Multiple sequence alignment - TraesCS1D01G041500

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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 TraesCS1D01G041500 chr1D 100.000 2567 0 0 1 2567 20060881 20063447 0.000000e+00 4741.0
1 TraesCS1D01G041500 chr1D 83.237 1897 197 52 473 2332 20184478 20186290 0.000000e+00 1629.0
2 TraesCS1D01G041500 chr1D 84.739 498 43 16 1 479 20182485 20182968 3.870000e-128 468.0
3 TraesCS1D01G041500 chr1D 78.165 632 89 29 998 1603 20193407 20194015 8.730000e-95 357.0
4 TraesCS1D01G041500 chr1B 89.858 2613 175 35 1 2567 33947780 33945212 0.000000e+00 3275.0
5 TraesCS1D01G041500 chr1B 86.379 2063 168 56 1 2013 33922566 33920567 0.000000e+00 2148.0
6 TraesCS1D01G041500 chr1B 78.328 646 89 31 996 1615 33857392 33856772 1.120000e-98 370.0
7 TraesCS1D01G041500 chr1B 92.462 199 10 1 650 843 33962776 33962578 1.940000e-71 279.0
8 TraesCS1D01G041500 chr1B 85.430 151 16 4 3 153 33963208 33963064 4.420000e-33 152.0
9 TraesCS1D01G041500 chr1B 90.698 86 8 0 840 925 33962299 33962214 5.800000e-22 115.0
10 TraesCS1D01G041500 chr1A 85.114 2405 232 55 8 2368 22283982 22281660 0.000000e+00 2342.0
11 TraesCS1D01G041500 chr1A 78.049 656 94 27 997 1612 22271964 22271319 4.040000e-98 368.0
12 TraesCS1D01G041500 chr1A 79.545 396 51 21 1152 1544 22074513 22074145 3.280000e-64 255.0
13 TraesCS1D01G041500 chr4B 84.932 219 22 6 1117 1325 434714057 434714274 7.200000e-51 211.0
14 TraesCS1D01G041500 chr5D 90.000 80 6 2 1117 1195 525302712 525302790 4.520000e-18 102.0
15 TraesCS1D01G041500 chr6B 96.970 33 1 0 937 969 253962101 253962133 3.570000e-04 56.5
16 TraesCS1D01G041500 chr3B 96.970 33 1 0 937 969 387795429 387795397 3.570000e-04 56.5


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 TraesCS1D01G041500 chr1D 20060881 20063447 2566 False 4741.0 4741 100.000 1 2567 1 chr1D.!!$F1 2566
1 TraesCS1D01G041500 chr1D 20182485 20186290 3805 False 1048.5 1629 83.988 1 2332 2 chr1D.!!$F3 2331
2 TraesCS1D01G041500 chr1D 20193407 20194015 608 False 357.0 357 78.165 998 1603 1 chr1D.!!$F2 605
3 TraesCS1D01G041500 chr1B 33945212 33947780 2568 True 3275.0 3275 89.858 1 2567 1 chr1B.!!$R3 2566
4 TraesCS1D01G041500 chr1B 33920567 33922566 1999 True 2148.0 2148 86.379 1 2013 1 chr1B.!!$R2 2012
5 TraesCS1D01G041500 chr1B 33856772 33857392 620 True 370.0 370 78.328 996 1615 1 chr1B.!!$R1 619
6 TraesCS1D01G041500 chr1A 22281660 22283982 2322 True 2342.0 2342 85.114 8 2368 1 chr1A.!!$R3 2360
7 TraesCS1D01G041500 chr1A 22271319 22271964 645 True 368.0 368 78.049 997 1612 1 chr1A.!!$R2 615

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
100 104 0.033306 TGGCATTTGGAGCAGGCATA 60.033 50.0 0.00 0.0 0.0 3.14 F
619 2175 0.037326 CTGAACTACTGAAGCGGCCA 60.037 55.0 2.24 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1360 3012 0.529337 TGCTTCTCTATCGCTGCTGC 60.529 55.0 5.34 5.34 0.0 5.25 R
1588 3263 1.170442 CTATTCGGCAAAAACCCGGT 58.830 50.0 0.00 0.00 45.6 5.28 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
100 104 0.033306 TGGCATTTGGAGCAGGCATA 60.033 50.000 0.00 0.00 0.00 3.14
131 135 9.566432 GTTTGATAAGATCATCATTAAGAGGGT 57.434 33.333 0.00 0.00 39.39 4.34
218 223 3.865745 CCTAGCTAGTCATGACCAAAACG 59.134 47.826 22.21 7.40 0.00 3.60
275 287 2.311542 TCAGTGGGCCACAATTTATCCT 59.688 45.455 36.28 11.47 36.74 3.24
304 316 4.662278 AGGAAAATGGGATCTTCGTTGAA 58.338 39.130 0.00 0.00 0.00 2.69
306 318 5.716703 AGGAAAATGGGATCTTCGTTGAAAT 59.283 36.000 0.00 0.00 0.00 2.17
308 320 7.561356 AGGAAAATGGGATCTTCGTTGAAATAT 59.439 33.333 0.00 0.00 0.00 1.28
317 329 9.490379 GGATCTTCGTTGAAATATAGTACCATT 57.510 33.333 0.00 0.00 0.00 3.16
332 344 6.342338 AGTACCATTCCGTCATAATCTACC 57.658 41.667 0.00 0.00 0.00 3.18
447 476 7.236432 AGTGCACTTGTTGATATCCTATCCTAT 59.764 37.037 15.25 0.00 0.00 2.57
448 477 8.531982 GTGCACTTGTTGATATCCTATCCTATA 58.468 37.037 10.32 0.00 0.00 1.31
530 2076 4.349342 AGAGGAGAAACAGTTGACCTTGAT 59.651 41.667 7.37 0.00 0.00 2.57
564 2112 3.346315 CCCTCATGAGTAATGTGCACAA 58.654 45.455 25.72 5.14 37.56 3.33
595 2143 4.424842 TGAATAAGCCCCTTTGGTTGATT 58.575 39.130 0.00 0.00 36.04 2.57
619 2175 0.037326 CTGAACTACTGAAGCGGCCA 60.037 55.000 2.24 0.00 0.00 5.36
631 2187 2.824041 CGGCCATGCACAGGTACC 60.824 66.667 2.73 2.73 0.00 3.34
687 2243 2.186384 GGATGCACTGAGCTCGCT 59.814 61.111 9.64 0.00 45.94 4.93
713 2269 0.893727 TGCGTGTGGCTCTAGAGTGA 60.894 55.000 20.75 5.25 44.05 3.41
822 2401 4.620982 AGTTGTGCATTTCTTTAACTGGC 58.379 39.130 0.00 0.00 0.00 4.85
868 2447 4.080469 TCACTACTGCCTAGCTACTACTGT 60.080 45.833 0.00 0.00 0.00 3.55
876 2455 5.655090 TGCCTAGCTACTACTGTGTGATTTA 59.345 40.000 0.00 0.00 0.00 1.40
877 2456 6.323996 TGCCTAGCTACTACTGTGTGATTTAT 59.676 38.462 0.00 0.00 0.00 1.40
887 2467 9.515226 ACTACTGTGTGATTTATTTTATGGTGT 57.485 29.630 0.00 0.00 0.00 4.16
950 2530 5.486526 TCTTCATCAGCTTCTTCTTCTTCC 58.513 41.667 0.00 0.00 0.00 3.46
953 2557 3.971245 TCAGCTTCTTCTTCTTCCTCC 57.029 47.619 0.00 0.00 0.00 4.30
1008 2612 2.290260 TGGGTTCAGAGCAATGACGAAT 60.290 45.455 0.00 0.00 0.00 3.34
1014 2618 4.433615 TCAGAGCAATGACGAATAGGTTC 58.566 43.478 0.00 0.00 0.00 3.62
1371 3023 4.529219 CCACCGGCAGCAGCGATA 62.529 66.667 0.00 0.00 43.41 2.92
1497 3167 4.796231 GACGAGTGCGGCCACGAT 62.796 66.667 2.24 0.00 46.62 3.73
1581 3254 2.679082 GTCTAGCTACCCCATTCTCCA 58.321 52.381 0.00 0.00 0.00 3.86
1588 3263 3.908103 GCTACCCCATTCTCCACCTATTA 59.092 47.826 0.00 0.00 0.00 0.98
1646 3322 2.226674 GTGCTCTTTGGCAGTAACTTCC 59.773 50.000 0.00 0.00 43.25 3.46
1720 3403 7.172190 CCATATTTTGTAGCAGTAGATGAGTGG 59.828 40.741 0.00 0.00 0.00 4.00
1730 3416 1.890552 AGATGAGTGGCCTGGAAGAT 58.109 50.000 3.32 0.00 34.07 2.40
1865 3555 5.583495 TGTCCGGTTATTGTTGACAAAAAG 58.417 37.500 0.00 0.00 39.55 2.27
1866 3556 5.125739 TGTCCGGTTATTGTTGACAAAAAGT 59.874 36.000 0.00 0.00 39.55 2.66
1867 3557 5.457473 GTCCGGTTATTGTTGACAAAAAGTG 59.543 40.000 0.00 0.00 39.55 3.16
1881 3573 4.180817 CAAAAAGTGAACCTTTGGTCCAC 58.819 43.478 0.00 0.00 42.62 4.02
1974 3666 0.035820 TTATCAGTTGGTGGCCCGAC 60.036 55.000 0.00 0.00 44.54 4.79
2006 3698 5.548406 ACCTCTTTTAGTATGTGCTCGTTT 58.452 37.500 0.00 0.00 0.00 3.60
2007 3699 6.694447 ACCTCTTTTAGTATGTGCTCGTTTA 58.306 36.000 0.00 0.00 0.00 2.01
2084 3776 2.872858 GTGAGGTCCAAGTTGAACTGTC 59.127 50.000 3.87 0.00 30.76 3.51
2118 3810 7.750947 AGGAACTATCTACATTAAACCCTGT 57.249 36.000 0.00 0.00 36.02 4.00
2128 3820 9.675464 TCTACATTAAACCCTGTAAATTCGATT 57.325 29.630 0.00 0.00 0.00 3.34
2177 3869 7.687941 ACCATTTAACATTAACTCAGACCTG 57.312 36.000 0.00 0.00 0.00 4.00
2402 4109 5.828299 TTTTTATTTCTCTATGCCCCACG 57.172 39.130 0.00 0.00 0.00 4.94
2452 4159 1.201429 AGACGAAGCCACCCTCCAAT 61.201 55.000 0.00 0.00 0.00 3.16
2460 4169 0.394352 CCACCCTCCAATCTTTCCCG 60.394 60.000 0.00 0.00 0.00 5.14
2495 4204 7.469537 TTTTTGTTCAAGTTAGGAGTTTCCA 57.530 32.000 0.00 0.00 39.61 3.53
2505 4214 6.784031 AGTTAGGAGTTTCCAGAACATGAAT 58.216 36.000 0.00 0.00 39.61 2.57
2511 4220 9.093458 AGGAGTTTCCAGAACATGAATAAAAAT 57.907 29.630 0.00 0.00 39.61 1.82
2512 4221 9.143631 GGAGTTTCCAGAACATGAATAAAAATG 57.856 33.333 0.00 0.00 36.28 2.32
2538 4247 8.239998 GCTAAAACAAGATATGGCTATGGATTC 58.760 37.037 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 46 7.670605 TCTCCGGATCTCTTTATTTTCCTTA 57.329 36.000 3.57 0.00 0.00 2.69
218 223 2.567615 ACTTGTGTCAGTACTCCCATCC 59.432 50.000 0.00 0.00 0.00 3.51
275 287 6.946009 ACGAAGATCCCATTTTCCTTTTCTTA 59.054 34.615 0.00 0.00 0.00 2.10
306 318 9.182214 GGTAGATTATGACGGAATGGTACTATA 57.818 37.037 0.00 0.00 0.00 1.31
308 320 7.005902 TGGTAGATTATGACGGAATGGTACTA 58.994 38.462 0.00 0.00 0.00 1.82
354 366 6.109156 TGACATGGTACTTTGTGTCTACAT 57.891 37.500 15.80 0.00 41.08 2.29
459 488 7.872483 GGGACTGAAAATTTCAAGAGCAAAATA 59.128 33.333 9.85 0.00 39.58 1.40
463 492 4.895297 AGGGACTGAAAATTTCAAGAGCAA 59.105 37.500 9.85 0.00 39.58 3.91
554 2102 3.023119 TCAGGTTTGACTTGTGCACATT 58.977 40.909 22.39 11.06 0.00 2.71
564 2112 2.649816 AGGGGCTTATTCAGGTTTGACT 59.350 45.455 0.00 0.00 31.71 3.41
595 2143 3.390135 CCGCTTCAGTAGTTCAGTTCAA 58.610 45.455 0.00 0.00 0.00 2.69
887 2467 6.649141 CCGCAGCTGTATTTATAGTCCATTTA 59.351 38.462 16.64 0.00 0.00 1.40
894 2474 5.424757 TCAAACCGCAGCTGTATTTATAGT 58.575 37.500 16.64 0.00 0.00 2.12
950 2530 7.780064 TCTGAAACTCTAAAGATGATGAGGAG 58.220 38.462 0.00 0.00 0.00 3.69
953 2557 9.467258 GATCTCTGAAACTCTAAAGATGATGAG 57.533 37.037 0.00 0.00 0.00 2.90
1014 2618 0.811915 TCTCCTTCTCCTCGAAAGCG 59.188 55.000 0.00 0.00 39.35 4.68
1069 2673 3.359523 CATCGGCATGGGCATCGG 61.360 66.667 0.00 0.00 43.71 4.18
1115 2761 3.542676 ACACGAACACCCGCTCCA 61.543 61.111 0.00 0.00 0.00 3.86
1360 3012 0.529337 TGCTTCTCTATCGCTGCTGC 60.529 55.000 5.34 5.34 0.00 5.25
1371 3023 2.270205 CCGCCACCATGCTTCTCT 59.730 61.111 0.00 0.00 0.00 3.10
1394 3049 2.456594 TTTCATGCCGACAACAGCGC 62.457 55.000 0.00 0.00 0.00 5.92
1576 3248 2.555732 AACCCGGTAATAGGTGGAGA 57.444 50.000 0.00 0.00 36.19 3.71
1581 3254 2.449464 GGCAAAAACCCGGTAATAGGT 58.551 47.619 0.00 0.00 38.27 3.08
1588 3263 1.170442 CTATTCGGCAAAAACCCGGT 58.830 50.000 0.00 0.00 45.60 5.28
1720 3403 1.202976 ACCATGGCATATCTTCCAGGC 60.203 52.381 13.04 0.00 35.57 4.85
1730 3416 6.498303 AGAGATGACTTATGTACCATGGCATA 59.502 38.462 13.04 9.79 0.00 3.14
1974 3666 7.043325 GCACATACTAAAAGAGGTAAGATGACG 60.043 40.741 0.00 0.00 0.00 4.35
2165 3857 3.971305 TCTTGGAAACCAGGTCTGAGTTA 59.029 43.478 0.00 0.00 33.81 2.24
2177 3869 9.573133 CATAAATACAAATCACTCTTGGAAACC 57.427 33.333 0.00 0.00 0.00 3.27
2380 4087 5.258051 ACGTGGGGCATAGAGAAATAAAAA 58.742 37.500 0.00 0.00 0.00 1.94
2386 4093 2.304761 AGAAACGTGGGGCATAGAGAAA 59.695 45.455 0.00 0.00 0.00 2.52
2425 4132 2.223745 GGTGGCTTCGTCTACCAAAAA 58.776 47.619 0.00 0.00 37.52 1.94
2452 4159 7.396418 ACAAAAATACTACATACCGGGAAAGA 58.604 34.615 6.32 0.00 0.00 2.52
2511 4220 6.600388 TCCATAGCCATATCTTGTTTTAGCA 58.400 36.000 0.00 0.00 0.00 3.49
2512 4221 7.693969 ATCCATAGCCATATCTTGTTTTAGC 57.306 36.000 0.00 0.00 0.00 3.09
2524 4233 3.007940 CAGGTTCCGAATCCATAGCCATA 59.992 47.826 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.