Multiple sequence alignment - TraesCS5B01G497600

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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 TraesCS5B01G497600 chr5B 100.000 3632 0 0 1 3632 664505503 664501872 0.000000e+00 6708.0
1 TraesCS5B01G497600 chr5B 91.071 1064 65 13 1701 2734 664475509 664474446 0.000000e+00 1411.0
2 TraesCS5B01G497600 chr5B 90.289 1071 67 14 1701 2734 664417090 664416020 0.000000e+00 1367.0
3 TraesCS5B01G497600 chr5B 92.800 750 44 1 1 750 592804730 592805469 0.000000e+00 1077.0
4 TraesCS5B01G497600 chr5B 91.763 607 21 11 1 606 210251667 210251089 0.000000e+00 817.0
5 TraesCS5B01G497600 chr5B 84.559 408 50 12 874 1271 664417606 664417202 3.400000e-105 392.0
6 TraesCS5B01G497600 chr5B 84.483 406 54 8 874 1271 664476025 664475621 3.400000e-105 392.0
7 TraesCS5B01G497600 chr5B 93.590 156 10 0 596 751 210250713 210250558 2.180000e-57 233.0
8 TraesCS5B01G497600 chr5B 82.353 153 26 1 587 738 15851258 15851410 8.180000e-27 132.0
9 TraesCS5B01G497600 chr3D 87.383 1490 116 34 1536 2970 2968872 2967400 0.000000e+00 1644.0
10 TraesCS5B01G497600 chr3D 92.857 168 8 3 3256 3423 2967326 2967163 1.300000e-59 241.0
11 TraesCS5B01G497600 chr3B 84.994 1586 141 48 1461 2970 2878579 2880143 0.000000e+00 1520.0
12 TraesCS5B01G497600 chr3B 84.752 282 31 6 1013 1290 2878147 2878420 4.620000e-69 272.0
13 TraesCS5B01G497600 chr3B 87.629 97 8 2 3117 3212 2880138 2880231 3.830000e-20 110.0
14 TraesCS5B01G497600 chr5A 92.564 1049 61 7 1686 2719 655189372 655188326 0.000000e+00 1489.0
15 TraesCS5B01G497600 chr5A 92.469 1049 62 7 1686 2719 655225534 655224488 0.000000e+00 1483.0
16 TraesCS5B01G497600 chr5A 91.742 775 49 8 1699 2458 654851791 654851017 0.000000e+00 1062.0
17 TraesCS5B01G497600 chr5A 87.993 558 45 12 752 1289 655226602 655226047 1.100000e-179 640.0
18 TraesCS5B01G497600 chr5A 88.462 286 22 8 3276 3558 655187901 655187624 5.810000e-88 335.0
19 TraesCS5B01G497600 chr5A 88.462 286 22 8 3276 3558 655224063 655223786 5.810000e-88 335.0
20 TraesCS5B01G497600 chr5A 83.750 240 18 11 3274 3511 654850323 654850103 1.320000e-49 207.0
21 TraesCS5B01G497600 chr5A 81.319 273 18 14 3157 3426 654849617 654849375 1.330000e-44 191.0
22 TraesCS5B01G497600 chr5A 85.057 87 11 1 3070 3156 705832929 705832845 1.800000e-13 87.9
23 TraesCS5B01G497600 chr5D 95.466 772 20 10 2088 2846 527841873 527841104 0.000000e+00 1218.0
24 TraesCS5B01G497600 chr5D 92.619 691 23 11 1353 2016 527842541 527841852 0.000000e+00 968.0
25 TraesCS5B01G497600 chr5D 93.974 531 31 1 764 1293 527843150 527842620 0.000000e+00 802.0
26 TraesCS5B01G497600 chr5D 95.000 80 3 1 3554 3632 527841112 527841033 1.370000e-24 124.0
27 TraesCS5B01G497600 chr7D 88.723 1002 87 17 1725 2710 401550930 401549939 0.000000e+00 1201.0
28 TraesCS5B01G497600 chr7D 81.667 300 43 10 995 1292 401552032 401551743 4.690000e-59 239.0
29 TraesCS5B01G497600 chr7A 87.984 982 89 21 1728 2683 459210151 459209173 0.000000e+00 1133.0
30 TraesCS5B01G497600 chr7A 84.444 225 35 0 999 1223 459211268 459211044 4.720000e-54 222.0
31 TraesCS5B01G497600 chr7B 95.721 444 19 0 1 444 616524144 616524587 0.000000e+00 715.0
32 TraesCS5B01G497600 chr7B 97.411 309 8 0 442 750 616532489 616532797 8.930000e-146 527.0
33 TraesCS5B01G497600 chr7B 79.305 604 84 21 150 751 583152641 583152077 5.690000e-103 385.0
34 TraesCS5B01G497600 chr7B 95.706 163 7 0 1 163 524051016 524051178 2.780000e-66 263.0
35 TraesCS5B01G497600 chr7B 85.590 229 32 1 996 1223 411061059 411060831 4.690000e-59 239.0
36 TraesCS5B01G497600 chr7B 90.909 88 7 1 3070 3156 211795496 211795409 2.290000e-22 117.0
37 TraesCS5B01G497600 chr7B 80.412 97 14 3 3070 3165 726345511 726345603 6.510000e-08 69.4
38 TraesCS5B01G497600 chr6D 87.206 383 45 4 1 381 186979844 186979464 2.000000e-117 433.0
39 TraesCS5B01G497600 chr6D 80.802 349 47 5 420 750 186979459 186979113 4.650000e-64 255.0
40 TraesCS5B01G497600 chr6B 79.104 603 84 14 150 750 233089773 233089211 9.520000e-101 377.0
41 TraesCS5B01G497600 chr6B 82.171 258 36 5 129 377 46008456 46008712 2.840000e-51 213.0
42 TraesCS5B01G497600 chr6B 84.444 90 14 0 3070 3159 284652742 284652653 5.000000e-14 89.8
43 TraesCS5B01G497600 chrUn 96.341 164 6 0 1 164 292093469 292093306 1.660000e-68 270.0
44 TraesCS5B01G497600 chrUn 88.333 180 18 2 21 198 455937759 455937581 2.840000e-51 213.0
45 TraesCS5B01G497600 chrUn 86.905 84 9 1 3070 3153 108358349 108358430 3.860000e-15 93.5
46 TraesCS5B01G497600 chrUn 100.000 28 0 0 3125 3152 39276719 39276746 7.000000e-03 52.8
47 TraesCS5B01G497600 chr4A 88.333 180 18 2 21 198 514808174 514807996 2.840000e-51 213.0
48 TraesCS5B01G497600 chr4B 87.778 180 19 2 21 198 190167567 190167745 1.320000e-49 207.0
49 TraesCS5B01G497600 chr1B 83.333 228 34 3 995 1221 628221203 628221427 1.320000e-49 207.0
50 TraesCS5B01G497600 chr2B 82.781 151 24 2 587 736 655594475 655594624 2.280000e-27 134.0
51 TraesCS5B01G497600 chr4D 81.699 153 27 1 599 750 126767371 126767523 3.810000e-25 126.0
52 TraesCS5B01G497600 chr6A 90.698 86 8 0 3070 3155 572166251 572166166 8.240000e-22 115.0


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 TraesCS5B01G497600 chr5B 664501872 664505503 3631 True 6708.000000 6708 100.000000 1 3632 1 chr5B.!!$R1 3631
1 TraesCS5B01G497600 chr5B 592804730 592805469 739 False 1077.000000 1077 92.800000 1 750 1 chr5B.!!$F2 749
2 TraesCS5B01G497600 chr5B 664474446 664476025 1579 True 901.500000 1411 87.777000 874 2734 2 chr5B.!!$R4 1860
3 TraesCS5B01G497600 chr5B 664416020 664417606 1586 True 879.500000 1367 87.424000 874 2734 2 chr5B.!!$R3 1860
4 TraesCS5B01G497600 chr5B 210250558 210251667 1109 True 525.000000 817 92.676500 1 751 2 chr5B.!!$R2 750
5 TraesCS5B01G497600 chr3D 2967163 2968872 1709 True 942.500000 1644 90.120000 1536 3423 2 chr3D.!!$R1 1887
6 TraesCS5B01G497600 chr3B 2878147 2880231 2084 False 634.000000 1520 85.791667 1013 3212 3 chr3B.!!$F1 2199
7 TraesCS5B01G497600 chr5A 655187624 655189372 1748 True 912.000000 1489 90.513000 1686 3558 2 chr5A.!!$R3 1872
8 TraesCS5B01G497600 chr5A 655223786 655226602 2816 True 819.333333 1483 89.641333 752 3558 3 chr5A.!!$R4 2806
9 TraesCS5B01G497600 chr5A 654849375 654851791 2416 True 486.666667 1062 85.603667 1699 3511 3 chr5A.!!$R2 1812
10 TraesCS5B01G497600 chr5D 527841033 527843150 2117 True 778.000000 1218 94.264750 764 3632 4 chr5D.!!$R1 2868
11 TraesCS5B01G497600 chr7D 401549939 401552032 2093 True 720.000000 1201 85.195000 995 2710 2 chr7D.!!$R1 1715
12 TraesCS5B01G497600 chr7A 459209173 459211268 2095 True 677.500000 1133 86.214000 999 2683 2 chr7A.!!$R1 1684
13 TraesCS5B01G497600 chr7B 583152077 583152641 564 True 385.000000 385 79.305000 150 751 1 chr7B.!!$R3 601
14 TraesCS5B01G497600 chr6D 186979113 186979844 731 True 344.000000 433 84.004000 1 750 2 chr6D.!!$R1 749
15 TraesCS5B01G497600 chr6B 233089211 233089773 562 True 377.000000 377 79.104000 150 750 1 chr6B.!!$R1 600

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
641 1065 0.248054 CGTGCGCGCAAGGAATAAAT 60.248 50.0 38.24 0.0 38.28 1.40 F
1304 1766 0.028902 GCATCCGGACGTTTATTGCC 59.971 55.0 6.12 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 3244 1.522580 GAGGATGCCAGCGGACTTC 60.523 63.158 0.00 0.0 0.00 3.01 R
2984 4394 0.605319 TCGACGGCTCCAAGCAAAAT 60.605 50.000 0.86 0.0 44.75 1.82 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
146 147 2.656002 TGGATTTTGTTGGAACCGTCA 58.344 42.857 0.00 0.00 0.00 4.35
148 149 3.639094 TGGATTTTGTTGGAACCGTCATT 59.361 39.130 0.00 0.00 0.00 2.57
165 166 5.218885 CGTCATTGATTTTTGCTACAACCA 58.781 37.500 0.00 0.00 0.00 3.67
167 168 6.446318 GTCATTGATTTTTGCTACAACCAGA 58.554 36.000 0.00 0.00 0.00 3.86
188 189 5.399301 CAGAAAATGTTTTTGCTACGTCCAG 59.601 40.000 0.00 0.00 28.98 3.86
451 459 3.209410 ACGGGATCTGCATCAGAAATTC 58.791 45.455 0.27 0.00 44.04 2.17
641 1065 0.248054 CGTGCGCGCAAGGAATAAAT 60.248 50.000 38.24 0.00 38.28 1.40
653 1077 5.448654 CAAGGAATAAATGAGTGGGGATGA 58.551 41.667 0.00 0.00 0.00 2.92
689 1113 0.521735 GGTTTCCACACTTCGCATCC 59.478 55.000 0.00 0.00 0.00 3.51
695 1119 1.596752 ACACTTCGCATCCAACGCA 60.597 52.632 0.00 0.00 0.00 5.24
751 1175 2.126071 GCGCAGAGTACTCGCCAA 60.126 61.111 24.20 0.00 42.71 4.52
752 1176 1.736645 GCGCAGAGTACTCGCCAAA 60.737 57.895 24.20 0.00 42.71 3.28
753 1177 1.289109 GCGCAGAGTACTCGCCAAAA 61.289 55.000 24.20 0.00 42.71 2.44
754 1178 1.144969 CGCAGAGTACTCGCCAAAAA 58.855 50.000 24.20 0.00 34.09 1.94
817 1242 0.249741 CTAGCGGATTGTAACGGGGG 60.250 60.000 0.00 0.00 0.00 5.40
872 1297 9.232473 GGATAAGAACTCTTTACCAACAAGATT 57.768 33.333 0.00 0.00 37.40 2.40
903 1331 2.115266 CCAAGCCAAACCTCCCGT 59.885 61.111 0.00 0.00 0.00 5.28
955 1387 4.202346 CCCAACTTCCAATCCAACAAACAT 60.202 41.667 0.00 0.00 0.00 2.71
1027 1484 3.679389 CCTCTTGGTGATACTGTTGCTT 58.321 45.455 0.00 0.00 0.00 3.91
1036 1493 0.764890 TACTGTTGCTTCTGTGGCCT 59.235 50.000 3.32 0.00 0.00 5.19
1038 1495 1.572085 CTGTTGCTTCTGTGGCCTCG 61.572 60.000 3.32 0.00 0.00 4.63
1234 1695 1.412710 AGGTACGCATGGATCAATCGT 59.587 47.619 10.89 10.89 37.19 3.73
1261 1722 5.243730 TCCGTGATAGCACATGATGATTCTA 59.756 40.000 12.28 0.00 45.41 2.10
1293 1755 1.680735 GTTTATTGCCATGCATCCGGA 59.319 47.619 6.61 6.61 38.76 5.14
1294 1756 1.317613 TTATTGCCATGCATCCGGAC 58.682 50.000 6.12 0.00 38.76 4.79
1295 1757 0.884259 TATTGCCATGCATCCGGACG 60.884 55.000 6.12 0.00 38.76 4.79
1296 1758 2.891941 ATTGCCATGCATCCGGACGT 62.892 55.000 6.12 0.00 38.76 4.34
1297 1759 2.824041 GCCATGCATCCGGACGTT 60.824 61.111 6.12 0.00 0.00 3.99
1298 1760 2.406616 GCCATGCATCCGGACGTTT 61.407 57.895 6.12 0.00 0.00 3.60
1299 1761 1.092921 GCCATGCATCCGGACGTTTA 61.093 55.000 6.12 0.00 0.00 2.01
1300 1762 1.593196 CCATGCATCCGGACGTTTAT 58.407 50.000 6.12 0.00 0.00 1.40
1301 1763 1.946768 CCATGCATCCGGACGTTTATT 59.053 47.619 6.12 0.00 0.00 1.40
1302 1764 2.286950 CCATGCATCCGGACGTTTATTG 60.287 50.000 6.12 0.00 0.00 1.90
1303 1765 0.730265 TGCATCCGGACGTTTATTGC 59.270 50.000 6.12 12.15 0.00 3.56
1304 1766 0.028902 GCATCCGGACGTTTATTGCC 59.971 55.000 6.12 0.00 0.00 4.52
1305 1767 1.374560 CATCCGGACGTTTATTGCCA 58.625 50.000 6.12 0.00 0.00 4.92
1306 1768 1.946768 CATCCGGACGTTTATTGCCAT 59.053 47.619 6.12 0.00 0.00 4.40
1307 1769 1.374560 TCCGGACGTTTATTGCCATG 58.625 50.000 0.00 0.00 0.00 3.66
1308 1770 0.248458 CCGGACGTTTATTGCCATGC 60.248 55.000 0.00 0.00 0.00 4.06
1309 1771 0.449786 CGGACGTTTATTGCCATGCA 59.550 50.000 0.00 0.00 36.47 3.96
1310 1772 1.065401 CGGACGTTTATTGCCATGCAT 59.935 47.619 0.00 0.00 38.76 3.96
1311 1773 2.731217 GGACGTTTATTGCCATGCATC 58.269 47.619 0.00 0.00 38.76 3.91
1346 1808 0.725117 GATCCGTTGTTTGGTAGGCG 59.275 55.000 0.00 0.00 0.00 5.52
1351 1813 0.948678 GTTGTTTGGTAGGCGCTGAA 59.051 50.000 7.64 0.00 0.00 3.02
1355 1817 0.107831 TTTGGTAGGCGCTGAACTGT 59.892 50.000 7.64 0.00 0.00 3.55
1356 1818 0.320421 TTGGTAGGCGCTGAACTGTC 60.320 55.000 7.64 0.00 0.00 3.51
1358 1820 1.805945 GTAGGCGCTGAACTGTCCG 60.806 63.158 7.64 0.00 0.00 4.79
1723 2833 6.426633 TCGCATATGAAATTGTAATCGGATGT 59.573 34.615 6.97 0.00 0.00 3.06
1730 2842 7.249858 TGAAATTGTAATCGGATGTTGATGTG 58.750 34.615 0.00 0.00 0.00 3.21
1898 3015 0.687920 TCATGTTCTACCGCAACCCA 59.312 50.000 0.00 0.00 0.00 4.51
2183 3394 2.840753 GGTGGCCTTCCTCACCCAA 61.841 63.158 3.32 0.00 45.60 4.12
2336 3547 1.227147 CAACACGGTCGACACCACT 60.227 57.895 18.91 0.00 44.02 4.00
2757 4079 3.873910 TGTGTAATTAAGGAGGCTGCTC 58.126 45.455 9.62 0.00 0.00 4.26
2759 4081 3.873952 GTGTAATTAAGGAGGCTGCTCAG 59.126 47.826 9.62 0.00 0.00 3.35
2846 4194 7.602517 AGAACATGCTCTACAAGATGTTTAC 57.397 36.000 0.00 0.00 36.61 2.01
2847 4195 6.595716 AGAACATGCTCTACAAGATGTTTACC 59.404 38.462 0.00 0.00 36.61 2.85
2848 4196 5.186198 ACATGCTCTACAAGATGTTTACCC 58.814 41.667 0.00 0.00 0.00 3.69
2849 4197 5.045578 ACATGCTCTACAAGATGTTTACCCT 60.046 40.000 0.00 0.00 0.00 4.34
2850 4198 4.832248 TGCTCTACAAGATGTTTACCCTG 58.168 43.478 0.00 0.00 0.00 4.45
2851 4199 4.192317 GCTCTACAAGATGTTTACCCTGG 58.808 47.826 0.00 0.00 0.00 4.45
2853 4201 5.803470 GCTCTACAAGATGTTTACCCTGGTT 60.803 44.000 0.00 0.00 0.00 3.67
2875 4284 6.703165 GGTTTAGAGTTTGTTTTCTAGTCGGA 59.297 38.462 0.00 0.00 0.00 4.55
2876 4285 7.387122 GGTTTAGAGTTTGTTTTCTAGTCGGAT 59.613 37.037 0.00 0.00 0.00 4.18
2877 4286 9.415544 GTTTAGAGTTTGTTTTCTAGTCGGATA 57.584 33.333 0.00 0.00 0.00 2.59
2878 4287 9.985730 TTTAGAGTTTGTTTTCTAGTCGGATAA 57.014 29.630 0.00 0.00 0.00 1.75
2925 4335 5.180117 TCTTGCTCTAAGTTTCAACATCAGC 59.820 40.000 0.00 0.00 37.65 4.26
2948 4358 5.679638 GCAATGATTTTATTCCTCTTGGCGT 60.680 40.000 0.00 0.00 0.00 5.68
2960 4370 2.824071 CTTGGCGTTTGCATCAGGCC 62.824 60.000 18.73 18.73 45.35 5.19
2966 4376 1.539388 CGTTTGCATCAGGCCTGTTTA 59.461 47.619 31.58 14.17 43.89 2.01
2967 4377 2.030363 CGTTTGCATCAGGCCTGTTTAA 60.030 45.455 31.58 18.90 43.89 1.52
2968 4378 3.551863 CGTTTGCATCAGGCCTGTTTAAA 60.552 43.478 31.58 22.86 43.89 1.52
2969 4379 4.568956 GTTTGCATCAGGCCTGTTTAAAT 58.431 39.130 31.58 15.18 43.89 1.40
2970 4380 4.888326 TTGCATCAGGCCTGTTTAAATT 57.112 36.364 31.58 7.00 43.89 1.82
2971 4381 4.454728 TGCATCAGGCCTGTTTAAATTC 57.545 40.909 31.58 12.83 43.89 2.17
2972 4382 3.831333 TGCATCAGGCCTGTTTAAATTCA 59.169 39.130 31.58 15.30 43.89 2.57
2973 4383 4.467082 TGCATCAGGCCTGTTTAAATTCAT 59.533 37.500 31.58 12.14 43.89 2.57
2974 4384 5.655974 TGCATCAGGCCTGTTTAAATTCATA 59.344 36.000 31.58 8.78 43.89 2.15
2975 4385 6.154192 TGCATCAGGCCTGTTTAAATTCATAA 59.846 34.615 31.58 8.56 43.89 1.90
2976 4386 7.147689 TGCATCAGGCCTGTTTAAATTCATAAT 60.148 33.333 31.58 10.63 43.89 1.28
2977 4387 7.712205 GCATCAGGCCTGTTTAAATTCATAATT 59.288 33.333 31.58 0.00 36.11 1.40
2978 4388 9.037737 CATCAGGCCTGTTTAAATTCATAATTG 57.962 33.333 31.58 0.76 0.00 2.32
2979 4389 8.359875 TCAGGCCTGTTTAAATTCATAATTGA 57.640 30.769 31.58 3.46 0.00 2.57
2980 4390 8.250332 TCAGGCCTGTTTAAATTCATAATTGAC 58.750 33.333 31.58 0.00 0.00 3.18
2981 4391 8.253113 CAGGCCTGTTTAAATTCATAATTGACT 58.747 33.333 25.53 0.00 0.00 3.41
2982 4392 8.815912 AGGCCTGTTTAAATTCATAATTGACTT 58.184 29.630 3.11 0.00 0.00 3.01
2983 4393 9.435688 GGCCTGTTTAAATTCATAATTGACTTT 57.564 29.630 0.00 0.00 38.08 2.66
3008 4418 1.811266 CTTGGAGCCGTCGACCATG 60.811 63.158 10.58 0.17 33.56 3.66
3012 4422 1.736586 GAGCCGTCGACCATGAGAT 59.263 57.895 10.58 0.00 0.00 2.75
3015 4425 0.460284 GCCGTCGACCATGAGATTGT 60.460 55.000 10.58 0.00 0.00 2.71
3016 4426 1.202371 GCCGTCGACCATGAGATTGTA 60.202 52.381 10.58 0.00 0.00 2.41
3017 4427 2.737359 GCCGTCGACCATGAGATTGTAA 60.737 50.000 10.58 0.00 0.00 2.41
3019 4429 3.507786 CGTCGACCATGAGATTGTAACA 58.492 45.455 10.58 0.00 0.00 2.41
3021 4431 3.865745 GTCGACCATGAGATTGTAACAGG 59.134 47.826 3.51 0.00 0.00 4.00
3022 4432 3.513912 TCGACCATGAGATTGTAACAGGT 59.486 43.478 0.00 0.00 0.00 4.00
3023 4433 3.618594 CGACCATGAGATTGTAACAGGTG 59.381 47.826 0.00 0.00 0.00 4.00
3024 4434 3.941483 GACCATGAGATTGTAACAGGTGG 59.059 47.826 0.00 0.00 0.00 4.61
3029 4439 3.146066 GAGATTGTAACAGGTGGCACAA 58.854 45.455 20.82 3.26 44.16 3.33
3041 4451 4.174411 GGTGGCACAACTATCCTTTTTC 57.826 45.455 20.82 0.00 46.61 2.29
3042 4452 3.056821 GGTGGCACAACTATCCTTTTTCC 60.057 47.826 20.82 0.00 46.61 3.13
3043 4453 3.826729 GTGGCACAACTATCCTTTTTCCT 59.173 43.478 13.86 0.00 44.16 3.36
3044 4454 5.007682 GTGGCACAACTATCCTTTTTCCTA 58.992 41.667 13.86 0.00 44.16 2.94
3045 4455 5.652452 GTGGCACAACTATCCTTTTTCCTAT 59.348 40.000 13.86 0.00 44.16 2.57
3046 4456 5.652014 TGGCACAACTATCCTTTTTCCTATG 59.348 40.000 0.00 0.00 31.92 2.23
3047 4457 5.652452 GGCACAACTATCCTTTTTCCTATGT 59.348 40.000 0.00 0.00 0.00 2.29
3048 4458 6.183360 GGCACAACTATCCTTTTTCCTATGTC 60.183 42.308 0.00 0.00 0.00 3.06
3049 4459 6.456988 GCACAACTATCCTTTTTCCTATGTCG 60.457 42.308 0.00 0.00 0.00 4.35
3050 4460 6.816640 CACAACTATCCTTTTTCCTATGTCGA 59.183 38.462 0.00 0.00 0.00 4.20
3051 4461 7.333423 CACAACTATCCTTTTTCCTATGTCGAA 59.667 37.037 0.00 0.00 0.00 3.71
3052 4462 7.881232 ACAACTATCCTTTTTCCTATGTCGAAA 59.119 33.333 0.00 0.00 0.00 3.46
3053 4463 8.391106 CAACTATCCTTTTTCCTATGTCGAAAG 58.609 37.037 0.00 0.00 31.22 2.62
3054 4464 7.848128 ACTATCCTTTTTCCTATGTCGAAAGA 58.152 34.615 0.00 0.00 31.22 2.52
3055 4465 8.319146 ACTATCCTTTTTCCTATGTCGAAAGAA 58.681 33.333 0.00 0.00 45.01 2.52
3056 4466 7.996098 ATCCTTTTTCCTATGTCGAAAGAAA 57.004 32.000 0.00 0.00 45.01 2.52
3057 4467 7.811117 TCCTTTTTCCTATGTCGAAAGAAAA 57.189 32.000 0.00 0.00 45.01 2.29
3058 4468 8.228035 TCCTTTTTCCTATGTCGAAAGAAAAA 57.772 30.769 11.39 11.39 45.01 1.94
3212 4624 2.844348 TCCTGAATTAAGGTCCAGTCCC 59.156 50.000 8.84 0.00 38.58 4.46
3213 4625 2.092375 CCTGAATTAAGGTCCAGTCCCC 60.092 54.545 0.00 0.00 32.17 4.81
3214 4626 2.846827 CTGAATTAAGGTCCAGTCCCCT 59.153 50.000 0.00 0.00 0.00 4.79
3215 4627 3.265489 TGAATTAAGGTCCAGTCCCCTT 58.735 45.455 0.00 0.00 43.41 3.95
3216 4628 3.660669 TGAATTAAGGTCCAGTCCCCTTT 59.339 43.478 0.00 0.00 41.30 3.11
3217 4629 4.107311 TGAATTAAGGTCCAGTCCCCTTTT 59.893 41.667 0.00 0.00 41.30 2.27
3218 4630 4.759793 ATTAAGGTCCAGTCCCCTTTTT 57.240 40.909 0.00 0.00 41.30 1.94
3244 4656 6.752335 TTTTGCTGAAAGTTCAATTCGATG 57.248 33.333 0.00 0.00 36.64 3.84
3245 4657 5.687770 TTGCTGAAAGTTCAATTCGATGA 57.312 34.783 0.00 0.00 36.64 2.92
3246 4658 5.885230 TGCTGAAAGTTCAATTCGATGAT 57.115 34.783 0.00 0.00 36.64 2.45
3247 4659 6.258230 TGCTGAAAGTTCAATTCGATGATT 57.742 33.333 0.00 0.00 36.64 2.57
3248 4660 6.088173 TGCTGAAAGTTCAATTCGATGATTG 58.912 36.000 3.82 3.82 36.64 2.67
3249 4661 6.088824 GCTGAAAGTTCAATTCGATGATTGT 58.911 36.000 9.14 0.00 36.64 2.71
3250 4662 7.094848 TGCTGAAAGTTCAATTCGATGATTGTA 60.095 33.333 9.14 0.00 36.64 2.41
3251 4663 7.750458 GCTGAAAGTTCAATTCGATGATTGTAA 59.250 33.333 9.14 1.83 36.64 2.41
3310 4722 9.699410 ACAAATCCCATCTTTTATCATTCTACA 57.301 29.630 0.00 0.00 0.00 2.74
3351 4765 1.898574 ACGCCTTGGCACCAAAGAG 60.899 57.895 12.45 1.93 35.33 2.85
3370 4784 4.082895 AAGAGATGATCTTGCACAGTTTGC 60.083 41.667 0.00 0.00 46.80 3.68
3372 4786 7.021724 AAGAGATGATCTTGCACAGTTTGCTA 61.022 38.462 2.46 0.00 46.80 3.49
3428 4842 6.360370 TCTCTTTTGCATCCACTAGTAAGT 57.640 37.500 0.00 0.00 35.91 2.24
3434 4848 9.113838 CTTTTGCATCCACTAGTAAGTATTCAT 57.886 33.333 0.00 0.00 33.48 2.57
3445 4859 6.704289 AGTAAGTATTCATGTGCAATGCAT 57.296 33.333 12.38 0.00 41.91 3.96
3448 4862 8.509690 AGTAAGTATTCATGTGCAATGCATATC 58.490 33.333 14.53 3.72 38.26 1.63
3497 4911 4.039245 CCTTTCGGGCATACTTCTCATCTA 59.961 45.833 0.00 0.00 0.00 1.98
3500 4914 4.215908 TCGGGCATACTTCTCATCTACTT 58.784 43.478 0.00 0.00 0.00 2.24
3505 4919 7.169982 CGGGCATACTTCTCATCTACTTTTAAG 59.830 40.741 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.558359 GACAGTGGTAGCAAAAATGGCT 59.442 45.455 0.00 0.00 45.18 4.75
73 74 7.973388 CAGTTCCAACAAAAACTAAGACAATGA 59.027 33.333 0.00 0.00 34.05 2.57
91 92 3.244044 GCAAAAATAGGTGCCAGTTCCAA 60.244 43.478 0.00 0.00 34.58 3.53
146 147 8.776470 CATTTTCTGGTTGTAGCAAAAATCAAT 58.224 29.630 0.00 0.00 31.12 2.57
148 149 7.271511 ACATTTTCTGGTTGTAGCAAAAATCA 58.728 30.769 0.00 0.00 31.12 2.57
165 166 5.067283 ACTGGACGTAGCAAAAACATTTTCT 59.933 36.000 0.00 0.00 0.00 2.52
167 168 5.163602 TGACTGGACGTAGCAAAAACATTTT 60.164 36.000 0.00 0.00 0.00 1.82
188 189 1.639298 GGGCAGCAACTCGTCATGAC 61.639 60.000 16.21 16.21 0.00 3.06
364 372 3.590824 CGAAGGTCCATGGTTGCC 58.409 61.111 12.58 12.61 0.00 4.52
451 459 2.434359 GGAACGTTCCCCGCTCTG 60.434 66.667 33.02 0.00 41.62 3.35
530 566 3.918220 CAGATCGCTGCCGTTCGC 61.918 66.667 0.00 0.00 38.03 4.70
531 567 3.257561 CCAGATCGCTGCCGTTCG 61.258 66.667 0.00 0.00 40.91 3.95
532 568 3.567797 GCCAGATCGCTGCCGTTC 61.568 66.667 0.00 0.00 40.91 3.95
533 569 3.899981 TTGCCAGATCGCTGCCGTT 62.900 57.895 0.00 0.00 40.91 4.44
534 570 4.393155 TTGCCAGATCGCTGCCGT 62.393 61.111 0.00 0.00 40.91 5.68
535 571 3.570638 CTTGCCAGATCGCTGCCG 61.571 66.667 0.00 0.00 40.91 5.69
536 572 3.885521 GCTTGCCAGATCGCTGCC 61.886 66.667 0.00 0.00 40.91 4.85
537 573 2.320339 GAAGCTTGCCAGATCGCTGC 62.320 60.000 2.10 0.00 40.91 5.25
538 574 1.720301 GAAGCTTGCCAGATCGCTG 59.280 57.895 2.10 0.00 41.93 5.18
539 575 1.812922 CGAAGCTTGCCAGATCGCT 60.813 57.895 2.10 0.00 0.00 4.93
631 1055 5.433051 TCTCATCCCCACTCATTTATTCCTT 59.567 40.000 0.00 0.00 0.00 3.36
641 1065 4.883759 TCTAAGAATCTCATCCCCACTCA 58.116 43.478 0.00 0.00 0.00 3.41
653 1077 5.422331 TGGAAACCGTCAGATCTAAGAATCT 59.578 40.000 0.00 0.00 36.41 2.40
689 1113 2.551912 GGTCCAACCCTGTGCGTTG 61.552 63.158 0.00 0.00 40.25 4.10
751 1175 6.139679 TCCTCTCTCTCTCTCTCTCTTTTT 57.860 41.667 0.00 0.00 0.00 1.94
752 1176 5.251700 ACTCCTCTCTCTCTCTCTCTCTTTT 59.748 44.000 0.00 0.00 0.00 2.27
753 1177 4.785376 ACTCCTCTCTCTCTCTCTCTCTTT 59.215 45.833 0.00 0.00 0.00 2.52
754 1178 4.366267 ACTCCTCTCTCTCTCTCTCTCTT 58.634 47.826 0.00 0.00 0.00 2.85
755 1179 4.000928 ACTCCTCTCTCTCTCTCTCTCT 57.999 50.000 0.00 0.00 0.00 3.10
756 1180 4.762289 AACTCCTCTCTCTCTCTCTCTC 57.238 50.000 0.00 0.00 0.00 3.20
850 1275 8.936864 CGATAATCTTGTTGGTAAAGAGTTCTT 58.063 33.333 0.00 0.00 37.10 2.52
955 1387 0.832135 GAGCCGGGGATGATAGGTGA 60.832 60.000 2.18 0.00 0.00 4.02
1155 1612 3.049674 CATGCGACGTTGGCAGGT 61.050 61.111 18.12 2.79 44.71 4.00
1234 1695 1.099689 TCATGTGCTATCACGGACGA 58.900 50.000 0.00 0.00 46.01 4.20
1261 1722 1.539827 GCAATAAACGCAAGGACAGGT 59.460 47.619 0.00 0.00 46.39 4.00
1293 1755 2.099592 CAGGATGCATGGCAATAAACGT 59.900 45.455 2.46 0.00 43.62 3.99
1294 1756 2.544277 CCAGGATGCATGGCAATAAACG 60.544 50.000 2.46 0.00 43.62 3.60
1295 1757 3.102052 CCAGGATGCATGGCAATAAAC 57.898 47.619 2.46 0.00 43.62 2.01
1304 1766 3.646976 CTCGCGCCAGGATGCATG 61.647 66.667 2.46 0.00 31.97 4.06
1309 1771 3.774959 CTAACGCTCGCGCCAGGAT 62.775 63.158 11.65 0.00 44.19 3.24
1310 1772 4.492160 CTAACGCTCGCGCCAGGA 62.492 66.667 11.65 0.00 44.19 3.86
1311 1773 3.774959 ATCTAACGCTCGCGCCAGG 62.775 63.158 11.65 0.00 44.19 4.45
1320 1782 2.073816 CCAAACAACGGATCTAACGCT 58.926 47.619 0.00 0.00 34.00 5.07
1346 1808 0.802607 GATCGGACGGACAGTTCAGC 60.803 60.000 0.00 0.00 0.00 4.26
1351 1813 1.001269 TGAGGATCGGACGGACAGT 60.001 57.895 0.00 0.00 38.61 3.55
1355 1817 0.835276 TCTAGTGAGGATCGGACGGA 59.165 55.000 0.00 0.00 38.61 4.69
1356 1818 0.945813 GTCTAGTGAGGATCGGACGG 59.054 60.000 0.00 0.00 38.61 4.79
1358 1820 1.950828 TCGTCTAGTGAGGATCGGAC 58.049 55.000 0.00 0.00 38.61 4.79
1519 2560 5.104610 AGTGGATTAGTGAGTTGAGATGCAT 60.105 40.000 0.00 0.00 0.00 3.96
1530 2571 7.962964 TTTGTGTTAAGAGTGGATTAGTGAG 57.037 36.000 0.00 0.00 0.00 3.51
1627 2700 7.851387 TTAACTCGTATTATTGATTGCACCA 57.149 32.000 0.00 0.00 0.00 4.17
1660 2734 7.018635 AGTCTAGACGAGAAATAACTACTGC 57.981 40.000 17.07 0.00 35.37 4.40
1898 3015 3.157217 GAGGAGCATGTCGGCGGAT 62.157 63.158 7.21 0.00 39.27 4.18
2033 3244 1.522580 GAGGATGCCAGCGGACTTC 60.523 63.158 0.00 0.00 0.00 3.01
2099 3310 4.783621 ATGCCATCACGTGCGGCT 62.784 61.111 34.22 23.10 46.39 5.52
2757 4079 1.202758 TGGGTGAAGGCTACAACACTG 60.203 52.381 11.56 0.00 34.28 3.66
2759 4081 1.975660 TTGGGTGAAGGCTACAACAC 58.024 50.000 0.00 0.00 0.00 3.32
2782 4123 4.271049 CGTCGCATTCAAGGTTCTGATAAT 59.729 41.667 0.00 0.00 0.00 1.28
2826 4174 5.295292 CAGGGTAAACATCTTGTAGAGCATG 59.705 44.000 0.00 0.00 0.00 4.06
2846 4194 6.771267 ACTAGAAAACAAACTCTAAACCAGGG 59.229 38.462 0.00 0.00 0.00 4.45
2847 4195 7.307219 CGACTAGAAAACAAACTCTAAACCAGG 60.307 40.741 0.00 0.00 0.00 4.45
2848 4196 7.307219 CCGACTAGAAAACAAACTCTAAACCAG 60.307 40.741 0.00 0.00 0.00 4.00
2849 4197 6.480981 CCGACTAGAAAACAAACTCTAAACCA 59.519 38.462 0.00 0.00 0.00 3.67
2850 4198 6.703165 TCCGACTAGAAAACAAACTCTAAACC 59.297 38.462 0.00 0.00 0.00 3.27
2851 4199 7.704789 TCCGACTAGAAAACAAACTCTAAAC 57.295 36.000 0.00 0.00 0.00 2.01
2925 4335 5.894807 ACGCCAAGAGGAATAAAATCATTG 58.105 37.500 0.00 0.00 36.89 2.82
2948 4358 4.888326 ATTTAAACAGGCCTGATGCAAA 57.112 36.364 39.19 27.22 43.89 3.68
2970 4380 9.859427 CTCCAAGCAAAATAAAGTCAATTATGA 57.141 29.630 0.00 0.00 0.00 2.15
2971 4381 8.598075 GCTCCAAGCAAAATAAAGTCAATTATG 58.402 33.333 0.00 0.00 41.89 1.90
2972 4382 7.765819 GGCTCCAAGCAAAATAAAGTCAATTAT 59.234 33.333 0.86 0.00 44.75 1.28
2973 4383 7.096551 GGCTCCAAGCAAAATAAAGTCAATTA 58.903 34.615 0.86 0.00 44.75 1.40
2974 4384 5.934043 GGCTCCAAGCAAAATAAAGTCAATT 59.066 36.000 0.86 0.00 44.75 2.32
2975 4385 5.482006 GGCTCCAAGCAAAATAAAGTCAAT 58.518 37.500 0.86 0.00 44.75 2.57
2976 4386 4.558496 CGGCTCCAAGCAAAATAAAGTCAA 60.558 41.667 0.86 0.00 44.75 3.18
2977 4387 3.057596 CGGCTCCAAGCAAAATAAAGTCA 60.058 43.478 0.86 0.00 44.75 3.41
2978 4388 3.057526 ACGGCTCCAAGCAAAATAAAGTC 60.058 43.478 0.86 0.00 44.75 3.01
2979 4389 2.890945 ACGGCTCCAAGCAAAATAAAGT 59.109 40.909 0.86 0.00 44.75 2.66
2980 4390 3.501950 GACGGCTCCAAGCAAAATAAAG 58.498 45.455 0.86 0.00 44.75 1.85
2981 4391 2.095466 CGACGGCTCCAAGCAAAATAAA 60.095 45.455 0.86 0.00 44.75 1.40
2982 4392 1.466950 CGACGGCTCCAAGCAAAATAA 59.533 47.619 0.86 0.00 44.75 1.40
2983 4393 1.083489 CGACGGCTCCAAGCAAAATA 58.917 50.000 0.86 0.00 44.75 1.40
2984 4394 0.605319 TCGACGGCTCCAAGCAAAAT 60.605 50.000 0.86 0.00 44.75 1.82
2985 4395 1.227704 TCGACGGCTCCAAGCAAAA 60.228 52.632 0.86 0.00 44.75 2.44
2986 4396 1.959226 GTCGACGGCTCCAAGCAAA 60.959 57.895 0.00 0.00 44.75 3.68
2987 4397 2.357034 GTCGACGGCTCCAAGCAA 60.357 61.111 0.00 0.00 44.75 3.91
2988 4398 4.373116 GGTCGACGGCTCCAAGCA 62.373 66.667 9.92 0.00 44.75 3.91
2989 4399 3.665675 ATGGTCGACGGCTCCAAGC 62.666 63.158 9.92 0.00 41.46 4.01
2990 4400 1.811266 CATGGTCGACGGCTCCAAG 60.811 63.158 9.92 0.00 34.80 3.61
2991 4401 2.225791 CTCATGGTCGACGGCTCCAA 62.226 60.000 9.92 0.00 34.80 3.53
2992 4402 2.678580 TCATGGTCGACGGCTCCA 60.679 61.111 9.92 1.19 35.64 3.86
2993 4403 1.739338 ATCTCATGGTCGACGGCTCC 61.739 60.000 9.92 0.00 0.00 4.70
3008 4418 2.778299 TGTGCCACCTGTTACAATCTC 58.222 47.619 0.00 0.00 0.00 2.75
3012 4422 2.428544 AGTTGTGCCACCTGTTACAA 57.571 45.000 0.00 0.00 0.00 2.41
3015 4425 2.910319 AGGATAGTTGTGCCACCTGTTA 59.090 45.455 0.00 0.00 0.00 2.41
3016 4426 1.705186 AGGATAGTTGTGCCACCTGTT 59.295 47.619 0.00 0.00 0.00 3.16
3017 4427 1.362224 AGGATAGTTGTGCCACCTGT 58.638 50.000 0.00 0.00 0.00 4.00
3019 4429 3.525800 AAAAGGATAGTTGTGCCACCT 57.474 42.857 0.00 0.00 0.00 4.00
3021 4431 3.826729 AGGAAAAAGGATAGTTGTGCCAC 59.173 43.478 0.00 0.00 0.00 5.01
3022 4432 4.112634 AGGAAAAAGGATAGTTGTGCCA 57.887 40.909 0.00 0.00 0.00 4.92
3023 4433 5.652452 ACATAGGAAAAAGGATAGTTGTGCC 59.348 40.000 0.00 0.00 0.00 5.01
3024 4434 6.456988 CGACATAGGAAAAAGGATAGTTGTGC 60.457 42.308 0.00 0.00 0.00 4.57
3029 4439 7.848128 TCTTTCGACATAGGAAAAAGGATAGT 58.152 34.615 0.00 0.00 33.37 2.12
3031 4441 9.509956 TTTTCTTTCGACATAGGAAAAAGGATA 57.490 29.630 3.85 0.00 34.41 2.59
3032 4442 7.996098 TTTCTTTCGACATAGGAAAAAGGAT 57.004 32.000 0.00 0.00 33.37 3.24
3033 4443 7.811117 TTTTCTTTCGACATAGGAAAAAGGA 57.189 32.000 3.85 0.00 34.41 3.36
3132 4542 6.146760 AGAAGTACTCCCTCCATCACATAAT 58.853 40.000 0.00 0.00 0.00 1.28
3138 4548 5.843019 AAAAAGAAGTACTCCCTCCATCA 57.157 39.130 0.00 0.00 0.00 3.07
3167 4578 8.994881 GGAAAATGTTTGTTTCGAATTTTGTTC 58.005 29.630 0.00 0.00 36.11 3.18
3220 4632 6.977502 TCATCGAATTGAACTTTCAGCAAAAA 59.022 30.769 0.00 0.00 38.61 1.94
3221 4633 6.502652 TCATCGAATTGAACTTTCAGCAAAA 58.497 32.000 0.00 0.00 38.61 2.44
3222 4634 6.070897 TCATCGAATTGAACTTTCAGCAAA 57.929 33.333 0.00 0.00 38.61 3.68
3223 4635 5.687770 TCATCGAATTGAACTTTCAGCAA 57.312 34.783 0.00 0.00 38.61 3.91
3224 4636 5.885230 ATCATCGAATTGAACTTTCAGCA 57.115 34.783 0.00 0.00 38.61 4.41
3225 4637 6.088824 ACAATCATCGAATTGAACTTTCAGC 58.911 36.000 15.09 0.00 38.64 4.26
3226 4638 9.778993 ATTACAATCATCGAATTGAACTTTCAG 57.221 29.630 15.09 0.00 38.64 3.02
3231 4643 9.342308 ACCATATTACAATCATCGAATTGAACT 57.658 29.630 15.09 3.53 38.64 3.01
3238 4650 8.556194 GCAAGTTACCATATTACAATCATCGAA 58.444 33.333 0.00 0.00 0.00 3.71
3239 4651 7.931407 AGCAAGTTACCATATTACAATCATCGA 59.069 33.333 0.00 0.00 0.00 3.59
3240 4652 8.087982 AGCAAGTTACCATATTACAATCATCG 57.912 34.615 0.00 0.00 0.00 3.84
3298 4710 9.527157 TTTGGTTGGATCTTTGTAGAATGATAA 57.473 29.630 1.51 0.00 33.20 1.75
3299 4711 9.699410 ATTTGGTTGGATCTTTGTAGAATGATA 57.301 29.630 1.51 0.00 33.20 2.15
3310 4722 2.825532 CCCGTGATTTGGTTGGATCTTT 59.174 45.455 0.00 0.00 0.00 2.52
3397 4811 6.510536 AGTGGATGCAAAAGAGAAAGAAAAG 58.489 36.000 0.00 0.00 0.00 2.27
3428 4842 8.098912 AGTCTAGATATGCATTGCACATGAATA 58.901 33.333 14.66 10.85 43.04 1.75
3434 4848 3.811497 GCAGTCTAGATATGCATTGCACA 59.189 43.478 21.60 1.68 43.04 4.57
3479 4893 4.592485 AAGTAGATGAGAAGTATGCCCG 57.408 45.455 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.