Multiple sequence alignment - TraesCS5A01G023600

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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 TraesCS5A01G023600 chr5A 100.000 4259 0 0 1 4259 18794384 18798642 0.000000e+00 7866.0
1 TraesCS5A01G023600 chr5A 82.767 1236 195 8 2865 4099 18814038 18812820 0.000000e+00 1086.0
2 TraesCS5A01G023600 chr5A 82.424 165 14 4 580 731 18795169 18795331 3.460000e-26 130.0
3 TraesCS5A01G023600 chr5A 96.970 33 0 1 1651 1682 657561824 657561856 2.000000e-03 54.7
4 TraesCS5A01G023600 chr5D 91.634 3873 189 56 371 4148 27467407 27471239 0.000000e+00 5232.0
5 TraesCS5A01G023600 chr5D 86.908 1245 151 9 2862 4103 27489483 27488248 0.000000e+00 1386.0
6 TraesCS5A01G023600 chr5D 84.529 1241 176 13 2864 4099 28162674 28163903 0.000000e+00 1214.0
7 TraesCS5A01G023600 chr5D 82.902 1199 191 6 2902 4099 27504115 27502930 0.000000e+00 1066.0
8 TraesCS5A01G023600 chr5D 90.037 271 26 1 678 948 27467621 27467890 2.440000e-92 350.0
9 TraesCS5A01G023600 chr5D 89.324 281 27 3 668 948 27467665 27467942 2.440000e-92 350.0
10 TraesCS5A01G023600 chr5D 99.123 114 1 0 1 114 27467295 27467408 5.580000e-49 206.0
11 TraesCS5A01G023600 chr1B 91.482 2477 169 23 1686 4148 631067282 631064834 0.000000e+00 3367.0
12 TraesCS5A01G023600 chr1B 90.537 782 51 9 580 1349 631068190 631067420 0.000000e+00 1013.0
13 TraesCS5A01G023600 chr1B 85.619 598 39 23 388 948 631068456 631067869 6.140000e-163 584.0
14 TraesCS5A01G023600 chr1B 89.161 286 30 1 663 948 631068205 631067921 5.240000e-94 355.0
15 TraesCS5A01G023600 chr1B 88.930 271 29 1 678 948 631068244 631067975 2.450000e-87 333.0
16 TraesCS5A01G023600 chr1B 96.053 76 3 0 1 76 631068534 631068459 1.610000e-24 124.0
17 TraesCS5A01G023600 chr1B 97.619 42 1 0 1637 1678 631067353 631067312 5.910000e-09 73.1
18 TraesCS5A01G023600 chr1B 100.000 36 0 0 1346 1381 631067399 631067364 2.750000e-07 67.6
19 TraesCS5A01G023600 chr5B 88.310 1976 115 50 371 2260 20149131 20151076 0.000000e+00 2263.0
20 TraesCS5A01G023600 chr5B 92.736 1473 94 7 2637 4108 20654218 20652758 0.000000e+00 2115.0
21 TraesCS5A01G023600 chr5B 83.702 1221 181 15 2880 4099 20730214 20731417 0.000000e+00 1136.0
22 TraesCS5A01G023600 chr5B 90.824 850 72 4 2492 3341 20154431 20155274 0.000000e+00 1133.0
23 TraesCS5A01G023600 chr5B 91.411 815 55 5 3335 4148 20166539 20167339 0.000000e+00 1103.0
24 TraesCS5A01G023600 chr5B 90.580 690 57 6 668 1356 20658595 20657913 0.000000e+00 907.0
25 TraesCS5A01G023600 chr5B 87.774 548 42 13 1679 2221 20657793 20657266 6.050000e-173 617.0
26 TraesCS5A01G023600 chr5B 92.857 420 29 1 2225 2643 20654815 20654396 3.640000e-170 608.0
27 TraesCS5A01G023600 chr5B 86.287 474 35 19 434 893 20658774 20658317 4.950000e-134 488.0
28 TraesCS5A01G023600 chr5B 90.785 293 22 5 657 948 20149367 20149655 1.860000e-103 387.0
29 TraesCS5A01G023600 chr5B 95.671 231 10 0 2245 2475 20151767 20151997 5.200000e-99 372.0
30 TraesCS5A01G023600 chr5B 94.737 114 6 0 1 114 20149019 20149132 1.220000e-40 178.0
31 TraesCS5A01G023600 chr5B 91.379 116 6 3 1 114 20659526 20659413 5.700000e-34 156.0
32 TraesCS5A01G023600 chr5B 91.398 93 8 0 4056 4148 20172987 20173079 1.240000e-25 128.0
33 TraesCS5A01G023600 chr5B 100.000 36 0 0 1346 1381 20657899 20657864 2.750000e-07 67.6
34 TraesCS5A01G023600 chr7A 95.038 262 12 1 112 372 108819419 108819680 1.100000e-110 411.0
35 TraesCS5A01G023600 chr7A 94.340 265 13 2 113 376 506291323 506291586 5.130000e-109 405.0
36 TraesCS5A01G023600 chr7A 81.343 134 22 3 1171 1304 136346166 136346036 5.820000e-19 106.0
37 TraesCS5A01G023600 chr3A 94.074 270 14 2 111 378 522717635 522717904 3.960000e-110 409.0
38 TraesCS5A01G023600 chr3A 96.970 33 0 1 1651 1682 58868868 58868900 2.000000e-03 54.7
39 TraesCS5A01G023600 chr2A 94.697 264 13 1 112 374 242038935 242039198 3.960000e-110 409.0
40 TraesCS5A01G023600 chr2A 94.382 267 13 2 112 377 625961209 625961474 3.960000e-110 409.0
41 TraesCS5A01G023600 chr2A 92.115 279 19 2 97 372 195810665 195810943 1.440000e-104 390.0
42 TraesCS5A01G023600 chr2A 76.211 227 37 8 1705 1922 19077941 19078159 2.090000e-18 104.0
43 TraesCS5A01G023600 chr4A 94.656 262 12 2 115 375 78157373 78157633 5.130000e-109 405.0
44 TraesCS5A01G023600 chr6A 94.007 267 14 1 116 380 584970742 584970476 1.840000e-108 403.0
45 TraesCS5A01G023600 chr1A 93.962 265 15 1 119 382 447114606 447114342 2.390000e-107 399.0
46 TraesCS5A01G023600 chr4B 75.738 305 56 14 1713 2008 618330565 618330860 2.070000e-28 137.0
47 TraesCS5A01G023600 chr7D 81.579 152 24 4 1172 1322 480002743 480002595 5.780000e-24 122.0
48 TraesCS5A01G023600 chr3D 76.404 267 34 15 1685 1930 433733282 433733024 2.690000e-22 117.0
49 TraesCS5A01G023600 chr3D 100.000 29 0 0 1650 1678 610026892 610026920 2.000000e-03 54.7
50 TraesCS5A01G023600 chr1D 80.795 151 25 3 1172 1322 137418299 137418445 9.680000e-22 115.0
51 TraesCS5A01G023600 chr2D 81.081 148 21 5 1172 1319 511526246 511526386 1.250000e-20 111.0
52 TraesCS5A01G023600 chr7B 84.762 105 16 0 1172 1276 380859509 380859405 5.820000e-19 106.0
53 TraesCS5A01G023600 chr7B 100.000 29 0 0 1650 1678 445659945 445659917 2.000000e-03 54.7


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 TraesCS5A01G023600 chr5A 18794384 18798642 4258 False 3998.000000 7866 91.212000 1 4259 2 chr5A.!!$F2 4258
1 TraesCS5A01G023600 chr5A 18812820 18814038 1218 True 1086.000000 1086 82.767000 2865 4099 1 chr5A.!!$R1 1234
2 TraesCS5A01G023600 chr5D 27467295 27471239 3944 False 1534.500000 5232 92.529500 1 4148 4 chr5D.!!$F2 4147
3 TraesCS5A01G023600 chr5D 27488248 27489483 1235 True 1386.000000 1386 86.908000 2862 4103 1 chr5D.!!$R1 1241
4 TraesCS5A01G023600 chr5D 28162674 28163903 1229 False 1214.000000 1214 84.529000 2864 4099 1 chr5D.!!$F1 1235
5 TraesCS5A01G023600 chr5D 27502930 27504115 1185 True 1066.000000 1066 82.902000 2902 4099 1 chr5D.!!$R2 1197
6 TraesCS5A01G023600 chr1B 631064834 631068534 3700 True 739.587500 3367 92.425125 1 4148 8 chr1B.!!$R1 4147
7 TraesCS5A01G023600 chr5B 20730214 20731417 1203 False 1136.000000 1136 83.702000 2880 4099 1 chr5B.!!$F3 1219
8 TraesCS5A01G023600 chr5B 20166539 20167339 800 False 1103.000000 1103 91.411000 3335 4148 1 chr5B.!!$F1 813
9 TraesCS5A01G023600 chr5B 20149019 20155274 6255 False 866.600000 2263 92.065400 1 3341 5 chr5B.!!$F4 3340
10 TraesCS5A01G023600 chr5B 20652758 20659526 6768 True 708.371429 2115 91.659000 1 4108 7 chr5B.!!$R1 4107

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
87 90 0.804989 AATTAACTGCGCCAGCTGAC 59.195 50.000 17.39 1.25 43.85 3.51 F
114 117 1.210478 ACAGAGAGCCGTTTGCCATAT 59.790 47.619 0.00 0.00 42.71 1.78 F
121 124 1.604278 GCCGTTTGCCATATTCTCTCC 59.396 52.381 0.00 0.00 0.00 3.71 F
2065 2841 0.253044 TAGTCTGGCATGCCTTGGTC 59.747 55.000 35.53 21.65 36.94 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2740 0.535335 GGCTCGTGTGAGATTGGGTA 59.465 55.000 0.00 0.00 45.57 3.69 R
2004 2778 0.840722 AAGTGGAGGTTGGACCGGAT 60.841 55.000 9.46 0.00 44.90 4.18 R
2151 2927 3.703052 TCTATAGGAAACACCGGAGAACC 59.297 47.826 9.46 7.05 44.74 3.62 R
3575 10129 0.247460 TGGATTCTCCGTGACAGCAG 59.753 55.000 0.00 0.00 40.17 4.24 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
87 90 0.804989 AATTAACTGCGCCAGCTGAC 59.195 50.000 17.39 1.25 43.85 3.51
114 117 1.210478 ACAGAGAGCCGTTTGCCATAT 59.790 47.619 0.00 0.00 42.71 1.78
115 118 2.292267 CAGAGAGCCGTTTGCCATATT 58.708 47.619 0.00 0.00 42.71 1.28
116 119 2.289002 CAGAGAGCCGTTTGCCATATTC 59.711 50.000 0.00 0.00 42.71 1.75
117 120 2.171448 AGAGAGCCGTTTGCCATATTCT 59.829 45.455 0.00 0.00 42.71 2.40
118 121 2.545946 GAGAGCCGTTTGCCATATTCTC 59.454 50.000 0.00 0.00 42.71 2.87
119 122 2.171448 AGAGCCGTTTGCCATATTCTCT 59.829 45.455 0.00 0.00 42.71 3.10
120 123 2.545946 GAGCCGTTTGCCATATTCTCTC 59.454 50.000 0.00 0.00 42.71 3.20
121 124 1.604278 GCCGTTTGCCATATTCTCTCC 59.396 52.381 0.00 0.00 0.00 3.71
122 125 1.867233 CCGTTTGCCATATTCTCTCCG 59.133 52.381 0.00 0.00 0.00 4.63
123 126 2.550978 CGTTTGCCATATTCTCTCCGT 58.449 47.619 0.00 0.00 0.00 4.69
124 127 2.936498 CGTTTGCCATATTCTCTCCGTT 59.064 45.455 0.00 0.00 0.00 4.44
125 128 3.374058 CGTTTGCCATATTCTCTCCGTTT 59.626 43.478 0.00 0.00 0.00 3.60
126 129 4.142687 CGTTTGCCATATTCTCTCCGTTTT 60.143 41.667 0.00 0.00 0.00 2.43
127 130 5.619086 CGTTTGCCATATTCTCTCCGTTTTT 60.619 40.000 0.00 0.00 0.00 1.94
128 131 6.402766 CGTTTGCCATATTCTCTCCGTTTTTA 60.403 38.462 0.00 0.00 0.00 1.52
129 132 7.480810 GTTTGCCATATTCTCTCCGTTTTTAT 58.519 34.615 0.00 0.00 0.00 1.40
130 133 7.639113 TTGCCATATTCTCTCCGTTTTTATT 57.361 32.000 0.00 0.00 0.00 1.40
131 134 7.639113 TGCCATATTCTCTCCGTTTTTATTT 57.361 32.000 0.00 0.00 0.00 1.40
132 135 8.740123 TGCCATATTCTCTCCGTTTTTATTTA 57.260 30.769 0.00 0.00 0.00 1.40
133 136 8.617809 TGCCATATTCTCTCCGTTTTTATTTAC 58.382 33.333 0.00 0.00 0.00 2.01
134 137 8.837389 GCCATATTCTCTCCGTTTTTATTTACT 58.163 33.333 0.00 0.00 0.00 2.24
138 141 6.963049 TCTCTCCGTTTTTATTTACTCTGC 57.037 37.500 0.00 0.00 0.00 4.26
139 142 6.460781 TCTCTCCGTTTTTATTTACTCTGCA 58.539 36.000 0.00 0.00 0.00 4.41
140 143 7.103641 TCTCTCCGTTTTTATTTACTCTGCAT 58.896 34.615 0.00 0.00 0.00 3.96
141 144 8.255206 TCTCTCCGTTTTTATTTACTCTGCATA 58.745 33.333 0.00 0.00 0.00 3.14
142 145 8.958119 TCTCCGTTTTTATTTACTCTGCATAT 57.042 30.769 0.00 0.00 0.00 1.78
143 146 9.391006 TCTCCGTTTTTATTTACTCTGCATATT 57.609 29.630 0.00 0.00 0.00 1.28
159 162 9.593134 CTCTGCATATTAGAGTTGACTAAAGTT 57.407 33.333 5.84 0.00 37.48 2.66
187 190 8.685838 ACTTCATAAAGTTGGCTAAGTTTACA 57.314 30.769 20.97 10.83 43.28 2.41
188 191 8.784043 ACTTCATAAAGTTGGCTAAGTTTACAG 58.216 33.333 20.97 18.32 43.28 2.74
189 192 8.911918 TTCATAAAGTTGGCTAAGTTTACAGA 57.088 30.769 20.97 18.42 41.80 3.41
190 193 8.911918 TCATAAAGTTGGCTAAGTTTACAGAA 57.088 30.769 20.97 5.24 41.80 3.02
191 194 9.344772 TCATAAAGTTGGCTAAGTTTACAGAAA 57.655 29.630 20.97 4.61 41.80 2.52
192 195 9.959749 CATAAAGTTGGCTAAGTTTACAGAAAA 57.040 29.630 20.97 3.98 41.80 2.29
333 336 6.330278 AAGTTTGTAAAGCTTGACTTTGACC 58.670 36.000 15.19 0.00 45.94 4.02
334 337 6.071616 AAGTTTGTAAAGCTTGACTTTGACCA 60.072 34.615 15.19 0.00 45.94 4.02
335 338 7.524698 AAGTTTGTAAAGCTTGACTTTGACCAA 60.525 33.333 15.19 0.00 45.94 3.67
350 353 7.281991 CTTTGACCAAAGCTAATATGCAAAC 57.718 36.000 9.25 0.00 40.94 2.93
351 354 6.588719 TTGACCAAAGCTAATATGCAAACT 57.411 33.333 0.00 0.00 34.99 2.66
352 355 7.695480 TTGACCAAAGCTAATATGCAAACTA 57.305 32.000 0.00 0.00 34.99 2.24
353 356 7.695480 TGACCAAAGCTAATATGCAAACTAA 57.305 32.000 0.00 0.00 34.99 2.24
354 357 8.116651 TGACCAAAGCTAATATGCAAACTAAA 57.883 30.769 0.00 0.00 34.99 1.85
355 358 8.748412 TGACCAAAGCTAATATGCAAACTAAAT 58.252 29.630 0.00 0.00 34.99 1.40
367 370 7.883229 ATGCAAACTAAATAAAAACGAAGGG 57.117 32.000 0.00 0.00 0.00 3.95
368 371 7.040473 TGCAAACTAAATAAAAACGAAGGGA 57.960 32.000 0.00 0.00 0.00 4.20
369 372 7.142680 TGCAAACTAAATAAAAACGAAGGGAG 58.857 34.615 0.00 0.00 0.00 4.30
370 373 7.143340 GCAAACTAAATAAAAACGAAGGGAGT 58.857 34.615 0.00 0.00 0.00 3.85
371 374 8.291740 GCAAACTAAATAAAAACGAAGGGAGTA 58.708 33.333 0.00 0.00 0.00 2.59
378 381 9.729281 AAATAAAAACGAAGGGAGTACTATTCA 57.271 29.630 0.00 0.00 0.00 2.57
429 1014 3.133003 TGCAGGAGTAAGGATGAAGCTAC 59.867 47.826 0.00 0.00 0.00 3.58
430 1015 3.386402 GCAGGAGTAAGGATGAAGCTACT 59.614 47.826 0.00 0.00 0.00 2.57
431 1016 4.500716 GCAGGAGTAAGGATGAAGCTACTC 60.501 50.000 1.16 1.16 39.60 2.59
604 1215 6.040054 AGAGGTTACCCAACACACAAATTTAC 59.960 38.462 0.00 0.00 36.29 2.01
619 1230 8.082242 ACACAAATTTACAATCTAGTTTGAGCC 58.918 33.333 18.30 0.00 32.53 4.70
671 1294 3.772025 ACACAGATTTAGACAGAGGGAGG 59.228 47.826 0.00 0.00 0.00 4.30
696 1319 2.310779 AGAGGCTACTCAGGACACAA 57.689 50.000 0.00 0.00 46.44 3.33
799 1422 2.567615 GAGAAGAAGAGGTTACCCAGCA 59.432 50.000 0.00 0.00 0.00 4.41
823 1446 8.717821 GCACACAGATTTAGAATGTAGTTACAA 58.282 33.333 0.00 0.00 39.99 2.41
843 1520 3.825908 ACAGAGGGAGAGAAGAAGAGT 57.174 47.619 0.00 0.00 0.00 3.24
844 1521 4.126520 ACAGAGGGAGAGAAGAAGAGTT 57.873 45.455 0.00 0.00 0.00 3.01
849 1526 4.098155 AGGGAGAGAAGAAGAGTTTACCC 58.902 47.826 0.00 0.00 0.00 3.69
851 1528 4.081365 GGGAGAGAAGAAGAGTTTACCCAG 60.081 50.000 0.00 0.00 34.43 4.45
852 1529 4.500127 GAGAGAAGAAGAGTTTACCCAGC 58.500 47.826 0.00 0.00 0.00 4.85
858 1535 2.550830 AGAGTTTACCCAGCACACAG 57.449 50.000 0.00 0.00 0.00 3.66
877 1554 8.717821 GCACACAGATTTAGAATGTAGTTACAA 58.282 33.333 0.00 0.00 39.99 2.41
893 1570 5.148502 AGTTACAACAGAGGGAGAGAAGAA 58.851 41.667 0.00 0.00 0.00 2.52
907 1584 5.394115 GGAGAGAAGAAAGAGGCTACTCAAG 60.394 48.000 0.00 0.00 46.44 3.02
956 1633 4.339247 CAGAGGGAGAGAAGAGATCAAGAC 59.661 50.000 0.00 0.00 0.00 3.01
1203 1880 7.598278 TCCGTTCACAAATATAACATGCTTTT 58.402 30.769 0.00 0.00 0.00 2.27
1610 2357 8.995027 TCCACTATTTTCATATACAAAGCCAT 57.005 30.769 0.00 0.00 0.00 4.40
1678 2425 3.190874 GTTGTTCTAATCCCGAGCTCAG 58.809 50.000 15.40 1.32 0.00 3.35
1679 2426 2.457598 TGTTCTAATCCCGAGCTCAGT 58.542 47.619 15.40 0.00 0.00 3.41
1680 2427 3.628008 TGTTCTAATCCCGAGCTCAGTA 58.372 45.455 15.40 0.00 0.00 2.74
1681 2428 4.021229 TGTTCTAATCCCGAGCTCAGTAA 58.979 43.478 15.40 0.00 0.00 2.24
1771 2540 7.304735 CAAAATTTCATCCTACAATGACGTGA 58.695 34.615 0.00 0.00 35.44 4.35
1864 2635 9.598517 TTTTGCCATATTTTCCAGAAATATCAC 57.401 29.630 2.01 0.00 32.24 3.06
1879 2650 6.316390 AGAAATATCACCTGGTGACGAAATTC 59.684 38.462 30.50 25.22 45.65 2.17
2004 2778 1.277273 CCTGAGATCAGAACAGCCACA 59.723 52.381 11.44 0.00 46.59 4.17
2058 2834 5.835113 TTATTTCCTTTAGTCTGGCATGC 57.165 39.130 9.90 9.90 0.00 4.06
2065 2841 0.253044 TAGTCTGGCATGCCTTGGTC 59.747 55.000 35.53 21.65 36.94 4.02
2072 2848 1.993653 CATGCCTTGGTCTCTCCCA 59.006 57.895 0.00 0.00 34.77 4.37
2151 2927 1.226547 GGTGTTTGCGTGGTGTGTG 60.227 57.895 0.00 0.00 0.00 3.82
2183 2960 2.638363 GTTTCCTATAGAATCCGCCCCT 59.362 50.000 0.00 0.00 33.44 4.79
2193 2970 1.201429 ATCCGCCCCTGATCCATACC 61.201 60.000 0.00 0.00 0.00 2.73
2302 6238 3.257393 ACAAGCTACAAGATTCGCTCAG 58.743 45.455 0.00 0.00 31.30 3.35
2323 6261 5.104693 TCAGGGTGTTTCTAGTCTCAAAACA 60.105 40.000 8.06 8.06 39.77 2.83
2455 6394 2.182537 GCGAGCAAAATGCCAGGG 59.817 61.111 0.00 0.00 46.52 4.45
2487 6426 0.040425 CAGCGTTGTTGGCACCTAAC 60.040 55.000 0.00 0.00 0.00 2.34
2532 8888 3.405592 TACTGCGCGTCGGGTCATC 62.406 63.158 8.43 0.00 0.00 2.92
2675 9222 5.335583 GGCATACTAACATTGACAACTGCAA 60.336 40.000 0.00 0.00 0.00 4.08
2676 9223 5.569059 GCATACTAACATTGACAACTGCAAC 59.431 40.000 0.00 0.00 0.00 4.17
2707 9254 1.068741 GATAACGGGCAGAAGGACGAT 59.931 52.381 0.00 0.00 0.00 3.73
2709 9256 1.827399 AACGGGCAGAAGGACGATGT 61.827 55.000 0.00 0.00 0.00 3.06
2723 9270 4.588951 AGGACGATGTAGCCAAGAATGATA 59.411 41.667 0.00 0.00 0.00 2.15
2730 9277 5.437060 TGTAGCCAAGAATGATAGGGAAAC 58.563 41.667 0.00 0.00 0.00 2.78
2736 9283 4.526438 AGAATGATAGGGAAACAAGGGG 57.474 45.455 0.00 0.00 0.00 4.79
2781 9328 3.217599 TGATGCTAGTGACGACAAGAC 57.782 47.619 0.00 0.00 0.00 3.01
2800 9347 1.760268 CGCAGGAAGAGCTCATTCGC 61.760 60.000 17.77 13.85 0.00 4.70
2813 9360 2.537625 CTCATTCGCCAAGAACTCGATC 59.462 50.000 0.00 0.00 42.39 3.69
2826 9373 1.172700 CTCGATCGAGACGTCAAACG 58.827 55.000 36.13 18.91 44.53 3.60
2843 9390 1.565591 CGTGGTTCGTTGCGCTTAA 59.434 52.632 9.73 0.00 34.52 1.85
2845 9392 0.584876 GTGGTTCGTTGCGCTTAACT 59.415 50.000 9.73 0.00 0.00 2.24
2937 9488 1.039068 CCATCTGCGACCTCTCTGAT 58.961 55.000 0.00 0.00 0.00 2.90
3135 9686 4.284550 GCCCAGTCCTTGGTGGCA 62.285 66.667 0.00 0.00 46.25 4.92
3258 9809 3.395702 ATCACCACCCGCGCCTAA 61.396 61.111 0.00 0.00 0.00 2.69
3484 10035 1.153823 CTGGACTTCCGCCTGTACG 60.154 63.158 0.00 0.00 39.43 3.67
3559 10113 2.174349 GCAAGAAGAACGCAGCCG 59.826 61.111 0.00 0.00 41.14 5.52
3802 10359 2.545946 GCGCTCACAAACTTCTTCTTCT 59.454 45.455 0.00 0.00 0.00 2.85
3921 10478 3.517100 AGCACATCCAGTACTTCATCAGT 59.483 43.478 0.00 0.00 39.87 3.41
4100 10657 1.756950 AGCTAATCCGGACGCTCCA 60.757 57.895 6.12 0.00 35.91 3.86
4148 10708 9.710818 TGATACTACTACCTCTGTTCCTAAATT 57.289 33.333 0.00 0.00 0.00 1.82
4184 10744 9.809096 TGACAAATAACTCAAAATTTTACTGCA 57.191 25.926 2.44 0.00 0.00 4.41
4203 10763 5.830912 CTGCAAGTACTTGAAATGTTTGGA 58.169 37.500 34.43 9.34 42.93 3.53
4204 10764 6.403866 TGCAAGTACTTGAAATGTTTGGAT 57.596 33.333 34.43 0.00 42.93 3.41
4205 10765 7.517614 TGCAAGTACTTGAAATGTTTGGATA 57.482 32.000 34.43 5.20 42.93 2.59
4206 10766 7.946207 TGCAAGTACTTGAAATGTTTGGATAA 58.054 30.769 34.43 3.44 42.93 1.75
4207 10767 8.584157 TGCAAGTACTTGAAATGTTTGGATAAT 58.416 29.630 34.43 0.00 42.93 1.28
4208 10768 9.423061 GCAAGTACTTGAAATGTTTGGATAATT 57.577 29.630 34.43 0.00 42.93 1.40
4255 10815 8.792633 TGGTCTTTGTTCTATGTTTAGAAATGG 58.207 33.333 0.00 0.00 44.12 3.16
4256 10816 9.010029 GGTCTTTGTTCTATGTTTAGAAATGGA 57.990 33.333 0.00 0.00 44.12 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 90 2.202492 CGGCTCTCTGTTCGACGG 60.202 66.667 0.00 0.00 0.00 4.79
114 117 6.932400 TGCAGAGTAAATAAAAACGGAGAGAA 59.068 34.615 0.00 0.00 0.00 2.87
115 118 6.460781 TGCAGAGTAAATAAAAACGGAGAGA 58.539 36.000 0.00 0.00 0.00 3.10
116 119 6.721571 TGCAGAGTAAATAAAAACGGAGAG 57.278 37.500 0.00 0.00 0.00 3.20
117 120 8.958119 ATATGCAGAGTAAATAAAAACGGAGA 57.042 30.769 0.00 0.00 0.00 3.71
133 136 9.593134 AACTTTAGTCAACTCTAATATGCAGAG 57.407 33.333 11.37 11.37 44.28 3.35
163 166 8.999431 TCTGTAAACTTAGCCAACTTTATGAAG 58.001 33.333 0.00 0.00 38.87 3.02
164 167 8.911918 TCTGTAAACTTAGCCAACTTTATGAA 57.088 30.769 0.00 0.00 0.00 2.57
165 168 8.911918 TTCTGTAAACTTAGCCAACTTTATGA 57.088 30.769 0.00 0.00 0.00 2.15
166 169 9.959749 TTTTCTGTAAACTTAGCCAACTTTATG 57.040 29.630 0.00 0.00 0.00 1.90
301 304 7.917505 AGTCAAGCTTTACAAACTTTGATCAAG 59.082 33.333 13.07 5.87 38.64 3.02
302 305 7.771183 AGTCAAGCTTTACAAACTTTGATCAA 58.229 30.769 13.07 3.38 0.00 2.57
303 306 7.333528 AGTCAAGCTTTACAAACTTTGATCA 57.666 32.000 13.07 0.00 0.00 2.92
304 307 8.634475 AAAGTCAAGCTTTACAAACTTTGATC 57.366 30.769 13.07 0.00 44.90 2.92
308 311 6.811665 GGTCAAAGTCAAGCTTTACAAACTTT 59.188 34.615 13.07 12.29 44.95 2.66
309 312 6.071616 TGGTCAAAGTCAAGCTTTACAAACTT 60.072 34.615 13.07 7.60 44.95 2.66
310 313 5.417580 TGGTCAAAGTCAAGCTTTACAAACT 59.582 36.000 13.07 2.11 44.95 2.66
311 314 5.646606 TGGTCAAAGTCAAGCTTTACAAAC 58.353 37.500 13.07 5.27 44.95 2.93
312 315 5.906113 TGGTCAAAGTCAAGCTTTACAAA 57.094 34.783 13.07 0.00 44.95 2.83
313 316 5.906113 TTGGTCAAAGTCAAGCTTTACAA 57.094 34.783 13.07 0.00 44.95 2.41
314 317 5.890334 CTTTGGTCAAAGTCAAGCTTTACA 58.110 37.500 13.07 0.00 44.95 2.41
327 330 6.991938 AGTTTGCATATTAGCTTTGGTCAAA 58.008 32.000 0.00 0.00 34.99 2.69
328 331 6.588719 AGTTTGCATATTAGCTTTGGTCAA 57.411 33.333 0.00 0.00 34.99 3.18
329 332 7.695480 TTAGTTTGCATATTAGCTTTGGTCA 57.305 32.000 0.00 0.00 34.99 4.02
341 344 9.581099 CCCTTCGTTTTTATTTAGTTTGCATAT 57.419 29.630 0.00 0.00 0.00 1.78
342 345 8.794553 TCCCTTCGTTTTTATTTAGTTTGCATA 58.205 29.630 0.00 0.00 0.00 3.14
343 346 7.662897 TCCCTTCGTTTTTATTTAGTTTGCAT 58.337 30.769 0.00 0.00 0.00 3.96
344 347 7.040473 TCCCTTCGTTTTTATTTAGTTTGCA 57.960 32.000 0.00 0.00 0.00 4.08
345 348 7.143340 ACTCCCTTCGTTTTTATTTAGTTTGC 58.857 34.615 0.00 0.00 0.00 3.68
346 349 9.603298 GTACTCCCTTCGTTTTTATTTAGTTTG 57.397 33.333 0.00 0.00 0.00 2.93
347 350 9.565090 AGTACTCCCTTCGTTTTTATTTAGTTT 57.435 29.630 0.00 0.00 0.00 2.66
352 355 9.729281 TGAATAGTACTCCCTTCGTTTTTATTT 57.271 29.630 0.00 0.00 0.00 1.40
353 356 9.901172 ATGAATAGTACTCCCTTCGTTTTTATT 57.099 29.630 0.00 0.00 0.00 1.40
354 357 9.326413 CATGAATAGTACTCCCTTCGTTTTTAT 57.674 33.333 0.00 0.00 0.00 1.40
355 358 8.316214 ACATGAATAGTACTCCCTTCGTTTTTA 58.684 33.333 0.00 0.00 0.00 1.52
356 359 7.166167 ACATGAATAGTACTCCCTTCGTTTTT 58.834 34.615 0.00 0.00 0.00 1.94
357 360 6.708285 ACATGAATAGTACTCCCTTCGTTTT 58.292 36.000 0.00 0.00 0.00 2.43
358 361 6.295719 ACATGAATAGTACTCCCTTCGTTT 57.704 37.500 0.00 0.00 0.00 3.60
359 362 5.934402 ACATGAATAGTACTCCCTTCGTT 57.066 39.130 0.00 0.00 0.00 3.85
360 363 6.127793 AGTACATGAATAGTACTCCCTTCGT 58.872 40.000 0.00 0.20 46.80 3.85
361 364 6.636562 AGTACATGAATAGTACTCCCTTCG 57.363 41.667 0.00 0.00 46.80 3.79
363 366 9.884814 AGAATAGTACATGAATAGTACTCCCTT 57.115 33.333 9.05 3.36 46.80 3.95
378 381 7.014326 TCAGCGACTTGGATTAGAATAGTACAT 59.986 37.037 0.00 0.00 0.00 2.29
429 1014 1.142748 GATCCACTCGCACCTGGAG 59.857 63.158 0.00 0.00 39.99 3.86
430 1015 2.359169 GGATCCACTCGCACCTGGA 61.359 63.158 6.95 0.00 40.92 3.86
431 1016 1.976132 ATGGATCCACTCGCACCTGG 61.976 60.000 18.99 0.00 0.00 4.45
432 1017 0.812811 CATGGATCCACTCGCACCTG 60.813 60.000 18.99 4.80 0.00 4.00
433 1018 1.524002 CATGGATCCACTCGCACCT 59.476 57.895 18.99 0.00 0.00 4.00
561 1170 4.454948 GCCTGTGGCGCATATGTA 57.545 55.556 10.83 0.00 39.62 2.29
604 1215 3.861840 TCCTTCGGCTCAAACTAGATTG 58.138 45.455 6.40 6.40 0.00 2.67
619 1230 5.385509 AAACTCTTCTTCTCTCTCCTTCG 57.614 43.478 0.00 0.00 0.00 3.79
624 1235 5.623596 GCTGGGTAAACTCTTCTTCTCTCTC 60.624 48.000 0.00 0.00 0.00 3.20
625 1236 4.221924 GCTGGGTAAACTCTTCTTCTCTCT 59.778 45.833 0.00 0.00 0.00 3.10
671 1294 2.429250 GTCCTGAGTAGCCTCTTCTTCC 59.571 54.545 0.00 0.00 38.61 3.46
696 1319 9.606631 CCTTCTGCTCTAACTACATTCTAAATT 57.393 33.333 0.00 0.00 0.00 1.82
799 1422 9.772973 TGTTGTAACTACATTCTAAATCTGTGT 57.227 29.630 0.00 0.00 35.89 3.72
823 1446 3.825908 ACTCTTCTTCTCTCCCTCTGT 57.174 47.619 0.00 0.00 0.00 3.41
843 1520 5.235850 TCTAAATCTGTGTGCTGGGTAAA 57.764 39.130 0.00 0.00 0.00 2.01
844 1521 4.901197 TCTAAATCTGTGTGCTGGGTAA 57.099 40.909 0.00 0.00 0.00 2.85
849 1526 6.974932 ACTACATTCTAAATCTGTGTGCTG 57.025 37.500 0.00 0.00 0.00 4.41
851 1528 8.251750 TGTAACTACATTCTAAATCTGTGTGC 57.748 34.615 0.00 0.00 0.00 4.57
858 1535 9.099454 CCCTCTGTTGTAACTACATTCTAAATC 57.901 37.037 0.00 0.00 35.89 2.17
877 1554 3.440127 CCTCTTTCTTCTCTCCCTCTGT 58.560 50.000 0.00 0.00 0.00 3.41
893 1570 3.501349 TCTGTGTCTTGAGTAGCCTCTT 58.499 45.455 0.00 0.00 38.61 2.85
907 1584 7.064728 GGTCCAACTACATTCTAAATCTGTGTC 59.935 40.741 0.00 0.00 0.00 3.67
956 1633 1.446272 GGTCGCTTCTCCTTCCGTG 60.446 63.158 0.00 0.00 0.00 4.94
1150 1827 1.330521 CTAACCAATGTCATTCGCGGG 59.669 52.381 6.13 0.00 0.00 6.13
1153 1830 4.270325 GGAGTACTAACCAATGTCATTCGC 59.730 45.833 0.00 0.00 0.00 4.70
1610 2357 2.691011 AGCGCCCTTAACTGAAACAAAA 59.309 40.909 2.29 0.00 0.00 2.44
1709 2478 5.738118 ACATTTGCCAATTTTTCACACAG 57.262 34.783 0.00 0.00 0.00 3.66
1855 2626 6.316390 AGAATTTCGTCACCAGGTGATATTTC 59.684 38.462 25.59 20.48 44.63 2.17
1864 2635 1.522668 TGCAGAATTTCGTCACCAGG 58.477 50.000 0.00 0.00 0.00 4.45
1879 2650 7.410800 TGAAAAATGTTTTGATAGCTTGCAG 57.589 32.000 0.00 0.00 0.00 4.41
1966 2740 0.535335 GGCTCGTGTGAGATTGGGTA 59.465 55.000 0.00 0.00 45.57 3.69
2004 2778 0.840722 AAGTGGAGGTTGGACCGGAT 60.841 55.000 9.46 0.00 44.90 4.18
2151 2927 3.703052 TCTATAGGAAACACCGGAGAACC 59.297 47.826 9.46 7.05 44.74 3.62
2183 2960 6.279682 AGGGAATACTAGGTAGGTATGGATCA 59.720 42.308 0.00 0.00 31.26 2.92
2193 2970 8.387813 AGATCACTTAGAGGGAATACTAGGTAG 58.612 40.741 0.00 0.00 27.39 3.18
2231 5461 6.855763 TCAATTAGTACTCCCTCCGTAAAA 57.144 37.500 0.00 0.00 0.00 1.52
2302 6238 4.515567 CCTGTTTTGAGACTAGAAACACCC 59.484 45.833 10.30 0.00 38.09 4.61
2386 6325 7.116948 ACACATACGAAGAAGCAAGCATATATC 59.883 37.037 0.00 0.00 0.00 1.63
2455 6394 1.893919 AACGCTGGAGGAGAAGAGGC 61.894 60.000 0.00 0.00 0.00 4.70
2532 8888 7.565398 ACCCTGATACCTATGCTATATAACAGG 59.435 40.741 0.00 0.00 39.43 4.00
2533 8889 8.540507 ACCCTGATACCTATGCTATATAACAG 57.459 38.462 0.00 0.00 0.00 3.16
2627 8990 7.096551 CCAATCAACAAACAAAATACCTAGGG 58.903 38.462 14.81 0.00 0.00 3.53
2675 9222 3.133901 TGCCCGTTATCTATGTCATGTGT 59.866 43.478 0.00 0.00 0.00 3.72
2676 9223 3.727726 TGCCCGTTATCTATGTCATGTG 58.272 45.455 0.00 0.00 0.00 3.21
2707 9254 5.045213 TGTTTCCCTATCATTCTTGGCTACA 60.045 40.000 0.00 0.00 0.00 2.74
2709 9256 5.708736 TGTTTCCCTATCATTCTTGGCTA 57.291 39.130 0.00 0.00 0.00 3.93
2723 9270 1.664956 AACTGGCCCCTTGTTTCCCT 61.665 55.000 0.00 0.00 0.00 4.20
2769 9316 0.596600 TTCCTGCGTCTTGTCGTCAC 60.597 55.000 0.00 0.00 0.00 3.67
2771 9318 0.039437 TCTTCCTGCGTCTTGTCGTC 60.039 55.000 0.00 0.00 0.00 4.20
2772 9319 0.039074 CTCTTCCTGCGTCTTGTCGT 60.039 55.000 0.00 0.00 0.00 4.34
2773 9320 1.347817 GCTCTTCCTGCGTCTTGTCG 61.348 60.000 0.00 0.00 0.00 4.35
2781 9328 1.760268 GCGAATGAGCTCTTCCTGCG 61.760 60.000 16.19 11.45 35.28 5.18
2800 9347 1.130749 ACGTCTCGATCGAGTTCTTGG 59.869 52.381 36.68 23.73 42.49 3.61
2826 9373 0.584876 AGTTAAGCGCAACGAACCAC 59.415 50.000 11.47 0.00 33.50 4.16
2832 9379 1.708680 GAAGCAAAGTTAAGCGCAACG 59.291 47.619 11.47 0.00 33.50 4.10
2843 9390 1.069227 GCATTCGAACGGAAGCAAAGT 60.069 47.619 0.00 0.00 38.24 2.66
2845 9392 0.239879 GGCATTCGAACGGAAGCAAA 59.760 50.000 0.00 0.00 38.24 3.68
2876 9427 1.091771 CACGCGGCCTGATTCAGATT 61.092 55.000 15.36 0.00 32.44 2.40
2937 9488 1.134310 TCGCAGATGTCGTACCTAGGA 60.134 52.381 17.98 0.00 0.00 2.94
3258 9809 2.600769 AACTGGACCTCGCCGTCT 60.601 61.111 0.00 0.00 33.07 4.18
3499 10050 4.477975 GTCGTCCGACGGGAGCAG 62.478 72.222 20.35 1.47 44.97 4.24
3515 10066 0.822164 CTTGTACGGGATTCCTCGGT 59.178 55.000 15.13 8.51 0.00 4.69
3559 10113 1.081242 CAGTGCCATTGTCGTTGCC 60.081 57.895 0.00 0.00 0.00 4.52
3575 10129 0.247460 TGGATTCTCCGTGACAGCAG 59.753 55.000 0.00 0.00 40.17 4.24
3670 10227 4.821589 CTCGAACCCGGCTGCCTC 62.822 72.222 17.92 6.34 36.24 4.70
4089 10646 2.439701 TACTCCTGGAGCGTCCGG 60.440 66.667 23.43 0.00 42.66 5.14
4100 10657 5.104193 TCACGTATCTAGTTTCCCTACTCCT 60.104 44.000 0.00 0.00 0.00 3.69
4158 10718 9.809096 TGCAGTAAAATTTTGAGTTATTTGTCA 57.191 25.926 13.76 1.79 0.00 3.58
4166 10726 9.301153 CAAGTACTTGCAGTAAAATTTTGAGTT 57.699 29.630 22.03 0.00 31.62 3.01
4167 10727 8.682710 TCAAGTACTTGCAGTAAAATTTTGAGT 58.317 29.630 27.49 9.45 40.24 3.41
4168 10728 9.515020 TTCAAGTACTTGCAGTAAAATTTTGAG 57.485 29.630 27.49 4.48 40.24 3.02
4169 10729 9.862371 TTTCAAGTACTTGCAGTAAAATTTTGA 57.138 25.926 27.49 5.47 40.24 2.69
4172 10732 9.816354 ACATTTCAAGTACTTGCAGTAAAATTT 57.184 25.926 27.49 17.58 40.24 1.82
4173 10733 9.816354 AACATTTCAAGTACTTGCAGTAAAATT 57.184 25.926 27.49 17.47 40.24 1.82
4174 10734 9.816354 AAACATTTCAAGTACTTGCAGTAAAAT 57.184 25.926 27.49 22.63 40.24 1.82
4175 10735 9.081997 CAAACATTTCAAGTACTTGCAGTAAAA 57.918 29.630 27.49 21.60 40.24 1.52
4176 10736 7.704472 CCAAACATTTCAAGTACTTGCAGTAAA 59.296 33.333 27.49 21.92 40.24 2.01
4177 10737 7.067615 TCCAAACATTTCAAGTACTTGCAGTAA 59.932 33.333 27.49 18.45 40.24 2.24
4178 10738 6.544197 TCCAAACATTTCAAGTACTTGCAGTA 59.456 34.615 27.49 10.36 40.24 2.74
4179 10739 5.359576 TCCAAACATTTCAAGTACTTGCAGT 59.640 36.000 27.49 19.20 40.24 4.40
4180 10740 5.830912 TCCAAACATTTCAAGTACTTGCAG 58.169 37.500 27.49 18.66 40.24 4.41
4181 10741 5.843673 TCCAAACATTTCAAGTACTTGCA 57.156 34.783 27.49 16.82 40.24 4.08
4182 10742 8.986477 ATTATCCAAACATTTCAAGTACTTGC 57.014 30.769 27.49 0.00 40.24 4.01
4229 10789 8.792633 CCATTTCTAAACATAGAACAAAGACCA 58.207 33.333 0.00 0.00 35.97 4.02
4230 10790 9.010029 TCCATTTCTAAACATAGAACAAAGACC 57.990 33.333 0.00 0.00 35.97 3.85


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

AutoCloner maintained by Alex Coulton.