Multiple sequence alignment - TraesCS7D01G288200

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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 TraesCS7D01G288200 chr7D 100.000 2555 0 0 1 2555 318857091 318859645 0.000000e+00 4719
1 TraesCS7D01G288200 chr7D 89.159 618 62 2 1 613 342642238 342641621 0.000000e+00 765
2 TraesCS7D01G288200 chr7D 90.588 85 7 1 1978 2062 318858993 318859076 7.470000e-21 111
3 TraesCS7D01G288200 chr6A 92.693 1177 61 5 612 1765 480459510 480460684 0.000000e+00 1674
4 TraesCS7D01G288200 chr6A 95.048 626 30 1 1931 2555 480460857 480461482 0.000000e+00 983
5 TraesCS7D01G288200 chr6A 94.495 109 4 2 1815 1921 480460704 480460812 1.570000e-37 167
6 TraesCS7D01G288200 chr6A 96.591 88 2 1 1900 1986 117401157 117401244 7.370000e-31 145
7 TraesCS7D01G288200 chr6A 94.382 89 3 2 1800 1887 480460769 480460856 4.430000e-28 135
8 TraesCS7D01G288200 chr6A 91.765 85 6 1 1903 1986 480460904 480460988 1.610000e-22 117
9 TraesCS7D01G288200 chr4A 92.432 1176 63 6 612 1762 500090442 500091616 0.000000e+00 1655
10 TraesCS7D01G288200 chr4A 95.645 574 24 1 1931 2503 500091693 500092266 0.000000e+00 920
11 TraesCS7D01G288200 chr4A 91.026 78 7 0 1807 1884 500091612 500091689 3.480000e-19 106
12 TraesCS7D01G288200 chr2D 95.652 920 39 1 846 1765 177444037 177443119 0.000000e+00 1476
13 TraesCS7D01G288200 chr2D 95.636 550 23 1 2007 2555 177443026 177442477 0.000000e+00 881
14 TraesCS7D01G288200 chr2D 89.251 614 63 3 1 613 114490480 114491091 0.000000e+00 765
15 TraesCS7D01G288200 chr2D 88.455 615 67 4 1 613 607157497 607156885 0.000000e+00 739
16 TraesCS7D01G288200 chr2D 97.026 269 6 2 609 875 528445941 528446209 3.880000e-123 451
17 TraesCS7D01G288200 chr2D 95.167 269 11 2 610 876 177444319 177444051 8.450000e-115 424
18 TraesCS7D01G288200 chr2D 94.521 73 4 0 1818 1890 177443096 177443024 2.080000e-21 113
19 TraesCS7D01G288200 chr7B 90.618 842 60 7 1057 1887 622460977 622461810 0.000000e+00 1099
20 TraesCS7D01G288200 chr7B 96.006 626 24 1 1931 2555 622461811 622462436 0.000000e+00 1016
21 TraesCS7D01G288200 chr7B 94.301 579 31 2 1978 2555 461210617 461210040 0.000000e+00 885
22 TraesCS7D01G288200 chr7B 88.946 579 39 10 608 1162 622460541 622461118 0.000000e+00 691
23 TraesCS7D01G288200 chr7B 86.034 580 68 6 1075 1643 461211303 461210726 6.040000e-171 610
24 TraesCS7D01G288200 chr7B 96.610 236 8 0 608 843 655058624 655058389 2.380000e-105 392
25 TraesCS7D01G288200 chr7B 94.231 104 2 3 1815 1916 622461659 622461760 3.400000e-34 156
26 TraesCS7D01G288200 chr7B 87.719 114 4 1 1662 1765 461210747 461210634 9.600000e-25 124
27 TraesCS7D01G288200 chr7B 91.667 84 6 1 1904 1986 622461859 622461942 5.780000e-22 115
28 TraesCS7D01G288200 chr6D 95.337 579 26 1 1978 2555 87581421 87580843 0.000000e+00 918
29 TraesCS7D01G288200 chr6D 88.548 620 62 6 1 613 248737934 248738551 0.000000e+00 743
30 TraesCS7D01G288200 chr6D 85.251 617 77 8 1038 1643 87582143 87581530 7.760000e-175 623
31 TraesCS7D01G288200 chr6D 95.833 96 3 1 1895 1989 87581429 87581334 1.220000e-33 154
32 TraesCS7D01G288200 chr6D 86.842 114 5 1 1662 1765 87581551 87581438 4.470000e-23 119
33 TraesCS7D01G288200 chr4D 95.046 545 26 1 2012 2555 498000079 498000623 0.000000e+00 856
34 TraesCS7D01G288200 chr4D 92.070 517 36 2 2040 2555 352496892 352497404 0.000000e+00 723
35 TraesCS7D01G288200 chr4D 86.034 580 68 6 1075 1643 497999369 497999946 6.040000e-171 610
36 TraesCS7D01G288200 chr4D 86.535 557 65 8 1019 1566 352487386 352487941 2.810000e-169 604
37 TraesCS7D01G288200 chr4D 87.719 114 4 1 1662 1765 497999925 498000038 9.600000e-25 124
38 TraesCS7D01G288200 chr3A 88.925 614 64 4 1 613 159538664 159538054 0.000000e+00 754
39 TraesCS7D01G288200 chr7A 88.655 617 66 2 1 613 352725812 352726428 0.000000e+00 749
40 TraesCS7D01G288200 chr7A 96.591 88 2 1 1900 1986 611912172 611912259 7.370000e-31 145
41 TraesCS7D01G288200 chr1D 88.331 617 68 4 1 613 473952342 473951726 0.000000e+00 737
42 TraesCS7D01G288200 chr1D 88.627 510 44 8 2057 2555 194178169 194178675 2.170000e-170 608
43 TraesCS7D01G288200 chr6B 88.543 611 65 5 4 613 349316341 349315735 0.000000e+00 736
44 TraesCS7D01G288200 chr6B 95.604 91 3 1 1900 1989 6473896 6473806 7.370000e-31 145
45 TraesCS7D01G288200 chr5B 88.293 615 68 4 1 613 252460302 252459690 0.000000e+00 734
46 TraesCS7D01G288200 chr5B 94.757 267 12 2 610 875 673670813 673671078 5.090000e-112 414
47 TraesCS7D01G288200 chr1A 88.802 509 44 10 2057 2555 369353036 369352531 1.680000e-171 612
48 TraesCS7D01G288200 chr1A 95.322 342 16 0 612 953 216480720 216481061 6.220000e-151 544
49 TraesCS7D01G288200 chr1A 94.118 340 18 2 1782 2119 216481115 216481454 1.360000e-142 516
50 TraesCS7D01G288200 chr5A 92.917 240 16 1 612 850 546706909 546706670 5.230000e-92 348
51 TraesCS7D01G288200 chr1B 97.727 88 1 1 1900 1986 22115250 22115337 1.580000e-32 150
52 TraesCS7D01G288200 chr3B 96.591 88 2 1 1900 1986 662510905 662510992 7.370000e-31 145


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 TraesCS7D01G288200 chr7D 318857091 318859645 2554 False 2415.000000 4719 95.294000 1 2555 2 chr7D.!!$F1 2554
1 TraesCS7D01G288200 chr7D 342641621 342642238 617 True 765.000000 765 89.159000 1 613 1 chr7D.!!$R1 612
2 TraesCS7D01G288200 chr6A 480459510 480461482 1972 False 615.200000 1674 93.676600 612 2555 5 chr6A.!!$F2 1943
3 TraesCS7D01G288200 chr4A 500090442 500092266 1824 False 893.666667 1655 93.034333 612 2503 3 chr4A.!!$F1 1891
4 TraesCS7D01G288200 chr2D 114490480 114491091 611 False 765.000000 765 89.251000 1 613 1 chr2D.!!$F1 612
5 TraesCS7D01G288200 chr2D 607156885 607157497 612 True 739.000000 739 88.455000 1 613 1 chr2D.!!$R1 612
6 TraesCS7D01G288200 chr2D 177442477 177444319 1842 True 723.500000 1476 95.244000 610 2555 4 chr2D.!!$R2 1945
7 TraesCS7D01G288200 chr7B 622460541 622462436 1895 False 615.400000 1099 92.293600 608 2555 5 chr7B.!!$F1 1947
8 TraesCS7D01G288200 chr7B 461210040 461211303 1263 True 539.666667 885 89.351333 1075 2555 3 chr7B.!!$R2 1480
9 TraesCS7D01G288200 chr6D 248737934 248738551 617 False 743.000000 743 88.548000 1 613 1 chr6D.!!$F1 612
10 TraesCS7D01G288200 chr6D 87580843 87582143 1300 True 453.500000 918 90.815750 1038 2555 4 chr6D.!!$R1 1517
11 TraesCS7D01G288200 chr4D 352496892 352497404 512 False 723.000000 723 92.070000 2040 2555 1 chr4D.!!$F2 515
12 TraesCS7D01G288200 chr4D 352487386 352487941 555 False 604.000000 604 86.535000 1019 1566 1 chr4D.!!$F1 547
13 TraesCS7D01G288200 chr4D 497999369 498000623 1254 False 530.000000 856 89.599667 1075 2555 3 chr4D.!!$F3 1480
14 TraesCS7D01G288200 chr3A 159538054 159538664 610 True 754.000000 754 88.925000 1 613 1 chr3A.!!$R1 612
15 TraesCS7D01G288200 chr7A 352725812 352726428 616 False 749.000000 749 88.655000 1 613 1 chr7A.!!$F1 612
16 TraesCS7D01G288200 chr1D 473951726 473952342 616 True 737.000000 737 88.331000 1 613 1 chr1D.!!$R1 612
17 TraesCS7D01G288200 chr1D 194178169 194178675 506 False 608.000000 608 88.627000 2057 2555 1 chr1D.!!$F1 498
18 TraesCS7D01G288200 chr6B 349315735 349316341 606 True 736.000000 736 88.543000 4 613 1 chr6B.!!$R2 609
19 TraesCS7D01G288200 chr5B 252459690 252460302 612 True 734.000000 734 88.293000 1 613 1 chr5B.!!$R1 612
20 TraesCS7D01G288200 chr1A 369352531 369353036 505 True 612.000000 612 88.802000 2057 2555 1 chr1A.!!$R1 498
21 TraesCS7D01G288200 chr1A 216480720 216481454 734 False 530.000000 544 94.720000 612 2119 2 chr1A.!!$F1 1507

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
174 178 0.167251 ACGGAATAAAACTTGCGCGG 59.833 50.0 8.83 0.0 42.8 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 2023 0.038599 TTGCATGCACACTCCTCCAT 59.961 50.0 22.58 0.0 0.0 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 5.153675 ACTAACCTATTAACCTAGAGCCCC 58.846 45.833 0.00 0.00 0.00 5.80
90 91 4.297427 AACCTATTAACCTAGAGCCCCT 57.703 45.455 0.00 0.00 0.00 4.79
153 157 5.536497 AAAGGAATACCAAATGGAGTCCT 57.464 39.130 11.33 11.17 41.51 3.85
169 173 5.935789 TGGAGTCCTAACGGAATAAAACTTG 59.064 40.000 11.33 0.00 42.08 3.16
174 178 0.167251 ACGGAATAAAACTTGCGCGG 59.833 50.000 8.83 0.00 42.80 6.46
176 180 1.400500 CGGAATAAAACTTGCGCGGTT 60.400 47.619 8.83 11.83 33.29 4.44
203 207 0.472471 TTGGACCAGAAGACACCCAC 59.528 55.000 0.00 0.00 0.00 4.61
259 263 1.746615 CCACAAGCCTGCTACGCAT 60.747 57.895 0.00 0.00 38.13 4.73
266 272 1.146041 CCTGCTACGCATGCCCTAA 59.854 57.895 13.15 0.00 38.13 2.69
270 276 1.830145 CTACGCATGCCCTAAGGGT 59.170 57.895 13.15 4.67 46.51 4.34
272 278 0.978667 TACGCATGCCCTAAGGGTGA 60.979 55.000 13.15 0.00 46.51 4.02
311 322 0.612174 CTCGAGAGTCCTCCAACCCA 60.612 60.000 6.58 0.00 36.04 4.51
315 326 2.500098 CGAGAGTCCTCCAACCCAAATA 59.500 50.000 0.00 0.00 36.04 1.40
372 384 3.689161 TCAGAAGCATCCACCAAAATACG 59.311 43.478 0.00 0.00 0.00 3.06
428 442 1.271926 CCATCTTGGGGACTTTTCCGT 60.272 52.381 0.00 0.00 43.94 4.69
431 445 1.702957 TCTTGGGGACTTTTCCGTCAT 59.297 47.619 0.00 0.00 43.94 3.06
466 480 4.271816 CGATCACGGAGGGCCTCG 62.272 72.222 26.54 22.46 35.72 4.63
487 501 0.971386 CATCAACCTTGCTGCCCTTT 59.029 50.000 0.00 0.00 0.00 3.11
508 522 3.242518 TCGATGAAGCGTGAGTAGTTTG 58.757 45.455 0.00 0.00 0.00 2.93
522 536 3.583086 AGTAGTTTGCCACAGACCTATGT 59.417 43.478 0.00 0.00 0.00 2.29
538 552 8.861086 CAGACCTATGTGTCCATAATTAGTAGT 58.139 37.037 0.00 0.00 35.83 2.73
638 652 1.039068 CCATCACAGTTTGTTGGGCA 58.961 50.000 0.00 0.00 40.30 5.36
686 700 1.747367 CCACGGAAATAGGGCGCAA 60.747 57.895 10.83 0.00 0.00 4.85
712 726 9.684702 ACTCCTTAACTATCCTATTAATTGGGA 57.315 33.333 14.81 12.66 0.00 4.37
830 846 3.445805 TGGGAATCGGTTTCTTATTTGCC 59.554 43.478 0.00 0.00 34.56 4.52
883 943 3.720601 TGCATGCGAGGCCTCCTT 61.721 61.111 27.20 14.37 31.76 3.36
943 1006 5.299028 TGTTTGCATTCACAAGTGTAGACAT 59.701 36.000 0.00 0.00 0.00 3.06
959 1022 9.435570 AGTGTAGACATCAGGGTACTATAAAAT 57.564 33.333 0.00 0.00 0.00 1.82
964 1027 6.838382 ACATCAGGGTACTATAAAATCCCAC 58.162 40.000 0.00 0.00 40.48 4.61
1059 1122 0.841961 CCATGGAGGAGATGCAAGGA 59.158 55.000 5.56 0.00 40.27 3.36
1101 1236 4.228567 GAGGGGCTAGGCGTGCTC 62.229 72.222 10.58 0.72 0.00 4.26
1104 1239 4.874977 GGGCTAGGCGTGCTCGAC 62.875 72.222 13.13 9.61 46.75 4.20
1110 1245 2.125512 GGCGTGCTCGACATTCCT 60.126 61.111 13.13 0.00 45.53 3.36
1111 1246 2.456119 GGCGTGCTCGACATTCCTG 61.456 63.158 13.13 0.00 45.53 3.86
1112 1247 3.084579 CGTGCTCGACATTCCTGC 58.915 61.111 1.00 0.00 39.71 4.85
1113 1248 2.456119 CGTGCTCGACATTCCTGCC 61.456 63.158 1.00 0.00 39.71 4.85
1114 1249 1.375908 GTGCTCGACATTCCTGCCA 60.376 57.895 0.00 0.00 0.00 4.92
1115 1250 0.745845 GTGCTCGACATTCCTGCCAT 60.746 55.000 0.00 0.00 0.00 4.40
1116 1251 0.745486 TGCTCGACATTCCTGCCATG 60.745 55.000 0.00 0.00 0.00 3.66
1117 1252 1.442526 GCTCGACATTCCTGCCATGG 61.443 60.000 7.63 7.63 0.00 3.66
1118 1253 0.178767 CTCGACATTCCTGCCATGGA 59.821 55.000 18.40 0.00 0.00 3.41
1119 1254 0.178767 TCGACATTCCTGCCATGGAG 59.821 55.000 18.40 10.04 37.43 3.86
1120 1255 0.816825 CGACATTCCTGCCATGGAGG 60.817 60.000 18.40 18.80 37.43 4.30
1121 1256 0.548031 GACATTCCTGCCATGGAGGA 59.452 55.000 22.10 22.10 41.22 3.71
1122 1257 0.549950 ACATTCCTGCCATGGAGGAG 59.450 55.000 23.66 18.35 40.79 3.69
1123 1258 0.178998 CATTCCTGCCATGGAGGAGG 60.179 60.000 23.66 19.95 40.79 4.30
1124 1259 0.625683 ATTCCTGCCATGGAGGAGGT 60.626 55.000 23.66 17.17 40.79 3.85
1125 1260 1.565390 TTCCTGCCATGGAGGAGGTG 61.565 60.000 23.66 4.82 40.79 4.00
1126 1261 2.124403 CTGCCATGGAGGAGGTGC 60.124 66.667 18.40 0.00 41.22 5.01
1127 1262 2.611800 TGCCATGGAGGAGGTGCT 60.612 61.111 18.40 0.00 41.22 4.40
1128 1263 1.306911 TGCCATGGAGGAGGTGCTA 60.307 57.895 18.40 0.00 41.22 3.49
1129 1264 1.340399 TGCCATGGAGGAGGTGCTAG 61.340 60.000 18.40 0.00 41.22 3.42
1130 1265 2.049627 GCCATGGAGGAGGTGCTAGG 62.050 65.000 18.40 0.00 41.22 3.02
1131 1266 1.449353 CATGGAGGAGGTGCTAGGC 59.551 63.158 0.00 0.00 0.00 3.93
1132 1267 2.136878 ATGGAGGAGGTGCTAGGCG 61.137 63.158 0.00 0.00 0.00 5.52
1253 1432 1.069227 GCAAGAGGTGGTACGCAAAAG 60.069 52.381 0.00 0.00 43.02 2.27
1294 1473 2.555325 ACTTGTGAGGTGTGCATTCATG 59.445 45.455 0.00 0.00 0.00 3.07
1423 1602 2.189594 TCCTTGCCTCTGTGACAATG 57.810 50.000 0.00 0.00 0.00 2.82
1771 2012 5.975693 GGTTCCATGATAAACCACTCAAA 57.024 39.130 15.58 0.00 43.63 2.69
1772 2013 6.530019 GGTTCCATGATAAACCACTCAAAT 57.470 37.500 15.58 0.00 43.63 2.32
1773 2014 6.332630 GGTTCCATGATAAACCACTCAAATG 58.667 40.000 15.58 0.00 43.63 2.32
1775 2016 7.147846 GGTTCCATGATAAACCACTCAAATGAT 60.148 37.037 15.58 0.00 43.63 2.45
1777 2018 7.348815 TCCATGATAAACCACTCAAATGATCT 58.651 34.615 0.00 0.00 0.00 2.75
1779 2020 9.123902 CCATGATAAACCACTCAAATGATCTTA 57.876 33.333 0.00 0.00 0.00 2.10
1782 2023 9.904198 TGATAAACCACTCAAATGATCTTATGA 57.096 29.630 0.00 0.00 0.00 2.15
1785 2026 7.578310 AACCACTCAAATGATCTTATGATGG 57.422 36.000 0.00 7.79 32.19 3.51
1786 2027 6.903516 ACCACTCAAATGATCTTATGATGGA 58.096 36.000 18.49 0.00 32.19 3.41
1787 2028 6.996879 ACCACTCAAATGATCTTATGATGGAG 59.003 38.462 18.49 0.00 32.19 3.86
1788 2029 6.430308 CCACTCAAATGATCTTATGATGGAGG 59.570 42.308 0.00 0.00 32.19 4.30
1789 2030 7.222161 CACTCAAATGATCTTATGATGGAGGA 58.778 38.462 0.00 0.00 32.19 3.71
1790 2031 7.388224 CACTCAAATGATCTTATGATGGAGGAG 59.612 40.741 0.00 0.00 32.19 3.69
1791 2032 7.072202 ACTCAAATGATCTTATGATGGAGGAGT 59.928 37.037 0.00 0.00 32.19 3.85
1792 2033 7.222161 TCAAATGATCTTATGATGGAGGAGTG 58.778 38.462 0.00 0.00 32.19 3.51
1793 2034 6.760440 AATGATCTTATGATGGAGGAGTGT 57.240 37.500 0.00 0.00 32.19 3.55
1794 2035 5.541953 TGATCTTATGATGGAGGAGTGTG 57.458 43.478 0.00 0.00 32.19 3.82
1795 2036 3.827008 TCTTATGATGGAGGAGTGTGC 57.173 47.619 0.00 0.00 0.00 4.57
1796 2037 3.106827 TCTTATGATGGAGGAGTGTGCA 58.893 45.455 0.00 0.00 0.00 4.57
1797 2038 3.713248 TCTTATGATGGAGGAGTGTGCAT 59.287 43.478 0.00 0.00 0.00 3.96
1798 2039 2.343484 ATGATGGAGGAGTGTGCATG 57.657 50.000 0.00 0.00 0.00 4.06
1799 2040 0.393402 TGATGGAGGAGTGTGCATGC 60.393 55.000 11.82 11.82 0.00 4.06
1800 2041 0.393402 GATGGAGGAGTGTGCATGCA 60.393 55.000 18.46 18.46 0.00 3.96
1801 2042 0.038599 ATGGAGGAGTGTGCATGCAA 59.961 50.000 24.58 10.26 0.00 4.08
1802 2043 0.607217 TGGAGGAGTGTGCATGCAAG 60.607 55.000 24.58 0.00 0.00 4.01
1803 2044 1.310933 GGAGGAGTGTGCATGCAAGG 61.311 60.000 24.58 0.00 0.00 3.61
1804 2045 1.303888 AGGAGTGTGCATGCAAGGG 60.304 57.895 24.58 0.00 0.00 3.95
1805 2046 1.303561 GGAGTGTGCATGCAAGGGA 60.304 57.895 24.58 3.72 0.00 4.20
1806 2047 1.310933 GGAGTGTGCATGCAAGGGAG 61.311 60.000 24.58 0.00 0.00 4.30
1807 2048 0.321919 GAGTGTGCATGCAAGGGAGA 60.322 55.000 24.58 0.00 0.00 3.71
1808 2049 0.111061 AGTGTGCATGCAAGGGAGAA 59.889 50.000 24.58 0.00 0.00 2.87
1809 2050 0.961019 GTGTGCATGCAAGGGAGAAA 59.039 50.000 24.58 0.00 0.00 2.52
1810 2051 1.340889 GTGTGCATGCAAGGGAGAAAA 59.659 47.619 24.58 0.00 0.00 2.29
1811 2052 2.037901 TGTGCATGCAAGGGAGAAAAA 58.962 42.857 24.58 0.00 0.00 1.94
1812 2053 2.224018 TGTGCATGCAAGGGAGAAAAAC 60.224 45.455 24.58 5.73 0.00 2.43
1813 2054 2.037901 TGCATGCAAGGGAGAAAAACA 58.962 42.857 20.30 0.00 0.00 2.83
1814 2055 2.633967 TGCATGCAAGGGAGAAAAACAT 59.366 40.909 20.30 0.00 0.00 2.71
1815 2056 3.831333 TGCATGCAAGGGAGAAAAACATA 59.169 39.130 20.30 0.00 0.00 2.29
1816 2057 4.282957 TGCATGCAAGGGAGAAAAACATAA 59.717 37.500 20.30 0.00 0.00 1.90
1871 2112 3.450457 ACTCAAATGCACCCTCAAAAACA 59.550 39.130 0.00 0.00 0.00 2.83
1878 2119 2.675844 GCACCCTCAAAAACAAAACACC 59.324 45.455 0.00 0.00 0.00 4.16
1919 2161 7.595311 AAATTTTCAGTTCAAAACAGTCCAC 57.405 32.000 0.00 0.00 0.00 4.02
2041 2319 5.995565 ACTAATACTCCAACAGTAGCACA 57.004 39.130 0.00 0.00 41.13 4.57
2110 2388 3.993081 CCTGCTCAACATATTCTCGATCC 59.007 47.826 0.00 0.00 0.00 3.36
2175 2453 3.553828 TTTCTTCAAGTGAGGAACCGT 57.446 42.857 5.44 0.00 39.41 4.83
2267 2545 2.582636 AGCTTTTGATGGGGGTACTCAT 59.417 45.455 0.00 0.00 0.00 2.90
2270 2548 3.931907 TTTGATGGGGGTACTCATCTG 57.068 47.619 18.03 0.00 38.78 2.90
2278 2556 1.421646 GGGTACTCATCTGGGGATTGG 59.578 57.143 0.00 0.00 0.00 3.16
2302 2580 6.542370 GGTTAACCTATGACACATAACAGCAT 59.458 38.462 17.83 0.00 0.00 3.79
2318 2596 4.553323 ACAGCATGAAAACTCAAATCAGC 58.447 39.130 0.00 0.00 39.69 4.26
2402 2693 3.054361 ACCTTTTGGACAATCTCGGCTAT 60.054 43.478 0.00 0.00 44.07 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 5.837438 GGCTCTAGGTTAATAGGTTAGTCCA 59.163 44.000 0.00 0.00 39.02 4.02
153 157 2.159680 CCGCGCAAGTTTTATTCCGTTA 60.160 45.455 8.75 0.00 41.68 3.18
169 173 2.247637 GTCCAAGAAAAATAACCGCGC 58.752 47.619 0.00 0.00 0.00 6.86
174 178 7.139392 GTGTCTTCTGGTCCAAGAAAAATAAC 58.861 38.462 0.00 0.00 35.79 1.89
176 180 5.768164 GGTGTCTTCTGGTCCAAGAAAAATA 59.232 40.000 0.00 0.00 35.79 1.40
203 207 2.674220 GCCCCCTCTCCAAGTCCTG 61.674 68.421 0.00 0.00 0.00 3.86
266 272 2.208349 AAGCCCTCAGGTCACCCT 59.792 61.111 0.00 0.00 44.02 4.34
270 276 2.528818 CCCACAAGCCCTCAGGTCA 61.529 63.158 0.00 0.00 34.57 4.02
272 278 3.971702 GCCCACAAGCCCTCAGGT 61.972 66.667 0.00 0.00 34.57 4.00
296 307 5.264395 CAAATATTTGGGTTGGAGGACTCT 58.736 41.667 18.72 0.00 34.59 3.24
335 347 6.024563 TGCTTCTGATTTTGGGGGAATATA 57.975 37.500 0.00 0.00 0.00 0.86
348 360 5.163622 CGTATTTTGGTGGATGCTTCTGATT 60.164 40.000 0.00 0.00 0.00 2.57
372 384 2.050077 GCTTGCAGTGGCGGAAAC 60.050 61.111 0.00 0.00 45.35 2.78
419 432 3.249687 GGCAGGATGACGGAAAAGT 57.750 52.632 0.00 0.00 39.69 2.66
487 501 3.242518 CAAACTACTCACGCTTCATCGA 58.757 45.455 0.00 0.00 0.00 3.59
522 536 8.492415 AGCCATCTAACTACTAATTATGGACA 57.508 34.615 0.00 0.00 35.48 4.02
530 544 8.776061 AGAGAAGAAGCCATCTAACTACTAAT 57.224 34.615 0.00 0.00 37.42 1.73
531 545 8.056400 AGAGAGAAGAAGCCATCTAACTACTAA 58.944 37.037 0.00 0.00 37.42 2.24
538 552 6.438741 TCAAAGAGAGAGAAGAAGCCATCTAA 59.561 38.462 0.00 0.00 37.42 2.10
686 700 9.684702 TCCCAATTAATAGGATAGTTAAGGAGT 57.315 33.333 3.53 0.00 0.00 3.85
843 859 0.953727 ATGTTCACACTTGCATGCGT 59.046 45.000 14.09 2.34 0.00 5.24
943 1006 5.163385 CGTGTGGGATTTTATAGTACCCTGA 60.163 44.000 0.00 0.00 40.98 3.86
964 1027 1.091771 GCCACATGGACTCCATCGTG 61.092 60.000 21.90 21.90 43.15 4.35
1059 1122 1.380302 GGCATGAACCTCCACCACT 59.620 57.895 0.00 0.00 0.00 4.00
1099 1234 0.178767 TCCATGGCAGGAATGTCGAG 59.821 55.000 6.96 0.00 33.93 4.04
1100 1235 0.178767 CTCCATGGCAGGAATGTCGA 59.821 55.000 6.96 0.00 37.20 4.20
1101 1236 0.816825 CCTCCATGGCAGGAATGTCG 60.817 60.000 19.95 0.00 37.20 4.35
1102 1237 0.548031 TCCTCCATGGCAGGAATGTC 59.452 55.000 23.13 0.00 37.09 3.06
1103 1238 0.549950 CTCCTCCATGGCAGGAATGT 59.450 55.000 24.48 0.00 39.69 2.71
1104 1239 0.178998 CCTCCTCCATGGCAGGAATG 60.179 60.000 24.48 17.75 39.69 2.67
1105 1240 0.625683 ACCTCCTCCATGGCAGGAAT 60.626 55.000 24.48 16.75 39.69 3.01
1106 1241 1.229951 ACCTCCTCCATGGCAGGAA 60.230 57.895 24.48 13.90 39.69 3.36
1107 1242 1.997311 CACCTCCTCCATGGCAGGA 60.997 63.158 23.94 23.73 37.75 3.86
1108 1243 2.593978 CACCTCCTCCATGGCAGG 59.406 66.667 19.03 19.03 38.37 4.85
1109 1244 1.340399 TAGCACCTCCTCCATGGCAG 61.340 60.000 6.96 5.54 35.26 4.85
1110 1245 1.306911 TAGCACCTCCTCCATGGCA 60.307 57.895 6.96 0.00 35.26 4.92
1111 1246 1.449353 CTAGCACCTCCTCCATGGC 59.551 63.158 6.96 0.00 35.26 4.40
1112 1247 2.049627 GCCTAGCACCTCCTCCATGG 62.050 65.000 4.97 4.97 37.10 3.66
1113 1248 1.449353 GCCTAGCACCTCCTCCATG 59.551 63.158 0.00 0.00 0.00 3.66
1114 1249 2.136878 CGCCTAGCACCTCCTCCAT 61.137 63.158 0.00 0.00 0.00 3.41
1115 1250 2.759973 CGCCTAGCACCTCCTCCA 60.760 66.667 0.00 0.00 0.00 3.86
1126 1261 1.582610 GGATCCTCGAGAGCGCCTAG 61.583 65.000 15.71 1.28 37.46 3.02
1127 1262 1.601197 GGATCCTCGAGAGCGCCTA 60.601 63.158 15.71 0.00 37.46 3.93
1128 1263 2.909965 GGATCCTCGAGAGCGCCT 60.910 66.667 15.71 0.00 37.46 5.52
1129 1264 2.909965 AGGATCCTCGAGAGCGCC 60.910 66.667 15.71 9.60 37.46 6.53
1130 1265 2.334653 CAGGATCCTCGAGAGCGC 59.665 66.667 12.69 0.00 37.46 5.92
1131 1266 2.334653 GCAGGATCCTCGAGAGCG 59.665 66.667 12.69 0.00 39.35 5.03
1132 1267 2.733945 GGCAGGATCCTCGAGAGC 59.266 66.667 12.69 12.07 0.00 4.09
1253 1432 1.255667 TGAGGTCGGGTTGGAGTAGC 61.256 60.000 0.00 0.00 0.00 3.58
1294 1473 0.109597 CACTTGAGGCACAAATCGGC 60.110 55.000 0.00 0.00 38.08 5.54
1296 1475 1.069022 CCACACTTGAGGCACAAATCG 60.069 52.381 0.00 0.00 38.08 3.34
1423 1602 1.522258 CGCACAATCTTTGCACCAAAC 59.478 47.619 0.00 0.00 40.20 2.93
1496 1675 6.971527 TTTCGTCCTCGAGATAGATAGATC 57.028 41.667 15.71 0.00 46.81 2.75
1765 2006 7.072202 ACTCCTCCATCATAAGATCATTTGAGT 59.928 37.037 0.00 0.00 30.20 3.41
1766 2007 7.388224 CACTCCTCCATCATAAGATCATTTGAG 59.612 40.741 0.00 0.00 30.20 3.02
1767 2008 7.147426 ACACTCCTCCATCATAAGATCATTTGA 60.147 37.037 0.00 0.00 30.20 2.69
1770 2011 6.531923 CACACTCCTCCATCATAAGATCATT 58.468 40.000 0.00 0.00 30.20 2.57
1771 2012 5.512749 GCACACTCCTCCATCATAAGATCAT 60.513 44.000 0.00 0.00 30.20 2.45
1772 2013 4.202295 GCACACTCCTCCATCATAAGATCA 60.202 45.833 0.00 0.00 30.20 2.92
1773 2014 4.202295 TGCACACTCCTCCATCATAAGATC 60.202 45.833 0.00 0.00 30.20 2.75
1775 2016 3.106827 TGCACACTCCTCCATCATAAGA 58.893 45.455 0.00 0.00 0.00 2.10
1777 2018 3.812262 CATGCACACTCCTCCATCATAA 58.188 45.455 0.00 0.00 0.00 1.90
1779 2020 1.749635 GCATGCACACTCCTCCATCAT 60.750 52.381 14.21 0.00 0.00 2.45
1780 2021 0.393402 GCATGCACACTCCTCCATCA 60.393 55.000 14.21 0.00 0.00 3.07
1781 2022 0.393402 TGCATGCACACTCCTCCATC 60.393 55.000 18.46 0.00 0.00 3.51
1782 2023 0.038599 TTGCATGCACACTCCTCCAT 59.961 50.000 22.58 0.00 0.00 3.41
1784 2025 1.310933 CCTTGCATGCACACTCCTCC 61.311 60.000 22.58 0.00 0.00 4.30
1785 2026 1.310933 CCCTTGCATGCACACTCCTC 61.311 60.000 22.58 0.00 0.00 3.71
1786 2027 1.303888 CCCTTGCATGCACACTCCT 60.304 57.895 22.58 0.00 0.00 3.69
1787 2028 1.303561 TCCCTTGCATGCACACTCC 60.304 57.895 22.58 0.00 0.00 3.85
1788 2029 0.321919 TCTCCCTTGCATGCACACTC 60.322 55.000 22.58 0.00 0.00 3.51
1789 2030 0.111061 TTCTCCCTTGCATGCACACT 59.889 50.000 22.58 0.00 0.00 3.55
1790 2031 0.961019 TTTCTCCCTTGCATGCACAC 59.039 50.000 22.58 0.00 0.00 3.82
1791 2032 1.702182 TTTTCTCCCTTGCATGCACA 58.298 45.000 22.58 11.00 0.00 4.57
1792 2033 2.224018 TGTTTTTCTCCCTTGCATGCAC 60.224 45.455 22.58 4.62 0.00 4.57
1793 2034 2.037901 TGTTTTTCTCCCTTGCATGCA 58.962 42.857 18.46 18.46 0.00 3.96
1794 2035 2.818130 TGTTTTTCTCCCTTGCATGC 57.182 45.000 11.82 11.82 0.00 4.06
1795 2036 7.910441 AATTTATGTTTTTCTCCCTTGCATG 57.090 32.000 0.00 0.00 0.00 4.06
1796 2037 8.922931 AAAATTTATGTTTTTCTCCCTTGCAT 57.077 26.923 0.00 0.00 0.00 3.96
1797 2038 8.744568 AAAAATTTATGTTTTTCTCCCTTGCA 57.255 26.923 0.00 0.00 36.79 4.08
1813 2054 9.883142 TGGACTGTTTTGAACTGAAAAATTTAT 57.117 25.926 0.00 0.00 34.78 1.40
1814 2055 9.145865 GTGGACTGTTTTGAACTGAAAAATTTA 57.854 29.630 0.00 0.00 34.78 1.40
1815 2056 7.877612 AGTGGACTGTTTTGAACTGAAAAATTT 59.122 29.630 4.97 0.00 34.78 1.82
1816 2057 7.386059 AGTGGACTGTTTTGAACTGAAAAATT 58.614 30.769 4.97 0.00 34.78 1.82
1871 2112 2.434336 GCTTTTCTCCCTTGGGTGTTTT 59.566 45.455 5.51 0.00 0.00 2.43
1878 2119 7.160726 TGAAAATTTATGCTTTTCTCCCTTGG 58.839 34.615 8.89 0.00 41.20 3.61
1953 2231 5.371526 CCTCATGTGATGGTGCTACTATTT 58.628 41.667 0.00 0.00 0.00 1.40
2041 2319 5.255687 TGATTTGTACTGCCTCATGTGATT 58.744 37.500 0.00 0.00 0.00 2.57
2087 2365 4.262207 GGATCGAGAATATGTTGAGCAGGA 60.262 45.833 0.00 0.00 0.00 3.86
2129 2407 4.161377 AGCATTAGAGAGACAAGGACTTCC 59.839 45.833 0.00 0.00 0.00 3.46
2267 2545 4.165372 GTCATAGGTTAACCAATCCCCAGA 59.835 45.833 26.26 9.38 38.89 3.86
2270 2548 4.204799 GTGTCATAGGTTAACCAATCCCC 58.795 47.826 26.26 9.83 38.89 4.81
2278 2556 6.978343 TGCTGTTATGTGTCATAGGTTAAC 57.022 37.500 0.00 0.00 0.00 2.01
2302 2580 6.151691 GCTTATGTGCTGATTTGAGTTTTCA 58.848 36.000 0.00 0.00 0.00 2.69
2402 2693 3.371917 CCATAGAAAGATGCCCAAGACCA 60.372 47.826 0.00 0.00 0.00 4.02
2431 2722 3.181466 GGTTGGTTTGCCTCAATTCAAGT 60.181 43.478 0.00 0.00 35.27 3.16


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

AutoCloner maintained by Alex Coulton.