Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004961.1 Kokia drynarioides strain JFW-HI SEQ_118688, 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: 1897
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Found at i:551 original size:216 final size:214
Alignment explanation
Indices: 83--1280 Score: 1179
Period size: 216 Copynumber: 5.7 Consensus size: 214
73 CAATGATGCG
* * * *
83 ATGTTCAAAAAATTGCAT-TAAGGAATCGATCGTCTTGAATACTTTAAGTAACCGAAGTTATAAA
1 ATGTTCGAAAAATTGC-TCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAA
* *
147 CGTACTCGAAAAAGTTTGACAAGTTCTGAATTTCGGCCAAGAACC-A-AGAGAAACAATTCTCAC
65 AGTACTCGAAAAAGTTTGACAAGTT-TGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCAC
* * *
210 ATAAAT-AGATTTTAA-TCCAAGAACCAAAAGTTGTTTACAAAATGACAGATTATTTGGACCAAA
129 ATAAATAAGTTTTTAATTCAAAG-ACCAAAAGTTGTTTACAAAAAGACAGATTATTTGGACCAAA
*
273 TGATGCGATTTCCCGAGAATGGA
193 TGATGAGATTT-CCGAGAATGGA
* * * * *
296 ATGTTCGAAAAGTTGTTCGACGAAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAA
1 ATGTTCGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAA
* * * *
361 GTACTCGAAAAAGTTTG-CAAAGTTTGGAAGTTCGGCCTAGAACCAAGAGTGAAATAATTATCAC
66 GTACTCGAAAAAGTTTGAC-AAGTTT-GAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCAC
* * * *
425 GTAAATAAGTTTTTAATTCAAAGACCGAATGTTTTTTACAAAAAGACTA-ATTATTTGGACCAAA
129 ATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAAGAC-AGATTATTTGGACCAAA
** *
489 TGATGAGATATTTAGAAAATGGA
193 TGATGAGAT-TTCCGAGAATGGA
* *
512 ATGTTCGAAAAATTGCTCGAATGAATTGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAA
1 ATGTTCGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAA
* * * **
577 GTACTCGAAAAAGTTTAACAAGTTCGGATGTTCAACCAAGAACC-AG-GAGAAACAATTCTCACA
66 GTACTCGAAAAAGTTTGACAAGTT-TGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACA
* * *
640 TAAATAAATTCTTAATGCAAAGACCAAAAGTTGTTTA-AAAAATGACAGATTATTTGGACCAAAT
130 TAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAA-GACAGATTATTTGGACCAAAT
* *
704 GATGCA-ATTTCCCAAGAACGGA
194 GATG-AGATTT-CCGAGAATGGA
* * * * * * * *
726 ATGTTCGAAAAATTGTTCGAAGAAATGGATCATCTTCAATACTTTAAGGAGCAAAAGTTAGAAAA
1 ATGTTCGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAA
* * * * * * * * *
791 GAACT-AAAGAAAGTTTG-CAAAG--T-AAGTTCGACCTAGTACCATGAGTGAAATAATTCTTAC
66 GTACTCGAA-AAAGTTTGAC-AAGTTTGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCAC
* * *
851 GTAAATAAGTTTTTAATTCAAAGACCGAAAG-T-TTT-C-----TACA-A--A--TGGAACCAAA
129 ATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAGATTATTTGG-ACCAAA
*
903 TGATGCGATTTCCCGAGAATGGA
193 TGATGAGATTT-CCGAGAATGGA
* * ** * * *
926 ATGTCCGAAAAATTGCTCGAAGGAATCTATAATCTTGAATACTTTGAGGAACCGAAGATATAAAA
1 ATGTTCGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAA
* * *
991 GTACTTGAAAAAGTTTGACAAGTTTAGAAGTTCAGCCAAGAACCAAGAGAGAAACAATTCTCACT
66 GTACTCGAAAAAGTTTGACAAGTTT-GAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACA
** * * * **
1056 TAAATAAAATTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGATAGATTATTTCTACCAAATG
130 TAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAGATTATTTGGACCAAATG
* *
1121 ATGAGATTTCCCGAGAACGAA
195 ATGAGATTT-CCGAGAATGGA
* *
1142 ATGTTCGAAAAATTGTTCGAATGG-A-C---CGTCTTGAATACTTTAGGGAACCAAAGTTATAAA
1 ATGTTCGAAAAATTGCTCGAA-GGAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAA
** * * * * *
1202 AAAACTCGAAAAAGTTTGTA-AAGTTCGGAAGTTTGGCCAAGAACGAAGAAAGAAATAATTCTCA
65 AGTACTCGAAAAAGTTTG-ACAAGTT-TGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCA
1266 CATAAATAAGTTTTT
128 CATAAATAAGTTTTT
1281 TACAAAAGGA
Statistics
Matches: 803, Mismatches: 138, Indels: 89
0.78 0.13 0.09
Matches are distributed among these distances:
199 3 0.00
200 92 0.11
201 4 0.00
202 1 0.00
203 1 0.00
204 58 0.07
205 1 0.00
206 3 0.00
207 1 0.00
210 16 0.02
211 2 0.00
212 136 0.17
213 104 0.13
214 146 0.18
215 24 0.03
216 199 0.25
217 12 0.01
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (214 bp):
ATGTTCGAAAAATTGCTCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAA
GTACTCGAAAAAGTTTGACAAGTTTGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACAT
AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAAGACAGATTATTTGGACCAAATGA
TGAGATTTCCGAGAATGGA
Found at i:1636 original size:630 final size:624
Alignment explanation
Indices: 102--1897 Score: 1662
Period size: 630 Copynumber: 2.9 Consensus size: 624
92 AAATTGCATT
* * * *
102 AAGGAATCGATCGTCTTGAATACTTTAAGTAACCGAAGTTATAAACGTACTCGAAAAAGTTTGAC
1 AAGGAATCGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAA-GAACTAG-AAAAGTTTGAC
*
167 AAGTTCTGAATTTCGGCCAAGAACCAAG-AGAAACAATTCTCACATAAATAGA-TTTTAATCCAA
64 AAGTTCTGAAGTTCGGCCAAGAACCAAGAAGAAACAATTCTCACATAAATA-ATTTTTAATCCAA
230 GAACCAAAAGTTGTTTACAAAATGACAGATTATTTGGACCAAATGATGCGATTTCCCGAGAATGG
128 G-ACCAAAAGTTGTTTACAAAAT-ACAGATTATTTGGACCAAATGATGCGATTTCCCGAGAATGG
* * * *
295 AATGTTCGAAAAGTTGTTCGACGAAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAA
191 AATGTTCGAAAAATTGTTCGAAGAAATTGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAA
* * * *
360 AGTACTCGAAAAAGTTTGCAAAGTTT-GGAAGTTCGGCCTAGAACCAAGAGTGAAATAATTATCA
256 AGTACTCGAAAAAGTTTGCAAAGTTTGGGAAGTTCAGCCAAGAACCAAGAGAGAAACAATTATCA
** * * * * *
424 CGTAAATAAGTTTTTAATTCAAAGACCGAATGTTTTTTACAAAAAGACTAATTATTTGGACCAAA
321 CGTAAATAAAATTTTAATCCAAAGACCAAAAGTTGTTTACAAAAAGACTAATTATTTCGACCAAA
* * * *
489 TGATGAGATATTTAGAAAATGGAATGTTCGAAAAATTGCTCGAATGAATTGATCGTCTTGAATAC
386 TGATGAGATATTCAGAAAACGAAATGTTCGAAAAATTGCTCGAATG-A--GACCGTCTTGAATAC
** *
554 TTTAAGGAACCAAAGTTATAAAAGTACTCGAAAAAGTTTAACAAGTTCGGATGTTCAACCAAGAA
448 TTTAAGGAACCAAAGTTATAAAAAAACTCGAAAAAGTTTAACAAGTTCGGAAGTTCAACCAAGAA
* *
619 CCAGGAGAAACAATTCTCACATAAATAAATTCTTAATGCAAAGACCAAAAGTTGTTTAAAAAATG
513 CAAGAAGAAACAATTCTCACATAAATAAATTCTT-AT----AGACCAAAAG-TG------AAAT-
* * * *
684 ACAGATTATTTGGACCAAATGATGCAATTTCCCAAGAACGGAATGTTCGAAAAATTGTTCG
565 A-AGACTATTTGGACCAAATGATGCAATTTCCCAAGAACGAAATGCTCGAAAAATTGCTCG
* * * * ** * *
745 AAGAAATGGATCATCTTCAATACTTTAAGGAGCAAAAGTTAGAAAAGAACTAAAGAAAGTTTG-C
1 AAGGAATCGATCATCTTGAATACTTTAAGGAACCGAAGTTA-TAAAGAACTAGA-AAAGTTTGAC
* * * * * * * *
809 AAAG---T-AAGTTCGACCTAGTACCATGAGTGAAATAATTCTTACGTAAATAAGTTTTTAATTC
64 -AAGTTCTGAAGTTCGGCCAAGAACCAAGA-AGAAACAATTCTCACATAAATAA-TTTTTAA-TC
* *
870 AAAGACCGAAAG-T-TTT-C----TACA-A--A--TGGAACCAAATGATGCGATTTCCCGAGAAT
125 CAAGACCAAAAGTTGTTTACAAAATACAGATTATTTGG-ACCAAATGATGCGATTTCCCGAGAAT
* * * * * * *
923 GGAATGTCCGAAAAATTGCTCGAAGGAATCT-ATAATCTTGAATACTTTGAGGAACCGAAGATAT
189 GGAATGTTCGAAAAATTGTTCGAAGAAAT-TGATCATCTTGAATACTTTAAGGAACCAAAGTTAT
* *
987 AAAAGTACTTGAAAAAGTTTG-ACAAGTTT-AGAAGTTCAGCCAAGAACCAAGAGAGAAACAATT
253 AAAAGTACTCGAAAAAGTTTGCA-AAGTTTGGGAAGTTCAGCCAAGAACCAAGAGAGAAACAATT
* * * *
1050 CTCACTTAAATAAAATTTTAATCCAAAGACCAAAAGTTGTTTACAAAATGA-TAGATTATTTCTA
317 ATCACGTAAATAAAATTTTAATCCAAAGACCAAAAGTTGTTTACAAAAAGACTA-ATTATTTCGA
* * *
1114 CCAAATGATGAGAT-TTCCCGAGAACGAAATGTTCGAAAAATTGTTCGAATG-GACCGTCTTGAA
381 CCAAATGATGAGATATT-CAGAAAACGAAATGTTCGAAAAATTGCTCGAATGAGACCGTCTTGAA
* * ***
1177 TACTTTAGGGAACCAAAGTTATAAAAAAACTCGAAAAAGTTTGTA-AAGTTCGGAAGTTTGGCCA
445 TACTTTAAGGAACCAAAGTTATAAAAAAACTCGAAAAAGTTT-AACAAGTTCGGAAGTTCAACCA
* * * *
1241 AGAACGAAGAAAGAAATAATTCTCACATAAATAAGTT-TT-T-TA-CAAAAG-G-ACT-A-ACTA
509 AGAAC-AAG-AAGAAACAATTCTCACATAAATAAATTCTTATAGACCAAAAGTGAAATAAGACTA
* * * * *
1298 TTTGGACCAAGTGATGCGATTTCCCGAGAATGAAATGCTC-ATAGAATTGCTCG
572 TTTGGACCAAATGATGCAATTTCCCAAGAACGAAATGCTCGA-AAAATTGCTCG
* * * *
1351 AAGGAATCGATCATCTTGAATACTCTAAGGAACCGAAGCTATAAGAGAACTTGAAAAGTTTGACT
1 AAGGAATCGATCATCTTGAATACTTTAAGGAACCGAAGTTATAA-AGAACTAGAAAAGTTTGACA
* ** *
1416 AGTTCTGAAGTTCGGTCAAGAACCAAGACAGAAACGTTTCCCACATAAATAATTTTTTAATCCAT
65 AGTTCTGAAGTTCGGCCAAGAACCAAGA-AGAAACAATTCTCACATAAATAA-TTTTTAATCCA-
* * * ***
1481 AGAGCAAAAGTTGTTTACAAAATAACAGATTATTTGGACCTAATAATGCGATTTCTTAAGAATGG
127 AGACCAAAAGTTGTTTACAAAAT-ACAGATTATTTGGACCAAATGATGCGATTTCCCGAGAATGG
*
1546 AATGTTCAAAAAATTGTTCGAAGAAATTGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAA
191 AATGTTCGAAAAATTGTTCGAAGAAATTGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAA
* * * * * *
1611 AGAACTCGAAAAAGTTTGCAAAGTTT-GGCAGTTCAGCCTAGAATCAAG-G-GTAAAGTAATTCT
256 AGTACTCGAAAAAGTTTGCAAAGTTTGGGAAGTTCAGCCAAGAACCAAGAGAG-AAA-CAATTAT
* ** * ** * * * * *
1673 CATGTAAATAAGTTTTTAATTCAAAGACTGAAAGTTTTTTACAAAAGGATTAGTTATTTGGACC-
319 CACGTAAATAAAATTTTAATCCAAAGACCAAAAGTTGTTTACAAAAAGACTAATTATTTCGACCA
* ** * * * * * * *
1737 AATGATGCGAT-TTCCCAAGAATGGAATGTTCAAAAAATTACGCGAAGGAATCGATCGTCTTGAA
384 AATGATGAGATATTCAGAA-AACGAAATGTTCGAAAAATTGCTCGAATG-A--GACCGTCTTGAA
*** * * * **
1801 TACTTTAAGGAACCGAAA-TTATAAACGTATTCAAAAAAGTTTAACAAGTTCTGAAGTTCGTCCA
445 TACTTTAAGGAACC-AAAGTTATAAAAAAACTCGAAAAAGTTTAACAAGTTCGGAAGTTCAACCA
1865 AGAACCAAG-AGAAACAATTCTCACATAAATAAA
509 AGAA-CAAGAAGAAACAATTCTCACATAAATAAA
Statistics
Matches: 938, Mismatches: 165, Indels: 121
0.77 0.13 0.10
Matches are distributed among these distances:
605 13 0.01
606 87 0.09
607 1 0.00
608 4 0.00
609 47 0.05
610 3 0.00
611 3 0.00
612 1 0.00
616 1 0.00
617 4 0.00
618 1 0.00
619 10 0.01
620 41 0.04
621 173 0.18
622 28 0.03
623 1 0.00
624 66 0.07
625 5 0.01
626 70 0.07
627 5 0.01
628 24 0.03
629 8 0.01
630 225 0.24
631 1 0.00
633 1 0.00
634 3 0.00
635 1 0.00
639 16 0.02
640 5 0.01
641 19 0.02
642 15 0.02
643 53 0.06
644 3 0.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (624 bp):
AAGGAATCGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAGAACTAGAAAAGTTTGACAA
GTTCTGAAGTTCGGCCAAGAACCAAGAAGAAACAATTCTCACATAAATAATTTTTAATCCAAGAC
CAAAAGTTGTTTACAAAATACAGATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGT
TCGAAAAATTGTTCGAAGAAATTGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGTAC
TCGAAAAAGTTTGCAAAGTTTGGGAAGTTCAGCCAAGAACCAAGAGAGAAACAATTATCACGTAA
ATAAAATTTTAATCCAAAGACCAAAAGTTGTTTACAAAAAGACTAATTATTTCGACCAAATGATG
AGATATTCAGAAAACGAAATGTTCGAAAAATTGCTCGAATGAGACCGTCTTGAATACTTTAAGGA
ACCAAAGTTATAAAAAAACTCGAAAAAGTTTAACAAGTTCGGAAGTTCAACCAAGAACAAGAAGA
AACAATTCTCACATAAATAAATTCTTATAGACCAAAAGTGAAATAAGACTATTTGGACCAAATGA
TGCAATTTCCCAAGAACGAAATGCTCGAAAAATTGCTCG
Found at i:1749 original size:215 final size:213
Alignment explanation
Indices: 1273--1896 Score: 627
Period size: 215 Copynumber: 2.9 Consensus size: 213
1263 TCACATAAAT
* ** * * *
1273 AAGTTTTTTACAAAAGGACTAACTATTTGGACCAAGTGATGCGATTTCCCGAGAATGAAATGCTC
1 AAGTTTTTTACAAAAGGAATAGTTATTTGGACCAA-TGATGCGATTTCCCAAGAATGGAATGTTC
* * * * * * *
1338 ATAGAATTGCTCGAAGGAATCGATCATCTTGAATACTCTAAGGAACCGAAGCTATAAGAGAACTT
65 AAAAAATTGCTCGAAGGAATCGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTC
* * *
1403 GAAAAGTTTGACTAGTTCTGAAGTTCGGTCAAGAACCAAGACAGAAACGTTTCCCACATAAATAA
130 GAAAAGTTTGACAAGTTCTGAAGTTCAGCCAAGAACCAAGA-AGAAACGTTTCCCACATAAATAA
* *
1468 TTTTTTAATCCATAGAGCAA
194 GTTTTTAATCCAAAGAGCAA
* * * * **
1488 AAGTTGTTTACAAAA-TAACAGATTATTTGGACCTAATAATGCGATTTCTTAAGAATGGAATGTT
1 AAGTTTTTTACAAAAGGAATAG-TTATTTGGACC-AATGATGCGATTTCCCAAGAATGGAATGTT
* * *
1552 CAAAAAATTGTTCGAAGAAATTGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACT
64 CAAAAAATTGCTCGAAGGAATCGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACT
* * * * * **
1617 CGAAAAAGTTTG-CAAAGTT-TGGCAGTTCAGCCTAGAATCAAG-GGTAAA-GTAATTCTCATGT
129 CG-AAAAGTTTGAC-AAGTTCT-GAAGTTCAGCCAAGAACCAAGAAG-AAACGT--TTCCCACAT
* *
1678 AAATAAGTTTTTAATTCAAAGA-CTGA
188 AAATAAGTTTTTAATCCAAAGAGC-AA
*
1704 AAGTTTTTTACAAAAGGATTAGTTATTTGGACCAATGATGCGATTTCCCAAGAATGGAATGTTCA
1 AAGTTTTTTACAAAAGGAATAGTTATTTGGACCAATGATGCGATTTCCCAAGAATGGAATGTTCA
* * * * * *
1769 AAAAATTACGCGAAGGAATCGATCGTCTTGAATACTTTAAGGAACCGAAA-TTATAAACGTATTC
66 AAAAATTGCTCGAAGGAATCGATCATCTTGAATACTTTAAGGAACC-AAAGTTATAAAAGAACTC
* * ** *
1833 AAAAAAGTTTAACAAGTTCTGAAGTTC-GTCCAAGAACCAAG-AGAAACAATTCTCACATAAATA
130 -GAAAAGTTTGACAAGTTCTGAAGTTCAG-CCAAGAACCAAGAAGAAACGTTTCCCACATAAATA
1896 A
193 A
1897 A
Statistics
Matches: 331, Mismatches: 62, Indels: 34
0.78 0.15 0.08
Matches are distributed among these distances:
213 13 0.04
214 9 0.03
215 219 0.66
216 87 0.26
217 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (213 bp):
AAGTTTTTTACAAAAGGAATAGTTATTTGGACCAATGATGCGATTTCCCAAGAATGGAATGTTCA
AAAAATTGCTCGAAGGAATCGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCG
AAAAGTTTGACAAGTTCTGAAGTTCAGCCAAGAACCAAGAAGAAACGTTTCCCACATAAATAAGT
TTTTAATCCAAAGAGCAA
Done.