Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003317.1 Kokia drynarioides strain JFW-HI SEQ_116009, 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: 3098
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Found at i:1775 original size:118 final size:117
Alignment explanation
Indices: 1653--1917 Score: 263
Period size: 118 Copynumber: 2.2 Consensus size: 117
1643 ACGTTGGGGG
* * *
1653 GTAAAATAATAATTTTTGAAAGTTTCGAGG-CCAAAACAGAGTTTTTGGACA-TTCGAG-GATAA
1 GTAAAATAATAATTTTTGAAAG-TTCGAGGTCAAAAACAAAATTTTTGGA-AGTTCGAGAG-TAA
* * *
1715 AAATGTACTTTTCAAAAAG-TCTCAGGGTCAAAAATGAAATTTTTGAAAGTTTGAGT
63 AAATGTAATTTT-AAAAAGAT-TCAGGGTCAAAAATGAAATTTTTGAAAGTTCGAGA
* * * *
1771 GTAAAA-ATGTAATTTTAGCAAGATTCGAGGTCAAAAATAAAATTTTTGGAAGTTCGAGAGTAAA
1 GTAAAATA-ATAATTTTTGAAAG-TTCGAGGTCAAAAACAAAATTTTTGGAAGTTCGAGAGTAAA
*** * *
1835 AATGTAATTTTTGGAAGATTCAGTGTTAAAAATGAAATTTTTGAAAGTTCGAGA
64 AATGTAATTTTAAAAAGATTCAGGGTCAAAAATGAAATTTTTGAAAGTTCGAGA
* *
1889 GTAAAAATGA-AATTTTTGGAAGTTCGAGG
1 GT-AAAATAATAATTTTTGAAAGTTCGAGG
1918 GTAAAAATGT
Statistics
Matches: 120, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
117 8 0.07
118 71 0.59
119 40 0.33
120 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (117 bp):
GTAAAATAATAATTTTTGAAAGTTCGAGGTCAAAAACAAAATTTTTGGAAGTTCGAGAGTAAAAA
TGTAATTTTAAAAAGATTCAGGGTCAAAAATGAAATTTTTGAAAGTTCGAGA
Found at i:1779 original size:29 final size:29
Alignment explanation
Indices: 1738--2050 Score: 258
Period size: 29 Copynumber: 10.6 Consensus size: 29
1728 AAAAAGTCTC
*
1738 AGGGTCAAAAATGAAATTTTTGAAAGTTTG
1 AGGGT-AAAAATGAAATTTTTGGAAGTTTG
* * * * *
1768 AGTGTAAAAATGTAATTTTAGCAAGATTCG
1 AGGGTAAAAATGAAATTTTTGGAAG-TTTG
* *
1798 A-GGTCAAAAATAAAATTTTTGGAAGTTCG
1 AGGGT-AAAAATGAAATTTTTGGAAGTTTG
* * * *
1827 AGAGTAAAAATGTAATTTTTGGAAGATTC
1 AGGGTAAAAATGAAATTTTTGGAAGTTTG
* * *
1856 AGTGTTAAAAATGAAATTTTTGAAAGTTCG
1 AG-GGTAAAAATGAAATTTTTGGAAGTTTG
* *
1886 AGAGTAAAAATGAAATTTTTGGAAGTTCG
1 AGGGTAAAAATGAAATTTTTGGAAGTTTG
* *
1915 AGGGTAAAAATGTAAA-TTTTAGAAGTTTT
1 AGGGTAAAAATG-AAATTTTTGGAAGTTTG
* *
1944 ATGGTCAAAATTG-AATTTTTGGAAGTTTG
1 AGGGT-AAAAATGAAATTTTTGGAAGTTTG
* * *
1973 AGGGTAAAAATGTAATTTTCGAAAGTTTCG
1 AGGGTAAAAATGAAATTTTTGGAAGTTT-G
* * *
2003 -GGGTCAATAATGGAATTTTTGGAAG-TTC
1 AGGGT-AAAAATGAAATTTTTGGAAGTTTG
2031 AGAGGTAAAAATGTAAATTT
1 AG-GGTAAAAATG-AAATTT
2051 CAGACAGTTT
Statistics
Matches: 225, Mismatches: 45, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
28 8 0.04
29 135 0.60
30 82 0.36
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (29 bp):
AGGGTAAAAATGAAATTTTTGGAAGTTTG
Found at i:1815 original size:59 final size:59
Alignment explanation
Indices: 1740--2050 Score: 293
Period size: 59 Copynumber: 5.3 Consensus size: 59
1730 AAAGTCTCAG
* * * *
1740 GGTCAAAAATGAAATTTTTGAAAGTTTGAGTGTAAAAATGTAATTTTAGCAAGATTCGA
1 GGTCAAAAATGAAATTTTTGAAAGTTCGAGAGTAAAAATGTAATTTTTGGAAGATTCGA
* *
1799 GGTCAAAAATAAAATTTTTGGAAGTTCGAGAGTAAAAATGTAATTTTTGGAAGATTC-A
1 GGTCAAAAATGAAATTTTTGAAAGTTCGAGAGTAAAAATGTAATTTTTGGAAGATTCGA
* *
1857 GTGTTAAAAATGAAATTTTTGAAAGTTCGAGAGTAAAAATGAAATTTTTGGAAG-TTCGA
1 G-GTCAAAAATGAAATTTTTGAAAGTTCGAGAGTAAAAATGTAATTTTTGGAAGATTCGA
* ** * *
1916 GGGT-AAAAATGTAAATTTTAG-AAGTTTTATG-GTCAAAAT-TGAATTTTTGGAAG-TTTGA
1 -GGTCAAAAATG-AAATTTTTGAAAGTTCGA-GAGTAAAAATGT-AATTTTTGGAAGATTCGA
* * * * *
1974 GGGT-AAAAATGTAATTTTCGAAAGTTTCG-GGGTCAATAATGGAATTTTTGGAAG-TTCAGA
1 -GGTCAAAAATGAAATTTTTGAAAG-TTCGAGAGT-AAAAATGTAATTTTTGGAAGATTC-GA
2034 GGT-AAAAATGTAAATTT
1 GGTCAAAAATG-AAATTT
2051 CAGACAGTTT
Statistics
Matches: 214, Mismatches: 25, Indels: 25
0.81 0.09 0.09
Matches are distributed among these distances:
57 8 0.04
58 57 0.27
59 141 0.66
60 8 0.04
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (59 bp):
GGTCAAAAATGAAATTTTTGAAAGTTCGAGAGTAAAAATGTAATTTTTGGAAGATTCGA
Found at i:1847 original size:88 final size:88
Alignment explanation
Indices: 1744--1942 Score: 260
Period size: 88 Copynumber: 2.3 Consensus size: 88
1734 TCTCAGGGTC
* * * *
1744 AAAAATGAAATTTTTGAAAGTTTGAGTG-TAAAAATGTAATTTTAGCAAGATTCGAG-GTCAAAA
1 AAAAATGTAATTTTTGAAAGTTTCAGTGTTAAAAATGAAATTTTAGAAAG-TTCGAGAGT-AAAA
1807 ATAAAATTTTTGGAAGTTCGAGAGT
64 ATAAAATTTTTGGAAGTTCGAGAGT
* * *
1832 AAAAATGTAATTTTTGGAAGATTCAGTGTTAAAAATGAAATTTTTGAAAGTTCGAGAGTAAAAAT
1 AAAAATGTAATTTTTGAAAGTTTCAGTGTTAAAAATGAAATTTTAGAAAGTTCGAGAGTAAAAAT
* *
1897 GAAATTTTTGGAAGTTCGAGGGT
66 AAAATTTTTGGAAGTTCGAGAGT
*
1920 AAAAATGTAAATTTT-AGAAGTTT
1 AAAAATGTAATTTTTGA-AAGTTT
1943 TATGGTCAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
88 76 0.79
89 20 0.21
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.34
Consensus pattern (88 bp):
AAAAATGTAATTTTTGAAAGTTTCAGTGTTAAAAATGAAATTTTAGAAAGTTCGAGAGTAAAAAT
AAAATTTTTGGAAGTTCGAGAGT
Done.