Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012595.1 Kokia drynarioides strain JFW-HI SEQ_127604, 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: 42883
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1721 original size:29 final size:29
Alignment explanation
Indices: 1679--1876 Score: 262
Period size: 29 Copynumber: 6.8 Consensus size: 29
1669 TTTTGAAAAC
1679 AAAAATGGAATTTTTGGAAGTTTAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTAGGGGT
*
1708 AAAAAT-GAATTTTTTGGAAGTTTCA-AGGT
1 AAAAATGGAA-TTTTTGGAAGTTT-AGGGGT
1737 CAAAAATGGAATTTTTGGAAGTTT-GAGGGT
1 -AAAAATGGAATTTTTGGAAGTTTAG-GGGT
*
1767 AAAAATGGAATTTTTGGAAGTTCAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTAGGGGT
* * *
1796 AAAAATGAAATTTTTGTAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGGAAG-TTTAGGGGT
1826 AAAAATGGAATTTTTGGAAGTTT-GAGGGT
1 AAAAATGGAATTTTTGGAAGTTTAG-GGGT
1855 AAAAATGGAA-TTTTGGAAGTTT
1 AAAAATGGAATTTTTGGAAGTTT
1877 CGCGACCTCC
Statistics
Matches: 150, Mismatches: 10, Indels: 19
0.84 0.06 0.11
Matches are distributed among these distances:
28 16 0.11
29 82 0.55
30 49 0.33
31 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTAGGGGT
Found at i:1770 original size:59 final size:57
Alignment explanation
Indices: 1679--1876 Score: 276
Period size: 59 Copynumber: 3.4 Consensus size: 57
1669 TTTTGAAAAC
*
1679 AAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAAT-GAATTTTTTGGAAGTTTCAAGGT
1 AAAAATGGAATTTTTGGAAGTTTA-GGGTAAAAATGGAA-TTTTTGGAAGTTTCAGGGT
1737 CAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAG-TTCAGGGGT
1 -AAAAATGGAATTTTTGGAAGTTT-AGGGTAAAAATGGAATTTTTGGAAGTTTCA-GGGT
* * *
1796 AAAAATGAAATTTTTGTAAGTTTTAGGGTTAAAAATGGAATTTTTGGAAGTTTGAGGGT
1 AAAAATGGAATTTTTGGAAG-TTTAGGG-TAAAAATGGAATTTTTGGAAGTTTCAGGGT
1855 AAAAATGGAA-TTTTGGAAGTTT
1 AAAAATGGAATTTTTGGAAGTTT
1877 CGCGACCTCC
Statistics
Matches: 127, Mismatches: 6, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
57 3 0.02
58 34 0.27
59 83 0.65
60 7 0.06
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.36
Consensus pattern (57 bp):
AAAAATGGAATTTTTGGAAGTTTAGGGTAAAAATGGAATTTTTGGAAGTTTCAGGGT
Found at i:1830 original size:88 final size:88
Alignment explanation
Indices: 1679--1875 Score: 333
Period size: 88 Copynumber: 2.2 Consensus size: 88
1669 TTTTGAAAAC
* *
1679 AAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGAATTTTTTGGAAGTTTCAAGGTCAAAAAT
1 AAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGAAATTTTTGGAAGTTTCAAGGTCAAAAAT
1744 GGAATTTTTGGAAGTTTGAGGGT
66 GGAATTTTTGGAAGTTTGAGGGT
* * * *
1767 AAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGAAATTTTTGTAAGTTTTAGGGTTAAAAAT
1 AAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGAAATTTTTGGAAGTTTCAAGGTCAAAAAT
1832 GGAATTTTTGGAAGTTTGAGGGT
66 GGAATTTTTGGAAGTTTGAGGGT
1855 AAAAATGGAA-TTTTGGAAGTT
1 AAAAATGGAATTTTTGGAAGTT
1876 TCGCGACCTC
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
87 11 0.11
88 92 0.89
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.36
Consensus pattern (88 bp):
AAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGAAATTTTTGGAAGTTTCAAGGTCAAAAAT
GGAATTTTTGGAAGTTTGAGGGT
Found at i:3264 original size:24 final size:23
Alignment explanation
Indices: 3227--3271 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
3217 ATTGGACTTG
*
3227 ATTTAAATAGATTTAAATTTTAA
1 ATTTAAATAAATTTAAATTTTAA
3250 ATTTATAATAAATTTAAATTTT
1 ATTTA-AATAAATTTAAATTTT
3272 CAGTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTTAAATAAATTTAAATTTTAA
Found at i:3265 original size:17 final size:17
Alignment explanation
Indices: 3240--3319 Score: 90
Period size: 17 Copynumber: 4.6 Consensus size: 17
3230 TAAATAGATT
3240 TAAATTTTAAATTTATAA
1 TAAA-TTTAAATTTATAA
*
3258 TAAATTTAAATTT-TCAG
1 TAAATTTAAATTTAT-AA
* *
3275 TAAATTTAAACTTATGA
1 TAAATTTAAATTTATAA
* *
3292 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTATAA
3309 TAAATTTAAAT
1 TAAATTTAAAT
3320 CTTTGTTGGG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
16 1 0.02
17 45 0.88
18 5 0.10
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:5298 original size:36 final size:36
Alignment explanation
Indices: 5251--5322 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
5241 TGATAGAGAA
5251 TATTAAAAGTTTCTGACCTCATTGAAACAATTGCAT
1 TATTAAAAGTTTCTGACCTCATTGAAACAATTGCAT
*
5287 TATTAAAAGTTTCTGACCTCATTGAAATAATTGCAT
1 TATTAAAAGTTTCTGACCTCATTGAAACAATTGCAT
5323 GTCAATATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (36 bp):
TATTAAAAGTTTCTGACCTCATTGAAACAATTGCAT
Found at i:14587 original size:13 final size:14
Alignment explanation
Indices: 14558--14587 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
14548 TTCAGTACAT
14558 TGACATTTAACCTC
1 TGACATTTAACCTC
14572 TGACATTTAA-CTC
1 TGACATTTAACCTC
14585 TGA
1 TGA
14588 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:25437 original size:27 final size:25
Alignment explanation
Indices: 25391--25444 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
25381 AACCTGAGGA
*
25391 GAAGAAGGAAAATAAAGAAGAGAAG
1 GAAGAAGGAAAACAAAGAAGAGAAG
*
25416 GAAGAAGAGAACAACAATGAAGAGAAG
1 GAAGAAG-GAA-AACAAAGAAGAGAAG
25443 GA
1 GA
25445 GGATGCCCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.28
26 3 0.12
27 15 0.60
ACGTcount: A:0.61, C:0.04, G:0.31, T:0.04
Consensus pattern (25 bp):
GAAGAAGGAAAACAAAGAAGAGAAG
Found at i:31139 original size:26 final size:26
Alignment explanation
Indices: 31110--31168 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
31100 CTTCTCCTAA
* *
31110 ATTTTAATTTGTTTT-AATTATTTAAC
1 ATTTTAATTTATTTTGAATT-GTTAAC
* *
31136 ATTTCAATTTATTTTGAATTGTTAAT
1 ATTTTAATTTATTTTGAATTGTTAAC
31162 ATTTTAA
1 ATTTTAA
31169 ACTAATTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (26 bp):
ATTTTAATTTATTTTGAATTGTTAAC
Done.