Multiple sequence alignment - TraesCS2A01G107500

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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 TraesCS2A01G107500 chr2A 100.000 3303 0 0 1 3303 59874936 59871634 0.000000e+00 6100.0
1 TraesCS2A01G107500 chr2A 97.030 2828 60 15 486 3303 59934473 59931660 0.000000e+00 4735.0
2 TraesCS2A01G107500 chr2A 84.231 1560 161 36 934 2434 59728627 59727094 0.000000e+00 1439.0
3 TraesCS2A01G107500 chr2A 82.788 581 91 7 1635 2209 59880131 59879554 8.180000e-141 510.0
4 TraesCS2A01G107500 chr2A 85.195 385 57 0 1822 2206 60078557 60078173 2.390000e-106 396.0
5 TraesCS2A01G107500 chr2A 87.455 279 29 4 485 762 59729226 59728953 1.910000e-82 316.0
6 TraesCS2A01G107500 chr2A 81.039 385 54 12 925 1299 59943583 59943208 4.170000e-74 289.0
7 TraesCS2A01G107500 chr2A 80.519 385 58 9 925 1299 59880913 59880536 2.510000e-71 279.0
8 TraesCS2A01G107500 chr2A 86.911 191 25 0 1385 1575 59723815 59724005 7.180000e-52 215.0
9 TraesCS2A01G107500 chr2A 83.784 74 9 2 485 558 59730189 59730119 2.130000e-07 67.6
10 TraesCS2A01G107500 chr2D 86.773 2442 171 65 501 2857 60016794 60014420 0.000000e+00 2580.0
11 TraesCS2A01G107500 chr2D 83.744 1095 109 35 1381 2434 59731313 59730247 0.000000e+00 972.0
12 TraesCS2A01G107500 chr2D 81.573 852 124 24 1388 2209 59658163 59659011 0.000000e+00 673.0
13 TraesCS2A01G107500 chr2D 75.595 840 176 22 1385 2198 59727423 59728259 4.000000e-104 388.0
14 TraesCS2A01G107500 chr2D 82.195 410 44 14 2863 3247 522499236 522499641 3.180000e-85 326.0
15 TraesCS2A01G107500 chr2D 96.907 97 1 2 391 487 60017309 60017215 9.490000e-36 161.0
16 TraesCS2A01G107500 chr2D 85.981 107 10 2 608 711 59734292 59734188 3.480000e-20 110.0
17 TraesCS2A01G107500 chr2D 90.566 53 2 3 341 392 1952604 1952654 2.130000e-07 67.6
18 TraesCS2A01G107500 chr2B 88.998 2045 142 45 485 2488 93690005 93688003 0.000000e+00 2453.0
19 TraesCS2A01G107500 chr2B 83.261 1846 179 66 693 2450 93639722 93637919 0.000000e+00 1578.0
20 TraesCS2A01G107500 chr2B 84.790 1407 140 27 1077 2434 93139383 93138002 0.000000e+00 1345.0
21 TraesCS2A01G107500 chr2B 88.775 1069 89 17 1639 2693 93446799 93445748 0.000000e+00 1280.0
22 TraesCS2A01G107500 chr2B 79.317 1083 148 46 1390 2433 93700771 93699726 0.000000e+00 689.0
23 TraesCS2A01G107500 chr2B 75.545 1100 211 40 1145 2198 94034295 94033208 3.830000e-134 488.0
24 TraesCS2A01G107500 chr2B 80.866 554 74 14 1034 1560 93447382 93446834 1.100000e-109 407.0
25 TraesCS2A01G107500 chr2B 81.723 383 51 14 2882 3248 27024316 27023937 5.360000e-78 302.0
26 TraesCS2A01G107500 chr2B 85.522 297 21 11 485 762 93140022 93139729 1.160000e-74 291.0
27 TraesCS2A01G107500 chr2B 86.628 172 14 4 2540 2703 93687991 93687821 7.280000e-42 182.0
28 TraesCS2A01G107500 chr2B 91.129 124 10 1 693 816 93453087 93452965 2.040000e-37 167.0
29 TraesCS2A01G107500 chr2B 91.753 97 6 2 391 487 93692182 93692088 2.070000e-27 134.0
30 TraesCS2A01G107500 chr3D 94.724 398 11 3 3 391 395150460 395150856 7.840000e-171 610.0
31 TraesCS2A01G107500 chr3D 83.473 357 43 10 2907 3249 383591689 383592043 5.320000e-83 318.0
32 TraesCS2A01G107500 chr4B 91.257 366 20 3 37 393 427221906 427221544 3.830000e-134 488.0
33 TraesCS2A01G107500 chr4B 78.364 379 60 17 2885 3249 88393652 88393282 3.320000e-55 226.0
34 TraesCS2A01G107500 chr3A 88.308 402 31 6 6 391 30991481 30991882 4.990000e-128 468.0
35 TraesCS2A01G107500 chr5B 87.651 413 17 9 4 390 642566089 642565685 1.810000e-122 449.0
36 TraesCS2A01G107500 chr5B 79.420 379 58 13 2882 3247 266015499 266015128 1.970000e-62 250.0
37 TraesCS2A01G107500 chr7D 93.617 235 6 3 22 247 572576068 572575834 3.160000e-90 342.0
38 TraesCS2A01G107500 chr7D 96.479 142 3 2 245 386 572567570 572567431 1.980000e-57 233.0
39 TraesCS2A01G107500 chr7D 85.333 150 8 5 241 390 629389516 629389651 3.440000e-30 143.0
40 TraesCS2A01G107500 chr7B 82.768 383 47 12 2882 3248 581266465 581266844 1.140000e-84 324.0
41 TraesCS2A01G107500 chr5A 84.776 335 36 10 2925 3247 682716946 682717277 4.110000e-84 322.0
42 TraesCS2A01G107500 chr5A 82.927 328 35 12 76 391 203499668 203499350 3.250000e-70 276.0
43 TraesCS2A01G107500 chr3B 81.510 384 48 15 2882 3245 654312210 654311830 8.960000e-76 294.0
44 TraesCS2A01G107500 chr3B 79.394 330 47 15 76 392 692888457 692888136 2.580000e-51 213.0
45 TraesCS2A01G107500 chr3B 74.359 351 60 19 2895 3229 659780455 659780791 4.480000e-24 122.0
46 TraesCS2A01G107500 chr6D 79.825 342 38 16 60 390 424650175 424650496 1.540000e-53 220.0
47 TraesCS2A01G107500 chr1A 76.590 346 37 20 68 398 57137245 57137561 2.050000e-32 150.0
48 TraesCS2A01G107500 chr1B 77.308 260 33 9 60 300 523002627 523002879 2.670000e-26 130.0
49 TraesCS2A01G107500 chr6B 91.667 60 5 0 4 63 692969985 692969926 2.110000e-12 84.2
50 TraesCS2A01G107500 chr6B 85.965 57 5 3 357 411 719748118 719748063 1.280000e-04 58.4
51 TraesCS2A01G107500 chr1D 91.667 60 5 0 4 63 21816068 21816127 2.110000e-12 84.2
52 TraesCS2A01G107500 chr1D 91.837 49 2 2 345 392 454522546 454522593 2.130000e-07 67.6


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 TraesCS2A01G107500 chr2A 59871634 59874936 3302 True 6100.000000 6100 100.000000 1 3303 1 chr2A.!!$R1 3302
1 TraesCS2A01G107500 chr2A 59931660 59934473 2813 True 4735.000000 4735 97.030000 486 3303 1 chr2A.!!$R2 2817
2 TraesCS2A01G107500 chr2A 59727094 59730189 3095 True 607.533333 1439 85.156667 485 2434 3 chr2A.!!$R5 1949
3 TraesCS2A01G107500 chr2A 59879554 59880913 1359 True 394.500000 510 81.653500 925 2209 2 chr2A.!!$R6 1284
4 TraesCS2A01G107500 chr2D 60014420 60017309 2889 True 1370.500000 2580 91.840000 391 2857 2 chr2D.!!$R2 2466
5 TraesCS2A01G107500 chr2D 59658163 59659011 848 False 673.000000 673 81.573000 1388 2209 1 chr2D.!!$F2 821
6 TraesCS2A01G107500 chr2D 59730247 59734292 4045 True 541.000000 972 84.862500 608 2434 2 chr2D.!!$R1 1826
7 TraesCS2A01G107500 chr2D 59727423 59728259 836 False 388.000000 388 75.595000 1385 2198 1 chr2D.!!$F3 813
8 TraesCS2A01G107500 chr2B 93637919 93639722 1803 True 1578.000000 1578 83.261000 693 2450 1 chr2B.!!$R3 1757
9 TraesCS2A01G107500 chr2B 93687821 93692182 4361 True 923.000000 2453 89.126333 391 2703 3 chr2B.!!$R8 2312
10 TraesCS2A01G107500 chr2B 93445748 93447382 1634 True 843.500000 1280 84.820500 1034 2693 2 chr2B.!!$R7 1659
11 TraesCS2A01G107500 chr2B 93138002 93140022 2020 True 818.000000 1345 85.156000 485 2434 2 chr2B.!!$R6 1949
12 TraesCS2A01G107500 chr2B 93699726 93700771 1045 True 689.000000 689 79.317000 1390 2433 1 chr2B.!!$R4 1043
13 TraesCS2A01G107500 chr2B 94033208 94034295 1087 True 488.000000 488 75.545000 1145 2198 1 chr2B.!!$R5 1053

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
240 241 0.654683 GGAGCAAGCTATTCTGCACG 59.345 55.000 10.57 0.0 34.99 5.34 F
879 5575 0.813184 TACCCGATCGAACAGGTGTC 59.187 55.000 18.66 0.0 33.70 3.67 F
1415 6268 1.067416 TGACGCGTCTGTTCTGCTT 59.933 52.632 36.27 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 6532 0.524816 GCACGCGAAGGATACGAAGA 60.525 55.000 15.93 0.0 46.39 2.87 R
2004 6943 1.003233 GGAGCCCCTTCTGTGACAC 60.003 63.158 0.00 0.0 0.00 3.67 R
3201 8217 1.020861 CATCTGCACCTGCGCTAACA 61.021 55.000 9.73 0.0 45.83 2.41 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
24 25 6.928348 ATTCCGTATGTGGTCTATAATGGA 57.072 37.500 0.00 0.00 0.00 3.41
25 26 6.734502 TTCCGTATGTGGTCTATAATGGAA 57.265 37.500 0.00 0.00 30.53 3.53
26 27 6.928348 TCCGTATGTGGTCTATAATGGAAT 57.072 37.500 0.00 0.00 0.00 3.01
27 28 6.931838 TCCGTATGTGGTCTATAATGGAATC 58.068 40.000 0.00 0.00 0.00 2.52
28 29 6.724441 TCCGTATGTGGTCTATAATGGAATCT 59.276 38.462 0.00 0.00 0.00 2.40
29 30 7.036220 CCGTATGTGGTCTATAATGGAATCTC 58.964 42.308 0.00 0.00 0.00 2.75
30 31 7.093727 CCGTATGTGGTCTATAATGGAATCTCT 60.094 40.741 0.00 0.00 0.00 3.10
31 32 8.957466 CGTATGTGGTCTATAATGGAATCTCTA 58.043 37.037 0.00 0.00 0.00 2.43
57 58 9.819267 ATAAAGACTTTTATCTAAGAACGGAGG 57.181 33.333 5.61 0.00 35.10 4.30
58 59 6.223351 AGACTTTTATCTAAGAACGGAGGG 57.777 41.667 0.00 0.00 0.00 4.30
59 60 5.956563 AGACTTTTATCTAAGAACGGAGGGA 59.043 40.000 0.00 0.00 0.00 4.20
60 61 6.097129 AGACTTTTATCTAAGAACGGAGGGAG 59.903 42.308 0.00 0.00 0.00 4.30
62 63 6.894103 ACTTTTATCTAAGAACGGAGGGAGTA 59.106 38.462 0.00 0.00 0.00 2.59
64 65 7.909485 TTTATCTAAGAACGGAGGGAGTAAT 57.091 36.000 0.00 0.00 0.00 1.89
65 66 7.521871 TTATCTAAGAACGGAGGGAGTAATC 57.478 40.000 0.00 0.00 0.00 1.75
66 67 4.213513 TCTAAGAACGGAGGGAGTAATCC 58.786 47.826 0.00 0.00 0.00 3.01
67 68 2.850695 AGAACGGAGGGAGTAATCCT 57.149 50.000 9.45 0.00 37.33 3.24
68 69 2.389715 AGAACGGAGGGAGTAATCCTG 58.610 52.381 9.45 0.00 34.21 3.86
69 70 2.024273 AGAACGGAGGGAGTAATCCTGA 60.024 50.000 9.45 0.00 34.21 3.86
70 71 2.074729 ACGGAGGGAGTAATCCTGAG 57.925 55.000 9.45 1.48 34.21 3.35
71 72 1.288335 ACGGAGGGAGTAATCCTGAGT 59.712 52.381 9.45 2.10 34.21 3.41
72 73 1.957877 CGGAGGGAGTAATCCTGAGTC 59.042 57.143 9.45 1.50 34.21 3.36
74 75 3.582164 GGAGGGAGTAATCCTGAGTCAT 58.418 50.000 9.45 0.00 34.21 3.06
75 76 3.970640 GGAGGGAGTAATCCTGAGTCATT 59.029 47.826 9.45 0.00 34.21 2.57
76 77 5.148502 GGAGGGAGTAATCCTGAGTCATTA 58.851 45.833 9.45 0.00 34.21 1.90
78 79 5.529289 AGGGAGTAATCCTGAGTCATTACA 58.471 41.667 9.45 0.00 37.76 2.41
80 81 6.617371 AGGGAGTAATCCTGAGTCATTACAAT 59.383 38.462 9.45 0.00 37.76 2.71
82 83 7.775561 GGGAGTAATCCTGAGTCATTACAATTT 59.224 37.037 9.45 0.00 37.76 1.82
83 84 8.616076 GGAGTAATCCTGAGTCATTACAATTTG 58.384 37.037 14.52 0.00 37.76 2.32
89 90 8.231692 TCCTGAGTCATTACAATTTGTTTCAA 57.768 30.769 7.45 0.00 0.00 2.69
90 91 8.690884 TCCTGAGTCATTACAATTTGTTTCAAA 58.309 29.630 7.45 0.00 0.00 2.69
91 92 9.480053 CCTGAGTCATTACAATTTGTTTCAAAT 57.520 29.630 7.45 0.00 0.00 2.32
189 190 9.415544 AGATTCATTGTAAAAGCTCATTGTTTC 57.584 29.630 0.00 0.00 0.00 2.78
190 191 7.621832 TTCATTGTAAAAGCTCATTGTTTCG 57.378 32.000 0.00 0.00 0.00 3.46
191 192 6.964908 TCATTGTAAAAGCTCATTGTTTCGA 58.035 32.000 0.00 0.00 0.00 3.71
192 193 7.421599 TCATTGTAAAAGCTCATTGTTTCGAA 58.578 30.769 0.00 0.00 0.00 3.71
193 194 7.918033 TCATTGTAAAAGCTCATTGTTTCGAAA 59.082 29.630 6.47 6.47 0.00 3.46
194 195 8.702438 CATTGTAAAAGCTCATTGTTTCGAAAT 58.298 29.630 14.69 0.00 0.00 2.17
195 196 9.906660 ATTGTAAAAGCTCATTGTTTCGAAATA 57.093 25.926 14.69 8.76 0.00 1.40
196 197 9.906660 TTGTAAAAGCTCATTGTTTCGAAATAT 57.093 25.926 14.69 8.14 0.00 1.28
197 198 9.906660 TGTAAAAGCTCATTGTTTCGAAATATT 57.093 25.926 14.69 5.04 0.00 1.28
220 221 8.918202 ATTACTTAGAACACAAATCCACTTGA 57.082 30.769 0.00 0.00 0.00 3.02
221 222 6.867662 ACTTAGAACACAAATCCACTTGAG 57.132 37.500 0.00 0.00 0.00 3.02
222 223 5.765182 ACTTAGAACACAAATCCACTTGAGG 59.235 40.000 0.00 0.00 0.00 3.86
223 224 4.437682 AGAACACAAATCCACTTGAGGA 57.562 40.909 0.00 0.00 43.01 3.71
224 225 4.392940 AGAACACAAATCCACTTGAGGAG 58.607 43.478 0.00 0.00 41.90 3.69
225 226 2.508526 ACACAAATCCACTTGAGGAGC 58.491 47.619 0.00 0.00 41.90 4.70
226 227 2.158623 ACACAAATCCACTTGAGGAGCA 60.159 45.455 0.00 0.00 41.90 4.26
227 228 2.886523 CACAAATCCACTTGAGGAGCAA 59.113 45.455 0.00 0.00 41.90 3.91
237 238 2.322355 TGAGGAGCAAGCTATTCTGC 57.678 50.000 0.00 0.00 0.00 4.26
238 239 1.556451 TGAGGAGCAAGCTATTCTGCA 59.444 47.619 10.57 0.00 34.99 4.41
239 240 1.939255 GAGGAGCAAGCTATTCTGCAC 59.061 52.381 10.57 4.13 34.99 4.57
240 241 0.654683 GGAGCAAGCTATTCTGCACG 59.345 55.000 10.57 0.00 34.99 5.34
241 242 1.645034 GAGCAAGCTATTCTGCACGA 58.355 50.000 10.57 0.00 34.99 4.35
242 243 2.208431 GAGCAAGCTATTCTGCACGAT 58.792 47.619 10.57 0.00 34.99 3.73
243 244 3.384668 GAGCAAGCTATTCTGCACGATA 58.615 45.455 10.57 0.00 34.99 2.92
244 245 3.797039 AGCAAGCTATTCTGCACGATAA 58.203 40.909 10.57 0.00 34.99 1.75
245 246 4.384056 AGCAAGCTATTCTGCACGATAAT 58.616 39.130 10.57 0.00 34.99 1.28
246 247 4.818546 AGCAAGCTATTCTGCACGATAATT 59.181 37.500 10.57 0.00 34.99 1.40
247 248 5.297776 AGCAAGCTATTCTGCACGATAATTT 59.702 36.000 10.57 0.00 34.99 1.82
248 249 5.397534 GCAAGCTATTCTGCACGATAATTTG 59.602 40.000 3.21 0.00 34.99 2.32
249 250 6.718388 CAAGCTATTCTGCACGATAATTTGA 58.282 36.000 0.00 0.00 34.99 2.69
250 251 6.925610 AGCTATTCTGCACGATAATTTGAA 57.074 33.333 0.00 0.00 34.99 2.69
251 252 6.719365 AGCTATTCTGCACGATAATTTGAAC 58.281 36.000 0.00 0.00 34.99 3.18
252 253 5.909610 GCTATTCTGCACGATAATTTGAACC 59.090 40.000 0.00 0.00 0.00 3.62
253 254 4.695217 TTCTGCACGATAATTTGAACCC 57.305 40.909 0.00 0.00 0.00 4.11
254 255 3.680490 TCTGCACGATAATTTGAACCCA 58.320 40.909 0.00 0.00 0.00 4.51
255 256 4.269183 TCTGCACGATAATTTGAACCCAT 58.731 39.130 0.00 0.00 0.00 4.00
256 257 4.096231 TCTGCACGATAATTTGAACCCATG 59.904 41.667 0.00 0.00 0.00 3.66
257 258 3.761218 TGCACGATAATTTGAACCCATGT 59.239 39.130 0.00 0.00 0.00 3.21
258 259 4.219507 TGCACGATAATTTGAACCCATGTT 59.780 37.500 0.00 0.00 37.42 2.71
259 260 5.416013 TGCACGATAATTTGAACCCATGTTA 59.584 36.000 0.00 0.00 33.97 2.41
260 261 6.096141 TGCACGATAATTTGAACCCATGTTAT 59.904 34.615 0.00 0.00 33.97 1.89
261 262 6.978080 GCACGATAATTTGAACCCATGTTATT 59.022 34.615 0.00 0.00 33.97 1.40
262 263 8.132362 GCACGATAATTTGAACCCATGTTATTA 58.868 33.333 0.00 0.00 33.97 0.98
333 334 5.629079 TTTTGTGTGTGTTGTGTGTATCA 57.371 34.783 0.00 0.00 0.00 2.15
334 335 4.873768 TTGTGTGTGTTGTGTGTATCAG 57.126 40.909 0.00 0.00 0.00 2.90
335 336 4.130286 TGTGTGTGTTGTGTGTATCAGA 57.870 40.909 0.00 0.00 0.00 3.27
336 337 4.508662 TGTGTGTGTTGTGTGTATCAGAA 58.491 39.130 0.00 0.00 0.00 3.02
337 338 4.938226 TGTGTGTGTTGTGTGTATCAGAAA 59.062 37.500 0.00 0.00 31.22 2.52
338 339 5.163804 TGTGTGTGTTGTGTGTATCAGAAAC 60.164 40.000 0.00 0.00 31.22 2.78
339 340 4.033472 TGTGTGTTGTGTGTATCAGAAACG 59.967 41.667 0.00 0.00 31.22 3.60
340 341 4.269123 GTGTGTTGTGTGTATCAGAAACGA 59.731 41.667 0.00 0.00 31.22 3.85
341 342 5.050363 GTGTGTTGTGTGTATCAGAAACGAT 60.050 40.000 0.00 0.00 31.22 3.73
342 343 5.525745 TGTGTTGTGTGTATCAGAAACGATT 59.474 36.000 0.00 0.00 31.22 3.34
343 344 6.702282 TGTGTTGTGTGTATCAGAAACGATTA 59.298 34.615 0.00 0.00 31.22 1.75
344 345 7.386573 TGTGTTGTGTGTATCAGAAACGATTAT 59.613 33.333 0.00 0.00 31.22 1.28
345 346 8.227791 GTGTTGTGTGTATCAGAAACGATTATT 58.772 33.333 0.00 0.00 31.22 1.40
346 347 9.425577 TGTTGTGTGTATCAGAAACGATTATTA 57.574 29.630 0.00 0.00 31.22 0.98
359 360 2.921754 CGATTATTATCGTTCTCGCCCC 59.078 50.000 5.95 0.00 46.62 5.80
360 361 2.825861 TTATTATCGTTCTCGCCCCC 57.174 50.000 0.00 0.00 36.96 5.40
377 378 3.160679 CCCCCTTATGCCTAAATCCTG 57.839 52.381 0.00 0.00 0.00 3.86
378 379 2.225117 CCCCCTTATGCCTAAATCCTGG 60.225 54.545 0.00 0.00 0.00 4.45
383 384 4.464262 GCCTAAATCCTGGCTCCG 57.536 61.111 0.00 0.00 45.26 4.63
384 385 1.894282 GCCTAAATCCTGGCTCCGC 60.894 63.158 0.00 0.00 45.26 5.54
469 471 5.652014 TCGGAAAAGGCTATGAAATGATTGT 59.348 36.000 0.00 0.00 0.00 2.71
624 2753 3.129287 CCACCACTATTCGTACGTAAGGT 59.871 47.826 16.05 12.43 46.39 3.50
875 5571 2.719426 GGTATACCCGATCGAACAGG 57.281 55.000 18.66 11.78 0.00 4.00
878 5574 1.481871 ATACCCGATCGAACAGGTGT 58.518 50.000 18.66 10.64 33.70 4.16
879 5575 0.813184 TACCCGATCGAACAGGTGTC 59.187 55.000 18.66 0.00 33.70 3.67
880 5576 1.516386 CCCGATCGAACAGGTGTCG 60.516 63.158 18.66 0.00 0.00 4.35
1415 6268 1.067416 TGACGCGTCTGTTCTGCTT 59.933 52.632 36.27 0.00 0.00 3.91
1628 6532 2.162809 GGATGCCATCGTTAACCGTTTT 59.837 45.455 0.00 0.00 37.94 2.43
1742 6669 3.155167 GACCTCCCAGGCCCTACG 61.155 72.222 0.00 0.00 39.63 3.51
2004 6943 0.179145 CGCCTACTACACCAACCTCG 60.179 60.000 0.00 0.00 0.00 4.63
2230 7179 7.199541 TGAATGACGAGCTACTACCTAATAC 57.800 40.000 0.00 0.00 0.00 1.89
2231 7180 6.206243 TGAATGACGAGCTACTACCTAATACC 59.794 42.308 0.00 0.00 0.00 2.73
2232 7181 5.301835 TGACGAGCTACTACCTAATACCT 57.698 43.478 0.00 0.00 0.00 3.08
2233 7182 5.061853 TGACGAGCTACTACCTAATACCTG 58.938 45.833 0.00 0.00 0.00 4.00
2309 7270 6.619464 ACCAATGGCCAATATAAATACCAGA 58.381 36.000 10.96 0.00 0.00 3.86
2375 7346 6.489361 TGCATGCATCCACATATTATGTAACA 59.511 34.615 18.46 4.48 42.70 2.41
2493 7468 1.184322 ATTTGGCATGACGTGGGCAA 61.184 50.000 13.98 13.98 46.16 4.52
2601 7579 7.412563 CGTGCTCGATTATTTTAGGAGAAAACA 60.413 37.037 1.00 0.00 39.71 2.83
2792 7801 7.062957 TCTCAATATTCTCCCATTTCCCTTTC 58.937 38.462 0.00 0.00 0.00 2.62
3045 8058 7.936496 AAAAAGACAAATTGGGTCAAAACAT 57.064 28.000 11.72 0.00 37.74 2.71
3078 8091 6.156429 ACAGTAAACATTTTTACAAACCCCCA 59.844 34.615 15.08 0.00 46.66 4.96
3157 8172 4.880759 TGCATCAAATTGTTTACCACAGG 58.119 39.130 0.00 0.00 36.48 4.00
3164 8179 7.616313 TCAAATTGTTTACCACAGGAAAAAGT 58.384 30.769 0.00 0.00 36.48 2.66
3165 8180 8.097662 TCAAATTGTTTACCACAGGAAAAAGTT 58.902 29.630 0.00 0.00 36.48 2.66
3233 8249 1.078918 CAGATGAGCTCGGGTGCAA 60.079 57.895 9.64 0.00 34.99 4.08
3246 8262 2.731968 CGGGTGCAAAGATGGATTTTCG 60.732 50.000 0.00 0.00 0.00 3.46
3257 8273 6.013842 AGATGGATTTTCGGTCTTTGAAAC 57.986 37.500 0.00 0.00 35.22 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.425237 TTCCATTATAGACCACATACGGAATA 57.575 34.615 0.00 0.00 0.00 1.75
1 2 6.928348 TCCATTATAGACCACATACGGAAT 57.072 37.500 0.00 0.00 0.00 3.01
3 4 6.724441 AGATTCCATTATAGACCACATACGGA 59.276 38.462 0.00 0.00 0.00 4.69
4 5 6.936279 AGATTCCATTATAGACCACATACGG 58.064 40.000 0.00 0.00 0.00 4.02
31 32 9.819267 CCTCCGTTCTTAGATAAAAGTCTTTAT 57.181 33.333 0.00 0.00 39.87 1.40
33 34 7.038516 TCCCTCCGTTCTTAGATAAAAGTCTTT 60.039 37.037 0.00 0.00 0.00 2.52
34 35 6.439692 TCCCTCCGTTCTTAGATAAAAGTCTT 59.560 38.462 0.00 0.00 0.00 3.01
35 36 5.956563 TCCCTCCGTTCTTAGATAAAAGTCT 59.043 40.000 0.00 0.00 0.00 3.24
36 37 6.127394 ACTCCCTCCGTTCTTAGATAAAAGTC 60.127 42.308 0.00 0.00 0.00 3.01
40 41 7.015001 GGATTACTCCCTCCGTTCTTAGATAAA 59.985 40.741 0.00 0.00 35.28 1.40
41 42 6.492772 GGATTACTCCCTCCGTTCTTAGATAA 59.507 42.308 0.00 0.00 35.28 1.75
42 43 6.008960 GGATTACTCCCTCCGTTCTTAGATA 58.991 44.000 0.00 0.00 35.28 1.98
43 44 4.833938 GGATTACTCCCTCCGTTCTTAGAT 59.166 45.833 0.00 0.00 35.28 1.98
44 45 4.079327 AGGATTACTCCCTCCGTTCTTAGA 60.079 45.833 0.00 0.00 43.21 2.10
46 47 3.958798 CAGGATTACTCCCTCCGTTCTTA 59.041 47.826 0.00 0.00 43.21 2.10
48 49 2.024273 TCAGGATTACTCCCTCCGTTCT 60.024 50.000 0.00 0.00 43.21 3.01
50 51 2.292323 ACTCAGGATTACTCCCTCCGTT 60.292 50.000 0.00 0.00 43.21 4.44
51 52 1.288335 ACTCAGGATTACTCCCTCCGT 59.712 52.381 0.00 0.00 43.21 4.69
52 53 1.957877 GACTCAGGATTACTCCCTCCG 59.042 57.143 0.00 0.00 43.21 4.63
54 55 5.598830 TGTAATGACTCAGGATTACTCCCTC 59.401 44.000 9.23 0.00 43.21 4.30
55 56 5.529289 TGTAATGACTCAGGATTACTCCCT 58.471 41.667 9.23 0.00 43.21 4.20
56 57 5.871396 TGTAATGACTCAGGATTACTCCC 57.129 43.478 9.23 0.00 43.21 4.30
57 58 8.616076 CAAATTGTAATGACTCAGGATTACTCC 58.384 37.037 9.23 0.00 42.43 3.85
58 59 9.167311 ACAAATTGTAATGACTCAGGATTACTC 57.833 33.333 0.00 0.00 36.43 2.59
59 60 9.520515 AACAAATTGTAATGACTCAGGATTACT 57.479 29.630 0.00 0.00 36.43 2.24
62 63 8.859090 TGAAACAAATTGTAATGACTCAGGATT 58.141 29.630 0.00 0.00 0.00 3.01
64 65 7.815840 TGAAACAAATTGTAATGACTCAGGA 57.184 32.000 0.00 0.00 0.00 3.86
65 66 8.870160 TTTGAAACAAATTGTAATGACTCAGG 57.130 30.769 0.00 0.00 0.00 3.86
164 165 8.368126 CGAAACAATGAGCTTTTACAATGAATC 58.632 33.333 0.00 0.00 0.00 2.52
165 166 8.081633 TCGAAACAATGAGCTTTTACAATGAAT 58.918 29.630 0.00 0.00 0.00 2.57
166 167 7.421599 TCGAAACAATGAGCTTTTACAATGAA 58.578 30.769 0.00 0.00 0.00 2.57
167 168 6.964908 TCGAAACAATGAGCTTTTACAATGA 58.035 32.000 0.00 0.00 0.00 2.57
170 171 9.906660 ATATTTCGAAACAATGAGCTTTTACAA 57.093 25.926 13.81 0.00 0.00 2.41
171 172 9.906660 AATATTTCGAAACAATGAGCTTTTACA 57.093 25.926 13.81 0.00 0.00 2.41
195 196 8.918202 TCAAGTGGATTTGTGTTCTAAGTAAT 57.082 30.769 0.00 0.00 0.00 1.89
196 197 7.444183 CCTCAAGTGGATTTGTGTTCTAAGTAA 59.556 37.037 0.00 0.00 0.00 2.24
197 198 6.934645 CCTCAAGTGGATTTGTGTTCTAAGTA 59.065 38.462 0.00 0.00 0.00 2.24
198 199 5.765182 CCTCAAGTGGATTTGTGTTCTAAGT 59.235 40.000 0.00 0.00 0.00 2.24
199 200 5.997746 TCCTCAAGTGGATTTGTGTTCTAAG 59.002 40.000 0.00 0.00 0.00 2.18
200 201 5.935945 TCCTCAAGTGGATTTGTGTTCTAA 58.064 37.500 0.00 0.00 0.00 2.10
201 202 5.551233 CTCCTCAAGTGGATTTGTGTTCTA 58.449 41.667 0.00 0.00 35.30 2.10
202 203 4.392940 CTCCTCAAGTGGATTTGTGTTCT 58.607 43.478 0.00 0.00 35.30 3.01
203 204 3.057946 GCTCCTCAAGTGGATTTGTGTTC 60.058 47.826 0.00 0.00 35.30 3.18
204 205 2.887152 GCTCCTCAAGTGGATTTGTGTT 59.113 45.455 0.00 0.00 35.30 3.32
205 206 2.158623 TGCTCCTCAAGTGGATTTGTGT 60.159 45.455 0.00 0.00 35.30 3.72
206 207 2.507484 TGCTCCTCAAGTGGATTTGTG 58.493 47.619 0.00 0.00 35.30 3.33
207 208 2.957402 TGCTCCTCAAGTGGATTTGT 57.043 45.000 0.00 0.00 35.30 2.83
208 209 3.844577 CTTGCTCCTCAAGTGGATTTG 57.155 47.619 0.00 0.00 45.48 2.32
217 218 2.026915 TGCAGAATAGCTTGCTCCTCAA 60.027 45.455 9.40 0.00 34.99 3.02
218 219 1.556451 TGCAGAATAGCTTGCTCCTCA 59.444 47.619 9.40 0.00 34.99 3.86
219 220 1.939255 GTGCAGAATAGCTTGCTCCTC 59.061 52.381 9.40 0.00 34.99 3.71
220 221 1.741732 CGTGCAGAATAGCTTGCTCCT 60.742 52.381 9.40 0.00 34.99 3.69
221 222 0.654683 CGTGCAGAATAGCTTGCTCC 59.345 55.000 9.40 0.15 34.99 4.70
222 223 1.645034 TCGTGCAGAATAGCTTGCTC 58.355 50.000 9.40 5.09 34.99 4.26
223 224 2.322355 ATCGTGCAGAATAGCTTGCT 57.678 45.000 9.40 0.00 34.99 3.91
224 225 4.739046 ATTATCGTGCAGAATAGCTTGC 57.261 40.909 1.00 1.00 34.99 4.01
225 226 6.718388 TCAAATTATCGTGCAGAATAGCTTG 58.282 36.000 0.00 0.00 34.99 4.01
226 227 6.925610 TCAAATTATCGTGCAGAATAGCTT 57.074 33.333 0.00 0.00 34.99 3.74
227 228 6.238484 GGTTCAAATTATCGTGCAGAATAGCT 60.238 38.462 0.00 0.00 34.99 3.32
228 229 5.909610 GGTTCAAATTATCGTGCAGAATAGC 59.090 40.000 0.00 0.00 0.00 2.97
229 230 6.038161 TGGGTTCAAATTATCGTGCAGAATAG 59.962 38.462 0.00 0.00 0.00 1.73
230 231 5.883115 TGGGTTCAAATTATCGTGCAGAATA 59.117 36.000 0.00 0.00 0.00 1.75
231 232 4.704540 TGGGTTCAAATTATCGTGCAGAAT 59.295 37.500 0.00 0.00 0.00 2.40
232 233 4.075682 TGGGTTCAAATTATCGTGCAGAA 58.924 39.130 0.00 0.00 0.00 3.02
233 234 3.680490 TGGGTTCAAATTATCGTGCAGA 58.320 40.909 0.00 0.00 0.00 4.26
234 235 4.142403 ACATGGGTTCAAATTATCGTGCAG 60.142 41.667 0.00 0.00 0.00 4.41
235 236 3.761218 ACATGGGTTCAAATTATCGTGCA 59.239 39.130 0.00 0.00 0.00 4.57
236 237 4.370364 ACATGGGTTCAAATTATCGTGC 57.630 40.909 0.00 0.00 0.00 5.34
310 311 6.013842 TGATACACACAACACACACAAAAA 57.986 33.333 0.00 0.00 0.00 1.94
311 312 5.412904 TCTGATACACACAACACACACAAAA 59.587 36.000 0.00 0.00 0.00 2.44
312 313 4.938226 TCTGATACACACAACACACACAAA 59.062 37.500 0.00 0.00 0.00 2.83
313 314 4.508662 TCTGATACACACAACACACACAA 58.491 39.130 0.00 0.00 0.00 3.33
314 315 4.130286 TCTGATACACACAACACACACA 57.870 40.909 0.00 0.00 0.00 3.72
315 316 5.263185 GTTTCTGATACACACAACACACAC 58.737 41.667 0.00 0.00 0.00 3.82
316 317 4.033472 CGTTTCTGATACACACAACACACA 59.967 41.667 0.00 0.00 0.00 3.72
317 318 4.269123 TCGTTTCTGATACACACAACACAC 59.731 41.667 0.00 0.00 0.00 3.82
318 319 4.434520 TCGTTTCTGATACACACAACACA 58.565 39.130 0.00 0.00 0.00 3.72
319 320 5.591643 ATCGTTTCTGATACACACAACAC 57.408 39.130 0.00 0.00 0.00 3.32
320 321 7.899178 ATAATCGTTTCTGATACACACAACA 57.101 32.000 0.00 0.00 0.00 3.33
339 340 3.259902 GGGGGCGAGAACGATAATAATC 58.740 50.000 0.00 0.00 42.66 1.75
340 341 3.329929 GGGGGCGAGAACGATAATAAT 57.670 47.619 0.00 0.00 42.66 1.28
341 342 2.825861 GGGGGCGAGAACGATAATAA 57.174 50.000 0.00 0.00 42.66 1.40
357 358 2.225117 CCAGGATTTAGGCATAAGGGGG 60.225 54.545 0.00 0.00 0.00 5.40
358 359 3.160679 CCAGGATTTAGGCATAAGGGG 57.839 52.381 0.00 0.00 0.00 4.79
418 420 0.037447 AGAGGAAAGTGAGGCCAAGC 59.963 55.000 5.01 0.00 0.00 4.01
624 2753 1.313772 CGTGGACACCAACCATTTGA 58.686 50.000 0.00 0.00 39.69 2.69
868 5564 1.162698 TAGTCTCCGACACCTGTTCG 58.837 55.000 0.00 0.00 34.60 3.95
873 5569 1.268899 CAACGTTAGTCTCCGACACCT 59.731 52.381 0.00 0.00 34.60 4.00
874 5570 1.668047 CCAACGTTAGTCTCCGACACC 60.668 57.143 0.00 0.00 34.60 4.16
875 5571 1.267806 TCCAACGTTAGTCTCCGACAC 59.732 52.381 0.00 0.00 34.60 3.67
878 5574 1.901591 AGTCCAACGTTAGTCTCCGA 58.098 50.000 0.00 0.00 0.00 4.55
879 5575 3.837213 TTAGTCCAACGTTAGTCTCCG 57.163 47.619 0.00 0.00 0.00 4.63
880 5576 4.430908 CCATTAGTCCAACGTTAGTCTCC 58.569 47.826 0.00 0.00 0.00 3.71
1316 6110 1.467543 CGTGACGGCTATCGGGATATG 60.468 57.143 0.00 0.00 44.45 1.78
1415 6268 1.269517 GCGTTTTGTTCCATGCCAGAA 60.270 47.619 0.00 0.00 0.00 3.02
1628 6532 0.524816 GCACGCGAAGGATACGAAGA 60.525 55.000 15.93 0.00 46.39 2.87
1742 6669 2.025155 TCAAGATCTGACCGGCTAGAC 58.975 52.381 10.14 0.00 0.00 2.59
1955 6894 4.986587 TTGGCCGTCGTCGTGTCG 62.987 66.667 0.00 0.00 35.01 4.35
2004 6943 1.003233 GGAGCCCCTTCTGTGACAC 60.003 63.158 0.00 0.00 0.00 3.67
2255 7208 5.128919 GCCTTATTCATTCATCAGGTGTCT 58.871 41.667 0.00 0.00 0.00 3.41
2375 7346 4.096984 GCATGAGAAAGTGGGAATTCGATT 59.903 41.667 0.00 0.00 0.00 3.34
2466 7441 3.364621 CACGTCATGCCAAATGTAAAAGC 59.635 43.478 0.00 0.00 0.00 3.51
2493 7468 7.556996 AGTGTTACGATTGATAGTAGTTCTCCT 59.443 37.037 0.00 0.00 0.00 3.69
2541 7519 4.451096 GCCAAATGTCGAAAGAGAAGTGTA 59.549 41.667 0.00 0.00 43.49 2.90
2542 7520 3.251004 GCCAAATGTCGAAAGAGAAGTGT 59.749 43.478 0.00 0.00 43.49 3.55
2659 7645 6.408092 GCAATGGGTGATATATAGGAATCGGA 60.408 42.308 0.00 0.00 0.00 4.55
2936 7949 5.508200 TTTCTACCGCACAGAAAAATTGT 57.492 34.783 2.76 0.00 38.68 2.71
2945 7958 3.853671 GCATCAAATTTTCTACCGCACAG 59.146 43.478 0.00 0.00 0.00 3.66
3033 8046 5.596361 ACTGTTCATGTAATGTTTTGACCCA 59.404 36.000 0.00 0.00 46.80 4.51
3085 8098 7.846644 ATTTGAACATCTAAGAAGCTCTCAG 57.153 36.000 0.00 0.00 0.00 3.35
3115 8128 3.119495 GCATGAGGTACGCTCCAATTTTT 60.119 43.478 0.00 0.00 0.00 1.94
3201 8217 1.020861 CATCTGCACCTGCGCTAACA 61.021 55.000 9.73 0.00 45.83 2.41
3210 8226 2.729479 CCCGAGCTCATCTGCACCT 61.729 63.158 15.40 0.00 34.99 4.00
3233 8249 6.447162 GTTTCAAAGACCGAAAATCCATCTT 58.553 36.000 0.00 0.00 34.32 2.40


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

AutoCloner maintained by Alex Coulton.