Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012085.1 Kokia drynarioides strain JFW-HI SEQ_127084, 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: 15188
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:494 original size:18 final size:18
Alignment explanation
Indices: 471--506 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
461 TTCAAATTTC
*
471 TAAAAAAATAATTAAAAT
1 TAAAAAAAAAATTAAAAT
*
489 TAAAAAAAAAATTCAAAT
1 TAAAAAAAAAATTAAAAT
507 GAAGAAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAAAAAAAATTAAAAT
Found at i:3871 original size:10 final size:10
Alignment explanation
Indices: 3856--3884 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3846 ATTTATTAAT
3856 TAATTAATAA
1 TAATTAATAA
3866 TAATTAATAA
1 TAATTAATAA
3876 TAA-TAATAA
1 TAATTAATAA
3885 AAATGAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAATTAATAA
Found at i:3878 original size:13 final size:14
Alignment explanation
Indices: 3852--3882 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3842 CTTTATTTAT
3852 TAATTAATTAATAA
1 TAATTAATTAATAA
3866 TAATTAA-TAATAA
1 TAATTAATTAATAA
3879 TAAT
1 TAAT
3883 AAAAATGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATTAATTAATAA
Found at i:4962 original size:30 final size:29
Alignment explanation
Indices: 4919--5355 Score: 254
Period size: 30 Copynumber: 14.8 Consensus size: 29
4909 AAGGTCCCTA
* *
4919 AACTATCTGAAAATTATCATTTTACCCCCG
1 AACT-TCTAAAAATTACCATTTTACCCCCG
* * *
4949 AACTTCCAAAAAATACCATTTTTAACCCCG
1 AACTTCTAAAAATTACCA-TTTTACCCCCG
* * * *
4979 AACCTTCCAAAAA-TCCCATTTTTAACCCCA
1 AA-CTTCTAAAAATTACCA-TTTTACCCCCG
* * *
5009 AACCTTCTAAAACTTACCATTTTACTCTCG
1 AA-CTTCTAAAAATTACCATTTTACCCCCG
* * *
5039 AAC-T-TACAAAACTCCCATTTTTAACCCCG
1 AACTTCTA-AAAATTACCA-TTTTACCCCCG
* *
5068 AACCTTCTAAAAATTATCATTTTACCCTCG
1 AA-CTTCTAAAAATTACCATTTTACCCCCG
* *
5098 AACTTCTAAAAA-TCCCATTTTTGA-CCCCA
1 AACTTCTAAAAATTACCA-TTTT-ACCCCCG
*
5127 AACATTCTAAAAATTACCATTTTACCCCCA
1 AAC-TTCTAAAAATTACCATTTTACCCCCG
* *
5157 AACTTCCAAAAA-T-CTCATTTTTGA-CCCCA
1 AACTTCTAAAAATTAC-CA-TTTT-ACCCCCG
5186 AACCTT-TCAAAAATTACCATTTTACCCCCG
1 AA-CTTCT-AAAAATTACCATTTTACCCCCG
* *
5216 AACTTCCAAAAA--ACCCTATTTTTAACCCCG
1 AACTTCTAAAAATTA-CC-A-TTTTACCCCCG
* *
5246 AACCTTCTAAAAATTACCATTTTACCCTCA
1 AA-CTTCTAAAAATTACCATTTTACCCCCG
* * * **
5276 AACTTCCATAAA-TCCCATTTTTGA-CCTTG
1 AACTTCTAAAAATTACCA-TTTT-ACCCCCG
* **
5305 AACCTTCTGAAAATTACCATTTTACCCTTG
1 AA-CTTCTAAAAATTACCATTTTACCCCCG
*
5335 AACTTCTAAAAA-TCCCATTTT
1 AACTTCTAAAAATTACCATTTT
5356 TGACTCCGAA
Statistics
Matches: 324, Mismatches: 50, Indels: 68
0.73 0.11 0.15
Matches are distributed among these distances:
27 4 0.01
28 28 0.09
29 98 0.30
30 145 0.45
31 43 0.13
32 5 0.02
33 1 0.00
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
AACTTCTAAAAATTACCATTTTACCCCCG
Found at i:5055 original size:59 final size:59
Alignment explanation
Indices: 4944--5385 Score: 532
Period size: 59 Copynumber: 7.5 Consensus size: 59
4934 ATCATTTTAC
* * *
4944 CCCCGAA-CTTCCAAAAAATACCATTTTTAACCC-CGAACCTTCCAAAAATCCCATTTTTAA
1 CCCCGAACCTTCTAAAAATTACCA-TTTT-ACCCTCGAA-CTTCCAAAAATCCCATTTTTGA
* * * * * *
5004 CCCCAAACCTTCTAAAACTTACCATTTTACTCTCGAACTTACAAAACTCCCATTTTTAA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* *
5063 CCCCGAACCTTCTAAAAATTATCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * * * *
5122 CCCCAAACATTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * * *
5181 CCCCAAACCTT-TCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAACCCTATTTTTAA
1 CCCCGAACCTTCT-AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCC-ATTTTTGA
* *
5241 CCCCGAACCTTCTAAAAATTACCATTTTACCCTCAAACTTCCATAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
** * * *
5300 CCTTGAACCTTCTGAAAATTACCATTTTACCCTTGAACTTCTAAAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * * *
5359 CTCCGAACTTTC-CAAAACTACCATTTT
1 CCCCGAACCTTCTAAAAATTACCATTTT
5386 GCCCCCGTGC
Statistics
Matches: 331, Mismatches: 46, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
58 14 0.04
59 238 0.72
60 65 0.20
61 14 0.04
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (59 bp):
CCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
Found at i:5293 original size:178 final size:177
Alignment explanation
Indices: 4956--5392 Score: 563
Period size: 178 Copynumber: 2.5 Consensus size: 177
4946 CCGAACTTCC
* * * *
4956 AAAAAATACCATTTTTAACCCCGAACCTTCCAAAAATCCCATTTTTAACCCCAAACC-TTCTAAA
1 AAAAATTACCA-TTTT-ACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTC-AAA
* * * ** *
5020 ACTTACCATTTTACTCTCGAACTTACAAAACTCCCATTTTTAACCCCGAACCTTCTAAAAATTAT
63 AATTACCATTTTACCCCCGAACTTACAAAAAACCCATTTTTAACCCCGAACCTTCTAAAAATTAC
* *
5085 CATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCCAAACATTCT
128 CATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAACATTCT
*
5135 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAACCTTTCAAAAAT
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTCAAAAAT
*
5200 TACCATTTTACCCCCGAACTTCCAAAAAACCCTATTTTTAACCCCGAACCTTCTAAAAATTACCA
66 TACCATTTTACCCCCGAACTTACAAAAAACCC-ATTTTTAACCCCGAACCTTCTAAAAATTACCA
* *** *
5265 TTTTACCCTCAAACTTCCATAAATCCCATTTTTGACCTTGAACCTTCT
130 TTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAACATTCT
* *** * * * * *
5313 GAAAATTACCATTTTACCCTTGAACTTCTAAAAATCCCATTTTTGACTCCGAA-CTTTCCAAAAC
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTCAAAAAT
*
5377 TACCATTTTGCCCCCG
66 TACCATTTTACCCCCG
5393 TGCATCCGAA
Statistics
Matches: 226, Mismatches: 30, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
177 92 0.41
178 124 0.55
179 10 0.04
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.32
Consensus pattern (177 bp):
AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTTCAAAAAT
TACCATTTTACCCCCGAACTTACAAAAAACCCATTTTTAACCCCGAACCTTCTAAAAATTACCAT
TTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAACATTCT
Done.