Multiple sequence alignment - TraesCS4A01G496000

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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 TraesCS4A01G496000 chr4A 100.000 2914 0 0 1 2914 742607817 742604904 0.000000e+00 5382.0
1 TraesCS4A01G496000 chr4A 98.246 57 1 0 255 311 742651574 742651518 1.850000e-17 100.0
2 TraesCS4A01G496000 chr4A 100.000 31 0 0 33 63 742651727 742651697 1.130000e-04 58.4
3 TraesCS4A01G496000 chr7D 89.140 2256 145 38 255 2442 2038171 2035948 0.000000e+00 2717.0
4 TraesCS4A01G496000 chr7D 83.333 456 36 19 2477 2912 2035744 2035309 4.560000e-103 385.0
5 TraesCS4A01G496000 chr7D 83.333 216 12 12 6 205 2038384 2038177 8.300000e-41 178.0
6 TraesCS4A01G496000 chrUn 87.783 1236 87 26 568 1771 81435351 81436554 0.000000e+00 1387.0
7 TraesCS4A01G496000 chrUn 87.783 1236 87 26 568 1771 336021913 336023116 0.000000e+00 1387.0
8 TraesCS4A01G496000 chrUn 84.891 1145 90 46 1737 2831 81436578 81437689 0.000000e+00 1079.0
9 TraesCS4A01G496000 chrUn 84.891 1145 90 46 1737 2831 336023140 336024251 0.000000e+00 1079.0
10 TraesCS4A01G496000 chrUn 88.509 322 16 10 255 573 81434987 81435290 1.280000e-98 370.0
11 TraesCS4A01G496000 chrUn 95.172 145 5 2 429 573 336021710 336021852 8.120000e-56 228.0
12 TraesCS4A01G496000 chrUn 77.725 422 42 29 384 774 423143800 423143400 8.180000e-51 211.0
13 TraesCS4A01G496000 chrUn 77.725 422 42 29 384 774 449239458 449239058 8.180000e-51 211.0
14 TraesCS4A01G496000 chrUn 83.182 220 13 12 1 205 81434771 81434981 2.310000e-41 180.0
15 TraesCS4A01G496000 chr5D 81.008 1727 177 74 448 2111 429290436 429292074 0.000000e+00 1232.0
16 TraesCS4A01G496000 chr5B 80.358 1787 198 80 384 2111 518482444 518484136 0.000000e+00 1214.0
17 TraesCS4A01G496000 chr5B 82.303 825 103 27 1314 2124 518474858 518475653 0.000000e+00 675.0
18 TraesCS4A01G496000 chr5B 74.265 680 73 52 141 774 310664417 310663794 2.960000e-45 193.0
19 TraesCS4A01G496000 chr5A 80.071 1681 190 79 384 2002 545074648 545076245 0.000000e+00 1114.0
20 TraesCS4A01G496000 chr5A 81.843 369 46 14 1757 2111 545060718 545061079 1.020000e-74 291.0
21 TraesCS4A01G496000 chr5A 78.302 424 37 16 794 1196 545059978 545060367 3.780000e-54 222.0
22 TraesCS4A01G496000 chr5A 82.877 146 10 8 1296 1429 545060544 545060686 1.830000e-22 117.0
23 TraesCS4A01G496000 chr1D 78.469 418 39 28 384 771 458737328 458737724 2.920000e-55 226.0
24 TraesCS4A01G496000 chr1D 78.095 420 39 29 384 771 26172289 26172687 1.760000e-52 217.0
25 TraesCS4A01G496000 chr1D 77.725 422 42 29 384 774 319537190 319536790 8.180000e-51 211.0
26 TraesCS4A01G496000 chr1D 77.830 424 39 32 384 774 319556401 319556000 8.180000e-51 211.0
27 TraesCS4A01G496000 chr6D 78.014 423 40 29 384 774 429327276 429326875 1.760000e-52 217.0
28 TraesCS4A01G496000 chr2D 77.962 422 41 28 384 774 1714400 1714000 1.760000e-52 217.0
29 TraesCS4A01G496000 chr2D 83.851 161 21 5 2604 2761 201953698 201953540 6.510000e-32 148.0
30 TraesCS4A01G496000 chr3D 77.778 423 41 29 384 774 53764355 53763954 8.180000e-51 211.0
31 TraesCS4A01G496000 chr3D 75.945 291 47 15 2603 2885 178590082 178590357 8.480000e-26 128.0
32 TraesCS4A01G496000 chr3D 80.328 122 18 6 2596 2715 96413537 96413654 1.440000e-13 87.9
33 TraesCS4A01G496000 chr7A 84.746 177 20 7 599 774 264052218 264052388 1.390000e-38 171.0
34 TraesCS4A01G496000 chr7A 86.916 107 9 4 225 331 138101793 138101692 6.600000e-22 115.0
35 TraesCS4A01G496000 chr4B 77.597 308 46 16 2604 2897 583757443 583757741 6.460000e-37 165.0
36 TraesCS4A01G496000 chr4B 84.672 137 20 1 2595 2730 596644387 596644523 5.070000e-28 135.0
37 TraesCS4A01G496000 chr3B 76.449 276 45 11 2603 2872 257035939 257036200 6.550000e-27 132.0
38 TraesCS4A01G496000 chr2B 86.667 105 9 4 225 329 49663464 49663365 8.540000e-21 111.0
39 TraesCS4A01G496000 chr1A 85.981 107 10 4 225 331 213900043 213900144 3.070000e-20 110.0
40 TraesCS4A01G496000 chr7B 84.762 105 10 4 225 329 79602952 79602854 1.850000e-17 100.0


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 TraesCS4A01G496000 chr4A 742604904 742607817 2913 True 5382.000000 5382 100.000000 1 2914 1 chr4A.!!$R1 2913
1 TraesCS4A01G496000 chr7D 2035309 2038384 3075 True 1093.333333 2717 85.268667 6 2912 3 chr7D.!!$R1 2906
2 TraesCS4A01G496000 chrUn 336021710 336024251 2541 False 898.000000 1387 89.282000 429 2831 3 chrUn.!!$F2 2402
3 TraesCS4A01G496000 chrUn 81434771 81437689 2918 False 754.000000 1387 86.091250 1 2831 4 chrUn.!!$F1 2830
4 TraesCS4A01G496000 chr5D 429290436 429292074 1638 False 1232.000000 1232 81.008000 448 2111 1 chr5D.!!$F1 1663
5 TraesCS4A01G496000 chr5B 518482444 518484136 1692 False 1214.000000 1214 80.358000 384 2111 1 chr5B.!!$F2 1727
6 TraesCS4A01G496000 chr5B 518474858 518475653 795 False 675.000000 675 82.303000 1314 2124 1 chr5B.!!$F1 810
7 TraesCS4A01G496000 chr5A 545074648 545076245 1597 False 1114.000000 1114 80.071000 384 2002 1 chr5A.!!$F1 1618
8 TraesCS4A01G496000 chr5A 545059978 545061079 1101 False 210.000000 291 81.007333 794 2111 3 chr5A.!!$F2 1317

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
115 116 1.599071 GTGTGTGTGTGTGTGATCCAG 59.401 52.381 0.00 0.0 0.0 3.86 F
1178 1330 0.972134 TCAGCTGGACCTTCACTCAG 59.028 55.000 15.13 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1705 0.107703 TGGATGGTGATCGTTGCCTC 60.108 55.0 0.00 0.0 0.00 4.70 R
2264 2631 0.613777 CACCTTGGTACCAGGTCCTC 59.386 60.0 24.81 0.0 32.95 3.71 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
71 72 4.022416 GTGTGCCAATTCTTACATGGACAA 60.022 41.667 0.00 0.00 36.27 3.18
95 96 9.814507 CAATTTGATTGTGTGGTTCATTAATTG 57.185 29.630 0.00 0.00 35.57 2.32
96 97 9.558396 AATTTGATTGTGTGGTTCATTAATTGT 57.442 25.926 0.00 0.00 0.00 2.71
97 98 7.943413 TTGATTGTGTGGTTCATTAATTGTG 57.057 32.000 0.00 0.00 0.00 3.33
98 99 7.048629 TGATTGTGTGGTTCATTAATTGTGT 57.951 32.000 0.00 0.00 0.00 3.72
99 100 6.922407 TGATTGTGTGGTTCATTAATTGTGTG 59.078 34.615 0.00 0.00 0.00 3.82
100 101 5.843673 TGTGTGGTTCATTAATTGTGTGT 57.156 34.783 0.00 0.00 0.00 3.72
101 102 5.586339 TGTGTGGTTCATTAATTGTGTGTG 58.414 37.500 0.00 0.00 0.00 3.82
115 116 1.599071 GTGTGTGTGTGTGTGATCCAG 59.401 52.381 0.00 0.00 0.00 3.86
131 132 6.166279 GTGATCCAGTGACTAAATTCAGTGA 58.834 40.000 9.11 0.00 46.10 3.41
132 133 6.650807 GTGATCCAGTGACTAAATTCAGTGAA 59.349 38.462 8.27 8.27 46.10 3.18
154 168 6.985059 TGAATAGTGCTGAAGAGAGAATGATG 59.015 38.462 0.00 0.00 0.00 3.07
205 224 7.009999 GTGAGTGAGTGAGAATGATGACAATAC 59.990 40.741 0.00 0.00 0.00 1.89
207 226 7.040494 AGTGAGTGAGAATGATGACAATACAG 58.960 38.462 0.00 0.00 0.00 2.74
208 227 7.038048 GTGAGTGAGAATGATGACAATACAGA 58.962 38.462 0.00 0.00 0.00 3.41
210 229 6.580788 AGTGAGAATGATGACAATACAGAGG 58.419 40.000 0.00 0.00 0.00 3.69
211 230 5.236047 GTGAGAATGATGACAATACAGAGGC 59.764 44.000 0.00 0.00 0.00 4.70
212 231 4.712476 AGAATGATGACAATACAGAGGCC 58.288 43.478 0.00 0.00 0.00 5.19
213 232 4.411540 AGAATGATGACAATACAGAGGCCT 59.588 41.667 3.86 3.86 0.00 5.19
214 233 4.785346 ATGATGACAATACAGAGGCCTT 57.215 40.909 6.77 0.00 0.00 4.35
215 234 3.877559 TGATGACAATACAGAGGCCTTG 58.122 45.455 6.77 10.13 0.00 3.61
216 235 2.787473 TGACAATACAGAGGCCTTGG 57.213 50.000 6.77 4.61 0.00 3.61
217 236 1.985159 TGACAATACAGAGGCCTTGGT 59.015 47.619 6.77 11.38 0.00 3.67
218 237 3.178046 TGACAATACAGAGGCCTTGGTA 58.822 45.455 6.77 13.44 0.00 3.25
219 238 3.780294 TGACAATACAGAGGCCTTGGTAT 59.220 43.478 19.24 19.24 0.00 2.73
220 239 4.141711 TGACAATACAGAGGCCTTGGTATC 60.142 45.833 23.00 15.61 0.00 2.24
221 240 3.780294 ACAATACAGAGGCCTTGGTATCA 59.220 43.478 23.00 6.08 0.00 2.15
222 241 4.130118 CAATACAGAGGCCTTGGTATCAC 58.870 47.826 23.00 3.59 0.00 3.06
223 242 1.958288 ACAGAGGCCTTGGTATCACT 58.042 50.000 6.77 0.00 0.00 3.41
224 243 3.116096 ACAGAGGCCTTGGTATCACTA 57.884 47.619 6.77 0.00 0.00 2.74
225 244 2.766828 ACAGAGGCCTTGGTATCACTAC 59.233 50.000 6.77 0.00 0.00 2.73
226 245 2.766263 CAGAGGCCTTGGTATCACTACA 59.234 50.000 6.77 0.00 0.00 2.74
227 246 3.389329 CAGAGGCCTTGGTATCACTACAT 59.611 47.826 6.77 0.00 0.00 2.29
228 247 4.040755 AGAGGCCTTGGTATCACTACATT 58.959 43.478 6.77 0.00 0.00 2.71
229 248 4.130118 GAGGCCTTGGTATCACTACATTG 58.870 47.826 6.77 0.00 0.00 2.82
230 249 3.523564 AGGCCTTGGTATCACTACATTGT 59.476 43.478 0.00 0.00 0.00 2.71
231 250 4.719773 AGGCCTTGGTATCACTACATTGTA 59.280 41.667 0.00 0.00 0.00 2.41
232 251 5.190925 AGGCCTTGGTATCACTACATTGTAA 59.809 40.000 0.00 0.00 0.00 2.41
233 252 5.296035 GGCCTTGGTATCACTACATTGTAAC 59.704 44.000 0.00 0.00 0.00 2.50
234 253 5.878116 GCCTTGGTATCACTACATTGTAACA 59.122 40.000 0.00 0.00 0.00 2.41
235 254 6.373216 GCCTTGGTATCACTACATTGTAACAA 59.627 38.462 0.00 0.00 0.00 2.83
236 255 7.094549 GCCTTGGTATCACTACATTGTAACAAA 60.095 37.037 0.00 0.00 0.00 2.83
237 256 8.956426 CCTTGGTATCACTACATTGTAACAAAT 58.044 33.333 0.00 0.00 0.00 2.32
322 346 5.121105 TCTCTTTCCTGATACATGCATGTG 58.879 41.667 36.72 22.23 41.89 3.21
350 374 5.180117 GTGGATCGATGATTAATGAAGGGTG 59.820 44.000 0.54 0.00 0.00 4.61
360 384 1.696063 ATGAAGGGTGCCATGCATAC 58.304 50.000 0.00 0.00 41.91 2.39
422 446 5.192327 CAAGCTTGGATCTTTGTTTCACT 57.808 39.130 19.14 0.00 0.00 3.41
423 447 4.843220 AGCTTGGATCTTTGTTTCACTG 57.157 40.909 0.00 0.00 0.00 3.66
424 448 4.210331 AGCTTGGATCTTTGTTTCACTGT 58.790 39.130 0.00 0.00 0.00 3.55
425 449 4.037208 AGCTTGGATCTTTGTTTCACTGTG 59.963 41.667 0.17 0.17 0.00 3.66
426 450 4.036734 GCTTGGATCTTTGTTTCACTGTGA 59.963 41.667 6.36 6.36 0.00 3.58
427 451 5.278660 GCTTGGATCTTTGTTTCACTGTGAT 60.279 40.000 11.86 0.00 0.00 3.06
646 765 5.215903 GCAGTCTAGCTTTTTCAAGGAAAC 58.784 41.667 0.00 0.00 30.83 2.78
656 775 4.195190 TTTTCAAGGAAACACAGGGGACC 61.195 47.826 0.00 0.00 39.24 4.46
822 950 6.908825 TGAATCAACTAAAAACCTTCCATCG 58.091 36.000 0.00 0.00 0.00 3.84
829 957 7.430992 ACTAAAAACCTTCCATCGTTTCTAC 57.569 36.000 0.00 0.00 31.09 2.59
833 961 2.027469 ACCTTCCATCGTTTCTACCACC 60.027 50.000 0.00 0.00 0.00 4.61
851 980 4.841246 ACCACCCAATTAAAGCCAACAATA 59.159 37.500 0.00 0.00 0.00 1.90
894 1023 2.433318 AGCTTTCGCTGCCTCGAC 60.433 61.111 0.00 0.00 46.86 4.20
915 1044 2.532723 CGAATCGACGGCTAATTTCGAA 59.467 45.455 7.55 0.00 44.39 3.71
930 1059 9.818796 GCTAATTTCGAATGAATATCTCTTTCC 57.181 33.333 0.00 0.00 35.67 3.13
1010 1139 6.556116 TCTCTCAATACATTCATGGAGGATGA 59.444 38.462 0.00 0.00 39.47 2.92
1062 1194 7.607991 ACAACAACAATAGTAGGAGATCAAAGG 59.392 37.037 0.00 0.00 0.00 3.11
1065 1197 5.289510 ACAATAGTAGGAGATCAAAGGGGT 58.710 41.667 0.00 0.00 0.00 4.95
1141 1293 5.036117 TGGGCTTGAGAATACTAATGGAC 57.964 43.478 0.00 0.00 0.00 4.02
1142 1294 4.473196 TGGGCTTGAGAATACTAATGGACA 59.527 41.667 0.00 0.00 0.00 4.02
1178 1330 0.972134 TCAGCTGGACCTTCACTCAG 59.028 55.000 15.13 0.00 0.00 3.35
1248 1505 7.718272 ATTTGGATAATTCATTTGCATTCCG 57.282 32.000 0.00 0.00 0.00 4.30
1260 1523 2.004017 TGCATTCCGGTTATTCGACAC 58.996 47.619 0.00 0.00 0.00 3.67
1269 1532 4.266976 CCGGTTATTCGACACTGACAATAC 59.733 45.833 0.00 0.00 0.00 1.89
1273 1536 6.401796 GGTTATTCGACACTGACAATACCAAC 60.402 42.308 0.00 0.00 0.00 3.77
1275 1538 5.456548 TTCGACACTGACAATACCAACTA 57.543 39.130 0.00 0.00 0.00 2.24
1276 1539 5.456548 TCGACACTGACAATACCAACTAA 57.543 39.130 0.00 0.00 0.00 2.24
1278 1541 6.460781 TCGACACTGACAATACCAACTAATT 58.539 36.000 0.00 0.00 0.00 1.40
1279 1542 7.604549 TCGACACTGACAATACCAACTAATTA 58.395 34.615 0.00 0.00 0.00 1.40
1281 1544 7.201496 CGACACTGACAATACCAACTAATTACC 60.201 40.741 0.00 0.00 0.00 2.85
1282 1545 7.455058 ACACTGACAATACCAACTAATTACCA 58.545 34.615 0.00 0.00 0.00 3.25
1283 1546 7.389607 ACACTGACAATACCAACTAATTACCAC 59.610 37.037 0.00 0.00 0.00 4.16
1287 1550 9.357161 TGACAATACCAACTAATTACCACTTTT 57.643 29.630 0.00 0.00 0.00 2.27
1288 1551 9.836076 GACAATACCAACTAATTACCACTTTTC 57.164 33.333 0.00 0.00 0.00 2.29
1289 1552 9.582648 ACAATACCAACTAATTACCACTTTTCT 57.417 29.630 0.00 0.00 0.00 2.52
1292 1555 7.284919 ACCAACTAATTACCACTTTTCTTGG 57.715 36.000 0.00 0.00 40.32 3.61
1294 1557 8.000127 ACCAACTAATTACCACTTTTCTTGGTA 59.000 33.333 0.00 0.00 46.01 3.25
1295 1558 9.020731 CCAACTAATTACCACTTTTCTTGGTAT 57.979 33.333 2.15 0.00 46.69 2.73
1359 1630 3.137728 TGCCACATCCTCTCATCATCATT 59.862 43.478 0.00 0.00 0.00 2.57
1420 1697 3.127721 TGACATCGACTACTCTTCTGCAG 59.872 47.826 7.63 7.63 0.00 4.41
1427 1704 2.499289 ACTACTCTTCTGCAGTCCATGG 59.501 50.000 14.67 4.97 0.00 3.66
1428 1705 0.617413 ACTCTTCTGCAGTCCATGGG 59.383 55.000 14.67 0.00 0.00 4.00
1429 1706 0.907486 CTCTTCTGCAGTCCATGGGA 59.093 55.000 14.67 0.00 0.00 4.37
1474 1754 0.032515 TCCTCGATGGCTTCCCTACA 60.033 55.000 0.00 0.00 35.26 2.74
1567 1847 2.515290 CCATCGCAGATGCTGGCA 60.515 61.111 11.51 0.00 45.12 4.92
1581 1861 1.073025 TGGCAACGGATGAGCAAGT 59.927 52.632 0.00 0.00 42.51 3.16
1582 1862 0.537143 TGGCAACGGATGAGCAAGTT 60.537 50.000 0.00 0.00 42.51 2.66
1694 1974 7.923878 AGAAGAAGAACAGAAAGTAAGTCTGAC 59.076 37.037 8.36 0.00 44.44 3.51
1733 2013 9.677567 TTTGACAACTACTTTATTTGCAGATTC 57.322 29.630 0.00 0.00 0.00 2.52
1749 2035 6.761312 TGCAGATTCCTTTTTCAATTGATGT 58.239 32.000 9.40 0.00 0.00 3.06
1775 2117 8.819974 TGAGCTTGAGTTTCAAATTTGAATTTC 58.180 29.630 29.13 26.30 45.65 2.17
1780 2122 8.870160 TGAGTTTCAAATTTGAATTTCGATGT 57.130 26.923 29.13 11.36 45.65 3.06
1877 2219 1.740025 AGATTCGCAAAGGCTAGCAAC 59.260 47.619 18.24 0.00 38.10 4.17
1926 2268 2.033662 GCAGGATAAATTCACGAGCGAC 60.034 50.000 0.00 0.00 0.00 5.19
1931 2273 1.641577 AAATTCACGAGCGACTAGGC 58.358 50.000 0.00 0.00 0.00 3.93
1983 2337 6.993786 TCCATTCGTTTTGCATATAGACAA 57.006 33.333 0.00 0.00 0.00 3.18
2090 2450 3.185880 TGCCTAGGTAGACCACTCTTT 57.814 47.619 11.31 0.00 38.89 2.52
2111 2471 4.844998 TTCCACACCACACAAATACATG 57.155 40.909 0.00 0.00 0.00 3.21
2171 2537 6.657117 AGATCTTAGCCCTTTTCTCAGTTTTC 59.343 38.462 0.00 0.00 0.00 2.29
2178 2544 6.070824 AGCCCTTTTCTCAGTTTTCTTTTTGA 60.071 34.615 0.00 0.00 0.00 2.69
2179 2545 6.593770 GCCCTTTTCTCAGTTTTCTTTTTGAA 59.406 34.615 0.00 0.00 0.00 2.69
2180 2546 7.280876 GCCCTTTTCTCAGTTTTCTTTTTGAAT 59.719 33.333 0.00 0.00 34.24 2.57
2248 2615 7.175641 CAGAGATAGTTTTGGGACACATTCTTT 59.824 37.037 0.00 0.00 39.29 2.52
2256 2623 5.269554 TGGGACACATTCTTTTTAGGGAT 57.730 39.130 0.00 0.00 0.00 3.85
2264 2631 9.449719 ACACATTCTTTTTAGGGATGTACTTAG 57.550 33.333 0.00 0.00 0.00 2.18
2269 2636 8.075761 TCTTTTTAGGGATGTACTTAGAGGAC 57.924 38.462 0.00 0.00 0.00 3.85
2316 2686 4.049186 GCCCTTGTCTATGTGTACATACG 58.951 47.826 0.00 0.00 37.76 3.06
2322 2692 9.955208 CCTTGTCTATGTGTACATACGTTATTA 57.045 33.333 0.00 0.00 37.76 0.98
2400 2800 7.156876 TGTGATTTTGGTGAATGTATTCTCC 57.843 36.000 15.37 15.37 45.79 3.71
2431 2832 7.727331 ATTGTTTCTTCAGAAGAGAGACAAG 57.273 36.000 26.17 1.09 38.63 3.16
2470 2871 3.861840 TGCCTGCAACTACATTCTCTAC 58.138 45.455 0.00 0.00 0.00 2.59
2536 3122 3.053991 TCTTTCACTCAGTTTTCCCCACA 60.054 43.478 0.00 0.00 0.00 4.17
2563 3149 2.038221 TCCAACCTCCAACCCCCA 60.038 61.111 0.00 0.00 0.00 4.96
2564 3150 1.467190 TCCAACCTCCAACCCCCAT 60.467 57.895 0.00 0.00 0.00 4.00
2565 3151 0.178828 TCCAACCTCCAACCCCCATA 60.179 55.000 0.00 0.00 0.00 2.74
2566 3152 0.258774 CCAACCTCCAACCCCCATAG 59.741 60.000 0.00 0.00 0.00 2.23
2567 3153 1.295020 CAACCTCCAACCCCCATAGA 58.705 55.000 0.00 0.00 0.00 1.98
2589 3177 6.561294 AGATTTTCCTGGTTTTTCATCCCTA 58.439 36.000 0.00 0.00 0.00 3.53
2719 3322 9.420118 ACATCTTTGATAACCCAATAAATAGCA 57.580 29.630 0.00 0.00 0.00 3.49
2737 3340 8.579850 AAATAGCAATAAATTCACTGTCCAGA 57.420 30.769 0.40 0.00 0.00 3.86
2738 3341 8.579850 AATAGCAATAAATTCACTGTCCAGAA 57.420 30.769 0.40 0.00 0.00 3.02
2739 3342 6.259550 AGCAATAAATTCACTGTCCAGAAC 57.740 37.500 0.40 0.00 0.00 3.01
2797 3407 8.080417 CCAATAAAGCAGAATAATCATGGACAG 58.920 37.037 0.00 0.00 0.00 3.51
2806 3416 9.814899 CAGAATAATCATGGACAGATACCTATC 57.185 37.037 0.00 0.00 0.00 2.08
2890 3501 7.784073 TCCTATTTCCCTATTTGATTTGCATCA 59.216 33.333 0.00 0.00 37.67 3.07
2912 3523 8.551440 CATCAAGATTTATCCCATATGGTCCTA 58.449 37.037 20.46 6.09 34.77 2.94
2913 3524 8.700145 TCAAGATTTATCCCATATGGTCCTAT 57.300 34.615 20.46 10.41 34.77 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 8.991026 CACAATTAATGAACCACACAATCAAAT 58.009 29.630 0.00 0.00 0.00 2.32
80 81 5.126222 ACACACACACAATTAATGAACCACA 59.874 36.000 0.00 0.00 0.00 4.17
84 85 6.020758 CACACACACACACACAATTAATGAAC 60.021 38.462 0.00 0.00 0.00 3.18
86 87 5.355350 TCACACACACACACACAATTAATGA 59.645 36.000 0.00 0.00 0.00 2.57
91 92 3.066621 GGATCACACACACACACACAATT 59.933 43.478 0.00 0.00 0.00 2.32
92 93 2.618241 GGATCACACACACACACACAAT 59.382 45.455 0.00 0.00 0.00 2.71
93 94 2.013400 GGATCACACACACACACACAA 58.987 47.619 0.00 0.00 0.00 3.33
95 96 1.599071 CTGGATCACACACACACACAC 59.401 52.381 0.00 0.00 0.00 3.82
96 97 1.209261 ACTGGATCACACACACACACA 59.791 47.619 0.00 0.00 0.00 3.72
97 98 1.599071 CACTGGATCACACACACACAC 59.401 52.381 0.00 0.00 0.00 3.82
98 99 1.484240 TCACTGGATCACACACACACA 59.516 47.619 0.00 0.00 0.00 3.72
99 100 1.867233 GTCACTGGATCACACACACAC 59.133 52.381 0.00 0.00 0.00 3.82
100 101 1.762370 AGTCACTGGATCACACACACA 59.238 47.619 0.00 0.00 0.00 3.72
101 102 2.533266 AGTCACTGGATCACACACAC 57.467 50.000 0.00 0.00 0.00 3.82
115 116 7.331934 TCAGCACTATTCACTGAATTTAGTCAC 59.668 37.037 9.57 3.71 37.49 3.67
131 132 6.985645 GTCATCATTCTCTCTTCAGCACTATT 59.014 38.462 0.00 0.00 0.00 1.73
132 133 6.462768 GGTCATCATTCTCTCTTCAGCACTAT 60.463 42.308 0.00 0.00 0.00 2.12
144 158 6.950842 TCACTTTGTATGGTCATCATTCTCT 58.049 36.000 0.00 0.00 37.30 3.10
154 168 4.926238 CACTCTCACTCACTTTGTATGGTC 59.074 45.833 0.00 0.00 0.00 4.02
205 224 2.766263 TGTAGTGATACCAAGGCCTCTG 59.234 50.000 5.23 6.85 0.00 3.35
207 226 4.130118 CAATGTAGTGATACCAAGGCCTC 58.870 47.826 5.23 0.00 0.00 4.70
208 227 3.523564 ACAATGTAGTGATACCAAGGCCT 59.476 43.478 0.00 0.00 0.00 5.19
210 229 5.878116 TGTTACAATGTAGTGATACCAAGGC 59.122 40.000 0.00 0.00 0.00 4.35
211 230 7.915293 TTGTTACAATGTAGTGATACCAAGG 57.085 36.000 0.00 0.00 0.00 3.61
238 257 8.982723 CACTCCCCACTTGCTTATATATATACT 58.017 37.037 1.73 0.00 0.00 2.12
239 258 8.759782 ACACTCCCCACTTGCTTATATATATAC 58.240 37.037 1.73 0.00 0.00 1.47
240 259 8.758829 CACACTCCCCACTTGCTTATATATATA 58.241 37.037 0.00 0.00 0.00 0.86
241 260 7.624549 CACACTCCCCACTTGCTTATATATAT 58.375 38.462 0.00 0.00 0.00 0.86
242 261 6.520061 GCACACTCCCCACTTGCTTATATATA 60.520 42.308 0.00 0.00 0.00 0.86
243 262 5.746065 GCACACTCCCCACTTGCTTATATAT 60.746 44.000 0.00 0.00 0.00 0.86
244 263 4.444306 GCACACTCCCCACTTGCTTATATA 60.444 45.833 0.00 0.00 0.00 0.86
245 264 3.685550 GCACACTCCCCACTTGCTTATAT 60.686 47.826 0.00 0.00 0.00 0.86
246 265 2.355716 GCACACTCCCCACTTGCTTATA 60.356 50.000 0.00 0.00 0.00 0.98
247 266 1.614317 GCACACTCCCCACTTGCTTAT 60.614 52.381 0.00 0.00 0.00 1.73
248 267 0.250727 GCACACTCCCCACTTGCTTA 60.251 55.000 0.00 0.00 0.00 3.09
249 268 1.529244 GCACACTCCCCACTTGCTT 60.529 57.895 0.00 0.00 0.00 3.91
250 269 1.127567 TAGCACACTCCCCACTTGCT 61.128 55.000 0.00 0.00 45.37 3.91
251 270 0.035056 ATAGCACACTCCCCACTTGC 60.035 55.000 0.00 0.00 0.00 4.01
252 271 1.556911 AGATAGCACACTCCCCACTTG 59.443 52.381 0.00 0.00 0.00 3.16
253 272 1.556911 CAGATAGCACACTCCCCACTT 59.443 52.381 0.00 0.00 0.00 3.16
290 313 6.882656 TGTATCAGGAAAGAGATCTTCCTTG 58.117 40.000 11.16 7.93 33.94 3.61
322 346 6.093219 CCTTCATTAATCATCGATCCACCATC 59.907 42.308 0.00 0.00 0.00 3.51
350 374 2.158842 AGGAGAAGTGAGTATGCATGGC 60.159 50.000 10.16 1.92 0.00 4.40
360 384 4.630940 GCAATCTTTCAGAGGAGAAGTGAG 59.369 45.833 0.00 0.00 0.00 3.51
417 441 4.751600 GTCATGTCAGTCAATCACAGTGAA 59.248 41.667 7.50 0.00 0.00 3.18
420 444 4.039609 TCAGTCATGTCAGTCAATCACAGT 59.960 41.667 0.00 0.00 0.00 3.55
421 445 4.563061 TCAGTCATGTCAGTCAATCACAG 58.437 43.478 0.00 0.00 0.00 3.66
422 446 4.281688 TCTCAGTCATGTCAGTCAATCACA 59.718 41.667 0.00 0.00 0.00 3.58
423 447 4.814147 TCTCAGTCATGTCAGTCAATCAC 58.186 43.478 0.00 0.00 0.00 3.06
424 448 5.672421 ATCTCAGTCATGTCAGTCAATCA 57.328 39.130 0.00 0.00 0.00 2.57
425 449 8.143193 AGATAATCTCAGTCATGTCAGTCAATC 58.857 37.037 0.00 0.00 0.00 2.67
426 450 8.020777 AGATAATCTCAGTCATGTCAGTCAAT 57.979 34.615 0.00 0.00 0.00 2.57
427 451 7.415592 AGATAATCTCAGTCATGTCAGTCAA 57.584 36.000 0.00 0.00 0.00 3.18
611 730 3.190118 AGCTAGACTGCAAAAGCACATTC 59.810 43.478 10.67 0.00 37.44 2.67
620 739 4.887071 TCCTTGAAAAAGCTAGACTGCAAA 59.113 37.500 0.00 0.00 34.99 3.68
646 765 0.104304 GTATGTAGCGGTCCCCTGTG 59.896 60.000 0.00 0.00 0.00 3.66
656 775 4.082949 TCGACCCATATGAAGTATGTAGCG 60.083 45.833 3.65 0.92 38.83 4.26
744 865 7.833183 GGGAAAGGCATCATTTCTCTATCATAT 59.167 37.037 4.36 0.00 34.84 1.78
745 866 7.017950 AGGGAAAGGCATCATTTCTCTATCATA 59.982 37.037 4.74 0.00 43.93 2.15
746 867 6.008960 GGGAAAGGCATCATTTCTCTATCAT 58.991 40.000 4.36 0.00 34.84 2.45
747 868 5.133322 AGGGAAAGGCATCATTTCTCTATCA 59.867 40.000 4.74 0.00 43.93 2.15
822 950 4.525100 TGGCTTTAATTGGGTGGTAGAAAC 59.475 41.667 0.00 0.00 0.00 2.78
829 957 3.760580 TTGTTGGCTTTAATTGGGTGG 57.239 42.857 0.00 0.00 0.00 4.61
833 961 5.979517 GCTAGCTATTGTTGGCTTTAATTGG 59.020 40.000 7.70 0.00 40.57 3.16
851 980 1.661341 GCATGCACTTGTAGCTAGCT 58.339 50.000 23.12 23.12 32.49 3.32
894 1023 2.114056 TCGAAATTAGCCGTCGATTCG 58.886 47.619 7.09 7.09 38.78 3.34
911 1040 7.726291 AGAGGTAGGAAAGAGATATTCATTCGA 59.274 37.037 0.00 0.00 34.99 3.71
930 1059 3.305471 GCGCCATCCTAGTTAAGAGGTAG 60.305 52.174 0.00 0.00 35.40 3.18
1010 1139 2.298610 TCGCATCGTCTATCTGAGGTT 58.701 47.619 0.00 0.00 32.81 3.50
1021 1150 1.463056 TGTTGTTCCATTCGCATCGTC 59.537 47.619 0.00 0.00 0.00 4.20
1062 1194 2.437359 CTGCTGCTGCTGGTACCC 60.437 66.667 17.00 0.00 40.48 3.69
1141 1293 4.022589 AGCTGAGTGATGACCAACAAATTG 60.023 41.667 0.00 0.00 35.40 2.32
1142 1294 4.022589 CAGCTGAGTGATGACCAACAAATT 60.023 41.667 8.42 0.00 33.12 1.82
1227 1484 4.648762 ACCGGAATGCAAATGAATTATCCA 59.351 37.500 9.46 0.00 0.00 3.41
1229 1486 8.816640 AATAACCGGAATGCAAATGAATTATC 57.183 30.769 9.46 0.00 0.00 1.75
1231 1488 6.915300 CGAATAACCGGAATGCAAATGAATTA 59.085 34.615 9.46 0.00 0.00 1.40
1236 1493 4.035017 GTCGAATAACCGGAATGCAAATG 58.965 43.478 9.46 0.00 0.00 2.32
1245 1502 1.887854 TGTCAGTGTCGAATAACCGGA 59.112 47.619 9.46 0.00 0.00 5.14
1248 1505 5.172934 TGGTATTGTCAGTGTCGAATAACC 58.827 41.667 0.00 0.00 0.00 2.85
1260 1523 8.561738 AAGTGGTAATTAGTTGGTATTGTCAG 57.438 34.615 0.00 0.00 0.00 3.51
1281 1544 8.925700 GCCAAGAAATTTATACCAAGAAAAGTG 58.074 33.333 0.00 0.00 0.00 3.16
1282 1545 8.646900 TGCCAAGAAATTTATACCAAGAAAAGT 58.353 29.630 0.00 0.00 0.00 2.66
1283 1546 9.143631 CTGCCAAGAAATTTATACCAAGAAAAG 57.856 33.333 0.00 0.00 0.00 2.27
1287 1550 5.714333 TGCTGCCAAGAAATTTATACCAAGA 59.286 36.000 0.00 0.00 0.00 3.02
1288 1551 5.964758 TGCTGCCAAGAAATTTATACCAAG 58.035 37.500 0.00 0.00 0.00 3.61
1289 1552 5.991933 TGCTGCCAAGAAATTTATACCAA 57.008 34.783 0.00 0.00 0.00 3.67
1290 1553 5.244851 TGTTGCTGCCAAGAAATTTATACCA 59.755 36.000 0.00 0.00 0.00 3.25
1291 1554 5.719173 TGTTGCTGCCAAGAAATTTATACC 58.281 37.500 0.00 0.00 0.00 2.73
1292 1555 5.289434 GCTGTTGCTGCCAAGAAATTTATAC 59.711 40.000 0.00 0.00 36.03 1.47
1293 1556 5.047448 TGCTGTTGCTGCCAAGAAATTTATA 60.047 36.000 0.00 0.00 40.48 0.98
1294 1557 4.248058 GCTGTTGCTGCCAAGAAATTTAT 58.752 39.130 0.00 0.00 36.03 1.40
1295 1558 3.069300 TGCTGTTGCTGCCAAGAAATTTA 59.931 39.130 0.00 0.00 40.48 1.40
1296 1559 2.158928 TGCTGTTGCTGCCAAGAAATTT 60.159 40.909 0.00 0.00 40.48 1.82
1359 1630 6.153510 CGAGGAGGATGGATTATAACATGAGA 59.846 42.308 0.00 0.00 0.00 3.27
1420 1697 0.815615 GATCGTTGCCTCCCATGGAC 60.816 60.000 15.22 0.36 0.00 4.02
1427 1704 0.815615 GGATGGTGATCGTTGCCTCC 60.816 60.000 0.00 0.00 0.00 4.30
1428 1705 0.107703 TGGATGGTGATCGTTGCCTC 60.108 55.000 0.00 0.00 0.00 4.70
1429 1706 0.548031 ATGGATGGTGATCGTTGCCT 59.452 50.000 0.00 0.00 0.00 4.75
1474 1754 4.692930 GGCATGGAAGGGCAGAAT 57.307 55.556 0.00 0.00 45.28 2.40
1567 1847 1.577328 CCGCAACTTGCTCATCCGTT 61.577 55.000 11.93 0.00 42.25 4.44
1581 1861 2.747460 GGTGATGAGCAGCCGCAA 60.747 61.111 0.00 0.00 42.27 4.85
1582 1862 3.963687 CTGGTGATGAGCAGCCGCA 62.964 63.158 0.00 0.00 44.28 5.69
1588 1868 1.407851 GGATCTTGCTGGTGATGAGCA 60.408 52.381 0.00 0.00 44.75 4.26
1717 1997 9.783081 ATTGAAAAAGGAATCTGCAAATAAAGT 57.217 25.926 0.00 0.00 0.00 2.66
1724 2004 7.171848 CACATCAATTGAAAAAGGAATCTGCAA 59.828 33.333 13.09 0.00 0.00 4.08
1732 2012 6.040729 TCAAGCTCACATCAATTGAAAAAGGA 59.959 34.615 13.09 5.50 0.00 3.36
1733 2013 6.218019 TCAAGCTCACATCAATTGAAAAAGG 58.782 36.000 13.09 4.67 0.00 3.11
1877 2219 4.304110 AGTGTAGTATGTGTTGGTGTTCG 58.696 43.478 0.00 0.00 0.00 3.95
2051 2409 6.791887 AGGCATGATCGACAGTAATATTTG 57.208 37.500 0.00 0.00 0.00 2.32
2052 2410 7.099764 CCTAGGCATGATCGACAGTAATATTT 58.900 38.462 0.00 0.00 0.00 1.40
2061 2421 2.885266 GTCTACCTAGGCATGATCGACA 59.115 50.000 9.30 0.00 0.00 4.35
2090 2450 3.005261 GCATGTATTTGTGTGGTGTGGAA 59.995 43.478 0.00 0.00 0.00 3.53
2111 2471 6.038714 CCTTCTCCACAAATTAAGAGGTATGC 59.961 42.308 0.00 0.00 0.00 3.14
2248 2615 5.897824 CAGGTCCTCTAAGTACATCCCTAAA 59.102 44.000 0.00 0.00 0.00 1.85
2256 2623 3.334581 TGGTACCAGGTCCTCTAAGTACA 59.665 47.826 11.60 4.53 36.71 2.90
2264 2631 0.613777 CACCTTGGTACCAGGTCCTC 59.386 60.000 24.81 0.00 32.95 3.71
2269 2636 6.419791 TGAATTATTACACCTTGGTACCAGG 58.580 40.000 21.94 21.94 0.00 4.45
2400 2800 9.752274 CTCTCTTCTGAAGAAACAATATTTTCG 57.248 33.333 19.73 5.12 39.96 3.46
2405 2805 9.434420 CTTGTCTCTCTTCTGAAGAAACAATAT 57.566 33.333 26.09 0.00 37.02 1.28
2502 3086 8.908786 AACTGAGTGAAAGATGAAACATTAGA 57.091 30.769 0.00 0.00 0.00 2.10
2507 3091 6.183360 GGGAAAACTGAGTGAAAGATGAAACA 60.183 38.462 0.00 0.00 0.00 2.83
2512 3096 4.022849 GTGGGGAAAACTGAGTGAAAGATG 60.023 45.833 0.00 0.00 0.00 2.90
2536 3122 1.759236 GAGGTTGGACGAAGGGGTT 59.241 57.895 0.00 0.00 0.00 4.11
2563 3149 7.191918 AGGGATGAAAAACCAGGAAAATCTAT 58.808 34.615 0.00 0.00 0.00 1.98
2564 3150 6.561294 AGGGATGAAAAACCAGGAAAATCTA 58.439 36.000 0.00 0.00 0.00 1.98
2565 3151 5.406163 AGGGATGAAAAACCAGGAAAATCT 58.594 37.500 0.00 0.00 0.00 2.40
2566 3152 5.745312 AGGGATGAAAAACCAGGAAAATC 57.255 39.130 0.00 0.00 0.00 2.17
2567 3153 6.211384 CAGTAGGGATGAAAAACCAGGAAAAT 59.789 38.462 0.00 0.00 0.00 1.82
2661 3264 5.952526 ACCAGGTTTTACCATAAGAAACG 57.047 39.130 0.00 0.00 41.95 3.60
2716 3319 5.769662 TGTTCTGGACAGTGAATTTATTGCT 59.230 36.000 0.00 0.00 33.40 3.91
2717 3320 6.012658 TGTTCTGGACAGTGAATTTATTGC 57.987 37.500 0.00 0.00 33.40 3.56
2718 3321 8.870160 TTTTGTTCTGGACAGTGAATTTATTG 57.130 30.769 0.00 0.00 39.94 1.90
2721 3324 9.126151 TGTATTTTGTTCTGGACAGTGAATTTA 57.874 29.630 0.00 0.00 39.94 1.40
2722 3325 8.006298 TGTATTTTGTTCTGGACAGTGAATTT 57.994 30.769 0.00 0.00 39.94 1.82
2723 3326 7.581213 TGTATTTTGTTCTGGACAGTGAATT 57.419 32.000 0.00 0.00 39.94 2.17
2724 3327 7.231317 ACATGTATTTTGTTCTGGACAGTGAAT 59.769 33.333 0.00 0.00 39.94 2.57
2725 3328 6.545666 ACATGTATTTTGTTCTGGACAGTGAA 59.454 34.615 0.00 0.00 39.94 3.18
2726 3329 6.061441 ACATGTATTTTGTTCTGGACAGTGA 58.939 36.000 0.00 0.00 39.94 3.41
2727 3330 6.317789 ACATGTATTTTGTTCTGGACAGTG 57.682 37.500 0.00 0.00 39.94 3.66
2728 3331 6.959639 AACATGTATTTTGTTCTGGACAGT 57.040 33.333 0.00 0.00 39.94 3.55
2729 3332 9.559958 GATTAACATGTATTTTGTTCTGGACAG 57.440 33.333 0.00 0.00 39.94 3.51
2730 3333 9.072375 TGATTAACATGTATTTTGTTCTGGACA 57.928 29.630 0.00 0.00 38.26 4.02
2746 3349 9.903682 GGGTTATCAAATGAGATGATTAACATG 57.096 33.333 0.00 0.00 39.56 3.21
2757 3360 7.833682 TCTGCTTTATTGGGTTATCAAATGAGA 59.166 33.333 0.00 0.00 0.00 3.27
2758 3361 7.999679 TCTGCTTTATTGGGTTATCAAATGAG 58.000 34.615 0.00 0.00 0.00 2.90
2759 3362 7.953005 TCTGCTTTATTGGGTTATCAAATGA 57.047 32.000 0.00 0.00 0.00 2.57
2848 3458 8.638873 GGGAAATAGGATTAGGTTTTGGTTATG 58.361 37.037 0.00 0.00 0.00 1.90
2866 3476 9.472361 CTTGATGCAAATCAAATAGGGAAATAG 57.528 33.333 4.41 0.00 39.73 1.73
2872 3482 9.991906 ATAAATCTTGATGCAAATCAAATAGGG 57.008 29.630 4.41 0.00 39.73 3.53
2881 3492 8.537016 CCATATGGGATAAATCTTGATGCAAAT 58.463 33.333 14.52 0.00 40.01 2.32


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

AutoCloner maintained by Alex Coulton.