Multiple sequence alignment - TraesCS5B01G036200

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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 TraesCS5B01G036200 chr5B 100.000 3056 0 0 1 3056 39743140 39740085 0.000000e+00 5644.0
1 TraesCS5B01G036200 chr5B 96.707 2126 66 4 1 2124 39545364 39543241 0.000000e+00 3535.0
2 TraesCS5B01G036200 chr5B 96.439 674 22 2 2359 3030 39543242 39542569 0.000000e+00 1110.0
3 TraesCS5B01G036200 chr5B 94.374 711 34 3 2344 3052 713054565 713053859 0.000000e+00 1086.0
4 TraesCS5B01G036200 chr7D 94.545 715 33 3 2344 3056 382021038 382020328 0.000000e+00 1099.0
5 TraesCS5B01G036200 chr7D 86.072 718 62 18 1 692 630113388 630112683 0.000000e+00 737.0
6 TraesCS5B01G036200 chr7D 85.106 282 27 5 427 696 630180543 630180821 1.080000e-69 274.0
7 TraesCS5B01G036200 chr7D 72.214 673 155 25 1388 2044 629450433 629449777 8.710000e-41 178.0
8 TraesCS5B01G036200 chr4D 94.406 715 34 3 2344 3056 123359278 123359988 0.000000e+00 1094.0
9 TraesCS5B01G036200 chr4D 86.790 704 63 16 1 691 428622025 428621339 0.000000e+00 758.0
10 TraesCS5B01G036200 chr4D 100.000 50 0 0 2280 2329 123570188 123570237 3.240000e-15 93.5
11 TraesCS5B01G036200 chr3D 94.266 715 35 3 2344 3056 202603583 202604293 0.000000e+00 1088.0
12 TraesCS5B01G036200 chr3D 100.000 50 0 0 2280 2329 202603551 202603600 3.240000e-15 93.5
13 TraesCS5B01G036200 chr2D 94.266 715 35 3 2344 3056 635027169 635027879 0.000000e+00 1088.0
14 TraesCS5B01G036200 chr2D 87.482 703 56 8 1 691 81395201 81394519 0.000000e+00 782.0
15 TraesCS5B01G036200 chr2D 86.490 718 59 17 1 692 573364271 573363566 0.000000e+00 754.0
16 TraesCS5B01G036200 chr2D 85.714 280 25 5 427 694 573453103 573453379 6.450000e-72 281.0
17 TraesCS5B01G036200 chr1B 94.374 711 34 3 2344 3052 461443911 461444617 0.000000e+00 1086.0
18 TraesCS5B01G036200 chr1B 100.000 50 0 0 2280 2329 338920054 338920103 3.240000e-15 93.5
19 TraesCS5B01G036200 chr1B 100.000 50 0 0 2280 2329 338995232 338995281 3.240000e-15 93.5
20 TraesCS5B01G036200 chr1B 100.000 50 0 0 2280 2329 461443879 461443928 3.240000e-15 93.5
21 TraesCS5B01G036200 chr1B 100.000 50 0 0 2280 2329 583509145 583509096 3.240000e-15 93.5
22 TraesCS5B01G036200 chr7A 94.233 711 35 3 2344 3052 120934201 120933495 0.000000e+00 1081.0
23 TraesCS5B01G036200 chr7A 74.003 727 128 49 1 692 689937102 689936402 3.940000e-59 239.0
24 TraesCS5B01G036200 chr5A 94.233 711 35 3 2344 3052 300040228 300040934 0.000000e+00 1081.0
25 TraesCS5B01G036200 chr5D 87.764 711 50 15 1 688 391329073 391329769 0.000000e+00 797.0
26 TraesCS5B01G036200 chr5D 84.874 714 60 23 1 691 356118808 356119496 0.000000e+00 676.0
27 TraesCS5B01G036200 chr5D 83.520 716 46 23 1 691 305761519 305762187 1.210000e-168 603.0
28 TraesCS5B01G036200 chr5D 74.740 673 154 12 1377 2044 524250253 524250914 1.390000e-73 287.0
29 TraesCS5B01G036200 chr5D 84.249 273 30 6 427 691 305736455 305736188 1.410000e-63 254.0
30 TraesCS5B01G036200 chr4B 86.932 704 47 15 1 691 187439803 187439132 0.000000e+00 749.0
31 TraesCS5B01G036200 chr4B 87.451 255 19 5 437 679 187462130 187462383 6.450000e-72 281.0
32 TraesCS5B01G036200 chr4B 90.000 170 16 1 523 691 526746588 526746419 5.130000e-53 219.0
33 TraesCS5B01G036200 chr4B 100.000 50 0 0 2280 2329 209157973 209157924 3.240000e-15 93.5
34 TraesCS5B01G036200 chr3A 85.486 689 54 27 1 671 22037514 22038174 0.000000e+00 676.0
35 TraesCS5B01G036200 chr4A 84.658 717 61 36 1 691 616787997 616788690 0.000000e+00 669.0
36 TraesCS5B01G036200 chrUn 100.000 50 0 0 2280 2329 390053597 390053646 3.240000e-15 93.5
37 TraesCS5B01G036200 chr6D 100.000 50 0 0 2280 2329 83963243 83963194 3.240000e-15 93.5


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 TraesCS5B01G036200 chr5B 39740085 39743140 3055 True 5644.00 5644 100.000 1 3056 1 chr5B.!!$R1 3055
1 TraesCS5B01G036200 chr5B 39542569 39545364 2795 True 2322.50 3535 96.573 1 3030 2 chr5B.!!$R3 3029
2 TraesCS5B01G036200 chr5B 713053859 713054565 706 True 1086.00 1086 94.374 2344 3052 1 chr5B.!!$R2 708
3 TraesCS5B01G036200 chr7D 382020328 382021038 710 True 1099.00 1099 94.545 2344 3056 1 chr7D.!!$R1 712
4 TraesCS5B01G036200 chr7D 630112683 630113388 705 True 737.00 737 86.072 1 692 1 chr7D.!!$R3 691
5 TraesCS5B01G036200 chr4D 123359278 123359988 710 False 1094.00 1094 94.406 2344 3056 1 chr4D.!!$F1 712
6 TraesCS5B01G036200 chr4D 428621339 428622025 686 True 758.00 758 86.790 1 691 1 chr4D.!!$R1 690
7 TraesCS5B01G036200 chr3D 202603551 202604293 742 False 590.75 1088 97.133 2280 3056 2 chr3D.!!$F1 776
8 TraesCS5B01G036200 chr2D 635027169 635027879 710 False 1088.00 1088 94.266 2344 3056 1 chr2D.!!$F2 712
9 TraesCS5B01G036200 chr2D 81394519 81395201 682 True 782.00 782 87.482 1 691 1 chr2D.!!$R1 690
10 TraesCS5B01G036200 chr2D 573363566 573364271 705 True 754.00 754 86.490 1 692 1 chr2D.!!$R2 691
11 TraesCS5B01G036200 chr1B 461443879 461444617 738 False 589.75 1086 97.187 2280 3052 2 chr1B.!!$F3 772
12 TraesCS5B01G036200 chr7A 120933495 120934201 706 True 1081.00 1081 94.233 2344 3052 1 chr7A.!!$R1 708
13 TraesCS5B01G036200 chr7A 689936402 689937102 700 True 239.00 239 74.003 1 692 1 chr7A.!!$R2 691
14 TraesCS5B01G036200 chr5A 300040228 300040934 706 False 1081.00 1081 94.233 2344 3052 1 chr5A.!!$F1 708
15 TraesCS5B01G036200 chr5D 391329073 391329769 696 False 797.00 797 87.764 1 688 1 chr5D.!!$F3 687
16 TraesCS5B01G036200 chr5D 356118808 356119496 688 False 676.00 676 84.874 1 691 1 chr5D.!!$F2 690
17 TraesCS5B01G036200 chr5D 305761519 305762187 668 False 603.00 603 83.520 1 691 1 chr5D.!!$F1 690
18 TraesCS5B01G036200 chr5D 524250253 524250914 661 False 287.00 287 74.740 1377 2044 1 chr5D.!!$F4 667
19 TraesCS5B01G036200 chr4B 187439132 187439803 671 True 749.00 749 86.932 1 691 1 chr4B.!!$R1 690
20 TraesCS5B01G036200 chr3A 22037514 22038174 660 False 676.00 676 85.486 1 671 1 chr3A.!!$F1 670
21 TraesCS5B01G036200 chr4A 616787997 616788690 693 False 669.00 669 84.658 1 691 1 chr4A.!!$F1 690

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
768 858 1.453928 GGGTTGGCATGCCCTAGAC 60.454 63.158 33.44 23.74 41.63 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2229 0.174389 TTAAGAGAGCGAGCAGGCAG 59.826 55.0 0.0 0.0 34.64 4.85 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
258 272 4.175489 CCATCTGCACGCTGCTGC 62.175 66.667 14.42 14.42 45.31 5.25
385 423 3.626930 ACAGAGGAAGAAGATAGCGAGT 58.373 45.455 0.00 0.00 0.00 4.18
400 438 1.608717 CGAGTTGGGGAGAGGAGTGG 61.609 65.000 0.00 0.00 0.00 4.00
511 585 2.507769 GCGCCGTTAGCCGTTAGT 60.508 61.111 0.00 0.00 38.78 2.24
549 635 3.057526 GCCATGTCAGGAAAGTGGTTAAC 60.058 47.826 0.00 0.00 32.56 2.01
655 742 2.803956 AGTGATAGTTCTGTGGGACGA 58.196 47.619 0.00 0.00 0.00 4.20
740 829 2.432628 GATATTCGGCCGGGAGCG 60.433 66.667 27.83 0.00 45.17 5.03
768 858 1.453928 GGGTTGGCATGCCCTAGAC 60.454 63.158 33.44 23.74 41.63 2.59
777 867 3.181450 GGCATGCCCTAGACTTGATACTT 60.181 47.826 27.24 0.00 0.00 2.24
778 868 4.455606 GCATGCCCTAGACTTGATACTTT 58.544 43.478 6.36 0.00 0.00 2.66
779 869 5.454755 GGCATGCCCTAGACTTGATACTTTA 60.455 44.000 27.24 0.00 0.00 1.85
916 1006 4.859304 TCTGATGTACCGTACAACAAGT 57.141 40.909 18.83 2.84 40.27 3.16
926 1016 9.787532 TGTACCGTACAACAAGTCTATAAATAC 57.212 33.333 8.99 0.00 35.38 1.89
934 1024 9.886132 ACAACAAGTCTATAAATACACCCTTAG 57.114 33.333 0.00 0.00 0.00 2.18
1005 1095 3.573967 AGCCCAATAATTAGGAAATGGCG 59.426 43.478 0.00 0.00 35.39 5.69
1051 1141 2.693762 TTGCAGCTCTCATTGGCGC 61.694 57.895 0.00 0.00 0.00 6.53
1079 1169 0.445436 CCAATGACACTCAAGAGCGC 59.555 55.000 0.00 0.00 0.00 5.92
1137 1227 2.892425 GGGAAGATGCTGTCGCCG 60.892 66.667 0.00 0.00 34.43 6.46
1342 1432 3.917760 CTTCCCTAGGCCCGCTCG 61.918 72.222 2.05 0.00 0.00 5.03
1490 1580 3.665848 CGATTCAACGGCGTGTTTAATGT 60.666 43.478 15.70 0.00 39.29 2.71
1693 1783 0.040067 CCAAGCGCCTTCTTTCACAC 60.040 55.000 2.29 0.00 0.00 3.82
1906 1996 1.260206 CGAGGTGAAGACGATGTTCG 58.740 55.000 0.00 0.00 46.93 3.95
2085 2175 0.110010 GTGCTTTCGAGCTTCCTTGC 60.110 55.000 0.00 0.00 35.49 4.01
2102 2192 3.061429 CCTTGCTTTCTCTCGATCGTTTC 59.939 47.826 15.94 0.00 0.00 2.78
2122 2212 2.942376 TCAGCGTGTGTCATGTCTTTTT 59.058 40.909 0.00 0.00 0.00 1.94
2145 2235 4.481930 TTTTGAATAACGTGTCTGCCTG 57.518 40.909 0.00 0.00 0.00 4.85
2146 2236 1.438651 TGAATAACGTGTCTGCCTGC 58.561 50.000 0.00 0.00 0.00 4.85
2147 2237 1.001974 TGAATAACGTGTCTGCCTGCT 59.998 47.619 0.00 0.00 0.00 4.24
2148 2238 1.661112 GAATAACGTGTCTGCCTGCTC 59.339 52.381 0.00 0.00 0.00 4.26
2149 2239 0.458543 ATAACGTGTCTGCCTGCTCG 60.459 55.000 0.00 0.00 0.00 5.03
2151 2241 4.731612 CGTGTCTGCCTGCTCGCT 62.732 66.667 0.00 0.00 0.00 4.93
2152 2242 2.813042 GTGTCTGCCTGCTCGCTC 60.813 66.667 0.00 0.00 0.00 5.03
2153 2243 2.993840 TGTCTGCCTGCTCGCTCT 60.994 61.111 0.00 0.00 0.00 4.09
2154 2244 2.202730 GTCTGCCTGCTCGCTCTC 60.203 66.667 0.00 0.00 0.00 3.20
2155 2245 2.362247 TCTGCCTGCTCGCTCTCT 60.362 61.111 0.00 0.00 0.00 3.10
2156 2246 1.981312 TCTGCCTGCTCGCTCTCTT 60.981 57.895 0.00 0.00 0.00 2.85
2157 2247 0.681243 TCTGCCTGCTCGCTCTCTTA 60.681 55.000 0.00 0.00 0.00 2.10
2158 2248 0.174389 CTGCCTGCTCGCTCTCTTAA 59.826 55.000 0.00 0.00 0.00 1.85
2159 2249 0.826715 TGCCTGCTCGCTCTCTTAAT 59.173 50.000 0.00 0.00 0.00 1.40
2160 2250 2.031870 TGCCTGCTCGCTCTCTTAATA 58.968 47.619 0.00 0.00 0.00 0.98
2161 2251 2.223829 TGCCTGCTCGCTCTCTTAATAC 60.224 50.000 0.00 0.00 0.00 1.89
2162 2252 2.864489 GCCTGCTCGCTCTCTTAATACC 60.864 54.545 0.00 0.00 0.00 2.73
2163 2253 2.288518 CCTGCTCGCTCTCTTAATACCC 60.289 54.545 0.00 0.00 0.00 3.69
2164 2254 1.337071 TGCTCGCTCTCTTAATACCCG 59.663 52.381 0.00 0.00 0.00 5.28
2165 2255 1.337387 GCTCGCTCTCTTAATACCCGT 59.663 52.381 0.00 0.00 0.00 5.28
2166 2256 2.223758 GCTCGCTCTCTTAATACCCGTT 60.224 50.000 0.00 0.00 0.00 4.44
2167 2257 3.372954 CTCGCTCTCTTAATACCCGTTG 58.627 50.000 0.00 0.00 0.00 4.10
2168 2258 1.859080 CGCTCTCTTAATACCCGTTGC 59.141 52.381 0.00 0.00 0.00 4.17
2169 2259 2.737359 CGCTCTCTTAATACCCGTTGCA 60.737 50.000 0.00 0.00 0.00 4.08
2170 2260 3.467803 GCTCTCTTAATACCCGTTGCAT 58.532 45.455 0.00 0.00 0.00 3.96
2171 2261 4.628074 GCTCTCTTAATACCCGTTGCATA 58.372 43.478 0.00 0.00 0.00 3.14
2172 2262 5.054477 GCTCTCTTAATACCCGTTGCATAA 58.946 41.667 0.00 0.00 0.00 1.90
2173 2263 5.701290 GCTCTCTTAATACCCGTTGCATAAT 59.299 40.000 0.00 0.00 0.00 1.28
2174 2264 6.204882 GCTCTCTTAATACCCGTTGCATAATT 59.795 38.462 0.00 0.00 0.00 1.40
2175 2265 7.255139 GCTCTCTTAATACCCGTTGCATAATTT 60.255 37.037 0.00 0.00 0.00 1.82
2176 2266 8.514330 TCTCTTAATACCCGTTGCATAATTTT 57.486 30.769 0.00 0.00 0.00 1.82
2177 2267 8.962679 TCTCTTAATACCCGTTGCATAATTTTT 58.037 29.630 0.00 0.00 0.00 1.94
2234 2324 9.865321 AAAGTCATGACAAGAATTATGAAATGG 57.135 29.630 27.02 0.00 31.98 3.16
2235 2325 8.812513 AGTCATGACAAGAATTATGAAATGGA 57.187 30.769 27.02 0.00 31.98 3.41
2236 2326 8.900781 AGTCATGACAAGAATTATGAAATGGAG 58.099 33.333 27.02 0.00 31.98 3.86
2237 2327 8.133627 GTCATGACAAGAATTATGAAATGGAGG 58.866 37.037 21.07 0.00 31.98 4.30
2238 2328 8.054572 TCATGACAAGAATTATGAAATGGAGGA 58.945 33.333 0.00 0.00 0.00 3.71
2239 2329 7.870509 TGACAAGAATTATGAAATGGAGGAG 57.129 36.000 0.00 0.00 0.00 3.69
2240 2330 7.405292 TGACAAGAATTATGAAATGGAGGAGT 58.595 34.615 0.00 0.00 0.00 3.85
2241 2331 7.890127 TGACAAGAATTATGAAATGGAGGAGTT 59.110 33.333 0.00 0.00 0.00 3.01
2242 2332 9.396022 GACAAGAATTATGAAATGGAGGAGTTA 57.604 33.333 0.00 0.00 0.00 2.24
2243 2333 9.927081 ACAAGAATTATGAAATGGAGGAGTTAT 57.073 29.630 0.00 0.00 0.00 1.89
2252 2342 9.872684 ATGAAATGGAGGAGTTATTATGTTGAT 57.127 29.630 0.00 0.00 0.00 2.57
2253 2343 9.123902 TGAAATGGAGGAGTTATTATGTTGATG 57.876 33.333 0.00 0.00 0.00 3.07
2254 2344 7.516198 AATGGAGGAGTTATTATGTTGATGC 57.484 36.000 0.00 0.00 0.00 3.91
2255 2345 5.376625 TGGAGGAGTTATTATGTTGATGCC 58.623 41.667 0.00 0.00 0.00 4.40
2256 2346 4.452455 GGAGGAGTTATTATGTTGATGCCG 59.548 45.833 0.00 0.00 0.00 5.69
2257 2347 5.290493 AGGAGTTATTATGTTGATGCCGA 57.710 39.130 0.00 0.00 0.00 5.54
2258 2348 5.300752 AGGAGTTATTATGTTGATGCCGAG 58.699 41.667 0.00 0.00 0.00 4.63
2259 2349 5.070446 AGGAGTTATTATGTTGATGCCGAGA 59.930 40.000 0.00 0.00 0.00 4.04
2260 2350 5.177696 GGAGTTATTATGTTGATGCCGAGAC 59.822 44.000 0.00 0.00 0.00 3.36
2261 2351 5.918608 AGTTATTATGTTGATGCCGAGACT 58.081 37.500 0.00 0.00 0.00 3.24
2262 2352 5.755375 AGTTATTATGTTGATGCCGAGACTG 59.245 40.000 0.00 0.00 0.00 3.51
2263 2353 3.610040 TTATGTTGATGCCGAGACTGT 57.390 42.857 0.00 0.00 0.00 3.55
2264 2354 2.479566 ATGTTGATGCCGAGACTGTT 57.520 45.000 0.00 0.00 0.00 3.16
2265 2355 2.254546 TGTTGATGCCGAGACTGTTT 57.745 45.000 0.00 0.00 0.00 2.83
2266 2356 1.872952 TGTTGATGCCGAGACTGTTTG 59.127 47.619 0.00 0.00 0.00 2.93
2267 2357 1.873591 GTTGATGCCGAGACTGTTTGT 59.126 47.619 0.00 0.00 0.00 2.83
2268 2358 3.064207 GTTGATGCCGAGACTGTTTGTA 58.936 45.455 0.00 0.00 0.00 2.41
2269 2359 3.610040 TGATGCCGAGACTGTTTGTAT 57.390 42.857 0.00 0.00 0.00 2.29
2270 2360 3.937814 TGATGCCGAGACTGTTTGTATT 58.062 40.909 0.00 0.00 0.00 1.89
2271 2361 4.323417 TGATGCCGAGACTGTTTGTATTT 58.677 39.130 0.00 0.00 0.00 1.40
2272 2362 4.391830 TGATGCCGAGACTGTTTGTATTTC 59.608 41.667 0.00 0.00 0.00 2.17
2273 2363 3.734463 TGCCGAGACTGTTTGTATTTCA 58.266 40.909 0.00 0.00 0.00 2.69
2274 2364 4.323417 TGCCGAGACTGTTTGTATTTCAT 58.677 39.130 0.00 0.00 0.00 2.57
2275 2365 5.483811 TGCCGAGACTGTTTGTATTTCATA 58.516 37.500 0.00 0.00 0.00 2.15
2276 2366 5.350365 TGCCGAGACTGTTTGTATTTCATAC 59.650 40.000 0.00 0.00 36.29 2.39
2277 2367 5.350365 GCCGAGACTGTTTGTATTTCATACA 59.650 40.000 0.00 0.00 43.54 2.29
2324 2414 9.413048 CGGATAGAGTATTAGAATGAAAAGACC 57.587 37.037 0.00 0.00 0.00 3.85
2331 2421 9.628500 AGTATTAGAATGAAAAGACCATTACCC 57.372 33.333 0.00 0.00 34.67 3.69
2332 2422 7.898014 ATTAGAATGAAAAGACCATTACCCC 57.102 36.000 0.00 0.00 34.67 4.95
2333 2423 4.270008 AGAATGAAAAGACCATTACCCCG 58.730 43.478 0.00 0.00 34.67 5.73
2334 2424 1.828979 TGAAAAGACCATTACCCCGC 58.171 50.000 0.00 0.00 0.00 6.13
2335 2425 1.074084 TGAAAAGACCATTACCCCGCA 59.926 47.619 0.00 0.00 0.00 5.69
2336 2426 2.164338 GAAAAGACCATTACCCCGCAA 58.836 47.619 0.00 0.00 0.00 4.85
2337 2427 2.296073 AAAGACCATTACCCCGCAAA 57.704 45.000 0.00 0.00 0.00 3.68
2338 2428 2.296073 AAGACCATTACCCCGCAAAA 57.704 45.000 0.00 0.00 0.00 2.44
2339 2429 2.296073 AGACCATTACCCCGCAAAAA 57.704 45.000 0.00 0.00 0.00 1.94
2446 2537 4.212636 GCTTTTACCTTTCTTGCGTACTCA 59.787 41.667 0.00 0.00 0.00 3.41
2523 2614 7.873505 AGTAAGATTCTTAAGCTTAATAGGCCG 59.126 37.037 18.93 6.93 40.63 6.13
2837 2928 2.036571 CGTGATCAAGGCTGCAGCA 61.037 57.895 37.63 19.79 44.36 4.41
2905 2998 2.134287 CCACCGATCCCGACCATCT 61.134 63.158 0.00 0.00 38.22 2.90
2914 3007 2.178273 CGACCATCTCGCGACACA 59.822 61.111 3.71 0.00 35.06 3.72
2984 3078 2.743538 GCAGCAGCACGGACATGA 60.744 61.111 0.00 0.00 41.58 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.026262 GGGCTTCTGGTTGAACCTGATA 60.026 50.000 22.04 13.06 44.15 2.15
258 272 1.467342 TGACGAGTACATGGACGAGTG 59.533 52.381 14.73 3.72 0.00 3.51
385 423 1.538876 CACCCACTCCTCTCCCCAA 60.539 63.158 0.00 0.00 0.00 4.12
400 438 1.470890 CTCACTCCTCTTCGTCTCACC 59.529 57.143 0.00 0.00 0.00 4.02
466 540 1.672854 CGGATGTTAGTGCCTCGGGA 61.673 60.000 0.00 0.00 0.00 5.14
542 628 4.022416 TCGTCGTTTTAGCTAGGTTAACCA 60.022 41.667 26.26 11.41 38.89 3.67
549 635 4.031426 GTGTTGATCGTCGTTTTAGCTAGG 59.969 45.833 0.00 0.00 0.00 3.02
768 858 9.239002 CGGTTCTCTTACAGATAAAGTATCAAG 57.761 37.037 0.00 0.00 37.65 3.02
777 867 6.318144 CCACTCTACGGTTCTCTTACAGATAA 59.682 42.308 0.00 0.00 0.00 1.75
778 868 5.821470 CCACTCTACGGTTCTCTTACAGATA 59.179 44.000 0.00 0.00 0.00 1.98
779 869 4.641094 CCACTCTACGGTTCTCTTACAGAT 59.359 45.833 0.00 0.00 0.00 2.90
789 879 3.881937 ATTGGTACCACTCTACGGTTC 57.118 47.619 16.04 0.00 37.99 3.62
796 886 4.715297 AGGATAACGAATTGGTACCACTCT 59.285 41.667 16.04 1.01 0.00 3.24
797 887 5.019785 AGGATAACGAATTGGTACCACTC 57.980 43.478 16.04 13.35 0.00 3.51
916 1006 7.070696 TCTGCTTGCTAAGGGTGTATTTATAGA 59.929 37.037 0.00 0.00 0.00 1.98
926 1016 1.446907 CAGTCTGCTTGCTAAGGGTG 58.553 55.000 0.00 0.00 0.00 4.61
1005 1095 3.003763 AAGGCCTCCCTGTCGTCC 61.004 66.667 5.23 0.00 41.90 4.79
1051 1141 2.205074 GAGTGTCATTGGCACGATAGG 58.795 52.381 15.25 0.00 41.36 2.57
1210 1300 0.731514 ACGATGTTGTACGACGCCAG 60.732 55.000 8.73 3.08 0.00 4.85
1251 1341 3.741476 GCAAGCAGGCCGTCCTTG 61.741 66.667 21.39 21.39 41.93 3.61
1342 1432 2.417515 GGATCTTGTCGTTCAGGAGGAC 60.418 54.545 0.00 0.00 42.17 3.85
1467 1557 0.164217 TAAACACGCCGTTGAATCGC 59.836 50.000 0.00 0.00 38.07 4.58
1693 1783 4.806481 GCTCACATGCTGCACGCG 62.806 66.667 3.57 3.53 43.27 6.01
1773 1863 2.338620 CAGTGCTCGTCGGTCCAA 59.661 61.111 0.00 0.00 0.00 3.53
1869 1959 2.686816 GGGCGTGTCATCCGGTTTG 61.687 63.158 0.00 0.36 0.00 2.93
1906 1996 4.268797 TGAGCATGAGAATATCCAGCTC 57.731 45.455 10.39 10.39 46.24 4.09
2085 2175 4.212949 ACGCTGAAACGATCGAGAGAAAG 61.213 47.826 24.34 11.82 39.33 2.62
2102 2192 3.338818 AAAAAGACATGACACACGCTG 57.661 42.857 0.00 0.00 0.00 5.18
2123 2213 4.791411 GCAGGCAGACACGTTATTCAAAAA 60.791 41.667 0.00 0.00 0.00 1.94
2124 2214 3.304391 GCAGGCAGACACGTTATTCAAAA 60.304 43.478 0.00 0.00 0.00 2.44
2125 2215 2.225491 GCAGGCAGACACGTTATTCAAA 59.775 45.455 0.00 0.00 0.00 2.69
2126 2216 1.804151 GCAGGCAGACACGTTATTCAA 59.196 47.619 0.00 0.00 0.00 2.69
2127 2217 1.001974 AGCAGGCAGACACGTTATTCA 59.998 47.619 0.00 0.00 0.00 2.57
2128 2218 1.661112 GAGCAGGCAGACACGTTATTC 59.339 52.381 0.00 0.00 0.00 1.75
2129 2219 1.726853 GAGCAGGCAGACACGTTATT 58.273 50.000 0.00 0.00 0.00 1.40
2130 2220 0.458543 CGAGCAGGCAGACACGTTAT 60.459 55.000 0.00 0.00 0.00 1.89
2131 2221 1.080772 CGAGCAGGCAGACACGTTA 60.081 57.895 0.00 0.00 0.00 3.18
2132 2222 2.356313 CGAGCAGGCAGACACGTT 60.356 61.111 0.00 0.00 0.00 3.99
2134 2224 4.731612 AGCGAGCAGGCAGACACG 62.732 66.667 0.00 0.00 34.64 4.49
2135 2225 2.813042 GAGCGAGCAGGCAGACAC 60.813 66.667 0.00 0.00 34.64 3.67
2136 2226 2.993840 AGAGCGAGCAGGCAGACA 60.994 61.111 0.00 0.00 34.64 3.41
2137 2227 2.202730 GAGAGCGAGCAGGCAGAC 60.203 66.667 0.00 0.00 34.64 3.51
2138 2228 0.681243 TAAGAGAGCGAGCAGGCAGA 60.681 55.000 0.00 0.00 34.64 4.26
2139 2229 0.174389 TTAAGAGAGCGAGCAGGCAG 59.826 55.000 0.00 0.00 34.64 4.85
2140 2230 0.826715 ATTAAGAGAGCGAGCAGGCA 59.173 50.000 0.00 0.00 34.64 4.75
2141 2231 2.399448 GTATTAAGAGAGCGAGCAGGC 58.601 52.381 0.00 0.00 0.00 4.85
2142 2232 2.288518 GGGTATTAAGAGAGCGAGCAGG 60.289 54.545 0.00 0.00 0.00 4.85
2143 2233 2.605823 CGGGTATTAAGAGAGCGAGCAG 60.606 54.545 0.00 0.00 0.00 4.24
2144 2234 1.337071 CGGGTATTAAGAGAGCGAGCA 59.663 52.381 0.00 0.00 0.00 4.26
2145 2235 1.337387 ACGGGTATTAAGAGAGCGAGC 59.663 52.381 0.00 0.00 0.00 5.03
2146 2236 3.372954 CAACGGGTATTAAGAGAGCGAG 58.627 50.000 0.00 0.00 0.00 5.03
2147 2237 2.480759 GCAACGGGTATTAAGAGAGCGA 60.481 50.000 0.00 0.00 0.00 4.93
2148 2238 1.859080 GCAACGGGTATTAAGAGAGCG 59.141 52.381 0.00 0.00 0.00 5.03
2149 2239 2.901249 TGCAACGGGTATTAAGAGAGC 58.099 47.619 0.00 0.00 0.00 4.09
2150 2240 7.730364 AATTATGCAACGGGTATTAAGAGAG 57.270 36.000 0.00 0.00 0.00 3.20
2151 2241 8.514330 AAAATTATGCAACGGGTATTAAGAGA 57.486 30.769 0.00 0.00 0.00 3.10
2208 2298 9.865321 CCATTTCATAATTCTTGTCATGACTTT 57.135 29.630 25.55 13.49 0.00 2.66
2209 2299 9.246670 TCCATTTCATAATTCTTGTCATGACTT 57.753 29.630 25.55 13.89 0.00 3.01
2210 2300 8.812513 TCCATTTCATAATTCTTGTCATGACT 57.187 30.769 25.55 7.77 0.00 3.41
2211 2301 8.133627 CCTCCATTTCATAATTCTTGTCATGAC 58.866 37.037 19.27 19.27 0.00 3.06
2212 2302 8.054572 TCCTCCATTTCATAATTCTTGTCATGA 58.945 33.333 0.00 0.00 0.00 3.07
2213 2303 8.229253 TCCTCCATTTCATAATTCTTGTCATG 57.771 34.615 0.00 0.00 0.00 3.07
2214 2304 8.057623 ACTCCTCCATTTCATAATTCTTGTCAT 58.942 33.333 0.00 0.00 0.00 3.06
2215 2305 7.405292 ACTCCTCCATTTCATAATTCTTGTCA 58.595 34.615 0.00 0.00 0.00 3.58
2216 2306 7.872113 ACTCCTCCATTTCATAATTCTTGTC 57.128 36.000 0.00 0.00 0.00 3.18
2217 2307 9.927081 ATAACTCCTCCATTTCATAATTCTTGT 57.073 29.630 0.00 0.00 0.00 3.16
2226 2316 9.872684 ATCAACATAATAACTCCTCCATTTCAT 57.127 29.630 0.00 0.00 0.00 2.57
2227 2317 9.123902 CATCAACATAATAACTCCTCCATTTCA 57.876 33.333 0.00 0.00 0.00 2.69
2228 2318 8.078596 GCATCAACATAATAACTCCTCCATTTC 58.921 37.037 0.00 0.00 0.00 2.17
2229 2319 7.014615 GGCATCAACATAATAACTCCTCCATTT 59.985 37.037 0.00 0.00 0.00 2.32
2230 2320 6.491403 GGCATCAACATAATAACTCCTCCATT 59.509 38.462 0.00 0.00 0.00 3.16
2231 2321 6.006449 GGCATCAACATAATAACTCCTCCAT 58.994 40.000 0.00 0.00 0.00 3.41
2232 2322 5.376625 GGCATCAACATAATAACTCCTCCA 58.623 41.667 0.00 0.00 0.00 3.86
2233 2323 4.452455 CGGCATCAACATAATAACTCCTCC 59.548 45.833 0.00 0.00 0.00 4.30
2234 2324 5.297547 TCGGCATCAACATAATAACTCCTC 58.702 41.667 0.00 0.00 0.00 3.71
2235 2325 5.070446 TCTCGGCATCAACATAATAACTCCT 59.930 40.000 0.00 0.00 0.00 3.69
2236 2326 5.177696 GTCTCGGCATCAACATAATAACTCC 59.822 44.000 0.00 0.00 0.00 3.85
2237 2327 5.986135 AGTCTCGGCATCAACATAATAACTC 59.014 40.000 0.00 0.00 0.00 3.01
2238 2328 5.755375 CAGTCTCGGCATCAACATAATAACT 59.245 40.000 0.00 0.00 0.00 2.24
2239 2329 5.523916 ACAGTCTCGGCATCAACATAATAAC 59.476 40.000 0.00 0.00 0.00 1.89
2240 2330 5.670485 ACAGTCTCGGCATCAACATAATAA 58.330 37.500 0.00 0.00 0.00 1.40
2241 2331 5.276461 ACAGTCTCGGCATCAACATAATA 57.724 39.130 0.00 0.00 0.00 0.98
2242 2332 4.142609 ACAGTCTCGGCATCAACATAAT 57.857 40.909 0.00 0.00 0.00 1.28
2243 2333 3.610040 ACAGTCTCGGCATCAACATAA 57.390 42.857 0.00 0.00 0.00 1.90
2244 2334 3.610040 AACAGTCTCGGCATCAACATA 57.390 42.857 0.00 0.00 0.00 2.29
2245 2335 2.479566 AACAGTCTCGGCATCAACAT 57.520 45.000 0.00 0.00 0.00 2.71
2246 2336 1.872952 CAAACAGTCTCGGCATCAACA 59.127 47.619 0.00 0.00 0.00 3.33
2247 2337 1.873591 ACAAACAGTCTCGGCATCAAC 59.126 47.619 0.00 0.00 0.00 3.18
2248 2338 2.254546 ACAAACAGTCTCGGCATCAA 57.745 45.000 0.00 0.00 0.00 2.57
2249 2339 3.610040 ATACAAACAGTCTCGGCATCA 57.390 42.857 0.00 0.00 0.00 3.07
2250 2340 4.391830 TGAAATACAAACAGTCTCGGCATC 59.608 41.667 0.00 0.00 0.00 3.91
2251 2341 4.323417 TGAAATACAAACAGTCTCGGCAT 58.677 39.130 0.00 0.00 0.00 4.40
2252 2342 3.734463 TGAAATACAAACAGTCTCGGCA 58.266 40.909 0.00 0.00 0.00 5.69
2253 2343 4.946784 ATGAAATACAAACAGTCTCGGC 57.053 40.909 0.00 0.00 0.00 5.54
2269 2359 9.944376 AGTTCTCAGTATTTAGCTTGTATGAAA 57.056 29.630 0.00 0.00 0.00 2.69
2270 2360 9.587772 GAGTTCTCAGTATTTAGCTTGTATGAA 57.412 33.333 0.00 0.00 0.00 2.57
2271 2361 8.972127 AGAGTTCTCAGTATTTAGCTTGTATGA 58.028 33.333 0.00 0.00 0.00 2.15
2272 2362 9.243637 GAGAGTTCTCAGTATTTAGCTTGTATG 57.756 37.037 4.30 0.00 42.42 2.39
2273 2363 8.132362 CGAGAGTTCTCAGTATTTAGCTTGTAT 58.868 37.037 9.61 0.00 43.00 2.29
2274 2364 7.415318 CCGAGAGTTCTCAGTATTTAGCTTGTA 60.415 40.741 9.61 0.00 43.00 2.41
2275 2365 6.326375 CGAGAGTTCTCAGTATTTAGCTTGT 58.674 40.000 9.61 0.00 43.00 3.16
2276 2366 5.746245 CCGAGAGTTCTCAGTATTTAGCTTG 59.254 44.000 9.61 0.00 43.00 4.01
2277 2367 5.652891 TCCGAGAGTTCTCAGTATTTAGCTT 59.347 40.000 9.61 0.00 43.00 3.74
2278 2368 5.194432 TCCGAGAGTTCTCAGTATTTAGCT 58.806 41.667 9.61 0.00 43.00 3.32
2311 2401 4.270008 CGGGGTAATGGTCTTTTCATTCT 58.730 43.478 0.00 0.00 36.40 2.40
2312 2402 3.181490 GCGGGGTAATGGTCTTTTCATTC 60.181 47.826 0.00 0.00 36.40 2.67
2313 2403 2.758423 GCGGGGTAATGGTCTTTTCATT 59.242 45.455 0.00 0.00 38.29 2.57
2314 2404 2.291282 TGCGGGGTAATGGTCTTTTCAT 60.291 45.455 0.00 0.00 0.00 2.57
2315 2405 1.074084 TGCGGGGTAATGGTCTTTTCA 59.926 47.619 0.00 0.00 0.00 2.69
2316 2406 1.828979 TGCGGGGTAATGGTCTTTTC 58.171 50.000 0.00 0.00 0.00 2.29
2317 2407 2.296073 TTGCGGGGTAATGGTCTTTT 57.704 45.000 0.00 0.00 0.00 2.27
2318 2408 2.296073 TTTGCGGGGTAATGGTCTTT 57.704 45.000 0.00 0.00 0.00 2.52
2319 2409 2.296073 TTTTGCGGGGTAATGGTCTT 57.704 45.000 0.00 0.00 0.00 3.01
2320 2410 2.296073 TTTTTGCGGGGTAATGGTCT 57.704 45.000 0.00 0.00 0.00 3.85
2446 2537 1.457346 GCTAGCAACTGGTTCAGCAT 58.543 50.000 10.63 0.00 34.37 3.79
2519 2610 2.028883 CGTACTTTTCGATCTTTCGGCC 59.971 50.000 0.00 0.00 45.53 6.13
2523 2614 4.240096 TGGTCCGTACTTTTCGATCTTTC 58.760 43.478 0.00 0.00 0.00 2.62
2837 2928 1.216710 GTTAGTCCTCGCAGCAGCT 59.783 57.895 0.00 0.00 39.10 4.24
2914 3007 0.894184 TGGAGGAGCTTTCGACGTCT 60.894 55.000 14.70 0.00 0.00 4.18
3007 3101 6.539826 TGCAGAATCGTTGATCATACTTCATT 59.460 34.615 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.