Multiple sequence alignment - TraesCS1D01G371800

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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 TraesCS1D01G371800 chr1D 100.000 2987 0 0 1 2987 449924588 449921602 0.000000e+00 5517.0
1 TraesCS1D01G371800 chr1D 86.222 1350 125 32 666 1975 449846523 449847851 0.000000e+00 1406.0
2 TraesCS1D01G371800 chr1D 85.210 1217 130 32 672 1864 449660074 449661264 0.000000e+00 1205.0
3 TraesCS1D01G371800 chr1D 81.798 1346 178 50 748 2051 449674403 449675723 0.000000e+00 1066.0
4 TraesCS1D01G371800 chr1D 84.892 973 90 28 924 1864 449752562 449753509 0.000000e+00 929.0
5 TraesCS1D01G371800 chr1D 83.628 623 73 19 662 1277 449983757 449983157 2.600000e-155 558.0
6 TraesCS1D01G371800 chr1D 94.872 39 1 1 2255 2292 256992661 256992699 3.220000e-05 60.2
7 TraesCS1D01G371800 chr1B 86.650 1558 114 52 622 2120 615745591 615744069 0.000000e+00 1639.0
8 TraesCS1D01G371800 chr1B 84.042 1435 148 48 622 2003 616133025 616131619 0.000000e+00 1306.0
9 TraesCS1D01G371800 chr1B 85.890 1056 102 31 831 1864 615581586 615582616 0.000000e+00 1081.0
10 TraesCS1D01G371800 chr1B 85.495 1041 114 27 853 1862 615625462 615626496 0.000000e+00 1051.0
11 TraesCS1D01G371800 chr1B 92.857 616 35 7 2376 2987 617921999 617922609 0.000000e+00 885.0
12 TraesCS1D01G371800 chr1B 89.490 647 53 9 1369 2003 615732517 615733160 0.000000e+00 804.0
13 TraesCS1D01G371800 chr1B 87.759 531 43 6 748 1272 615731921 615732435 4.260000e-168 601.0
14 TraesCS1D01G371800 chr1B 81.051 628 79 24 653 1277 616136975 616136385 5.830000e-127 464.0
15 TraesCS1D01G371800 chr1B 80.172 464 75 14 2525 2979 541975783 541976238 6.170000e-87 331.0
16 TraesCS1D01G371800 chr1B 93.122 189 13 0 394 582 616133308 616133120 8.150000e-71 278.0
17 TraesCS1D01G371800 chr1B 92.593 189 14 0 394 582 615745874 615745686 3.790000e-69 272.0
18 TraesCS1D01G371800 chr1B 90.955 199 16 1 1 199 615753833 615753637 1.770000e-67 267.0
19 TraesCS1D01G371800 chr1B 90.476 126 11 1 2189 2314 615744065 615743941 6.620000e-37 165.0
20 TraesCS1D01G371800 chr1A 87.372 1465 110 38 666 2072 545009850 545008403 0.000000e+00 1611.0
21 TraesCS1D01G371800 chr1A 89.671 881 73 10 1000 1863 544748298 544749177 0.000000e+00 1107.0
22 TraesCS1D01G371800 chr1A 82.250 1369 160 48 652 2003 545025575 545024273 0.000000e+00 1105.0
23 TraesCS1D01G371800 chr1A 87.197 742 63 17 1128 1864 544927966 544928680 0.000000e+00 815.0
24 TraesCS1D01G371800 chr1A 91.141 587 28 10 1 582 545010545 545009978 0.000000e+00 774.0
25 TraesCS1D01G371800 chr1A 87.752 645 61 9 1369 2001 545000589 545001227 0.000000e+00 737.0
26 TraesCS1D01G371800 chr1A 84.355 620 48 29 661 1272 544999878 545000456 2.010000e-156 562.0
27 TraesCS1D01G371800 chr1A 83.491 424 41 14 666 1076 544927558 544927965 4.700000e-98 368.0
28 TraesCS1D01G371800 chr4D 80.300 467 79 12 2529 2987 455196010 455195549 1.030000e-89 340.0
29 TraesCS1D01G371800 chr4D 79.574 470 77 14 2525 2982 2768106 2768568 4.800000e-83 318.0
30 TraesCS1D01G371800 chr2B 80.000 470 83 10 2525 2987 743308629 743309094 1.330000e-88 337.0
31 TraesCS1D01G371800 chrUn 79.701 468 80 12 2529 2987 397841701 397841240 1.030000e-84 324.0
32 TraesCS1D01G371800 chrUn 97.222 36 1 0 2254 2289 56923933 56923968 8.940000e-06 62.1
33 TraesCS1D01G371800 chr3A 79.701 468 80 12 2529 2987 30284188 30284649 1.030000e-84 324.0
34 TraesCS1D01G371800 chr3A 79.701 468 80 12 2529 2987 30303479 30303940 1.030000e-84 324.0
35 TraesCS1D01G371800 chr3A 79.739 459 79 11 2529 2978 30250492 30250945 1.340000e-83 320.0
36 TraesCS1D01G371800 chr7A 83.871 93 14 1 2253 2345 232745456 232745365 1.480000e-13 87.9
37 TraesCS1D01G371800 chr2A 87.013 77 9 1 2252 2328 102688037 102688112 5.310000e-13 86.1
38 TraesCS1D01G371800 chr5A 83.951 81 9 4 2262 2341 33929235 33929158 1.150000e-09 75.0
39 TraesCS1D01G371800 chr5D 81.928 83 7 8 2262 2341 43962157 43962080 2.490000e-06 63.9
40 TraesCS1D01G371800 chr5D 77.679 112 18 7 2253 2360 50780433 50780541 8.940000e-06 62.1
41 TraesCS1D01G371800 chr4A 97.143 35 1 0 2255 2289 628332778 628332812 3.220000e-05 60.2


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 TraesCS1D01G371800 chr1D 449921602 449924588 2986 True 5517.000000 5517 100.000000 1 2987 1 chr1D.!!$R1 2986
1 TraesCS1D01G371800 chr1D 449846523 449847851 1328 False 1406.000000 1406 86.222000 666 1975 1 chr1D.!!$F5 1309
2 TraesCS1D01G371800 chr1D 449660074 449661264 1190 False 1205.000000 1205 85.210000 672 1864 1 chr1D.!!$F2 1192
3 TraesCS1D01G371800 chr1D 449674403 449675723 1320 False 1066.000000 1066 81.798000 748 2051 1 chr1D.!!$F3 1303
4 TraesCS1D01G371800 chr1D 449752562 449753509 947 False 929.000000 929 84.892000 924 1864 1 chr1D.!!$F4 940
5 TraesCS1D01G371800 chr1D 449983157 449983757 600 True 558.000000 558 83.628000 662 1277 1 chr1D.!!$R2 615
6 TraesCS1D01G371800 chr1B 615581586 615582616 1030 False 1081.000000 1081 85.890000 831 1864 1 chr1B.!!$F2 1033
7 TraesCS1D01G371800 chr1B 615625462 615626496 1034 False 1051.000000 1051 85.495000 853 1862 1 chr1B.!!$F3 1009
8 TraesCS1D01G371800 chr1B 617921999 617922609 610 False 885.000000 885 92.857000 2376 2987 1 chr1B.!!$F4 611
9 TraesCS1D01G371800 chr1B 615731921 615733160 1239 False 702.500000 804 88.624500 748 2003 2 chr1B.!!$F5 1255
10 TraesCS1D01G371800 chr1B 615743941 615745874 1933 True 692.000000 1639 89.906333 394 2314 3 chr1B.!!$R2 1920
11 TraesCS1D01G371800 chr1B 616131619 616136975 5356 True 682.666667 1306 86.071667 394 2003 3 chr1B.!!$R3 1609
12 TraesCS1D01G371800 chr1A 545008403 545010545 2142 True 1192.500000 1611 89.256500 1 2072 2 chr1A.!!$R2 2071
13 TraesCS1D01G371800 chr1A 544748298 544749177 879 False 1107.000000 1107 89.671000 1000 1863 1 chr1A.!!$F1 863
14 TraesCS1D01G371800 chr1A 545024273 545025575 1302 True 1105.000000 1105 82.250000 652 2003 1 chr1A.!!$R1 1351
15 TraesCS1D01G371800 chr1A 544999878 545001227 1349 False 649.500000 737 86.053500 661 2001 2 chr1A.!!$F3 1340
16 TraesCS1D01G371800 chr1A 544927558 544928680 1122 False 591.500000 815 85.344000 666 1864 2 chr1A.!!$F2 1198

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
288 293 1.081242 CTGCATTTGGACGCACACC 60.081 57.895 0.0 0.0 33.75 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 5757 0.101219 GGAGAAATGGATGTTGCCGC 59.899 55.0 0.0 0.0 0.0 6.53 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
33 34 1.907240 AATGGTATAGGTGCACCCCT 58.093 50.000 32.29 21.40 38.70 4.79
224 229 3.119096 GCCGCTGTCCTTCGGTTC 61.119 66.667 2.58 0.00 46.79 3.62
288 293 1.081242 CTGCATTTGGACGCACACC 60.081 57.895 0.00 0.00 33.75 4.16
338 343 1.210155 GCACGCACCCTGATTGAAC 59.790 57.895 0.00 0.00 0.00 3.18
366 371 3.512516 GCAGGGCCGCTGATTCAC 61.513 66.667 21.37 3.50 0.00 3.18
367 372 2.825836 CAGGGCCGCTGATTCACC 60.826 66.667 14.21 0.00 0.00 4.02
389 394 1.333115 CGCGACGTGATTTGTGACTA 58.667 50.000 0.00 0.00 0.00 2.59
418 3693 2.568956 TCAATTAGTGAGCTGAGCCACT 59.431 45.455 24.54 24.54 40.82 4.00
427 3702 3.390311 TGAGCTGAGCCACTGATGATTAT 59.610 43.478 0.00 0.00 0.00 1.28
546 3821 1.472480 GCATTGATGGCTTACGGTTGT 59.528 47.619 0.00 0.00 0.00 3.32
582 3857 1.602377 GCCGTGTTAAGTTGCTCTTGT 59.398 47.619 5.28 0.00 37.56 3.16
680 4017 1.789054 GCGCACGGCACACTATTTTAC 60.789 52.381 0.30 0.00 42.87 2.01
699 4036 2.199652 CCCACGGTGTGCCACAAAT 61.200 57.895 0.00 0.00 35.86 2.32
919 4308 2.049433 CGACCATACCGATCGCCC 60.049 66.667 10.32 0.00 0.00 6.13
941 4343 1.640428 ACATACATCGACGTTGCCTG 58.360 50.000 5.84 6.35 0.00 4.85
1098 4543 1.825474 CTCTACAACCACATCCTCCGT 59.175 52.381 0.00 0.00 0.00 4.69
1304 4767 4.097714 CGCAATGCATTCAGTTCGTATTT 58.902 39.130 9.53 0.00 0.00 1.40
1352 4852 1.470098 CAGCGGAAAGATTTGGGACAG 59.530 52.381 0.00 0.00 42.39 3.51
1354 4854 0.447801 CGGAAAGATTTGGGACAGCG 59.552 55.000 0.00 0.00 42.39 5.18
1365 4884 2.476051 GACAGCGTGTTGATGCGG 59.524 61.111 0.00 0.00 37.55 5.69
1373 4892 0.668096 GTGTTGATGCGGGTCGTGTA 60.668 55.000 0.00 0.00 0.00 2.90
1473 4992 0.396435 TCAAGAAGAAGCTCCGGCAA 59.604 50.000 0.00 0.00 41.70 4.52
1803 5348 2.442272 GGCTACGGGGAGAGCTCA 60.442 66.667 17.77 0.00 38.79 4.26
2067 5647 3.805207 AGAGAAACGTTAGTGCCACTTT 58.195 40.909 1.02 0.00 0.00 2.66
2068 5648 3.808174 AGAGAAACGTTAGTGCCACTTTC 59.192 43.478 1.02 0.00 0.00 2.62
2069 5649 3.537580 AGAAACGTTAGTGCCACTTTCA 58.462 40.909 1.02 0.00 0.00 2.69
2071 5651 1.878953 ACGTTAGTGCCACTTTCAGG 58.121 50.000 1.02 0.00 0.00 3.86
2080 5660 2.730550 CCACTTTCAGGCACCAATTC 57.269 50.000 0.00 0.00 0.00 2.17
2084 5664 1.547372 CTTTCAGGCACCAATTCCAGG 59.453 52.381 0.00 0.00 0.00 4.45
2085 5665 0.482446 TTCAGGCACCAATTCCAGGT 59.518 50.000 0.00 0.00 40.85 4.00
2086 5666 0.482446 TCAGGCACCAATTCCAGGTT 59.518 50.000 0.00 0.00 37.23 3.50
2088 5668 2.109128 TCAGGCACCAATTCCAGGTTTA 59.891 45.455 0.00 0.00 37.23 2.01
2089 5669 3.099141 CAGGCACCAATTCCAGGTTTAT 58.901 45.455 0.00 0.00 37.23 1.40
2090 5670 3.515104 CAGGCACCAATTCCAGGTTTATT 59.485 43.478 0.00 0.00 37.23 1.40
2091 5671 4.709397 CAGGCACCAATTCCAGGTTTATTA 59.291 41.667 0.00 0.00 37.23 0.98
2092 5672 5.363580 CAGGCACCAATTCCAGGTTTATTAT 59.636 40.000 0.00 0.00 37.23 1.28
2093 5673 6.549364 CAGGCACCAATTCCAGGTTTATTATA 59.451 38.462 0.00 0.00 37.23 0.98
2120 5701 4.104086 AGGTGATACAGAACAAGGATGGA 58.896 43.478 0.00 0.00 0.00 3.41
2122 5703 4.192317 GTGATACAGAACAAGGATGGACC 58.808 47.826 0.00 0.00 39.35 4.46
2123 5704 3.199946 TGATACAGAACAAGGATGGACCC 59.800 47.826 0.00 0.00 40.05 4.46
2124 5705 1.747444 ACAGAACAAGGATGGACCCT 58.253 50.000 0.00 0.00 40.05 4.34
2125 5706 2.065799 ACAGAACAAGGATGGACCCTT 58.934 47.619 0.00 0.00 46.91 3.95
2126 5707 2.040412 ACAGAACAAGGATGGACCCTTC 59.960 50.000 0.00 0.00 44.30 3.46
2127 5708 1.279271 AGAACAAGGATGGACCCTTCG 59.721 52.381 0.00 0.00 44.30 3.79
2128 5709 1.278127 GAACAAGGATGGACCCTTCGA 59.722 52.381 0.00 0.00 44.30 3.71
2129 5710 0.905357 ACAAGGATGGACCCTTCGAG 59.095 55.000 0.00 0.00 44.30 4.04
2130 5711 0.179000 CAAGGATGGACCCTTCGAGG 59.821 60.000 0.00 0.00 44.30 4.63
2131 5712 0.252742 AAGGATGGACCCTTCGAGGT 60.253 55.000 0.00 0.00 42.62 3.85
2132 5713 0.635009 AGGATGGACCCTTCGAGGTA 59.365 55.000 0.00 0.00 41.42 3.08
2133 5714 1.007963 AGGATGGACCCTTCGAGGTAA 59.992 52.381 0.00 0.00 41.42 2.85
2134 5715 2.047830 GGATGGACCCTTCGAGGTAAT 58.952 52.381 0.00 0.00 41.42 1.89
2135 5716 2.438392 GGATGGACCCTTCGAGGTAATT 59.562 50.000 0.00 0.00 41.42 1.40
2136 5717 3.118000 GGATGGACCCTTCGAGGTAATTT 60.118 47.826 0.00 0.00 41.42 1.82
2137 5718 3.622166 TGGACCCTTCGAGGTAATTTC 57.378 47.619 0.00 0.00 41.42 2.17
2138 5719 3.178865 TGGACCCTTCGAGGTAATTTCT 58.821 45.455 0.00 0.00 41.42 2.52
2139 5720 4.355549 TGGACCCTTCGAGGTAATTTCTA 58.644 43.478 0.00 0.00 41.42 2.10
2140 5721 4.404715 TGGACCCTTCGAGGTAATTTCTAG 59.595 45.833 0.00 0.00 41.42 2.43
2141 5722 4.202233 GGACCCTTCGAGGTAATTTCTAGG 60.202 50.000 0.00 0.00 41.42 3.02
2142 5723 3.134262 ACCCTTCGAGGTAATTTCTAGGC 59.866 47.826 0.00 0.00 38.79 3.93
2143 5724 3.494573 CCCTTCGAGGTAATTTCTAGGCC 60.495 52.174 0.00 0.00 31.93 5.19
2144 5725 3.494573 CCTTCGAGGTAATTTCTAGGCCC 60.495 52.174 0.00 0.00 0.00 5.80
2145 5726 3.042059 TCGAGGTAATTTCTAGGCCCT 57.958 47.619 0.00 0.00 0.00 5.19
2146 5727 3.381335 TCGAGGTAATTTCTAGGCCCTT 58.619 45.455 0.00 0.00 0.00 3.95
2147 5728 3.387050 TCGAGGTAATTTCTAGGCCCTTC 59.613 47.826 0.00 0.00 0.00 3.46
2148 5729 3.729966 GAGGTAATTTCTAGGCCCTTCG 58.270 50.000 0.00 0.00 0.00 3.79
2149 5730 3.381335 AGGTAATTTCTAGGCCCTTCGA 58.619 45.455 0.00 0.00 0.00 3.71
2150 5731 3.388350 AGGTAATTTCTAGGCCCTTCGAG 59.612 47.826 0.00 0.00 0.00 4.04
2151 5732 3.387050 GGTAATTTCTAGGCCCTTCGAGA 59.613 47.826 0.00 0.00 0.00 4.04
2152 5733 4.040584 GGTAATTTCTAGGCCCTTCGAGAT 59.959 45.833 0.00 0.00 0.00 2.75
2153 5734 5.245526 GGTAATTTCTAGGCCCTTCGAGATA 59.754 44.000 0.00 0.00 0.00 1.98
2154 5735 4.875561 ATTTCTAGGCCCTTCGAGATAC 57.124 45.455 0.00 0.00 0.00 2.24
2155 5736 3.308035 TTCTAGGCCCTTCGAGATACA 57.692 47.619 0.00 0.00 0.00 2.29
2156 5737 2.865079 TCTAGGCCCTTCGAGATACAG 58.135 52.381 0.00 0.00 0.00 2.74
2157 5738 2.442126 TCTAGGCCCTTCGAGATACAGA 59.558 50.000 0.00 0.00 0.00 3.41
2158 5739 2.160721 AGGCCCTTCGAGATACAGAA 57.839 50.000 0.00 0.00 0.00 3.02
2159 5740 1.757699 AGGCCCTTCGAGATACAGAAC 59.242 52.381 0.00 0.00 0.00 3.01
2160 5741 1.480954 GGCCCTTCGAGATACAGAACA 59.519 52.381 0.00 0.00 0.00 3.18
2161 5742 2.093658 GGCCCTTCGAGATACAGAACAA 60.094 50.000 0.00 0.00 0.00 2.83
2162 5743 3.190874 GCCCTTCGAGATACAGAACAAG 58.809 50.000 0.00 0.00 0.00 3.16
2163 5744 3.786635 CCCTTCGAGATACAGAACAAGG 58.213 50.000 0.00 0.00 0.00 3.61
2164 5745 3.447586 CCCTTCGAGATACAGAACAAGGA 59.552 47.826 0.00 0.00 32.16 3.36
2165 5746 4.100189 CCCTTCGAGATACAGAACAAGGAT 59.900 45.833 0.00 0.00 32.16 3.24
2166 5747 5.046529 CCTTCGAGATACAGAACAAGGATG 58.953 45.833 0.00 0.00 32.16 3.51
2167 5748 4.655762 TCGAGATACAGAACAAGGATGG 57.344 45.455 0.00 0.00 0.00 3.51
2168 5749 4.023980 TCGAGATACAGAACAAGGATGGT 58.976 43.478 0.00 0.00 0.00 3.55
2169 5750 4.115516 CGAGATACAGAACAAGGATGGTG 58.884 47.826 0.00 0.00 0.00 4.17
2170 5751 3.873952 GAGATACAGAACAAGGATGGTGC 59.126 47.826 0.00 0.00 0.00 5.01
2171 5752 2.093306 TACAGAACAAGGATGGTGCG 57.907 50.000 0.00 0.00 0.00 5.34
2172 5753 1.237285 ACAGAACAAGGATGGTGCGC 61.237 55.000 0.00 0.00 0.00 6.09
2173 5754 2.034879 AGAACAAGGATGGTGCGCG 61.035 57.895 0.00 0.00 0.00 6.86
2174 5755 2.281484 AACAAGGATGGTGCGCGT 60.281 55.556 8.43 0.00 0.00 6.01
2175 5756 1.852067 GAACAAGGATGGTGCGCGTT 61.852 55.000 8.43 0.00 0.00 4.84
2176 5757 2.128853 AACAAGGATGGTGCGCGTTG 62.129 55.000 8.43 3.94 36.33 4.10
2177 5758 3.737172 AAGGATGGTGCGCGTTGC 61.737 61.111 8.43 0.00 46.70 4.17
2250 5831 7.333528 TGAAGTTCAAATTGCAAGACTAACT 57.666 32.000 4.94 9.43 0.00 2.24
2251 5832 7.195646 TGAAGTTCAAATTGCAAGACTAACTG 58.804 34.615 16.20 3.06 0.00 3.16
2258 5839 9.890629 TCAAATTGCAAGACTAACTGATATACT 57.109 29.630 4.94 0.00 0.00 2.12
2260 5841 9.890629 AAATTGCAAGACTAACTGATATACTCA 57.109 29.630 4.94 0.00 0.00 3.41
2269 5850 8.152309 ACTAACTGATATACTCACTCCGTAAC 57.848 38.462 0.00 0.00 0.00 2.50
2314 5895 7.840342 AGAATTATGACAGTGTCAGAACATC 57.160 36.000 30.03 27.63 44.56 3.06
2315 5896 7.619050 AGAATTATGACAGTGTCAGAACATCT 58.381 34.615 30.03 28.94 44.56 2.90
2316 5897 7.763528 AGAATTATGACAGTGTCAGAACATCTC 59.236 37.037 30.03 22.74 44.56 2.75
2317 5898 6.596309 TTATGACAGTGTCAGAACATCTCT 57.404 37.500 28.54 12.80 46.04 3.10
2318 5899 4.944619 TGACAGTGTCAGAACATCTCTT 57.055 40.909 22.06 0.00 37.67 2.85
2319 5900 6.596309 ATGACAGTGTCAGAACATCTCTTA 57.404 37.500 28.54 2.99 46.04 2.10
2320 5901 6.596309 TGACAGTGTCAGAACATCTCTTAT 57.404 37.500 22.06 0.00 37.67 1.73
2321 5902 7.703058 TGACAGTGTCAGAACATCTCTTATA 57.297 36.000 22.06 0.00 37.67 0.98
2322 5903 8.298729 TGACAGTGTCAGAACATCTCTTATAT 57.701 34.615 22.06 0.00 37.67 0.86
2323 5904 8.753133 TGACAGTGTCAGAACATCTCTTATATT 58.247 33.333 22.06 0.00 37.67 1.28
2336 5917 8.820831 ACATCTCTTATATTAAGTCATGGAGGG 58.179 37.037 0.00 0.00 0.00 4.30
2337 5918 9.040259 CATCTCTTATATTAAGTCATGGAGGGA 57.960 37.037 0.00 0.00 0.00 4.20
2338 5919 8.657387 TCTCTTATATTAAGTCATGGAGGGAG 57.343 38.462 0.00 0.00 0.00 4.30
2339 5920 8.235230 TCTCTTATATTAAGTCATGGAGGGAGT 58.765 37.037 0.00 0.00 0.00 3.85
2340 5921 9.535170 CTCTTATATTAAGTCATGGAGGGAGTA 57.465 37.037 0.00 0.00 0.00 2.59
2345 5926 4.510167 AAGTCATGGAGGGAGTATTTGG 57.490 45.455 0.00 0.00 0.00 3.28
2346 5927 3.464828 AGTCATGGAGGGAGTATTTGGT 58.535 45.455 0.00 0.00 0.00 3.67
2347 5928 4.631234 AGTCATGGAGGGAGTATTTGGTA 58.369 43.478 0.00 0.00 0.00 3.25
2348 5929 5.036916 AGTCATGGAGGGAGTATTTGGTAA 58.963 41.667 0.00 0.00 0.00 2.85
2349 5930 5.672194 AGTCATGGAGGGAGTATTTGGTAAT 59.328 40.000 0.00 0.00 0.00 1.89
2350 5931 6.849697 AGTCATGGAGGGAGTATTTGGTAATA 59.150 38.462 0.00 0.00 0.00 0.98
2351 5932 7.349859 AGTCATGGAGGGAGTATTTGGTAATAA 59.650 37.037 0.00 0.00 0.00 1.40
2352 5933 8.164070 GTCATGGAGGGAGTATTTGGTAATAAT 58.836 37.037 0.00 0.00 0.00 1.28
2353 5934 8.732854 TCATGGAGGGAGTATTTGGTAATAATT 58.267 33.333 0.00 0.00 0.00 1.40
2354 5935 8.796475 CATGGAGGGAGTATTTGGTAATAATTG 58.204 37.037 0.00 0.00 0.00 2.32
2355 5936 8.108378 TGGAGGGAGTATTTGGTAATAATTGA 57.892 34.615 0.00 0.00 0.00 2.57
2356 5937 8.561769 TGGAGGGAGTATTTGGTAATAATTGAA 58.438 33.333 0.00 0.00 0.00 2.69
2357 5938 9.416284 GGAGGGAGTATTTGGTAATAATTGAAA 57.584 33.333 0.00 0.00 0.00 2.69
2434 6015 2.606308 CGATCCCTGTATTACCGAACGG 60.606 54.545 11.83 11.83 42.03 4.44
2480 6061 2.001872 CATGAATTTTTCAAGCGCCCC 58.998 47.619 2.29 0.00 43.95 5.80
2481 6062 0.320050 TGAATTTTTCAAGCGCCCCC 59.680 50.000 2.29 0.00 36.59 5.40
2612 6194 4.911514 AATGTTTTGTAGCTCAAACCGT 57.088 36.364 9.83 3.87 44.39 4.83
2614 6196 3.271729 TGTTTTGTAGCTCAAACCGTCA 58.728 40.909 9.83 6.14 44.39 4.35
2615 6197 3.880490 TGTTTTGTAGCTCAAACCGTCAT 59.120 39.130 9.83 0.00 44.39 3.06
2617 6199 4.481930 TTTGTAGCTCAAACCGTCATTG 57.518 40.909 0.00 0.00 40.56 2.82
2682 6264 5.749462 AGACCTTCAAAACTAGATCCCATG 58.251 41.667 0.00 0.00 0.00 3.66
2693 6275 8.682936 AAACTAGATCCCATGTTGATATGTTC 57.317 34.615 0.00 0.00 0.00 3.18
2697 6279 3.804036 TCCCATGTTGATATGTTCCGAC 58.196 45.455 0.00 0.00 0.00 4.79
2700 6282 4.058124 CCATGTTGATATGTTCCGACGAT 58.942 43.478 0.00 0.00 0.00 3.73
2735 6317 3.181527 GTAAAAAGTTACCACGCCTAGCG 60.182 47.826 7.54 7.54 44.34 4.26
2738 6320 7.606925 GTAAAAAGTTACCACGCCTAGCGTAT 61.607 42.308 14.91 8.64 46.84 3.06
2739 6321 9.496289 GTAAAAAGTTACCACGCCTAGCGTATG 62.496 44.444 14.91 11.26 46.84 2.39
2751 6333 5.526115 GCCTAGCGTATGTAAGTTATCACA 58.474 41.667 0.00 0.00 0.00 3.58
2800 6382 5.818336 TGATTAAATAGGCGAATTCCGAACA 59.182 36.000 0.00 0.00 41.76 3.18
2832 6414 4.635699 TTTCTCCAACTTTCTCCCTACC 57.364 45.455 0.00 0.00 0.00 3.18
2886 6468 6.494666 TGTCATCGTAGATTCCCCTATTTT 57.505 37.500 0.00 0.00 45.12 1.82
2933 6516 4.476628 ACCATCTGCCCAATTCAAAATC 57.523 40.909 0.00 0.00 0.00 2.17
2942 6525 6.297582 TGCCCAATTCAAAATCTGTTTTCAT 58.702 32.000 0.00 0.00 35.41 2.57
2944 6527 7.935755 TGCCCAATTCAAAATCTGTTTTCATAA 59.064 29.630 0.00 0.00 35.41 1.90
2983 6568 6.994221 GAGACCTTCGAAATTAGATCCCATA 58.006 40.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.181419 TCTAGGGGTGCACCTATACCAT 59.819 50.000 33.91 17.70 42.03 3.55
21 22 0.616679 GGTGTCTAGGGGTGCACCTA 60.617 60.000 33.91 19.09 45.64 3.08
22 23 1.918800 GGTGTCTAGGGGTGCACCT 60.919 63.158 33.91 18.99 45.64 4.00
49 50 2.597510 GTTTGCTTCGTGGGGGCT 60.598 61.111 0.00 0.00 0.00 5.19
117 118 2.688446 CGATCAGTGAACCTAGGCACTA 59.312 50.000 18.41 9.98 43.06 2.74
224 229 2.480037 TGCAGTGCAAACTAATCACTCG 59.520 45.455 17.26 0.00 38.85 4.18
266 271 2.945510 TGCGTCCAAATGCAGACAT 58.054 47.368 4.88 0.00 42.47 3.06
318 323 1.514678 TTCAATCAGGGTGCGTGCAC 61.515 55.000 16.40 16.40 45.49 4.57
319 324 1.228094 TTCAATCAGGGTGCGTGCA 60.228 52.632 0.00 0.00 0.00 4.57
320 325 1.210155 GTTCAATCAGGGTGCGTGC 59.790 57.895 0.00 0.00 0.00 5.34
321 326 1.227999 ACGTTCAATCAGGGTGCGTG 61.228 55.000 0.00 0.00 0.00 5.34
322 327 0.949105 GACGTTCAATCAGGGTGCGT 60.949 55.000 0.00 0.00 0.00 5.24
324 329 0.605319 TGGACGTTCAATCAGGGTGC 60.605 55.000 0.00 0.00 0.00 5.01
325 330 1.442769 CTGGACGTTCAATCAGGGTG 58.557 55.000 0.00 0.00 0.00 4.61
326 331 0.324943 CCTGGACGTTCAATCAGGGT 59.675 55.000 0.00 0.00 42.12 4.34
367 372 3.773630 ACAAATCACGTCGCGCGG 61.774 61.111 31.69 17.77 46.52 6.46
371 376 2.341760 GTCTAGTCACAAATCACGTCGC 59.658 50.000 0.00 0.00 0.00 5.19
389 394 6.291648 TCAGCTCACTAATTGATCAAGTCT 57.708 37.500 12.35 0.00 32.17 3.24
525 3800 1.102978 AACCGTAAGCCATCAATGCC 58.897 50.000 0.00 0.00 0.00 4.40
531 3806 1.530323 AACCACAACCGTAAGCCATC 58.470 50.000 0.00 0.00 0.00 3.51
546 3821 1.164411 CGGCACTGCTAATCAAACCA 58.836 50.000 0.00 0.00 0.00 3.67
664 4001 1.351683 TGGGGTAAAATAGTGTGCCGT 59.648 47.619 0.00 0.00 0.00 5.68
699 4036 1.211969 GAGCTTACGACACCTGCGA 59.788 57.895 0.00 0.00 0.00 5.10
805 4187 1.221466 TGTGAAGAACCGCAAGCTCG 61.221 55.000 0.00 0.00 0.00 5.03
919 4308 3.242944 CAGGCAACGTCGATGTATGTAAG 59.757 47.826 11.40 0.00 46.39 2.34
941 4343 1.943293 CTAGCTACTCCGACGAGCC 59.057 63.158 0.00 0.00 40.03 4.70
982 4401 0.831966 ATTGCAGGCTCCTCTCTCTG 59.168 55.000 0.00 0.00 0.00 3.35
984 4403 0.179051 CCATTGCAGGCTCCTCTCTC 60.179 60.000 0.00 0.00 0.00 3.20
985 4404 1.633915 CCCATTGCAGGCTCCTCTCT 61.634 60.000 0.00 0.00 0.00 3.10
1352 4852 4.147322 CGACCCGCATCAACACGC 62.147 66.667 0.00 0.00 0.00 5.34
1354 4854 0.668096 TACACGACCCGCATCAACAC 60.668 55.000 0.00 0.00 0.00 3.32
1365 4884 3.467119 CTGCACGCGTACACGACC 61.467 66.667 13.44 0.91 43.02 4.79
1473 4992 4.778143 GCGGGGTCGATGCCTTGT 62.778 66.667 0.00 0.00 39.00 3.16
1803 5348 0.752743 TCCAGTTGCTGCTGTTGCTT 60.753 50.000 0.00 0.00 40.48 3.91
1909 5478 2.325583 AACGAGAACTTGTGCTCCAA 57.674 45.000 3.37 0.00 0.00 3.53
2051 5631 2.218603 CCTGAAAGTGGCACTAACGTT 58.781 47.619 22.37 11.53 0.00 3.99
2067 5647 0.482446 AACCTGGAATTGGTGCCTGA 59.518 50.000 0.00 0.00 37.93 3.86
2068 5648 1.341080 AAACCTGGAATTGGTGCCTG 58.659 50.000 0.00 0.00 37.93 4.85
2069 5649 2.990740 TAAACCTGGAATTGGTGCCT 57.009 45.000 0.00 0.00 37.93 4.75
2093 5673 8.378565 CCATCCTTGTTCTGTATCACCTATAAT 58.621 37.037 0.00 0.00 0.00 1.28
2104 5685 2.915869 AGGGTCCATCCTTGTTCTGTA 58.084 47.619 0.00 0.00 32.13 2.74
2108 5689 1.278127 TCGAAGGGTCCATCCTTGTTC 59.722 52.381 0.00 0.00 46.31 3.18
2120 5701 3.134262 GCCTAGAAATTACCTCGAAGGGT 59.866 47.826 1.56 1.56 40.58 4.34
2122 5703 3.494573 GGGCCTAGAAATTACCTCGAAGG 60.495 52.174 0.84 0.00 42.49 3.46
2123 5704 3.388350 AGGGCCTAGAAATTACCTCGAAG 59.612 47.826 2.82 0.00 0.00 3.79
2124 5705 3.381335 AGGGCCTAGAAATTACCTCGAA 58.619 45.455 2.82 0.00 0.00 3.71
2125 5706 3.042059 AGGGCCTAGAAATTACCTCGA 57.958 47.619 2.82 0.00 0.00 4.04
2126 5707 3.729966 GAAGGGCCTAGAAATTACCTCG 58.270 50.000 6.41 0.00 0.00 4.63
2127 5708 3.387050 TCGAAGGGCCTAGAAATTACCTC 59.613 47.826 6.41 0.00 0.00 3.85
2128 5709 3.381335 TCGAAGGGCCTAGAAATTACCT 58.619 45.455 6.41 0.00 0.00 3.08
2129 5710 3.387050 TCTCGAAGGGCCTAGAAATTACC 59.613 47.826 6.41 0.00 0.00 2.85
2130 5711 4.667519 TCTCGAAGGGCCTAGAAATTAC 57.332 45.455 6.41 0.00 0.00 1.89
2131 5712 5.836898 TGTATCTCGAAGGGCCTAGAAATTA 59.163 40.000 6.41 0.00 0.00 1.40
2132 5713 4.654262 TGTATCTCGAAGGGCCTAGAAATT 59.346 41.667 6.41 0.00 0.00 1.82
2133 5714 4.223953 TGTATCTCGAAGGGCCTAGAAAT 58.776 43.478 6.41 4.64 0.00 2.17
2134 5715 3.637229 CTGTATCTCGAAGGGCCTAGAAA 59.363 47.826 6.41 0.00 0.00 2.52
2135 5716 3.117625 TCTGTATCTCGAAGGGCCTAGAA 60.118 47.826 6.41 1.69 0.00 2.10
2136 5717 2.442126 TCTGTATCTCGAAGGGCCTAGA 59.558 50.000 6.41 6.74 0.00 2.43
2137 5718 2.865079 TCTGTATCTCGAAGGGCCTAG 58.135 52.381 6.41 4.20 0.00 3.02
2138 5719 2.957006 GTTCTGTATCTCGAAGGGCCTA 59.043 50.000 6.41 0.00 0.00 3.93
2139 5720 1.757699 GTTCTGTATCTCGAAGGGCCT 59.242 52.381 0.00 0.00 0.00 5.19
2140 5721 1.480954 TGTTCTGTATCTCGAAGGGCC 59.519 52.381 0.00 0.00 0.00 5.80
2141 5722 2.961526 TGTTCTGTATCTCGAAGGGC 57.038 50.000 0.00 0.00 0.00 5.19
2142 5723 3.447586 TCCTTGTTCTGTATCTCGAAGGG 59.552 47.826 0.00 0.00 31.25 3.95
2143 5724 4.720649 TCCTTGTTCTGTATCTCGAAGG 57.279 45.455 0.00 0.00 0.00 3.46
2144 5725 5.046529 CCATCCTTGTTCTGTATCTCGAAG 58.953 45.833 0.00 0.00 0.00 3.79
2145 5726 4.466370 ACCATCCTTGTTCTGTATCTCGAA 59.534 41.667 0.00 0.00 0.00 3.71
2146 5727 4.023980 ACCATCCTTGTTCTGTATCTCGA 58.976 43.478 0.00 0.00 0.00 4.04
2147 5728 4.115516 CACCATCCTTGTTCTGTATCTCG 58.884 47.826 0.00 0.00 0.00 4.04
2148 5729 3.873952 GCACCATCCTTGTTCTGTATCTC 59.126 47.826 0.00 0.00 0.00 2.75
2149 5730 3.679917 CGCACCATCCTTGTTCTGTATCT 60.680 47.826 0.00 0.00 0.00 1.98
2150 5731 2.609459 CGCACCATCCTTGTTCTGTATC 59.391 50.000 0.00 0.00 0.00 2.24
2151 5732 2.632377 CGCACCATCCTTGTTCTGTAT 58.368 47.619 0.00 0.00 0.00 2.29
2152 5733 1.943968 GCGCACCATCCTTGTTCTGTA 60.944 52.381 0.30 0.00 0.00 2.74
2153 5734 1.237285 GCGCACCATCCTTGTTCTGT 61.237 55.000 0.30 0.00 0.00 3.41
2154 5735 1.503542 GCGCACCATCCTTGTTCTG 59.496 57.895 0.30 0.00 0.00 3.02
2155 5736 2.034879 CGCGCACCATCCTTGTTCT 61.035 57.895 8.75 0.00 0.00 3.01
2156 5737 1.852067 AACGCGCACCATCCTTGTTC 61.852 55.000 5.73 0.00 0.00 3.18
2157 5738 1.896660 AACGCGCACCATCCTTGTT 60.897 52.632 5.73 0.00 0.00 2.83
2158 5739 2.281484 AACGCGCACCATCCTTGT 60.281 55.556 5.73 0.00 0.00 3.16
2159 5740 2.176546 CAACGCGCACCATCCTTG 59.823 61.111 5.73 0.00 0.00 3.61
2160 5741 3.737172 GCAACGCGCACCATCCTT 61.737 61.111 5.73 0.00 41.79 3.36
2171 5752 2.817470 AATGGATGTTGCCGCAACGC 62.817 55.000 26.80 21.29 46.13 4.84
2172 5753 0.388391 AAATGGATGTTGCCGCAACG 60.388 50.000 26.80 0.00 46.13 4.10
2173 5754 1.067635 AGAAATGGATGTTGCCGCAAC 60.068 47.619 26.21 26.21 43.78 4.17
2174 5755 1.202114 GAGAAATGGATGTTGCCGCAA 59.798 47.619 0.38 0.38 0.00 4.85
2175 5756 0.810648 GAGAAATGGATGTTGCCGCA 59.189 50.000 0.00 0.00 0.00 5.69
2176 5757 0.101219 GGAGAAATGGATGTTGCCGC 59.899 55.000 0.00 0.00 0.00 6.53
2177 5758 0.378257 CGGAGAAATGGATGTTGCCG 59.622 55.000 0.00 0.00 0.00 5.69
2178 5759 1.401905 GTCGGAGAAATGGATGTTGCC 59.598 52.381 0.00 0.00 39.69 4.52
2179 5760 2.096496 CAGTCGGAGAAATGGATGTTGC 59.904 50.000 0.00 0.00 39.69 4.17
2180 5761 3.599343 TCAGTCGGAGAAATGGATGTTG 58.401 45.455 0.00 0.00 39.69 3.33
2181 5762 3.981071 TCAGTCGGAGAAATGGATGTT 57.019 42.857 0.00 0.00 39.69 2.71
2182 5763 3.261897 AGTTCAGTCGGAGAAATGGATGT 59.738 43.478 0.00 0.00 39.69 3.06
2183 5764 3.866651 AGTTCAGTCGGAGAAATGGATG 58.133 45.455 0.00 0.00 39.69 3.51
2184 5765 5.878406 ATAGTTCAGTCGGAGAAATGGAT 57.122 39.130 0.00 0.00 39.69 3.41
2185 5766 6.127101 TCTATAGTTCAGTCGGAGAAATGGA 58.873 40.000 0.00 0.00 39.69 3.41
2186 5767 6.392625 TCTATAGTTCAGTCGGAGAAATGG 57.607 41.667 0.00 0.00 39.69 3.16
2187 5768 8.879342 ATTTCTATAGTTCAGTCGGAGAAATG 57.121 34.615 6.24 0.00 39.48 2.32
2224 5805 9.066892 AGTTAGTCTTGCAATTTGAACTTCATA 57.933 29.630 0.00 0.00 0.00 2.15
2246 5827 8.743085 AAGTTACGGAGTGAGTATATCAGTTA 57.257 34.615 0.00 0.00 45.73 2.24
2258 5839 8.213518 ACGTCTTATATTAAGTTACGGAGTGA 57.786 34.615 11.01 0.00 45.73 3.41
2289 5870 8.099537 AGATGTTCTGACACTGTCATAATTCTT 58.900 33.333 12.34 0.56 41.94 2.52
2291 5872 7.763528 AGAGATGTTCTGACACTGTCATAATTC 59.236 37.037 12.34 11.75 41.94 2.17
2292 5873 7.619050 AGAGATGTTCTGACACTGTCATAATT 58.381 34.615 12.34 4.36 41.94 1.40
2311 5892 9.040259 TCCCTCCATGACTTAATATAAGAGATG 57.960 37.037 0.00 5.53 0.00 2.90
2314 5895 8.429237 ACTCCCTCCATGACTTAATATAAGAG 57.571 38.462 0.00 0.00 0.00 2.85
2319 5900 8.386264 CCAAATACTCCCTCCATGACTTAATAT 58.614 37.037 0.00 0.00 0.00 1.28
2320 5901 7.349859 ACCAAATACTCCCTCCATGACTTAATA 59.650 37.037 0.00 0.00 0.00 0.98
2321 5902 6.160459 ACCAAATACTCCCTCCATGACTTAAT 59.840 38.462 0.00 0.00 0.00 1.40
2322 5903 5.491078 ACCAAATACTCCCTCCATGACTTAA 59.509 40.000 0.00 0.00 0.00 1.85
2323 5904 5.036916 ACCAAATACTCCCTCCATGACTTA 58.963 41.667 0.00 0.00 0.00 2.24
2324 5905 3.852578 ACCAAATACTCCCTCCATGACTT 59.147 43.478 0.00 0.00 0.00 3.01
2325 5906 3.464828 ACCAAATACTCCCTCCATGACT 58.535 45.455 0.00 0.00 0.00 3.41
2326 5907 3.933861 ACCAAATACTCCCTCCATGAC 57.066 47.619 0.00 0.00 0.00 3.06
2327 5908 7.699709 TTATTACCAAATACTCCCTCCATGA 57.300 36.000 0.00 0.00 0.00 3.07
2328 5909 8.796475 CAATTATTACCAAATACTCCCTCCATG 58.204 37.037 0.00 0.00 0.00 3.66
2329 5910 8.732854 TCAATTATTACCAAATACTCCCTCCAT 58.267 33.333 0.00 0.00 0.00 3.41
2330 5911 8.108378 TCAATTATTACCAAATACTCCCTCCA 57.892 34.615 0.00 0.00 0.00 3.86
2331 5912 8.990163 TTCAATTATTACCAAATACTCCCTCC 57.010 34.615 0.00 0.00 0.00 4.30
2362 5943 9.847224 ATCGTTTGGAATATATTACTGTCCTTT 57.153 29.630 9.13 0.00 0.00 3.11
2363 5944 9.847224 AATCGTTTGGAATATATTACTGTCCTT 57.153 29.630 9.13 0.00 0.00 3.36
2364 5945 9.847224 AAATCGTTTGGAATATATTACTGTCCT 57.153 29.630 9.13 0.00 0.00 3.85
2365 5946 9.878599 CAAATCGTTTGGAATATATTACTGTCC 57.121 33.333 9.13 1.68 37.01 4.02
2368 5949 9.169468 GCACAAATCGTTTGGAATATATTACTG 57.831 33.333 9.13 0.00 44.81 2.74
2369 5950 8.349983 GGCACAAATCGTTTGGAATATATTACT 58.650 33.333 9.13 0.00 44.81 2.24
2370 5951 8.349983 AGGCACAAATCGTTTGGAATATATTAC 58.650 33.333 0.18 0.18 44.81 1.89
2371 5952 8.458573 AGGCACAAATCGTTTGGAATATATTA 57.541 30.769 12.79 0.00 44.81 0.98
2372 5953 7.346751 AGGCACAAATCGTTTGGAATATATT 57.653 32.000 0.00 0.00 44.81 1.28
2373 5954 6.959639 AGGCACAAATCGTTTGGAATATAT 57.040 33.333 12.79 0.00 44.81 0.86
2374 5955 8.349245 CAATAGGCACAAATCGTTTGGAATATA 58.651 33.333 12.79 3.17 44.81 0.86
2464 6045 1.182385 TCGGGGGCGCTTGAAAAATT 61.182 50.000 7.64 0.00 0.00 1.82
2480 6061 4.158025 ACACAATTAGTACAGAGGAGTCGG 59.842 45.833 0.00 0.00 0.00 4.79
2481 6062 5.312120 ACACAATTAGTACAGAGGAGTCG 57.688 43.478 0.00 0.00 0.00 4.18
2605 6187 2.610219 TCAATCGCAATGACGGTTTG 57.390 45.000 0.00 0.00 33.18 2.93
2642 6224 2.223377 GGTCTCGTCGCAACAAATCTTT 59.777 45.455 0.00 0.00 0.00 2.52
2649 6231 0.103390 TTGAAGGTCTCGTCGCAACA 59.897 50.000 0.00 0.00 0.00 3.33
2713 6295 4.332186 GCTAGGCGTGGTAACTTTTTAC 57.668 45.455 0.00 0.00 37.46 2.01
2751 6333 7.828508 TCGTGGTAACTTATGTACCATAGAT 57.171 36.000 6.59 0.00 44.58 1.98
2886 6468 9.698309 TTTCAGTACAAACATTTCAAAGTTTCA 57.302 25.926 0.00 0.00 35.90 2.69
2951 6536 4.598257 CGAAGGTCTCGCCATTGT 57.402 55.556 0.00 0.00 41.49 2.71


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

AutoCloner maintained by Alex Coulton.