Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007123.1 Kokia drynarioides strain JFW-HI SEQ_121734, 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: 19796
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:567 original size:30 final size:30
Alignment explanation
Indices: 474--860 Score: 135
Period size: 30 Copynumber: 13.1 Consensus size: 30
464 GGAAGGTTTG
* * * *
474 GGGTC-AAATTTGAATTTTGGAAAGTTCAA
1 GGGTCAAAATATGATTTTTGAAAAGTTTAA
* **
503 -GGTCAAAATATGATTTTT-AGAAAG-ATCG
1 GGGTCAAAATATGATTTTTGA-AAAGTTTAA
531 GAGGTCAAAATATGATTTTTGAAAAGTTTAA
1 G-GGTCAAAATATGATTTTTGAAAAGTTTAA
* * * * * * *
562 GGGTC-AATTCTAAAATTTGGGAAAGTTT-G
1 GGGTCAAAATAT-GATTTTTGAAAAGTTTAA
* *
591 GTGGTCATAATGTAT-TTTTTTG-AAAG-TTAA
1 G-GGTCA-AA-ATATGATTTTTGAAAAGTTTAA
* * * *
621 GAGTCAAAATGTGATTTCT-AGAAAG-TTAGG
1 GGGTCAAAATATGATTTTTGA-AAAGTTTA-A
* *
651 GGGTTAAAATATGATTTTTGAAAAGTTTAT
1 GGGTCAAAATATGATTTTTGAAAAGTTTAA
* * * **
681 GGGTTAAAATGTAATTTTTGAAAAG--TGC
1 GGGTCAAAATATGATTTTTGAAAAGTTTAA
* * * * *
709 GGGAGCCAAATTTGAATTTTTGGAACGTTT-A
1 GGG-TCAAAATATG-ATTTTTGAAAAGTTTAA
* * * *
740 GGAGTTAAAATGTAATTTTTTAAAAGTTT-A
1 GG-GTCAAAATATGATTTTTGAAAAGTTTAA
* **
770 GGGTC-AAA-ATGAATTTTTGAAATGTTTGG
1 GGGTCAAAATATG-ATTTTTGAAAAGTTTAA
799 GGGTCAAAATATGATTTTTGAAAAGTTTGAA
1 GGGTCAAAATATGATTTTTGAAAAGTTT-AA
* * ** *
830 -AGTTAAAATATGATTTTAAAAAAGTTCAA
1 GGGTCAAAATATGATTTTTGAAAAGTTTAA
859 GG
1 GG
861 ACTTCTTGGA
Statistics
Matches: 260, Mismatches: 69, Indels: 57
0.67 0.18 0.15
Matches are distributed among these distances:
27 3 0.01
28 30 0.12
29 47 0.18
30 153 0.59
31 21 0.08
32 4 0.02
33 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.37
Consensus pattern (30 bp):
GGGTCAAAATATGATTTTTGAAAAGTTTAA
Found at i:706 original size:60 final size:59
Alignment explanation
Indices: 607--825 Score: 162
Period size: 60 Copynumber: 3.7 Consensus size: 59
597 ATAATGTATT
* * * * * *
607 TTTTTG-AAAGTTAAGAGTCAAAATGTGATTTCT-AGAAAGTTAGGGGGTTAAAATATG-A
1 TTTTTGAAAAGTTTAGGGTTAAAATGTAATTTTTGA-AAAGTTAGGGAG-TAAAATATGAA
** ** *
665 TTTTTGAAAAGTTTATGGGTTAAAATGTAATTTTTGAAAAGTGCGGGAGCCAAATTTGAA
1 TTTTTGAAAAGTTTA-GGGTTAAAATGTAATTTTTGAAAAGTTAGGGAGTAAAATATGAA
* * * *
725 TTTTTGGAACGTTTAGGAGTTAAAATGTAATTTTTTAAAAGTTTA-GG-GTCAAA-ATGAA
1 TTTTTGAAAAGTTTAGG-GTTAAAATGTAATTTTTGAAAAG-TTAGGGAGTAAAATATGAA
* * * * *
783 TTTTTGAAATGTTTGGGGGTCAAAATATGATTTTTGAAAAGTT
1 TTTTTGAAAAGTTT-AGGGTTAAAATGTAATTTTTGAAAAGTT
826 TGAAAGTTAA
Statistics
Matches: 129, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
57 2 0.02
58 41 0.32
59 22 0.17
60 62 0.48
61 2 0.02
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (59 bp):
TTTTTGAAAAGTTTAGGGTTAAAATGTAATTTTTGAAAAGTTAGGGAGTAAAATATGAA
Found at i:729 original size:119 final size:119
Alignment explanation
Indices: 478--824 Score: 282
Period size: 119 Copynumber: 2.9 Consensus size: 119
468 GGTTTGGGGT
* * * * *
478 CAAATTTGAA-TTTTGGAAAGTTCAAG-GTCAAAATATGATTTTTAGAAAGATCGGAGGTCAAAA
1 CAAATTTGAATTTTTGGAAAGTT-AAGAGTCAAAATGTGATTTTTAGAAAGTTAGGGGGTTAAAA
* * * * * * ** *
541 TATGATTTTTGAAAAGTTTAAGGG-TCAATTCTAAAATTTGGGAAAGTTTGGTGGT
65 TATGATTTTTGAAAAGTTTAAGGGTTAAAATAT-AATTTTTGAAAAGTGCGGTGGC
* * * *
596 CATAATGT-ATTTTTTTGAAAGTTAAGAGTCAAAATGTGATTTCTAGAAAGTTAGGGGGTTAAAA
1 CA-AATTTGAATTTTTGGAAAGTTAAGAGTCAAAATGTGATTTTTAGAAAGTTAGGGGGTTAAAA
* *
660 TATGATTTTTGAAAAGTTTATGGGTTAAAATGTAATTTTTGAAAAGTGCGG-GAGC
65 TATGATTTTTGAAAAGTTTAAGGGTTAAAATATAATTTTTGAAAAGTGCGGTG-GC
* * * * *
715 CAAATTTGAATTTTTGGAACGTTTAGGAGTTAAAATGTAATTTTTTA-AAAGTTTA--GGG-TCA
1 CAAATTTGAATTTTTGGAAAG-TTAAGAGTCAAAATGTGA-TTTTTAGAAAG-TTAGGGGGTTAA
* ** * *
776 AA-ATGAATTTTTGAAATGTTTGGGGGTCAAAATATGATTTTTGAAAAGT
63 AATATG-ATTTTTGAAAAGTTTAAGGGTTAAAATATAATTTTTGAAAAGT
825 TTGAAAGTTA
Statistics
Matches: 185, Mismatches: 34, Indels: 20
0.77 0.14 0.08
Matches are distributed among these distances:
117 3 0.02
118 52 0.28
119 98 0.53
120 24 0.13
121 8 0.04
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (119 bp):
CAAATTTGAATTTTTGGAAAGTTAAGAGTCAAAATGTGATTTTTAGAAAGTTAGGGGGTTAAAAT
ATGATTTTTGAAAAGTTTAAGGGTTAAAATATAATTTTTGAAAAGTGCGGTGGC
Found at i:846 original size:88 final size:90
Alignment explanation
Indices: 653--855 Score: 225
Period size: 88 Copynumber: 2.3 Consensus size: 90
643 AAGTTAGGGG
* * *
653 GTTAAAATATGATTTTTGAAAAGTTTATGGGTTAAAATGTAATTTTTGAAAAGTGCGGGAGCCAA
1 GTTAAAATATGATTTTTAAAAAGTTTATGGGTCAAAATGTAATTTTTGAAAAGTGCGGGAGCAAA
* * * *
718 ATTTGAATTTTTGGAACGTTTAGGA
66 ATATGAATTTTTGAAAAGTTTAGAA
* * * * ** *
743 GTTAAAATGTAATTTTTTAAAAGTTTA-GGGTCAAAATG-AATTTTTGAAATGTTTGGGGGTCAA
1 GTTAAAATATGATTTTTAAAAAGTTTATGGGTCAAAATGTAATTTTTGAAAAGTGCGGGAG-CAA
806 AATATG-ATTTTTGAAAAGTTT-GAAA
65 AATATGAATTTTTGAAAAGTTTAG-AA
*
831 GTTAAAATATGATTTTAAAAAAGTT
1 GTTAAAATATGATTTTTAAAAAGTT
856 CAAGGACTTC
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
87 1 0.01
88 52 0.55
89 17 0.18
90 24 0.26
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (90 bp):
GTTAAAATATGATTTTTAAAAAGTTTATGGGTCAAAATGTAATTTTTGAAAAGTGCGGGAGCAAA
ATATGAATTTTTGAAAAGTTTAGAA
Found at i:1998 original size:19 final size:19
Alignment explanation
Indices: 1967--2039 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
1957 AAAAATATAA
1967 ATTTTGAAATTTTTTTAAAT
1 ATTTTG-AATTTTTTTAAAT
*** *
1987 ATTTTGAATTTTAAGAATT
1 ATTTTGAATTTTTTTAAAT
* *
2006 ATTTTAAATTTTTTAAAAAT
1 ATTTTGAATTTTTT-TAAAT
*
2026 ATTTT-TATTTTTTT
1 ATTTTGAATTTTTTT
2040 GTAATTTTTG
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 27 0.66
20 14 0.34
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
ATTTTGAATTTTTTTAAAT
Found at i:2005 original size:28 final size:27
Alignment explanation
Indices: 1943--2022 Score: 81
Period size: 28 Copynumber: 3.0 Consensus size: 27
1933 TTTAAAAAAA
* * *
1943 TTTATAATTTTTTTAAA-AATATAAAT
1 TTTAAAATTTTTTTAAATATTTTAAAT
* *
1969 TTTGAAATTTTTTTAAATATTTTGAAT
1 TTTAAAATTTTTTTAAATATTTTAAAT
* *
1996 TTTAAGAATTATTTTAAATTTTTTAAA
1 TTTAA-AATTTTTTTAAATATTTTAAA
2023 AATATTTTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
26 15 0.35
27 10 0.23
28 18 0.42
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (27 bp):
TTTAAAATTTTTTTAAATATTTTAAAT
Found at i:2037 original size:20 final size:20
Alignment explanation
Indices: 1929--2039 Score: 70
Period size: 20 Copynumber: 5.3 Consensus size: 20
1919 TCTTTAGAAT
*
1929 TTTTTTTAAAAAAATTTATAA
1 TTTTTTTAAAAATATTT-TAA
1950 TTTTTTTAAAAATATAAATTTTGAAA
1 TTTTTTT-AAAA-AT--ATTTT--AA
1976 TTTTTTT--AAATATTTTGAA
1 TTTTTTTAAAAATATTTT-AA
*
1995 ---TTTTAAGAATTATTTTAA
1 TTTTTTTAA-AAATATTTTAA
* *
2013 ATTTTTTAAAAATATTTTTA
1 TTTTTTTAAAAATATTTTAA
2033 TTTTTTT
1 TTTTTTT
2040 GTAATTTTTG
Statistics
Matches: 72, Mismatches: 6, Indels: 25
0.70 0.06 0.24
Matches are distributed among these distances:
16 4 0.06
18 2 0.03
19 10 0.14
20 20 0.28
21 13 0.18
22 6 0.08
23 3 0.04
24 1 0.01
25 4 0.06
26 9 0.12
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTTTAAAAATATTTTAA
Found at i:5576 original size:23 final size:23
Alignment explanation
Indices: 5525--5576 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
5515 ATTTTAAAAA
* *
5525 TATATATTTATATTCTTTTAATT
1 TATATATTTATATTCTTTGAAAT
*
5548 TA-ATATTTTTATT-TATTGAAAT
1 TATATATTTATATTCT-TTGAAAT
5570 TATATAT
1 TATATAT
5577 ATAGTCATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 1 0.04
22 17 0.71
23 6 0.25
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
TATATATTTATATTCTTTGAAAT
Found at i:6147 original size:5 final size:5
Alignment explanation
Indices: 6139--6167 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
6129 GAGGCATGCA
6139 TCACC TCACC TCACC TCACC TCACC TCAC
1 TCACC TCACC TCACC TCACC TCACC TCAC
6168 TTTTCTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21
Consensus pattern (5 bp):
TCACC
Found at i:12243 original size:19 final size:18
Alignment explanation
Indices: 12204--12245 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
12194 TTTATGCAAT
*
12204 GAAAAATATGAGAAGAGA
1 GAAAAATATGAAAAGAGA
12222 GAAAAATAATGGAAAAGA-A
1 GAAAAAT-AT-GAAAAGAGA
12241 GAAAA
1 GAAAA
12246 GGAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 8 0.38
20 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.10
Consensus pattern (18 bp):
GAAAAATATGAAAAGAGA
Found at i:17126 original size:30 final size:30
Alignment explanation
Indices: 17067--17131 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 30
17057 TGGGTGTCTG
*
17067 ATTTTTTGAAAGTTAGTATGACTTATTTGTT
1 ATTTTTTGAAAGTTAG-ATGACTTATTTGTC
17098 ATTTTTTGAAAGTT-GAGTGACTGT-TTTGTC
1 ATTTTTTGAAAGTTAGA-TGACT-TATTTGTC
17128 ATTT
1 ATTT
17132 ACCTTTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
29 1 0.03
30 15 0.48
31 15 0.48
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (30 bp):
ATTTTTTGAAAGTTAGATGACTTATTTGTC
Done.