Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001738.1 Kokia drynarioides strain JFW-HI SEQ_113445, 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, 780
Length: 1300
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.28
Found at i:545 original size:28 final size:28
Alignment explanation
Indices: 514--573 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
504 AAAATGTGAT
** *
514 TTTTGGATGCTCGAGGGTAAAACGGTAA
1 TTTTGGACACTCGAGGGCAAAACGGTAA
* *
542 TTTTGGACACTTGAGGGCAAAATGGTAA
1 TTTTGGACACTCGAGGGCAAAACGGTAA
570 TTTT
1 TTTT
574 TGGAAAGTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.33
Consensus pattern (28 bp):
TTTTGGACACTCGAGGGCAAAACGGTAA
Found at i:660 original size:58 final size:58
Alignment explanation
Indices: 532--692 Score: 171
Period size: 58 Copynumber: 2.7 Consensus size: 58
522 GCTCGAGGGT
* *
532 AAAACGGTAATTTTGGACACTT-GAGGGCAAAATGGTAATTTTTGGAAAGTTCGAAGTCA
1 AAAACGG-AATTTTAGACA-TTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGAAGTCA
* * * * ** *
591 AAAATGAAATTTTAGACGTTCGAGGGTAAAATCGTAATTTTTGGAAAGTTCGGTGTTA
1 AAAACGGAATTTTAGACATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGAAGTCA
* ** *
649 AAAACGGAATTTCTAGATACCCGTGGGTAAAATGGTAATTTTTG
1 AAAACGGAATTT-TAGACATTCGAGGGTAAAATGGTAATTTTTG
693 AAAAATAGGG
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
57 2 0.02
58 51 0.61
59 30 0.36
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (58 bp):
AAAACGGAATTTTAGACATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGAAGTCA
Found at i:775 original size:29 final size:27
Alignment explanation
Indices: 743--956 Score: 103
Period size: 29 Copynumber: 7.3 Consensus size: 27
733 TGAAATGATA
743 AATTTTGGAAAAATTAGGGTCAACAATGG
1 AATTTTGGAAAAATTAGGGT-AA-AATGG
* * *
772 AATTATT-G-AAAGTTCGAGGGTGAAATAGTA
1 AATT-TTGGAAAAATT--AGGGTAAAAT-G-G
*
802 AATTTTGGAAAAAAAATTGGGGTCAAAAATGG
1 AATTTTGG---AAAAATTAGGGT--AAAATGG
** *
834 AATTTTGGAAATTTTAGGGTAAAATGT
1 AATTTTGGAAAAATTAGGGTAAAATGG
*
861 AATTTTTGGAAAATTTAGGGTTAAAATGG
1 AA-TTTTGGAAAAATTAGGG-TAAAATGG
**
890 AATTTT--AAAAAGTTTAGGGGGTAAAAATTT
1 AATTTTGGAAAAA--TTA--GGGT-AAAATGG
* *
920 ATTTTTGGAAAATTTAGGGTCATAAATGG
1 AATTTTGGAAAAATTAGGGT-A-AAATGG
949 AATTTTGG
1 AATTTTGG
957 GTAAGTTCAG
Statistics
Matches: 141, Mismatches: 22, Indels: 44
0.68 0.11 0.21
Matches are distributed among these distances:
26 4 0.03
27 8 0.06
28 36 0.26
29 39 0.28
30 28 0.20
32 16 0.11
33 1 0.01
34 9 0.06
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (27 bp):
AATTTTGGAAAAATTAGGGTAAAATGG
Found at i:775 original size:59 final size:58
Alignment explanation
Indices: 685--954 Score: 212
Period size: 59 Copynumber: 4.6 Consensus size: 58
675 GTAAAATGGT
* *
685 AATTTTTGAAAAA-TAGGGTCAAAAATAGAATTTTT-AGAAGTTCGGTGGTGAAATGATA
1 AATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGA-AAGTTCGG-GGTGAAATGATA
* *
743 AATTTTGGAAAAATTAGGGTCAACAATGGAATTATTGAAAGTTCGAGGGTGAAAT-AGTA
1 AATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGAAAGTTCG-GGGTGAAATGA-TA
* * * ** *
802 AATTTTGGAAAAAAAATTGGGGTCAAAAATGGAATTTTGGAAATTTTAGGGTAAAATG-TA
1 AATTTTGG---AAAAATTAGGGTCAAAAATGGAATTTTTGAAAGTTCGGGGTGAAATGATA
* * * ** * * *
862 ATTTTTGGAAAATTTAGGGT-TAAAATGGAATTTTAAAAAGTTTAGGGG-GTAAA-AATTT
1 AATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGAAAG-TTCGGGGTG-AAATGA-TA
* * *
920 ATTTTTGGAAAATTTAGGGTCATAAATGGAATTTT
1 AATTTTGGAAAAATTAGGGTCAAAAATGGAATTTT
955 GGGTAAGTTC
Statistics
Matches: 173, Mismatches: 26, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
56 16 0.09
57 18 0.10
58 34 0.20
59 56 0.32
60 11 0.06
61 8 0.05
62 30 0.17
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (58 bp):
AATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGAAAGTTCGGGGTGAAATGATA
Found at i:868 original size:28 final size:29
Alignment explanation
Indices: 821--954 Score: 125
Period size: 28 Copynumber: 4.6 Consensus size: 29
811 AAAAAAATTG
*
821 GGGTCAAAAATGGAA-TTTTGGAAATTTTA
1 GGGT-AAAAATGGAATTTTTGGAAAATTTA
*
850 GGGT-AAAATGTAATTTTTGGAAAATTTA
1 GGGTAAAAATGGAATTTTTGGAAAATTTA
* *
878 GGGTTAAAATGGAA-TTTT-AAAAAGTTTA
1 GGGTAAAAATGGAATTTTTGGAAAA-TTTA
**
906 GGGGGTAAAAAT-TTATTTTTGGAAAATTTA
1 --GGGTAAAAATGGAATTTTTGGAAAATTTA
*
936 GGGTCATAAATGGAATTTT
1 GGGT-AAAAATGGAATTTT
955 GGGTAAGTTC
Statistics
Matches: 85, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
27 12 0.14
28 29 0.34
29 18 0.21
30 22 0.26
31 4 0.05
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.37
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAAATTTA
Done.