Multiple sequence alignment - TraesCS7B01G201500

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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 TraesCS7B01G201500 chr7B 100.000 5510 0 0 1 5510 368158449 368152940 0.000000e+00 10176.0
1 TraesCS7B01G201500 chr7D 94.834 4723 140 34 838 5510 372906843 372902175 0.000000e+00 7275.0
2 TraesCS7B01G201500 chr7D 89.463 484 39 10 1 479 372907848 372907372 7.900000e-168 601.0
3 TraesCS7B01G201500 chr7D 82.842 373 28 15 499 838 372907250 372906881 8.970000e-78 302.0
4 TraesCS7B01G201500 chr7D 84.858 317 22 7 4429 4730 36515692 36515997 4.170000e-76 296.0
5 TraesCS7B01G201500 chr7A 95.108 3291 105 21 1396 4666 418115751 418112497 0.000000e+00 5134.0
6 TraesCS7B01G201500 chr7A 93.226 871 23 20 4669 5510 418106661 418105798 0.000000e+00 1249.0
7 TraesCS7B01G201500 chr7A 93.860 570 20 12 838 1405 418116412 418115856 0.000000e+00 845.0
8 TraesCS7B01G201500 chr7A 89.073 302 30 3 1 300 418130864 418130564 6.740000e-99 372.0
9 TraesCS7B01G201500 chr7A 88.649 185 17 3 298 480 418117435 418117253 7.180000e-54 222.0
10 TraesCS7B01G201500 chr7A 81.176 255 28 8 501 755 418117136 418116902 2.620000e-43 187.0
11 TraesCS7B01G201500 chr7A 96.154 78 3 0 761 838 418116527 418116450 1.610000e-25 128.0
12 TraesCS7B01G201500 chr6A 83.648 318 24 9 4429 4730 21160575 21160880 1.960000e-69 274.0
13 TraesCS7B01G201500 chr1B 92.683 41 3 0 4682 4722 597450742 597450702 5.960000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G201500 chr7B 368152940 368158449 5509 True 10176.0 10176 100.000000 1 5510 1 chr7B.!!$R1 5509
1 TraesCS7B01G201500 chr7D 372902175 372907848 5673 True 2726.0 7275 89.046333 1 5510 3 chr7D.!!$R1 5509
2 TraesCS7B01G201500 chr7A 418112497 418117435 4938 True 1303.2 5134 90.989400 298 4666 5 chr7A.!!$R3 4368
3 TraesCS7B01G201500 chr7A 418105798 418106661 863 True 1249.0 1249 93.226000 4669 5510 1 chr7A.!!$R1 841

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
359 362 0.247419 TCGCGAGCGACTACGTAAAG 60.247 55.000 16.64 0.0 44.01 1.85 F
2082 2739 0.413037 TGGGTGCATCCATTTTCCCT 59.587 50.000 16.81 0.0 38.11 4.20 F
3582 4239 1.734465 GAGCTTCATGTACTGTGCCAC 59.266 52.381 0.00 0.0 0.00 5.01 F
3700 4357 0.249120 CCCTGATCACAACCGCAGTA 59.751 55.000 0.00 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2942 1.407437 CCAAGCAGATGTACACCTCCC 60.407 57.143 0.00 0.00 0.00 4.30 R
3700 4357 0.035630 GAGTGCCAAGGTCAGCTGAT 60.036 55.000 21.47 0.83 0.00 2.90 R
4451 5118 0.336048 ACATTTCCCTGGGATGTGGG 59.664 55.000 17.93 7.49 44.66 4.61 R
4862 5539 1.774300 GGGGGAGGAAGAGCCAAAA 59.226 57.895 0.00 0.00 40.02 2.44 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
50 51 3.533691 GTCGTAGCACGCACTCGC 61.534 66.667 4.15 0.00 42.21 5.03
82 83 3.437795 CGGCCGTCGTAGTCCACT 61.438 66.667 19.50 0.00 0.00 4.00
83 84 2.488820 GGCCGTCGTAGTCCACTC 59.511 66.667 0.00 0.00 0.00 3.51
84 85 2.488820 GCCGTCGTAGTCCACTCC 59.511 66.667 0.00 0.00 0.00 3.85
85 86 2.338015 GCCGTCGTAGTCCACTCCA 61.338 63.158 0.00 0.00 0.00 3.86
91 93 1.611977 TCGTAGTCCACTCCAACACAG 59.388 52.381 0.00 0.00 0.00 3.66
103 105 1.600636 AACACAGCATCCACCACCG 60.601 57.895 0.00 0.00 0.00 4.94
109 111 2.896854 CATCCACCACCGCCATCG 60.897 66.667 0.00 0.00 0.00 3.84
117 119 2.746277 ACCGCCATCGAAAGCACC 60.746 61.111 10.25 0.00 38.10 5.01
125 127 2.481276 CCATCGAAAGCACCAGATCGTA 60.481 50.000 0.00 0.00 36.70 3.43
149 151 2.118132 CAACACCTGCAGTTGCCTT 58.882 52.632 11.68 0.00 39.76 4.35
153 155 2.437897 CCTGCAGTTGCCTTCCCT 59.562 61.111 13.81 0.00 41.18 4.20
154 156 1.676967 CCTGCAGTTGCCTTCCCTC 60.677 63.158 13.81 0.00 41.18 4.30
155 157 1.676967 CTGCAGTTGCCTTCCCTCC 60.677 63.158 5.25 0.00 41.18 4.30
156 158 2.134630 CTGCAGTTGCCTTCCCTCCT 62.135 60.000 5.25 0.00 41.18 3.69
157 159 1.377856 GCAGTTGCCTTCCCTCCTC 60.378 63.158 0.00 0.00 34.31 3.71
168 170 0.621571 TCCCTCCTCCCTGATTGTGG 60.622 60.000 0.00 0.00 0.00 4.17
169 171 1.225704 CCTCCTCCCTGATTGTGGC 59.774 63.158 0.00 0.00 0.00 5.01
170 172 1.153289 CTCCTCCCTGATTGTGGCG 60.153 63.158 0.00 0.00 0.00 5.69
171 173 2.825836 CCTCCCTGATTGTGGCGC 60.826 66.667 0.00 0.00 0.00 6.53
172 174 2.046023 CTCCCTGATTGTGGCGCA 60.046 61.111 10.83 0.00 0.00 6.09
173 175 2.359850 TCCCTGATTGTGGCGCAC 60.360 61.111 10.83 6.37 34.56 5.34
174 176 3.803082 CCCTGATTGTGGCGCACG 61.803 66.667 10.83 0.00 37.14 5.34
175 177 3.049674 CCTGATTGTGGCGCACGT 61.050 61.111 10.83 0.00 37.14 4.49
177 179 2.280457 TGATTGTGGCGCACGTCA 60.280 55.556 10.83 5.70 37.14 4.35
212 214 1.318576 GTTGGTGTGGTTGAAGGGAG 58.681 55.000 0.00 0.00 0.00 4.30
226 228 1.213296 AGGGAGTCAGGTGTGTTGTT 58.787 50.000 0.00 0.00 0.00 2.83
235 237 1.283613 AGGTGTGTTGTTGGTTGAGGA 59.716 47.619 0.00 0.00 0.00 3.71
236 238 2.096248 GGTGTGTTGTTGGTTGAGGAA 58.904 47.619 0.00 0.00 0.00 3.36
261 263 1.338674 TGTAGATGCGTTGGGTTCCAG 60.339 52.381 0.00 0.00 33.81 3.86
280 282 0.321122 GCCGATAAGGATGAGGGCAG 60.321 60.000 0.00 0.00 45.00 4.85
300 302 1.385206 AGAGAAGGATGGGAGGGGC 60.385 63.158 0.00 0.00 0.00 5.80
348 351 0.926174 GTGAGTCACTATCGCGAGCG 60.926 60.000 16.66 11.64 41.35 5.03
359 362 0.247419 TCGCGAGCGACTACGTAAAG 60.247 55.000 16.64 0.00 44.01 1.85
426 430 0.710588 TAGTGCTCCTCTTCCTGGGA 59.289 55.000 0.00 0.00 0.00 4.37
474 514 2.341846 TTTGAGGGAACTTGCGAAGT 57.658 45.000 0.00 0.00 44.43 3.01
476 516 2.743636 TGAGGGAACTTGCGAAGTAG 57.256 50.000 2.60 0.00 44.43 2.57
479 519 3.260884 TGAGGGAACTTGCGAAGTAGATT 59.739 43.478 2.60 0.00 44.43 2.40
488 528 9.464714 GAACTTGCGAAGTAGATTATGAGATAA 57.535 33.333 2.60 0.00 41.91 1.75
489 529 8.804688 ACTTGCGAAGTAGATTATGAGATAAC 57.195 34.615 0.00 0.00 40.69 1.89
490 530 8.634444 ACTTGCGAAGTAGATTATGAGATAACT 58.366 33.333 0.00 0.00 40.69 2.24
492 532 9.894783 TTGCGAAGTAGATTATGAGATAACTAC 57.105 33.333 0.00 0.00 33.93 2.73
493 533 9.063615 TGCGAAGTAGATTATGAGATAACTACA 57.936 33.333 0.00 0.00 34.92 2.74
494 534 9.332301 GCGAAGTAGATTATGAGATAACTACAC 57.668 37.037 0.00 0.00 34.92 2.90
583 696 2.202919 GGGGATGGCAATTTGCGC 60.203 61.111 14.83 0.00 46.21 6.09
584 705 2.578128 GGGATGGCAATTTGCGCA 59.422 55.556 5.66 5.66 46.21 6.09
586 707 1.216178 GGATGGCAATTTGCGCAGT 59.784 52.632 11.31 0.00 46.21 4.40
630 751 6.843069 ACTGTCATGGCATTTTGTTTAAAC 57.157 33.333 11.54 11.54 0.00 2.01
636 757 5.091261 TGGCATTTTGTTTAAACTGTGGT 57.909 34.783 18.72 0.00 31.31 4.16
641 762 7.868415 GGCATTTTGTTTAAACTGTGGTATGTA 59.132 33.333 18.72 0.00 31.31 2.29
642 763 9.418045 GCATTTTGTTTAAACTGTGGTATGTAT 57.582 29.630 18.72 0.00 31.31 2.29
709 830 4.257267 GCTTTTGCCAGGTTTTGATACT 57.743 40.909 0.00 0.00 40.15 2.12
736 857 5.509716 ACATCCGTCAGATAACATTACGA 57.490 39.130 0.00 0.00 35.66 3.43
773 1263 8.574737 ACTAAGAATAGTGACTTTTGAGTACGT 58.425 33.333 0.00 0.00 40.88 3.57
815 1305 3.264450 CCTCCCCAATATATGACCAGTCC 59.736 52.174 0.00 0.00 0.00 3.85
864 1392 1.525077 GTGAACCCTGTGGCGTCAA 60.525 57.895 0.00 0.00 32.40 3.18
891 1419 7.121168 TCTGCTCCAGACAATAAATAAAAGTGG 59.879 37.037 0.00 0.00 35.39 4.00
983 1512 2.097038 CCAGCCTCGCTCAAACTCG 61.097 63.158 0.00 0.00 36.40 4.18
1212 1741 2.765689 TCTTCATCTCCCTCCTCCTC 57.234 55.000 0.00 0.00 0.00 3.71
1252 1783 1.544246 GCCCAATCCGTAAGCTTGTTT 59.456 47.619 9.86 0.00 0.00 2.83
1365 1896 5.348259 TGGGAAGGATTTTTAGTCCCTTT 57.652 39.130 8.44 0.00 46.97 3.11
1380 1911 4.021007 TCCCTTTAGGATTCATGGGAGA 57.979 45.455 0.00 0.00 40.93 3.71
1381 1912 3.976654 TCCCTTTAGGATTCATGGGAGAG 59.023 47.826 0.00 0.00 40.93 3.20
1382 1913 3.976654 CCCTTTAGGATTCATGGGAGAGA 59.023 47.826 0.00 0.00 38.24 3.10
1383 1914 4.041444 CCCTTTAGGATTCATGGGAGAGAG 59.959 50.000 0.00 0.00 38.24 3.20
1384 1915 4.904251 CCTTTAGGATTCATGGGAGAGAGA 59.096 45.833 0.00 0.00 37.39 3.10
1385 1916 5.011943 CCTTTAGGATTCATGGGAGAGAGAG 59.988 48.000 0.00 0.00 37.39 3.20
1386 1917 3.989600 AGGATTCATGGGAGAGAGAGA 57.010 47.619 0.00 0.00 0.00 3.10
1547 2200 1.842562 CCTGTGATGGAGACCCTGAAT 59.157 52.381 0.00 0.00 0.00 2.57
1567 2220 7.309194 CCTGAATTTTTATCCGGGGATATTCAC 60.309 40.741 15.01 5.48 37.02 3.18
1583 2236 2.839486 TCACGTCAGATCAGCCTTTT 57.161 45.000 0.00 0.00 0.00 2.27
1590 2243 1.084018 AGATCAGCCTTTTTCCCCCA 58.916 50.000 0.00 0.00 0.00 4.96
1591 2244 1.648037 AGATCAGCCTTTTTCCCCCAT 59.352 47.619 0.00 0.00 0.00 4.00
1592 2245 2.858768 AGATCAGCCTTTTTCCCCCATA 59.141 45.455 0.00 0.00 0.00 2.74
1593 2246 2.525105 TCAGCCTTTTTCCCCCATAC 57.475 50.000 0.00 0.00 0.00 2.39
1594 2247 1.713647 TCAGCCTTTTTCCCCCATACA 59.286 47.619 0.00 0.00 0.00 2.29
1595 2248 2.314549 TCAGCCTTTTTCCCCCATACAT 59.685 45.455 0.00 0.00 0.00 2.29
1623 2278 2.558800 GGGAATCTTTTTACCTGCCCCA 60.559 50.000 0.00 0.00 0.00 4.96
1624 2279 2.760650 GGAATCTTTTTACCTGCCCCAG 59.239 50.000 0.00 0.00 0.00 4.45
1748 2403 6.206634 TGATTTGTGGTGTTGGAGATAAGAAC 59.793 38.462 0.00 0.00 0.00 3.01
1773 2429 4.804139 GTGTATCATCAGTCCTTTGTACCG 59.196 45.833 0.00 0.00 0.00 4.02
1778 2434 1.758280 TCAGTCCTTTGTACCGTGTGT 59.242 47.619 0.00 0.00 0.00 3.72
1790 2446 1.902508 ACCGTGTGTTCTCCATGATCT 59.097 47.619 0.00 0.00 0.00 2.75
1791 2447 3.096852 ACCGTGTGTTCTCCATGATCTA 58.903 45.455 0.00 0.00 0.00 1.98
1792 2448 3.131223 ACCGTGTGTTCTCCATGATCTAG 59.869 47.826 0.00 0.00 0.00 2.43
1793 2449 3.491619 CCGTGTGTTCTCCATGATCTAGG 60.492 52.174 0.00 0.00 0.00 3.02
1794 2450 3.131223 CGTGTGTTCTCCATGATCTAGGT 59.869 47.826 0.00 0.00 0.00 3.08
1795 2451 4.688021 GTGTGTTCTCCATGATCTAGGTC 58.312 47.826 0.00 0.00 0.00 3.85
1796 2452 4.160439 GTGTGTTCTCCATGATCTAGGTCA 59.840 45.833 8.45 8.45 0.00 4.02
1797 2453 4.160439 TGTGTTCTCCATGATCTAGGTCAC 59.840 45.833 8.14 0.00 0.00 3.67
1798 2454 4.160439 GTGTTCTCCATGATCTAGGTCACA 59.840 45.833 8.14 0.00 0.00 3.58
1799 2455 4.403752 TGTTCTCCATGATCTAGGTCACAG 59.596 45.833 8.14 5.04 0.00 3.66
1800 2456 4.526438 TCTCCATGATCTAGGTCACAGA 57.474 45.455 8.14 7.39 0.00 3.41
1801 2457 5.072129 TCTCCATGATCTAGGTCACAGAT 57.928 43.478 8.14 0.00 35.43 2.90
1802 2458 4.831710 TCTCCATGATCTAGGTCACAGATG 59.168 45.833 8.14 2.43 32.86 2.90
1803 2459 3.323115 TCCATGATCTAGGTCACAGATGC 59.677 47.826 8.14 0.00 32.86 3.91
1804 2460 3.070590 CCATGATCTAGGTCACAGATGCA 59.929 47.826 8.14 0.00 32.86 3.96
1805 2461 4.443881 CCATGATCTAGGTCACAGATGCAA 60.444 45.833 8.14 0.00 32.86 4.08
1806 2462 4.824479 TGATCTAGGTCACAGATGCAAA 57.176 40.909 0.14 0.00 32.86 3.68
1807 2463 5.164620 TGATCTAGGTCACAGATGCAAAA 57.835 39.130 0.14 0.00 32.86 2.44
1808 2464 5.559770 TGATCTAGGTCACAGATGCAAAAA 58.440 37.500 0.14 0.00 32.86 1.94
2010 2667 3.058570 TGCGTGTTAACCAAATAGCACAG 60.059 43.478 2.48 0.00 36.98 3.66
2082 2739 0.413037 TGGGTGCATCCATTTTCCCT 59.587 50.000 16.81 0.00 38.11 4.20
2131 2788 1.742761 AGATGCGTTTGGATCAGTGG 58.257 50.000 0.00 0.00 44.70 4.00
2142 2799 6.425721 CGTTTGGATCAGTGGTTTCTAGTTTA 59.574 38.462 0.00 0.00 0.00 2.01
2167 2824 5.424121 AAAGTACGATTGCTTATGGATGC 57.576 39.130 0.00 0.00 0.00 3.91
2178 2835 4.065789 GCTTATGGATGCTACTAACCACC 58.934 47.826 0.00 0.00 35.19 4.61
2179 2836 4.202367 GCTTATGGATGCTACTAACCACCT 60.202 45.833 0.00 0.00 35.19 4.00
2244 2901 3.192422 TCCATTTGCCCATTTGTCTTACG 59.808 43.478 0.00 0.00 0.00 3.18
2257 2914 5.462530 TTGTCTTACGTCCTCTTTGATGA 57.537 39.130 0.00 0.00 0.00 2.92
2285 2942 6.316140 TCAGGTGGTGATCATTCTTTTTATCG 59.684 38.462 0.00 0.00 0.00 2.92
2563 3220 2.202046 GACGATTGCACACACGCG 60.202 61.111 3.53 3.53 33.35 6.01
2946 3603 6.494666 TCTATTGGAAACATATCCGGTTCT 57.505 37.500 0.00 0.00 42.76 3.01
3072 3729 6.226787 GGTTAGTCCTGATGTAATGGAGATG 58.773 44.000 0.00 0.00 0.00 2.90
3086 3743 8.608598 TGTAATGGAGATGGATATTGATGATGT 58.391 33.333 0.00 0.00 0.00 3.06
3162 3819 6.458210 CCAAGAAGTGAAACATAAGGCAATT 58.542 36.000 0.00 0.00 41.43 2.32
3405 4062 5.460646 ACCATGCTTTAAAGTGTTCATTCG 58.539 37.500 16.38 6.50 0.00 3.34
3559 4216 3.121030 GCACGAGCAATCACGGCT 61.121 61.111 0.00 0.00 46.07 5.52
3582 4239 1.734465 GAGCTTCATGTACTGTGCCAC 59.266 52.381 0.00 0.00 0.00 5.01
3630 4287 2.989909 TGGAAGCATGTCGATGATGTT 58.010 42.857 8.64 1.20 0.00 2.71
3634 4291 4.036027 GGAAGCATGTCGATGATGTTGAAT 59.964 41.667 8.64 0.00 0.00 2.57
3700 4357 0.249120 CCCTGATCACAACCGCAGTA 59.751 55.000 0.00 0.00 0.00 2.74
3729 4386 0.803117 CTTGGCACTCACAGCTCATG 59.197 55.000 0.00 0.00 0.00 3.07
3772 4429 1.542915 GCCACTGTGACAGCAATCATT 59.457 47.619 13.37 0.00 34.37 2.57
3856 4513 1.227527 CTGGAGTGCCGTGTTCACA 60.228 57.895 3.87 0.00 36.93 3.58
3942 4599 2.751806 GAGGAAAGCTGTCTTCCAATGG 59.248 50.000 16.25 0.00 0.00 3.16
3982 4639 1.801178 GCACAAACTACCTGCTCAGAC 59.199 52.381 0.00 0.00 0.00 3.51
4038 4703 5.260424 TGTGGTATTATGCACTGGAAACAT 58.740 37.500 0.00 0.00 41.51 2.71
4123 4788 1.270358 GGTTTCCGAGTGACTTGCTCT 60.270 52.381 0.00 0.00 0.00 4.09
4153 4818 2.023984 TCCAGGAATGACTAGCAGAGGA 60.024 50.000 0.00 0.00 0.00 3.71
4164 4829 6.634805 TGACTAGCAGAGGATAGAAAAGTTG 58.365 40.000 0.00 0.00 36.51 3.16
4169 4834 4.092091 GCAGAGGATAGAAAAGTTGTGTCG 59.908 45.833 0.00 0.00 0.00 4.35
4228 4893 4.082571 CCAAAAGTTTCTGAGCCCACATAG 60.083 45.833 0.00 0.00 0.00 2.23
4238 4905 4.079253 TGAGCCCACATAGTTTCTTTTCC 58.921 43.478 0.00 0.00 0.00 3.13
4348 5015 9.154632 TGATTGCTGTTTAGGGTAGATATAAGA 57.845 33.333 0.00 0.00 0.00 2.10
4377 5044 3.505680 CCCTCTACAAGATGAGATCCGAG 59.494 52.174 0.00 0.00 32.44 4.63
4421 5088 9.762381 TTGATCCCCTTTTGTACTTGTAAATAT 57.238 29.630 0.00 0.00 0.00 1.28
4449 5116 9.008965 TCGAGTTGATAAAATTTGGAATTGAGA 57.991 29.630 0.00 0.00 0.00 3.27
4450 5117 9.793252 CGAGTTGATAAAATTTGGAATTGAGAT 57.207 29.630 0.00 0.00 0.00 2.75
4453 5120 9.317936 GTTGATAAAATTTGGAATTGAGATCCC 57.682 33.333 0.00 0.00 36.04 3.85
4454 5121 8.606754 TGATAAAATTTGGAATTGAGATCCCA 57.393 30.769 0.00 0.00 36.04 4.37
4455 5122 8.477256 TGATAAAATTTGGAATTGAGATCCCAC 58.523 33.333 0.00 0.00 36.04 4.61
4483 5150 3.897505 AGGGAAATGTTGGTCCAAGAAAG 59.102 43.478 3.96 0.00 35.44 2.62
4515 5182 8.076178 GGTGTACTGATTATTTGTTCATATGCC 58.924 37.037 0.00 0.00 0.00 4.40
4563 5233 4.032104 CGTATGGTTTACACGCCTAACTTC 59.968 45.833 0.00 0.00 0.00 3.01
4570 5240 2.522185 ACACGCCTAACTTCTGGAGTA 58.478 47.619 0.00 0.00 37.72 2.59
4586 5256 8.768501 TTCTGGAGTAATCTGATATACACTGT 57.231 34.615 0.00 0.00 0.00 3.55
4724 5400 7.589395 TGCAAACATCGACAACACTAAATATT 58.411 30.769 0.00 0.00 0.00 1.28
4895 5577 3.349879 CCCCCGCTTGGTTAAGAAA 57.650 52.632 0.00 0.00 35.92 2.52
4896 5578 1.847328 CCCCCGCTTGGTTAAGAAAT 58.153 50.000 0.00 0.00 35.92 2.17
4959 5664 4.473559 TCCAAACAGAGTATAAAGAGGGGG 59.526 45.833 0.00 0.00 0.00 5.40
5078 5785 6.706270 ACAATTTCACAGTACAGGTCTAACTG 59.294 38.462 0.00 9.66 44.89 3.16
5139 5846 0.735978 TCATAGCGCACAACTCACCG 60.736 55.000 11.47 0.00 0.00 4.94
5160 5867 7.860373 TCACCGATGAAATTAACAACAAAAGAG 59.140 33.333 0.00 0.00 0.00 2.85
5447 6154 8.485392 TCTCATCATATCCTGTGACATAAACAA 58.515 33.333 0.00 0.00 0.00 2.83
5490 6197 4.693283 TCACAGATTCGTGACAGAAAAGT 58.307 39.130 7.08 0.00 40.94 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.064324 GCACATGCTGGGACCACC 61.064 66.667 0.00 0.00 38.21 4.61
28 29 2.049526 TGCGTGCTACGACCACAG 60.050 61.111 11.94 0.00 46.05 3.66
45 46 3.240134 ATGCTCAACCACGGCGAGT 62.240 57.895 16.62 7.86 0.00 4.18
50 51 3.803082 CCGCATGCTCAACCACGG 61.803 66.667 17.13 2.60 0.00 4.94
71 72 1.611977 CTGTGTTGGAGTGGACTACGA 59.388 52.381 0.00 0.00 0.00 3.43
77 78 0.036732 GGATGCTGTGTTGGAGTGGA 59.963 55.000 0.00 0.00 0.00 4.02
82 83 0.537143 GTGGTGGATGCTGTGTTGGA 60.537 55.000 0.00 0.00 0.00 3.53
83 84 1.526575 GGTGGTGGATGCTGTGTTGG 61.527 60.000 0.00 0.00 0.00 3.77
84 85 1.855213 CGGTGGTGGATGCTGTGTTG 61.855 60.000 0.00 0.00 0.00 3.33
85 86 1.600636 CGGTGGTGGATGCTGTGTT 60.601 57.895 0.00 0.00 0.00 3.32
91 93 3.211963 GATGGCGGTGGTGGATGC 61.212 66.667 0.00 0.00 0.00 3.91
103 105 0.659957 GATCTGGTGCTTTCGATGGC 59.340 55.000 3.59 3.59 0.00 4.40
149 151 0.621571 CCACAATCAGGGAGGAGGGA 60.622 60.000 0.00 0.00 0.00 4.20
153 155 2.989639 CGCCACAATCAGGGAGGA 59.010 61.111 0.00 0.00 0.00 3.71
154 156 2.825836 GCGCCACAATCAGGGAGG 60.826 66.667 0.00 0.00 0.00 4.30
155 157 2.046023 TGCGCCACAATCAGGGAG 60.046 61.111 4.18 0.00 0.00 4.30
156 158 2.359850 GTGCGCCACAATCAGGGA 60.360 61.111 4.18 0.00 34.08 4.20
157 159 3.803082 CGTGCGCCACAATCAGGG 61.803 66.667 4.18 0.00 33.40 4.45
171 173 4.789075 CCCCGCTACCGTGACGTG 62.789 72.222 3.64 0.00 0.00 4.49
190 192 0.744281 CCTTCAACCACACCAACACC 59.256 55.000 0.00 0.00 0.00 4.16
196 198 0.472471 TGACTCCCTTCAACCACACC 59.528 55.000 0.00 0.00 0.00 4.16
212 214 2.088423 TCAACCAACAACACACCTGAC 58.912 47.619 0.00 0.00 0.00 3.51
226 228 2.696775 TCTACAACCCTTCCTCAACCA 58.303 47.619 0.00 0.00 0.00 3.67
235 237 1.613255 CCCAACGCATCTACAACCCTT 60.613 52.381 0.00 0.00 0.00 3.95
236 238 0.035439 CCCAACGCATCTACAACCCT 60.035 55.000 0.00 0.00 0.00 4.34
261 263 0.321122 CTGCCCTCATCCTTATCGGC 60.321 60.000 0.00 0.00 36.91 5.54
275 277 1.153005 CCATCCTTCTCTGCTGCCC 60.153 63.158 0.00 0.00 0.00 5.36
280 282 1.704007 CCCCTCCCATCCTTCTCTGC 61.704 65.000 0.00 0.00 0.00 4.26
300 302 4.373116 CCACACGGGTCACCCTCG 62.373 72.222 12.38 3.78 42.67 4.63
348 351 0.912528 CGGCTTCGCTTTACGTAGTC 59.087 55.000 0.00 0.00 43.93 2.59
352 355 1.138047 CGATCGGCTTCGCTTTACGT 61.138 55.000 7.38 0.00 44.19 3.57
359 362 3.313257 GTCGTCGATCGGCTTCGC 61.313 66.667 18.81 9.07 41.33 4.70
426 430 4.488126 AATATATGCTTCGCACGCAAAT 57.512 36.364 0.00 0.00 43.04 2.32
445 449 8.527810 TCGCAAGTTCCCTCAAATAAATAAAAT 58.472 29.630 0.00 0.00 39.48 1.82
466 506 9.894783 GTAGTTATCTCATAATCTACTTCGCAA 57.105 33.333 0.00 0.00 32.65 4.85
476 516 9.803315 TGACAGTTGTGTAGTTATCTCATAATC 57.197 33.333 0.00 0.00 36.88 1.75
479 519 8.349568 AGTGACAGTTGTGTAGTTATCTCATA 57.650 34.615 0.00 0.00 36.88 2.15
488 528 7.201785 CCCAAATTTAAGTGACAGTTGTGTAGT 60.202 37.037 5.75 0.00 36.88 2.73
489 529 7.012894 TCCCAAATTTAAGTGACAGTTGTGTAG 59.987 37.037 5.75 0.00 36.88 2.74
490 530 6.829298 TCCCAAATTTAAGTGACAGTTGTGTA 59.171 34.615 5.75 0.00 36.88 2.90
491 531 5.654650 TCCCAAATTTAAGTGACAGTTGTGT 59.345 36.000 5.75 0.00 40.71 3.72
492 532 5.977129 GTCCCAAATTTAAGTGACAGTTGTG 59.023 40.000 5.75 0.00 0.00 3.33
493 533 5.068591 GGTCCCAAATTTAAGTGACAGTTGT 59.931 40.000 5.75 0.00 0.00 3.32
494 534 5.508994 GGGTCCCAAATTTAAGTGACAGTTG 60.509 44.000 1.78 0.00 0.00 3.16
495 535 4.587262 GGGTCCCAAATTTAAGTGACAGTT 59.413 41.667 1.78 0.34 0.00 3.16
496 536 4.149598 GGGTCCCAAATTTAAGTGACAGT 58.850 43.478 1.78 0.00 0.00 3.55
540 647 1.065273 GCGCTTGCCATCATTCCTG 59.935 57.895 0.00 0.00 0.00 3.86
565 678 3.016541 GCGCAAATTGCCATCCCCA 62.017 57.895 12.80 0.00 41.12 4.96
566 679 2.202919 GCGCAAATTGCCATCCCC 60.203 61.111 12.80 0.00 41.12 4.81
567 680 1.519898 CTGCGCAAATTGCCATCCC 60.520 57.895 13.05 0.00 41.12 3.85
583 696 1.138069 GAAAAACACCACCCCCAACTG 59.862 52.381 0.00 0.00 0.00 3.16
584 705 1.273324 TGAAAAACACCACCCCCAACT 60.273 47.619 0.00 0.00 0.00 3.16
586 707 1.952621 TTGAAAAACACCACCCCCAA 58.047 45.000 0.00 0.00 0.00 4.12
597 718 5.989551 ATGCCATGACAGTTTTGAAAAAC 57.010 34.783 10.07 10.07 46.54 2.43
630 751 5.047377 AGTTTTTGCCCAATACATACCACAG 60.047 40.000 0.00 0.00 0.00 3.66
663 784 4.520874 CCAGAGCCGTCAGATTTAGATCTA 59.479 45.833 0.00 0.00 40.67 1.98
700 821 3.331150 ACGGATGTTCGCAGTATCAAAA 58.669 40.909 0.00 0.00 0.00 2.44
709 830 2.094442 TGTTATCTGACGGATGTTCGCA 60.094 45.455 7.05 0.00 35.98 5.10
748 869 8.851416 CACGTACTCAAAAGTCACTATTCTTAG 58.149 37.037 0.00 0.00 36.92 2.18
755 876 6.331845 TCAAACACGTACTCAAAAGTCACTA 58.668 36.000 0.00 0.00 36.92 2.74
756 877 5.172934 TCAAACACGTACTCAAAAGTCACT 58.827 37.500 0.00 0.00 36.92 3.41
759 1249 5.901884 CACATCAAACACGTACTCAAAAGTC 59.098 40.000 0.00 0.00 36.92 3.01
773 1263 1.881973 GCTCTCAAGCCACATCAAACA 59.118 47.619 0.00 0.00 43.10 2.83
838 1328 1.480137 CCACAGGGTTCACAAGCAAAA 59.520 47.619 0.00 0.00 0.00 2.44
840 1330 1.391157 GCCACAGGGTTCACAAGCAA 61.391 55.000 0.00 0.00 36.17 3.91
864 1392 8.680903 CACTTTTATTTATTGTCTGGAGCAGAT 58.319 33.333 0.00 0.00 42.73 2.90
891 1419 2.310538 CCTTGGACCATATTGCCCTTC 58.689 52.381 0.00 0.00 0.00 3.46
977 1506 2.035237 TTGGGTGGCTCGACGAGTTT 62.035 55.000 24.80 0.00 31.39 2.66
983 1512 0.670854 GAGAGTTTGGGTGGCTCGAC 60.671 60.000 0.00 0.00 34.69 4.20
1026 1555 0.796927 GAAGGAGGGCGTTTCTTTCG 59.203 55.000 0.00 0.00 0.00 3.46
1212 1741 2.941720 GCTGCAGAATCAGTAAGGAAGG 59.058 50.000 20.43 0.00 36.49 3.46
1252 1783 3.074412 GACGATCCAAAGAAGCAAAGGA 58.926 45.455 0.00 0.00 0.00 3.36
1365 1896 4.667382 TCTCTCTCTCTCCCATGAATCCTA 59.333 45.833 0.00 0.00 0.00 2.94
1378 1909 3.632333 TCGTCTCTCTCTCTCTCTCTCT 58.368 50.000 0.00 0.00 0.00 3.10
1379 1910 4.592485 ATCGTCTCTCTCTCTCTCTCTC 57.408 50.000 0.00 0.00 0.00 3.20
1380 1911 6.495181 AGATTATCGTCTCTCTCTCTCTCTCT 59.505 42.308 0.00 0.00 0.00 3.10
1381 1912 6.692486 AGATTATCGTCTCTCTCTCTCTCTC 58.308 44.000 0.00 0.00 0.00 3.20
1382 1913 6.672266 AGATTATCGTCTCTCTCTCTCTCT 57.328 41.667 0.00 0.00 0.00 3.10
1383 1914 6.952935 GAGATTATCGTCTCTCTCTCTCTC 57.047 45.833 0.00 0.00 41.12 3.20
1547 2200 5.038651 ACGTGAATATCCCCGGATAAAAA 57.961 39.130 0.73 0.00 40.07 1.94
1567 2220 1.740025 GGGAAAAAGGCTGATCTGACG 59.260 52.381 3.42 0.00 0.00 4.35
1583 2236 1.568597 CCAAGTGGATGTATGGGGGAA 59.431 52.381 0.00 0.00 37.39 3.97
1590 2243 7.342026 GGTAAAAAGATTCCCAAGTGGATGTAT 59.658 37.037 0.00 0.00 44.66 2.29
1591 2244 6.661805 GGTAAAAAGATTCCCAAGTGGATGTA 59.338 38.462 0.00 0.00 44.66 2.29
1592 2245 5.480422 GGTAAAAAGATTCCCAAGTGGATGT 59.520 40.000 0.00 0.00 44.66 3.06
1593 2246 5.716703 AGGTAAAAAGATTCCCAAGTGGATG 59.283 40.000 0.00 0.00 44.66 3.51
1594 2247 5.716703 CAGGTAAAAAGATTCCCAAGTGGAT 59.283 40.000 0.00 0.00 44.66 3.41
1595 2248 5.076873 CAGGTAAAAAGATTCCCAAGTGGA 58.923 41.667 0.00 0.00 43.18 4.02
1605 2260 3.542969 ACTGGGGCAGGTAAAAAGATT 57.457 42.857 0.00 0.00 35.51 2.40
1748 2403 5.812642 GGTACAAAGGACTGATGATACACTG 59.187 44.000 0.00 0.00 0.00 3.66
1773 2429 4.160439 TGACCTAGATCATGGAGAACACAC 59.840 45.833 10.44 0.00 0.00 3.82
1778 2434 4.871822 TCTGTGACCTAGATCATGGAGAA 58.128 43.478 10.44 0.00 0.00 2.87
2010 2667 3.404899 TCCGTTAATCCCAACACAACTC 58.595 45.455 0.00 0.00 0.00 3.01
2045 2702 6.165577 GCACCCAATAATTCAACACATTTCT 58.834 36.000 0.00 0.00 0.00 2.52
2046 2703 5.931146 TGCACCCAATAATTCAACACATTTC 59.069 36.000 0.00 0.00 0.00 2.17
2142 2799 7.445402 AGCATCCATAAGCAATCGTACTTTAAT 59.555 33.333 0.00 0.00 0.00 1.40
2149 2806 5.468540 AGTAGCATCCATAAGCAATCGTA 57.531 39.130 0.00 0.00 0.00 3.43
2167 2824 9.796180 AGTTATACATCTCTAGGTGGTTAGTAG 57.204 37.037 0.00 0.00 0.00 2.57
2210 2867 2.351157 GGCAAATGGAGCGATTCTATGC 60.351 50.000 0.00 0.00 0.00 3.14
2244 2901 4.397417 CCACCTGAAATCATCAAAGAGGAC 59.603 45.833 0.00 0.00 37.67 3.85
2257 2914 6.923199 AAAAGAATGATCACCACCTGAAAT 57.077 33.333 0.00 0.00 30.60 2.17
2285 2942 1.407437 CCAAGCAGATGTACACCTCCC 60.407 57.143 0.00 0.00 0.00 4.30
3072 3729 7.227156 AGTTTACCTCCACATCATCAATATCC 58.773 38.462 0.00 0.00 0.00 2.59
3086 3743 1.621814 CCTTGTCCGAGTTTACCTCCA 59.378 52.381 0.00 0.00 36.82 3.86
3099 3756 3.274288 CTCCTTTGCAGTATCCTTGTCC 58.726 50.000 0.00 0.00 0.00 4.02
3162 3819 1.213678 CTCCATGCCTCCAAGAATCCA 59.786 52.381 0.00 0.00 0.00 3.41
3405 4062 3.255642 TGAAACAAGCAAAGGCCTATCAC 59.744 43.478 5.16 0.00 42.56 3.06
3559 4216 1.713597 CACAGTACATGAAGCTCGCA 58.286 50.000 0.00 0.00 0.00 5.10
3582 4239 2.554032 CTGTACAAGAAAAGGGCAGGTG 59.446 50.000 0.00 0.00 0.00 4.00
3630 4287 6.604396 AGTGATGAACATGAGGCAAATATTCA 59.396 34.615 0.00 0.00 0.00 2.57
3634 4291 4.641541 CCAGTGATGAACATGAGGCAAATA 59.358 41.667 0.00 0.00 0.00 1.40
3700 4357 0.035630 GAGTGCCAAGGTCAGCTGAT 60.036 55.000 21.47 0.83 0.00 2.90
3729 4386 1.947456 GTGCCCGAGAATTACCATTCC 59.053 52.381 0.00 0.00 39.95 3.01
3856 4513 0.245539 GTGCTGCTGCCATCAACATT 59.754 50.000 13.47 0.00 38.71 2.71
3942 4599 2.281484 TGGCGACAACCTTGCTCC 60.281 61.111 0.00 0.00 37.44 4.70
4010 4667 6.493189 TCCAGTGCATAATACCACATCTTA 57.507 37.500 0.00 0.00 34.48 2.10
4011 4668 5.372343 TCCAGTGCATAATACCACATCTT 57.628 39.130 0.00 0.00 34.48 2.40
4012 4669 5.372343 TTCCAGTGCATAATACCACATCT 57.628 39.130 0.00 0.00 34.48 2.90
4123 4788 4.974645 AGTCATTCCTGGAGTTTGTACA 57.025 40.909 0.00 0.00 0.00 2.90
4228 4893 3.889538 ACAAGGCACTAGGGAAAAGAAAC 59.110 43.478 0.00 0.00 38.49 2.78
4238 4905 6.238374 CCAATTCGTATTTACAAGGCACTAGG 60.238 42.308 0.00 0.00 38.49 3.02
4348 5015 7.202084 GGATCTCATCTTGTAGAGGGAGATTTT 60.202 40.741 17.49 4.80 43.43 1.82
4377 5044 2.103771 TCAAGATGGCCAGCAGATAGAC 59.896 50.000 25.38 0.00 0.00 2.59
4422 5089 9.793252 CTCAATTCCAAATTTTATCAACTCGAT 57.207 29.630 0.00 0.00 38.21 3.59
4451 5118 0.336048 ACATTTCCCTGGGATGTGGG 59.664 55.000 17.93 7.49 44.66 4.61
4452 5119 1.826720 CAACATTTCCCTGGGATGTGG 59.173 52.381 19.96 14.56 34.47 4.17
4453 5120 1.826720 CCAACATTTCCCTGGGATGTG 59.173 52.381 19.96 20.16 34.47 3.21
4454 5121 1.432807 ACCAACATTTCCCTGGGATGT 59.567 47.619 17.93 16.15 35.65 3.06
4455 5122 2.102578 GACCAACATTTCCCTGGGATG 58.897 52.381 17.93 15.44 34.31 3.51
4467 5134 5.838521 ACCATTTACTTTCTTGGACCAACAT 59.161 36.000 1.69 0.00 33.36 2.71
4541 5211 5.063060 CAGAAGTTAGGCGTGTAAACCATAC 59.937 44.000 0.00 0.00 0.00 2.39
4543 5213 4.000988 CAGAAGTTAGGCGTGTAAACCAT 58.999 43.478 0.00 0.00 0.00 3.55
4788 5465 7.921214 AGAATATATCAACGTCTACAACACCAG 59.079 37.037 0.00 0.00 0.00 4.00
4862 5539 1.774300 GGGGGAGGAAGAGCCAAAA 59.226 57.895 0.00 0.00 40.02 2.44
4959 5664 5.774498 AGTTTGTGGAAGAACTGGATTTC 57.226 39.130 0.00 0.00 34.96 2.17
5139 5846 8.593492 AAGCCTCTTTTGTTGTTAATTTCATC 57.407 30.769 0.00 0.00 0.00 2.92
5160 5867 8.338986 GTGAGAAATATTGAGCTAGTTTAAGCC 58.661 37.037 0.00 0.00 43.86 4.35


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

AutoCloner maintained by Alex Coulton.