Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007021.1 Kokia drynarioides strain JFW-HI SEQ_121627, 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: 26416
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:9074 original size:20 final size:20
Alignment explanation
Indices: 9043--9083 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
9033 AAGCAATAAG
9043 AAGAAAAAGAAGCAGA-AAC
1 AAGAAAAAGAAGCAGAGAAC
9062 AAGAAACAAGAAGCAGAGAAC
1 AAGAAA-AAGAAGCAGAGAAC
9083 A
1 A
9084 CACCTTGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 10 0.50
21 4 0.20
ACGTcount: A:0.66, C:0.12, G:0.22, T:0.00
Consensus pattern (20 bp):
AAGAAAAAGAAGCAGAGAAC
Found at i:16123 original size:68 final size:68
Alignment explanation
Indices: 16014--16158 Score: 281
Period size: 68 Copynumber: 2.1 Consensus size: 68
16004 CAAAGGTTCA
16014 AATCCTACCAAGAGTATGACACTCACGTCCCATTGGTAGATGGTCATGCATAGCGCTCTTACTCT
1 AATCCTACCAAGAGTATGACACTCACGTCCCATTGGTAGATGGTCATGCATAGCGCTCTTACTCT
16079 GTG
66 GTG
*
16082 AATCCTACCAAGAGTATGACACTCACGTCCCATTGGTAGATGGTCATGCATAGCGTTCTTACTCT
1 AATCCTACCAAGAGTATGACACTCACGTCCCATTGGTAGATGGTCATGCATAGCGCTCTTACTCT
16147 GTG
66 GTG
16150 AATCCTACC
1 AATCCTACC
16159 TTAGGGTCTA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 76 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (68 bp):
AATCCTACCAAGAGTATGACACTCACGTCCCATTGGTAGATGGTCATGCATAGCGCTCTTACTCT
GTG
Found at i:16860 original size:236 final size:226
Alignment explanation
Indices: 16479--16922 Score: 717
Period size: 236 Copynumber: 1.9 Consensus size: 226
16469 CAAAAAAAAA
*
16479 AAAAAAAAGGAAAAACAATGATGGAAGAGTTTTTCGAATATTAATATATTGATAAGTTTGTTTTT
1 AAAAAAAAGGAAAAACAATGATGGAAGAGTTTTTCGAACATTAATATATTGATAAGTTTGTTTTT
* *
16544 TATACAATGTCTATAATTTTCATCCCTTAAATATAATGCGTTTCAATATACTCAAACTCATGTCC
66 TATACAATGTCTAGAATTTTCATCCCTTAAATATAATACGTTTCAATATACTCAAACTCATGTCC
16609 TTTTGCATTAATAATAATACCGATATCAATCAAATTAAGACTCAATCAATAATTAAAAGAAGAGT
131 TTTTGCATTAATAATAATACCGATATCAATCAAATTAAGACTCAATCAATAATTAAAAGAAGAGT
16674 TATAACACTTAAAAAGGAAGCATTCAAATAC
196 TATAACACTTAAAAAGGAAGCATTCAAATAC
16705 AAAANNNNNNNNNNAAAAGGAAAAACAATGATGGAAGAGTTTTTCGAACATTAATATATTGATAA
1 AAAA----------AAAAGGAAAAACAATGATGGAAGAGTTTTTCGAACATTAATATATTGATAA
*
16770 GTTTGTTTTTTATACAATGTCTAGAATTTTCATCCCTTAAATATAATATGTTTCAATATACTCAA
56 GTTTGTTTTTTATACAATGTCTAGAATTTTCATCCCTTAAATATAATACGTTTCAATATACTCAA
* * * * *
16835 ATTCATGTCTTTTTGCATTAATAATAATACCGATATCAATCAAGTTAAGATTCACTCAATAATTA
121 ACTCATGTCCTTTTGCATTAATAATAATACCGATATCAATCAAATTAAGACTCAATCAATAATTA
16900 AAAGAAGAGTTATAACACTTAAA
186 AAAGAAGAGTTATAACACTTAAA
16923 CGCTTAGGCT
Statistics
Matches: 199, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
226 4 0.02
236 195 0.98
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.34
Consensus pattern (226 bp):
AAAAAAAAGGAAAAACAATGATGGAAGAGTTTTTCGAACATTAATATATTGATAAGTTTGTTTTT
TATACAATGTCTAGAATTTTCATCCCTTAAATATAATACGTTTCAATATACTCAAACTCATGTCC
TTTTGCATTAATAATAATACCGATATCAATCAAATTAAGACTCAATCAATAATTAAAAGAAGAGT
TATAACACTTAAAAAGGAAGCATTCAAATAC
Found at i:25236 original size:31 final size:31
Alignment explanation
Indices: 25198--25259 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
25188 AAGGCAAAGT
25198 AAGATTATTCAAAACAATAAACATAATCAAC
1 AAGATTATTCAAAACAATAAACATAATCAAC
25229 AAGATTATTCAAAACAATAAACATAATCAAC
1 AAGATTATTCAAAACAATAAACATAATCAAC
25260 TCTAATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.23
Consensus pattern (31 bp):
AAGATTATTCAAAACAATAAACATAATCAAC
Found at i:25500 original size:18 final size:16
Alignment explanation
Indices: 25470--25519 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 16
25460 TAAAATTAAC
25470 ATAATTATTTT-AATT
1 ATAATTATTTTAAATT
25485 AATAATTATATATTAAATT
1 -ATAATTAT-T-TTAAATT
25504 ATAATTATTTTTAAAT
1 ATAATTA-TTTTAAAT
25520 ATTTTTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.27
17 7 0.23
18 10 0.33
19 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATAATTATTTTAAATT
Found at i:26223 original size:11 final size:11
Alignment explanation
Indices: 26209--26242 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
26199 AAATTGAATA
26209 AAAAAAGAAAG
1 AAAAAAGAAAG
*
26220 AAAAAAGAGA-
1 AAAAAAGAAAG
26230 AAAAAAGAAAG
1 AAAAAAGAAAG
26241 AA
1 AA
26243 GAAGGAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:26238 original size:17 final size:18
Alignment explanation
Indices: 26211--26244 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
26201 ATTGAATAAA
26211 AAAAGAAAGAAAAAAGAG
1 AAAAGAAAGAAAAAAGAG
*
26229 AAAA-AAAGAAAGAAGA
1 AAAAGAAAGAAAAAAGA
26245 AGGAAGAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAGAAAGAAAAAAGAG
Done.