Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007913.1 Kokia drynarioides strain JFW-HI SEQ_122557, 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: 7188
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Found at i:403 original size:31 final size:34
Alignment explanation
Indices: 368--429 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 34
358 ATGTATTCGA
*
368 TCCTTT-CATTTTTTTTATTT-TTTT-AATTTAG
1 TCCTTTCCATTTTTTTAATTTATTTTCAATTTAG
399 TCCTTTCCATTTTTTTAATTTATTTTCAATT
1 TCCTTTCCATTTTTTTAATTTATTTTCAATT
430 GGCCCAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 6 0.22
32 13 0.48
33 4 0.15
34 4 0.15
ACGTcount: A:0.18, C:0.13, G:0.02, T:0.68
Consensus pattern (34 bp):
TCCTTTCCATTTTTTTAATTTATTTTCAATTTAG
Found at i:786 original size:30 final size:29
Alignment explanation
Indices: 716--930 Score: 116
Period size: 29 Copynumber: 7.3 Consensus size: 29
706 GAAATCATAA
* * **
716 TTTGACCCCTTAACTTTCCAAAATTCTATTT
1 TTTGACCCC-TAAATTTCCAAAAAT-TACAT
*
747 TTTTA-CCCTAAATTTTCCAAAAATTACAT
1 TTTGACCCCTAAA-TTTCCAAAAATTACAT
* * **
776 TTTGACCCCTAAACTTTTCTAAAATTTTAT
1 TTTGACCCCTAAA-TTTCCAAAAATTACAT
* *
806 CTTTGACCTCGAAATTTCCAAAAATTACAT
1 -TTTGACCCCTAAATTTCCAAAAATTACAT
* ** * *
836 TTTTACCCCCGAACTTCCAAAAATTACCAC
1 TTTGACCCCTAAATTTCCAAAAATTA-CAT
** * *
866 TTT-ACCCCCGAATATCCAAAAATT-CTGT
1 TTTGACCCCTAAATTTCCAAAAATTAC-AT
* *
894 TTTGA-CCTTAAAATTTCCAAAAAATACCAT
1 TTTGACCCCT-AAATTTCCAAAAATTA-CAT
924 TTT-ACCC
1 TTTGACCC
931 TCGAATGTTT
Statistics
Matches: 141, Mismatches: 33, Indels: 21
0.72 0.17 0.11
Matches are distributed among these distances:
27 1 0.01
28 5 0.04
29 64 0.45
30 55 0.39
31 16 0.11
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (29 bp):
TTTGACCCCTAAATTTCCAAAAATTACAT
Found at i:791 original size:60 final size:59
Alignment explanation
Indices: 716--857 Score: 162
Period size: 60 Copynumber: 2.4 Consensus size: 59
706 GAAATCATAA
* * * *
716 TTTGACCCCTTAACTTTCCAAAATTCTATTTTTTTACC-CTAAATTTTCCAAAAATTACAT
1 TTTGACCCCTAAACTTTCCAAAATTCTA-TCTTTGACCTCGAAA-TTTCCAAAAATTACAT
* *
776 TTTGACCCCTAAACTTTTCTAAAATTTTATCTTTGACCTCGAAATTTCCAAAAATTACAT
1 TTTGACCCCTAAAC-TTTCCAAAATTCTATCTTTGACCTCGAAATTTCCAAAAATTACAT
* **
836 TTTTACCCCCGAAC-TTCCAAAA
1 TTTGACCCCTAAACTTTCCAAAA
858 ATTACCACTT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
58 7 0.10
60 47 0.67
61 16 0.23
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (59 bp):
TTTGACCCCTAAACTTTCCAAAATTCTATCTTTGACCTCGAAATTTCCAAAAATTACAT
Found at i:5280 original size:49 final size:49
Alignment explanation
Indices: 5161--5685 Score: 470
Period size: 49 Copynumber: 10.8 Consensus size: 49
5151 TCAGTTCCAC
* *
5161 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-
1 GAAGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCTCA
* * * *
5209 GGAG-ATTGGAGGGAAAGATTTAAGTCGCAACGACGAA-CCTTGTACCTCA
1 GAAGCA-TGAAGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTACCTCA
* *
5258 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACA
1 GAAGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCTCA
* * *
5307 -AAG-ATACAAAGGGAAAGACTTAAGTCGCAACGGCGAA-CCTTGTACCTCA
1 GAAGCAT--GAAGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTACCTCA
* * *
5356 AAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-
1 GAAGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCTCA
* * * *
5404 GAAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAA-CCTTGTACCTCA
1 GAAG-CATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTACCTCA
* * *
5454 G-AGACATGAAGGGAAACATTTAAGTCGCAACGGCGAATCCAATACCAC-
1 GAAG-CATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCTCA
* * * * *
5502 GAAGACACGAAAGGAAAAATTTAAGTCGCAATGGCGAA-CTTA-TACCTCA
1 GAAG-CATGAAGGGAAAGATTTAAGTCGCAACGGCGAATC-CAGTACCTCA
** * * *
5551 GAAATATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACC-AA
1 GAAGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCTCA
* * * *
5599 TAAGACAAGAAGGGAAAG-GTTAAGTCGCAATGGCGAA-CCTTA-TACCTCA
1 GAAG-CATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCC--AGTACCTCA
* * * *
5648 GAAGCATGAAAGAAAAAATTTAAGCCGCAACGGCGAAT
1 GAAGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAAT
5686 TTAGTACCAT
Statistics
Matches: 382, Mismatches: 69, Indels: 50
0.76 0.14 0.10
Matches are distributed among these distances:
47 7 0.02
48 112 0.29
49 250 0.65
50 11 0.03
51 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (49 bp):
GAAGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCTCA
Found at i:5283 original size:97 final size:97
Alignment explanation
Indices: 5161--5694 Score: 698
Period size: 98 Copynumber: 5.5 Consensus size: 97
5151 TCAGTTCCAC
* * *
5161 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGGAGATTGGAGGGAAAG
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATCGAAGGGAAAG
*
5226 ATTTAAGTCGCAACGACGAACCTTGTACCTCA
66 ATTTAAGTCGCAACGGCGAACCTTGTACCTCA
* *
5258 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGATACAAAGGGAAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGAT-CGAAGGGAAA
*
5323 GACTTAAGTCGCAACGGCGAACCTTGTACCTCA
65 GATTTAAGTCGCAACGGCGAACCTTGTACCTCA
* *
5356 AAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGAT-CGAAGGGAAA
* *
5421 GGTTTAAGTCGCAACGACGAACCTTGTACCTCA
65 GATTTAAGTCGCAACGGCGAACCTTGTACCTCA
* * * * *
5454 G-AGACATGAAGGGAAACATTTAAGTCGCAACGGCGAATCCAATACCACGAAGACACGAAAGGAA
1 GAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGA-TCGAAGGGAA
* * *
5518 AAATTTAAGTCGCAATGGCGAA-CTTATACCTCA
64 AGATTTAAGTCGCAACGGCGAACCTTGTACCTCA
** * **
5551 GAAATATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCAATAAGA-CAAGAAGGGAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATC--GAAGGGAA
* * *
5615 AG-GTTAAGTCGCAATGGCGAACCTTATACCTCA
64 AGATTTAAGTCGCAACGGCGAACCTTGTACCTCA
* * * **
5648 GAAGCATGAAAGAAAAAATTTAAGCCGCAACGGCGAATTTAGTACCA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
5695 TGCGGATTGA
Statistics
Matches: 385, Mismatches: 45, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
95 1 0.00
96 18 0.05
97 165 0.43
98 201 0.52
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.16
Consensus pattern (97 bp):
GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATCGAAGGGAAAG
ATTTAAGTCGCAACGGCGAACCTTGTACCTCA
Found at i:6171 original size:18 final size:17
Alignment explanation
Indices: 6148--6185 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
6138 ATAAATTGGT
*
6148 TTTAAATTTATTTTTAAA
1 TTTAAATTT-TGTTTAAA
6166 TTTAAATTTTGTTTAAA
1 TTTAAATTTTGTTTAAA
6183 TTT
1 TTT
6186 GAAACGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTAAATTTTGTTTAAA
Found at i:6940 original size:3 final size:3
Alignment explanation
Indices: 6932--6992 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
6922 CATTGATTTT
* * *
6932 TAA TAA TAA TAA TAA TAA TAA TAA -ATA TAA TAT TAA TAA CAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
6977 TAA TAA TAAA TAA TAA
1 TAA TAA T-AA TAA TAA
6993 AAAGGGAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 1 0.02
3 44 0.90
4 4 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Done.