Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006559.1 Kokia drynarioides strain JFW-HI SEQ_121145, 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: 47239
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 257 characters in sequence are not A, C, G, or T
Found at i:2204 original size:6 final size:6
Alignment explanation
Indices: 2193--2288 Score: 147
Period size: 6 Copynumber: 16.0 Consensus size: 6
2183 TAAATAAATA
2193 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
* * * * *
2241 AATAAT AATAAT AATAAT AGTAAT AGTAAT AGTAAT AGTAAT AGTAAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
2289 GTAAATATTG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (6 bp):
AATAAT
Found at i:7253 original size:10 final size:10
Alignment explanation
Indices: 7223--7270 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
7213 ATTGAGGGTG
*
7223 TTATAATAAA
1 TTATAAAAAA
* *
7233 TTCTAATAAA
1 TTATAAAAAA
7243 TTATAAAAAA
1 TTATAAAAAA
7253 -TAT-AAAAA
1 TTATAAAAAA
7261 TTATAAAAAA
1 TTATAAAAAA
7271 GTCATTTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 5 0.15
9 6 0.18
10 22 0.67
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:7261 original size:8 final size:9
Alignment explanation
Indices: 7223--7269 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
7213 ATTGAGGGTG
7223 TTATAATAAA
1 TTATAA-AAA
*
7233 TTCTAATAAA
1 TTATAA-AAA
7243 TTATAAAAA
1 TTATAAAAA
*
7252 ATATAAAAA
1 TTATAAAAA
7261 TTATAAAAA
1 TTATAAAAA
7270 AGTCATTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
9 19 0.58
10 14 0.42
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:9095 original size:21 final size:21
Alignment explanation
Indices: 9069--9109 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
9059 CTCCACCACT
9069 GATTCCAAAATTATTCGTACA
1 GATTCCAAAATTATTCGTACA
*
9090 GATTCCAGAATTATTCGTAC
1 GATTCCAAAATTATTCGTAC
9110 TGAGTGCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (21 bp):
GATTCCAAAATTATTCGTACA
Found at i:25776 original size:30 final size:30
Alignment explanation
Indices: 25690--25821 Score: 113
Period size: 30 Copynumber: 4.4 Consensus size: 30
25680 TTTCGAGGCC
* * *
25690 AAAATGTAATTTTAGGAAAGTTTGA-GGAT
1 AAAATGTAATTTTAGAAAAGTTTAAGGGTT
* * * * *
25719 CAAATATAATCTTGGAAAAGTTCAAGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAAGGGTT
*
25749 AAAATGTAATTTTAGAAAAATTTAAGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAAGGGTT
* * * * *
25779 GAAATGTAATTTTTGGAAAGTTTAATGGTC
1 AAAATGTAATTTTAGAAAAGTTTAAGGGTT
**
25809 AAAACATAATTTT
1 AAAATGTAATTTT
25822 TGGATAGTTT
Statistics
Matches: 79, Mismatches: 23, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
29 18 0.23
30 61 0.77
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAGTTTAAGGGTT
Found at i:36836 original size:22 final size:20
Alignment explanation
Indices: 36787--36837 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
36777 TAGGAAGGAA
*
36787 AGAAAAAG-GAAGCGCAAGG
1 AGAAAAAGAGAAGCACAAGG
*
36806 ACAAAAAGAAGAAGCACAAGG
1 AGAAAAAG-AGAAGCACAAGG
36827 AGGAAAAAGAG
1 A-GAAAAAGAG
36838 TGCATAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 7 0.27
21 13 0.50
22 6 0.23
ACGTcount: A:0.59, C:0.10, G:0.31, T:0.00
Consensus pattern (20 bp):
AGAAAAAGAGAAGCACAAGG
Found at i:39924 original size:37 final size:37
Alignment explanation
Indices: 39872--39948 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
39862 CAGAGTTAGA
39872 AAAATTATCCAGTTTTGTTAAACGATAAGAATTTAAT
1 AAAATTATCCAGTTTTGTTAAACGATAAGAATTTAAT
*
39909 AAAATTATCCGGTTTTGTTAAACGATAAGAATTTAAT
1 AAAATTATCCAGTTTTGTTAAACGATAAGAATTTAAT
39946 AAA
1 AAA
39949 TTAAAACCCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (37 bp):
AAAATTATCCAGTTTTGTTAAACGATAAGAATTTAAT
Found at i:40182 original size:12 final size:13
Alignment explanation
Indices: 40142--40185 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
40132 TTTTTTTATT
*
40142 CCACAATTTGAAG
1 CCACAATTTAAAG
*
40155 CTACAATTTAAAG
1 CCACAATTTAAAG
*
40168 CCACAA-TTAAGG
1 CCACAATTTAAAG
40180 CCACAA
1 CCACAA
40186 AACACAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.20
Consensus pattern (13 bp):
CCACAATTTAAAG
Found at i:40467 original size:79 final size:76
Alignment explanation
Indices: 40344--40566 Score: 187
Period size: 77 Copynumber: 2.9 Consensus size: 76
40334 AACTAAATCA
* * * * * *
40344 AAATCAAATCAAATATGTTGAATGGGGGGAATAAATCTCAAAATAGAATTATTTAATTTTAATTT
1 AAATCAAATCAAATATGTTAAATGAGGGGAAGAAATCTCAAAATAAAATTATTCAA--TTAATTC
*
40409 TTATTTGGAAACT
64 TTATTCGGAAACT
* * *
40422 AAATCAGAATCAAATCTGTTAAATGATGGGAAGAAATC-CTGAAATAAAATTATTCAATTAATTC
1 AAATCA-AATCAAATATGTTAAATGAGGGGAAGAAATCTC-AAAATAAAATTATTCAATTAATTC
**
40486 TTATTCGGAAAAA
64 TTATTCGGAAACT
** * * *** * * * *
40499 AAATCCAAATCATTTTTGTTGAATGACAAGAATAAATCTCGAAACAAAATTATTCAATTAATTAT
1 AAAT-CAAATCAAATATGTTAAATGAGGGGAAGAAATCTCAAAATAAAATTATTCAATTAATTCT
40564 TAT
65 TAT
40567 AAAATCTAAA
Statistics
Matches: 119, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
77 69 0.58
78 10 0.08
79 40 0.34
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (76 bp):
AAATCAAATCAAATATGTTAAATGAGGGGAAGAAATCTCAAAATAAAATTATTCAATTAATTCTT
ATTCGGAAACT
Found at i:40904 original size:50 final size:50
Alignment explanation
Indices: 40850--40956 Score: 114
Period size: 51 Copynumber: 2.1 Consensus size: 50
40840 ATAAATATAA
*
40850 ATATTTATATTAAATACA-AGATCTT-AACAAAAT-A-ATATAAACAAATATTT
1 ATATTTATA-TAAAAACACAGAT-TTAAAC-AAATCACAT-TAAACAAATATTT
* *
40900 ATATTGATATAAAAACACCAGATTTAAACAAATCACATTAAATAAATATTT
1 ATATTTATATAAAAACA-CAGATTTAAACAAATCACATTAAACAAATATTT
40951 ATATTT
1 ATATTT
40957 TTTAAAACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
49 7 0.15
50 14 0.29
51 25 0.52
52 2 0.04
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (50 bp):
ATATTTATATAAAAACACAGATTTAAACAAATCACATTAAACAAATATTT
Done.