Multiple sequence alignment - TraesCS5D01G317500

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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 TraesCS5D01G317500 chr5D 100.000 2681 0 0 1 2681 410639237 410636557 0.000000e+00 4951.0
1 TraesCS5D01G317500 chr5D 83.361 1214 112 41 872 2040 410607261 410606093 0.000000e+00 1040.0
2 TraesCS5D01G317500 chr5D 84.962 911 90 26 966 1860 410874255 410873376 0.000000e+00 880.0
3 TraesCS5D01G317500 chr5D 80.536 560 63 26 1077 1613 410843249 410842713 3.240000e-104 388.0
4 TraesCS5D01G317500 chr5D 81.843 369 48 10 1077 1443 411170955 411170604 2.610000e-75 292.0
5 TraesCS5D01G317500 chr5D 88.312 154 13 3 2381 2533 380078774 380078923 2.120000e-41 180.0
6 TraesCS5D01G317500 chr5D 78.571 210 34 7 1506 1711 410620973 410621175 7.790000e-26 128.0
7 TraesCS5D01G317500 chr5A 93.255 1883 82 11 766 2638 522357866 522356019 0.000000e+00 2732.0
8 TraesCS5D01G317500 chr5A 85.168 1072 91 30 872 1909 522124731 522123694 0.000000e+00 1037.0
9 TraesCS5D01G317500 chr5A 84.286 910 97 29 966 1859 522868860 522867981 0.000000e+00 846.0
10 TraesCS5D01G317500 chr5A 77.674 215 35 10 1509 1720 522083375 522083579 4.690000e-23 119.0
11 TraesCS5D01G317500 chr5A 89.610 77 5 2 1967 2041 522114210 522114135 7.900000e-16 95.3
12 TraesCS5D01G317500 chr5B 95.603 1410 40 10 778 2165 493125623 493124214 0.000000e+00 2241.0
13 TraesCS5D01G317500 chr5B 87.442 868 77 19 995 1852 492820193 492819348 0.000000e+00 970.0
14 TraesCS5D01G317500 chr5B 86.328 768 71 10 966 1727 493286658 493285919 0.000000e+00 806.0
15 TraesCS5D01G317500 chr5B 89.228 557 40 12 216 766 42140929 42140387 0.000000e+00 678.0
16 TraesCS5D01G317500 chr5B 92.259 478 29 5 2163 2638 493123928 493123457 0.000000e+00 671.0
17 TraesCS5D01G317500 chr5B 78.155 206 35 6 1509 1714 493086034 493085839 3.620000e-24 122.0
18 TraesCS5D01G317500 chr5B 100.000 36 0 0 2646 2681 493123431 493123396 1.720000e-07 67.6
19 TraesCS5D01G317500 chr5B 100.000 33 0 0 769 801 493126260 493126228 8.010000e-06 62.1
20 TraesCS5D01G317500 chr7D 94.737 551 23 5 216 765 73176375 73175830 0.000000e+00 852.0
21 TraesCS5D01G317500 chr7D 81.788 302 38 12 71 368 406795146 406795434 1.240000e-58 237.0
22 TraesCS5D01G317500 chr7D 88.312 154 13 5 2381 2533 192549761 192549612 2.120000e-41 180.0
23 TraesCS5D01G317500 chr7B 88.393 560 42 15 213 765 544883420 544882877 0.000000e+00 652.0
24 TraesCS5D01G317500 chr1B 88.551 559 35 14 213 765 278474985 278474450 0.000000e+00 651.0
25 TraesCS5D01G317500 chr1B 86.929 482 53 8 63 541 192223322 192222848 1.410000e-147 532.0
26 TraesCS5D01G317500 chr4B 86.404 559 54 14 215 766 371979556 371980099 2.300000e-165 592.0
27 TraesCS5D01G317500 chr4B 88.235 153 15 3 2382 2533 516951178 516951328 2.120000e-41 180.0
28 TraesCS5D01G317500 chr6D 93.910 312 12 4 216 527 412485938 412486242 5.230000e-127 464.0
29 TraesCS5D01G317500 chr3A 91.837 294 22 2 482 774 120174061 120173769 2.480000e-110 409.0
30 TraesCS5D01G317500 chr3A 94.262 122 7 0 1 122 734029272 734029393 1.270000e-43 187.0
31 TraesCS5D01G317500 chr3A 89.041 146 15 1 2388 2533 71122157 71122301 2.120000e-41 180.0
32 TraesCS5D01G317500 chr2A 90.429 303 23 4 215 513 686298020 686297720 6.960000e-106 394.0
33 TraesCS5D01G317500 chr2A 92.793 111 8 0 14 124 194135565 194135675 7.680000e-36 161.0
34 TraesCS5D01G317500 chr3B 91.197 284 20 3 482 765 662805146 662805424 5.420000e-102 381.0
35 TraesCS5D01G317500 chr3B 89.583 288 14 5 482 769 482003412 482003141 4.250000e-93 351.0
36 TraesCS5D01G317500 chr3B 89.085 284 15 6 482 765 675570025 675570292 3.310000e-89 339.0
37 TraesCS5D01G317500 chr3B 90.826 109 10 0 16 124 754307071 754307179 2.150000e-31 147.0
38 TraesCS5D01G317500 chr3D 89.542 153 10 4 2382 2533 368949699 368949552 3.520000e-44 189.0
39 TraesCS5D01G317500 chr4D 84.103 195 22 7 1 189 3746352 3746543 2.120000e-41 180.0
40 TraesCS5D01G317500 chr2D 86.928 153 16 4 2381 2533 535622598 535622450 4.590000e-38 169.0
41 TraesCS5D01G317500 chr2D 92.593 108 8 0 16 123 336514449 336514342 3.570000e-34 156.0
42 TraesCS5D01G317500 chr1D 86.928 153 16 4 2382 2533 199327787 199327936 4.590000e-38 169.0
43 TraesCS5D01G317500 chrUn 92.793 111 8 0 14 124 101303935 101304045 7.680000e-36 161.0
44 TraesCS5D01G317500 chr7A 92.793 111 8 0 14 124 692722577 692722467 7.680000e-36 161.0
45 TraesCS5D01G317500 chr6B 91.071 112 9 1 14 124 35205225 35205114 1.660000e-32 150.0


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 TraesCS5D01G317500 chr5D 410636557 410639237 2680 True 4951.000 4951 100.0000 1 2681 1 chr5D.!!$R2 2680
1 TraesCS5D01G317500 chr5D 410606093 410607261 1168 True 1040.000 1040 83.3610 872 2040 1 chr5D.!!$R1 1168
2 TraesCS5D01G317500 chr5D 410873376 410874255 879 True 880.000 880 84.9620 966 1860 1 chr5D.!!$R4 894
3 TraesCS5D01G317500 chr5D 410842713 410843249 536 True 388.000 388 80.5360 1077 1613 1 chr5D.!!$R3 536
4 TraesCS5D01G317500 chr5A 522356019 522357866 1847 True 2732.000 2732 93.2550 766 2638 1 chr5A.!!$R3 1872
5 TraesCS5D01G317500 chr5A 522123694 522124731 1037 True 1037.000 1037 85.1680 872 1909 1 chr5A.!!$R2 1037
6 TraesCS5D01G317500 chr5A 522867981 522868860 879 True 846.000 846 84.2860 966 1859 1 chr5A.!!$R4 893
7 TraesCS5D01G317500 chr5B 492819348 492820193 845 True 970.000 970 87.4420 995 1852 1 chr5B.!!$R2 857
8 TraesCS5D01G317500 chr5B 493285919 493286658 739 True 806.000 806 86.3280 966 1727 1 chr5B.!!$R4 761
9 TraesCS5D01G317500 chr5B 493123396 493126260 2864 True 760.425 2241 96.9655 769 2681 4 chr5B.!!$R5 1912
10 TraesCS5D01G317500 chr5B 42140387 42140929 542 True 678.000 678 89.2280 216 766 1 chr5B.!!$R1 550
11 TraesCS5D01G317500 chr7D 73175830 73176375 545 True 852.000 852 94.7370 216 765 1 chr7D.!!$R1 549
12 TraesCS5D01G317500 chr7B 544882877 544883420 543 True 652.000 652 88.3930 213 765 1 chr7B.!!$R1 552
13 TraesCS5D01G317500 chr1B 278474450 278474985 535 True 651.000 651 88.5510 213 765 1 chr1B.!!$R2 552
14 TraesCS5D01G317500 chr4B 371979556 371980099 543 False 592.000 592 86.4040 215 766 1 chr4B.!!$F1 551

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
83 84 0.096454 GCGGAATGCTACAACCGTTC 59.904 55.0 14.52 0.0 45.91 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 2474 1.497716 TCCCCCGATGCTTACTCTCTA 59.502 52.381 0.0 0.0 0.0 2.43 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
39 40 7.681939 AAAAAGCTTCAACCAGATATACGAA 57.318 32.000 0.00 0.00 0.00 3.85
40 41 7.681939 AAAAGCTTCAACCAGATATACGAAA 57.318 32.000 0.00 0.00 0.00 3.46
41 42 7.681939 AAAGCTTCAACCAGATATACGAAAA 57.318 32.000 0.00 0.00 0.00 2.29
42 43 6.910536 AGCTTCAACCAGATATACGAAAAG 57.089 37.500 0.00 0.00 0.00 2.27
43 44 5.294552 AGCTTCAACCAGATATACGAAAAGC 59.705 40.000 0.00 0.00 36.52 3.51
44 45 5.294552 GCTTCAACCAGATATACGAAAAGCT 59.705 40.000 0.00 0.00 34.18 3.74
45 46 6.662414 TTCAACCAGATATACGAAAAGCTG 57.338 37.500 0.00 0.00 0.00 4.24
46 47 4.570772 TCAACCAGATATACGAAAAGCTGC 59.429 41.667 0.00 0.00 0.00 5.25
47 48 4.137116 ACCAGATATACGAAAAGCTGCA 57.863 40.909 1.02 0.00 0.00 4.41
48 49 4.513442 ACCAGATATACGAAAAGCTGCAA 58.487 39.130 1.02 0.00 0.00 4.08
49 50 4.572389 ACCAGATATACGAAAAGCTGCAAG 59.428 41.667 1.02 0.00 0.00 4.01
66 67 4.021650 GCATTCATTGCCATGGCG 57.978 55.556 30.87 17.51 46.15 5.69
67 68 1.593209 GCATTCATTGCCATGGCGG 60.593 57.895 30.87 22.21 46.15 6.13
68 69 2.018727 GCATTCATTGCCATGGCGGA 62.019 55.000 30.87 24.05 46.15 5.54
69 70 0.460722 CATTCATTGCCATGGCGGAA 59.539 50.000 30.87 29.79 45.51 4.30
70 71 1.069513 CATTCATTGCCATGGCGGAAT 59.930 47.619 30.23 30.23 45.51 3.01
71 72 0.460722 TTCATTGCCATGGCGGAATG 59.539 50.000 30.52 30.52 45.51 2.67
72 73 1.593209 CATTGCCATGGCGGAATGC 60.593 57.895 30.87 6.57 45.51 3.56
73 74 1.759299 ATTGCCATGGCGGAATGCT 60.759 52.632 30.87 7.84 45.51 3.79
74 75 0.467844 ATTGCCATGGCGGAATGCTA 60.468 50.000 30.87 8.74 45.51 3.49
75 76 1.383456 TTGCCATGGCGGAATGCTAC 61.383 55.000 30.87 1.83 45.51 3.58
76 77 1.823470 GCCATGGCGGAATGCTACA 60.823 57.895 23.48 0.00 45.43 2.74
77 78 1.383456 GCCATGGCGGAATGCTACAA 61.383 55.000 23.48 0.00 45.43 2.41
78 79 0.381801 CCATGGCGGAATGCTACAAC 59.618 55.000 0.00 0.00 45.43 3.32
79 80 0.381801 CATGGCGGAATGCTACAACC 59.618 55.000 0.00 0.00 45.43 3.77
80 81 1.095228 ATGGCGGAATGCTACAACCG 61.095 55.000 0.00 0.00 46.74 4.44
81 82 1.743995 GGCGGAATGCTACAACCGT 60.744 57.895 14.52 0.00 45.91 4.83
82 83 1.303091 GGCGGAATGCTACAACCGTT 61.303 55.000 14.52 0.00 45.91 4.44
83 84 0.096454 GCGGAATGCTACAACCGTTC 59.904 55.000 14.52 0.00 45.91 3.95
84 85 1.434555 CGGAATGCTACAACCGTTCA 58.565 50.000 0.00 0.00 40.42 3.18
85 86 1.127951 CGGAATGCTACAACCGTTCAC 59.872 52.381 0.00 0.00 40.42 3.18
86 87 2.147958 GGAATGCTACAACCGTTCACA 58.852 47.619 0.00 0.00 31.43 3.58
87 88 2.747446 GGAATGCTACAACCGTTCACAT 59.253 45.455 0.00 0.00 31.43 3.21
88 89 3.936453 GGAATGCTACAACCGTTCACATA 59.064 43.478 0.00 0.00 31.43 2.29
89 90 4.393680 GGAATGCTACAACCGTTCACATAA 59.606 41.667 0.00 0.00 31.43 1.90
90 91 5.106475 GGAATGCTACAACCGTTCACATAAA 60.106 40.000 0.00 0.00 31.43 1.40
91 92 5.950758 ATGCTACAACCGTTCACATAAAA 57.049 34.783 0.00 0.00 0.00 1.52
92 93 5.950758 TGCTACAACCGTTCACATAAAAT 57.049 34.783 0.00 0.00 0.00 1.82
93 94 5.694816 TGCTACAACCGTTCACATAAAATG 58.305 37.500 0.00 0.00 0.00 2.32
94 95 4.557301 GCTACAACCGTTCACATAAAATGC 59.443 41.667 0.00 0.00 0.00 3.56
95 96 4.846779 ACAACCGTTCACATAAAATGCT 57.153 36.364 0.00 0.00 0.00 3.79
96 97 5.950758 ACAACCGTTCACATAAAATGCTA 57.049 34.783 0.00 0.00 0.00 3.49
97 98 5.695818 ACAACCGTTCACATAAAATGCTAC 58.304 37.500 0.00 0.00 0.00 3.58
98 99 5.239744 ACAACCGTTCACATAAAATGCTACA 59.760 36.000 0.00 0.00 0.00 2.74
99 100 5.950758 ACCGTTCACATAAAATGCTACAA 57.049 34.783 0.00 0.00 0.00 2.41
100 101 6.509418 ACCGTTCACATAAAATGCTACAAT 57.491 33.333 0.00 0.00 0.00 2.71
101 102 6.551736 ACCGTTCACATAAAATGCTACAATC 58.448 36.000 0.00 0.00 0.00 2.67
102 103 5.971202 CCGTTCACATAAAATGCTACAATCC 59.029 40.000 0.00 0.00 0.00 3.01
103 104 6.183360 CCGTTCACATAAAATGCTACAATCCT 60.183 38.462 0.00 0.00 0.00 3.24
104 105 7.011950 CCGTTCACATAAAATGCTACAATCCTA 59.988 37.037 0.00 0.00 0.00 2.94
105 106 8.064222 CGTTCACATAAAATGCTACAATCCTAG 58.936 37.037 0.00 0.00 0.00 3.02
106 107 9.109393 GTTCACATAAAATGCTACAATCCTAGA 57.891 33.333 0.00 0.00 0.00 2.43
107 108 9.851686 TTCACATAAAATGCTACAATCCTAGAT 57.148 29.630 0.00 0.00 0.00 1.98
131 132 3.996150 AAATGCTTCAACCAGACACTG 57.004 42.857 0.00 0.00 0.00 3.66
132 133 2.645838 ATGCTTCAACCAGACACTGT 57.354 45.000 0.00 0.00 0.00 3.55
133 134 1.667236 TGCTTCAACCAGACACTGTG 58.333 50.000 6.19 6.19 0.00 3.66
134 135 1.209261 TGCTTCAACCAGACACTGTGA 59.791 47.619 15.86 0.00 0.00 3.58
135 136 2.288666 GCTTCAACCAGACACTGTGAA 58.711 47.619 15.86 0.00 29.93 3.18
136 137 2.682856 GCTTCAACCAGACACTGTGAAA 59.317 45.455 15.86 0.00 30.14 2.69
137 138 3.128589 GCTTCAACCAGACACTGTGAAAA 59.871 43.478 15.86 0.00 30.14 2.29
138 139 4.731773 GCTTCAACCAGACACTGTGAAAAG 60.732 45.833 15.86 3.15 30.14 2.27
139 140 4.214986 TCAACCAGACACTGTGAAAAGA 57.785 40.909 15.86 0.41 0.00 2.52
140 141 4.584874 TCAACCAGACACTGTGAAAAGAA 58.415 39.130 15.86 0.00 0.00 2.52
141 142 5.007034 TCAACCAGACACTGTGAAAAGAAA 58.993 37.500 15.86 0.00 0.00 2.52
142 143 5.475220 TCAACCAGACACTGTGAAAAGAAAA 59.525 36.000 15.86 0.00 0.00 2.29
143 144 5.975693 ACCAGACACTGTGAAAAGAAAAA 57.024 34.783 15.86 0.00 0.00 1.94
144 145 5.954335 ACCAGACACTGTGAAAAGAAAAAG 58.046 37.500 15.86 0.00 0.00 2.27
145 146 5.105756 ACCAGACACTGTGAAAAGAAAAAGG 60.106 40.000 15.86 4.15 0.00 3.11
146 147 5.105756 CCAGACACTGTGAAAAGAAAAAGGT 60.106 40.000 15.86 0.00 0.00 3.50
147 148 6.389906 CAGACACTGTGAAAAGAAAAAGGTT 58.610 36.000 15.86 0.00 0.00 3.50
148 149 6.308766 CAGACACTGTGAAAAGAAAAAGGTTG 59.691 38.462 15.86 0.00 0.00 3.77
149 150 4.929211 ACACTGTGAAAAGAAAAAGGTTGC 59.071 37.500 15.86 0.00 0.00 4.17
150 151 4.928615 CACTGTGAAAAGAAAAAGGTTGCA 59.071 37.500 0.32 0.00 0.00 4.08
151 152 5.407995 CACTGTGAAAAGAAAAAGGTTGCAA 59.592 36.000 0.32 0.00 0.00 4.08
152 153 5.408299 ACTGTGAAAAGAAAAAGGTTGCAAC 59.592 36.000 21.59 21.59 0.00 4.17
153 154 5.300752 TGTGAAAAGAAAAAGGTTGCAACA 58.699 33.333 29.55 2.13 0.00 3.33
154 155 5.760253 TGTGAAAAGAAAAAGGTTGCAACAA 59.240 32.000 29.55 0.00 0.00 2.83
155 156 6.429385 TGTGAAAAGAAAAAGGTTGCAACAAT 59.571 30.769 29.55 15.65 0.00 2.71
156 157 7.040823 TGTGAAAAGAAAAAGGTTGCAACAATT 60.041 29.630 29.55 20.34 0.00 2.32
157 158 7.271008 GTGAAAAGAAAAAGGTTGCAACAATTG 59.729 33.333 29.55 3.24 0.00 2.32
158 159 7.173907 TGAAAAGAAAAAGGTTGCAACAATTGA 59.826 29.630 29.55 3.80 0.00 2.57
159 160 6.421377 AAGAAAAAGGTTGCAACAATTGAC 57.579 33.333 29.55 18.50 0.00 3.18
160 161 5.486526 AGAAAAAGGTTGCAACAATTGACA 58.513 33.333 29.55 4.47 0.00 3.58
161 162 5.936956 AGAAAAAGGTTGCAACAATTGACAA 59.063 32.000 29.55 10.45 0.00 3.18
162 163 6.429385 AGAAAAAGGTTGCAACAATTGACAAA 59.571 30.769 29.55 0.00 31.82 2.83
163 164 6.566197 AAAAGGTTGCAACAATTGACAAAA 57.434 29.167 29.55 0.00 31.82 2.44
164 165 6.566197 AAAGGTTGCAACAATTGACAAAAA 57.434 29.167 29.55 0.00 31.82 1.94
183 184 3.831715 AAAAGCTTCAACCGTAGATGC 57.168 42.857 0.00 0.00 0.00 3.91
184 185 2.472695 AAGCTTCAACCGTAGATGCA 57.527 45.000 0.00 0.00 0.00 3.96
185 186 2.472695 AGCTTCAACCGTAGATGCAA 57.527 45.000 0.00 0.00 0.00 4.08
186 187 2.778299 AGCTTCAACCGTAGATGCAAA 58.222 42.857 0.00 0.00 0.00 3.68
187 188 3.146066 AGCTTCAACCGTAGATGCAAAA 58.854 40.909 0.00 0.00 0.00 2.44
188 189 3.189287 AGCTTCAACCGTAGATGCAAAAG 59.811 43.478 0.00 0.00 0.00 2.27
189 190 3.492313 CTTCAACCGTAGATGCAAAAGC 58.508 45.455 0.00 0.00 0.00 3.51
190 191 1.810151 TCAACCGTAGATGCAAAAGCC 59.190 47.619 0.00 0.00 0.00 4.35
191 192 1.812571 CAACCGTAGATGCAAAAGCCT 59.187 47.619 0.00 0.00 0.00 4.58
192 193 2.200373 ACCGTAGATGCAAAAGCCTT 57.800 45.000 0.00 0.00 0.00 4.35
193 194 2.084546 ACCGTAGATGCAAAAGCCTTC 58.915 47.619 0.00 0.00 0.00 3.46
194 195 2.083774 CCGTAGATGCAAAAGCCTTCA 58.916 47.619 0.00 0.00 0.00 3.02
195 196 2.487762 CCGTAGATGCAAAAGCCTTCAA 59.512 45.455 0.00 0.00 0.00 2.69
196 197 3.129287 CCGTAGATGCAAAAGCCTTCAAT 59.871 43.478 0.00 0.00 0.00 2.57
197 198 4.346129 CGTAGATGCAAAAGCCTTCAATC 58.654 43.478 0.00 0.00 0.00 2.67
198 199 4.142622 CGTAGATGCAAAAGCCTTCAATCA 60.143 41.667 0.00 0.00 0.00 2.57
199 200 4.451629 AGATGCAAAAGCCTTCAATCAG 57.548 40.909 0.00 0.00 0.00 2.90
200 201 3.194968 AGATGCAAAAGCCTTCAATCAGG 59.805 43.478 0.00 0.00 36.95 3.86
207 208 3.635433 CCTTCAATCAGGCATTGCG 57.365 52.632 1.91 0.00 41.72 4.85
208 209 0.526954 CCTTCAATCAGGCATTGCGC 60.527 55.000 0.00 0.00 41.72 6.09
209 210 0.171679 CTTCAATCAGGCATTGCGCA 59.828 50.000 5.66 5.66 45.17 6.09
210 211 0.602060 TTCAATCAGGCATTGCGCAA 59.398 45.000 27.24 27.24 45.17 4.85
211 212 0.602060 TCAATCAGGCATTGCGCAAA 59.398 45.000 28.81 9.99 45.17 3.68
851 1504 4.453177 AGTGAGAGTGTGATGTCATCTG 57.547 45.455 13.90 0.00 0.00 2.90
915 1572 3.265221 GCCATCCTCCTATCATCCATTCA 59.735 47.826 0.00 0.00 0.00 2.57
916 1573 4.625805 GCCATCCTCCTATCATCCATTCAG 60.626 50.000 0.00 0.00 0.00 3.02
1557 2254 3.755526 CTGGATCGGCGGCATGGAA 62.756 63.158 10.53 0.00 0.00 3.53
1788 2501 0.323451 AAGCATCGGGGGAAAGGTTC 60.323 55.000 0.00 0.00 0.00 3.62
1855 2577 7.811713 GCACAAATGAGCTTCTTTCTTTATTCT 59.188 33.333 0.00 0.00 0.00 2.40
1962 2713 1.115467 CCTACCACTAGGACTGCCAG 58.885 60.000 0.00 0.00 42.34 4.85
2433 3485 4.803908 GGGTAGCTGCCAGCCCAC 62.804 72.222 23.21 11.70 43.77 4.61
2441 3493 3.712907 GCCAGCCCACCCGAGTTA 61.713 66.667 0.00 0.00 0.00 2.24
2444 3496 1.550130 CCAGCCCACCCGAGTTAGAA 61.550 60.000 0.00 0.00 0.00 2.10
2450 3502 1.077265 ACCCGAGTTAGAACCCCGA 59.923 57.895 6.43 0.00 0.00 5.14
2478 3530 1.885850 ACGGTGCTCGCGAAGTTTT 60.886 52.632 11.33 0.00 43.89 2.43
2527 3579 0.178873 TAGCCCTTGGGTTGGTCTCT 60.179 55.000 7.61 0.00 34.28 3.10
2558 3611 1.674359 ATTCGTCAGTTGTGTTGGCA 58.326 45.000 0.00 0.00 0.00 4.92
2599 3652 1.255882 ACAATGCCTGAAAATCCGCA 58.744 45.000 0.00 0.00 35.35 5.69
2610 3663 3.243704 TGAAAATCCGCAAACAAAGGGAG 60.244 43.478 0.00 0.00 30.92 4.30
2638 3691 3.954258 TGTCGGAGATGCTCATTTCTCTA 59.046 43.478 0.00 0.00 40.67 2.43
2639 3692 4.037327 TGTCGGAGATGCTCATTTCTCTAG 59.963 45.833 0.00 0.00 40.67 2.43
2640 3693 4.037446 GTCGGAGATGCTCATTTCTCTAGT 59.963 45.833 0.00 0.00 40.67 2.57
2641 3694 4.277174 TCGGAGATGCTCATTTCTCTAGTC 59.723 45.833 0.00 0.00 38.71 2.59
2642 3695 4.545610 GGAGATGCTCATTTCTCTAGTCG 58.454 47.826 0.00 0.00 38.71 4.18
2643 3696 4.277174 GGAGATGCTCATTTCTCTAGTCGA 59.723 45.833 0.00 0.00 38.71 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.681939 TTCGTATATCTGGTTGAAGCTTTTT 57.318 32.000 0.00 0.00 0.00 1.94
16 17 7.681939 TTTCGTATATCTGGTTGAAGCTTTT 57.318 32.000 0.00 0.00 0.00 2.27
17 18 7.626452 GCTTTTCGTATATCTGGTTGAAGCTTT 60.626 37.037 0.00 0.00 34.54 3.51
18 19 6.183360 GCTTTTCGTATATCTGGTTGAAGCTT 60.183 38.462 0.00 0.00 34.54 3.74
19 20 5.294552 GCTTTTCGTATATCTGGTTGAAGCT 59.705 40.000 0.00 0.00 34.54 3.74
20 21 5.294552 AGCTTTTCGTATATCTGGTTGAAGC 59.705 40.000 0.00 0.00 36.84 3.86
21 22 6.709643 CAGCTTTTCGTATATCTGGTTGAAG 58.290 40.000 0.00 0.00 0.00 3.02
22 23 5.064707 GCAGCTTTTCGTATATCTGGTTGAA 59.935 40.000 0.00 0.00 0.00 2.69
23 24 4.570772 GCAGCTTTTCGTATATCTGGTTGA 59.429 41.667 0.00 0.00 0.00 3.18
24 25 4.332543 TGCAGCTTTTCGTATATCTGGTTG 59.667 41.667 0.00 0.00 0.00 3.77
25 26 4.513442 TGCAGCTTTTCGTATATCTGGTT 58.487 39.130 0.00 0.00 0.00 3.67
26 27 4.137116 TGCAGCTTTTCGTATATCTGGT 57.863 40.909 0.00 0.00 0.00 4.00
27 28 4.553547 GCTTGCAGCTTTTCGTATATCTGG 60.554 45.833 0.00 0.00 38.45 3.86
28 29 4.034394 TGCTTGCAGCTTTTCGTATATCTG 59.966 41.667 9.12 0.00 42.97 2.90
29 30 4.191544 TGCTTGCAGCTTTTCGTATATCT 58.808 39.130 9.12 0.00 42.97 1.98
30 31 4.536364 TGCTTGCAGCTTTTCGTATATC 57.464 40.909 9.12 0.00 42.97 1.63
31 32 5.066375 TGAATGCTTGCAGCTTTTCGTATAT 59.934 36.000 0.87 0.00 42.97 0.86
32 33 4.394610 TGAATGCTTGCAGCTTTTCGTATA 59.605 37.500 0.87 0.00 42.97 1.47
33 34 3.191162 TGAATGCTTGCAGCTTTTCGTAT 59.809 39.130 0.87 0.00 42.97 3.06
34 35 2.551887 TGAATGCTTGCAGCTTTTCGTA 59.448 40.909 0.87 0.00 42.97 3.43
35 36 1.337703 TGAATGCTTGCAGCTTTTCGT 59.662 42.857 0.87 0.00 42.97 3.85
36 37 2.054687 TGAATGCTTGCAGCTTTTCG 57.945 45.000 0.87 0.00 42.97 3.46
37 38 4.322101 CAATGAATGCTTGCAGCTTTTC 57.678 40.909 0.87 11.22 42.97 2.29
50 51 0.460722 TTCCGCCATGGCAATGAATG 59.539 50.000 34.93 17.21 42.06 2.67
51 52 1.069513 CATTCCGCCATGGCAATGAAT 59.930 47.619 31.82 29.69 42.06 2.57
52 53 0.460722 CATTCCGCCATGGCAATGAA 59.539 50.000 31.82 29.05 42.06 2.57
53 54 2.018727 GCATTCCGCCATGGCAATGA 62.019 55.000 36.22 26.88 42.06 2.57
54 55 1.593209 GCATTCCGCCATGGCAATG 60.593 57.895 31.38 31.38 42.06 2.82
55 56 0.467844 TAGCATTCCGCCATGGCAAT 60.468 50.000 34.93 24.47 44.04 3.56
56 57 1.077140 TAGCATTCCGCCATGGCAA 60.077 52.632 34.93 23.33 44.04 4.52
57 58 1.823470 GTAGCATTCCGCCATGGCA 60.823 57.895 34.93 17.72 44.04 4.92
58 59 1.383456 TTGTAGCATTCCGCCATGGC 61.383 55.000 27.67 27.67 44.04 4.40
59 60 0.381801 GTTGTAGCATTCCGCCATGG 59.618 55.000 7.63 7.63 44.04 3.66
60 61 0.381801 GGTTGTAGCATTCCGCCATG 59.618 55.000 0.00 0.00 44.04 3.66
61 62 1.095228 CGGTTGTAGCATTCCGCCAT 61.095 55.000 0.00 0.00 44.04 4.40
62 63 1.743623 CGGTTGTAGCATTCCGCCA 60.744 57.895 0.00 0.00 44.04 5.69
63 64 1.303091 AACGGTTGTAGCATTCCGCC 61.303 55.000 0.00 0.00 45.76 6.13
64 65 0.096454 GAACGGTTGTAGCATTCCGC 59.904 55.000 0.00 0.00 45.76 5.54
65 66 1.127951 GTGAACGGTTGTAGCATTCCG 59.872 52.381 0.00 0.00 46.98 4.30
66 67 2.147958 TGTGAACGGTTGTAGCATTCC 58.852 47.619 0.00 0.00 0.00 3.01
67 68 5.539582 TTATGTGAACGGTTGTAGCATTC 57.460 39.130 0.00 0.00 0.00 2.67
68 69 5.950758 TTTATGTGAACGGTTGTAGCATT 57.049 34.783 0.00 0.00 0.00 3.56
69 70 5.950758 TTTTATGTGAACGGTTGTAGCAT 57.049 34.783 0.00 0.25 0.00 3.79
70 71 5.694816 CATTTTATGTGAACGGTTGTAGCA 58.305 37.500 0.00 0.00 0.00 3.49
71 72 4.557301 GCATTTTATGTGAACGGTTGTAGC 59.443 41.667 0.00 0.00 0.00 3.58
72 73 5.938322 AGCATTTTATGTGAACGGTTGTAG 58.062 37.500 0.00 0.00 0.00 2.74
73 74 5.950758 AGCATTTTATGTGAACGGTTGTA 57.049 34.783 0.00 0.00 0.00 2.41
74 75 4.846779 AGCATTTTATGTGAACGGTTGT 57.153 36.364 0.00 0.00 0.00 3.32
75 76 5.694816 TGTAGCATTTTATGTGAACGGTTG 58.305 37.500 0.00 0.00 0.00 3.77
76 77 5.950758 TGTAGCATTTTATGTGAACGGTT 57.049 34.783 0.00 0.00 0.00 4.44
77 78 5.950758 TTGTAGCATTTTATGTGAACGGT 57.049 34.783 0.00 0.00 0.00 4.83
78 79 5.971202 GGATTGTAGCATTTTATGTGAACGG 59.029 40.000 0.00 0.00 0.00 4.44
79 80 6.785191 AGGATTGTAGCATTTTATGTGAACG 58.215 36.000 0.00 0.00 0.00 3.95
80 81 9.109393 TCTAGGATTGTAGCATTTTATGTGAAC 57.891 33.333 0.00 0.00 0.00 3.18
81 82 9.851686 ATCTAGGATTGTAGCATTTTATGTGAA 57.148 29.630 0.00 0.00 0.00 3.18
109 110 4.160252 ACAGTGTCTGGTTGAAGCATTTTT 59.840 37.500 0.00 0.00 35.51 1.94
110 111 3.701040 ACAGTGTCTGGTTGAAGCATTTT 59.299 39.130 0.00 0.00 35.51 1.82
111 112 3.067180 CACAGTGTCTGGTTGAAGCATTT 59.933 43.478 0.00 0.00 35.51 2.32
112 113 2.620115 CACAGTGTCTGGTTGAAGCATT 59.380 45.455 0.00 0.00 35.51 3.56
113 114 2.158769 TCACAGTGTCTGGTTGAAGCAT 60.159 45.455 0.00 0.00 35.51 3.79
114 115 1.209261 TCACAGTGTCTGGTTGAAGCA 59.791 47.619 0.00 0.00 35.51 3.91
115 116 1.953559 TCACAGTGTCTGGTTGAAGC 58.046 50.000 0.00 0.00 35.51 3.86
116 117 4.635765 TCTTTTCACAGTGTCTGGTTGAAG 59.364 41.667 0.00 0.00 35.51 3.02
117 118 4.584874 TCTTTTCACAGTGTCTGGTTGAA 58.415 39.130 0.00 0.00 35.51 2.69
118 119 4.214986 TCTTTTCACAGTGTCTGGTTGA 57.785 40.909 0.00 0.00 35.51 3.18
119 120 4.963276 TTCTTTTCACAGTGTCTGGTTG 57.037 40.909 0.00 0.00 35.51 3.77
120 121 5.975693 TTTTCTTTTCACAGTGTCTGGTT 57.024 34.783 0.00 0.00 35.51 3.67
121 122 5.105756 CCTTTTTCTTTTCACAGTGTCTGGT 60.106 40.000 0.00 0.00 35.51 4.00
122 123 5.105756 ACCTTTTTCTTTTCACAGTGTCTGG 60.106 40.000 0.00 0.00 35.51 3.86
123 124 5.954335 ACCTTTTTCTTTTCACAGTGTCTG 58.046 37.500 0.00 0.00 37.52 3.51
124 125 6.389906 CAACCTTTTTCTTTTCACAGTGTCT 58.610 36.000 0.00 0.00 0.00 3.41
125 126 5.062183 GCAACCTTTTTCTTTTCACAGTGTC 59.938 40.000 0.00 0.00 0.00 3.67
126 127 4.929211 GCAACCTTTTTCTTTTCACAGTGT 59.071 37.500 0.00 0.00 0.00 3.55
127 128 4.928615 TGCAACCTTTTTCTTTTCACAGTG 59.071 37.500 0.00 0.00 0.00 3.66
128 129 5.146010 TGCAACCTTTTTCTTTTCACAGT 57.854 34.783 0.00 0.00 0.00 3.55
129 130 5.407995 TGTTGCAACCTTTTTCTTTTCACAG 59.592 36.000 26.14 0.00 0.00 3.66
130 131 5.300752 TGTTGCAACCTTTTTCTTTTCACA 58.699 33.333 26.14 0.00 0.00 3.58
131 132 5.854431 TGTTGCAACCTTTTTCTTTTCAC 57.146 34.783 26.14 0.00 0.00 3.18
132 133 7.173907 TCAATTGTTGCAACCTTTTTCTTTTCA 59.826 29.630 26.14 0.07 0.00 2.69
133 134 7.481483 GTCAATTGTTGCAACCTTTTTCTTTTC 59.519 33.333 26.14 0.00 0.00 2.29
134 135 7.040823 TGTCAATTGTTGCAACCTTTTTCTTTT 60.041 29.630 26.14 4.54 0.00 2.27
135 136 6.429385 TGTCAATTGTTGCAACCTTTTTCTTT 59.571 30.769 26.14 5.97 0.00 2.52
136 137 5.936956 TGTCAATTGTTGCAACCTTTTTCTT 59.063 32.000 26.14 6.78 0.00 2.52
137 138 5.486526 TGTCAATTGTTGCAACCTTTTTCT 58.513 33.333 26.14 1.69 0.00 2.52
138 139 5.793026 TGTCAATTGTTGCAACCTTTTTC 57.207 34.783 26.14 13.11 0.00 2.29
139 140 6.566197 TTTGTCAATTGTTGCAACCTTTTT 57.434 29.167 26.14 11.56 0.00 1.94
140 141 6.566197 TTTTGTCAATTGTTGCAACCTTTT 57.434 29.167 26.14 13.92 0.00 2.27
141 142 6.566197 TTTTTGTCAATTGTTGCAACCTTT 57.434 29.167 26.14 16.33 0.00 3.11
162 163 3.568007 TGCATCTACGGTTGAAGCTTTTT 59.432 39.130 17.66 0.00 0.00 1.94
163 164 3.146066 TGCATCTACGGTTGAAGCTTTT 58.854 40.909 17.66 0.00 0.00 2.27
164 165 2.778299 TGCATCTACGGTTGAAGCTTT 58.222 42.857 17.66 0.00 0.00 3.51
165 166 2.472695 TGCATCTACGGTTGAAGCTT 57.527 45.000 17.66 0.00 0.00 3.74
166 167 2.472695 TTGCATCTACGGTTGAAGCT 57.527 45.000 17.66 0.00 0.00 3.74
167 168 3.492313 CTTTTGCATCTACGGTTGAAGC 58.508 45.455 11.78 11.78 0.00 3.86
168 169 3.492313 GCTTTTGCATCTACGGTTGAAG 58.508 45.455 0.00 0.00 46.58 3.02
169 170 3.552604 GCTTTTGCATCTACGGTTGAA 57.447 42.857 0.00 0.00 46.58 2.69
189 190 0.526954 GCGCAATGCCTGATTGAAGG 60.527 55.000 0.30 0.00 43.87 3.46
190 191 0.171679 TGCGCAATGCCTGATTGAAG 59.828 50.000 8.16 0.00 43.87 3.02
191 192 0.602060 TTGCGCAATGCCTGATTGAA 59.398 45.000 21.02 0.00 43.87 2.69
192 193 0.602060 TTTGCGCAATGCCTGATTGA 59.398 45.000 25.64 0.97 43.87 2.57
193 194 0.996462 CTTTGCGCAATGCCTGATTG 59.004 50.000 25.64 2.36 45.60 2.67
194 195 0.889994 TCTTTGCGCAATGCCTGATT 59.110 45.000 25.64 0.00 45.60 2.57
195 196 0.889994 TTCTTTGCGCAATGCCTGAT 59.110 45.000 25.64 0.00 45.60 2.90
196 197 0.889994 ATTCTTTGCGCAATGCCTGA 59.110 45.000 25.64 13.88 45.60 3.86
197 198 1.717194 AATTCTTTGCGCAATGCCTG 58.283 45.000 25.64 11.82 45.60 4.85
198 199 2.460757 AAATTCTTTGCGCAATGCCT 57.539 40.000 25.64 13.21 45.60 4.75
199 200 3.541071 AAAAATTCTTTGCGCAATGCC 57.459 38.095 25.64 0.00 45.60 4.40
566 590 2.692741 CTCCCCCTTCCCCTCCAC 60.693 72.222 0.00 0.00 0.00 4.02
567 591 4.038804 CCTCCCCCTTCCCCTCCA 62.039 72.222 0.00 0.00 0.00 3.86
696 720 3.195698 GCGGCCGTTGGATCTGAC 61.196 66.667 28.70 0.93 0.00 3.51
915 1572 0.707616 AGGTGGAGAGGTGTAGCTCT 59.292 55.000 12.96 12.96 0.00 4.09
916 1573 1.107945 GAGGTGGAGAGGTGTAGCTC 58.892 60.000 2.98 2.98 0.00 4.09
1557 2254 3.885521 GCGTAGTACGAGCCGGCT 61.886 66.667 33.48 33.48 46.05 5.52
1761 2474 1.497716 TCCCCCGATGCTTACTCTCTA 59.502 52.381 0.00 0.00 0.00 2.43
1962 2713 2.808543 CCTACCGCTGAATTCTATTGCC 59.191 50.000 7.05 0.00 0.00 4.52
2433 3485 0.969409 AGTCGGGGTTCTAACTCGGG 60.969 60.000 1.05 0.00 31.32 5.14
2533 3585 5.212194 CCAACACAACTGACGAATTTTAGG 58.788 41.667 0.00 0.00 0.00 2.69
2545 3598 1.538512 CCATCTCTGCCAACACAACTG 59.461 52.381 0.00 0.00 0.00 3.16
2558 3611 6.889198 TGTTTCCGATTATTTCTCCATCTCT 58.111 36.000 0.00 0.00 0.00 3.10
2599 3652 2.489329 CGACATGCATCTCCCTTTGTTT 59.511 45.455 0.00 0.00 0.00 2.83
2638 3691 6.098409 TGCTCCTCTAAAATTTAGGATCGACT 59.902 38.462 12.29 0.00 38.70 4.18
2639 3692 6.281405 TGCTCCTCTAAAATTTAGGATCGAC 58.719 40.000 12.29 1.63 38.70 4.20
2640 3693 6.479972 TGCTCCTCTAAAATTTAGGATCGA 57.520 37.500 12.29 0.00 38.70 3.59
2641 3694 7.410485 GTTTGCTCCTCTAAAATTTAGGATCG 58.590 38.462 12.29 0.92 38.70 3.69
2642 3695 7.410485 CGTTTGCTCCTCTAAAATTTAGGATC 58.590 38.462 12.29 5.73 38.70 3.36
2643 3696 6.318900 CCGTTTGCTCCTCTAAAATTTAGGAT 59.681 38.462 12.29 0.00 38.70 3.24


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

AutoCloner maintained by Alex Coulton.