Multiple sequence alignment - TraesCS1D01G027100

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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 TraesCS1D01G027100 chr1D 100.000 3711 0 0 1 3711 10928949 10932659 0.000000e+00 6854.0
1 TraesCS1D01G027100 chr1D 88.713 2277 190 38 1461 3711 10775143 10772908 0.000000e+00 2719.0
2 TraesCS1D01G027100 chr1D 87.705 976 84 21 2749 3711 10762302 10761350 0.000000e+00 1105.0
3 TraesCS1D01G027100 chr1D 84.606 864 79 25 2749 3603 10845853 10846671 0.000000e+00 809.0
4 TraesCS1D01G027100 chr1D 97.619 252 4 2 15 265 10922264 10922014 7.360000e-117 431.0
5 TraesCS1D01G027100 chr1D 80.038 521 64 31 1054 1552 10764214 10763712 2.120000e-92 350.0
6 TraesCS1D01G027100 chr1D 80.421 475 66 18 981 1446 10776959 10776503 1.650000e-88 337.0
7 TraesCS1D01G027100 chr1D 92.742 124 9 0 3588 3711 10846714 10846837 2.940000e-41 180.0
8 TraesCS1D01G027100 chr1A 96.163 3492 57 14 258 3711 22762755 22759303 0.000000e+00 5635.0
9 TraesCS1D01G027100 chr1A 91.147 2067 125 32 754 2777 13271845 13273896 0.000000e+00 2750.0
10 TraesCS1D01G027100 chr1A 88.352 2318 201 42 1415 3711 13212988 13215257 0.000000e+00 2721.0
11 TraesCS1D01G027100 chr1A 88.480 2118 187 35 1415 3506 13229599 13231685 0.000000e+00 2507.0
12 TraesCS1D01G027100 chr1A 89.451 1621 135 20 1415 3017 13009308 13007706 0.000000e+00 2013.0
13 TraesCS1D01G027100 chr1A 91.953 932 66 4 2781 3711 13273868 13274791 0.000000e+00 1297.0
14 TraesCS1D01G027100 chr1A 87.743 514 46 13 3208 3711 13007696 13007190 5.340000e-163 584.0
15 TraesCS1D01G027100 chr1A 86.186 485 45 11 256 727 57298885 57299360 4.280000e-139 505.0
16 TraesCS1D01G027100 chr1A 81.326 573 62 35 1001 1552 13009850 13009302 1.230000e-114 424.0
17 TraesCS1D01G027100 chr1A 82.439 410 55 11 981 1381 13250410 13250811 3.550000e-90 342.0
18 TraesCS1D01G027100 chr1A 79.423 520 62 35 1054 1552 13229110 13229605 3.570000e-85 326.0
19 TraesCS1D01G027100 chr1A 90.909 44 3 1 885 927 13228938 13228981 1.440000e-04 58.4
20 TraesCS1D01G027100 chr1B 91.220 2073 154 15 1488 3544 39814816 39816876 0.000000e+00 2795.0
21 TraesCS1D01G027100 chr1B 91.367 2027 129 22 1611 3626 16400954 16402945 0.000000e+00 2732.0
22 TraesCS1D01G027100 chr1B 87.725 2330 207 48 1415 3711 16225064 16222781 0.000000e+00 2645.0
23 TraesCS1D01G027100 chr1B 87.512 2066 177 36 1433 3474 39732828 39734836 0.000000e+00 2311.0
24 TraesCS1D01G027100 chr1B 79.882 845 95 41 2878 3711 23776929 23777709 1.950000e-152 549.0
25 TraesCS1D01G027100 chr1B 86.523 512 40 14 3206 3711 39808730 39809218 1.520000e-148 536.0
26 TraesCS1D01G027100 chr1B 86.022 372 41 6 889 1256 39814095 39814459 4.490000e-104 388.0
27 TraesCS1D01G027100 chr1B 95.397 239 10 1 3474 3711 39816847 39817085 2.700000e-101 379.0
28 TraesCS1D01G027100 chr6A 88.382 482 46 5 255 728 453118573 453118094 4.160000e-159 571.0
29 TraesCS1D01G027100 chr6A 85.339 457 55 9 255 703 137169429 137169881 2.610000e-126 462.0
30 TraesCS1D01G027100 chr6A 83.542 480 67 10 255 728 560563522 560563995 4.400000e-119 438.0
31 TraesCS1D01G027100 chr5B 89.955 448 35 6 255 696 291839105 291838662 1.500000e-158 569.0
32 TraesCS1D01G027100 chr2A 87.292 480 43 7 256 728 692528322 692528790 1.960000e-147 532.0
33 TraesCS1D01G027100 chrUn 94.769 325 17 0 3387 3711 261630582 261630258 1.190000e-139 507.0
34 TraesCS1D01G027100 chr6B 85.193 466 47 9 255 703 216689310 216689770 3.380000e-125 459.0
35 TraesCS1D01G027100 chr3D 85.455 440 52 9 261 695 309928326 309928758 7.310000e-122 448.0
36 TraesCS1D01G027100 chr3D 98.024 253 5 0 1 253 577385423 577385171 1.220000e-119 440.0
37 TraesCS1D01G027100 chr3D 95.273 275 10 3 1 273 550441220 550441493 2.050000e-117 433.0
38 TraesCS1D01G027100 chr3D 97.925 241 5 0 12 252 577392000 577392240 5.730000e-113 418.0
39 TraesCS1D01G027100 chr3D 99.550 222 1 0 15 236 550434616 550434395 4.460000e-109 405.0
40 TraesCS1D01G027100 chr7D 99.163 239 2 0 15 253 600059554 600059316 7.360000e-117 431.0
41 TraesCS1D01G027100 chr2D 97.244 254 6 1 1 253 481548007 481548260 2.650000e-116 429.0
42 TraesCS1D01G027100 chr2D 98.745 239 3 0 15 253 481541234 481540996 3.430000e-115 425.0
43 TraesCS1D01G027100 chr7B 93.281 253 17 0 1 253 516874591 516874843 1.260000e-99 374.0


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 TraesCS1D01G027100 chr1D 10928949 10932659 3710 False 6854.000000 6854 100.000000 1 3711 1 chr1D.!!$F1 3710
1 TraesCS1D01G027100 chr1D 10772908 10776959 4051 True 1528.000000 2719 84.567000 981 3711 2 chr1D.!!$R3 2730
2 TraesCS1D01G027100 chr1D 10761350 10764214 2864 True 727.500000 1105 83.871500 1054 3711 2 chr1D.!!$R2 2657
3 TraesCS1D01G027100 chr1D 10845853 10846837 984 False 494.500000 809 88.674000 2749 3711 2 chr1D.!!$F2 962
4 TraesCS1D01G027100 chr1A 22759303 22762755 3452 True 5635.000000 5635 96.163000 258 3711 1 chr1A.!!$R1 3453
5 TraesCS1D01G027100 chr1A 13212988 13215257 2269 False 2721.000000 2721 88.352000 1415 3711 1 chr1A.!!$F1 2296
6 TraesCS1D01G027100 chr1A 13271845 13274791 2946 False 2023.500000 2750 91.550000 754 3711 2 chr1A.!!$F5 2957
7 TraesCS1D01G027100 chr1A 13007190 13009850 2660 True 1007.000000 2013 86.173333 1001 3711 3 chr1A.!!$R2 2710
8 TraesCS1D01G027100 chr1A 13228938 13231685 2747 False 963.800000 2507 86.270667 885 3506 3 chr1A.!!$F4 2621
9 TraesCS1D01G027100 chr1B 16400954 16402945 1991 False 2732.000000 2732 91.367000 1611 3626 1 chr1B.!!$F1 2015
10 TraesCS1D01G027100 chr1B 16222781 16225064 2283 True 2645.000000 2645 87.725000 1415 3711 1 chr1B.!!$R1 2296
11 TraesCS1D01G027100 chr1B 39732828 39734836 2008 False 2311.000000 2311 87.512000 1433 3474 1 chr1B.!!$F3 2041
12 TraesCS1D01G027100 chr1B 39814095 39817085 2990 False 1187.333333 2795 90.879667 889 3711 3 chr1B.!!$F5 2822
13 TraesCS1D01G027100 chr1B 23776929 23777709 780 False 549.000000 549 79.882000 2878 3711 1 chr1B.!!$F2 833

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
260 261 0.096454 GGCAATTAACTCACGGCGAC 59.904 55.0 16.62 0.0 0.0 5.19 F
674 675 2.971660 TTATCAAATCCGACGGCTCA 57.028 45.0 9.66 0.0 0.0 4.26 F
1733 3242 0.532573 TTGGGCTAGAAGACTCTGCG 59.467 55.0 0.00 0.0 32.7 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 2992 2.357009 GAGAGTAAACTATCGTCCCGCA 59.643 50.000 0.0 0.0 0.00 5.69 R
2516 4049 4.051922 CAGATAGTAATGACACTTCGCCC 58.948 47.826 0.0 0.0 0.00 6.13 R
2876 4498 7.654568 TCAGTATAACACTCCACCATAATACG 58.345 38.462 0.0 0.0 34.26 3.06 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
19 20 4.760047 GCGAAGAGGGCGAGCCAA 62.760 66.667 16.65 0.00 37.98 4.52
20 21 2.815647 CGAAGAGGGCGAGCCAAC 60.816 66.667 16.65 8.85 37.98 3.77
21 22 2.347490 GAAGAGGGCGAGCCAACA 59.653 61.111 16.65 0.00 37.98 3.33
22 23 1.743252 GAAGAGGGCGAGCCAACAG 60.743 63.158 16.65 0.00 37.98 3.16
23 24 2.172483 GAAGAGGGCGAGCCAACAGA 62.172 60.000 16.65 0.00 37.98 3.41
24 25 2.125350 GAGGGCGAGCCAACAGAG 60.125 66.667 16.65 0.00 37.98 3.35
25 26 2.925170 AGGGCGAGCCAACAGAGT 60.925 61.111 16.65 0.00 37.98 3.24
26 27 2.032681 GGGCGAGCCAACAGAGTT 59.967 61.111 16.65 0.00 37.98 3.01
27 28 2.328099 GGGCGAGCCAACAGAGTTG 61.328 63.158 16.65 3.00 37.98 3.16
28 29 1.301716 GGCGAGCCAACAGAGTTGA 60.302 57.895 9.58 0.00 35.81 3.18
29 30 1.569479 GGCGAGCCAACAGAGTTGAC 61.569 60.000 9.58 0.00 35.81 3.18
30 31 1.891060 GCGAGCCAACAGAGTTGACG 61.891 60.000 11.19 13.12 0.00 4.35
31 32 0.318699 CGAGCCAACAGAGTTGACGA 60.319 55.000 11.19 0.00 0.00 4.20
32 33 1.423395 GAGCCAACAGAGTTGACGAG 58.577 55.000 11.19 0.00 0.00 4.18
33 34 0.601311 AGCCAACAGAGTTGACGAGC 60.601 55.000 11.19 6.18 0.00 5.03
34 35 1.891060 GCCAACAGAGTTGACGAGCG 61.891 60.000 11.19 0.00 0.00 5.03
35 36 1.284982 CCAACAGAGTTGACGAGCGG 61.285 60.000 11.19 0.00 0.00 5.52
36 37 1.006102 AACAGAGTTGACGAGCGGG 60.006 57.895 0.00 0.00 0.00 6.13
37 38 2.125912 CAGAGTTGACGAGCGGGG 60.126 66.667 0.00 0.00 0.00 5.73
38 39 3.382832 AGAGTTGACGAGCGGGGG 61.383 66.667 0.00 0.00 0.00 5.40
39 40 3.379445 GAGTTGACGAGCGGGGGA 61.379 66.667 0.00 0.00 0.00 4.81
40 41 2.920912 AGTTGACGAGCGGGGGAA 60.921 61.111 0.00 0.00 0.00 3.97
41 42 2.031465 GTTGACGAGCGGGGGAAA 59.969 61.111 0.00 0.00 0.00 3.13
42 43 2.031465 TTGACGAGCGGGGGAAAC 59.969 61.111 0.00 0.00 0.00 2.78
43 44 3.869473 TTGACGAGCGGGGGAAACG 62.869 63.158 0.00 0.00 0.00 3.60
70 71 4.530857 CCTCCGCCGTTAGCCCTG 62.531 72.222 0.00 0.00 38.78 4.45
71 72 4.530857 CTCCGCCGTTAGCCCTGG 62.531 72.222 0.00 0.00 38.78 4.45
77 78 4.388499 CGTTAGCCCTGGCCACGT 62.388 66.667 17.94 0.00 40.93 4.49
78 79 2.746277 GTTAGCCCTGGCCACGTG 60.746 66.667 9.08 9.08 43.17 4.49
79 80 4.028490 TTAGCCCTGGCCACGTGG 62.028 66.667 30.66 30.66 43.17 4.94
89 90 4.373116 CCACGTGGTCCCGACAGG 62.373 72.222 26.95 0.00 37.24 4.00
107 108 4.100084 CGGGCCAGGCATGTCAGA 62.100 66.667 15.19 0.00 0.00 3.27
108 109 2.599597 GGGCCAGGCATGTCAGAT 59.400 61.111 15.19 0.00 0.00 2.90
109 110 1.076485 GGGCCAGGCATGTCAGATT 60.076 57.895 15.19 0.00 0.00 2.40
110 111 1.105759 GGGCCAGGCATGTCAGATTC 61.106 60.000 15.19 0.00 0.00 2.52
111 112 1.442526 GGCCAGGCATGTCAGATTCG 61.443 60.000 15.19 0.00 0.00 3.34
112 113 2.020131 CCAGGCATGTCAGATTCGC 58.980 57.895 0.00 0.00 0.00 4.70
113 114 0.745486 CCAGGCATGTCAGATTCGCA 60.745 55.000 0.00 0.00 0.00 5.10
114 115 0.376152 CAGGCATGTCAGATTCGCAC 59.624 55.000 0.00 0.00 0.00 5.34
115 116 0.251354 AGGCATGTCAGATTCGCACT 59.749 50.000 0.00 0.00 0.00 4.40
116 117 1.089920 GGCATGTCAGATTCGCACTT 58.910 50.000 0.00 0.00 0.00 3.16
117 118 2.093500 AGGCATGTCAGATTCGCACTTA 60.093 45.455 0.00 0.00 0.00 2.24
118 119 2.286294 GGCATGTCAGATTCGCACTTAG 59.714 50.000 0.00 0.00 0.00 2.18
119 120 2.286067 GCATGTCAGATTCGCACTTAGC 60.286 50.000 0.00 0.00 40.87 3.09
120 121 2.010145 TGTCAGATTCGCACTTAGCC 57.990 50.000 0.00 0.00 41.38 3.93
121 122 0.924090 GTCAGATTCGCACTTAGCCG 59.076 55.000 0.00 0.00 41.38 5.52
122 123 0.806102 TCAGATTCGCACTTAGCCGC 60.806 55.000 0.00 0.00 41.38 6.53
128 129 4.752879 GCACTTAGCCGCGGGTCA 62.753 66.667 36.11 23.26 37.23 4.02
129 130 2.813908 CACTTAGCCGCGGGTCAC 60.814 66.667 36.11 13.55 0.00 3.67
130 131 3.307906 ACTTAGCCGCGGGTCACA 61.308 61.111 36.11 14.77 0.00 3.58
131 132 2.509336 CTTAGCCGCGGGTCACAG 60.509 66.667 36.11 23.41 0.00 3.66
132 133 4.752879 TTAGCCGCGGGTCACAGC 62.753 66.667 36.11 13.77 0.00 4.40
138 139 2.719354 GCGGGTCACAGCGTTTTT 59.281 55.556 0.00 0.00 0.00 1.94
139 140 1.943293 GCGGGTCACAGCGTTTTTA 59.057 52.632 0.00 0.00 0.00 1.52
140 141 0.110373 GCGGGTCACAGCGTTTTTAG 60.110 55.000 0.00 0.00 0.00 1.85
141 142 1.223187 CGGGTCACAGCGTTTTTAGT 58.777 50.000 0.00 0.00 0.00 2.24
142 143 2.406130 CGGGTCACAGCGTTTTTAGTA 58.594 47.619 0.00 0.00 0.00 1.82
143 144 2.156310 CGGGTCACAGCGTTTTTAGTAC 59.844 50.000 0.00 0.00 0.00 2.73
144 145 3.396560 GGGTCACAGCGTTTTTAGTACT 58.603 45.455 0.00 0.00 0.00 2.73
145 146 4.559153 GGGTCACAGCGTTTTTAGTACTA 58.441 43.478 0.00 0.00 0.00 1.82
146 147 5.173664 GGGTCACAGCGTTTTTAGTACTAT 58.826 41.667 2.79 0.00 0.00 2.12
147 148 6.332630 GGGTCACAGCGTTTTTAGTACTATA 58.667 40.000 2.79 0.00 0.00 1.31
148 149 6.982724 GGGTCACAGCGTTTTTAGTACTATAT 59.017 38.462 2.79 0.00 0.00 0.86
149 150 7.042925 GGGTCACAGCGTTTTTAGTACTATATG 60.043 40.741 2.79 0.00 0.00 1.78
150 151 7.490402 GGTCACAGCGTTTTTAGTACTATATGT 59.510 37.037 2.79 0.00 0.00 2.29
151 152 8.866956 GTCACAGCGTTTTTAGTACTATATGTT 58.133 33.333 2.79 0.00 0.00 2.71
164 165 8.888579 AGTACTATATGTTATTCACTTGCCAC 57.111 34.615 0.00 0.00 0.00 5.01
165 166 8.482943 AGTACTATATGTTATTCACTTGCCACA 58.517 33.333 0.00 0.00 0.00 4.17
166 167 7.792374 ACTATATGTTATTCACTTGCCACAG 57.208 36.000 0.00 0.00 0.00 3.66
167 168 7.564793 ACTATATGTTATTCACTTGCCACAGA 58.435 34.615 0.00 0.00 0.00 3.41
168 169 8.046708 ACTATATGTTATTCACTTGCCACAGAA 58.953 33.333 0.00 0.00 0.00 3.02
169 170 5.633830 ATGTTATTCACTTGCCACAGAAG 57.366 39.130 0.00 0.00 0.00 2.85
170 171 4.460263 TGTTATTCACTTGCCACAGAAGT 58.540 39.130 0.00 0.00 33.82 3.01
182 183 1.330521 CACAGAAGTGGTGGTTGTTCG 59.669 52.381 0.00 0.00 42.13 3.95
183 184 1.065709 ACAGAAGTGGTGGTTGTTCGT 60.066 47.619 0.00 0.00 0.00 3.85
184 185 2.014128 CAGAAGTGGTGGTTGTTCGTT 58.986 47.619 0.00 0.00 0.00 3.85
185 186 3.199677 CAGAAGTGGTGGTTGTTCGTTA 58.800 45.455 0.00 0.00 0.00 3.18
186 187 3.813166 CAGAAGTGGTGGTTGTTCGTTAT 59.187 43.478 0.00 0.00 0.00 1.89
187 188 4.274950 CAGAAGTGGTGGTTGTTCGTTATT 59.725 41.667 0.00 0.00 0.00 1.40
188 189 4.885325 AGAAGTGGTGGTTGTTCGTTATTT 59.115 37.500 0.00 0.00 0.00 1.40
189 190 5.358725 AGAAGTGGTGGTTGTTCGTTATTTT 59.641 36.000 0.00 0.00 0.00 1.82
190 191 5.177725 AGTGGTGGTTGTTCGTTATTTTC 57.822 39.130 0.00 0.00 0.00 2.29
191 192 3.969981 GTGGTGGTTGTTCGTTATTTTCG 59.030 43.478 0.00 0.00 0.00 3.46
192 193 3.875727 TGGTGGTTGTTCGTTATTTTCGA 59.124 39.130 0.00 0.00 35.50 3.71
193 194 4.213674 GGTGGTTGTTCGTTATTTTCGAC 58.786 43.478 0.00 0.00 37.05 4.20
194 195 4.213674 GTGGTTGTTCGTTATTTTCGACC 58.786 43.478 0.00 0.00 37.05 4.79
195 196 3.875727 TGGTTGTTCGTTATTTTCGACCA 59.124 39.130 0.00 0.00 37.05 4.02
196 197 4.334759 TGGTTGTTCGTTATTTTCGACCAA 59.665 37.500 0.00 0.00 37.37 3.67
197 198 4.907582 GGTTGTTCGTTATTTTCGACCAAG 59.092 41.667 0.00 0.00 39.49 3.61
198 199 5.504392 GTTGTTCGTTATTTTCGACCAAGT 58.496 37.500 0.00 0.00 39.49 3.16
199 200 5.738118 TGTTCGTTATTTTCGACCAAGTT 57.262 34.783 0.00 0.00 37.05 2.66
200 201 5.503498 TGTTCGTTATTTTCGACCAAGTTG 58.497 37.500 0.00 0.00 37.05 3.16
201 202 4.735662 TCGTTATTTTCGACCAAGTTGG 57.264 40.909 20.76 20.76 45.02 3.77
212 213 2.888834 CCAAGTTGGTGGTTTTGGAG 57.111 50.000 14.21 0.00 42.05 3.86
213 214 2.107366 CCAAGTTGGTGGTTTTGGAGT 58.893 47.619 14.21 0.00 42.05 3.85
214 215 3.292460 CCAAGTTGGTGGTTTTGGAGTA 58.708 45.455 14.21 0.00 42.05 2.59
215 216 3.067601 CCAAGTTGGTGGTTTTGGAGTAC 59.932 47.826 14.21 0.00 42.05 2.73
216 217 2.940158 AGTTGGTGGTTTTGGAGTACC 58.060 47.619 0.00 0.00 34.93 3.34
217 218 1.958579 GTTGGTGGTTTTGGAGTACCC 59.041 52.381 0.00 0.00 33.34 3.69
218 219 1.525175 TGGTGGTTTTGGAGTACCCT 58.475 50.000 0.00 0.00 33.34 4.34
219 220 2.703947 TGGTGGTTTTGGAGTACCCTA 58.296 47.619 0.00 0.00 33.34 3.53
220 221 2.640826 TGGTGGTTTTGGAGTACCCTAG 59.359 50.000 0.00 0.00 33.34 3.02
221 222 2.617276 GGTGGTTTTGGAGTACCCTAGC 60.617 54.545 0.00 0.00 33.34 3.42
222 223 1.631898 TGGTTTTGGAGTACCCTAGCC 59.368 52.381 0.00 0.00 33.34 3.93
223 224 1.631898 GGTTTTGGAGTACCCTAGCCA 59.368 52.381 0.00 0.00 35.38 4.75
224 225 2.617276 GGTTTTGGAGTACCCTAGCCAC 60.617 54.545 0.00 0.00 35.38 5.01
225 226 2.032965 TTTGGAGTACCCTAGCCACA 57.967 50.000 0.00 0.00 35.38 4.17
226 227 2.032965 TTGGAGTACCCTAGCCACAA 57.967 50.000 0.00 0.00 35.38 3.33
227 228 2.032965 TGGAGTACCCTAGCCACAAA 57.967 50.000 0.00 0.00 35.38 2.83
228 229 2.557869 TGGAGTACCCTAGCCACAAAT 58.442 47.619 0.00 0.00 35.38 2.32
229 230 2.504175 TGGAGTACCCTAGCCACAAATC 59.496 50.000 0.00 0.00 35.38 2.17
230 231 2.772515 GGAGTACCCTAGCCACAAATCT 59.227 50.000 0.00 0.00 0.00 2.40
231 232 3.432326 GGAGTACCCTAGCCACAAATCTG 60.432 52.174 0.00 0.00 0.00 2.90
232 233 2.505819 AGTACCCTAGCCACAAATCTGG 59.494 50.000 0.00 0.00 0.00 3.86
233 234 1.372501 ACCCTAGCCACAAATCTGGT 58.627 50.000 0.00 0.00 33.30 4.00
234 235 1.004745 ACCCTAGCCACAAATCTGGTG 59.995 52.381 0.00 0.00 33.30 4.17
242 243 3.110447 CACAAATCTGGTGGTTTTGGG 57.890 47.619 0.00 0.00 38.33 4.12
243 244 1.416030 ACAAATCTGGTGGTTTTGGGC 59.584 47.619 0.00 0.00 38.33 5.36
244 245 1.415659 CAAATCTGGTGGTTTTGGGCA 59.584 47.619 0.00 0.00 33.41 5.36
245 246 1.799933 AATCTGGTGGTTTTGGGCAA 58.200 45.000 0.00 0.00 0.00 4.52
246 247 2.028561 ATCTGGTGGTTTTGGGCAAT 57.971 45.000 0.00 0.00 0.00 3.56
247 248 1.799933 TCTGGTGGTTTTGGGCAATT 58.200 45.000 0.00 0.00 0.00 2.32
248 249 2.964209 TCTGGTGGTTTTGGGCAATTA 58.036 42.857 0.00 0.00 0.00 1.40
249 250 3.309296 TCTGGTGGTTTTGGGCAATTAA 58.691 40.909 0.00 0.00 0.00 1.40
250 251 3.070302 TCTGGTGGTTTTGGGCAATTAAC 59.930 43.478 0.00 0.00 0.00 2.01
251 252 3.041946 TGGTGGTTTTGGGCAATTAACT 58.958 40.909 0.00 0.00 0.00 2.24
252 253 3.070302 TGGTGGTTTTGGGCAATTAACTC 59.930 43.478 0.00 0.00 0.00 3.01
253 254 3.070302 GGTGGTTTTGGGCAATTAACTCA 59.930 43.478 0.00 0.00 0.00 3.41
254 255 4.055360 GTGGTTTTGGGCAATTAACTCAC 58.945 43.478 0.00 0.00 0.00 3.51
255 256 3.243569 TGGTTTTGGGCAATTAACTCACG 60.244 43.478 0.00 0.00 0.00 4.35
256 257 3.313690 GTTTTGGGCAATTAACTCACGG 58.686 45.455 0.00 0.00 0.00 4.94
257 258 0.885196 TTGGGCAATTAACTCACGGC 59.115 50.000 0.00 0.00 0.00 5.68
258 259 1.302383 TGGGCAATTAACTCACGGCG 61.302 55.000 4.80 4.80 0.00 6.46
259 260 1.022451 GGGCAATTAACTCACGGCGA 61.022 55.000 16.62 0.00 0.00 5.54
260 261 0.096454 GGCAATTAACTCACGGCGAC 59.904 55.000 16.62 0.00 0.00 5.19
389 390 6.971184 GGAAGATTTCTGCAACATTAGTCATG 59.029 38.462 0.00 0.00 39.07 3.07
604 605 9.817365 CAAGATAATCTGTCTTACAAGTGTTTG 57.183 33.333 0.00 0.00 35.82 2.93
613 614 7.872881 TGTCTTACAAGTGTTTGTACAACAAA 58.127 30.769 8.07 1.21 46.53 2.83
631 632 4.439057 ACAAAGTCTCTGTTGCGAAGTAA 58.561 39.130 0.00 0.00 0.00 2.24
674 675 2.971660 TTATCAAATCCGACGGCTCA 57.028 45.000 9.66 0.00 0.00 4.26
858 859 5.485708 ACTCTCTTAATTAAGGGCTGACACT 59.514 40.000 22.11 0.78 33.78 3.55
1209 1248 3.257624 ACGTCTACACCCGATTCTTTCTT 59.742 43.478 0.00 0.00 0.00 2.52
1266 1320 5.929415 GTGTAAGCAGCCTCTATATTTCTCC 59.071 44.000 0.00 0.00 0.00 3.71
1403 1626 7.544622 ACATGCCATGCTCATCATTAAATATC 58.455 34.615 4.17 0.00 31.79 1.63
1733 3242 0.532573 TTGGGCTAGAAGACTCTGCG 59.467 55.000 0.00 0.00 32.70 5.18
2810 4428 5.734720 AGTGATGTGGTCCACTAAGTTATG 58.265 41.667 22.56 0.00 41.38 1.90
2965 4591 2.857104 GCACTTGGCGTTTTGTTAGACC 60.857 50.000 0.00 0.00 0.00 3.85
3608 5387 7.649306 AGACAAACAACTCATGATTTTTACAGC 59.351 33.333 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.760047 TTGGCTCGCCCTCTTCGC 62.760 66.667 5.33 0.00 34.56 4.70
6 7 2.604686 TCTGTTGGCTCGCCCTCT 60.605 61.111 5.33 0.00 34.56 3.69
7 8 2.125350 CTCTGTTGGCTCGCCCTC 60.125 66.667 5.33 0.00 34.56 4.30
8 9 2.520536 AACTCTGTTGGCTCGCCCT 61.521 57.895 5.33 0.00 34.56 5.19
9 10 2.032681 AACTCTGTTGGCTCGCCC 59.967 61.111 5.33 0.00 34.56 6.13
10 11 1.301716 TCAACTCTGTTGGCTCGCC 60.302 57.895 10.05 0.00 0.00 5.54
11 12 1.862806 GTCAACTCTGTTGGCTCGC 59.137 57.895 7.66 0.00 0.00 5.03
12 13 0.318699 TCGTCAACTCTGTTGGCTCG 60.319 55.000 12.23 12.54 0.00 5.03
13 14 1.423395 CTCGTCAACTCTGTTGGCTC 58.577 55.000 12.23 3.45 0.00 4.70
14 15 0.601311 GCTCGTCAACTCTGTTGGCT 60.601 55.000 12.23 0.00 0.00 4.75
15 16 1.862806 GCTCGTCAACTCTGTTGGC 59.137 57.895 10.05 7.65 0.00 4.52
16 17 1.284982 CCGCTCGTCAACTCTGTTGG 61.285 60.000 10.05 0.00 0.00 3.77
17 18 1.284982 CCCGCTCGTCAACTCTGTTG 61.285 60.000 4.25 4.25 0.00 3.33
18 19 1.006102 CCCGCTCGTCAACTCTGTT 60.006 57.895 0.00 0.00 0.00 3.16
19 20 2.651361 CCCGCTCGTCAACTCTGT 59.349 61.111 0.00 0.00 0.00 3.41
20 21 2.125912 CCCCGCTCGTCAACTCTG 60.126 66.667 0.00 0.00 0.00 3.35
21 22 3.382832 CCCCCGCTCGTCAACTCT 61.383 66.667 0.00 0.00 0.00 3.24
22 23 2.444700 TTTCCCCCGCTCGTCAACTC 62.445 60.000 0.00 0.00 0.00 3.01
23 24 2.513259 TTTCCCCCGCTCGTCAACT 61.513 57.895 0.00 0.00 0.00 3.16
24 25 2.031465 TTTCCCCCGCTCGTCAAC 59.969 61.111 0.00 0.00 0.00 3.18
25 26 2.031465 GTTTCCCCCGCTCGTCAA 59.969 61.111 0.00 0.00 0.00 3.18
26 27 4.367023 CGTTTCCCCCGCTCGTCA 62.367 66.667 0.00 0.00 0.00 4.35
53 54 4.530857 CAGGGCTAACGGCGGAGG 62.531 72.222 13.24 0.91 42.94 4.30
54 55 4.530857 CCAGGGCTAACGGCGGAG 62.531 72.222 13.24 9.45 42.94 4.63
61 62 2.746277 CACGTGGCCAGGGCTAAC 60.746 66.667 28.01 10.23 41.60 2.34
62 63 4.028490 CCACGTGGCCAGGGCTAA 62.028 66.667 28.01 0.00 41.60 3.09
72 73 4.373116 CCTGTCGGGACCACGTGG 62.373 72.222 32.83 32.83 42.17 4.94
90 91 2.898920 AATCTGACATGCCTGGCCCG 62.899 60.000 17.53 9.64 0.00 6.13
91 92 1.076485 AATCTGACATGCCTGGCCC 60.076 57.895 17.53 3.41 0.00 5.80
92 93 1.442526 CGAATCTGACATGCCTGGCC 61.443 60.000 17.53 0.00 0.00 5.36
93 94 2.020131 CGAATCTGACATGCCTGGC 58.980 57.895 12.87 12.87 0.00 4.85
94 95 0.745486 TGCGAATCTGACATGCCTGG 60.745 55.000 0.00 0.00 0.00 4.45
95 96 0.376152 GTGCGAATCTGACATGCCTG 59.624 55.000 0.00 0.00 0.00 4.85
96 97 0.251354 AGTGCGAATCTGACATGCCT 59.749 50.000 0.00 0.00 0.00 4.75
97 98 1.089920 AAGTGCGAATCTGACATGCC 58.910 50.000 0.00 0.00 0.00 4.40
98 99 2.286067 GCTAAGTGCGAATCTGACATGC 60.286 50.000 0.00 0.00 0.00 4.06
99 100 2.286294 GGCTAAGTGCGAATCTGACATG 59.714 50.000 0.00 0.00 44.05 3.21
100 101 2.555199 GGCTAAGTGCGAATCTGACAT 58.445 47.619 0.00 0.00 44.05 3.06
101 102 1.735700 CGGCTAAGTGCGAATCTGACA 60.736 52.381 0.00 0.00 44.05 3.58
102 103 0.924090 CGGCTAAGTGCGAATCTGAC 59.076 55.000 0.00 0.00 44.05 3.51
103 104 0.806102 GCGGCTAAGTGCGAATCTGA 60.806 55.000 0.00 0.00 44.05 3.27
104 105 1.638467 GCGGCTAAGTGCGAATCTG 59.362 57.895 0.00 0.00 44.05 2.90
105 106 4.110493 GCGGCTAAGTGCGAATCT 57.890 55.556 0.00 0.00 44.05 2.40
111 112 4.752879 TGACCCGCGGCTAAGTGC 62.753 66.667 22.85 7.14 41.94 4.40
112 113 2.813908 GTGACCCGCGGCTAAGTG 60.814 66.667 22.85 7.58 0.00 3.16
113 114 3.296709 CTGTGACCCGCGGCTAAGT 62.297 63.158 22.85 12.87 0.00 2.24
114 115 2.509336 CTGTGACCCGCGGCTAAG 60.509 66.667 22.85 8.91 0.00 2.18
115 116 4.752879 GCTGTGACCCGCGGCTAA 62.753 66.667 22.85 3.19 42.28 3.09
121 122 0.110373 CTAAAAACGCTGTGACCCGC 60.110 55.000 0.00 0.00 0.00 6.13
122 123 1.223187 ACTAAAAACGCTGTGACCCG 58.777 50.000 0.00 0.00 0.00 5.28
123 124 3.396560 AGTACTAAAAACGCTGTGACCC 58.603 45.455 0.00 0.00 0.00 4.46
124 125 7.490402 ACATATAGTACTAAAAACGCTGTGACC 59.510 37.037 6.70 0.00 0.00 4.02
125 126 8.403606 ACATATAGTACTAAAAACGCTGTGAC 57.596 34.615 6.70 0.00 0.00 3.67
126 127 8.991243 AACATATAGTACTAAAAACGCTGTGA 57.009 30.769 6.70 0.00 0.00 3.58
138 139 9.976511 GTGGCAAGTGAATAACATATAGTACTA 57.023 33.333 4.77 4.77 0.00 1.82
139 140 8.482943 TGTGGCAAGTGAATAACATATAGTACT 58.517 33.333 0.00 0.00 0.00 2.73
140 141 8.657074 TGTGGCAAGTGAATAACATATAGTAC 57.343 34.615 0.00 0.00 0.00 2.73
141 142 8.700973 TCTGTGGCAAGTGAATAACATATAGTA 58.299 33.333 0.00 0.00 0.00 1.82
142 143 7.564793 TCTGTGGCAAGTGAATAACATATAGT 58.435 34.615 0.00 0.00 0.00 2.12
143 144 8.437360 TTCTGTGGCAAGTGAATAACATATAG 57.563 34.615 0.00 0.00 0.00 1.31
144 145 8.046708 ACTTCTGTGGCAAGTGAATAACATATA 58.953 33.333 0.00 0.00 32.65 0.86
145 146 6.886459 ACTTCTGTGGCAAGTGAATAACATAT 59.114 34.615 0.00 0.00 32.65 1.78
146 147 6.237901 ACTTCTGTGGCAAGTGAATAACATA 58.762 36.000 0.00 0.00 32.65 2.29
147 148 5.072741 ACTTCTGTGGCAAGTGAATAACAT 58.927 37.500 0.00 0.00 32.65 2.71
148 149 4.460263 ACTTCTGTGGCAAGTGAATAACA 58.540 39.130 0.00 0.00 32.65 2.41
162 163 1.330521 CGAACAACCACCACTTCTGTG 59.669 52.381 0.00 0.00 43.45 3.66
163 164 1.065709 ACGAACAACCACCACTTCTGT 60.066 47.619 0.00 0.00 0.00 3.41
164 165 1.663695 ACGAACAACCACCACTTCTG 58.336 50.000 0.00 0.00 0.00 3.02
165 166 2.413310 AACGAACAACCACCACTTCT 57.587 45.000 0.00 0.00 0.00 2.85
166 167 4.823790 AATAACGAACAACCACCACTTC 57.176 40.909 0.00 0.00 0.00 3.01
167 168 5.584442 GAAAATAACGAACAACCACCACTT 58.416 37.500 0.00 0.00 0.00 3.16
168 169 4.260866 CGAAAATAACGAACAACCACCACT 60.261 41.667 0.00 0.00 0.00 4.00
169 170 3.969981 CGAAAATAACGAACAACCACCAC 59.030 43.478 0.00 0.00 0.00 4.16
170 171 3.875727 TCGAAAATAACGAACAACCACCA 59.124 39.130 0.00 0.00 36.84 4.17
171 172 4.213674 GTCGAAAATAACGAACAACCACC 58.786 43.478 0.00 0.00 41.31 4.61
172 173 4.213674 GGTCGAAAATAACGAACAACCAC 58.786 43.478 0.00 0.00 45.18 4.16
173 174 4.471157 GGTCGAAAATAACGAACAACCA 57.529 40.909 0.00 0.00 45.18 3.67
178 179 4.907582 CCAACTTGGTCGAAAATAACGAAC 59.092 41.667 0.00 0.00 45.90 3.95
179 180 5.098218 CCAACTTGGTCGAAAATAACGAA 57.902 39.130 0.00 0.00 41.31 3.85
180 181 4.735662 CCAACTTGGTCGAAAATAACGA 57.264 40.909 0.00 0.00 37.43 3.85
193 194 2.107366 ACTCCAAAACCACCAACTTGG 58.893 47.619 6.24 6.24 45.02 3.61
194 195 3.067601 GGTACTCCAAAACCACCAACTTG 59.932 47.826 0.00 0.00 35.73 3.16
195 196 3.293337 GGTACTCCAAAACCACCAACTT 58.707 45.455 0.00 0.00 35.73 2.66
196 197 2.423803 GGGTACTCCAAAACCACCAACT 60.424 50.000 0.00 0.00 37.51 3.16
197 198 1.958579 GGGTACTCCAAAACCACCAAC 59.041 52.381 0.00 0.00 37.51 3.77
198 199 1.854280 AGGGTACTCCAAAACCACCAA 59.146 47.619 0.00 0.00 37.51 3.67
199 200 1.525175 AGGGTACTCCAAAACCACCA 58.475 50.000 0.00 0.00 37.51 4.17
200 201 2.617276 GCTAGGGTACTCCAAAACCACC 60.617 54.545 0.00 0.00 37.51 4.61
201 202 2.617276 GGCTAGGGTACTCCAAAACCAC 60.617 54.545 0.00 0.00 37.51 4.16
202 203 1.631898 GGCTAGGGTACTCCAAAACCA 59.368 52.381 0.00 0.00 37.51 3.67
203 204 1.631898 TGGCTAGGGTACTCCAAAACC 59.368 52.381 0.00 0.00 38.24 3.27
204 205 2.039348 TGTGGCTAGGGTACTCCAAAAC 59.961 50.000 0.00 0.00 38.24 2.43
205 206 2.340731 TGTGGCTAGGGTACTCCAAAA 58.659 47.619 0.00 0.00 38.24 2.44
206 207 2.032965 TGTGGCTAGGGTACTCCAAA 57.967 50.000 0.00 0.00 38.24 3.28
207 208 2.032965 TTGTGGCTAGGGTACTCCAA 57.967 50.000 0.00 0.00 38.24 3.53
208 209 2.032965 TTTGTGGCTAGGGTACTCCA 57.967 50.000 0.00 0.00 38.24 3.86
209 210 2.772515 AGATTTGTGGCTAGGGTACTCC 59.227 50.000 0.00 0.00 0.00 3.85
210 211 3.432326 CCAGATTTGTGGCTAGGGTACTC 60.432 52.174 0.00 0.00 0.00 2.59
211 212 2.505819 CCAGATTTGTGGCTAGGGTACT 59.494 50.000 0.00 0.00 0.00 2.73
212 213 2.238898 ACCAGATTTGTGGCTAGGGTAC 59.761 50.000 0.00 0.00 41.90 3.34
213 214 2.238646 CACCAGATTTGTGGCTAGGGTA 59.761 50.000 0.00 0.00 41.90 3.69
214 215 1.004745 CACCAGATTTGTGGCTAGGGT 59.995 52.381 0.00 0.00 41.90 4.34
215 216 1.683011 CCACCAGATTTGTGGCTAGGG 60.683 57.143 0.00 0.00 46.13 3.53
216 217 1.755179 CCACCAGATTTGTGGCTAGG 58.245 55.000 0.00 0.00 46.13 3.02
222 223 2.806382 GCCCAAAACCACCAGATTTGTG 60.806 50.000 0.00 0.00 33.31 3.33
223 224 1.416030 GCCCAAAACCACCAGATTTGT 59.584 47.619 0.00 0.00 33.31 2.83
224 225 1.415659 TGCCCAAAACCACCAGATTTG 59.584 47.619 0.00 0.00 34.60 2.32
225 226 1.799933 TGCCCAAAACCACCAGATTT 58.200 45.000 0.00 0.00 0.00 2.17
226 227 1.799933 TTGCCCAAAACCACCAGATT 58.200 45.000 0.00 0.00 0.00 2.40
227 228 2.028561 ATTGCCCAAAACCACCAGAT 57.971 45.000 0.00 0.00 0.00 2.90
228 229 1.799933 AATTGCCCAAAACCACCAGA 58.200 45.000 0.00 0.00 0.00 3.86
229 230 3.070878 AGTTAATTGCCCAAAACCACCAG 59.929 43.478 0.00 0.00 0.00 4.00
230 231 3.041946 AGTTAATTGCCCAAAACCACCA 58.958 40.909 0.00 0.00 0.00 4.17
231 232 3.070302 TGAGTTAATTGCCCAAAACCACC 59.930 43.478 0.00 0.00 0.00 4.61
232 233 4.055360 GTGAGTTAATTGCCCAAAACCAC 58.945 43.478 0.00 0.00 0.00 4.16
233 234 3.243569 CGTGAGTTAATTGCCCAAAACCA 60.244 43.478 0.00 0.00 0.00 3.67
234 235 3.313690 CGTGAGTTAATTGCCCAAAACC 58.686 45.455 0.00 0.00 0.00 3.27
235 236 3.313690 CCGTGAGTTAATTGCCCAAAAC 58.686 45.455 0.00 0.00 0.00 2.43
236 237 2.288518 GCCGTGAGTTAATTGCCCAAAA 60.289 45.455 0.00 0.00 0.00 2.44
237 238 1.271102 GCCGTGAGTTAATTGCCCAAA 59.729 47.619 0.00 0.00 0.00 3.28
238 239 0.885196 GCCGTGAGTTAATTGCCCAA 59.115 50.000 0.00 0.00 0.00 4.12
239 240 1.302383 CGCCGTGAGTTAATTGCCCA 61.302 55.000 0.00 0.00 0.00 5.36
240 241 1.022451 TCGCCGTGAGTTAATTGCCC 61.022 55.000 0.00 0.00 0.00 5.36
241 242 0.096454 GTCGCCGTGAGTTAATTGCC 59.904 55.000 0.00 0.00 0.00 4.52
242 243 0.247145 CGTCGCCGTGAGTTAATTGC 60.247 55.000 0.00 0.00 0.00 3.56
243 244 0.247145 GCGTCGCCGTGAGTTAATTG 60.247 55.000 5.75 0.00 36.15 2.32
244 245 2.075761 GCGTCGCCGTGAGTTAATT 58.924 52.632 5.75 0.00 36.15 1.40
245 246 3.776656 GCGTCGCCGTGAGTTAAT 58.223 55.556 5.75 0.00 36.15 1.40
257 258 2.586079 ATCCTTGCCATCGCGTCG 60.586 61.111 5.77 0.00 38.08 5.12
258 259 2.537560 CCATCCTTGCCATCGCGTC 61.538 63.158 5.77 0.00 38.08 5.19
259 260 2.514592 CCATCCTTGCCATCGCGT 60.515 61.111 5.77 0.00 38.08 6.01
260 261 3.282157 CCCATCCTTGCCATCGCG 61.282 66.667 0.00 0.00 38.08 5.87
261 262 3.599704 GCCCATCCTTGCCATCGC 61.600 66.667 0.00 0.00 0.00 4.58
613 614 4.585955 TCTTTACTTCGCAACAGAGACT 57.414 40.909 0.00 0.00 0.00 3.24
631 632 0.320771 AGCGGATGCACGTCTTTCTT 60.321 50.000 0.00 0.00 46.23 2.52
674 675 0.252197 AAAAAGATCCGCCGCCTAGT 59.748 50.000 0.00 0.00 0.00 2.57
701 702 3.261951 CTACGCATCGGCCGTTGG 61.262 66.667 31.52 24.08 36.38 3.77
703 704 4.444838 TGCTACGCATCGGCCGTT 62.445 61.111 27.15 15.26 36.38 4.44
704 705 4.873129 CTGCTACGCATCGGCCGT 62.873 66.667 27.15 10.00 38.13 5.68
830 831 5.421056 TCAGCCCTTAATTAAGAGAGTTCGA 59.579 40.000 23.95 9.65 35.33 3.71
858 859 3.050089 GGCCAATGGTCCAACTGAA 57.950 52.632 0.00 0.00 0.00 3.02
1209 1248 5.977489 TGTCAAAGACGGAGAAATCTCTA 57.023 39.130 10.09 0.00 42.48 2.43
1403 1626 4.968626 TCGTTGTTTACTGCTATGCATTG 58.031 39.130 3.54 3.55 38.13 2.82
1521 2992 2.357009 GAGAGTAAACTATCGTCCCGCA 59.643 50.000 0.00 0.00 0.00 5.69
2516 4049 4.051922 CAGATAGTAATGACACTTCGCCC 58.948 47.826 0.00 0.00 0.00 6.13
2876 4498 7.654568 TCAGTATAACACTCCACCATAATACG 58.345 38.462 0.00 0.00 34.26 3.06
2919 4544 8.749499 GCACTAATCTGCTTTAATTATGCAAAG 58.251 33.333 12.62 5.02 36.59 2.77
2965 4591 7.672983 ATGTTCATATTTCCGCCTAATACAG 57.327 36.000 0.00 0.00 0.00 2.74
3434 5112 9.151471 GTCGTAAATTAGCATATCCACATATGT 57.849 33.333 1.41 1.41 42.84 2.29
3608 5387 9.955208 TGCATAACTTAAGAGCAAAATCATATG 57.045 29.630 10.09 0.00 31.42 1.78


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

AutoCloner maintained by Alex Coulton.