Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010258.1 Kokia drynarioides strain JFW-HI SEQ_125095, 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: 2120
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Found at i:336 original size:96 final size:95
Alignment explanation
Indices: 147--338 Score: 219
Period size: 96 Copynumber: 2.0 Consensus size: 95
137 TCTTTGGGAA
* ** *
147 AAGGATATTTGATTATCTTGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
* * *
212 GAATTGAAGATAAGGAAACATTGTCTCGATT
66 AAATCGAAGATAAGG-AACATTGCCTCGATT
* * *
243 AAGGGTATTCGATTATTTTGATTTGAGGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTC
*
307 AAAACTCGAA-ATAAAAGG-ATATTGCCTCGATT
65 AAAA-TCGAAGAT--AAGGAACATTGCCTCGATT
339 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 1 0.01
96 72 0.89
97 4 0.05
98 4 0.05
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (95 bp):
AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
AAATCGAAGATAAGGAACATTGCCTCGATT
Found at i:764 original size:29 final size:29
Alignment explanation
Indices: 688--1057 Score: 186
Period size: 30 Copynumber: 12.6 Consensus size: 29
678 ACATCCGGAA
*
688 GTAAAATGGTAATTTTTTGGAAGTGTCG-GG
1 GTAAAATGGTAA-TTTTTAGAAGT-TCGAGG
*
718 GTTAAAAAT-G-AGACTTTTAGAAGTTCGAGG
1 G-T-AAAATGGTA-ATTTTTAGAAGTTCGAGG
748 GTAAAATGGTAATTTTTAGAAGTTTCGA-G
1 GTAAAATGGTAATTTTTAGAAG-TTCGAGG
* * *
777 GTAAAAAATGG-AACTTTTGGAAGTTCGAGA
1 GT--AAAATGGTAATTTTTAGAAGTTCGAGG
* *
807 GTAAAACGGTAA-TTTTAGGAAGTTTTG-GG
1 GTAAAATGGTAATTTTTA-GAAG-TTCGAGG
* * *
836 GTAAAAAATGG-GATTTTTGGAAGTTCGGGG
1 GT--AAAATGGTAATTTTTAGAAGTTCGAGG
*
866 GTAAAATGGTAA-TTTTAGGAAGGTT-TAGG
1 GTAAAATGGTAATTTTTA-GAA-GTTCGAGG
* * * *
895 GTCAAAATGG-GATTTTTGGAAGTTTGGGG
1 GT-AAAATGGTAATTTTTAGAAGTTCGAGG
*
924 GT-AAATGGTAA-TTTTAGGAAGTTTTG-GG
1 GTAAAATGGTAATTTTTA-GAAG-TTCGAGG
* * *
952 GTCAAAAAT-G-AGATTTTTGGAAGTTTGGGG
1 GT--AAAATGGTA-ATTTTTAGAAGTTCGAGG
*
982 GTAAAATGGTAA-TTTTAGGAAGTTTTGA-G
1 GTAAAATGGTAATTTTTA-GAAG-TTCGAGG
*
1011 GTAAAAAAT-G-AGATTTTTGGAAGTTCGAGG
1 GT--AAAATGGTA-ATTTTTAGAAGTTCGAGG
1041 GTAAAATGGTAATTTTT
1 GTAAAATGGTAATTTTT
1058 GGATAGTTTA
Statistics
Matches: 268, Mismatches: 29, Indels: 87
0.70 0.08 0.23
Matches are distributed among these distances:
27 10 0.04
28 52 0.19
29 81 0.30
30 83 0.31
31 37 0.14
32 5 0.02
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
GTAAAATGGTAATTTTTAGAAGTTCGAGG
Found at i:777 original size:30 final size:30
Alignment explanation
Indices: 688--1066 Score: 273
Period size: 29 Copynumber: 12.8 Consensus size: 30
678 ACATCCGGAA
*
688 GTAAAATGGTAATTTTTTGGAAGTGTCG-GG
1 GTAAAATGGTAA-TTTTTGGAAGTTTCGAGG
* *
718 GTTAAAAAT-G-AGACTTTTAGAAG-TTCGAGG
1 G-T-AAAATGGTA-ATTTTTGGAAGTTTCGAGG
*
748 GTAAAATGGTAATTTTTAGAAGTTTCGA-G
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGG
* *
777 GTAAAAAATGG-AACTTTTGGAAG-TTCGAGA
1 GT--AAAATGGTAATTTTTGGAAGTTTCGAGG
* * *
807 GTAAAACGGTAATTTTAGGAAGTTTTG-GG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGG
* *
836 GTAAAAAATGG-GATTTTTGGAAG-TTCGGGG
1 GT--AAAATGGTAATTTTTGGAAGTTTCGAGG
*
866 GTAAAATGGTAATTTTAGGAAGGTTT--AGG
1 GTAAAATGGTAATTTTTGGAA-GTTTCGAGG
* *
895 GTCAAAATGG-GATTTTTGGAAGTTT-GGGG
1 GT-AAAATGGTAATTTTTGGAAGTTTCGAGG
* *
924 GT-AAATGGTAATTTTAGGAAGTTTTG-GG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGG
*
952 GTCAAAAAT-G-AGATTTTTGGAAGTTT-GGGG
1 GT--AAAATGGTA-ATTTTTGGAAGTTTCGAGG
* *
982 GTAAAATGGTAATTTTAGGAAGTTTTGA-G
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGG
1011 GTAAAAAAT-G-AGATTTTTGGAAG-TTCGAGG
1 GT--AAAATGGTA-ATTTTTGGAAGTTTCGAGG
1041 GTAAAATGGTAATTTTTGGATAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
1067 AGGGACCTCC
Statistics
Matches: 282, Mismatches: 29, Indels: 75
0.73 0.08 0.19
Matches are distributed among these distances:
27 6 0.02
28 49 0.17
29 100 0.35
30 93 0.33
31 29 0.10
32 5 0.02
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (30 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGAGG
Found at i:786 original size:59 final size:59
Alignment explanation
Indices: 688--1066 Score: 478
Period size: 59 Copynumber: 6.4 Consensus size: 59
678 ACATCCGGAA
* * * * * *
688 GTAAAATGGTAATTTTTTGGAAGTGTCGGGGTTAAAAATGAGACTTTTAGAAGTTCGAGG
1 GTAAAATGGTAA-TTTTAGGAAGTTTTGGGGTAAAAAATGAGATTTTTGGAAGTTCGAGG
* * * *
748 GTAAAATGGTAATTTTTA-GAAGTTTCGAGGTAAAAAATG-GAACTTTTGGAAGTTCGAGA
1 GTAAAATGGTAA-TTTTAGGAAGTTTTGGGGTAAAAAATGAG-ATTTTTGGAAGTTCGAGG
* * *
807 GTAAAACGGTAATTTTAGGAAGTTTTGGGGTAAAAAATGGGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTAGGAAGTTTTGGGGTAAAAAATGAGATTTTTGGAAGTTCGAGG
* * * * * *
866 GTAAAATGGTAATTTTAGGAAGGTTTAGGGT-CAAAATGGGATTTTTGGAAGTTTGGGG
1 GTAAAATGGTAATTTTAGGAAGTTTTGGGGTAAAAAATGAGATTTTTGGAAGTTCGAGG
* * *
924 GT-AAATGGTAATTTTAGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTTGGGG
1 GTAAAATGGTAATTTTAGGAAGTTTTGGGGTAAAAAATGAGATTTTTGGAAGTTCGAGG
*
982 GTAAAATGGTAATTTTAGGAAGTTTTGAGGTAAAAAATGAGATTTTTGGAAGTTCGAGG
1 GTAAAATGGTAATTTTAGGAAGTTTTGGGGTAAAAAATGAGATTTTTGGAAGTTCGAGG
*
1041 GTAAAATGGTAATTTTTGGATAGTTT
1 GTAAAATGGTAATTTTAGGA-AGTTT
1067 AGGGACCTCC
Statistics
Matches: 287, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
57 26 0.09
58 60 0.21
59 178 0.62
60 23 0.08
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (59 bp):
GTAAAATGGTAATTTTAGGAAGTTTTGGGGTAAAAAATGAGATTTTTGGAAGTTCGAGG
Found at i:961 original size:175 final size:176
Alignment explanation
Indices: 722--1070 Score: 490
Period size: 175 Copynumber: 2.0 Consensus size: 176
712 GTCGGGGTTA
722 AAAATGAGACTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTAAAAAATG
1 AAAATGAGACTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTAAAAAATG
* *
787 -GAACTTTTGGAAGTTCGAGAGTAAAACGGTAATTTTAGGAAGTTTTGGGGTAAAAAATGGGATT
66 AG-ACTTTTGGAAGTTCGAGAGTAAAACGGTAATTTTAGGAAGTTTTGAGGTAAAAAATGAGATT
*
851 TTTGGAAGTTCGGGGGTAAAATGGTAATTTTAGGA-AGGTTTAGGGTC
130 TTTGGAAGTTCGAGGGTAAAATGGTAATTTTAGGATA-GTTTAGGGTC
* * * * * * * *
898 AAAATGGGATTTTTGGAAGTTTGGGGGT-AAATGGTAA-TTTTAGGAAGTTTTGGGGTCAAAAAT
1 AAAATGAGACTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTA-GAAGTTTCGAGGTAAAAAAT
* * * * *
961 GAGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTAGGAAGTTTTGAGGTAAAAAATGAGATT
65 GAGACTTTTGGAAGTTCGAGAGTAAAACGGTAATTTTAGGAAGTTTTGAGGTAAAAAATGAGATT
*
1026 TTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGATAGTTTAGGG
130 TTTGGAAGTTCGAGGGTAAAATGGTAATTTTAGGATAGTTTAGGG
1071 ACCTCCGGGG
Statistics
Matches: 153, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
174 5 0.03
175 123 0.80
176 25 0.16
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.34
Consensus pattern (176 bp):
AAAATGAGACTTTTAGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTAAAAAATG
AGACTTTTGGAAGTTCGAGAGTAAAACGGTAATTTTAGGAAGTTTTGAGGTAAAAAATGAGATTT
TTGGAAGTTCGAGGGTAAAATGGTAATTTTAGGATAGTTTAGGGTC
Found at i:2078 original size:13 final size:13
Alignment explanation
Indices: 2055--2093 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2045 TTTTTATTCT
*
2055 TAATAATTAATAC
1 TAATTATTAATAC
* *
2068 TGATTATTAATAA
1 TAATTATTAATAC
2081 TAATTATTAATAC
1 TAATTATTAATAC
2094 AGTTATCAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (13 bp):
TAATTATTAATAC
Done.