Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012666.1 Kokia drynarioides strain JFW-HI SEQ_127677, 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: 2715
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Found at i:918 original size:29 final size:28
Alignment explanation
Indices: 765--1037 Score: 112
Period size: 29 Copynumber: 9.4 Consensus size: 28
755 GTAAAATGTT
**
765 AATTTTGGAAAATTACA-GTAAAAAATGG
1 AATTTTGGAAAATTTGAGGT-AAAAATGG
* * *
793 AATGTTAGG-AAATTCGAGGGT-AAAATAGT
1 AAT-TTTGGAAAATTTGA-GGTAAAAAT-GG
* *
822 AACTTTTGCAAAAATTGAGGTCAAAAATGG
1 AA-TTTTGGAAAATTTGAGGT-AAAAATGG
* * *
852 AATTTTGGAAAGTTCGAAGGGGTAAAAATGTA
1 AATTTTGGAAAATTTG-A--GGTAAAAATG-G
884 AATTTTGGAAAATTTGAGGTCAAAAATGG
1 AATTTTGGAAAATTTGAGGT-AAAAATGG
* * *
913 AATTTTGGAAAGTTTGGGGGT-AAAATGTA
1 AATTTTGGAAAATTT-GAGGTAAAAATG-G
** *
942 AATTTTATAAAATTT-AGGGTTAAAAATAG
1 AATTTTGGAAAATTTGA-GG-TAAAAATGG
* * * **
971 AATTTT-AAAAAGTTCAGGGT-AAAATTT
1 AATTTTGGAAAATTTGA-GGTAAAAATGG
** *
998 AATTTAT-GAAAAGTTCAAGGTTAAAATGG
1 AATTT-TGGAAAA-TTTGAGGTAAAAATGG
1027 AATTTTGGAAA
1 AATTTTGGAAA
1038 TTCGAGGACC
Statistics
Matches: 186, Mismatches: 36, Indels: 45
0.70 0.13 0.17
Matches are distributed among these distances:
27 10 0.05
28 38 0.20
29 79 0.42
30 29 0.16
31 13 0.07
32 17 0.09
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (28 bp):
AATTTTGGAAAATTTGAGGTAAAAATGG
Found at i:923 original size:119 final size:113
Alignment explanation
Indices: 752--1044 Score: 299
Period size: 119 Copynumber: 2.5 Consensus size: 113
742 TAGACACTCA
* *
752 AGGGTAAAATGTTAATTTTGGAAAATTACA-GTAAAAAATGGAATGTTAGGAAATTCGAGGGTAA
1 AGGGTAAAATGTTAATTTTGGAAAATTAAAGGT-AAAAATGGAAT-TTTGGAAATTCGAGGGTAA
* * **
816 AATAGTAACTTTTGCA-AAAATTGA-GGTCAAAAATGGAATTTTGGAAAGTTC
64 AAT-GTAAATTTT--ATAAAATTGAGGGTCAAAAATAGAATTTTAAAAAGTTC
* ** * *
867 GAAGGGGTAAAAATGTAAATTTTGGAAAATTTGAGGTCAAAAATGGAATTTTGGAAAGTTTGGGG
1 --A-GGGT-AAAATGTTAATTTTGGAAAATTAAAGGT-AAAAATGGAATTTTGGAAA-TTCGAGG
* *
932 GTAAAATGTAAATTTTATAAAATTTAGGGTTAAAAATAGAATTTTAAAAAGTTC
60 GTAAAATGTAAATTTTATAAAATTGAGGGTCAAAAATAGAATTTTAAAAAGTTC
* *
986 AGGGTAAAAT-TTAATTTAT-GAAAAGTTCAAGGTTAAAATGGAATTTTGGAAATTCGAGG
1 AGGGTAAAATGTTAATTT-TGGAAAA-TTAAAGGTAAAAATGGAATTTTGGAAATTCGAGG
1045 ACCTCCGGGG
Statistics
Matches: 149, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
113 5 0.03
114 29 0.19
115 12 0.08
116 4 0.03
117 3 0.02
118 11 0.07
119 60 0.40
120 25 0.17
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.31
Consensus pattern (113 bp):
AGGGTAAAATGTTAATTTTGGAAAATTAAAGGTAAAAATGGAATTTTGGAAATTCGAGGGTAAAA
TGTAAATTTTATAAAATTGAGGGTCAAAAATAGAATTTTAAAAAGTTC
Found at i:967 original size:58 final size:58
Alignment explanation
Indices: 752--1044 Score: 246
Period size: 58 Copynumber: 5.1 Consensus size: 58
742 TAGACACTCA
* * ** * *
752 AGGGTAAAATGTTAATTTTGGAAAA-TTACAGTAAAAAATGGAATGTTAGGAAA-TTCG
1 AGGGTAAAATGTAAATTTTAGAAAATTTAGGGTCAAAAATGGAAT-TTTGGAAAGTTCG
* *
809 AGGGTAAAATAGTAACTTTT-GCAAAAATT-GAGGTCAAAAATGGAATTTTGGAAAGTTCG
1 AGGGTAAAAT-GTAAATTTTAG-AAAATTTAG-GGTCAAAAATGGAATTTTGGAAAGTTCG
* *
868 AAGGGGTAAAAATGTAAATTTTGGAAAATTT-GAGGTCAAAAATGGAATTTTGGAAAGTTTG
1 -A-GGGT-AAAATGTAAATTTTAGAAAATTTAG-GGTCAAAAATGGAATTTTGGAAAGTTCG
* * * * **
929 GGGGTAAAATGTAAATTTTATAAAATTTAGGGTTAAAAATAGAATTTTAAAAAGTTC-
1 AGGGTAAAATGTAAATTTTAGAAAATTTAGGGTCAAAAATGGAATTTTGGAAAGTTCG
* * * *
986 AGGGTAAAAT-TTAA-TTTATGAAAAGTTCAAGGT-TAAAATGGAATTTTGGAAA-TTCG
1 AGGGTAAAATGTAAATTTTA-GAAAA-TTTAGGGTCAAAAATGGAATTTTGGAAAGTTCG
1042 AGG
1 AGG
1045 ACCTCCGGGG
Statistics
Matches: 197, Mismatches: 26, Indels: 27
0.79 0.10 0.11
Matches are distributed among these distances:
55 7 0.04
56 25 0.13
57 26 0.13
58 61 0.31
59 24 0.12
60 1 0.01
61 47 0.24
62 6 0.03
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.31
Consensus pattern (58 bp):
AGGGTAAAATGTAAATTTTAGAAAATTTAGGGTCAAAAATGGAATTTTGGAAAGTTCG
Found at i:1869 original size:18 final size:17
Alignment explanation
Indices: 1846--1879 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1836 AATCTTTGAA
1846 TTTGTTCTTTCTTTTTAT
1 TTTGTT-TTTCTTTTTAT
*
1864 TTTGTTTTTGTTTTTA
1 TTTGTTTTTCTTTTTA
1880 AAAAGAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.06, C:0.06, G:0.09, T:0.79
Consensus pattern (17 bp):
TTTGTTTTTCTTTTTAT
Done.