Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013679.1 Kokia drynarioides strain JFW-HI SEQ_128707, 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, 823
Length: 1372
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Found at i:872 original size:424 final size:423
Alignment explanation
Indices: 305--1346 Score: 1312
Period size: 440 Copynumber: 2.4 Consensus size: 423
295 TATTTACGTG
* * * * * *
305 AGAATTGTTACTCCTTTGGTTCTTTGACAACCTTCTGAACTAGTCAAACTTTTTACGAGTTCTTT
1 AGAATTGTTTCT-CTTTTGTTCTTAGACAAACTTCTGAACTAGTCAAAC-TTTTACTATTTCTTT
* * * * *
370 TATAATTTTGGTTCATTAAAGTATTCAAGACGATCCATTCCTTCGATCAATATTCCGAACATTCC
64 TATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATATTCCGAACATTCC
*
435 ATGCTCAGGAAATAGCATCATCCGGTCTAAATAGTTTGTCATTTTGCAAACAACTTTTTGGTCCT
129 ATGCTCGGGAAATAGCATCATCCGGTCTAAATAGTTTGTCATTTTGCAAACAACTTTTTGGTCCT
*
500 TG-A-ATGTAA-AATTATTTCTCTTTTGATTCTTAGACAAACTTCTAAACTTGTCAAGCTTTTAC
194 TGAATATGAAAGAATTATTTCTCTTTTGATTCTTAGACAAACTTCTAAACTTGTCAAGCTTTTAC
*
562 TATTTTTTCTATGATAACTTCGGTTCCTTAAACTATCCAAGATGATCCAATCCTTCGAGCAATAT
259 TATTTCTTCTATGATAACTTCGGTTCCTTAAACTATCCAAGATGATCCAATCCTTCGAGCAATAT
* ** ** *
627 TCCGAACATTCCAAGCTCGGGAAATCGCATCATCCGGTCTAAATAGTTTGTTATTT-TGCAAACA
324 TCCGAACATTCCAAGCTCGGGAAATCGCATCATCCGGTCAAAATAGTTTGCCATTTCTAAAAAAA
691 ACTTTTTGGTC-CTTGAATTAAA-AATATATTTA-TGAA
389 AC-TTTTGGTCAC-TGAATTAAATAAT-TATTTATTG-A
* *
727 AGAATTATTTCTCTTTTGATTCTTAGACAAACTTCTGAACTTGTCAAACTTTTACTATTTCTTCT
1 AGAATTGTTTCTCTTTTG-TTCTTAGACAAACTTCTGAACTAGTCAAACTTTTACTATTTCTT-T
* * *
792 ATGATAACTTCGGTTCCTTAAACTATCCAAGATGATCCAGTCCTTCGAGCAATATTCCGAACATT
64 -T-ATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATATTCCGAACATT
857 CCATGCTCGGGAAATAGCATCATCCGGTCTAAATAGTTTGTCATTTTGCAAACAACTTTTTGGTC
127 CCATGCTCGGGAAATAGCATCATCCGGTCTAAATAGTTTGTCATTTTGCAAACAACTTTTTGGTC
*
922 CTTGAATTTAAAATATATTTATGAAAGAATTATTTCTCTTTTGATTCTTAGACAAACTTCTGAAC
192 CTTG----------A-A--TATGAAAGAATTATTTCTCTTTTGATTCTTAGACAAACTTCTAAAC
* *
987 TTGTCAAGCTTTTACTATTTCTTCTATGGTAACTTCGGTTCCTTAAACTATCCAAGATGATTCAA
244 TTGTCAAGCTTTTACTATTTCTTCTATGATAACTTCGGTTCCTTAAACTATCCAAGATGATCCAA
* * * * *
1052 TCCTTCGAGCAATATTCCTAACATTCCATGCTCGGGAAATCGCTTCTTTCGGTCAAAATAGTTTG
309 TCCTTCGAGCAATATTCCGAACATTCCAAGCTCGGGAAATCGCATCATCCGGTCAAAATAGTTTG
* *
1117 CCATTTCGTAAAAAAAACTTTTGGTCACTGAATTAAATACTTATTTATTTGT
374 CCATTTC-TAAAAAAAACTTTTGGTCACTGAATTAAATAATTATTTA-TTGA
* * * * ** *
1169 A-AATTGTTTCTCTCCTTGTTCTTGGACGAACTTTTGAACTAGGAAAACTTTTACTATTTCTGTT
1 AGAATTGTTTCTCT-TTTGTTCTTAGACAAACTTCTGAACTAGTCAAACTTTTACTATTTCTTTT
* **
1233 ATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAA-ATTTATGAACATTCC
65 ATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATA-TTCCGAACATTCC
* * * ** *
1297 ATGCTCGAGAAATTGCATCTTTTGGTCTAAATAG-TTGTCATTTTGAAAAC
129 ATGCTCGGGAAATAGCATCATCCGGTCTAAATAGTTTGTCATTTTGCAAAC
1347 CAAGTTTTGG
Statistics
Matches: 536, Mismatches: 56, Indels: 41
0.85 0.09 0.06
Matches are distributed among these distances:
421 17 0.03
422 38 0.07
423 1 0.00
424 122 0.23
436 1 0.00
437 16 0.03
438 85 0.16
439 6 0.01
440 163 0.30
441 71 0.13
442 14 0.03
443 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (423 bp):
AGAATTGTTTCTCTTTTGTTCTTAGACAAACTTCTGAACTAGTCAAACTTTTACTATTTCTTTTA
TAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATATTCCGAACATTCCAT
GCTCGGGAAATAGCATCATCCGGTCTAAATAGTTTGTCATTTTGCAAACAACTTTTTGGTCCTTG
AATATGAAAGAATTATTTCTCTTTTGATTCTTAGACAAACTTCTAAACTTGTCAAGCTTTTACTA
TTTCTTCTATGATAACTTCGGTTCCTTAAACTATCCAAGATGATCCAATCCTTCGAGCAATATTC
CGAACATTCCAAGCTCGGGAAATCGCATCATCCGGTCAAAATAGTTTGCCATTTCTAAAAAAAAC
TTTTGGTCACTGAATTAAATAATTATTTATTGA
Found at i:891 original size:220 final size:220
Alignment explanation
Indices: 509--1346 Score: 1140
Period size: 220 Copynumber: 3.8 Consensus size: 220
499 TTGAATGTAA
* * *
509 AATTATTTCTCTTTTGATTCTTAGACAAACTTCTAAACTTGTCAAGCTTTTACTATTTTTTCTAT
1 AATTATTTCTCTTTTGATTCTTAGACAAACTTCTGAACTTGTCAAACTTTTACTATTTCTTCTAT
574 GATAACTTCGGTTCCTTAAACTATCCAAGATGATCCAATCCTTCGAGCAATATTCCGAACATTCC
66 GATAACTTCGGTTCCTTAAACTATCCAAGATGATCCAATCCTTCGAGCAATATTCCGAACATTCC
* * *
639 AAGCTCGGGAAATCGCATCATCCGGTCTAAATAGTTTGTTATTTTGCAAACAACTTTTTGGTCCT
131 ATGCTCGGGAAATCGCATCATCCGGTCTAAATAGTTTGTCATTTTGAAAACAACTTTTTGGTCCT
704 TGAATTAAAAATATATTTATGAAAG
196 TGAATTAAAAATATATTTATGAAAG
729 AATTATTTCTCTTTTGATTCTTAGACAAACTTCTGAACTTGTCAAACTTTTACTATTTCTTCTAT
1 AATTATTTCTCTTTTGATTCTTAGACAAACTTCTGAACTTGTCAAACTTTTACTATTTCTTCTAT
*
794 GATAACTTCGGTTCCTTAAACTATCCAAGATGATCCAGTCCTTCGAGCAATATTCCGAACATTCC
66 GATAACTTCGGTTCCTTAAACTATCCAAGATGATCCAATCCTTCGAGCAATATTCCGAACATTCC
* *
859 ATGCTCGGGAAATAGCATCATCCGGTCTAAATAGTTTGTCATTTTGCAAACAACTTTTTGGTCCT
131 ATGCTCGGGAAATCGCATCATCCGGTCTAAATAGTTTGTCATTTTGAAAACAACTTTTTGGTCCT
*
924 TGAATTTAAAATATATTTATGAAAG
196 TGAATTAAAAATATATTTATGAAAG
*
949 AATTATTTCTCTTTTGATTCTTAGACAAACTTCTGAACTTGTCAAGCTTTTACTATTTCTTCTAT
1 AATTATTTCTCTTTTGATTCTTAGACAAACTTCTGAACTTGTCAAACTTTTACTATTTCTTCTAT
* * *
1014 GGTAACTTCGGTTCCTTAAACTATCCAAGATGATTCAATCCTTCGAGCAATATTCCTAACATTCC
66 GATAACTTCGGTTCCTTAAACTATCCAAGATGATCCAATCCTTCGAGCAATATTCCGAACATTCC
* * * * * * *
1079 ATGCTCGGGAAATCGCTTCTTTCGGTCAAAATAGTTTGCCATTTCGTAAAAAAAAC-TTTTGGTC
131 ATGCTCGGGAAATCGCATCATCCGGTCTAAATAGTTTGTCATTT--TGAAAACAACTTTTTGGTC
* *
1143 AC-TGAATTAAATACT-TATTTATTTG-TA-
194 -CTTGAATTAAA-AATATATTTA--TGAAAG
* * * * * * ** *
1170 AATTGTTTCTCTCCTTG-TTCTTGGACGAACTTTTGAACTAGGAAAACTTTTACTATTTC-TGT-
1 AATTATTTCTCT-TTTGATTCTTAGACAAACTTCTGAACTTGTCAAACTTTTACTATTTCTTCTA
* * * * **
1232 T-ATAACTTCGGTTCCTTAAAGTATTCAAGATGATCCATTTCTTCGAGCAA-ATTTATGAACATT
65 TGATAACTTCGGTTCCTTAAACTATCCAAGATGATCCAATCCTTCGAGCAATA-TTCCGAACATT
* * * **
1295 CCATGCTCGAGAAATTGCATCTTTTGGTCTAAATAG-TTGTCATTTTGAAAAC
129 CCATGCTCGGGAAATCGCATCATCCGGTCTAAATAGTTTGTCATTTTGAAAAC
1347 CAAGTTTTGG
Statistics
Matches: 558, Mismatches: 52, Indels: 21
0.88 0.08 0.03
Matches are distributed among these distances:
215 5 0.01
217 9 0.02
218 82 0.15
219 1 0.00
220 377 0.68
221 68 0.12
222 14 0.03
223 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (220 bp):
AATTATTTCTCTTTTGATTCTTAGACAAACTTCTGAACTTGTCAAACTTTTACTATTTCTTCTAT
GATAACTTCGGTTCCTTAAACTATCCAAGATGATCCAATCCTTCGAGCAATATTCCGAACATTCC
ATGCTCGGGAAATCGCATCATCCGGTCTAAATAGTTTGTCATTTTGAAAACAACTTTTTGGTCCT
TGAATTAAAAATATATTTATGAAAG
Done.