Multiple sequence alignment - TraesCS6D01G316900

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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 TraesCS6D01G316900 chr6D 100.000 4214 0 0 1 4214 425983703 425987916 0.000000e+00 7782
1 TraesCS6D01G316900 chr6D 95.025 1769 53 10 1261 3022 101454805 101456545 0.000000e+00 2747
2 TraesCS6D01G316900 chr6D 98.336 1262 19 2 1 1260 124519125 124517864 0.000000e+00 2213
3 TraesCS6D01G316900 chr6D 89.400 1783 128 29 1261 3033 15498334 15496603 0.000000e+00 2189
4 TraesCS6D01G316900 chr6D 98.135 1019 17 2 3197 4214 124517120 124516103 0.000000e+00 1775
5 TraesCS6D01G316900 chr6D 98.857 175 2 0 3022 3196 124517868 124517694 3.160000e-81 313
6 TraesCS6D01G316900 chr5D 95.190 1767 50 8 1261 3021 396666952 396665215 0.000000e+00 2760
7 TraesCS6D01G316900 chr5D 95.127 1765 51 10 1261 3021 97031380 97033113 0.000000e+00 2750
8 TraesCS6D01G316900 chr5D 94.734 1766 54 13 1261 3021 97359580 97357849 0.000000e+00 2710
9 TraesCS6D01G316900 chr5D 94.076 422 18 3 2607 3021 418729782 418729361 5.940000e-178 634
10 TraesCS6D01G316900 chr4D 95.071 1765 55 10 1260 3021 118394374 118396109 0.000000e+00 2748
11 TraesCS6D01G316900 chr4D 98.257 1262 20 2 1 1260 123551529 123550268 0.000000e+00 2207
12 TraesCS6D01G316900 chr4D 93.495 661 14 4 2364 3022 378407028 378406395 0.000000e+00 955
13 TraesCS6D01G316900 chr4D 92.432 370 22 5 2656 3022 135145711 135145345 1.340000e-144 523
14 TraesCS6D01G316900 chr4D 98.857 175 2 0 3022 3196 123550272 123550098 3.160000e-81 313
15 TraesCS6D01G316900 chr3D 95.020 1767 54 9 1261 3024 328894733 328896468 0.000000e+00 2745
16 TraesCS6D01G316900 chr2D 94.955 1764 59 5 1261 3022 476394650 476392915 0.000000e+00 2737
17 TraesCS6D01G316900 chr7D 96.401 1445 42 8 1260 2699 222190443 222189004 0.000000e+00 2372
18 TraesCS6D01G316900 chr7D 90.965 1782 118 35 1261 3021 10584902 10586661 0.000000e+00 2359
19 TraesCS6D01G316900 chr7D 98.653 1262 15 2 1 1260 203501602 203500341 0.000000e+00 2235
20 TraesCS6D01G316900 chr7D 98.574 1262 16 2 1 1260 381925604 381924343 0.000000e+00 2230
21 TraesCS6D01G316900 chr7D 98.494 1262 17 2 1 1260 382051682 382050421 0.000000e+00 2224
22 TraesCS6D01G316900 chr7D 98.177 1262 18 3 1 1260 381972167 381973425 0.000000e+00 2198
23 TraesCS6D01G316900 chr7D 98.430 1019 15 1 3197 4214 381974165 381975183 0.000000e+00 1792
24 TraesCS6D01G316900 chr7D 98.430 1019 15 1 3197 4214 382049677 382048659 0.000000e+00 1792
25 TraesCS6D01G316900 chr7D 98.857 175 2 0 3022 3196 203500345 203500171 3.160000e-81 313
26 TraesCS6D01G316900 chr7D 98.857 175 2 0 3022 3196 381973421 381973595 3.160000e-81 313
27 TraesCS6D01G316900 chr7D 98.286 175 3 0 3022 3196 381924347 381924173 1.470000e-79 307
28 TraesCS6D01G316900 chr7D 98.295 176 2 1 3022 3196 382050425 382050250 1.470000e-79 307
29 TraesCS6D01G316900 chr5A 98.574 1262 16 2 1 1260 19247240 19248501 0.000000e+00 2230
30 TraesCS6D01G316900 chr5A 98.430 1019 15 1 3197 4214 19249252 19250270 0.000000e+00 1792
31 TraesCS6D01G316900 chr5A 85.276 1107 108 36 1933 3021 490479783 490480852 0.000000e+00 1090
32 TraesCS6D01G316900 chr1A 98.494 1262 17 2 1 1260 498689624 498690885 0.000000e+00 2224
33 TraesCS6D01G316900 chr1A 98.135 1019 17 2 3197 4214 498691629 498692646 0.000000e+00 1775
34 TraesCS6D01G316900 chr1A 98.857 175 2 0 3022 3196 498690881 498691055 3.160000e-81 313
35 TraesCS6D01G316900 chr7B 98.414 1261 19 1 1 1260 716877178 716878438 0.000000e+00 2217
36 TraesCS6D01G316900 chr7B 98.037 1019 19 1 3197 4214 716879184 716880202 0.000000e+00 1770
37 TraesCS6D01G316900 chr4A 87.451 1801 143 53 1261 3033 98530175 98531920 0.000000e+00 1997
38 TraesCS6D01G316900 chrUn 98.430 1019 15 1 3197 4214 413952171 413951153 0.000000e+00 1792
39 TraesCS6D01G316900 chr7A 98.234 1019 17 1 3197 4214 120841561 120842579 0.000000e+00 1781
40 TraesCS6D01G316900 chr7A 90.748 1016 56 12 2029 3037 473000322 472999338 0.000000e+00 1321
41 TraesCS6D01G316900 chr7A 98.857 175 2 0 3022 3196 60279659 60279485 3.160000e-81 313
42 TraesCS6D01G316900 chr7A 98.851 174 2 0 3023 3196 120840815 120840988 1.140000e-80 311
43 TraesCS6D01G316900 chr1D 98.234 1019 17 1 3197 4214 269406400 269405382 0.000000e+00 1781
44 TraesCS6D01G316900 chr6B 84.175 1801 190 65 1261 3022 13688155 13689899 0.000000e+00 1659


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 TraesCS6D01G316900 chr6D 425983703 425987916 4213 False 7782.000000 7782 100.000000 1 4214 1 chr6D.!!$F2 4213
1 TraesCS6D01G316900 chr6D 101454805 101456545 1740 False 2747.000000 2747 95.025000 1261 3022 1 chr6D.!!$F1 1761
2 TraesCS6D01G316900 chr6D 15496603 15498334 1731 True 2189.000000 2189 89.400000 1261 3033 1 chr6D.!!$R1 1772
3 TraesCS6D01G316900 chr6D 124516103 124519125 3022 True 1433.666667 2213 98.442667 1 4214 3 chr6D.!!$R2 4213
4 TraesCS6D01G316900 chr5D 396665215 396666952 1737 True 2760.000000 2760 95.190000 1261 3021 1 chr5D.!!$R2 1760
5 TraesCS6D01G316900 chr5D 97031380 97033113 1733 False 2750.000000 2750 95.127000 1261 3021 1 chr5D.!!$F1 1760
6 TraesCS6D01G316900 chr5D 97357849 97359580 1731 True 2710.000000 2710 94.734000 1261 3021 1 chr5D.!!$R1 1760
7 TraesCS6D01G316900 chr4D 118394374 118396109 1735 False 2748.000000 2748 95.071000 1260 3021 1 chr4D.!!$F1 1761
8 TraesCS6D01G316900 chr4D 123550098 123551529 1431 True 1260.000000 2207 98.557000 1 3196 2 chr4D.!!$R3 3195
9 TraesCS6D01G316900 chr4D 378406395 378407028 633 True 955.000000 955 93.495000 2364 3022 1 chr4D.!!$R2 658
10 TraesCS6D01G316900 chr3D 328894733 328896468 1735 False 2745.000000 2745 95.020000 1261 3024 1 chr3D.!!$F1 1763
11 TraesCS6D01G316900 chr2D 476392915 476394650 1735 True 2737.000000 2737 94.955000 1261 3022 1 chr2D.!!$R1 1761
12 TraesCS6D01G316900 chr7D 222189004 222190443 1439 True 2372.000000 2372 96.401000 1260 2699 1 chr7D.!!$R1 1439
13 TraesCS6D01G316900 chr7D 10584902 10586661 1759 False 2359.000000 2359 90.965000 1261 3021 1 chr7D.!!$F1 1760
14 TraesCS6D01G316900 chr7D 382048659 382051682 3023 True 1441.000000 2224 98.406333 1 4214 3 chr7D.!!$R4 4213
15 TraesCS6D01G316900 chr7D 381972167 381975183 3016 False 1434.333333 2198 98.488000 1 4214 3 chr7D.!!$F2 4213
16 TraesCS6D01G316900 chr7D 203500171 203501602 1431 True 1274.000000 2235 98.755000 1 3196 2 chr7D.!!$R2 3195
17 TraesCS6D01G316900 chr7D 381924173 381925604 1431 True 1268.500000 2230 98.430000 1 3196 2 chr7D.!!$R3 3195
18 TraesCS6D01G316900 chr5A 19247240 19250270 3030 False 2011.000000 2230 98.502000 1 4214 2 chr5A.!!$F2 4213
19 TraesCS6D01G316900 chr5A 490479783 490480852 1069 False 1090.000000 1090 85.276000 1933 3021 1 chr5A.!!$F1 1088
20 TraesCS6D01G316900 chr1A 498689624 498692646 3022 False 1437.333333 2224 98.495333 1 4214 3 chr1A.!!$F1 4213
21 TraesCS6D01G316900 chr7B 716877178 716880202 3024 False 1993.500000 2217 98.225500 1 4214 2 chr7B.!!$F1 4213
22 TraesCS6D01G316900 chr4A 98530175 98531920 1745 False 1997.000000 1997 87.451000 1261 3033 1 chr4A.!!$F1 1772
23 TraesCS6D01G316900 chrUn 413951153 413952171 1018 True 1792.000000 1792 98.430000 3197 4214 1 chrUn.!!$R1 1017
24 TraesCS6D01G316900 chr7A 472999338 473000322 984 True 1321.000000 1321 90.748000 2029 3037 1 chr7A.!!$R2 1008
25 TraesCS6D01G316900 chr7A 120840815 120842579 1764 False 1046.000000 1781 98.542500 3023 4214 2 chr7A.!!$F1 1191
26 TraesCS6D01G316900 chr1D 269405382 269406400 1018 True 1781.000000 1781 98.234000 3197 4214 1 chr1D.!!$R1 1017
27 TraesCS6D01G316900 chr6B 13688155 13689899 1744 False 1659.000000 1659 84.175000 1261 3022 1 chr6B.!!$F1 1761

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
832 834 0.320683 CCATCAGACGGCTGTTCACA 60.321 55.0 19.93 0.0 42.84 3.58 F
1978 2063 0.324645 GGTAACCCCTCGGTACTCCA 60.325 60.0 0.00 0.0 43.71 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 2156 2.418609 GGATGTGATCACGGACATGACA 60.419 50.0 20.54 0.28 32.85 3.58 R
3347 4103 0.608035 GCGACCCAATGACCTTTCCA 60.608 55.0 0.00 0.00 0.00 3.53 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
171 172 2.269605 GCTACAAAAGCCGGCTAACGA 61.270 52.381 33.07 13.53 46.25 3.85
269 270 6.095440 GCCCAAATCCGCTATATATTTGACAT 59.905 38.462 8.75 0.00 41.14 3.06
669 671 1.036707 GAGAGATTGAGTCCGAGGGG 58.963 60.000 0.00 0.00 0.00 4.79
735 737 2.031508 CCACAAGTTGTTAATTCGCCGT 60.032 45.455 5.57 0.00 0.00 5.68
748 750 2.874751 GCCGTTGGGGAATTCACG 59.125 61.111 7.93 8.33 38.47 4.35
773 775 6.153510 GCAAAAGGGAAGGACTTATTCTCAAT 59.846 38.462 0.00 0.00 28.99 2.57
832 834 0.320683 CCATCAGACGGCTGTTCACA 60.321 55.000 19.93 0.00 42.84 3.58
863 865 6.097554 CCACTCTCGGCTTGGATTATATATCT 59.902 42.308 0.00 0.00 31.39 1.98
1120 1122 8.194104 TCTTCCTTTTCGATGAAAAACAAATCA 58.806 29.630 6.23 0.00 40.34 2.57
1318 1321 3.197265 CACACGCAAGATCATGGTGATA 58.803 45.455 19.56 0.00 37.20 2.15
1406 1412 4.841443 ACGCGGTTGATGTAGTCATATA 57.159 40.909 12.47 0.00 36.54 0.86
1470 1478 1.071239 CGAGTTCAGCACACGTTCAAG 60.071 52.381 0.00 0.00 35.01 3.02
1494 1502 0.611062 TGACGTCCCTCGAACTCCAT 60.611 55.000 14.12 0.00 42.86 3.41
1948 2031 1.526225 GAGGCCCAATAACCTCCGC 60.526 63.158 0.00 0.00 45.71 5.54
1951 2034 2.904905 CCCAATAACCTCCGCGGA 59.095 61.111 29.03 29.03 36.31 5.54
1978 2063 0.324645 GGTAACCCCTCGGTACTCCA 60.325 60.000 0.00 0.00 43.71 3.86
2056 2141 9.636879 CAATATATCAATCTTCATGTCTCGACT 57.363 33.333 0.00 0.00 0.00 4.18
2099 2184 1.029681 CGTGATCACATCCGGGACTA 58.970 55.000 24.93 0.00 0.00 2.59
2100 2185 1.407618 CGTGATCACATCCGGGACTAA 59.592 52.381 24.93 0.00 0.00 2.24
2113 2198 2.751806 CGGGACTAAGAACTACCTTCGT 59.248 50.000 0.00 0.00 33.60 3.85
2417 2507 7.023575 GTCTCTTTACTCGTTCCGTAATACAA 58.976 38.462 0.00 0.00 0.00 2.41
2616 2707 1.529438 CGTTGTGACGTTTGGTAGCAT 59.471 47.619 0.00 0.00 44.08 3.79
2767 2929 3.366052 AAGCTAACGGAATGGGTCAAT 57.634 42.857 0.00 0.00 0.00 2.57
3132 3304 5.243954 GGATTACAAAAAGAGGGTGCTTTCT 59.756 40.000 0.00 0.00 37.12 2.52
3142 3314 1.069049 GGGTGCTTTCTTGTGTTGCAT 59.931 47.619 0.00 0.00 36.04 3.96
3238 3994 4.844349 ATAGGCAGGCTTCTTTCAGTAA 57.156 40.909 0.00 0.00 0.00 2.24
3347 4103 3.195661 GGCGACGAATACTTCCAATTCT 58.804 45.455 0.00 0.00 32.29 2.40
3400 4157 1.796459 GCGAAAGTTGTAGAAAGCCGA 59.204 47.619 0.00 0.00 0.00 5.54
3519 4276 5.131642 TCTGACTGAATCCATCCATAAAGCT 59.868 40.000 0.00 0.00 0.00 3.74
3739 4497 3.808218 TTGGGCTGCTGTGAACCCC 62.808 63.158 0.00 0.00 42.07 4.95
4140 4898 1.415374 TGAGTTTCACGCGCTCTAAC 58.585 50.000 5.73 5.93 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 172 6.688144 ATGTTCTCATACGCAGGAATACCCT 61.688 44.000 0.00 0.00 37.97 4.34
269 270 1.247419 CCAGCATTACGGCAAACCCA 61.247 55.000 0.00 0.00 35.83 4.51
341 343 8.970859 AACCATAGAAGGAATTCAATCACTAG 57.029 34.615 7.93 0.00 0.00 2.57
669 671 0.032117 CCCCAAGAAAATCCCCCTCC 60.032 60.000 0.00 0.00 0.00 4.30
677 679 1.909302 TCTCTCGAGCCCCAAGAAAAT 59.091 47.619 7.81 0.00 0.00 1.82
735 737 1.342819 CCTTTTGCGTGAATTCCCCAA 59.657 47.619 2.27 0.99 0.00 4.12
748 750 5.010282 TGAGAATAAGTCCTTCCCTTTTGC 58.990 41.667 0.00 0.00 0.00 3.68
832 834 1.482593 CCAAGCCGAGAGTGGAGTTAT 59.517 52.381 0.00 0.00 34.05 1.89
1120 1122 2.932614 CGCTTTCGGAGATTGAGATGTT 59.067 45.455 0.00 0.00 35.04 2.71
1255 1258 0.604511 CTACGTTCCCCAACACACCC 60.605 60.000 0.00 0.00 32.14 4.61
1256 1259 0.107268 ACTACGTTCCCCAACACACC 59.893 55.000 0.00 0.00 32.14 4.16
1257 1260 2.818130 TACTACGTTCCCCAACACAC 57.182 50.000 0.00 0.00 32.14 3.82
1258 1261 4.354893 AATTACTACGTTCCCCAACACA 57.645 40.909 0.00 0.00 32.14 3.72
1318 1321 1.115467 CTCCCCTCTCGTTGCTATGT 58.885 55.000 0.00 0.00 0.00 2.29
1470 1478 0.522915 GTTCGAGGGACGTCATCGAC 60.523 60.000 32.00 24.75 44.43 4.20
1494 1502 0.537188 CCCTCAAAGCTCGGCTAGAA 59.463 55.000 0.00 0.00 38.25 2.10
2071 2156 2.418609 GGATGTGATCACGGACATGACA 60.419 50.000 20.54 0.28 32.85 3.58
2099 2184 7.496591 TGTTTTGATGTAACGAAGGTAGTTCTT 59.503 33.333 0.00 0.00 32.33 2.52
2100 2185 6.987992 TGTTTTGATGTAACGAAGGTAGTTCT 59.012 34.615 0.00 0.00 32.33 3.01
2315 2405 5.321516 GCAAGTAACATACCGATGACAAAC 58.678 41.667 0.00 0.00 36.48 2.93
2417 2507 3.350219 AATGAGTTAGTTGCGGGATGT 57.650 42.857 0.00 0.00 0.00 3.06
2457 2547 6.646653 CACTCGGTAATGCACATCACTATAAT 59.353 38.462 0.00 0.00 0.00 1.28
2616 2707 5.051816 CGTTTACTGGAGGAACACTTTGTA 58.948 41.667 0.00 0.00 0.00 2.41
2701 2826 9.008965 TGTTGCTATTGCTTTCTTTATGACTTA 57.991 29.630 0.00 0.00 40.48 2.24
2702 2827 7.885297 TGTTGCTATTGCTTTCTTTATGACTT 58.115 30.769 0.00 0.00 40.48 3.01
2703 2828 7.452880 TGTTGCTATTGCTTTCTTTATGACT 57.547 32.000 0.00 0.00 40.48 3.41
2704 2829 9.226345 GTATGTTGCTATTGCTTTCTTTATGAC 57.774 33.333 0.00 0.00 40.48 3.06
2705 2830 9.177608 AGTATGTTGCTATTGCTTTCTTTATGA 57.822 29.630 0.00 0.00 40.48 2.15
2709 2834 9.626045 GTTTAGTATGTTGCTATTGCTTTCTTT 57.374 29.630 0.00 0.00 40.48 2.52
2710 2835 7.962918 CGTTTAGTATGTTGCTATTGCTTTCTT 59.037 33.333 0.00 0.00 40.48 2.52
2711 2836 7.333423 TCGTTTAGTATGTTGCTATTGCTTTCT 59.667 33.333 0.00 0.00 40.48 2.52
2712 2837 7.461107 TCGTTTAGTATGTTGCTATTGCTTTC 58.539 34.615 0.00 0.00 40.48 2.62
2713 2838 7.372451 TCGTTTAGTATGTTGCTATTGCTTT 57.628 32.000 0.00 0.00 40.48 3.51
2714 2839 6.978343 TCGTTTAGTATGTTGCTATTGCTT 57.022 33.333 0.00 0.00 40.48 3.91
2715 2840 6.761242 TGATCGTTTAGTATGTTGCTATTGCT 59.239 34.615 0.00 0.00 40.48 3.91
2716 2841 6.943981 TGATCGTTTAGTATGTTGCTATTGC 58.056 36.000 0.00 0.00 40.20 3.56
2717 2842 8.604035 ACTTGATCGTTTAGTATGTTGCTATTG 58.396 33.333 0.00 0.00 0.00 1.90
2718 2843 8.604035 CACTTGATCGTTTAGTATGTTGCTATT 58.396 33.333 0.00 0.00 0.00 1.73
2719 2844 7.254455 GCACTTGATCGTTTAGTATGTTGCTAT 60.254 37.037 0.00 0.00 0.00 2.97
2720 2845 6.035650 GCACTTGATCGTTTAGTATGTTGCTA 59.964 38.462 0.00 0.00 0.00 3.49
2721 2846 5.163854 GCACTTGATCGTTTAGTATGTTGCT 60.164 40.000 0.00 0.00 0.00 3.91
2722 2847 5.022021 GCACTTGATCGTTTAGTATGTTGC 58.978 41.667 0.00 0.00 0.00 4.17
2827 2991 8.335532 TCAAAGATGGTTATGTTTCCTAACTG 57.664 34.615 0.00 0.00 35.24 3.16
3238 3994 5.719173 CCCGGTGAAAATGAATATGTTTGT 58.281 37.500 0.00 0.00 0.00 2.83
3347 4103 0.608035 GCGACCCAATGACCTTTCCA 60.608 55.000 0.00 0.00 0.00 3.53
3519 4276 0.941542 CGAACTTCGTTTCCTTGGCA 59.058 50.000 2.84 0.00 34.72 4.92
3695 4453 3.068691 CCGCCTGGAAGTCCGAGA 61.069 66.667 0.00 0.00 39.43 4.04
3739 4497 1.506493 GCTGTATTGGCGAGATCCAG 58.494 55.000 0.00 0.00 37.44 3.86
4172 4930 1.688772 GGTGGTACCGCTCAGATAGA 58.311 55.000 24.21 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.