Multiple sequence alignment - TraesCS7A01G062600

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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 TraesCS7A01G062600 chr7A 100.000 3897 0 0 1 3897 31103739 31099843 0.000000e+00 7197
1 TraesCS7A01G062600 chr4A 90.406 3648 238 37 316 3894 697951149 697954753 0.000000e+00 4695
2 TraesCS7A01G062600 chr4A 90.506 1580 89 24 1890 3422 698040586 698042151 0.000000e+00 2030
3 TraesCS7A01G062600 chr4A 89.820 1552 121 15 316 1852 698038984 698040513 0.000000e+00 1956
4 TraesCS7A01G062600 chr4A 91.915 235 19 0 1 235 698038752 698038986 2.900000e-86 329
5 TraesCS7A01G062600 chr4A 90.756 238 19 1 1 235 697950914 697951151 8.130000e-82 315
6 TraesCS7A01G062600 chr7D 91.648 2203 128 24 1711 3897 30839837 30837675 0.000000e+00 2998
7 TraesCS7A01G062600 chr7D 89.927 1370 83 10 316 1674 30841162 30839837 0.000000e+00 1714
8 TraesCS7A01G062600 chr7D 94.087 575 31 2 3323 3897 30525234 30524663 0.000000e+00 870
9 TraesCS7A01G062600 chr7D 88.830 188 20 1 1 187 30841374 30841187 3.030000e-56 230
10 TraesCS7A01G062600 chr7D 90.909 88 8 0 231 318 16713333 16713246 6.840000e-23 119
11 TraesCS7A01G062600 chr7D 91.011 89 7 1 233 320 633878851 633878763 6.840000e-23 119
12 TraesCS7A01G062600 chr5B 95.294 85 4 0 233 317 629934766 629934850 6.790000e-28 135
13 TraesCS7A01G062600 chr2A 94.318 88 5 0 233 320 753429650 753429737 6.790000e-28 135
14 TraesCS7A01G062600 chr2D 92.308 91 7 0 231 321 615394355 615394265 3.160000e-26 130
15 TraesCS7A01G062600 chr2D 92.222 90 6 1 229 317 95418732 95418643 4.090000e-25 126
16 TraesCS7A01G062600 chr1A 92.941 85 6 0 233 317 552322369 552322453 1.470000e-24 124
17 TraesCS7A01G062600 chr1A 91.860 86 7 0 232 317 442798964 442799049 1.900000e-23 121
18 TraesCS7A01G062600 chr7B 91.111 90 7 1 233 322 43549669 43549581 1.900000e-23 121


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 TraesCS7A01G062600 chr7A 31099843 31103739 3896 True 7197.000000 7197 100.000 1 3897 1 chr7A.!!$R1 3896
1 TraesCS7A01G062600 chr4A 697950914 697954753 3839 False 2505.000000 4695 90.581 1 3894 2 chr4A.!!$F1 3893
2 TraesCS7A01G062600 chr4A 698038752 698042151 3399 False 1438.333333 2030 90.747 1 3422 3 chr4A.!!$F2 3421
3 TraesCS7A01G062600 chr7D 30837675 30841374 3699 True 1647.333333 2998 90.135 1 3897 3 chr7D.!!$R4 3896
4 TraesCS7A01G062600 chr7D 30524663 30525234 571 True 870.000000 870 94.087 3323 3897 1 chr7D.!!$R2 574

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
273 278 0.111253 AAGTTGCTGGGGGAGTTCAG 59.889 55.0 0.0 0.0 0.00 3.02 F
275 280 0.178990 GTTGCTGGGGGAGTTCAGTT 60.179 55.0 0.0 0.0 33.81 3.16 F
1221 1241 0.541863 CCTACGGCATGACCTCCTTT 59.458 55.0 0.0 0.0 35.61 3.11 F
1479 1499 0.745845 CCAGCTTCTTCCACATCGGG 60.746 60.0 0.0 0.0 34.36 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1731 0.398664 ATCCTACGCTGGCCTAGGTT 60.399 55.000 11.31 4.93 32.59 3.50 R
1876 1925 1.065109 GGTGCACCACGGTTTGAAC 59.935 57.895 31.23 0.00 34.83 3.18 R
2026 2105 1.352017 TCTTGCATGCTCTTCTTCCCA 59.648 47.619 20.33 0.00 0.00 4.37 R
3298 3421 0.249699 TGTGACAAATCTGCGTCGGT 60.250 50.000 0.00 0.00 34.78 4.69 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
30 31 3.708563 TTAAGTTGAGTTGGCTGTTGC 57.291 42.857 0.00 0.00 38.76 4.17
50 51 5.743026 TGCAAACGAGTTAATTGTCAGAA 57.257 34.783 0.00 0.00 0.00 3.02
52 53 6.556212 TGCAAACGAGTTAATTGTCAGAAAA 58.444 32.000 0.00 0.00 0.00 2.29
169 174 6.489700 TGGCATTTCATCCGTATACATTGAAT 59.510 34.615 3.32 0.00 0.00 2.57
225 230 5.594317 GTGGTATATGCCCAAACTTTCTGAT 59.406 40.000 7.44 0.00 32.72 2.90
232 237 3.316308 GCCCAAACTTTCTGATGCGATAT 59.684 43.478 0.00 0.00 0.00 1.63
233 238 4.515191 GCCCAAACTTTCTGATGCGATATA 59.485 41.667 0.00 0.00 0.00 0.86
234 239 5.182001 GCCCAAACTTTCTGATGCGATATAT 59.818 40.000 0.00 0.00 0.00 0.86
235 240 6.294176 GCCCAAACTTTCTGATGCGATATATT 60.294 38.462 0.00 0.00 0.00 1.28
236 241 7.094805 GCCCAAACTTTCTGATGCGATATATTA 60.095 37.037 0.00 0.00 0.00 0.98
237 242 8.230486 CCCAAACTTTCTGATGCGATATATTAC 58.770 37.037 0.00 0.00 0.00 1.89
238 243 8.230486 CCAAACTTTCTGATGCGATATATTACC 58.770 37.037 0.00 0.00 0.00 2.85
239 244 8.993121 CAAACTTTCTGATGCGATATATTACCT 58.007 33.333 0.00 0.00 0.00 3.08
242 247 9.809096 ACTTTCTGATGCGATATATTACCTATG 57.191 33.333 0.00 0.00 0.00 2.23
243 248 9.809096 CTTTCTGATGCGATATATTACCTATGT 57.191 33.333 0.00 0.00 0.00 2.29
248 253 9.936759 TGATGCGATATATTACCTATGTTTTGA 57.063 29.630 0.00 0.00 0.00 2.69
263 268 9.520204 CCTATGTTTTGAAATATAAGTTGCTGG 57.480 33.333 0.00 0.00 0.00 4.85
264 269 9.520204 CTATGTTTTGAAATATAAGTTGCTGGG 57.480 33.333 0.00 0.00 0.00 4.45
265 270 6.696411 TGTTTTGAAATATAAGTTGCTGGGG 58.304 36.000 0.00 0.00 0.00 4.96
266 271 5.930837 TTTGAAATATAAGTTGCTGGGGG 57.069 39.130 0.00 0.00 0.00 5.40
267 272 4.871871 TGAAATATAAGTTGCTGGGGGA 57.128 40.909 0.00 0.00 0.00 4.81
268 273 4.792068 TGAAATATAAGTTGCTGGGGGAG 58.208 43.478 0.00 0.00 0.00 4.30
269 274 4.229582 TGAAATATAAGTTGCTGGGGGAGT 59.770 41.667 0.00 0.00 0.00 3.85
270 275 4.881157 AATATAAGTTGCTGGGGGAGTT 57.119 40.909 0.00 0.00 0.00 3.01
271 276 2.808906 ATAAGTTGCTGGGGGAGTTC 57.191 50.000 0.00 0.00 0.00 3.01
272 277 1.440618 TAAGTTGCTGGGGGAGTTCA 58.559 50.000 0.00 0.00 0.00 3.18
273 278 0.111253 AAGTTGCTGGGGGAGTTCAG 59.889 55.000 0.00 0.00 0.00 3.02
274 279 1.062488 AGTTGCTGGGGGAGTTCAGT 61.062 55.000 0.00 0.00 33.81 3.41
275 280 0.178990 GTTGCTGGGGGAGTTCAGTT 60.179 55.000 0.00 0.00 33.81 3.16
276 281 0.555769 TTGCTGGGGGAGTTCAGTTT 59.444 50.000 0.00 0.00 33.81 2.66
277 282 1.440618 TGCTGGGGGAGTTCAGTTTA 58.559 50.000 0.00 0.00 33.81 2.01
278 283 1.073284 TGCTGGGGGAGTTCAGTTTAC 59.927 52.381 0.00 0.00 33.81 2.01
279 284 1.073284 GCTGGGGGAGTTCAGTTTACA 59.927 52.381 0.00 0.00 33.81 2.41
280 285 2.779506 CTGGGGGAGTTCAGTTTACAC 58.220 52.381 0.00 0.00 0.00 2.90
281 286 2.372172 CTGGGGGAGTTCAGTTTACACT 59.628 50.000 0.00 0.00 0.00 3.55
282 287 2.370849 TGGGGGAGTTCAGTTTACACTC 59.629 50.000 0.00 0.00 36.91 3.51
286 291 3.055209 GAGTTCAGTTTACACTCCCCC 57.945 52.381 0.00 0.00 32.26 5.40
287 292 2.370849 GAGTTCAGTTTACACTCCCCCA 59.629 50.000 0.00 0.00 32.26 4.96
288 293 2.781174 AGTTCAGTTTACACTCCCCCAA 59.219 45.455 0.00 0.00 0.00 4.12
289 294 2.882761 GTTCAGTTTACACTCCCCCAAC 59.117 50.000 0.00 0.00 0.00 3.77
290 295 1.071071 TCAGTTTACACTCCCCCAACG 59.929 52.381 0.00 0.00 0.00 4.10
291 296 1.071071 CAGTTTACACTCCCCCAACGA 59.929 52.381 0.00 0.00 0.00 3.85
292 297 1.071228 AGTTTACACTCCCCCAACGAC 59.929 52.381 0.00 0.00 0.00 4.34
293 298 1.071228 GTTTACACTCCCCCAACGACT 59.929 52.381 0.00 0.00 0.00 4.18
294 299 1.426751 TTACACTCCCCCAACGACTT 58.573 50.000 0.00 0.00 0.00 3.01
295 300 2.307496 TACACTCCCCCAACGACTTA 57.693 50.000 0.00 0.00 0.00 2.24
296 301 1.652947 ACACTCCCCCAACGACTTAT 58.347 50.000 0.00 0.00 0.00 1.73
297 302 2.823959 ACACTCCCCCAACGACTTATA 58.176 47.619 0.00 0.00 0.00 0.98
298 303 3.381335 ACACTCCCCCAACGACTTATAT 58.619 45.455 0.00 0.00 0.00 0.86
299 304 3.778629 ACACTCCCCCAACGACTTATATT 59.221 43.478 0.00 0.00 0.00 1.28
300 305 4.226620 ACACTCCCCCAACGACTTATATTT 59.773 41.667 0.00 0.00 0.00 1.40
301 306 5.426185 ACACTCCCCCAACGACTTATATTTA 59.574 40.000 0.00 0.00 0.00 1.40
302 307 5.989777 CACTCCCCCAACGACTTATATTTAG 59.010 44.000 0.00 0.00 0.00 1.85
303 308 5.071384 ACTCCCCCAACGACTTATATTTAGG 59.929 44.000 0.00 0.00 0.00 2.69
304 309 5.218179 TCCCCCAACGACTTATATTTAGGA 58.782 41.667 0.00 0.00 0.00 2.94
305 310 5.666718 TCCCCCAACGACTTATATTTAGGAA 59.333 40.000 0.00 0.00 0.00 3.36
306 311 5.761726 CCCCCAACGACTTATATTTAGGAAC 59.238 44.000 0.00 0.00 0.00 3.62
307 312 6.350906 CCCCAACGACTTATATTTAGGAACA 58.649 40.000 0.00 0.00 0.00 3.18
308 313 6.482308 CCCCAACGACTTATATTTAGGAACAG 59.518 42.308 0.00 0.00 0.00 3.16
309 314 7.270047 CCCAACGACTTATATTTAGGAACAGA 58.730 38.462 0.00 0.00 0.00 3.41
310 315 7.438459 CCCAACGACTTATATTTAGGAACAGAG 59.562 40.741 0.00 0.00 0.00 3.35
311 316 7.438459 CCAACGACTTATATTTAGGAACAGAGG 59.562 40.741 0.00 0.00 0.00 3.69
312 317 7.052142 ACGACTTATATTTAGGAACAGAGGG 57.948 40.000 0.00 0.00 0.00 4.30
313 318 6.837568 ACGACTTATATTTAGGAACAGAGGGA 59.162 38.462 0.00 0.00 0.00 4.20
314 319 7.014422 ACGACTTATATTTAGGAACAGAGGGAG 59.986 40.741 0.00 0.00 0.00 4.30
371 376 6.055588 GCTTTAAGCACATCTCTACCCAATA 58.944 40.000 12.54 0.00 41.89 1.90
410 415 1.724545 TCCCCTCTCAAAAAGGACGA 58.275 50.000 0.00 0.00 35.83 4.20
426 440 8.617290 AAAAGGACGAATACTTGTTCTTGTAT 57.383 30.769 0.00 0.00 34.19 2.29
429 443 9.886132 AAGGACGAATACTTGTTCTTGTATAAT 57.114 29.630 0.00 0.00 32.69 1.28
626 640 5.658190 CCAACCATCCTATCAATTTTGTCCT 59.342 40.000 0.00 0.00 0.00 3.85
658 672 5.479724 TGTTGATGGTGCAATTATCTCCAAA 59.520 36.000 0.00 0.00 31.80 3.28
709 723 1.625818 GTGCCCCATATAGACAGGGAG 59.374 57.143 0.00 0.00 45.80 4.30
721 739 9.521841 CATATAGACAGGGAGAAACTAGACATA 57.478 37.037 0.00 0.00 0.00 2.29
815 834 1.464687 CGCTCTCGGTGCATTGAAAAG 60.465 52.381 0.00 0.00 0.00 2.27
831 850 5.627499 TGAAAAGATTGATAGCTTTGCGT 57.373 34.783 0.00 0.00 38.96 5.24
840 859 5.369685 TGATAGCTTTGCGTGATTGAAAA 57.630 34.783 0.00 0.00 0.00 2.29
882 901 1.136110 TGAGATGGCGCGACAAAGATA 59.864 47.619 23.46 1.04 0.00 1.98
893 912 3.375299 GCGACAAAGATATGAACCTGCTT 59.625 43.478 0.00 0.00 0.00 3.91
915 934 1.729131 CAACGTGCCAAATGCGACC 60.729 57.895 0.00 0.00 45.60 4.79
1035 1055 1.067916 GTTGGTGTTGGCTGCCTTG 59.932 57.895 21.03 0.00 0.00 3.61
1221 1241 0.541863 CCTACGGCATGACCTCCTTT 59.458 55.000 0.00 0.00 35.61 3.11
1224 1244 2.409870 CGGCATGACCTCCTTTGGC 61.410 63.158 0.00 0.00 35.61 4.52
1479 1499 0.745845 CCAGCTTCTTCCACATCGGG 60.746 60.000 0.00 0.00 34.36 5.14
1533 1553 1.216444 CAGCCTCGAAGTGCAGCTA 59.784 57.895 0.00 0.00 31.23 3.32
1627 1649 5.011329 ACAGTGGATTGAACTGAAAATGCAT 59.989 36.000 10.35 0.00 46.55 3.96
1663 1695 4.966787 GCTGCCACCCGGGTTTGA 62.967 66.667 27.83 9.45 39.65 2.69
1683 1715 7.281549 GGTTTGAAGAAGTACTGGTTAAGTCAA 59.718 37.037 0.00 0.00 40.56 3.18
1699 1731 8.038944 GGTTAAGTCAACTGATTATGGTCACTA 58.961 37.037 0.00 0.00 37.30 2.74
1887 1964 8.616942 TGGTAATGATATATTGTTCAAACCGTG 58.383 33.333 0.00 0.00 35.94 4.94
1890 1967 6.429791 TGATATATTGTTCAAACCGTGGTG 57.570 37.500 0.00 0.00 0.00 4.17
1891 1968 3.569250 ATATTGTTCAAACCGTGGTGC 57.431 42.857 0.00 0.00 0.00 5.01
1978 2057 3.194116 GCAAGGATTTCTTTGGCAGATCA 59.806 43.478 4.82 0.00 34.05 2.92
2026 2105 4.147321 TCAACGACTACCACTACTCCTTT 58.853 43.478 0.00 0.00 0.00 3.11
2054 2133 5.194432 AGAAGAGCATGCAAGAAATCAGAT 58.806 37.500 21.98 0.00 0.00 2.90
2147 2226 1.197721 CATGTCACTCCGGCTGTTTTC 59.802 52.381 0.00 0.00 0.00 2.29
2177 2256 5.730289 GCGTACATGCATGTTAACATCATGT 60.730 40.000 36.02 36.02 45.54 3.21
2393 2472 2.659016 CGTCCAGAAGCTGCAGGA 59.341 61.111 17.12 0.56 0.00 3.86
2466 2545 1.817099 GATGGTCAAGGCGCCTGAG 60.817 63.158 33.60 25.74 0.00 3.35
2495 2574 9.909644 ATTCGGTCAGTATAATTCTGTGTATAC 57.090 33.333 0.00 0.00 34.66 1.47
2526 2605 2.158475 TGTTGGAAGTGCCCTGAGATTT 60.158 45.455 0.00 0.00 34.97 2.17
2529 2608 4.156455 TGGAAGTGCCCTGAGATTTATC 57.844 45.455 0.00 0.00 34.97 1.75
2573 2652 7.656707 AACATATTGCACACCTTTTTGAATC 57.343 32.000 0.00 0.00 0.00 2.52
2872 2963 3.600388 GCTCAACACCATAGTAAGCAGT 58.400 45.455 0.00 0.00 0.00 4.40
2885 2976 1.884235 AAGCAGTCTGCCTACAACAC 58.116 50.000 21.32 0.00 46.52 3.32
2886 2977 1.051812 AGCAGTCTGCCTACAACACT 58.948 50.000 21.32 0.00 46.52 3.55
3063 3185 4.352893 ACCAATAAAAAGGATGGTGGAGG 58.647 43.478 0.00 0.00 44.25 4.30
3170 3292 2.063266 GACGGCATCACGACACTTTTA 58.937 47.619 0.00 0.00 37.61 1.52
3171 3293 2.066262 ACGGCATCACGACACTTTTAG 58.934 47.619 0.00 0.00 37.61 1.85
3172 3294 2.066262 CGGCATCACGACACTTTTAGT 58.934 47.619 0.00 0.00 35.47 2.24
3173 3295 3.247442 CGGCATCACGACACTTTTAGTA 58.753 45.455 0.00 0.00 35.47 1.82
3174 3296 3.863424 CGGCATCACGACACTTTTAGTAT 59.137 43.478 0.00 0.00 35.47 2.12
3175 3297 4.259810 CGGCATCACGACACTTTTAGTATG 60.260 45.833 0.00 0.00 35.47 2.39
3176 3298 4.630069 GGCATCACGACACTTTTAGTATGT 59.370 41.667 0.00 0.00 0.00 2.29
3177 3299 5.445939 GGCATCACGACACTTTTAGTATGTG 60.446 44.000 0.00 0.00 37.78 3.21
3178 3300 5.550981 CATCACGACACTTTTAGTATGTGC 58.449 41.667 0.00 0.00 35.81 4.57
3179 3301 4.623002 TCACGACACTTTTAGTATGTGCA 58.377 39.130 0.00 0.00 35.81 4.57
3224 3347 3.587797 TGTCACGGACTCCTATTGAAC 57.412 47.619 5.77 0.00 33.15 3.18
3231 3354 2.673368 GGACTCCTATTGAACACTTGCG 59.327 50.000 0.00 0.00 0.00 4.85
3242 3365 5.324784 TGAACACTTGCGAGTATAGATGT 57.675 39.130 6.21 0.00 33.90 3.06
3245 3368 5.073311 ACACTTGCGAGTATAGATGTGTT 57.927 39.130 6.21 0.00 34.32 3.32
3249 3372 3.186909 TGCGAGTATAGATGTGTTGCAC 58.813 45.455 0.00 0.00 34.56 4.57
3252 3375 5.221244 TGCGAGTATAGATGTGTTGCACTAT 60.221 40.000 0.00 0.00 35.11 2.12
3259 3382 2.549064 TGTGTTGCACTATGCTCACT 57.451 45.000 20.74 0.00 45.31 3.41
3260 3383 2.145536 TGTGTTGCACTATGCTCACTG 58.854 47.619 20.74 0.00 45.31 3.66
3261 3384 2.224257 TGTGTTGCACTATGCTCACTGA 60.224 45.455 20.74 7.75 45.31 3.41
3262 3385 3.005554 GTGTTGCACTATGCTCACTGAT 58.994 45.455 16.34 0.00 45.31 2.90
3263 3386 3.063180 GTGTTGCACTATGCTCACTGATC 59.937 47.826 16.34 0.00 45.31 2.92
3264 3387 3.264947 GTTGCACTATGCTCACTGATCA 58.735 45.455 2.02 0.00 45.31 2.92
3265 3388 3.175109 TGCACTATGCTCACTGATCAG 57.825 47.619 21.37 21.37 45.31 2.90
3282 3405 3.564053 TCAGTGATCATAGCCATTGCA 57.436 42.857 0.00 0.00 41.13 4.08
3286 3409 4.519350 CAGTGATCATAGCCATTGCATCTT 59.481 41.667 0.00 0.00 41.13 2.40
3298 3421 3.507162 TTGCATCTTCTCTTGGAACCA 57.493 42.857 0.00 0.00 0.00 3.67
3346 3469 9.244799 CATTGAAGACGTACAAGTAGCATATAA 57.755 33.333 0.00 0.00 0.00 0.98
3405 3528 7.784633 TTCAAGATCGATATGTGCATACAAA 57.215 32.000 0.00 0.00 40.84 2.83
3454 3577 5.394115 GGTCAACCAAGTCACTGACAAAATT 60.394 40.000 11.80 0.00 39.97 1.82
3547 3670 5.117592 GCACAAACAAAAGATTGATTCCTCG 59.882 40.000 0.00 0.00 38.94 4.63
3558 3685 6.096036 AGATTGATTCCTCGCTATTGATACG 58.904 40.000 0.00 0.00 0.00 3.06
3572 3699 2.616960 TGATACGACTGCAACACCATC 58.383 47.619 0.00 0.00 0.00 3.51
3645 3772 5.239306 GCACTATGTATGCTGCCAAGATAAA 59.761 40.000 0.00 0.00 40.08 1.40
3646 3773 6.072286 GCACTATGTATGCTGCCAAGATAAAT 60.072 38.462 0.00 0.00 40.08 1.40
3683 3810 3.276857 AGTGATCATGACTTGATGCACC 58.723 45.455 19.02 0.00 45.29 5.01
3703 3830 2.345876 CACGATGTTGCACCATACTGA 58.654 47.619 0.00 0.00 0.00 3.41
3707 3834 4.751600 ACGATGTTGCACCATACTGATATG 59.248 41.667 0.00 0.00 38.38 1.78
3752 3879 3.074412 CGCATCCTTGAAGGTAAACACT 58.926 45.455 11.60 0.00 36.53 3.55
3754 3881 4.378459 CGCATCCTTGAAGGTAAACACTTC 60.378 45.833 11.60 0.00 43.52 3.01
3812 3939 0.685097 TTTACTGGCGTGGCTCTTCT 59.315 50.000 0.00 0.00 0.00 2.85
3836 3963 5.509605 AGTTGCGTTGTTGTTTTCTTTTC 57.490 34.783 0.00 0.00 0.00 2.29
3861 3988 4.403734 TGGAAACCAAACCTAGTGATTCC 58.596 43.478 0.00 0.00 34.73 3.01
3890 4017 9.713684 TCTAAATATCCCAAATGGTTTTGATCT 57.286 29.630 0.00 0.00 44.11 2.75
3894 4021 5.467035 TCCCAAATGGTTTTGATCTTGTC 57.533 39.130 0.00 0.00 44.11 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.100503 ACTCGTTTGCAACAGCCAAC 59.899 50.000 0.00 0.00 32.34 3.77
50 51 7.038088 AGGCCAAGGAGATCAACATTTATTTTT 60.038 33.333 5.01 0.00 0.00 1.94
52 53 5.960202 AGGCCAAGGAGATCAACATTTATTT 59.040 36.000 5.01 0.00 0.00 1.40
87 92 6.417258 TGTGATAAGATTTGCTTGATCCTCA 58.583 36.000 0.00 0.00 37.42 3.86
174 179 4.843220 AGCTGTGCAATTTAGGATATGC 57.157 40.909 0.00 0.00 39.22 3.14
237 242 9.520204 CCAGCAACTTATATTTCAAAACATAGG 57.480 33.333 0.00 0.00 0.00 2.57
238 243 9.520204 CCCAGCAACTTATATTTCAAAACATAG 57.480 33.333 0.00 0.00 0.00 2.23
239 244 8.474025 CCCCAGCAACTTATATTTCAAAACATA 58.526 33.333 0.00 0.00 0.00 2.29
240 245 7.330262 CCCCAGCAACTTATATTTCAAAACAT 58.670 34.615 0.00 0.00 0.00 2.71
241 246 6.295575 CCCCCAGCAACTTATATTTCAAAACA 60.296 38.462 0.00 0.00 0.00 2.83
242 247 6.071051 TCCCCCAGCAACTTATATTTCAAAAC 60.071 38.462 0.00 0.00 0.00 2.43
243 248 6.019748 TCCCCCAGCAACTTATATTTCAAAA 58.980 36.000 0.00 0.00 0.00 2.44
244 249 5.584913 TCCCCCAGCAACTTATATTTCAAA 58.415 37.500 0.00 0.00 0.00 2.69
245 250 5.199982 TCCCCCAGCAACTTATATTTCAA 57.800 39.130 0.00 0.00 0.00 2.69
246 251 4.229582 ACTCCCCCAGCAACTTATATTTCA 59.770 41.667 0.00 0.00 0.00 2.69
247 252 4.793201 ACTCCCCCAGCAACTTATATTTC 58.207 43.478 0.00 0.00 0.00 2.17
248 253 4.881157 ACTCCCCCAGCAACTTATATTT 57.119 40.909 0.00 0.00 0.00 1.40
249 254 4.229582 TGAACTCCCCCAGCAACTTATATT 59.770 41.667 0.00 0.00 0.00 1.28
250 255 3.785887 TGAACTCCCCCAGCAACTTATAT 59.214 43.478 0.00 0.00 0.00 0.86
251 256 3.186283 TGAACTCCCCCAGCAACTTATA 58.814 45.455 0.00 0.00 0.00 0.98
252 257 1.992557 TGAACTCCCCCAGCAACTTAT 59.007 47.619 0.00 0.00 0.00 1.73
253 258 1.351017 CTGAACTCCCCCAGCAACTTA 59.649 52.381 0.00 0.00 0.00 2.24
254 259 0.111253 CTGAACTCCCCCAGCAACTT 59.889 55.000 0.00 0.00 0.00 2.66
255 260 1.062488 ACTGAACTCCCCCAGCAACT 61.062 55.000 0.00 0.00 33.90 3.16
256 261 0.178990 AACTGAACTCCCCCAGCAAC 60.179 55.000 0.00 0.00 33.90 4.17
257 262 0.555769 AAACTGAACTCCCCCAGCAA 59.444 50.000 0.00 0.00 33.90 3.91
258 263 1.073284 GTAAACTGAACTCCCCCAGCA 59.927 52.381 0.00 0.00 33.90 4.41
259 264 1.073284 TGTAAACTGAACTCCCCCAGC 59.927 52.381 0.00 0.00 33.90 4.85
260 265 2.372172 AGTGTAAACTGAACTCCCCCAG 59.628 50.000 0.00 0.00 36.53 4.45
261 266 2.370849 GAGTGTAAACTGAACTCCCCCA 59.629 50.000 0.00 0.00 35.36 4.96
262 267 3.055209 GAGTGTAAACTGAACTCCCCC 57.945 52.381 0.00 0.00 35.36 5.40
266 271 2.370849 TGGGGGAGTGTAAACTGAACTC 59.629 50.000 0.00 0.00 39.70 3.01
267 272 2.414612 TGGGGGAGTGTAAACTGAACT 58.585 47.619 0.00 0.00 0.00 3.01
268 273 2.882761 GTTGGGGGAGTGTAAACTGAAC 59.117 50.000 0.00 0.00 0.00 3.18
269 274 2.485835 CGTTGGGGGAGTGTAAACTGAA 60.486 50.000 0.00 0.00 0.00 3.02
270 275 1.071071 CGTTGGGGGAGTGTAAACTGA 59.929 52.381 0.00 0.00 0.00 3.41
271 276 1.071071 TCGTTGGGGGAGTGTAAACTG 59.929 52.381 0.00 0.00 0.00 3.16
272 277 1.071228 GTCGTTGGGGGAGTGTAAACT 59.929 52.381 0.00 0.00 0.00 2.66
273 278 1.071228 AGTCGTTGGGGGAGTGTAAAC 59.929 52.381 0.00 0.00 0.00 2.01
274 279 1.426751 AGTCGTTGGGGGAGTGTAAA 58.573 50.000 0.00 0.00 0.00 2.01
275 280 1.426751 AAGTCGTTGGGGGAGTGTAA 58.573 50.000 0.00 0.00 0.00 2.41
276 281 2.307496 TAAGTCGTTGGGGGAGTGTA 57.693 50.000 0.00 0.00 0.00 2.90
277 282 1.652947 ATAAGTCGTTGGGGGAGTGT 58.347 50.000 0.00 0.00 0.00 3.55
278 283 4.417426 AATATAAGTCGTTGGGGGAGTG 57.583 45.455 0.00 0.00 0.00 3.51
279 284 5.071384 CCTAAATATAAGTCGTTGGGGGAGT 59.929 44.000 0.00 0.00 0.00 3.85
280 285 5.306160 TCCTAAATATAAGTCGTTGGGGGAG 59.694 44.000 0.00 0.00 0.00 4.30
281 286 5.218179 TCCTAAATATAAGTCGTTGGGGGA 58.782 41.667 0.00 0.00 0.00 4.81
282 287 5.556006 TCCTAAATATAAGTCGTTGGGGG 57.444 43.478 0.00 0.00 0.00 5.40
283 288 6.350906 TGTTCCTAAATATAAGTCGTTGGGG 58.649 40.000 0.00 0.00 0.00 4.96
284 289 7.270047 TCTGTTCCTAAATATAAGTCGTTGGG 58.730 38.462 0.00 0.00 0.00 4.12
285 290 7.438459 CCTCTGTTCCTAAATATAAGTCGTTGG 59.562 40.741 0.00 0.00 0.00 3.77
286 291 7.438459 CCCTCTGTTCCTAAATATAAGTCGTTG 59.562 40.741 0.00 0.00 0.00 4.10
287 292 7.343833 TCCCTCTGTTCCTAAATATAAGTCGTT 59.656 37.037 0.00 0.00 0.00 3.85
288 293 6.837568 TCCCTCTGTTCCTAAATATAAGTCGT 59.162 38.462 0.00 0.00 0.00 4.34
289 294 7.014422 ACTCCCTCTGTTCCTAAATATAAGTCG 59.986 40.741 0.00 0.00 0.00 4.18
290 295 8.252624 ACTCCCTCTGTTCCTAAATATAAGTC 57.747 38.462 0.00 0.00 0.00 3.01
291 296 9.900112 ATACTCCCTCTGTTCCTAAATATAAGT 57.100 33.333 0.00 0.00 0.00 2.24
296 301 9.892444 TGAATATACTCCCTCTGTTCCTAAATA 57.108 33.333 0.00 0.00 0.00 1.40
297 302 8.798975 TGAATATACTCCCTCTGTTCCTAAAT 57.201 34.615 0.00 0.00 0.00 1.40
298 303 8.618240 TTGAATATACTCCCTCTGTTCCTAAA 57.382 34.615 0.00 0.00 0.00 1.85
299 304 7.844779 ACTTGAATATACTCCCTCTGTTCCTAA 59.155 37.037 0.00 0.00 0.00 2.69
300 305 7.363031 ACTTGAATATACTCCCTCTGTTCCTA 58.637 38.462 0.00 0.00 0.00 2.94
301 306 6.206042 ACTTGAATATACTCCCTCTGTTCCT 58.794 40.000 0.00 0.00 0.00 3.36
302 307 6.487299 ACTTGAATATACTCCCTCTGTTCC 57.513 41.667 0.00 0.00 0.00 3.62
303 308 8.697292 ACTTACTTGAATATACTCCCTCTGTTC 58.303 37.037 0.00 0.00 0.00 3.18
304 309 8.611051 ACTTACTTGAATATACTCCCTCTGTT 57.389 34.615 0.00 0.00 0.00 3.16
305 310 9.134055 GTACTTACTTGAATATACTCCCTCTGT 57.866 37.037 0.00 0.00 0.00 3.41
306 311 8.291032 CGTACTTACTTGAATATACTCCCTCTG 58.709 40.741 0.00 0.00 0.00 3.35
307 312 7.997803 ACGTACTTACTTGAATATACTCCCTCT 59.002 37.037 0.00 0.00 0.00 3.69
308 313 8.074972 CACGTACTTACTTGAATATACTCCCTC 58.925 40.741 0.00 0.00 0.00 4.30
309 314 7.776969 TCACGTACTTACTTGAATATACTCCCT 59.223 37.037 0.00 0.00 32.47 4.20
310 315 7.934457 TCACGTACTTACTTGAATATACTCCC 58.066 38.462 0.00 0.00 32.47 4.30
426 440 5.369699 AGCAGGAAGTTGGCTCCTTATATTA 59.630 40.000 0.00 0.00 30.74 0.98
429 443 3.115390 AGCAGGAAGTTGGCTCCTTATA 58.885 45.455 0.00 0.00 30.74 0.98
654 668 7.420800 GTCAAGATATAAAGCACTCCATTTGG 58.579 38.462 0.00 0.00 0.00 3.28
658 672 6.161855 TCGTCAAGATATAAAGCACTCCAT 57.838 37.500 0.00 0.00 0.00 3.41
692 706 4.235372 AGTTTCTCCCTGTCTATATGGGG 58.765 47.826 0.00 0.00 41.22 4.96
815 834 5.160699 TCAATCACGCAAAGCTATCAATC 57.839 39.130 0.00 0.00 0.00 2.67
831 850 3.243670 TGGCTTTGCATCGTTTTCAATCA 60.244 39.130 0.00 0.00 0.00 2.57
840 859 1.337074 CCATTGTTGGCTTTGCATCGT 60.337 47.619 0.00 0.00 35.85 3.73
942 961 8.708378 TGATGATGAGCTATGTATTTATAGGGG 58.292 37.037 0.00 0.00 32.47 4.79
1107 1127 2.799176 GCCAAAGGCGAAGATGGAT 58.201 52.632 0.00 0.00 39.62 3.41
1342 1362 4.142600 GCCTTGAGCTGAAAATCATACGTT 60.143 41.667 0.00 0.00 38.99 3.99
1425 1445 2.841160 GCCACCAACGGCGAAGTTT 61.841 57.895 16.62 0.00 43.52 2.66
1503 1523 2.121963 AGGCTGGTGTTGAGGGGA 60.122 61.111 0.00 0.00 0.00 4.81
1533 1553 2.284258 AGCTCCTCGAACCAGCCT 60.284 61.111 6.35 0.00 33.28 4.58
1627 1649 8.293867 GTGGCAGCCGTTTCATATTAATTTATA 58.706 33.333 7.03 0.00 0.00 0.98
1663 1695 7.120923 TCAGTTGACTTAACCAGTACTTCTT 57.879 36.000 0.00 0.00 40.24 2.52
1699 1731 0.398664 ATCCTACGCTGGCCTAGGTT 60.399 55.000 11.31 4.93 32.59 3.50
1876 1925 1.065109 GGTGCACCACGGTTTGAAC 59.935 57.895 31.23 0.00 34.83 3.18
1887 1964 2.364002 AGTGTTTGGTTAATGGTGCACC 59.636 45.455 29.67 29.67 0.00 5.01
1890 1967 4.314740 TCAAGTGTTTGGTTAATGGTGC 57.685 40.909 0.00 0.00 34.97 5.01
1891 1968 5.691305 CACATCAAGTGTTTGGTTAATGGTG 59.309 40.000 0.00 0.00 43.40 4.17
1978 2057 1.705873 ACTCACCCACGAAGAAGAGT 58.294 50.000 0.00 0.00 0.00 3.24
2026 2105 1.352017 TCTTGCATGCTCTTCTTCCCA 59.648 47.619 20.33 0.00 0.00 4.37
2054 2133 2.224137 GGATGAGATCTGGCACGAATGA 60.224 50.000 0.00 0.00 0.00 2.57
2147 2226 1.362768 ACATGCATGTACGCTGACTG 58.637 50.000 30.50 1.88 39.68 3.51
2390 2469 2.765807 CATCGGGGTGCTCCTCCT 60.766 66.667 4.53 0.00 35.33 3.69
2393 2472 2.284625 TCACATCGGGGTGCTCCT 60.285 61.111 4.53 0.00 38.66 3.69
2466 2545 8.197988 ACACAGAATTATACTGACCGAATTTC 57.802 34.615 0.00 0.00 38.55 2.17
2495 2574 2.666619 GCACTTCCAACAATGAAGAGCG 60.667 50.000 6.99 0.00 43.17 5.03
2526 2605 5.654603 TGGACAAAACTCTAAGCGAGATA 57.345 39.130 0.00 0.00 42.62 1.98
2529 2608 4.773510 GTTTGGACAAAACTCTAAGCGAG 58.226 43.478 0.00 0.00 44.10 5.03
2536 2615 6.183360 TGTGCAATATGTTTGGACAAAACTCT 60.183 34.615 12.86 0.00 45.42 3.24
2573 2652 5.319140 TCAAGATTCATGCTGAACAATGG 57.681 39.130 1.44 0.00 39.45 3.16
2620 2711 3.769739 TCTGCAATGTTCACCACTACT 57.230 42.857 0.00 0.00 0.00 2.57
2621 2712 3.815401 ACTTCTGCAATGTTCACCACTAC 59.185 43.478 0.00 0.00 0.00 2.73
2622 2713 4.085357 ACTTCTGCAATGTTCACCACTA 57.915 40.909 0.00 0.00 0.00 2.74
2776 2867 4.522405 CAGAATAGATGAGTGGACGGATCT 59.478 45.833 0.00 0.00 0.00 2.75
2872 2963 3.165875 AGAGCTAAGTGTTGTAGGCAGA 58.834 45.455 0.00 0.00 0.00 4.26
2936 3027 4.521639 GGTGATATGATGGACTACCGTGTA 59.478 45.833 0.00 0.00 39.42 2.90
3123 3245 7.184067 AGTAGGTCTAAATTTTCTCGATGGT 57.816 36.000 0.00 0.00 0.00 3.55
3170 3292 8.512138 GGTAAAACATCTAAACTTGCACATACT 58.488 33.333 0.00 0.00 0.00 2.12
3171 3293 7.480542 CGGTAAAACATCTAAACTTGCACATAC 59.519 37.037 0.00 0.00 0.00 2.39
3172 3294 7.361371 CCGGTAAAACATCTAAACTTGCACATA 60.361 37.037 0.00 0.00 0.00 2.29
3173 3295 6.378582 CGGTAAAACATCTAAACTTGCACAT 58.621 36.000 0.00 0.00 0.00 3.21
3174 3296 5.278071 CCGGTAAAACATCTAAACTTGCACA 60.278 40.000 0.00 0.00 0.00 4.57
3175 3297 5.151389 CCGGTAAAACATCTAAACTTGCAC 58.849 41.667 0.00 0.00 0.00 4.57
3176 3298 4.822896 ACCGGTAAAACATCTAAACTTGCA 59.177 37.500 4.49 0.00 0.00 4.08
3177 3299 5.366829 ACCGGTAAAACATCTAAACTTGC 57.633 39.130 4.49 0.00 0.00 4.01
3178 3300 8.036273 ACATACCGGTAAAACATCTAAACTTG 57.964 34.615 20.22 9.36 0.00 3.16
3179 3301 8.508875 CAACATACCGGTAAAACATCTAAACTT 58.491 33.333 20.22 0.00 0.00 2.66
3224 3347 4.259970 GCAACACATCTATACTCGCAAGTG 60.260 45.833 0.00 0.00 36.92 3.16
3231 3354 6.459257 GCATAGTGCAACACATCTATACTC 57.541 41.667 0.00 0.00 44.26 2.59
3242 3365 7.535624 ACTGATCAGTGAGCATAGTGCAACA 62.536 44.000 27.37 1.73 42.67 3.33
3245 3368 2.498885 ACTGATCAGTGAGCATAGTGCA 59.501 45.455 27.37 0.00 42.67 4.57
3259 3382 4.070009 GCAATGGCTATGATCACTGATCA 58.930 43.478 21.43 21.43 43.86 2.92
3260 3383 4.070009 TGCAATGGCTATGATCACTGATC 58.930 43.478 11.59 11.59 41.91 2.92
3261 3384 4.094830 TGCAATGGCTATGATCACTGAT 57.905 40.909 0.00 0.00 41.91 2.90
3262 3385 3.564053 TGCAATGGCTATGATCACTGA 57.436 42.857 0.00 0.00 41.91 3.41
3263 3386 4.072839 AGATGCAATGGCTATGATCACTG 58.927 43.478 0.00 0.00 41.91 3.66
3264 3387 4.368565 AGATGCAATGGCTATGATCACT 57.631 40.909 0.00 0.00 41.91 3.41
3265 3388 4.760715 AGAAGATGCAATGGCTATGATCAC 59.239 41.667 0.00 0.00 41.91 3.06
3282 3405 2.028020 GTCGGTGGTTCCAAGAGAAGAT 60.028 50.000 0.00 0.00 34.29 2.40
3286 3409 1.663739 CGTCGGTGGTTCCAAGAGA 59.336 57.895 0.00 0.00 35.57 3.10
3298 3421 0.249699 TGTGACAAATCTGCGTCGGT 60.250 50.000 0.00 0.00 34.78 4.69
3405 3528 5.842907 AGCTAAGAAAAAGCCGTGAATTTT 58.157 33.333 0.00 0.00 41.02 1.82
3410 3533 2.552315 CCAAGCTAAGAAAAAGCCGTGA 59.448 45.455 0.00 0.00 41.02 4.35
3454 3577 1.001974 ACTTATCTCACTTGCACGCCA 59.998 47.619 0.00 0.00 0.00 5.69
3547 3670 3.001330 GGTGTTGCAGTCGTATCAATAGC 59.999 47.826 0.00 0.00 0.00 2.97
3558 3685 0.729116 CCGATGATGGTGTTGCAGTC 59.271 55.000 0.00 0.00 0.00 3.51
3572 3699 2.492019 TCATAGCGTCTTCACCGATG 57.508 50.000 0.00 0.00 0.00 3.84
3645 3772 7.486407 TGATCACTATGTGCACCATCTATAT 57.514 36.000 15.69 1.25 34.86 0.86
3646 3773 6.916360 TGATCACTATGTGCACCATCTATA 57.084 37.500 15.69 4.00 34.86 1.31
3683 3810 2.345876 TCAGTATGGTGCAACATCGTG 58.654 47.619 23.14 19.19 39.98 4.35
3703 3830 7.228507 TCTGTTGCAGTAAACAACTCAACATAT 59.771 33.333 16.26 0.00 45.07 1.78
3707 3834 5.229921 TCTGTTGCAGTAAACAACTCAAC 57.770 39.130 7.99 10.71 46.03 3.18
3812 3939 6.183359 CGAAAAGAAAACAACAACGCAACTAA 60.183 34.615 0.00 0.00 0.00 2.24
3836 3963 3.207778 TCACTAGGTTTGGTTTCCAACG 58.792 45.455 0.35 0.00 43.82 4.10
3861 3988 8.757877 TCAAAACCATTTGGGATATTTAGAAGG 58.242 33.333 0.96 0.00 44.88 3.46


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

AutoCloner maintained by Alex Coulton.