Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011154.1 Kokia drynarioides strain JFW-HI SEQ_126128, 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, 870
Length: 1450
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Found at i:428 original size:208 final size:211
Alignment explanation
Indices: 1--459 Score: 572
Period size: 208 Copynumber: 2.2 Consensus size: 211
* * * * * * *
1 TGGACCAAATA-ATGTGATTTCTTGAGCATGGAATGTTCATGAAATTGCTCGAAGGAATGGATTG
1 TGGACCAAA-AGATGCGACTTCTCGAGCATGGAATGCTCAGGAAATTGCTCGAAGGAAAGGATCG
* *
65 CCTTGAATACTTTGAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCGGAAGTT
65 CCTTGAATACTTTAAGGAACCGAAGTTAGAAAAGAACTCGTAAAAGTTTG--AA--TC-GAAGTT
* * *
130 CGTCCAGGAACCAGGAGAGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTT
125 CATCCAAGAACCAAGAGAGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTT
195 GTTTACAAAATGAAAAACAATT
190 GTTTACAAAATGAAAAACAATT
*
217 TGGACCAAAAGATGCGACTTC-CAGAGCATGGAATGCTCGGGAAA-TGTCTCGAAGGAAAGGATC
1 TGGACCAAAAGATGCGACTTCTC-GAGCATGGAATGCTCAGGAAATTG-CTCGAAGGAAAGGATC
* ** * *
280 GCCTTGAATACTTTAAGGAACCGAAGTTAGAAAAGAAGTTTTAAATGTTTG-A-C-AGGTTCATC
64 GCCTTGAATACTTTAAGGAACCGAAGTTAGAAAAGAACTCGTAAAAGTTTGAATCGAAGTTCATC
*
342 CAAGAACCAAGAGAGATACA-ATTCTCACATAAATAAGTTTTTATTTCAAAGACCAAAAGTTGTT
129 CAAGAACCAAGAGAGATA-ATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTT
* *
406 TACAAAATGACAAACTATT
193 TACAAAATGAAAAACAATT
* * *
425 TGGACCAAATGATGCGATTTCTCGAGCATGAAATG
1 TGGACCAAAAGATGCGACTTCTCGAGCATGGAATG
460 TTCAAAAAAT
Statistics
Matches: 214, Mismatches: 24, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
208 113 0.53
209 2 0.01
210 1 0.00
213 1 0.00
215 3 0.01
216 94 0.44
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (211 bp):
TGGACCAAAAGATGCGACTTCTCGAGCATGGAATGCTCAGGAAATTGCTCGAAGGAAAGGATCGC
CTTGAATACTTTAAGGAACCGAAGTTAGAAAAGAACTCGTAAAAGTTTGAATCGAAGTTCATCCA
AGAACCAAGAGAGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAC
AAAATGAAAAACAATT
Found at i:487 original size:61 final size:61
Alignment explanation
Indices: 417--535 Score: 229
Period size: 61 Copynumber: 2.0 Consensus size: 61
407 ACAAAATGAC
417 AAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGAAATGTTCAAAAAATAGCTTAAA
1 AAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGAAATGTTCAAAAAATAGCTTAAA
*
478 AAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGAAATGTTCAGAAAATAGCTT
1 AAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGAAATGTTCAAAAAATAGCTT
536 GAAGGAATGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (61 bp):
AAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGAAATGTTCAAAAAATAGCTTAAA
Found at i:890 original size:208 final size:208
Alignment explanation
Indices: 478--1450 Score: 790
Period size: 208 Copynumber: 4.6 Consensus size: 208
468 ATAGCTTAAA
* * * * *
478 AAACTATTTGGACCAAATGATGCGATTTCTC-GAGCATGAAATGTTCAGAAAATAGCTTGAAGGA
1 AAACTATTTGGACCAAAAGATGCGATTTC-CAGAGCATGGAATGTTCAGGAAAT-TCTCGAAGGA
* * * * * * * *
542 ATGAATCATCTTGAATACTTTGAGGAGCCGAAGCTATAAAAGAACTCGTAAAAGTTTGAAAAGTT
64 ATGGATCGTCTTGAATACTTTAAGGAACCGATGTTACAAAAGAACTCGTAAAAGTTTGACAA---
* * * *
607 TAGATGTTCGTCTAGGAACC-AGAAGAGATA-ATATTCTCACATAAATAAGTTTTAAATTAAAAG
126 T-G--GTTCGTCCAAGAACCAAG-AGAGATACA-ATTCTCACATAAATAAGTTTTTAATTCAAAG
*
670 ACCAAAAGTTGTTTACAAAATGAA
186 ACCAAAAGTTGTTTAC-AAATGAC
* * * * *
694 AAACAATTTGGACCAAAAGATGCGACTTCCAGAGCATGGAATGCTCGGGTAATGTCTCGAAGGAA
1 AAACTATTTGGACCAAAAGATGCGATTTCCAGAGCATGGAATGTTCAGGAAAT-TCTCGAAGGAA
* * * * ** *
759 AGGATCGTCTTAAATACTTTAAGGAACCGATGTTAGAAAAGAAGTTTTAAATGTTTGAC-A-GGT
65 TGGATCGTCTTGAATACTTTAAGGAACCGATGTTACAAAAGAACTCGTAAAAGTTTGACAATGGT
*
822 TCGTCCAAGAACCAAGAGAGATACAATTCTCACATAAATAAGTTTTTAATTCAAATACCAAAAGT
130 TCGTCCAAGAACCAAGAGAGATACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGT
887 TGTTTACAAAATGAC
195 TGTTTAC-AAATGAC
* * * * *
902 AAACTATTCGGTA-CAAATGATGCGATTTCTC-GAGCATGAAATGTTCAGAAAATATCTTGAAGG
1 AAACTATTTGG-ACCAAAAGATGCGATTTC-CAGAGCATGGAATGTTCAGGAAAT-TCTCGAAGG
* * * * * *
965 AATGAATCATCTCGAATACTTTAAGGAACTGAAT-TTATAAATGAACTCGTAAAAGTTTGACAAG
63 AATGGATCGTCTTGAATACTTTAAGGAACCG-ATGTTACAAAAGAACTCGTAAAAGTTTGACAA-
* * * * **
1029 TTGGAAATTTTGTCCAAGAACCAAGAGTA-TTAAAATTCCCAGGTAAATAAGTTTTTAATTCAAA
126 -TGG----TTCGTCCAAGAACCAAGAG-AGATACAATTCTCACATAAATAAGTTTTTAATTCAAA
* * *
1093 TAACAAAATTTGTTTAC-AA-GAC
185 GACCAAAAGTTGTTTACAAATGAC
* * **
1115 AAACTATTTGGACCAAACA-ATGCGATTTATCA-AGCGTGGAATGTTCTTGAAATTGCTCGAAGG
1 AAACTATTTGGACCAAA-AGATGCGATTT-CCAGAGCATGGAATGTTCAGGAAATT-CTCGAAGG
* * * *
1178 AATGGATCGTCTTGAACACTTTAAGGAACCAAAAG-AACAAAAGAACTCGTAAAAGTTTGACTAG
63 AATGGATCGTCTTGAATACTTTAAGGAACC-GATGTTACAAAAGAACTCGTAAAAGTTTGAC-A-
* **
1242 TTCGAAAGTTCGTCCAAGAACCAAGAGAGATACAATTCTCATGTAAATAAGTTTTTAATTCAAAG
125 AT-G---GTTCGTCCAAGAACCAAGAGAGATACAATTCTCACATAAATAAGTTTTTAATTCAAAG
*
1307 ACCAAAAGTTGGTTACAAATGAC
186 ACCAAAAGTTGTTTACAAATGAC
* * * *** ** *
1330 AAACTATTTGGACCAAACGATACGATTTCTC-GAGCATGAAATACCCAAAAAATAGT-TCGAAGA
1 AAACTATTTGGACCAAAAGATGCGATTTC-CAGAGCATGGAATGTTCAGGAAAT--TCTCGAAGG
* * * * * * *
1393 AATTGATCGCCTTGAATATTTTAAGTAACCGAAGTTATAAAAGAACTCGAAAAAGTTT
63 AATGGATCGTCTTGAATACTTTAAGGAACCGATGTTACAAAAGAACTCGTAAAAGTTT
Statistics
Matches: 608, Mismatches: 112, Indels: 75
0.76 0.14 0.09
Matches are distributed among these distances:
208 165 0.27
209 8 0.01
210 1 0.00
212 5 0.01
213 162 0.27
214 9 0.01
215 95 0.16
216 160 0.26
217 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (208 bp):
AAACTATTTGGACCAAAAGATGCGATTTCCAGAGCATGGAATGTTCAGGAAATTCTCGAAGGAAT
GGATCGTCTTGAATACTTTAAGGAACCGATGTTACAAAAGAACTCGTAAAAGTTTGACAATGGTT
CGTCCAAGAACCAAGAGAGATACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTT
GTTTACAAATGAC
Found at i:921 original size:485 final size:485
Alignment explanation
Indices: 1--955 Score: 1626
Period size: 485 Copynumber: 2.0 Consensus size: 485
* * * * * **
1 TGGACCAAATAATGTGATTTCTTGAGCATGGAATGTTCATGAAATTGCTCGAAGGAATGGATTGC
1 TGGACCAAATAATGCGATTTCTCGAGCATGAAATGTTCATGAAATAGCTCGAAGGAATGAATCAC
* *
66 CTTGAATACTTTGAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCGGAAGTTC
66 CTTGAATACTTTGAGGAACCGAAGCTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGAAGTTC
* * *
131 GTCCAGGAACCAGGAGAGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTG
131 GTCCAGGAACCAGAAGAGATAATATTCTCACATAAATAAGTTTTAAATTAAAAGACCAAAAGTTG
196 TTTACAAAATGAAAAACAATTTGGACCAAAAGATGCGACTTCCAGAGCATGGAATGCTCGGGAAA
196 TTTACAAAATGAAAAACAATTTGGACCAAAAGATGCGACTTCCAGAGCATGGAATGCTCGGGAAA
*
261 TGTCTCGAAGGAAAGGATCGCCTTGAATACTTTAAGGAACCGAAGTTAGAAAAGAAGTTTTAAAT
261 TGTCTCGAAGGAAAGGATCGCCTTAAATACTTTAAGGAACCGAAGTTAGAAAAGAAGTTTTAAAT
*
326 GTTTGACAGGTTCATCCAAGAACCAAGAGAGATACAATTCTCACATAAATAAGTTTTTATTTCAA
326 GTTTGACAGGTTCATCCAAGAACCAAGAGAGATACAATTCTCACATAAATAAGTTTTTAATTCAA
*
391 AGACCAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGA
391 AGACCAAAAGTTGTTTACAAAATGACAAACTATTCGGACCAAATGATGCGATTTCTCGAGCATGA
456 AATGTTCAAAAAATAGCTTAAAAAACTATT
456 AATGTTCAAAAAATAGCTTAAAAAACTATT
* *
486 TGGACCAAATGATGCGATTTCTCGAGCATGAAATGTTCA-GAAAATAGCTTGAAGGAATGAATCA
1 TGGACCAAATAATGCGATTTCTCGAGCATGAAATGTTCATG-AAATAGCTCGAAGGAATGAATCA
* * * *
550 TCTTGAATACTTTGAGGAGCCGAAGCTATAAAAGAACTCGTAAAAGTTTGAAAAGTTTAGATGTT
65 CCTTGAATACTTTGAGGAACCGAAGCTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGAAGTT
*
615 CGTCTAGGAACCAGAAGAGATAATATTCTCACATAAATAAGTTTTAAATTAAAAGACCAAAAGTT
130 CGTCCAGGAACCAGAAGAGATAATATTCTCACATAAATAAGTTTTAAATTAAAAGACCAAAAGTT
*
680 GTTTACAAAATGAAAAACAATTTGGACCAAAAGATGCGACTTCCAGAGCATGGAATGCTCGGGTA
195 GTTTACAAAATGAAAAACAATTTGGACCAAAAGATGCGACTTCCAGAGCATGGAATGCTCGGGAA
* *
745 ATGTCTCGAAGGAAAGGATCGTCTTAAATACTTTAAGGAACCGATGTTAGAAAAGAAGTTTTAAA
260 ATGTCTCGAAGGAAAGGATCGCCTTAAATACTTTAAGGAACCGAAGTTAGAAAAGAAGTTTTAAA
*
810 TGTTTGACAGGTTCGTCCAAGAACCAAGAGAGATACAATTCTCACATAAATAAGTTTTTAATTCA
325 TGTTTGACAGGTTCATCCAAGAACCAAGAGAGATACAATTCTCACATAAATAAGTTTTTAATTCA
*
875 AATACCAAAAGTTGTTTACAAAATGACAAACTATTCGGTA-CAAATGATGCGATTTCTCGAGCAT
390 AAGACCAAAAGTTGTTTACAAAATGACAAACTATTCGG-ACCAAATGATGCGATTTCTCGAGCAT
*
939 GAAATGTTCAGAAAATA
454 GAAATGTTCAAAAAATA
956 TCTTGAAGGA
Statistics
Matches: 440, Mismatches: 28, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
484 1 0.00
485 438 1.00
486 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (485 bp):
TGGACCAAATAATGCGATTTCTCGAGCATGAAATGTTCATGAAATAGCTCGAAGGAATGAATCAC
CTTGAATACTTTGAGGAACCGAAGCTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGAAGTTC
GTCCAGGAACCAGAAGAGATAATATTCTCACATAAATAAGTTTTAAATTAAAAGACCAAAAGTTG
TTTACAAAATGAAAAACAATTTGGACCAAAAGATGCGACTTCCAGAGCATGGAATGCTCGGGAAA
TGTCTCGAAGGAAAGGATCGCCTTAAATACTTTAAGGAACCGAAGTTAGAAAAGAAGTTTTAAAT
GTTTGACAGGTTCATCCAAGAACCAAGAGAGATACAATTCTCACATAAATAAGTTTTTAATTCAA
AGACCAAAAGTTGTTTACAAAATGACAAACTATTCGGACCAAATGATGCGATTTCTCGAGCATGA
AATGTTCAAAAAATAGCTTAAAAAACTATT
Found at i:1226 original size:213 final size:215
Alignment explanation
Indices: 478--1371 Score: 793
Period size: 213 Copynumber: 4.2 Consensus size: 215
468 ATAGCTTAAA
* * * * *
478 AAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGAAATGTTCAGAAAATAGCTTGAAGGAA
1 AAACTATTTGGACCAAACGATGCGATTTATCAAGCATGAAATGTTCAGAAAATATCTCGAAGGAA
* * * * * * * *
543 TGAATCATCTTGAATACTTTGAGGAGCC-GAAGCTATAAAAGAACTCGTAAAAGTTTGAAAAGTT
66 TGAATCATCTCGAACACTTTAAGGAACCAAAAG-AACAAAAGAACTCGTAAAAGTTTGACAAGTT
* * * * * * *
607 -TAGATGTTCGTCTAGGAACC-AGAAGAGATA-ATATTCTCACATAAATAAGTTTTAAATTAAAA
130 CGA-AAGTTCGTCCAAGAACCAAG-AGAGATACA-ATTCTCACGTAAATAAGTTTTTAATTCAAA
* *
669 GACCAAAAGTTGTTTACAAAATGAA
192 TACCAAAAGTTGTTTAC-AAATGAC
* * * * * * * ** *
694 AAACAATTTGGACCAAAAGATGCGACTT-CCAGAGCATGGAATGCTCGGGTAATGTCTCGAAGGA
1 AAACTATTTGGACCAAACGATGCGATTTATCA-AGCATGAAATGTTCAGAAAATATCTCGAAGGA
* * * ** * * * * * * ** *
758 AAGGATCGTCTTAAATACTTTAAGGAACC-GATGTTAGAAAAGAAGTTTTAAATGTTTGAC-A--
65 ATGAATCATCTCGAACACTTTAAGGAACCAAAAG-AACAAAAGAACTCGTAAAAGTTTGACAAGT
*
819 --G---GTTCGTCCAAGAACCAAGAGAGATACAATTCTCACATAAATAAGTTTTTAATTCAAATA
129 TCGAAAGTTCGTCCAAGAACCAAGAGAGATACAATTCTCACGTAAATAAGTTTTTAATTCAAATA
879 CCAAAAGTTGTTTACAAAATGAC
194 CCAAAAGTTGTTTAC-AAATGAC
* * * * *
902 AAACTATTCGGTA-CAAATGATGCGATTTCTCGAGCATGAAATGTTCAGAAAATATCTTGAAGGA
1 AAACTATTTGG-ACCAAACGATGCGATTTATCAAGCATGAAATGTTCAGAAAATATCTCGAAGGA
* ** *** * *
966 ATGAATCATCTCGAATACTTTAAGGAACTGAATTTATAAATGAACTCGTAAAAGTTTGACAAGTT
65 ATGAATCATCTCGAACACTTTAAGGAACCAAAAGAACAAAAGAACTCGTAAAAGTTTGACAAGTT
* * * * * * *
1031 GGAAATTTTGTCCAAGAACCAAGAGTA-TTAAAATTCCCAGGTAAATAAGTTTTTAATTCAAATA
130 CGAAAGTTCGTCCAAGAACCAAGAG-AGATACAATTCTCACGTAAATAAGTTTTTAATTCAAATA
* *
1095 ACAAAATTTGTTTAC-AA-GAC
194 CCAAAAGTTGTTTACAAATGAC
* * * *
1115 AAACTATTTGGACCAAACAATGCGATTTATCAAGCGTGGAATGTTCTTG-AAAT-TGCTCGAAGG
1 AAACTATTTGGACCAAACGATGCGATTTATCAAGCATGAAATGTTC-AGAAAATAT-CTCGAAGG
* * * *
1178 AATGGATCGTCTTGAACACTTTAAGGAACCAAAAGAACAAAAGAACTCGTAAAAGTTTGACTAGT
64 AATGAATCATCTCGAACACTTTAAGGAACCAAAAGAACAAAAGAACTCGTAAAAGTTTGACAAGT
* *
1243 TCGAAAGTTCGTCCAAGAACCAAGAGAGATACAATTCTCATGTAAATAAGTTTTTAATTCAAAGA
129 TCGAAAGTTCGTCCAAGAACCAAGAGAGATACAATTCTCACGTAAATAAGTTTTTAATTCAAATA
*
1308 CCAAAAGTTGGTTACAAATGAC
194 CCAAAAGTTGTTTACAAATGAC
* * *
1330 AAACTATTTGGACCAAACGATACGATTTCTCGAGCATGAAAT
1 AAACTATTTGGACCAAACGATGCGATTTATCAAGCATGAAAT
1372 ACCCAAAAAA
Statistics
Matches: 549, Mismatches: 108, Indels: 43
0.78 0.15 0.06
Matches are distributed among these distances:
208 161 0.29
209 8 0.01
212 3 0.01
213 172 0.31
214 5 0.01
215 41 0.07
216 158 0.29
217 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (215 bp):
AAACTATTTGGACCAAACGATGCGATTTATCAAGCATGAAATGTTCAGAAAATATCTCGAAGGAA
TGAATCATCTCGAACACTTTAAGGAACCAAAAGAACAAAAGAACTCGTAAAAGTTTGACAAGTTC
GAAAGTTCGTCCAAGAACCAAGAGAGATACAATTCTCACGTAAATAAGTTTTTAATTCAAATACC
AAAAGTTGTTTACAAATGAC
Done.