Multiple sequence alignment - TraesCS1B01G041900

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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 TraesCS1B01G041900 chr1B 100.000 2406 0 0 1 2406 21803581 21805986 0.000000e+00 4444
1 TraesCS1B01G041900 chr1B 97.039 608 14 4 1 605 91536210 91536816 0.000000e+00 1020
2 TraesCS1B01G041900 chr1B 96.154 182 6 1 613 793 91537573 91537754 1.810000e-76 296
3 TraesCS1B01G041900 chr1B 96.133 181 6 1 613 792 98560952 98560772 6.500000e-76 294
4 TraesCS1B01G041900 chr1B 96.591 176 5 1 616 790 554790966 554790791 8.410000e-75 291
5 TraesCS1B01G041900 chr1B 95.531 179 7 1 613 790 400467758 400467936 3.910000e-73 285
6 TraesCS1B01G041900 chr1B 97.581 124 3 0 2272 2395 623107059 623107182 1.870000e-51 213
7 TraesCS1B01G041900 chr1D 89.849 995 40 21 791 1755 15519750 15520713 0.000000e+00 1221
8 TraesCS1B01G041900 chr1D 86.233 523 54 10 1752 2270 15520750 15521258 3.500000e-153 551
9 TraesCS1B01G041900 chr1A 87.959 980 50 28 816 1751 16038321 16039276 0.000000e+00 1094
10 TraesCS1B01G041900 chr1A 84.601 526 57 12 1752 2270 16039318 16039826 3.570000e-138 501
11 TraesCS1B01G041900 chr1A 97.581 124 3 0 2272 2395 320509480 320509603 1.870000e-51 213
12 TraesCS1B01G041900 chr2B 97.533 608 11 4 2 605 120600093 120599486 0.000000e+00 1037
13 TraesCS1B01G041900 chr2B 96.705 607 16 3 1 605 635757927 635757323 0.000000e+00 1007
14 TraesCS1B01G041900 chr2B 96.089 179 6 1 613 790 764546188 764546010 8.410000e-75 291
15 TraesCS1B01G041900 chr2B 95.109 184 7 2 613 794 774820309 774820126 3.030000e-74 289
16 TraesCS1B01G041900 chr2B 93.382 136 8 1 2261 2395 6740183 6740048 1.460000e-47 200
17 TraesCS1B01G041900 chr7B 97.364 607 13 3 1 605 529678515 529677910 0.000000e+00 1029
18 TraesCS1B01G041900 chr7B 95.531 179 7 1 614 791 529677164 529676986 3.910000e-73 285
19 TraesCS1B01G041900 chr4A 97.035 607 16 2 1 605 656470325 656470931 0.000000e+00 1020
20 TraesCS1B01G041900 chr4A 96.546 608 17 4 1 605 656027702 656028308 0.000000e+00 1003
21 TraesCS1B01G041900 chr4A 96.523 604 19 2 1 602 691663000 691662397 0.000000e+00 998
22 TraesCS1B01G041900 chr4A 96.667 180 5 1 615 793 691661632 691661453 5.030000e-77 298
23 TraesCS1B01G041900 chr5B 96.705 607 16 4 1 605 231005415 231006019 0.000000e+00 1007
24 TraesCS1B01G041900 chr3B 96.563 611 15 4 1 605 729375490 729376100 0.000000e+00 1007
25 TraesCS1B01G041900 chr4B 97.207 179 4 1 615 792 16673073 16673251 3.890000e-78 302
26 TraesCS1B01G041900 chr4B 91.608 143 8 4 2256 2395 13941832 13941691 6.790000e-46 195
27 TraesCS1B01G041900 chr7A 97.581 124 3 0 2272 2395 736543736 736543613 1.870000e-51 213
28 TraesCS1B01G041900 chr3D 97.561 123 3 0 2270 2392 238618437 238618559 6.740000e-51 211
29 TraesCS1B01G041900 chr3D 96.800 125 4 0 2269 2393 282978915 282978791 2.420000e-50 209
30 TraesCS1B01G041900 chr3A 96.825 126 3 1 2268 2392 699994224 699994099 2.420000e-50 209
31 TraesCS1B01G041900 chr6B 94.776 134 6 1 2271 2403 448665610 448665743 8.720000e-50 207


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 TraesCS1B01G041900 chr1B 21803581 21805986 2405 False 4444.0 4444 100.0000 1 2406 1 chr1B.!!$F1 2405
1 TraesCS1B01G041900 chr1B 91536210 91537754 1544 False 658.0 1020 96.5965 1 793 2 chr1B.!!$F4 792
2 TraesCS1B01G041900 chr1D 15519750 15521258 1508 False 886.0 1221 88.0410 791 2270 2 chr1D.!!$F1 1479
3 TraesCS1B01G041900 chr1A 16038321 16039826 1505 False 797.5 1094 86.2800 816 2270 2 chr1A.!!$F2 1454
4 TraesCS1B01G041900 chr2B 120599486 120600093 607 True 1037.0 1037 97.5330 2 605 1 chr2B.!!$R2 603
5 TraesCS1B01G041900 chr2B 635757323 635757927 604 True 1007.0 1007 96.7050 1 605 1 chr2B.!!$R3 604
6 TraesCS1B01G041900 chr7B 529676986 529678515 1529 True 657.0 1029 96.4475 1 791 2 chr7B.!!$R1 790
7 TraesCS1B01G041900 chr4A 656470325 656470931 606 False 1020.0 1020 97.0350 1 605 1 chr4A.!!$F2 604
8 TraesCS1B01G041900 chr4A 656027702 656028308 606 False 1003.0 1003 96.5460 1 605 1 chr4A.!!$F1 604
9 TraesCS1B01G041900 chr4A 691661453 691663000 1547 True 648.0 998 96.5950 1 793 2 chr4A.!!$R1 792
10 TraesCS1B01G041900 chr5B 231005415 231006019 604 False 1007.0 1007 96.7050 1 605 1 chr5B.!!$F1 604
11 TraesCS1B01G041900 chr3B 729375490 729376100 610 False 1007.0 1007 96.5630 1 605 1 chr3B.!!$F1 604

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
845 1619 0.911769 CTGGGGTAACAGCATCAGGA 59.088 55.0 0.0 0.0 39.74 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 3150 0.030369 CGAGTATTTCCGGACGGAGG 59.97 60.0 13.64 0.0 46.06 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
440 449 7.746916 CACGACCAACACGATAAAAATCAATAA 59.253 33.333 0.00 0.00 34.70 1.40
532 541 1.614241 ATCGTTCCCAGGAAGGACCG 61.614 60.000 20.78 11.37 46.90 4.79
798 1572 3.887621 TTAGTGATTTCGGGAGGTGAG 57.112 47.619 0.00 0.00 0.00 3.51
804 1578 4.671590 TCGGGAGGTGAGGTCGCA 62.672 66.667 0.00 0.00 0.00 5.10
809 1583 1.064946 GAGGTGAGGTCGCATCTCG 59.935 63.158 0.00 0.00 36.40 4.04
845 1619 0.911769 CTGGGGTAACAGCATCAGGA 59.088 55.000 0.00 0.00 39.74 3.86
856 1630 1.457643 CATCAGGACCTCGGCCCTA 60.458 63.158 0.00 0.00 0.00 3.53
895 1670 7.267128 CCCTTTTATATTTCTGCTTGCATCAA 58.733 34.615 0.00 0.00 0.00 2.57
1119 1904 4.409218 GCCCGTGACTCGTACGCA 62.409 66.667 11.24 0.00 40.04 5.24
1184 1987 0.807667 CTCTAATGGCGTCGCTTGCT 60.808 55.000 18.11 2.17 0.00 3.91
1545 2368 3.658351 CGAACCACGGATTCTGAATTC 57.342 47.619 4.11 1.05 38.46 2.17
1546 2369 3.262420 CGAACCACGGATTCTGAATTCT 58.738 45.455 7.05 0.00 38.46 2.40
1547 2370 3.062639 CGAACCACGGATTCTGAATTCTG 59.937 47.826 7.05 6.50 38.46 3.02
1548 2371 3.981071 ACCACGGATTCTGAATTCTGA 57.019 42.857 10.68 10.68 0.00 3.27
1549 2372 4.494091 ACCACGGATTCTGAATTCTGAT 57.506 40.909 14.89 6.46 0.00 2.90
1550 2373 4.194640 ACCACGGATTCTGAATTCTGATG 58.805 43.478 14.89 10.00 0.00 3.07
1552 2375 3.624410 CACGGATTCTGAATTCTGATGCA 59.376 43.478 14.89 2.24 0.00 3.96
1554 2377 3.303857 CGGATTCTGAATTCTGATGCAGC 60.304 47.826 14.89 0.00 38.62 5.25
1555 2378 3.004524 GGATTCTGAATTCTGATGCAGCC 59.995 47.826 14.89 9.37 38.62 4.85
1556 2379 3.361281 TTCTGAATTCTGATGCAGCCT 57.639 42.857 14.89 0.00 38.62 4.58
1557 2380 3.361281 TCTGAATTCTGATGCAGCCTT 57.639 42.857 10.68 0.00 38.62 4.35
1558 2381 3.693807 TCTGAATTCTGATGCAGCCTTT 58.306 40.909 10.68 0.00 38.62 3.11
1559 2382 4.084287 TCTGAATTCTGATGCAGCCTTTT 58.916 39.130 10.68 0.00 38.62 2.27
1560 2383 4.082408 TCTGAATTCTGATGCAGCCTTTTG 60.082 41.667 10.68 0.00 38.62 2.44
1561 2384 3.056393 TGAATTCTGATGCAGCCTTTTGG 60.056 43.478 7.05 0.00 44.18 3.28
1562 2385 1.259609 TTCTGATGCAGCCTTTTGGG 58.740 50.000 0.00 0.00 40.82 4.12
1605 2428 1.908066 GAACCACACCACGGATTCGC 61.908 60.000 0.00 0.00 40.63 4.70
1610 2433 0.949105 ACACCACGGATTCGCAACTC 60.949 55.000 0.00 0.00 40.63 3.01
1613 2436 2.813908 ACGGATTCGCAACTCGGC 60.814 61.111 0.00 0.00 40.63 5.54
1614 2437 3.564027 CGGATTCGCAACTCGGCC 61.564 66.667 0.00 0.00 39.05 6.13
1658 2481 9.908152 GTTTCCATGCTTTACAAACTTAGTATT 57.092 29.630 0.00 0.00 0.00 1.89
1698 2521 2.821378 TGTCATGCATTTCCTTGTCTGG 59.179 45.455 0.00 0.00 0.00 3.86
1702 2525 1.962807 TGCATTTCCTTGTCTGGTTGG 59.037 47.619 0.00 0.00 0.00 3.77
1707 2530 2.472695 TCCTTGTCTGGTTGGAATCG 57.527 50.000 0.00 0.00 0.00 3.34
1723 2546 1.909700 ATCGGTTGCTTCCATGTGTT 58.090 45.000 0.00 0.00 0.00 3.32
1724 2547 1.686355 TCGGTTGCTTCCATGTGTTT 58.314 45.000 0.00 0.00 0.00 2.83
1739 2562 8.272545 TCCATGTGTTTATTCAGAATTCAGAG 57.727 34.615 8.44 0.00 0.00 3.35
1775 2639 1.073098 ACAGTTTCCGGATTTCCCCT 58.927 50.000 4.15 0.00 0.00 4.79
1776 2640 1.004394 ACAGTTTCCGGATTTCCCCTC 59.996 52.381 4.15 0.00 0.00 4.30
1780 2644 3.162666 GTTTCCGGATTTCCCCTCTTTT 58.837 45.455 4.15 0.00 0.00 2.27
1781 2645 3.536075 TTCCGGATTTCCCCTCTTTTT 57.464 42.857 4.15 0.00 0.00 1.94
1811 2675 5.081032 GTCTCATAGCCTGGTATAAGGTCT 58.919 45.833 0.00 0.00 39.75 3.85
1848 2712 4.328983 CCATGATGTTGATTTGAAGCTTGC 59.671 41.667 2.10 0.00 0.00 4.01
1849 2713 4.859304 TGATGTTGATTTGAAGCTTGCT 57.141 36.364 2.10 0.00 0.00 3.91
1850 2714 4.801891 TGATGTTGATTTGAAGCTTGCTC 58.198 39.130 2.10 0.00 0.00 4.26
1863 2727 3.871485 AGCTTGCTCAGATTCGATTTCT 58.129 40.909 0.00 0.00 0.00 2.52
1865 2729 5.423015 AGCTTGCTCAGATTCGATTTCTTA 58.577 37.500 0.00 0.00 0.00 2.10
1868 2732 6.202570 GCTTGCTCAGATTCGATTTCTTATCT 59.797 38.462 0.00 0.00 0.00 1.98
1904 2769 2.163412 TCTTTTGCCGTCATATGCCAAC 59.837 45.455 0.00 0.00 0.00 3.77
1911 2776 2.355756 CCGTCATATGCCAACCTTGAAG 59.644 50.000 0.00 0.00 0.00 3.02
1934 2799 9.107177 GAAGCTCCATGTCATATGATAAATAGG 57.893 37.037 9.02 7.77 0.00 2.57
1969 2839 5.833406 TTGTGTCAACAACTCAACATGAT 57.167 34.783 0.00 0.00 41.41 2.45
1973 2843 4.338964 TGTCAACAACTCAACATGATTGCT 59.661 37.500 0.00 0.00 0.00 3.91
1990 2860 1.307097 GCTATCAAGCTCTTGCCCTG 58.693 55.000 4.81 0.00 45.85 4.45
1991 2861 1.307097 CTATCAAGCTCTTGCCCTGC 58.693 55.000 4.81 0.00 40.24 4.85
1993 2863 0.914644 ATCAAGCTCTTGCCCTGCTA 59.085 50.000 4.81 0.00 40.24 3.49
2030 2900 7.502696 TGTTACAACTTACAACCAGTACTCAT 58.497 34.615 0.00 0.00 30.91 2.90
2079 2949 6.017275 GCCTCAAATGATAGGATCTGAACTTG 60.017 42.308 0.00 0.00 34.58 3.16
2129 2999 9.683069 AACTTCAGATGATGATACAACAAAAAC 57.317 29.630 3.01 0.00 37.89 2.43
2176 3046 4.937620 CAGCAGAGTAATGTAGCAAAGGAA 59.062 41.667 0.00 0.00 0.00 3.36
2187 3057 6.515272 TGTAGCAAAGGAAAAATGGATCTC 57.485 37.500 0.00 0.00 0.00 2.75
2246 3117 4.163078 AGGAGAACCTCATGTATTCAGTGG 59.837 45.833 0.00 0.00 44.13 4.00
2247 3118 3.873952 GAGAACCTCATGTATTCAGTGGC 59.126 47.826 0.00 0.00 0.00 5.01
2257 3128 2.211250 ATTCAGTGGCTGCACATCTT 57.789 45.000 0.50 0.00 0.00 2.40
2260 3131 1.202794 TCAGTGGCTGCACATCTTCAA 60.203 47.619 0.50 0.00 0.00 2.69
2270 3141 6.038603 GGCTGCACATCTTCAATCTGTATAAA 59.961 38.462 0.50 0.00 0.00 1.40
2271 3142 7.255381 GGCTGCACATCTTCAATCTGTATAAAT 60.255 37.037 0.50 0.00 0.00 1.40
2272 3143 8.133627 GCTGCACATCTTCAATCTGTATAAATT 58.866 33.333 0.00 0.00 0.00 1.82
2284 3155 9.587772 CAATCTGTATAAATTATACTCCCTCCG 57.412 37.037 20.02 4.00 41.21 4.63
2285 3156 8.896722 ATCTGTATAAATTATACTCCCTCCGT 57.103 34.615 20.02 0.91 41.21 4.69
2286 3157 8.345724 TCTGTATAAATTATACTCCCTCCGTC 57.654 38.462 20.02 0.00 41.21 4.79
2287 3158 7.395489 TCTGTATAAATTATACTCCCTCCGTCC 59.605 40.741 20.02 0.00 41.21 4.79
2288 3159 5.656213 ATAAATTATACTCCCTCCGTCCG 57.344 43.478 0.00 0.00 0.00 4.79
2289 3160 1.920610 ATTATACTCCCTCCGTCCGG 58.079 55.000 0.00 0.00 0.00 5.14
2290 3161 0.846015 TTATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
2291 3162 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
2292 3163 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2293 3164 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2294 3165 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2295 3166 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2296 3167 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2297 3168 0.388294 CCCTCCGTCCGGAAATACTC 59.612 60.000 5.23 0.00 44.66 2.59
2298 3169 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.000 5.23 3.90 44.66 4.18
2299 3170 0.737219 CTCCGTCCGGAAATACTCGT 59.263 55.000 5.23 0.00 44.66 4.18
2300 3171 0.734889 TCCGTCCGGAAATACTCGTC 59.265 55.000 5.23 0.00 42.05 4.20
2301 3172 0.590732 CCGTCCGGAAATACTCGTCG 60.591 60.000 5.23 1.25 37.50 5.12
2302 3173 0.590732 CGTCCGGAAATACTCGTCGG 60.591 60.000 5.23 0.00 41.80 4.79
2303 3174 0.734889 GTCCGGAAATACTCGTCGGA 59.265 55.000 5.23 0.00 46.06 4.55
2304 3175 1.019673 TCCGGAAATACTCGTCGGAG 58.980 55.000 0.00 0.00 43.84 4.63
2305 3176 0.030369 CCGGAAATACTCGTCGGAGG 59.970 60.000 0.00 0.00 44.93 4.30
2306 3177 1.019673 CGGAAATACTCGTCGGAGGA 58.980 55.000 0.00 0.00 44.93 3.71
2307 3178 1.402968 CGGAAATACTCGTCGGAGGAA 59.597 52.381 1.73 0.00 44.93 3.36
2308 3179 2.034305 CGGAAATACTCGTCGGAGGAAT 59.966 50.000 1.73 0.00 44.93 3.01
2309 3180 3.381949 GGAAATACTCGTCGGAGGAATG 58.618 50.000 1.73 0.00 44.93 2.67
2310 3181 3.067742 GGAAATACTCGTCGGAGGAATGA 59.932 47.826 1.73 0.00 44.93 2.57
2311 3182 4.441079 GGAAATACTCGTCGGAGGAATGAA 60.441 45.833 1.73 0.00 44.93 2.57
2312 3183 4.939052 AATACTCGTCGGAGGAATGAAT 57.061 40.909 1.73 0.00 44.93 2.57
2313 3184 2.586258 ACTCGTCGGAGGAATGAATG 57.414 50.000 1.73 0.00 44.93 2.67
2314 3185 1.825474 ACTCGTCGGAGGAATGAATGT 59.175 47.619 1.73 0.00 44.93 2.71
2315 3186 3.021695 ACTCGTCGGAGGAATGAATGTA 58.978 45.455 1.73 0.00 44.93 2.29
2316 3187 3.637229 ACTCGTCGGAGGAATGAATGTAT 59.363 43.478 1.73 0.00 44.93 2.29
2317 3188 4.230657 CTCGTCGGAGGAATGAATGTATC 58.769 47.826 1.73 0.00 36.61 2.24
2318 3189 3.889538 TCGTCGGAGGAATGAATGTATCT 59.110 43.478 0.00 0.00 0.00 1.98
2319 3190 5.067954 TCGTCGGAGGAATGAATGTATCTA 58.932 41.667 0.00 0.00 0.00 1.98
2320 3191 5.181433 TCGTCGGAGGAATGAATGTATCTAG 59.819 44.000 0.00 0.00 0.00 2.43
2321 3192 5.181433 CGTCGGAGGAATGAATGTATCTAGA 59.819 44.000 0.00 0.00 0.00 2.43
2322 3193 6.127869 CGTCGGAGGAATGAATGTATCTAGAT 60.128 42.308 10.73 10.73 0.00 1.98
2323 3194 7.032580 GTCGGAGGAATGAATGTATCTAGATG 58.967 42.308 15.79 0.00 0.00 2.90
2324 3195 6.721668 TCGGAGGAATGAATGTATCTAGATGT 59.278 38.462 15.79 0.00 0.00 3.06
2325 3196 7.888546 TCGGAGGAATGAATGTATCTAGATGTA 59.111 37.037 15.79 4.44 0.00 2.29
2326 3197 8.690884 CGGAGGAATGAATGTATCTAGATGTAT 58.309 37.037 15.79 6.61 0.00 2.29
2364 3235 7.760131 ACATTCATTTTTATGCATTTCTCCG 57.240 32.000 3.54 0.00 0.00 4.63
2365 3236 7.546358 ACATTCATTTTTATGCATTTCTCCGA 58.454 30.769 3.54 0.00 0.00 4.55
2366 3237 7.489113 ACATTCATTTTTATGCATTTCTCCGAC 59.511 33.333 3.54 0.00 0.00 4.79
2367 3238 6.507958 TCATTTTTATGCATTTCTCCGACA 57.492 33.333 3.54 0.00 0.00 4.35
2368 3239 6.918626 TCATTTTTATGCATTTCTCCGACAA 58.081 32.000 3.54 0.00 0.00 3.18
2369 3240 7.028962 TCATTTTTATGCATTTCTCCGACAAG 58.971 34.615 3.54 0.00 0.00 3.16
2370 3241 5.957842 TTTTATGCATTTCTCCGACAAGT 57.042 34.783 3.54 0.00 0.00 3.16
2371 3242 7.441890 TTTTTATGCATTTCTCCGACAAGTA 57.558 32.000 3.54 0.00 0.00 2.24
2372 3243 7.624360 TTTTATGCATTTCTCCGACAAGTAT 57.376 32.000 3.54 0.00 0.00 2.12
2373 3244 7.624360 TTTATGCATTTCTCCGACAAGTATT 57.376 32.000 3.54 0.00 0.00 1.89
2374 3245 7.624360 TTATGCATTTCTCCGACAAGTATTT 57.376 32.000 3.54 0.00 0.00 1.40
2375 3246 5.545658 TGCATTTCTCCGACAAGTATTTC 57.454 39.130 0.00 0.00 0.00 2.17
2376 3247 5.245531 TGCATTTCTCCGACAAGTATTTCT 58.754 37.500 0.00 0.00 0.00 2.52
2377 3248 5.122239 TGCATTTCTCCGACAAGTATTTCTG 59.878 40.000 0.00 0.00 0.00 3.02
2378 3249 5.447818 GCATTTCTCCGACAAGTATTTCTGG 60.448 44.000 0.00 0.00 0.00 3.86
2379 3250 5.477607 TTTCTCCGACAAGTATTTCTGGA 57.522 39.130 0.00 0.00 0.00 3.86
2380 3251 4.451629 TCTCCGACAAGTATTTCTGGAC 57.548 45.455 0.00 0.00 0.00 4.02
2381 3252 3.830178 TCTCCGACAAGTATTTCTGGACA 59.170 43.478 0.00 0.00 0.00 4.02
2382 3253 4.082190 TCTCCGACAAGTATTTCTGGACAG 60.082 45.833 0.00 0.00 0.00 3.51
2383 3254 3.830178 TCCGACAAGTATTTCTGGACAGA 59.170 43.478 0.00 0.00 35.27 3.41
2384 3255 4.082190 TCCGACAAGTATTTCTGGACAGAG 60.082 45.833 1.92 0.00 38.88 3.35
2385 3256 4.177026 CGACAAGTATTTCTGGACAGAGG 58.823 47.826 1.92 0.00 38.88 3.69
2386 3257 4.508662 GACAAGTATTTCTGGACAGAGGG 58.491 47.826 1.92 0.00 38.88 4.30
2387 3258 4.168101 ACAAGTATTTCTGGACAGAGGGA 58.832 43.478 1.92 0.00 38.88 4.20
2388 3259 4.223923 ACAAGTATTTCTGGACAGAGGGAG 59.776 45.833 1.92 0.00 38.88 4.30
2389 3260 4.067944 AGTATTTCTGGACAGAGGGAGT 57.932 45.455 1.92 0.00 38.88 3.85
2390 3261 5.208294 AGTATTTCTGGACAGAGGGAGTA 57.792 43.478 1.92 0.00 38.88 2.59
2391 3262 5.782925 AGTATTTCTGGACAGAGGGAGTAT 58.217 41.667 1.92 0.00 38.88 2.12
2392 3263 6.923670 AGTATTTCTGGACAGAGGGAGTATA 58.076 40.000 1.92 0.00 38.88 1.47
2393 3264 7.540183 AGTATTTCTGGACAGAGGGAGTATAT 58.460 38.462 1.92 0.00 38.88 0.86
2394 3265 8.679725 AGTATTTCTGGACAGAGGGAGTATATA 58.320 37.037 1.92 0.00 38.88 0.86
2395 3266 9.310449 GTATTTCTGGACAGAGGGAGTATATAA 57.690 37.037 1.92 0.00 38.88 0.98
2396 3267 7.598759 TTTCTGGACAGAGGGAGTATATAAC 57.401 40.000 1.92 0.00 38.88 1.89
2397 3268 6.275692 TCTGGACAGAGGGAGTATATAACA 57.724 41.667 0.00 0.00 32.82 2.41
2398 3269 6.069331 TCTGGACAGAGGGAGTATATAACAC 58.931 44.000 0.00 0.00 32.82 3.32
2399 3270 5.773091 TGGACAGAGGGAGTATATAACACA 58.227 41.667 0.00 0.00 0.00 3.72
2400 3271 5.833667 TGGACAGAGGGAGTATATAACACAG 59.166 44.000 0.00 0.00 0.00 3.66
2401 3272 6.069331 GGACAGAGGGAGTATATAACACAGA 58.931 44.000 0.00 0.00 0.00 3.41
2402 3273 6.550108 GGACAGAGGGAGTATATAACACAGAA 59.450 42.308 0.00 0.00 0.00 3.02
2403 3274 7.069578 GGACAGAGGGAGTATATAACACAGAAA 59.930 40.741 0.00 0.00 0.00 2.52
2404 3275 8.375493 ACAGAGGGAGTATATAACACAGAAAA 57.625 34.615 0.00 0.00 0.00 2.29
2405 3276 8.993424 ACAGAGGGAGTATATAACACAGAAAAT 58.007 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
440 449 7.537596 TTGAACATTATGGAACTTGGATTGT 57.462 32.000 0.00 0.00 0.00 2.71
532 541 1.197721 CGTGTGAGGAGCAAATTCCAC 59.802 52.381 0.00 0.00 39.84 4.02
611 1098 3.055021 GGTTTCCCTTTGTGGTTTTTCCA 60.055 43.478 0.00 0.00 45.01 3.53
809 1583 1.542547 CCAGTTACGGCCCATATGGTC 60.543 57.143 20.46 7.73 36.04 4.02
812 1586 0.250727 CCCCAGTTACGGCCCATATG 60.251 60.000 0.00 0.00 0.00 1.78
813 1587 0.696485 ACCCCAGTTACGGCCCATAT 60.696 55.000 0.00 0.00 0.00 1.78
814 1588 0.031313 TACCCCAGTTACGGCCCATA 60.031 55.000 0.00 0.00 0.00 2.74
845 1619 2.158295 AGAAGACATATAGGGCCGAGGT 60.158 50.000 0.00 0.00 0.00 3.85
881 1656 1.252904 GGGCCTTGATGCAAGCAGAA 61.253 55.000 0.84 0.00 39.85 3.02
966 1748 2.204244 GGGGGAGAAGTGGGGGAA 60.204 66.667 0.00 0.00 0.00 3.97
967 1749 3.135716 TTGGGGGAGAAGTGGGGGA 62.136 63.158 0.00 0.00 0.00 4.81
1147 1950 0.854218 AGGAGCTAATCGAGAGGGGA 59.146 55.000 0.00 0.00 0.00 4.81
1380 2183 3.771491 CCTCGTCGTCGTCGTCGT 61.771 66.667 18.44 0.00 45.27 4.34
1554 2377 3.437741 GCAATCAATTGAAGCCCAAAAGG 59.562 43.478 19.87 1.65 40.14 3.11
1555 2378 3.123959 CGCAATCAATTGAAGCCCAAAAG 59.876 43.478 22.80 9.91 40.14 2.27
1556 2379 3.065655 CGCAATCAATTGAAGCCCAAAA 58.934 40.909 22.80 0.00 40.14 2.44
1557 2380 2.612471 CCGCAATCAATTGAAGCCCAAA 60.612 45.455 22.80 0.00 40.14 3.28
1558 2381 1.067000 CCGCAATCAATTGAAGCCCAA 60.067 47.619 22.80 0.00 40.14 4.12
1559 2382 0.531657 CCGCAATCAATTGAAGCCCA 59.468 50.000 22.80 0.00 40.14 5.36
1560 2383 0.807275 GCCGCAATCAATTGAAGCCC 60.807 55.000 22.80 14.25 40.14 5.19
1561 2384 0.174162 AGCCGCAATCAATTGAAGCC 59.826 50.000 22.80 13.94 40.14 4.35
1562 2385 1.274596 CAGCCGCAATCAATTGAAGC 58.725 50.000 20.36 20.36 40.14 3.86
1563 2386 2.642139 ACAGCCGCAATCAATTGAAG 57.358 45.000 13.09 9.43 40.14 3.02
1564 2387 3.242706 CGATACAGCCGCAATCAATTGAA 60.243 43.478 13.09 0.00 40.14 2.69
1565 2388 2.287644 CGATACAGCCGCAATCAATTGA 59.712 45.455 11.26 11.26 40.14 2.57
1566 2389 2.287644 TCGATACAGCCGCAATCAATTG 59.712 45.455 0.00 0.00 40.66 2.32
1567 2390 2.560504 TCGATACAGCCGCAATCAATT 58.439 42.857 0.00 0.00 0.00 2.32
1605 2428 2.331893 TTTGCATCCGGCCGAGTTG 61.332 57.895 30.73 21.13 43.89 3.16
1610 2433 1.932011 TTCATGTTTGCATCCGGCCG 61.932 55.000 21.04 21.04 43.89 6.13
1613 2436 1.477700 ACCATTCATGTTTGCATCCGG 59.522 47.619 0.00 0.00 31.99 5.14
1614 2437 2.945447 ACCATTCATGTTTGCATCCG 57.055 45.000 0.00 0.00 31.99 4.18
1702 2525 1.812571 ACACATGGAAGCAACCGATTC 59.187 47.619 0.00 0.00 36.79 2.52
1707 2530 5.048083 TCTGAATAAACACATGGAAGCAACC 60.048 40.000 0.00 0.00 0.00 3.77
1723 2546 8.403236 CAATGCACATCTCTGAATTCTGAATAA 58.597 33.333 14.97 5.60 0.00 1.40
1724 2547 7.771826 TCAATGCACATCTCTGAATTCTGAATA 59.228 33.333 14.97 7.72 0.00 1.75
1759 2623 2.509166 AAGAGGGGAAATCCGGAAAC 57.491 50.000 9.01 2.40 36.71 2.78
1760 2624 3.536075 AAAAGAGGGGAAATCCGGAAA 57.464 42.857 9.01 0.00 36.71 3.13
1780 2644 3.181434 ACCAGGCTATGAGACAAACCAAA 60.181 43.478 0.00 0.00 0.00 3.28
1781 2645 2.375174 ACCAGGCTATGAGACAAACCAA 59.625 45.455 0.00 0.00 0.00 3.67
1782 2646 1.985159 ACCAGGCTATGAGACAAACCA 59.015 47.619 0.00 0.00 0.00 3.67
1783 2647 2.789409 ACCAGGCTATGAGACAAACC 57.211 50.000 0.00 0.00 0.00 3.27
1784 2648 5.992217 CCTTATACCAGGCTATGAGACAAAC 59.008 44.000 0.00 0.00 0.00 2.93
1811 2675 8.522542 TCAACATCATGGATCATTGTTGATTA 57.477 30.769 17.25 4.06 42.01 1.75
1865 2729 8.398665 GGCAAAAGATGTAGTCGAATTTTAGAT 58.601 33.333 0.00 0.00 0.00 1.98
1868 2732 6.148150 ACGGCAAAAGATGTAGTCGAATTTTA 59.852 34.615 0.00 0.00 0.00 1.52
1873 2737 2.991190 GACGGCAAAAGATGTAGTCGAA 59.009 45.455 0.00 0.00 31.56 3.71
1875 2739 2.333926 TGACGGCAAAAGATGTAGTCG 58.666 47.619 0.00 0.00 39.08 4.18
1880 2744 2.358898 GGCATATGACGGCAAAAGATGT 59.641 45.455 6.97 0.00 0.00 3.06
1904 2769 4.711399 TCATATGACATGGAGCTTCAAGG 58.289 43.478 0.00 0.00 0.00 3.61
1911 2776 7.223582 CGACCTATTTATCATATGACATGGAGC 59.776 40.741 7.78 3.18 0.00 4.70
1934 2799 5.795939 TTGTTGACACAATGTTGTAAACGAC 59.204 36.000 0.00 4.47 43.49 4.34
1947 2812 5.833406 ATCATGTTGAGTTGTTGACACAA 57.167 34.783 0.00 0.00 40.82 3.33
1973 2843 0.914644 AGCAGGGCAAGAGCTTGATA 59.085 50.000 14.04 0.00 42.93 2.15
1980 2850 2.425143 TGGAAATAGCAGGGCAAGAG 57.575 50.000 0.00 0.00 0.00 2.85
1981 2851 3.748668 GCTATGGAAATAGCAGGGCAAGA 60.749 47.826 11.83 0.00 46.49 3.02
1983 2853 2.586425 GCTATGGAAATAGCAGGGCAA 58.414 47.619 11.83 0.00 46.49 4.52
1990 2860 5.823045 AGTTGTAACAGGCTATGGAAATAGC 59.177 40.000 8.85 8.85 46.52 2.97
1991 2861 7.865706 AAGTTGTAACAGGCTATGGAAATAG 57.134 36.000 0.00 0.00 0.00 1.73
1993 2863 7.172342 TGTAAGTTGTAACAGGCTATGGAAAT 58.828 34.615 0.00 0.00 0.00 2.17
2007 2877 7.959175 AGATGAGTACTGGTTGTAAGTTGTAA 58.041 34.615 0.00 0.00 32.25 2.41
2008 2878 7.450634 AGAGATGAGTACTGGTTGTAAGTTGTA 59.549 37.037 0.00 0.00 32.25 2.41
2009 2879 6.267928 AGAGATGAGTACTGGTTGTAAGTTGT 59.732 38.462 0.00 0.00 32.25 3.32
2010 2880 6.587990 CAGAGATGAGTACTGGTTGTAAGTTG 59.412 42.308 0.00 0.00 32.25 3.16
2011 2881 6.493802 TCAGAGATGAGTACTGGTTGTAAGTT 59.506 38.462 0.00 0.00 32.25 2.66
2012 2882 6.010850 TCAGAGATGAGTACTGGTTGTAAGT 58.989 40.000 0.00 0.00 32.25 2.24
2013 2883 6.516739 TCAGAGATGAGTACTGGTTGTAAG 57.483 41.667 0.00 0.00 32.25 2.34
2079 2949 9.361315 GTTTCTCTAAACTCTTATTCTGAGGAC 57.639 37.037 0.00 0.00 41.52 3.85
2129 2999 9.350357 CTGAACCATAATTCTTGAACAAATCAG 57.650 33.333 0.00 0.00 39.77 2.90
2145 3015 6.049149 GCTACATTACTCTGCTGAACCATAA 58.951 40.000 0.00 0.00 0.00 1.90
2176 3046 7.396907 TGGTTGTATTCACATGAGATCCATTTT 59.603 33.333 0.00 0.00 33.76 1.82
2187 3057 7.012610 TGCTGATATCTTGGTTGTATTCACATG 59.987 37.037 3.98 0.00 33.76 3.21
2220 3091 6.097554 CACTGAATACATGAGGTTCTCCTACT 59.902 42.308 0.00 0.00 45.24 2.57
2246 3117 6.609237 TTATACAGATTGAAGATGTGCAGC 57.391 37.500 0.00 0.00 0.00 5.25
2260 3131 8.896722 ACGGAGGGAGTATAATTTATACAGAT 57.103 34.615 22.44 7.61 42.68 2.90
2270 3141 1.426598 TCCGGACGGAGGGAGTATAAT 59.573 52.381 9.76 0.00 39.76 1.28
2271 3142 0.846015 TCCGGACGGAGGGAGTATAA 59.154 55.000 9.76 0.00 39.76 0.98
2272 3143 0.846015 TTCCGGACGGAGGGAGTATA 59.154 55.000 13.64 0.00 46.06 1.47
2273 3144 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
2274 3145 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2275 3146 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2276 3147 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2277 3148 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2278 3149 0.388294 GAGTATTTCCGGACGGAGGG 59.612 60.000 13.64 0.00 46.06 4.30
2279 3150 0.030369 CGAGTATTTCCGGACGGAGG 59.970 60.000 13.64 0.00 46.06 4.30
2280 3151 0.737219 ACGAGTATTTCCGGACGGAG 59.263 55.000 13.64 3.15 46.06 4.63
2281 3152 0.734889 GACGAGTATTTCCGGACGGA 59.265 55.000 1.83 9.76 43.52 4.69
2282 3153 0.590732 CGACGAGTATTTCCGGACGG 60.591 60.000 1.83 3.96 0.00 4.79
2283 3154 0.590732 CCGACGAGTATTTCCGGACG 60.591 60.000 1.83 5.89 42.49 4.79
2284 3155 0.734889 TCCGACGAGTATTTCCGGAC 59.265 55.000 1.83 0.00 43.47 4.79
2285 3156 1.019673 CTCCGACGAGTATTTCCGGA 58.980 55.000 0.00 0.00 45.74 5.14
2286 3157 0.030369 CCTCCGACGAGTATTTCCGG 59.970 60.000 0.00 0.00 41.36 5.14
2287 3158 1.019673 TCCTCCGACGAGTATTTCCG 58.980 55.000 0.00 0.00 33.93 4.30
2288 3159 3.067742 TCATTCCTCCGACGAGTATTTCC 59.932 47.826 0.00 0.00 33.93 3.13
2289 3160 4.303086 TCATTCCTCCGACGAGTATTTC 57.697 45.455 0.00 0.00 33.93 2.17
2290 3161 4.730949 TTCATTCCTCCGACGAGTATTT 57.269 40.909 0.00 0.00 33.93 1.40
2291 3162 4.099573 ACATTCATTCCTCCGACGAGTATT 59.900 41.667 0.00 0.00 33.93 1.89
2292 3163 3.637229 ACATTCATTCCTCCGACGAGTAT 59.363 43.478 0.00 0.00 33.93 2.12
2293 3164 3.021695 ACATTCATTCCTCCGACGAGTA 58.978 45.455 0.00 0.00 33.93 2.59
2294 3165 1.825474 ACATTCATTCCTCCGACGAGT 59.175 47.619 0.00 0.00 33.93 4.18
2295 3166 2.586258 ACATTCATTCCTCCGACGAG 57.414 50.000 0.00 0.00 35.72 4.18
2296 3167 3.889538 AGATACATTCATTCCTCCGACGA 59.110 43.478 0.00 0.00 0.00 4.20
2297 3168 4.244425 AGATACATTCATTCCTCCGACG 57.756 45.455 0.00 0.00 0.00 5.12
2298 3169 6.576662 TCTAGATACATTCATTCCTCCGAC 57.423 41.667 0.00 0.00 0.00 4.79
2299 3170 6.721668 ACATCTAGATACATTCATTCCTCCGA 59.278 38.462 4.54 0.00 0.00 4.55
2300 3171 6.929625 ACATCTAGATACATTCATTCCTCCG 58.070 40.000 4.54 0.00 0.00 4.63
2338 3209 9.467258 CGGAGAAATGCATAAAAATGAATGTAT 57.533 29.630 0.00 0.00 30.86 2.29
2339 3210 8.681806 TCGGAGAAATGCATAAAAATGAATGTA 58.318 29.630 0.00 0.00 0.00 2.29
2340 3211 7.489113 GTCGGAGAAATGCATAAAAATGAATGT 59.511 33.333 0.00 0.00 39.69 2.71
2341 3212 7.488792 TGTCGGAGAAATGCATAAAAATGAATG 59.511 33.333 0.00 0.00 39.69 2.67
2342 3213 7.546358 TGTCGGAGAAATGCATAAAAATGAAT 58.454 30.769 0.00 0.00 39.69 2.57
2343 3214 6.918626 TGTCGGAGAAATGCATAAAAATGAA 58.081 32.000 0.00 0.00 39.69 2.57
2344 3215 6.507958 TGTCGGAGAAATGCATAAAAATGA 57.492 33.333 0.00 0.00 39.69 2.57
2345 3216 6.808212 ACTTGTCGGAGAAATGCATAAAAATG 59.192 34.615 0.00 0.00 39.69 2.32
2346 3217 6.924111 ACTTGTCGGAGAAATGCATAAAAAT 58.076 32.000 0.00 0.00 39.69 1.82
2347 3218 6.325919 ACTTGTCGGAGAAATGCATAAAAA 57.674 33.333 0.00 0.00 39.69 1.94
2348 3219 5.957842 ACTTGTCGGAGAAATGCATAAAA 57.042 34.783 0.00 0.00 39.69 1.52
2349 3220 7.624360 AATACTTGTCGGAGAAATGCATAAA 57.376 32.000 0.00 0.00 39.69 1.40
2350 3221 7.552687 AGAAATACTTGTCGGAGAAATGCATAA 59.447 33.333 0.00 0.00 39.69 1.90
2351 3222 7.011389 CAGAAATACTTGTCGGAGAAATGCATA 59.989 37.037 0.00 0.00 39.69 3.14
2352 3223 5.882557 AGAAATACTTGTCGGAGAAATGCAT 59.117 36.000 0.00 0.00 39.69 3.96
2353 3224 5.122239 CAGAAATACTTGTCGGAGAAATGCA 59.878 40.000 0.00 0.00 39.69 3.96
2354 3225 5.447818 CCAGAAATACTTGTCGGAGAAATGC 60.448 44.000 0.00 0.00 39.69 3.56
2355 3226 5.874810 TCCAGAAATACTTGTCGGAGAAATG 59.125 40.000 0.00 0.00 39.69 2.32
2356 3227 5.875359 GTCCAGAAATACTTGTCGGAGAAAT 59.125 40.000 0.00 0.00 39.69 2.17
2357 3228 5.221561 TGTCCAGAAATACTTGTCGGAGAAA 60.222 40.000 0.00 0.00 39.69 2.52
2358 3229 4.282449 TGTCCAGAAATACTTGTCGGAGAA 59.718 41.667 0.00 0.00 39.69 2.87
2359 3230 3.830178 TGTCCAGAAATACTTGTCGGAGA 59.170 43.478 0.00 0.00 0.00 3.71
2360 3231 4.082190 TCTGTCCAGAAATACTTGTCGGAG 60.082 45.833 0.00 0.00 33.91 4.63
2361 3232 3.830178 TCTGTCCAGAAATACTTGTCGGA 59.170 43.478 0.00 0.00 33.91 4.55
2362 3233 4.177026 CTCTGTCCAGAAATACTTGTCGG 58.823 47.826 0.00 0.00 36.94 4.79
2363 3234 4.177026 CCTCTGTCCAGAAATACTTGTCG 58.823 47.826 0.00 0.00 36.94 4.35
2364 3235 4.223032 TCCCTCTGTCCAGAAATACTTGTC 59.777 45.833 0.00 0.00 36.94 3.18
2365 3236 4.168101 TCCCTCTGTCCAGAAATACTTGT 58.832 43.478 0.00 0.00 36.94 3.16
2366 3237 4.223923 ACTCCCTCTGTCCAGAAATACTTG 59.776 45.833 0.00 0.00 36.94 3.16
2367 3238 4.430441 ACTCCCTCTGTCCAGAAATACTT 58.570 43.478 0.00 0.00 36.94 2.24
2368 3239 4.067944 ACTCCCTCTGTCCAGAAATACT 57.932 45.455 0.00 0.00 36.94 2.12
2369 3240 7.784470 ATATACTCCCTCTGTCCAGAAATAC 57.216 40.000 0.00 0.00 36.94 1.89
2370 3241 9.310449 GTTATATACTCCCTCTGTCCAGAAATA 57.690 37.037 0.00 0.00 36.94 1.40
2371 3242 7.789831 TGTTATATACTCCCTCTGTCCAGAAAT 59.210 37.037 0.00 0.00 36.94 2.17
2372 3243 7.069578 GTGTTATATACTCCCTCTGTCCAGAAA 59.930 40.741 0.00 0.00 36.94 2.52
2373 3244 6.550108 GTGTTATATACTCCCTCTGTCCAGAA 59.450 42.308 0.00 0.00 36.94 3.02
2374 3245 6.069331 GTGTTATATACTCCCTCTGTCCAGA 58.931 44.000 0.00 0.00 35.85 3.86
2375 3246 5.833667 TGTGTTATATACTCCCTCTGTCCAG 59.166 44.000 0.00 0.00 0.00 3.86
2376 3247 5.773091 TGTGTTATATACTCCCTCTGTCCA 58.227 41.667 0.00 0.00 0.00 4.02
2377 3248 6.069331 TCTGTGTTATATACTCCCTCTGTCC 58.931 44.000 0.00 0.00 0.00 4.02
2378 3249 7.584122 TTCTGTGTTATATACTCCCTCTGTC 57.416 40.000 0.00 0.00 0.00 3.51
2379 3250 7.973048 TTTCTGTGTTATATACTCCCTCTGT 57.027 36.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.