Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007193.1 Kokia drynarioides strain JFW-HI SEQ_121807, 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: 23258
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:5535 original size:58 final size:58
Alignment explanation
Indices: 5416--5535 Score: 143
Period size: 58 Copynumber: 2.1 Consensus size: 58
5406 TTGTTCCGTA
* * * * *
5416 AAGTCCGTCAGGGACTAACAAATGAAGAGGATGTCCGTTAGGACTACCTAGGGTTGGG
1 AAGTCCGCCAAGGACTAACAAATGAAGAGGATGTCCGTTAAGACTACCTAGGATTGAG
* * * *
5474 AAGTCCGCCAAGGACTAA-AGAATGAAGAGGATGTTCGTTAAGACTATCTAGTATTTAG
1 AAGTCCGCCAAGGACTAACA-AATGAAGAGGATGTCCGTTAAGACTACCTAGGATTGAG
5532 AAGT
1 AAGT
5536 TCGCTAAAGA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 1 0.02
58 51 0.98
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.23
Consensus pattern (58 bp):
AAGTCCGCCAAGGACTAACAAATGAAGAGGATGTCCGTTAAGACTACCTAGGATTGAG
Found at i:5548 original size:58 final size:58
Alignment explanation
Indices: 5428--5548 Score: 136
Period size: 58 Copynumber: 2.1 Consensus size: 58
5418 GTCCGTCAGG
* * * *
5428 GACTAACAAATGAAGAGGATGTCCGTTAGGACTACCTAGGGTTGGGAAGTCCGCCAAG
1 GACTAACAAATGAAGAGGATGTCCGTTAAGACTACCTAGGATTGAGAAGTCCGCCAAA
* * * * * *
5486 GACTAA-AGAATGAAGAGGATGTTCGTTAAGACTATCTAGTATTTAGAAGTTCGCTAAA
1 GACTAACA-AATGAAGAGGATGTCCGTTAAGACTACCTAGGATTGAGAAGTCCGCCAAA
5544 GACTA
1 GACTA
5549 TCTTATAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
57 1 0.02
58 51 0.98
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (58 bp):
GACTAACAAATGAAGAGGATGTCCGTTAAGACTACCTAGGATTGAGAAGTCCGCCAAA
Found at i:10709 original size:221 final size:225
Alignment explanation
Indices: 10207--10779 Score: 759
Period size: 221 Copynumber: 2.6 Consensus size: 225
10197 AACAAAAATC
* * * * * * **
10207 TATACCTATATATTACAACCCGATATTTTATATATTCGTGTTGTATTCATATTTTTTTTATGTTA
1 TATACATATATATTAGAACCCGATAATTTGTATATTTGTGTTGTGTTCATATACTTTTTATGTTA
* * * * *
10272 TTATCATCTTTAAGATATTTTAAATTCATTTAAAATTTTATATGTAATTGTTTTGTATGTATGTA
66 TTATCGTGTTTAAGATATTTTAAATTCATATAAAACTTTATATGTAATTGTTCTGTATGTA--TA
* * *
10337 TGAATATATGAATGAAAGAGAGAAAAATTGGAGAAAATCAAGTGTTAAAGAAGAAGGTCAAGGTG
129 -GAATATATGAATGAAAGAGAGAAAAATTGGAGAAAATCAAGTGCTAAAGAAGAAGGCCAAGATG
*
10402 GTGGTGAGTCGATGATAGTAGAATATATATATA
193 GTGGTGAGTCGATAATAGTAGAATATATATATA
* **
10435 TATATATATATATTAGAATTCGATAATTTGTATATTTGTGTTGTGTTCATATACTTTTTATGTTA
1 TATACATATATATTAGAACCCGATAATTTGTATATTTGTGTTGTGTTCATATACTTTTTATGTTA
* *
10500 TTATCGTGTTTAAGATATTTTAAATTCGTATAAAACTTTATATGTAATTATTCTGTATG-A-A-A
66 TTATCGTGTTTAAGATATTTTAAATTCATATAAAACTTTATATGTAATTGTTCTGTATGTATAGA
10562 A-A-ATGAATGAAAGAGAG-AAAATT-GAGAAAATCGAA-TGCTAGAA-AAGAAGGCCAAGATGG
131 ATATATGAATGAAAGAGAGAAAAATTGGAGAAAATC-AAGTGCTA-AAGAAGAAGGCCAAGATGG
10621 TGGTGAGTCGATAATAGTAGAAATATATATATACA
194 TGGTGAGTCGATAATAGTAG-AATATATATAT--A
* * * *
10656 TATACATATCTATTAGAACCCGATAATTTGTATGTTTATGTTATGTTCATATACTTTTTATGTTA
1 TATACATATATATTAGAACCCGATAATTTGTATATTTGTGTTGTGTTCATATACTTTTTATGTTA
* *
10721 TTATCGCGTTTAAGATATTTTAAATTTATATAAAACTTTATATGTAATTGTTCTGTATG
66 TTATCGTGTTTAAGATATTTTAAATTCATATAAAACTTTATATGTAATTGTTCTGTATG
10780 CGTGTATGTA
Statistics
Matches: 307, Mismatches: 33, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
218 46 0.15
219 21 0.07
220 15 0.05
221 115 0.37
222 2 0.01
224 1 0.00
227 1 0.00
228 106 0.35
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (225 bp):
TATACATATATATTAGAACCCGATAATTTGTATATTTGTGTTGTGTTCATATACTTTTTATGTTA
TTATCGTGTTTAAGATATTTTAAATTCATATAAAACTTTATATGTAATTGTTCTGTATGTATAGA
ATATATGAATGAAAGAGAGAAAAATTGGAGAAAATCAAGTGCTAAAGAAGAAGGCCAAGATGGTG
GTGAGTCGATAATAGTAGAATATATATATA
Found at i:11228 original size:13 final size:13
Alignment explanation
Indices: 11210--11234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11200 AATATAATAA
11210 AATATTTAAAAAT
1 AATATTTAAAAAT
11223 AATATTTAAAAA
1 AATATTTAAAAA
11235 AAAGGAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATTTAAAAAT
Found at i:13051 original size:2 final size:2
Alignment explanation
Indices: 13044--13074 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13034 TTGATGGGTT
13044 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13075 TGATGTTGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14978 original size:3 final size:3
Alignment explanation
Indices: 14970--14997 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
14960 GATAGCAGTT
14970 GTA GTA GTA GTA GTA GTA GTA GTA GTA G
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA G
14998 GTGGTGGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GTA
Found at i:16377 original size:7 final size:7
Alignment explanation
Indices: 16367--16407 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
16357 AGATAAGATC
16367 GAAGAGA
1 GAAGAGA
16374 GAAGAGA
1 GAAGAGA
16381 GAAGAGA
1 GAAGAGA
16388 GAAGAGA
1 GAAGAGA
16395 GAAGAGA
1 GAAGAGA
16402 GAAGAG
1 GAAGAG
16408 TTAGTGGTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (7 bp):
GAAGAGA
Found at i:21911 original size:6 final size:6
Alignment explanation
Indices: 21902--22019 Score: 73
Period size: 6 Copynumber: 20.0 Consensus size: 6
21892 GATTTATTTC
* * * **
21902 TAAATT TAAATT T-ACTG TAAATT TAAATT TAAATT CATTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
** * * * *
21949 TAAATT T-GTTT TAAATT TTAATT T-AGTT TAAATT TAAA-A TAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
21994 TAAAACT TAAACTT TAAAAT TAAATT
1 T-AAATT TAAA-TT TAAATT TAAATT
22020 CAAAGTCCAT
Statistics
Matches: 81, Mismatches: 25, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
5 13 0.16
6 59 0.73
7 9 0.11
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:21950 original size:41 final size:41
Alignment explanation
Indices: 21888--21973 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
21878 TTTAAATTAT
* *
21888 TTTAGATTTATTTCTAAATTTAAATTTACTGTAAATTTAAA
1 TTTAAATTCATTTCTAAATTTAAATTTACTGTAAATTTAAA
* ** * *
21929 TTTAAATTCATTTTTAAATTTAAATTTGTTTTAAATTTTAA
1 TTTAAATTCATTTCTAAATTTAAATTTACTGTAAATTTAAA
21970 TTTA
1 TTTA
21974 GTTTAAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (41 bp):
TTTAAATTCATTTCTAAATTTAAATTTACTGTAAATTTAAA
Found at i:21995 original size:17 final size:17
Alignment explanation
Indices: 21878--21997 Score: 82
Period size: 17 Copynumber: 7.0 Consensus size: 17
21868 TACTTTTGAG
*
21878 TTTAAATT-ATTTTAGA
1 TTTAAATTAATTTTAAA
** *
21894 TTTATTTCTAAATTTAAA
1 TTTAAAT-TAATTTTAAA
* *
21912 TTT-ACTGTAAATTTAAA
1 TTTAAAT-TAATTTTAAA
*
21929 TTTAAATTCATTTTTAAA
1 TTTAAATT-AATTTTAAA
**
21947 TTTAAATTTGTTTTAAA
1 TTTAAATTAATTTTAAA
* * *
21964 TTTTAATTTAGTTTAAA
1 TTTAAATTAATTTTAAA
*
21981 TTTAAAATAATTTTAAA
1 TTTAAATTAATTTTAAA
21998 ACTTAAACTT
Statistics
Matches: 81, Mismatches: 19, Indels: 7
0.76 0.18 0.07
Matches are distributed among these distances:
16 5 0.06
17 50 0.62
18 26 0.32
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTAATTTTAAA
Done.