Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014732.1 Kokia drynarioides strain JFW-HI SEQ_129771, 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: 6657
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:5483 original size:617 final size:600
Alignment explanation
Indices: 4111--5530 Score: 1655
Period size: 614 Copynumber: 2.3 Consensus size: 600
4101 ACACGGCTCT
* * * * * *
4111 GACACAACCATGTGATAGGCCAAATCGATTTCACGGAATTGCACACCAAACAACGAAAAATCAAA
1 GACACGACCATGTGGTAGGCCATATCGATATCACGGAATTGCACACCAAACAATGGAAAATCAAA
* * * * *
4176 TTTTTTAGGTTTTCCGGGCATTCTAAGATGTATATATGAAAAAAATAAGAAAATTA-GAGGGAGA
66 -ATTTTAGGTTTT-CGGGCATTCTAAGACGTATATATGACAAAAATAA-AAAACTAGGAGGGAGC
* * *
4240 CATCAGAGAACATTCAAGAAAATAACTTGAAAAACACCATTGAAGCCGACTTTGAAGCATATTTG
128 CATCAGAGAATATTCAAGAAAAAAACTCGAAAAACACCATTGAAGCCGACTTT---G-A-A----
*
4305 CGTCAAGATTGAAGATTCTCATTTGATTTGATAGCAGATTATCATGAGTTTCTTTATTTTTTTGG
184 -G-CAAGA-TGAAGATTCTCATTTGATTTGATAGCAGATTATCATGAGTTTCTTTATTTTTTCGG
*
4370 TTATATTGTCTCTTGGATGTTTTTACTTTCAAGAATGAACTAATTTTCTAAATACCTAGGGGAGA
246 TTATATTGTCTCTTGGATGTTTTTACTTTCAAGAATGAACTAATTTCCTAAATACCTAGGGGAGA
* *
4435 TGAAACCAATGATGGATTATGATGTTTGATTTTTATTTTGCAGTTTTTCTCTCAATTATGTGTTC
311 TGAAACCAATGATAGATTATGATGTTTGATTTTTATTTTGCAGTTTTTCTCTCAATTATGTGTAC
* *
4500 TTAAATCGTGAATATTCGATGTTCATTGTAAATGTTATGCTCCTAATCCTTTCAATTCATGTTTT
376 TTAAATCGTGAATATTCGATGTTCATTGTAAATGTTATGCTCCTAATCCTTTCAATACATGATTT
* **
4565 TATGCTTAATATAGCACTAGAAATCAAAAGGAGAGAAAAATGAGTGAAAAAAAAATCGGAGCAAG
441 TATGCCTAATATAGCACTAGAAATCAAAAGGAGAGAAAAATGAGCAAAAAAAAAATCGGAGCAAG
* * * * *
4630 CTATAGGAGCCACACGGGTTGAACCATTCCACTTGGCCATATTATCCGCACGAGCAAAACCATTC
506 CTAAAGGAGCCACACGGGCTGAACCATTCCACATGGCCATATGATCCGCACAAGCAAAACCATTC
* *
4695 CACACGGCCAGACCACACGGTTGTGTGACC
571 CACACGACCAGACCACACGATTGTGTGACC
* * * *
4725 CACACGACCATGTGGTAAGCCATATCGATATCATGTAATTGCACACCAAACAATGGAAAATCAAA
1 GACACGACCATGTGGTAGGCCATATCGATATCACGGAATTGCACACCAAACAATGGAAAATC-AA
* * * **
4790 AATTTTAGGTATTTCGAGCATTCTAAGACGTACATATGAC-AAAATAAGAAACTAGGAATGAGCC
65 AATTTTAGGT-TTTCGGGCATTCTAAGACGTATATATGACAAAAATAAAAAACTAGGAGGGAGCC
* * *
4854 AAT-AGGGAATATTCAAGAAAAAAAATCGAAAAACACCATTGAAGTCGACTTTGAAGCAA-A-GA
129 -ATCAGAGAATATTCAAGAAAAAAACTCGAAAAACACCATTGAAGCCGACTTTGAAGCAAGATGA
* *
4916 ATATTC-CAATTTGATTTGATAGGAGATTATCATGAGTTTCTTTATTTCTTTCGGTTATATTGTC
193 AGATTCTC-ATTTGATTTGATAGCAGATTATCATGAGTTTCTTTATTT-TTTCGGTTATATTGTC
*
4980 TCCTT-GATGTTTTTTCCTTTCAAGAATGAACTAATTTCCTAAATACCTAGGGGAGATG-AACC-
256 T-CTTGGATG-TTTTTACTTTCAAGAATGAACTAATTTCCTAAATACCTAGGGGAGATGAAACCA
* *
5042 TTGTAATAGATTATGTTGTTTGATTTTTATTTTGCGCAAAAAATGCTTAGTTTTTTCTCTCAATT
319 ATG--ATAGATTATGATGTTTGATTTTTA-TTT----------TGC--AG-TTTTTCTCTCAATT
* * * * * *
5107 ATGAT-TACTTAAATTGTGATTATTCGATGTTCATTGTGAATTTTATGCTCTTAATCTTTTCAAT
368 ATG-TGTACTTAAATCGTGAATATTCGATGTTCATTGTAAATGTTATGCTCCTAATCCTTTCAAT
* * *
5171 ACAT-ATTTTATGCCTAATA-AGGCACTTGAAATCAACAGGAGTGAAAAATGAGCAAAAATCGAA
432 ACATGATTTTATGCCTAATATA-GCACTAGAAATCAAAAGGAGAGAAAAATGAGCAAAAA---AA
* * *
5234 AAATTGGAGCAAGCTACAAGG-GCCACATGGGCTGGACCATTCCACATGGCCATATGATCCGCAC
493 AAATCGGAGCAAGCTA-AAGGAGCCACACGGGCTGAACCATTCCACATGGCCATATGATCCGCAC
* * *
5298 AAGCTAAAGCATTCCACACGACCTA-ACCACATGATTGTGTGA-C
557 AAGCAAAACCATTCCACACGACC-AGACCACACGATTGTGTGACC
* *
5341 GACACGACCATGTGGTAGGCCATATCGATATCACGGAATTGCACACCAAATAGTGGAAAATCACA
1 GACACGACCATGTGGTAGGCCATATCGATATCACGGAATTGCACACCAAACAATGGAAAATCA-A
* * *
5406 AATTTTAGGCTTTTCGGGCATTTTAAGACATATATATGACAAAAATAACAAACTAGGAGGGAGCC
65 AATTTTAGG-TTTTCGGGCATTCTAAGACGTATATATGACAAAAATAAAAAACTAGGAGGGAGCC
* * * *
5471 ATCAAAGAATATTCAAGAAAACAACTCAAAAAAAAATCCATTGAAGCCGACTTTGAAGCA
129 ATCAGAGAATATTCAAGAAAAAAACTC-GAAAAACA-CCATTGAAGCCGACTTTGAAGCA
5531 GATTTCCGTC
Statistics
Matches: 687, Mismatches: 82, Indels: 69
0.82 0.10 0.08
Matches are distributed among these distances:
598 1 0.00
599 47 0.07
600 24 0.03
601 72 0.10
602 6 0.01
603 1 0.00
608 1 0.00
609 1 0.00
610 1 0.00
612 8 0.01
613 57 0.08
614 131 0.19
615 79 0.11
616 95 0.14
617 131 0.19
618 10 0.01
619 22 0.03
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (600 bp):
GACACGACCATGTGGTAGGCCATATCGATATCACGGAATTGCACACCAAACAATGGAAAATCAAA
ATTTTAGGTTTTCGGGCATTCTAAGACGTATATATGACAAAAATAAAAAACTAGGAGGGAGCCAT
CAGAGAATATTCAAGAAAAAAACTCGAAAAACACCATTGAAGCCGACTTTGAAGCAAGATGAAGA
TTCTCATTTGATTTGATAGCAGATTATCATGAGTTTCTTTATTTTTTCGGTTATATTGTCTCTTG
GATGTTTTTACTTTCAAGAATGAACTAATTTCCTAAATACCTAGGGGAGATGAAACCAATGATAG
ATTATGATGTTTGATTTTTATTTTGCAGTTTTTCTCTCAATTATGTGTACTTAAATCGTGAATAT
TCGATGTTCATTGTAAATGTTATGCTCCTAATCCTTTCAATACATGATTTTATGCCTAATATAGC
ACTAGAAATCAAAAGGAGAGAAAAATGAGCAAAAAAAAAATCGGAGCAAGCTAAAGGAGCCACAC
GGGCTGAACCATTCCACATGGCCATATGATCCGCACAAGCAAAACCATTCCACACGACCAGACCA
CACGATTGTGTGACC
Done.