Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010924.1 Kokia drynarioides strain JFW-HI SEQ_125892, 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: 11061
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Found at i:2199 original size:21 final size:21
Alignment explanation
Indices: 2175--2218 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2165 AAGATAAGGT
2175 CAAGGCAATAGAAGGGGCTAA
1 CAAGGCAATAGAAGGGGCTAA
2196 CAAGGCAATAGAAGGGGCTAA
1 CAAGGCAATAGAAGGGGCTAA
2217 CA
1 CA
2219 CCTGCTGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.16, G:0.32, T:0.09
Consensus pattern (21 bp):
CAAGGCAATAGAAGGGGCTAA
Found at i:8463 original size:16 final size:16
Alignment explanation
Indices: 8442--8473 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
8432 TACATATCAA
8442 GCAGGAAGATGATCCT
1 GCAGGAAGATGATCCT
8458 GCAGGAAGATGATCCT
1 GCAGGAAGATGATCCT
8474 CAGATCAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (16 bp):
GCAGGAAGATGATCCT
Found at i:9163 original size:98 final size:98
Alignment explanation
Indices: 8963--9300 Score: 292
Period size: 98 Copynumber: 3.5 Consensus size: 98
8953 TTAGAGGTCT
* * * * *
8963 CAGTACCAC-GA-AGCATGAAGGGAAAGATCTAAACTGCAACGGCGGATCTAGTACTGCGAAGAC
1 CAGTACCACAGAGA-CACGAAGGGAAGGATCTAAACCGCAACGGCGGATCCAGTACTGCAAAGAC
* * * *
9026 ATAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-C
65 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * * *
9059 TTAGTACCTCAGAGACATGAAGGGGAGGATCTAAGCCGCAACGGCGGATCCAATACTGCAAAGAC
1 -CAGTACCACAGAGACACGAAGGGAAGGATCTAAACCGCAACGGCGGATCCAGTACTGCAAAGAC
** *
9124 ATGAAGGGAAAGATTTAAGCCATAACGGTGAATC
65 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * * * *
9158 CAGTACCAC-GAAGACACGAGGGGAAGGGTTTAAATCGTAACGGC-GAACCTTGTACCT-CAAAG
1 CAGTACCACAG-AGACACGAAGGGAAGGATCTAAACCGCAACGGCGGATCC-AGTA-CTGCAAAG
*
9220 ACATGAAGGGAAAGATCTAAGCCGCAACGGCGAATC
63 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * * **
9256 CAGTACCGCAAAGACACAAAGGGAAGGGTTTAAGTCGCAACGGCG
1 CAGTACCACAGAGACACGAAGGGAAGGATCTAAACCGCAACGGCG
9301 AACCTTGTAC
Statistics
Matches: 194, Mismatches: 39, Indels: 14
0.79 0.16 0.06
Matches are distributed among these distances:
97 12 0.06
98 178 0.92
99 4 0.02
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.15
Consensus pattern (98 bp):
CAGTACCACAGAGACACGAAGGGAAGGATCTAAACCGCAACGGCGGATCCAGTACTGCAAAGACA
TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
Found at i:9301 original size:98 final size:98
Alignment explanation
Indices: 9117--9312 Score: 302
Period size: 98 Copynumber: 2.0 Consensus size: 98
9107 TCCAATACTG
* * * * * *
9117 CAAAGACATGAAGGGAAAGATTTAAGCCATAACGGTGAATCCAGTACCACGAAGACACGAGGGGA
1 CAAAGACATGAAGGGAAAGATCTAAGCCACAACGGCGAATCCAGTACCACAAAGACACAAAGGGA
*
9182 AGGGTTTAAATCGTAACGGCGAACCTTGTACCT
66 AGGGTTTAAATCGCAACGGCGAACCTTGTACCT
* *
9215 CAAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCGCAAAGACACAAAGGGA
1 CAAAGACATGAAGGGAAAGATCTAAGCCACAACGGCGAATCCAGTACCACAAAGACACAAAGGGA
*
9280 AGGGTTTAAGTCGCAACGGCGAACCTTGTACCT
66 AGGGTTTAAATCGCAACGGCGAACCTTGTACCT
9313 TAGAAACATA
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.37, C:0.21, G:0.27, T:0.15
Consensus pattern (98 bp):
CAAAGACATGAAGGGAAAGATCTAAGCCACAACGGCGAATCCAGTACCACAAAGACACAAAGGGA
AGGGTTTAAATCGCAACGGCGAACCTTGTACCT
Found at i:9311 original size:49 final size:49
Alignment explanation
Indices: 8976--9311 Score: 255
Period size: 49 Copynumber: 6.9 Consensus size: 49
8966 TACCACGAAG
* * * * * * *
8976 CATGAAGGGAAAGATCTAAACTGCAACGGCGGATCTAGTACTGCGAAGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCGCAAAGA
* * * * * * *
9025 CATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACTTAGTACCTCAGAGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCGCAAAGA
* * * * * *
9074 CATGAAGGGGAGGATCTAAGCCGCAACGGCGGATCC-AATACTGCAAAGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGC-GAACCTAGTACCGCAAAGA
** * * *
9123 CATGAAGGGAAAGATTTAAGCCATAACGGTGAATCC-AGTACCACGAAGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCGCAAAGA
* * * * ** * * *
9172 CACGAGGGGAAGGGTTTAAATCGTAACGGCGAACCTTGTACCTCAAAGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCGCAAAGA
*
9221 CATGAAGGGAAAGATCTAAGCCGCAACGGCGAATCC-AGTACCGCAAAGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAA-CCTAGTACCGCAAAGA
** * * * *
9270 CACAAAGGGAAGGGTTTAAGTCGCAACGGCGAACCTTGTACC
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACC
9312 TTAGAAACAT
Statistics
Matches: 216, Mismatches: 66, Indels: 10
0.74 0.23 0.03
Matches are distributed among these distances:
48 6 0.03
49 205 0.95
50 5 0.02
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.16
Consensus pattern (49 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTAGTACCGCAAAGA
Found at i:9311 original size:147 final size:147
Alignment explanation
Indices: 8980--9302 Score: 369
Period size: 147 Copynumber: 2.2 Consensus size: 147
8970 ACGAAGCATG
* * ** * * ** ** * *
8980 AAGGGAAAGATCTAAACTGCAACGGCGGATCTAGTACTGCGAAGACATAAAGGGAAAGGTTTAAG
1 AAGGGAAAGATTTAAGCCACAACGGCGAATCCAGTACCACGAAGACACGAGGGGAAAGGTTTAAA
* * * * *
9045 TCGCAATGGCGAACTTAGTACCTCAGAGACATGAAGGGGAGGATCTAAGCCGCAACGGCGGATCC
66 TCGCAACGGCGAACTTAGTACCTCAAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGAATCC
* **
9110 AATACTGCAAAGACATG
131 AATACCGCAAAGACACA
* * *
9127 AAGGGAAAGATTTAAGCCATAACGGTGAATCCAGTACCACGAAGACACGAGGGGAAGGGTTTAAA
1 AAGGGAAAGATTTAAGCCACAACGGCGAATCCAGTACCACGAAGACACGAGGGGAAAGGTTTAAA
*
9192 TCGTAACGGCGAACCTT-GTACCTCAAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGAATC
66 TCGCAACGGCGAA-CTTAGTACCTCAAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGAATC
*
9256 CAGTACCGCAAAGACACA
130 CAATACCGCAAAGACACA
* * * *
9274 AAGGGAAGGGTTTAAGTCGCAACGGCGAA
1 AAGGGAAAGATTTAAGCCACAACGGCGAA
9303 CCTTGTACCT
Statistics
Matches: 144, Mismatches: 31, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
147 141 0.98
148 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.28, T:0.15
Consensus pattern (147 bp):
AAGGGAAAGATTTAAGCCACAACGGCGAATCCAGTACCACGAAGACACGAGGGGAAAGGTTTAAA
TCGCAACGGCGAACTTAGTACCTCAAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGAATCC
AATACCGCAAAGACACA
Found at i:9995 original size:17 final size:17
Alignment explanation
Indices: 9973--10036 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
9963 CAAACACATT
9973 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAAGA
*
9990 TTAAATTTGTTTTAA-A
1 TTAAATTTATTTTAAGA
* *
10006 TTTAAATTTAATTTAAGT
1 -TTAAATTTATTTTAAGA
10024 TTAAATTTATTTT
1 TTAAATTTATTTT
10037 TAAATTCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
16 1 0.03
17 39 0.98
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:10009 original size:6 final size:6
Alignment explanation
Indices: 10000--10042 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
9990 TTAAATTTGT
* **
10000 TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA TTTATT TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
10043 CAAAATTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:10010 original size:34 final size:35
Alignment explanation
Indices: 9972--10052 Score: 110
Period size: 34 Copynumber: 2.3 Consensus size: 35
9962 CCAAACACAT
9972 TTTAAATTTATTTTAAGATTAAATTT-GTTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTAGTTTTAAA
* * *
10006 TTTAAATTTAATTTAAGTTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTAGTTTTAAA
* *
10041 TTCAAAATTATT
1 TTTAAATTTATT
10053 ATAATTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
34 24 0.60
35 16 0.40
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.56
Consensus pattern (35 bp):
TTTAAATTTATTTTAAGATTAAATTTAGTTTTAAA
Done.