Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005613.1 Kokia drynarioides strain JFW-HI SEQ_119763, 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: 22301
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:487 original size:16 final size:16
Alignment explanation
Indices: 466--504 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
456 CTGTTCTTCC
* * *
466 TTCTTTTGTTTTTTTT
1 TTCTTTTCTTTATTTA
482 TTCTTTTCTTTATTTA
1 TTCTTTTCTTTATTTA
498 TTCTTTT
1 TTCTTTT
505 ATTTCTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82
Consensus pattern (16 bp):
TTCTTTTCTTTATTTA
Found at i:2525 original size:20 final size:21
Alignment explanation
Indices: 2501--2554 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
2491 TTTTTTATAT
2501 TTTTTTAAAAATATT-TATGAA
1 TTTTTTAAAAAT-TTATATGAA
* *
2522 -TTTTTATAAATTTATTTGAA
1 TTTTTTAAAAATTTATATGAA
2542 TTTTTTAAAAATT
1 TTTTTTAAAAATT
2555 ATAACCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTTTTAAAAATTTATATGAA
Found at i:2873 original size:6 final size:6
Alignment explanation
Indices: 2862--2889 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2852 AGAAACAAAG
2862 ATTGCT ATTGCT ATTGCT ATTGCT ATTG
1 ATTGCT ATTGCT ATTGCT ATTGCT ATTG
2890 GTTCTTTNTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (6 bp):
ATTGCT
Found at i:13260 original size:14 final size:14
Alignment explanation
Indices: 13223--13269 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
13213 TGGAAAAAAT
*
13223 AAAAAGAAAT-TAA
1 AAAAAAAAATCTAA
13236 AAAATATAAAATCTAA
1 AAAA-A-AAAATCTAA
13252 AAAAAAAAATCTTAA
1 AAAAAAAAATC-TAA
13267 AAA
1 AAA
13270 GTGTATTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 4 0.14
14 7 0.24
15 11 0.38
16 7 0.24
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.19
Consensus pattern (14 bp):
AAAAAAAAATCTAA
Found at i:19619 original size:263 final size:265
Alignment explanation
Indices: 19150--19679 Score: 974
Period size: 263 Copynumber: 2.0 Consensus size: 265
19140 GGGTGTTCTA
19150 TATAATTATTTAAATTAAATGTTTAGGTTGTTGGCAAAAATAAATAAAAAAGTCAACTCCTAATT
1 TATAATTATTTAAATTAAATGTTTAGGTTGTTGGCAAAAATAAATAAAAAAGTCAACTCCTAATT
* * *
19215 TTGGTTTATTTTATTTTTCTGCTATTAATTTATAAAAAATTATGTTTTAGTTATTAACGTTATCG
66 TTGGTTTATTTTATTTTTCTGCCATTAATTTATAAAAAATTAAGTTTTAGTTATTAACGGTATCG
19280 ATTTTTAATATTTTGGTCATTCGTCCATTAACAATCATTAGAGTCCTAAAGGAAAAGTGACGTGA
131 ATTTTTAATATTTTGGTCATTCGTCCATTAACAATCATTAGAGTCCTAAAGGAAAAGTGACGTGA
19345 CGCTTTAACTCAAGGGTTAATATTTAATTTGATATTTGAATTATAGCTGAAATATTCAAGTTGAT
196 CGCTTTAACTCAAGGGTTAATATTTAATTTGATATTTGAATTATAGCTGAAATATTCAAGTTGAT
19410 ATTTT
261 ATTTT
*
19415 TATAATTATTTAAATTAAATGTTTAGGTTGTTGGCAAAAAT-AA-AAAAAGGTCAACTCCTAATT
1 TATAATTATTTAAATTAAATGTTTAGGTTGTTGGCAAAAATAAATAAAAAAGTCAACTCCTAATT
* *
19478 TTGGTTTATTTTATTTTTCTGCCATTAATTTATAAAAAGTTAAGTTTTGGTTATTAACGGTATCG
66 TTGGTTTATTTTATTTTTCTGCCATTAATTTATAAAAAATTAAGTTTTAGTTATTAACGGTATCG
* *
19543 ATTTTTAATATTTTGGTCATTCGTCCATTAACAGTCATTAGAGTTCTAAAGGAAAAGTGACGTGA
131 ATTTTTAATATTTTGGTCATTCGTCCATTAACAATCATTAGAGTCCTAAAGGAAAAGTGACGTGA
19608 CGCTTTAACTCAAGGGTTAATATTTAATTTGATATTTGAATTATAGCTGAAATATTCAAGTTGAT
196 CGCTTTAACTCAAGGGTTAATATTTAATTTGATATTTGAATTATAGCTGAAATATTCAAGTTGAT
19673 ATTTT
261 ATTTT
19678 TA
1 TA
19680 CAACTTTTTT
Statistics
Matches: 257, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
263 214 0.83
264 2 0.01
265 41 0.16
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (265 bp):
TATAATTATTTAAATTAAATGTTTAGGTTGTTGGCAAAAATAAATAAAAAAGTCAACTCCTAATT
TTGGTTTATTTTATTTTTCTGCCATTAATTTATAAAAAATTAAGTTTTAGTTATTAACGGTATCG
ATTTTTAATATTTTGGTCATTCGTCCATTAACAATCATTAGAGTCCTAAAGGAAAAGTGACGTGA
CGCTTTAACTCAAGGGTTAATATTTAATTTGATATTTGAATTATAGCTGAAATATTCAAGTTGAT
ATTTT
Found at i:19980 original size:94 final size:94
Alignment explanation
Indices: 19819--20006 Score: 349
Period size: 94 Copynumber: 2.0 Consensus size: 94
19809 TCATATTCAT
19819 CTCTCGATTCTTCAAAAGAAGAGCTCAACAATTTGATTCTACAAACTACATTCCCATGCATTATT
1 CTCTCGATTCTTCAAAAGAAGAGCTCAACAATTTGATTCTACAAACTACATTCCCATGCATTATT
*
19884 TTTTAGGTAAGTTTTTACTCTTTGGTAAA
66 TTTTACGTAAGTTTTTACTCTTTGGTAAA
* *
19913 CTCTCGATTCTTCAAAAGAAGAGCTCAACAATTTGATTCTACGATCTACATTCCCATGCATTATT
1 CTCTCGATTCTTCAAAAGAAGAGCTCAACAATTTGATTCTACAAACTACATTCCCATGCATTATT
19978 TTTTACGTAAGTTTTTACTCTTTGGTAAA
66 TTTTACGTAAGTTTTTACTCTTTGGTAAA
20007 GCATATATCT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.39
Consensus pattern (94 bp):
CTCTCGATTCTTCAAAAGAAGAGCTCAACAATTTGATTCTACAAACTACATTCCCATGCATTATT
TTTTACGTAAGTTTTTACTCTTTGGTAAA
Found at i:22293 original size:286 final size:291
Alignment explanation
Indices: 21564--22301 Score: 1067
Period size: 298 Copynumber: 2.5 Consensus size: 291
21554 CTACTCCCTA
*
21564 AGTATTATAGTACACTAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACAT
1 AGTATTATAGTGCACTAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACAT
* * * ** * *
21629 TACTTGTAGGTCCTAGGTTCTCTGTAGTAGGTAAATTAGGTTCGTCGAGTTTCCAATAGCCTTTA
66 TACTTGTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTAGGTTCGTCAAGTTTCCAACAGCCTTTA
* * * * * *
21694 TATCGCTAGAGAATTATGAAAAATGAGAATACATGTGAAAGATTTCATATGAGATATATGCATGA
131 TATCGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAAATTCCATATAAGATATATGCATGA
* * *
21759 TTCAAGAAATGATCATTGACAAGCTGTGAAATGATCCAAATTTTTTGAATGATATATAGTCGAAT
196 TTCAAGAAATGAGCATTGACAAGCCGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAAT
* *
21824 ATGCAGCCTGAATAATACATGATTGACCGTACCGCTTG
261 AT----CC---ATAACACATGATTGACCGTACCGCCTG
* *
21862 AGTATTATAGTGCATTAAAGTTAAAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACAT
1 AGTATTATAGTGCACTAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACAT
* *
21927 TACTTGTAGGTTTTAGGTCCTTTGTAGTGGGTGCATTAGGTTCGTCGAA-TTTCCAACAGCCTTT
66 TACTTGTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTAGGTTCGTC-AAGTTTCCAACAGCCTTT
21991 ATATCGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAAATTCCATATAAGATATATGCATG
130 ATATCGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAAATTCCATATAAGATATATGCATG
22056 ATTCAAGAAATGAGCATTGACAAGCCGTGAAATGATCCAAATTTTCTGAATGATATATAGTCG-A
195 ATTCAAGAAATGAGCATTGACAAGCCGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAA
*
22120 -AT-C-TAACA-ATGATTGGGCC-TACCGCCTG
260 TATCCATAACACATGATT-GACCGTACCGCCTG
*
22148 AGTATTATAGTGCACTAAACTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACAT
1 AGTATTATAGTGCACTAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACAT
* * * * *
22213 TACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTGGGCTCGTCAAGTTTTCAACAACCTTTA
66 TACTTGTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTAGGTTCGTCAAGTTTCCAACAGCCTTTA
*
22278 TGTCGCTAGAGAATTATGCAAAAC
131 TATCGCTAGAGAATTATGCAAAAC
Statistics
Matches: 402, Mismatches: 35, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
285 2 0.00
286 154 0.38
287 7 0.02
291 1 0.00
296 2 0.00
297 1 0.00
298 234 0.58
299 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (291 bp):
AGTATTATAGTGCACTAAAGTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACAT
TACTTGTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTAGGTTCGTCAAGTTTCCAACAGCCTTTA
TATCGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAAATTCCATATAAGATATATGCATGA
TTCAAGAAATGAGCATTGACAAGCCGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAAT
ATCCATAACACATGATTGACCGTACCGCCTG
Done.