Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011516.1 Kokia drynarioides strain JFW-HI SEQ_126501, 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: 7613
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Found at i:6629 original size:29 final size:30
Alignment explanation
Indices: 6562--6990 Score: 257
Period size: 29 Copynumber: 14.6 Consensus size: 30
6552 TGACATCCGG
* *
6562 GGGT-AAAATGGTAATTTTAGGAAGTTTCGA
1 GGGTAAAAATGG-AATTTTTGGAAGTTTTGA
* * *
6592 -AGTCAAAAATGGAATTTTGGGAAG-TTCGA
1 GGGT-AAAAATGGAATTTTTGGAAGTTTTGA
* * * *
6621 GGCTAAAAATAGATTTTTTAGAAGTTTTG-
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGA
*
6650 GGGTTAAAAAAT-GAA-TTTTGGAAG-TTTCA
1 GGG-T-AAAAATGGAATTTTTGGAAGTTTTGA
* * * * *
6679 AGGTCAAAATGGGATTTTTAGAAG-TTTGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGA
*
6708 GGGTAAAAATGGAATTTTTGGAGGTTTTG-
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGA
* *
6737 GGGTCAAAAATGAGAA-TTTTAGAAG-TTTGG
1 GGGT-AAAAATG-GAATTTTTGGAAGTTTTGA
* *
6767 GGGTAAAAATGGGATTTTTGGAAG-TTTCA
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGA
** * ** * *
6796 GGAAAAAAATGGGATTTTTAAAAG-TTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGA
* * *
6825 GGGTAAAGATGGGATTTTTGGAGGTTTTG-
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGA
* *
6854 GGGTTAAAAATGGGATTTTTAGAAGTTTT-A
1 GGG-TAAAAATGGAATTTTTGGAAGTTTTGA
* *
6884 GGGTAAAAAT-GAGATTTTTGAAAG-TTTGT
1 GGGTAAAAATGGA-ATTTTTGGAAGTTTTGA
* * *
6913 TGGTAAAAATGGGATTTTTGGAAGTTTAG-
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGA
* * * * *
6942 GGGTCAAAATGGGATTTTTAGAAGCTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGA
*
6972 -GGTCAAAAATGGGATTTTT
1 GGGT-AAAAATGGAATTTTT
6991 AAACGTTCGG
Statistics
Matches: 315, Mismatches: 61, Indels: 46
0.75 0.14 0.11
Matches are distributed among these distances:
27 5 0.02
28 12 0.04
29 196 0.62
30 86 0.27
31 16 0.05
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (30 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTTGA
Found at i:6645 original size:59 final size:57
Alignment explanation
Indices: 6576--7029 Score: 301
Period size: 59 Copynumber: 7.7 Consensus size: 57
6566 AAAATGGTAA
** *
6576 TTTTAGGAAGTTTCGAAGTCAAAAATGGAATTTTGGGAAG-TTCGAGGCTAAAAAT-AGATT
1 TTTTA-GAAGTTTCGGGGT-AAAAATGGAATTTT-GGAAGTTTCAAGG-TAAAAATGAGA-T
* * *
6636 TTTTAGAAGTTTTGGGGTTAAAAAAT-GAATTTTGGAAGTTTCAAGGTCAAAATGGGAT
1 TTTTAGAAGTTTCGGGG-T-AAAAATGGAATTTTGGAAGTTTCAAGGTAAAAATGAGAT
* * *** *
6694 TTTTAGAAGTTTGGGGGTAAAAATGGAATTTTTGGAGGTTTTGGGGTCAAAAATGAGAA
1 TTTTAGAAGTTTCGGGGTAAAAATGGAA-TTTTGGAAGTTTCAAGGT-AAAAATGAGAT
* * * *
6753 TTTTAGAAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTC-AGGAAAAAAATGGGAT
1 TTTTAGAAGTTTCGGGGTAAAAAT-GGAATTTTGGAAGTTTCAAGG-TAAAAATGAGAT
* * * * *** *
6811 TTTTAAAAG-TTCGGGGGTAAAGATGGGATTTTTGGAGGTTTTGGGGTTAAAAATGGGAT
1 TTTTAGAAGTTTC-GGGGTAAAAAT-GGAATTTTGGAAGTTTCAAGG-TAAAAATGAGAT
** * * *** *
6870 TTTTAGAAGTTTTAGGGTAAAAATGAGATTTTTGAAAGTTTGTTGGTAAAAATGGGAT
1 TTTTAGAAGTTTCGGGGTAAAAATG-GAATTTTGGAAGTTTCAAGGTAAAAATGAGAT
* * * * * * * *
6928 TTTTGGAAGTTTAGGGGTCAAAATGGGATTTTTAGAAGCTTCGAGGTCAAAAATGGGAT
1 TTTTAGAAGTTTCGGGGTAAAAAT-GGAATTTTGGAAGTTTCAAGGT-AAAAATGAGAT
* *
6987 TTTTA-AACG-TTCGGGGGTAAAAACGAGATTTTTGGAAGTTTCA
1 TTTTAGAA-GTTTC-GGGGTAAAAATG-GAATTTTGGAAGTTTCA
7030 GGATCCTCGG
Statistics
Matches: 321, Mismatches: 56, Indels: 35
0.78 0.14 0.08
Matches are distributed among these distances:
56 6 0.02
57 6 0.02
58 140 0.44
59 152 0.47
60 17 0.05
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (57 bp):
TTTTAGAAGTTTCGGGGTAAAAATGGAATTTTGGAAGTTTCAAGGTAAAAATGAGAT
Found at i:6653 original size:88 final size:88
Alignment explanation
Indices: 6561--7028 Score: 300
Period size: 88 Copynumber: 5.3 Consensus size: 88
6551 TTGACATCCG
* *
6561 GGGGT-AAAATGGTAATTTTAGGAAGTTTCGAAGTCAAAAATGGAATTTTGGGAAGTTCGAGGCT
1 GGGGTAAAAATGG-AATTTTAGGAAGTTTCGAAGTCAAAAATGGGATTTTTGGAAGTTCGAGGCT
*
6625 AAAAATAGATTTTTTAGAAGTTTT
65 AAAAATAGAATTTTTAGAAGTTTT
* * *
6649 GGGGTTAAAAAAT-GAATTTT-GGAAGTTTC-AAGGTC-AAAATGGGATTTTTAGAAGTTTGGGG
1 GGGG-T-AAAAATGGAATTTTAGGAAGTTTCGAA-GTCAAAAATGGGATTTTTGGAAGTTCGAGG
* * * *
6710 GTAAAAATGGAATTTTTGGAGGTTTT
63 CTAAAAATAGAATTTTTAGAAGTTTT
* **
6736 GGGGTCAAAAATGAGAATTTTA-GAAGTTTGGGGGT-AAAAATGGGATTTTTGGAAGTTTC-AGG
1 GGGGT-AAAAATG-GAATTTTAGGAAGTTTCGAAGTCAAAAATGGGATTTTTGGAAG-TTCGAGG
** * * * **
6798 AAAAAAATGGGATTTTTAAAAGTTCG
63 CTAAAAATAGAATTTTTAGAAGTTTT
* * * * * ** * * ** *
6824 GGGGTAAAGATGGGATTTTTGGAGGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTTTAGGGTA
1 GGGGTAAAAATGGAATTTTAGGAAGTTTCGAAGTCAAAAATGGGATTTTTGGAAGTTCGAGGCTA
6889 AAAAT-GAGATTTTT-GAAAG-TTT
66 AAAATAGA-ATTTTTAG-AAGTTTT
* * * * ** *
6911 GTTGGTAAAAATGGGATTTTTGGAAGTTTAGGGGTC-AAAATGGGATTTTTAGAAGCTTCGAGG-
1 G-GGGTAAAAATGGAATTTTAGGAAGTTTCGAAGTCAAAAATGGGATTTTTGGAAG-TTCGAGGC
* * **
6974 TCAAAAATGGGATTTTTA-AACGTTCG
64 T-AAAAATAGAATTTTTAGAA-GTTTT
* *
7000 GGGGTAAAAA-CGAGATTTTTGGAAGTTTC
1 GGGGTAAAAATGGA-ATTTTAGGAAGTTTC
7029 AGGATCCTCG
Statistics
Matches: 305, Mismatches: 52, Indels: 46
0.76 0.13 0.11
Matches are distributed among these distances:
86 13 0.04
87 93 0.30
88 181 0.59
89 12 0.04
90 1 0.00
91 5 0.02
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (88 bp):
GGGGTAAAAATGGAATTTTAGGAAGTTTCGAAGTCAAAAATGGGATTTTTGGAAGTTCGAGGCTA
AAAATAGAATTTTTAGAAGTTTT
Found at i:6727 original size:117 final size:114
Alignment explanation
Indices: 6596--7031 Score: 430
Period size: 117 Copynumber: 3.7 Consensus size: 114
6586 TTTCGAAGTC
*
6596 AAAAATGGAATTTTGGGAAG-TTCGAGG-CTAAAAAT-AGATTTTTTAGAAGTTTTGGGGTTAAA
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC-AAAAATGAGA-TTTTTAGAAGTTTTGGGG-T-AA
*
6658 AAATGAATTTTGGAAGTTTCAAGGTCAAAATGGGATTTTTAGAAGTTTGGGGGT
62 AAATGAATTTTGGAAGTTTC-AGGTAAAAATGGGATTTTTAGAAGTTTGGGGGT
* * * * *
6712 AAAAATGGAATTTTTGGAGGTTTTGGGGTCAAAAATGAGAATTTTAGAAGTTTGGGGGTAAAAAT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTAGAAGTTTTGGGGTAAAAAT
* * * *
6777 GGGATTTTTGGAAGTTTCAGGAAAAAAATGGGATTTTTAAAAGTTCGGGGGT
66 --GAATTTTGGAAGTTTCAGG-TAAAAATGGGATTTTTAGAAGTTTGGGGGT
* * * * * * * *
6829 AAAGATGGGATTTTTGGAGGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTTTAGGGTAAAAAT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTAGAAGTTTTGGGGTAAAAAT
* ** * *
6894 GAGATTTTTGAAAGTTTGTTGGTAAAAATGGGATTTTTGGAAGTTTAGGGGT
66 GA-A-TTTTGGAAGTTT-CAGGTAAAAATGGGATTTTTAGAAGTTTGGGGGT
* * * * * **
6946 CAAAATGGGATTTTTAGAAGCTTCGAGGTCAAAAATGGGATTTTTA-AACGTTCGGGGGTAAAAA
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTAGAA-GTTTTGGGGTAAAAA
*
7010 CGAGATTTTTGGAAGTTTCAGG
65 TGA-A-TTTTGGAAGTTTCAGG
7032 ATCCTCGGGG
Statistics
Matches: 268, Mismatches: 42, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
115 8 0.03
116 26 0.10
117 228 0.85
118 6 0.02
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (114 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTAGAAGTTTTGGGGTAAAAAT
GAATTTTGGAAGTTTCAGGTAAAAATGGGATTTTTAGAAGTTTGGGGGT
Done.