Multiple sequence alignment - TraesCS6B01G356100

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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 TraesCS6B01G356100 chr6B 100.000 2792 0 0 1 2792 624478943 624481734 0.000000e+00 5156
1 TraesCS6B01G356100 chr6B 90.714 420 33 4 265 682 624398949 624399364 3.140000e-154 555
2 TraesCS6B01G356100 chr6B 84.647 482 56 10 310 786 624266200 624266668 5.450000e-127 464
3 TraesCS6B01G356100 chr6B 83.742 326 49 4 168 492 239337431 239337109 3.490000e-79 305
4 TraesCS6B01G356100 chr6B 94.545 165 3 1 1 159 624398634 624398798 1.660000e-62 250
5 TraesCS6B01G356100 chr6B 92.121 165 7 1 1 159 624231951 624232115 7.780000e-56 228
6 TraesCS6B01G356100 chr6B 95.327 107 5 0 680 786 624400467 624400573 1.330000e-38 171
7 TraesCS6B01G356100 chr1B 94.218 1989 97 6 812 2792 589083206 589081228 0.000000e+00 3020
8 TraesCS6B01G356100 chr1B 93.696 1983 116 3 813 2792 592967358 592965382 0.000000e+00 2961
9 TraesCS6B01G356100 chr5A 90.443 1988 184 4 809 2792 23616084 23618069 0.000000e+00 2614
10 TraesCS6B01G356100 chr5A 88.440 1263 132 11 813 2066 437072864 437074121 0.000000e+00 1511
11 TraesCS6B01G356100 chr5A 92.371 603 45 1 2089 2691 437147888 437148489 0.000000e+00 857
12 TraesCS6B01G356100 chr5A 80.831 433 61 14 207 623 317244586 317244160 1.250000e-83 320
13 TraesCS6B01G356100 chr7B 90.167 1912 180 6 885 2792 624242239 624240332 0.000000e+00 2483
14 TraesCS6B01G356100 chr7B 84.523 995 143 11 818 1807 613904218 613905206 0.000000e+00 974
15 TraesCS6B01G356100 chr7B 84.422 995 144 11 818 1807 613927733 613928721 0.000000e+00 968
16 TraesCS6B01G356100 chr7B 86.575 797 105 2 1997 2792 45292335 45293130 0.000000e+00 878
17 TraesCS6B01G356100 chr7B 79.911 672 129 6 2111 2779 104781931 104781263 3.230000e-134 488
18 TraesCS6B01G356100 chr7B 80.465 430 67 8 205 622 454793930 454793506 2.090000e-81 313
19 TraesCS6B01G356100 chr3B 87.475 1988 218 18 812 2792 737706356 737708319 0.000000e+00 2263
20 TraesCS6B01G356100 chr2A 93.878 882 38 5 812 1693 4397734 4396869 0.000000e+00 1315
21 TraesCS6B01G356100 chr2A 94.311 334 19 0 2459 2792 4396864 4396531 1.920000e-141 512
22 TraesCS6B01G356100 chr2A 76.702 382 71 9 249 616 22193725 22194102 2.190000e-46 196
23 TraesCS6B01G356100 chr6D 85.215 629 81 11 168 786 414247751 414248377 1.090000e-178 636
24 TraesCS6B01G356100 chr6D 83.746 646 68 12 168 786 414107669 414108304 6.710000e-161 577
25 TraesCS6B01G356100 chr6D 92.727 165 6 1 1 159 414246332 414246496 1.670000e-57 233
26 TraesCS6B01G356100 chr6A 80.921 456 68 14 171 616 24275544 24275098 2.660000e-90 342
27 TraesCS6B01G356100 chr6A 79.341 455 73 11 168 613 558511978 558512420 1.630000e-77 300
28 TraesCS6B01G356100 chr6A 92.949 156 4 2 1 150 559154935 559155089 1.300000e-53 220
29 TraesCS6B01G356100 chrUn 79.258 458 74 11 168 616 286967766 286967321 1.630000e-77 300
30 TraesCS6B01G356100 chr5B 81.818 330 52 8 2107 2433 643409671 643409995 1.270000e-68 270


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 TraesCS6B01G356100 chr6B 624478943 624481734 2791 False 5156.000000 5156 100.000000 1 2792 1 chr6B.!!$F3 2791
1 TraesCS6B01G356100 chr6B 624398634 624400573 1939 False 325.333333 555 93.528667 1 786 3 chr6B.!!$F4 785
2 TraesCS6B01G356100 chr1B 589081228 589083206 1978 True 3020.000000 3020 94.218000 812 2792 1 chr1B.!!$R1 1980
3 TraesCS6B01G356100 chr1B 592965382 592967358 1976 True 2961.000000 2961 93.696000 813 2792 1 chr1B.!!$R2 1979
4 TraesCS6B01G356100 chr5A 23616084 23618069 1985 False 2614.000000 2614 90.443000 809 2792 1 chr5A.!!$F1 1983
5 TraesCS6B01G356100 chr5A 437072864 437074121 1257 False 1511.000000 1511 88.440000 813 2066 1 chr5A.!!$F2 1253
6 TraesCS6B01G356100 chr5A 437147888 437148489 601 False 857.000000 857 92.371000 2089 2691 1 chr5A.!!$F3 602
7 TraesCS6B01G356100 chr7B 624240332 624242239 1907 True 2483.000000 2483 90.167000 885 2792 1 chr7B.!!$R3 1907
8 TraesCS6B01G356100 chr7B 613904218 613905206 988 False 974.000000 974 84.523000 818 1807 1 chr7B.!!$F2 989
9 TraesCS6B01G356100 chr7B 613927733 613928721 988 False 968.000000 968 84.422000 818 1807 1 chr7B.!!$F3 989
10 TraesCS6B01G356100 chr7B 45292335 45293130 795 False 878.000000 878 86.575000 1997 2792 1 chr7B.!!$F1 795
11 TraesCS6B01G356100 chr7B 104781263 104781931 668 True 488.000000 488 79.911000 2111 2779 1 chr7B.!!$R1 668
12 TraesCS6B01G356100 chr3B 737706356 737708319 1963 False 2263.000000 2263 87.475000 812 2792 1 chr3B.!!$F1 1980
13 TraesCS6B01G356100 chr2A 4396531 4397734 1203 True 913.500000 1315 94.094500 812 2792 2 chr2A.!!$R1 1980
14 TraesCS6B01G356100 chr6D 414107669 414108304 635 False 577.000000 577 83.746000 168 786 1 chr6D.!!$F1 618
15 TraesCS6B01G356100 chr6D 414246332 414248377 2045 False 434.500000 636 88.971000 1 786 2 chr6D.!!$F2 785

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
247 1502 0.039798 CAGCAACACAGGCACATCAC 60.04 55.0 0.0 0.0 0.0 3.06 F
249 1504 0.039798 GCAACACAGGCACATCACAG 60.04 55.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 4396 0.179097 GTTCTCATCCTCGAGTGCCC 60.179 60.000 12.31 0.00 34.46 5.36 R
2155 4784 1.135139 GAGTAGACTCATTGCGCCTGA 59.865 52.381 4.18 7.32 42.42 3.86 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
162 169 2.198969 TGCCTTGCGCATGTTCCAA 61.199 52.632 12.75 0.00 44.64 3.53
163 170 1.006337 GCCTTGCGCATGTTCCAAA 60.006 52.632 12.75 0.00 37.47 3.28
164 171 0.599728 GCCTTGCGCATGTTCCAAAA 60.600 50.000 12.75 0.00 37.47 2.44
165 172 1.139163 CCTTGCGCATGTTCCAAAAC 58.861 50.000 12.75 0.00 35.85 2.43
178 1433 0.527565 CCAAAACTTGGCGATGAGGG 59.472 55.000 0.00 0.00 45.17 4.30
179 1434 1.247567 CAAAACTTGGCGATGAGGGT 58.752 50.000 0.00 0.00 0.00 4.34
189 1444 1.533625 CGATGAGGGTTTTGCTTGGA 58.466 50.000 0.00 0.00 0.00 3.53
197 1452 4.479158 AGGGTTTTGCTTGGACATTCTTA 58.521 39.130 0.00 0.00 0.00 2.10
198 1453 4.524328 AGGGTTTTGCTTGGACATTCTTAG 59.476 41.667 0.00 0.00 0.00 2.18
199 1454 4.522789 GGGTTTTGCTTGGACATTCTTAGA 59.477 41.667 0.00 0.00 0.00 2.10
200 1455 5.010617 GGGTTTTGCTTGGACATTCTTAGAA 59.989 40.000 0.00 0.00 0.00 2.10
202 1457 5.705609 TTTGCTTGGACATTCTTAGAACC 57.294 39.130 0.00 0.00 0.00 3.62
203 1458 3.686016 TGCTTGGACATTCTTAGAACCC 58.314 45.455 0.00 0.08 0.00 4.11
205 1460 4.534500 TGCTTGGACATTCTTAGAACCCTA 59.466 41.667 0.00 0.00 0.00 3.53
206 1461 5.119694 GCTTGGACATTCTTAGAACCCTAG 58.880 45.833 0.00 6.85 0.00 3.02
207 1462 4.755266 TGGACATTCTTAGAACCCTAGC 57.245 45.455 0.00 0.00 0.00 3.42
208 1463 4.101114 TGGACATTCTTAGAACCCTAGCA 58.899 43.478 0.00 0.00 0.00 3.49
209 1464 4.162320 TGGACATTCTTAGAACCCTAGCAG 59.838 45.833 0.00 0.00 0.00 4.24
210 1465 4.123506 GACATTCTTAGAACCCTAGCAGC 58.876 47.826 0.00 0.00 0.00 5.25
211 1466 2.961526 TTCTTAGAACCCTAGCAGCG 57.038 50.000 0.00 0.00 0.00 5.18
212 1467 1.112113 TCTTAGAACCCTAGCAGCGG 58.888 55.000 0.00 0.00 0.00 5.52
213 1468 0.530870 CTTAGAACCCTAGCAGCGGC 60.531 60.000 0.00 0.00 41.61 6.53
214 1469 1.261938 TTAGAACCCTAGCAGCGGCA 61.262 55.000 12.44 0.00 44.61 5.69
215 1470 1.048724 TAGAACCCTAGCAGCGGCAT 61.049 55.000 12.44 0.00 44.61 4.40
216 1471 1.889573 GAACCCTAGCAGCGGCATC 60.890 63.158 12.44 0.00 44.61 3.91
217 1472 3.740128 AACCCTAGCAGCGGCATCG 62.740 63.158 12.44 0.00 44.61 3.84
218 1473 4.976925 CCCTAGCAGCGGCATCGG 62.977 72.222 12.44 7.81 44.61 4.18
220 1475 4.897357 CTAGCAGCGGCATCGGCA 62.897 66.667 12.44 0.00 44.61 5.69
221 1476 4.465480 TAGCAGCGGCATCGGCAA 62.465 61.111 12.44 0.00 44.61 4.52
224 1479 4.170062 CAGCGGCATCGGCAAGTG 62.170 66.667 1.45 0.00 43.71 3.16
225 1480 4.393155 AGCGGCATCGGCAAGTGA 62.393 61.111 1.45 0.00 43.71 3.41
226 1481 3.204827 GCGGCATCGGCAAGTGAT 61.205 61.111 0.00 0.00 43.71 3.06
227 1482 2.711311 CGGCATCGGCAAGTGATG 59.289 61.111 0.00 0.00 44.77 3.07
238 1493 2.046283 CAAGTGATGCAGCAACACAG 57.954 50.000 30.85 21.16 39.16 3.66
239 1494 0.956633 AAGTGATGCAGCAACACAGG 59.043 50.000 30.85 0.00 39.16 4.00
240 1495 1.080974 GTGATGCAGCAACACAGGC 60.081 57.895 26.32 3.35 37.17 4.85
241 1496 1.528776 TGATGCAGCAACACAGGCA 60.529 52.632 0.00 0.00 41.00 4.75
242 1497 1.080974 GATGCAGCAACACAGGCAC 60.081 57.895 0.00 0.00 39.34 5.01
243 1498 1.798234 GATGCAGCAACACAGGCACA 61.798 55.000 0.00 0.00 39.34 4.57
244 1499 1.183030 ATGCAGCAACACAGGCACAT 61.183 50.000 0.00 0.00 39.34 3.21
245 1500 1.080974 GCAGCAACACAGGCACATC 60.081 57.895 0.00 0.00 0.00 3.06
246 1501 1.798234 GCAGCAACACAGGCACATCA 61.798 55.000 0.00 0.00 0.00 3.07
247 1502 0.039798 CAGCAACACAGGCACATCAC 60.040 55.000 0.00 0.00 0.00 3.06
248 1503 0.466007 AGCAACACAGGCACATCACA 60.466 50.000 0.00 0.00 0.00 3.58
249 1504 0.039798 GCAACACAGGCACATCACAG 60.040 55.000 0.00 0.00 0.00 3.66
250 1505 1.596603 CAACACAGGCACATCACAGA 58.403 50.000 0.00 0.00 0.00 3.41
251 1506 1.534163 CAACACAGGCACATCACAGAG 59.466 52.381 0.00 0.00 0.00 3.35
252 1507 0.761187 ACACAGGCACATCACAGAGT 59.239 50.000 0.00 0.00 0.00 3.24
253 1508 1.270518 ACACAGGCACATCACAGAGTC 60.271 52.381 0.00 0.00 0.00 3.36
254 1509 1.001746 CACAGGCACATCACAGAGTCT 59.998 52.381 0.00 0.00 0.00 3.24
255 1510 1.696336 ACAGGCACATCACAGAGTCTT 59.304 47.619 0.00 0.00 0.00 3.01
256 1511 2.899900 ACAGGCACATCACAGAGTCTTA 59.100 45.455 0.00 0.00 0.00 2.10
257 1512 3.056250 ACAGGCACATCACAGAGTCTTAG 60.056 47.826 0.00 0.00 0.00 2.18
258 1513 2.093764 AGGCACATCACAGAGTCTTAGC 60.094 50.000 0.00 0.00 0.00 3.09
259 1514 2.093764 GGCACATCACAGAGTCTTAGCT 60.094 50.000 0.00 0.00 0.00 3.32
260 1515 3.594134 GCACATCACAGAGTCTTAGCTT 58.406 45.455 0.00 0.00 0.00 3.74
261 1516 3.999663 GCACATCACAGAGTCTTAGCTTT 59.000 43.478 0.00 0.00 0.00 3.51
262 1517 4.092675 GCACATCACAGAGTCTTAGCTTTC 59.907 45.833 0.00 0.00 0.00 2.62
263 1518 4.325741 CACATCACAGAGTCTTAGCTTTCG 59.674 45.833 0.00 0.00 0.00 3.46
278 1533 2.352715 GCTTTCGGGGTGAAAATCCAAG 60.353 50.000 0.00 0.00 45.59 3.61
300 1555 3.153919 GTCTGGCCTTAATTGGTTGTGA 58.846 45.455 3.32 0.00 0.00 3.58
321 1576 2.023673 CTGGCAGTGACCTTGTTGAAA 58.976 47.619 6.28 0.00 0.00 2.69
329 1584 6.088824 CAGTGACCTTGTTGAAAGCATTATC 58.911 40.000 0.00 0.00 0.00 1.75
337 1592 6.187125 TGTTGAAAGCATTATCTTGAGAGC 57.813 37.500 0.00 0.00 0.00 4.09
349 1604 2.948979 TCTTGAGAGCGAGGATCTTCTC 59.051 50.000 3.09 0.00 41.19 2.87
350 1605 2.727123 TGAGAGCGAGGATCTTCTCT 57.273 50.000 3.09 0.00 42.59 3.10
351 1606 2.296792 TGAGAGCGAGGATCTTCTCTG 58.703 52.381 1.56 0.00 40.90 3.35
378 1633 7.173390 GGGTGAAAATCTAAGATTTAGGATCGG 59.827 40.741 0.00 0.00 0.00 4.18
407 1662 2.407361 CGGTACTTGCGTACTGTTTCTG 59.593 50.000 3.32 0.00 44.41 3.02
413 1668 1.864711 TGCGTACTGTTTCTGTCTTGC 59.135 47.619 0.00 0.00 0.00 4.01
417 1672 2.717639 ACTGTTTCTGTCTTGCAGGT 57.282 45.000 0.00 0.00 45.08 4.00
421 1676 1.261619 GTTTCTGTCTTGCAGGTGTCG 59.738 52.381 0.00 0.00 45.08 4.35
422 1677 0.880278 TTCTGTCTTGCAGGTGTCGC 60.880 55.000 0.00 0.00 45.08 5.19
428 1683 0.662619 CTTGCAGGTGTCGCTTTTGA 59.337 50.000 0.00 0.00 0.00 2.69
440 1695 4.097135 TGTCGCTTTTGAAGAATTTGGACA 59.903 37.500 0.00 0.00 0.00 4.02
442 1697 3.735746 CGCTTTTGAAGAATTTGGACACC 59.264 43.478 0.00 0.00 0.00 4.16
489 1744 4.878397 GTGCTGTAGCTACAAGGAATTGAT 59.122 41.667 25.95 0.00 42.66 2.57
490 1745 5.007136 GTGCTGTAGCTACAAGGAATTGATC 59.993 44.000 25.95 6.58 42.66 2.92
494 1749 7.418337 TGTAGCTACAAGGAATTGATCACTA 57.582 36.000 24.15 0.00 32.40 2.74
538 1795 3.234596 GTCTTTTGACTGTGTGCGTAC 57.765 47.619 0.00 0.00 45.55 3.67
539 1796 1.855978 TCTTTTGACTGTGTGCGTACG 59.144 47.619 11.84 11.84 0.00 3.67
540 1797 1.591158 CTTTTGACTGTGTGCGTACGT 59.409 47.619 17.90 0.00 0.00 3.57
541 1798 1.202203 TTTGACTGTGTGCGTACGTC 58.798 50.000 17.90 9.82 0.00 4.34
542 1799 0.595567 TTGACTGTGTGCGTACGTCC 60.596 55.000 17.90 8.20 0.00 4.79
575 1832 3.064207 ACGACATTACGTTGTTGCAGAT 58.936 40.909 7.41 0.00 44.14 2.90
581 1838 2.324330 CGTTGTTGCAGATGCCGGA 61.324 57.895 5.05 0.00 41.18 5.14
599 1856 3.057736 CCGGATGTAATTCGTATCTCCGT 60.058 47.826 0.00 0.00 46.20 4.69
617 1874 7.520451 TCTCCGTGATATTAATATATCCCCG 57.480 40.000 7.97 6.41 41.24 5.73
630 1887 1.525941 ATCCCCGTTGTTGTTTACCG 58.474 50.000 0.00 0.00 0.00 4.02
657 1914 7.696035 TGTGCATAACAAGCAAGATATAAAACG 59.304 33.333 0.00 0.00 44.64 3.60
686 3048 9.768662 AAAAAGAAGAATATGACAATGTGCTTT 57.231 25.926 0.00 0.00 0.00 3.51
695 3057 5.330455 TGACAATGTGCTTTGTACCAAAA 57.670 34.783 0.00 0.00 39.85 2.44
747 3109 1.004745 TCCTGGGCCTCATTCAGTTTC 59.995 52.381 4.53 0.00 0.00 2.78
787 3149 9.589461 TGTAAGATTTAGGAATAGTAGAGGAGG 57.411 37.037 0.00 0.00 0.00 4.30
788 3150 7.547697 AAGATTTAGGAATAGTAGAGGAGGC 57.452 40.000 0.00 0.00 0.00 4.70
789 3151 6.869930 AGATTTAGGAATAGTAGAGGAGGCT 58.130 40.000 0.00 0.00 0.00 4.58
790 3152 6.951778 AGATTTAGGAATAGTAGAGGAGGCTC 59.048 42.308 5.78 5.78 0.00 4.70
791 3153 3.536075 AGGAATAGTAGAGGAGGCTCC 57.464 52.381 26.42 26.42 36.58 4.70
792 3154 2.792370 AGGAATAGTAGAGGAGGCTCCA 59.208 50.000 33.86 13.87 39.61 3.86
793 3155 3.404425 AGGAATAGTAGAGGAGGCTCCAT 59.596 47.826 33.86 23.77 39.61 3.41
794 3156 3.767131 GGAATAGTAGAGGAGGCTCCATC 59.233 52.174 33.86 25.60 39.61 3.51
795 3157 4.510205 GGAATAGTAGAGGAGGCTCCATCT 60.510 50.000 33.86 29.94 39.61 2.90
796 3158 5.281297 GGAATAGTAGAGGAGGCTCCATCTA 60.281 48.000 33.86 29.03 39.61 1.98
797 3159 3.806949 AGTAGAGGAGGCTCCATCTAG 57.193 52.381 33.86 0.00 39.61 2.43
798 3160 2.167662 GTAGAGGAGGCTCCATCTAGC 58.832 57.143 33.86 22.64 39.61 3.42
799 3161 0.539438 AGAGGAGGCTCCATCTAGCG 60.539 60.000 33.86 0.00 43.74 4.26
800 3162 2.153547 GAGGAGGCTCCATCTAGCGC 62.154 65.000 33.86 0.00 43.74 5.92
801 3163 2.341911 GAGGCTCCATCTAGCGCC 59.658 66.667 2.29 0.00 43.74 6.53
802 3164 3.565910 GAGGCTCCATCTAGCGCCG 62.566 68.421 2.29 0.00 46.85 6.46
803 3165 3.917760 GGCTCCATCTAGCGCCGT 61.918 66.667 2.29 0.00 43.74 5.68
804 3166 2.355244 GCTCCATCTAGCGCCGTC 60.355 66.667 2.29 0.00 31.76 4.79
805 3167 2.336809 CTCCATCTAGCGCCGTCC 59.663 66.667 2.29 0.00 0.00 4.79
806 3168 2.123854 TCCATCTAGCGCCGTCCT 60.124 61.111 2.29 0.00 0.00 3.85
807 3169 0.889638 CTCCATCTAGCGCCGTCCTA 60.890 60.000 2.29 0.00 0.00 2.94
810 3172 1.150992 ATCTAGCGCCGTCCTAGGT 59.849 57.895 9.08 0.00 34.43 3.08
875 3240 1.616921 CCCACCGTAGAGACCCCTA 59.383 63.158 0.00 0.00 0.00 3.53
886 3251 1.233659 GACCCCTAGTCCCCTCTCC 59.766 68.421 0.00 0.00 39.84 3.71
937 3303 4.008933 GACCTCTGGTGCGGCTGT 62.009 66.667 0.00 0.00 35.25 4.40
1027 3395 4.908877 GCGCGTCTAGCTCGGGAC 62.909 72.222 21.08 8.92 45.59 4.46
1060 3428 3.203710 TCTGGAAGCCATGATGAAGGAAT 59.796 43.478 0.00 0.00 30.82 3.01
1113 3481 0.624254 TCGTTGAGGAGGAGGAGCTA 59.376 55.000 0.00 0.00 0.00 3.32
1114 3482 1.215673 TCGTTGAGGAGGAGGAGCTAT 59.784 52.381 0.00 0.00 0.00 2.97
1190 3558 6.213600 ACATACAGTCAGTATTGGTTCTTCCT 59.786 38.462 0.00 0.00 41.47 3.36
1261 3629 5.334105 CCACTTGAAGACAATCTTTACACGG 60.334 44.000 0.00 0.00 36.73 4.94
1267 3635 2.151202 ACAATCTTTACACGGTGCAGG 58.849 47.619 8.30 0.00 0.00 4.85
1353 3721 3.106672 CGTAGTGATTGCTCCTTACGAC 58.893 50.000 0.00 0.00 36.00 4.34
1390 3758 2.375174 TCAACCATAGGCCTCAACAAGT 59.625 45.455 9.68 0.00 0.00 3.16
1656 4275 1.066257 CTGGTGTGCAGTTTGTGGC 59.934 57.895 0.00 0.00 0.00 5.01
1699 4318 0.041090 GTGTGGGGATGGGGTTCATT 59.959 55.000 0.00 0.00 35.97 2.57
1875 4498 1.548357 ATGCAACCGAGTCTGAGGCT 61.548 55.000 0.00 0.00 0.00 4.58
2035 4658 0.187117 TGCCCCAAAGTCCATCAACA 59.813 50.000 0.00 0.00 0.00 3.33
2127 4750 2.522836 AACAAAACCAATGATGCGCA 57.477 40.000 14.96 14.96 0.00 6.09
2635 5322 2.788191 GAACCGGAGTCAGGCACAGG 62.788 65.000 9.46 0.00 0.00 4.00
2664 5351 2.325583 TTCGTGATGCCCTTGATACC 57.674 50.000 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 167 1.247567 ACCCTCATCGCCAAGTTTTG 58.752 50.000 0.00 0.00 0.00 2.44
162 169 1.995376 AAACCCTCATCGCCAAGTTT 58.005 45.000 0.00 0.00 0.00 2.66
163 170 1.613437 CAAAACCCTCATCGCCAAGTT 59.387 47.619 0.00 0.00 0.00 2.66
164 171 1.247567 CAAAACCCTCATCGCCAAGT 58.752 50.000 0.00 0.00 0.00 3.16
165 172 0.109132 GCAAAACCCTCATCGCCAAG 60.109 55.000 0.00 0.00 0.00 3.61
178 1433 5.920840 GGTTCTAAGAATGTCCAAGCAAAAC 59.079 40.000 0.00 0.00 0.00 2.43
179 1434 5.010617 GGGTTCTAAGAATGTCCAAGCAAAA 59.989 40.000 0.00 0.00 0.00 2.44
189 1444 3.430929 CGCTGCTAGGGTTCTAAGAATGT 60.431 47.826 0.00 0.00 0.00 2.71
197 1452 2.317149 GATGCCGCTGCTAGGGTTCT 62.317 60.000 0.70 0.00 38.71 3.01
198 1453 1.889573 GATGCCGCTGCTAGGGTTC 60.890 63.158 0.70 0.00 38.71 3.62
199 1454 2.190578 GATGCCGCTGCTAGGGTT 59.809 61.111 0.70 0.00 38.71 4.11
200 1455 4.227134 CGATGCCGCTGCTAGGGT 62.227 66.667 0.70 0.00 38.71 4.34
203 1458 4.897357 TGCCGATGCCGCTGCTAG 62.897 66.667 0.70 0.00 38.71 3.42
207 1462 4.170062 CACTTGCCGATGCCGCTG 62.170 66.667 0.00 0.00 36.33 5.18
208 1463 3.687321 ATCACTTGCCGATGCCGCT 62.687 57.895 0.00 0.00 36.33 5.52
209 1464 3.204827 ATCACTTGCCGATGCCGC 61.205 61.111 0.00 0.00 36.33 6.53
210 1465 2.711311 CATCACTTGCCGATGCCG 59.289 61.111 0.00 0.00 34.32 5.69
219 1474 1.335597 CCTGTGTTGCTGCATCACTTG 60.336 52.381 31.96 25.52 35.74 3.16
220 1475 0.956633 CCTGTGTTGCTGCATCACTT 59.043 50.000 31.96 0.00 35.74 3.16
221 1476 1.521450 GCCTGTGTTGCTGCATCACT 61.521 55.000 31.96 0.00 35.74 3.41
222 1477 1.080974 GCCTGTGTTGCTGCATCAC 60.081 57.895 28.19 28.19 35.41 3.06
223 1478 1.528776 TGCCTGTGTTGCTGCATCA 60.529 52.632 9.22 9.22 0.00 3.07
224 1479 1.080974 GTGCCTGTGTTGCTGCATC 60.081 57.895 1.84 2.97 35.96 3.91
225 1480 1.183030 ATGTGCCTGTGTTGCTGCAT 61.183 50.000 1.84 0.00 35.96 3.96
226 1481 1.798234 GATGTGCCTGTGTTGCTGCA 61.798 55.000 0.00 0.00 0.00 4.41
227 1482 1.080974 GATGTGCCTGTGTTGCTGC 60.081 57.895 0.00 0.00 0.00 5.25
228 1483 0.039798 GTGATGTGCCTGTGTTGCTG 60.040 55.000 0.00 0.00 0.00 4.41
229 1484 0.466007 TGTGATGTGCCTGTGTTGCT 60.466 50.000 0.00 0.00 0.00 3.91
230 1485 0.039798 CTGTGATGTGCCTGTGTTGC 60.040 55.000 0.00 0.00 0.00 4.17
231 1486 1.534163 CTCTGTGATGTGCCTGTGTTG 59.466 52.381 0.00 0.00 0.00 3.33
232 1487 1.141657 ACTCTGTGATGTGCCTGTGTT 59.858 47.619 0.00 0.00 0.00 3.32
233 1488 0.761187 ACTCTGTGATGTGCCTGTGT 59.239 50.000 0.00 0.00 0.00 3.72
234 1489 1.001746 AGACTCTGTGATGTGCCTGTG 59.998 52.381 0.00 0.00 0.00 3.66
235 1490 1.346062 AGACTCTGTGATGTGCCTGT 58.654 50.000 0.00 0.00 0.00 4.00
236 1491 2.469274 AAGACTCTGTGATGTGCCTG 57.531 50.000 0.00 0.00 0.00 4.85
237 1492 2.093764 GCTAAGACTCTGTGATGTGCCT 60.094 50.000 0.00 0.00 0.00 4.75
238 1493 2.093764 AGCTAAGACTCTGTGATGTGCC 60.094 50.000 0.00 0.00 0.00 5.01
239 1494 3.244033 AGCTAAGACTCTGTGATGTGC 57.756 47.619 0.00 0.00 0.00 4.57
240 1495 4.325741 CGAAAGCTAAGACTCTGTGATGTG 59.674 45.833 0.00 0.00 0.00 3.21
241 1496 4.489810 CGAAAGCTAAGACTCTGTGATGT 58.510 43.478 0.00 0.00 0.00 3.06
242 1497 3.862267 CCGAAAGCTAAGACTCTGTGATG 59.138 47.826 0.00 0.00 0.00 3.07
243 1498 3.118956 CCCGAAAGCTAAGACTCTGTGAT 60.119 47.826 0.00 0.00 0.00 3.06
244 1499 2.231478 CCCGAAAGCTAAGACTCTGTGA 59.769 50.000 0.00 0.00 0.00 3.58
245 1500 2.611518 CCCGAAAGCTAAGACTCTGTG 58.388 52.381 0.00 0.00 0.00 3.66
246 1501 1.550976 CCCCGAAAGCTAAGACTCTGT 59.449 52.381 0.00 0.00 0.00 3.41
247 1502 1.550976 ACCCCGAAAGCTAAGACTCTG 59.449 52.381 0.00 0.00 0.00 3.35
248 1503 1.550976 CACCCCGAAAGCTAAGACTCT 59.449 52.381 0.00 0.00 0.00 3.24
249 1504 1.549170 TCACCCCGAAAGCTAAGACTC 59.451 52.381 0.00 0.00 0.00 3.36
250 1505 1.640917 TCACCCCGAAAGCTAAGACT 58.359 50.000 0.00 0.00 0.00 3.24
251 1506 2.467566 TTCACCCCGAAAGCTAAGAC 57.532 50.000 0.00 0.00 0.00 3.01
252 1507 3.495434 TTTTCACCCCGAAAGCTAAGA 57.505 42.857 0.00 0.00 44.32 2.10
253 1508 3.128764 GGATTTTCACCCCGAAAGCTAAG 59.871 47.826 0.00 0.00 44.32 2.18
254 1509 3.086282 GGATTTTCACCCCGAAAGCTAA 58.914 45.455 0.00 0.00 44.32 3.09
255 1510 2.040545 TGGATTTTCACCCCGAAAGCTA 59.959 45.455 0.00 0.00 44.32 3.32
256 1511 1.203001 TGGATTTTCACCCCGAAAGCT 60.203 47.619 0.00 0.00 44.32 3.74
257 1512 1.253100 TGGATTTTCACCCCGAAAGC 58.747 50.000 0.00 0.00 44.32 3.51
258 1513 2.231235 CCTTGGATTTTCACCCCGAAAG 59.769 50.000 0.00 0.00 44.32 2.62
259 1514 2.243810 CCTTGGATTTTCACCCCGAAA 58.756 47.619 0.00 0.00 41.95 3.46
260 1515 1.146152 ACCTTGGATTTTCACCCCGAA 59.854 47.619 0.00 0.00 0.00 4.30
261 1516 0.774908 ACCTTGGATTTTCACCCCGA 59.225 50.000 0.00 0.00 0.00 5.14
262 1517 1.173913 GACCTTGGATTTTCACCCCG 58.826 55.000 0.00 0.00 0.00 5.73
263 1518 2.171003 CAGACCTTGGATTTTCACCCC 58.829 52.381 0.00 0.00 0.00 4.95
278 1533 2.231235 CACAACCAATTAAGGCCAGACC 59.769 50.000 5.01 0.00 39.61 3.85
300 1555 0.546122 TCAACAAGGTCACTGCCAGT 59.454 50.000 0.00 0.00 0.00 4.00
321 1576 2.961741 TCCTCGCTCTCAAGATAATGCT 59.038 45.455 0.00 0.00 0.00 3.79
329 1584 2.951642 AGAGAAGATCCTCGCTCTCAAG 59.048 50.000 0.00 0.00 38.19 3.02
337 1592 0.749649 CACCCCAGAGAAGATCCTCG 59.250 60.000 0.00 0.00 38.19 4.63
349 1604 7.346471 TCCTAAATCTTAGATTTTCACCCCAG 58.654 38.462 22.92 13.09 0.00 4.45
350 1605 7.278724 TCCTAAATCTTAGATTTTCACCCCA 57.721 36.000 22.92 4.98 0.00 4.96
351 1606 7.173390 CGATCCTAAATCTTAGATTTTCACCCC 59.827 40.741 22.92 9.49 0.00 4.95
378 1633 2.514013 CGCAAGTACCGTCATCGCC 61.514 63.158 0.00 0.00 35.54 5.54
407 1662 0.663153 AAAAGCGACACCTGCAAGAC 59.337 50.000 0.00 0.00 34.07 3.01
413 1668 3.904136 ATTCTTCAAAAGCGACACCTG 57.096 42.857 0.00 0.00 0.00 4.00
417 1672 4.097135 TGTCCAAATTCTTCAAAAGCGACA 59.903 37.500 0.00 0.00 0.00 4.35
421 1676 3.735746 CGGTGTCCAAATTCTTCAAAAGC 59.264 43.478 0.00 0.00 0.00 3.51
422 1677 4.298332 CCGGTGTCCAAATTCTTCAAAAG 58.702 43.478 0.00 0.00 0.00 2.27
428 1683 1.133606 ACACCCGGTGTCCAAATTCTT 60.134 47.619 18.00 0.00 43.92 2.52
440 1695 1.477685 CCACCTAGACAACACCCGGT 61.478 60.000 0.00 0.00 0.00 5.28
442 1697 0.320421 CACCACCTAGACAACACCCG 60.320 60.000 0.00 0.00 0.00 5.28
527 1784 0.385849 TTACGGACGTACGCACACAG 60.386 55.000 22.56 7.92 37.37 3.66
535 1792 6.418956 TGTCGTAAAGATATTACGGACGTAC 58.581 40.000 17.51 10.29 45.40 3.67
537 1794 5.484173 TGTCGTAAAGATATTACGGACGT 57.516 39.130 17.51 1.98 45.40 4.34
538 1795 6.981379 AATGTCGTAAAGATATTACGGACG 57.019 37.500 17.51 6.84 45.40 4.79
559 1816 1.130373 CGGCATCTGCAACAACGTAAT 59.870 47.619 4.33 0.00 44.36 1.89
564 1821 0.179156 CATCCGGCATCTGCAACAAC 60.179 55.000 0.00 0.00 44.36 3.32
575 1832 3.305813 GGAGATACGAATTACATCCGGCA 60.306 47.826 0.00 0.00 0.00 5.69
613 1870 0.308376 CACGGTAAACAACAACGGGG 59.692 55.000 0.00 0.00 0.00 5.73
617 1874 2.546195 TGCACACGGTAAACAACAAC 57.454 45.000 0.00 0.00 0.00 3.32
630 1887 8.798153 GTTTTATATCTTGCTTGTTATGCACAC 58.202 33.333 0.00 0.00 40.40 3.82
657 1914 7.276438 GCACATTGTCATATTCTTCTTTTTCCC 59.724 37.037 0.00 0.00 0.00 3.97
709 3071 4.524053 CAGGAAGGAACCATAGGTTTACC 58.476 47.826 2.55 0.99 46.95 2.85
747 3109 7.968405 CCTAAATCTTACATTTTGGTTTCCTCG 59.032 37.037 0.00 0.00 32.06 4.63
762 3124 8.525316 GCCTCCTCTACTATTCCTAAATCTTAC 58.475 40.741 0.00 0.00 0.00 2.34
786 3148 3.850095 GACGGCGCTAGATGGAGCC 62.850 68.421 6.90 0.77 46.24 4.70
787 3149 2.355244 GACGGCGCTAGATGGAGC 60.355 66.667 6.90 0.00 39.20 4.70
788 3150 0.889638 TAGGACGGCGCTAGATGGAG 60.890 60.000 6.90 0.00 0.00 3.86
789 3151 0.889638 CTAGGACGGCGCTAGATGGA 60.890 60.000 6.90 0.00 0.00 3.41
790 3152 1.581954 CTAGGACGGCGCTAGATGG 59.418 63.158 6.90 0.00 0.00 3.51
791 3153 1.173444 ACCTAGGACGGCGCTAGATG 61.173 60.000 17.98 8.86 0.00 2.90
792 3154 1.150992 ACCTAGGACGGCGCTAGAT 59.849 57.895 17.98 3.24 0.00 1.98
793 3155 1.822613 CACCTAGGACGGCGCTAGA 60.823 63.158 17.98 0.00 0.00 2.43
794 3156 2.061182 GACACCTAGGACGGCGCTAG 62.061 65.000 17.98 10.71 0.00 3.42
795 3157 2.044650 ACACCTAGGACGGCGCTA 60.045 61.111 17.98 0.00 0.00 4.26
796 3158 3.450115 GACACCTAGGACGGCGCT 61.450 66.667 17.98 0.00 0.00 5.92
797 3159 4.509737 GGACACCTAGGACGGCGC 62.510 72.222 17.98 0.00 0.00 6.53
798 3160 3.834799 GGGACACCTAGGACGGCG 61.835 72.222 17.98 4.80 0.00 6.46
799 3161 3.468140 GGGGACACCTAGGACGGC 61.468 72.222 17.98 8.13 36.80 5.68
884 3249 1.686110 GAGAGAAGAAGGCCGGGGA 60.686 63.158 2.18 0.00 0.00 4.81
886 3251 2.904131 GGAGAGAAGAAGGCCGGG 59.096 66.667 2.18 0.00 0.00 5.73
933 3298 1.739562 CTCCAGCGTCTTCCACAGC 60.740 63.158 0.00 0.00 0.00 4.40
937 3303 0.895530 CTAACCTCCAGCGTCTTCCA 59.104 55.000 0.00 0.00 0.00 3.53
1027 3395 0.811281 GCTTCCAGATCGGTTTTGGG 59.189 55.000 0.90 0.00 35.57 4.12
1060 3428 2.025321 GGGTTTCCTCATTGAGCCCTAA 60.025 50.000 15.95 3.44 32.05 2.69
1113 3481 0.978146 ACCTGGTAGCTTCAGCCGAT 60.978 55.000 0.00 0.00 43.38 4.18
1114 3482 1.609501 ACCTGGTAGCTTCAGCCGA 60.610 57.895 0.00 0.00 43.38 5.54
1190 3558 1.379916 CAGGCCACCCTCATGTTCA 59.620 57.895 5.01 0.00 40.33 3.18
1267 3635 1.205417 CCAATCACCCAGGCATGAAAC 59.795 52.381 0.00 0.00 0.00 2.78
1335 3703 1.135083 CCGTCGTAAGGAGCAATCACT 60.135 52.381 0.00 0.00 38.47 3.41
1353 3721 0.948623 TTGATGGTCGTGTGAAGCCG 60.949 55.000 0.00 0.00 0.00 5.52
1390 3758 6.778559 TCATGAATTTGCATCCAGATATCCAA 59.221 34.615 0.00 0.00 0.00 3.53
1656 4275 2.148446 TGAAAAGATGGCCCAGATGG 57.852 50.000 0.00 0.00 37.09 3.51
1699 4318 0.685097 AAGACAAGCTTGCTCGGGTA 59.315 50.000 26.27 0.00 34.93 3.69
1731 4350 2.283173 CCCTTGAACCAGGTGGCC 60.283 66.667 0.00 0.00 39.32 5.36
1776 4396 0.179097 GTTCTCATCCTCGAGTGCCC 60.179 60.000 12.31 0.00 34.46 5.36
1840 4463 2.038659 TGCATCCATACGGTCATCAGA 58.961 47.619 0.00 0.00 0.00 3.27
1875 4498 2.026915 CCCATCAGTGTCCATCTGTTCA 60.027 50.000 0.00 0.00 34.86 3.18
2035 4658 3.202151 TGGTTCTCTTCACCTCCTGTTTT 59.798 43.478 0.00 0.00 35.07 2.43
2127 4750 4.431131 CTTGGAGGCCCGCCACAT 62.431 66.667 5.38 0.00 38.92 3.21
2155 4784 1.135139 GAGTAGACTCATTGCGCCTGA 59.865 52.381 4.18 7.32 42.42 3.86
2335 4964 4.528920 CTCCTACCAGAGCTACTAACAGT 58.471 47.826 0.00 0.00 0.00 3.55
2606 5293 2.122324 TCCGGTTCCCCACTCCAA 60.122 61.111 0.00 0.00 0.00 3.53
2664 5351 3.117888 ACCCAATATCAGTTAGCCCACAG 60.118 47.826 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.