Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001973.1 Kokia drynarioides strain JFW-HI SEQ_113818, 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, 750
Length: 1250
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Found at i:549 original size:216 final size:216
Alignment explanation
Indices: 1--1247 Score: 1404
Period size: 216 Copynumber: 5.8 Consensus size: 216
* ** *
1 TTCTTGGATGAAGTTCCGAACTTGTCAAACATTTACTAAATCTTTTATAACTTCGGTTCCTGATA
1 TTCTTGGACGAAGTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGA
* * * * * *
66 GTAGTCAAGACGATCCATTCCTTTGACCAATTTTCCGCAGATTCCATTATCGGGAAATCGCATTA
66 GTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAAGATTCCATGATCGAGAAATCGCATCA
*
131 TTTGGTC-AAAATAG--TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAATACTTTTTTAC
131 TTTGGTCTAAAA-AGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTAC
* *
193 GTGAGAATTGTTGC-CTTCTT-G
195 GTGAGAATTCTTTCTC-TCTTGG
** * * * * * *
214 AAC--GGAC--A--TACGAACTAGTCAAACTTTTACAAGTTCTATTATAACTTCGGTTCTTGAGA
1 TTCTTGGACGAAGTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGA
* * * *
273 GCATTCAAGACGATCCACTCCGTTGACCATTTTTTCGAAGATTCCATGATC-AGGAAATCGCATC
66 GTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAAGATTCCATGATCGA-GAAATCGCATC
*
337 ATTTGGTCTAAAACGTTTGTCATTTTGTAAA-AAGCTTTTGGTCTTTGAATTAAAAACTTTTTTA
130 ATTTGGTCTAAAAAGTTTGTCATTTTGTAAACAA-CTTTTGGTCTTTGAATTAAAAACTTTTTTA
*
401 CGTGAGAATTGTTTCTCTCTTGG
194 CGTGAGAATTCTTTCTCTCTTGG
* *
424 TTCTTGGATGAAGTTCCGAACTTATCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGA
1 TTCTTGGACGAAGTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGA
* *
489 GTATTCAAGACGATCCATTCCTTTGACCAA-TTCTCTGAAGATTCCATTATCGAGAAATCGCATC
66 GTATTCAAGACGATCCATTCCTTTGACCAATTTTTC-GAAGATTCCATGATCGAGAAATCGCATC
* * ** * *
553 ATTTGGT-AAAAATAGTTTGCCA-TTTGTAATTAAATTTTGGTCTTTGACTTAAAAACTTTTTTA
130 ATTTGGTCTAAAA-AGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTA
* *
616 CATTG-CAATTCTTTCTCTCTTGG
194 C-GTGAGAATTCTTTCTCTCTTGG
* * * * * * *
639 TTCTTTGACGAAGTTTCGAACTTGTCAAACATTTACTAGTTCTTTAACAACTTCGATCCCTGATA
1 TTCTTGGACGAAGTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGA
* * * ** *
704 GTAGTCAAGATGATCCATTCCTTCGACCAATTTTTCGATCATTCCATGATC-AGGAAATCGTATC
66 GTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAAGATTCCATGATCGA-GAAATCGCATC
* * *
768 ATTTGGTATAAATAGTTTGTCATTTTGTAAACAACTTTGGGTCTTTGAATTAAAAACTTTTTTAC
130 ATTTGGTCTAAAAAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTAC
* *
833 GAGAGAATTATTTCTCTCTTGG
195 GTGAGAATTCTTTCTCTCTTGG
* ** * * * * *
855 TTCTTGGACGAACTTTTGAACTGGTTAAACATTTACAAGTTATTTTATAACTTCGGTTCTTGAGA
1 TTCTTGGACGAAGTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGA
* * *
920 GTATTCAAGTCGATCCATTCCTTTGACCAATTTTT-GAAGATTCCATGACCGGGAAATCGCATCA
66 GTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAAGATTCCATGATCGAGAAATCGCATCA
* *
984 TTTTGGTC-AAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATT-AAAAGTGTTTTT
131 -TTTGGTCTAAAA-AGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACT-TTTTT
* *
1047 ACGTTAGAATTCTTTCTTTCTTGG
193 ACGTGAGAATTCTTTCTCTCTTGG
* * * * *
1071 TTCTTGGACGAACATT-TGAACTTGTTAAACATTTACGAGTTCTTTTATAACTTCAGTTCCTGAG
1 TTCTTGGACGAA-GTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAG
* * * ** * * * ** *
1135 AGTATTTAATACGATCCATTCCTTCGACTTATTTTTCAAACATTTCATTCTCGGGAAATCGCATC
65 AGTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAAGATTCCATGATCGAGAAATCGCATC
* * * *
1200 ACTTGGTCTAAAAAGTTTGGCATGTTGTAAAAAACTTTTGGTCTTTGA
130 ATTTGGTCTAAAAAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGA
1248 TTT
Statistics
Matches: 872, Mismatches: 132, Indels: 57
0.82 0.12 0.05
Matches are distributed among these distances:
207 104 0.12
208 6 0.01
209 62 0.07
210 3 0.00
211 3 0.00
212 3 0.00
213 1 0.00
214 2 0.00
215 212 0.24
216 446 0.51
217 30 0.03
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.40
Consensus pattern (216 bp):
TTCTTGGACGAAGTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGA
GTATTCAAGACGATCCATTCCTTTGACCAATTTTTCGAAGATTCCATGATCGAGAAATCGCATCA
TTTGGTCTAAAAAGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACG
TGAGAATTCTTTCTCTCTTGG
Found at i:887 original size:431 final size:426
Alignment explanation
Indices: 1--1247 Score: 1500
Period size: 431 Copynumber: 2.9 Consensus size: 426
* * ** *
1 TTCTTGGATGAAGTTCCGAACTTGTCAAACATTTACTAAATCTTTTATAACTTCGGTTCCTGATA
1 TTCTTGGACGAACTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGA
* * * *
66 GTAGTCAAGACGATCCATTCCTTTGACCAATTTTCCGCAGATTCCATTATCGGGAAATCGCATTA
66 GTATTCAAGACGATCCATTCCTTTGACCAA-TTTCTGAAGATTCCATTATCGGGAAATCGCATCA
* *
131 TTTGGTCAAAATAG--TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAATACTTTTTTACG
130 TTTGGTCAAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTTTTTTAC-
* * * * * * *
194 TGAGAATT-GTT-GC-C----TTC-TTGAACGGACA-TACGAACTAGTCAAACTTTTACAAGTTC
194 T-TGAATTCTTTCTCTCTTGGTTCTTTG-AC-GAAATTTCGAACTTGTCAAACATTTACAAGTTC
* * * * * *
250 TATTATAACTTCGGTTCTTGAGAGCATTCAAGACGATCCACTCCGTT-GACCATTTTTTCGAAGA
256 T-TTATAACTTCGATTCCTGAGAGTATTCAAGACGATCCATTCC-TTCGACCAATTTTTCGAACA
314 TTCCATGATCAGGAAATCGCATCATTTGGTCTAAAACGTTTGTCATTTTGTAAAAAGCTTTTGGT
319 TTCCATGATCAGGAAATCGCATCATTTGGTCTAAAA-GTTTGTCATTTTGTAAAAA-CTTTTGGT
* *
379 CTTTGAATTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGG
382 CTTTGAATTAAAAACTTTTTTACGAGAGAATTATTTCTCTCTTGG
* * *
424 TTCTTGGATGAAGTTCCGAACTTATCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGA
1 TTCTTGGACGAACTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGA
*
489 GTATTCAAGACGATCCATTCCTTTGACCAATTCTCTGAAGATTCCATTATCGAGAAATCGCATCA
66 GTATTCAAGACGATCCATTCCTTTGACCAATT-TCTGAAGATTCCATTATCGGGAAATCGCATCA
* * * * *
554 TTTGGTAAAAATAGTTTGCCA-TTTGTAATTAAATTTTGGTCTTTGACTTAAAAACTTTTTTACA
130 TTTGGTCAAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTTTTTTAC-
* *
618 TTGCAATTCTTTCTCTCTTGGTTCTTTGACGAAGTTTCGAACTTGTCAAACATTTACTAGTTCTT
194 TTG-AATTCTTTCTCTCTTGGTTCTTTGACGAAATTTCGAACTTGTCAAACATTTACAAGTTCTT
* * * * * *
683 TAACAACTTCGATCCCTGATAGTAGTCAAGATGATCCATTCCTTCGACCAATTTTTCGATCATTC
258 T-ATAACTTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACCAATTTTTCGAACATTC
* * *
748 CATGATCAGGAAATCGTATCATTTGGTATAAATAGTTTGTCATTTTGTAAACAACTTTGGGTCTT
322 CATGATCAGGAAATCGCATCATTTGGTCTAAA-AGTTTGTCATTTTGTAAA-AACTTTTGGTCTT
813 TGAATTAAAAACTTTTTTACGAGAGAATTATTTCTCTCTTGG
385 TGAATTAAAAACTTTTTTACGAGAGAATTATTTCTCTCTTGG
** * * * * *
855 TTCTTGGACGAACTTTTGAACTGGTTAAACATTTACAAGTTATTTTATAACTTCGGTTCTTGAGA
1 TTCTTGGACGAACTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGA
* * * *
920 GTATTCAAGTCGATCCATTCCTTTGACCAATTTTTGAAGATTCCATGACCGGGAAATCGCATCAT
66 GTATTCAAGACGATCCATTCCTTTGACCAATTTCTGAAGATTCCATTATCGGGAAATCGCATCA-
*
985 TTTGGTCAAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATT-AAAAGTGTTTTTAC
130 TTTGGTCAAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACT-TTTTTAC
* * * *
1049 GTTAGAATTCTTTCTTTCTTGGTTCTTGGACGAACATTT-GAACTTGTTAAACATTTACGAGTTC
194 -TT-GAATTCTTTCTCTCTTGGTTCTTTGACGAA-ATTTCGAACTTGTCAAACATTTACAAGTTC
* * ** *
1113 TTTTATAACTTC-AGTTCCTGAGAGTATTTAATACGATCCATTCCTTCGACTTATTTTTCAAACA
256 -TTTATAACTTCGA-TTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACCAATTTTTCGAACA
* ** * * * *
1177 TTTCATTCTCGGGAAATCGCATCACTTGGTCTAAAAAGTTTGGCATGTTGTAAAAAACTTTTGGT
319 TTCCATGATCAGGAAATCGCATCATTTGGTCT-AAAAGTTTGTCATTTTGT-AAAAACTTTTGGT
1242 CTTTGA
382 CTTTGA
1248 TTT
Statistics
Matches: 707, Mismatches: 91, Indels: 43
0.84 0.11 0.05
Matches are distributed among these distances:
422 2 0.00
423 132 0.19
424 42 0.06
425 6 0.01
426 1 0.00
427 1 0.00
430 34 0.05
431 286 0.40
432 190 0.27
433 13 0.02
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.40
Consensus pattern (426 bp):
TTCTTGGACGAACTTCCGAACTTGTCAAACATTTACTAGTTCTTTTATAACTTCGGTTCCTGAGA
GTATTCAAGACGATCCATTCCTTTGACCAATTTCTGAAGATTCCATTATCGGGAAATCGCATCAT
TTGGTCAAAATAGTTTGTCATTTTGTAAATAACTTTTGGTCTTTGAATTAAAAACTTTTTTACTT
GAATTCTTTCTCTCTTGGTTCTTTGACGAAATTTCGAACTTGTCAAACATTTACAAGTTCTTTAT
AACTTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTCGACCAATTTTTCGAACATTCCATG
ATCAGGAAATCGCATCATTTGGTCTAAAAGTTTGTCATTTTGTAAAAACTTTTGGTCTTTGAATT
AAAAACTTTTTTACGAGAGAATTATTTCTCTCTTGG
Done.