Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011694.1 Kokia drynarioides strain JFW-HI SEQ_126688, 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, 1000
Length: 5674
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:4621 original size:810 final size:760
Alignment explanation
Indices: 3062--4631 Score: 1499
Period size: 810 Copynumber: 2.0 Consensus size: 760
3052 AATGTGCTTG
3062 CTGCATTCCATAATTAAGGGTCACAGGATTGATGTCAGCACAATCTTACATAAAGAGATTGCTGA
1 CTGCATTCCATAATTAAGGGTCACAGGATTGATGTCAGCACAATCTTACATAAAGAGATTGCTGA
*
3127 GACAGCAACAAAACAAATAGGTATCCTACCCTTTCCTTCTTTGATAATGCTGCTATGTAAATAAA
66 GACAGCAACAAAACAAATAAGTATCCTACCCTTTCCTTCTTTGATAATGCTGCTATGTAAATAAA
3192 GAGGCATTGTGCCTCGTGAAGGGGAGGAAACTGTGGAGAACAAGGGCCCAATTAATGATGTATCA
131 GAGGCATTGTGCCTCGTGAAGGGGAGGAAACTGTGGAGAACAAGGGCCCAATTAATGATGTATCA
3257 GTGGAACGATGACTGGGGGACAAGAAACCCTTATAGTGAAAGAGGCTCCAAAGAAAAAAGAAAAA
196 GTGGAACGATGACTGGGGGACAAGAAACCCTTATAGTGAAAGAGGCTCCAAAGAAAAAAGAAAAA
* *
3322 AGGCAAAGGGAAGAAAAAGGCCGCTCAGACTAATGCGCCCACAGATCCTCTGATCTGGAGGAAAC
261 AAGCAAAGGGAAGAAAAAGGCCGCTCAGACTAATGCGCCCACAGATCCTCTAATCTGGAGGAAAC
3387 TTGTAGAGATTGAAAAATGTATGGATCGAACAAGCTGTAAACAAATTCAACTTGTCGGCGTAATA
326 TTGTAGAGATTGAAAAATGTATGGATCGAACAAGCTGTAAACAAATTCAACTTGTCGGCGTAATA
**
3452 GAGGAGATATAGTACAGGCAAATTTTATTTTATGCCTATACCATGGTATGGATCAAAGCTATTGT
391 GAGGAGATATAGTACAGGCAAAACTTATTTTATGCCTATACCATGGTATGGATCAAAGCTATTGT
3517 CGCCACATTACGCGGTTTAAGCACACAACCGATGCCAGATTTCCTTGTTTTTCCTCCCATTACCA
456 CGCCACATTACGCGGTTTAAGCACACAACCGATGCCAGATTTCCTTGTTTTTCCTCCCATTACCA
3582 AGGAAGCCACTACATCCTTCGAGCAGCACACTTCAGATGAATGAACCAAATTCGTCCAATCCCCA
521 AGGAAGCCACTACATCCTTCGAGCAGCACACTTCAGATGAATGAACCAAATTCGTCCAATCCCCA
3647 AATCGAATCCACATCTCTGATGATGATGAGAAAGAGGTGCAATCCAAGGAAGTGGAAGATTGCTT
586 AATCGAATCCACATCTCTGATGATGATGAGAAAGAGGTGCAATCCAAGGAAGTGGAAGATTGCTT
3712 CCGCAATATAGCAAGCCTCTTTGACAATGACCAGTCAAATAGTTTTGGTGCTAACATGGTGGAAC
651 CCGCAATATAGCAAGCCTCTTTGACAATGACCAGTCAAATAGTTTTGGTGCTAACATGGTGGAAC
3777 GAGAGGTCGCTACTGCTGTTGGGGAGGAGCAAACACCAGTCGCAT
716 GAGAGGTCGCTACTGCTGTTGGGGAGGAGCAAACACCAGTCGCAT
*********************************** * * *
3822 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGCATTCCATAATT
1 ---------------CTGCATTCCATAATTAAGGGTCACAGGATTGATGTCAGCA--CAAT-CTT
* * * * * * * * *
3887 A-AGGGTCACAG-GATTGATGTCAGCACAATCTTACATAAAGAGAT-TGCTGAGACAGCAACAAA
48 ACA---T-AAAGAGATTGCTG--AG-AC-AGC-AACA-AAACAAATAAG-T-A-TC--CTAC---
* * ** * * * * ** *** *
3949 ACAAATAAGTATCCTACCCT--T--TCCTTCT-T-T-GATAATGCTGC-TATGT---AAATAAAG
95 -C--CT---T-TCCTTCTTTGATAATGCTGCTATGTAAATAAAGAGGCAT-TGTGCCTCGTGAAG
* *** * * ** * *** * * *
4003 AGGCATTGTGCCTCGTGAAGGGGAGGAA-ACTGTGG-AGAA-CAA-G--GGCCCAAT-TAATGAT
152 -GGGA--G-GAAAC-T---GTGGA-GAACA-AG-GGCCCAATTAATGATGTATCAGTGGAACGAT
* * * * ******* * *
4061 GTATCAGTGGAACGATGACTGGGGGACAAGAAACCCTTATAGTGAAAGAGGCTCCAAAGAAAAAA
206 G-A-CTGGGGGAC-AAGAAACCCTTA-TAG--T----------GAAAGAGGCTCCAAAGAAAAAA
4126 GAAAAAAAGCAAAGGGAAGAAAAAGGCCGCTCAGACTAATGCGCCCACAGATCCTCTAATCTGGA
255 GAAAAAAAGCAAAGGGAAGAAAAAGGCCGCTCAGACTAATGCGCCCACAGATCCTCTAATCTGGA
*
4191 GGAAACTTGTAGAGATTGAAAAATGTGTGGATCGAACAAGCTGTAAACAAATTCAACTTGTCGGC
320 GGAAACTTGTAGAGATTGAAAAATGTATGGATCGAACAAGCTGTAAACAAATTCAACTTGTCGGC
4256 GTAATAGAGGAGATATAGTACAGGCAAAACTTATTTTATGCCTATACCATGGTATGGATCAAAGC
385 GTAATAGAGGAGATATAGTACAGGCAAAACTTATTTTATGCCTATACCATGGTATGGATCAAAGC
4321 TATTGTCGCCACATTACGCGGTTTAAGCACACAACCGATGCCAGATTTCCTTGTTTTTCCTCCCA
450 TATTGTCGCCACATTACGCGGTTTAAGCACACAACCGATGCCAGATTTCCTTGTTTTTCCTCCCA
4386 TTACCAAGGAAGCCACTACATCCTTCGAGCAGCACACTTCAGATGAATGAACCAAATTCGTCCAA
515 TTACCAAGGAAGCCACTACATCCTTCGAGCAGCACACTTCAGATGAATGAACCAAATTCGTCCAA
4451 TCCCCAAATCGAATCCACATCTCTGATGATGATGAGAAAGAGGTGCAATCCAAGGAAGTGGAAGA
580 TCCCCAAATCGAATCCACATCTCTGATGATGATGAGAAAGAGGTGCAATCCAAGGAAGTGGAAGA
4516 TTGCTTCCGCAATATAGCAAGCCTCTTTGACAATGACCAGTCAAATAGTTTTGGTGCTAACATGG
645 TTGCTTCCGCAATATAGCAAGCCTCTTTGACAATGACCAGTCAAATAGTTTTGGTGCTAACATGG
4581 TGGAACGAGAGGTCGCTACTGCTGTTGGGGAGGAGCAAACACCAGTCGCAT
710 TGGAACGAGAGGTCGCTACTGCTGTTGGGGAGGAGCAAACACCAGTCGCAT
4632 TTGTGGATAT
Statistics
Matches: 645, Mismatches: 94, Indels: 77
0.79 0.12 0.09
Matches are distributed among these distances:
775 4 0.01
777 4 0.01
778 3 0.00
780 8 0.01
781 3 0.00
782 2 0.00
783 2 0.00
784 2 0.00
785 4 0.01
786 7 0.01
787 1 0.00
788 1 0.00
790 7 0.01
791 3 0.00
792 1 0.00
793 11 0.02
794 10 0.02
795 7 0.01
796 12 0.02
797 5 0.01
798 10 0.02
799 7 0.01
800 8 0.01
810 523 0.81
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.22
Consensus pattern (760 bp):
CTGCATTCCATAATTAAGGGTCACAGGATTGATGTCAGCACAATCTTACATAAAGAGATTGCTGA
GACAGCAACAAAACAAATAAGTATCCTACCCTTTCCTTCTTTGATAATGCTGCTATGTAAATAAA
GAGGCATTGTGCCTCGTGAAGGGGAGGAAACTGTGGAGAACAAGGGCCCAATTAATGATGTATCA
GTGGAACGATGACTGGGGGACAAGAAACCCTTATAGTGAAAGAGGCTCCAAAGAAAAAAGAAAAA
AAGCAAAGGGAAGAAAAAGGCCGCTCAGACTAATGCGCCCACAGATCCTCTAATCTGGAGGAAAC
TTGTAGAGATTGAAAAATGTATGGATCGAACAAGCTGTAAACAAATTCAACTTGTCGGCGTAATA
GAGGAGATATAGTACAGGCAAAACTTATTTTATGCCTATACCATGGTATGGATCAAAGCTATTGT
CGCCACATTACGCGGTTTAAGCACACAACCGATGCCAGATTTCCTTGTTTTTCCTCCCATTACCA
AGGAAGCCACTACATCCTTCGAGCAGCACACTTCAGATGAATGAACCAAATTCGTCCAATCCCCA
AATCGAATCCACATCTCTGATGATGATGAGAAAGAGGTGCAATCCAAGGAAGTGGAAGATTGCTT
CCGCAATATAGCAAGCCTCTTTGACAATGACCAGTCAAATAGTTTTGGTGCTAACATGGTGGAAC
GAGAGGTCGCTACTGCTGTTGGGGAGGAGCAAACACCAGTCGCAT
Found at i:5154 original size:15 final size:16
Alignment explanation
Indices: 5120--5162 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5110 GCATGCATTT
5120 ATTTTAATTGTCATTGC
1 ATTTTAATTGTCA-TGC
*
5137 ATTTTTATTGTC-TGC
1 ATTTTAATTGTCATGC
*
5152 ATTTTATTTGT
1 ATTTTAATTGT
5163 TTTAGCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 12 0.52
17 11 0.48
ACGTcount: A:0.19, C:0.09, G:0.12, T:0.60
Consensus pattern (16 bp):
ATTTTAATTGTCATGC
Done.