Multiple sequence alignment - TraesCS2B01G430400

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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 TraesCS2B01G430400 chr2B 100.000 2819 0 0 1 2819 619387034 619389852 0.000000e+00 5206
1 TraesCS2B01G430400 chr2B 93.412 759 42 3 1 753 351831774 351832530 0.000000e+00 1118
2 TraesCS2B01G430400 chr2B 87.597 129 8 3 2383 2504 619389327 619389454 2.930000e-30 143
3 TraesCS2B01G430400 chr2B 87.597 129 8 3 2294 2421 619389416 619389537 2.930000e-30 143
4 TraesCS2B01G430400 chr2D 93.899 1262 51 10 907 2143 524033995 524035255 0.000000e+00 1881
5 TraesCS2B01G430400 chr2D 84.073 496 54 13 2340 2819 524036004 524036490 3.310000e-124 455
6 TraesCS2B01G430400 chr2D 91.165 249 20 2 2175 2421 524035931 524036179 1.250000e-88 337
7 TraesCS2B01G430400 chr2A 93.566 1259 55 16 907 2143 669624638 669625892 0.000000e+00 1853
8 TraesCS2B01G430400 chr5D 89.820 943 55 15 1 906 7586732 7587670 0.000000e+00 1171
9 TraesCS2B01G430400 chr5D 89.396 943 61 14 1 906 7588671 7589611 0.000000e+00 1151
10 TraesCS2B01G430400 chr5D 89.375 160 9 3 755 906 560185523 560185682 7.970000e-46 195
11 TraesCS2B01G430400 chr4B 93.316 763 43 2 1 756 591488535 591487774 0.000000e+00 1120
12 TraesCS2B01G430400 chr5B 93.493 753 43 2 1 747 644472117 644472869 0.000000e+00 1114
13 TraesCS2B01G430400 chr5B 91.617 167 7 3 753 913 644472906 644473071 1.020000e-54 224
14 TraesCS2B01G430400 chr1B 92.999 757 44 6 1 753 143443603 143444354 0.000000e+00 1096
15 TraesCS2B01G430400 chr6B 92.632 760 47 4 1 753 25968754 25969511 0.000000e+00 1085
16 TraesCS2B01G430400 chr6B 90.909 154 10 3 756 906 544634036 544633884 1.320000e-48 204
17 TraesCS2B01G430400 chr4A 92.026 765 47 7 2 754 705228476 705229238 0.000000e+00 1062
18 TraesCS2B01G430400 chr3B 93.093 666 37 5 1 660 62014712 62014050 0.000000e+00 966
19 TraesCS2B01G430400 chr3B 89.605 760 46 3 1 753 390915584 390914851 0.000000e+00 935
20 TraesCS2B01G430400 chr3B 98.901 91 1 0 817 907 227108694 227108604 2.250000e-36 163
21 TraesCS2B01G430400 chrUn 92.994 157 10 1 753 908 2232118 2232274 7.860000e-56 228
22 TraesCS2B01G430400 chr7B 91.176 136 6 2 777 906 348282297 348282162 2.230000e-41 180
23 TraesCS2B01G430400 chr7B 92.647 68 5 0 756 823 348282381 348282314 6.430000e-17 99
24 TraesCS2B01G430400 chr5A 84.713 157 19 4 754 906 520622298 520622143 4.860000e-33 152
25 TraesCS2B01G430400 chr3D 84.076 157 19 4 756 908 19334107 19334261 2.260000e-31 147


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 TraesCS2B01G430400 chr2B 619387034 619389852 2818 False 1830.666667 5206 91.731333 1 2819 3 chr2B.!!$F2 2818
1 TraesCS2B01G430400 chr2B 351831774 351832530 756 False 1118.000000 1118 93.412000 1 753 1 chr2B.!!$F1 752
2 TraesCS2B01G430400 chr2D 524033995 524036490 2495 False 891.000000 1881 89.712333 907 2819 3 chr2D.!!$F1 1912
3 TraesCS2B01G430400 chr2A 669624638 669625892 1254 False 1853.000000 1853 93.566000 907 2143 1 chr2A.!!$F1 1236
4 TraesCS2B01G430400 chr5D 7586732 7589611 2879 False 1161.000000 1171 89.608000 1 906 2 chr5D.!!$F2 905
5 TraesCS2B01G430400 chr4B 591487774 591488535 761 True 1120.000000 1120 93.316000 1 756 1 chr4B.!!$R1 755
6 TraesCS2B01G430400 chr5B 644472117 644473071 954 False 669.000000 1114 92.555000 1 913 2 chr5B.!!$F1 912
7 TraesCS2B01G430400 chr1B 143443603 143444354 751 False 1096.000000 1096 92.999000 1 753 1 chr1B.!!$F1 752
8 TraesCS2B01G430400 chr6B 25968754 25969511 757 False 1085.000000 1085 92.632000 1 753 1 chr6B.!!$F1 752
9 TraesCS2B01G430400 chr4A 705228476 705229238 762 False 1062.000000 1062 92.026000 2 754 1 chr4A.!!$F1 752
10 TraesCS2B01G430400 chr3B 62014050 62014712 662 True 966.000000 966 93.093000 1 660 1 chr3B.!!$R1 659
11 TraesCS2B01G430400 chr3B 390914851 390915584 733 True 935.000000 935 89.605000 1 753 1 chr3B.!!$R3 752

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
933 2951 0.419865 TACTCCCACTTCCCCCATCA 59.58 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2144 4194 0.586802 GACACAAGTTGCGTTCCTCC 59.413 55.0 1.81 0.0 0.0 4.3 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
226 238 6.018588 GGTGGTTTTAAAGTTTTTGAATCCCG 60.019 38.462 0.00 0.00 0.00 5.14
271 284 8.404000 CAAATTTTGTTCATGGGTGAAAAATCA 58.596 29.630 0.78 0.00 45.38 2.57
566 2523 5.355630 TGGAACTTCGAAACATTTCTTCACA 59.644 36.000 0.00 0.00 35.07 3.58
677 2634 6.922957 GTGTTGAATTCTGGCAAAATGACTAA 59.077 34.615 7.05 0.00 0.00 2.24
705 2662 5.288543 AGATATTAGCGCTGCAAATTAGC 57.711 39.130 22.90 3.56 37.80 3.09
748 2705 1.673168 GGCTATTGGGAGCACTTCAG 58.327 55.000 0.00 0.00 44.76 3.02
810 2822 1.800805 CTTCCCATCGCGCTTGATAT 58.199 50.000 5.56 0.00 0.00 1.63
814 2826 1.404717 CCCATCGCGCTTGATATAGCT 60.405 52.381 5.56 0.00 39.03 3.32
933 2951 0.419865 TACTCCCACTTCCCCCATCA 59.580 55.000 0.00 0.00 0.00 3.07
1051 3069 2.097038 CGAAGAGCCGCAACTCCTG 61.097 63.158 0.00 0.00 37.39 3.86
1057 3075 2.626780 GCCGCAACTCCTGAAACCC 61.627 63.158 0.00 0.00 0.00 4.11
1162 3180 0.036294 AGTAACGGAAGAAGCCCTGC 60.036 55.000 0.00 0.00 0.00 4.85
1379 3398 2.980233 GGACAGCCACAGCCACAC 60.980 66.667 0.00 0.00 41.25 3.82
1574 3599 2.657237 CTTCGAGTTCACGGGCCT 59.343 61.111 0.84 0.00 0.00 5.19
1898 3936 7.544566 TGTGAAGTTGAAGTTAAGTATCGATCC 59.455 37.037 0.00 0.00 0.00 3.36
1958 4000 8.936864 AGTTTCTGAATAAATACTCGGTTTCAG 58.063 33.333 0.00 0.00 40.72 3.02
1959 4001 8.718734 GTTTCTGAATAAATACTCGGTTTCAGT 58.281 33.333 9.52 0.00 40.41 3.41
1960 4002 8.475331 TTCTGAATAAATACTCGGTTTCAGTC 57.525 34.615 9.52 0.00 40.41 3.51
1966 4011 5.723672 AATACTCGGTTTCAGTCTCTTGA 57.276 39.130 0.00 0.00 0.00 3.02
2091 4141 4.866508 TGACTGATTTGTCCTAAGTCGT 57.133 40.909 0.00 0.00 40.10 4.34
2102 4152 1.405821 CCTAAGTCGTACCAGCCTCAG 59.594 57.143 0.00 0.00 0.00 3.35
2131 4181 2.423892 AGTGCACTAGTCTCCATGTACG 59.576 50.000 20.16 0.00 33.49 3.67
2139 4189 4.392921 AGTCTCCATGTACGAAATCAGG 57.607 45.455 0.00 0.00 0.00 3.86
2143 4193 2.434336 TCCATGTACGAAATCAGGAGGG 59.566 50.000 0.00 0.00 0.00 4.30
2144 4194 2.485479 CCATGTACGAAATCAGGAGGGG 60.485 54.545 0.00 0.00 0.00 4.79
2145 4195 1.200519 TGTACGAAATCAGGAGGGGG 58.799 55.000 0.00 0.00 0.00 5.40
2146 4196 1.273381 TGTACGAAATCAGGAGGGGGA 60.273 52.381 0.00 0.00 0.00 4.81
2147 4197 1.413077 GTACGAAATCAGGAGGGGGAG 59.587 57.143 0.00 0.00 0.00 4.30
2148 4198 0.983378 ACGAAATCAGGAGGGGGAGG 60.983 60.000 0.00 0.00 0.00 4.30
2150 4200 1.596496 GAAATCAGGAGGGGGAGGAA 58.404 55.000 0.00 0.00 0.00 3.36
2152 4202 0.983378 AATCAGGAGGGGGAGGAACG 60.983 60.000 0.00 0.00 0.00 3.95
2153 4203 3.787001 CAGGAGGGGGAGGAACGC 61.787 72.222 0.00 0.00 0.00 4.84
2154 4204 4.332543 AGGAGGGGGAGGAACGCA 62.333 66.667 0.00 0.00 0.00 5.24
2156 4206 2.046217 GAGGGGGAGGAACGCAAC 60.046 66.667 0.00 0.00 0.00 4.17
2159 4209 1.971695 GGGGGAGGAACGCAACTTG 60.972 63.158 0.00 0.00 0.00 3.16
2160 4210 1.228154 GGGGAGGAACGCAACTTGT 60.228 57.895 0.00 0.00 0.00 3.16
2162 4212 0.818040 GGGAGGAACGCAACTTGTGT 60.818 55.000 1.94 1.94 43.87 3.72
2163 4213 0.586802 GGAGGAACGCAACTTGTGTC 59.413 55.000 8.41 3.14 40.68 3.67
2164 4214 1.583054 GAGGAACGCAACTTGTGTCT 58.417 50.000 8.41 2.78 40.68 3.41
2166 4216 2.354821 GAGGAACGCAACTTGTGTCTTT 59.645 45.455 8.41 0.00 40.68 2.52
2167 4217 2.354821 AGGAACGCAACTTGTGTCTTTC 59.645 45.455 8.41 3.25 40.68 2.62
2168 4218 2.354821 GGAACGCAACTTGTGTCTTTCT 59.645 45.455 8.41 0.00 40.68 2.52
2169 4219 3.181500 GGAACGCAACTTGTGTCTTTCTT 60.181 43.478 8.41 0.00 40.68 2.52
2170 4220 4.412207 GAACGCAACTTGTGTCTTTCTTT 58.588 39.130 8.41 0.00 40.68 2.52
2171 4221 5.448089 GGAACGCAACTTGTGTCTTTCTTTA 60.448 40.000 8.41 0.00 40.68 1.85
2173 4223 6.854496 ACGCAACTTGTGTCTTTCTTTATA 57.146 33.333 1.94 0.00 36.11 0.98
2174 4224 7.435068 ACGCAACTTGTGTCTTTCTTTATAT 57.565 32.000 1.94 0.00 36.11 0.86
2175 4225 8.542497 ACGCAACTTGTGTCTTTCTTTATATA 57.458 30.769 1.94 0.00 36.11 0.86
2176 4226 8.440833 ACGCAACTTGTGTCTTTCTTTATATAC 58.559 33.333 1.94 0.00 36.11 1.47
2177 4227 8.440059 CGCAACTTGTGTCTTTCTTTATATACA 58.560 33.333 0.00 0.00 0.00 2.29
2220 4914 0.524816 GATGTTTGCTCATGCCAGCG 60.525 55.000 2.31 0.00 42.92 5.18
2224 4918 1.588824 TTTGCTCATGCCAGCGGAAG 61.589 55.000 2.31 0.00 42.92 3.46
2234 4928 3.406682 CAGCGGAAGATGTTTTGCC 57.593 52.632 0.00 0.00 43.76 4.52
2238 4932 1.202114 GCGGAAGATGTTTTGCCATGA 59.798 47.619 0.00 0.00 0.00 3.07
2262 4957 4.504858 ACCGAAGATGTTAGCTAAAGTGG 58.495 43.478 7.99 6.23 0.00 4.00
2279 4974 1.000274 GTGGGTTGTCATGGCAACTTC 60.000 52.381 34.86 27.47 45.69 3.01
2284 4979 2.728690 TGTCATGGCAACTTCAATGC 57.271 45.000 0.00 0.00 43.08 3.56
2290 4985 4.452795 TCATGGCAACTTCAATGCATTTTG 59.547 37.500 9.83 12.76 45.60 2.44
2319 5014 3.018856 CAACTGAAGATGCCTTGGCATA 58.981 45.455 24.97 10.36 31.62 3.14
2323 5018 1.607628 GAAGATGCCTTGGCATAGCAG 59.392 52.381 24.97 0.00 40.40 4.24
2327 5022 0.255604 TGCCTTGGCATAGCAGCTTA 59.744 50.000 10.65 0.00 34.17 3.09
2328 5023 1.340893 TGCCTTGGCATAGCAGCTTAA 60.341 47.619 10.65 0.00 34.17 1.85
2354 5049 4.696877 TGTCAGCCATGTCAACTTAAGATG 59.303 41.667 10.09 8.06 0.00 2.90
2366 5061 4.032960 ACTTAAGATGTGTTGCCATGGA 57.967 40.909 18.40 0.00 0.00 3.41
2377 5072 5.069648 TGTGTTGCCATGGAAACTGAAAATA 59.930 36.000 31.58 10.89 34.80 1.40
2409 5105 5.624344 CAAAAATATGTTTTGGCATGGCA 57.376 34.783 19.43 19.43 37.59 4.92
2410 5106 6.010294 CAAAAATATGTTTTGGCATGGCAA 57.990 33.333 29.00 29.00 37.59 4.52
2411 5107 5.625921 AAAATATGTTTTGGCATGGCAAC 57.374 34.783 32.02 23.17 36.24 4.17
2412 5108 4.556592 AATATGTTTTGGCATGGCAACT 57.443 36.364 32.02 19.15 37.61 3.16
2413 5109 2.934886 ATGTTTTGGCATGGCAACTT 57.065 40.000 32.02 18.33 37.61 2.66
2414 5110 5.674052 ATATGTTTTGGCATGGCAACTTA 57.326 34.783 32.02 23.15 37.61 2.24
2415 5111 3.827008 TGTTTTGGCATGGCAACTTAA 57.173 38.095 32.02 21.45 37.61 1.85
2416 5112 3.726607 TGTTTTGGCATGGCAACTTAAG 58.273 40.909 32.02 0.00 37.61 1.85
2417 5113 3.386078 TGTTTTGGCATGGCAACTTAAGA 59.614 39.130 32.02 19.90 37.61 2.10
2418 5114 4.040217 TGTTTTGGCATGGCAACTTAAGAT 59.960 37.500 32.02 0.00 37.61 2.40
2419 5115 3.872511 TTGGCATGGCAACTTAAGATG 57.127 42.857 29.00 9.09 37.61 2.90
2420 5116 2.806434 TGGCATGGCAACTTAAGATGT 58.194 42.857 21.13 0.00 37.61 3.06
2421 5117 2.754552 TGGCATGGCAACTTAAGATGTC 59.245 45.455 21.13 10.14 37.61 3.06
2422 5118 2.754552 GGCATGGCAACTTAAGATGTCA 59.245 45.455 20.47 20.47 36.88 3.58
2423 5119 3.181493 GGCATGGCAACTTAAGATGTCAG 60.181 47.826 22.18 15.65 35.94 3.51
2424 5120 3.733077 GCATGGCAACTTAAGATGTCAGC 60.733 47.826 22.18 20.04 35.94 4.26
2425 5121 2.436417 TGGCAACTTAAGATGTCAGCC 58.564 47.619 15.23 14.20 38.31 4.85
2426 5122 2.224744 TGGCAACTTAAGATGTCAGCCA 60.225 45.455 15.23 16.18 42.25 4.75
2427 5123 3.019564 GGCAACTTAAGATGTCAGCCAT 58.980 45.455 12.02 0.00 37.97 4.40
2428 5124 3.181493 GGCAACTTAAGATGTCAGCCATG 60.181 47.826 12.02 0.00 37.97 3.66
2429 5125 3.441572 GCAACTTAAGATGTCAGCCATGT 59.558 43.478 10.09 0.00 32.56 3.21
2430 5126 4.437930 GCAACTTAAGATGTCAGCCATGTC 60.438 45.833 10.09 0.00 32.56 3.06
2431 5127 4.558226 ACTTAAGATGTCAGCCATGTCA 57.442 40.909 10.09 0.00 32.56 3.58
2432 5128 4.910195 ACTTAAGATGTCAGCCATGTCAA 58.090 39.130 10.09 0.00 32.56 3.18
2433 5129 4.940046 ACTTAAGATGTCAGCCATGTCAAG 59.060 41.667 10.09 0.00 32.56 3.02
2434 5130 3.708403 AAGATGTCAGCCATGTCAAGA 57.292 42.857 0.00 0.00 32.56 3.02
2435 5131 3.928005 AGATGTCAGCCATGTCAAGAT 57.072 42.857 0.00 0.00 32.56 2.40
2436 5132 3.542648 AGATGTCAGCCATGTCAAGATG 58.457 45.455 0.00 0.00 32.56 2.90
2437 5133 2.865119 TGTCAGCCATGTCAAGATGT 57.135 45.000 0.00 0.00 0.00 3.06
2438 5134 2.429478 TGTCAGCCATGTCAAGATGTG 58.571 47.619 0.00 0.00 0.00 3.21
2439 5135 2.224597 TGTCAGCCATGTCAAGATGTGT 60.225 45.455 0.00 0.00 0.00 3.72
2440 5136 2.816087 GTCAGCCATGTCAAGATGTGTT 59.184 45.455 0.00 0.00 0.00 3.32
2441 5137 2.815503 TCAGCCATGTCAAGATGTGTTG 59.184 45.455 0.00 0.00 0.00 3.33
2442 5138 1.542915 AGCCATGTCAAGATGTGTTGC 59.457 47.619 0.00 0.00 0.00 4.17
2443 5139 1.403249 GCCATGTCAAGATGTGTTGCC 60.403 52.381 0.00 0.00 0.00 4.52
2444 5140 1.887854 CCATGTCAAGATGTGTTGCCA 59.112 47.619 0.00 0.00 0.00 4.92
2445 5141 2.494471 CCATGTCAAGATGTGTTGCCAT 59.506 45.455 0.00 0.00 0.00 4.40
2446 5142 3.507786 CATGTCAAGATGTGTTGCCATG 58.492 45.455 0.58 0.58 0.00 3.66
2447 5143 1.887854 TGTCAAGATGTGTTGCCATGG 59.112 47.619 7.63 7.63 0.00 3.66
2448 5144 2.161855 GTCAAGATGTGTTGCCATGGA 58.838 47.619 18.40 0.00 0.00 3.41
2449 5145 2.557924 GTCAAGATGTGTTGCCATGGAA 59.442 45.455 18.40 0.00 0.00 3.53
2450 5146 3.005684 GTCAAGATGTGTTGCCATGGAAA 59.994 43.478 18.40 9.10 0.00 3.13
2451 5147 3.005684 TCAAGATGTGTTGCCATGGAAAC 59.994 43.478 26.71 26.71 34.32 2.78
2452 5148 2.880443 AGATGTGTTGCCATGGAAACT 58.120 42.857 31.58 15.50 34.80 2.66
2453 5149 2.559668 AGATGTGTTGCCATGGAAACTG 59.440 45.455 31.58 0.00 34.80 3.16
2454 5150 2.064434 TGTGTTGCCATGGAAACTGA 57.936 45.000 31.58 17.78 34.80 3.41
2455 5151 2.382882 TGTGTTGCCATGGAAACTGAA 58.617 42.857 31.58 16.89 34.80 3.02
2456 5152 2.762887 TGTGTTGCCATGGAAACTGAAA 59.237 40.909 31.58 12.66 34.80 2.69
2457 5153 3.196469 TGTGTTGCCATGGAAACTGAAAA 59.804 39.130 31.58 12.30 34.80 2.29
2458 5154 4.187694 GTGTTGCCATGGAAACTGAAAAA 58.812 39.130 31.58 11.59 34.80 1.94
2459 5155 4.815846 GTGTTGCCATGGAAACTGAAAAAT 59.184 37.500 31.58 0.00 34.80 1.82
2460 5156 4.815308 TGTTGCCATGGAAACTGAAAAATG 59.185 37.500 31.58 0.00 34.80 2.32
2461 5157 4.686191 TGCCATGGAAACTGAAAAATGT 57.314 36.364 18.40 0.00 0.00 2.71
2462 5158 5.033589 TGCCATGGAAACTGAAAAATGTT 57.966 34.783 18.40 0.00 0.00 2.71
2463 5159 4.815308 TGCCATGGAAACTGAAAAATGTTG 59.185 37.500 18.40 0.00 0.00 3.33
2464 5160 4.213906 GCCATGGAAACTGAAAAATGTTGG 59.786 41.667 18.40 0.00 0.00 3.77
2465 5161 4.213906 CCATGGAAACTGAAAAATGTTGGC 59.786 41.667 5.56 0.00 0.00 4.52
2466 5162 4.478206 TGGAAACTGAAAAATGTTGGCA 57.522 36.364 0.00 0.00 0.00 4.92
2467 5163 5.033589 TGGAAACTGAAAAATGTTGGCAT 57.966 34.783 0.00 0.00 36.80 4.40
2468 5164 4.815308 TGGAAACTGAAAAATGTTGGCATG 59.185 37.500 0.00 0.00 35.15 4.06
2469 5165 4.319694 GGAAACTGAAAAATGTTGGCATGC 60.320 41.667 9.90 9.90 35.15 4.06
2470 5166 2.769893 ACTGAAAAATGTTGGCATGCC 58.230 42.857 30.54 30.54 35.15 4.40
2471 5167 2.104451 ACTGAAAAATGTTGGCATGCCA 59.896 40.909 35.59 35.59 45.63 4.92
2484 5180 5.624344 TGGCATGCCAAAAATATGTTTTG 57.376 34.783 36.95 5.39 44.12 2.44
2551 5247 6.790232 TTTCTGTCCATTCAAGGTTTTCTT 57.210 33.333 0.00 0.00 35.79 2.52
2558 5254 6.986231 GTCCATTCAAGGTTTTCTTTTGTGAT 59.014 34.615 0.00 0.00 32.41 3.06
2584 5280 7.769272 TTTAGATGGCAACTTTTTGTTTCTG 57.231 32.000 1.54 0.00 36.63 3.02
2586 5282 5.351458 AGATGGCAACTTTTTGTTTCTGTC 58.649 37.500 0.00 0.00 36.63 3.51
2587 5283 4.527509 TGGCAACTTTTTGTTTCTGTCA 57.472 36.364 0.00 0.00 36.63 3.58
2588 5284 4.887748 TGGCAACTTTTTGTTTCTGTCAA 58.112 34.783 0.00 0.00 36.63 3.18
2589 5285 5.486526 TGGCAACTTTTTGTTTCTGTCAAT 58.513 33.333 0.00 0.00 36.63 2.57
2590 5286 5.936956 TGGCAACTTTTTGTTTCTGTCAATT 59.063 32.000 0.00 0.00 36.63 2.32
2633 5329 8.856153 ACATCATGTGTGTTGGTAGTTTATTA 57.144 30.769 0.00 0.00 40.28 0.98
2635 5331 7.372451 TCATGTGTGTTGGTAGTTTATTAGC 57.628 36.000 0.00 0.00 0.00 3.09
2664 5360 7.807977 AATTGGGCAACTCTAAGTATATGTG 57.192 36.000 0.00 0.00 0.00 3.21
2669 5365 6.821665 GGGCAACTCTAAGTATATGTGTGAAA 59.178 38.462 0.00 0.00 0.00 2.69
2682 5378 2.917701 TGTGAAACAGTTGCAGTGTG 57.082 45.000 0.00 0.00 45.67 3.82
2685 5381 3.044855 GTGAAACAGTTGCAGTGTGCAG 61.045 50.000 0.00 0.00 46.62 4.41
2696 5392 2.350522 CAGTGTGCAGACCATACTTCC 58.649 52.381 10.88 0.00 42.44 3.46
2713 5409 7.382218 CCATACTTCCTTTCATTTCACAAACAC 59.618 37.037 0.00 0.00 0.00 3.32
2715 5411 4.974368 TCCTTTCATTTCACAAACACGT 57.026 36.364 0.00 0.00 0.00 4.49
2720 5416 8.788806 TCCTTTCATTTCACAAACACGTTATAT 58.211 29.630 0.00 0.00 0.00 0.86
2776 5472 6.072175 TGGCACACTCATGGTAAACTATTTTC 60.072 38.462 0.00 0.00 0.00 2.29
2777 5473 6.021596 GCACACTCATGGTAAACTATTTTCG 58.978 40.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.703892 TCGAATTCATAACATGTTTTCCAATTT 57.296 25.926 17.78 2.82 0.00 1.82
162 174 6.335777 ACTCCTGAGCATATTTTGAATTTGC 58.664 36.000 7.66 7.66 0.00 3.68
178 190 9.846248 CACCAATATTTTTAGAAAACTCCTGAG 57.154 33.333 0.00 0.00 0.00 3.35
296 309 3.454082 ACCCCTTGAGCAATTTTGAAACA 59.546 39.130 0.00 0.00 0.00 2.83
356 2311 6.650239 TTTTCCTTTTTGTAAAAGCGAACC 57.350 33.333 6.42 0.00 0.00 3.62
426 2383 8.816640 AACATATTTTCCAATTGTGAACACTC 57.183 30.769 4.43 0.00 0.00 3.51
550 2507 9.712410 CGAATAAAATTGTGAAGAAATGTTTCG 57.288 29.630 0.24 0.00 41.92 3.46
677 2634 7.678947 ATTTGCAGCGCTAATATCTAAGAAT 57.321 32.000 10.99 0.00 32.90 2.40
705 2662 5.692204 CGTGTGAGCTAATAATCCTAAGTGG 59.308 44.000 0.00 0.00 37.10 4.00
810 2822 2.423898 GGCAGACGGGTGCTAGCTA 61.424 63.158 17.23 0.00 43.45 3.32
814 2826 2.584064 CATGGCAGACGGGTGCTA 59.416 61.111 10.64 5.58 43.45 3.49
955 2973 1.291877 GATTTCTGCGTGCCTCGTGT 61.292 55.000 0.83 0.00 42.13 4.49
1073 3091 1.947146 GGCGGTTTTGTTGCGGTTC 60.947 57.895 0.00 0.00 0.00 3.62
1074 3092 2.105328 GGCGGTTTTGTTGCGGTT 59.895 55.556 0.00 0.00 0.00 4.44
1121 3139 4.680237 CGGCAGTGGCGTTCTCCA 62.680 66.667 29.14 0.00 46.33 3.86
1145 3163 1.298667 GGCAGGGCTTCTTCCGTTA 59.701 57.895 0.00 0.00 0.00 3.18
1256 3275 2.747855 GGGAGTTCAGCGCCTTGG 60.748 66.667 2.29 0.00 37.22 3.61
1665 3690 2.879907 GCGGTAGTACCTGTCGCA 59.120 61.111 17.29 0.00 44.87 5.10
1666 3691 1.063811 GAGCGGTAGTACCTGTCGC 59.936 63.158 17.29 14.43 45.72 5.19
1761 3786 0.589223 CGGCAAACTCTAACGCCAAA 59.411 50.000 0.00 0.00 45.14 3.28
1898 3936 5.473504 ACACTTGTACTGAATAAAGCAAGGG 59.526 40.000 0.00 0.00 41.51 3.95
1966 4011 9.942850 CATTAAAGGAGGTTAAATTGATGGTTT 57.057 29.630 0.00 0.00 0.00 3.27
2008 4053 7.832503 ATGCATAACAGAAAGGCAAATTTAC 57.167 32.000 0.00 0.00 38.08 2.01
2091 4141 3.195610 CACTACACAATCTGAGGCTGGTA 59.804 47.826 0.00 0.00 0.00 3.25
2131 4181 1.213182 GTTCCTCCCCCTCCTGATTTC 59.787 57.143 0.00 0.00 0.00 2.17
2139 4189 2.046217 GTTGCGTTCCTCCCCCTC 60.046 66.667 0.00 0.00 0.00 4.30
2143 4193 0.818040 ACACAAGTTGCGTTCCTCCC 60.818 55.000 1.81 0.00 0.00 4.30
2144 4194 0.586802 GACACAAGTTGCGTTCCTCC 59.413 55.000 1.81 0.00 0.00 4.30
2145 4195 1.583054 AGACACAAGTTGCGTTCCTC 58.417 50.000 1.81 0.00 0.00 3.71
2146 4196 2.038387 AAGACACAAGTTGCGTTCCT 57.962 45.000 1.81 0.00 0.00 3.36
2147 4197 2.354821 AGAAAGACACAAGTTGCGTTCC 59.645 45.455 1.81 0.00 0.00 3.62
2148 4198 3.675467 AGAAAGACACAAGTTGCGTTC 57.325 42.857 1.81 1.54 0.00 3.95
2150 4200 5.751243 ATAAAGAAAGACACAAGTTGCGT 57.249 34.783 1.81 0.00 0.00 5.24
2166 4216 9.226606 CCACCTGTGTCTTTTTGTATATAAAGA 57.773 33.333 1.85 1.85 37.88 2.52
2167 4217 7.968405 GCCACCTGTGTCTTTTTGTATATAAAG 59.032 37.037 0.00 0.00 33.65 1.85
2168 4218 7.448777 TGCCACCTGTGTCTTTTTGTATATAAA 59.551 33.333 0.00 0.00 0.00 1.40
2169 4219 6.943146 TGCCACCTGTGTCTTTTTGTATATAA 59.057 34.615 0.00 0.00 0.00 0.98
2170 4220 6.477253 TGCCACCTGTGTCTTTTTGTATATA 58.523 36.000 0.00 0.00 0.00 0.86
2171 4221 5.321102 TGCCACCTGTGTCTTTTTGTATAT 58.679 37.500 0.00 0.00 0.00 0.86
2173 4223 3.561143 TGCCACCTGTGTCTTTTTGTAT 58.439 40.909 0.00 0.00 0.00 2.29
2174 4224 3.006112 TGCCACCTGTGTCTTTTTGTA 57.994 42.857 0.00 0.00 0.00 2.41
2175 4225 1.846007 TGCCACCTGTGTCTTTTTGT 58.154 45.000 0.00 0.00 0.00 2.83
2176 4226 2.957491 TTGCCACCTGTGTCTTTTTG 57.043 45.000 0.00 0.00 0.00 2.44
2177 4227 3.260632 AGTTTTGCCACCTGTGTCTTTTT 59.739 39.130 0.00 0.00 0.00 1.94
2186 4880 3.457610 AACATCAAGTTTTGCCACCTG 57.542 42.857 0.00 0.00 37.03 4.00
2220 4914 3.996363 GGTTTCATGGCAAAACATCTTCC 59.004 43.478 14.73 0.00 38.16 3.46
2224 4918 3.296322 TCGGTTTCATGGCAAAACATC 57.704 42.857 14.73 0.67 38.16 3.06
2234 4928 6.662414 TTAGCTAACATCTTCGGTTTCATG 57.338 37.500 0.86 0.00 0.00 3.07
2238 4932 5.411669 CCACTTTAGCTAACATCTTCGGTTT 59.588 40.000 5.45 0.00 0.00 3.27
2284 4979 2.756829 TCAGTTGGCATGTGCAAAATG 58.243 42.857 14.55 14.55 44.36 2.32
2290 4985 1.734707 GCATCTTCAGTTGGCATGTGC 60.735 52.381 0.00 0.00 41.14 4.57
2319 5014 1.280133 TGGCTGACATCTTAAGCTGCT 59.720 47.619 6.23 0.00 37.12 4.24
2323 5018 3.273434 TGACATGGCTGACATCTTAAGC 58.727 45.455 0.00 0.00 37.84 3.09
2327 5022 3.430042 AGTTGACATGGCTGACATCTT 57.570 42.857 0.00 0.00 37.84 2.40
2328 5023 3.430042 AAGTTGACATGGCTGACATCT 57.570 42.857 0.00 0.00 37.84 2.90
2366 5061 5.163281 TGGCATGCCAATATTTTCAGTTT 57.837 34.783 36.95 0.00 44.12 2.66
2402 5098 3.733077 GCTGACATCTTAAGTTGCCATGC 60.733 47.826 12.51 9.74 0.00 4.06
2407 5103 3.441572 ACATGGCTGACATCTTAAGTTGC 59.558 43.478 12.51 7.09 37.84 4.17
2408 5104 4.696877 TGACATGGCTGACATCTTAAGTTG 59.303 41.667 11.26 11.26 37.84 3.16
2409 5105 4.910195 TGACATGGCTGACATCTTAAGTT 58.090 39.130 0.00 0.00 37.84 2.66
2410 5106 4.558226 TGACATGGCTGACATCTTAAGT 57.442 40.909 0.00 0.00 37.84 2.24
2411 5107 5.181009 TCTTGACATGGCTGACATCTTAAG 58.819 41.667 0.00 0.00 37.84 1.85
2412 5108 5.164620 TCTTGACATGGCTGACATCTTAA 57.835 39.130 0.00 0.00 37.84 1.85
2413 5109 4.824479 TCTTGACATGGCTGACATCTTA 57.176 40.909 0.00 0.00 37.84 2.10
2414 5110 3.708403 TCTTGACATGGCTGACATCTT 57.292 42.857 0.00 0.00 37.84 2.40
2415 5111 3.054582 ACATCTTGACATGGCTGACATCT 60.055 43.478 0.00 0.00 37.84 2.90
2416 5112 3.064958 CACATCTTGACATGGCTGACATC 59.935 47.826 0.00 0.00 37.84 3.06
2417 5113 3.014623 CACATCTTGACATGGCTGACAT 58.985 45.455 0.00 0.00 41.57 3.06
2418 5114 2.224597 ACACATCTTGACATGGCTGACA 60.225 45.455 0.00 0.00 0.00 3.58
2419 5115 2.430465 ACACATCTTGACATGGCTGAC 58.570 47.619 0.00 0.00 0.00 3.51
2420 5116 2.815503 CAACACATCTTGACATGGCTGA 59.184 45.455 0.00 0.00 0.00 4.26
2421 5117 2.670229 GCAACACATCTTGACATGGCTG 60.670 50.000 0.00 0.00 0.00 4.85
2422 5118 1.542915 GCAACACATCTTGACATGGCT 59.457 47.619 0.00 0.00 0.00 4.75
2423 5119 1.403249 GGCAACACATCTTGACATGGC 60.403 52.381 0.00 0.00 0.00 4.40
2424 5120 1.887854 TGGCAACACATCTTGACATGG 59.112 47.619 0.00 0.00 46.17 3.66
2438 5134 4.815846 ACATTTTTCAGTTTCCATGGCAAC 59.184 37.500 18.37 18.37 0.00 4.17
2439 5135 5.033589 ACATTTTTCAGTTTCCATGGCAA 57.966 34.783 6.96 0.00 0.00 4.52
2440 5136 4.686191 ACATTTTTCAGTTTCCATGGCA 57.314 36.364 6.96 0.00 0.00 4.92
2441 5137 4.213906 CCAACATTTTTCAGTTTCCATGGC 59.786 41.667 6.96 0.00 0.00 4.40
2442 5138 4.213906 GCCAACATTTTTCAGTTTCCATGG 59.786 41.667 4.97 4.97 0.00 3.66
2443 5139 4.815308 TGCCAACATTTTTCAGTTTCCATG 59.185 37.500 0.00 0.00 0.00 3.66
2444 5140 5.033589 TGCCAACATTTTTCAGTTTCCAT 57.966 34.783 0.00 0.00 0.00 3.41
2445 5141 4.478206 TGCCAACATTTTTCAGTTTCCA 57.522 36.364 0.00 0.00 0.00 3.53
2446 5142 4.319694 GCATGCCAACATTTTTCAGTTTCC 60.320 41.667 6.36 0.00 32.87 3.13
2447 5143 4.319694 GGCATGCCAACATTTTTCAGTTTC 60.320 41.667 32.08 0.00 32.87 2.78
2448 5144 3.565063 GGCATGCCAACATTTTTCAGTTT 59.435 39.130 32.08 0.00 32.87 2.66
2449 5145 3.140623 GGCATGCCAACATTTTTCAGTT 58.859 40.909 32.08 0.00 32.87 3.16
2450 5146 2.104451 TGGCATGCCAACATTTTTCAGT 59.896 40.909 36.95 0.00 44.12 3.41
2451 5147 2.768698 TGGCATGCCAACATTTTTCAG 58.231 42.857 36.95 0.00 44.12 3.02
2452 5148 2.924757 TGGCATGCCAACATTTTTCA 57.075 40.000 36.95 9.68 44.12 2.69
2462 5158 5.624344 CAAAACATATTTTTGGCATGCCA 57.376 34.783 35.59 35.59 45.63 4.92
2470 5166 5.624344 TGCCATGCCAAAACATATTTTTG 57.376 34.783 12.42 12.42 35.79 2.44
2471 5167 5.769162 AGTTGCCATGCCAAAACATATTTTT 59.231 32.000 0.00 0.00 35.79 1.94
2472 5168 5.315348 AGTTGCCATGCCAAAACATATTTT 58.685 33.333 0.00 0.00 38.61 1.82
2473 5169 4.909001 AGTTGCCATGCCAAAACATATTT 58.091 34.783 0.00 0.00 0.00 1.40
2474 5170 4.556592 AGTTGCCATGCCAAAACATATT 57.443 36.364 0.00 0.00 0.00 1.28
2475 5171 4.556592 AAGTTGCCATGCCAAAACATAT 57.443 36.364 0.00 0.00 0.00 1.78
2476 5172 5.186603 TCATAAGTTGCCATGCCAAAACATA 59.813 36.000 0.00 0.00 0.00 2.29
2477 5173 2.934886 AAGTTGCCATGCCAAAACAT 57.065 40.000 0.00 0.00 0.00 2.71
2478 5174 3.323115 TCATAAGTTGCCATGCCAAAACA 59.677 39.130 0.00 0.00 0.00 2.83
2479 5175 3.924144 TCATAAGTTGCCATGCCAAAAC 58.076 40.909 0.00 0.00 0.00 2.43
2480 5176 4.020396 ACATCATAAGTTGCCATGCCAAAA 60.020 37.500 0.00 0.00 0.00 2.44
2481 5177 3.514706 ACATCATAAGTTGCCATGCCAAA 59.485 39.130 0.00 0.00 0.00 3.28
2482 5178 3.098377 ACATCATAAGTTGCCATGCCAA 58.902 40.909 0.00 0.00 0.00 4.52
2483 5179 2.737544 ACATCATAAGTTGCCATGCCA 58.262 42.857 0.00 0.00 0.00 4.92
2484 5180 3.806625 AACATCATAAGTTGCCATGCC 57.193 42.857 0.00 0.00 0.00 4.40
2485 5181 7.115378 GCTAATTAACATCATAAGTTGCCATGC 59.885 37.037 0.00 0.00 29.61 4.06
2486 5182 7.596248 GGCTAATTAACATCATAAGTTGCCATG 59.404 37.037 12.58 0.00 44.98 3.66
2487 5183 7.661040 GGCTAATTAACATCATAAGTTGCCAT 58.339 34.615 12.58 0.00 44.98 4.40
2488 5184 7.038154 GGCTAATTAACATCATAAGTTGCCA 57.962 36.000 12.58 0.00 44.98 4.92
2489 5185 7.038154 TGGCTAATTAACATCATAAGTTGCC 57.962 36.000 11.20 11.20 45.45 4.52
2530 5226 6.154363 ACAAAAGAAAACCTTGAATGGACAGA 59.846 34.615 0.00 0.00 34.79 3.41
2531 5227 6.256321 CACAAAAGAAAACCTTGAATGGACAG 59.744 38.462 0.00 0.00 34.79 3.51
2532 5228 6.071108 TCACAAAAGAAAACCTTGAATGGACA 60.071 34.615 0.00 0.00 34.79 4.02
2534 5230 6.537453 TCACAAAAGAAAACCTTGAATGGA 57.463 33.333 0.00 0.00 34.79 3.41
2535 5231 9.492973 AATATCACAAAAGAAAACCTTGAATGG 57.507 29.630 0.00 0.00 34.79 3.16
2543 5239 9.087424 GCCATCTAAATATCACAAAAGAAAACC 57.913 33.333 0.00 0.00 0.00 3.27
2544 5240 9.638239 TGCCATCTAAATATCACAAAAGAAAAC 57.362 29.630 0.00 0.00 0.00 2.43
2551 5247 9.995003 AAAAAGTTGCCATCTAAATATCACAAA 57.005 25.926 0.00 0.00 0.00 2.83
2558 5254 9.474920 CAGAAACAAAAAGTTGCCATCTAAATA 57.525 29.630 0.00 0.00 41.19 1.40
2565 5261 5.083533 TGACAGAAACAAAAAGTTGCCAT 57.916 34.783 0.00 0.00 41.19 4.40
2567 5263 6.421377 AATTGACAGAAACAAAAAGTTGCC 57.579 33.333 0.00 0.00 41.19 4.52
2633 5329 2.041701 AGAGTTGCCCAATTTGTTGCT 58.958 42.857 8.89 0.00 0.00 3.91
2635 5331 5.200368 ACTTAGAGTTGCCCAATTTGTTG 57.800 39.130 0.00 0.00 0.00 3.33
2664 5360 1.548986 GCACACTGCAACTGTTTCAC 58.451 50.000 0.00 0.00 44.26 3.18
2677 5373 2.260822 AGGAAGTATGGTCTGCACACT 58.739 47.619 0.00 0.00 0.00 3.55
2682 5378 5.415701 TGAAATGAAAGGAAGTATGGTCTGC 59.584 40.000 0.00 0.00 0.00 4.26
2685 5381 6.817765 TGTGAAATGAAAGGAAGTATGGTC 57.182 37.500 0.00 0.00 0.00 4.02
2740 5436 5.766670 CCATGAGTGTGCCATAATATTGACT 59.233 40.000 0.00 0.00 0.00 3.41
2745 5441 7.290061 AGTTTACCATGAGTGTGCCATAATAT 58.710 34.615 0.00 0.00 0.00 1.28
2753 5449 6.021596 CGAAAATAGTTTACCATGAGTGTGC 58.978 40.000 0.00 0.00 0.00 4.57
2756 5452 8.664798 TCATTCGAAAATAGTTTACCATGAGTG 58.335 33.333 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.