Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012536.1 Kokia drynarioides strain JFW-HI SEQ_127544, 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: 3218
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1808 original size:30 final size:29
Alignment explanation
Indices: 1748--2089 Score: 335
Period size: 30 Copynumber: 11.4 Consensus size: 29
1738 GTCCTCATAA
1748 TTTTCCAAAATTACA-TTTAAGCCCCCTAAAC
1 TTTTCCAAAATTACATTTTAA---CCCTAAAC
*
1779 TTTTCCAACATTACATTTTAACTCCTAAAC
1 TTTTCCAAAATTACATTTTAAC-CCTAAAC
*
1809 TTTTCCAAAATTACATTTTAACCCTTTAAC
1 TTTTCCAAAATTACATTTTAACCC-TAAAC
*
1839 TTTTCCAAAATTACATTTTAACCACCAAAC
1 TTTTCCAAAATTACATTTTAACC-CTAAAC
* * * *
1869 TTTTCCAAAATAATATTTTGACCACCAAAC
1 TTTTCCAAAATTACATTTTAACC-CTAAAC
* * * *
1899 TTTTCCAAAATCATATATTAACCCCTGAAC
1 TTTTCCAAAATTACATTTTAA-CCCTAAAC
** *
1929 TTTTTTAAAATTACATTTTAAACCTTAAAC
1 TTTTCCAAAATTACATTTT-AACCCTAAAC
* * * *
1959 CTTTCCAAAATCATATTTTGAGCCCTAAAC
1 TTTTCCAAAATTACATTTT-AACCCTAAAC
*
1989 TTTTCCAAAATTACATTTTGACCCCTAAAC
1 TTTTCCAAAATTACATTTT-AACCCTAAAC
* * * *
2019 ATTTCCAAAATCATATTTTGACACCTAAAC
1 TTTTCCAAAATTACATTTTAAC-CCTAAAC
* *
2049 TTTTCCAAATTTACATTTTAACCCCAAAAC
1 TTTTCCAAAATTACATTTTAA-CCCTAAAC
2079 TTTTCCAAAAT
1 TTTTCCAAAAT
2090 CATNNNNNNN
Statistics
Matches: 259, Mismatches: 44, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
29 4 0.02
30 230 0.89
31 20 0.08
32 5 0.02
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (29 bp):
TTTTCCAAAATTACATTTTAACCCTAAAC
Found at i:1854 original size:60 final size:59
Alignment explanation
Indices: 1748--2092 Score: 388
Period size: 60 Copynumber: 5.7 Consensus size: 59
1738 GTCCTCATAA
* * *
1748 TTTTCCAAAATTACA-TTTAAGCCCCCTAAACTTTTCCAACATTACATTTTAACTCCTAAAC
1 TTTTCCAAAATTACATTTTAA--CCCCTAAACTTTTCCAAAATCATATTTTAAC-CCTAAAC
* * * * *
1809 TTTTCCAAAATTACATTTTAACCCTTTAACTTTTCCAAAATTACATTTTAACCACCAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTAACC-CTAAAC
* * * * *
1869 TTTTCCAAAATAATATTTTGACCACC-AAACTTTTCCAAAATCATATATTAACCCCTGAAC
1 TTTTCCAAAATTACATTTTAACC-CCTAAACTTTTCCAAAATCATATTTTAA-CCCTAAAC
** * * * *
1929 TTTTTTAAAATTACATTTTAAACCTTAAACCTTTCCAAAATCATATTTTGAGCCCTAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTT-AACCCTAAAC
* * *
1989 TTTTCCAAAATTACATTTTGACCCCTAAACATTTCCAAAATCATATTTTGACACCTAAAC
1 TTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTAAC-CCTAAAC
* *
2049 TTTTCCAAATTTACATTTTAACCCCAAAACTTTTCCAAAATCAT
1 TTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCAT
2093 NNNNNNNNNN
Statistics
Matches: 240, Mismatches: 37, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
59 3 0.01
60 213 0.89
61 19 0.08
62 5 0.02
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (59 bp):
TTTTCCAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTAACCCTAAAC
Found at i:2248 original size:60 final size:60
Alignment explanation
Indices: 2149--2599 Score: 499
Period size: 60 Copynumber: 7.5 Consensus size: 60
2139 NNNNACCACC
* * * * *
2149 AAACTTTTCCAAAATAATATTTTGACCAC-CAAACTTTTCCAAAATCATATGTTGACCCCT
1 AAACTTTTCCAAAATTACATTTTAACC-CTTAAACTTTTCCAAAATCATATTTTGACCCCT
* * * *
2209 GAACTTTTCTAAAATTACATTTTAACCCTTAAACCTTTCCAAAATCATATTTTGAGCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTGACCCCT
* * *
2269 AAACTTTTCCAAAATTACATTTTAACCCCTAAACATTTCCAAAATCATATTTTGACACCT
1 AAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTGACCCCT
* **
2329 AAACTTTTCCAAATTTACATTTTAACCCCAAAACTTTTCCAAAATCATATTTTGACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTGACCCCT
* * * *
2389 AAACTTTTCTAAATTTACATTTTTACCCCTAAACTTTTCCAAAATCATATTTTGACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTGACCCCT
* ** * * * * * * *
2449 AAATTTTTAAAAAAAATCATATTTTGACCCTTAAACTATTCCAAAATTACATTTTGACCTCT
1 AAACTTTT--CCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTGACCCCT
* * * * * * * * *
2511 AAACTTTTCTAAAATCATATTTTGATCCTCAAACTTTTCCAAAATCACATTTTAACCCCC
1 AAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTGACCCCT
* * *
2571 GAACTTTTCCAAAATCACATTTTGACCCT
1 AAACTTTTCCAAAATTACATTTTAACCCT
2600 CGAACTTGTC
Statistics
Matches: 340, Mismatches: 48, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
59 1 0.00
60 291 0.86
62 48 0.14
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.37
Consensus pattern (60 bp):
AAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTGACCCCT
Found at i:2369 original size:284 final size:234
Alignment explanation
Indices: 2143--2598 Score: 454
Period size: 242 Copynumber: 1.9 Consensus size: 234
2133 NNNNNNNNNN
* *
2143 ACCACCAAACTTTTCCAAAATAATATTTTGACCACCAAACTTTTCCAAAATCATATGTTGACCCC
1 ACCACCAAACTTTTCCAAAATAATATTTTGACCACCAAACTTTTCCAAAATCATATATTAACCCC
*
2208 TGAACTTTTCTAAAATTACATTTTAACCCTTAAACCTTTCCAAAATCATATTTTGAGCCCTAAAC
66 TGAACTTTTCTAAAATTACATTTTAAACCTTAAACCTTTCCAAAATCATATTTTGAGCCCTAAAC
2273 TTTTCCAAAATTACATTTTAACCCCTAAACATTTCCAAAATCATATTTTGACACCTAAACTTTTC
131 TTTTCCAAAATTACATTTTAACCCCTAAACATTTCCAAAATCATATTTTGACACCTAAACTTTTC
2338 CAAATTTACATTTTAACCCCAAAACTTTTCCAAAATCATATTTT
196 CAAATTTACATTTTAACCCCAAAACTTTTCCAAAATC--A---T
* * * * * * *
2382 GACC-CCTAAACTTTTCTAAATTTACATTTTTACC-CCTAAACTTTTCCAAAATCATATTTTGAC
1 -ACCACC-AAACTTTTCCAAAATAATATTTTGACCACC-AAACTTTTCCAAAATCATATATTAAC
* * ** * * * * * *
2445 CCCTAAATTTTTAAAAAAAATCATATTTTGACCCTTAAA-CTATTCCAAAATTACATTTTGA-CC
63 CCCTGAACTTTT--CTAAAATTACATTTTAAACCTTAAACCT-TTCCAAAATCATATTTTGAGCC
* * * * * * * * * **
2508 TCTAAACTTTTCTAAAATCATATTTTGA-TCCTCAAACTTTTCCAAAATCACATTTTAACCCCCG
125 -CTAAACTTTTCCAAAATTACATTTTAACCCCT-AAACATTTCCAAAATCATATTTTGACACCTA
* * *
2572 AACTTTTCCAAAATCACATTTTGACCC
188 AACTTTTCCAAATTTACATTTTAACCC
2599 TCGAACTTGT
Statistics
Matches: 180, Mismatches: 29, Indels: 12
0.81 0.13 0.05
Matches are distributed among these distances:
239 4 0.02
240 60 0.33
241 7 0.04
242 109 0.61
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (234 bp):
ACCACCAAACTTTTCCAAAATAATATTTTGACCACCAAACTTTTCCAAAATCATATATTAACCCC
TGAACTTTTCTAAAATTACATTTTAAACCTTAAACCTTTCCAAAATCATATTTTGAGCCCTAAAC
TTTTCCAAAATTACATTTTAACCCCTAAACATTTCCAAAATCATATTTTGACACCTAAACTTTTC
CAAATTTACATTTTAACCCCAAAACTTTTCCAAAATCAT
Found at i:2606 original size:30 final size:29
Alignment explanation
Indices: 2147--2598 Score: 418
Period size: 30 Copynumber: 15.0 Consensus size: 29
2137 NNNNNNACCA
*
2147 CCAAACTTTTCCAAAATAATATTTTGACC
1 CCAAACTTTTCCAAAATCATATTTTGACC
*
2176 ACCAAACTTTTCCAAAATCATATGTTGACC
1 -CCAAACTTTTCCAAAATCATATTTTGACC
* * * * *
2206 CCTGAACTTTTCTAAAATTACATTTTAACC
1 CC-AAACTTTTCCAAAATCATATTTTGACC
* *
2236 CTTAAACCTTTCCAAAATCATATTTTGAGCC
1 C-CAAACTTTTCCAAAATCATATTTTGA-CC
* * * *
2267 CTAAACTTTTCCAAAATTACATTTTAACC
1 CCAAACTTTTCCAAAATCATATTTTGACC
*
2296 CCTAAACATTTCCAAAATCATATTTTGACAC
1 CC-AAACTTTTCCAAAATCATATTTTGAC-C
* * * * *
2327 CTAAACTTTTCCAAATTTACATTTTAACC
1 CCAAACTTTTCCAAAATCATATTTTGACC
2356 CCAAAACTTTTCCAAAATCATATTTTGACC
1 CC-AAACTTTTCCAAAATCATATTTTGACC
* * * * *
2386 CCTAAACTTTTCTAAATTTACATTTTTACC
1 CC-AAACTTTTCCAAAATCATATTTTGACC
2416 CCTAAACTTTTCCAAAATCATATTTTGACC
1 CC-AAACTTTTCCAAAATCATATTTTGACC
* **
2446 CCTAAATTTTTAAAAAAAATCATATTTTGACC
1 CC-AAACTTTT--CCAAAATCATATTTTGACC
* * * *
2478 CTTAAACTATTCCAAAATTACATTTTGACC
1 C-CAAACTTTTCCAAAATCATATTTTGACC
* *
2508 TCTAAACTTTTCTAAAATCATATTTTGATCC
1 -CCAAACTTTTCCAAAATCATATTTTGA-CC
* * *
2539 TCAAACTTTTCCAAAATCACATTTTAACCC
1 CCAAACTTTTCCAAAATCATATTTTGA-CC
* *
2569 CCGAACTTTTCCAAAATCACATTTTGACC
1 CCAAACTTTTCCAAAATCATATTTTGACC
2598 C
1 C
2599 TCGAACTTGT
Statistics
Matches: 342, Mismatches: 69, Indels: 23
0.79 0.16 0.05
Matches are distributed among these distances:
29 10 0.03
30 300 0.88
31 8 0.02
32 24 0.07
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
CCAAACTTTTCCAAAATCATATTTTGACC
Found at i:2623 original size:90 final size:90
Alignment explanation
Indices: 2148--2615 Score: 505
Period size: 90 Copynumber: 5.2 Consensus size: 90
2138 NNNNNACCAC
* * *
2148 CAAACTTTTCCAAAATAATATTTTGACCACC-AAACTTTTCCAAAATCATATGTTGACCCCTGAA
1 CAAACTTTTCCAAAATCATATTTTGACC-CCTAAACTTTTCCAAAATCATATTTTGACCCCTAAA
* *
2212 CTTTTCTAAAATTACATTTTAACCCT
65 CTTTTCCAAAATTACATTTTGACCCT
* * * * * *
2238 TAAACCTTTCCAAAATCATATTTTGAGCCCTAAACTTTTCCAAAATTACATTTTAACCCCTAAAC
1 CAAACTTTTCCAAAATCATATTTTGACCCCTAAACTTTTCCAAAATCATATTTTGACCCCTAAAC
* * *
2303 ATTTCCAAAATCATATTTTGACACCT
66 TTTTCCAAAATTACATTTTGAC-CCT
* * * * *
2329 -AAACTTTTCCAAATTTACATTTTAACCCCAAAACTTTTCCAAAATCATATTTTGACCCCTAAAC
1 CAAACTTTTCCAAAATCATATTTTGACCCCTAAACTTTTCCAAAATCATATTTTGACCCCTAAAC
* * *
2393 TTTTCTAAATTTACATTTTTACCC-
66 TTTTCCAAAATTACATTTTGACCCT
* ** *
2417 CTAAACTTTTCCAAAATCATATTTTGACCCCTAAATTTTTAAAAAAAATCATATTTTGACCCTTA
1 C-AAACTTTTCCAAAATCATATTTTGACCCCTAAACTTTT--CCAAAATCATATTTTGACCCCTA
*
2482 AACTATTCCAAAATTACATTTTGA-CCT
63 AACTTTTCCAAAATTACATTTTGACCCT
* * * * **
2509 CTAAACTTTTCTAAAATCATATTTTGA-TCCTCAAACTTTTCCAAAATCACATTTTAACCCCCGA
1 C-AAACTTTTCCAAAATCATATTTTGACCCCT-AAACTTTTCCAAAATCATATTTTGACCCCTAA
*
2573 ACTTTTCCAAAATCACATTTTGACCCT
64 ACTTTTCCAAAATTACATTTTGACCCT
* * *
2600 CGAACTTGTCTAAAAT
1 CAAACTTTTCCAAAAT
2616 TTTATTTTCA
Statistics
Matches: 312, Mismatches: 57, Indels: 18
0.81 0.15 0.05
Matches are distributed among these distances:
89 4 0.01
90 223 0.71
91 12 0.04
92 73 0.23
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.37
Consensus pattern (90 bp):
CAAACTTTTCCAAAATCATATTTTGACCCCTAAACTTTTCCAAAATCATATTTTGACCCCTAAAC
TTTTCCAAAATTACATTTTGACCCT
Done.