Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007319.1 Kokia drynarioides strain JFW-HI SEQ_121935, 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, 951
Length: 1585
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Found at i:974 original size:50 final size:50
Alignment explanation
Indices: 907--1336 Score: 282
Period size: 50 Copynumber: 8.7 Consensus size: 50
897 ACCATAAAGC
* * *
907 ATGAAGGGAAATA-TTTAAGCCGTAACGGTGAATCCAGTACCACGAAGATA
1 ATGAAGGGAAA-AGTTTAAGTCGCAACGGCGAATCCAGTACCACGAAGATA
* * * * * * *
957 ATGGAGGGAAAAGTTTAAGTCGTAACGAC-AAACCTTGTACCTCAGAAG--C
1 ATGAAGGGAAAAGTTTAAGTCGCAACGGCGAATCC-AGTACCAC-GAAGATA
* ** *
1006 ATGAAGGG-AAAGATTTAAGCCGCAACGATGAATTCAGTACCACGAAGATA
1 ATGAAGGGAAAAG-TTTAAGTCGCAACGGCGAATCCAGTACCACGAAGATA
* * * * *
1056 ATGGAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCTCAGAA-A-C
1 ATGAAGGGAAAAGTTTAAGTCGCAACGGCGAATCC-AGTACCAC-GAAGATA
* * *
1105 ATGAAGGG-AAAGATTTACG-CTGCAACGGCGAATCTAGTACCACGAAGATG
1 ATGAAGGGAAAAG-TTTAAGTC-GCAACGGCGAATCCAGTACCACGAAGATA
* * *
1155 AT-AGAGGGAAAAGTTTAAGTCGCAACGGCGAA-CCTTGTACCTCAGAAG--C
1 ATGA-AGGGAAAAGTTTAAGTCGCAACGGCGAATCC-AGTACCAC-GAAGATA
* * *
1204 ATGAAGGGAAAAATTTAAGTCGCAACGACGAATCTAGTACCACGAAGATA
1 ATGAAGGGAAAAGTTTAAGTCGCAACGGCGAATCCAGTACCACGAAGATA
* * * * * * **
1254 ATGAAGGGAAAGGCTTAAGTCGCAACAGCGAA-CCTTGTACCTC-AAAAGC
1 ATGAAGGGAAAAGTTTAAGTCGCAACGGCGAATCC-AGTACCACGAAGATA
* *
1303 ATGGAGGG-AAAGATTTAAGCCGCAACGGCGAATC
1 ATGAAGGGAAAAG-TTTAAGTCGCAACGGCGAATC
1337 TAATACTGCG
Statistics
Matches: 293, Mismatches: 60, Indels: 54
0.72 0.15 0.13
Matches are distributed among these distances:
48 22 0.08
49 125 0.43
50 127 0.43
51 19 0.06
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (50 bp):
ATGAAGGGAAAAGTTTAAGTCGCAACGGCGAATCCAGTACCACGAAGATA
Found at i:1033 original size:49 final size:49
Alignment explanation
Indices: 961--1334 Score: 318
Period size: 49 Copynumber: 7.6 Consensus size: 49
951 AAGATAATGG
* *
961 AGGGAAA-AGTTTAAGTCGTAACGACAAACCTTGTACCTCAGAAGCATGA
1 AGGGAAAGA-TTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
* * * * *
1010 AGGGAAAGATTTAAGCCGCAACGATGAA--TTCAGTACCAC-GAAGATAATGG
1 AGGGAAAGATTTAAGTCGCAACGACGAACCTT--GTACCTCAGAAG--CATGA
* * *
1060 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
* * * * *
1109 AGGGAAAGATTTACG-CTGCAACGGCGAATCTAGTACCAC-GAAG-ATGATA
1 AGGGAAAGATTTAAGTC-GCAACGACGAACCTTGTACCTCAGAAGCATG--A
*
1158 GAGGGAAA-AGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGA
1 -AGGGAAAGA-TTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
* * * * *
1208 AGGGAAAAATTTAAGTCGCAACGACGAATCTAGTACCAC-GAAGATAATGA
1 AGGGAAAGATTTAAGTCGCAACGACGAACCTTGTACCTCAGAAG--CATGA
** * *
1258 AGGGAAAGGCTTAAGTCGCAAC-AGCGAACCTTGTACCTCAAAAGCATGG
1 AGGGAAAGATTTAAGTCGCAACGA-CGAACCTTGTACCTCAGAAGCATGA
* *
1307 AGGGAAAGATTTAAGCCGCAACGGCGAA
1 AGGGAAAGATTTAAGTCGCAACGACGAA
1335 TCTAATACTG
Statistics
Matches: 260, Mismatches: 43, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
47 5 0.02
48 12 0.05
49 125 0.48
50 102 0.39
51 11 0.04
52 5 0.02
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.18
Consensus pattern (49 bp):
AGGGAAAGATTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
Found at i:1074 original size:99 final size:99
Alignment explanation
Indices: 903--1338 Score: 615
Period size: 99 Copynumber: 4.4 Consensus size: 99
893 CATTACCATA
* * ** *
903 AAGCATGAAGGGAAATATTTAAGCCGTAACGGTGAATCCAGTACCACGAAGATAATGGAGGGAAA
1 AAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATAATGGAGGGAAA
* *
968 AGTTTAAGTCGTAACGACAAACCTTGTACCTCAG
66 AGTTTAAGTCGCAACGACGAACCTTGTACCTCAG
*
1002 AAGCATGAAGGGAAAGATTTAAGCCGCAACGATGAAT-TCAGTACCACGAAGATAATGGAGGGAA
1 AAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCT-AGTACCACGAAGATAATGGAGGGAA
* *
1066 AGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAG
65 AAGTTTAAGTCGCAACGACGAACCTTGTACCTCAG
* * * * * *
1101 AAACATGAAGGGAAAGATTTACGCTGCAACGGCGAATCTAGTACCACGAAGATGATAGAGGGAAA
1 AAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATAATGGAGGGAAA
*
1166 AGTTTAAGTCGCAACGGCGAACCTTGTACCTCAG
66 AGTTTAAGTCGCAACGACGAACCTTGTACCTCAG
* * *
1200 AAGCATGAAGGGAAAAATTTAAGTCGCAACGACGAATCTAGTACCACGAAGATAATGAAGGGAAA
1 AAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATAATGGAGGGAAA
* * *
1265 GGCTTAAGTCGCAAC-AGCGAACCTTGTACCTCAA
66 AGTTTAAGTCGCAACGA-CGAACCTTGTACCTCAG
* *
1299 AAGCATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCTA
1 AAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTA
1339 ATACTGCGAA
Statistics
Matches: 301, Mismatches: 33, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
99 300 1.00
100 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (99 bp):
AAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATAATGGAGGGAAA
AGTTTAAGTCGCAACGACGAACCTTGTACCTCAG
Found at i:1245 original size:198 final size:198
Alignment explanation
Indices: 902--1338 Score: 680
Period size: 198 Copynumber: 2.2 Consensus size: 198
892 TCATTACCAT
* * * * *
902 AAAGCATGAAGGGAAATATTTAAGCCGTAACGGTGAATCCAGTACCACGAAGATAATGGAGGGAA
1 AAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATAATAGAGGGAA
* *
967 AAGTTTAAGTCGTAACGACAAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAAC
66 AAGTTTAAGTCGCAACGACAAACCTTGTACCTCAGAAGCATGAAGGGAAAAATTTAAGCCGCAAC
* * * *
1032 GATGAATTCAGTACCACGAAGATAATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACC
131 GACGAATTCAGTACCACGAAGATAATGAAGGGAAAGGCTTAAGTCGCAACAGCGAACCTTGTACC
1097 TCA
196 TCA
* * *
1100 GAAA-CATGAAGGGAAAGATTTACGCTGCAACGGCGAATCTAGTACCACGAAGATGATAGAGGGA
1 -AAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATAATAGAGGGA
* * *
1164 AAAGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAAATTTAAGTCGCAA
65 AAAGTTTAAGTCGCAACGACAAACCTTGTACCTCAGAAGCATGAAGGGAAAAATTTAAGCCGCAA
1229 CGACGAA-TCTAGTACCACGAAGATAATGAAGGGAAAGGCTTAAGTCGCAACAGCGAACCTTGTA
130 CGACGAATTC-AGTACCACGAAGATAATGAAGGGAAAGGCTTAAGTCGCAACAGCGAACCTTGTA
1293 CCTCA
194 CCTCA
*
1298 AAAGCATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCTA
1 AAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTA
1339 ATACTGCGAA
Statistics
Matches: 216, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
197 5 0.02
198 208 0.96
199 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (198 bp):
AAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATAATAGAGGGAA
AAGTTTAAGTCGCAACGACAAACCTTGTACCTCAGAAGCATGAAGGGAAAAATTTAAGCCGCAAC
GACGAATTCAGTACCACGAAGATAATGAAGGGAAAGGCTTAAGTCGCAACAGCGAACCTTGTACC
TCA
Done.