Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002795.1 Kokia drynarioides strain JFW-HI SEQ_115135, 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: 4790
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1641 original size:101 final size:101
Alignment explanation
Indices: 1531--1887 Score: 464
Period size: 101 Copynumber: 3.5 Consensus size: 101
1521 ACAGTTGTGG
* * * * *
1531 ATCTGAATCTCCCTGAAGTTGCAGTGGAATGGAGGGAAGGTACAACACCAAATGCTATATCCTTG
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAACACCAAATCCTATATCCCTG
*
1596 AAGTTGTAGTGGATTGGATTAAAACTACGATAACGA
66 AAGTTGTAGTGGATCGGATTAAAACTACGATAACGA
* * *
1632 ATTTCAATCTCCCTGAAGTTACAGTGGAGTGGAGTGAAGATACAACACCAAATCCTATATCCCTG
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAACACCAAATCCTATATCCCTG
* *
1697 AAGTTGTTGTGGATCGGATTAAAATTACGATAACGA
66 AAGTTGTAGTGGATCGGATTAAAACTACGATAACGA
* * * * * * *
1733 ATCTCAATCTTCCTAAAGTTGTAGTGGAATAGAGTAAAGTTACAATACCAAATCCTATATCCCTG
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAACACCAAATCCTATATCCCTG
** * *
1798 AAGTTGCGGTGGATCGGATTAAAACTATGATAGCGA
66 AAGTTGTAGTGGATCGGATTAAAACTACGATAACGA
* * * *
1834 ATCTCAATCTCCTTGAAGTTGTAGTGGAATGAAGTGAAGCTACAACGA-CAAATC
1 ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAAC-ACCAAATC
1888 TTATCTCATT
Statistics
Matches: 221, Mismatches: 34, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
101 220 1.00
102 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (101 bp):
ATCTCAATCTCCCTGAAGTTGCAGTGGAATGGAGTGAAGATACAACACCAAATCCTATATCCCTG
AAGTTGTAGTGGATCGGATTAAAACTACGATAACGA
Found at i:1754 original size:51 final size:51
Alignment explanation
Indices: 1594--1861 Score: 179
Period size: 51 Copynumber: 5.3 Consensus size: 51
1584 GCTATATCCT
* * * *
1594 TGAAGTTGTAGTGGATTGGATTAAAACTACGATAACGAATTTCAATCTCCC
1 TGAAGTTGTAGTGGATCGGATTAAAATTACGATAACGAATCTCAATCTTCC
** * * * * * * * * *
1645 TGAAGTTACAGTGGAGT-GGAGTGAAGA-TACAACACCAAATC-CTATATCCC
1 TGAAGTTGTAGTGGA-TCGGA-TTAAAATTACGATAACGAATCTCAATCTTCC
*
1695 TGAAGTTGTTGTGGATCGGATTAAAATTACGATAACGAATCTCAATCTTCC
1 TGAAGTTGTAGTGGATCGGATTAAAATTACGATAACGAATCTCAATCTTCC
* * * * * * * * * *
1746 TAAAGTTGTAGTGGAAT-AGAGTAAAGTTACAATACCAAATC-CTATATCCC
1 TGAAGTTGTAGTGG-ATCGGATTAAAATTACGATAACGAATCTCAATCTTCC
** * * *
1796 TGAAGTTGCGGTGGATCGGATTAAAACTATGATAGCGAATCTCAATC-TCC
1 TGAAGTTGTAGTGGATCGGATTAAAATTACGATAACGAATCTCAATCTTCC
1846 TTGAAGTTGTAGTGGA
1 -TGAAGTTGTAGTGGA
1862 ATGAAGTGAA
Statistics
Matches: 158, Mismatches: 50, Indels: 18
0.70 0.22 0.08
Matches are distributed among these distances:
49 7 0.04
50 67 0.42
51 77 0.49
52 7 0.04
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (51 bp):
TGAAGTTGTAGTGGATCGGATTAAAATTACGATAACGAATCTCAATCTTCC
Found at i:1810 original size:50 final size:50
Alignment explanation
Indices: 1540--1810 Score: 184
Period size: 50 Copynumber: 5.4 Consensus size: 50
1530 GATCTGAATC
** * * *
1540 TCCCTGAAGTTGCAGTGGAATGGAGGGAAGGTACAACACCAAATGCTATA
1 TCCCTGAAGTTGCAGTGGAATGGAGTAAAGTTACAATACCAAATCCTATA
* * * * ** * * * * * *
1590 TCCTTGAAGTTGTAGTGGATTGGATTAAAACTACGATAACGAATTTCAATC
1 TCCCTGAAGTTGCAGTGGAATGGAGTAAAGTTACAAT-ACCAAATCCTATA
* * * * *
1641 TCCCTGAAGTTACAGTGGAGTGGAGTGAAGATACAACACCAAATCCTATA
1 TCCCTGAAGTTGCAGTGGAATGGAGTAAAGTTACAATACCAAATCCTATA
** * * * * * * *
1691 TCCCTGAAGTTGTTGTGG-ATCGGATTAAAATTACGATAACGAATCTCAATC
1 TCCCTGAAGTTGCAGTGGAAT-GGAGTAAAGTTACAATACCAAATC-CTATA
* * * *
1742 TTCCTAAAGTTGTAGTGGAATAGAGTAAAGTTACAATACCAAATCCTATA
1 TCCCTGAAGTTGCAGTGGAATGGAGTAAAGTTACAATACCAAATCCTATA
*
1792 TCCCTGAAGTTGCGGTGGA
1 TCCCTGAAGTTGCAGTGGA
1811 TCGGATTAAA
Statistics
Matches: 158, Mismatches: 59, Indels: 8
0.70 0.26 0.04
Matches are distributed among these distances:
49 1 0.01
50 84 0.53
51 71 0.45
52 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (50 bp):
TCCCTGAAGTTGCAGTGGAATGGAGTAAAGTTACAATACCAAATCCTATA
Found at i:1903 original size:202 final size:202
Alignment explanation
Indices: 1473--1903 Score: 490
Period size: 202 Copynumber: 2.1 Consensus size: 202
1463 GGACCAGTGA
* * ** * *** * *
1473 AACAACAAATCCTATATCAAC-GAAGGTGCAGTGGATCAGATTAAAATTAC-AGTTGTGGATCTG
1 AACACCAAATCCTATATC-ACTGAAGTTGTTGTGGATCGGATTAAAATTACGA-TAACGAATCTC
* * * * *
1536 AATCTCCCTGAAGTTGCAGTGGAATGGAGGGAAGGTACAACACCAAATGCTATATCCTTGAAGTT
64 AATCTCCCTAAAGTTGCAGTGGAATAGAGGAAAGGTACAACACCAAATCCTATATCCCTGAAGTT
* * * * *
1601 GTAGTGGATTGGATTAAAACTACGATAACGAATTTCAATCTCCCTGAAGTTACAGTGGAGTGGAG
129 GCAGTGGATCGGATTAAAACTACGATAACGAATCTCAATCTCCCTGAAGTTACAGTGGAATGAAG
1666 TGAAGATAC
194 TGAAGATAC
*
1675 AACACCAAATCCTATATCCCTGAAGTTGTTGTGGATCGGATTAAAATTACGATAACGAATCTCAA
1 AACACCAAATCCTATATCACTGAAGTTGTTGTGGATCGGATTAAAATTACGATAACGAATCTCAA
* * * * *
1740 TCTTCCTAAAGTTGTAGTGGAATAGAGTAAAGTTACAATACCAAATCCTATATCCCTGAAGTTGC
66 TCTCCCTAAAGTTGCAGTGGAATAGAGGAAAGGTACAACACCAAATCCTATATCCCTGAAGTTGC
* * * * **
1805 GGTGGATCGGATTAAAACTATGATAGCGAATCTCAATCTCCTTGAAGTTGTAGTGGAATGAAGTG
131 AGTGGATCGGATTAAAACTACGATAACGAATCTCAATCTCCCTGAAGTTACAGTGGAATGAAGTG
*
1870 AAGCTAC
196 AAGATAC
* * *
1877 AACGA-CAAATCTTATCTCATTGAAGTT
1 AAC-ACCAAATCCTATATCACTGAAGTT
1904 ACCATGGGGC
Statistics
Matches: 189, Mismatches: 37, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
201 1 0.01
202 186 0.98
203 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (202 bp):
AACACCAAATCCTATATCACTGAAGTTGTTGTGGATCGGATTAAAATTACGATAACGAATCTCAA
TCTCCCTAAAGTTGCAGTGGAATAGAGGAAAGGTACAACACCAAATCCTATATCCCTGAAGTTGC
AGTGGATCGGATTAAAACTACGATAACGAATCTCAATCTCCCTGAAGTTACAGTGGAATGAAGTG
AAGATAC
Done.