Multiple sequence alignment - TraesCS4B01G235900

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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 TraesCS4B01G235900 chr4B 100.000 5662 0 0 1 5662 493526173 493531834 0.000000e+00 10456
1 TraesCS4B01G235900 chr4B 95.455 550 25 0 5113 5662 133610960 133611509 0.000000e+00 878
2 TraesCS4B01G235900 chr4B 87.437 398 28 13 2748 3136 184601009 184601393 6.730000e-119 438
3 TraesCS4B01G235900 chr4B 83.983 231 31 3 1 228 616753596 616753369 3.440000e-52 217
4 TraesCS4B01G235900 chr4D 93.970 4677 159 60 298 4898 399530479 399535108 0.000000e+00 6961
5 TraesCS4B01G235900 chr4D 86.692 263 30 2 2 259 399530211 399530473 2.580000e-73 287
6 TraesCS4B01G235900 chr4D 82.383 193 12 8 4947 5117 399535105 399535297 1.270000e-31 148
7 TraesCS4B01G235900 chr4A 92.470 4847 180 54 294 5045 57162505 57167261 0.000000e+00 6758
8 TraesCS4B01G235900 chr4A 95.795 547 23 0 5116 5662 701948074 701947528 0.000000e+00 883
9 TraesCS4B01G235900 chr4A 84.314 204 24 4 2 201 629355576 629355775 5.790000e-45 193
10 TraesCS4B01G235900 chr2B 96.350 548 18 2 5116 5662 229782057 229782603 0.000000e+00 900
11 TraesCS4B01G235900 chr7B 95.795 547 23 0 5116 5662 439997024 439997570 0.000000e+00 883
12 TraesCS4B01G235900 chr7B 95.430 547 25 0 5116 5662 192454529 192453983 0.000000e+00 872
13 TraesCS4B01G235900 chr7B 95.430 547 24 1 5116 5662 66170677 66170132 0.000000e+00 870
14 TraesCS4B01G235900 chr5B 95.596 545 24 0 5114 5658 542208995 542209539 0.000000e+00 874
15 TraesCS4B01G235900 chr5B 94.909 550 28 0 5113 5662 89742935 89743484 0.000000e+00 861
16 TraesCS4B01G235900 chr5B 86.614 127 15 2 4033 4158 585475640 585475765 7.650000e-29 139
17 TraesCS4B01G235900 chr1B 95.082 549 26 1 5114 5662 38013342 38013889 0.000000e+00 863
18 TraesCS4B01G235900 chr1D 87.282 401 25 15 2748 3136 403278531 403278145 8.710000e-118 435
19 TraesCS4B01G235900 chr2D 87.250 400 26 16 2748 3136 579178649 579179034 3.130000e-117 433
20 TraesCS4B01G235900 chr3A 86.611 239 26 5 6 242 712530493 712530727 5.630000e-65 259
21 TraesCS4B01G235900 chr3A 80.198 303 45 12 1 296 522265848 522266142 4.440000e-51 213
22 TraesCS4B01G235900 chr3D 84.127 252 36 3 6 254 550687477 550687227 2.040000e-59 241
23 TraesCS4B01G235900 chr3D 80.405 296 42 12 6 293 401891568 401891855 1.600000e-50 211
24 TraesCS4B01G235900 chr3D 79.530 298 50 9 2 293 523531837 523532129 9.620000e-48 202
25 TraesCS4B01G235900 chr6D 84.279 229 28 5 6 234 362992553 362992773 3.440000e-52 217
26 TraesCS4B01G235900 chr5A 88.387 155 11 2 2748 2896 615832928 615832775 4.510000e-41 180
27 TraesCS4B01G235900 chr5A 85.827 127 16 2 4033 4158 597256923 597257048 3.560000e-27 134
28 TraesCS4B01G235900 chr7D 82.938 211 19 13 2930 3136 559288468 559288271 2.100000e-39 174
29 TraesCS4B01G235900 chr7D 90.625 128 5 2 2748 2869 559288594 559288468 4.540000e-36 163
30 TraesCS4B01G235900 chr5D 85.827 127 16 2 4033 4158 477986488 477986613 3.560000e-27 134


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 TraesCS4B01G235900 chr4B 493526173 493531834 5661 False 10456.000000 10456 100.000000 1 5662 1 chr4B.!!$F3 5661
1 TraesCS4B01G235900 chr4B 133610960 133611509 549 False 878.000000 878 95.455000 5113 5662 1 chr4B.!!$F1 549
2 TraesCS4B01G235900 chr4D 399530211 399535297 5086 False 2465.333333 6961 87.681667 2 5117 3 chr4D.!!$F1 5115
3 TraesCS4B01G235900 chr4A 57162505 57167261 4756 False 6758.000000 6758 92.470000 294 5045 1 chr4A.!!$F1 4751
4 TraesCS4B01G235900 chr4A 701947528 701948074 546 True 883.000000 883 95.795000 5116 5662 1 chr4A.!!$R1 546
5 TraesCS4B01G235900 chr2B 229782057 229782603 546 False 900.000000 900 96.350000 5116 5662 1 chr2B.!!$F1 546
6 TraesCS4B01G235900 chr7B 439997024 439997570 546 False 883.000000 883 95.795000 5116 5662 1 chr7B.!!$F1 546
7 TraesCS4B01G235900 chr7B 192453983 192454529 546 True 872.000000 872 95.430000 5116 5662 1 chr7B.!!$R2 546
8 TraesCS4B01G235900 chr7B 66170132 66170677 545 True 870.000000 870 95.430000 5116 5662 1 chr7B.!!$R1 546
9 TraesCS4B01G235900 chr5B 542208995 542209539 544 False 874.000000 874 95.596000 5114 5658 1 chr5B.!!$F2 544
10 TraesCS4B01G235900 chr5B 89742935 89743484 549 False 861.000000 861 94.909000 5113 5662 1 chr5B.!!$F1 549
11 TraesCS4B01G235900 chr1B 38013342 38013889 547 False 863.000000 863 95.082000 5114 5662 1 chr1B.!!$F1 548

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
220 226 0.036952 ATGTGGACGCAGGACAGAAG 60.037 55.0 0.00 0.0 0.00 2.85 F
1016 1044 0.179065 TTGATGAGAGCGATGGCCAG 60.179 55.0 13.05 0.0 41.24 4.85 F
1140 1171 0.824109 CTATGTCCGCTTCTCCCACA 59.176 55.0 0.00 0.0 0.00 4.17 F
2476 2577 0.329596 ACCTGATTGAACCTGCCTCC 59.670 55.0 0.00 0.0 0.00 4.30 F
3337 3451 0.039527 AAAACAATCTCAACGCGCCC 60.040 50.0 5.73 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 1635 0.395311 TCTTGGTAGATCGCCTCCGT 60.395 55.000 10.06 0.00 35.54 4.69 R
1999 2049 1.621317 TGAGCAAGTTGGGATCGTACA 59.379 47.619 4.75 0.00 0.00 2.90 R
2871 2979 2.618816 CCTGGCAGCCTTGTCTTCATTA 60.619 50.000 14.15 0.00 0.00 1.90 R
4049 4177 1.226575 CTTGATCGCGGCTACGTCA 60.227 57.895 6.13 0.00 43.45 4.35 R
5000 5144 0.318529 CATCAGCTCAGTCCCGATCG 60.319 60.000 8.51 8.51 0.00 3.69 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
36 37 4.649692 GATCTTGTGGAGCATATGTGGAT 58.350 43.478 4.29 0.00 0.00 3.41
119 120 7.838771 AACAAGACCTATGTATTTTCGGTAC 57.161 36.000 0.00 0.00 0.00 3.34
121 122 5.192327 AGACCTATGTATTTTCGGTACCG 57.808 43.478 28.66 28.66 41.35 4.02
137 140 3.867493 GGTACCGACATTTGCTACTTACC 59.133 47.826 0.00 0.00 0.00 2.85
140 143 3.007614 ACCGACATTTGCTACTTACCTGT 59.992 43.478 0.00 0.00 0.00 4.00
150 153 4.039852 TGCTACTTACCTGTGACATTGACA 59.960 41.667 0.00 0.00 0.00 3.58
163 166 4.739716 TGACATTGACATGTATGATCGACG 59.260 41.667 14.22 0.00 44.22 5.12
164 167 4.932146 ACATTGACATGTATGATCGACGA 58.068 39.130 14.22 0.00 42.24 4.20
165 168 4.978580 ACATTGACATGTATGATCGACGAG 59.021 41.667 14.22 0.00 42.24 4.18
176 179 3.261580 TGATCGACGAGCATGAATTTGT 58.738 40.909 12.49 0.00 0.00 2.83
191 197 7.095940 GCATGAATTTGTATGAATTTGATCCGG 60.096 37.037 0.00 0.00 29.75 5.14
208 214 6.464222 TGATCCGGATTTAAGATATGTGGAC 58.536 40.000 20.22 0.00 0.00 4.02
214 220 4.746535 TTTAAGATATGTGGACGCAGGA 57.253 40.909 0.00 0.00 0.00 3.86
220 226 0.036952 ATGTGGACGCAGGACAGAAG 60.037 55.000 0.00 0.00 0.00 2.85
225 231 2.101415 TGGACGCAGGACAGAAGATATG 59.899 50.000 0.00 0.00 0.00 1.78
226 232 2.362397 GGACGCAGGACAGAAGATATGA 59.638 50.000 0.00 0.00 0.00 2.15
227 233 3.551863 GGACGCAGGACAGAAGATATGAG 60.552 52.174 0.00 0.00 0.00 2.90
234 240 1.342074 CAGAAGATATGAGGGGCCGA 58.658 55.000 0.00 0.00 0.00 5.54
259 265 0.956633 GCCATCCACGGACGTATAGA 59.043 55.000 0.00 0.00 0.00 1.98
261 267 2.671351 GCCATCCACGGACGTATAGATG 60.671 54.545 17.55 17.55 33.18 2.90
262 268 2.817844 CCATCCACGGACGTATAGATGA 59.182 50.000 22.40 6.23 34.25 2.92
263 269 3.254903 CCATCCACGGACGTATAGATGAA 59.745 47.826 22.40 0.00 34.25 2.57
264 270 3.976793 TCCACGGACGTATAGATGAAC 57.023 47.619 0.00 0.00 0.00 3.18
265 271 3.281158 TCCACGGACGTATAGATGAACA 58.719 45.455 0.00 0.00 0.00 3.18
266 272 3.314357 TCCACGGACGTATAGATGAACAG 59.686 47.826 0.00 0.00 0.00 3.16
267 273 3.314357 CCACGGACGTATAGATGAACAGA 59.686 47.826 0.00 0.00 0.00 3.41
268 274 4.023107 CCACGGACGTATAGATGAACAGAT 60.023 45.833 0.00 0.00 0.00 2.90
269 275 5.507482 CCACGGACGTATAGATGAACAGATT 60.507 44.000 0.00 0.00 0.00 2.40
270 276 5.977725 CACGGACGTATAGATGAACAGATTT 59.022 40.000 0.00 0.00 0.00 2.17
271 277 5.977725 ACGGACGTATAGATGAACAGATTTG 59.022 40.000 0.00 0.00 0.00 2.32
272 278 5.107837 CGGACGTATAGATGAACAGATTTGC 60.108 44.000 0.00 0.00 0.00 3.68
273 279 5.177696 GGACGTATAGATGAACAGATTTGCC 59.822 44.000 0.00 0.00 0.00 4.52
274 280 5.670485 ACGTATAGATGAACAGATTTGCCA 58.330 37.500 0.00 0.00 0.00 4.92
275 281 6.112734 ACGTATAGATGAACAGATTTGCCAA 58.887 36.000 0.00 0.00 0.00 4.52
276 282 6.258727 ACGTATAGATGAACAGATTTGCCAAG 59.741 38.462 0.00 0.00 0.00 3.61
277 283 6.258727 CGTATAGATGAACAGATTTGCCAAGT 59.741 38.462 0.00 0.00 0.00 3.16
278 284 6.690194 ATAGATGAACAGATTTGCCAAGTC 57.310 37.500 0.00 0.00 0.00 3.01
279 285 3.760684 AGATGAACAGATTTGCCAAGTCC 59.239 43.478 0.00 0.00 0.00 3.85
280 286 1.879380 TGAACAGATTTGCCAAGTCCG 59.121 47.619 0.00 0.00 0.00 4.79
281 287 1.200020 GAACAGATTTGCCAAGTCCGG 59.800 52.381 0.00 0.00 0.00 5.14
289 295 2.360350 CCAAGTCCGGCTGCACAT 60.360 61.111 0.50 0.00 0.00 3.21
290 296 2.693762 CCAAGTCCGGCTGCACATG 61.694 63.158 0.50 0.00 0.00 3.21
291 297 3.058160 AAGTCCGGCTGCACATGC 61.058 61.111 0.50 0.00 42.50 4.06
292 298 3.557903 AAGTCCGGCTGCACATGCT 62.558 57.895 5.31 0.00 42.66 3.79
296 302 1.137404 CCGGCTGCACATGCTTTAC 59.863 57.895 5.31 0.00 42.66 2.01
313 319 1.108776 TACCGGATACACTCACCTGC 58.891 55.000 9.46 0.00 0.00 4.85
316 322 1.107114 CGGATACACTCACCTGCTCT 58.893 55.000 0.00 0.00 0.00 4.09
462 468 1.136695 GAGTGAGATGGAGAGGCACTG 59.863 57.143 0.00 0.00 41.55 3.66
601 617 1.272480 CCCCAGTAAAAAGAGGGTGGG 60.272 57.143 0.00 0.00 43.80 4.61
660 678 6.128007 ACACGACATCTTTTATCCAATCCAAC 60.128 38.462 0.00 0.00 0.00 3.77
688 706 1.070758 CCCCATGGAACGAGAGGTATG 59.929 57.143 15.22 0.00 0.00 2.39
735 754 4.872691 CCTAGATTTTATATGCCCGCTCTG 59.127 45.833 0.00 0.00 0.00 3.35
834 858 3.074390 TCCCTCTCATTCCTTTTGCTCAA 59.926 43.478 0.00 0.00 0.00 3.02
1016 1044 0.179065 TTGATGAGAGCGATGGCCAG 60.179 55.000 13.05 0.00 41.24 4.85
1017 1045 1.960250 GATGAGAGCGATGGCCAGC 60.960 63.158 12.07 12.07 41.24 4.85
1018 1046 3.804153 ATGAGAGCGATGGCCAGCG 62.804 63.158 37.66 37.66 43.89 5.18
1038 1066 2.033602 GGCGGCAACTGGTTAGGT 59.966 61.111 3.07 0.00 0.00 3.08
1099 1130 3.934391 GAACCCGACCACGCTCAGG 62.934 68.421 0.00 0.00 38.29 3.86
1102 1133 4.803426 CCGACCACGCTCAGGCTC 62.803 72.222 0.00 0.00 38.29 4.70
1103 1134 4.056125 CGACCACGCTCAGGCTCA 62.056 66.667 0.00 0.00 36.09 4.26
1104 1135 2.343758 GACCACGCTCAGGCTCAA 59.656 61.111 0.00 0.00 36.09 3.02
1140 1171 0.824109 CTATGTCCGCTTCTCCCACA 59.176 55.000 0.00 0.00 0.00 4.17
1270 1301 1.954258 GCGTCTACTACTCCCACCACT 60.954 57.143 0.00 0.00 0.00 4.00
1319 1350 1.340308 CCTGTGCATCATGGAAGGTCA 60.340 52.381 0.00 0.00 0.00 4.02
1355 1386 6.350949 GCACTTCTCTCTCTATCTCTTGGTTT 60.351 42.308 0.00 0.00 0.00 3.27
1358 1389 5.832221 TCTCTCTCTATCTCTTGGTTTCCA 58.168 41.667 0.00 0.00 0.00 3.53
1376 1408 1.534028 CATTGTTGCAACGCCGATAC 58.466 50.000 23.79 0.00 0.00 2.24
1399 1431 0.955428 TCTTTCGTGCTGCCATCACC 60.955 55.000 0.00 0.00 0.00 4.02
1413 1445 1.701292 CATCACCTAGGGATGATGCCA 59.299 52.381 24.95 0.00 44.13 4.92
1458 1490 4.292145 TTGGGTGGCGGCAATGGA 62.292 61.111 15.50 0.00 0.00 3.41
1591 1635 1.134220 ACTTCCAGCACTTGACGGAAA 60.134 47.619 0.00 0.00 37.10 3.13
1612 1656 1.693627 GGAGGCGATCTACCAAGAGA 58.306 55.000 4.63 0.00 34.49 3.10
1902 1952 2.328099 CCAGAAGCAGCCCGTTCAC 61.328 63.158 0.00 0.00 0.00 3.18
2008 2058 2.943033 CCTTTGGGTTCATGTACGATCC 59.057 50.000 0.00 0.00 0.00 3.36
2069 2155 5.404096 TGCTGATCATGTGCAAATAAACTG 58.596 37.500 5.70 0.00 33.48 3.16
2157 2253 5.121811 TGTAGTGGCAGTACTAGTACTAGC 58.878 45.833 30.34 30.00 43.98 3.42
2212 2309 5.869649 TGTCCTAGTTAGCAGCATTGATA 57.130 39.130 0.00 0.00 0.00 2.15
2306 2403 6.171921 TCCAAAACAAATTAATGCCATGGAG 58.828 36.000 18.40 0.00 29.99 3.86
2330 2430 6.375455 AGCAGTTAGATTTATTCACCCACAAG 59.625 38.462 0.00 0.00 0.00 3.16
2355 2455 4.761739 TGCTTAGTTTGTTTCATCCCTCAG 59.238 41.667 0.00 0.00 0.00 3.35
2465 2565 6.047870 TGTTTTTGACCAAATCACCTGATTG 58.952 36.000 1.23 0.00 43.41 2.67
2476 2577 0.329596 ACCTGATTGAACCTGCCTCC 59.670 55.000 0.00 0.00 0.00 4.30
2743 2850 2.706339 ATGTCAACATCTCTGGCTCC 57.294 50.000 0.00 0.00 28.78 4.70
2871 2979 2.487775 TGTGGGCTAGGTGGTTATGAT 58.512 47.619 0.00 0.00 0.00 2.45
2919 3027 3.801698 TGATCTGGCTGCTCTGAAATAC 58.198 45.455 0.00 0.00 0.00 1.89
2969 3077 2.872245 CGGTATGGATGACAACATGGAC 59.128 50.000 0.00 0.00 36.82 4.02
2993 3101 4.645588 TGGTTCATGGAAACTAAAACCGTT 59.354 37.500 0.00 0.00 37.97 4.44
3030 3138 9.481340 TCTATAATGTGAACTGATATGTTGAGC 57.519 33.333 0.00 0.00 0.00 4.26
3118 3226 5.646606 GTTGCACACTTGAGAAGGTAAAAA 58.353 37.500 0.00 0.00 0.00 1.94
3263 3372 4.051922 CGAGGTAAGATGCCTACACATTC 58.948 47.826 0.00 0.00 36.29 2.67
3272 3381 2.237143 TGCCTACACATTCTCCCTCAAG 59.763 50.000 0.00 0.00 0.00 3.02
3337 3451 0.039527 AAAACAATCTCAACGCGCCC 60.040 50.000 5.73 0.00 0.00 6.13
3439 3553 2.155155 CGGCACTTTCAGTAAGAACGAC 59.845 50.000 0.00 0.00 37.30 4.34
3440 3554 3.128349 GGCACTTTCAGTAAGAACGACA 58.872 45.455 0.00 0.00 37.30 4.35
3441 3555 3.746492 GGCACTTTCAGTAAGAACGACAT 59.254 43.478 0.00 0.00 37.30 3.06
3442 3556 4.213482 GGCACTTTCAGTAAGAACGACATT 59.787 41.667 0.00 0.00 37.30 2.71
3443 3557 5.277828 GGCACTTTCAGTAAGAACGACATTT 60.278 40.000 0.00 0.00 37.30 2.32
3544 3661 3.828875 GCTAATCTCAAGTAGCAGGGT 57.171 47.619 0.45 0.00 45.95 4.34
3617 3736 5.009210 GCTAGAGAATGTAGTAGACACCCAG 59.991 48.000 0.00 0.00 42.17 4.45
3697 3818 4.111375 ACTTTAGCTCGTGGAGTACATG 57.889 45.455 0.00 0.00 37.44 3.21
3698 3819 3.762288 ACTTTAGCTCGTGGAGTACATGA 59.238 43.478 0.00 0.00 42.69 3.07
3792 3916 2.224305 GGCTGTGACCTCTGTACAAAGT 60.224 50.000 0.00 0.00 0.00 2.66
3796 3920 5.701290 GCTGTGACCTCTGTACAAAGTTATT 59.299 40.000 0.00 0.00 0.00 1.40
3832 3956 4.140900 TGAATACCCCCTTGGACTGAAAAA 60.141 41.667 0.00 0.00 38.00 1.94
3970 4095 7.576287 CGTCTTCTAAAGTAACATACCTCACCA 60.576 40.741 0.00 0.00 0.00 4.17
3973 4098 9.449719 CTTCTAAAGTAACATACCTCACCATTT 57.550 33.333 0.00 0.00 0.00 2.32
3974 4099 8.786826 TCTAAAGTAACATACCTCACCATTTG 57.213 34.615 0.00 0.00 0.00 2.32
3975 4100 8.380099 TCTAAAGTAACATACCTCACCATTTGT 58.620 33.333 0.00 0.00 0.00 2.83
4028 4156 4.713553 TGAATCTTTGTACAGCCACTCAA 58.286 39.130 0.00 0.00 0.00 3.02
4049 4177 1.341156 AAGAAGCAGCCGAGGCCTAT 61.341 55.000 4.42 0.00 43.17 2.57
4253 4381 0.615331 ATGCCGAAGAAGGAAGCTCA 59.385 50.000 0.00 0.00 0.00 4.26
4421 4552 2.788176 CGCGCATGACATCGACGTT 61.788 57.895 8.75 0.00 0.00 3.99
4433 4564 2.163818 TCGACGTTTCAGGCAAGATT 57.836 45.000 0.00 0.00 0.00 2.40
4626 4757 0.250510 GCCGAATTCCTCCATCCCTC 60.251 60.000 0.00 0.00 0.00 4.30
4652 4783 1.077140 TGTGTTTGCTGCCTGGACA 60.077 52.632 0.00 0.00 0.00 4.02
4699 4830 0.610232 AATCTTGCTGTCACTGGCCC 60.610 55.000 0.00 0.00 0.00 5.80
4706 4837 0.886490 CTGTCACTGGCCCTGTTGTC 60.886 60.000 0.00 0.00 0.00 3.18
4711 4842 0.250166 ACTGGCCCTGTTGTCGTAAC 60.250 55.000 0.00 0.00 0.00 2.50
4753 4884 0.675633 GGTTGCTCATGCCACTTGTT 59.324 50.000 0.00 0.00 38.71 2.83
4756 4887 3.243704 GGTTGCTCATGCCACTTGTTTTA 60.244 43.478 0.00 0.00 38.71 1.52
4881 5018 6.081872 AGCAGTACGTAGTGTTCTTACTTT 57.918 37.500 26.80 4.27 45.73 2.66
4883 5020 6.016443 AGCAGTACGTAGTGTTCTTACTTTCT 60.016 38.462 26.80 11.72 45.73 2.52
5000 5144 4.123497 AGAAAAGTGAAAGGGTTTGTGC 57.877 40.909 0.00 0.00 0.00 4.57
5035 5179 3.448686 CTGATGTGTCTTCATCCGTACC 58.551 50.000 4.59 0.00 42.24 3.34
5036 5180 3.096852 TGATGTGTCTTCATCCGTACCT 58.903 45.455 4.59 0.00 42.24 3.08
5039 5183 4.345859 TGTGTCTTCATCCGTACCTTTT 57.654 40.909 0.00 0.00 0.00 2.27
5076 5242 8.304596 GGTATAGATTCACAGGATTACAATCGA 58.695 37.037 0.00 0.00 36.27 3.59
5079 5245 6.045318 AGATTCACAGGATTACAATCGACAG 58.955 40.000 0.00 0.00 36.27 3.51
5081 5247 3.056179 TCACAGGATTACAATCGACAGCA 60.056 43.478 0.00 0.00 36.27 4.41
5090 5256 3.990092 ACAATCGACAGCAACTAGTTCA 58.010 40.909 4.77 0.00 0.00 3.18
5095 5261 1.721926 GACAGCAACTAGTTCAGCGAC 59.278 52.381 4.77 1.54 0.00 5.19
5096 5262 1.071605 CAGCAACTAGTTCAGCGACC 58.928 55.000 4.77 0.00 0.00 4.79
5165 5332 0.601558 CGCCTAAATAGAGCGGCCTA 59.398 55.000 0.00 0.00 45.88 3.93
5197 5364 2.365105 CTAGTTCGGCCCCTGGGA 60.365 66.667 16.20 0.00 37.50 4.37
5282 5449 1.872237 CGTTCCCGCTCTCAAAAGACA 60.872 52.381 0.00 0.00 0.00 3.41
5284 5451 1.048601 TCCCGCTCTCAAAAGACACT 58.951 50.000 0.00 0.00 0.00 3.55
5295 5462 1.981256 AAAGACACTGCAAATCCGGT 58.019 45.000 0.00 0.00 0.00 5.28
5296 5463 2.851263 AAGACACTGCAAATCCGGTA 57.149 45.000 0.00 0.00 0.00 4.02
5300 5467 3.006940 GACACTGCAAATCCGGTAATCA 58.993 45.455 0.00 0.00 0.00 2.57
5449 5616 2.809861 CTTCGGTGCTGGGCTGTGAT 62.810 60.000 0.00 0.00 0.00 3.06
5512 5679 4.382320 GGGCTTGGCGTCCGTGTA 62.382 66.667 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.740832 CACAAGATCGTTGAGTAGTTGCA 59.259 43.478 10.61 0.00 0.00 4.08
7 8 1.344438 TGCTCCACAAGATCGTTGAGT 59.656 47.619 10.61 0.00 32.59 3.41
36 37 7.589958 TTAGCTCTTTGGTTTTTATTGTGGA 57.410 32.000 0.00 0.00 0.00 4.02
45 46 9.860898 CAGCTTAAATATTAGCTCTTTGGTTTT 57.139 29.630 9.37 0.00 45.54 2.43
90 91 9.537192 CCGAAAATACATAGGTCTTGTTACATA 57.463 33.333 0.00 0.00 0.00 2.29
115 116 3.867493 GGTAAGTAGCAAATGTCGGTACC 59.133 47.826 0.16 0.16 37.93 3.34
119 120 3.370978 CACAGGTAAGTAGCAAATGTCGG 59.629 47.826 0.00 0.00 0.00 4.79
121 122 4.994852 TGTCACAGGTAAGTAGCAAATGTC 59.005 41.667 0.00 0.00 0.00 3.06
137 140 5.750067 TCGATCATACATGTCAATGTCACAG 59.250 40.000 0.00 0.00 43.85 3.66
140 143 4.739716 CGTCGATCATACATGTCAATGTCA 59.260 41.667 0.00 0.00 43.85 3.58
150 153 3.923017 TCATGCTCGTCGATCATACAT 57.077 42.857 10.99 1.06 0.00 2.29
163 166 8.975439 GGATCAAATTCATACAAATTCATGCTC 58.025 33.333 0.00 0.00 0.00 4.26
164 167 7.650504 CGGATCAAATTCATACAAATTCATGCT 59.349 33.333 0.00 0.00 0.00 3.79
165 168 7.095940 CCGGATCAAATTCATACAAATTCATGC 60.096 37.037 0.00 0.00 0.00 4.06
191 197 5.177696 GTCCTGCGTCCACATATCTTAAATC 59.822 44.000 0.00 0.00 0.00 2.17
203 209 0.247736 ATCTTCTGTCCTGCGTCCAC 59.752 55.000 0.00 0.00 0.00 4.02
208 214 2.288702 CCCTCATATCTTCTGTCCTGCG 60.289 54.545 0.00 0.00 0.00 5.18
214 220 1.051812 CGGCCCCTCATATCTTCTGT 58.948 55.000 0.00 0.00 0.00 3.41
220 226 0.250513 GTCCATCGGCCCCTCATATC 59.749 60.000 0.00 0.00 0.00 1.63
243 249 3.887110 TGTTCATCTATACGTCCGTGGAT 59.113 43.478 1.98 1.48 0.00 3.41
247 253 5.769484 AATCTGTTCATCTATACGTCCGT 57.231 39.130 0.00 0.00 0.00 4.69
253 259 7.254932 GGACTTGGCAAATCTGTTCATCTATAC 60.255 40.741 8.72 0.00 0.00 1.47
259 265 2.489329 CGGACTTGGCAAATCTGTTCAT 59.511 45.455 9.28 0.00 0.00 2.57
261 267 1.200020 CCGGACTTGGCAAATCTGTTC 59.800 52.381 15.57 1.50 0.00 3.18
262 268 1.247567 CCGGACTTGGCAAATCTGTT 58.752 50.000 15.57 0.00 0.00 3.16
263 269 2.946947 CCGGACTTGGCAAATCTGT 58.053 52.632 15.57 3.20 0.00 3.41
272 278 2.360350 ATGTGCAGCCGGACTTGG 60.360 61.111 5.05 0.00 33.94 3.61
273 279 2.872557 CATGTGCAGCCGGACTTG 59.127 61.111 5.05 0.18 33.94 3.16
274 280 3.058160 GCATGTGCAGCCGGACTT 61.058 61.111 5.05 0.00 41.59 3.01
275 281 3.557903 AAGCATGTGCAGCCGGACT 62.558 57.895 5.05 0.00 45.16 3.85
276 282 1.305219 TAAAGCATGTGCAGCCGGAC 61.305 55.000 5.05 0.00 45.16 4.79
277 283 1.002746 TAAAGCATGTGCAGCCGGA 60.003 52.632 5.05 0.00 45.16 5.14
278 284 1.137404 GTAAAGCATGTGCAGCCGG 59.863 57.895 7.83 0.00 45.16 6.13
279 285 1.137404 GGTAAAGCATGTGCAGCCG 59.863 57.895 7.83 0.00 45.16 5.52
280 286 1.137404 CGGTAAAGCATGTGCAGCC 59.863 57.895 7.83 2.98 45.16 4.85
281 287 1.137404 CCGGTAAAGCATGTGCAGC 59.863 57.895 7.83 0.00 45.16 5.25
282 288 1.382522 ATCCGGTAAAGCATGTGCAG 58.617 50.000 0.00 0.00 45.16 4.41
283 289 2.285083 GTATCCGGTAAAGCATGTGCA 58.715 47.619 0.00 0.00 45.16 4.57
284 290 2.031683 GTGTATCCGGTAAAGCATGTGC 59.968 50.000 0.00 0.00 42.49 4.57
285 291 3.531538 AGTGTATCCGGTAAAGCATGTG 58.468 45.455 0.00 0.00 0.00 3.21
286 292 3.196901 TGAGTGTATCCGGTAAAGCATGT 59.803 43.478 0.00 0.00 0.00 3.21
287 293 3.555956 GTGAGTGTATCCGGTAAAGCATG 59.444 47.826 0.00 0.00 0.00 4.06
288 294 3.431766 GGTGAGTGTATCCGGTAAAGCAT 60.432 47.826 0.00 0.00 0.00 3.79
289 295 2.093869 GGTGAGTGTATCCGGTAAAGCA 60.094 50.000 0.00 0.00 0.00 3.91
290 296 2.167900 AGGTGAGTGTATCCGGTAAAGC 59.832 50.000 0.00 0.00 0.00 3.51
291 297 3.782046 CAGGTGAGTGTATCCGGTAAAG 58.218 50.000 0.00 0.00 0.00 1.85
292 298 2.093869 GCAGGTGAGTGTATCCGGTAAA 60.094 50.000 0.00 0.00 0.00 2.01
296 302 0.103208 GAGCAGGTGAGTGTATCCGG 59.897 60.000 0.00 0.00 0.00 5.14
313 319 2.168521 ACGTGAGAGGAGAGAGAGAGAG 59.831 54.545 0.00 0.00 0.00 3.20
316 322 3.516300 AGTTACGTGAGAGGAGAGAGAGA 59.484 47.826 0.00 0.00 0.00 3.10
462 468 2.128507 CAGCCTCCTCCTACCGTCC 61.129 68.421 0.00 0.00 0.00 4.79
601 617 2.439245 GTCCCTTGGGTTCCCACC 59.561 66.667 10.41 0.00 43.37 4.61
619 635 1.324435 CGTGTGTGTGTGTGTCTTCAG 59.676 52.381 0.00 0.00 0.00 3.02
660 678 0.464373 CGTTCCATGGGGATCTGTGG 60.464 60.000 13.02 0.00 44.48 4.17
688 706 0.469144 TGTTTGTTCTTGGCCTCCCC 60.469 55.000 3.32 0.00 0.00 4.81
735 754 4.261909 CCTGAGCCCTAATGCAATTTCATC 60.262 45.833 0.00 0.00 37.87 2.92
1038 1066 2.121832 TGCGGGGAGAGGGAGAAA 59.878 61.111 0.00 0.00 0.00 2.52
1270 1301 2.186644 CGTGATGGGCATGACGGA 59.813 61.111 0.00 0.00 43.07 4.69
1319 1350 1.415659 AGAGAAGTGCAACAGTGAGCT 59.584 47.619 12.21 0.00 41.43 4.09
1355 1386 1.240641 ATCGGCGTTGCAACAATGGA 61.241 50.000 28.01 18.54 0.00 3.41
1358 1389 1.448985 AGTATCGGCGTTGCAACAAT 58.551 45.000 28.01 16.99 0.00 2.71
1376 1408 2.938451 TGATGGCAGCACGAAAGATTAG 59.062 45.455 0.00 0.00 0.00 1.73
1399 1431 1.066573 GGACGATGGCATCATCCCTAG 60.067 57.143 27.81 12.19 45.20 3.02
1413 1445 3.127352 GAGCTTCGGCGAGGACGAT 62.127 63.158 23.87 5.62 44.78 3.73
1591 1635 0.395311 TCTTGGTAGATCGCCTCCGT 60.395 55.000 10.06 0.00 35.54 4.69
1593 1637 1.338655 GTCTCTTGGTAGATCGCCTCC 59.661 57.143 10.06 2.23 0.00 4.30
1902 1952 2.444624 CGTGTCGATGGACTTGCGG 61.445 63.158 9.41 0.00 43.79 5.69
1994 2044 3.181510 GCAAGTTGGGATCGTACATGAAC 60.182 47.826 4.75 0.00 0.00 3.18
1999 2049 1.621317 TGAGCAAGTTGGGATCGTACA 59.379 47.619 4.75 0.00 0.00 2.90
2003 2053 3.535561 ACTATTGAGCAAGTTGGGATCG 58.464 45.455 4.75 0.00 0.00 3.69
2054 2137 6.985117 AGTTGACATCAGTTTATTTGCACAT 58.015 32.000 0.00 0.00 0.00 3.21
2128 2217 5.017490 ACTAGTACTGCCACTACATGTTCT 58.983 41.667 2.30 0.00 0.00 3.01
2132 2221 6.293516 GCTAGTACTAGTACTGCCACTACATG 60.294 46.154 35.52 17.33 45.25 3.21
2142 2236 6.678409 GCTCAAACAGGCTAGTACTAGTACTG 60.678 46.154 35.52 32.46 45.25 2.74
2157 2253 3.989817 GCAAAACATAAGGCTCAAACAGG 59.010 43.478 0.00 0.00 0.00 4.00
2270 2367 6.642707 ATTTGTTTTGGAACGAAGTATGGA 57.357 33.333 0.00 0.00 45.00 3.41
2276 2373 6.201806 TGGCATTAATTTGTTTTGGAACGAAG 59.798 34.615 0.00 0.00 41.28 3.79
2306 2403 6.374333 TCTTGTGGGTGAATAAATCTAACTGC 59.626 38.462 0.00 0.00 0.00 4.40
2330 2430 5.415701 TGAGGGATGAAACAAACTAAGCATC 59.584 40.000 0.00 0.00 33.29 3.91
2355 2455 3.790123 GCATTGCGCTCAGTCTTTAATCC 60.790 47.826 9.73 0.00 37.77 3.01
2465 2565 5.656859 ACAATATAAAAAGGGAGGCAGGTTC 59.343 40.000 0.00 0.00 0.00 3.62
2743 2850 3.996150 AACTGCAAGAAGACACCATTG 57.004 42.857 0.00 0.00 37.43 2.82
2871 2979 2.618816 CCTGGCAGCCTTGTCTTCATTA 60.619 50.000 14.15 0.00 0.00 1.90
2969 3077 4.277423 ACGGTTTTAGTTTCCATGAACCAG 59.723 41.667 8.79 4.97 37.07 4.00
2993 3101 9.476202 CAGTTCACATTATAGAAACCGATATCA 57.524 33.333 3.12 0.00 0.00 2.15
3010 3118 6.093219 GTGAAGCTCAACATATCAGTTCACAT 59.907 38.462 6.94 0.00 41.31 3.21
3022 3130 3.969287 TCTAGCTGTGAAGCTCAACAT 57.031 42.857 3.00 0.00 45.00 2.71
3030 3138 7.168972 CCTCTCGATAATTTTCTAGCTGTGAAG 59.831 40.741 0.00 0.00 0.00 3.02
3263 3372 8.055279 TGCAATATTTTTCTTACTTGAGGGAG 57.945 34.615 0.00 0.00 0.00 4.30
3337 3451 3.239587 TGATGCCTGAAATGCAACATG 57.760 42.857 0.00 0.00 41.86 3.21
3544 3661 8.507524 AGCATACTAGCATCGATAATAGTACA 57.492 34.615 21.93 10.59 34.49 2.90
3617 3736 6.017026 AGAGGTTTAACAGTAAAAGCTTCTGC 60.017 38.462 12.30 0.00 42.88 4.26
3792 3916 6.657541 GGGTATTCAAGACAGTCAACCAATAA 59.342 38.462 2.66 0.00 0.00 1.40
3796 3920 3.244770 GGGGTATTCAAGACAGTCAACCA 60.245 47.826 2.66 0.00 0.00 3.67
3832 3956 2.530177 CGTCGTGCTAGTGTGATTGAT 58.470 47.619 0.00 0.00 0.00 2.57
3973 4098 9.500785 TTTGTTAAGATCTTCATACATGTGACA 57.499 29.630 12.24 0.00 0.00 3.58
4028 4156 2.267324 GCCTCGGCTGCTTCTTCT 59.733 61.111 0.00 0.00 38.26 2.85
4049 4177 1.226575 CTTGATCGCGGCTACGTCA 60.227 57.895 6.13 0.00 43.45 4.35
4253 4381 2.039624 ACCATCCTCCAGACGCCT 59.960 61.111 0.00 0.00 0.00 5.52
4403 4534 2.278659 AAACGTCGATGTCATGCGCG 62.279 55.000 11.41 0.00 34.81 6.86
4421 4552 5.755409 TGGAGTAGTTAATCTTGCCTGAA 57.245 39.130 0.00 0.00 0.00 3.02
4433 4564 3.760684 GGGAAGACGAGTTGGAGTAGTTA 59.239 47.826 0.00 0.00 0.00 2.24
4552 4683 2.203252 CCATCCACGGGCTCATGG 60.203 66.667 0.00 0.00 37.32 3.66
4626 4757 1.290955 CAGCAAACACAGGCATGGG 59.709 57.895 0.00 0.00 35.24 4.00
4699 4830 1.000955 AGCTCCAGGTTACGACAACAG 59.999 52.381 0.00 0.00 0.00 3.16
4706 4837 2.431057 ACTAATCCAGCTCCAGGTTACG 59.569 50.000 0.00 0.00 0.00 3.18
4711 4842 1.000283 CGCTACTAATCCAGCTCCAGG 60.000 57.143 0.00 0.00 35.57 4.45
4753 4884 1.923356 CCTTGCCTTCCCAGCTTAAA 58.077 50.000 0.00 0.00 0.00 1.52
4756 4887 2.283460 GCCTTGCCTTCCCAGCTT 60.283 61.111 0.00 0.00 0.00 3.74
4799 4930 4.080356 TCCTACGTACCACTACCACTACAT 60.080 45.833 0.00 0.00 0.00 2.29
4908 5045 9.023962 GCATGATAATACATTCCCAGGAAATTA 57.976 33.333 2.65 4.15 37.69 1.40
4910 5047 7.011994 TGCATGATAATACATTCCCAGGAAAT 58.988 34.615 2.65 0.00 37.69 2.17
4911 5048 6.372104 TGCATGATAATACATTCCCAGGAAA 58.628 36.000 2.65 0.00 37.69 3.13
4912 5049 5.951204 TGCATGATAATACATTCCCAGGAA 58.049 37.500 0.68 0.68 38.59 3.36
4942 5079 4.276642 TCCATGCATTGTTGTAAGCCATA 58.723 39.130 0.00 0.00 0.00 2.74
4977 5121 4.566759 GCACAAACCCTTTCACTTTTCTTC 59.433 41.667 0.00 0.00 0.00 2.87
5000 5144 0.318529 CATCAGCTCAGTCCCGATCG 60.319 60.000 8.51 8.51 0.00 3.69
5046 5190 4.792521 ATCCTGTGAATCTATACCTCGC 57.207 45.455 0.00 0.00 0.00 5.03
5047 5191 7.215719 TGTAATCCTGTGAATCTATACCTCG 57.784 40.000 0.00 0.00 0.00 4.63
5048 5192 9.646427 GATTGTAATCCTGTGAATCTATACCTC 57.354 37.037 0.00 0.00 0.00 3.85
5049 5193 8.307483 CGATTGTAATCCTGTGAATCTATACCT 58.693 37.037 0.00 0.00 31.68 3.08
5050 5194 8.304596 TCGATTGTAATCCTGTGAATCTATACC 58.695 37.037 0.00 0.00 31.68 2.73
5051 5195 9.130312 GTCGATTGTAATCCTGTGAATCTATAC 57.870 37.037 0.00 0.00 31.68 1.47
5052 5196 8.856103 TGTCGATTGTAATCCTGTGAATCTATA 58.144 33.333 0.00 0.00 31.68 1.31
5054 5198 7.107639 TGTCGATTGTAATCCTGTGAATCTA 57.892 36.000 0.00 0.00 31.68 1.98
5076 5242 1.605712 GGTCGCTGAACTAGTTGCTGT 60.606 52.381 14.14 0.00 0.00 4.40
5079 5245 0.320421 TGGGTCGCTGAACTAGTTGC 60.320 55.000 14.14 10.33 0.00 4.17
5081 5247 1.002087 CCTTGGGTCGCTGAACTAGTT 59.998 52.381 8.13 8.13 0.00 2.24
5096 5262 1.143970 TTACCCAACCTCCCCCTTGG 61.144 60.000 0.00 0.00 37.30 3.61
5197 5364 1.755008 GACTGGGAGCTAGGTCGCT 60.755 63.158 31.19 17.73 44.33 4.93
5236 5403 5.126384 CCAAGTTTAAATTTCCCGCATCCTA 59.874 40.000 0.00 0.00 0.00 2.94
5282 5449 3.270877 GTCTGATTACCGGATTTGCAGT 58.729 45.455 9.46 0.00 31.82 4.40
5284 5451 2.276201 CGTCTGATTACCGGATTTGCA 58.724 47.619 9.46 0.00 31.82 4.08
5300 5467 1.527034 TGTAACGCCAGACTACGTCT 58.473 50.000 0.00 0.00 44.44 4.18
5555 5722 2.202932 CGGCCTCATCCTGAACGG 60.203 66.667 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.