Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001546.1 Kokia drynarioides strain JFW-HI SEQ_113123, 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: 27666
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2166 original size:383 final size:383
Alignment explanation
Indices: 1444--2167 Score: 1193
Period size: 383 Copynumber: 1.9 Consensus size: 383
1434 GAATGAATTT
* * *
1444 AGGATTAGGTCATTAGGTTAGTTTTTAATTCTTGTATAATAAATTAAGAGGTTGAAGACAGTAAT
1 AGGATTAGATCATTAGGTTAGTTTTTAATTCTTGCATAATAAATTAAGAGGTTGAAGACAATAAT
* * * * *
1509 TGAACAACCTAGAAAAATAAGAGTGTGACAATATATATGTACATTTATAAGATAGGACGTTGAAA
66 TGAACAACCTAAAAAAATAAAAGTGTGACAATATATATGTACATGTATAAGATAGAACATTGAAA
*
1574 GAGCTTGGTACTTGGAATGATGAAAATATATAAACTTTTTCAAACCCTTTTTAACATAAATTCAA
131 GAGCTTGGTACTTGGAACGATGAAAATATATAAACTTTTTCAAACCCTTTTTAACATAAATTCAA
** *
1639 GCACGTTCTGAGAAATTAACATCGAAAAATATAATTTAATGATAAAATAATTAATTTGTGCAAAA
196 GCAAATTCTGAGAAATTAACATCGAAAAATACAATTTAATGATAAAATAATTAATTTGTGCAAAA
1704 ATTTACAACATATTGATTTTTAATTATTTTTACAAATATAAAGCATGAATTTGATGATTTTTTTG
261 ATTTACAACATATTGATTTTTAATTATTTTTACAAATATAAAGCATGAATTTGATGATTTTTTTG
1769 ATATTTTGGCACAATTGGTGCACTACAAGAAAATAGGTTTTTAGCGGCTTTTTGTAAG
326 ATATTTTGGCACAATTGGTGCACTACAAGAAAATAGGTTTTTAGCGGCTTTTTGTAAG
*
1827 AGGATTTGATCATTAGGTTAAG-TTTTAATTCTTGCATAATAAATTAAGAGGTTGAAGACAATAA
1 AGGATTAGATCATTAGGTT-AGTTTTTAATTCTTGCATAATAAATTAAGAGGTTGAAGACAATAA
* *
1891 TTGAACAACCTAAAAAAATAAAAGTGTGACAATATATATGTACATGTATAGGATTGAACATTGAA
65 TTGAACAACCTAAAAAAATAAAAGTGTGACAATATATATGTACATGTATAAGATAGAACATTGAA
*
1956 AGAGCTTGGTACTTGGAACGATGAAAATATATAGACTTTTTCAAACCCTTTTTAATC-TAAATTC
130 AGAGCTTGGTACTTGGAACGATGAAAATATATAAACTTTTTCAAACCCTTTTTAA-CATAAATTC
** * * *
2020 AAGCAAATTCTGAGAAATTAATGTCGAAAAATACAATTTAATTATAAAATAATTATTTTGTGCTA
194 AAGCAAATTCTGAGAAATTAACATCGAAAAATACAATTTAATGATAAAATAATTAATTTGTGCAA
* *
2085 AAATTTCCAACATATTGATTTTTAATTATTTTTATAAATATAAAGCATGAATTTGATGATTTTTT
259 AAATTTACAACATATTGATTTTTAATTATTTTTACAAATATAAAGCATGAATTTGATGATTTTTT
2150 TGATAGTTTT-GCACAATT
324 TGATA-TTTTGGCACAATT
2168 TGTGAAAATC
Statistics
Matches: 315, Mismatches: 23, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
383 308 0.98
384 7 0.02
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (383 bp):
AGGATTAGATCATTAGGTTAGTTTTTAATTCTTGCATAATAAATTAAGAGGTTGAAGACAATAAT
TGAACAACCTAAAAAAATAAAAGTGTGACAATATATATGTACATGTATAAGATAGAACATTGAAA
GAGCTTGGTACTTGGAACGATGAAAATATATAAACTTTTTCAAACCCTTTTTAACATAAATTCAA
GCAAATTCTGAGAAATTAACATCGAAAAATACAATTTAATGATAAAATAATTAATTTGTGCAAAA
ATTTACAACATATTGATTTTTAATTATTTTTACAAATATAAAGCATGAATTTGATGATTTTTTTG
ATATTTTGGCACAATTGGTGCACTACAAGAAAATAGGTTTTTAGCGGCTTTTTGTAAG
Found at i:4920 original size:23 final size:21
Alignment explanation
Indices: 4866--4921 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
4856 CTGGCCTCGA
*
4866 TGTCGTGACACACCTAGCATT
1 TGTCGCGACACACCTAGCATT
*
4887 TGTCGCGACACACCTATCATT
1 TGTCGCGACACACCTAGCATT
4908 TGTCGCGACACACC
1 TGTCGCGACACACC
4922 AACATAACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (21 bp):
TGTCGCGACACACCTAGCATT
Found at i:8302 original size:6 final size:7
Alignment explanation
Indices: 8273--8301 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
8263 ATACTATTTA
8273 TTAGTTT
1 TTAGTTT
8280 TTAGTTT
1 TTAGTTT
8287 TTAGTTT
1 TTAGTTT
8294 TTAGTTT
1 TTAGTTT
8301 T
1 T
8302 ATTTTGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (7 bp):
TTAGTTT
Found at i:8314 original size:13 final size:13
Alignment explanation
Indices: 8267--8318 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
8257 TTAAACATAC
8267 TATTTATTAGTTTT
1 TATTT-TTAGTTTT
8281 TAGTTTTTAGTTTT
1 TA-TTTTTAGTTTT
*
8295 TAGTTTTA-TTTT
1 TATTTTTAGTTTT
8307 GTATTTTT-GTTT
1 -TATTTTTAGTTT
8319 GAAACGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 4 0.12
13 14 0.42
14 12 0.36
15 3 0.09
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (13 bp):
TATTTTTAGTTTT
Found at i:24117 original size:21 final size:21
Alignment explanation
Indices: 24091--24151 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
24081 GCAAGCTGAA
24091 GAAGAAGAAGAAGAAGATCCT
1 GAAGAAGAAGAAGAAGATCCT
*
24112 GAAGAAGAAGAAGAAGACCCT
1 GAAGAAGAAGAAGAAGATCCT
* *
24133 GTAGAA-ATTGAAGAAGATC
1 GAAGAAGA-AGAAGAAGATC
24152 TTTCGGTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.51, C:0.10, G:0.28, T:0.11
Consensus pattern (21 bp):
GAAGAAGAAGAAGAAGATCCT
Found at i:26506 original size:3 final size:3
Alignment explanation
Indices: 26498--26557 Score: 56
Period size: 3 Copynumber: 20.0 Consensus size: 3
26488 GTATTGAGGC
26498 AGA AGA AGA AGAA AGA A-A AGA AGA AG- AGAA AGA AG- AGA AGAA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AG-A AGA AGA AGA AG-A AGA
26543 A-A AGAA AGA AGA AGA
1 AGA AG-A AGA AGA AGA
26558 TATTGCCCCG
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
2 8 0.16
3 30 0.61
4 11 0.22
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:27632 original size:2 final size:2
Alignment explanation
Indices: 27625--27666 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
27615 TGATAAAAAG
27625 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.