Multiple sequence alignment - TraesCS6B01G024200

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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 TraesCS6B01G024200 chr6B 100.000 2462 0 0 1 2462 14623040 14620579 0.000000e+00 4547
1 TraesCS6B01G024200 chr6B 88.011 1443 144 14 262 1676 14330391 14331832 0.000000e+00 1679
2 TraesCS6B01G024200 chr6B 85.671 1319 160 19 392 1687 14550129 14548817 0.000000e+00 1362
3 TraesCS6B01G024200 chr6B 91.579 760 41 14 1714 2462 14548741 14547994 0.000000e+00 1027
4 TraesCS6B01G024200 chr6B 84.454 714 46 32 1714 2415 14331919 14332579 0.000000e+00 643
5 TraesCS6B01G024200 chr6B 76.036 1231 251 35 286 1492 14323509 14324719 1.260000e-167 599
6 TraesCS6B01G024200 chr6B 85.507 138 7 6 1 137 14329884 14330009 5.520000e-27 132
7 TraesCS6B01G024200 chr6D 91.833 2498 127 41 1 2462 7994543 7992087 0.000000e+00 3411
8 TraesCS6B01G024200 chr6D 90.367 2014 128 28 494 2462 7715858 7717850 0.000000e+00 2584
9 TraesCS6B01G024200 chr6D 94.760 229 8 3 1 227 7715633 7715859 1.080000e-93 353
10 TraesCS6B01G024200 chr6D 75.531 801 117 43 1405 2167 9545650 9544891 1.100000e-83 320
11 TraesCS6B01G024200 chr6A 89.064 2350 168 35 177 2462 8202477 8200153 0.000000e+00 2833
12 TraesCS6B01G024200 chr6A 90.995 1999 129 18 1 1958 7986468 7988456 0.000000e+00 2647
13 TraesCS6B01G024200 chr6A 75.797 1223 235 49 278 1468 7977707 7978900 1.650000e-156 562
14 TraesCS6B01G024200 chr6A 86.069 524 33 11 1950 2462 7988642 7989136 6.030000e-146 527
15 TraesCS6B01G024200 chr1B 87.615 1736 158 31 392 2080 27752870 27751145 0.000000e+00 1962
16 TraesCS6B01G024200 chr1B 88.102 1496 152 17 209 1687 27678219 27676733 0.000000e+00 1753
17 TraesCS6B01G024200 chr1B 88.728 346 25 9 1714 2055 27676657 27676322 6.340000e-111 411
18 TraesCS6B01G024200 chr1B 90.058 171 10 4 2249 2415 27675986 27675819 5.330000e-52 215
19 TraesCS6B01G024200 chr5A 86.547 1561 160 17 278 1805 650824531 650826074 0.000000e+00 1674
20 TraesCS6B01G024200 chr5A 89.153 378 30 8 1987 2354 650826075 650826451 6.200000e-126 460
21 TraesCS6B01G024200 chr5D 86.355 1561 164 15 278 1805 524577505 524579049 0.000000e+00 1657
22 TraesCS6B01G024200 chr5D 88.594 377 33 7 1987 2354 524579050 524579425 1.340000e-122 449


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 TraesCS6B01G024200 chr6B 14620579 14623040 2461 True 4547.0 4547 100.000000 1 2462 1 chr6B.!!$R1 2461
1 TraesCS6B01G024200 chr6B 14547994 14550129 2135 True 1194.5 1362 88.625000 392 2462 2 chr6B.!!$R2 2070
2 TraesCS6B01G024200 chr6B 14329884 14332579 2695 False 818.0 1679 85.990667 1 2415 3 chr6B.!!$F2 2414
3 TraesCS6B01G024200 chr6B 14323509 14324719 1210 False 599.0 599 76.036000 286 1492 1 chr6B.!!$F1 1206
4 TraesCS6B01G024200 chr6D 7992087 7994543 2456 True 3411.0 3411 91.833000 1 2462 1 chr6D.!!$R1 2461
5 TraesCS6B01G024200 chr6D 7715633 7717850 2217 False 1468.5 2584 92.563500 1 2462 2 chr6D.!!$F1 2461
6 TraesCS6B01G024200 chr6D 9544891 9545650 759 True 320.0 320 75.531000 1405 2167 1 chr6D.!!$R2 762
7 TraesCS6B01G024200 chr6A 8200153 8202477 2324 True 2833.0 2833 89.064000 177 2462 1 chr6A.!!$R1 2285
8 TraesCS6B01G024200 chr6A 7986468 7989136 2668 False 1587.0 2647 88.532000 1 2462 2 chr6A.!!$F2 2461
9 TraesCS6B01G024200 chr6A 7977707 7978900 1193 False 562.0 562 75.797000 278 1468 1 chr6A.!!$F1 1190
10 TraesCS6B01G024200 chr1B 27751145 27752870 1725 True 1962.0 1962 87.615000 392 2080 1 chr1B.!!$R1 1688
11 TraesCS6B01G024200 chr1B 27675819 27678219 2400 True 793.0 1753 88.962667 209 2415 3 chr1B.!!$R2 2206
12 TraesCS6B01G024200 chr5A 650824531 650826451 1920 False 1067.0 1674 87.850000 278 2354 2 chr5A.!!$F1 2076
13 TraesCS6B01G024200 chr5D 524577505 524579425 1920 False 1053.0 1657 87.474500 278 2354 2 chr5D.!!$F1 2076

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
276 343 0.604511 CAACGCGTTCCCCTTTACCT 60.605 55.000 23.92 0.0 0.00 3.08 F
477 863 1.142097 GTCTCTACCTGCGGGCTTC 59.858 63.158 12.89 0.0 35.63 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1241 1642 4.408396 TTAGCCGGCCCTCCAGGA 62.408 66.667 26.15 0.0 38.24 3.86 R
1544 1956 9.640952 TCAATCACTATTTAGGGGGAAAAATAG 57.359 33.333 11.40 11.4 45.17 1.73 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
101 102 5.014858 AGATCAAATGTGCTCCAAATGAGT 58.985 37.500 0.00 0.00 43.48 3.41
220 234 2.519622 CCACTCCAGAGCACCCACA 61.520 63.158 0.00 0.00 0.00 4.17
237 271 1.734465 CACAGAAATCTTCTCCACGGC 59.266 52.381 0.00 0.00 38.11 5.68
239 273 1.065854 CAGAAATCTTCTCCACGGCCT 60.066 52.381 0.00 0.00 38.11 5.19
240 274 1.208293 AGAAATCTTCTCCACGGCCTC 59.792 52.381 0.00 0.00 34.07 4.70
272 339 2.190841 CACCAACGCGTTCCCCTTT 61.191 57.895 23.92 0.00 0.00 3.11
273 340 0.885596 CACCAACGCGTTCCCCTTTA 60.886 55.000 23.92 0.00 0.00 1.85
274 341 0.886043 ACCAACGCGTTCCCCTTTAC 60.886 55.000 23.92 0.00 0.00 2.01
275 342 1.579964 CCAACGCGTTCCCCTTTACC 61.580 60.000 23.92 0.00 0.00 2.85
276 343 0.604511 CAACGCGTTCCCCTTTACCT 60.605 55.000 23.92 0.00 0.00 3.08
386 769 1.532794 CTCCCAGCTCCTCGGCTAT 60.533 63.158 0.00 0.00 41.00 2.97
433 819 2.902846 CGCCGTTTCCACCAACCA 60.903 61.111 0.00 0.00 0.00 3.67
473 859 2.482333 CCTCGTCTCTACCTGCGGG 61.482 68.421 11.02 11.02 38.88 6.13
476 862 2.711922 CGTCTCTACCTGCGGGCTT 61.712 63.158 12.89 0.00 35.63 4.35
477 863 1.142097 GTCTCTACCTGCGGGCTTC 59.858 63.158 12.89 0.00 35.63 3.86
530 916 3.256960 GCCCACCTCAAGTCCCCA 61.257 66.667 0.00 0.00 0.00 4.96
536 922 1.142688 ACCTCAAGTCCCCAGCCAAT 61.143 55.000 0.00 0.00 0.00 3.16
684 1070 3.649277 CTCACCGGCCTTGGTCTCG 62.649 68.421 0.00 0.00 41.38 4.04
703 1089 2.810887 GTGCTCTGACATCGCGCA 60.811 61.111 8.75 0.00 34.52 6.09
712 1098 2.584418 CATCGCGCACCTCCTCTG 60.584 66.667 8.75 0.00 0.00 3.35
758 1156 4.102681 GTCCCCAATATACACTACTGCCTT 59.897 45.833 0.00 0.00 0.00 4.35
1241 1642 1.340248 CCCCGTAATGCTCTCGTACAT 59.660 52.381 0.00 0.00 0.00 2.29
1544 1956 9.542462 TCATAGTAAGCTGGTAATTCACATTAC 57.458 33.333 0.00 0.00 42.94 1.89
2192 3146 1.002430 ACGGCCCTGATATATGCTGTG 59.998 52.381 0.00 0.00 41.53 3.66
2452 3416 4.572389 CCGCTAGCTGTTTCTGTTATGAAT 59.428 41.667 13.93 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 234 1.208293 GAGGCCGTGGAGAAGATTTCT 59.792 52.381 0.00 0.0 44.21 2.52
237 271 2.066393 TGCGGGAATGAGGAGGAGG 61.066 63.158 0.00 0.0 0.00 4.30
239 273 2.367202 GGTGCGGGAATGAGGAGGA 61.367 63.158 0.00 0.0 0.00 3.71
240 274 2.190578 GGTGCGGGAATGAGGAGG 59.809 66.667 0.00 0.0 0.00 4.30
386 769 3.071206 GAGAGGAGGCGGCTGTGA 61.071 66.667 19.63 0.0 0.00 3.58
481 867 4.729918 CCTTGAGGGCCTGCGCTT 62.730 66.667 12.95 0.0 39.38 4.68
505 891 2.738213 CTTGAGGTGGGCGAGCTTGT 62.738 60.000 1.96 0.0 30.42 3.16
677 1063 2.983592 TCAGAGCACGCGAGACCA 60.984 61.111 15.93 0.0 0.00 4.02
684 1070 3.906649 CGCGATGTCAGAGCACGC 61.907 66.667 0.00 0.0 44.64 5.34
687 1073 2.810887 GTGCGCGATGTCAGAGCA 60.811 61.111 12.10 0.0 41.82 4.26
715 1101 2.764637 GATGGAACTTGTGGGGGCGT 62.765 60.000 0.00 0.0 0.00 5.68
721 1119 0.676782 GGGGACGATGGAACTTGTGG 60.677 60.000 0.00 0.0 0.00 4.17
723 1121 0.768622 TTGGGGACGATGGAACTTGT 59.231 50.000 0.00 0.0 0.00 3.16
725 1123 4.410883 TGTATATTGGGGACGATGGAACTT 59.589 41.667 0.00 0.0 35.53 2.66
728 1126 3.971305 AGTGTATATTGGGGACGATGGAA 59.029 43.478 0.00 0.0 35.53 3.53
758 1156 0.535335 GTAGGACCCGAAGATGCACA 59.465 55.000 0.00 0.0 0.00 4.57
851 1252 2.023461 CTCGTAGGAGCGCGACAG 59.977 66.667 12.10 0.0 32.61 3.51
1241 1642 4.408396 TTAGCCGGCCCTCCAGGA 62.408 66.667 26.15 0.0 38.24 3.86
1544 1956 9.640952 TCAATCACTATTTAGGGGGAAAAATAG 57.359 33.333 11.40 11.4 45.17 1.73


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

AutoCloner maintained by Alex Coulton.