Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000704.1 Kokia drynarioides strain JFW-HI SEQ_111707, 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: 1757
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Found at i:851 original size:59 final size:57
Alignment explanation
Indices: 784--1272 Score: 412
Period size: 59 Copynumber: 8.3 Consensus size: 57
774 TGACATCCGG
784 GGGT-AAAATGGTAACTTTTT-GAAGTTTTGGGGTAAAAAAGGAATTTTTGGAAGTTCGA
1 GGGTAAAAATGG-AA-TTTTTAGAAGTTTTGGGGTAAAAAAGG-ATTTTTGGAAGTTCGA
** * * * ** * *
842 GGCCAAAAATTGAATTTTTGGAAG-TTCGAGGGTAAAATTGGGATTTTTTGAAAGTTCAA
1 GGGTAAAAATGGAATTTTTAGAAGTTTTG-GGGTAAAA-AAGGA-TTTTTGGAAGTTCGA
** * * * *
901 GGGTAAAAATATAATTTATGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT-TA
1 GGGTAAAAATGGAATTTTTAGAAGTTTTGGGGT-AAAAA-AGGATTTTTGGAAGTTCGA
* * * *
959 GGGGT-AAAATGGAATTTTTAGAAGTTTTGGGCTTAAAAATGGGATTTTTGGAAGTACGG
1 -GGGTAAAAATGGAATTTTTAGAAGTTTTGGG-GTAAAAA-AGGATTTTTGGAAGTTCGA
* * * * * *
1018 GGGTAAAAATAGAATTTTTAGAAGTTTCGAGGTCAAAAATGGATTTTTGGATGTACGA
1 GGGTAAAAATGGAATTTTTAGAAGTTTTGGGGT-AAAAAAGGATTTTTGGAAGTTCGA
* * * * *
1076 GGGTAAAAATAGAATATTTAGAAGTTTTGGGGTTAAAAATAGGATTTTTAGAAGTTTGG
1 GGGTAAAAATGGAATTTTTAGAAGTTTTGGGG-TAAAAA-AGGATTTTTGGAAGTTCGA
* * *
1135 GGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATAGGATTCTTGGAAGTTTTGG
1 GGGTAAAAATGGAATTTTTAGAAGTTTTGGGGT-AAAAA-AGGATTTTTGGAAG-TTCGA
* * ** * *
1195 GGGTAAAAATGGAATTTTTAGAAGTTTCGAGGTTTAAAATGGGATTTTTGGAAGTACAA
1 GGGTAAAAATGGAATTTTTAGAAGTTTTG-GG-GTAAAAAAGGATTTTTGGAAGTTCGA
*
1254 GGGTAAAAATAGAATTTTT
1 GGGTAAAAATGGAATTTTT
1273 TGGATAGTTT
Statistics
Matches: 357, Mismatches: 55, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
57 8 0.02
58 117 0.33
59 169 0.47
60 56 0.16
61 6 0.02
62 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (57 bp):
GGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTAAAAAAGGATTTTTGGAAGTTCGA
Found at i:890 original size:117 final size:117
Alignment explanation
Indices: 759--1272 Score: 474
Period size: 117 Copynumber: 4.4 Consensus size: 117
749 TTACGAAGTC
*
759 AAAAAT-GGAGTTTTTTGACA-TCCGGGGGT-AAAATGGTAACTTTTT-GAAGTTTTGGGGT-AA
1 AAAAATGGGA-TTTTTTGA-AGTTCGGGGGTAAAAATGG-AA-TTTTTAGAAGTTTTGGGGTCAA
** * *
819 AAAAGGAATTTTTGGAAGTTCGAGGCCAAAAATTGAATTTTTGGAAG-TTCGAGG-GT
62 AAAAGG-ATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTCG-GGCGT
* ** ** * *
875 AAAATTGGGATTTTTTGAAAGTTCAAGGGTAAAAATATAATTTATGGAAGTTTTGGGGTCAAAAA
1 AAAAATGGGATTTTTTG-AAGTTCGGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAA
* * * *
940 TGGGATTTTTGGAAGTT-TAGGGGT-AAAATGGAATTTTTAGAAGTTTTGGGCTT
65 -AGGATTTTTGGAAGTTCGA-GGGTAAAAATGGAATTTTTAGAAGTTTCGGGCGT
* * * * * *
993 AAAAATGGGATTTTTGGAAGTACGGGGGTAAAAATAGAATTTTTAGAAGTTTCGAGGTCAAAAAT
1 AAAAATGGGATTTTTTGAAGTTCGGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAAA
* * * * *
1058 GGATTTTTGGATGTACGAGGGTAAAAATAGAATATTTAGAAGTTTTGGG-GTT
66 GGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTCGGGCG-T
* * *
1110 AAAAATAGGATTTTTAGAAGTTTGGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAAT
1 AAAAATGGGATTTTTTGAAGTTCGGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAA-
* * * *
1175 AGGATTCTTGGAAGTTTTGGGGGTAAAAATGGAATTTTTAGAAGTTTCGAGG-TT
65 AGGATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTCG-GGCGT
* * * ** *
1229 TAAAATGGGATTTTTGGAAGTACAAGGGTAAAAATAGAATTTTT
1 AAAAATGGGATTTTTTGAAGTTCGGGGGTAAAAATGGAATTTTT
1273 TGGATAGTTT
Statistics
Matches: 325, Mismatches: 57, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
116 34 0.10
117 167 0.51
118 55 0.17
119 67 0.21
120 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (117 bp):
AAAAATGGGATTTTTTGAAGTTCGGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAAA
GGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTCGGGCGT
Found at i:953 original size:30 final size:29
Alignment explanation
Indices: 783--1282 Score: 361
Period size: 30 Copynumber: 17.0 Consensus size: 29
773 TTGACATCCG
783 GGGGT-AAAATGGTAACTTTTT-GAAGTTTT
1 GGGGTAAAAATGG-AA-TTTTTGGAAGTTTT
* *
812 GGGGTAAAAAAGGAATTTTTGGAAG-TTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
** * *
840 GAGGCCAAAAATTGAATTTTTGGAAG-TTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
* * * **
869 GAGGGTAAAATTGGGATTTTTTGAAAGTTCA
1 G-GGGTAAAAAT-GGAATTTTTGGAAGTTTT
* ** *
900 AGGGTAAAAATATAATTTATGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* *
929 GGGGTCAAAAATGGGATTTTTGGAAGTTTA
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
*
959 GGGGT-AAAATGGAATTTTTAGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* * ***
987 GGGCTTAAAAATGGGATTTTTGGAAGTACG
1 GGG-GTAAAAATGGAATTTTTGGAAGTTTT
* * *
1017 GGGGTAAAAATAGAATTTTTAGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* * **
1046 GAGGTCAAAAATGG-ATTTTTGGATG-TAC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
* * *
1074 GAGGGTAAAAATAGAATATTTAGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
* *
1104 GGGGTTAAAAATAGG-ATTTTTAGAAGTTTG
1 GGGG-TAAAAAT-GGAATTTTTGGAAGTTTT
*
1134 GGGGTAAAAATGGAATTTTTAGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
*
1163 GGGGTCAAAAATAGG-ATTCTTGGAAGTTTT
1 GGGGT-AAAAAT-GGAATTTTTGGAAGTTTT
* *
1193 GGGGGTAAAAATGGAATTTTTAGAAGTTTC
1 -GGGGTAAAAATGGAATTTTTGGAAGTTTT
* * * ***
1223 GAGGTTTAAAATGGGATTTTTGGAAGTACA
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
* *
1253 AGGGTAAAAATAGAATTTTTTGGATAGTTT
1 GGGGTAAAAATGGAA-TTTTTGGA-AGTTT
1283 AGGGACCTCC
Statistics
Matches: 369, Mismatches: 80, Indels: 42
0.75 0.16 0.09
Matches are distributed among these distances:
28 43 0.12
29 144 0.39
30 170 0.46
31 12 0.03
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTT
Done.