Multiple sequence alignment - TraesCS3D01G012200

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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 TraesCS3D01G012200 chr3D 100.000 1484 0 0 1 1484 4289648 4291131 0.000000e+00 2741.0
1 TraesCS3D01G012200 chr3D 100.000 1483 0 0 1796 3278 4291443 4292925 0.000000e+00 2739.0
2 TraesCS3D01G012200 chr3D 78.175 559 88 20 2672 3218 4195045 4195581 3.150000e-85 326.0
3 TraesCS3D01G012200 chr3D 79.418 447 79 13 2149 2591 4194526 4194963 1.480000e-78 303.0
4 TraesCS3D01G012200 chr3D 93.151 73 5 0 186 258 371366964 371367036 1.240000e-19 108.0
5 TraesCS3D01G012200 chr3D 96.825 63 0 2 186 247 280387049 280387110 1.610000e-18 104.0
6 TraesCS3D01G012200 chr3D 96.825 63 0 2 186 247 365000882 365000821 1.610000e-18 104.0
7 TraesCS3D01G012200 chr3A 95.581 1471 46 4 1810 3278 9881884 9883337 0.000000e+00 2338.0
8 TraesCS3D01G012200 chr3A 96.528 1152 34 2 336 1481 9880471 9881622 0.000000e+00 1901.0
9 TraesCS3D01G012200 chr3A 79.281 1419 233 33 1871 3275 10166832 10168203 0.000000e+00 935.0
10 TraesCS3D01G012200 chr3A 76.497 1119 188 48 2149 3236 9853995 9855069 1.030000e-149 540.0
11 TraesCS3D01G012200 chr3A 88.710 186 21 0 2672 2857 9933128 9933313 9.150000e-56 228.0
12 TraesCS3D01G012200 chr3A 78.717 343 52 16 973 1300 9931668 9932004 3.310000e-50 209.0
13 TraesCS3D01G012200 chr3A 86.702 188 23 2 1 186 9879525 9879712 1.190000e-49 207.0
14 TraesCS3D01G012200 chr3A 96.774 93 3 0 236 328 9879716 9879808 4.380000e-34 156.0
15 TraesCS3D01G012200 chrUn 96.080 1148 30 8 336 1481 288187696 288188830 0.000000e+00 1857.0
16 TraesCS3D01G012200 chrUn 96.370 909 33 0 2370 3278 35856079 35855171 0.000000e+00 1496.0
17 TraesCS3D01G012200 chrUn 96.370 909 33 0 2370 3278 299959362 299960270 0.000000e+00 1496.0
18 TraesCS3D01G012200 chrUn 82.773 1428 207 28 1865 3278 35374341 35372939 0.000000e+00 1238.0
19 TraesCS3D01G012200 chrUn 77.578 669 99 34 839 1470 35376407 35375753 1.120000e-94 357.0
20 TraesCS3D01G012200 chr3B 82.773 1428 207 28 1865 3278 6556715 6558117 0.000000e+00 1238.0
21 TraesCS3D01G012200 chr3B 77.578 669 99 34 839 1470 6554649 6555303 1.120000e-94 357.0
22 TraesCS3D01G012200 chr3B 77.878 556 92 20 2672 3218 6679658 6680191 1.900000e-82 316.0
23 TraesCS3D01G012200 chr3B 79.821 446 76 13 2149 2589 6679138 6679574 2.460000e-81 313.0
24 TraesCS3D01G012200 chr3B 92.000 50 4 0 134 183 822114141 822114092 1.630000e-08 71.3
25 TraesCS3D01G012200 chr7D 79.178 730 103 35 2149 2857 499886355 499887056 8.290000e-126 460.0
26 TraesCS3D01G012200 chr7D 91.781 73 5 1 186 257 234351299 234351371 2.080000e-17 100.0
27 TraesCS3D01G012200 chr7D 87.500 88 9 2 186 272 436663685 436663599 2.080000e-17 100.0
28 TraesCS3D01G012200 chr7D 92.308 39 3 0 1811 1849 39131736 39131774 4.570000e-04 56.5
29 TraesCS3D01G012200 chr7B 86.992 123 16 0 1167 1289 527856250 527856372 4.410000e-29 139.0
30 TraesCS3D01G012200 chr7B 100.000 30 0 0 1801 1830 2907482 2907453 4.570000e-04 56.5
31 TraesCS3D01G012200 chr7A 86.087 115 16 0 1175 1289 565797594 565797708 1.230000e-24 124.0
32 TraesCS3D01G012200 chr7A 80.342 117 20 1 3114 3230 54722999 54723112 5.830000e-13 86.1
33 TraesCS3D01G012200 chr5B 100.000 59 0 0 186 244 472118222 472118280 3.460000e-20 110.0
34 TraesCS3D01G012200 chr6A 92.754 69 5 0 186 254 602454172 602454240 2.080000e-17 100.0
35 TraesCS3D01G012200 chr6A 89.333 75 8 0 186 260 87299430 87299504 9.680000e-16 95.3
36 TraesCS3D01G012200 chr6A 98.039 51 1 0 1798 1848 2218197 2218247 4.510000e-14 89.8
37 TraesCS3D01G012200 chr2D 90.541 74 5 2 186 258 62293348 62293276 2.690000e-16 97.1
38 TraesCS3D01G012200 chr2D 95.000 40 2 0 1807 1846 245521913 245521874 2.730000e-06 63.9
39 TraesCS3D01G012200 chr2D 94.444 36 0 2 1814 1848 636789319 636789353 2.000000e-03 54.7
40 TraesCS3D01G012200 chr1D 97.674 43 1 0 144 186 29724148 29724106 1.260000e-09 75.0
41 TraesCS3D01G012200 chr1D 97.674 43 1 0 144 186 29891817 29891859 1.260000e-09 75.0
42 TraesCS3D01G012200 chr1D 94.872 39 2 0 1813 1851 80277876 80277914 9.820000e-06 62.1
43 TraesCS3D01G012200 chr1A 97.674 43 1 0 144 186 589498552 589498594 1.260000e-09 75.0
44 TraesCS3D01G012200 chr1A 90.385 52 5 0 132 183 351605441 351605492 5.870000e-08 69.4
45 TraesCS3D01G012200 chr4D 92.157 51 4 0 1798 1848 451167899 451167849 4.540000e-09 73.1
46 TraesCS3D01G012200 chr4D 92.000 50 4 0 137 186 3470396 3470347 1.630000e-08 71.3
47 TraesCS3D01G012200 chr5A 95.349 43 2 0 144 186 429750519 429750477 5.870000e-08 69.4
48 TraesCS3D01G012200 chr6B 89.091 55 5 1 133 186 400075933 400075879 2.110000e-07 67.6
49 TraesCS3D01G012200 chr4B 100.000 30 0 0 1817 1846 187434268 187434297 4.570000e-04 56.5


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 TraesCS3D01G012200 chr3D 4289648 4292925 3277 False 2740.0 2741 100.00000 1 3278 2 chr3D.!!$F4 3277
1 TraesCS3D01G012200 chr3D 4194526 4195581 1055 False 314.5 326 78.79650 2149 3218 2 chr3D.!!$F3 1069
2 TraesCS3D01G012200 chr3A 9879525 9883337 3812 False 1150.5 2338 93.89625 1 3278 4 chr3A.!!$F3 3277
3 TraesCS3D01G012200 chr3A 10166832 10168203 1371 False 935.0 935 79.28100 1871 3275 1 chr3A.!!$F2 1404
4 TraesCS3D01G012200 chr3A 9853995 9855069 1074 False 540.0 540 76.49700 2149 3236 1 chr3A.!!$F1 1087
5 TraesCS3D01G012200 chr3A 9931668 9933313 1645 False 218.5 228 83.71350 973 2857 2 chr3A.!!$F4 1884
6 TraesCS3D01G012200 chrUn 288187696 288188830 1134 False 1857.0 1857 96.08000 336 1481 1 chrUn.!!$F1 1145
7 TraesCS3D01G012200 chrUn 35855171 35856079 908 True 1496.0 1496 96.37000 2370 3278 1 chrUn.!!$R1 908
8 TraesCS3D01G012200 chrUn 299959362 299960270 908 False 1496.0 1496 96.37000 2370 3278 1 chrUn.!!$F2 908
9 TraesCS3D01G012200 chrUn 35372939 35376407 3468 True 797.5 1238 80.17550 839 3278 2 chrUn.!!$R2 2439
10 TraesCS3D01G012200 chr3B 6554649 6558117 3468 False 797.5 1238 80.17550 839 3278 2 chr3B.!!$F1 2439
11 TraesCS3D01G012200 chr3B 6679138 6680191 1053 False 314.5 316 78.84950 2149 3218 2 chr3B.!!$F2 1069
12 TraesCS3D01G012200 chr7D 499886355 499887056 701 False 460.0 460 79.17800 2149 2857 1 chr7D.!!$F3 708

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
57 58 0.749649 AAAAGGCGAACACCATTGCA 59.250 45.000 0.00 0.00 0.00 4.08 F
75 77 1.000506 GCAAGTCTAGGACGTGGACAA 59.999 52.381 13.23 0.00 41.09 3.18 F
1076 1755 0.179100 CTCATCGCTGGATCAACGGT 60.179 55.000 0.00 0.00 0.00 4.83 F
1085 1764 1.066430 TGGATCAACGGTGTTCCTAGC 60.066 52.381 26.67 5.52 42.17 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1063 1742 0.321653 AGGAACACCGTTGATCCAGC 60.322 55.000 11.78 0.0 45.26 4.85 R
1985 3871 2.166459 TCTAGTCCAAAGTCCTCATGCG 59.834 50.000 0.00 0.0 0.00 4.73 R
2276 4174 2.761208 TGGTTTTGATTCACACCCGTTT 59.239 40.909 10.45 0.0 0.00 3.60 R
2782 4747 3.133014 CTCGGGCGGATGATGACT 58.867 61.111 0.00 0.0 0.00 3.41 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
51 52 1.194772 CGAGAGAAAAAGGCGAACACC 59.805 52.381 0.00 0.00 0.00 4.16
52 53 2.218603 GAGAGAAAAAGGCGAACACCA 58.781 47.619 0.00 0.00 0.00 4.17
53 54 2.814336 GAGAGAAAAAGGCGAACACCAT 59.186 45.455 0.00 0.00 0.00 3.55
57 58 0.749649 AAAAGGCGAACACCATTGCA 59.250 45.000 0.00 0.00 0.00 4.08
68 70 2.002586 CACCATTGCAAGTCTAGGACG 58.997 52.381 4.94 0.00 37.67 4.79
75 77 1.000506 GCAAGTCTAGGACGTGGACAA 59.999 52.381 13.23 0.00 41.09 3.18
80 82 2.496470 GTCTAGGACGTGGACAAGGAAT 59.504 50.000 6.76 0.00 36.66 3.01
95 97 9.607333 TGGACAAGGAATCTAACTATATGAGAT 57.393 33.333 0.00 0.00 0.00 2.75
141 144 7.226441 TGTAGGGATTTGACATGATTAGATGG 58.774 38.462 0.00 0.00 0.00 3.51
142 145 5.075493 AGGGATTTGACATGATTAGATGGC 58.925 41.667 0.00 0.00 0.00 4.40
147 150 6.441093 TTTGACATGATTAGATGGCACTTC 57.559 37.500 0.00 0.00 41.26 3.01
152 155 4.679373 TGATTAGATGGCACTTCCTCTC 57.321 45.455 0.00 0.00 35.26 3.20
157 160 4.751767 AGATGGCACTTCCTCTCTAAAG 57.248 45.455 0.00 0.00 35.26 1.85
191 194 8.688151 AGAGTGTTTAGATCACTACTTACATCC 58.312 37.037 0.00 0.00 44.68 3.51
192 195 8.362464 AGTGTTTAGATCACTACTTACATCCA 57.638 34.615 0.00 0.00 43.17 3.41
203 206 9.862149 TCACTACTTACATCCATATCTAGACAA 57.138 33.333 0.00 0.00 0.00 3.18
224 227 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
225 228 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
226 229 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
227 230 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
228 231 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
229 232 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
230 233 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
231 234 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
232 235 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
233 236 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
234 237 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
235 238 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
236 239 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
237 240 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
238 241 1.961133 TTTGGGACGGAGGGAGTATT 58.039 50.000 0.00 0.00 0.00 1.89
239 242 1.961133 TTGGGACGGAGGGAGTATTT 58.039 50.000 0.00 0.00 0.00 1.40
240 243 1.200519 TGGGACGGAGGGAGTATTTG 58.799 55.000 0.00 0.00 0.00 2.32
241 244 1.201424 GGGACGGAGGGAGTATTTGT 58.799 55.000 0.00 0.00 0.00 2.83
254 257 5.132144 GGGAGTATTTGTTTATGGAGGGAGA 59.868 44.000 0.00 0.00 0.00 3.71
328 331 7.041916 TCCAACTATTTTACGTGACGTTCATTT 60.042 33.333 18.28 0.62 41.54 2.32
331 334 9.584839 AACTATTTTACGTGACGTTCATTTTAC 57.415 29.630 18.28 0.00 41.54 2.01
332 335 7.946237 ACTATTTTACGTGACGTTCATTTTACG 59.054 33.333 18.28 0.00 41.54 3.18
349 1007 1.722011 ACGTGAAGGTAGAAATGGCG 58.278 50.000 0.00 0.00 0.00 5.69
389 1047 4.682589 GCATACCACCAAGTCCTTACTACC 60.683 50.000 0.00 0.00 33.75 3.18
398 1056 3.633418 AGTCCTTACTACCAGGCTACAG 58.367 50.000 0.00 0.00 32.84 2.74
669 1327 3.060473 GTGCGAACTGTTCAGTAACACTC 60.060 47.826 19.56 7.93 40.69 3.51
686 1344 9.141400 AGTAACACTCGAGATATGAAAAAGTTC 57.859 33.333 21.68 3.26 0.00 3.01
1063 1742 0.883814 GGGCAAGAGCATCCTCATCG 60.884 60.000 0.00 0.00 44.61 3.84
1076 1755 0.179100 CTCATCGCTGGATCAACGGT 60.179 55.000 0.00 0.00 0.00 4.83
1085 1764 1.066430 TGGATCAACGGTGTTCCTAGC 60.066 52.381 26.67 5.52 42.17 3.42
1177 1916 5.125100 TCTTTCTTGCATGATTTGTGGAC 57.875 39.130 2.75 0.00 0.00 4.02
1985 3871 1.826385 CCTTTGGTGGGAGACATCAC 58.174 55.000 0.00 0.00 40.67 3.06
2178 4076 9.932699 TTGCTCAAAATGTGATGTTAATTTTTG 57.067 25.926 0.00 0.00 35.07 2.44
2276 4174 5.474532 AGCTCAAGATGTTGCTTCATGTTTA 59.525 36.000 0.00 0.00 30.68 2.01
2605 4544 7.016268 AGAGGTCAGACATAGGAAACTTTACAA 59.984 37.037 2.17 0.00 43.67 2.41
2607 4546 7.661847 AGGTCAGACATAGGAAACTTTACAAAG 59.338 37.037 2.17 0.13 43.67 2.77
2626 4567 6.569780 ACAAAGAGGAAAACAACAACATACC 58.430 36.000 0.00 0.00 0.00 2.73
2782 4747 2.353610 GCGAGGGGACTTTCCGGTA 61.354 63.158 0.00 0.00 44.43 4.02
2836 4801 2.056223 CAAGGAGCCATTGCCTGGG 61.056 63.158 4.72 0.00 46.06 4.45
2878 4847 7.495606 AGGTGTTGAAACTCAAAATTGAATTCC 59.504 33.333 2.27 2.45 38.22 3.01
2892 4861 7.729124 AATTGAATTCCTGATCCTTCACAAT 57.271 32.000 2.27 0.00 0.00 2.71
2897 4876 4.849813 TCCTGATCCTTCACAATGACAT 57.150 40.909 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.542595 GTGTTCGCCTTTTTCTCTCGAA 59.457 45.455 0.00 0.0 36.91 3.71
30 31 2.132762 GTGTTCGCCTTTTTCTCTCGA 58.867 47.619 0.00 0.0 0.00 4.04
51 52 2.002586 CCACGTCCTAGACTTGCAATG 58.997 52.381 0.00 0.0 31.73 2.82
52 53 1.899814 TCCACGTCCTAGACTTGCAAT 59.100 47.619 0.00 0.0 31.73 3.56
53 54 1.000506 GTCCACGTCCTAGACTTGCAA 59.999 52.381 0.00 0.0 31.73 4.08
57 58 1.893801 CCTTGTCCACGTCCTAGACTT 59.106 52.381 0.00 0.0 0.00 3.01
68 70 8.861086 TCTCATATAGTTAGATTCCTTGTCCAC 58.139 37.037 0.00 0.0 0.00 4.02
95 97 2.933495 AGCACGAACTGAGCGTATTA 57.067 45.000 0.00 0.0 40.44 0.98
96 98 2.933495 TAGCACGAACTGAGCGTATT 57.067 45.000 0.00 0.0 40.44 1.89
104 107 3.735237 ATCCCTACATAGCACGAACTG 57.265 47.619 0.00 0.0 0.00 3.16
198 201 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.0 28.79 3.41
199 202 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.0 28.79 3.18
200 203 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.0 28.79 2.83
201 204 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.0 29.84 2.32
202 205 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.0 0.00 2.17
203 206 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.0 0.00 2.40
204 207 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.0 0.00 1.98
205 208 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.0 0.00 2.10
206 209 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.0 0.00 2.18
207 210 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.0 0.00 2.10
208 211 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.0 0.00 3.01
209 212 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.0 0.00 3.41
210 213 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.0 0.00 3.18
211 214 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.0 0.00 3.16
212 215 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.0 0.00 3.02
213 216 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.0 0.00 2.52
214 217 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.0 0.00 2.40
215 218 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.0 0.00 2.17
216 219 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.0 0.00 1.82
217 220 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.0 0.00 1.82
218 221 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.0 0.00 2.44
219 222 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.0 0.00 3.28
220 223 1.557832 CAAATACTCCCTCCGTCCCAA 59.442 52.381 0.00 0.0 0.00 4.12
221 224 1.200519 CAAATACTCCCTCCGTCCCA 58.799 55.000 0.00 0.0 0.00 4.37
222 225 1.201424 ACAAATACTCCCTCCGTCCC 58.799 55.000 0.00 0.0 0.00 4.46
223 226 3.345508 AAACAAATACTCCCTCCGTCC 57.654 47.619 0.00 0.0 0.00 4.79
224 227 4.814771 CCATAAACAAATACTCCCTCCGTC 59.185 45.833 0.00 0.0 0.00 4.79
225 228 4.472108 TCCATAAACAAATACTCCCTCCGT 59.528 41.667 0.00 0.0 0.00 4.69
226 229 5.031066 TCCATAAACAAATACTCCCTCCG 57.969 43.478 0.00 0.0 0.00 4.63
227 230 5.377478 CCTCCATAAACAAATACTCCCTCC 58.623 45.833 0.00 0.0 0.00 4.30
228 231 5.132144 TCCCTCCATAAACAAATACTCCCTC 59.868 44.000 0.00 0.0 0.00 4.30
229 232 5.043762 TCCCTCCATAAACAAATACTCCCT 58.956 41.667 0.00 0.0 0.00 4.20
230 233 5.132144 TCTCCCTCCATAAACAAATACTCCC 59.868 44.000 0.00 0.0 0.00 4.30
231 234 6.248569 TCTCCCTCCATAAACAAATACTCC 57.751 41.667 0.00 0.0 0.00 3.85
232 235 7.339482 AGTTCTCCCTCCATAAACAAATACTC 58.661 38.462 0.00 0.0 0.00 2.59
233 236 7.272144 AGTTCTCCCTCCATAAACAAATACT 57.728 36.000 0.00 0.0 0.00 2.12
234 237 7.555306 GAGTTCTCCCTCCATAAACAAATAC 57.445 40.000 0.00 0.0 0.00 1.89
254 257 2.817844 GCCCGTCTACAAAAATGGAGTT 59.182 45.455 0.00 0.0 0.00 3.01
328 331 3.056678 TCGCCATTTCTACCTTCACGTAA 60.057 43.478 0.00 0.0 0.00 3.18
331 334 2.004583 TCGCCATTTCTACCTTCACG 57.995 50.000 0.00 0.0 0.00 4.35
332 335 3.531538 TCATCGCCATTTCTACCTTCAC 58.468 45.455 0.00 0.0 0.00 3.18
334 337 4.060038 TCTCATCGCCATTTCTACCTTC 57.940 45.455 0.00 0.0 0.00 3.46
349 1007 1.953559 TGCCTTTGCCGTATCTCATC 58.046 50.000 0.00 0.0 36.33 2.92
398 1056 1.224592 CCATCTGGGTGTACTGGGC 59.775 63.158 0.00 0.0 0.00 5.36
622 1280 0.250338 GGGTTGACTGAAACGCCTCT 60.250 55.000 0.00 0.0 37.10 3.69
627 1285 0.817634 TGCCAGGGTTGACTGAAACG 60.818 55.000 0.00 0.0 40.97 3.60
669 1327 7.278211 TGTTCTCGAACTTTTTCATATCTCG 57.722 36.000 10.75 0.0 41.67 4.04
1063 1742 0.321653 AGGAACACCGTTGATCCAGC 60.322 55.000 11.78 0.0 45.26 4.85
1076 1755 6.717289 ACACATATACCTTTTGCTAGGAACA 58.283 36.000 0.00 0.0 38.73 3.18
1177 1916 5.105063 TCAATATCTTCTCGACAAGCACTG 58.895 41.667 0.00 0.0 0.00 3.66
1187 1926 4.054671 GCTGAACCCTCAATATCTTCTCG 58.945 47.826 0.00 0.0 0.00 4.04
1985 3871 2.166459 TCTAGTCCAAAGTCCTCATGCG 59.834 50.000 0.00 0.0 0.00 4.73
2178 4076 4.993584 ACATCGAAAGCCACATCATATCTC 59.006 41.667 0.00 0.0 0.00 2.75
2276 4174 2.761208 TGGTTTTGATTCACACCCGTTT 59.239 40.909 10.45 0.0 0.00 3.60
2326 4235 3.439857 AACTGCATGATACACCAACCT 57.560 42.857 0.00 0.0 0.00 3.50
2387 4304 4.202245 TGTTCACCAACTACATAGGCTC 57.798 45.455 0.00 0.0 33.17 4.70
2478 4397 5.535753 TGATCAGATTTAGCTCGGATTCA 57.464 39.130 0.00 0.0 31.44 2.57
2605 4544 7.255486 GCTTAGGTATGTTGTTGTTTTCCTCTT 60.255 37.037 0.00 0.0 0.00 2.85
2607 4546 6.016610 TGCTTAGGTATGTTGTTGTTTTCCTC 60.017 38.462 0.00 0.0 0.00 3.71
2626 4567 6.510799 CGGCAGAAAAGAGTATGAATGCTTAG 60.511 42.308 0.00 0.0 33.09 2.18
2782 4747 3.133014 CTCGGGCGGATGATGACT 58.867 61.111 0.00 0.0 0.00 3.41
2836 4801 4.236527 ACACCTAATTCCTTCCATCCAC 57.763 45.455 0.00 0.0 0.00 4.02
2878 4847 6.505044 TTCAATGTCATTGTGAAGGATCAG 57.495 37.500 22.01 0.0 41.02 2.90
2892 4861 7.634671 AATGCTCAGTAATCATTCAATGTCA 57.365 32.000 0.00 0.0 0.00 3.58
3077 5061 4.035558 CCAACAACGCATCACATATAGCTT 59.964 41.667 0.00 0.0 0.00 3.74
3173 5157 7.170277 TGATCTGACCTTTTTGATCATCTGAA 58.830 34.615 0.00 0.0 39.91 3.02


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

AutoCloner maintained by Alex Coulton.