561 CGGGAAATCGCATCATTTGGTCTAAA-ACGTTTGTCATTTTTTAAA-AAGCCTTTGGTCTTTGAA
130 CGGGAAATCGCATCATTTGGTCTAAATA-GTTTGTCATTTTGTAAACAA-CTTTTGGTCTTTGAA
***
624 TTAAATTGTTTTTTACGTGAGAAT
193 TTAAAAACTTTTTTACGTGAGAAT
* * * * **
648 TGTTTCTCTCTTGTTTCTTGGATGAAGTTCCGAACTTGTCAAACATTTACTAAATCTTTTATAAC
1 TGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAAC
* * * * * *
713 TTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCGACCAATTTTTCAAACATTCCATGATC
66 TTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATC
* * * *
778 GGGAAATCACAACATTTGGTCTAAATAGTTTGTCATTTTGCAATCAACTTTTGGTCTTTGAATTA
131 GGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTA
* **
843 AAAACTTTATTACGAAAGAAT
196 AAAACTTTTTTACGTGAGAAT
* * * *
864 TGTTTCTCTCTTGGCTCTTGGACAAACTTCCGAA-TTGGTTAAACATTTACGAGTTCTTTCATAA
1 TGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTT-GTCAAACATTTACGAGTTCTTTTATAA
* * * * *
928 CCTCGGTTCCTGAGAGGT-TTC-A-A-GAT-CATTCCTTTGACCAATTTTTTGAAGATTTCATGA
65 CTTCGATTCCTGAGA-GTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGA
* * * * * *
988 CCGGGAAATCGCATCATCTGGTCAAAATAG--TGTCATTTTGTAAATAAATTTTGGTCTTTGACT
129 TCGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAAT
* *
1051 TAAAAGCTTTTTTACGTTAGAAT
194 TAAAAACTTTTTTACGTGAGAAT
* *
1074 TCTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAATATTTACGAGTTCTTTTATAAC
1 TGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAAC
* * * * ** * * **
1139 TT-TAGTTCCTGAGAGTATTTAATACGATCCATTCCTTCGACTTATTTTTCGAGCATTTCATTCT
66 TTCGA-TTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGAT
* * * * * * * *
1203 CGAGAAATCGTATCACTTGGTCTAAAAAGTTTGGCATGTTGTAAAAAACTTTTGGTCTTTGATTT
130 CGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATT
1268 AAAAACTTTTTTACGTGAGAAT
195 AAAAACTTTTTTACGTGAGAAT
* * * * * *
1290 TGATTCCCTCTTGGTTCTCGGACAAACTTCCGAACTTATCAAACATTTATGAGTTCTTTTATAAC
1 TGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAAC
* * * * * * *
1355 TTTGGTTTCTAAGAGTATTCAATACGATCCATTCCTTTGACCAATTTTTTC-AACATTCCACGCT
66 TTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAA-TTTTTCGAACATTCCATGAT
* * * * * * * * *
1419 TGGGAAATCACATCATTGGGTCTAAAAAGTCTGTCATTTTATAAACAACATTTAGTCTTTTAATT
130 CGGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATT
* * *
1484 AAAAACTTTATTATGTGAAAAT
195 AAAAACTTTTTTACGTGAGAAT
** * *
1506 TGTTTCTCTCTCAGTTCTTGGACGAAGTGT-CGAACTTGTCAAACATTT-CGTAGATCTTTTATA
1 TGTTTCTCTCTTGGTTCTTGGACGAACT-TCCGAACTTGTCAAACATTTACG-AGTTCTTTTATA
* * * * * * *
1569 ACTTCGATCCCAGATAGTAGTCAAGATGATCCATTCCTTTG-CCAATTTTTTGAACATTCCATGC
64 ACTTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGA
*
1633 TCAGGAAATCGCATCATTTGGTCTAAA-ACGTTTGTCATTTTGTAAA-AACCTTTTGGTCTTTGA
129 TCGGGAAATCGCATCATTTGGTCTAAATA-GTTTGTCATTTTGTAAACAA-CTTTTGGTCTTTGA
* *
1696 ATTAAAATCTTTCTTACGTGAGAAT
192 ATTAAAAACTTTTTTACGTGAGAAT
*
1721 TGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAATATTTACGAGTTCTTTTATAAC
1 TGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAAC
*
1786 TT-TAGTTCCTGAGAGTATT
66 TTCGA-TTCCTGAGAGTATT
1805 TA
Statistics
Matches: 1327, Mismatches: 232, Indels: 60
0.82 0.14 0.04
Matches are distributed among these distances:
209 2 0.00
210 115 0.09
211 3 0.00
212 54 0.04
213 6 0.00
214 60 0.05
215 300 0.23
216 775 0.58
217 12 0.01
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (216 bp):
TGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACATTTACGAGTTCTTTTATAAC
TTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATC
GGGAAATCGCATCATTTGGTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTA
AAAACTTTTTTACGTGAGAAT
Found at i:1259 original size:642 final size:643
Alignment explanation
Indices: 1--1806 Score: 2260
Period size: 642 Copynumber: 2.8 Consensus size: 643
1 TGTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAAC
1 TGTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAAC
* * *
66 TTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTCTGAAGATTCCATTATC
66 TTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTT-TCAACATTCCATGATC
* ** ** * * *
131 GAGAAATTGCATCATTTGGTAAAAATAGTTTGCCA-TTTGTAAAT-AAATTTTGGTCTTTGACTT
130 GGGAAATCACATCATTTGGTCTAAATAGTTTGTCATTTTG-AAATCAACTTTTGGTCTTTGAATT
* ** *
194 AAAAACTTTTTTAC-ATTGCAATTCTTTCTCTCTTGGTTCTTGGACGAAGTTTCGAACTTGTCAA
194 AAAAACTTTATTACGAAAG-AATTGTTTCTCTCTTGGTTCTTGGACGAAG-TTCGAACTTGTCAA
* * *
258 ACATTTACTAGTTCTTTAACAACTTCGATCCCTGATAGTAGTCAAGATGATCCATTCCTTCGACC
257 ACATTTACGAGTTCTTTAATAACTTCGATCCCTGATAGTAGTCAAGATGATCCATTCCTTTGACC
* * * *
323 AATTTTTCGATCATTCCATGATCAGGAAATCGTATCATTTGGT-ATAAATAGTTTGTCATTTTGT
322 AATTTTTTGAACATTCCATGACCAGGAAATCGCATCATTTGGTCA-AAATAG--TGTCATTTTGT
*
387 AAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGAGAGAATTATTTCTCTCTTGGTTCTTG
384 AAA-AACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCTTG
* ** * * * * * *
452 GATGAACTTTTGAACTGGTTAAACATTTACGAGTTCTTTTATAACTTCAGTTCTTGAGAGTATTC
448 GACGAACTTCCGAACTTGTCAAATATTTACGAGTTCTTTTATAACTTTAGTTCCTGAGAGTATTT
* * * *
517 AAGACGATCCATTCCTTTGACCAATTTTTTGAACATTCCATGCTCGGGAAATCGCATCATTTGGT
513 AAGACGATCCATTCCTTCGACCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCACTTGGT
* * * * * ***
582 CTAAAACGTTTGTCATTTTTTAAAAAGCCTTTGGTCTTTGAATTAAATTGTTTTTTACGTGAGAA
578 CTAAAAAGTTTGGCATGTTGTAAAAAACCTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAA
647 T
643 T
* **
648 TGTTTCTCTCTTGTTTCTTGGATGAAGTTCCGAACTTGTCAAACATTTACTAAATCTTTTATAAC
1 TGTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAAC
* * * *
713 TTCGGTTCCTGATAGTAGTCAAGACGATCCATTTCTTCGACCAATTTTTCAAACATTCCATGATC
66 TTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTC-AACATTCCATGATC
* *
778 GGGAAATCACAACATTTGGTCTAAATAGTTTGTCATTTTGCAATCAACTTTTGGTCTTTGAATTA
130 GGGAAATCACATCATTTGGTCTAAATAGTTTGTCATTTTGAAATCAACTTTTGGTCTTTGAATTA
* * * *
843 AAAACTTTATTACGAAAGAATTGTTTCTCTCTTGGCTCTTGGACAAACTTCCGAA-TTGGTTAAA
195 AAAACTTTATTACGAAAGAATTGTTTCTCTCTTGGTTCTTGGACGAAGTT-CGAACTT-GTCAAA
* * * * * *
907 CATTTACGAGTTCTTTCATAACCTCGGTTCCTGAGAGGT-TTC-A-A-GAT-CATTCCTTTGACC
258 CATTTACGAGTTCTTTAATAACTTCGATCCCTGATA-GTAGTCAAGATGATCCATTCCTTTGACC
* * * *
967 AATTTTTTGAAGATTTCATGACCGGGAAATCGCATCATCTGGTCAAAATAGTGTCATTTTGTAAA
322 AATTTTTTGAACATTCCATGACCAGGAAATCGCATCATTTGGTCAAAATAGTGTCATTTTGTAAA
* * * * *
1032 TAAATTTTGGTCTTTGACTTAAAAGCTTTTTTACGTTAGAATTCTTTCTCTCTTGGTTCTTGGAC
387 -AACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGAC
*
1097 GAACTTCCGAACTTGTCAAATATTTACGAGTTCTTTTATAACTTTAGTTCCTGAGAGTATTTAAT
451 GAACTTCCGAACTTGTCAAATATTTACGAGTTCTTTTATAACTTTAGTTCCTGAGAGTATTTAAG
** * * * *
1162 ACGATCCATTCCTTCGACTTATTTTTCGAGCATTTCATTCTCGAGAAATCGTATCACTTGGTCTA
516 ACGATCCATTCCTTCGACCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCACTTGGTCTA
* *
1227 AAAAGTTTGGCATGTTGTAAAAAACTTTTGGTCTTTGATTTAAAAACTTTTTTACGTGAGAAT
581 AAAAGTTTGGCATGTTGTAAAAAACCTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAAT
* * * ** * *
1290 TGATTCCCTCTTGGTTCTCGGACAAACTTCCGAACTTATCAAACATTTA-TGAGTTCTTTTATAA
1 TGTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACTTGTCAAACATTTACT-AGTTCTTTTATAA
* * * * * *
1354 CTTTGGTTTCTAAGAGTATTCAATACGATCCATTCCTTTGACCAATTTTTTCAACATTCCACGCT
65 CTTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAA-TTTTTCAACATTCCATGAT
* * * * * * * *
1419 TGGGAAATCACATCATTGGGTCTAAAAAGTCTGTCATTTT-ATAAACAACATTTAGTCTTTTAAT
129 CGGGAAATCACATCATTTGGTCTAAATAGTTTGTCATTTTGA-AATCAACTTTTGGTCTTTGAAT
* * **
1483 TAAAAACTTTATTATGTGAA-AATTGTTTCTCTCTCAGTTCTTGGACGAAGTGTCGAACTTGTCA
193 TAAAAACTTTATTACG-AAAGAATTGTTTCTCTCTTGGTTCTTGGACGAAGT-TCGAACTTGTCA
* * *
1547 AACATTT-CGTAGATCTTTTATAACTTCGATCCCAGATAGTAGTCAAGATGATCCATTCCTTTG-
256 AACATTTACG-AGTTCTTTAATAACTTCGATCCCTGATAGTAGTCAAGATGATCCATTCCTTTGA
*
1610 CCAATTTTTTGAACATTCCATG-CTCAGGAAATCGCATCATTTGGTCTAAAACGT-TTGTCATTT
320 CCAATTTTTTGAACATTCCATGAC-CAGGAAATCGCATCATTTGGTC-AAAA--TAGTGTCATTT
* * *
1673 TGTAAAAACCTTTTGGTCTTTGAATTAAAATCTTTCTTACGTGAGAATTGTTTCTCTCTTGGTTC
381 TGTAAAAA-CTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTC
1738 TTGGACGAACTTCCGAACTTGTCAAATATTTACGAGTTCTTTTATAACTTTAGTTCCTGAGAGTA
445 TTGGACGAACTTCCGAACTTGTCAAATATTTACGAGTTCTTTTATAACTTTAGTTCCTGAGAGTA
1803 TTTA
510 TTTA
Statistics
Matches: 995, Mismatches: 139, Indels: 50
0.84 0.12 0.04
Matches are distributed among these distances:
641 5 0.01
642 466 0.47
643 12 0.01
644 55 0.06
645 47 0.05
646 18 0.02
647 287 0.29
648 101 0.10
649 4 0.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (643 bp):
TGTTTCTCTCTTGGTTCTTGGATGAAGTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAAC
TTCGGTTCCTGAGAGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCAACATTCCATGATCG
GGAAATCACATCATTTGGTCTAAATAGTTTGTCATTTTGAAATCAACTTTTGGTCTTTGAATTAA
AAACTTTATTACGAAAGAATTGTTTCTCTCTTGGTTCTTGGACGAAGTTCGAACTTGTCAAACAT
TTACGAGTTCTTTAATAACTTCGATCCCTGATAGTAGTCAAGATGATCCATTCCTTTGACCAATT
TTTTGAACATTCCATGACCAGGAAATCGCATCATTTGGTCAAAATAGTGTCATTTTGTAAAAACT
TTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACT
TCCGAACTTGTCAAATATTTACGAGTTCTTTTATAACTTTAGTTCCTGAGAGTATTTAAGACGAT
CCATTCCTTCGACCAATTTTTCGAACATTCCATGCTCGAGAAATCGCATCACTTGGTCTAAAAAG
TTTGGCATGTTGTAAAAAACCTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAAT
Done.