Multiple sequence alignment - TraesCS5A01G202400

Loading Multiple Alignment...

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 TraesCS5A01G202400 chr5A 100.000 2195 0 0 1 2195 409324085 409326279 0.000000e+00 4054.0
1 TraesCS5A01G202400 chr5D 83.131 1316 138 33 321 1598 315206351 315207620 0.000000e+00 1123.0
2 TraesCS5A01G202400 chr5D 91.135 564 37 7 1632 2183 315207620 315208182 0.000000e+00 752.0
3 TraesCS5A01G202400 chr5D 85.284 299 42 2 492 788 262843659 262843957 7.610000e-80 307.0
4 TraesCS5A01G202400 chr5D 76.480 608 98 31 1023 1592 158164796 158164196 2.760000e-74 289.0
5 TraesCS5A01G202400 chr5D 94.304 158 9 0 80 237 315205672 315205829 2.180000e-60 243.0
6 TraesCS5A01G202400 chr2D 79.280 806 100 30 784 1553 192726386 192727160 3.250000e-138 501.0
7 TraesCS5A01G202400 chr2D 82.427 478 70 10 320 788 313715495 313715967 2.620000e-109 405.0
8 TraesCS5A01G202400 chr2D 77.401 708 122 21 320 996 59170733 59171433 9.500000e-104 387.0
9 TraesCS5A01G202400 chr2D 83.208 399 61 5 391 785 477631099 477631495 5.760000e-96 361.0
10 TraesCS5A01G202400 chr2D 80.042 471 71 11 436 889 187041517 187041981 5.840000e-86 327.0
11 TraesCS5A01G202400 chr2D 94.444 36 0 2 210 243 446268069 446268034 1.000000e-03 54.7
12 TraesCS5A01G202400 chr2D 94.444 36 0 2 210 243 446271734 446271699 1.000000e-03 54.7
13 TraesCS5A01G202400 chr4B 85.281 462 57 7 1057 1508 171826896 171826436 1.190000e-127 466.0
14 TraesCS5A01G202400 chr4B 80.897 602 94 13 1005 1593 517496092 517495499 2.570000e-124 455.0
15 TraesCS5A01G202400 chr4B 79.027 596 103 14 1010 1595 338449833 338450416 2.640000e-104 388.0
16 TraesCS5A01G202400 chr4B 93.651 63 4 0 239 301 107240732 107240670 6.450000e-16 95.3
17 TraesCS5A01G202400 chr3D 81.218 591 83 17 1005 1587 590675159 590674589 3.320000e-123 451.0
18 TraesCS5A01G202400 chr3D 84.633 436 58 8 358 788 590675847 590675416 2.010000e-115 425.0
19 TraesCS5A01G202400 chr3D 78.705 587 83 16 320 889 416912872 416913433 9.640000e-94 353.0
20 TraesCS5A01G202400 chr3D 81.546 401 66 6 395 788 83892804 83892405 7.560000e-85 324.0
21 TraesCS5A01G202400 chr3D 82.963 135 21 2 1804 1936 20339726 20339860 1.060000e-23 121.0
22 TraesCS5A01G202400 chr5B 86.667 405 29 12 1599 1987 363262329 363262724 2.010000e-115 425.0
23 TraesCS5A01G202400 chr5B 84.737 190 22 3 1601 1785 15007840 15008027 1.340000e-42 183.0
24 TraesCS5A01G202400 chr5B 96.386 83 3 0 2042 2124 363262731 363262813 1.060000e-28 137.0
25 TraesCS5A01G202400 chr3B 82.571 459 67 9 1105 1553 132638689 132639144 2.040000e-105 392.0
26 TraesCS5A01G202400 chr3B 80.303 132 21 4 1804 1934 32738088 32738215 6.450000e-16 95.3
27 TraesCS5A01G202400 chr3B 81.731 104 8 2 201 294 62792749 62792851 2.340000e-10 76.8
28 TraesCS5A01G202400 chr7D 77.211 588 94 20 1025 1593 422871144 422871710 7.610000e-80 307.0
29 TraesCS5A01G202400 chr7D 93.443 61 4 0 921 981 2367862 2367922 8.350000e-15 91.6
30 TraesCS5A01G202400 chr6D 81.714 350 62 2 439 787 99803629 99803977 7.670000e-75 291.0
31 TraesCS5A01G202400 chr6D 75.261 671 103 38 784 1410 293053778 293053127 6.010000e-66 261.0
32 TraesCS5A01G202400 chr6D 84.946 93 3 3 198 280 352898312 352898403 1.400000e-12 84.2
33 TraesCS5A01G202400 chr6D 97.059 34 1 0 207 240 89236640 89236607 8.460000e-05 58.4
34 TraesCS5A01G202400 chr2B 75.318 551 95 25 1019 1534 508415485 508414941 2.190000e-55 226.0
35 TraesCS5A01G202400 chr2B 85.714 147 21 0 1023 1169 742328020 742327874 2.920000e-34 156.0
36 TraesCS5A01G202400 chr7A 78.571 364 59 16 1202 1553 609406166 609406522 2.840000e-54 222.0
37 TraesCS5A01G202400 chr7A 79.355 310 43 17 1294 1589 284739937 284740239 4.780000e-47 198.0
38 TraesCS5A01G202400 chr7A 74.615 390 67 23 1219 1590 129274814 129275189 2.270000e-30 143.0
39 TraesCS5A01G202400 chr7A 73.278 479 88 29 1601 2061 533330269 533330725 2.940000e-29 139.0
40 TraesCS5A01G202400 chr7A 84.821 112 16 1 1805 1915 288898368 288898479 6.410000e-21 111.0
41 TraesCS5A01G202400 chr7A 80.180 111 12 5 207 307 410502301 410502191 8.400000e-10 75.0
42 TraesCS5A01G202400 chr1A 79.197 274 41 9 1647 1909 277618378 277618110 2.240000e-40 176.0
43 TraesCS5A01G202400 chr1A 79.197 274 41 9 1647 1909 277620360 277620092 2.240000e-40 176.0
44 TraesCS5A01G202400 chr1A 79.197 274 41 9 1647 1909 277622343 277622075 2.240000e-40 176.0
45 TraesCS5A01G202400 chr1A 78.832 274 42 8 1647 1909 277616396 277616128 1.040000e-38 171.0
46 TraesCS5A01G202400 chr1A 84.828 145 15 3 1647 1786 277624405 277624263 2.940000e-29 139.0
47 TraesCS5A01G202400 chr1A 78.977 176 26 7 1740 1909 277624228 277624058 2.300000e-20 110.0
48 TraesCS5A01G202400 chr6B 90.361 83 8 0 236 318 136109370 136109288 2.300000e-20 110.0
49 TraesCS5A01G202400 chr6B 83.810 105 7 4 207 301 137430165 137430061 8.350000e-15 91.6
50 TraesCS5A01G202400 chr4D 82.114 123 15 4 8 124 54674535 54674656 4.990000e-17 99.0
51 TraesCS5A01G202400 chr6A 84.615 104 6 3 207 300 80914918 80914815 6.450000e-16 95.3
52 TraesCS5A01G202400 chr4A 86.905 84 11 0 235 318 668303576 668303659 6.450000e-16 95.3
53 TraesCS5A01G202400 chr1B 82.759 116 10 6 205 310 498039502 498039387 6.450000e-16 95.3
54 TraesCS5A01G202400 chr2A 90.323 62 6 0 240 301 519532275 519532336 5.020000e-12 82.4


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 TraesCS5A01G202400 chr5A 409324085 409326279 2194 False 4054 4054 100.000000 1 2195 1 chr5A.!!$F1 2194
1 TraesCS5A01G202400 chr5D 315205672 315208182 2510 False 706 1123 89.523333 80 2183 3 chr5D.!!$F2 2103
2 TraesCS5A01G202400 chr5D 158164196 158164796 600 True 289 289 76.480000 1023 1592 1 chr5D.!!$R1 569
3 TraesCS5A01G202400 chr2D 192726386 192727160 774 False 501 501 79.280000 784 1553 1 chr2D.!!$F3 769
4 TraesCS5A01G202400 chr2D 59170733 59171433 700 False 387 387 77.401000 320 996 1 chr2D.!!$F1 676
5 TraesCS5A01G202400 chr4B 517495499 517496092 593 True 455 455 80.897000 1005 1593 1 chr4B.!!$R3 588
6 TraesCS5A01G202400 chr4B 338449833 338450416 583 False 388 388 79.027000 1010 1595 1 chr4B.!!$F1 585
7 TraesCS5A01G202400 chr3D 590674589 590675847 1258 True 438 451 82.925500 358 1587 2 chr3D.!!$R2 1229
8 TraesCS5A01G202400 chr3D 416912872 416913433 561 False 353 353 78.705000 320 889 1 chr3D.!!$F2 569
9 TraesCS5A01G202400 chr7D 422871144 422871710 566 False 307 307 77.211000 1025 1593 1 chr7D.!!$F2 568
10 TraesCS5A01G202400 chr6D 293053127 293053778 651 True 261 261 75.261000 784 1410 1 chr6D.!!$R2 626
11 TraesCS5A01G202400 chr2B 508414941 508415485 544 True 226 226 75.318000 1019 1534 1 chr2B.!!$R1 515

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
307 325 0.099791 CCAAAACGCGTCCACTTTGT 59.9 50.0 24.52 2.02 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1255 1835 1.00358 GGCCAGTGAGGTTGATCAGAA 59.996 52.381 0.0 0.0 40.61 3.02 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
56 57 9.239002 TCCAAAATAACTTCAAACATAAACACG 57.761 29.630 0.00 0.00 0.00 4.49
57 58 9.239002 CCAAAATAACTTCAAACATAAACACGA 57.761 29.630 0.00 0.00 0.00 4.35
63 64 8.918961 AACTTCAAACATAAACACGAAATTGA 57.081 26.923 0.00 0.00 0.00 2.57
64 65 8.918961 ACTTCAAACATAAACACGAAATTGAA 57.081 26.923 0.00 0.00 35.14 2.69
65 66 9.528018 ACTTCAAACATAAACACGAAATTGAAT 57.472 25.926 0.00 0.00 35.67 2.57
77 78 8.336498 ACACGAAATTGAATATCTACACTACG 57.664 34.615 0.00 0.00 0.00 3.51
78 79 8.186163 ACACGAAATTGAATATCTACACTACGA 58.814 33.333 0.00 0.00 0.00 3.43
143 144 9.869844 GCATCTTCATGTACAACTTATATTGAC 57.130 33.333 0.00 0.00 31.50 3.18
147 148 7.694388 TCATGTACAACTTATATTGACTCGC 57.306 36.000 0.00 0.00 33.57 5.03
150 151 8.691727 CATGTACAACTTATATTGACTCGCTAC 58.308 37.037 0.00 0.00 33.57 3.58
184 185 6.187727 AGATTAGAAGGAAAGTGGTGAACA 57.812 37.500 0.00 0.00 0.00 3.18
192 193 5.690865 AGGAAAGTGGTGAACAAGATTACA 58.309 37.500 0.00 0.00 0.00 2.41
193 194 6.306987 AGGAAAGTGGTGAACAAGATTACAT 58.693 36.000 0.00 0.00 0.00 2.29
196 197 8.184192 GGAAAGTGGTGAACAAGATTACATATG 58.816 37.037 0.00 0.00 0.00 1.78
237 238 2.677003 CGCAGCGACCCAAATCGTT 61.677 57.895 9.98 0.00 44.13 3.85
238 239 1.134694 GCAGCGACCCAAATCGTTC 59.865 57.895 0.00 0.00 44.13 3.95
240 241 1.005394 AGCGACCCAAATCGTTCGT 60.005 52.632 0.00 0.00 44.13 3.85
243 253 1.945207 CGACCCAAATCGTTCGTTTG 58.055 50.000 10.67 10.67 37.33 2.93
251 261 0.250124 ATCGTTCGTTTGGGTCTGCA 60.250 50.000 0.00 0.00 0.00 4.41
252 262 1.155424 TCGTTCGTTTGGGTCTGCAC 61.155 55.000 0.00 0.00 0.00 4.57
261 271 0.394488 TGGGTCTGCACGGACAAAAA 60.394 50.000 11.53 0.00 37.91 1.94
266 276 1.879380 TCTGCACGGACAAAAATGGAG 59.121 47.619 0.00 0.00 32.29 3.86
268 278 0.388520 GCACGGACAAAAATGGAGGC 60.389 55.000 0.00 0.00 0.00 4.70
269 279 1.247567 CACGGACAAAAATGGAGGCT 58.752 50.000 0.00 0.00 0.00 4.58
273 291 2.351738 CGGACAAAAATGGAGGCTCAAC 60.352 50.000 17.69 0.00 0.00 3.18
275 293 1.000274 ACAAAAATGGAGGCTCAACGC 60.000 47.619 17.69 0.00 38.13 4.84
296 314 0.388006 CCGATCCAAACCCAAAACGC 60.388 55.000 0.00 0.00 0.00 4.84
299 317 0.312729 ATCCAAACCCAAAACGCGTC 59.687 50.000 14.44 0.00 0.00 5.19
301 319 1.433879 CAAACCCAAAACGCGTCCA 59.566 52.632 14.44 0.00 0.00 4.02
307 325 0.099791 CCAAAACGCGTCCACTTTGT 59.900 50.000 24.52 2.02 0.00 2.83
311 329 1.433837 AACGCGTCCACTTTGTGTCC 61.434 55.000 14.44 0.00 0.00 4.02
313 331 1.885850 GCGTCCACTTTGTGTCCGT 60.886 57.895 0.00 0.00 31.00 4.69
345 786 2.284921 CCACCCTCTGCTCCCTCA 60.285 66.667 0.00 0.00 0.00 3.86
346 787 2.365586 CCACCCTCTGCTCCCTCAG 61.366 68.421 0.00 0.00 35.46 3.35
432 886 4.787280 CTCGCCACCCCTCTCCCT 62.787 72.222 0.00 0.00 0.00 4.20
433 887 4.332543 TCGCCACCCCTCTCCCTT 62.333 66.667 0.00 0.00 0.00 3.95
437 891 2.660064 CCACCCCTCTCCCTTGTCG 61.660 68.421 0.00 0.00 0.00 4.35
438 892 2.284699 ACCCCTCTCCCTTGTCGG 60.285 66.667 0.00 0.00 0.00 4.79
441 895 3.382832 CCTCTCCCTTGTCGGCGT 61.383 66.667 6.85 0.00 0.00 5.68
442 896 2.050350 CCTCTCCCTTGTCGGCGTA 61.050 63.158 6.85 0.00 0.00 4.42
444 898 0.460311 CTCTCCCTTGTCGGCGTATT 59.540 55.000 6.85 0.00 0.00 1.89
446 900 1.276989 TCTCCCTTGTCGGCGTATTTT 59.723 47.619 6.85 0.00 0.00 1.82
506 980 2.987547 GTGTGGCACTGGCAGCAT 60.988 61.111 19.83 0.00 43.71 3.79
562 1037 2.754472 CACGACTGTCACTTGGATTCA 58.246 47.619 8.73 0.00 0.00 2.57
583 1058 0.629596 AGAGGATCCCAGTGTCGGTA 59.370 55.000 8.55 0.00 33.66 4.02
587 1062 0.753262 GATCCCAGTGTCGGTAGCAT 59.247 55.000 0.00 0.00 0.00 3.79
592 1067 2.101575 GTGTCGGTAGCATCGCGA 59.898 61.111 13.09 13.09 0.00 5.87
609 1084 4.435436 ATCGGCAAGAGCGCACGA 62.435 61.111 11.47 9.92 43.41 4.35
684 1160 2.451167 CCTACGACGTCGACTCGCT 61.451 63.158 41.52 22.01 43.02 4.93
691 1167 1.326852 GACGTCGACTCGCTCTATTGA 59.673 52.381 14.70 0.00 0.00 2.57
761 1237 0.748729 CGAAGTCTCCCGTAGCTCCT 60.749 60.000 0.00 0.00 0.00 3.69
766 1242 4.435970 TCCCGTAGCTCCTCGCCA 62.436 66.667 0.00 0.00 40.39 5.69
857 1374 3.733507 ATACGAGGAGGAGGCGGCA 62.734 63.158 13.08 0.00 0.00 5.69
911 1456 3.075005 GCTAGCCCTGTCGTCCCA 61.075 66.667 2.29 0.00 0.00 4.37
942 1487 1.533273 GCCGGAGCCTACCCTCATA 60.533 63.158 5.05 0.00 33.47 2.15
985 1530 3.545574 TGTGCGAGTGGGTGAGCA 61.546 61.111 0.00 0.00 37.26 4.26
1003 1548 2.492012 GCACCTTGCTGATCTAGATGG 58.508 52.381 10.74 6.47 40.96 3.51
1007 1552 0.767375 TTGCTGATCTAGATGGGGGC 59.233 55.000 10.74 9.06 0.00 5.80
1230 1810 2.280524 TTGTCTGGAACACGGCGG 60.281 61.111 13.24 2.35 37.70 6.13
1271 1851 3.428180 CGTCGATTCTGATCAACCTCACT 60.428 47.826 0.00 0.00 32.33 3.41
1283 1866 0.617820 ACCTCACTGGCCCTAACGAT 60.618 55.000 0.00 0.00 40.22 3.73
1451 2053 3.626028 ATTCTTTTTCTTTCGCGCACT 57.374 38.095 8.75 0.00 0.00 4.40
1559 2163 0.031994 AAAAGCGGACAAAGCGCATT 59.968 45.000 11.47 0.00 40.04 3.56
1571 2178 1.006688 GCGCATTTCCGTTTGGGTT 60.007 52.632 0.30 0.00 37.00 4.11
1575 2182 0.390860 CATTTCCGTTTGGGTTGGCA 59.609 50.000 0.00 0.00 37.00 4.92
1598 2205 6.622896 GCACGTTGAAGTTGCTATTAGGAATT 60.623 38.462 0.71 0.00 0.00 2.17
1599 2206 6.742718 CACGTTGAAGTTGCTATTAGGAATTG 59.257 38.462 0.71 0.00 0.00 2.32
1600 2207 6.653320 ACGTTGAAGTTGCTATTAGGAATTGA 59.347 34.615 0.71 0.00 0.00 2.57
1602 2209 8.184192 CGTTGAAGTTGCTATTAGGAATTGATT 58.816 33.333 0.71 0.00 0.00 2.57
1605 2212 9.679661 TGAAGTTGCTATTAGGAATTGATTACA 57.320 29.630 0.71 0.00 0.00 2.41
1607 2214 9.686683 AAGTTGCTATTAGGAATTGATTACAGT 57.313 29.630 0.71 0.00 0.00 3.55
1611 2218 9.542462 TGCTATTAGGAATTGATTACAGTACAC 57.458 33.333 0.00 0.00 0.00 2.90
1612 2219 9.765795 GCTATTAGGAATTGATTACAGTACACT 57.234 33.333 0.00 0.00 0.00 3.55
1628 2235 7.517614 CAGTACACTGGTCATATGTAGATCT 57.482 40.000 0.00 0.00 40.20 2.75
1629 2236 8.622948 CAGTACACTGGTCATATGTAGATCTA 57.377 38.462 1.90 0.00 40.20 1.98
1630 2237 8.508062 CAGTACACTGGTCATATGTAGATCTAC 58.492 40.741 23.53 23.53 40.20 2.59
1631 2238 8.441572 AGTACACTGGTCATATGTAGATCTACT 58.558 37.037 28.53 18.21 37.00 2.57
1632 2239 7.753309 ACACTGGTCATATGTAGATCTACTC 57.247 40.000 28.53 8.68 37.00 2.59
1633 2240 7.290813 ACACTGGTCATATGTAGATCTACTCA 58.709 38.462 28.53 18.42 37.00 3.41
1634 2241 7.947332 ACACTGGTCATATGTAGATCTACTCAT 59.053 37.037 28.53 18.97 37.00 2.90
1635 2242 8.458052 CACTGGTCATATGTAGATCTACTCATC 58.542 40.741 28.53 15.70 37.00 2.92
1666 2273 3.924073 GTGAAACAGAAAACCCACAACAC 59.076 43.478 0.00 0.00 36.32 3.32
1688 2298 2.981859 AAGTTGTGTCAGACGAGGTT 57.018 45.000 0.00 0.00 0.00 3.50
1696 2306 3.190953 GTGTCAGACGAGGTTAAGCTACT 59.809 47.826 7.26 5.07 0.00 2.57
1759 2369 8.386606 TGAATGTCAAAATTTTCGTCCAAAAAG 58.613 29.630 0.00 0.00 37.52 2.27
1832 2442 5.343307 TGAATGGAATCAGAACATCGAGA 57.657 39.130 0.00 0.00 0.00 4.04
1872 2482 8.946085 TGTATAACTTTTCTTGAATCGAAGCAT 58.054 29.630 0.00 0.00 0.00 3.79
1884 2494 7.880059 TGAATCGAAGCATGATTATGTAGAG 57.120 36.000 0.00 0.00 36.24 2.43
1893 2503 5.063186 GCATGATTATGTAGAGGCGATGAAG 59.937 44.000 0.00 0.00 36.65 3.02
1912 2522 8.768955 CGATGAAGGAGATTAAAAGGTGATTAG 58.231 37.037 0.00 0.00 0.00 1.73
1945 2555 2.138596 CAAACCACTTGCATGTGTCC 57.861 50.000 25.77 0.00 36.30 4.02
1950 2565 0.877071 CACTTGCATGTGTCCTCCAC 59.123 55.000 21.36 0.00 44.78 4.02
1971 2586 0.798776 CACGTGGGTTTGAGAGCATC 59.201 55.000 7.95 0.00 0.00 3.91
1992 2607 2.282462 CGGGCCTGGCTGAAAACT 60.282 61.111 19.68 0.00 0.00 2.66
1995 2610 1.115326 GGGCCTGGCTGAAAACTGTT 61.115 55.000 19.68 0.00 0.00 3.16
2011 2626 6.822073 AAACTGTTAATTTGAGCGTTTTCC 57.178 33.333 0.00 0.00 0.00 3.13
2015 2630 5.044558 TGTTAATTTGAGCGTTTTCCAACC 58.955 37.500 0.00 0.00 0.00 3.77
2028 2643 4.329462 TTTCCAACCATACAGGCAAAAC 57.671 40.909 0.00 0.00 43.14 2.43
2064 2680 3.872603 TCGTGCAGGCCCAACTGT 61.873 61.111 0.00 0.00 40.59 3.55
2071 2687 2.027460 GGCCCAACTGTGTTTGCG 59.973 61.111 0.00 0.00 0.00 4.85
2134 2750 1.338136 GGCTACCAAGGCCTGAGCTA 61.338 60.000 21.80 5.16 45.57 3.32
2146 2762 3.450457 GGCCTGAGCTATATGCAGACTAT 59.550 47.826 0.00 0.00 45.94 2.12
2170 2789 3.134574 ACACGTCCTAGGAAATGCAAA 57.865 42.857 14.65 0.00 0.00 3.68
2173 2792 3.074412 ACGTCCTAGGAAATGCAAAGTG 58.926 45.455 14.65 0.00 0.00 3.16
2183 2802 9.474920 CTAGGAAATGCAAAGTGAAAACATTTA 57.525 29.630 0.00 0.00 40.13 1.40
2184 2803 8.729805 AGGAAATGCAAAGTGAAAACATTTAA 57.270 26.923 0.00 0.00 40.13 1.52
2185 2804 8.829612 AGGAAATGCAAAGTGAAAACATTTAAG 58.170 29.630 0.00 0.00 40.13 1.85
2186 2805 8.069574 GGAAATGCAAAGTGAAAACATTTAAGG 58.930 33.333 0.00 0.00 40.13 2.69
2187 2806 8.729805 AAATGCAAAGTGAAAACATTTAAGGA 57.270 26.923 0.00 0.00 38.73 3.36
2188 2807 7.713764 ATGCAAAGTGAAAACATTTAAGGAC 57.286 32.000 0.00 0.00 0.00 3.85
2189 2808 6.634805 TGCAAAGTGAAAACATTTAAGGACA 58.365 32.000 0.00 0.00 0.00 4.02
2190 2809 7.099764 TGCAAAGTGAAAACATTTAAGGACAA 58.900 30.769 0.00 0.00 0.00 3.18
2191 2810 7.064016 TGCAAAGTGAAAACATTTAAGGACAAC 59.936 33.333 0.00 0.00 0.00 3.32
2192 2811 7.064016 GCAAAGTGAAAACATTTAAGGACAACA 59.936 33.333 0.00 0.00 0.00 3.33
2193 2812 9.097257 CAAAGTGAAAACATTTAAGGACAACAT 57.903 29.630 0.00 0.00 0.00 2.71
2194 2813 8.647143 AAGTGAAAACATTTAAGGACAACATG 57.353 30.769 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.239002 CGTGTTTATGTTTGAAGTTATTTTGGA 57.761 29.630 0.00 0.00 0.00 3.53
31 32 9.239002 TCGTGTTTATGTTTGAAGTTATTTTGG 57.761 29.630 0.00 0.00 0.00 3.28
38 39 8.918961 TCAATTTCGTGTTTATGTTTGAAGTT 57.081 26.923 0.00 0.00 0.00 2.66
39 40 8.918961 TTCAATTTCGTGTTTATGTTTGAAGT 57.081 26.923 0.00 0.00 30.72 3.01
51 52 8.804743 CGTAGTGTAGATATTCAATTTCGTGTT 58.195 33.333 0.00 0.00 0.00 3.32
52 53 8.186163 TCGTAGTGTAGATATTCAATTTCGTGT 58.814 33.333 0.00 0.00 0.00 4.49
53 54 8.556517 TCGTAGTGTAGATATTCAATTTCGTG 57.443 34.615 0.00 0.00 0.00 4.35
54 55 9.017669 GTTCGTAGTGTAGATATTCAATTTCGT 57.982 33.333 0.00 0.00 0.00 3.85
55 56 8.199462 CGTTCGTAGTGTAGATATTCAATTTCG 58.801 37.037 0.00 0.00 0.00 3.46
56 57 9.229784 TCGTTCGTAGTGTAGATATTCAATTTC 57.770 33.333 0.00 0.00 0.00 2.17
57 58 9.577110 TTCGTTCGTAGTGTAGATATTCAATTT 57.423 29.630 0.00 0.00 0.00 1.82
58 59 9.017669 GTTCGTTCGTAGTGTAGATATTCAATT 57.982 33.333 0.00 0.00 0.00 2.32
59 60 7.646922 GGTTCGTTCGTAGTGTAGATATTCAAT 59.353 37.037 0.00 0.00 0.00 2.57
60 61 6.968904 GGTTCGTTCGTAGTGTAGATATTCAA 59.031 38.462 0.00 0.00 0.00 2.69
61 62 6.093909 TGGTTCGTTCGTAGTGTAGATATTCA 59.906 38.462 0.00 0.00 0.00 2.57
62 63 6.489675 TGGTTCGTTCGTAGTGTAGATATTC 58.510 40.000 0.00 0.00 0.00 1.75
63 64 6.441093 TGGTTCGTTCGTAGTGTAGATATT 57.559 37.500 0.00 0.00 0.00 1.28
64 65 6.441093 TTGGTTCGTTCGTAGTGTAGATAT 57.559 37.500 0.00 0.00 0.00 1.63
65 66 5.878332 TTGGTTCGTTCGTAGTGTAGATA 57.122 39.130 0.00 0.00 0.00 1.98
66 67 4.771590 TTGGTTCGTTCGTAGTGTAGAT 57.228 40.909 0.00 0.00 0.00 1.98
67 68 4.771590 ATTGGTTCGTTCGTAGTGTAGA 57.228 40.909 0.00 0.00 0.00 2.59
68 69 4.682860 ACAATTGGTTCGTTCGTAGTGTAG 59.317 41.667 10.83 0.00 0.00 2.74
69 70 4.619973 ACAATTGGTTCGTTCGTAGTGTA 58.380 39.130 10.83 0.00 0.00 2.90
70 71 3.460103 ACAATTGGTTCGTTCGTAGTGT 58.540 40.909 10.83 0.00 0.00 3.55
71 72 4.461992 AACAATTGGTTCGTTCGTAGTG 57.538 40.909 10.83 0.00 33.35 2.74
72 73 4.571580 TCAAACAATTGGTTCGTTCGTAGT 59.428 37.500 5.55 0.00 39.29 2.73
73 74 5.085636 TCAAACAATTGGTTCGTTCGTAG 57.914 39.130 5.55 0.00 39.29 3.51
74 75 5.481200 TTCAAACAATTGGTTCGTTCGTA 57.519 34.783 5.55 0.00 39.29 3.43
75 76 4.358494 TTCAAACAATTGGTTCGTTCGT 57.642 36.364 5.55 0.00 39.29 3.85
76 77 4.148000 CCATTCAAACAATTGGTTCGTTCG 59.852 41.667 5.55 0.00 39.29 3.95
77 78 5.285651 TCCATTCAAACAATTGGTTCGTTC 58.714 37.500 5.55 0.00 39.29 3.95
78 79 5.269505 TCCATTCAAACAATTGGTTCGTT 57.730 34.783 5.55 0.00 39.29 3.85
140 141 2.134201 CACAACTGTGTAGCGAGTCA 57.866 50.000 1.51 0.00 40.96 3.41
173 174 8.862325 TTCATATGTAATCTTGTTCACCACTT 57.138 30.769 1.90 0.00 0.00 3.16
192 193 6.556495 TGGAGTTGCTCTAATCTCCTTCATAT 59.444 38.462 10.66 0.00 44.57 1.78
193 194 5.899547 TGGAGTTGCTCTAATCTCCTTCATA 59.100 40.000 10.66 0.00 44.57 2.15
196 197 4.744795 TGGAGTTGCTCTAATCTCCTTC 57.255 45.455 10.66 0.00 44.57 3.46
237 238 2.280524 CCGTGCAGACCCAAACGA 60.281 61.111 0.00 0.00 38.27 3.85
238 239 2.280524 TCCGTGCAGACCCAAACG 60.281 61.111 0.00 0.00 35.85 3.60
240 241 0.394488 TTTGTCCGTGCAGACCCAAA 60.394 50.000 3.85 1.34 35.83 3.28
243 253 0.958822 ATTTTTGTCCGTGCAGACCC 59.041 50.000 3.85 0.00 35.83 4.46
247 257 1.068333 CCTCCATTTTTGTCCGTGCAG 60.068 52.381 0.00 0.00 0.00 4.41
251 261 1.202879 TGAGCCTCCATTTTTGTCCGT 60.203 47.619 0.00 0.00 0.00 4.69
252 262 1.533625 TGAGCCTCCATTTTTGTCCG 58.466 50.000 0.00 0.00 0.00 4.79
268 278 2.387445 TTTGGATCGGCGCGTTGAG 61.387 57.895 8.43 0.00 0.00 3.02
269 279 2.357638 TTTGGATCGGCGCGTTGA 60.358 55.556 8.43 6.41 0.00 3.18
275 293 0.388006 GTTTTGGGTTTGGATCGGCG 60.388 55.000 0.00 0.00 0.00 6.46
281 299 1.726533 GGACGCGTTTTGGGTTTGGA 61.727 55.000 15.53 0.00 44.90 3.53
296 314 1.931551 CACGGACACAAAGTGGACG 59.068 57.895 12.02 12.02 40.54 4.79
299 317 3.030652 GGCACGGACACAAAGTGG 58.969 61.111 1.93 0.00 37.94 4.00
318 336 4.554036 GAGGGTGGCGAGATGGGC 62.554 72.222 0.00 0.00 0.00 5.36
343 784 1.880894 CTAGGGTTGTCGTCGCTGA 59.119 57.895 0.00 0.00 0.00 4.26
345 786 2.572284 GCTAGGGTTGTCGTCGCT 59.428 61.111 0.00 0.00 0.00 4.93
346 787 2.508663 GGCTAGGGTTGTCGTCGC 60.509 66.667 0.00 0.00 0.00 5.19
349 790 2.939261 CGGTGGCTAGGGTTGTCGT 61.939 63.158 0.00 0.00 0.00 4.34
352 793 1.839747 TGTCGGTGGCTAGGGTTGT 60.840 57.895 0.00 0.00 0.00 3.32
416 870 4.332543 AAGGGAGAGGGGTGGCGA 62.333 66.667 0.00 0.00 0.00 5.54
463 937 3.677527 GCACTGGCAAGCTCATGT 58.322 55.556 4.50 0.00 40.72 3.21
483 957 4.015406 CCAGTGCCACACCGCCTA 62.015 66.667 0.00 0.00 34.49 3.93
490 964 2.674033 GATGCTGCCAGTGCCACA 60.674 61.111 0.00 0.00 36.33 4.17
506 980 2.124403 GTAGGGAGAGGGACGCGA 60.124 66.667 15.93 0.00 0.00 5.87
550 1025 3.708631 GGATCCTCTCTGAATCCAAGTGA 59.291 47.826 3.84 0.00 0.00 3.41
562 1037 0.396417 CCGACACTGGGATCCTCTCT 60.396 60.000 12.58 0.00 0.00 3.10
583 1058 2.963854 CTTGCCGATCGCGATGCT 60.964 61.111 29.09 2.35 42.08 3.79
592 1067 4.435436 TCGTGCGCTCTTGCCGAT 62.435 61.111 9.73 0.00 34.31 4.18
684 1160 1.933181 CGAACCAATGCGCTCAATAGA 59.067 47.619 9.73 0.00 0.00 1.98
766 1242 4.789075 CGAACGACGATGGGCGGT 62.789 66.667 8.18 0.00 46.49 5.68
786 1297 4.101448 GAGGACAGCCGCCATGGT 62.101 66.667 14.67 0.00 41.21 3.55
835 1346 2.873525 GCCTCCTCCTCGTATGCCC 61.874 68.421 0.00 0.00 0.00 5.36
857 1374 2.516930 GCCATGCGTGCCTGGTAT 60.517 61.111 16.00 0.00 34.76 2.73
897 1442 2.526873 ACTTGGGACGACAGGGCT 60.527 61.111 0.00 0.00 0.00 5.19
902 1447 1.070786 GCCTTGACTTGGGACGACA 59.929 57.895 0.00 0.00 0.00 4.35
942 1487 2.115911 CGTCCAGGAGTAGCGCTCT 61.116 63.158 16.34 11.61 43.62 4.09
985 1530 2.053244 CCCCATCTAGATCAGCAAGGT 58.947 52.381 1.03 0.00 0.00 3.50
986 1531 1.350351 CCCCCATCTAGATCAGCAAGG 59.650 57.143 1.03 0.00 0.00 3.61
987 1532 1.271271 GCCCCCATCTAGATCAGCAAG 60.271 57.143 1.03 0.00 0.00 4.01
988 1533 0.767375 GCCCCCATCTAGATCAGCAA 59.233 55.000 1.03 0.00 0.00 3.91
989 1534 1.475169 CGCCCCCATCTAGATCAGCA 61.475 60.000 1.03 0.00 0.00 4.41
990 1535 1.188219 TCGCCCCCATCTAGATCAGC 61.188 60.000 1.03 2.73 0.00 4.26
991 1536 0.894141 CTCGCCCCCATCTAGATCAG 59.106 60.000 1.03 0.00 0.00 2.90
992 1537 1.188219 GCTCGCCCCCATCTAGATCA 61.188 60.000 1.03 0.00 0.00 2.92
993 1538 1.188219 TGCTCGCCCCCATCTAGATC 61.188 60.000 1.03 0.00 0.00 2.75
994 1539 1.152247 TGCTCGCCCCCATCTAGAT 60.152 57.895 0.00 0.00 0.00 1.98
995 1540 2.134287 GTGCTCGCCCCCATCTAGA 61.134 63.158 0.00 0.00 0.00 2.43
996 1541 2.423446 GTGCTCGCCCCCATCTAG 59.577 66.667 0.00 0.00 0.00 2.43
997 1542 3.161450 GGTGCTCGCCCCCATCTA 61.161 66.667 0.00 0.00 0.00 1.98
1062 1608 4.105733 CGCTTGCGCCATTGCTCA 62.106 61.111 4.18 0.00 35.36 4.26
1200 1779 2.264794 GACAAGGCGATGTCGGGT 59.735 61.111 10.03 0.00 40.23 5.28
1214 1794 3.509137 GACCGCCGTGTTCCAGACA 62.509 63.158 0.00 0.00 35.42 3.41
1251 1831 3.118992 CCAGTGAGGTTGATCAGAATCGA 60.119 47.826 0.00 0.00 34.39 3.59
1255 1835 1.003580 GGCCAGTGAGGTTGATCAGAA 59.996 52.381 0.00 0.00 40.61 3.02
1271 1851 1.672854 CCTCGTCATCGTTAGGGCCA 61.673 60.000 6.18 0.00 38.33 5.36
1283 1866 4.277552 CCCTAGGCATCCTCGTCA 57.722 61.111 2.05 0.00 34.61 4.35
1335 1931 7.643764 CCAAGCGTCCACATTACATTAATTAAG 59.356 37.037 3.94 0.00 0.00 1.85
1440 2038 1.710249 CATTTTGACAGTGCGCGAAAG 59.290 47.619 12.10 0.00 0.00 2.62
1451 2053 2.862541 CTGACCTGACCCATTTTGACA 58.137 47.619 0.00 0.00 0.00 3.58
1483 2087 3.402095 TTCCACGTTTGGGTCGGCA 62.402 57.895 0.00 0.00 44.11 5.69
1559 2163 2.482333 CGTGCCAACCCAAACGGAA 61.482 57.895 0.00 0.00 34.64 4.30
1571 2178 1.890876 ATAGCAACTTCAACGTGCCA 58.109 45.000 0.00 0.00 0.00 4.92
1575 2182 6.653320 TCAATTCCTAATAGCAACTTCAACGT 59.347 34.615 0.00 0.00 0.00 3.99
1598 2205 7.418337 ACATATGACCAGTGTACTGTAATCA 57.582 36.000 10.38 10.95 42.27 2.57
1599 2206 8.847196 TCTACATATGACCAGTGTACTGTAATC 58.153 37.037 10.38 6.33 42.27 1.75
1600 2207 8.762481 TCTACATATGACCAGTGTACTGTAAT 57.238 34.615 10.38 4.49 42.27 1.89
1602 2209 8.218488 AGATCTACATATGACCAGTGTACTGTA 58.782 37.037 10.38 0.00 42.27 2.74
1603 2210 7.063593 AGATCTACATATGACCAGTGTACTGT 58.936 38.462 10.38 0.00 42.27 3.55
1604 2211 7.517614 AGATCTACATATGACCAGTGTACTG 57.482 40.000 10.38 5.05 43.40 2.74
1605 2212 8.441572 AGTAGATCTACATATGACCAGTGTACT 58.558 37.037 29.85 6.37 38.48 2.73
1606 2213 8.624367 AGTAGATCTACATATGACCAGTGTAC 57.376 38.462 29.85 4.17 38.48 2.90
1607 2214 8.437575 TGAGTAGATCTACATATGACCAGTGTA 58.562 37.037 29.85 0.00 38.48 2.90
1608 2215 7.290813 TGAGTAGATCTACATATGACCAGTGT 58.709 38.462 29.85 8.60 38.48 3.55
1609 2216 7.751768 TGAGTAGATCTACATATGACCAGTG 57.248 40.000 29.85 0.00 38.48 3.66
1610 2217 8.390143 AGATGAGTAGATCTACATATGACCAGT 58.610 37.037 29.85 9.26 38.48 4.00
1611 2218 8.806429 AGATGAGTAGATCTACATATGACCAG 57.194 38.462 29.85 3.72 38.48 4.00
1626 2233 9.591792 CTGTTTCACAAATCATAGATGAGTAGA 57.408 33.333 0.00 0.00 40.64 2.59
1627 2234 9.591792 TCTGTTTCACAAATCATAGATGAGTAG 57.408 33.333 0.00 0.00 40.64 2.57
1628 2235 9.942850 TTCTGTTTCACAAATCATAGATGAGTA 57.057 29.630 0.00 0.00 40.64 2.59
1629 2236 8.853077 TTCTGTTTCACAAATCATAGATGAGT 57.147 30.769 0.00 0.00 40.64 3.41
1631 2238 9.897744 GTTTTCTGTTTCACAAATCATAGATGA 57.102 29.630 0.00 0.00 41.70 2.92
1632 2239 9.132521 GGTTTTCTGTTTCACAAATCATAGATG 57.867 33.333 0.00 0.00 0.00 2.90
1633 2240 8.306761 GGGTTTTCTGTTTCACAAATCATAGAT 58.693 33.333 0.00 0.00 0.00 1.98
1634 2241 7.286546 TGGGTTTTCTGTTTCACAAATCATAGA 59.713 33.333 0.00 0.00 0.00 1.98
1635 2242 7.382218 GTGGGTTTTCTGTTTCACAAATCATAG 59.618 37.037 0.00 0.00 0.00 2.23
1666 2273 1.787155 CCTCGTCTGACACAACTTTCG 59.213 52.381 8.73 0.00 0.00 3.46
1688 2298 7.959175 TGAAGTTTCCTTTGACTAGTAGCTTA 58.041 34.615 0.00 0.00 0.00 3.09
1696 2306 5.187687 ACCGTTTGAAGTTTCCTTTGACTA 58.812 37.500 0.00 0.00 0.00 2.59
1786 2396 6.101650 AGCGATCATACTTCCATTCATGTA 57.898 37.500 0.00 0.00 0.00 2.29
1787 2397 4.965814 AGCGATCATACTTCCATTCATGT 58.034 39.130 0.00 0.00 0.00 3.21
1789 2399 5.614308 TCAAGCGATCATACTTCCATTCAT 58.386 37.500 0.00 0.00 0.00 2.57
1794 2404 4.129380 CCATTCAAGCGATCATACTTCCA 58.871 43.478 0.00 0.00 0.00 3.53
1796 2406 5.991328 TTCCATTCAAGCGATCATACTTC 57.009 39.130 0.00 0.00 0.00 3.01
1799 2409 5.698089 TCTGATTCCATTCAAGCGATCATAC 59.302 40.000 0.00 0.00 0.00 2.39
1806 2416 4.595116 GATGTTCTGATTCCATTCAAGCG 58.405 43.478 0.00 0.00 0.00 4.68
1844 2454 8.227791 GCTTCGATTCAAGAAAAGTTATACACA 58.772 33.333 0.00 0.00 0.00 3.72
1860 2470 6.870439 CCTCTACATAATCATGCTTCGATTCA 59.130 38.462 0.00 0.00 35.39 2.57
1861 2471 6.183360 GCCTCTACATAATCATGCTTCGATTC 60.183 42.308 0.00 0.00 35.39 2.52
1872 2482 4.832823 TCCTTCATCGCCTCTACATAATCA 59.167 41.667 0.00 0.00 0.00 2.57
1884 2494 4.035675 CACCTTTTAATCTCCTTCATCGCC 59.964 45.833 0.00 0.00 0.00 5.54
1893 2503 9.462606 TTTTCCTCTAATCACCTTTTAATCTCC 57.537 33.333 0.00 0.00 0.00 3.71
1912 2522 3.826729 AGTGGTTTGCAGGTATTTTCCTC 59.173 43.478 0.00 0.00 35.37 3.71
1992 2607 5.044558 GGTTGGAAAACGCTCAAATTAACA 58.955 37.500 0.00 0.00 0.00 2.41
1995 2610 4.920640 TGGTTGGAAAACGCTCAAATTA 57.079 36.364 0.00 0.00 35.09 1.40
2011 2626 1.611491 ACCGTTTTGCCTGTATGGTTG 59.389 47.619 0.00 0.00 38.35 3.77
2015 2630 4.759516 AAAGTACCGTTTTGCCTGTATG 57.240 40.909 0.00 0.00 0.00 2.39
2028 2643 4.029861 CACGACACGATTCTTAAAGTACCG 59.970 45.833 0.00 0.00 0.00 4.02
2130 2746 5.923114 CGTGTTTGATAGTCTGCATATAGCT 59.077 40.000 0.00 0.00 45.94 3.32
2134 2750 5.050490 GGACGTGTTTGATAGTCTGCATAT 58.950 41.667 0.00 0.00 34.34 1.78
2146 2762 3.071479 GCATTTCCTAGGACGTGTTTGA 58.929 45.455 12.22 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.