Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012159.1 Kokia drynarioides strain JFW-HI SEQ_127160, 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: 2853
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.38
Warning! 180 characters in sequence are not A, C, G, or T
Found at i:745 original size:215 final size:214
Alignment explanation
Indices: 252--1617 Score: 1799
Period size: 215 Copynumber: 6.3 Consensus size: 214
242 NNNNNNNNNN
* *
252 TTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTCTTTTTTGGTTCTTGGACGAACTTC
1 TTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTA
* ** * * *
317 CAAACTTGTCAAACTTTTACGTGTTCATTTT-TAACTTTGGTTCCTTAATGTAGTCACGACGATC
66 CGAACTTGTCAAACTTTTACAAGTTC-TTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATC
** * *
381 CATTCCTTCGAGC-CGTTTTCGAACATTCCATGATCGGGAAATCGTATCATTTGGTCCAAAT-GC
130 CATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAG-
*
444 TTTGTCATTTCGTAGACAACTT
194 TTTGTCATTT-GTAAACAACTT
* *
466 TTGGTCTTTGAATTTAAAACTTATTTACGTCAGATTGTTTCTGTTTTGGTTCTTGGACGAACTTA
1 TTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTA
* * * *
531 TGAACTTGTGAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATACAAGATGATCC
66 CGAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCC
* *
596 ATTCCTTCGAGTAATTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCCAAATAGTT
131 ATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTT
*
661 TGTCATTTGTAAGCAACTT
196 TGTCATTTGTAAACAACTT
* * * * *
680 TTGGTTTTTAAATTAAAAACTTATTTAAGTGAGACTTGTTTCTCTTTTGGTTCTTGGATGAACTT
1 TTGGTCTTTAAATTTAAAACTTATTTACGTCAGA-TTGTTTCTCTTTTGGTTCTTGGACGAACTT
* * * * * * * * *
745 ACGAGCTTGTTAAAATGTTACAAGTTCTTTTACAGCTTCGATTCCTTAAAGTATTCAAAACGATC
65 ACGAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATC
* * * *
810 CATTCCTTTGAGCAATTTTTCCGAGCATTCCATGCTCGAGAAATCGCATCTTTTGGTCCAAAATA
130 CATTCCTTCGAGCAATTTTT-CGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCC-AAATA
875 GTTTGTCATTTTGTAAACAACTTT
193 GTTTGTCA-TTTGTAAACAAC-TT
* ** * ** * * *
899 TTGGTCTTTGAATAAAAAACTAATTTGTGTCAGAATTGTCTCTC-TTTGGGT-TTGGATGAACTT
1 TTGGTCTTTAAATTTAAAACTTATTTACGTCAG-ATTGTTTCTCTTTTGGTTCTTGGACGAACTT
* * * * * * *
962 CCAAACTTGTCAAGCTTTTACGAGTTATTTTATAACTTTGGTTCCTTCAAGTATTCATGACGATC
65 ACGAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATC
* * *
1027 CATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCAGGAAATCGCATCATTTGGTCCAAATGGT
130 CATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGT
1092 TTGTCATTTTGTAAACAACTTT
195 TTGTCA-TTTGTAAACAAC-TT
* * *
1114 TTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTCTCTTTTAGTGCTTGGACGAACTTC
1 TTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTA
* * ** * *
1179 CAAACCTGTCAAACTTTTAGGAGTTCTTTTATAACTTTGGTTCCTTCAAGTATTCACGACGATCC
66 CGAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCC
* *
1244 ATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCGGGAAATCGTATCATTTGGTCCAAAT-GCT
131 ATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAG-T
1308 TTGTCATTTCGTAAACAACTT
195 TTGTCATTT-GTAAACAACTT
* *
1329 TTGGTCTTTGAATTTAAAACTTATTTACGTCAGATTGTTTCTGTTTTGGTTCTTGGACGAACTTA
1 TTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTA
* * * *
1394 TGAACTTGTGAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATACAAGATGATCC
66 CGAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCC
* *
1459 ATTCCTTCGAGTAATTTTTCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCCAAATAGTT
131 ATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTT
*
1524 TGTCATTTGTAAGCAACTT
196 TGTCATTTGTAAACAACTT
* * * * *
1543 TTGGTTTTTAAATTAAAAACTTATTTAAGTGAGACTTGTTTCTCTTTTGGTTCTTGGATGAACTT
1 TTGGTCTTTAAATTTAAAACTTATTTACGTCAGA-TTGTTTCTCTTTTGGTTCTTGGACGAACTT
*
1608 ACGAGCTTGT
65 ACGAACTTGT
1618 TAAANNNNNN
Statistics
Matches: 1011, Mismatches: 126, Indels: 29
0.87 0.11 0.02
Matches are distributed among these distances:
213 4 0.00
214 209 0.21
215 435 0.43
216 217 0.21
217 92 0.09
218 17 0.02
219 36 0.04
220 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (214 bp):
TTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTA
CGAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCC
ATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCCAAATAGTT
TGTCATTTGTAAACAACTT
Found at i:1245 original size:648 final size:644
Alignment explanation
Indices: 252--1607 Score: 1898
Period size: 648 Copynumber: 2.1 Consensus size: 644
242 NNNNNNNNNN
** * * * * * *
252 TTGGTCTTTAAATTTAAAACTTATTTACGTCAG-ATTGTTTCTTTTTTGGTTCTTGGACGAACTT
1 TTGGTCTTTAAATAAAAAACTAATTTAAGTCAGAATTGTCTCTCTTTTGGGTCTTGGATGAACTT
*
316 CCAAACTTGTCAAACTTTTACGTGTTCATTTTTAACTTTGGTTCCTTAATGTAGTCACGACGATC
66 CCAAACTTGTCAAACTTTTACGAGTTCATTTTTAACTTTGGTTCCTTAATGTAGTCACGACGATC
* *
381 CATTCCTTCGAGCCGTTTTCGAACATTCCATGATCGGGAAATCGTATCATTTGGTCCAAATGCTT
131 CATTCCTTCGAGCCGTTTTCGAACATTCCATGATCAGGAAATCGCATCATTTGGTCCAAATGCTT
* * *
446 TGTCATTTCGTAGACAACTTTTGGTCTTTGAATTTAAAACTTATTTACGTCAGATTGTTTCTGTT
196 TGTCATTTCGTAAACAACTTTTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTCTCTT
* * ** * *
511 TTGGTTCTTGGACGAACTTATGAACTTGTGAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCT
261 TTAGTGCTTGGACGAACTTACAAACCTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCT
* * *
576 TAAAGTATACAAGATGATCCATTCCTTCGAGTAATTTTTCGAACATTCCATGCTTGGGAAATCGC
326 TAAAGTATACAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGC
* *
641 ATCATTTGGTCCAAATAG-TTTGTCATTT-GTAAGCAACTTTTGGTTTTTAAATTAAAAACTTAT
391 ATCATTTGGTCCAAAT-GCTTTGTCATTTCGTAAACAACTTTTGGTCTTTAAATTAAAAACTTAT
* * * *
704 TTAAGTGAGACTTGTTTCTCTTTTGGTTCTTGGATGAACTTACGAGCTTGTTAAAATGTTACAAG
455 TTAAGTCAGA-TTGTTTCTCTTTTGGTTCTTGGACGAACTTACGAACTTGTGAAAATGTTACAAG
* * *
769 TTCTTTTACAGCTTCGATTCCTTAAAGTATTCAAAACGATCCATTCCTTTGAGCAATTTTTCCGA
519 TTCTTTTACAACTTCGATTCCTTAAAGTATACAAAACGATCCATTCCTTCGAGCAATTTTT-CGA
* *
834 GCATTCCATGCTCGAGAAATCGCATCTTTTGGTCCAAAATAGTTTGTCATTTTGTAAACAACTTT
583 ACATTCCATGCTCGAGAAATCGCATCATTTGGTCC-AAATAGTTTGTCA-TTTGTAAACAAC-TT
* **
899 TTGGTCTTTGAATAAAAAACTAATTTGTGTCAGAATTGTCTCTC-TTTGGGT-TTGGATGAACTT
1 TTGGTCTTTAAATAAAAAACTAATTTAAGTCAGAATTGTCTCTCTTTTGGGTCTTGGATGAACTT
* * *
962 CCAAACTTGTCAAGCTTTTACGAGTT-ATTTTATAACTTTGGTTCCTTCAA-GTATTCATGACGA
66 CCAAACTTGTCAAACTTTTACGAGTTCATTTT-TAACTTTGGTTCCTT-AATGTAGTCACGACGA
* *
1025 TCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCAGGAAATCGCATCATTTGGTCCAAATG
129 TCCATTCCTTCGAGCC-GTTTTCGAACATTCCATGATCAGGAAATCGCATCATTTGGTCCAAATG
* *
1090 GTTTGTCATTTTGTAAACAACTTTTTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTC
193 CTTTGTCATTTCGTAAACAAC-TTTTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTC
* **
1155 TCTTTTAGTGCTTGGACGAACTTCCAAACCTGTCAAACTTTTAGGAGTTCTTTTATAACTTTGGT
257 TCTTTTAGTGCTTGGACGAACTTACAAACCTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGT
* * * *
1220 TCCTTCAAGTATTCACGACGATCCATTCCTTCGAGCCATTTTTCGAACATTCCATGCTCGGGAAA
322 TCCTTAAAGTATACAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAA
* * *
1285 TCGTATCATTTGGTCCAAATGCTTTGTCATTTCGTAAACAACTTTTGGTCTTTGAATTTAAAACT
387 TCGCATCATTTGGTCCAAATGCTTTGTCATTTCGTAAACAACTTTTGGTCTTTAAATTAAAAACT
* * * * *
1350 TATTTACGTCAGATTGTTTCTGTTTTGGTTCTTGGACGAACTTATGAACTTGTGAAACTTTTACA
452 TATTTAAGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTACGAACTTGTGAAAATGTTACA
* * * * * *
1415 AGTTCTTTTATAACTTTGGTTCCTTAAAGTATACAAGATGATCCATTCCTTCGAGTAATTTTTCG
517 AGTTCTTTTACAACTTCGATTCCTTAAAGTATACAAAACGATCCATTCCTTCGAGCAATTTTTCG
* * *
1480 AACATTCCATGCTTGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTGTAAGCAACTT
582 AACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTGTAAACAACTT
* * * * * * *
1543 TTGGTTTTTAAATTAAAAACTTATTTAAGTGAGACTTGTTTCTCTTTTGGTTCTTGGATGAACTT
1 TTGGTCTTTAAATAAAAAACTAATTTAAGTCAGAATTGTCTCTCTTTTGGGTCTTGGATGAACTT
1608 ACGAGCTTGT
Statistics
Matches: 623, Mismatches: 77, Indels: 19
0.87 0.11 0.03
Matches are distributed among these distances:
644 37 0.06
645 22 0.04
646 102 0.16
647 132 0.21
648 291 0.47
649 39 0.06
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.41
Consensus pattern (644 bp):
TTGGTCTTTAAATAAAAAACTAATTTAAGTCAGAATTGTCTCTCTTTTGGGTCTTGGATGAACTT
CCAAACTTGTCAAACTTTTACGAGTTCATTTTTAACTTTGGTTCCTTAATGTAGTCACGACGATC
CATTCCTTCGAGCCGTTTTCGAACATTCCATGATCAGGAAATCGCATCATTTGGTCCAAATGCTT
TGTCATTTCGTAAACAACTTTTGGTCTTTAAATTTAAAACTTATTTACGTCAGATTGTTTCTCTT
TTAGTGCTTGGACGAACTTACAAACCTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCT
TAAAGTATACAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGC
ATCATTTGGTCCAAATGCTTTGTCATTTCGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATT
TAAGTCAGATTGTTTCTCTTTTGGTTCTTGGACGAACTTACGAACTTGTGAAAATGTTACAAGTT
CTTTTACAACTTCGATTCCTTAAAGTATACAAAACGATCCATTCCTTCGAGCAATTTTTCGAACA
TTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTGTAAACAACTT
Found at i:2663 original size:216 final size:215
Alignment explanation
Indices: 1969--2853 Score: 1031
Period size: 216 Copynumber: 4.1 Consensus size: 215
1959 NNNNNNNNNN
* * ** *
1969 ACTTATTTACGTCAGATTGTTTCTGTTTTGGTTCTTGGACGAACTTATGAACTTGTGAAACTTTT
1 ACTTATTTACGTCAGATTGTTTCTCTTTTGGTGCTTGGACGAACTTACAAACTTGTCAAACTTTT
* * * *
2034 ACAAGTTCTTTTATAACTTGGGTTCCTTAAAGTATACAAGATGATCCATTCCTTCGAGTAATTTT
66 ACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTT
* * *
2099 TCGAACATTCCATGCTTGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCA-TTTGTAAGCAAC
131 TCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAAC
*
2163 TTTTGGTTTTTAAATTAAAA
196 TTTTGGTCTTTAAATTAAAA
* * * * * * * * *
2183 ACTTATTTAAGTGAGACTTGTTTCTCTTTTGGTTCTTGGATGAACTTACGAGCTTGTTAAAATGT
1 ACTTATTTACGTCAGA-TTGTTTCTCTTTTGGTGCTTGGACGAACTTACAAACTTGTCAAACTTT
* * * * * *
2248 TACAAGTTCTTTTACAGCTTCGATTCCTTAAAGTATTCAAAACGATCCATTCCTTTGAGCAATTT
65 TACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTT
*
2313 TTCCGAGCATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAAATAGTTTGTCATTTTGTAAAC
130 TT-CGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCC-AAATAGTTTGTCATTTTGTAAAC
* *
2378 AACTTTTTGGTCTTTGAATAAAAA
193 AAC-TTTTGGTCTTTAAATTAAAA
* ** * * * * *
2402 ACTAATTTGTGTCAGAATTGTCTCTC-TTTGG-GTTTGGATGAACTTCCAAACTTGTCAAGCTTT
1 ACTTATTTACGTCAG-ATTGTTTCTCTTTTGGTGCTTGGACGAACTTACAAACTTGTCAAACTTT
* * * * *
2465 TACGAGTTATTTTATAACTTTGGTTCCTTCAAGTATTCATGACGATCCATTCCTTCGAGCCATTT
65 TACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTT
*********** *
2530 TTCGAACATTCCATGNNNNNNNNNNNGCATCATTTGGTCCAAATGGTTTGTCATTTTGTAAACAA
130 TTCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAA
*
2595 CTTTTTGGTCTTTAAATTTAAA
195 C-TTTTGGTCTTTAAATTAAAA
* * *
2617 ACTTATTTACGTCAGATTGTTTCTCTTTTAGTGCTTGGACGAACTTCCAAACCTGTCAAACTTTT
1 ACTTATTTACGTCAGATTGTTTCTCTTTTGGTGCTTGGACGAACTTACAAACTTGTCAAACTTTT
** * * *
2682 AGGAGTTCTTTTATAACTTTGGTTCCTTCAAGTATTCACGACGATCCATTCCTTCGAGCCATTTT
66 ACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTT
* * * * *
2747 TCGAACATTCCATGCTCAAGAAGTTGTATCATTTGGTCCAAAT-GCTTTGTCATTTCGTAAACAA
131 TCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAG-TTTGTCATTTTGTAAACAA
* *
2811 CTTTTGGTCTTTGAATTTAAA
195 CTTTTGGTCTTTAAATTAAAA
2832 ACTTATTTACGTCAGATTGTTT
1 ACTTATTTACGTCAGATTGTTT
Statistics
Matches: 570, Mismatches: 92, Indels: 17
0.84 0.14 0.03
Matches are distributed among these distances:
214 23 0.04
215 200 0.35
216 202 0.35
217 92 0.16
218 16 0.03
219 36 0.06
220 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (215 bp):
ACTTATTTACGTCAGATTGTTTCTCTTTTGGTGCTTGGACGAACTTACAAACTTGTCAAACTTTT
ACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTT
TCGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAAC
TTTTGGTCTTTAAATTAAAA
Done.