Multiple sequence alignment - TraesCS2D01G364400

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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 TraesCS2D01G364400 chr2D 100.000 3116 0 0 1 3116 469999004 470002119 0.000000e+00 5755.0
1 TraesCS2D01G364400 chr2B 91.025 2440 128 49 273 2661 548649989 548652388 0.000000e+00 3208.0
2 TraesCS2D01G364400 chr2B 83.607 244 21 7 367 604 548630301 548630531 8.760000e-51 211.0
3 TraesCS2D01G364400 chr2A 93.401 2182 101 21 273 2447 611309698 611311843 0.000000e+00 3192.0
4 TraesCS2D01G364400 chr2A 88.204 373 27 9 2754 3116 611312192 611312557 2.220000e-116 429.0
5 TraesCS2D01G364400 chr2A 83.273 275 17 9 2460 2725 611311824 611312078 3.130000e-55 226.0
6 TraesCS2D01G364400 chr7D 90.954 608 46 6 683 1288 418398831 418398231 0.000000e+00 809.0
7 TraesCS2D01G364400 chr7D 96.296 270 9 1 1 269 78862451 78862182 2.850000e-120 442.0
8 TraesCS2D01G364400 chr7D 96.269 268 9 1 1 267 16184624 16184357 3.690000e-119 438.0
9 TraesCS2D01G364400 chr7D 85.000 80 8 3 2662 2737 42837304 42837383 9.260000e-11 78.7
10 TraesCS2D01G364400 chr7D 88.000 50 2 3 3028 3076 27423349 27423395 4.340000e-04 56.5
11 TraesCS2D01G364400 chr5D 80.387 724 110 28 1045 1750 292698750 292698041 3.560000e-144 521.0
12 TraesCS2D01G364400 chr5D 84.132 334 48 3 1784 2116 292695793 292695464 5.010000e-83 318.0
13 TraesCS2D01G364400 chr5D 85.542 83 6 4 2662 2739 386689276 386689195 7.160000e-12 82.4
14 TraesCS2D01G364400 chr5A 82.248 614 87 18 1146 1750 385398457 385397857 7.710000e-141 510.0
15 TraesCS2D01G364400 chr5A 83.284 341 50 6 1778 2116 385395798 385395463 1.090000e-79 307.0
16 TraesCS2D01G364400 chr5B 81.506 611 96 13 1146 1750 333256470 333255871 1.300000e-133 486.0
17 TraesCS2D01G364400 chr5B 83.234 334 51 3 1784 2116 333252579 333252250 5.050000e-78 302.0
18 TraesCS2D01G364400 chr5B 86.667 75 10 0 2662 2736 654927017 654926943 1.990000e-12 84.2
19 TraesCS2D01G364400 chr5B 88.889 63 2 3 2680 2737 638487222 638487284 4.310000e-09 73.1
20 TraesCS2D01G364400 chr5B 83.824 68 10 1 3031 3098 610023417 610023483 2.590000e-06 63.9
21 TraesCS2D01G364400 chr6D 95.699 279 10 2 1 277 10676312 10676590 6.130000e-122 448.0
22 TraesCS2D01G364400 chr6D 95.588 272 11 1 1 271 386157087 386156816 4.770000e-118 435.0
23 TraesCS2D01G364400 chr6A 96.654 269 8 1 1 268 286335693 286335425 2.200000e-121 446.0
24 TraesCS2D01G364400 chr6A 86.047 86 7 5 3029 3112 78565292 78565374 1.540000e-13 87.9
25 TraesCS2D01G364400 chr1D 96.241 266 9 1 1 265 425566549 425566814 4.770000e-118 435.0
26 TraesCS2D01G364400 chr1D 94.796 269 14 0 1 269 29804033 29803765 1.340000e-113 420.0
27 TraesCS2D01G364400 chr1D 88.571 70 5 3 2670 2737 382919612 382919544 7.160000e-12 82.4
28 TraesCS2D01G364400 chr4D 95.849 265 11 0 1 265 28419971 28420235 2.220000e-116 429.0
29 TraesCS2D01G364400 chr4A 95.539 269 11 1 1 268 471170064 471170332 2.220000e-116 429.0
30 TraesCS2D01G364400 chr3A 83.721 86 9 4 2657 2737 46569216 46569131 3.330000e-10 76.8
31 TraesCS2D01G364400 chr3D 86.567 67 8 1 3028 3094 588210558 588210493 4.310000e-09 73.1
32 TraesCS2D01G364400 chr3D 88.000 50 5 1 3039 3088 612677378 612677330 1.210000e-04 58.4
33 TraesCS2D01G364400 chr7A 82.143 84 12 3 3031 3113 222232680 222232599 5.580000e-08 69.4
34 TraesCS2D01G364400 chr1A 91.304 46 2 1 3032 3077 445549886 445549843 9.330000e-06 62.1
35 TraesCS2D01G364400 chr6B 82.192 73 9 3 3030 3099 255468980 255468909 3.360000e-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 TraesCS2D01G364400 chr2D 469999004 470002119 3115 False 5755.000000 5755 100.000000 1 3116 1 chr2D.!!$F1 3115
1 TraesCS2D01G364400 chr2B 548649989 548652388 2399 False 3208.000000 3208 91.025000 273 2661 1 chr2B.!!$F2 2388
2 TraesCS2D01G364400 chr2A 611309698 611312557 2859 False 1282.333333 3192 88.292667 273 3116 3 chr2A.!!$F1 2843
3 TraesCS2D01G364400 chr7D 418398231 418398831 600 True 809.000000 809 90.954000 683 1288 1 chr7D.!!$R3 605
4 TraesCS2D01G364400 chr5D 292695464 292698750 3286 True 419.500000 521 82.259500 1045 2116 2 chr5D.!!$R2 1071
5 TraesCS2D01G364400 chr5A 385395463 385398457 2994 True 408.500000 510 82.766000 1146 2116 2 chr5A.!!$R1 970
6 TraesCS2D01G364400 chr5B 333252250 333256470 4220 True 394.000000 486 82.370000 1146 2116 2 chr5B.!!$R2 970

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
158 159 0.179097 TGAACTACATATGCCGCGCA 60.179 50.0 8.75 2.46 44.86 6.09 F
159 160 0.232303 GAACTACATATGCCGCGCAC 59.768 55.0 8.75 0.00 43.04 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1453 2.124819 AGCGATGGGAGCAAGCAG 60.125 61.111 0.0 0.0 37.01 4.24 R
2247 5727 5.064325 GCCATTTTACCGTAGTAACTCAAGG 59.936 44.000 0.0 0.0 38.19 3.61 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
55 56 3.813724 GCTGGATGGGGGTGGGAG 61.814 72.222 0.00 0.00 0.00 4.30
56 57 2.286425 CTGGATGGGGGTGGGAGT 60.286 66.667 0.00 0.00 0.00 3.85
57 58 1.930656 CTGGATGGGGGTGGGAGTT 60.931 63.158 0.00 0.00 0.00 3.01
58 59 2.215451 CTGGATGGGGGTGGGAGTTG 62.215 65.000 0.00 0.00 0.00 3.16
59 60 2.043953 GATGGGGGTGGGAGTTGC 60.044 66.667 0.00 0.00 0.00 4.17
60 61 3.995506 GATGGGGGTGGGAGTTGCG 62.996 68.421 0.00 0.00 0.00 4.85
62 63 4.410400 GGGGGTGGGAGTTGCGAG 62.410 72.222 0.00 0.00 0.00 5.03
65 66 4.373116 GGTGGGAGTTGCGAGCGA 62.373 66.667 0.00 0.00 0.00 4.93
66 67 2.811317 GTGGGAGTTGCGAGCGAG 60.811 66.667 0.00 0.00 0.00 5.03
67 68 4.742201 TGGGAGTTGCGAGCGAGC 62.742 66.667 0.00 0.00 37.71 5.03
114 115 2.951227 GCAGCAAATAAGCGGCGC 60.951 61.111 26.86 26.86 45.03 6.53
115 116 2.648724 CAGCAAATAAGCGGCGCG 60.649 61.111 27.59 12.27 40.15 6.86
126 127 4.147322 CGGCGCGCGATTGAGTTT 62.147 61.111 37.18 0.00 0.00 2.66
127 128 2.276680 GGCGCGCGATTGAGTTTC 60.277 61.111 37.18 12.28 0.00 2.78
128 129 2.641663 GCGCGCGATTGAGTTTCG 60.642 61.111 37.18 0.41 39.55 3.46
129 130 2.020016 CGCGCGATTGAGTTTCGG 59.980 61.111 28.94 0.00 37.10 4.30
130 131 2.276680 GCGCGATTGAGTTTCGGC 60.277 61.111 12.10 0.00 37.10 5.54
131 132 2.399611 CGCGATTGAGTTTCGGCC 59.600 61.111 0.00 0.00 37.10 6.13
132 133 2.791927 GCGATTGAGTTTCGGCCC 59.208 61.111 0.00 0.00 37.10 5.80
133 134 3.089784 CGATTGAGTTTCGGCCCG 58.910 61.111 0.00 0.00 33.05 6.13
134 135 2.791927 GATTGAGTTTCGGCCCGC 59.208 61.111 0.00 0.00 0.00 6.13
135 136 3.095898 GATTGAGTTTCGGCCCGCG 62.096 63.158 0.00 0.00 0.00 6.46
145 146 4.752879 GGCCCGCGCACTGAACTA 62.753 66.667 8.75 0.00 36.38 2.24
146 147 3.488090 GCCCGCGCACTGAACTAC 61.488 66.667 8.75 0.00 34.03 2.73
147 148 2.048597 CCCGCGCACTGAACTACA 60.049 61.111 8.75 0.00 0.00 2.74
148 149 1.447838 CCCGCGCACTGAACTACAT 60.448 57.895 8.75 0.00 0.00 2.29
149 150 0.179121 CCCGCGCACTGAACTACATA 60.179 55.000 8.75 0.00 0.00 2.29
150 151 1.538204 CCCGCGCACTGAACTACATAT 60.538 52.381 8.75 0.00 0.00 1.78
151 152 1.522676 CCGCGCACTGAACTACATATG 59.477 52.381 8.75 0.00 0.00 1.78
152 153 1.071239 CGCGCACTGAACTACATATGC 60.071 52.381 8.75 0.00 37.24 3.14
153 154 1.261619 GCGCACTGAACTACATATGCC 59.738 52.381 0.30 0.00 37.27 4.40
154 155 1.522676 CGCACTGAACTACATATGCCG 59.477 52.381 1.58 0.00 37.27 5.69
155 156 1.261619 GCACTGAACTACATATGCCGC 59.738 52.381 1.58 0.00 35.68 6.53
156 157 1.522676 CACTGAACTACATATGCCGCG 59.477 52.381 1.58 0.00 0.00 6.46
157 158 0.508641 CTGAACTACATATGCCGCGC 59.491 55.000 0.00 0.00 0.00 6.86
158 159 0.179097 TGAACTACATATGCCGCGCA 60.179 50.000 8.75 2.46 44.86 6.09
159 160 0.232303 GAACTACATATGCCGCGCAC 59.768 55.000 8.75 0.00 43.04 5.34
160 161 1.487452 AACTACATATGCCGCGCACG 61.487 55.000 8.75 0.00 43.04 5.34
161 162 3.281751 CTACATATGCCGCGCACGC 62.282 63.158 8.75 9.14 43.04 5.34
162 163 3.783478 TACATATGCCGCGCACGCT 62.783 57.895 16.45 5.98 43.04 5.07
163 164 4.654904 CATATGCCGCGCACGCTG 62.655 66.667 16.45 7.82 43.04 5.18
169 170 3.385999 CCGCGCACGCTGTTTTTG 61.386 61.111 13.70 0.00 39.32 2.44
170 171 4.033481 CGCGCACGCTGTTTTTGC 62.033 61.111 13.70 0.00 39.32 3.68
189 190 2.434185 CGCCCGCTGAAGCAACTA 60.434 61.111 2.79 0.00 42.21 2.24
190 191 1.815421 CGCCCGCTGAAGCAACTAT 60.815 57.895 2.79 0.00 42.21 2.12
191 192 0.529773 CGCCCGCTGAAGCAACTATA 60.530 55.000 2.79 0.00 42.21 1.31
192 193 0.938008 GCCCGCTGAAGCAACTATAC 59.062 55.000 2.79 0.00 42.21 1.47
193 194 1.583054 CCCGCTGAAGCAACTATACC 58.417 55.000 2.79 0.00 42.21 2.73
194 195 1.209128 CCGCTGAAGCAACTATACCG 58.791 55.000 2.79 0.00 42.21 4.02
195 196 1.209128 CGCTGAAGCAACTATACCGG 58.791 55.000 0.00 0.00 42.21 5.28
196 197 1.470979 CGCTGAAGCAACTATACCGGT 60.471 52.381 13.98 13.98 42.21 5.28
197 198 2.629051 GCTGAAGCAACTATACCGGTT 58.371 47.619 15.04 3.05 41.59 4.44
198 199 2.351726 GCTGAAGCAACTATACCGGTTG 59.648 50.000 15.04 5.42 44.60 3.77
199 200 3.596214 CTGAAGCAACTATACCGGTTGT 58.404 45.455 15.04 7.13 43.93 3.32
200 201 3.331150 TGAAGCAACTATACCGGTTGTG 58.669 45.455 15.04 5.55 43.93 3.33
201 202 1.734163 AGCAACTATACCGGTTGTGC 58.266 50.000 15.04 15.46 43.93 4.57
202 203 0.372334 GCAACTATACCGGTTGTGCG 59.628 55.000 15.04 6.42 43.93 5.34
203 204 0.372334 CAACTATACCGGTTGTGCGC 59.628 55.000 15.04 0.00 39.14 6.09
204 205 1.079875 AACTATACCGGTTGTGCGCG 61.080 55.000 15.04 0.00 0.00 6.86
205 206 2.867091 CTATACCGGTTGTGCGCGC 61.867 63.158 27.26 27.26 0.00 6.86
220 221 2.483288 CGCGCTAAAACGGGCAAT 59.517 55.556 5.56 0.00 42.32 3.56
221 222 1.154112 CGCGCTAAAACGGGCAATT 60.154 52.632 5.56 0.00 42.32 2.32
222 223 0.731174 CGCGCTAAAACGGGCAATTT 60.731 50.000 5.56 0.00 42.32 1.82
223 224 1.424403 GCGCTAAAACGGGCAATTTT 58.576 45.000 0.00 3.81 41.86 1.82
224 225 1.125930 GCGCTAAAACGGGCAATTTTG 59.874 47.619 0.00 0.00 41.86 2.44
251 252 4.166011 GCTAGTTTGGCGCGGCTG 62.166 66.667 33.23 16.16 0.00 4.85
252 253 2.742372 CTAGTTTGGCGCGGCTGT 60.742 61.111 33.23 16.80 0.00 4.40
253 254 2.281208 TAGTTTGGCGCGGCTGTT 60.281 55.556 33.23 17.83 0.00 3.16
254 255 2.513065 CTAGTTTGGCGCGGCTGTTG 62.513 60.000 33.23 14.34 0.00 3.33
255 256 4.999939 GTTTGGCGCGGCTGTTGG 63.000 66.667 33.23 0.00 0.00 3.77
260 261 3.869272 GCGCGGCTGTTGGAGATG 61.869 66.667 8.83 0.00 0.00 2.90
261 262 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
262 263 2.437359 GCGGCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 0.00 3.79
263 264 2.467826 GCGGCTGTTGGAGATGCTC 61.468 63.158 0.00 0.00 0.00 4.26
264 265 1.220206 CGGCTGTTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
265 266 0.392193 CGGCTGTTGGAGATGCTCTT 60.392 55.000 0.00 0.00 0.00 2.85
266 267 1.134699 CGGCTGTTGGAGATGCTCTTA 60.135 52.381 0.00 0.00 0.00 2.10
267 268 2.559440 GGCTGTTGGAGATGCTCTTAG 58.441 52.381 0.00 0.00 0.00 2.18
268 269 1.939255 GCTGTTGGAGATGCTCTTAGC 59.061 52.381 0.00 0.00 42.82 3.09
284 285 5.041951 TCTTAGCACGGCAAATTTAGTTG 57.958 39.130 0.00 0.00 0.00 3.16
289 290 3.793801 GCACGGCAAATTTAGTTGTCACA 60.794 43.478 0.00 0.00 32.46 3.58
294 295 4.038642 GGCAAATTTAGTTGTCACAAGGGA 59.961 41.667 0.00 0.00 33.19 4.20
307 308 4.275196 GTCACAAGGGACAAGTTCCTTTAC 59.725 45.833 10.12 5.88 41.80 2.01
312 313 3.462205 AGGGACAAGTTCCTTTACCAAGT 59.538 43.478 0.00 0.00 45.09 3.16
313 314 4.661709 AGGGACAAGTTCCTTTACCAAGTA 59.338 41.667 0.00 0.00 45.09 2.24
314 315 5.312443 AGGGACAAGTTCCTTTACCAAGTAT 59.688 40.000 0.00 0.00 45.09 2.12
318 319 7.282450 GGACAAGTTCCTTTACCAAGTATATGG 59.718 40.741 0.00 0.00 42.93 2.74
321 322 6.727394 AGTTCCTTTACCAAGTATATGGCAA 58.273 36.000 0.00 0.00 44.75 4.52
326 327 8.004215 TCCTTTACCAAGTATATGGCAATTCAT 58.996 33.333 0.00 0.00 44.75 2.57
330 331 9.814899 TTACCAAGTATATGGCAATTCATTTTG 57.185 29.630 0.00 0.00 44.75 2.44
338 339 4.378774 TGGCAATTCATTTTGTTGTCAGG 58.621 39.130 0.00 0.00 33.03 3.86
352 353 4.832266 TGTTGTCAGGATTTGCCATACTTT 59.168 37.500 0.00 0.00 40.02 2.66
354 355 6.072175 TGTTGTCAGGATTTGCCATACTTTAC 60.072 38.462 0.00 0.00 40.02 2.01
389 391 4.080863 CCTCCTCACTACACCTAAATTGCT 60.081 45.833 0.00 0.00 0.00 3.91
392 394 7.015292 CCTCCTCACTACACCTAAATTGCTATA 59.985 40.741 0.00 0.00 0.00 1.31
471 474 2.257974 TCGCTTATGTGACGACTGAC 57.742 50.000 0.00 0.00 0.00 3.51
492 495 0.467290 ACGTCAAATGGCTGTGGGTT 60.467 50.000 0.00 0.00 0.00 4.11
500 517 2.613506 GGCTGTGGGTTGTACGTGC 61.614 63.158 0.00 0.00 0.00 5.34
532 549 8.571461 TTTACTGTCTCTTCGATTAGGACTTA 57.429 34.615 0.00 0.00 0.00 2.24
581 598 2.180432 GGCCAGTAAACCGAAACTCT 57.820 50.000 0.00 0.00 0.00 3.24
586 603 4.566004 CCAGTAAACCGAAACTCTGATCA 58.434 43.478 0.00 0.00 0.00 2.92
639 656 2.486504 CGCTGGACGCAATGCAAT 59.513 55.556 5.91 0.00 39.08 3.56
673 690 3.654201 GTCAGCACGACATGGCAA 58.346 55.556 0.00 0.00 44.69 4.52
722 740 1.672356 AGCGGCGCAATTCTTCACT 60.672 52.632 35.02 5.79 0.00 3.41
841 861 2.227388 CCAAGCATCACAGAGGTCAAAC 59.773 50.000 0.00 0.00 0.00 2.93
873 893 4.368315 GGTTTCCATCACAAACCTTGTTC 58.632 43.478 7.02 0.00 46.47 3.18
877 897 3.138304 CCATCACAAACCTTGTTCGAGA 58.862 45.455 0.00 0.00 43.23 4.04
951 972 0.673644 GTCAGGCACGCACTACCAAT 60.674 55.000 0.00 0.00 0.00 3.16
961 982 5.565695 CACGCACTACCAATTACCAAATAC 58.434 41.667 0.00 0.00 0.00 1.89
1419 1453 2.280052 GCTCCTGCAGCTCGATCC 60.280 66.667 8.66 0.00 45.83 3.36
2247 5727 6.867662 TTTGGCTCTTCTATAATAAGCTGC 57.132 37.500 0.00 0.00 33.50 5.25
2251 5731 5.411053 GGCTCTTCTATAATAAGCTGCCTTG 59.589 44.000 15.86 0.00 38.78 3.61
2357 5845 8.523658 GGTAAAATAAGAGCTGAAGGTTTGATT 58.476 33.333 0.00 0.00 0.00 2.57
2416 5904 2.169978 GGTGCGGTAGTTTCTCCCTTAT 59.830 50.000 0.00 0.00 0.00 1.73
2417 5905 3.385755 GGTGCGGTAGTTTCTCCCTTATA 59.614 47.826 0.00 0.00 0.00 0.98
2418 5906 4.141869 GGTGCGGTAGTTTCTCCCTTATAA 60.142 45.833 0.00 0.00 0.00 0.98
2419 5907 5.454329 GGTGCGGTAGTTTCTCCCTTATAAT 60.454 44.000 0.00 0.00 0.00 1.28
2421 5909 7.212274 GTGCGGTAGTTTCTCCCTTATAATTA 58.788 38.462 0.00 0.00 0.00 1.40
2422 5910 7.384387 GTGCGGTAGTTTCTCCCTTATAATTAG 59.616 40.741 0.00 0.00 0.00 1.73
2423 5911 7.070322 TGCGGTAGTTTCTCCCTTATAATTAGT 59.930 37.037 0.00 0.00 0.00 2.24
2424 5912 8.579863 GCGGTAGTTTCTCCCTTATAATTAGTA 58.420 37.037 0.00 0.00 0.00 1.82
2445 5933 9.695526 TTAGTAATTTTGCATCCATCATTATGC 57.304 29.630 0.00 0.00 46.92 3.14
2446 5934 7.959175 AGTAATTTTGCATCCATCATTATGCT 58.041 30.769 8.57 0.00 46.87 3.79
2447 5935 8.426489 AGTAATTTTGCATCCATCATTATGCTT 58.574 29.630 8.57 0.00 46.87 3.91
2448 5936 9.048446 GTAATTTTGCATCCATCATTATGCTTT 57.952 29.630 8.57 1.48 46.87 3.51
2449 5937 8.514330 AATTTTGCATCCATCATTATGCTTTT 57.486 26.923 8.57 0.00 46.87 2.27
2450 5938 7.925043 TTTTGCATCCATCATTATGCTTTTT 57.075 28.000 8.57 0.00 46.87 1.94
2451 5939 7.542534 TTTGCATCCATCATTATGCTTTTTC 57.457 32.000 8.57 0.00 46.87 2.29
2452 5940 6.474140 TGCATCCATCATTATGCTTTTTCT 57.526 33.333 8.57 0.00 46.87 2.52
2453 5941 6.880484 TGCATCCATCATTATGCTTTTTCTT 58.120 32.000 8.57 0.00 46.87 2.52
2454 5942 7.332557 TGCATCCATCATTATGCTTTTTCTTT 58.667 30.769 8.57 0.00 46.87 2.52
2455 5943 7.825270 TGCATCCATCATTATGCTTTTTCTTTT 59.175 29.630 8.57 0.00 46.87 2.27
2456 5944 9.316730 GCATCCATCATTATGCTTTTTCTTTTA 57.683 29.630 0.00 0.00 44.08 1.52
2526 6014 7.540474 AGGCTTATTTCCTTCGAGTGATATA 57.460 36.000 0.00 0.00 0.00 0.86
2527 6015 8.140112 AGGCTTATTTCCTTCGAGTGATATAT 57.860 34.615 0.00 0.00 0.00 0.86
2528 6016 8.598041 AGGCTTATTTCCTTCGAGTGATATATT 58.402 33.333 0.00 0.00 0.00 1.28
2537 6030 8.462811 TCCTTCGAGTGATATATTAAGAGATGC 58.537 37.037 0.00 0.00 0.00 3.91
2571 6064 7.547370 AGTGTTATGCATCTTCTCTTTACTGTC 59.453 37.037 0.19 0.00 0.00 3.51
2582 6078 6.665474 TCTCTTTACTGTCGTCTCTATGTC 57.335 41.667 0.00 0.00 0.00 3.06
2584 6080 4.639310 TCTTTACTGTCGTCTCTATGTCCC 59.361 45.833 0.00 0.00 0.00 4.46
2586 6082 3.928005 ACTGTCGTCTCTATGTCCCTA 57.072 47.619 0.00 0.00 0.00 3.53
2677 6191 4.412528 ACAAAAAGGGAGTGTCTAGGTCTT 59.587 41.667 0.00 0.00 0.00 3.01
2684 6198 3.622612 GGAGTGTCTAGGTCTTAGTCGAC 59.377 52.174 7.70 7.70 0.00 4.20
2685 6199 4.506758 GAGTGTCTAGGTCTTAGTCGACT 58.493 47.826 23.66 23.66 34.38 4.18
2731 6245 9.944663 GTCAAGTGACATAACATGTAAGAAAAA 57.055 29.630 0.00 0.00 45.03 1.94
2759 6273 4.568152 TTCCTCGCAAAAAGGAAGAAAG 57.432 40.909 0.51 0.00 45.74 2.62
2763 6362 5.126384 TCCTCGCAAAAAGGAAGAAAGAAAA 59.874 36.000 0.00 0.00 39.99 2.29
2800 6399 9.757227 AAATTTTGAACGGATCTTGATGTAAAA 57.243 25.926 0.00 0.00 0.00 1.52
2801 6400 9.927668 AATTTTGAACGGATCTTGATGTAAAAT 57.072 25.926 0.00 0.00 0.00 1.82
2802 6401 8.964420 TTTTGAACGGATCTTGATGTAAAATC 57.036 30.769 0.00 0.00 0.00 2.17
2803 6402 6.677781 TGAACGGATCTTGATGTAAAATCC 57.322 37.500 0.00 0.00 33.93 3.01
2804 6403 5.588648 TGAACGGATCTTGATGTAAAATCCC 59.411 40.000 0.00 0.00 33.75 3.85
2805 6404 5.110814 ACGGATCTTGATGTAAAATCCCA 57.889 39.130 0.00 0.00 33.75 4.37
2808 6407 5.048504 CGGATCTTGATGTAAAATCCCATGG 60.049 44.000 4.14 4.14 33.75 3.66
2816 6415 7.118723 TGATGTAAAATCCCATGGATATAGCC 58.881 38.462 15.22 0.00 42.27 3.93
2831 6430 6.327365 TGGATATAGCCTTGATTGAGACTTGA 59.673 38.462 8.79 0.00 0.00 3.02
2876 6482 7.875554 AGCAATCCCGTAACAAAATACAAAAAT 59.124 29.630 0.00 0.00 0.00 1.82
3004 6613 1.079750 GAGGCCTGGTCTCAACGAC 60.080 63.158 22.99 0.00 42.07 4.34
3010 6619 2.100197 CCTGGTCTCAACGACATCCTA 58.900 52.381 0.00 0.00 44.68 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.813724 CTCCCACCCCCATCCAGC 61.814 72.222 0.00 0.00 0.00 4.85
39 40 1.930656 AACTCCCACCCCCATCCAG 60.931 63.158 0.00 0.00 0.00 3.86
40 41 2.212761 AACTCCCACCCCCATCCA 59.787 61.111 0.00 0.00 0.00 3.41
41 42 2.683475 CAACTCCCACCCCCATCC 59.317 66.667 0.00 0.00 0.00 3.51
42 43 2.043953 GCAACTCCCACCCCCATC 60.044 66.667 0.00 0.00 0.00 3.51
43 44 4.047125 CGCAACTCCCACCCCCAT 62.047 66.667 0.00 0.00 0.00 4.00
45 46 4.410400 CTCGCAACTCCCACCCCC 62.410 72.222 0.00 0.00 0.00 5.40
48 49 4.373116 TCGCTCGCAACTCCCACC 62.373 66.667 0.00 0.00 0.00 4.61
49 50 2.811317 CTCGCTCGCAACTCCCAC 60.811 66.667 0.00 0.00 0.00 4.61
50 51 4.742201 GCTCGCTCGCAACTCCCA 62.742 66.667 0.00 0.00 0.00 4.37
89 90 2.652893 CTTATTTGCTGCGCCCGCTC 62.653 60.000 17.83 6.41 42.51 5.03
90 91 2.749839 TTATTTGCTGCGCCCGCT 60.750 55.556 17.83 2.93 42.51 5.52
91 92 2.278142 CTTATTTGCTGCGCCCGC 60.278 61.111 4.18 8.60 42.35 6.13
92 93 2.278142 GCTTATTTGCTGCGCCCG 60.278 61.111 4.18 0.00 0.00 6.13
93 94 2.278142 CGCTTATTTGCTGCGCCC 60.278 61.111 4.18 0.00 43.08 6.13
97 98 2.951227 GCGCCGCTTATTTGCTGC 60.951 61.111 0.00 0.00 39.28 5.25
98 99 2.648724 CGCGCCGCTTATTTGCTG 60.649 61.111 7.78 0.00 0.00 4.41
109 110 4.147322 AAACTCAATCGCGCGCCG 62.147 61.111 27.95 20.60 38.61 6.46
110 111 2.276680 GAAACTCAATCGCGCGCC 60.277 61.111 27.95 8.11 0.00 6.53
111 112 2.641663 CGAAACTCAATCGCGCGC 60.642 61.111 27.95 23.91 33.07 6.86
112 113 2.020016 CCGAAACTCAATCGCGCG 59.980 61.111 26.76 26.76 38.93 6.86
113 114 2.276680 GCCGAAACTCAATCGCGC 60.277 61.111 0.00 0.00 38.93 6.86
114 115 2.399611 GGCCGAAACTCAATCGCG 59.600 61.111 0.00 0.00 38.93 5.87
115 116 2.791927 GGGCCGAAACTCAATCGC 59.208 61.111 0.00 0.00 38.93 4.58
116 117 3.089784 CGGGCCGAAACTCAATCG 58.910 61.111 24.41 0.00 39.92 3.34
117 118 2.791927 GCGGGCCGAAACTCAATC 59.208 61.111 33.44 4.02 0.00 2.67
118 119 3.124921 CGCGGGCCGAAACTCAAT 61.125 61.111 33.44 0.00 40.02 2.57
128 129 4.752879 TAGTTCAGTGCGCGGGCC 62.753 66.667 22.70 13.09 38.85 5.80
129 130 3.488090 GTAGTTCAGTGCGCGGGC 61.488 66.667 18.81 18.81 40.52 6.13
130 131 0.179121 TATGTAGTTCAGTGCGCGGG 60.179 55.000 8.83 0.00 0.00 6.13
131 132 1.522676 CATATGTAGTTCAGTGCGCGG 59.477 52.381 8.83 0.00 0.00 6.46
132 133 1.071239 GCATATGTAGTTCAGTGCGCG 60.071 52.381 0.00 0.00 34.00 6.86
133 134 1.261619 GGCATATGTAGTTCAGTGCGC 59.738 52.381 0.00 0.00 40.29 6.09
134 135 1.522676 CGGCATATGTAGTTCAGTGCG 59.477 52.381 4.29 0.00 40.29 5.34
135 136 1.261619 GCGGCATATGTAGTTCAGTGC 59.738 52.381 4.29 2.52 39.36 4.40
136 137 1.522676 CGCGGCATATGTAGTTCAGTG 59.477 52.381 4.29 0.00 0.00 3.66
137 138 1.852942 CGCGGCATATGTAGTTCAGT 58.147 50.000 4.29 0.00 0.00 3.41
138 139 0.508641 GCGCGGCATATGTAGTTCAG 59.491 55.000 8.83 0.00 0.00 3.02
139 140 0.179097 TGCGCGGCATATGTAGTTCA 60.179 50.000 8.83 0.00 31.71 3.18
140 141 0.232303 GTGCGCGGCATATGTAGTTC 59.768 55.000 8.83 0.00 41.91 3.01
141 142 1.487452 CGTGCGCGGCATATGTAGTT 61.487 55.000 12.87 0.00 41.91 2.24
142 143 1.949133 CGTGCGCGGCATATGTAGT 60.949 57.895 12.87 0.00 41.91 2.73
143 144 2.846224 CGTGCGCGGCATATGTAG 59.154 61.111 12.87 0.00 41.91 2.74
144 145 3.334751 GCGTGCGCGGCATATGTA 61.335 61.111 22.73 0.00 41.91 2.29
172 173 0.529773 TATAGTTGCTTCAGCGGGCG 60.530 55.000 0.00 0.00 45.83 6.13
173 174 0.938008 GTATAGTTGCTTCAGCGGGC 59.062 55.000 0.00 0.00 45.83 6.13
174 175 1.583054 GGTATAGTTGCTTCAGCGGG 58.417 55.000 0.00 0.00 45.83 6.13
175 176 1.209128 CGGTATAGTTGCTTCAGCGG 58.791 55.000 0.00 0.00 45.83 5.52
176 177 1.209128 CCGGTATAGTTGCTTCAGCG 58.791 55.000 0.00 0.00 45.83 5.18
177 178 2.311124 ACCGGTATAGTTGCTTCAGC 57.689 50.000 4.49 0.00 42.50 4.26
178 179 3.370978 CACAACCGGTATAGTTGCTTCAG 59.629 47.826 8.00 0.00 46.85 3.02
179 180 3.331150 CACAACCGGTATAGTTGCTTCA 58.669 45.455 8.00 0.00 46.85 3.02
180 181 2.095372 GCACAACCGGTATAGTTGCTTC 59.905 50.000 8.00 0.00 46.85 3.86
181 182 2.081462 GCACAACCGGTATAGTTGCTT 58.919 47.619 8.00 0.00 46.85 3.91
182 183 1.734163 GCACAACCGGTATAGTTGCT 58.266 50.000 8.00 0.00 46.85 3.91
183 184 0.372334 CGCACAACCGGTATAGTTGC 59.628 55.000 8.00 11.48 46.85 4.17
185 186 1.079875 CGCGCACAACCGGTATAGTT 61.080 55.000 8.00 0.00 0.00 2.24
186 187 1.517694 CGCGCACAACCGGTATAGT 60.518 57.895 8.00 4.14 0.00 2.12
187 188 2.867091 GCGCGCACAACCGGTATAG 61.867 63.158 29.10 3.36 0.00 1.31
188 189 2.886604 GCGCGCACAACCGGTATA 60.887 61.111 29.10 0.00 0.00 1.47
202 203 3.677099 ATTGCCCGTTTTAGCGCGC 62.677 57.895 26.66 26.66 36.35 6.86
203 204 0.731174 AAATTGCCCGTTTTAGCGCG 60.731 50.000 0.00 0.00 0.00 6.86
204 205 1.125930 CAAAATTGCCCGTTTTAGCGC 59.874 47.619 0.00 0.00 0.00 5.92
234 235 4.166011 CAGCCGCGCCAAACTAGC 62.166 66.667 0.00 0.00 0.00 3.42
235 236 2.325082 AACAGCCGCGCCAAACTAG 61.325 57.895 0.00 0.00 0.00 2.57
236 237 2.281208 AACAGCCGCGCCAAACTA 60.281 55.556 0.00 0.00 0.00 2.24
237 238 3.964875 CAACAGCCGCGCCAAACT 61.965 61.111 0.00 0.00 0.00 2.66
238 239 4.999939 CCAACAGCCGCGCCAAAC 63.000 66.667 0.00 0.00 0.00 2.93
243 244 3.869272 CATCTCCAACAGCCGCGC 61.869 66.667 0.00 0.00 0.00 6.86
244 245 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
245 246 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
246 247 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
260 261 2.636768 AAATTTGCCGTGCTAAGAGC 57.363 45.000 0.00 0.00 42.82 4.09
261 262 4.946784 ACTAAATTTGCCGTGCTAAGAG 57.053 40.909 0.00 0.00 0.00 2.85
262 263 4.517453 ACAACTAAATTTGCCGTGCTAAGA 59.483 37.500 0.00 0.00 0.00 2.10
263 264 4.794169 ACAACTAAATTTGCCGTGCTAAG 58.206 39.130 0.00 0.00 0.00 2.18
264 265 4.276183 TGACAACTAAATTTGCCGTGCTAA 59.724 37.500 0.00 0.00 0.00 3.09
265 266 3.815962 TGACAACTAAATTTGCCGTGCTA 59.184 39.130 0.00 0.00 0.00 3.49
266 267 2.621055 TGACAACTAAATTTGCCGTGCT 59.379 40.909 0.00 0.00 0.00 4.40
267 268 2.724174 GTGACAACTAAATTTGCCGTGC 59.276 45.455 0.00 0.00 0.00 5.34
268 269 3.958704 TGTGACAACTAAATTTGCCGTG 58.041 40.909 0.00 0.00 0.00 4.94
269 270 4.499019 CCTTGTGACAACTAAATTTGCCGT 60.499 41.667 0.00 0.00 0.00 5.68
270 271 3.980775 CCTTGTGACAACTAAATTTGCCG 59.019 43.478 0.00 0.00 0.00 5.69
271 272 4.038642 TCCCTTGTGACAACTAAATTTGCC 59.961 41.667 0.00 0.00 0.00 4.52
294 295 6.602009 GCCATATACTTGGTAAAGGAACTTGT 59.398 38.462 0.00 0.00 43.35 3.16
297 298 6.321821 TGCCATATACTTGGTAAAGGAACT 57.678 37.500 0.00 0.00 38.97 3.01
307 308 8.605746 CAACAAAATGAATTGCCATATACTTGG 58.394 33.333 0.00 0.00 39.94 3.61
312 313 7.980662 CCTGACAACAAAATGAATTGCCATATA 59.019 33.333 0.00 0.00 33.52 0.86
313 314 6.819649 CCTGACAACAAAATGAATTGCCATAT 59.180 34.615 0.00 0.00 33.52 1.78
314 315 6.014755 TCCTGACAACAAAATGAATTGCCATA 60.015 34.615 0.00 0.00 33.52 2.74
318 319 6.790285 AATCCTGACAACAAAATGAATTGC 57.210 33.333 0.00 0.00 33.52 3.56
321 322 5.702209 GGCAAATCCTGACAACAAAATGAAT 59.298 36.000 0.00 0.00 30.79 2.57
364 366 3.555117 TTTAGGTGTAGTGAGGAGGGT 57.445 47.619 0.00 0.00 0.00 4.34
366 368 4.080863 AGCAATTTAGGTGTAGTGAGGAGG 60.081 45.833 0.00 0.00 0.00 4.30
367 369 5.091261 AGCAATTTAGGTGTAGTGAGGAG 57.909 43.478 0.00 0.00 0.00 3.69
423 426 6.764308 AATGTTGAAAATCCGATGTCAGAT 57.236 33.333 0.00 0.00 0.00 2.90
424 427 7.254421 CGATAATGTTGAAAATCCGATGTCAGA 60.254 37.037 0.00 0.00 0.00 3.27
430 433 6.618592 GCGATCGATAATGTTGAAAATCCGAT 60.619 38.462 21.57 0.00 0.00 4.18
440 443 6.292129 GTCACATAAGCGATCGATAATGTTG 58.708 40.000 21.57 16.05 0.00 3.33
471 474 1.497278 CCACAGCCATTTGACGTCG 59.503 57.895 11.62 0.00 0.00 5.12
492 495 3.738830 AGTAAAACTGAGGCACGTACA 57.261 42.857 0.00 0.00 0.00 2.90
500 517 5.715070 ATCGAAGAGACAGTAAAACTGAGG 58.285 41.667 13.72 0.00 45.40 3.86
532 549 8.192110 TCGAGCCTTAAAAACAGTAAAAACAAT 58.808 29.630 0.00 0.00 0.00 2.71
574 591 4.499183 ACTGACGGATTGATCAGAGTTTC 58.501 43.478 8.18 0.00 44.32 2.78
581 598 5.147330 AGTACAAACTGACGGATTGATCA 57.853 39.130 10.94 0.00 33.57 2.92
625 642 1.882311 GTCCATTGCATTGCGTCCA 59.118 52.632 3.84 0.00 0.00 4.02
629 646 2.580326 GGCGTCCATTGCATTGCG 60.580 61.111 3.84 4.03 0.00 4.85
660 677 2.577644 CGCATTGCCATGTCGTGC 60.578 61.111 2.41 0.00 32.28 5.34
662 679 4.164664 CGCGCATTGCCATGTCGT 62.165 61.111 8.75 0.00 42.08 4.34
693 711 3.272334 CGCCGCTGCTATTGACCC 61.272 66.667 0.00 0.00 34.43 4.46
722 740 2.798283 GTCTGGATCGAACACGAACAAA 59.202 45.455 0.00 0.00 39.45 2.83
841 861 1.811965 TGATGGAAACCATGCAACTCG 59.188 47.619 8.06 0.00 45.26 4.18
873 893 0.811915 ACAGTTCGGAGGTGATCTCG 59.188 55.000 0.00 0.00 43.34 4.04
877 897 0.608640 GGTGACAGTTCGGAGGTGAT 59.391 55.000 0.00 0.00 0.00 3.06
951 972 3.687125 TGCGTGGATTGGTATTTGGTAA 58.313 40.909 0.00 0.00 0.00 2.85
961 982 0.463295 AGCTCTGATGCGTGGATTGG 60.463 55.000 0.00 0.00 38.13 3.16
1419 1453 2.124819 AGCGATGGGAGCAAGCAG 60.125 61.111 0.00 0.00 37.01 4.24
2247 5727 5.064325 GCCATTTTACCGTAGTAACTCAAGG 59.936 44.000 0.00 0.00 38.19 3.61
2251 5731 6.148315 ACAAAGCCATTTTACCGTAGTAACTC 59.852 38.462 0.00 0.00 38.19 3.01
2357 5845 9.956720 GTAATAAGTATTAAGCCGACTGACTTA 57.043 33.333 0.00 0.00 32.17 2.24
2419 5907 9.695526 GCATAATGATGGATGCAAAATTACTAA 57.304 29.630 7.48 0.00 46.29 2.24
2472 5960 2.440517 AATGCATGTCACCCAGCATA 57.559 45.000 0.00 0.00 46.10 3.14
2512 6000 8.246871 TGCATCTCTTAATATATCACTCGAAGG 58.753 37.037 0.00 0.00 0.00 3.46
2548 6041 6.531948 ACGACAGTAAAGAGAAGATGCATAAC 59.468 38.462 0.00 0.00 0.00 1.89
2562 6055 4.641094 AGGGACATAGAGACGACAGTAAAG 59.359 45.833 0.00 0.00 0.00 1.85
2571 6064 6.982852 ACATGTATTTAGGGACATAGAGACG 58.017 40.000 0.00 0.00 34.52 4.18
2582 6078 4.178540 ACGACAACGACATGTATTTAGGG 58.821 43.478 0.00 0.00 42.66 3.53
2584 6080 5.445407 CCCAACGACAACGACATGTATTTAG 60.445 44.000 0.00 0.00 42.66 1.85
2586 6082 3.187637 CCCAACGACAACGACATGTATTT 59.812 43.478 0.00 0.00 42.66 1.40
2640 6151 8.739972 ACTCCCTTTTTGTTAGCATAATTGTAG 58.260 33.333 0.00 0.00 0.00 2.74
2661 6175 2.944349 CGACTAAGACCTAGACACTCCC 59.056 54.545 0.00 0.00 0.00 4.30
2677 6191 8.282455 AGATTTGATTAAGTCTCAGTCGACTA 57.718 34.615 19.57 0.00 43.14 2.59
2732 6246 4.729227 TCCTTTTTGCGAGGAAGTTTTT 57.271 36.364 0.00 0.00 40.27 1.94
2733 6247 4.729227 TTCCTTTTTGCGAGGAAGTTTT 57.271 36.364 1.61 0.00 45.81 2.43
2739 6253 3.815809 TCTTTCTTCCTTTTTGCGAGGA 58.184 40.909 0.00 0.00 41.46 3.71
2740 6254 4.568152 TTCTTTCTTCCTTTTTGCGAGG 57.432 40.909 0.00 0.00 35.53 4.63
2741 6255 6.531594 AGTTTTTCTTTCTTCCTTTTTGCGAG 59.468 34.615 0.00 0.00 0.00 5.03
2743 6257 6.647212 AGTTTTTCTTTCTTCCTTTTTGCG 57.353 33.333 0.00 0.00 0.00 4.85
2792 6391 7.349598 AGGCTATATCCATGGGATTTTACATC 58.650 38.462 13.02 0.00 39.79 3.06
2800 6399 5.493613 TCAATCAAGGCTATATCCATGGGAT 59.506 40.000 13.02 8.57 45.40 3.85
2801 6400 4.851540 TCAATCAAGGCTATATCCATGGGA 59.148 41.667 13.02 0.00 35.55 4.37
2802 6401 5.045359 TCTCAATCAAGGCTATATCCATGGG 60.045 44.000 13.02 0.00 0.00 4.00
2803 6402 5.879223 GTCTCAATCAAGGCTATATCCATGG 59.121 44.000 4.97 4.97 0.00 3.66
2804 6403 6.709281 AGTCTCAATCAAGGCTATATCCATG 58.291 40.000 0.00 0.00 26.75 3.66
2805 6404 6.949117 AGTCTCAATCAAGGCTATATCCAT 57.051 37.500 0.00 0.00 26.75 3.41
2808 6407 8.845413 AATCAAGTCTCAATCAAGGCTATATC 57.155 34.615 0.00 0.00 29.06 1.63
2813 6412 6.479884 ACTTAATCAAGTCTCAATCAAGGCT 58.520 36.000 0.00 0.00 41.25 4.58
2831 6430 7.439655 GGATTGCTAAATCTCACTCGACTTAAT 59.560 37.037 0.00 0.00 41.74 1.40
2841 6446 4.873827 TGTTACGGGATTGCTAAATCTCAC 59.126 41.667 0.00 0.00 42.61 3.51
2894 6500 9.399797 AGATGCATCATAAGTGTCAATTTTAGA 57.600 29.630 27.81 0.00 0.00 2.10
2906 6512 9.081204 TGCCAAATATTTAGATGCATCATAAGT 57.919 29.630 27.81 19.33 0.00 2.24
2935 6541 7.473735 TGCTTGGTTTGGTATCAATATTTGA 57.526 32.000 0.00 0.00 45.01 2.69
2946 6554 2.356665 TTCAGCTGCTTGGTTTGGTA 57.643 45.000 9.47 0.00 0.00 3.25
3001 6610 7.499232 AGTGATTAAGGGAAAATTAGGATGTCG 59.501 37.037 0.00 0.00 0.00 4.35
3004 6613 8.752005 TGAGTGATTAAGGGAAAATTAGGATG 57.248 34.615 0.00 0.00 0.00 3.51
3083 6692 7.551617 AGGCTAGCGTGTACTTATTATGTTTTT 59.448 33.333 9.56 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.