Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009966.1 Kokia drynarioides strain JFW-HI SEQ_124715, 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: 12373
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Found at i:11702 original size:29 final size:29
Alignment explanation
Indices: 11606--11981 Score: 259
Period size: 29 Copynumber: 12.8 Consensus size: 29
11596 AATTCAAGGT
* *
11606 TAAAAATGGATTTTTTGGATA-TCCGG-GG
1 TAAAAATGGAATTTTTGGA-AGTTCGGAGG
* * * *
11634 GAAAAATGGTAATTTTAGGAATTTTCAGA-G
1 TAAAAATGG-AATTTTTGGAA-GTTCGGAGG
* *
11664 TCAAAAATGGAATTTTGGGAAGTTCGGAGC
1 T-AAAAATGGAATTTTTGGAAGTTCGGAGG
*
11694 TAAAAATGGAATTTTTAGAAGTTTCGG-GG
1 TAAAAATGGAATTTTTGGAAG-TTCGGAGG
**
11723 TTAAAAATGGAA-TTTTGGAAGTTCCAAGG
1 -TAAAAATGGAATTTTTGGAAGTTCGGAGG
* * * *
11752 TCAAAAATGGGATTTTTAGAAGTTTGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTCGGAGG
* * *
11782 TAAAAATGGGATTTTTGGAATTTTC-GAGA
1 TAAAAATGGAATTTTTGGAA-GTTCGGAGG
* * *
11811 TAAAAAATGGGATTTTTAGAAGTTCGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTCGGAGG
* *
11841 TAAAAATGGAATTTTTTGAGGTTTC-GAGG
1 TAAAAATGGAATTTTTGGAAG-TTCGGAGG
* * *
11870 TTAATAATGGAATTTTTGAAAGTT-TGAGGG
1 -TAAAAATGGAATTTTTGGAAGTTCGGA-GG
* *
11900 TAAAAATGGGATTTTTGGAAGTTTTGG-GG
1 TAAAAATGGAATTTTTGGAAG-TTCGGAGG
* * *
11929 CAAAAATGGGATTTTTGGAAGTT-TGAGGG
1 TAAAAATGGAATTTTTGGAAGTTCGGA-GG
*
11958 TAAAAAATGGGATTTTTGGAAGTT
1 T-AAAAATGGAATTTTTGGAAGTT
11982 TCAAGACCCT
Statistics
Matches: 279, Mismatches: 46, Indels: 44
0.76 0.12 0.12
Matches are distributed among these distances:
27 1 0.00
28 15 0.05
29 141 0.51
30 113 0.41
31 9 0.03
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTCGGAGG
Found at i:11707 original size:59 final size:59
Alignment explanation
Indices: 11635--11981 Score: 182
Period size: 59 Copynumber: 5.9 Consensus size: 59
11625 TATCCGGGGG
*
11635 AAAAATGGTAA-TTTTAGGAATTTTCAGAGTCAAAAATGGAATTTTGGGAAGTTCGGAGCT
1 AAAAATGGTAATTTTTA-GAAGTTTCAGAGTCAAAAATGGAATTTT-GGAAGTTCGGAGCT
* * * ** *
11695 AAAAATGG-AATTTTTAGAAGTTTCGGGGTTAAAAATGGAATTTTGGAAGTTCCAAGGT
1 AAAAATGGTAATTTTTAGAAGTTTCAGAGTCAAAAATGGAATTTTGGAAGTTCGGAGCT
* ** * * * *
11753 CAAAAATGG-GATTTTTAGAAGTTTGGGGGT-AAAAATGGGATTTTTGGAATTTTC-GAGAT
1 -AAAAATGGTAATTTTTAGAAGTTTCAGAGTCAAAAAT-GGAATTTTGGAA-GTTCGGAGCT
* * * * * *
11812 AAAAAATGG-GATTTTTAGAAG-TTCGGGGGT-AAAAATGGAATTTTTTGAGGTTTC-GAGGTT
1 -AAAAATGGTAATTTTTAGAAGTTTC-AGAGTCAAAAATGGAA-TTTTGGAAG-TTCGGA-GCT
* * * * * *
11872 AATAATGG-AATTTTT-GAAAGTTTGAGGGT-AAAAATGGGATTTTTGGAAGTTTTGGGGC-
1 AAAAATGGTAATTTTTAG-AAGTTTCAGAGTCAAAAAT-GGAATTTTGGAAG-TTCGGAGCT
* * * * * *
11930 AAAAATGG-GATTTTTGGAAGTTTGAGGGTAAAAAATGGGATTTTTGGAAGTT
1 AAAAATGGTAATTTTTAGAAGTTTCAGAGTCAAAAAT-GGAATTTTGGAAGTT
11982 TCAAGACCCT
Statistics
Matches: 241, Mismatches: 32, Indels: 30
0.80 0.11 0.10
Matches are distributed among these distances:
58 50 0.21
59 167 0.69
60 24 0.10
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
AAAAATGGTAATTTTTAGAAGTTTCAGAGTCAAAAATGGAATTTTGGAAGTTCGGAGCT
Found at i:11796 original size:147 final size:146
Alignment explanation
Indices: 11630--11981 Score: 456
Period size: 147 Copynumber: 2.4 Consensus size: 146
11620 TTGGATATCC
* * * * *
11630 GGGGGAAAAATGGTAATTTTAGGAATTTTCAGAGTCAAAAATGGAATTTTGGGAAGTTCGGAGCT
1 GGGGGAAAAATGG-GATTTTTGGAATTTTCAGAGTAAAAAATGGGATTTTTGGAAGTTCGGAGCT
* *
11695 AAAAATGGAATTTTTAGAAGTTTCGGGGTTAAAAATGGAA-TTTTGGAAGTTCCAAGGTCAAAAA
65 AAAAATGGAATTTTTAGAAGTTTCGAGGTTAAAAATGGAATTTTTGAAAGTTCCAAGGT-AAAAA
11759 TGGGATTTTTAGAAGTTT
129 TGGGATTTTTAGAAGTTT
* * *
11777 GGGGGTAAAAATGGGATTTTTGGAATTTTC-GAGATAAAAAATGGGATTTTTAGAAGTTCGGGGG
1 GGGGG-AAAAATGGGATTTTTGGAATTTTCAGAG-TAAAAAATGGGATTTTTGGAAGTTCGGAGC
* * * ** *
11841 TAAAAATGGAATTTTTTGAGGTTTCGAGGTTAATAATGGAATTTTTGAAAGTTTGAGGGTAAAAA
64 TAAAAATGGAATTTTTAGAAGTTTCGAGGTTAAAAATGGAATTTTTGAAAGTTCCAAGGTAAAAA
*
11906 TGGGATTTTTGGAAGTTTT
129 TGGGATTTTTAGAAG-TTT
* * * *
11925 GGGGCAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAAAATGGGATTTTTGGAAGTT
1 GGGGGAAAAATGGGATTTTTGGAATTTTCAGAGTAAAAAATGGGATTTTTGGAAGTT
11982 TCAAGACCCT
Statistics
Matches: 178, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
146 3 0.02
147 144 0.81
148 31 0.17
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (146 bp):
GGGGGAAAAATGGGATTTTTGGAATTTTCAGAGTAAAAAATGGGATTTTTGGAAGTTCGGAGCTA
AAAATGGAATTTTTAGAAGTTTCGAGGTTAAAAATGGAATTTTTGAAAGTTCCAAGGTAAAAATG
GGATTTTTAGAAGTTT
Found at i:11807 original size:88 final size:87
Alignment explanation
Indices: 11629--11983 Score: 313
Period size: 88 Copynumber: 4.0 Consensus size: 87
11619 TTTGGATATC
* * * * * *
11629 CGGGGGAAAAATGGTAATTTTAGGAATTTTCAGAGTCAAAAATGGAATTTTGGGAAGTTCG-GAG
1 CGGGGTAAAAATGGGAATTTT-GGAAGTTCCAG-GTCAAAAATGGAATTTTTGGAAGTTTGAG-G
* * *
11693 CTAAAAATGGAATTTTTAGAAGTTT
63 GTAAAAATGGGATTTTTGGAAGTTT
* * *
11718 CGGGGTTAAAAAT-GGAATTTTGGAAGTTCCAAGGTCAAAAATGGGATTTTTAGAAGTTTGGGGG
1 CGGGG-TAAAAATGGGAATTTTGGAAGTTCC-AGGTCAAAAATGGAATTTTTGGAAGTTTGAGGG
*
11782 TAAAAATGGGATTTTTGGAATTTT
64 TAAAAATGGGATTTTTGGAAGTTT
* * * * ** * *
11806 CGAGATAAAAAATGGGATTTTTAGAAGTTCGGGGGT-AAAAATGGAATTTTTTGAGGTTTCGAGG
1 CGGGGT-AAAAATGGGAATTTTGGAAGTTC-CAGGTCAAAAATGGAATTTTTGGAAGTTT-GAGG
* * * *
11870 TTAATAATGGAATTTTTGAAAGTTT
63 GTAAAAATGGGATTTTTGGAAGTTT
* *** * *
11895 -GAGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGCAAAAATGGGATTTTTGGAAGTTTGAGGGT
1 CG-GGGTAAAAATGGGAATTTTGGAAGTTCCAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGT
11959 AAAAAATGGGATTTTTGGAAGTTT
65 -AAAAATGGGATTTTTGGAAGTTT
11983 C
1 C
11984 AAGACCCTCG
Statistics
Matches: 215, Mismatches: 40, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
87 9 0.04
88 143 0.67
89 57 0.27
90 6 0.03
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (87 bp):
CGGGGTAAAAATGGGAATTTTGGAAGTTCCAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTA
AAAATGGGATTTTTGGAAGTTT
Done.