Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010759.1 Kokia drynarioides strain JFW-HI SEQ_125718, 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, 796
Length: 1327
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.26
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1051 original size:215 final size:216
Alignment explanation
Indices: 271--1327 Score: 1302
Period size: 215 Copynumber: 5.0 Consensus size: 216
261 NNNNNNNTAT
* * * * *
271 GACAAAGACCAAGAGAGAAACAATTCTCACGTAAAAAAGATTTTAATTCAGAGACTACAAGTTGT
1 GACAAAGACCAAGAGAGTAACAATTCTCACGTAAAAAAGATTTTAATTCAAAGACCAAAAATTGT
* *
336 TTACAAAATGACAAATTATTTTGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAAAAT
66 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAAAAT
401 TGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAG
131 TGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAG
* *
466 TTTGACTAGTTCGAAAGATCG
196 TTTGACTAGTTCGAAAGTTAG
* * * * *
487 G-CCAAGAACCAAGAGAGTAACTATTCTGAC-TTAATAAG-TTTATAATTCAAAGACCAAAAATT
1 GACAAAG-ACCAAGAGAGTAACAATTCTCACGTAAAAAAGATTT-TAATTCAAAGACCAAAAATT
* * * * * *
549 GTTTACGAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAA
64 GTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAAA
* * * * * ** * *
614 GTTGCTCAAAGGAATGGATCGTCCTGAATAC-TTAGAATAATCGAAGTTGTAAAAGAACTCGTAA
129 ATTGTTCGAAGGAATGGATAGTCTTGAATACTTTA-AGGAACCGAAGTTATAAAAGAACTCGTAA
*
678 AAGTTT-A--A----G-AAGTTAT
193 AAGTTTGACTAGTTCGAAAGTTAG
* ** * *
694 GACAAAGACCAAGAGAGAAACAATTCTCACGTAAAAAAGATTTTAATTCAAAGAGTACAAGTTGT
1 GACAAAGACCAAGAGAGTAACAATTCTCACGTAAAAAAGATTTTAATTCAAAGACCAAAAATTGT
*
759 TTACAAAATGACAAACTATTTTGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAAAAT
66 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAAAAT
*
824 TGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAA
131 TGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAG
*
889 TTTGACTAGTTCGAAAGTTCG
196 TTTGACTAGTTCGAAAGTTAG
* * * * * *
910 G-CCAAGAACCAAGAGAGTAACGATTCTGAC-TTAATAAG-TTTATATTTCAAAGACCAAAAATT
1 GACAAAG-ACCAAGAGAGTAACAATTCTCACGTAAAAAAGATTT-TAATTCAAAGACCAAAAATT
** * * * * *
972 GTTTACGCAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGATCGGAAA
64 GTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAAA
* * * * ** * *
1037 GTTGCTCAAAGGAATGGATCGTCTTGAATAC-TTAGAATAATCGAAGTTGTAAAAGAACTCGTAA
129 ATTGTTCGAAGGAATGGATAGTCTTGAATACTTTA-AGGAACCGAAGTTATAAAAGAACTCGTAA
*
1101 AAGTTT-A--A----G-AAGTTAT
193 AAGTTTGACTAGTTCGAAAGTTAG
* * * *
1117 GACAAAGACCAAGAGA--AACAATTCTCACGTAAAAAAGATTTTAATTCAGAGACTACAAGTTGT
1 GACAAAGACCAAGAGAGTAACAATTCTCACGTAAAAAAGATTTTAATTCAAAGACCAAAAATTGT
1180 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAAAAT
66 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAAAAT
1245 TGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAG
131 TGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAG
1310 TTTGACTAGTTCGAAAGT
196 TTTGACTAGTTCGAAAGT
Statistics
Matches: 697, Mismatches: 114, Indels: 62
0.80 0.13 0.07
Matches are distributed among these distances:
205 10 0.01
206 137 0.20
207 47 0.07
208 146 0.21
209 8 0.01
211 1 0.00
212 2 0.00
213 1 0.00
214 18 0.03
215 280 0.40
216 47 0.07
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (216 bp):
GACAAAGACCAAGAGAGTAACAATTCTCACGTAAAAAAGATTTTAATTCAAAGACCAAAAATTGT
TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAAAAT
TGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAG
TTTGACTAGTTCGAAAGTTAG
Found at i:1054 original size:423 final size:423
Alignment explanation
Indices: 268--1327 Score: 1998
Period size: 423 Copynumber: 2.5 Consensus size: 423
258 NNNNNNNNNN
268 TATGACAAAGACCAAGAGAGAAACAATTCTCACGTAAAAAAGATTTTAATTCAGAGACTACAAGT
1 TATGACAAAGACCAAGAGAGAAACAATTCTCACGTAAAAAAGATTTTAATTCAGAGACTACAAGT
*
333 TGTTTACAAAATGACAAATTATTTTGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAA
66 TGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAA
398 AATTGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
131 AATTGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
* *
463 AAGTTTGACTAGTTCGAAAGATCGGCCAAGAACCAAGAGAGTAACTATTCTGACTTAATAAGTTT
196 AAGTTTGACTAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGTAACGATTCTGACTTAATAAGTTT
528 ATAATTCAAAGACCAAAAATTGTTTACGAAATGAAAAACTATTTAGACCAAATGATGCGATTTCC
261 ATAATTCAAAGACCAAAAATTGTTTACGAAATGAAAAACTATTTAGACCAAATGATGCGATTTCC
* *
593 CGAGCATGGAATGTTTGGAAAGTTGCTCAAAGGAATGGATCGTCCTGAATACTTAGAATAATCGA
326 CGAGCATGGAATGATCGGAAAGTTGCTCAAAGGAATGGATCGTCCTGAATACTTAGAATAATCGA
658 AGTTGTAAAAGAACTCGTAAAAGTTTAAGAAGT
391 AGTTGTAAAAGAACTCGTAAAAGTTTAAGAAGT
* *
691 TATGACAAAGACCAAGAGAGAAACAATTCTCACGTAAAAAAGATTTTAATTCAAAGAGTACAAGT
1 TATGACAAAGACCAAGAGAGAAACAATTCTCACGTAAAAAAGATTTTAATTCAGAGACTACAAGT
756 TGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAA
66 TGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAA
821 AATTGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
131 AATTGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
*
886 AAATTTGACTAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGTAACGATTCTGACTTAATAAGTTT
196 AAGTTTGACTAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGTAACGATTCTGACTTAATAAGTTT
* *
951 ATATTTCAAAGACCAAAAATTGTTTACGCAATGAAAAACTATTTAGACCAAATGATGCGATTTCC
261 ATAATTCAAAGACCAAAAATTGTTTACGAAATGAAAAACTATTTAGACCAAATGATGCGATTTCC
*
1016 CGAGCATGGAATGATCGGAAAGTTGCTCAAAGGAATGGATCGTCTTGAATACTTAGAATAATCGA
326 CGAGCATGGAATGATCGGAAAGTTGCTCAAAGGAATGGATCGTCCTGAATACTTAGAATAATCGA
1081 AGTTGTAAAAGAACTCGTAAAAGTTTAAGAAGT
391 AGTTGTAAAAGAACTCGTAAAAGTTTAAGAAGT
1114 TATGACAAAGACC-A-AGAGAAACAATTCTCACGTAAAAAAGATTTTAATTCAGAGACTACAAGT
1 TATGACAAAGACCAAGAGAGAAACAATTCTCACGTAAAAAAGATTTTAATTCAGAGACTACAAGT
*
1177 TGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAA
66 TGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAA
1242 AATTGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
131 AATTGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
1307 AAGTTTGACTAGTTCGAAAGT
196 AAGTTTGACTAGTTCGAAAGT
Statistics
Matches: 622, Mismatches: 15, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
421 196 0.32
422 1 0.00
423 425 0.68
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (423 bp):
TATGACAAAGACCAAGAGAGAAACAATTCTCACGTAAAAAAGATTTTAATTCAGAGACTACAAGT
TGTTTACAAAATGACAAACTATTTTGACCAAATGATGCGATTTCCCGAGAAAGGAATGTTCGAAA
AATTGTTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
AAGTTTGACTAGTTCGAAAGTTCGGCCAAGAACCAAGAGAGTAACGATTCTGACTTAATAAGTTT
ATAATTCAAAGACCAAAAATTGTTTACGAAATGAAAAACTATTTAGACCAAATGATGCGATTTCC
CGAGCATGGAATGATCGGAAAGTTGCTCAAAGGAATGGATCGTCCTGAATACTTAGAATAATCGA
AGTTGTAAAAGAACTCGTAAAAGTTTAAGAAGT
Done.