Multiple sequence alignment - TraesCS3B01G210700

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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 TraesCS3B01G210700 chr3B 100.000 3263 0 0 1 3263 248247684 248250946 0.000000e+00 6026.0
1 TraesCS3B01G210700 chr3B 97.066 2045 27 12 1242 3263 248580830 248582864 0.000000e+00 3413.0
2 TraesCS3B01G210700 chr3B 98.994 795 6 2 450 1243 248579937 248580730 0.000000e+00 1423.0
3 TraesCS3B01G210700 chr3B 82.520 1270 188 17 1002 2265 184963250 184962009 0.000000e+00 1085.0
4 TraesCS3B01G210700 chr3B 82.075 1272 193 17 1002 2265 186095088 186093844 0.000000e+00 1053.0
5 TraesCS3B01G210700 chr3B 88.660 97 10 1 2978 3073 154213772 154213868 2.060000e-22 117.0
6 TraesCS3B01G210700 chr3B 82.707 133 15 2 2712 2836 52556217 52556349 9.570000e-21 111.0
7 TraesCS3B01G210700 chr3B 98.000 50 1 0 2571 2620 248250206 248250255 1.610000e-13 87.9
8 TraesCS3B01G210700 chr3B 98.000 50 1 0 2523 2572 248250254 248250303 1.610000e-13 87.9
9 TraesCS3B01G210700 chr3B 98.000 50 1 0 2571 2620 248582113 248582162 1.610000e-13 87.9
10 TraesCS3B01G210700 chr3B 98.000 50 1 0 2523 2572 248582161 248582210 1.610000e-13 87.9
11 TraesCS3B01G210700 chr3B 100.000 37 0 0 1589 1625 248243511 248243547 5.840000e-08 69.4
12 TraesCS3B01G210700 chr3B 100.000 37 0 0 1589 1625 248557874 248557910 5.840000e-08 69.4
13 TraesCS3B01G210700 chr3B 97.297 37 1 0 1589 1625 248577610 248577646 2.720000e-06 63.9
14 TraesCS3B01G210700 chr3B 90.909 44 2 2 2695 2738 643854971 643854930 1.260000e-04 58.4
15 TraesCS3B01G210700 chr1A 97.143 455 13 0 1 455 561115534 561115080 0.000000e+00 769.0
16 TraesCS3B01G210700 chr1A 85.600 125 11 3 2712 2836 465208498 465208615 1.230000e-24 124.0
17 TraesCS3B01G210700 chr1A 91.209 91 7 1 2980 3070 63515491 63515402 4.420000e-24 122.0
18 TraesCS3B01G210700 chr1A 83.721 129 14 4 2711 2839 65267152 65267031 7.400000e-22 115.0
19 TraesCS3B01G210700 chr1A 79.310 145 14 6 2708 2836 582281533 582281389 1.610000e-13 87.9
20 TraesCS3B01G210700 chr2B 97.130 453 12 1 1 452 614113528 614113980 0.000000e+00 763.0
21 TraesCS3B01G210700 chr2B 90.625 96 8 1 2976 3070 25284894 25284799 3.420000e-25 126.0
22 TraesCS3B01G210700 chr6A 96.903 452 14 0 1 452 324283477 324283928 0.000000e+00 758.0
23 TraesCS3B01G210700 chr6B 96.499 457 15 1 1 456 427639735 427639279 0.000000e+00 754.0
24 TraesCS3B01G210700 chr6B 88.889 99 7 3 2969 3065 543229230 543229326 5.720000e-23 119.0
25 TraesCS3B01G210700 chr5A 96.460 452 16 0 1 452 490870085 490870536 0.000000e+00 747.0
26 TraesCS3B01G210700 chr7A 96.460 452 14 1 1 452 399518219 399518668 0.000000e+00 745.0
27 TraesCS3B01G210700 chr5B 96.247 453 16 1 1 453 436552066 436552517 0.000000e+00 741.0
28 TraesCS3B01G210700 chr1D 95.633 458 14 2 1 453 304333237 304332781 0.000000e+00 730.0
29 TraesCS3B01G210700 chr1D 86.667 60 8 0 2717 2776 463321754 463321813 2.100000e-07 67.6
30 TraesCS3B01G210700 chr7D 95.585 453 19 1 1 453 156773442 156772991 0.000000e+00 725.0
31 TraesCS3B01G210700 chr1B 86.614 127 10 3 2712 2838 611680423 611680542 2.040000e-27 134.0
32 TraesCS3B01G210700 chr1B 84.000 125 13 3 2712 2836 576063422 576063305 2.660000e-21 113.0
33 TraesCS3B01G210700 chr5D 85.606 132 12 1 2709 2840 416427887 416428011 7.350000e-27 132.0
34 TraesCS3B01G210700 chr2D 86.047 129 9 4 2712 2839 408776383 408776263 2.640000e-26 130.0
35 TraesCS3B01G210700 chr6D 92.135 89 7 0 2979 3067 29232380 29232292 3.420000e-25 126.0
36 TraesCS3B01G210700 chr3A 92.135 89 7 0 2978 3066 194703879 194703967 3.420000e-25 126.0
37 TraesCS3B01G210700 chr3A 91.111 90 8 0 2981 3070 57262236 57262147 4.420000e-24 122.0
38 TraesCS3B01G210700 chr7B 90.323 93 9 0 2977 3069 639796195 639796287 4.420000e-24 122.0
39 TraesCS3B01G210700 chr7B 83.721 129 14 4 2711 2839 526866277 526866156 7.400000e-22 115.0
40 TraesCS3B01G210700 chrUn 81.250 144 24 3 2263 2406 100201602 100201462 2.660000e-21 113.0
41 TraesCS3B01G210700 chr4B 81.720 93 13 4 2744 2836 601768369 601768281 1.260000e-09 75.0


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 TraesCS3B01G210700 chr3B 248247684 248250946 3262 False 2067.266667 6026 98.666667 1 3263 3 chr3B.!!$F5 3262
1 TraesCS3B01G210700 chr3B 184962009 184963250 1241 True 1085.000000 1085 82.520000 1002 2265 1 chr3B.!!$R1 1263
2 TraesCS3B01G210700 chr3B 186093844 186095088 1244 True 1053.000000 1053 82.075000 1002 2265 1 chr3B.!!$R2 1263
3 TraesCS3B01G210700 chr3B 248577610 248582864 5254 False 1015.140000 3413 97.871400 450 3263 5 chr3B.!!$F6 2813

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
177 178 0.038067 GGCACGGCCCGTTTAATTTT 60.038 50.0 5.76 0.00 44.06 1.82 F
268 269 0.323725 AAAATCAGATGGGCCAGCGT 60.324 50.0 17.28 3.68 0.00 5.07 F
1904 3885 0.038744 CATGAGCTTGGTGGGGAACT 59.961 55.0 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 3886 2.099141 TGCAGAAGAAAGTAGCGCAT 57.901 45.0 11.47 0.0 0.00 4.73 R
1949 3935 6.102663 GGGACCAATATATCTCTTGTCATCG 58.897 44.0 0.00 0.0 0.00 3.84 R
3145 5155 0.105778 CACATTTTGCCGTTTGGGGT 59.894 50.0 0.00 0.0 35.78 4.95 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 4.073052 CCAAACAGGCCGTGCTAA 57.927 55.556 0.00 0.00 0.00 3.09
25 26 2.566824 CCAAACAGGCCGTGCTAAT 58.433 52.632 0.00 0.00 0.00 1.73
27 28 1.402720 CCAAACAGGCCGTGCTAATTG 60.403 52.381 0.00 0.00 0.00 2.32
28 29 0.887933 AAACAGGCCGTGCTAATTGG 59.112 50.000 0.00 0.00 0.00 3.16
29 30 0.965363 AACAGGCCGTGCTAATTGGG 60.965 55.000 0.00 0.00 0.00 4.12
32 33 3.887868 GCCGTGCTAATTGGGCCG 61.888 66.667 0.00 0.00 39.67 6.13
33 34 3.209097 CCGTGCTAATTGGGCCGG 61.209 66.667 0.00 0.00 37.26 6.13
50 51 4.752879 GCCCGGTAGCACGCAGAA 62.753 66.667 0.00 0.00 0.00 3.02
52 53 2.388232 CCCGGTAGCACGCAGAAAC 61.388 63.158 0.00 0.00 0.00 2.78
53 54 2.726691 CCGGTAGCACGCAGAAACG 61.727 63.158 0.00 0.00 39.50 3.60
54 55 2.726691 CGGTAGCACGCAGAAACGG 61.727 63.158 0.00 0.00 37.37 4.44
55 56 2.474712 GTAGCACGCAGAAACGGC 59.525 61.111 0.00 0.00 37.37 5.68
57 58 2.314647 TAGCACGCAGAAACGGCAC 61.315 57.895 0.00 0.00 37.37 5.01
86 87 4.770874 GGCACGGCCCGAGCTAAA 62.771 66.667 24.26 0.00 44.06 1.85
87 88 3.497031 GCACGGCCCGAGCTAAAC 61.497 66.667 18.56 0.00 40.03 2.01
88 89 3.186047 CACGGCCCGAGCTAAACG 61.186 66.667 11.71 0.00 39.73 3.60
94 95 4.732106 CCGAGCTAAACGGGCTAG 57.268 61.111 4.45 0.00 45.65 3.42
95 96 1.067582 CCGAGCTAAACGGGCTAGG 59.932 63.158 4.45 0.00 45.65 3.02
96 97 1.591863 CGAGCTAAACGGGCTAGGC 60.592 63.158 8.00 8.00 40.40 3.93
134 135 4.119363 GGCCATGCCTGAGCCTGA 62.119 66.667 0.00 0.00 46.69 3.86
135 136 2.044650 GCCATGCCTGAGCCTGAA 60.045 61.111 0.00 0.00 36.81 3.02
136 137 2.119655 GCCATGCCTGAGCCTGAAG 61.120 63.158 0.00 0.00 36.81 3.02
137 138 1.453379 CCATGCCTGAGCCTGAAGG 60.453 63.158 0.00 0.00 36.81 3.46
175 176 3.280211 GGCACGGCCCGTTTAATT 58.720 55.556 5.76 0.00 44.06 1.40
176 177 1.587568 GGCACGGCCCGTTTAATTT 59.412 52.632 5.76 0.00 44.06 1.82
177 178 0.038067 GGCACGGCCCGTTTAATTTT 60.038 50.000 5.76 0.00 44.06 1.82
178 179 1.605968 GGCACGGCCCGTTTAATTTTT 60.606 47.619 5.76 0.00 44.06 1.94
224 225 5.690865 TGACCTAAATTACAGCCCAATAGG 58.309 41.667 0.00 0.00 35.62 2.57
238 239 3.826729 CCCAATAGGCCTAAAATACAGCC 59.173 47.826 18.42 0.00 46.13 4.85
243 244 2.452505 GGCCTAAAATACAGCCCAACA 58.547 47.619 0.00 0.00 39.60 3.33
244 245 2.427095 GGCCTAAAATACAGCCCAACAG 59.573 50.000 0.00 0.00 39.60 3.16
245 246 2.427095 GCCTAAAATACAGCCCAACAGG 59.573 50.000 0.00 0.00 39.47 4.00
259 260 5.002464 CCCAACAGGCTAAAAATCAGATG 57.998 43.478 0.00 0.00 0.00 2.90
260 261 4.142093 CCCAACAGGCTAAAAATCAGATGG 60.142 45.833 0.00 0.00 0.00 3.51
262 263 3.026694 ACAGGCTAAAAATCAGATGGGC 58.973 45.455 0.00 0.00 0.00 5.36
263 264 2.363359 CAGGCTAAAAATCAGATGGGCC 59.637 50.000 0.00 0.00 38.71 5.80
264 265 2.024080 AGGCTAAAAATCAGATGGGCCA 60.024 45.455 9.61 9.61 40.61 5.36
265 266 2.363359 GGCTAAAAATCAGATGGGCCAG 59.637 50.000 13.78 0.00 38.35 4.85
266 267 2.223900 GCTAAAAATCAGATGGGCCAGC 60.224 50.000 15.39 15.39 0.00 4.85
267 268 0.819582 AAAAATCAGATGGGCCAGCG 59.180 50.000 17.28 11.59 0.00 5.18
268 269 0.323725 AAAATCAGATGGGCCAGCGT 60.324 50.000 17.28 3.68 0.00 5.07
270 271 4.783621 TCAGATGGGCCAGCGTGC 62.784 66.667 17.28 0.47 0.00 5.34
271 272 4.790962 CAGATGGGCCAGCGTGCT 62.791 66.667 17.28 2.99 0.00 4.40
273 274 2.124736 GATGGGCCAGCGTGCTAA 60.125 61.111 13.78 0.00 0.00 3.09
275 276 1.993369 GATGGGCCAGCGTGCTAAAC 61.993 60.000 13.78 0.00 0.00 2.01
301 302 4.239162 GGCCGGCCCGTTTAATAA 57.761 55.556 36.64 0.00 0.00 1.40
302 303 2.723231 GGCCGGCCCGTTTAATAAT 58.277 52.632 36.64 0.00 0.00 1.28
306 307 1.877443 CCGGCCCGTTTAATAATCAGG 59.123 52.381 0.85 0.00 0.00 3.86
307 308 1.265905 CGGCCCGTTTAATAATCAGGC 59.734 52.381 0.00 0.78 38.21 4.85
310 311 2.567985 CCCGTTTAATAATCAGGCCGT 58.432 47.619 0.00 0.00 0.00 5.68
311 312 2.289547 CCCGTTTAATAATCAGGCCGTG 59.710 50.000 0.00 0.00 0.00 4.94
326 327 4.792804 GTGCCTGGGCCAGAGAGC 62.793 72.222 34.84 27.58 41.09 4.09
363 364 4.244463 GGCACGGCCCGGCTATTA 62.244 66.667 8.57 0.00 44.06 0.98
365 366 1.820481 GCACGGCCCGGCTATTAAA 60.820 57.895 8.57 0.00 0.00 1.52
366 367 2.019337 CACGGCCCGGCTATTAAAC 58.981 57.895 8.57 0.00 0.00 2.01
367 368 1.522130 ACGGCCCGGCTATTAAACG 60.522 57.895 8.57 4.87 0.00 3.60
368 369 1.522130 CGGCCCGGCTATTAAACGT 60.522 57.895 9.86 0.00 0.00 3.99
369 370 1.768112 CGGCCCGGCTATTAAACGTG 61.768 60.000 9.86 0.00 0.00 4.49
370 371 1.354155 GCCCGGCTATTAAACGTGC 59.646 57.895 0.71 0.00 0.00 5.34
371 372 2.019337 CCCGGCTATTAAACGTGCC 58.981 57.895 0.00 2.35 41.76 5.01
372 373 0.745128 CCCGGCTATTAAACGTGCCA 60.745 55.000 12.24 0.00 45.13 4.92
373 374 0.375803 CCGGCTATTAAACGTGCCAC 59.624 55.000 12.24 0.00 45.13 5.01
404 405 2.902343 GGGCCAGGCACGATTAGC 60.902 66.667 15.19 0.00 0.00 3.09
406 407 2.472909 GGCCAGGCACGATTAGCAC 61.473 63.158 15.19 0.00 0.00 4.40
407 408 2.813179 GCCAGGCACGATTAGCACG 61.813 63.158 6.55 0.00 0.00 5.34
408 409 2.173669 CCAGGCACGATTAGCACGG 61.174 63.158 0.00 0.00 34.93 4.94
409 410 2.173669 CAGGCACGATTAGCACGGG 61.174 63.158 0.00 0.00 37.22 5.28
451 452 2.672996 CCCGTTTGGCCAGGTCTG 60.673 66.667 5.11 0.00 0.00 3.51
762 2642 4.895224 TGTGTGCTCCTATACTAAGACG 57.105 45.455 0.00 0.00 0.00 4.18
1066 2946 3.600388 GAGGAATTGTTGGACGAGATGT 58.400 45.455 0.00 0.00 0.00 3.06
1180 3060 1.092921 TGTTCGTGCACACCTCCAAC 61.093 55.000 18.64 9.29 0.00 3.77
1787 3768 2.898920 AATCAGCCATGCTCCCCACG 62.899 60.000 0.00 0.00 36.40 4.94
1903 3884 0.967380 CCATGAGCTTGGTGGGGAAC 60.967 60.000 0.00 0.00 31.74 3.62
1904 3885 0.038744 CATGAGCTTGGTGGGGAACT 59.961 55.000 0.00 0.00 0.00 3.01
1905 3886 1.281867 CATGAGCTTGGTGGGGAACTA 59.718 52.381 0.00 0.00 0.00 2.24
1949 3935 6.442952 AGAGTATGCAACGAGTATTGATCTC 58.557 40.000 0.00 0.00 0.00 2.75
2112 4101 8.421249 TGAAGGATCATGGTGTAAAAGAAAAT 57.579 30.769 0.00 0.00 0.00 1.82
2371 4360 5.415077 GCAGAGGTGTCTAAGTAAGTGTCTA 59.585 44.000 0.00 0.00 0.00 2.59
2669 4663 6.421801 GTGCATGTTAATTTTCTGCTGTTTCT 59.578 34.615 0.00 0.00 34.02 2.52
2740 4734 2.613474 CCGTCCGAAAATACTTGTCCCA 60.613 50.000 0.00 0.00 0.00 4.37
2781 4775 8.731275 TGGATGTATTTACCACTAACTTGATG 57.269 34.615 0.00 0.00 0.00 3.07
2782 4776 8.325787 TGGATGTATTTACCACTAACTTGATGT 58.674 33.333 0.00 0.00 0.00 3.06
2783 4777 9.174166 GGATGTATTTACCACTAACTTGATGTT 57.826 33.333 0.00 0.00 42.31 2.71
2814 4808 2.834638 AGATCCATTTGGGGGACAAG 57.165 50.000 0.00 0.00 40.82 3.16
2876 4886 4.212214 GCTAGCATCCAGTTTCTAATTCCG 59.788 45.833 10.63 0.00 0.00 4.30
2887 4897 6.856426 CAGTTTCTAATTCCGTTTCTTTGTCC 59.144 38.462 0.00 0.00 0.00 4.02
2903 4913 6.533730 TCTTTGTCCAGCTCATTCTCTTTTA 58.466 36.000 0.00 0.00 0.00 1.52
3070 5080 5.148651 TCTTTACAGAGGGAGTAGTTTGC 57.851 43.478 0.00 0.00 0.00 3.68
3080 5090 7.011857 CAGAGGGAGTAGTTTGCAGAATAAATC 59.988 40.741 0.00 0.00 0.00 2.17
3081 5091 6.122964 AGGGAGTAGTTTGCAGAATAAATCC 58.877 40.000 8.08 8.08 0.00 3.01
3145 5155 3.998341 GTCTGGTACGGTGCTATTTTGAA 59.002 43.478 0.00 0.00 35.30 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.402720 CCAATTAGCACGGCCTGTTTG 60.403 52.381 0.00 2.02 0.00 2.93
9 10 0.887933 CCAATTAGCACGGCCTGTTT 59.112 50.000 0.00 0.00 0.00 2.83
10 11 0.965363 CCCAATTAGCACGGCCTGTT 60.965 55.000 0.00 0.00 0.00 3.16
11 12 1.378514 CCCAATTAGCACGGCCTGT 60.379 57.895 0.00 0.00 0.00 4.00
12 13 2.774799 GCCCAATTAGCACGGCCTG 61.775 63.158 0.00 0.00 35.23 4.85
13 14 2.440247 GCCCAATTAGCACGGCCT 60.440 61.111 0.00 0.00 35.23 5.19
15 16 3.887868 CGGCCCAATTAGCACGGC 61.888 66.667 0.00 0.00 40.85 5.68
16 17 3.209097 CCGGCCCAATTAGCACGG 61.209 66.667 0.00 12.06 37.59 4.94
17 18 3.887868 GCCGGCCCAATTAGCACG 61.888 66.667 18.11 3.66 0.00 5.34
18 19 3.527427 GGCCGGCCCAATTAGCAC 61.527 66.667 36.64 5.01 0.00 4.40
33 34 4.752879 TTCTGCGTGCTACCGGGC 62.753 66.667 6.32 0.00 0.00 6.13
36 37 2.726691 CCGTTTCTGCGTGCTACCG 61.727 63.158 0.00 0.00 0.00 4.02
37 38 3.023591 GCCGTTTCTGCGTGCTACC 62.024 63.158 0.00 0.00 0.00 3.18
38 39 2.314647 TGCCGTTTCTGCGTGCTAC 61.315 57.895 0.00 0.00 0.00 3.58
39 40 2.029815 TGCCGTTTCTGCGTGCTA 59.970 55.556 0.00 0.00 0.00 3.49
40 41 3.649986 GTGCCGTTTCTGCGTGCT 61.650 61.111 0.00 0.00 0.00 4.40
42 43 4.368808 CCGTGCCGTTTCTGCGTG 62.369 66.667 0.00 0.00 0.00 5.34
71 72 3.186047 CGTTTAGCTCGGGCCGTG 61.186 66.667 27.32 24.90 39.73 4.94
72 73 4.446413 CCGTTTAGCTCGGGCCGT 62.446 66.667 27.32 9.60 43.68 5.68
77 78 1.067582 CCTAGCCCGTTTAGCTCGG 59.932 63.158 5.38 5.38 46.49 4.63
78 79 1.591863 GCCTAGCCCGTTTAGCTCG 60.592 63.158 0.00 0.00 41.83 5.03
79 80 1.227586 GGCCTAGCCCGTTTAGCTC 60.228 63.158 0.00 0.00 44.06 4.09
80 81 2.908796 GGCCTAGCCCGTTTAGCT 59.091 61.111 0.00 0.00 44.06 3.32
159 160 1.785768 AAAAATTAAACGGGCCGTGC 58.214 45.000 34.87 0.00 39.99 5.34
198 199 8.109634 CCTATTGGGCTGTAATTTAGGTCATAT 58.890 37.037 0.00 0.00 0.00 1.78
199 200 7.458397 CCTATTGGGCTGTAATTTAGGTCATA 58.542 38.462 0.00 0.00 0.00 2.15
200 201 6.306987 CCTATTGGGCTGTAATTTAGGTCAT 58.693 40.000 0.00 0.00 0.00 3.06
224 225 2.427095 CCTGTTGGGCTGTATTTTAGGC 59.573 50.000 0.00 0.00 39.76 3.93
238 239 4.142093 CCCATCTGATTTTTAGCCTGTTGG 60.142 45.833 0.00 0.00 0.00 3.77
239 240 4.678840 GCCCATCTGATTTTTAGCCTGTTG 60.679 45.833 0.00 0.00 0.00 3.33
241 242 3.026694 GCCCATCTGATTTTTAGCCTGT 58.973 45.455 0.00 0.00 0.00 4.00
243 244 2.024080 TGGCCCATCTGATTTTTAGCCT 60.024 45.455 0.00 0.00 39.90 4.58
244 245 2.363359 CTGGCCCATCTGATTTTTAGCC 59.637 50.000 0.00 0.00 39.64 3.93
245 246 2.223900 GCTGGCCCATCTGATTTTTAGC 60.224 50.000 0.00 0.00 0.00 3.09
246 247 2.033801 CGCTGGCCCATCTGATTTTTAG 59.966 50.000 0.00 0.00 0.00 1.85
248 249 0.819582 CGCTGGCCCATCTGATTTTT 59.180 50.000 0.00 0.00 0.00 1.94
249 250 0.323725 ACGCTGGCCCATCTGATTTT 60.324 50.000 0.00 0.00 0.00 1.82
251 252 1.452651 CACGCTGGCCCATCTGATT 60.453 57.895 0.00 0.00 0.00 2.57
252 253 2.191375 CACGCTGGCCCATCTGAT 59.809 61.111 0.00 0.00 0.00 2.90
253 254 4.783621 GCACGCTGGCCCATCTGA 62.784 66.667 0.00 0.00 0.00 3.27
254 255 2.874648 TTAGCACGCTGGCCCATCTG 62.875 60.000 0.00 0.00 0.00 2.90
256 257 1.748879 TTTAGCACGCTGGCCCATC 60.749 57.895 0.00 0.00 0.00 3.51
258 259 2.671619 GTTTAGCACGCTGGCCCA 60.672 61.111 0.00 0.00 0.00 5.36
259 260 3.799755 CGTTTAGCACGCTGGCCC 61.800 66.667 0.00 0.00 43.37 5.80
267 268 2.554272 CCGTGGCACGTTTAGCAC 59.446 61.111 34.74 0.00 40.58 4.40
268 269 2.666862 CCCGTGGCACGTTTAGCA 60.667 61.111 34.74 0.00 40.58 3.49
285 286 1.265905 CTGATTATTAAACGGGCCGGC 59.734 52.381 31.78 21.18 0.00 6.13
286 287 1.877443 CCTGATTATTAAACGGGCCGG 59.123 52.381 31.78 12.53 0.00 6.13
291 292 2.286772 GCACGGCCTGATTATTAAACGG 60.287 50.000 0.00 0.00 0.00 4.44
292 293 2.286772 GGCACGGCCTGATTATTAAACG 60.287 50.000 0.00 0.00 46.69 3.60
293 294 3.349488 GGCACGGCCTGATTATTAAAC 57.651 47.619 0.00 0.00 46.69 2.01
308 309 4.463879 CTCTCTGGCCCAGGCACG 62.464 72.222 11.68 0.35 44.11 5.34
347 348 1.820481 TTTAATAGCCGGGCCGTGC 60.820 57.895 26.32 25.86 0.00 5.34
348 349 1.768112 CGTTTAATAGCCGGGCCGTG 61.768 60.000 26.32 17.25 0.00 4.94
351 352 2.019337 CACGTTTAATAGCCGGGCC 58.981 57.895 17.02 0.00 0.00 5.80
352 353 1.354155 GCACGTTTAATAGCCGGGC 59.646 57.895 12.11 12.11 44.35 6.13
353 354 2.019337 GGCACGTTTAATAGCCGGG 58.981 57.895 2.18 0.00 37.41 5.73
358 359 0.025770 CGCCGTGGCACGTTTAATAG 59.974 55.000 34.74 20.30 40.58 1.73
359 360 1.360194 CCGCCGTGGCACGTTTAATA 61.360 55.000 34.74 0.00 40.58 0.98
361 362 3.347405 CCGCCGTGGCACGTTTAA 61.347 61.111 34.74 0.00 40.58 1.52
385 386 4.169696 TAATCGTGCCTGGCCCGG 62.170 66.667 22.84 9.24 0.00 5.73
386 387 2.588877 CTAATCGTGCCTGGCCCG 60.589 66.667 17.67 17.67 0.00 6.13
387 388 2.902343 GCTAATCGTGCCTGGCCC 60.902 66.667 17.53 2.94 0.00 5.80
389 390 2.813179 CGTGCTAATCGTGCCTGGC 61.813 63.158 12.87 12.87 0.00 4.85
390 391 2.173669 CCGTGCTAATCGTGCCTGG 61.174 63.158 0.00 0.00 0.00 4.45
391 392 2.173669 CCCGTGCTAATCGTGCCTG 61.174 63.158 0.00 0.00 0.00 4.85
392 393 2.186903 CCCGTGCTAATCGTGCCT 59.813 61.111 0.00 0.00 0.00 4.75
393 394 3.573491 GCCCGTGCTAATCGTGCC 61.573 66.667 0.00 0.00 33.53 5.01
434 435 2.672996 CAGACCTGGCCAAACGGG 60.673 66.667 7.01 7.12 42.81 5.28
435 436 2.672996 CCAGACCTGGCCAAACGG 60.673 66.667 7.01 7.56 44.73 4.44
444 445 3.324713 CCCTTAGGGCCAGACCTG 58.675 66.667 3.52 0.00 42.02 4.00
454 455 2.107141 CTCTTCGGCGCCCTTAGG 59.893 66.667 23.46 6.36 0.00 2.69
455 456 1.066587 CTCTCTTCGGCGCCCTTAG 59.933 63.158 23.46 15.61 0.00 2.18
637 2517 7.148853 CGGAAAAATGATTTGCTTCTCTCAAAG 60.149 37.037 0.00 0.00 36.93 2.77
1066 2946 2.158813 GCCGGATTAAGATCTCCCACAA 60.159 50.000 5.05 0.00 32.66 3.33
1180 3060 2.842208 TGTTGTTTCTGTTTGGAGCG 57.158 45.000 0.00 0.00 0.00 5.03
1787 3768 2.282180 TGAAACGAAGCAGCCCCC 60.282 61.111 0.00 0.00 0.00 5.40
1903 3884 3.190079 TGCAGAAGAAAGTAGCGCATAG 58.810 45.455 11.47 0.00 0.00 2.23
1904 3885 3.245518 TGCAGAAGAAAGTAGCGCATA 57.754 42.857 11.47 0.00 0.00 3.14
1905 3886 2.099141 TGCAGAAGAAAGTAGCGCAT 57.901 45.000 11.47 0.00 0.00 4.73
1949 3935 6.102663 GGGACCAATATATCTCTTGTCATCG 58.897 44.000 0.00 0.00 0.00 3.84
2371 4360 3.255642 ACCGTTGCTTATTTGTTGAGCAT 59.744 39.130 0.00 0.00 45.36 3.79
2450 4442 0.675083 CAAGCAAACACATCAGGCCA 59.325 50.000 5.01 0.00 0.00 5.36
2621 4615 6.034470 CACAAAACAAAGCATCGTTTAAGTGT 59.966 34.615 14.90 7.78 36.96 3.55
2669 4663 6.054860 AGATTAGCTGGCAGAGTTTCTTTA 57.945 37.500 20.86 0.00 0.00 1.85
2740 4734 3.181418 ACATCCATTTGAGGGACAAGGTT 60.181 43.478 0.00 0.00 39.77 3.50
2781 4775 9.442047 CCCAAATGGATCTATCTAACATCTAAC 57.558 37.037 0.00 0.00 37.39 2.34
2782 4776 8.605947 CCCCAAATGGATCTATCTAACATCTAA 58.394 37.037 0.00 0.00 37.39 2.10
2783 4777 7.182749 CCCCCAAATGGATCTATCTAACATCTA 59.817 40.741 0.00 0.00 37.39 1.98
2784 4778 6.012157 CCCCCAAATGGATCTATCTAACATCT 60.012 42.308 0.00 0.00 37.39 2.90
2785 4779 6.012508 TCCCCCAAATGGATCTATCTAACATC 60.013 42.308 0.00 0.00 37.39 3.06
2786 4780 5.857283 TCCCCCAAATGGATCTATCTAACAT 59.143 40.000 0.00 0.00 37.39 2.71
2787 4781 5.073144 GTCCCCCAAATGGATCTATCTAACA 59.927 44.000 0.00 0.00 37.39 2.41
2828 4822 2.127708 CACCCTTGGCTATTACTCCCT 58.872 52.381 0.00 0.00 0.00 4.20
2876 4886 4.759183 AGAGAATGAGCTGGACAAAGAAAC 59.241 41.667 0.00 0.00 0.00 2.78
2887 4897 8.939929 TGTACTGATTTAAAAGAGAATGAGCTG 58.060 33.333 0.00 0.00 0.00 4.24
2931 4941 4.679654 CCGTTTTTCACAGCTATTTTCCAC 59.320 41.667 0.00 0.00 0.00 4.02
2934 4944 6.665465 ACTACCGTTTTTCACAGCTATTTTC 58.335 36.000 0.00 0.00 0.00 2.29
3070 5080 8.359642 TCTTTTTCTGTGGTTGGATTTATTCTG 58.640 33.333 0.00 0.00 0.00 3.02
3080 5090 4.935352 TCCATTCTTTTTCTGTGGTTGG 57.065 40.909 0.00 0.00 0.00 3.77
3081 5091 4.687483 GCATCCATTCTTTTTCTGTGGTTG 59.313 41.667 0.00 0.00 34.39 3.77
3145 5155 0.105778 CACATTTTGCCGTTTGGGGT 59.894 50.000 0.00 0.00 35.78 4.95


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

AutoCloner maintained by Alex Coulton.