Multiple sequence alignment - TraesCS6B01G046700

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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 TraesCS6B01G046700 chr6B 100.000 3527 0 0 1 3527 27821239 27817713 0.000000e+00 6514
1 TraesCS6B01G046700 chr6B 92.692 2559 176 9 326 2881 27806939 27804389 0.000000e+00 3679
2 TraesCS6B01G046700 chr6B 89.504 343 20 6 3185 3527 27804184 27803858 1.510000e-113 420
3 TraesCS6B01G046700 chr6B 95.370 216 9 1 2907 3121 27804392 27804177 3.370000e-90 342
4 TraesCS6B01G046700 chr6D 92.031 3200 236 13 326 3520 15799938 15796753 0.000000e+00 4479
5 TraesCS6B01G046700 chr6D 91.253 2458 190 9 326 2777 15809503 15807065 0.000000e+00 3325
6 TraesCS6B01G046700 chr6D 85.915 1775 202 28 1015 2779 15783831 15782095 0.000000e+00 1849
7 TraesCS6B01G046700 chr6D 84.926 1758 251 8 778 2530 15419831 15418083 0.000000e+00 1766
8 TraesCS6B01G046700 chr6D 84.876 1739 251 8 797 2530 15385360 15383629 0.000000e+00 1744
9 TraesCS6B01G046700 chr6D 87.805 779 70 11 280 1055 15784715 15783959 0.000000e+00 889
10 TraesCS6B01G046700 chr6A 92.447 2979 208 11 326 3299 16401365 16398399 0.000000e+00 4239
11 TraesCS6B01G046700 chr6A 90.247 2635 227 13 150 2779 16410866 16408257 0.000000e+00 3415
12 TraesCS6B01G046700 chr6A 87.453 1586 192 5 953 2531 16388242 16386657 0.000000e+00 1820
13 TraesCS6B01G046700 chr6A 84.669 1735 254 7 797 2526 15953615 15951888 0.000000e+00 1720
14 TraesCS6B01G046700 chr6A 85.890 163 13 5 3 164 16412511 16412358 7.830000e-37 165


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 TraesCS6B01G046700 chr6B 27817713 27821239 3526 True 6514.000000 6514 100.0000 1 3527 1 chr6B.!!$R1 3526
1 TraesCS6B01G046700 chr6B 27803858 27806939 3081 True 1480.333333 3679 92.5220 326 3527 3 chr6B.!!$R2 3201
2 TraesCS6B01G046700 chr6D 15796753 15799938 3185 True 4479.000000 4479 92.0310 326 3520 1 chr6D.!!$R3 3194
3 TraesCS6B01G046700 chr6D 15807065 15809503 2438 True 3325.000000 3325 91.2530 326 2777 1 chr6D.!!$R4 2451
4 TraesCS6B01G046700 chr6D 15418083 15419831 1748 True 1766.000000 1766 84.9260 778 2530 1 chr6D.!!$R2 1752
5 TraesCS6B01G046700 chr6D 15383629 15385360 1731 True 1744.000000 1744 84.8760 797 2530 1 chr6D.!!$R1 1733
6 TraesCS6B01G046700 chr6D 15782095 15784715 2620 True 1369.000000 1849 86.8600 280 2779 2 chr6D.!!$R5 2499
7 TraesCS6B01G046700 chr6A 16398399 16401365 2966 True 4239.000000 4239 92.4470 326 3299 1 chr6A.!!$R3 2973
8 TraesCS6B01G046700 chr6A 16386657 16388242 1585 True 1820.000000 1820 87.4530 953 2531 1 chr6A.!!$R2 1578
9 TraesCS6B01G046700 chr6A 16408257 16412511 4254 True 1790.000000 3415 88.0685 3 2779 2 chr6A.!!$R4 2776
10 TraesCS6B01G046700 chr6A 15951888 15953615 1727 True 1720.000000 1720 84.6690 797 2526 1 chr6A.!!$R1 1729

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
387 1896 1.080995 GCTCGCTGTAACCTGCAGAG 61.081 60.000 17.39 8.04 38.22 3.35 F
1371 3072 0.311790 CAGCGGTGTTTTGCATGTCT 59.688 50.000 6.41 0.00 0.00 3.41 F
1558 3259 1.134491 CACAGCTCATCATGCCTCTCA 60.134 52.381 0.00 0.00 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1958 3659 1.141881 ATGCCGAAGTACCGAGCAG 59.858 57.895 11.13 0.0 38.42 4.24 R
2469 4170 0.032952 GTACGGCGAGGATGGCATTA 59.967 55.000 16.62 0.0 43.90 1.90 R
2891 4606 0.108662 CATCTACGAGCAGCACCACA 60.109 55.000 0.00 0.0 0.00 4.17 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
31 32 1.542492 ACAGAGGCATGCAAAGGAAG 58.458 50.000 21.36 4.65 0.00 3.46
48 49 7.412237 GCAAAGGAAGCAATTCAACATCAATAC 60.412 37.037 0.00 0.00 0.00 1.89
49 50 6.839124 AGGAAGCAATTCAACATCAATACA 57.161 33.333 0.00 0.00 0.00 2.29
56 57 6.694411 GCAATTCAACATCAATACAGATCCAC 59.306 38.462 0.00 0.00 0.00 4.02
92 93 2.813754 GTTTGCCACTACTCAATGCTGA 59.186 45.455 0.00 0.00 0.00 4.26
93 94 3.354948 TTGCCACTACTCAATGCTGAT 57.645 42.857 0.00 0.00 0.00 2.90
98 99 5.098211 GCCACTACTCAATGCTGATTTTTC 58.902 41.667 0.00 0.00 0.00 2.29
104 105 9.453572 ACTACTCAATGCTGATTTTTCTCATAA 57.546 29.630 0.00 0.00 0.00 1.90
181 1688 9.113876 CATGACCTTCGTAACAACTTATTTTTC 57.886 33.333 0.00 0.00 0.00 2.29
182 1689 7.641760 TGACCTTCGTAACAACTTATTTTTCC 58.358 34.615 0.00 0.00 0.00 3.13
193 1700 8.587952 ACAACTTATTTTTCCGGATTTTCTTG 57.412 30.769 4.15 2.70 0.00 3.02
194 1701 7.170828 ACAACTTATTTTTCCGGATTTTCTTGC 59.829 33.333 4.15 0.00 0.00 4.01
232 1739 4.471904 TCTCACTTGTGTTTCACTGTCT 57.528 40.909 0.46 0.00 35.11 3.41
309 1816 7.613585 ACATGCATTCTATTTTTGACATGGAA 58.386 30.769 0.00 0.00 38.33 3.53
317 1824 8.792830 TCTATTTTTGACATGGAAAGAGTAGG 57.207 34.615 0.00 0.00 0.00 3.18
387 1896 1.080995 GCTCGCTGTAACCTGCAGAG 61.081 60.000 17.39 8.04 38.22 3.35
439 1948 8.989980 AGTCAACTCTTAATTTGTACTTAGCAC 58.010 33.333 0.00 0.00 0.00 4.40
440 1949 8.770828 GTCAACTCTTAATTTGTACTTAGCACA 58.229 33.333 0.00 0.00 0.00 4.57
458 1967 5.488341 AGCACATAGGATCAAGTACGTTTT 58.512 37.500 0.00 0.00 0.00 2.43
525 2035 4.705507 CCCTACAGCTAGTGTCAACTCTTA 59.294 45.833 0.00 0.00 40.94 2.10
531 2041 4.021104 AGCTAGTGTCAACTCTTATGCACA 60.021 41.667 0.00 0.00 37.88 4.57
536 2046 1.350684 TCAACTCTTATGCACAGCCCA 59.649 47.619 0.00 0.00 0.00 5.36
537 2047 2.161855 CAACTCTTATGCACAGCCCAA 58.838 47.619 0.00 0.00 0.00 4.12
543 2053 1.948104 TATGCACAGCCCAATACGTC 58.052 50.000 0.00 0.00 0.00 4.34
546 2056 1.090052 GCACAGCCCAATACGTCCTC 61.090 60.000 0.00 0.00 0.00 3.71
564 2074 2.627945 CTCGCAACAGTTAATGCCCTA 58.372 47.619 0.00 0.00 39.39 3.53
586 2111 8.300286 CCCTACCACTGCATATATATTATCTCG 58.700 40.741 0.00 0.00 0.00 4.04
684 2210 8.795786 TGGACAATCTCAAAAATTAAGAAACG 57.204 30.769 0.00 0.00 0.00 3.60
704 2230 3.006110 ACGGAGGAGAACGTCAAACATAA 59.994 43.478 0.00 0.00 39.40 1.90
738 2264 7.362920 GGAGTAATGGTGTGCATTAATTTGAGT 60.363 37.037 0.00 0.00 0.00 3.41
880 2408 5.106396 CCTTCTCATCTTTTCGAGCACAAAT 60.106 40.000 0.00 0.00 0.00 2.32
951 2480 1.944892 GCACATTGCAGCTCTGAGAGT 60.945 52.381 11.64 0.00 44.26 3.24
1164 2865 0.588252 CCTTCTTCACCTGCGTTGTG 59.412 55.000 0.00 0.00 35.01 3.33
1371 3072 0.311790 CAGCGGTGTTTTGCATGTCT 59.688 50.000 6.41 0.00 0.00 3.41
1558 3259 1.134491 CACAGCTCATCATGCCTCTCA 60.134 52.381 0.00 0.00 0.00 3.27
1740 3441 5.041191 ACATGAACAAGGACAAGTTCTCT 57.959 39.130 0.00 0.00 43.38 3.10
1958 3659 2.836793 GCTACCTCTCCGACCTCGC 61.837 68.421 0.00 0.00 38.18 5.03
2142 3843 2.088950 ACGGTGTTATCCCTTTCGTG 57.911 50.000 0.00 0.00 0.00 4.35
2157 3858 2.963371 GTGTCTCGACGCTCCCTT 59.037 61.111 3.50 0.00 38.69 3.95
2202 3903 2.672295 GGTGGTAATGTGGGCGGA 59.328 61.111 0.00 0.00 0.00 5.54
2494 4195 4.753662 TCCTCGCCGTACCTGCCT 62.754 66.667 0.00 0.00 0.00 4.75
2534 4235 6.012858 ACCCCTCAACATGTATAAGACTCAAA 60.013 38.462 0.00 0.00 0.00 2.69
2613 4323 0.178955 TGTACGTTCCTCCAGGGTCA 60.179 55.000 0.00 0.00 36.25 4.02
2641 4351 3.746045 TGATGCCCTATTAAGACGGTC 57.254 47.619 0.00 0.00 0.00 4.79
2779 4494 2.092211 CGTACCTTCACATTTCTCGTGC 59.908 50.000 0.00 0.00 34.27 5.34
2823 4538 6.141560 TGTACTTTTGCACATGTTTGATGA 57.858 33.333 0.00 0.00 0.00 2.92
2878 4593 2.304761 TGGTTAGCCGACCTCTGAAAAT 59.695 45.455 7.53 0.00 40.47 1.82
2884 4599 3.197766 AGCCGACCTCTGAAAATATCACA 59.802 43.478 0.00 0.00 33.47 3.58
2891 4606 6.773638 ACCTCTGAAAATATCACACTCTGTT 58.226 36.000 0.00 0.00 33.47 3.16
2896 4611 6.061441 TGAAAATATCACACTCTGTTGTGGT 58.939 36.000 10.73 7.45 45.93 4.16
2904 4619 1.563435 CTCTGTTGTGGTGCTGCTCG 61.563 60.000 0.00 0.00 0.00 5.03
2986 4702 0.899717 GGCCAAATTCCAGCTCACCA 60.900 55.000 0.00 0.00 0.00 4.17
3079 4795 2.054232 AGCCTCTTGGATGATTGCAG 57.946 50.000 0.00 0.00 34.57 4.41
3104 4820 7.977853 AGCAGGAATGCATTAGTTGAATAAAAG 59.022 33.333 12.97 0.00 37.25 2.27
3139 4855 6.597280 TCCCACAAAAAGAAAAACAAATGGAG 59.403 34.615 0.00 0.00 0.00 3.86
3206 4922 5.031066 TCCCTACATGTTGTAGCATAACC 57.969 43.478 2.30 0.00 46.72 2.85
3207 4923 4.719773 TCCCTACATGTTGTAGCATAACCT 59.280 41.667 2.30 0.00 46.72 3.50
3376 5092 9.247861 AGCTAAAAACAGAAATAAGACCATGAT 57.752 29.630 0.00 0.00 0.00 2.45
3404 5120 6.663734 TGATACATGGAGAAGAGTCAGACTA 58.336 40.000 2.00 0.00 0.00 2.59
3413 5129 8.282982 TGGAGAAGAGTCAGACTATAGGTTATT 58.717 37.037 2.00 0.00 0.00 1.40
3460 5176 1.375523 GCAACCACCCTACTCCGTG 60.376 63.158 0.00 0.00 0.00 4.94
3499 5215 2.816083 TGAACGGGCCGTAATGCG 60.816 61.111 34.37 3.29 39.99 4.73
3505 5221 1.367840 GGGCCGTAATGCGAGAGAT 59.632 57.895 0.00 0.00 44.77 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.221441 TGCATGCCTCTGTAACGAATATACT 60.221 40.000 16.68 0.00 0.00 2.12
1 2 4.988540 TGCATGCCTCTGTAACGAATATAC 59.011 41.667 16.68 0.00 0.00 1.47
13 14 0.172803 GCTTCCTTTGCATGCCTCTG 59.827 55.000 16.68 1.37 0.00 3.35
14 15 0.251474 TGCTTCCTTTGCATGCCTCT 60.251 50.000 16.68 0.00 35.31 3.69
31 32 6.694411 GTGGATCTGTATTGATGTTGAATTGC 59.306 38.462 0.00 0.00 0.00 3.56
160 161 6.073112 TCCGGAAAAATAAGTTGTTACGAAGG 60.073 38.462 0.00 0.00 0.00 3.46
165 1672 9.687210 AGAAAATCCGGAAAAATAAGTTGTTAC 57.313 29.630 9.01 0.00 0.00 2.50
169 1676 7.170658 TGCAAGAAAATCCGGAAAAATAAGTTG 59.829 33.333 9.01 6.50 0.00 3.16
181 1688 7.087639 TGTTTATAAGTTGCAAGAAAATCCGG 58.912 34.615 0.00 0.00 0.00 5.14
182 1689 8.687824 ATGTTTATAAGTTGCAAGAAAATCCG 57.312 30.769 0.00 0.00 0.00 4.18
193 1700 9.760660 CAAGTGAGAACTATGTTTATAAGTTGC 57.239 33.333 0.00 0.00 0.00 4.17
323 1832 1.066716 ACTTAACGCGTCATTAGGCCA 60.067 47.619 14.44 0.00 32.81 5.36
324 1833 1.326548 CACTTAACGCGTCATTAGGCC 59.673 52.381 14.44 0.00 32.81 5.19
387 1896 2.970576 GCTGCAGAGCTAGCTGTAC 58.029 57.895 24.99 14.22 42.52 2.90
411 1920 8.657729 GCTAAGTACAAATTAAGAGTTGACTCC 58.342 37.037 7.50 0.00 43.88 3.85
439 1948 5.345702 TCCGAAAACGTACTTGATCCTATG 58.654 41.667 0.00 0.00 0.00 2.23
440 1949 5.587388 TCCGAAAACGTACTTGATCCTAT 57.413 39.130 0.00 0.00 0.00 2.57
458 1967 1.687563 TGCAGGTCGAGATATTCCGA 58.312 50.000 0.00 0.00 0.00 4.55
489 1998 7.002879 ACTAGCTGTAGGGTTTATTCGATCTA 58.997 38.462 0.00 0.00 0.00 1.98
525 2035 0.748005 GGACGTATTGGGCTGTGCAT 60.748 55.000 0.00 0.00 0.00 3.96
531 2041 1.895020 TTGCGAGGACGTATTGGGCT 61.895 55.000 0.00 0.00 41.98 5.19
536 2046 2.450609 AACTGTTGCGAGGACGTATT 57.549 45.000 0.00 0.00 41.98 1.89
537 2047 3.581024 TTAACTGTTGCGAGGACGTAT 57.419 42.857 2.69 0.00 41.98 3.06
543 2053 0.451783 GGGCATTAACTGTTGCGAGG 59.548 55.000 2.69 0.00 39.78 4.63
546 2056 1.400494 GGTAGGGCATTAACTGTTGCG 59.600 52.381 2.69 0.00 39.78 4.85
684 2210 5.469084 AGTTTTATGTTTGACGTTCTCCTCC 59.531 40.000 0.00 0.00 0.00 4.30
704 2230 5.321102 TGCACACCATTACTCCATTAGTTT 58.679 37.500 0.00 0.00 39.80 2.66
817 2343 4.685924 CATGCTTGAACCACTTCAGTTTT 58.314 39.130 0.00 0.00 37.70 2.43
951 2480 2.711009 TCTTCTTCCTTGCTCCTTGGAA 59.289 45.455 0.00 0.00 38.10 3.53
1371 3072 2.275089 CCGGGGCCATCAATGACA 59.725 61.111 4.39 0.00 0.00 3.58
1410 3111 2.550855 GGCAAGTGAGACACCAATGAGA 60.551 50.000 0.00 0.00 34.49 3.27
1958 3659 1.141881 ATGCCGAAGTACCGAGCAG 59.858 57.895 11.13 0.00 38.42 4.24
2142 3843 2.182030 CCAAGGGAGCGTCGAGAC 59.818 66.667 0.00 0.00 0.00 3.36
2202 3903 2.390225 AGAGGAACTGTGTGAGACCT 57.610 50.000 0.00 0.00 41.55 3.85
2355 4056 2.124403 TAGTCCTCCTCGGTCGCC 60.124 66.667 0.00 0.00 0.00 5.54
2469 4170 0.032952 GTACGGCGAGGATGGCATTA 59.967 55.000 16.62 0.00 43.90 1.90
2494 4195 2.920912 GGTGACGTGAGGTGGGGA 60.921 66.667 0.00 0.00 0.00 4.81
2534 4235 2.621668 GCAGCAGGGAGGTAGGAAAAAT 60.622 50.000 0.00 0.00 0.00 1.82
2540 4241 2.586792 GTGCAGCAGGGAGGTAGG 59.413 66.667 0.00 0.00 0.00 3.18
2613 4323 5.652452 GTCTTAATAGGGCATCAAACACCTT 59.348 40.000 0.00 0.00 34.59 3.50
2779 4494 6.768029 ACAAAACAACGATGAAAATGGATG 57.232 33.333 0.00 0.00 0.00 3.51
2823 4538 3.159213 TCCATTGTCACCTGCTTGAAT 57.841 42.857 0.00 0.00 0.00 2.57
2884 4599 0.533755 GAGCAGCACCACAACAGAGT 60.534 55.000 0.00 0.00 0.00 3.24
2891 4606 0.108662 CATCTACGAGCAGCACCACA 60.109 55.000 0.00 0.00 0.00 4.17
2896 4611 3.694566 TCTTAGTTCATCTACGAGCAGCA 59.305 43.478 0.00 0.00 0.00 4.41
2904 4619 8.679100 TCAGAAGCTAGTTCTTAGTTCATCTAC 58.321 37.037 5.23 0.00 43.54 2.59
2944 4659 5.698089 CCGATCTGTACACATGCTGAATTAT 59.302 40.000 0.00 0.00 0.00 1.28
3104 4820 5.576447 TCTTTTTGTGGGAAACTTGAGAC 57.424 39.130 0.00 0.00 0.00 3.36
3139 4855 3.945434 CGCAGCGTGGCATCATCC 61.945 66.667 6.65 0.00 0.00 3.51
3224 4940 4.002982 CAGCTAAATGGTACTGCACAAGA 58.997 43.478 0.00 0.00 0.00 3.02
3260 4976 3.657398 ATGCATGTCCTCTTCATCCAA 57.343 42.857 0.00 0.00 0.00 3.53
3376 5092 7.067615 GTCTGACTCTTCTCCATGTATCAAGTA 59.932 40.741 0.00 0.00 0.00 2.24
3378 5094 6.096705 AGTCTGACTCTTCTCCATGTATCAAG 59.903 42.308 4.06 0.00 0.00 3.02
3379 5095 5.954752 AGTCTGACTCTTCTCCATGTATCAA 59.045 40.000 4.06 0.00 0.00 2.57
3380 5096 5.514169 AGTCTGACTCTTCTCCATGTATCA 58.486 41.667 4.06 0.00 0.00 2.15
3381 5097 7.759489 ATAGTCTGACTCTTCTCCATGTATC 57.241 40.000 14.62 0.00 0.00 2.24
3395 5111 7.720074 TCGTCATCAATAACCTATAGTCTGACT 59.280 37.037 15.57 15.57 0.00 3.41
3404 5120 5.391449 CGTCGATCGTCATCAATAACCTAT 58.609 41.667 15.94 0.00 34.52 2.57
3413 5129 0.248094 GACTGCGTCGATCGTCATCA 60.248 55.000 15.94 9.23 42.13 3.07
3431 5147 2.856231 AGGGTGGTTGCTTATATTGGGA 59.144 45.455 0.00 0.00 0.00 4.37
3460 5176 3.806521 ACATGCAAGATCATCGAGTAAGC 59.193 43.478 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.