Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012881.1 Kokia drynarioides strain JFW-HI SEQ_127895, 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: 6637
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:3466 original size:831 final size:780
Alignment explanation
Indices: 1866--3476 Score: 2103
Period size: 831 Copynumber: 2.0 Consensus size: 780
1856 AAAATAAAAC
1866 ATCAGCAACAATATGCTTTATATTTAAAAGAATTTGAACATCATTAGGACCAAAAAGAACATACC
1 ATCAGCAACAATATGCTTTATATTTAAAAGAATTTGAACATCATTAGGACCAAAAAGAACATACC
1931 TTCCTAAATCTATTATTTGCAAGATAGAAGCAAGGTTTTTCTTTAAGCCAAGAACATGATAAACA
66 TTCCTAAATCTATTATTTGCAAGATAGAAGCAAGGTTTTTCTTTAAGCCAAGAACATGATAAACA
1996 TTCTTAAGAAAAACTTCTCCATCATTCAAATCACCTTCTTTTATCATAGGATATAGTGAATTATC
131 TTCTTAAGAAAAACTTCTCCATCATTCAAATCACCTTCTTTTATCATAGGATATAGTGAATTATC
2061 AGCGGTTACGATAACCTTTTTCATATGATGTGGACGAACATCCGATAAAAGAGTATCATTCCAGA
196 AGCGGTTACGATAACCTTTTTCATATGATGTGGACGAACATCCGATAAAAGAGTATCATTCCAGA
2126 TAGCATGGTGAGAATAACCGGAATCAACAATCACTCTTCGTCATAGTTGATAAAAGCATGGGCAT
261 TAGCATGGTGAGAATAACCGGAATCAACAATCACTCTTCGTCATAGTTGATAAAAGCATGGGCAT
2191 CAATTGGTACATCATCTTGGTGCACAAGAGAAGTCACATTTGTTGGCTGATCAAACACCTCAATA
326 CAATTGGTACATCATCTTGGTGCACAAGAGAAGTCACATTTGTTGGCTGATCAAACACCTCAATA
*
2256 GATAAACATTTCTCCTAATTTGGTTGTTGAAACTCATTATTGTCAAGTACAACCTTTGCTGCTTC
391 GATAAACATTTCTCCCAATTTGGTTGTTGAAACTCATTATTGTCAAGTACAACCTTTGCTGCTTC
* *
2321 CTCTTGCATTTTGACTTGACAATTCACCTTAATAGGGCCTGGCTTCCCACATCGATCACACACCA
456 CTCTTGCATTTTGACTCGACAATTCACCTTAATAGGGCCTGGCTTCCCACATCAATCACACACCA
* *
2386 CTTTCACTCGACAATCTCATTTGATATGTCCAAGTTTTTCACACCTGTAGCAAGATTTGAAACAT
521 CTTTCACTCAACAATCTCATTTGATATGTCCAAGTTTTCCACACCTGTAGCAAGATTTGAAACAT
*
2451 CTTTTTGGCCGCTCCTCACTTCTAGATTGGTTTCTGTCACTTGAAGAAGACTTCGAGTAGAAATT
586 CTTTTTGGCCGCTCCTCACTTCTAGACTGGTTTCTGTCACTTGAAGAAGACTTCGAGTAGAAATT
* *
2516 TTTCCTCCTTTGATCCTTGACGAATAACACATCCTTTGACTTGGAAGAAAGCTTAGTGCTTGTCA
651 TTTCCTCCTTTCATCCTTGACGAACAACACATCCTTTGACTTGGAAGAAAGCTTAGTGCTTGTCA
*
2581 TTTGCTTTATCAAAGCTTCCTTATTAGAGAGCAAATTCTCTAACTCAAAAATTGAAGGTTGATTT
716 TTTGCTTTATCAAAGCTTCCTGATTAGAGAGCAAATTCTCTAACTCAAAAATTGAAGGTTGATTT
******************************* **
2646 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATCAGCAACAATATG
1 -------------------ATCAGCAACAATATGCTTTATATTTAAAAGAATTTG-AAC---AT-
* * ** * * *** * * *
2711 CTTTA-TATTTAAAAGAATTTGAACAT-CATTAGGACCAAAAAGAACATACCTTCCTAA-ATCTA
42 CATTAGGA--CCAAA-AA---GAACATACCTT----CCTAAATCTA-TTA-TTTGC-AAGA--TA
* *
2773 TTATTTGCAAGATAGAAGCAAGGTTTTTCTTTAAGCCAAGAACATGATAAACATTCTTAAGAAAA
92 -GA--AGCAAG-----------GTTTTTCTTTAAGCCAAGAACATGATAAACATTCTTAAGAAAA
2838 ACTTCTCCATCATTCAAATCACCTTCTTTTATCATAGGATATAGTGAATTATCAGCGGTTACGAT
143 ACTTCTCCATCATTCAAATCACCTTCTTTTATCATAGGATATAGTGAATTATCAGCGGTTACGAT
2903 AACCTTTTTCATATGATGTGGACGAACATCCGATAAAAGAGTATCATTCCAGATAGCATGGTGAG
208 AACCTTTTTCATATGATGTGGACGAACATCCGATAAAAGAGTATCATTCCAGATAGCATGGTGAG
2968 AATAACCGGAATCAACAATCCACTCTTCGTCATAGTTGATAAAAGCATGGGCATCAATTGGTACA
273 AATAACCGGAATCAACAAT-CACTCTTCGTCATAGTTGATAAAAGCATGGGCATCAATTGGTACA
3033 TCATCTTGGTGCACAAGAGAAGTCACATTTGTTGGCTGATCAAACACCTCAATAGATAAACATTT
337 TCATCTTGGTGCACAAGAGAAGTCACATTTGTTGGCTGATCAAACACCTCAATAGATAAACATTT
3098 CTCCCAATTTGGTTGTTGAAACTCATTATTGTCAAGTACAACCTTTGCTGCTTCCTCTTGCATTT
402 CTCCCAATTTGGTTGTTGAAACTCATTATTGTCAAGTACAACCTTTGCTGCTTCCTCTTGCATTT
* * * *
3163 TGACTCGACAATTCGCCTTAATATGGCCTGGCTTCCCACATCAATCACATACCACTTTCAGTCAA
467 TGACTCGACAATTCACCTTAATAGGGCCTGGCTTCCCACATCAATCACACACCACTTTCACTCAA
* **
3228 CAATCTCGTTTGATATGTCCAAGTTTTCCACACCTGTAGCAAGATTTGAAACATCTTTTTGGTTG
532 CAATCTCATTTGATATGTCCAAGTTTTCCACACCTGTAGCAAGATTTGAAACATCTTTTTGGCCG
* * *
3293 TTCCTCACTTTTAGACTGGTTTCTGTCACTTGAAGAAGGCTTCGAGTAGAAATTTTTCCTCCTTT
597 CTCCTCACTTCTAGACTGGTTTCTGTCACTTGAAGAAGACTTCGAGTAGAAATTTTTCCTCCTTT
*
3358 CATCCTTGACGAACAACACATCCTTTGACTTGGAAGAAAGCTTAGTGTTTGTCATTTGCTTTATC
662 CATCCTTGACGAACAACACATCCTTTGACTTGGAAGAAAGCTTAGTGCTTGTCATTTGCTTTATC
*
3423 AAAGCTTCCTGATTAGAGATCAAATTCTCTAACTCAAAAATTGAAGGTTGATTT
727 AAAGCTTCCTGATTAGAGAGCAAATTCTCTAACTCAAAAATTGAAGGTTGATTT
3477 GCCCACCCTT
Statistics
Matches: 709, Mismatches: 68, Indels: 38
0.87 0.08 0.05
Matches are distributed among these distances:
799 3 0.00
800 3 0.00
803 3 0.00
804 4 0.01
805 3 0.00
806 2 0.00
808 3 0.00
809 6 0.01
812 6 0.01
813 2 0.00
814 4 0.01
815 2 0.00
816 2 0.00
817 1 0.00
819 5 0.01
830 192 0.27
831 468 0.66
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.32
Consensus pattern (780 bp):
ATCAGCAACAATATGCTTTATATTTAAAAGAATTTGAACATCATTAGGACCAAAAAGAACATACC
TTCCTAAATCTATTATTTGCAAGATAGAAGCAAGGTTTTTCTTTAAGCCAAGAACATGATAAACA
TTCTTAAGAAAAACTTCTCCATCATTCAAATCACCTTCTTTTATCATAGGATATAGTGAATTATC
AGCGGTTACGATAACCTTTTTCATATGATGTGGACGAACATCCGATAAAAGAGTATCATTCCAGA
TAGCATGGTGAGAATAACCGGAATCAACAATCACTCTTCGTCATAGTTGATAAAAGCATGGGCAT
CAATTGGTACATCATCTTGGTGCACAAGAGAAGTCACATTTGTTGGCTGATCAAACACCTCAATA
GATAAACATTTCTCCCAATTTGGTTGTTGAAACTCATTATTGTCAAGTACAACCTTTGCTGCTTC
CTCTTGCATTTTGACTCGACAATTCACCTTAATAGGGCCTGGCTTCCCACATCAATCACACACCA
CTTTCACTCAACAATCTCATTTGATATGTCCAAGTTTTCCACACCTGTAGCAAGATTTGAAACAT
CTTTTTGGCCGCTCCTCACTTCTAGACTGGTTTCTGTCACTTGAAGAAGACTTCGAGTAGAAATT
TTTCCTCCTTTCATCCTTGACGAACAACACATCCTTTGACTTGGAAGAAAGCTTAGTGCTTGTCA
TTTGCTTTATCAAAGCTTCCTGATTAGAGAGCAAATTCTCTAACTCAAAAATTGAAGGTTGATTT
Found at i:6241 original size:38 final size:38
Alignment explanation
Indices: 6190--6268 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
6180 AATGGATTAA
6190 ACTGTGTAGAATAATTAATCATTATACCAGTTTTTTAT
1 ACTGTGTAGAATAATTAATCATTATACCAGTTTTTTAT
6228 ACTGTGTAGAATAATTAATCATTATACCAGTTTTTTAT
1 ACTGTGTAGAATAATTAATCATTATACCAGTTTTTTAT
6266 ACT
1 ACT
6269 TATTTTTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (38 bp):
ACTGTGTAGAATAATTAATCATTATACCAGTTTTTTAT
Done.