Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012379.1 Kokia drynarioides strain JFW-HI SEQ_127383, 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, 955
Length: 1593
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Found at i:824 original size:30 final size:30
Alignment explanation
Indices: 749--1003 Score: 204
Period size: 30 Copynumber: 8.6 Consensus size: 30
739 GGAAAGTTCA
* * * *
749 AGGTTAAAAATAGAATTTTAGG--CATTCG
1 AGGTTAAAAATGGAATTTTTGGAAGAATCG
*
777 AGGGT-AAAATGGTAATTTTTGGAAGAATCG
1 AGGTTAAAAATGG-AATTTTTGGAAGAATCG
* ** *
807 GGGTTAAAAATGGAATTTTTGGAAGTTTAG
1 AGGTTAAAAATGGAATTTTTGGAAGAATCG
* *
837 -GGGT-AAAATGGTAATTTTTAAGAAGAATCG
1 AGGTTAAAAATGG-AATTTTT-GGAAGAATCG
* *
867 AGGTCAAAAATGGAATTTTTTGGAAG-TTCG
1 AGGTTAAAAATGGAA-TTTTTGGAAGAATCG
*
897 AGGTT-AAAATGGTAATTTTTGGAAAAATCG
1 AGGTTAAAAATGG-AATTTTTGGAAGAATCG
* * *
927 AGGTCAAAAATGGAATTTTTGGAAG-TTTG
1 AGGTTAAAAATGGAATTTTTGGAAGAATCG
* * *
956 AGGGT-AAAATGGTATTTTTGGAAAAATCG
1 AGGTTAAAAATGGAATTTTTGGAAGAATCG
*
985 AGGTTAAAAAAAGGAATTT
1 AGGTT-AAAAATGGAATTT
1004 GGGAAAGTTT
Statistics
Matches: 177, Mismatches: 35, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
27 6 0.03
28 36 0.20
29 37 0.21
30 54 0.31
31 32 0.18
32 12 0.07
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (30 bp):
AGGTTAAAAATGGAATTTTTGGAAGAATCG
Found at i:1012 original size:59 final size:59
Alignment explanation
Indices: 724--1096 Score: 361
Period size: 59 Copynumber: 6.3 Consensus size: 59
714 ATCCAGGGGC
* ** * * * * * *
724 AAAATGGTAATTTTGGGAAAGTTCAAGGTTAAAAATAGAATTTTAGGCA-TTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGT
* * *
782 AAAATGGTAATTTTTGGAAGAATCGGGGTTAAAAATGGAATTTTTGGAAGTTT-AGGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTTGA-GGGT
* * * *
841 AAAATGGTAATTTTTAAGAAGAATCGAGGTCAAAAATGGAATTTTTTGGAAGTTCGAGGTT
1 AAAATGGTAATTTTT-GGAAAAATCGAGGTCAAAAATGGAA-TTTTTGGAAGTTTGAGGGT
902 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGT
* * * *
961 AAAATGGT-ATTTTTGGAAAAATCGAGGTTAAAAAAAGGAA-TTTGGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGG-TCAAAAATGGAATTTTTGG-AAGTTTGAGGGT
** *
1020 AAAAAT-GTAA-TTTTGGAAAGTTCGAGGGTCAAAATAT--AATTTTGGAGAAGTTT-AGGGGT
1 -AAAATGGTAATTTTTGGAAAAATCGA-GGTCAAAA-ATGGAATTTTTG-GAAGTTTGA-GGGT
*
1079 CAAAAT-ATAATTTTTGGA
1 -AAAATGGTAATTTTTGGA
1097 CAATTTAGGG
Statistics
Matches: 270, Mismatches: 30, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
58 67 0.25
59 110 0.41
60 62 0.23
61 30 0.11
62 1 0.00
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGT
Found at i:1079 original size:30 final size:29
Alignment explanation
Indices: 999--1106 Score: 121
Period size: 29 Copynumber: 3.7 Consensus size: 29
989 TAAAAAAAGG
* * * *
999 AATTTGGGAAAGTTTGGGGGTAAAAATGT
1 AATTTTGGAAAGTTTAGGGGTCAAAATAT
*
1028 AATTTTGGAAAG-TTCGAGGGTCAAAATAT
1 AATTTTGGAAAGTTTAG-GGGTCAAAATAT
1057 AATTTTGGAGAAGTTTAGGGGTCAAAATAT
1 AATTTTGGA-AAGTTTAGGGGTCAAAATAT
1087 AATTTTTGGACAA-TTTAGGG
1 AA-TTTTGGA-AAGTTTAGGG
1107 ACCTTTAGGG
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
28 3 0.04
29 30 0.43
30 24 0.35
31 12 0.17
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (29 bp):
AATTTTGGAAAGTTTAGGGGTCAAAATAT
Done.