Multiple sequence alignment - TraesCS5D01G252700

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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 TraesCS5D01G252700 chr5D 100.000 2480 0 0 1 2480 358797386 358799865 0.000000e+00 4580.0
1 TraesCS5D01G252700 chr5A 86.435 2219 191 33 3 2168 459541695 459543856 0.000000e+00 2329.0
2 TraesCS5D01G252700 chr5A 92.903 155 6 2 2282 2435 459543889 459544039 1.150000e-53 220.0
3 TraesCS5D01G252700 chr5B 89.310 1478 105 31 613 2067 423795796 423797243 0.000000e+00 1805.0
4 TraesCS5D01G252700 chr5B 88.702 416 38 7 1 413 423792121 423792530 1.320000e-137 499.0
5 TraesCS5D01G252700 chr5B 93.714 175 10 1 2216 2390 423797341 423797514 6.800000e-66 261.0
6 TraesCS5D01G252700 chr5B 89.375 160 17 0 411 570 423795452 423795611 4.180000e-48 202.0
7 TraesCS5D01G252700 chr4B 85.317 756 79 24 731 1463 436098192 436098938 0.000000e+00 752.0
8 TraesCS5D01G252700 chr4B 95.023 442 22 0 1022 1463 436102581 436103022 0.000000e+00 695.0
9 TraesCS5D01G252700 chr4B 87.288 118 14 1 96 212 10898054 10898171 1.550000e-27 134.0
10 TraesCS5D01G252700 chr4A 85.112 759 77 29 731 1463 112858345 112857597 0.000000e+00 743.0
11 TraesCS5D01G252700 chr4A 95.853 434 18 0 1025 1458 112847011 112846578 0.000000e+00 702.0
12 TraesCS5D01G252700 chr4A 95.444 439 20 0 1025 1463 112853360 112852922 0.000000e+00 701.0
13 TraesCS5D01G252700 chr4A 92.857 42 3 0 562 603 362116160 362116201 7.410000e-06 62.1
14 TraesCS5D01G252700 chr4D 95.249 442 21 0 1022 1463 352580006 352580447 0.000000e+00 701.0
15 TraesCS5D01G252700 chr4D 87.288 118 14 1 96 212 42123456 42123339 1.550000e-27 134.0
16 TraesCS5D01G252700 chr6B 92.521 468 29 3 997 1458 145043634 145044101 0.000000e+00 665.0
17 TraesCS5D01G252700 chrUn 81.063 602 85 20 20 603 297428320 297428910 1.050000e-123 453.0
18 TraesCS5D01G252700 chrUn 81.063 602 85 20 20 603 297433272 297433862 1.050000e-123 453.0
19 TraesCS5D01G252700 chr3A 83.019 212 33 3 16 225 662954838 662955048 3.260000e-44 189.0
20 TraesCS5D01G252700 chr1D 91.111 45 4 0 563 607 468720479 468720523 7.410000e-06 62.1


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 TraesCS5D01G252700 chr5D 358797386 358799865 2479 False 4580.00 4580 100.00000 1 2480 1 chr5D.!!$F1 2479
1 TraesCS5D01G252700 chr5A 459541695 459544039 2344 False 1274.50 2329 89.66900 3 2435 2 chr5A.!!$F1 2432
2 TraesCS5D01G252700 chr5B 423792121 423797514 5393 False 691.75 1805 90.27525 1 2390 4 chr5B.!!$F1 2389
3 TraesCS5D01G252700 chr4B 436098192 436103022 4830 False 723.50 752 90.17000 731 1463 2 chr4B.!!$F2 732
4 TraesCS5D01G252700 chr4A 112857597 112858345 748 True 743.00 743 85.11200 731 1463 1 chr4A.!!$R3 732
5 TraesCS5D01G252700 chrUn 297428320 297428910 590 False 453.00 453 81.06300 20 603 1 chrUn.!!$F1 583
6 TraesCS5D01G252700 chrUn 297433272 297433862 590 False 453.00 453 81.06300 20 603 1 chrUn.!!$F2 583

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
54 55 0.320374 ACGAATGACGAAGGGAGCAA 59.68 50.0 0.0 0.0 45.77 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 8976 1.373748 GAGCCGAACAACTGCCGTA 60.374 57.895 0.0 0.0 0.0 4.02 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
54 55 0.320374 ACGAATGACGAAGGGAGCAA 59.680 50.000 0.00 0.00 45.77 3.91
120 129 3.050275 GCGAACTTCTGCCGCCTT 61.050 61.111 0.00 0.00 42.77 4.35
149 158 4.069232 CTCCCCGTCGCTCAAGCA 62.069 66.667 2.50 0.00 42.21 3.91
279 290 2.039624 TCCTCTCCAGCACCCTCC 59.960 66.667 0.00 0.00 0.00 4.30
294 305 1.343478 CCCTCCTGTACCACCATCTCT 60.343 57.143 0.00 0.00 0.00 3.10
359 370 8.439993 TCTAGTATGCTAGTATGCTAGTATGC 57.560 38.462 30.56 23.26 45.77 3.14
378 392 8.094798 AGTATGCTTGAACTGTTTAATTTCGA 57.905 30.769 0.00 0.00 0.00 3.71
423 3363 5.853936 TGTATGGCATGTAGTATGAACTCC 58.146 41.667 10.98 0.00 37.15 3.85
424 3364 3.838244 TGGCATGTAGTATGAACTCCC 57.162 47.619 0.00 0.00 37.15 4.30
425 3365 3.384168 TGGCATGTAGTATGAACTCCCT 58.616 45.455 0.00 0.00 37.15 4.20
426 3366 3.780294 TGGCATGTAGTATGAACTCCCTT 59.220 43.478 0.00 0.00 37.15 3.95
471 3411 3.100817 TCTATGTTTACGCGCGAACTAC 58.899 45.455 39.36 25.80 0.00 2.73
508 3448 5.505985 GCGGTATCGGTATGAAGGATCTATC 60.506 48.000 0.00 0.00 36.79 2.08
545 3485 5.121768 CCGACATCCTGTAAAAATCGTTTCT 59.878 40.000 0.00 0.00 0.00 2.52
548 3488 7.133891 ACATCCTGTAAAAATCGTTTCTGAG 57.866 36.000 0.00 0.00 0.00 3.35
588 3528 4.778143 GACGGCCAGTTGCGGGAT 62.778 66.667 2.24 0.00 44.08 3.85
603 3543 2.441410 CGGGATCTGCTAGAGATGCTA 58.559 52.381 16.99 0.00 46.30 3.49
607 3547 5.126222 CGGGATCTGCTAGAGATGCTATTAA 59.874 44.000 16.99 0.00 46.30 1.40
680 3770 3.637714 GCGAAACTCACCGCTTGA 58.362 55.556 0.00 0.00 46.96 3.02
681 3771 1.204312 GCGAAACTCACCGCTTGAC 59.796 57.895 0.00 0.00 46.96 3.18
682 3772 1.860078 CGAAACTCACCGCTTGACC 59.140 57.895 0.00 0.00 0.00 4.02
683 3773 1.860078 GAAACTCACCGCTTGACCG 59.140 57.895 0.00 0.00 0.00 4.79
728 3820 1.684983 CGGTAGGCGGGAAAATAGAGA 59.315 52.381 0.00 0.00 0.00 3.10
741 3833 4.678509 AAATAGAGACGCAAAATTCGCA 57.321 36.364 1.28 0.00 0.00 5.10
787 3879 4.097361 GTCCAACCGAGCCTCCCC 62.097 72.222 0.00 0.00 0.00 4.81
815 3907 2.046314 CTCCCCAAACCGCATCGT 60.046 61.111 0.00 0.00 0.00 3.73
908 4001 3.385111 CCGTCTGAAGCTCTAAATACCCT 59.615 47.826 0.00 0.00 0.00 4.34
1435 8684 1.789576 GCCCAAGTCCCCCAAGAAGA 61.790 60.000 0.00 0.00 0.00 2.87
1488 8739 1.490574 AGAAGGCCTAAGAGATGCGT 58.509 50.000 5.16 0.00 0.00 5.24
1493 8744 1.137086 GGCCTAAGAGATGCGTTCTGA 59.863 52.381 0.00 0.00 33.74 3.27
1496 8747 3.677424 GCCTAAGAGATGCGTTCTGAGTT 60.677 47.826 0.00 0.00 33.74 3.01
1503 8754 4.632153 AGATGCGTTCTGAGTTGTTTAGT 58.368 39.130 0.00 0.00 31.79 2.24
1561 8814 4.745620 GTGAAGGTGTTCTGTCTAGTTGTC 59.254 45.833 0.00 0.00 33.38 3.18
1568 8821 6.147581 GTGTTCTGTCTAGTTGTCGATGTAA 58.852 40.000 0.00 0.00 0.00 2.41
1579 8834 3.127589 TGTCGATGTAACCTGTGTTGTG 58.872 45.455 0.00 0.00 35.87 3.33
1637 8902 2.096220 ATGCTGCTGTCTTGAGTCAG 57.904 50.000 0.00 1.61 34.96 3.51
1643 8908 1.506493 CTGTCTTGAGTCAGTGCACC 58.494 55.000 14.63 0.00 0.00 5.01
1647 8912 0.249868 CTTGAGTCAGTGCACCGGAA 60.250 55.000 14.63 0.00 0.00 4.30
1653 8918 0.313672 TCAGTGCACCGGAAATTTGC 59.686 50.000 14.63 7.96 36.76 3.68
1658 8923 1.549620 TGCACCGGAAATTTGCATCAT 59.450 42.857 9.46 0.00 41.29 2.45
1660 8925 3.002102 GCACCGGAAATTTGCATCATTT 58.998 40.909 9.46 4.45 36.22 2.32
1662 8927 4.268405 GCACCGGAAATTTGCATCATTTAG 59.732 41.667 9.46 3.38 36.22 1.85
1698 8963 1.689959 GTGTCGCTGAAATTGGCAAG 58.310 50.000 5.96 0.00 0.00 4.01
1708 8973 5.093169 TGAAATTGGCAAGCGAATTTTTG 57.907 34.783 22.51 0.00 41.83 2.44
1756 9021 3.674997 TGTGGATTCAGTTTACTGCTCC 58.325 45.455 17.47 17.47 43.46 4.70
1765 9030 4.825085 TCAGTTTACTGCTCCGGAATTTTT 59.175 37.500 5.23 0.00 43.46 1.94
1804 9069 3.914555 CAGAGCAGTAAACTATGCACG 57.085 47.619 0.00 0.00 45.01 5.34
1900 9165 7.229506 GGAGGGAATTGAATAACCTGTCAATAG 59.770 40.741 5.44 0.00 42.30 1.73
1904 9169 6.949352 ATTGAATAACCTGTCAATAGCTGG 57.051 37.500 0.00 0.00 41.54 4.85
1977 9243 1.000283 CACAGAAGTCGCCTTGTCTCT 60.000 52.381 0.00 0.00 0.00 3.10
2036 9302 0.037605 CGACTCCGGGCTTTACTTGT 60.038 55.000 0.00 0.00 0.00 3.16
2045 9311 1.439679 GCTTTACTTGTGCTAGCGGT 58.560 50.000 10.77 8.73 0.00 5.68
2091 9388 1.475280 GGGGGTTAATTTCCGAACAGC 59.525 52.381 0.00 0.00 0.00 4.40
2094 9391 2.163613 GGGTTAATTTCCGAACAGCAGG 59.836 50.000 0.00 0.00 0.00 4.85
2097 9394 2.514458 AATTTCCGAACAGCAGGGAT 57.486 45.000 0.00 0.00 0.00 3.85
2100 9397 2.124570 CCGAACAGCAGGGATGGG 60.125 66.667 0.00 0.00 0.00 4.00
2114 9411 0.035056 GATGGGTGGAGAGGGTTGTG 60.035 60.000 0.00 0.00 0.00 3.33
2121 9418 0.107945 GGAGAGGGTTGTGCTAGCAG 60.108 60.000 20.03 0.00 0.00 4.24
2133 9430 5.405935 TGTGCTAGCAGATCTCTGTAAAA 57.594 39.130 20.03 0.00 45.45 1.52
2155 9452 3.778618 AGTATTAGCTCCGTTCGGAAAC 58.221 45.455 14.79 9.99 33.41 2.78
2159 9456 0.602905 AGCTCCGTTCGGAAACAAGG 60.603 55.000 14.79 3.82 34.93 3.61
2168 9465 1.164041 CGGAAACAAGGGACGCTGTT 61.164 55.000 0.00 0.00 40.10 3.16
2169 9466 1.029681 GGAAACAAGGGACGCTGTTT 58.970 50.000 15.05 15.05 46.43 2.83
2170 9467 1.407618 GGAAACAAGGGACGCTGTTTT 59.592 47.619 15.76 8.93 44.79 2.43
2171 9468 2.619646 GGAAACAAGGGACGCTGTTTTA 59.380 45.455 15.76 0.00 44.79 1.52
2172 9469 3.304458 GGAAACAAGGGACGCTGTTTTAG 60.304 47.826 15.76 0.00 44.79 1.85
2173 9470 2.632987 ACAAGGGACGCTGTTTTAGT 57.367 45.000 0.00 0.00 0.00 2.24
2174 9471 2.927028 ACAAGGGACGCTGTTTTAGTT 58.073 42.857 0.00 0.00 0.00 2.24
2175 9472 2.876550 ACAAGGGACGCTGTTTTAGTTC 59.123 45.455 0.00 0.00 0.00 3.01
2176 9473 3.139077 CAAGGGACGCTGTTTTAGTTCT 58.861 45.455 0.00 0.00 0.00 3.01
2177 9474 3.041508 AGGGACGCTGTTTTAGTTCTC 57.958 47.619 0.00 0.00 0.00 2.87
2178 9475 2.367567 AGGGACGCTGTTTTAGTTCTCA 59.632 45.455 0.00 0.00 0.00 3.27
2179 9476 2.479275 GGGACGCTGTTTTAGTTCTCAC 59.521 50.000 0.00 0.00 0.00 3.51
2180 9477 3.391049 GGACGCTGTTTTAGTTCTCACT 58.609 45.455 0.00 0.00 36.99 3.41
2181 9478 3.808174 GGACGCTGTTTTAGTTCTCACTT 59.192 43.478 0.00 0.00 34.06 3.16
2182 9479 4.318831 GGACGCTGTTTTAGTTCTCACTTG 60.319 45.833 0.00 0.00 34.06 3.16
2183 9480 4.189231 ACGCTGTTTTAGTTCTCACTTGT 58.811 39.130 0.00 0.00 34.06 3.16
2184 9481 4.634443 ACGCTGTTTTAGTTCTCACTTGTT 59.366 37.500 0.00 0.00 34.06 2.83
2185 9482 5.123344 ACGCTGTTTTAGTTCTCACTTGTTT 59.877 36.000 0.00 0.00 34.06 2.83
2186 9483 5.677178 CGCTGTTTTAGTTCTCACTTGTTTC 59.323 40.000 0.00 0.00 34.06 2.78
2187 9484 5.971792 GCTGTTTTAGTTCTCACTTGTTTCC 59.028 40.000 0.00 0.00 34.06 3.13
2188 9485 6.114221 TGTTTTAGTTCTCACTTGTTTCCG 57.886 37.500 0.00 0.00 34.06 4.30
2189 9486 5.875910 TGTTTTAGTTCTCACTTGTTTCCGA 59.124 36.000 0.00 0.00 34.06 4.55
2190 9487 6.372103 TGTTTTAGTTCTCACTTGTTTCCGAA 59.628 34.615 0.00 0.00 34.06 4.30
2191 9488 5.978934 TTAGTTCTCACTTGTTTCCGAAC 57.021 39.130 0.00 0.00 34.06 3.95
2192 9489 2.864343 AGTTCTCACTTGTTTCCGAACG 59.136 45.455 0.00 0.00 38.65 3.95
2193 9490 1.860676 TCTCACTTGTTTCCGAACGG 58.139 50.000 6.94 6.94 38.65 4.44
2194 9491 1.409790 TCTCACTTGTTTCCGAACGGA 59.590 47.619 12.04 12.04 43.52 4.69
2195 9492 1.792949 CTCACTTGTTTCCGAACGGAG 59.207 52.381 15.34 6.93 46.06 4.63
2196 9493 0.865769 CACTTGTTTCCGAACGGAGG 59.134 55.000 15.34 7.95 46.06 4.30
2197 9494 0.250166 ACTTGTTTCCGAACGGAGGG 60.250 55.000 15.34 8.23 46.06 4.30
2198 9495 0.034337 CTTGTTTCCGAACGGAGGGA 59.966 55.000 15.34 4.36 46.06 4.20
2199 9496 0.034337 TTGTTTCCGAACGGAGGGAG 59.966 55.000 15.34 0.00 46.06 4.30
2200 9497 1.117142 TGTTTCCGAACGGAGGGAGT 61.117 55.000 15.34 0.00 46.06 3.85
2201 9498 0.890683 GTTTCCGAACGGAGGGAGTA 59.109 55.000 15.34 0.00 46.06 2.59
2202 9499 1.135170 GTTTCCGAACGGAGGGAGTAG 60.135 57.143 15.34 0.00 46.06 2.57
2203 9500 0.038744 TTCCGAACGGAGGGAGTAGT 59.961 55.000 15.34 0.00 46.06 2.73
2204 9501 0.911769 TCCGAACGGAGGGAGTAGTA 59.088 55.000 12.04 0.00 39.76 1.82
2205 9502 1.134280 TCCGAACGGAGGGAGTAGTAG 60.134 57.143 12.04 0.00 39.76 2.57
2206 9503 0.662085 CGAACGGAGGGAGTAGTAGC 59.338 60.000 0.00 0.00 0.00 3.58
2207 9504 1.746516 CGAACGGAGGGAGTAGTAGCT 60.747 57.143 0.00 0.00 0.00 3.32
2208 9505 2.484417 CGAACGGAGGGAGTAGTAGCTA 60.484 54.545 0.00 0.00 0.00 3.32
2209 9506 3.753815 GAACGGAGGGAGTAGTAGCTAT 58.246 50.000 0.00 0.00 0.00 2.97
2210 9507 3.421919 ACGGAGGGAGTAGTAGCTATC 57.578 52.381 0.00 0.00 0.00 2.08
2211 9508 2.040145 ACGGAGGGAGTAGTAGCTATCC 59.960 54.545 0.00 0.00 0.00 2.59
2214 9511 2.994957 GGGAGTAGTAGCTATCCCCA 57.005 55.000 16.55 0.00 44.89 4.96
2215 9512 2.810164 GGGAGTAGTAGCTATCCCCAG 58.190 57.143 16.55 0.00 44.89 4.45
2216 9513 2.172679 GGAGTAGTAGCTATCCCCAGC 58.827 57.143 0.00 0.00 42.12 4.85
2256 9553 1.384525 CTCAACCCCGTTGTGAACAA 58.615 50.000 4.56 0.00 43.23 2.83
2371 9669 1.267806 CTTCTTCGCCACATTGCAGTT 59.732 47.619 0.00 0.00 0.00 3.16
2390 9688 2.816087 GTTTGCCAGAGAATCAGCTTCA 59.184 45.455 0.00 0.00 37.52 3.02
2391 9689 2.865119 TGCCAGAGAATCAGCTTCAA 57.135 45.000 0.00 0.00 37.52 2.69
2392 9690 3.361281 TGCCAGAGAATCAGCTTCAAT 57.639 42.857 0.00 0.00 37.52 2.57
2393 9691 3.276857 TGCCAGAGAATCAGCTTCAATC 58.723 45.455 0.00 0.00 37.52 2.67
2430 9728 4.781934 AGCAAACTTACTGAAGGTGAACT 58.218 39.130 0.00 0.00 36.95 3.01
2435 9733 3.325135 ACTTACTGAAGGTGAACTCCAGG 59.675 47.826 0.00 0.00 36.95 4.45
2436 9734 2.103153 ACTGAAGGTGAACTCCAGGA 57.897 50.000 0.00 0.00 0.00 3.86
2437 9735 2.625639 ACTGAAGGTGAACTCCAGGAT 58.374 47.619 0.00 0.00 0.00 3.24
2438 9736 3.791320 ACTGAAGGTGAACTCCAGGATA 58.209 45.455 0.00 0.00 0.00 2.59
2439 9737 3.772025 ACTGAAGGTGAACTCCAGGATAG 59.228 47.826 0.00 0.00 0.00 2.08
2440 9738 4.026744 CTGAAGGTGAACTCCAGGATAGA 58.973 47.826 0.00 0.00 0.00 1.98
2441 9739 3.769844 TGAAGGTGAACTCCAGGATAGAC 59.230 47.826 0.00 0.00 0.00 2.59
2442 9740 3.474798 AGGTGAACTCCAGGATAGACA 57.525 47.619 0.00 0.00 0.00 3.41
2443 9741 3.791320 AGGTGAACTCCAGGATAGACAA 58.209 45.455 0.00 0.00 0.00 3.18
2444 9742 4.168101 AGGTGAACTCCAGGATAGACAAA 58.832 43.478 0.00 0.00 0.00 2.83
2445 9743 4.223923 AGGTGAACTCCAGGATAGACAAAG 59.776 45.833 0.00 0.00 0.00 2.77
2446 9744 4.508662 GTGAACTCCAGGATAGACAAAGG 58.491 47.826 0.00 0.00 0.00 3.11
2447 9745 3.055094 TGAACTCCAGGATAGACAAAGGC 60.055 47.826 0.00 0.00 0.00 4.35
2448 9746 1.840635 ACTCCAGGATAGACAAAGGCC 59.159 52.381 0.00 0.00 0.00 5.19
2449 9747 2.122768 CTCCAGGATAGACAAAGGCCT 58.877 52.381 0.00 0.00 0.00 5.19
2450 9748 2.103941 CTCCAGGATAGACAAAGGCCTC 59.896 54.545 5.23 0.00 0.00 4.70
2451 9749 1.141858 CCAGGATAGACAAAGGCCTCC 59.858 57.143 5.23 0.00 0.00 4.30
2452 9750 2.122768 CAGGATAGACAAAGGCCTCCT 58.877 52.381 5.23 2.12 33.43 3.69
2464 9762 3.358111 AGGCCTCCTTTCTTCTAAAGC 57.642 47.619 0.00 0.00 0.00 3.51
2465 9763 2.644798 AGGCCTCCTTTCTTCTAAAGCA 59.355 45.455 0.00 0.00 0.00 3.91
2466 9764 3.268072 AGGCCTCCTTTCTTCTAAAGCAT 59.732 43.478 0.00 0.00 0.00 3.79
2467 9765 4.019858 GGCCTCCTTTCTTCTAAAGCATT 58.980 43.478 0.00 0.00 0.00 3.56
2468 9766 4.142293 GGCCTCCTTTCTTCTAAAGCATTG 60.142 45.833 0.00 0.00 0.00 2.82
2469 9767 4.702131 GCCTCCTTTCTTCTAAAGCATTGA 59.298 41.667 0.00 0.00 0.00 2.57
2470 9768 5.163673 GCCTCCTTTCTTCTAAAGCATTGAG 60.164 44.000 0.00 0.00 0.00 3.02
2471 9769 6.176183 CCTCCTTTCTTCTAAAGCATTGAGA 58.824 40.000 0.00 0.00 0.00 3.27
2472 9770 6.827762 CCTCCTTTCTTCTAAAGCATTGAGAT 59.172 38.462 0.00 0.00 0.00 2.75
2473 9771 7.201714 CCTCCTTTCTTCTAAAGCATTGAGATG 60.202 40.741 0.00 0.00 36.32 2.90
2474 9772 7.397221 TCCTTTCTTCTAAAGCATTGAGATGA 58.603 34.615 0.00 0.00 35.16 2.92
2475 9773 8.051535 TCCTTTCTTCTAAAGCATTGAGATGAT 58.948 33.333 0.00 0.00 35.16 2.45
2476 9774 8.344098 CCTTTCTTCTAAAGCATTGAGATGATC 58.656 37.037 0.00 0.00 35.16 2.92
2477 9775 8.797350 TTTCTTCTAAAGCATTGAGATGATCA 57.203 30.769 0.00 0.00 35.16 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.747686 GGCGGAGGAAGTGTTGGA 59.252 61.111 0.00 0.00 0.00 3.53
40 41 2.048222 CGCTTGCTCCCTTCGTCA 60.048 61.111 0.00 0.00 0.00 4.35
120 129 2.721167 CGGGGAGAAGATGCGGTCA 61.721 63.158 0.00 0.00 0.00 4.02
199 209 2.496341 CCGCAGCTTCATCTCCGA 59.504 61.111 0.00 0.00 0.00 4.55
226 236 2.125512 CCTTGAAGAGCGTCGGGG 60.126 66.667 0.00 0.00 0.00 5.73
279 290 2.760650 TGCTGTAGAGATGGTGGTACAG 59.239 50.000 0.00 4.35 41.80 2.74
320 331 5.777223 AGCATACTAGATCTACTTGCCATCA 59.223 40.000 17.17 0.00 0.00 3.07
353 364 8.094798 TCGAAATTAAACAGTTCAAGCATACT 57.905 30.769 0.00 0.00 29.36 2.12
354 365 8.895932 ATCGAAATTAAACAGTTCAAGCATAC 57.104 30.769 0.00 0.00 29.36 2.39
356 367 8.702438 CAAATCGAAATTAAACAGTTCAAGCAT 58.298 29.630 0.00 0.00 29.36 3.79
357 368 7.704472 ACAAATCGAAATTAAACAGTTCAAGCA 59.296 29.630 0.00 0.00 29.36 3.91
358 369 8.061125 ACAAATCGAAATTAAACAGTTCAAGC 57.939 30.769 0.00 0.00 29.36 4.01
389 405 5.573380 ACATGCCATACAGGAGTTCATAT 57.427 39.130 0.00 0.00 41.22 1.78
400 416 5.221641 GGGAGTTCATACTACATGCCATACA 60.222 44.000 0.00 0.00 36.91 2.29
423 3363 5.882557 ACTGGAGTTCAAACATAGCATAAGG 59.117 40.000 0.00 0.00 0.00 2.69
424 3364 6.595326 TCACTGGAGTTCAAACATAGCATAAG 59.405 38.462 0.00 0.00 0.00 1.73
425 3365 6.472016 TCACTGGAGTTCAAACATAGCATAA 58.528 36.000 0.00 0.00 0.00 1.90
426 3366 6.048732 TCACTGGAGTTCAAACATAGCATA 57.951 37.500 0.00 0.00 0.00 3.14
471 3411 5.757886 ACCGATACCGCATATTCAAATTTG 58.242 37.500 12.15 12.15 0.00 2.32
508 3448 2.128035 GATGTCGGACGCTTAATCAGG 58.872 52.381 3.34 0.00 0.00 3.86
512 3452 2.225068 CAGGATGTCGGACGCTTAAT 57.775 50.000 3.34 0.00 0.00 1.40
545 3485 5.062934 CGCAAAACTCATTTACGGTATCTCA 59.937 40.000 0.00 0.00 0.00 3.27
548 3488 4.495184 CCCGCAAAACTCATTTACGGTATC 60.495 45.833 10.63 0.00 42.19 2.24
588 3528 7.353414 ACTTGTTAATAGCATCTCTAGCAGA 57.647 36.000 0.00 0.00 34.78 4.26
603 3543 3.914435 AGGGACTGGGTGTACTTGTTAAT 59.086 43.478 0.00 0.00 37.18 1.40
607 3547 2.708037 TAGGGACTGGGTGTACTTGT 57.292 50.000 0.00 0.00 41.52 3.16
682 3772 2.770048 ATCTGGGGAAGAGGGGCG 60.770 66.667 0.00 0.00 38.67 6.13
683 3773 1.385206 AGATCTGGGGAAGAGGGGC 60.385 63.158 0.00 0.00 38.67 5.80
688 3780 0.326618 GGGGTGAGATCTGGGGAAGA 60.327 60.000 0.00 0.00 39.94 2.87
723 3815 1.999735 CCTGCGAATTTTGCGTCTCTA 59.000 47.619 4.22 0.00 34.24 2.43
728 3820 1.210155 GAGCCTGCGAATTTTGCGT 59.790 52.632 4.22 0.00 34.24 5.24
741 3833 0.107459 GCGAGGAGATTTTGGAGCCT 60.107 55.000 0.00 0.00 0.00 4.58
934 4027 3.714871 GACTGCCGGAGAGCTCTGC 62.715 68.421 23.91 24.08 34.69 4.26
936 4029 2.051518 CAGACTGCCGGAGAGCTCT 61.052 63.158 18.28 18.28 0.00 4.09
937 4030 2.493973 CAGACTGCCGGAGAGCTC 59.506 66.667 5.05 5.27 0.00 4.09
1476 8725 4.489810 ACAACTCAGAACGCATCTCTTAG 58.510 43.478 0.00 0.00 35.73 2.18
1488 8739 4.570772 GCACACAGACTAAACAACTCAGAA 59.429 41.667 0.00 0.00 0.00 3.02
1493 8744 3.623060 CACAGCACACAGACTAAACAACT 59.377 43.478 0.00 0.00 0.00 3.16
1496 8747 3.260475 ACACAGCACACAGACTAAACA 57.740 42.857 0.00 0.00 0.00 2.83
1503 8754 2.798145 CGAACACTACACAGCACACAGA 60.798 50.000 0.00 0.00 0.00 3.41
1561 8814 3.125146 CCATCACAACACAGGTTACATCG 59.875 47.826 0.00 0.00 34.87 3.84
1568 8821 3.576078 TTCTTCCATCACAACACAGGT 57.424 42.857 0.00 0.00 0.00 4.00
1605 8867 4.081406 ACAGCAGCATATTTGGAAACTCA 58.919 39.130 0.00 0.00 0.00 3.41
1608 8870 4.708726 AGACAGCAGCATATTTGGAAAC 57.291 40.909 0.00 0.00 0.00 2.78
1643 8908 3.486841 CGCCTAAATGATGCAAATTTCCG 59.513 43.478 12.53 10.67 0.00 4.30
1647 8912 2.098934 TCGCGCCTAAATGATGCAAATT 59.901 40.909 0.00 0.00 0.00 1.82
1653 8918 1.665679 ACAAGTCGCGCCTAAATGATG 59.334 47.619 0.00 0.00 0.00 3.07
1658 8923 1.572447 GCAACAAGTCGCGCCTAAA 59.428 52.632 0.00 0.00 0.00 1.85
1660 8925 2.740826 GGCAACAAGTCGCGCCTA 60.741 61.111 0.00 0.00 41.50 3.93
1708 8973 1.423845 CCGAACAACTGCCGTATGC 59.576 57.895 0.00 0.00 41.77 3.14
1711 8976 1.373748 GAGCCGAACAACTGCCGTA 60.374 57.895 0.00 0.00 0.00 4.02
1765 9030 5.643777 GCTCTGCTGGTACTTTCTCAAATAA 59.356 40.000 0.00 0.00 0.00 1.40
1778 9043 4.680708 GCATAGTTTACTGCTCTGCTGGTA 60.681 45.833 1.90 0.00 35.49 3.25
1780 9045 2.611292 GCATAGTTTACTGCTCTGCTGG 59.389 50.000 1.90 0.00 35.49 4.85
1804 9069 2.210116 TCAGTTCACTGCTCCGTTTTC 58.790 47.619 1.74 0.00 43.46 2.29
1849 9114 8.755018 CCAACACAATTTCATAGAAAGTGTTTC 58.245 33.333 19.08 0.00 43.68 2.78
1900 9165 3.121030 ACAGCGAACGATGCCAGC 61.121 61.111 12.19 0.00 34.49 4.85
1977 9243 1.685224 GGAATCACAGGGTCCAGCA 59.315 57.895 0.00 0.00 0.00 4.41
2067 9333 0.035247 TCGGAAATTAACCCCCGGTG 60.035 55.000 0.00 0.00 42.03 4.94
2091 9388 2.074948 CCCTCTCCACCCATCCCTG 61.075 68.421 0.00 0.00 0.00 4.45
2094 9391 1.208165 ACAACCCTCTCCACCCATCC 61.208 60.000 0.00 0.00 0.00 3.51
2097 9394 2.829384 GCACAACCCTCTCCACCCA 61.829 63.158 0.00 0.00 0.00 4.51
2100 9397 0.391793 GCTAGCACAACCCTCTCCAC 60.392 60.000 10.63 0.00 0.00 4.02
2121 9418 7.921745 ACGGAGCTAATACTTTTTACAGAGATC 59.078 37.037 0.00 0.00 0.00 2.75
2133 9430 4.179298 GTTTCCGAACGGAGCTAATACTT 58.821 43.478 15.34 0.00 46.06 2.24
2155 9452 3.139077 AGAACTAAAACAGCGTCCCTTG 58.861 45.455 0.00 0.00 0.00 3.61
2159 9456 3.391049 AGTGAGAACTAAAACAGCGTCC 58.609 45.455 0.00 0.00 0.00 4.79
2168 9465 5.005971 CGTTCGGAAACAAGTGAGAACTAAA 59.994 40.000 0.00 0.00 34.93 1.85
2169 9466 4.505191 CGTTCGGAAACAAGTGAGAACTAA 59.495 41.667 0.00 0.00 34.93 2.24
2170 9467 4.046462 CGTTCGGAAACAAGTGAGAACTA 58.954 43.478 0.00 0.00 34.93 2.24
2171 9468 2.864343 CGTTCGGAAACAAGTGAGAACT 59.136 45.455 0.00 0.00 34.93 3.01
2172 9469 2.033151 CCGTTCGGAAACAAGTGAGAAC 60.033 50.000 5.19 0.00 34.93 3.01
2173 9470 2.159071 TCCGTTCGGAAACAAGTGAGAA 60.159 45.455 11.66 0.00 34.93 2.87
2174 9471 1.409790 TCCGTTCGGAAACAAGTGAGA 59.590 47.619 11.66 0.00 34.93 3.27
2175 9472 1.792949 CTCCGTTCGGAAACAAGTGAG 59.207 52.381 14.79 0.00 34.93 3.51
2176 9473 1.539496 CCTCCGTTCGGAAACAAGTGA 60.539 52.381 14.79 0.00 34.93 3.41
2177 9474 0.865769 CCTCCGTTCGGAAACAAGTG 59.134 55.000 14.79 1.97 34.93 3.16
2178 9475 0.250166 CCCTCCGTTCGGAAACAAGT 60.250 55.000 14.79 0.00 34.93 3.16
2179 9476 0.034337 TCCCTCCGTTCGGAAACAAG 59.966 55.000 14.79 3.31 34.93 3.16
2180 9477 0.034337 CTCCCTCCGTTCGGAAACAA 59.966 55.000 14.79 1.25 34.93 2.83
2181 9478 1.117142 ACTCCCTCCGTTCGGAAACA 61.117 55.000 14.79 1.28 34.93 2.83
2182 9479 0.890683 TACTCCCTCCGTTCGGAAAC 59.109 55.000 14.79 0.00 33.41 2.78
2183 9480 1.180029 CTACTCCCTCCGTTCGGAAA 58.820 55.000 14.79 3.49 33.41 3.13
2184 9481 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
2185 9482 0.911769 TACTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
2186 9483 1.307097 CTACTACTCCCTCCGTTCGG 58.693 60.000 4.74 4.74 0.00 4.30
2187 9484 0.662085 GCTACTACTCCCTCCGTTCG 59.338 60.000 0.00 0.00 0.00 3.95
2188 9485 2.055684 AGCTACTACTCCCTCCGTTC 57.944 55.000 0.00 0.00 0.00 3.95
2189 9486 3.498301 GGATAGCTACTACTCCCTCCGTT 60.498 52.174 0.00 0.00 0.00 4.44
2190 9487 2.040145 GGATAGCTACTACTCCCTCCGT 59.960 54.545 0.00 0.00 0.00 4.69
2191 9488 2.618559 GGGATAGCTACTACTCCCTCCG 60.619 59.091 19.15 0.00 43.45 4.63
2192 9489 2.291735 GGGGATAGCTACTACTCCCTCC 60.292 59.091 23.50 12.24 45.65 4.30
2193 9490 2.379226 TGGGGATAGCTACTACTCCCTC 59.621 54.545 23.50 16.25 45.65 4.30
2194 9491 2.380590 CTGGGGATAGCTACTACTCCCT 59.619 54.545 23.50 0.00 45.65 4.20
2195 9492 2.810164 CTGGGGATAGCTACTACTCCC 58.190 57.143 18.47 18.47 45.64 4.30
2196 9493 2.172679 GCTGGGGATAGCTACTACTCC 58.827 57.143 0.00 0.00 40.52 3.85
2205 9502 1.041437 ACTAACGAGCTGGGGATAGC 58.959 55.000 0.00 0.00 44.01 2.97
2206 9503 2.307768 TCACTAACGAGCTGGGGATAG 58.692 52.381 0.00 2.66 0.00 2.08
2207 9504 2.447408 TCACTAACGAGCTGGGGATA 57.553 50.000 0.00 0.00 0.00 2.59
2208 9505 1.414181 CATCACTAACGAGCTGGGGAT 59.586 52.381 0.00 0.00 0.00 3.85
2209 9506 0.824109 CATCACTAACGAGCTGGGGA 59.176 55.000 0.00 0.00 0.00 4.81
2210 9507 0.537188 ACATCACTAACGAGCTGGGG 59.463 55.000 0.00 0.00 0.00 4.96
2211 9508 1.204704 TGACATCACTAACGAGCTGGG 59.795 52.381 0.00 0.00 0.00 4.45
2212 9509 2.654749 TGACATCACTAACGAGCTGG 57.345 50.000 0.00 0.00 0.00 4.85
2213 9510 4.990543 TTTTGACATCACTAACGAGCTG 57.009 40.909 0.00 0.00 0.00 4.24
2214 9511 4.142816 GCATTTTGACATCACTAACGAGCT 60.143 41.667 0.00 0.00 0.00 4.09
2215 9512 4.091424 GCATTTTGACATCACTAACGAGC 58.909 43.478 0.00 0.00 0.00 5.03
2216 9513 5.120674 TGAGCATTTTGACATCACTAACGAG 59.879 40.000 0.00 0.00 0.00 4.18
2217 9514 4.994217 TGAGCATTTTGACATCACTAACGA 59.006 37.500 0.00 0.00 0.00 3.85
2218 9515 5.281693 TGAGCATTTTGACATCACTAACG 57.718 39.130 0.00 0.00 0.00 3.18
2219 9516 5.858581 GGTTGAGCATTTTGACATCACTAAC 59.141 40.000 0.00 0.00 0.00 2.34
2220 9517 5.048083 GGGTTGAGCATTTTGACATCACTAA 60.048 40.000 0.00 0.00 0.00 2.24
2221 9518 4.458989 GGGTTGAGCATTTTGACATCACTA 59.541 41.667 0.00 0.00 0.00 2.74
2288 9585 3.007182 AGTTTTTACATGCTGCTGCCAAT 59.993 39.130 13.47 0.00 38.71 3.16
2371 9669 2.865119 TGAAGCTGATTCTCTGGCAA 57.135 45.000 7.22 0.00 38.83 4.52
2405 9703 4.776349 TCACCTTCAGTAAGTTTGCTTCA 58.224 39.130 0.00 0.00 36.22 3.02
2430 9728 2.119495 GAGGCCTTTGTCTATCCTGGA 58.881 52.381 6.77 0.00 0.00 3.86
2444 9742 2.644798 TGCTTTAGAAGAAAGGAGGCCT 59.355 45.455 3.86 3.86 33.87 5.19
2445 9743 3.073274 TGCTTTAGAAGAAAGGAGGCC 57.927 47.619 0.00 0.00 0.00 5.19
2446 9744 4.702131 TCAATGCTTTAGAAGAAAGGAGGC 59.298 41.667 0.00 0.00 31.27 4.70
2447 9745 6.176183 TCTCAATGCTTTAGAAGAAAGGAGG 58.824 40.000 0.00 0.00 31.27 4.30
2448 9746 7.551974 TCATCTCAATGCTTTAGAAGAAAGGAG 59.448 37.037 0.00 0.00 31.27 3.69
2449 9747 7.397221 TCATCTCAATGCTTTAGAAGAAAGGA 58.603 34.615 0.00 0.00 32.58 3.36
2450 9748 7.621428 TCATCTCAATGCTTTAGAAGAAAGG 57.379 36.000 0.00 0.00 32.58 3.11
2451 9749 8.890718 TGATCATCTCAATGCTTTAGAAGAAAG 58.109 33.333 0.00 0.00 32.58 2.62
2452 9750 8.797350 TGATCATCTCAATGCTTTAGAAGAAA 57.203 30.769 0.00 0.00 32.58 2.52
2453 9751 8.671921 GTTGATCATCTCAATGCTTTAGAAGAA 58.328 33.333 0.00 0.00 45.36 2.52
2454 9752 8.206325 GTTGATCATCTCAATGCTTTAGAAGA 57.794 34.615 0.00 0.00 45.36 2.87


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

AutoCloner maintained by Alex Coulton.