Multiple sequence alignment - TraesCS2B01G214900

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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 TraesCS2B01G214900 chr2B 100.000 2948 0 0 1 2948 200083380 200080433 0.000000e+00 5445.0
1 TraesCS2B01G214900 chr2B 79.703 202 40 1 2745 2945 177133997 177134198 8.520000e-31 145.0
2 TraesCS2B01G214900 chr2B 87.597 129 10 4 1760 1882 200081567 200081439 8.520000e-31 145.0
3 TraesCS2B01G214900 chr2B 87.597 129 10 4 1814 1942 200081621 200081499 8.520000e-31 145.0
4 TraesCS2B01G214900 chr2D 93.157 2718 99 30 104 2792 142065521 142062862 0.000000e+00 3908.0
5 TraesCS2B01G214900 chr2D 83.168 202 29 5 2745 2945 192744342 192744145 2.330000e-41 180.0
6 TraesCS2B01G214900 chr2D 82.162 185 31 2 2745 2928 325808387 325808570 1.090000e-34 158.0
7 TraesCS2B01G214900 chr2D 88.372 129 9 4 1760 1882 142063815 142063687 1.830000e-32 150.0
8 TraesCS2B01G214900 chr2D 89.535 86 3 3 1 86 142065580 142065501 1.450000e-18 104.0
9 TraesCS2B01G214900 chr2A 91.609 2884 119 40 104 2945 159066212 159069014 0.000000e+00 3871.0
10 TraesCS2B01G214900 chr7A 86.709 158 18 3 2771 2927 547106933 547107088 3.910000e-39 172.0
11 TraesCS2B01G214900 chr6A 84.270 178 27 1 2756 2933 575556989 575556813 3.910000e-39 172.0
12 TraesCS2B01G214900 chr5D 82.500 200 32 3 2743 2940 104624706 104624508 3.910000e-39 172.0
13 TraesCS2B01G214900 chr5D 88.889 72 8 0 2650 2721 485911075 485911146 4.050000e-14 89.8
14 TraesCS2B01G214900 chr7D 82.323 198 29 4 2745 2940 235795396 235795589 1.820000e-37 167.0
15 TraesCS2B01G214900 chr7B 81.868 182 31 2 2745 2924 643380296 643380115 5.090000e-33 152.0
16 TraesCS2B01G214900 chr7B 85.714 77 9 2 2650 2725 320327188 320327263 2.440000e-11 80.5
17 TraesCS2B01G214900 chr3B 80.102 196 35 4 2755 2948 707446328 707446135 3.060000e-30 143.0


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 TraesCS2B01G214900 chr2B 200080433 200083380 2947 True 1911.666667 5445 91.731333 1 2948 3 chr2B.!!$R1 2947
1 TraesCS2B01G214900 chr2D 142062862 142065580 2718 True 1387.333333 3908 90.354667 1 2792 3 chr2D.!!$R2 2791
2 TraesCS2B01G214900 chr2A 159066212 159069014 2802 False 3871.000000 3871 91.609000 104 2945 1 chr2A.!!$F1 2841

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
40 41 0.239082 TCGCGAATCACTGTGTACGT 59.761 50.0 6.2 0.0 0.0 3.57 F
670 697 0.510359 GTGTCGCTTTGCTCTCTGTG 59.490 55.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1719 0.816825 CGGTCTTGCCCATGGATCTG 60.817 60.0 15.22 0.0 0.00 2.90 R
2626 2683 0.740868 ACATGATTGAGGGACGCACG 60.741 55.0 0.00 0.0 38.28 5.34 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
34 35 3.181967 GCGCTCGCGAATCACTGT 61.182 61.111 16.26 0.00 42.83 3.55
40 41 0.239082 TCGCGAATCACTGTGTACGT 59.761 50.000 6.20 0.00 0.00 3.57
41 42 1.464219 TCGCGAATCACTGTGTACGTA 59.536 47.619 6.20 0.00 0.00 3.57
42 43 1.838345 CGCGAATCACTGTGTACGTAG 59.162 52.381 0.00 7.24 0.00 3.51
44 45 3.484065 CGCGAATCACTGTGTACGTAGTA 60.484 47.826 0.00 0.00 45.11 1.82
75 76 9.534565 TTGACATTCTACTACTAAATCATGAGC 57.465 33.333 0.09 0.00 0.00 4.26
76 77 8.695456 TGACATTCTACTACTAAATCATGAGCA 58.305 33.333 0.09 0.00 0.00 4.26
77 78 9.190858 GACATTCTACTACTAAATCATGAGCAG 57.809 37.037 0.09 0.46 0.00 4.24
78 79 8.918116 ACATTCTACTACTAAATCATGAGCAGA 58.082 33.333 0.09 0.00 0.00 4.26
79 80 9.409312 CATTCTACTACTAAATCATGAGCAGAG 57.591 37.037 0.09 0.00 0.00 3.35
80 81 8.753497 TTCTACTACTAAATCATGAGCAGAGA 57.247 34.615 0.09 0.00 0.00 3.10
81 82 8.753497 TCTACTACTAAATCATGAGCAGAGAA 57.247 34.615 0.09 0.00 0.00 2.87
82 83 9.190317 TCTACTACTAAATCATGAGCAGAGAAA 57.810 33.333 0.09 0.00 0.00 2.52
83 84 9.462174 CTACTACTAAATCATGAGCAGAGAAAG 57.538 37.037 0.09 2.88 0.00 2.62
84 85 7.846066 ACTACTAAATCATGAGCAGAGAAAGT 58.154 34.615 0.09 3.42 0.00 2.66
85 86 8.317679 ACTACTAAATCATGAGCAGAGAAAGTT 58.682 33.333 0.09 0.00 0.00 2.66
86 87 7.608308 ACTAAATCATGAGCAGAGAAAGTTC 57.392 36.000 0.09 0.00 0.00 3.01
87 88 7.164122 ACTAAATCATGAGCAGAGAAAGTTCA 58.836 34.615 0.09 0.00 0.00 3.18
88 89 6.889301 AAATCATGAGCAGAGAAAGTTCAA 57.111 33.333 0.09 0.00 30.07 2.69
89 90 6.889301 AATCATGAGCAGAGAAAGTTCAAA 57.111 33.333 0.09 0.00 30.07 2.69
90 91 6.889301 ATCATGAGCAGAGAAAGTTCAAAA 57.111 33.333 0.09 0.00 30.07 2.44
91 92 6.698008 TCATGAGCAGAGAAAGTTCAAAAA 57.302 33.333 0.00 0.00 30.07 1.94
151 152 1.447838 GCAGCGAAATCACGAGGGA 60.448 57.895 0.00 0.00 35.09 4.20
197 202 2.050691 GCAATAAATGCGGTTATGCGG 58.949 47.619 0.00 0.00 46.87 5.69
216 221 3.179265 CAACCCGTACGCTGCTCG 61.179 66.667 10.49 0.00 45.38 5.03
238 243 3.815962 GTCAGGTCATGATCGAGCTAGTA 59.184 47.826 0.90 0.00 41.69 1.82
240 245 3.818210 CAGGTCATGATCGAGCTAGTAGT 59.182 47.826 0.90 0.00 41.69 2.73
241 246 4.277174 CAGGTCATGATCGAGCTAGTAGTT 59.723 45.833 0.90 0.00 41.69 2.24
243 248 4.541779 GTCATGATCGAGCTAGTAGTTGG 58.458 47.826 0.90 0.00 0.00 3.77
244 249 4.276183 GTCATGATCGAGCTAGTAGTTGGA 59.724 45.833 0.90 1.38 0.00 3.53
245 250 4.517075 TCATGATCGAGCTAGTAGTTGGAG 59.483 45.833 0.90 0.00 0.00 3.86
246 251 4.152284 TGATCGAGCTAGTAGTTGGAGA 57.848 45.455 0.90 0.00 0.00 3.71
247 252 3.878103 TGATCGAGCTAGTAGTTGGAGAC 59.122 47.826 0.90 3.09 0.00 3.36
248 253 3.630892 TCGAGCTAGTAGTTGGAGACT 57.369 47.619 0.00 0.00 42.55 3.24
249 254 3.533547 TCGAGCTAGTAGTTGGAGACTC 58.466 50.000 0.00 0.00 39.86 3.36
250 255 3.198200 TCGAGCTAGTAGTTGGAGACTCT 59.802 47.826 1.74 0.00 39.86 3.24
251 256 3.942748 CGAGCTAGTAGTTGGAGACTCTT 59.057 47.826 1.74 0.00 39.86 2.85
252 257 4.396790 CGAGCTAGTAGTTGGAGACTCTTT 59.603 45.833 1.74 0.00 39.86 2.52
253 258 5.585445 CGAGCTAGTAGTTGGAGACTCTTTA 59.415 44.000 1.74 0.00 39.86 1.85
254 259 6.261381 CGAGCTAGTAGTTGGAGACTCTTTAT 59.739 42.308 1.74 0.00 39.86 1.40
255 260 7.201750 CGAGCTAGTAGTTGGAGACTCTTTATT 60.202 40.741 1.74 0.00 39.86 1.40
256 261 8.368962 AGCTAGTAGTTGGAGACTCTTTATTT 57.631 34.615 1.74 0.00 39.86 1.40
257 262 8.817876 AGCTAGTAGTTGGAGACTCTTTATTTT 58.182 33.333 1.74 0.00 39.86 1.82
258 263 9.438228 GCTAGTAGTTGGAGACTCTTTATTTTT 57.562 33.333 1.74 0.00 39.86 1.94
268 273 3.822167 ACTCTTTATTTTTCGGGCGGAAA 59.178 39.130 15.25 15.25 42.75 3.13
335 340 8.922058 AACCAACTGTACGAGTAGTATTTATG 57.078 34.615 0.00 0.00 37.69 1.90
336 341 8.284945 ACCAACTGTACGAGTAGTATTTATGA 57.715 34.615 0.00 0.00 37.69 2.15
337 342 8.186821 ACCAACTGTACGAGTAGTATTTATGAC 58.813 37.037 0.00 0.00 37.69 3.06
338 343 8.404000 CCAACTGTACGAGTAGTATTTATGACT 58.596 37.037 0.00 0.00 37.69 3.41
365 370 3.036084 CTCGACGCGCAACCAACT 61.036 61.111 5.73 0.00 0.00 3.16
386 393 2.227089 GATCGACGGCAAGGGTGTCT 62.227 60.000 0.00 0.00 0.00 3.41
432 439 1.369625 CTCGTGGATTACTTGGTGCC 58.630 55.000 0.00 0.00 0.00 5.01
441 448 3.530265 TTACTTGGTGCCGATTCGTAT 57.470 42.857 5.20 0.00 0.00 3.06
463 474 8.617809 CGTATAAAACTATGGGTTTGCTGTTAT 58.382 33.333 1.78 0.00 46.18 1.89
464 475 9.730420 GTATAAAACTATGGGTTTGCTGTTATG 57.270 33.333 1.78 0.00 46.18 1.90
476 487 6.183360 GGTTTGCTGTTATGCTTAGAAATTGC 60.183 38.462 0.00 0.00 0.00 3.56
482 493 7.189693 TGTTATGCTTAGAAATTGCTATCGG 57.810 36.000 0.00 0.00 0.00 4.18
518 529 4.397103 TCGAGTTATACGTCACCACTGATT 59.603 41.667 0.00 0.00 0.00 2.57
552 563 1.497991 ATCGTGATTATCCGGTTGCG 58.502 50.000 0.00 0.00 0.00 4.85
670 697 0.510359 GTGTCGCTTTGCTCTCTGTG 59.490 55.000 0.00 0.00 0.00 3.66
767 797 1.890625 TACACCGGGTCAATCGTGGG 61.891 60.000 6.32 0.00 0.00 4.61
809 839 6.669631 TGAATAGTACTATCTGACACCTCCA 58.330 40.000 15.72 0.37 0.00 3.86
916 960 7.094205 CCACAGAGGAACAGCTAAACAAATTAT 60.094 37.037 0.00 0.00 41.22 1.28
940 984 1.870580 CGACACCGGAGCAAGTTACAA 60.871 52.381 9.46 0.00 0.00 2.41
1018 1069 2.799126 TATGCCGGAAGAAATGGTGT 57.201 45.000 5.05 0.00 0.00 4.16
1029 1080 1.106351 AAATGGTGTTCTGCGGCACA 61.106 50.000 0.00 0.00 37.35 4.57
1112 1163 1.276705 GAAGGAGAAGAAGAAGCCGGT 59.723 52.381 1.90 0.00 0.00 5.28
1114 1165 0.608640 GGAGAAGAAGAAGCCGGTCA 59.391 55.000 1.90 0.00 0.00 4.02
1293 1344 2.507102 ATCGTCGTCAAGCTGCCG 60.507 61.111 0.00 0.00 0.00 5.69
1294 1345 2.989881 ATCGTCGTCAAGCTGCCGA 61.990 57.895 0.00 0.00 0.00 5.54
1340 1391 1.268079 GCCCAAGAAGAAGTGCAAGTC 59.732 52.381 0.00 0.00 0.00 3.01
1353 1404 2.281761 AAGTCCAAGCTGGCCGTG 60.282 61.111 0.00 0.00 37.47 4.94
1668 1719 3.551407 GGCGAGGATGGAGGACCC 61.551 72.222 0.00 0.00 34.81 4.46
1740 1791 2.690173 AGATCGGCGAGAAGATTACG 57.310 50.000 17.22 0.00 0.00 3.18
1871 1922 1.594862 GATTTCGCCCAGAAGATCACG 59.405 52.381 0.00 0.00 40.40 4.35
1948 1999 2.755103 GCACATGGGAAGAAAGGGTAAG 59.245 50.000 0.00 0.00 0.00 2.34
1995 2046 0.597637 AGTCGTCAAACAGAGTGGCG 60.598 55.000 0.00 0.00 45.25 5.69
2004 2055 4.021456 TCAAACAGAGTGGCGAGAAAGATA 60.021 41.667 0.00 0.00 0.00 1.98
2031 2082 8.950007 AATTTCAGGTTTTATCTTTCCTACCA 57.050 30.769 0.00 0.00 0.00 3.25
2038 2089 7.184753 AGGTTTTATCTTTCCTACCATTCTCCT 59.815 37.037 0.00 0.00 0.00 3.69
2185 2240 2.323959 CAACATGCGCAACGGTTTTAT 58.676 42.857 17.11 0.00 0.00 1.40
2196 2251 6.469595 GCGCAACGGTTTTATGTATAAATTCA 59.530 34.615 0.30 0.00 32.78 2.57
2326 2381 1.469703 TGGATGACTGCTGAAAATGCG 59.530 47.619 0.00 0.00 0.00 4.73
2369 2424 5.415701 ACGGAGATAAACATGTGAATTGCTT 59.584 36.000 0.00 0.00 0.00 3.91
2415 2470 7.011482 GTCATACATTGGTCATTGGTCTACTTC 59.989 40.741 0.00 0.00 0.00 3.01
2555 2611 1.381872 AGTGGGTCCCCTCTCATCG 60.382 63.158 5.13 0.00 35.24 3.84
2558 2614 2.367202 GGGTCCCCTCTCATCGCAA 61.367 63.158 0.00 0.00 0.00 4.85
2559 2615 1.700042 GGGTCCCCTCTCATCGCAAT 61.700 60.000 0.00 0.00 0.00 3.56
2580 2637 7.121759 CGCAATTCCCCATAGATTTATTCATCT 59.878 37.037 0.00 0.00 37.31 2.90
2616 2673 7.959658 TTTTCCACCACATCATATTTGATCT 57.040 32.000 0.00 0.00 40.70 2.75
2626 2683 5.310409 TCATATTTGATCTCACCTTCCCC 57.690 43.478 0.00 0.00 0.00 4.81
2632 2689 4.003788 CTCACCTTCCCCGTGCGT 62.004 66.667 0.00 0.00 0.00 5.24
2643 2700 1.153369 CCGTGCGTCCCTCAATCAT 60.153 57.895 0.00 0.00 0.00 2.45
2677 2734 3.891366 ACCTTCTGAACCAATTTCACCTG 59.109 43.478 0.00 0.00 39.45 4.00
2731 2788 2.433436 GGTAAATCACCGCACCTTTCT 58.567 47.619 0.00 0.00 37.63 2.52
2732 2789 2.161609 GGTAAATCACCGCACCTTTCTG 59.838 50.000 0.00 0.00 37.63 3.02
2733 2790 2.270352 AAATCACCGCACCTTTCTGA 57.730 45.000 0.00 0.00 0.00 3.27
2761 2818 9.055248 GCGCTGCTTAATCATATTAATTACTTG 57.945 33.333 0.00 0.00 0.00 3.16
2830 2887 9.180678 CATCAAATTATAAAGTAAATCACGGGC 57.819 33.333 0.00 0.00 0.00 6.13
2831 2888 8.282455 TCAAATTATAAAGTAAATCACGGGCA 57.718 30.769 0.00 0.00 0.00 5.36
2832 2889 8.402472 TCAAATTATAAAGTAAATCACGGGCAG 58.598 33.333 0.00 0.00 0.00 4.85
2833 2890 8.402472 CAAATTATAAAGTAAATCACGGGCAGA 58.598 33.333 0.00 0.00 0.00 4.26
2862 2919 5.692654 GGTAAACATTTATTTGCACAACCGT 59.307 36.000 0.00 0.00 0.00 4.83
2874 2931 7.575414 TTTGCACAACCGTATTAATATGGAT 57.425 32.000 31.77 21.58 41.06 3.41
2945 3002 5.038683 CGCACGAACATGGTTCTACTATAA 58.961 41.667 7.43 0.00 0.00 0.98
2946 3003 5.517411 CGCACGAACATGGTTCTACTATAAA 59.483 40.000 7.43 0.00 0.00 1.40
2947 3004 6.200286 CGCACGAACATGGTTCTACTATAAAT 59.800 38.462 7.43 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 7.912056 AGAATGTCAAGTAGTACTACGTACA 57.088 36.000 26.17 26.17 41.03 2.90
49 50 9.534565 GCTCATGATTTAGTAGTAGAATGTCAA 57.465 33.333 0.00 0.00 0.00 3.18
59 60 7.846066 ACTTTCTCTGCTCATGATTTAGTAGT 58.154 34.615 0.00 0.00 0.00 2.73
65 66 6.889301 TTGAACTTTCTCTGCTCATGATTT 57.111 33.333 0.00 0.00 0.00 2.17
66 67 6.889301 TTTGAACTTTCTCTGCTCATGATT 57.111 33.333 0.00 0.00 0.00 2.57
67 68 6.889301 TTTTGAACTTTCTCTGCTCATGAT 57.111 33.333 0.00 0.00 0.00 2.45
68 69 6.698008 TTTTTGAACTTTCTCTGCTCATGA 57.302 33.333 0.00 0.00 0.00 3.07
90 91 9.603921 TCTGCTCATGATTTTCTTTTTCTTTTT 57.396 25.926 0.00 0.00 0.00 1.94
91 92 9.257651 CTCTGCTCATGATTTTCTTTTTCTTTT 57.742 29.630 0.00 0.00 0.00 2.27
92 93 8.636213 TCTCTGCTCATGATTTTCTTTTTCTTT 58.364 29.630 0.00 0.00 0.00 2.52
93 94 8.174733 TCTCTGCTCATGATTTTCTTTTTCTT 57.825 30.769 0.00 0.00 0.00 2.52
94 95 7.756395 TCTCTGCTCATGATTTTCTTTTTCT 57.244 32.000 0.00 0.00 0.00 2.52
95 96 8.807667 TTTCTCTGCTCATGATTTTCTTTTTC 57.192 30.769 0.00 0.00 0.00 2.29
96 97 9.774413 ATTTTCTCTGCTCATGATTTTCTTTTT 57.226 25.926 0.00 0.00 0.00 1.94
97 98 9.774413 AATTTTCTCTGCTCATGATTTTCTTTT 57.226 25.926 0.00 0.00 0.00 2.27
98 99 9.204570 CAATTTTCTCTGCTCATGATTTTCTTT 57.795 29.630 0.00 0.00 0.00 2.52
99 100 7.817962 CCAATTTTCTCTGCTCATGATTTTCTT 59.182 33.333 0.00 0.00 0.00 2.52
100 101 7.321153 CCAATTTTCTCTGCTCATGATTTTCT 58.679 34.615 0.00 0.00 0.00 2.52
101 102 6.534079 CCCAATTTTCTCTGCTCATGATTTTC 59.466 38.462 0.00 0.00 0.00 2.29
102 103 6.403878 CCCAATTTTCTCTGCTCATGATTTT 58.596 36.000 0.00 0.00 0.00 1.82
137 138 0.170561 ACGTCTCCCTCGTGATTTCG 59.829 55.000 0.00 0.00 40.07 3.46
178 183 2.660490 CCCGCATAACCGCATTTATTG 58.340 47.619 0.00 0.00 0.00 1.90
182 187 1.599606 TTGCCCGCATAACCGCATTT 61.600 50.000 0.00 0.00 0.00 2.32
216 221 2.621055 ACTAGCTCGATCATGACCTGAC 59.379 50.000 0.00 0.00 36.48 3.51
238 243 5.705905 CCCGAAAAATAAAGAGTCTCCAACT 59.294 40.000 0.00 0.00 42.42 3.16
240 245 4.457949 GCCCGAAAAATAAAGAGTCTCCAA 59.542 41.667 0.00 0.00 0.00 3.53
241 246 4.007659 GCCCGAAAAATAAAGAGTCTCCA 58.992 43.478 0.00 0.00 0.00 3.86
243 248 3.063588 CCGCCCGAAAAATAAAGAGTCTC 59.936 47.826 0.00 0.00 0.00 3.36
244 249 3.007635 CCGCCCGAAAAATAAAGAGTCT 58.992 45.455 0.00 0.00 0.00 3.24
245 250 3.004862 TCCGCCCGAAAAATAAAGAGTC 58.995 45.455 0.00 0.00 0.00 3.36
246 251 3.062122 TCCGCCCGAAAAATAAAGAGT 57.938 42.857 0.00 0.00 0.00 3.24
247 252 4.428615 TTTCCGCCCGAAAAATAAAGAG 57.571 40.909 0.00 0.00 37.53 2.85
248 253 5.449451 GCTATTTCCGCCCGAAAAATAAAGA 60.449 40.000 0.00 0.00 43.61 2.52
249 254 4.738252 GCTATTTCCGCCCGAAAAATAAAG 59.262 41.667 0.00 3.70 43.61 1.85
250 255 4.399934 AGCTATTTCCGCCCGAAAAATAAA 59.600 37.500 0.00 0.00 43.61 1.40
251 256 3.949113 AGCTATTTCCGCCCGAAAAATAA 59.051 39.130 0.00 0.00 43.61 1.40
252 257 3.314080 CAGCTATTTCCGCCCGAAAAATA 59.686 43.478 0.00 0.00 43.61 1.40
253 258 2.099098 CAGCTATTTCCGCCCGAAAAAT 59.901 45.455 0.00 0.00 43.61 1.82
254 259 1.470890 CAGCTATTTCCGCCCGAAAAA 59.529 47.619 0.00 0.00 43.61 1.94
255 260 1.091537 CAGCTATTTCCGCCCGAAAA 58.908 50.000 0.00 0.00 43.61 2.29
256 261 0.746563 CCAGCTATTTCCGCCCGAAA 60.747 55.000 0.00 0.00 44.49 3.46
257 262 1.153249 CCAGCTATTTCCGCCCGAA 60.153 57.895 0.00 0.00 0.00 4.30
258 263 2.028125 CTCCAGCTATTTCCGCCCGA 62.028 60.000 0.00 0.00 0.00 5.14
268 273 3.107402 TGACTCCAAGTCTCCAGCTAT 57.893 47.619 8.44 0.00 45.27 2.97
335 340 0.926174 CGTCGAGCTCGCACATAGTC 60.926 60.000 30.97 11.55 39.60 2.59
336 341 1.062685 CGTCGAGCTCGCACATAGT 59.937 57.895 30.97 0.00 39.60 2.12
337 342 3.895204 CGTCGAGCTCGCACATAG 58.105 61.111 30.97 13.47 39.60 2.23
365 370 3.000819 ACCCTTGCCGTCGATCCA 61.001 61.111 0.00 0.00 0.00 3.41
386 393 1.531677 GCGTACGTAACTGCGTATCCA 60.532 52.381 17.90 0.00 46.81 3.41
432 439 6.849305 GCAAACCCATAGTTTTATACGAATCG 59.151 38.462 0.00 0.00 46.79 3.34
441 448 6.435904 AGCATAACAGCAAACCCATAGTTTTA 59.564 34.615 0.00 0.00 46.79 1.52
463 474 4.127171 GGACCGATAGCAATTTCTAAGCA 58.873 43.478 0.00 0.00 0.00 3.91
464 475 3.184581 CGGACCGATAGCAATTTCTAAGC 59.815 47.826 8.64 0.00 0.00 3.09
476 487 0.666913 ATCAACCGACGGACCGATAG 59.333 55.000 23.38 10.50 0.00 2.08
482 493 0.109412 AACTCGATCAACCGACGGAC 60.109 55.000 23.38 5.40 34.56 4.79
518 529 6.516739 AATCACGATTTGTAGAGAGACTGA 57.483 37.500 0.00 0.00 0.00 3.41
670 697 5.674933 AAGAAAACGGTGAGAATCTTCAC 57.325 39.130 4.87 4.87 45.28 3.18
767 797 6.815142 ACTATTCAATTTTCATGCCTTGCTTC 59.185 34.615 0.00 0.00 0.00 3.86
916 960 3.573772 CTTGCTCCGGTGTCGCTCA 62.574 63.158 0.00 0.00 34.56 4.26
1029 1080 0.886490 CAACGTCCTTGAAGCTGGCT 60.886 55.000 0.00 0.00 30.42 4.75
1112 1163 0.974383 GTTCTCCTTCTTCCCGGTGA 59.026 55.000 0.00 0.00 0.00 4.02
1114 1165 1.199425 GGGTTCTCCTTCTTCCCGGT 61.199 60.000 0.00 0.00 0.00 5.28
1152 1203 1.168714 GCACCATGGAGAACTTGTCC 58.831 55.000 21.47 0.00 34.31 4.02
1340 1391 4.988598 ACGACACGGCCAGCTTGG 62.989 66.667 2.24 0.00 41.55 3.61
1668 1719 0.816825 CGGTCTTGCCCATGGATCTG 60.817 60.000 15.22 0.00 0.00 2.90
1871 1922 3.685272 GGAGCTACTACTTTTCTTGCCAC 59.315 47.826 0.00 0.00 0.00 5.01
1948 1999 1.335689 ACACGACCTTCTAAGTGCGAC 60.336 52.381 0.00 0.00 38.08 5.19
2031 2082 8.846943 AAAAAGAACAACAAAAACAGGAGAAT 57.153 26.923 0.00 0.00 0.00 2.40
2038 2089 8.555361 CCTTTGAGAAAAAGAACAACAAAAACA 58.445 29.630 0.00 0.00 0.00 2.83
2196 2251 7.120923 TGAACCAAGAAGTTCTTAGTGTACT 57.879 36.000 17.62 2.06 45.25 2.73
2374 2429 7.977293 CCAATGTATGACATCAAACATCACAAT 59.023 33.333 3.38 0.00 37.97 2.71
2375 2430 7.039853 ACCAATGTATGACATCAAACATCACAA 60.040 33.333 3.38 0.00 37.97 3.33
2509 2564 3.633986 AGAGTTTTGCCTCACAGGAAAAG 59.366 43.478 0.00 0.00 43.56 2.27
2510 2565 3.631250 AGAGTTTTGCCTCACAGGAAAA 58.369 40.909 0.00 0.00 41.15 2.29
2511 2566 3.297134 AGAGTTTTGCCTCACAGGAAA 57.703 42.857 0.00 0.00 37.67 3.13
2512 2567 3.297134 AAGAGTTTTGCCTCACAGGAA 57.703 42.857 0.00 0.00 37.67 3.36
2513 2568 2.951642 CAAAGAGTTTTGCCTCACAGGA 59.048 45.455 0.00 0.00 37.47 3.86
2514 2569 2.689983 ACAAAGAGTTTTGCCTCACAGG 59.310 45.455 0.25 0.00 46.05 4.00
2515 2570 3.378112 TGACAAAGAGTTTTGCCTCACAG 59.622 43.478 0.25 0.00 46.05 3.66
2516 2571 3.351740 TGACAAAGAGTTTTGCCTCACA 58.648 40.909 0.25 0.00 46.05 3.58
2517 2572 3.378427 ACTGACAAAGAGTTTTGCCTCAC 59.622 43.478 0.25 0.00 46.05 3.51
2518 2573 3.378112 CACTGACAAAGAGTTTTGCCTCA 59.622 43.478 0.25 0.00 46.05 3.86
2519 2574 3.243201 CCACTGACAAAGAGTTTTGCCTC 60.243 47.826 0.25 0.00 46.05 4.70
2555 2611 8.358582 AGATGAATAAATCTATGGGGAATTGC 57.641 34.615 0.00 0.00 35.09 3.56
2559 2615 9.621239 AGTCTAGATGAATAAATCTATGGGGAA 57.379 33.333 0.00 0.00 38.25 3.97
2580 2637 9.967451 TGATGTGGTGGAAAAATAAATAGTCTA 57.033 29.630 0.00 0.00 0.00 2.59
2590 2647 8.984855 AGATCAAATATGATGTGGTGGAAAAAT 58.015 29.630 0.00 0.00 46.30 1.82
2616 2673 3.998672 GACGCACGGGGAAGGTGA 61.999 66.667 0.00 0.00 37.60 4.02
2626 2683 0.740868 ACATGATTGAGGGACGCACG 60.741 55.000 0.00 0.00 38.28 5.34
2632 2689 7.054124 GGTAAGTAATCAACATGATTGAGGGA 58.946 38.462 14.23 0.00 45.77 4.20
2643 2700 6.833041 TGGTTCAGAAGGTAAGTAATCAACA 58.167 36.000 0.00 0.00 0.00 3.33
2731 2788 6.799926 TTAATATGATTAAGCAGCGCATCA 57.200 33.333 11.47 9.44 0.00 3.07
2732 2789 9.214953 GTAATTAATATGATTAAGCAGCGCATC 57.785 33.333 11.47 2.75 0.00 3.91
2733 2790 8.950210 AGTAATTAATATGATTAAGCAGCGCAT 58.050 29.630 11.47 0.00 0.00 4.73
2761 2818 3.956744 AGGTGGAATTGGTTTAGAGAGC 58.043 45.455 0.00 0.00 0.00 4.09
2763 2820 8.950007 AAATTAAGGTGGAATTGGTTTAGAGA 57.050 30.769 0.00 0.00 0.00 3.10
2806 2863 8.282455 TGCCCGTGATTTACTTTATAATTTGA 57.718 30.769 0.00 0.00 0.00 2.69
2811 2868 8.514330 AATTCTGCCCGTGATTTACTTTATAA 57.486 30.769 0.00 0.00 0.00 0.98
2819 2876 3.426615 ACCAAATTCTGCCCGTGATTTA 58.573 40.909 0.00 0.00 0.00 1.40
2820 2877 2.247358 ACCAAATTCTGCCCGTGATTT 58.753 42.857 0.00 0.00 0.00 2.17
2821 2878 1.923356 ACCAAATTCTGCCCGTGATT 58.077 45.000 0.00 0.00 0.00 2.57
2822 2879 2.799126 TACCAAATTCTGCCCGTGAT 57.201 45.000 0.00 0.00 0.00 3.06
2823 2880 2.554893 GTTTACCAAATTCTGCCCGTGA 59.445 45.455 0.00 0.00 0.00 4.35
2824 2881 2.294791 TGTTTACCAAATTCTGCCCGTG 59.705 45.455 0.00 0.00 0.00 4.94
2825 2882 2.588620 TGTTTACCAAATTCTGCCCGT 58.411 42.857 0.00 0.00 0.00 5.28
2826 2883 3.866883 ATGTTTACCAAATTCTGCCCG 57.133 42.857 0.00 0.00 0.00 6.13
2827 2884 8.450180 CAAATAAATGTTTACCAAATTCTGCCC 58.550 33.333 0.00 0.00 0.00 5.36
2828 2885 7.962373 GCAAATAAATGTTTACCAAATTCTGCC 59.038 33.333 0.00 0.00 0.00 4.85
2829 2886 8.502387 TGCAAATAAATGTTTACCAAATTCTGC 58.498 29.630 0.00 0.00 0.00 4.26
2830 2887 9.810231 GTGCAAATAAATGTTTACCAAATTCTG 57.190 29.630 0.00 0.00 0.00 3.02
2831 2888 9.553064 TGTGCAAATAAATGTTTACCAAATTCT 57.447 25.926 0.00 0.00 0.00 2.40
2833 2890 9.943163 GTTGTGCAAATAAATGTTTACCAAATT 57.057 25.926 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.