Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001976.1 Kokia drynarioides strain JFW-HI SEQ_113822, 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, 889
Length: 1483
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Found at i:394 original size:216 final size:216
Alignment explanation
Indices: 1--447 Score: 623
Period size: 216 Copynumber: 2.1 Consensus size: 216
* *
1 TTCTCACGTAAATAAGTTTTTAATTCAAAGTGCAAAACTTGTTTACAAAATGACAAATTATTTAG
1 TTCTCACGTAAATAAGTTTTTAATTCAAAGTACAAAACTTGTTTACAAAATGACAAACTATTTAG
** * * ** * *
66 ACCAAATGATGCGATTTCCTGAGCATGGAATGTTCGAGAAATTGCTCTAAGGAATGGATCGTGTT
66 ACCAAATGATGCGATTTCCCAAGCACGAAAAATTCGAAAAATTGCTCAAAGGAATGGATCGTGTT
*
131 GAATACTTTAGGGAAACGAAGTTAAAAAATAACATGTAAAAGTTTGACAAGTTCGAAAGTTCGTA
131 GAATACTTTAGGGAAACGAAGTTAAAAAATAACATGTAAAAGTTTGACAAGTTCGAAAGTTCATA
196 CAA-AGGAAAAGAGAGAAACAA
196 CAACA-GAAAAGAGAGAAACAA
* *
217 TTCTCACGTAAATAAGTTTTTAATTCAAAG-ACAAAAACTTGTTTACAAAATGAGAAACTATTTT
1 TTCTCACGTAAATAAGTTTTTAATTCAAAGTAC-AAAACTTGTTTACAAAATGACAAACTATTTA
* *
281 GACCAAATGATGCGATTTCCCAAGTACGAAAAATTCGAAAAATTGCTCAAAGGAATGGATCTTGT
65 GACCAAATGATGCGATTTCCCAAGCACGAAAAATTCGAAAAATTGCTCAAAGGAATGGATCGTGT
* * * *
346 TGAATAGTTTAGGG-AACTGAAGTTAAAGAATAAC-TCGTGAATGTTTGACAAGTTCGAAAGTTC
130 TGAATACTTTAGGGAAAC-GAAGTTAAAAAATAACAT-GTAAAAGTTTGACAAGTTCGAAAGTTC
* * *
409 ATCCAACAGCAAAGAGATAAACAA
193 ATACAACAGAAAAGAGAGAAACAA
*
433 TTCTTACGTAAATAA
1 TTCTCACGTAAATAA
448 CTCATAAAAG
Statistics
Matches: 204, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
215 5 0.02
216 198 0.97
217 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (216 bp):
TTCTCACGTAAATAAGTTTTTAATTCAAAGTACAAAACTTGTTTACAAAATGACAAACTATTTAG
ACCAAATGATGCGATTTCCCAAGCACGAAAAATTCGAAAAATTGCTCAAAGGAATGGATCGTGTT
GAATACTTTAGGGAAACGAAGTTAAAAAATAACATGTAAAAGTTTGACAAGTTCGAAAGTTCATA
CAACAGAAAAGAGAGAAACAA
Found at i:679 original size:285 final size:285
Alignment explanation
Indices: 167--732 Score: 692
Period size: 285 Copynumber: 2.0 Consensus size: 285
157 AAATAACATG
*
167 TAAAAGTTTGACAAGTTCGAAAGTTCGTACAAAGGAAAAGAGAGAAACAATTCTCACGTAAATAA
1 TAAAAGTTTGACAAGTACGAAAGTTCGTACAAAGGAAAAGAGAGAAACAATTCTCACGTAAATAA
* * *
232 GTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGAGAAACTATTTTGACCAAATGATGCGAT
66 GTTTTTAATTCAAAGACAAAAACCTGTTTACAAAATGACAAACTACTTTGACCAAATGATGCGAT
* * * * * * *
297 TTCCCAAGTACGAAAAATTCGAAAAATTGCTCAAAGGAATGGATCTTGTTGAATAGTTTAGGGAA
131 CTCCCAAGCACGAAAAATTCGAAAAATTGCTCAAAGGAATCGATCGTCTTGAATACTTTAGAGAA
** * * * * * *
362 CTGAAGTTAAAGAATAACTCGTGAATGTTTGACAAGTTC-GAAAGTTCATCCAACAGCAAAGAGA
196 CCAAAGTTAAAGAAGAACTAGTAAAAGTTTGACAAGCTCAG-AAGTTCATCCAACAACAAAGAGA
* *
426 TAAACAATTCTTACGTAAATAACTCA
260 GAAACAATTCTTACATAAATAACTCA
* * * * *
452 TAAAAGTTTGACAAGTACGAAAGTTTGTATAGA-GACAAAGAGAGAAGCAATTGTCACGTAAATA
1 TAAAAGTTTGACAAGTACGAAAGTTCGTACAAAGGA-AAAGAGAGAAACAATTCTCACGTAAATA
* *
516 AGTTTTTAATTCAAAGACCAAAACCTGTTTGCAAAATGACAAACTACTTTGACCAAATGATGCGA
65 AGTTTTTAATTCAAAGACAAAAACCTGTTTACAAAATGACAAACTACTTTGACCAAATGATGCGA
* * * ** *
581 TCTGCCGAGCATGAAATGTTCGAAAAGTTGCTCGAAA-GAATCGATCGTCTTGAATACTTT-GAG
130 TCTCCCAAGCACGAAAAATTCGAAAAATTGCTC-AAAGGAATCGATCGTCTTGAATACTTTAGAG
* * * * *
644 AATCCAAAGTTATCA-AAGGACTAGTAAAAGTTTGACAAGCTCAGAAGTTCGTCCAAGAACAGAG
194 AA-CCAAAGTTA-AAGAAGAACTAGTAAAAGTTTGACAAGCTCAGAAGTTCATCCAACAACAAAG
*
708 GGAGAAACAATTCTTACATAAATAA
257 AGAGAAACAATTCTTACATAAATAA
733 GTTCTTAATT
Statistics
Matches: 236, Mismatches: 40, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
284 6 0.03
285 225 0.95
286 5 0.02
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (285 bp):
TAAAAGTTTGACAAGTACGAAAGTTCGTACAAAGGAAAAGAGAGAAACAATTCTCACGTAAATAA
GTTTTTAATTCAAAGACAAAAACCTGTTTACAAAATGACAAACTACTTTGACCAAATGATGCGAT
CTCCCAAGCACGAAAAATTCGAAAAATTGCTCAAAGGAATCGATCGTCTTGAATACTTTAGAGAA
CCAAAGTTAAAGAAGAACTAGTAAAAGTTTGACAAGCTCAGAAGTTCATCCAACAACAAAGAGAG
AAACAATTCTTACATAAATAACTCA
Found at i:892 original size:213 final size:215
Alignment explanation
Indices: 486--1439 Score: 999
Period size: 213 Copynumber: 4.4 Consensus size: 215
476 TTGTATAGAG
* * * * * *
486 ACAAAGAGAGAAGCAATTGTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACCTGTTTGCAAA
1 ACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGTCCAAAACTTGTTTACAAA
* * *
551 ATGACAAACTACTTTGACCAAATGATGCGATCTGCCGAGCATGAAATGTTCGAAAAGTTGCTCGA
66 ATGAC-AACTACTTTGACCAAATGATGCGATCTCCCGAGCATGAAATGTTCGAAAAATTGCTCTA
* * ** *
616 AAGAATCGATCGTCTTGAATACTTTGA-GAATCCAAAGTTATCAAAGGACTAGTAAAAGTTTGAC
130 AAGAATGGATCGTCTTGAATACTTTAAGGAA-CCAAAGTTAAAAAAGAACTAGTAAAAGTTTGAC
*
680 AAGCTCAGAAGTTCGTCCAAGA
194 AAGCTCAGAAGTTCGTCCAAAA
* * * * *
702 ACAGAGGGAGAAACAATTCTTACATAAATAAGTTCTTAATTCAAAGTTCAAAACTTGTTTACAAA
1 ACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGTCCAAAACTTGTTTACAAA
* * * * * *
767 ATGAC-A-TATTTTGATCAATTGATGCGCTTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAA
66 ATGACAACTACTTTGACCAAATGATGCGATCTCCCGAGCATGAAATGTTCGAAAAATTGCTCTAA
* ** * * * * * *
830 GGAATGGATTTTGTTGAATGCTTTAAGGAACCAAAGTTAAAAAATAACTTGTAGAAGTTTGACCA
131 AGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAAAAAAGAACTAGTAAAAGTTTGACAA
* ** *
895 GTTTGGATGTTCGTCCAAAA
196 GCTCAGAAGTTCGTCCAAAA
** * *
915 ACAAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAA-TACCAAAACCTGTTTGCAA
1 ACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGT-CCAAAACTTGTTTACAA
*
979 AATGACAAACTACTTTGACCAAATGATGCGATCTGCCGAGCATGAAATGTTCGAAAAATTGCT-T
65 AATGAC-AACTACTTTGACCAAATGATGCGATCTCCCGAGCATGAAATGTTCGAAAAATTGCTCT
* * * **
1043 GAAAGAATGGATCGTCTTGAATACTTTGAGGATCCGAAGTTATCAAAGAACTAGTAAAAGTTTGA
129 -AAAGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAAAAAAGAACTAGTAAAAGTTTGA
* **
1108 GAAGCTCAGAAGTTCGTCCAAGT
193 CAAGCTCAGAAGTTCGTCCAAAA
* * * *
1131 ACAGAGGGAGAAACAATTCTCACATAAATAAGTTCTTAATTCAAAGTTCAAAACTTGTTTACAAA
1 ACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGTCCAAAACTTGTTTACAAA
* * * * * * * *
1196 ATAAC-A-TATTTTGATCGATTGATGCGCTTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAA
66 ATGACAACTACTTTGACCAAATGATGCGATCTCCCGAGCATGAAATGTTCGAAAAATTGCTCTAA
* ** * * * * * ** *
1259 GGAATGGATTTTATTGAATGCTTTAGGGAACCAAAGTTAAAAAATAACTTGTAGTAGTTTGACCA
131 AGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAAAAAAGAACTAGTAAAAGTTTGACAA
* ** *
1324 GTTTGGATGTTCGTCCAAAA
196 GCTCAGAAGTTCGTCCAAAA
* * * * *
1344 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATACAACGACCAAAACTCGTTTACAAA
1 ACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGTCCAAAACTTGTTTACAAA
* *
1409 ACGA-AAATA-TATTCAGACCAAATGATGCGAT
66 ATGACAACTACT-TT--GACCAAATGATGCGAT
1440 TTCTTGAGCA
Statistics
Matches: 594, Mismatches: 131, Indels: 26
0.79 0.17 0.03
Matches are distributed among these distances:
212 1 0.00
213 338 0.57
214 10 0.02
215 2 0.00
216 242 0.41
217 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (215 bp):
ACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGTCCAAAACTTGTTTACAAA
ATGACAACTACTTTGACCAAATGATGCGATCTCCCGAGCATGAAATGTTCGAAAAATTGCTCTAA
AGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTAAAAAAGAACTAGTAAAAGTTTGACAA
GCTCAGAAGTTCGTCCAAAA
Found at i:1035 original size:429 final size:429
Alignment explanation
Indices: 486--1439 Score: 1646
Period size: 429 Copynumber: 2.2 Consensus size: 429
476 TTGTATAGAG
* *
486 ACAAAGAGAGAAGCAATTGTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACCTGTTTGCAAA
1 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACCTGTTTGCAAA
*
551 ATGACAAACTACTTTGACCAAATGATGCGATCTGCCGAGCATGAAATGTTCGAAAAGTTGCTCGA
66 ATGACAAACTACTTTGACCAAATGATGCGATCTGCCGAGCATGAAATGTTCGAAAAATTGCTCGA
*
616 AAGAATCGATCGTCTTGAATACTTTGAGAATCCAAAGTTATCAAAGGACTAGTAAAAGTTTGACA
131 AAGAATCGATCGTCTTGAATACTTTGAGAATCCAAAGTTATCAAAGAACTAGTAAAAGTTTGACA
*
681 AGCTCAGAAGTTCGTCCAAGAACAGAGGGAGAAACAATTCTTACATAAATAAGTTCTTAATTCAA
196 AGCTCAGAAGTTCGTCCAAGAACAGAGGGAGAAACAATTCTCACATAAATAAGTTCTTAATTCAA
*
746 AGTTCAAAACTTGTTTACAAAATGACATATTTTGATCAATTGATGCGCTTTCCCGAGCATGGAAT
261 AGTTCAAAACTTGTTTACAAAATAACATATTTTGATCAATTGATGCGCTTTCCCGAGCATGGAAT
*
811 GTTCGAAAAATTGCTCTAAGGAATGGATTTTGTTGAATGCTTTAAGGAACCAAAGTTAAAAAATA
326 GTTCGAAAAATTGCTCTAAGGAATGGATTTTATTGAATGCTTTAAGGAACCAAAGTTAAAAAATA
876 ACTTGTAGAAGTTTGACCAGTTTGGATGTTCGTCCAAAA
391 ACTTGTAGAAGTTTGACCAGTTTGGATGTTCGTCCAAAA
* *
915 ACAAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAATACCAAAACCTGTTTGCAAA
1 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACCTGTTTGCAAA
*
980 ATGACAAACTACTTTGACCAAATGATGCGATCTGCCGAGCATGAAATGTTCGAAAAATTGCTTGA
66 ATGACAAACTACTTTGACCAAATGATGCGATCTGCCGAGCATGAAATGTTCGAAAAATTGCTCGA
* * * *
1045 AAGAATGGATCGTCTTGAATACTTTGAGGATCCGAAGTTATCAAAGAACTAGTAAAAGTTTGAGA
131 AAGAATCGATCGTCTTGAATACTTTGAGAATCCAAAGTTATCAAAGAACTAGTAAAAGTTTGACA
*
1110 AGCTCAGAAGTTCGTCCAAGTACAGAGGGAGAAACAATTCTCACATAAATAAGTTCTTAATTCAA
196 AGCTCAGAAGTTCGTCCAAGAACAGAGGGAGAAACAATTCTCACATAAATAAGTTCTTAATTCAA
*
1175 AGTTCAAAACTTGTTTACAAAATAACATATTTTGATCGATTGATGCGCTTTCCCGAGCATGGAAT
261 AGTTCAAAACTTGTTTACAAAATAACATATTTTGATCAATTGATGCGCTTTCCCGAGCATGGAAT
*
1240 GTTCGAAAAATTGCTCTAAGGAATGGATTTTATTGAATGCTTTAGGGAACCAAAGTTAAAAAATA
326 GTTCGAAAAATTGCTCTAAGGAATGGATTTTATTGAATGCTTTAAGGAACCAAAGTTAAAAAATA
*
1305 ACTTGTAGTAGTTTGACCAGTTTGGATGTTCGTCCAAAA
391 ACTTGTAGAAGTTTGACCAGTTTGGATGTTCGTCCAAAA
* * *
1344 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATACAACGACCAAAA-CTCGTTTACAA
1 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACCT-GTTTGCAA
*
1408 AACGA-AAA-TA-TATTCAGACCAAATGATGCGAT
65 AATGACAAACTACT-TT--GACCAAATGATGCGAT
1440 TTCTTGAGCA
Statistics
Matches: 497, Mismatches: 24, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
426 1 0.00
427 4 0.01
428 5 0.01
429 487 0.98
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (429 bp):
ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACCTGTTTGCAAA
ATGACAAACTACTTTGACCAAATGATGCGATCTGCCGAGCATGAAATGTTCGAAAAATTGCTCGA
AAGAATCGATCGTCTTGAATACTTTGAGAATCCAAAGTTATCAAAGAACTAGTAAAAGTTTGACA
AGCTCAGAAGTTCGTCCAAGAACAGAGGGAGAAACAATTCTCACATAAATAAGTTCTTAATTCAA
AGTTCAAAACTTGTTTACAAAATAACATATTTTGATCAATTGATGCGCTTTCCCGAGCATGGAAT
GTTCGAAAAATTGCTCTAAGGAATGGATTTTATTGAATGCTTTAAGGAACCAAAGTTAAAAAATA
ACTTGTAGAAGTTTGACCAGTTTGGATGTTCGTCCAAAA
Done.