Multiple sequence alignment - TraesCS4D01G258400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G258400 chr4D 100.000 2918 0 0 1 2918 428529574 428532491 0.000000e+00 5389.0
1 TraesCS4D01G258400 chr4D 96.219 2645 75 13 286 2918 507114494 507111863 0.000000e+00 4307.0
2 TraesCS4D01G258400 chr1D 96.823 2644 62 10 286 2918 475528296 475525664 0.000000e+00 4397.0
3 TraesCS4D01G258400 chr1D 94.834 2652 93 23 281 2918 6491899 6489278 0.000000e+00 4098.0
4 TraesCS4D01G258400 chr1D 94.041 688 30 5 2241 2918 37519621 37520307 0.000000e+00 1033.0
5 TraesCS4D01G258400 chr3D 96.260 2647 72 14 286 2918 85226134 85228767 0.000000e+00 4314.0
6 TraesCS4D01G258400 chr3D 96.068 2645 78 16 286 2918 359622499 359625129 0.000000e+00 4285.0
7 TraesCS4D01G258400 chr3D 95.206 2649 83 20 286 2918 574856805 574854185 0.000000e+00 4148.0
8 TraesCS4D01G258400 chr3D 97.283 1656 30 7 1270 2918 11274709 11276356 0.000000e+00 2795.0
9 TraesCS4D01G258400 chr6D 95.623 2650 71 21 286 2918 472510963 472513584 0.000000e+00 4209.0
10 TraesCS4D01G258400 chr6D 95.049 2646 91 21 285 2918 367564538 367561921 0.000000e+00 4124.0
11 TraesCS4D01G258400 chr6D 96.142 2359 60 14 286 2623 7981042 7978694 0.000000e+00 3823.0
12 TraesCS4D01G258400 chr2D 95.425 2645 94 17 285 2918 382702779 382700151 0.000000e+00 4189.0
13 TraesCS4D01G258400 chr2D 95.458 2642 86 16 286 2918 182632456 182629840 0.000000e+00 4183.0
14 TraesCS4D01G258400 chr2D 95.308 2664 71 23 286 2918 74953112 74955752 0.000000e+00 4178.0
15 TraesCS4D01G258400 chr2D 95.855 1737 42 10 1188 2918 634823627 634821915 0.000000e+00 2782.0
16 TraesCS4D01G258400 chr5D 95.208 2650 81 22 286 2918 480824254 480821634 0.000000e+00 4148.0
17 TraesCS4D01G258400 chr5D 81.000 100 14 4 154 251 446684564 446684660 1.120000e-09 75.0
18 TraesCS4D01G258400 chr1B 89.429 700 43 12 2235 2918 664032283 664032967 0.000000e+00 854.0
19 TraesCS4D01G258400 chr5A 87.234 47 5 1 200 246 573083711 573083666 5.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G258400 chr4D 428529574 428532491 2917 False 5389 5389 100.000 1 2918 1 chr4D.!!$F1 2917
1 TraesCS4D01G258400 chr4D 507111863 507114494 2631 True 4307 4307 96.219 286 2918 1 chr4D.!!$R1 2632
2 TraesCS4D01G258400 chr1D 475525664 475528296 2632 True 4397 4397 96.823 286 2918 1 chr1D.!!$R2 2632
3 TraesCS4D01G258400 chr1D 6489278 6491899 2621 True 4098 4098 94.834 281 2918 1 chr1D.!!$R1 2637
4 TraesCS4D01G258400 chr1D 37519621 37520307 686 False 1033 1033 94.041 2241 2918 1 chr1D.!!$F1 677
5 TraesCS4D01G258400 chr3D 85226134 85228767 2633 False 4314 4314 96.260 286 2918 1 chr3D.!!$F2 2632
6 TraesCS4D01G258400 chr3D 359622499 359625129 2630 False 4285 4285 96.068 286 2918 1 chr3D.!!$F3 2632
7 TraesCS4D01G258400 chr3D 574854185 574856805 2620 True 4148 4148 95.206 286 2918 1 chr3D.!!$R1 2632
8 TraesCS4D01G258400 chr3D 11274709 11276356 1647 False 2795 2795 97.283 1270 2918 1 chr3D.!!$F1 1648
9 TraesCS4D01G258400 chr6D 472510963 472513584 2621 False 4209 4209 95.623 286 2918 1 chr6D.!!$F1 2632
10 TraesCS4D01G258400 chr6D 367561921 367564538 2617 True 4124 4124 95.049 285 2918 1 chr6D.!!$R2 2633
11 TraesCS4D01G258400 chr6D 7978694 7981042 2348 True 3823 3823 96.142 286 2623 1 chr6D.!!$R1 2337
12 TraesCS4D01G258400 chr2D 382700151 382702779 2628 True 4189 4189 95.425 285 2918 1 chr2D.!!$R2 2633
13 TraesCS4D01G258400 chr2D 182629840 182632456 2616 True 4183 4183 95.458 286 2918 1 chr2D.!!$R1 2632
14 TraesCS4D01G258400 chr2D 74953112 74955752 2640 False 4178 4178 95.308 286 2918 1 chr2D.!!$F1 2632
15 TraesCS4D01G258400 chr2D 634821915 634823627 1712 True 2782 2782 95.855 1188 2918 1 chr2D.!!$R3 1730
16 TraesCS4D01G258400 chr5D 480821634 480824254 2620 True 4148 4148 95.208 286 2918 1 chr5D.!!$R1 2632
17 TraesCS4D01G258400 chr1B 664032283 664032967 684 False 854 854 89.429 2235 2918 1 chr1B.!!$F1 683

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
46 47 0.035739 TGGCCACGAAAGAAGTACCC 59.964 55.0 0.0 0.0 0.00 3.69 F
278 279 0.108585 TGCTTCGGCTTATCATCCCC 59.891 55.0 0.0 0.0 42.37 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1240 1277 7.11839 AGAGCAACTTGTCAACATAATACTGTC 59.882 37.037 0.0 0.0 0.0 3.51 R
2178 2236 4.16204 AGATTAGCTTCACATTCCCCAG 57.838 45.455 0.0 0.0 0.0 4.45 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.947464 TCAAGAGGAGGTATTTCTTTACTGG 58.053 40.000 0.00 0.00 0.00 4.00
25 26 5.959583 AGAGGAGGTATTTCTTTACTGGG 57.040 43.478 0.00 0.00 0.00 4.45
26 27 5.351405 AGAGGAGGTATTTCTTTACTGGGT 58.649 41.667 0.00 0.00 0.00 4.51
27 28 5.791141 AGAGGAGGTATTTCTTTACTGGGTT 59.209 40.000 0.00 0.00 0.00 4.11
28 29 5.816682 AGGAGGTATTTCTTTACTGGGTTG 58.183 41.667 0.00 0.00 0.00 3.77
29 30 4.948004 GGAGGTATTTCTTTACTGGGTTGG 59.052 45.833 0.00 0.00 0.00 3.77
30 31 4.341487 AGGTATTTCTTTACTGGGTTGGC 58.659 43.478 0.00 0.00 0.00 4.52
31 32 3.446161 GGTATTTCTTTACTGGGTTGGCC 59.554 47.826 0.00 0.00 0.00 5.36
32 33 2.757894 TTTCTTTACTGGGTTGGCCA 57.242 45.000 0.00 0.00 36.17 5.36
33 34 1.989706 TTCTTTACTGGGTTGGCCAC 58.010 50.000 3.88 0.00 36.17 5.01
34 35 0.250553 TCTTTACTGGGTTGGCCACG 60.251 55.000 3.88 0.00 36.17 4.94
35 36 0.250553 CTTTACTGGGTTGGCCACGA 60.251 55.000 3.88 0.00 36.17 4.35
36 37 0.183014 TTTACTGGGTTGGCCACGAA 59.817 50.000 3.88 0.00 36.17 3.85
37 38 0.183014 TTACTGGGTTGGCCACGAAA 59.817 50.000 3.88 0.00 36.17 3.46
38 39 0.250553 TACTGGGTTGGCCACGAAAG 60.251 55.000 3.88 3.75 36.17 2.62
39 40 1.228124 CTGGGTTGGCCACGAAAGA 60.228 57.895 3.88 0.00 36.17 2.52
40 41 0.821711 CTGGGTTGGCCACGAAAGAA 60.822 55.000 3.88 0.00 36.17 2.52
41 42 0.821711 TGGGTTGGCCACGAAAGAAG 60.822 55.000 3.88 0.00 36.17 2.85
42 43 0.822121 GGGTTGGCCACGAAAGAAGT 60.822 55.000 3.88 0.00 36.17 3.01
43 44 1.543871 GGGTTGGCCACGAAAGAAGTA 60.544 52.381 3.88 0.00 36.17 2.24
44 45 1.534163 GGTTGGCCACGAAAGAAGTAC 59.466 52.381 3.88 0.00 34.09 2.73
45 46 1.534163 GTTGGCCACGAAAGAAGTACC 59.466 52.381 3.88 0.00 0.00 3.34
46 47 0.035739 TGGCCACGAAAGAAGTACCC 59.964 55.000 0.00 0.00 0.00 3.69
47 48 0.675837 GGCCACGAAAGAAGTACCCC 60.676 60.000 0.00 0.00 0.00 4.95
48 49 1.017701 GCCACGAAAGAAGTACCCCG 61.018 60.000 0.00 0.00 0.00 5.73
49 50 1.017701 CCACGAAAGAAGTACCCCGC 61.018 60.000 0.00 0.00 0.00 6.13
50 51 1.017701 CACGAAAGAAGTACCCCGCC 61.018 60.000 0.00 0.00 0.00 6.13
51 52 1.294138 CGAAAGAAGTACCCCGCCA 59.706 57.895 0.00 0.00 0.00 5.69
52 53 0.320946 CGAAAGAAGTACCCCGCCAA 60.321 55.000 0.00 0.00 0.00 4.52
53 54 1.677820 CGAAAGAAGTACCCCGCCAAT 60.678 52.381 0.00 0.00 0.00 3.16
54 55 1.743394 GAAAGAAGTACCCCGCCAATG 59.257 52.381 0.00 0.00 0.00 2.82
55 56 0.988832 AAGAAGTACCCCGCCAATGA 59.011 50.000 0.00 0.00 0.00 2.57
56 57 0.988832 AGAAGTACCCCGCCAATGAA 59.011 50.000 0.00 0.00 0.00 2.57
57 58 1.564348 AGAAGTACCCCGCCAATGAAT 59.436 47.619 0.00 0.00 0.00 2.57
58 59 2.025321 AGAAGTACCCCGCCAATGAATT 60.025 45.455 0.00 0.00 0.00 2.17
59 60 3.201266 AGAAGTACCCCGCCAATGAATTA 59.799 43.478 0.00 0.00 0.00 1.40
60 61 2.927028 AGTACCCCGCCAATGAATTAC 58.073 47.619 0.00 0.00 0.00 1.89
61 62 2.508300 AGTACCCCGCCAATGAATTACT 59.492 45.455 0.00 0.00 0.00 2.24
62 63 3.712733 AGTACCCCGCCAATGAATTACTA 59.287 43.478 0.00 0.00 0.00 1.82
63 64 3.876309 ACCCCGCCAATGAATTACTAT 57.124 42.857 0.00 0.00 0.00 2.12
64 65 4.986054 ACCCCGCCAATGAATTACTATA 57.014 40.909 0.00 0.00 0.00 1.31
65 66 5.313280 ACCCCGCCAATGAATTACTATAA 57.687 39.130 0.00 0.00 0.00 0.98
66 67 5.697067 ACCCCGCCAATGAATTACTATAAA 58.303 37.500 0.00 0.00 0.00 1.40
67 68 6.130569 ACCCCGCCAATGAATTACTATAAAA 58.869 36.000 0.00 0.00 0.00 1.52
68 69 6.608002 ACCCCGCCAATGAATTACTATAAAAA 59.392 34.615 0.00 0.00 0.00 1.94
184 185 8.422973 CTCATGAGCCATTATATTAGCTTCTC 57.577 38.462 10.38 0.00 35.23 2.87
185 186 8.143673 TCATGAGCCATTATATTAGCTTCTCT 57.856 34.615 0.00 0.00 35.23 3.10
186 187 9.259832 TCATGAGCCATTATATTAGCTTCTCTA 57.740 33.333 0.00 0.00 35.23 2.43
202 203 8.541133 AGCTTCTCTATTAGAGTGTTCAAAAC 57.459 34.615 18.06 2.80 42.83 2.43
203 204 8.371699 AGCTTCTCTATTAGAGTGTTCAAAACT 58.628 33.333 18.06 4.70 42.83 2.66
204 205 9.640963 GCTTCTCTATTAGAGTGTTCAAAACTA 57.359 33.333 18.06 0.00 42.83 2.24
215 216 9.444600 AGAGTGTTCAAAACTAGTAACAGAAAA 57.555 29.630 8.81 0.00 32.83 2.29
218 219 9.836076 GTGTTCAAAACTAGTAACAGAAAAAGT 57.164 29.630 8.81 0.00 32.83 2.66
222 223 9.221933 TCAAAACTAGTAACAGAAAAAGTCACA 57.778 29.630 0.00 0.00 0.00 3.58
223 224 9.834628 CAAAACTAGTAACAGAAAAAGTCACAA 57.165 29.630 0.00 0.00 0.00 3.33
225 226 7.247929 ACTAGTAACAGAAAAAGTCACAAGC 57.752 36.000 0.00 0.00 0.00 4.01
226 227 6.821665 ACTAGTAACAGAAAAAGTCACAAGCA 59.178 34.615 0.00 0.00 0.00 3.91
227 228 6.509418 AGTAACAGAAAAAGTCACAAGCAA 57.491 33.333 0.00 0.00 0.00 3.91
228 229 7.100458 AGTAACAGAAAAAGTCACAAGCAAT 57.900 32.000 0.00 0.00 0.00 3.56
229 230 8.220755 AGTAACAGAAAAAGTCACAAGCAATA 57.779 30.769 0.00 0.00 0.00 1.90
230 231 8.850156 AGTAACAGAAAAAGTCACAAGCAATAT 58.150 29.630 0.00 0.00 0.00 1.28
256 257 7.686438 ATAACAATCATCAAACACAGTAGCA 57.314 32.000 0.00 0.00 0.00 3.49
257 258 5.618056 ACAATCATCAAACACAGTAGCAG 57.382 39.130 0.00 0.00 0.00 4.24
258 259 4.083110 ACAATCATCAAACACAGTAGCAGC 60.083 41.667 0.00 0.00 0.00 5.25
259 260 3.407424 TCATCAAACACAGTAGCAGCT 57.593 42.857 0.00 0.00 0.00 4.24
260 261 3.069289 TCATCAAACACAGTAGCAGCTG 58.931 45.455 10.11 10.11 41.92 4.24
261 262 1.229428 TCAAACACAGTAGCAGCTGC 58.771 50.000 31.53 31.53 39.96 5.25
271 272 3.819188 GCAGCTGCTTCGGCTTAT 58.181 55.556 31.33 0.00 44.48 1.73
272 273 1.645997 GCAGCTGCTTCGGCTTATC 59.354 57.895 31.33 0.00 44.48 1.75
273 274 1.091771 GCAGCTGCTTCGGCTTATCA 61.092 55.000 31.33 0.00 44.48 2.15
274 275 1.590932 CAGCTGCTTCGGCTTATCAT 58.409 50.000 0.00 0.00 44.48 2.45
275 276 1.530293 CAGCTGCTTCGGCTTATCATC 59.470 52.381 0.00 0.00 44.48 2.92
276 277 0.871057 GCTGCTTCGGCTTATCATCC 59.129 55.000 0.00 0.00 42.37 3.51
277 278 1.517242 CTGCTTCGGCTTATCATCCC 58.483 55.000 0.00 0.00 42.37 3.85
278 279 0.108585 TGCTTCGGCTTATCATCCCC 59.891 55.000 0.00 0.00 42.37 4.81
279 280 0.951040 GCTTCGGCTTATCATCCCCG 60.951 60.000 0.00 0.00 41.97 5.73
280 281 0.679505 CTTCGGCTTATCATCCCCGA 59.320 55.000 0.00 0.00 46.94 5.14
281 282 3.067011 TCGGCTTATCATCCCCGAT 57.933 52.632 0.00 0.00 44.13 4.18
282 283 1.348064 TCGGCTTATCATCCCCGATT 58.652 50.000 0.00 0.00 44.13 3.34
283 284 1.275291 TCGGCTTATCATCCCCGATTC 59.725 52.381 0.00 0.00 44.13 2.52
322 330 2.895404 ACTACCACTTTTCGTGCTAGGA 59.105 45.455 0.00 0.00 42.42 2.94
326 334 3.008049 ACCACTTTTCGTGCTAGGATTCT 59.992 43.478 0.00 0.00 42.42 2.40
380 391 1.271656 CCTACCACTTTTCTCGTCGGT 59.728 52.381 0.00 0.00 0.00 4.69
820 856 9.973450 GCTAGATTAGATTAGTGTTCATCTTGA 57.027 33.333 0.00 0.00 31.89 3.02
963 1000 9.342308 GGGAATTAATTTGTGATCTATGTCTGA 57.658 33.333 1.43 0.00 0.00 3.27
965 1002 9.875675 GAATTAATTTGTGATCTATGTCTGAGC 57.124 33.333 1.43 0.00 0.00 4.26
966 1003 9.624373 AATTAATTTGTGATCTATGTCTGAGCT 57.376 29.630 0.00 0.00 0.00 4.09
969 1006 8.659925 AATTTGTGATCTATGTCTGAGCTAAG 57.340 34.615 0.00 0.00 0.00 2.18
988 1025 6.113411 GCTAAGGTGAGCTAAGGTGATTTTA 58.887 40.000 0.00 0.00 39.50 1.52
1240 1277 1.972872 AGTTGCTGTTCTGAACCCAG 58.027 50.000 17.26 10.30 41.74 4.45
1910 1955 1.518903 GCCAAGGAACAGAGGTGCAC 61.519 60.000 8.80 8.80 0.00 4.57
1915 1960 4.074970 CAAGGAACAGAGGTGCACTTTAT 58.925 43.478 17.98 0.00 0.00 1.40
2112 2169 2.104622 TGTGTTCTGCAGATGGTGAAGA 59.895 45.455 19.04 0.00 39.36 2.87
2178 2236 5.680619 TGTGAAGATATGGGGTGTACATTC 58.319 41.667 0.00 0.00 0.00 2.67
2351 2413 3.452264 TGATAAGCACTGCTGGACTATGT 59.548 43.478 3.73 0.00 39.62 2.29
2444 2516 8.995577 AGTTATATTTACAAACCTAGGCCTACA 58.004 33.333 8.91 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.116126 CCCAGTAAAGAAATACCTCCTCTTG 58.884 44.000 0.00 0.00 29.93 3.02
2 3 5.791141 ACCCAGTAAAGAAATACCTCCTCTT 59.209 40.000 0.00 0.00 0.00 2.85
3 4 5.351405 ACCCAGTAAAGAAATACCTCCTCT 58.649 41.667 0.00 0.00 0.00 3.69
5 6 5.281037 CCAACCCAGTAAAGAAATACCTCCT 60.281 44.000 0.00 0.00 0.00 3.69
6 7 4.948004 CCAACCCAGTAAAGAAATACCTCC 59.052 45.833 0.00 0.00 0.00 4.30
7 8 4.398358 GCCAACCCAGTAAAGAAATACCTC 59.602 45.833 0.00 0.00 0.00 3.85
8 9 4.341487 GCCAACCCAGTAAAGAAATACCT 58.659 43.478 0.00 0.00 0.00 3.08
9 10 3.446161 GGCCAACCCAGTAAAGAAATACC 59.554 47.826 0.00 0.00 0.00 2.73
10 11 4.082408 GTGGCCAACCCAGTAAAGAAATAC 60.082 45.833 7.24 0.00 46.54 1.89
11 12 4.083565 GTGGCCAACCCAGTAAAGAAATA 58.916 43.478 7.24 0.00 46.54 1.40
12 13 2.897326 GTGGCCAACCCAGTAAAGAAAT 59.103 45.455 7.24 0.00 46.54 2.17
13 14 2.312390 GTGGCCAACCCAGTAAAGAAA 58.688 47.619 7.24 0.00 46.54 2.52
14 15 1.816183 CGTGGCCAACCCAGTAAAGAA 60.816 52.381 7.24 0.00 46.54 2.52
15 16 0.250553 CGTGGCCAACCCAGTAAAGA 60.251 55.000 7.24 0.00 46.54 2.52
16 17 0.250553 TCGTGGCCAACCCAGTAAAG 60.251 55.000 7.24 0.00 46.54 1.85
17 18 0.183014 TTCGTGGCCAACCCAGTAAA 59.817 50.000 7.24 0.00 46.54 2.01
18 19 0.183014 TTTCGTGGCCAACCCAGTAA 59.817 50.000 7.24 0.00 46.54 2.24
19 20 0.250553 CTTTCGTGGCCAACCCAGTA 60.251 55.000 7.24 0.00 46.54 2.74
20 21 1.528309 CTTTCGTGGCCAACCCAGT 60.528 57.895 7.24 0.00 46.54 4.00
21 22 0.821711 TTCTTTCGTGGCCAACCCAG 60.822 55.000 7.24 1.30 46.54 4.45
22 23 0.821711 CTTCTTTCGTGGCCAACCCA 60.822 55.000 7.24 0.00 42.79 4.51
23 24 0.822121 ACTTCTTTCGTGGCCAACCC 60.822 55.000 7.24 0.00 33.59 4.11
24 25 1.534163 GTACTTCTTTCGTGGCCAACC 59.466 52.381 7.24 0.00 0.00 3.77
25 26 1.534163 GGTACTTCTTTCGTGGCCAAC 59.466 52.381 7.24 0.15 0.00 3.77
26 27 1.543871 GGGTACTTCTTTCGTGGCCAA 60.544 52.381 7.24 0.00 0.00 4.52
27 28 0.035739 GGGTACTTCTTTCGTGGCCA 59.964 55.000 0.00 0.00 0.00 5.36
28 29 0.675837 GGGGTACTTCTTTCGTGGCC 60.676 60.000 0.00 0.00 0.00 5.36
29 30 1.017701 CGGGGTACTTCTTTCGTGGC 61.018 60.000 0.00 0.00 0.00 5.01
30 31 1.017701 GCGGGGTACTTCTTTCGTGG 61.018 60.000 0.00 0.00 0.00 4.94
31 32 1.017701 GGCGGGGTACTTCTTTCGTG 61.018 60.000 0.00 0.00 0.00 4.35
32 33 1.294459 GGCGGGGTACTTCTTTCGT 59.706 57.895 0.00 0.00 0.00 3.85
33 34 0.320946 TTGGCGGGGTACTTCTTTCG 60.321 55.000 0.00 0.00 0.00 3.46
34 35 1.743394 CATTGGCGGGGTACTTCTTTC 59.257 52.381 0.00 0.00 0.00 2.62
35 36 1.353022 TCATTGGCGGGGTACTTCTTT 59.647 47.619 0.00 0.00 0.00 2.52
36 37 0.988832 TCATTGGCGGGGTACTTCTT 59.011 50.000 0.00 0.00 0.00 2.52
37 38 0.988832 TTCATTGGCGGGGTACTTCT 59.011 50.000 0.00 0.00 0.00 2.85
38 39 2.052782 ATTCATTGGCGGGGTACTTC 57.947 50.000 0.00 0.00 0.00 3.01
39 40 2.525105 AATTCATTGGCGGGGTACTT 57.475 45.000 0.00 0.00 0.00 2.24
40 41 2.508300 AGTAATTCATTGGCGGGGTACT 59.492 45.455 0.00 0.00 0.00 2.73
41 42 2.927028 AGTAATTCATTGGCGGGGTAC 58.073 47.619 0.00 0.00 0.00 3.34
42 43 4.986054 ATAGTAATTCATTGGCGGGGTA 57.014 40.909 0.00 0.00 0.00 3.69
43 44 3.876309 ATAGTAATTCATTGGCGGGGT 57.124 42.857 0.00 0.00 0.00 4.95
44 45 6.642707 TTTTATAGTAATTCATTGGCGGGG 57.357 37.500 0.00 0.00 0.00 5.73
159 160 8.259411 AGAGAAGCTAATATAATGGCTCATGAG 58.741 37.037 18.84 18.84 33.63 2.90
160 161 8.143673 AGAGAAGCTAATATAATGGCTCATGA 57.856 34.615 0.00 0.00 33.63 3.07
176 177 9.640963 GTTTTGAACACTCTAATAGAGAAGCTA 57.359 33.333 22.83 4.62 45.07 3.32
177 178 8.371699 AGTTTTGAACACTCTAATAGAGAAGCT 58.628 33.333 22.83 10.16 45.07 3.74
178 179 8.541133 AGTTTTGAACACTCTAATAGAGAAGC 57.459 34.615 22.83 8.25 45.07 3.86
189 190 9.444600 TTTTCTGTTACTAGTTTTGAACACTCT 57.555 29.630 0.00 0.00 0.00 3.24
192 193 9.836076 ACTTTTTCTGTTACTAGTTTTGAACAC 57.164 29.630 0.00 0.00 0.00 3.32
196 197 9.221933 TGTGACTTTTTCTGTTACTAGTTTTGA 57.778 29.630 0.00 0.00 0.00 2.69
197 198 9.834628 TTGTGACTTTTTCTGTTACTAGTTTTG 57.165 29.630 0.00 0.00 0.00 2.44
199 200 8.182227 GCTTGTGACTTTTTCTGTTACTAGTTT 58.818 33.333 0.00 0.00 32.63 2.66
200 201 7.335924 TGCTTGTGACTTTTTCTGTTACTAGTT 59.664 33.333 0.00 0.00 32.63 2.24
201 202 6.821665 TGCTTGTGACTTTTTCTGTTACTAGT 59.178 34.615 0.00 0.00 32.63 2.57
202 203 7.246674 TGCTTGTGACTTTTTCTGTTACTAG 57.753 36.000 0.00 0.00 32.97 2.57
203 204 7.618502 TTGCTTGTGACTTTTTCTGTTACTA 57.381 32.000 0.00 0.00 0.00 1.82
204 205 6.509418 TTGCTTGTGACTTTTTCTGTTACT 57.491 33.333 0.00 0.00 0.00 2.24
230 231 9.225436 TGCTACTGTGTTTGATGATTGTTATTA 57.775 29.630 0.00 0.00 0.00 0.98
231 232 8.109705 TGCTACTGTGTTTGATGATTGTTATT 57.890 30.769 0.00 0.00 0.00 1.40
232 233 7.627088 GCTGCTACTGTGTTTGATGATTGTTAT 60.627 37.037 0.00 0.00 0.00 1.89
233 234 6.348458 GCTGCTACTGTGTTTGATGATTGTTA 60.348 38.462 0.00 0.00 0.00 2.41
234 235 5.563475 GCTGCTACTGTGTTTGATGATTGTT 60.563 40.000 0.00 0.00 0.00 2.83
235 236 4.083110 GCTGCTACTGTGTTTGATGATTGT 60.083 41.667 0.00 0.00 0.00 2.71
236 237 4.155462 AGCTGCTACTGTGTTTGATGATTG 59.845 41.667 0.00 0.00 0.00 2.67
237 238 4.155462 CAGCTGCTACTGTGTTTGATGATT 59.845 41.667 0.00 0.00 32.78 2.57
238 239 3.688185 CAGCTGCTACTGTGTTTGATGAT 59.312 43.478 0.00 0.00 32.78 2.45
239 240 3.069289 CAGCTGCTACTGTGTTTGATGA 58.931 45.455 0.00 0.00 32.78 2.92
240 241 2.413765 GCAGCTGCTACTGTGTTTGATG 60.414 50.000 31.33 0.00 39.96 3.07
241 242 1.808945 GCAGCTGCTACTGTGTTTGAT 59.191 47.619 31.33 0.00 39.96 2.57
242 243 1.229428 GCAGCTGCTACTGTGTTTGA 58.771 50.000 31.33 0.00 39.96 2.69
243 244 3.761481 GCAGCTGCTACTGTGTTTG 57.239 52.632 31.33 0.00 39.96 2.93
254 255 1.091771 TGATAAGCCGAAGCAGCTGC 61.092 55.000 31.53 31.53 40.49 5.25
255 256 1.530293 GATGATAAGCCGAAGCAGCTG 59.470 52.381 10.11 10.11 40.49 4.24
256 257 1.542108 GGATGATAAGCCGAAGCAGCT 60.542 52.381 0.00 0.00 44.19 4.24
257 258 0.871057 GGATGATAAGCCGAAGCAGC 59.129 55.000 0.00 0.00 43.56 5.25
258 259 1.517242 GGGATGATAAGCCGAAGCAG 58.483 55.000 0.00 0.00 43.56 4.24
259 260 0.108585 GGGGATGATAAGCCGAAGCA 59.891 55.000 0.00 0.00 43.56 3.91
260 261 0.951040 CGGGGATGATAAGCCGAAGC 60.951 60.000 0.00 0.00 40.32 3.86
261 262 0.679505 TCGGGGATGATAAGCCGAAG 59.320 55.000 0.00 0.00 0.00 3.79
262 263 1.348064 ATCGGGGATGATAAGCCGAA 58.652 50.000 0.00 0.00 33.57 4.30
263 264 1.275291 GAATCGGGGATGATAAGCCGA 59.725 52.381 0.00 0.00 0.00 5.54
264 265 1.276421 AGAATCGGGGATGATAAGCCG 59.724 52.381 0.00 0.00 0.00 5.52
265 266 2.303022 TCAGAATCGGGGATGATAAGCC 59.697 50.000 0.00 0.00 0.00 4.35
266 267 3.007398 ACTCAGAATCGGGGATGATAAGC 59.993 47.826 0.00 0.00 0.00 3.09
267 268 4.881019 ACTCAGAATCGGGGATGATAAG 57.119 45.455 0.00 0.00 0.00 1.73
268 269 6.740944 TTTACTCAGAATCGGGGATGATAA 57.259 37.500 0.00 0.00 0.00 1.75
269 270 6.935240 ATTTACTCAGAATCGGGGATGATA 57.065 37.500 0.00 0.00 0.00 2.15
270 271 5.832539 ATTTACTCAGAATCGGGGATGAT 57.167 39.130 0.00 0.00 0.00 2.45
271 272 5.279506 GCTATTTACTCAGAATCGGGGATGA 60.280 44.000 0.00 0.00 0.00 2.92
272 273 4.932200 GCTATTTACTCAGAATCGGGGATG 59.068 45.833 0.00 0.00 0.00 3.51
273 274 4.593206 TGCTATTTACTCAGAATCGGGGAT 59.407 41.667 0.00 0.00 0.00 3.85
274 275 3.964688 TGCTATTTACTCAGAATCGGGGA 59.035 43.478 0.00 0.00 0.00 4.81
275 276 4.336889 TGCTATTTACTCAGAATCGGGG 57.663 45.455 0.00 0.00 0.00 5.73
276 277 7.962964 TTTATGCTATTTACTCAGAATCGGG 57.037 36.000 0.00 0.00 0.00 5.14
277 278 9.046296 AGTTTTATGCTATTTACTCAGAATCGG 57.954 33.333 0.00 0.00 0.00 4.18
282 283 9.595823 GTGGTAGTTTTATGCTATTTACTCAGA 57.404 33.333 0.00 0.00 0.00 3.27
283 284 9.601217 AGTGGTAGTTTTATGCTATTTACTCAG 57.399 33.333 0.00 0.00 0.00 3.35
677 713 0.252513 TCCCCGTCATTCCAGGAAGA 60.253 55.000 8.20 2.83 0.00 2.87
718 754 2.565046 TGTCCATGCTTGTGATGTCA 57.435 45.000 0.00 0.00 0.00 3.58
804 840 7.215789 CCTAGCTCATCAAGATGAACACTAAT 58.784 38.462 13.25 0.00 46.10 1.73
964 1001 3.828875 ATCACCTTAGCTCACCTTAGC 57.171 47.619 0.00 0.00 43.11 3.09
965 1002 8.616076 CAATAAAATCACCTTAGCTCACCTTAG 58.384 37.037 0.00 0.00 0.00 2.18
966 1003 8.325787 TCAATAAAATCACCTTAGCTCACCTTA 58.674 33.333 0.00 0.00 0.00 2.69
967 1004 7.175104 TCAATAAAATCACCTTAGCTCACCTT 58.825 34.615 0.00 0.00 0.00 3.50
968 1005 6.721318 TCAATAAAATCACCTTAGCTCACCT 58.279 36.000 0.00 0.00 0.00 4.00
969 1006 7.067494 ACATCAATAAAATCACCTTAGCTCACC 59.933 37.037 0.00 0.00 0.00 4.02
988 1025 3.693085 GTCTCCTGCATGAACACATCAAT 59.307 43.478 0.00 0.00 42.54 2.57
1240 1277 7.118390 AGAGCAACTTGTCAACATAATACTGTC 59.882 37.037 0.00 0.00 0.00 3.51
2112 2169 6.576778 ACTATAAAGGCCTTGGATGTACTT 57.423 37.500 21.33 1.71 0.00 2.24
2113 2170 7.292591 ACATACTATAAAGGCCTTGGATGTACT 59.707 37.037 23.49 8.21 0.00 2.73
2114 2171 7.387948 CACATACTATAAAGGCCTTGGATGTAC 59.612 40.741 24.02 0.00 0.00 2.90
2178 2236 4.162040 AGATTAGCTTCACATTCCCCAG 57.838 45.455 0.00 0.00 0.00 4.45
2444 2516 3.450457 CAGTGGAGAGGCATCTAGAGTTT 59.550 47.826 0.00 0.00 35.30 2.66
2892 2972 6.179906 AGTGGAAGGGATACATAGTTCATG 57.820 41.667 0.00 0.00 40.78 3.07


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.