Multiple sequence alignment - TraesCS3D01G042400

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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 TraesCS3D01G042400 chr3D 100.000 3318 0 0 1 3318 16194462 16191145 0.000000e+00 6128.0
1 TraesCS3D01G042400 chr3D 88.735 1225 121 7 1033 2250 16159994 16158780 0.000000e+00 1482.0
2 TraesCS3D01G042400 chr3D 83.879 397 41 7 1970 2366 16155951 16155578 1.130000e-94 357.0
3 TraesCS3D01G042400 chr3D 87.363 182 18 2 2856 3032 16142234 16142053 1.560000e-48 204.0
4 TraesCS3D01G042400 chr3D 83.708 178 19 9 2373 2549 16155516 16155348 3.430000e-35 159.0
5 TraesCS3D01G042400 chr3D 87.500 112 9 4 2523 2634 16158099 16157993 1.250000e-24 124.0
6 TraesCS3D01G042400 chr3D 86.111 108 10 4 2373 2480 16158277 16158175 9.730000e-21 111.0
7 TraesCS3D01G042400 chr3B 91.939 1253 79 6 1012 2259 23714851 23713616 0.000000e+00 1735.0
8 TraesCS3D01G042400 chr3B 93.421 380 20 4 2338 2714 23713444 23713067 2.890000e-155 558.0
9 TraesCS3D01G042400 chr3B 85.634 355 35 5 1970 2324 23701141 23700803 3.150000e-95 359.0
10 TraesCS3D01G042400 chr3B 88.172 279 25 2 3040 3318 23693199 23693469 3.190000e-85 326.0
11 TraesCS3D01G042400 chr3B 95.288 191 8 1 2699 2888 23713052 23712862 5.380000e-78 302.0
12 TraesCS3D01G042400 chr3B 85.424 295 16 8 3043 3318 23709567 23709281 7.010000e-72 281.0
13 TraesCS3D01G042400 chr3B 84.420 276 32 5 3043 3318 23702411 23702147 9.130000e-66 261.0
14 TraesCS3D01G042400 chr3B 92.442 172 8 2 2871 3037 23702992 23702821 1.190000e-59 241.0
15 TraesCS3D01G042400 chr3B 86.885 183 18 3 2856 3032 23689982 23689800 2.020000e-47 200.0
16 TraesCS3D01G042400 chr3B 89.209 139 9 3 2904 3037 23710107 23709970 5.690000e-38 169.0
17 TraesCS3D01G042400 chr3B 94.000 50 3 0 2701 2750 23690793 23690744 3.550000e-10 76.8
18 TraesCS3D01G042400 chr3A 90.393 1322 107 9 1012 2319 20189005 20190320 0.000000e+00 1720.0
19 TraesCS3D01G042400 chr3A 92.381 315 16 8 2318 2632 20206354 20206660 3.040000e-120 442.0
20 TraesCS3D01G042400 chr3A 89.349 169 14 1 3040 3208 20207263 20207427 3.350000e-50 209.0
21 TraesCS3D01G042400 chr3A 86.813 182 19 2 2856 3032 20288829 20289010 7.260000e-47 198.0
22 TraesCS3D01G042400 chr3A 96.226 53 2 0 3266 3318 20207427 20207479 1.640000e-13 87.9
23 TraesCS3D01G042400 chr3A 97.222 36 1 0 2667 2702 20248287 20248322 9.940000e-06 62.1
24 TraesCS3D01G042400 chr1D 93.690 1046 34 9 1 1014 462731453 462730408 0.000000e+00 1537.0
25 TraesCS3D01G042400 chr1D 91.910 1063 35 3 1 1012 199590416 199591478 0.000000e+00 1439.0
26 TraesCS3D01G042400 chr2D 92.681 1052 43 6 1 1018 178522965 178524016 0.000000e+00 1485.0
27 TraesCS3D01G042400 chr2D 100.000 28 0 0 2050 2077 431394589 431394616 6.000000e-03 52.8
28 TraesCS3D01G042400 chr4D 92.891 1041 43 4 1 1011 192980482 192979443 0.000000e+00 1483.0
29 TraesCS3D01G042400 chr4D 91.541 1064 39 8 1 1013 167494942 167496005 0.000000e+00 1419.0
30 TraesCS3D01G042400 chr6D 91.831 1065 33 13 1 1011 419870646 419869582 0.000000e+00 1435.0
31 TraesCS3D01G042400 chr6D 91.952 994 31 4 1 946 79588241 79589233 0.000000e+00 1347.0
32 TraesCS3D01G042400 chr6D 93.581 888 30 3 1 861 38170794 38169907 0.000000e+00 1299.0
33 TraesCS3D01G042400 chr5D 91.808 1062 35 15 1 1011 421114481 421113421 0.000000e+00 1432.0
34 TraesCS3D01G042400 chr5D 91.800 1061 36 9 1 1010 133813867 133814927 0.000000e+00 1430.0
35 TraesCS3D01G042400 chr5D 91.431 1062 35 13 5 1011 83356472 83355412 0.000000e+00 1406.0
36 TraesCS3D01G042400 chr7D 91.682 1058 40 13 1 1011 595152908 595151852 0.000000e+00 1423.0
37 TraesCS3D01G042400 chr7D 91.588 1058 42 13 1 1011 141568327 141567270 0.000000e+00 1417.0
38 TraesCS3D01G042400 chr7D 91.268 1065 37 5 1 1011 126034585 126033523 0.000000e+00 1400.0
39 TraesCS3D01G042400 chr7D 93.468 888 30 3 1 861 446932759 446933645 0.000000e+00 1293.0
40 TraesCS3D01G042400 chr2A 92.432 185 10 4 834 1015 605274019 605274202 9.130000e-66 261.0


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 TraesCS3D01G042400 chr3D 16191145 16194462 3317 True 6128.0 6128 100.000000 1 3318 1 chr3D.!!$R2 3317
1 TraesCS3D01G042400 chr3D 16155348 16159994 4646 True 446.6 1482 85.986600 1033 2634 5 chr3D.!!$R3 1601
2 TraesCS3D01G042400 chr3B 23709281 23714851 5570 True 609.0 1735 91.056200 1012 3318 5 chr3B.!!$R3 2306
3 TraesCS3D01G042400 chr3B 23700803 23702992 2189 True 287.0 359 87.498667 1970 3318 3 chr3B.!!$R2 1348
4 TraesCS3D01G042400 chr3A 20189005 20190320 1315 False 1720.0 1720 90.393000 1012 2319 1 chr3A.!!$F1 1307
5 TraesCS3D01G042400 chr3A 20206354 20207479 1125 False 246.3 442 92.652000 2318 3318 3 chr3A.!!$F4 1000
6 TraesCS3D01G042400 chr1D 462730408 462731453 1045 True 1537.0 1537 93.690000 1 1014 1 chr1D.!!$R1 1013
7 TraesCS3D01G042400 chr1D 199590416 199591478 1062 False 1439.0 1439 91.910000 1 1012 1 chr1D.!!$F1 1011
8 TraesCS3D01G042400 chr2D 178522965 178524016 1051 False 1485.0 1485 92.681000 1 1018 1 chr2D.!!$F1 1017
9 TraesCS3D01G042400 chr4D 192979443 192980482 1039 True 1483.0 1483 92.891000 1 1011 1 chr4D.!!$R1 1010
10 TraesCS3D01G042400 chr4D 167494942 167496005 1063 False 1419.0 1419 91.541000 1 1013 1 chr4D.!!$F1 1012
11 TraesCS3D01G042400 chr6D 419869582 419870646 1064 True 1435.0 1435 91.831000 1 1011 1 chr6D.!!$R2 1010
12 TraesCS3D01G042400 chr6D 79588241 79589233 992 False 1347.0 1347 91.952000 1 946 1 chr6D.!!$F1 945
13 TraesCS3D01G042400 chr6D 38169907 38170794 887 True 1299.0 1299 93.581000 1 861 1 chr6D.!!$R1 860
14 TraesCS3D01G042400 chr5D 421113421 421114481 1060 True 1432.0 1432 91.808000 1 1011 1 chr5D.!!$R2 1010
15 TraesCS3D01G042400 chr5D 133813867 133814927 1060 False 1430.0 1430 91.800000 1 1010 1 chr5D.!!$F1 1009
16 TraesCS3D01G042400 chr5D 83355412 83356472 1060 True 1406.0 1406 91.431000 5 1011 1 chr5D.!!$R1 1006
17 TraesCS3D01G042400 chr7D 595151852 595152908 1056 True 1423.0 1423 91.682000 1 1011 1 chr7D.!!$R3 1010
18 TraesCS3D01G042400 chr7D 141567270 141568327 1057 True 1417.0 1417 91.588000 1 1011 1 chr7D.!!$R2 1010
19 TraesCS3D01G042400 chr7D 126033523 126034585 1062 True 1400.0 1400 91.268000 1 1011 1 chr7D.!!$R1 1010
20 TraesCS3D01G042400 chr7D 446932759 446933645 886 False 1293.0 1293 93.468000 1 861 1 chr7D.!!$F1 860

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
299 300 1.336440 CATCATCGCGAAGAGGAGAGT 59.664 52.381 20.0 0.0 43.38 3.24 F
1067 1153 1.167155 AGCGACTATGGCGACGATCT 61.167 55.000 0.0 0.0 35.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 1580 0.032130 GGATGCTATCGGCGACAAGA 59.968 55.0 21.35 9.49 45.43 3.02 R
3037 9218 0.036388 GAGGGAAATCACGGCTGACA 60.036 55.0 0.00 0.00 0.00 3.58 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
147 148 2.358003 GTGCTCGGACTGCTGCTT 60.358 61.111 0.00 0.00 0.00 3.91
233 234 3.030168 TTCATGGAGGCGGCGATGT 62.030 57.895 12.98 0.00 0.00 3.06
299 300 1.336440 CATCATCGCGAAGAGGAGAGT 59.664 52.381 20.00 0.00 43.38 3.24
306 307 2.035940 AAGAGGAGAGTCGGCGGT 59.964 61.111 7.21 0.00 0.00 5.68
307 308 1.596895 GAAGAGGAGAGTCGGCGGTT 61.597 60.000 7.21 0.00 0.00 4.44
309 310 2.282958 AGGAGAGTCGGCGGTTGA 60.283 61.111 7.21 0.00 0.00 3.18
339 340 1.614241 GCGAGGGCCTTGACCTTCTA 61.614 60.000 25.47 0.00 43.92 2.10
555 560 1.973281 CCAGCGTCCACCATTGCTT 60.973 57.895 0.00 0.00 34.99 3.91
1050 1135 3.408288 ACGTAGAAGACAGATCGAAGC 57.592 47.619 0.00 0.00 0.00 3.86
1067 1153 1.167155 AGCGACTATGGCGACGATCT 61.167 55.000 0.00 0.00 35.00 2.75
1137 1223 2.396955 CGTCCTACCTCGAGCACGT 61.397 63.158 6.99 2.14 40.69 4.49
1352 1445 3.512516 GCCGGTGCTTCCTGATGC 61.513 66.667 1.90 0.00 33.53 3.91
1409 1502 1.982395 CCCGAGTACCTCTGTGCCA 60.982 63.158 0.00 0.00 0.00 4.92
1486 1580 1.050988 CCCCTCGACAGATCACCCAT 61.051 60.000 0.00 0.00 0.00 4.00
1543 1637 2.202453 GACCTCGTCGCCGTTCTC 60.202 66.667 0.00 0.00 35.01 2.87
1574 1668 0.246757 GCACACGAGCAATAACGTCG 60.247 55.000 0.00 0.00 40.76 5.12
1582 1676 3.318017 GAGCAATAACGTCGGCATCTAT 58.682 45.455 0.00 0.00 0.00 1.98
1758 1852 2.808543 GAGAATCCGTCCAATGCATACC 59.191 50.000 0.00 0.00 0.00 2.73
1786 1880 1.741770 GCCGCCAACAAGAGTCGAT 60.742 57.895 0.00 0.00 0.00 3.59
1801 1895 0.968901 TCGATGAGGGCTACAACCGT 60.969 55.000 0.00 0.00 0.00 4.83
1813 1907 2.084681 CAACCGTGTACGCGAGGTC 61.085 63.158 29.24 0.00 35.68 3.85
1814 1908 3.273080 AACCGTGTACGCGAGGTCC 62.273 63.158 29.24 0.00 35.68 4.46
1829 1923 1.516423 GTCCGCTTCTACCTGGTCC 59.484 63.158 0.63 0.00 0.00 4.46
1864 1958 2.029380 CCTACTCATGGTCGAACACACA 60.029 50.000 4.62 0.00 0.00 3.72
1972 2075 1.229529 ACGGTGGAGGGAGGTTGAT 60.230 57.895 0.00 0.00 0.00 2.57
2079 2182 2.681344 TCTACTTTATGAGCGAGCGTCA 59.319 45.455 0.00 0.00 0.00 4.35
2149 2252 2.304761 GGGGGTGTACAACATGAGAGAA 59.695 50.000 14.02 0.00 0.00 2.87
2154 2257 4.080863 GGTGTACAACATGAGAGAAGGGAT 60.081 45.833 5.89 0.00 0.00 3.85
2167 2270 4.593206 AGAGAAGGGATGATAATAACGCCA 59.407 41.667 0.00 0.00 0.00 5.69
2240 2343 1.530655 ACTTGGCTTTTCCCACCGG 60.531 57.895 0.00 0.00 33.82 5.28
2263 8383 1.774110 TTTGAGGTTTTGAGCTGGCA 58.226 45.000 0.00 0.00 0.00 4.92
2264 8384 1.774110 TTGAGGTTTTGAGCTGGCAA 58.226 45.000 0.00 0.00 0.00 4.52
2437 8612 5.341617 TGAACAAAATACACAAACCGGTTC 58.658 37.500 22.53 2.98 34.33 3.62
2604 8780 8.794335 AGAGAAAAATGAACTAACCTATGACC 57.206 34.615 0.00 0.00 0.00 4.02
2624 8800 7.750229 TGACCATGAGCTTCCATATTTAATC 57.250 36.000 0.00 0.00 0.00 1.75
2632 8808 5.308237 AGCTTCCATATTTAATCTCCTCCGT 59.692 40.000 0.00 0.00 0.00 4.69
2633 8809 5.998363 GCTTCCATATTTAATCTCCTCCGTT 59.002 40.000 0.00 0.00 0.00 4.44
2634 8810 6.147985 GCTTCCATATTTAATCTCCTCCGTTC 59.852 42.308 0.00 0.00 0.00 3.95
2635 8811 6.740944 TCCATATTTAATCTCCTCCGTTCA 57.259 37.500 0.00 0.00 0.00 3.18
2636 8812 7.316393 TCCATATTTAATCTCCTCCGTTCAT 57.684 36.000 0.00 0.00 0.00 2.57
2637 8813 7.161404 TCCATATTTAATCTCCTCCGTTCATG 58.839 38.462 0.00 0.00 0.00 3.07
2638 8814 6.372659 CCATATTTAATCTCCTCCGTTCATGG 59.627 42.308 0.00 0.00 0.00 3.66
2639 8815 2.910688 TAATCTCCTCCGTTCATGGC 57.089 50.000 0.00 0.00 0.00 4.40
2640 8816 0.179073 AATCTCCTCCGTTCATGGCG 60.179 55.000 0.00 0.00 0.00 5.69
2646 8822 3.499737 CCGTTCATGGCGGCACTC 61.500 66.667 16.34 4.09 42.82 3.51
2647 8823 3.499737 CGTTCATGGCGGCACTCC 61.500 66.667 16.34 1.35 0.00 3.85
2648 8824 3.134127 GTTCATGGCGGCACTCCC 61.134 66.667 16.34 0.00 27.74 4.30
2671 8847 0.401738 CAAGGAGAAGTTGAGGCCCA 59.598 55.000 0.00 0.00 0.00 5.36
2672 8848 0.695347 AAGGAGAAGTTGAGGCCCAG 59.305 55.000 0.00 0.00 0.00 4.45
2673 8849 0.178891 AGGAGAAGTTGAGGCCCAGA 60.179 55.000 0.00 0.00 0.00 3.86
2674 8850 0.251634 GGAGAAGTTGAGGCCCAGAG 59.748 60.000 0.00 0.00 0.00 3.35
2675 8851 0.251634 GAGAAGTTGAGGCCCAGAGG 59.748 60.000 0.00 0.00 0.00 3.69
2676 8852 0.474660 AGAAGTTGAGGCCCAGAGGT 60.475 55.000 0.00 0.00 34.57 3.85
2677 8853 0.322008 GAAGTTGAGGCCCAGAGGTG 60.322 60.000 0.00 0.00 34.57 4.00
2678 8854 2.360475 GTTGAGGCCCAGAGGTGC 60.360 66.667 0.00 0.00 34.57 5.01
2684 8860 4.864334 GCCCAGAGGTGCCGGATG 62.864 72.222 5.05 0.00 34.57 3.51
2685 8861 3.402681 CCCAGAGGTGCCGGATGT 61.403 66.667 5.05 0.00 0.00 3.06
2686 8862 2.063979 CCCAGAGGTGCCGGATGTA 61.064 63.158 5.05 0.00 0.00 2.29
2687 8863 1.443407 CCAGAGGTGCCGGATGTAG 59.557 63.158 5.05 0.00 0.00 2.74
2688 8864 1.227380 CAGAGGTGCCGGATGTAGC 60.227 63.158 5.05 0.00 0.00 3.58
2689 8865 2.109181 GAGGTGCCGGATGTAGCC 59.891 66.667 5.05 0.00 0.00 3.93
2690 8866 3.462199 GAGGTGCCGGATGTAGCCC 62.462 68.421 5.05 0.00 0.00 5.19
2691 8867 3.480133 GGTGCCGGATGTAGCCCT 61.480 66.667 5.05 0.00 0.00 5.19
2692 8868 2.590092 GTGCCGGATGTAGCCCTT 59.410 61.111 5.05 0.00 0.00 3.95
2693 8869 1.077716 GTGCCGGATGTAGCCCTTT 60.078 57.895 5.05 0.00 0.00 3.11
2694 8870 0.679960 GTGCCGGATGTAGCCCTTTT 60.680 55.000 5.05 0.00 0.00 2.27
2695 8871 0.679640 TGCCGGATGTAGCCCTTTTG 60.680 55.000 5.05 0.00 0.00 2.44
2696 8872 2.004808 GCCGGATGTAGCCCTTTTGC 62.005 60.000 5.05 0.00 0.00 3.68
2697 8873 1.384222 CCGGATGTAGCCCTTTTGCC 61.384 60.000 0.00 0.00 0.00 4.52
2698 8874 0.679640 CGGATGTAGCCCTTTTGCCA 60.680 55.000 0.00 0.00 0.00 4.92
2699 8875 1.780503 GGATGTAGCCCTTTTGCCAT 58.219 50.000 0.00 0.00 0.00 4.40
2700 8876 2.110578 GGATGTAGCCCTTTTGCCATT 58.889 47.619 0.00 0.00 0.00 3.16
2701 8877 2.501316 GGATGTAGCCCTTTTGCCATTT 59.499 45.455 0.00 0.00 0.00 2.32
2702 8878 3.704061 GGATGTAGCCCTTTTGCCATTTA 59.296 43.478 0.00 0.00 0.00 1.40
2703 8879 4.202151 GGATGTAGCCCTTTTGCCATTTAG 60.202 45.833 0.00 0.00 0.00 1.85
2704 8880 2.495669 TGTAGCCCTTTTGCCATTTAGC 59.504 45.455 0.00 0.00 0.00 3.09
2705 8881 1.643310 AGCCCTTTTGCCATTTAGCA 58.357 45.000 0.00 0.00 42.17 3.49
2706 8882 1.276138 AGCCCTTTTGCCATTTAGCAC 59.724 47.619 0.00 0.00 43.97 4.40
2707 8883 1.001860 GCCCTTTTGCCATTTAGCACA 59.998 47.619 0.00 0.00 43.97 4.57
2708 8884 2.355007 GCCCTTTTGCCATTTAGCACAT 60.355 45.455 0.00 0.00 43.97 3.21
2709 8885 3.118811 GCCCTTTTGCCATTTAGCACATA 60.119 43.478 0.00 0.00 43.97 2.29
2710 8886 4.432712 CCCTTTTGCCATTTAGCACATAC 58.567 43.478 0.00 0.00 43.97 2.39
2711 8887 4.104776 CCTTTTGCCATTTAGCACATACG 58.895 43.478 0.00 0.00 43.97 3.06
2712 8888 4.380444 CCTTTTGCCATTTAGCACATACGT 60.380 41.667 0.00 0.00 43.97 3.57
2713 8889 5.163703 CCTTTTGCCATTTAGCACATACGTA 60.164 40.000 0.00 0.00 43.97 3.57
2714 8890 5.881777 TTTGCCATTTAGCACATACGTAA 57.118 34.783 0.00 0.00 43.97 3.18
2715 8891 5.478233 TTGCCATTTAGCACATACGTAAG 57.522 39.130 0.00 0.00 43.97 2.34
2716 8892 3.311322 TGCCATTTAGCACATACGTAAGC 59.689 43.478 0.00 4.58 38.54 3.09
2717 8893 3.560068 GCCATTTAGCACATACGTAAGCT 59.440 43.478 19.73 19.73 45.62 3.74
2718 8894 4.035208 GCCATTTAGCACATACGTAAGCTT 59.965 41.667 20.63 3.48 45.62 3.74
2719 8895 5.448632 GCCATTTAGCACATACGTAAGCTTT 60.449 40.000 20.63 8.20 45.62 3.51
2720 8896 5.965334 CCATTTAGCACATACGTAAGCTTTG 59.035 40.000 20.63 16.06 45.62 2.77
2721 8897 5.539582 TTTAGCACATACGTAAGCTTTGG 57.460 39.130 20.63 0.00 45.62 3.28
2722 8898 1.737793 AGCACATACGTAAGCTTTGGC 59.262 47.619 3.20 2.56 45.62 4.52
2723 8899 1.529010 GCACATACGTAAGCTTTGGCG 60.529 52.381 3.20 10.15 44.37 5.69
2724 8900 1.996898 CACATACGTAAGCTTTGGCGA 59.003 47.619 19.51 7.94 44.37 5.54
2725 8901 1.997606 ACATACGTAAGCTTTGGCGAC 59.002 47.619 19.51 5.66 44.37 5.19
2726 8902 1.326548 CATACGTAAGCTTTGGCGACC 59.673 52.381 19.51 0.00 44.37 4.79
2727 8903 0.604578 TACGTAAGCTTTGGCGACCT 59.395 50.000 19.51 5.22 44.37 3.85
2728 8904 0.604578 ACGTAAGCTTTGGCGACCTA 59.395 50.000 19.51 0.00 44.37 3.08
2729 8905 1.001181 ACGTAAGCTTTGGCGACCTAA 59.999 47.619 19.51 0.00 44.37 2.69
2730 8906 1.659098 CGTAAGCTTTGGCGACCTAAG 59.341 52.381 3.20 12.93 44.37 2.18
2731 8907 2.696506 GTAAGCTTTGGCGACCTAAGT 58.303 47.619 3.20 5.66 44.37 2.24
2732 8908 2.271944 AAGCTTTGGCGACCTAAGTT 57.728 45.000 16.50 10.84 44.37 2.66
2733 8909 3.412237 AAGCTTTGGCGACCTAAGTTA 57.588 42.857 16.50 0.00 44.37 2.24
2734 8910 2.973945 AGCTTTGGCGACCTAAGTTAG 58.026 47.619 16.50 2.65 44.37 2.34
2735 8911 2.565834 AGCTTTGGCGACCTAAGTTAGA 59.434 45.455 11.66 0.00 44.37 2.10
2736 8912 2.671888 GCTTTGGCGACCTAAGTTAGAC 59.328 50.000 11.66 4.54 38.32 2.59
2737 8913 3.259902 CTTTGGCGACCTAAGTTAGACC 58.740 50.000 11.66 7.67 33.06 3.85
2738 8914 1.188863 TGGCGACCTAAGTTAGACCC 58.811 55.000 11.66 6.37 0.00 4.46
2739 8915 1.272872 TGGCGACCTAAGTTAGACCCT 60.273 52.381 11.66 0.00 0.00 4.34
2740 8916 1.136500 GGCGACCTAAGTTAGACCCTG 59.864 57.143 11.66 0.00 0.00 4.45
2741 8917 2.097825 GCGACCTAAGTTAGACCCTGA 58.902 52.381 11.66 0.00 0.00 3.86
2742 8918 2.494870 GCGACCTAAGTTAGACCCTGAA 59.505 50.000 11.66 0.00 0.00 3.02
2743 8919 3.132467 GCGACCTAAGTTAGACCCTGAAT 59.868 47.826 11.66 0.00 0.00 2.57
2744 8920 4.737055 GCGACCTAAGTTAGACCCTGAATC 60.737 50.000 11.66 0.00 0.00 2.52
2745 8921 4.401519 CGACCTAAGTTAGACCCTGAATCA 59.598 45.833 11.66 0.00 0.00 2.57
2746 8922 5.069251 CGACCTAAGTTAGACCCTGAATCAT 59.931 44.000 11.66 0.00 0.00 2.45
2747 8923 6.240549 ACCTAAGTTAGACCCTGAATCATG 57.759 41.667 11.66 0.00 0.00 3.07
2748 8924 5.726793 ACCTAAGTTAGACCCTGAATCATGT 59.273 40.000 11.66 0.00 0.00 3.21
2749 8925 6.127026 ACCTAAGTTAGACCCTGAATCATGTC 60.127 42.308 11.66 5.29 0.00 3.06
2750 8926 5.762179 AAGTTAGACCCTGAATCATGTCA 57.238 39.130 13.23 0.00 0.00 3.58
2751 8927 5.762179 AGTTAGACCCTGAATCATGTCAA 57.238 39.130 13.23 5.43 0.00 3.18
2752 8928 5.491982 AGTTAGACCCTGAATCATGTCAAC 58.508 41.667 13.23 13.45 0.00 3.18
2753 8929 5.013079 AGTTAGACCCTGAATCATGTCAACA 59.987 40.000 13.23 0.00 0.00 3.33
2754 8930 4.581309 AGACCCTGAATCATGTCAACAT 57.419 40.909 13.23 0.00 36.96 2.71
2755 8931 4.521146 AGACCCTGAATCATGTCAACATC 58.479 43.478 13.23 0.00 33.61 3.06
2756 8932 4.226846 AGACCCTGAATCATGTCAACATCT 59.773 41.667 13.23 0.00 33.61 2.90
2757 8933 4.267536 ACCCTGAATCATGTCAACATCTG 58.732 43.478 0.00 0.00 33.61 2.90
2758 8934 4.263639 ACCCTGAATCATGTCAACATCTGT 60.264 41.667 0.00 0.00 33.61 3.41
2759 8935 4.095932 CCCTGAATCATGTCAACATCTGTG 59.904 45.833 0.00 0.00 33.61 3.66
2760 8936 4.698780 CCTGAATCATGTCAACATCTGTGT 59.301 41.667 0.00 0.00 41.28 3.72
2761 8937 5.163784 CCTGAATCATGTCAACATCTGTGTC 60.164 44.000 0.00 0.00 37.67 3.67
2762 8938 4.696877 TGAATCATGTCAACATCTGTGTCC 59.303 41.667 0.00 0.00 37.67 4.02
2763 8939 4.564782 ATCATGTCAACATCTGTGTCCT 57.435 40.909 0.00 0.00 37.67 3.85
2764 8940 4.356405 TCATGTCAACATCTGTGTCCTT 57.644 40.909 0.00 0.00 37.67 3.36
2765 8941 4.717877 TCATGTCAACATCTGTGTCCTTT 58.282 39.130 0.00 0.00 37.67 3.11
2766 8942 5.132502 TCATGTCAACATCTGTGTCCTTTT 58.867 37.500 0.00 0.00 37.67 2.27
2767 8943 5.239306 TCATGTCAACATCTGTGTCCTTTTC 59.761 40.000 0.00 0.00 37.67 2.29
2768 8944 4.780815 TGTCAACATCTGTGTCCTTTTCT 58.219 39.130 0.00 0.00 37.67 2.52
2769 8945 5.192927 TGTCAACATCTGTGTCCTTTTCTT 58.807 37.500 0.00 0.00 37.67 2.52
2770 8946 5.652014 TGTCAACATCTGTGTCCTTTTCTTT 59.348 36.000 0.00 0.00 37.67 2.52
2771 8947 6.152661 TGTCAACATCTGTGTCCTTTTCTTTT 59.847 34.615 0.00 0.00 37.67 2.27
2772 8948 7.338196 TGTCAACATCTGTGTCCTTTTCTTTTA 59.662 33.333 0.00 0.00 37.67 1.52
2773 8949 7.644157 GTCAACATCTGTGTCCTTTTCTTTTAC 59.356 37.037 0.00 0.00 37.67 2.01
2774 8950 7.556275 TCAACATCTGTGTCCTTTTCTTTTACT 59.444 33.333 0.00 0.00 37.67 2.24
2775 8951 8.836413 CAACATCTGTGTCCTTTTCTTTTACTA 58.164 33.333 0.00 0.00 37.67 1.82
2776 8952 8.379457 ACATCTGTGTCCTTTTCTTTTACTAC 57.621 34.615 0.00 0.00 31.41 2.73
2777 8953 7.444487 ACATCTGTGTCCTTTTCTTTTACTACC 59.556 37.037 0.00 0.00 31.41 3.18
2778 8954 7.133133 TCTGTGTCCTTTTCTTTTACTACCT 57.867 36.000 0.00 0.00 0.00 3.08
2779 8955 8.253867 TCTGTGTCCTTTTCTTTTACTACCTA 57.746 34.615 0.00 0.00 0.00 3.08
2780 8956 8.707449 TCTGTGTCCTTTTCTTTTACTACCTAA 58.293 33.333 0.00 0.00 0.00 2.69
2781 8957 9.333724 CTGTGTCCTTTTCTTTTACTACCTAAA 57.666 33.333 0.00 0.00 0.00 1.85
2782 8958 9.683870 TGTGTCCTTTTCTTTTACTACCTAAAA 57.316 29.630 0.00 0.00 33.93 1.52
2808 8984 3.679389 GAGGCAATCTCTTTGTTGAGGA 58.321 45.455 0.00 0.00 39.38 3.71
2809 8985 4.074970 GAGGCAATCTCTTTGTTGAGGAA 58.925 43.478 0.00 0.00 39.38 3.36
2810 8986 4.473444 AGGCAATCTCTTTGTTGAGGAAA 58.527 39.130 0.00 0.00 37.65 3.13
2811 8987 4.895297 AGGCAATCTCTTTGTTGAGGAAAA 59.105 37.500 0.00 0.00 37.65 2.29
2812 8988 5.363580 AGGCAATCTCTTTGTTGAGGAAAAA 59.636 36.000 0.00 0.00 37.65 1.94
2869 9045 3.042481 AAAAAGAGTCAGGCCAGGC 57.958 52.632 5.01 1.26 0.00 4.85
2873 9049 4.828925 GAGTCAGGCCAGGCGAGC 62.829 72.222 5.01 0.00 0.00 5.03
2907 9083 5.990668 ACAAGACTTTCCATGTAGGGTATC 58.009 41.667 0.00 0.00 38.24 2.24
2909 9085 5.615925 AGACTTTCCATGTAGGGTATCAC 57.384 43.478 0.00 0.00 38.24 3.06
2910 9086 5.030147 AGACTTTCCATGTAGGGTATCACA 58.970 41.667 0.00 0.00 38.24 3.58
2962 9139 5.042463 TCAAGTTCAACTAACCCATGACA 57.958 39.130 0.00 0.00 39.03 3.58
2963 9140 4.819630 TCAAGTTCAACTAACCCATGACAC 59.180 41.667 0.00 0.00 39.03 3.67
2964 9141 3.751518 AGTTCAACTAACCCATGACACC 58.248 45.455 0.00 0.00 39.03 4.16
2979 9156 1.337387 GACACCGGTATCTCAGCCTAC 59.663 57.143 6.87 0.00 0.00 3.18
3019 9200 0.743688 AGCTCACCTGCAGATCGTAG 59.256 55.000 17.39 6.24 34.99 3.51
3026 9207 3.191182 TGCAGATCGTAGAGGCAGA 57.809 52.632 0.00 0.00 43.63 4.26
3029 9210 1.317613 CAGATCGTAGAGGCAGAGCT 58.682 55.000 0.00 0.00 43.63 4.09
3037 9218 2.875094 AGAGGCAGAGCTTGACATTT 57.125 45.000 4.83 0.00 37.23 2.32
3130 9724 9.742552 GTAGAATTTATTGTCTCTCAAACGAAC 57.257 33.333 0.00 0.00 39.62 3.95
3137 9731 4.617959 TGTCTCTCAAACGAACGAAGAAT 58.382 39.130 0.14 0.00 0.00 2.40
3175 9769 1.306148 CATGCCACAGCGAAGATCAT 58.694 50.000 0.00 0.00 44.31 2.45
3184 9778 0.861837 GCGAAGATCATGGCCTAACG 59.138 55.000 3.32 0.00 0.00 3.18
3258 9858 3.718210 GATCGACGTCCCTGGTGGC 62.718 68.421 10.58 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 0.970937 CCACTACGAGGCCCTTCAGA 60.971 60.000 0.00 0.00 0.00 3.27
299 300 2.180769 CTCGATGTCAACCGCCGA 59.819 61.111 0.00 0.00 0.00 5.54
309 310 3.069980 GCCCTCGCTGACTCGATGT 62.070 63.158 0.00 0.00 37.87 3.06
339 340 0.826256 TCCCGCTGGCGAGTATATGT 60.826 55.000 16.79 0.00 42.83 2.29
555 560 1.808531 CGTGTCCAACCCCGACTACA 61.809 60.000 0.00 0.00 0.00 2.74
998 1083 4.250464 GTTTTGGCCCTGTTAAAATAGGC 58.750 43.478 0.00 0.00 36.10 3.93
1018 1103 6.005583 TGTCTTCTACGTACAATTCTCGTT 57.994 37.500 0.00 0.00 38.69 3.85
1050 1135 0.386100 CCAGATCGTCGCCATAGTCG 60.386 60.000 0.00 0.00 0.00 4.18
1352 1445 4.436998 GTCGCCGGAGTGAGGGTG 62.437 72.222 5.05 0.00 31.79 4.61
1409 1502 1.476007 AAGTCGCTGAACTGGAGGCT 61.476 55.000 0.00 0.00 0.00 4.58
1486 1580 0.032130 GGATGCTATCGGCGACAAGA 59.968 55.000 21.35 9.49 45.43 3.02
1543 1637 1.440850 CGTGTGCAAACGCCTGATG 60.441 57.895 17.88 0.00 36.65 3.07
1574 1668 0.388649 CCGCCACGAGTATAGATGCC 60.389 60.000 0.00 0.00 0.00 4.40
1582 1676 1.017177 GCATTGTTCCGCCACGAGTA 61.017 55.000 0.00 0.00 0.00 2.59
1786 1880 0.604578 GTACACGGTTGTAGCCCTCA 59.395 55.000 0.00 0.00 38.95 3.86
1813 1907 2.901042 GGGACCAGGTAGAAGCGG 59.099 66.667 0.00 0.00 0.00 5.52
1864 1958 5.000591 TGTTGATACGTCATGTGGTCAATT 58.999 37.500 0.00 0.00 38.18 2.32
2094 2197 4.715130 TGGTAGCGTCCCTGGCCT 62.715 66.667 3.32 0.00 0.00 5.19
2149 2252 3.758554 GCAATGGCGTTATTATCATCCCT 59.241 43.478 0.00 0.00 0.00 4.20
2154 2257 2.621055 GGTGGCAATGGCGTTATTATCA 59.379 45.455 1.51 0.00 42.47 2.15
2167 2270 4.397348 GTCTCCAACGGTGGCAAT 57.603 55.556 16.88 0.00 45.54 3.56
2240 2343 2.589014 CAGCTCAAAACCTCAAATCGC 58.411 47.619 0.00 0.00 0.00 4.58
2330 8450 7.253950 CCGTCTCTCTAAACTACTACGAACTAC 60.254 44.444 0.00 0.00 0.00 2.73
2437 8612 2.920964 CGATCATCGCTTGCGTCGG 61.921 63.158 14.70 6.03 32.79 4.79
2472 8647 7.280205 GCTCCGACAGAAATTCCTAAAATTCTA 59.720 37.037 0.00 0.00 33.31 2.10
2473 8648 6.094186 GCTCCGACAGAAATTCCTAAAATTCT 59.906 38.462 0.00 0.00 35.46 2.40
2474 8649 6.128007 TGCTCCGACAGAAATTCCTAAAATTC 60.128 38.462 0.00 0.00 0.00 2.17
2475 8650 5.710099 TGCTCCGACAGAAATTCCTAAAATT 59.290 36.000 0.00 0.00 0.00 1.82
2476 8651 5.253330 TGCTCCGACAGAAATTCCTAAAAT 58.747 37.500 0.00 0.00 0.00 1.82
2479 8654 3.973206 TGCTCCGACAGAAATTCCTAA 57.027 42.857 0.00 0.00 0.00 2.69
2480 8655 3.861840 CTTGCTCCGACAGAAATTCCTA 58.138 45.455 0.00 0.00 0.00 2.94
2482 8657 1.131315 GCTTGCTCCGACAGAAATTCC 59.869 52.381 0.00 0.00 0.00 3.01
2529 8705 3.418684 AATACAGGCCAACGAGTTCTT 57.581 42.857 5.01 0.00 0.00 2.52
2602 8778 6.944862 GGAGATTAAATATGGAAGCTCATGGT 59.055 38.462 13.94 0.00 39.34 3.55
2603 8779 7.173722 AGGAGATTAAATATGGAAGCTCATGG 58.826 38.462 13.94 0.00 39.34 3.66
2604 8780 7.336427 GGAGGAGATTAAATATGGAAGCTCATG 59.664 40.741 13.94 0.00 39.34 3.07
2632 8808 4.776322 CGGGAGTGCCGCCATGAA 62.776 66.667 11.14 0.00 33.83 2.57
2640 8816 4.329545 TCCTTGTGCGGGAGTGCC 62.330 66.667 0.00 0.00 0.00 5.01
2641 8817 2.743928 CTCCTTGTGCGGGAGTGC 60.744 66.667 0.00 0.00 43.77 4.40
2645 8821 0.250295 CAACTTCTCCTTGTGCGGGA 60.250 55.000 0.00 0.00 0.00 5.14
2646 8822 0.250295 TCAACTTCTCCTTGTGCGGG 60.250 55.000 0.00 0.00 0.00 6.13
2647 8823 1.151668 CTCAACTTCTCCTTGTGCGG 58.848 55.000 0.00 0.00 0.00 5.69
2648 8824 1.151668 CCTCAACTTCTCCTTGTGCG 58.848 55.000 0.00 0.00 0.00 5.34
2649 8825 0.877743 GCCTCAACTTCTCCTTGTGC 59.122 55.000 0.00 0.00 0.00 4.57
2653 8829 0.695347 CTGGGCCTCAACTTCTCCTT 59.305 55.000 4.53 0.00 0.00 3.36
2671 8847 2.435693 GGCTACATCCGGCACCTCT 61.436 63.158 0.00 0.00 0.00 3.69
2672 8848 2.109181 GGCTACATCCGGCACCTC 59.891 66.667 0.00 0.00 0.00 3.85
2673 8849 3.480133 GGGCTACATCCGGCACCT 61.480 66.667 0.00 0.00 0.00 4.00
2674 8850 2.552231 AAAGGGCTACATCCGGCACC 62.552 60.000 0.00 0.00 31.31 5.01
2675 8851 0.679960 AAAAGGGCTACATCCGGCAC 60.680 55.000 0.00 0.00 0.00 5.01
2676 8852 0.679640 CAAAAGGGCTACATCCGGCA 60.680 55.000 0.00 0.00 0.00 5.69
2677 8853 2.004808 GCAAAAGGGCTACATCCGGC 62.005 60.000 0.00 0.00 0.00 6.13
2678 8854 1.384222 GGCAAAAGGGCTACATCCGG 61.384 60.000 0.00 0.00 39.42 5.14
2679 8855 0.679640 TGGCAAAAGGGCTACATCCG 60.680 55.000 0.00 0.00 43.83 4.18
2680 8856 1.780503 ATGGCAAAAGGGCTACATCC 58.219 50.000 0.00 0.00 43.83 3.51
2681 8857 3.893326 AAATGGCAAAAGGGCTACATC 57.107 42.857 0.00 0.00 43.83 3.06
2682 8858 3.132824 GCTAAATGGCAAAAGGGCTACAT 59.867 43.478 0.00 0.00 43.83 2.29
2683 8859 2.495669 GCTAAATGGCAAAAGGGCTACA 59.504 45.455 0.00 0.00 43.83 2.74
2684 8860 2.495669 TGCTAAATGGCAAAAGGGCTAC 59.504 45.455 0.00 0.00 43.83 3.58
2685 8861 2.495669 GTGCTAAATGGCAAAAGGGCTA 59.504 45.455 0.00 0.00 44.18 3.93
2686 8862 1.276138 GTGCTAAATGGCAAAAGGGCT 59.724 47.619 0.00 0.00 44.18 5.19
2687 8863 1.001860 TGTGCTAAATGGCAAAAGGGC 59.998 47.619 0.00 0.00 44.18 5.19
2688 8864 3.615224 ATGTGCTAAATGGCAAAAGGG 57.385 42.857 0.00 0.00 44.18 3.95
2689 8865 4.104776 CGTATGTGCTAAATGGCAAAAGG 58.895 43.478 0.00 0.00 44.18 3.11
2690 8866 4.732784 ACGTATGTGCTAAATGGCAAAAG 58.267 39.130 0.00 0.00 44.18 2.27
2691 8867 4.775058 ACGTATGTGCTAAATGGCAAAA 57.225 36.364 0.00 0.00 44.18 2.44
2692 8868 5.675071 GCTTACGTATGTGCTAAATGGCAAA 60.675 40.000 9.88 0.00 44.18 3.68
2693 8869 4.201871 GCTTACGTATGTGCTAAATGGCAA 60.202 41.667 9.88 0.00 44.18 4.52
2694 8870 3.311322 GCTTACGTATGTGCTAAATGGCA 59.689 43.478 9.88 0.00 40.15 4.92
2695 8871 3.560068 AGCTTACGTATGTGCTAAATGGC 59.440 43.478 13.96 0.00 33.64 4.40
2696 8872 5.734855 AAGCTTACGTATGTGCTAAATGG 57.265 39.130 15.31 0.00 35.09 3.16
2697 8873 5.965334 CCAAAGCTTACGTATGTGCTAAATG 59.035 40.000 15.31 14.01 35.09 2.32
2698 8874 5.448632 GCCAAAGCTTACGTATGTGCTAAAT 60.449 40.000 15.31 6.02 35.09 1.40
2699 8875 4.142773 GCCAAAGCTTACGTATGTGCTAAA 60.143 41.667 15.31 0.00 35.09 1.85
2700 8876 3.372822 GCCAAAGCTTACGTATGTGCTAA 59.627 43.478 15.31 0.00 35.09 3.09
2701 8877 2.933906 GCCAAAGCTTACGTATGTGCTA 59.066 45.455 15.31 0.00 35.09 3.49
2702 8878 1.737793 GCCAAAGCTTACGTATGTGCT 59.262 47.619 0.00 10.47 37.37 4.40
2703 8879 1.529010 CGCCAAAGCTTACGTATGTGC 60.529 52.381 0.00 8.56 36.60 4.57
2704 8880 1.996898 TCGCCAAAGCTTACGTATGTG 59.003 47.619 0.00 0.00 36.60 3.21
2705 8881 1.997606 GTCGCCAAAGCTTACGTATGT 59.002 47.619 0.00 0.00 36.60 2.29
2706 8882 1.326548 GGTCGCCAAAGCTTACGTATG 59.673 52.381 0.00 0.00 36.60 2.39
2707 8883 1.206371 AGGTCGCCAAAGCTTACGTAT 59.794 47.619 0.00 0.00 36.60 3.06
2708 8884 0.604578 AGGTCGCCAAAGCTTACGTA 59.395 50.000 0.00 0.00 36.60 3.57
2709 8885 0.604578 TAGGTCGCCAAAGCTTACGT 59.395 50.000 0.00 0.00 36.60 3.57
2710 8886 1.659098 CTTAGGTCGCCAAAGCTTACG 59.341 52.381 0.00 4.63 36.60 3.18
2711 8887 2.696506 ACTTAGGTCGCCAAAGCTTAC 58.303 47.619 0.00 0.00 36.60 2.34
2712 8888 3.412237 AACTTAGGTCGCCAAAGCTTA 57.588 42.857 0.00 0.00 36.60 3.09
2713 8889 2.271944 AACTTAGGTCGCCAAAGCTT 57.728 45.000 0.00 0.00 36.60 3.74
2714 8890 2.565834 TCTAACTTAGGTCGCCAAAGCT 59.434 45.455 0.00 0.00 36.60 3.74
2715 8891 2.671888 GTCTAACTTAGGTCGCCAAAGC 59.328 50.000 0.00 0.00 0.00 3.51
2716 8892 3.259902 GGTCTAACTTAGGTCGCCAAAG 58.740 50.000 0.00 0.00 0.00 2.77
2717 8893 2.027837 GGGTCTAACTTAGGTCGCCAAA 60.028 50.000 0.00 0.00 0.00 3.28
2718 8894 1.551883 GGGTCTAACTTAGGTCGCCAA 59.448 52.381 0.00 0.00 0.00 4.52
2719 8895 1.188863 GGGTCTAACTTAGGTCGCCA 58.811 55.000 0.00 0.00 0.00 5.69
2720 8896 1.136500 CAGGGTCTAACTTAGGTCGCC 59.864 57.143 0.00 0.00 0.00 5.54
2721 8897 2.097825 TCAGGGTCTAACTTAGGTCGC 58.902 52.381 0.00 0.11 0.00 5.19
2722 8898 4.401519 TGATTCAGGGTCTAACTTAGGTCG 59.598 45.833 0.00 0.00 0.00 4.79
2723 8899 5.934402 TGATTCAGGGTCTAACTTAGGTC 57.066 43.478 0.00 0.00 0.00 3.85
2724 8900 5.726793 ACATGATTCAGGGTCTAACTTAGGT 59.273 40.000 0.00 0.00 0.00 3.08
2725 8901 6.127054 TGACATGATTCAGGGTCTAACTTAGG 60.127 42.308 17.20 0.00 0.00 2.69
2726 8902 6.878317 TGACATGATTCAGGGTCTAACTTAG 58.122 40.000 17.20 0.00 0.00 2.18
2727 8903 6.867519 TGACATGATTCAGGGTCTAACTTA 57.132 37.500 17.20 0.25 0.00 2.24
2728 8904 5.762179 TGACATGATTCAGGGTCTAACTT 57.238 39.130 17.20 0.00 0.00 2.66
2729 8905 5.013079 TGTTGACATGATTCAGGGTCTAACT 59.987 40.000 17.20 0.00 0.00 2.24
2730 8906 5.245531 TGTTGACATGATTCAGGGTCTAAC 58.754 41.667 17.20 17.42 0.00 2.34
2731 8907 5.497464 TGTTGACATGATTCAGGGTCTAA 57.503 39.130 17.20 10.18 0.00 2.10
2732 8908 5.426509 AGATGTTGACATGATTCAGGGTCTA 59.573 40.000 17.20 10.35 36.57 2.59
2733 8909 4.226846 AGATGTTGACATGATTCAGGGTCT 59.773 41.667 17.20 0.00 36.57 3.85
2734 8910 4.334759 CAGATGTTGACATGATTCAGGGTC 59.665 45.833 0.00 12.10 36.57 4.46
2735 8911 4.263639 ACAGATGTTGACATGATTCAGGGT 60.264 41.667 0.00 0.00 36.57 4.34
2736 8912 4.095932 CACAGATGTTGACATGATTCAGGG 59.904 45.833 0.00 0.00 36.57 4.45
2737 8913 4.698780 ACACAGATGTTGACATGATTCAGG 59.301 41.667 0.00 0.00 34.46 3.86
2738 8914 5.163784 GGACACAGATGTTGACATGATTCAG 60.164 44.000 0.00 0.00 39.95 3.02
2739 8915 4.696877 GGACACAGATGTTGACATGATTCA 59.303 41.667 0.00 0.00 39.95 2.57
2740 8916 4.940046 AGGACACAGATGTTGACATGATTC 59.060 41.667 0.00 0.00 39.95 2.52
2741 8917 4.914983 AGGACACAGATGTTGACATGATT 58.085 39.130 0.00 0.00 39.95 2.57
2742 8918 4.564782 AGGACACAGATGTTGACATGAT 57.435 40.909 0.00 0.00 39.95 2.45
2743 8919 4.356405 AAGGACACAGATGTTGACATGA 57.644 40.909 0.00 0.00 39.95 3.07
2744 8920 5.240183 AGAAAAGGACACAGATGTTGACATG 59.760 40.000 0.57 0.00 39.95 3.21
2745 8921 5.380043 AGAAAAGGACACAGATGTTGACAT 58.620 37.500 0.00 0.00 39.95 3.06
2746 8922 4.780815 AGAAAAGGACACAGATGTTGACA 58.219 39.130 0.00 0.00 39.95 3.58
2747 8923 5.757850 AAGAAAAGGACACAGATGTTGAC 57.242 39.130 0.00 0.00 39.95 3.18
2748 8924 6.773976 AAAAGAAAAGGACACAGATGTTGA 57.226 33.333 0.00 0.00 39.95 3.18
2749 8925 7.707104 AGTAAAAGAAAAGGACACAGATGTTG 58.293 34.615 0.00 0.00 39.95 3.33
2750 8926 7.881775 AGTAAAAGAAAAGGACACAGATGTT 57.118 32.000 0.00 0.00 39.95 2.71
2751 8927 7.444487 GGTAGTAAAAGAAAAGGACACAGATGT 59.556 37.037 0.00 0.00 43.71 3.06
2752 8928 7.661847 AGGTAGTAAAAGAAAAGGACACAGATG 59.338 37.037 0.00 0.00 0.00 2.90
2753 8929 7.746703 AGGTAGTAAAAGAAAAGGACACAGAT 58.253 34.615 0.00 0.00 0.00 2.90
2754 8930 7.133133 AGGTAGTAAAAGAAAAGGACACAGA 57.867 36.000 0.00 0.00 0.00 3.41
2755 8931 8.897872 TTAGGTAGTAAAAGAAAAGGACACAG 57.102 34.615 0.00 0.00 0.00 3.66
2756 8932 9.683870 TTTTAGGTAGTAAAAGAAAAGGACACA 57.316 29.630 0.00 0.00 35.97 3.72
2787 8963 3.679389 TCCTCAACAAAGAGATTGCCTC 58.321 45.455 0.00 0.00 43.13 4.70
2788 8964 3.795688 TCCTCAACAAAGAGATTGCCT 57.204 42.857 0.00 0.00 43.13 4.75
2789 8965 4.853924 TTTCCTCAACAAAGAGATTGCC 57.146 40.909 0.00 0.00 43.13 4.52
2851 9027 0.890996 CGCCTGGCCTGACTCTTTTT 60.891 55.000 14.12 0.00 0.00 1.94
2852 9028 1.302832 CGCCTGGCCTGACTCTTTT 60.303 57.895 14.12 0.00 0.00 2.27
2853 9029 2.177594 CTCGCCTGGCCTGACTCTTT 62.178 60.000 14.12 0.00 0.00 2.52
2854 9030 2.604686 TCGCCTGGCCTGACTCTT 60.605 61.111 14.12 0.00 0.00 2.85
2855 9031 3.073735 CTCGCCTGGCCTGACTCT 61.074 66.667 14.12 0.00 0.00 3.24
2856 9032 4.828925 GCTCGCCTGGCCTGACTC 62.829 72.222 14.12 0.00 0.00 3.36
2869 9045 4.717629 TGTTCCAGTCGGCGCTCG 62.718 66.667 7.64 9.90 40.90 5.03
2873 9049 0.600255 AAGTCTTGTTCCAGTCGGCG 60.600 55.000 0.00 0.00 0.00 6.46
2885 9061 5.817816 GTGATACCCTACATGGAAAGTCTTG 59.182 44.000 0.00 0.00 38.35 3.02
2896 9072 7.200434 ACTTCTTCAATGTGATACCCTACAT 57.800 36.000 0.00 0.00 39.08 2.29
2901 9077 6.170506 TGTGTACTTCTTCAATGTGATACCC 58.829 40.000 0.00 0.00 0.00 3.69
2907 9083 6.128172 GGAAGGATGTGTACTTCTTCAATGTG 60.128 42.308 4.52 0.00 43.63 3.21
2909 9085 5.939883 TGGAAGGATGTGTACTTCTTCAATG 59.060 40.000 4.52 0.00 43.63 2.82
2910 9086 6.126863 TGGAAGGATGTGTACTTCTTCAAT 57.873 37.500 4.52 0.00 43.63 2.57
2962 9139 1.214673 TGAGTAGGCTGAGATACCGGT 59.785 52.381 13.98 13.98 0.00 5.28
2963 9140 1.982660 TGAGTAGGCTGAGATACCGG 58.017 55.000 0.00 0.00 0.00 5.28
2964 9141 4.038042 TGAATTGAGTAGGCTGAGATACCG 59.962 45.833 0.00 0.00 0.00 4.02
2979 9156 4.384846 GCTGACAAATGCTTGTGAATTGAG 59.615 41.667 0.00 0.00 45.98 3.02
3019 9200 2.157738 ACAAATGTCAAGCTCTGCCTC 58.842 47.619 0.00 0.00 0.00 4.70
3037 9218 0.036388 GAGGGAAATCACGGCTGACA 60.036 55.000 0.00 0.00 0.00 3.58
3041 9626 0.181350 GATGGAGGGAAATCACGGCT 59.819 55.000 0.00 0.00 0.00 5.52
3130 9724 5.475719 TGTACAAGGTAGTCCAATTCTTCG 58.524 41.667 0.00 0.00 35.89 3.79
3137 9731 4.260985 CATGCATGTACAAGGTAGTCCAA 58.739 43.478 18.91 0.00 35.89 3.53
3175 9769 2.044451 CCCCATTGCGTTAGGCCA 60.044 61.111 5.01 0.00 42.61 5.36
3184 9778 2.994417 TTCCCAACGCCCCATTGC 60.994 61.111 0.00 0.00 0.00 3.56
3258 9858 1.579964 GGCGTACCTTTTCAACCCCG 61.580 60.000 0.00 0.00 0.00 5.73
3282 9882 1.961277 GTGCTTGTCCCCACAGACG 60.961 63.158 0.00 0.00 39.77 4.18


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

AutoCloner maintained by Alex Coulton.