Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005274.1 Kokia drynarioides strain JFW-HI SEQ_119194, 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: 27646
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:221 original size:28 final size:30
Alignment explanation
Indices: 186--245 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
176 AATTTGGAAT
*
186 TTAATCCTTATAC-TTTTAT-TTTTAAGAA
1 TTAATCCTTATACATTTTATATTTTAAAAA
* *
214 TTAATCCTTCTACATTTTTTATTTTAAAAA
1 TTAATCCTTATACATTTTATATTTTAAAAA
244 TT
1 TT
246 TAAGTCCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 5 0.19
30 10 0.37
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.55
Consensus pattern (30 bp):
TTAATCCTTATACATTTTATATTTTAAAAA
Found at i:963 original size:54 final size:54
Alignment explanation
Indices: 881--993 Score: 190
Period size: 54 Copynumber: 2.1 Consensus size: 54
871 TTCTACATTG
*
881 GTAATAATACCGATGGCAATCGAACTAAACACCCTTACTATAATTAATATTATA
1 GTAATAATACCGATGGCAATCGAACTAAACACCCTTAATATAATTAATATTATA
** *
935 GTAATAATACCGATGTTAATCGAGCTAAACACCCTTAATATAATTAATATTATA
1 GTAATAATACCGATGGCAATCGAACTAAACACCCTTAATATAATTAATATTATA
989 GTAAT
1 GTAAT
994 TAATCTATCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (54 bp):
GTAATAATACCGATGGCAATCGAACTAAACACCCTTAATATAATTAATATTATA
Found at i:2439 original size:30 final size:31
Alignment explanation
Indices: 2370--2449 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
2360 TTAAATTAAT
* *
2370 AATAAT-AAAATTACATTTTAATTTTTTAAAA
1 AATAATAAAAATTA-AATTTAACTTTTTAAAA
2401 AATAATAAAAATTAAATTTAACTTTTT-AAA
1 AATAATAAAAATTAAATTTAACTTTTTAAAA
*
2431 AATTATAAAAATATAAATT
1 AATAATAAAAAT-TAAATT
2450 ATAAAAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 14 0.32
31 23 0.52
32 7 0.16
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (31 bp):
AATAATAAAAATTAAATTTAACTTTTTAAAA
Found at i:2450 original size:15 final size:17
Alignment explanation
Indices: 2429--2469 Score: 68
Period size: 15 Copynumber: 2.5 Consensus size: 17
2419 TAACTTTTTA
2429 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
2445 -AAATTATAAAAATAAT
1 AAAATTATAAAAATAAT
2461 AAAATTATA
1 AAAATTATA
2470 TTTTCTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.57
16 2 0.09
17 8 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:6215 original size:26 final size:28
Alignment explanation
Indices: 6186--6237 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
6176 ATTTATATAG
* *
6186 TCTCGAATTCA-A-ATTATTTTAAATTA
1 TCTCAAATTCATATATTATTATAAATTA
6212 TCTCAAATTCATATATTATTATAAAT
1 TCTCAAATTCATATATTATTATAAAT
6238 CAAAAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 1 0.05
28 11 0.50
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (28 bp):
TCTCAAATTCATATATTATTATAAATTA
Found at i:8348 original size:39 final size:39
Alignment explanation
Indices: 8294--8374 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
8284 TTTTTTATAT
*
8294 ATATAATGTCTAAAACTACTCATAGCCTTTTCTCAACCC
1 ATATAATGTCTAAAACTACTCATAGCCTTTCCTCAACCC
*
8333 ATATAATGTCTAAAACTATTCATAGCCTTTCCTCAACCC
1 ATATAATGTCTAAAACTACTCATAGCCTTTCCTCAACCC
8372 ATA
1 ATA
8375 AATAGGAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (39 bp):
ATATAATGTCTAAAACTACTCATAGCCTTTCCTCAACCC
Found at i:10163 original size:3 final size:3
Alignment explanation
Indices: 10155--10183 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10145 TTTATTTGGG
10155 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
10184 AGGTAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:13358 original size:20 final size:19
Alignment explanation
Indices: 13314--13362 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
13304 ATAAATATTT
*
13314 TAATATTTTCGAATAAAAA
1 TAATATTTTCAAATAAAAA
13333 TAAATATTTT-AAATAAAATAA
1 T-AATATTTTCAAAT-AAA-AA
13354 TAATATTTT
1 TAATATTTT
13363 TTGAGATTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.15
20 19 0.73
21 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TAATATTTTCAAATAAAAA
Found at i:17034 original size:22 final size:23
Alignment explanation
Indices: 17009--17063 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
16999 AAAATACTTC
*
17009 TTATATTTATTATCATAATTT-A
1 TTATTTTTATTATCATAATTTAA
*
17031 TTATTTTTCA-TATCATATTTTAA
1 TTATTTTT-ATTATCATAATTTAA
17054 TTATTTTTAT
1 TTATTTTTAT
17064 GTAGCATGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATTTTTATTATCATAATTTAA
Done.