Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012450.1 Kokia drynarioides strain JFW-HI SEQ_127454, 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: 1670
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.39
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:379 original size:214 final size:214
Alignment explanation
Indices: 3--449 Score: 576
Period size: 214 Copynumber: 2.1 Consensus size: 214
1 TC
* * * * *
3 TAGAAATCGCATCATTTAGTCTGAATAGTTGCCATTATGTATACGACTTTTGGTCTTTGAATTAA
1 TAGAAATCTCATCATTTGGTCTAAATAGTTGCCATTATGTAAACAACTTTTGGTCTTTGAATTAA
* * * *
68 ATACTTATTTAGGTGAGAATAGTTTTTCTCCTGGTTCTAGGCCGAACATCCGAAGTTGACAAACT
66 AAACTTATTTACGTGAGAATAATTTCTCTCCTGGTTCTAGGCCGAACATCCGAAGTTGACAAACT
* *
133 TTTACGAGTTCTTTTACAACTTCGGCTCCTTAAAGTATCCAAGGCAAACCATTCCTTCGAGCAAT
131 TTTACGAGTTCTTTTACAACTTCGACTCCTTAAAGTATCCAAGACAAACCATTCCTTCGAGCAAT
198 TTTCT-GAACATTCCAAGCT
196 TTT-TGGAACATTCCAAGCT
* * *
217 TAGAAATCTCATCATTTGGTCTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTTTAATTAA
1 TAGAAATCTCATCATTTGGTCTAAATAGTTGCCATTATGTAAACAACTTTTGGTCTTTGAATTAA
* * **
282 AAACTTATTTACGTGAGAATAATTTCTCTCTTGGTTCTGGGCCGAAC-TGTTGAAGTTGACAAAC
66 AAACTTATTTACGTGAGAATAATTTCTCTCCTGGTTCTAGGCCGAACAT-CCGAAGTTGACAAAC
* * * * ** * * *
346 TTTTACGAGTTCTTTTATATCTTTGATTCCTTAAAGTATTTAAGACGAGCCATTCCTTCGAGGAA
130 TTTTACGAGTTCTTTTACAACTTCGACTCCTTAAAGTATCCAAGACAAACCATTCCTTCGAGCAA
**
411 TTTTTGGAACATTCCGTGCT
195 TTTTTGGAACATTCCAAGCT
*
431 TGGAAATCGT-ATCATTTGG
1 TAGAAATC-TCATCATTTGG
450 NNNNNNNNNN
Statistics
Matches: 200, Mismatches: 30, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
213 2 0.01
214 197 0.99
215 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (214 bp):
TAGAAATCTCATCATTTGGTCTAAATAGTTGCCATTATGTAAACAACTTTTGGTCTTTGAATTAA
AAACTTATTTACGTGAGAATAATTTCTCTCCTGGTTCTAGGCCGAACATCCGAAGTTGACAAACT
TTTACGAGTTCTTTTACAACTTCGACTCCTTAAAGTATCCAAGACAAACCATTCCTTCGAGCAAT
TTTTGGAACATTCCAAGCT
Found at i:881 original size:214 final size:212
Alignment explanation
Indices: 500--1670 Score: 1002
Period size: 214 Copynumber: 5.6 Consensus size: 212
490 NNNNNNNNNN
* * * ** ***
500 AAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAATTTCTCTCTTGGTTCTGG
1 AAACAAATTTTGGTCTTTGAATTAAAAAATTATTTATGTGAGAATTGTTTCTCTCTTGGTTCACA
* * * *
565 GCCGAACTGTCGAAGTTGACAAACTTTTACGAGTTCTTTTATAACTTTGATTCCTTCAAGTATTT
66 GCCGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTTTAACTTTG-TTCCTT-AAGTATTC
* * * *
630 AAGACGAGCCATTCATTCGAG-GATTTTTTCGAACATTCCATGCTTGGAAATCGTATCATTTGGT
129 AAGACGATCCATTCCTTCGAGCAATTTTTT-GAACATTCCATGCTTGGAAATCGCATCATTTGGT
*
694 CTAAATAGTTGTCCTTCTGT
193 CTAAATAGTTGTCATTCTGT
* * *
714 AAACAAATTTTGGTCTTTGAATTAAAAAATTCTTTATGTGAGAATTGTTTCTCTATTTGTTCACA
1 AAACAAATTTTGGTCTTTGAATTAAAAAATTATTTATGTGAGAATTGTTTCTCTCTTGGTTCACA
** *
779 GTTGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTTTAACTTCTGTTCCTTATAGAATTC
66 GCCGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTTTAACTT-TGTTCCTTA-AGTATTC
* * * * *
844 AAGATGATCCATTCCTTCGAGCAATTTTTTAAACATTCCATGCTCGGGAAATCGCATCACTTGTT
129 AAGACGATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCT-TGGAAATCGCATCATTTGGT
*
909 CTTAATAGATTGTCAATT-TGT
193 CTAAATAG-TTGTC-ATTCTGT
* ** * * * * * * * *
930 AAAAAAAAGTT-AT-TTATG--TT--AGAATT-GTT-TCT-----TTCTTTGT-TCTCGGTTGAA
1 AAACAAATTTTGGTCTT-TGAATTAAAAAATTATTTATGTGAGAATTGTTTCTCTCTTGGTT-CA
** * * *
981 CTTCCGAAC-TT-G------ACAAACTTTAACGAGTTCTTTTATAACTTTTGTTCATTAAAGTAT
64 CAGCCGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTTTAAC-TTTGTTCCTT-AAGTAT
* * *** * * * *
1038 TCAGGACGATCCATTCTTTCGAGCAA-TTTCCCATACAGTCCATGCTTGGGAGATCACATCATTA
127 TCAAGACGATCCATTCCTTCGAGCAATTTTTTGA-ACATTCCATGCTT-GGAAATCGCATCATTT
* *
1102 GATCTAAATAGTTGTCATTTTGT
190 GGTCTAAATAGTTGTCATTCTGT
* * * * ** * *
1125 AAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAGTAATATCTCTCCTGGTTCTA-
1 AAACAAATTTTGGTCTTTGAATTAAAAAATTATTTATGTGAGAATTGTTTCTCTCTTGGTTC-AC
* * * * * *
1189 GGCCAAACTGTCGAAGTTGACAAACTTTTACAAGTTCTTTTATAACTTTGATTCCTTAAAGTATT
65 AGCCGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTTTAACTTTG-TTCCTT-AAGTATT
* * * * *
1254 TAAGACGAGCCATTCCTTCGAGGAATTTTTCGAACATTCCATGCTTGGAAATCGTATCATTTGGT
128 CAAGACGATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTTGGAAATCGCATCATTTGGT
*
1319 CTAAATAGTTGTCATTTTGT
193 CTAAATAGTTGTCATTCTGT
* * * *
1339 AAACAAATTTTGGTCTTTGAATTAAAAAATTCTTTATGTGAGAATTGTTTCTTTCTTGGATCTCA
1 AAACAAATTTTGGTCTTTGAATTAAAAAATTATTTATGTGAGAATTGTTTCTCTCTTGGTTCACA
* * * * * *
1404 GCCAAACTTT-AAACTTGACAAAATTTT-CAAGTTCTTTTTTAAAATTT-TTCATTAAAGTATTC
66 GCCGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTTT-AACTTTGTTCCTT-AAGTATTC
* * * * * * *
1466 AAGGCGATCCATTCCTTC-AGCAATTTATTGTACAGTCCATGCTTGGGAAATCACATTATTAGGT
129 AAGACGATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTT-GGAAATCGCATCATTTGGT
*
1530 CTAAATTGTTGTCATTCTGT
193 CTAAATAGTTGTCATTCTGT
* * * * *
1550 AAACTACTTTTGGTTTTTCAATTAAAAACA-TATTT-TCGTGAGAATTGTTTCTCTATTGGTTCA
1 AAACAAATTTTGGTCTTTGAATTAAAAA-ATTATTTAT-GTGAGAATTGTTTCTCTCTTGGTTCA
**
1613 CAGTTGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTTTAACTTATGTTCCTT
64 CAGCCGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTTTAACTT-TGTTCCTT
Statistics
Matches: 758, Mismatches: 152, Indels: 94
0.75 0.15 0.09
Matches are distributed among these distances:
194 3 0.00
195 19 0.03
196 94 0.12
197 5 0.01
198 2 0.00
200 4 0.01
201 2 0.00
202 2 0.00
203 7 0.01
204 12 0.02
207 9 0.01
208 8 0.01
209 3 0.00
210 24 0.03
211 126 0.17
212 32 0.04
213 35 0.05
214 243 0.32
215 105 0.14
216 21 0.03
217 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (212 bp):
AAACAAATTTTGGTCTTTGAATTAAAAAATTATTTATGTGAGAATTGTTTCTCTCTTGGTTCACA
GCCGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTTTAACTTTGTTCCTTAAGTATTCAA
GACGATCCATTCCTTCGAGCAATTTTTTGAACATTCCATGCTTGGAAATCGCATCATTTGGTCTA
AATAGTTGTCATTCTGT
Found at i:1082 original size:196 final size:194
Alignment explanation
Indices: 737--1127 Score: 505
Period size: 196 Copynumber: 2.0 Consensus size: 194
727 TCTTTGAATT
* *
737 AAAAAATTCTTTATGTGAGAATTGTTTCTCTATTTGTTCACAGTTGAACTTTCGAACTTGACAAA
1 AAAAAATTATTTATGTGAGAATTGTTTCTCTATTTGTTCACAGTTGAACTTCCGAACTTGACAAA
* * * * *
802 CTTTTACGAGTTCTTTTTTAACTTCTGTTCCTTATAGAATTCAAGATGATCCATTCCTTCGAGCA
66 CTTTAACGAGTTCTTTTATAACTTCTGTTCATTAAAGAATTCAAGACGATCCATTCCTTCGAGCA
*** * * * *
867 ATTTTTTAAACATTCCATGCTCGGGAAATCGCATCACTT-GTTCTTAATAGATTGTCAATTTGTA
131 ATTTCCCAAACAGTCCATGCTCGGGAAATCACATCA-TTAGATCTAAATAG-TTGTCAATTTGTA
931 A
194 A
* * * * *
932 AAAAAAGTTATTTATGTTAGAATTGTTTCTTTCTTTGTTCTCGGTTGAACTTCCGAACTTGACAA
1 AAAAAA-TTATTTATGTGAGAATTGTTTCTCTATTTGTTCACAGTTGAACTTCCGAACTTGACAA
* * * *
997 ACTTTAACGAGTTCTTTTATAACTTTTGTTCATTAAAGTATTCAGGACGATCCATTCTTTCGAGC
65 ACTTTAACGAGTTCTTTTATAACTTCTGTTCATTAAAGAATTCAAGACGATCCATTCCTTCGAGC
* * * *
1062 AATTTCCCATACAGTCCATGCTTGGGAGATCACATCATTAGATCTAAATAGTTGTCATTTTGTAA
130 AATTTCCCAAACAGTCCATGCTCGGGAAATCACATCATTAGATCTAAATAGTTGTCAATTTGTAA
1127 A
1 A
1128 CAACTTTTGG
Statistics
Matches: 167, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
195 22 0.13
196 145 0.87
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (194 bp):
AAAAAATTATTTATGTGAGAATTGTTTCTCTATTTGTTCACAGTTGAACTTCCGAACTTGACAAA
CTTTAACGAGTTCTTTTATAACTTCTGTTCATTAAAGAATTCAAGACGATCCATTCCTTCGAGCA
ATTTCCCAAACAGTCCATGCTCGGGAAATCACATCATTAGATCTAAATAGTTGTCAATTTGTAA
Found at i:1292 original size:411 final size:416
Alignment explanation
Indices: 516--1670 Score: 1084
Period size: 411 Copynumber: 2.8 Consensus size: 416
506 CTTTTGGTCT
* * ** * * ** * *
516 TTGAATTAAAAACTTATTTAGGTGAGAATAATTTCTCTCTTGGTTCTGGGCCGAACTGTCGAAGT
1 TTGAA-TAAAAAATTATTTATGTGAGAATTGTTTCTTTCTTGGATCTCAGCCAAACT-TCGAACT
* * * * *
581 TGACAAACTTTTACGAGTTCTTTTATAACTTTGATTCCTTCAAGTATTTAAGACGAGCCATTCAT
64 TGACAAAC-TTTACGAGTTCTTTTATAACTTTG-TTCATTAAAGTATTCAGGACGATCCATTCAT
* * * * * ** * *
646 TCGAGGATTTTTTCGA-ACATTCCATGCTT-GGAAATCGTATCATTTGGTCTAAATAGTTGTCCT
127 TCGAGCA-ATTTACCATACAGTCCATGCTTGGGAAATCACATCATTAGGTCTAAATAGTTGTCAT
* * * * ** * * *
709 TCTGTAAACAAATTTTGGTCTTTGAATTAAAAAATTCTTTATGTGAGAATTGTTTCTCTATTTGT
191 TCTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAATATCTCTACTGGT
*** * * * *
774 TCACAGTTGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTTTAACTTCTGTTCCTTATAG
256 TCACAGCCAAACTGTCGAACTTGACAAACTTTTACAAGTTCTTTTATAACTTCTGTTCCTTAAAG
* * *
839 AATTCAAGATGATCCATTCCTTCGAGCAATTTTTTAAACATTCCATGCTCGGGAAATCGCATCAC
321 AATTCAAGACGAGCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCT-GGGAAATCGCATCAC
* *
904 TTGTTCTTAATA-G-A-TTGT-C-AA-TTT-G
385 TTGGTCTAAATATGCATTTGTACAAATTTTGG
* * * * ***
929 -T-AA-AAAAAAGTTATTTATGTTAGAATTGTTTCTTTCTTTGTTCTCGGTTGAACTTCCGAACT
1 TTGAATAAAAAA-TTATTTATGTGAGAATTGTTTCTTTCTTGGATCTCAGCCAAACTT-CGAACT
*
991 TGACAAACTTTAACGAGTTCTTTTATAACTTTTGTTCATTAAAGTATTCAGGACGATCCATTCTT
64 TGACAAACTTT-ACGAGTTCTTTTATAAC-TTTGTTCATTAAAGTATTCAGGACGATCCATTCAT
* * *
1056 TCGAGCAATTTCCCATACAGTCCATGCTTGGGAGATCACATCATTAGATCTAAATAGTTGTCATT
127 TCGAGCAATTTACCATACAGTCCATGCTTGGGAAATCACATCATTAGGTCTAAATAGTTGTCATT
* * *
1121 TTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAGTAATATCTCTCCTGGTT
192 CTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAATATCTCTACTGGTT
* *
1186 CTA-GGCCAAACTGTCGAAGTTGACAAACTTTTACAAGTTCTTTTATAACTT-TGATTCCTTAAA
257 C-ACAGCCAAACTGTCGAACTTGACAAACTTTTACAAGTTCTTTTATAACTTCTG-TTCCTTAAA
* * * * * * *
1249 GTATTTAAGACGAGCCATTCCTTCGAGGAATTTTTCGAACATTCCATGCTTGGAAATCGTATCAT
320 GAATTCAAGACGAGCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTGGGAAATCGCATCAC
1314 TTGGTCTAAATAGTTGTCATTTTGTAAACAAATTTTGG
385 TTGGTCTAAATA--TG-CA-TTTGT--ACAAATTTTGG
* **
1352 TCTTTGAATTAAAAAATTCTTTATGTGAGAATTGTTTCTTTCTTGGATCTCAGCCAAACTTTAAA
1 ---TTGAA-TAAAAAATTATTTATGTGAGAATTGTTTCTTTCTTGGATCTCAGCCAAACTTCGAA
* * * * *
1417 CTTGACAAAATTTTCAAGTTCTTTTTTAAAATTT-TTCATTAAAGTATTCAAGG-CGATCCATTC
62 CTTGACAAACTTTACGAGTTCTTTTAT-AACTTTGTTCATTAAAGTATTC-AGGACGATCCATTC
* *** * *
1480 CTTC-AGCAATTTATTGTACAGTCCATGCTTGGGAAATCACATTATTAGGTCTAAATTGTTGTCA
125 ATTCGAGCAATTTACCATACAGTCCATGCTTGGGAAATCACATCATTAGGTCTAAATAGTTGTCA
* * * * ** ** * *
1544 TTCTGTAAACTACTTTTGGTTTTTCAATTAAAAACATATTTTCGTGAGAATTGTTTCTCTATTGG
190 TTCTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAATATCTCTACTGG
*** * * * *
1609 TTCACAGTTGAACTTTCGAACTTGACAAACTTTTACGAGTTCTTTTTTAACTTATGTTCCTT
255 TTCACAGCCAAACTGTCGAACTTGACAAACTTTTACAAGTTCTTTTATAACTTCTGTTCCTT
Statistics
Matches: 604, Mismatches: 106, Indels: 52
0.79 0.14 0.07
Matches are distributed among these distances:
409 14 0.02
410 132 0.22
411 180 0.30
412 2 0.00
413 1 0.00
415 1 0.00
417 4 0.01
420 1 0.00
421 2 0.00
422 3 0.00
423 1 0.00
424 1 0.00
425 153 0.25
426 30 0.05
427 18 0.03
428 18 0.03
429 37 0.06
430 6 0.01
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (416 bp):
TTGAATAAAAAATTATTTATGTGAGAATTGTTTCTTTCTTGGATCTCAGCCAAACTTCGAACTTG
ACAAACTTTACGAGTTCTTTTATAACTTTGTTCATTAAAGTATTCAGGACGATCCATTCATTCGA
GCAATTTACCATACAGTCCATGCTTGGGAAATCACATCATTAGGTCTAAATAGTTGTCATTCTGT
AAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATAATATCTCTACTGGTTCACA
GCCAAACTGTCGAACTTGACAAACTTTTACAAGTTCTTTTATAACTTCTGTTCCTTAAAGAATTC
AAGACGAGCCATTCCTTCGAGCAATTTTTCAAACATTCCATGCTGGGAAATCGCATCACTTGGTC
TAAATATGCATTTGTACAAATTTTGG
Done.