Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004032.1 Kokia drynarioides strain JFW-HI SEQ_117165, 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, 914
Length: 1524
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Found at i:214 original size:96 final size:96
Alignment explanation
Indices: 30--221 Score: 210
Period size: 96 Copynumber: 2.0 Consensus size: 96
20 TCTTTACAAA
* ** *
30 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTACACCTAGTAAGTTAAAGCGTAATATTTCG
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAAGCGAAATATTTCG
* *
95 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 AAATCGAAGATAAAGAAACATTGCCTCGATT
* * * * * *
126 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAAAT-TTTT
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAAGCG-AAATATTTC
* *
190 GAAACTCGAA-ATGAAAG-AATATTGCTTCGATT
65 GAAA-TCGAAGAT-AAAGAAACATTGCCTCGATT
222 TTAAAGTTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
96 68 0.86
97 11 0.14
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAAGCGAAATATTTCG
AAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:578 original size:30 final size:28
Alignment explanation
Indices: 540--1015 Score: 229
Period size: 30 Copynumber: 16.1 Consensus size: 28
530 TGACATCCGG
540 GGGT-AAAATGGTAATTTTAGGAAGTTTC
1 GGGTAAAAATGG-AATTTTAGGAAGTTTC
* *
568 GGAGTCAAAATTGGAATTTTGGGAAG-TTC
1 GG-GT-AAAAATGGAATTTTAGGAAGTTTC
*
597 AGGGCTAAAAATGGAATTTTTA-GAAGTTTTG
1 -GGG-TAAAAATGGAA-TTTTAGGAAG-TTTC
*
628 GGGTTAAAAATGGAATTTT-GGAAGTTCC
1 GGG-TAAAAATGGAATTTTAGGAAGTTTC
* * *
656 AAGGTCAAAAATGGGATTTTTA-GAAGTTTGG
1 -GGGT-AAAAAT-GGAATTTTAGGAAGTTT-C
* *
687 GGGTAAAAA-CGAGATTTTTGGAAGTTTC
1 GGGTAAAAATGGA-ATTTTAGGAAGTTTC
* *
715 GGGATCAAAAATGGGATTTTTA-GAAGTTTGG
1 GGG-T-AAAAAT-GGAATTTTAGGAAGTTT-C
* * *
746 GGGTAAAAATGGAATTTTTGGAGGTTTT
1 GGGTAAAAATGGAATTTTAGGAAGTTTC
* * * *
774 GAGGTCAAAAATGGGATTTTTGAAAGTTTA
1 G-GGT-AAAAATGGAATTTTAGGAAGTTTC
* *
804 GTGGTAAAAATGGGATTTTTGGAAGTTTC
1 G-GGTAAAAATGGAATTTTAGGAAGTTTC
*
833 GGGATCAAAAATGGGATTTTTA-GAAG-TTC
1 GGG-T-AAAAAT-GGAATTTTAGGAAGTTTC
*
862 GAGGGTAAAAATGGAATTTTTA-GAGGTTTC
1 --GGGTAAAAATGGAA-TTTTAGGAAGTTTC
* * * *
892 AGGGTCAAAAATGGGATTTTTGAAAGTTTTGGG
1 -GGGT-AAAAATGGAATTTTAGGAAG-TTT--C
* * * *
925 GGGTAAAAATGGGATATTGGGAAGTTTTG
1 GGGTAAAAATGGAATTTTAGGAAG-TTTC
*
954 GGGTAAAAAAT-GAGATTTTTGGAAGTTTC
1 GGGT-AAAAATGGA-ATTTTAGGAAGTTTC
* * *
983 GAGGTTAAAAA-CGAGATTTTTGTAAGTTTC
1 G-GG-TAAAAATGGA-ATTTTAGGAAGTTTC
1013 GGG
1 GGG
1016 ACCCTCGGGG
Statistics
Matches: 357, Mismatches: 50, Indels: 81
0.73 0.10 0.17
Matches are distributed among these distances:
27 2 0.01
28 25 0.07
29 125 0.35
30 150 0.42
31 49 0.14
32 6 0.02
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (28 bp):
GGGTAAAAATGGAATTTTAGGAAGTTTC
Found at i:625 original size:59 final size:59
Alignment explanation
Indices: 544--1012 Score: 447
Period size: 59 Copynumber: 7.9 Consensus size: 59
534 ATCCGGGGGT
* * * * *
544 AAAATGGTAATTTTAGGAAGTTTCGGAGTCAAAATTGGAATTTTGGGAAG-TTCAGGG-CTA
1 AAAATGGGATTTTTA-GAAGTTTCGGGGT-AAAAATGGAATTTTTGGAAGTTTCAGGGTC-A
* * * *
604 AAAATGGAATTTTTAGAAGTTTTGGGGTTAAAAATGGAA-TTTTGGAAGTTCCAAGGTCA
1 AAAATGGGATTTTTAGAAGTTTCGGGG-TAAAAATGGAATTTTTGGAAGTTTCAGGGTCA
* *
663 AAAATGGGATTTTTAGAAGTTTGGGGGTAAAAA-CGAGATTTTTGGAAGTTTC-GGGATCA
1 AAAATGGGATTTTTAGAAGTTTCGGGGTAAAAATGGA-ATTTTTGGAAGTTTCAGGG-TCA
* * *
722 AAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATGGAATTTTTGGAGGTTT-TGAGGTCA
1 AAAATGGGATTTTTAGAAGTTTCGGGGTAAAAATGGAATTTTTGGAAGTTTCAG-GGTCA
* * *
781 AAAATGGGATTTTT-GAAAGTTTAGTGGTAAAAATGGGATTTTTGGAAGTTTC-GGGATCA
1 AAAATGGGATTTTTAG-AAGTTTCGGGGTAAAAATGGAATTTTTGGAAGTTTCAGGG-TCA
* *
840 AAAATGGGATTTTTAGAAG-TTCGAGGGTAAAAATGGAATTTTTAGAGGTTTCAGGGTCA
1 AAAATGGGATTTTTAGAAGTTTCG-GGGTAAAAATGGAATTTTTGGAAGTTTCAGGGTCA
* * * * ** *
899 AAAATGGGATTTTT-GAAAGTTTTGGGGGGTAAAAATGGGATATTGGGAAGTTTTGGGGTAA
1 AAAATGGGATTTTTAG-AAG-TTT-CGGGGTAAAAATGGAATTTTTGGAAGTTTCAGGGTCA
* * * * *
960 AAAATGAGATTTTTGGAAGTTTCGAGGTTAAAAA-CGAGATTTTTGTAAGTTTC
1 AAAATGGGATTTTTAGAAGTTTCG-GGGTAAAAATGGA-ATTTTTGGAAGTTTC
1013 GGGACCCTCG
Statistics
Matches: 345, Mismatches: 42, Indels: 44
0.80 0.10 0.10
Matches are distributed among these distances:
57 2 0.01
58 24 0.07
59 227 0.66
60 45 0.13
61 45 0.13
62 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (59 bp):
AAAATGGGATTTTTAGAAGTTTCGGGGTAAAAATGGAATTTTTGGAAGTTTCAGGGTCA
Found at i:706 original size:118 final size:118
Alignment explanation
Indices: 603--993 Score: 493
Period size: 118 Copynumber: 3.3 Consensus size: 118
593 GTTCAGGGCT
* * *
603 AAAAATGGAATTTTTAGAAGTTTTGGGGTTAAAAATGGAA-TTTTGGAAGTTCCAAGGTCAAAAA
1 AAAAATGGAATTTTTAGAAG-TTCGGGGTTAAAAATGGAATTTTTGGAGGTTTCAAGGTCAAAAA
* *
667 TGGGATTTTT-AGAAGTTTGGGGGTAAAAACGAGATTTTTGGAAGTTTCGGGATC
65 TGGGATTTTTGA-AAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGATC
* * * **
721 AAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATGGAATTTTTGGAGGTTTTGAGGTCAAAAAT
1 AAAAATGGAATTTTTAGAAGTTCGGGGTTAAAAATGGAATTTTTGGAGGTTTCAAGGTCAAAAAT
* *
786 GGGATTTTTGAAAGTTTAGTGGTAAAAATGGGATTTTTGGAAGTTTCGGGATC
66 GGGATTTTTGAAAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGATC
* * *
839 AAAAATGGGATTTTTAGAAGTTCGAGGG-TAAAAATGGAATTTTTAGAGGTTTCAGGGTCAAAAA
1 AAAAATGGAATTTTTAGAAGTTCG-GGGTTAAAAATGGAATTTTTGGAGGTTTCAAGGTCAAAAA
* * * * *
903 TGGGATTTTTGAAAGTTTTGGGGGGTAAAAATGGGATATTGGGAAGTTTTGGGGTA
65 TGGGATTTTTGAAAG-TTT-GGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGATC
* *
959 AAAAAT-GAGATTTTTGGAAGTTTCGAGGTTAAAAA
1 AAAAATGGA-ATTTTTAGAAG-TTCGGGGTTAAAAA
994 CGAGATTTTT
Statistics
Matches: 240, Mismatches: 25, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
117 18 0.08
118 157 0.65
119 8 0.03
120 47 0.20
121 10 0.04
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (118 bp):
AAAAATGGAATTTTTAGAAGTTCGGGGTTAAAAATGGAATTTTTGGAGGTTTCAAGGTCAAAAAT
GGGATTTTTGAAAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGATC
Done.