Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007320.1 Kokia drynarioides strain JFW-HI SEQ_121936, 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: 1846
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: 273
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-AAAGATTTAAGCCGCAACGATGAATCCAGTACCACGAAGATA
1 ATGAAGGGAAAAG-TTTAAGTCGCAACGGCGAATCCAGTACCACGAAGATA
* * * * *
1056 ATGGAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCTC-AA-AAA
1 ATGAAGGGAAAAGTTTAAGTCGCAACGGCGAATCC-AGTACCACGAAGATA
* * *
1104 CATGAAGGG-AAAGATTTATG-CTGCAACGGCGAATCTAGTACCACGAAGATG
1 -ATGAAGGGAAAAG-TTTAAGTC-GCAACGGCGAATCCAGTACCACGAAGATA
* * * *
1155 AT-AGAGGGAAAAGTTTAAGTCGCAACGGTGAA-CCTTGTACCTCAGAAG--C
1 ATGA-AGGGAAAAGTTTAAGTCGCAACGGCGAATCC-AGTACCAC-GAAGATA
* * **
1204 ATGAAGGGAAAAATTTAAGTCGCAACGACGAATTTAGTACCACGAAGATA
1 ATGAAGGGAAAAGTTTAAGTCGCAACGGCGAATCCAGTACCACGAAGATA
* * * * * * **
1254 ATGAAGGGAAAGGCTTAAGTCGCAACAGCGAA-CCTTGTACCTC-AAAAGC
1 ATGAAGGGAAAAGTTTAAGTCGCAACGGCGAATCC-AGTACCACGAAGATA
* *
1303 ATGGAGGG-AAAGATTTAAGCCGCAACGGCGAATC
1 ATGAAGGGAAAAG-TTTAAGTCGCAACGGCGAATC
1337 TAATAATGCG
Statistics
Matches: 290, Mismatches: 63, Indels: 54
0.71 0.15 0.13
Matches are distributed among these distances:
48 21 0.07
49 125 0.43
50 127 0.44
51 17 0.06
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.19
Consensus pattern (50 bp):
ATGAAGGGAAAAGTTTAAGTCGCAACGGCGAATCCAGTACCACGAAGATA
Found at i:1033 original size:49 final size:49
Alignment explanation
Indices: 961--1334 Score: 300
Period size: 49 Copynumber: 7.6 Consensus size: 49
951 AAGATAATGG
* *
961 AGGGAAA-AGTTTAAGTCGTAACGACAAACCTTGTACCTCAGAAGCATGA
1 AGGGAAAGA-TTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
* * * * * *
1010 AGGGAAAGATTTAAGCCGCAACGATGAATCC-AGTACCAC-GAAGATAATGG
1 AGGGAAAGATTTAAGTCGCAACGACGAA-CCTTGTACCTCAGAAG--CATGA
* * * *
1060 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
* * * * *
1109 AGGGAAAGATTTATG-CTGCAACGGCGAATCTAGTACCAC-GAAG-ATGATA
1 AGGGAAAGATTTAAGTC-GCAACGACGAACCTTGTACCTCAGAAGCATG--A
**
1158 GAGGGAAA-AGTTTAAGTCGCAACGGTGAACCTTGTACCTCAGAAGCATGA
1 -AGGGAAAGA-TTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
* * * *
1208 AGGGAAAAATTTAAGTCGCAACGACGAA-TTTAGTACCAC-GAAGATAATGA
1 AGGGAAAGATTTAAGTCGCAACGACGAACCTT-GTACCTCAGAAG--CATGA
** * *
1258 AGGGAAAGGCTTAAGTCGCAAC-AGCGAACCTTGTACCTCAAAAGCATGG
1 AGGGAAAGATTTAAGTCGCAACGA-CGAACCTTGTACCTCAGAAGCATGA
* *
1307 AGGGAAAGATTTAAGCCGCAACGGCGAA
1 AGGGAAAGATTTAAGTCGCAACGACGAA
1335 TCTAATAATG
Statistics
Matches: 256, Mismatches: 47, Indels: 44
0.74 0.14 0.13
Matches are distributed among these distances:
47 3 0.01
48 13 0.05
49 124 0.48
50 101 0.39
51 12 0.05
52 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (49 bp):
AGGGAAAGATTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
Found at i:1245 original size:198 final size:198
Alignment explanation
Indices: 906--1338 Score: 668
Period size: 198 Copynumber: 2.2 Consensus size: 198
896 TACCATAAAG
* * * * *
906 CATGAAGGGAAATATTTAAGCCGTAACGGTGAATCCAGTACCACGAAGATAATGGAGGGAAAAGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATAATAGAGGGAAAAGT
* * *
971 TTAAGTCGTAACGACAAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGATG
66 TTAAGTCGCAACGACAAACCTTGTACCTCAGAAGCATGAAGGGAAAAATTTAAGCCGCAACGACG
* * *
1036 AATCCAGTACCACGAAGATAATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAA
131 AATCCAGTACCACGAAGATAATGAAGGGAAAGGCTTAAGTCGCAACAGCGAACCTTGTACCTCAA
1101 AAA
196 AAA
* * *
1104 CATGAAGGGAAAGATTTATGCTGCAACGGCGAATCTAGTACCACGAAGATGATAGAGGGAAAAGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATAATAGAGGGAAAAGT
*** *
1169 TTAAGTCGCAACGGTGAACCTTGTACCTCAGAAGCATGAAGGGAAAAATTTAAGTCGCAACGACG
66 TTAAGTCGCAACGACAAACCTTGTACCTCAGAAGCATGAAGGGAAAAATTTAAGCCGCAACGACG
**
1234 AATTTAGTACCACGAAGATAATGAAGGGAAAGGCTTAAGTCGCAACAGCGAACCTTGTACCTCAA
131 AATCCAGTACCACGAAGATAATGAAGGGAAAGGCTTAAGTCGCAACAGCGAACCTTGTACCTCAA
*
1299 AAG
196 AAA
*
1302 CATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCTA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTA
1339 ATAATGCGAA
Statistics
Matches: 211, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
198 211 1.00
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (198 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATAATAGAGGGAAAAGT
TTAAGTCGCAACGACAAACCTTGTACCTCAGAAGCATGAAGGGAAAAATTTAAGCCGCAACGACG
AATCCAGTACCACGAAGATAATGAAGGGAAAGGCTTAAGTCGCAACAGCGAACCTTGTACCTCAA
AAA
Found at i:1350 original size:99 final size:99
Alignment explanation
Indices: 902--1338 Score: 606
Period size: 99 Copynumber: 4.4 Consensus size: 99
892 TCATTACCAT
* * * * *
902 AAAGCATGAAGGGAAATATTTAAGCCGTAACGGTGAATCCAGTACCACGAAGATAATGGAGGGAA
1 AAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATAATGAAGGGAA
* * *
967 AAGTTTAAGTCGTAACGACAAACCTTGTACCTCA
66 AAGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
* ** * *
1001 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGATGAATCCAGTACCACGAAGATAATGGAGGGAA
1 AAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATAATGAAGGGAA
*
1066 AGGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
66 AAGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
* * * *
1100 AAAACATGAAGGGAAAGATTTATGCTGCAACGGCGAATCTAGTACCACGAAGATGAT-AGAGGGA
1 AAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATAATGA-AGGGA
*
1164 AAAGTTTAAGTCGCAACGGTGAACCTTGTACCTCA
65 AAAGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
* * * * *
1199 GAAGCATGAAGGGAAAAATTTAAGTCGCAACGACGAATTTAGTACCACGAAGATAATGAAGGGAA
1 AAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATAATGAAGGGAA
* * *
1264 AGGCTTAAGTCGCAACAGCGAACCTTGTACCTCA
66 AAGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
*
1298 AAAGCATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCTA
1 AAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTA
1339 ATAATGCGAA
Statistics
Matches: 298, Mismatches: 38, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
99 297 1.00
100 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (99 bp):
AAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATAATGAAGGGAA
AAGTTTAAGTCGCAACGGCGAACCTTGTACCTCA
Done.