Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008524.1 Kokia drynarioides strain JFW-HI SEQ_123201, 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, 831
Length: 1385
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Found at i:481 original size:215 final size:214
Alignment explanation
Indices: 3--1377 Score: 1316
Period size: 215 Copynumber: 6.5 Consensus size: 214
1 GG
* * * *
3 AATAAGTTTTTAATGCAAAGACCAAAACTTTTTTACAAAGTGACAAACAATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAAACCAAAAC-TTTTTACAAAATGACAAACTATTTAGACCAAATGAT
** * * ** * *
68 ATGATTTC-CTGAGCATGGAATGTTTAGAATATTGCTCGAATTAAAGGATCGTCATGAATACTTT
65 GCGATTTCTC-GAGCATGGAATGTTTA-AAAATTGCTAGAAGGAATGGATCGTCTTGAATACTTT
** * * * * *
132 TTGGAATCGAAGTTAT-AAAGAACTCGTAAAAGTTGGAAAAGTTCGGAAGTTCGTCCAAGAACCA
128 AAGGAACCAAAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCA
*
196 AGACA-AAA-AATTCTCACGTA
193 AGAGAGAAACAATTCTCACGTA
* *
216 AATAAGTTTTTAATTCAAACAA-CGAAACTTTTTTTACAAAATGACAAACTATTTAGACTAAATG
1 AATAAGTTTTTAATTCAAA-AACCAAAAC--TTTTTACAAAATGACAAACTATTTAGACCAAATG
* * * * * *
280 ATGTGATATCTCGAGCATAGAATGTTTGAAAAATTACTAGAAGGAATGAATCGTCTTGATTACTT
63 ATGCGATTTCTCGAGCATGGAATGTTT-AAAAATTGCTAGAAGGAATGGATCGTCTTGAATACTT
345 TAAGGAACCAAAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACC
127 TAAGGAACCAAAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACC
*
410 AAGAGAGAAACAATTCTCACTTA
192 AAGAGAGAAACAATTCTCACGTA
* * *
433 AATAAGTTTTTAATTCAAACAACCAAACCTTTTTACAAAATG-CAAACTATTTAAAACAAATGAT
1 AATAAGTTTTTAATTCAAA-AACCAAAACTTTTTACAAAATGACAAACTATTTAGACCAAATGAT
* * ** * * * *
497 GCGATTTCCCGAGCATGGAAAGTTCGGAAAATTGCTCA-AAGGAATGGATCATCTAGAACACTGT
65 GCGATTTCTCGAGCATGGAATGTT-TAAAAATTGCT-AGAAGGAATGGATCGTCTTGAATACTTT
* * * * * * *
561 ATGGAA-CAGAAATTATAAAAGAACTCGTAAAATTTTGACAAGTTGGGAAGTTCATCCAAGAACC
128 AAGGAACCA-AAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACC
625 AA-ATGAGAAACAATTCTCACGTA
192 AAGA-GAGAAACAATTCTCACGTA
* *
648 AATAAGTATTTAATTCAAAAACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAAACCAAAACTT-TTTACAAAATGACAAACTATTTAGACCAAATGAT
* * *
713 GCGATTTCTCGAGCATGGAATGTTCAAAAAATTGCT----CGAA--G---GTCTTGAATACTCTA
65 GCGATTTCTCGAGCATGGAATGTT-TAAAAATTGCTAGAAGGAATGGATCGTCTTGAATACTTTA
* * * * * * *
769 AGAAACCGAAGTTATAAAAGAACTCGTAAGAGTTTGAAAAGTTCGAAAGTTCGTCAAAAAACCAA
129 AGGAACCAAAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAA
*
834 GAGAGAAACGATTCTCACGT-
194 GAGAGAAACAATTCTCACGTA
* * * * * * ** * *
854 AATAAGTGTTTAATCCAAAGACAAAAAATTATTTACATAATGACGCACTATTTATACAAAATGAT
1 AATAAGTTTTTAATTCAAAAACCAAAACTT-TTTACAAAATGACAAACTATTTAGACCAAATGAT
* * * * * *
919 GCCATTTCCCGAGCATGTAATGTTTAGAAAATTGCTTGAAGGAATGGATCATCTTGAATACTGTA
65 GCGATTTCTCGAGCATGGAATGTTTA-AAAATTGCTAGAAGGAATGGATCGTCTTGAATACTTTA
* * *
984 AGGAACCGAAGTTATTG-AAGAACTCGTAAAAGTTTGACAAGTTTGAAGGTTCGTCCAAGAACC-
129 AGGAACCAAAGTTA-TGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCA
1047 A-AGAGAAACAATTCTCACG-A
193 AGAGAGAAACAATTCTCACGTA
* * * * * * *
1067 AATAAGTTTTTGATTCAAAGACCAAAACTTGTTCCAAAATGA-AGAACTATTTTGATCAAATGTT
1 AATAAGTTTTTAATTCAAAAACCAAAACTTTTTACAAAATGACA-AACTATTTAGACCAAATGAT
* * * * * *
1131 GCTATTTC-C---C---GAA-----AAAAGTTGCTCGAAGGAATGGGTAGTTTTGAATACTTTAA
65 GCGATTTCTCGAGCATGGAATGTTTAAAAATTGCTAGAAGGAATGGATCGTCTTGAATACTTTAA
* * * *
1184 GGAACCAAACTTGTGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGGCCAAGAACAAAA
130 GGAACCAAAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAAC--CA
* *
1249 ATAGAGAAACAATTCTCTCGTA
193 AGAGAGAAACAATTCTCACGTA
*
1271 AATAAGTTTTTAATTCAAATAA-CAAAACTATTTTACAAAATTACAAACTATTTAGACCAAATGA
1 AATAAGTTTTTAATTCAAA-AACCAAAACT-TTTTACAAAATGACAAACTATTTAGACCAAATGA
** * * *
1335 CACGATTTC-CTGAGCA-CGAACTGTTCGAAAAAATGCTAGAAGG
64 TGCGATTTCTC-GAGCATGGAA-TGTT-TAAAAATTGCTAGAAGG
1378 TGTGGATC
Statistics
Matches: 957, Mismatches: 154, Indels: 97
0.79 0.13 0.08
Matches are distributed among these distances:
198 2 0.00
199 84 0.09
200 1 0.00
202 1 0.00
203 17 0.02
204 26 0.03
205 37 0.04
206 85 0.09
207 79 0.08
208 3 0.00
209 1 0.00
210 4 0.00
211 4 0.00
212 34 0.04
213 65 0.07
214 108 0.11
215 286 0.30
216 70 0.07
217 33 0.03
218 17 0.02
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (214 bp):
AATAAGTTTTTAATTCAAAAACCAAAACTTTTTACAAAATGACAAACTATTTAGACCAAATGATG
CGATTTCTCGAGCATGGAATGTTTAAAAATTGCTAGAAGGAATGGATCGTCTTGAATACTTTAAG
GAACCAAAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGA
GAGAAACAATTCTCACGTA
Found at i:842 original size:422 final size:417
Alignment explanation
Indices: 3--1350 Score: 1421
Period size: 422 Copynumber: 3.2 Consensus size: 417
1 GG
* * * * * *
3 AATAAGTTTTTAATGCAAAGACCAAAACTTTTTTACAAAGTGACAAACAATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAAACCAAAAC-TTTTTACAAAATGACAAACTATTTAAAACAAATGAT
* * * ** * * *
68 ATGATTTCCTGAGCATGGAATGTTTAGAATATTGCTCGAATTAAAGGATCGTC-ATGAATACTTT
65 ACGATTTCCCGAGCATGGAATGTTTAGAAAATTGCTCGAAGGAATGGATCATCTA-GAATACTGT
* * *
132 TTGGAATCGAAGTTATAAAGAACTCGTAAAAGTTGGAAAAGTTCGGAAGTTCGTCCAAGAACCAA
129 ATGGAA-CGAAGTTATAAAGAACTCGTAAAAGTTTGACAAGTT-GGAAGTTCGTCCAAGAACCAA
* * * *
197 GACAAAAAATTCTCACGTAAATAAGTTTTTAATTCAAACAA-CGAAACTTTTTTTACAAAATGAC
192 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA-AACCAAAAC-TTGTTTACAAAATGAC
* * * ** *
261 AAACTATTTAGACTAAATGATGTGATATCTCGAGCATAGAATGTTTGAAAAATTACTAGAAGGAA
255 AAACTATTTAGACCAAATGATGCGATTTCTCGAGCATAGAATGTTCAAAAAATTGCT----GGAA
*
326 TGAATCGTCTTGATTACTTTAAGGAACCAAAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTC
316 -G----GTCTTGAATACTTTAAGGAACCAAAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTC
* * *
391 GAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACTTA
376 GAAAGTTCGTCAAAAAACCAAGAGAGAAACAATTCTCACGTA
*
433 AATAAGTTTTTAATTCAAACAACCAAACCTTTTTACAAAATG-CAAACTATTTAAAACAAATGAT
1 AATAAGTTTTTAATTCAAA-AACCAAAACTTTTTACAAAATGACAAACTATTTAAAACAAATGAT
* * ** * *
497 GCGATTTCCCGAGCATGGAAAGTTCGGAAAATTGCTCAAAGGAATGGATCATCTAGAACACTGTA
65 ACGATTTCCCGAGCATGGAATGTTTAGAAAATTGCTCGAAGGAATGGATCATCTAGAATACTGTA
* * *
562 TGGAACAGAAATTATAAAAGAACTCGTAAAATTTTGACAAGTTGGGAAGTTCATCCAAGAACCAA
130 TGGAAC-GAAGTTAT-AAAGAACTCGTAAAAGTTTGACAAGTT-GGAAGTTCGTCCAAGAACC-A
* *
627 ATGAGAAACAATTCTCACGTAAATAAGTATTTAATTCAAAAACCAAAAGTTGTTTACAAAATGAC
191 A-GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACCAAAACTTGTTTACAAAATGAC
* *
692 AAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCAAAAAATTGCTCGAAGGTC
255 AAACTATTTAGACCAAATGATGCGATTTCTCGAGCATAGAATGTTCAAAAAATTGCTGGAAGGTC
* * * * * *
757 TTGAATACTCTAAGAAACCGAAGTTATAAAAGAACTCGTAAGAGTTTGAAAAGTTCGAAAGTTCG
320 TTGAATACTTTAAGGAACCAAAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCG
*
822 TCAAAAAACCAAGAGAGAAACGATTCTCACGT-
385 TCAAAAAACCAAGAGAGAAACAATTCTCACGTA
* * * * * * ** *
854 AATAAGTGTTTAATCCAAAGACAAAAAATTATTTACATAATGACGCACTATTT-ATACAAAATGA
1 AATAAGTTTTTAATTCAAAAACCAAAACTT-TTTACAAAATGACAAACTATTTAAAAC-AAATGA
* * * * *
918 TGCCATTTCCCGAGCATGTAATGTTTAGAAAATTGCTTGAAGGAATGGATCATCTTGAATACTGT
64 TACGATTTCCCGAGCATGGAATGTTTAGAAAATTGCTCGAAGGAATGGATCATCTAGAATACTGT
* * *
983 AAGGAACCGAAGTTATTGAAGAACTCGTAAAAGTTTGACAAGTTTGAAGGTTCGTCCAAGAACCA
129 ATGGAA-CGAAGTTA-TAAAGAACTCGTAAAAGTTTGACAAGTTGGAA-GTTCGTCCAAGAACCA
* * *
1048 AGAGAAACAATTCTCACG-AAATAAGTTTTTGATTCAAAGACCAAAACTTG-TTCCAAAATGA-A
191 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACCAAAACTTGTTTACAAAATGACA
* * * * * ** * * * ** *
1110 GAACTATTTTGATCAAATGTTGCTATTTCCCGAAAAAAG-TTGCTCGAAGGAA-TG--GGTA-GT
256 -AACTATTTAGACCAAATGATGCGATTTCTCGAGCATAGAATGTTC-AAAAAATTGCTGGAAGGT
* * *
1170 TTTGAATACTTTAAGGAACCAAACTTGTGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTC
319 CTTGAATACTTTAAGGAACCAAAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTC
* * * *
1235 GGCCAAGAACAA-AAATAGAGAAACAATTCTCTCGTA
384 -GTCAA-AA-AACCAAGAGAGAAACAATTCTCACGTA
* * *
1271 AATAAGTTTTTAATTCAAATAA-CAAAACTATTTTACAAAATTACAAACTATTTAGACCAAATGA
1 AATAAGTTTTTAATTCAAA-AACCAAAACT-TTTTACAAAATGACAAACTATTTAAAACAAATGA
* *
1335 CACGATTTCCTGAGCA
64 TACGATTTCCCGAGCA
1351 CGAACTGTTC
Statistics
Matches: 768, Mismatches: 128, Indels: 57
0.81 0.13 0.06
Matches are distributed among these distances:
414 58 0.08
415 6 0.01
416 21 0.03
417 67 0.09
418 46 0.06
419 28 0.04
420 24 0.03
421 35 0.05
422 209 0.27
423 2 0.00
426 1 0.00
427 3 0.00
428 1 0.00
429 79 0.10
430 73 0.10
431 76 0.10
432 39 0.05
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (417 bp):
AATAAGTTTTTAATTCAAAAACCAAAACTTTTTACAAAATGACAAACTATTTAAAACAAATGATA
CGATTTCCCGAGCATGGAATGTTTAGAAAATTGCTCGAAGGAATGGATCATCTAGAATACTGTAT
GGAACGAAGTTATAAAGAACTCGTAAAAGTTTGACAAGTTGGAAGTTCGTCCAAGAACCAAGAGA
AACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACCAAAACTTGTTTACAAAATGACAAACTA
TTTAGACCAAATGATGCGATTTCTCGAGCATAGAATGTTCAAAAAATTGCTGGAAGGTCTTGAAT
ACTTTAAGGAACCAAAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCAAAA
AACCAAGAGAGAAACAATTCTCACGTA
Found at i:1332 original size:21 final size:21
Alignment explanation
Indices: 1286--1332 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1276 GTTTTTAATT
*
1286 CAAATAACAAAACTATTTTAC
1 CAAATAACAAAACTATTTGAC
* *
1307 AAAATTAC-AAACTATTTAGAC
1 CAAATAACAAAACTATTT-GAC
1328 CAAAT
1 CAAAT
1333 GACACGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (21 bp):
CAAATAACAAAACTATTTGAC
Done.