Multiple sequence alignment - TraesCS3D01G264100

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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 TraesCS3D01G264100 chr3D 100.000 3727 0 0 1 3727 365908438 365912164 0 6883
1 TraesCS3D01G264100 chr3A 93.011 3806 166 40 2 3727 487856647 487860432 0 5463
2 TraesCS3D01G264100 chr3B 91.559 2014 93 34 559 2557 476948617 476950568 0 2706
3 TraesCS3D01G264100 chr3B 92.188 1216 54 18 2541 3725 476950582 476951787 0 1681
4 TraesCS3D01G264100 chr3B 91.833 502 29 8 1 495 476947825 476948321 0 689


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 TraesCS3D01G264100 chr3D 365908438 365912164 3726 False 6883 6883 100.000 1 3727 1 chr3D.!!$F1 3726
1 TraesCS3D01G264100 chr3A 487856647 487860432 3785 False 5463 5463 93.011 2 3727 1 chr3A.!!$F1 3725
2 TraesCS3D01G264100 chr3B 476947825 476951787 3962 False 1692 2706 91.860 1 3725 3 chr3B.!!$F1 3724

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
486 517 0.038890 AGCCCTTCTTCCCTTCTTGC 59.961 55.0 0.00 0.0 0.0 4.01 F
487 518 0.967887 GCCCTTCTTCCCTTCTTGCC 60.968 60.0 0.00 0.0 0.0 4.52 F
2058 2391 0.108233 CTTCTCACTGCAGGAGAGCC 60.108 60.0 25.26 0.0 42.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2391 0.721718 GATTCGCTGGTGTTTCTCCG 59.278 55.000 0.00 0.0 0.00 4.63 R
2105 2438 1.153309 CCAGCAGCATGATCACCGA 60.153 57.895 0.00 0.0 39.69 4.69 R
2968 3355 0.036010 CACTCACACTTGCCTAGGGG 60.036 60.000 11.72 0.0 0.00 4.79 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
99 102 5.508200 AATTCGTCTCCAGTCTGTCTATC 57.492 43.478 0.00 0.00 0.00 2.08
100 103 2.920524 TCGTCTCCAGTCTGTCTATCC 58.079 52.381 0.00 0.00 0.00 2.59
101 104 2.506231 TCGTCTCCAGTCTGTCTATCCT 59.494 50.000 0.00 0.00 0.00 3.24
102 105 3.710165 TCGTCTCCAGTCTGTCTATCCTA 59.290 47.826 0.00 0.00 0.00 2.94
194 199 7.118101 GCATTTCATTTCACAGATAAGGCAAAA 59.882 33.333 0.00 0.00 0.00 2.44
235 243 1.666011 GACTGACGGGAGCAGACAA 59.334 57.895 0.00 0.00 37.41 3.18
268 287 1.754803 TGTAGGACTGCCCAACGATAG 59.245 52.381 0.00 0.00 39.14 2.08
415 441 3.243367 CGATCTCTTGCTTCTCTACTGGG 60.243 52.174 0.00 0.00 0.00 4.45
476 507 1.857638 GCTCCTCCCAAGCCCTTCTT 61.858 60.000 0.00 0.00 33.53 2.52
486 517 0.038890 AGCCCTTCTTCCCTTCTTGC 59.961 55.000 0.00 0.00 0.00 4.01
487 518 0.967887 GCCCTTCTTCCCTTCTTGCC 60.968 60.000 0.00 0.00 0.00 4.52
529 564 2.112691 ACTCTCCTCTTCCTTCTTCCCA 59.887 50.000 0.00 0.00 0.00 4.37
573 881 4.324874 GGCTTGCATATCATATCCTCCCTT 60.325 45.833 0.00 0.00 0.00 3.95
608 917 3.769739 TCACTCAAGCCAAGCTCTTTA 57.230 42.857 0.00 0.00 38.25 1.85
762 1071 3.074412 CAGTTCATAGCCCTTTTCGTGT 58.926 45.455 0.00 0.00 0.00 4.49
763 1072 4.250464 CAGTTCATAGCCCTTTTCGTGTA 58.750 43.478 0.00 0.00 0.00 2.90
805 1116 1.031571 TGGGCGCATGGCTCTTTTAG 61.032 55.000 10.83 0.00 44.88 1.85
930 1249 2.839975 TGTCATGTGGTGCGACTTAAA 58.160 42.857 0.00 0.00 0.00 1.52
931 1250 3.206964 TGTCATGTGGTGCGACTTAAAA 58.793 40.909 0.00 0.00 0.00 1.52
987 1306 3.256136 CCTCCTTTTCGATATAGCGTCCT 59.744 47.826 10.57 0.00 0.00 3.85
994 1313 7.254795 CCTTTTCGATATAGCGTCCTTGAAAAT 60.255 37.037 10.57 0.00 34.67 1.82
995 1314 6.764877 TTCGATATAGCGTCCTTGAAAATC 57.235 37.500 10.57 0.00 0.00 2.17
996 1315 5.838529 TCGATATAGCGTCCTTGAAAATCA 58.161 37.500 10.57 0.00 0.00 2.57
997 1316 6.455647 TCGATATAGCGTCCTTGAAAATCAT 58.544 36.000 10.57 0.00 0.00 2.45
998 1317 6.366061 TCGATATAGCGTCCTTGAAAATCATG 59.634 38.462 10.57 0.00 0.00 3.07
999 1318 6.401474 CGATATAGCGTCCTTGAAAATCATGG 60.401 42.308 1.35 6.05 41.54 3.66
1036 1355 2.929641 TCCACAGCTGTGTTTCAATCA 58.070 42.857 37.55 13.58 44.21 2.57
1080 1399 1.078759 CGGACCACTTCGTGCTCATC 61.079 60.000 0.00 0.00 31.34 2.92
1104 1423 2.355126 CGGATGATCACGGAGGCG 60.355 66.667 0.00 0.00 0.00 5.52
1116 1435 4.070552 GAGGCGACGCTTCAGGGT 62.071 66.667 25.04 0.00 44.25 4.34
1242 1561 1.280133 TGCCAGGAAGAAGGTGATCAG 59.720 52.381 0.00 0.00 0.00 2.90
1335 1654 8.301720 GCTTGATGATTCCATATGCTATGAAAA 58.698 33.333 0.00 0.00 32.09 2.29
1351 1670 8.646356 TGCTATGAAAATTTGCTTAATTGTTCG 58.354 29.630 0.00 0.00 36.57 3.95
1405 1724 8.956426 GTTGAGAACCCACTTATTATTCATCAA 58.044 33.333 0.00 0.00 0.00 2.57
1472 1792 2.092158 TCCATATCAAAATGCCACCGGA 60.092 45.455 9.46 0.00 0.00 5.14
1484 1804 2.131972 GCCACCGGAAACACAAATTTC 58.868 47.619 9.46 0.00 37.78 2.17
1485 1805 2.223947 GCCACCGGAAACACAAATTTCT 60.224 45.455 9.46 0.00 38.43 2.52
1486 1806 3.004944 GCCACCGGAAACACAAATTTCTA 59.995 43.478 9.46 0.00 38.43 2.10
1487 1807 4.321675 GCCACCGGAAACACAAATTTCTAT 60.322 41.667 9.46 0.00 38.43 1.98
1488 1808 5.778862 CCACCGGAAACACAAATTTCTATT 58.221 37.500 9.46 0.00 38.43 1.73
1559 1885 3.304382 CGAATCGGATTTTTCGAGGTG 57.696 47.619 4.47 0.00 45.68 4.00
1576 1904 2.370849 AGGTGTTATCCTTGTGTCGGTT 59.629 45.455 0.00 0.00 33.52 4.44
1582 1910 1.790755 TCCTTGTGTCGGTTGAATCG 58.209 50.000 0.00 0.00 0.00 3.34
1649 1978 2.435069 TGCCCATTTATTCCTGCCAATG 59.565 45.455 0.00 0.00 0.00 2.82
1671 2004 9.626045 CAATGGAGGTTTTATTTGAACTAGTTC 57.374 33.333 25.73 25.73 39.91 3.01
1767 2100 7.383572 GTGAGATATGCTTACAGGTGAGTAATG 59.616 40.741 0.00 0.00 33.82 1.90
1997 2330 6.252995 TGGTGCTTAAGATCCTTGGTAATTT 58.747 36.000 6.67 0.00 0.00 1.82
2058 2391 0.108233 CTTCTCACTGCAGGAGAGCC 60.108 60.000 25.26 0.00 42.00 4.70
2094 2427 3.372206 CGAATCTCAACGCTGGAGAAAAT 59.628 43.478 5.52 0.00 44.01 1.82
2105 2438 4.561326 CGCTGGAGAAAATGTTTCCCAAAT 60.561 41.667 10.28 0.00 0.00 2.32
2258 2610 3.687212 CCAACTAACGCATATGTGTTCCA 59.313 43.478 32.07 18.29 44.53 3.53
2268 2620 4.689812 GCATATGTGTTCCAAAACATGCAA 59.310 37.500 4.29 0.00 46.58 4.08
2531 2883 2.815503 CAGTTGTCACATTGCTCCATCA 59.184 45.455 0.00 0.00 0.00 3.07
2574 2956 0.036765 TTACCCATGTCCAGTCACGC 60.037 55.000 0.00 0.00 0.00 5.34
2585 2969 3.311596 GTCCAGTCACGCATATAAAACCC 59.688 47.826 0.00 0.00 0.00 4.11
2586 2970 3.055021 TCCAGTCACGCATATAAAACCCA 60.055 43.478 0.00 0.00 0.00 4.51
2726 3110 3.118149 AGCATGTCATCAGCATCCAGTAA 60.118 43.478 0.00 0.00 0.00 2.24
2863 3250 6.073440 GCAAGTGTAAAGATGTTCCGTAGAAA 60.073 38.462 0.00 0.00 32.58 2.52
2864 3251 7.288672 CAAGTGTAAAGATGTTCCGTAGAAAC 58.711 38.462 0.00 0.00 32.58 2.78
2865 3252 6.756221 AGTGTAAAGATGTTCCGTAGAAACT 58.244 36.000 0.00 0.00 32.58 2.66
2877 3264 7.066043 TGTTCCGTAGAAACTTTGTACACAAAT 59.934 33.333 7.91 0.00 38.21 2.32
2906 3293 4.876107 AGTAGGAACAACACACTTGACTTG 59.124 41.667 0.00 0.00 0.00 3.16
2960 3347 7.282224 TGAAGTGGGCATGTGTATATAAAGTTC 59.718 37.037 0.00 0.00 0.00 3.01
2967 3354 9.503427 GGCATGTGTATATAAAGTTCAAGAAAC 57.497 33.333 0.00 0.00 38.21 2.78
2968 3355 9.503427 GCATGTGTATATAAAGTTCAAGAAACC 57.497 33.333 0.00 0.00 38.76 3.27
3045 3432 0.764890 TTGTGCCCAGCTACAGAAGT 59.235 50.000 0.00 0.00 0.00 3.01
3246 3645 2.572290 AGGCTACAACAACAACCTGAC 58.428 47.619 0.00 0.00 0.00 3.51
3270 3669 8.718102 ACGATAAAATTGAGCTACAACATAGT 57.282 30.769 0.00 0.00 41.52 2.12
3278 3684 7.658179 TTGAGCTACAACATAGTGAGAAAAG 57.342 36.000 0.00 0.00 33.18 2.27
3297 3703 1.090728 GCACTCTTAAGCTGGCCTTC 58.909 55.000 3.32 0.00 34.95 3.46
3298 3704 1.611673 GCACTCTTAAGCTGGCCTTCA 60.612 52.381 3.32 0.00 34.95 3.02
3299 3705 2.079925 CACTCTTAAGCTGGCCTTCAC 58.920 52.381 3.32 0.00 34.95 3.18
3300 3706 1.699634 ACTCTTAAGCTGGCCTTCACA 59.300 47.619 3.32 0.00 34.95 3.58
3519 3926 4.832248 TGATGTTATGACCTGAAGACACC 58.168 43.478 0.00 0.00 0.00 4.16
3542 3949 5.584649 CCAGCATAAGTTTCAATTCTACGGA 59.415 40.000 0.00 0.00 0.00 4.69
3544 3951 7.361713 CCAGCATAAGTTTCAATTCTACGGAAA 60.362 37.037 0.00 0.00 34.90 3.13
3577 3985 4.142609 AGAGTTTCAGAGAGTTTGCACA 57.857 40.909 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 134 3.006430 TCCACCGCTGTATATATGGTGTG 59.994 47.826 14.73 8.73 46.77 3.82
132 135 3.006537 GTCCACCGCTGTATATATGGTGT 59.993 47.826 14.73 0.00 46.77 4.16
165 170 6.183360 GCCTTATCTGTGAAATGAAATGCTCT 60.183 38.462 0.00 0.00 0.00 4.09
168 173 5.653507 TGCCTTATCTGTGAAATGAAATGC 58.346 37.500 0.00 0.00 0.00 3.56
194 199 2.022527 GGGATGGATAGATAGGCCCTCT 60.023 54.545 10.14 10.14 0.00 3.69
235 243 4.817874 AGTCCTACAAGATAGGGCTACT 57.182 45.455 5.29 0.00 46.93 2.57
342 361 0.707822 CGTTGCGTTTATTTGGCTGC 59.292 50.000 0.00 0.00 0.00 5.25
345 364 1.613270 CTCCGTTGCGTTTATTTGGC 58.387 50.000 0.00 0.00 0.00 4.52
476 507 0.821711 CCAACAACGGCAAGAAGGGA 60.822 55.000 0.00 0.00 0.00 4.20
486 517 3.365265 GAGGCAGGCCAACAACGG 61.365 66.667 13.63 0.00 38.92 4.44
487 518 2.281761 AGAGGCAGGCCAACAACG 60.282 61.111 13.63 0.00 38.92 4.10
541 576 0.396139 ATATGCAAGCCACACCAGGG 60.396 55.000 0.00 0.00 0.00 4.45
547 582 4.566278 GGAGGATATGATATGCAAGCCACA 60.566 45.833 6.72 0.00 0.00 4.17
548 583 3.944015 GGAGGATATGATATGCAAGCCAC 59.056 47.826 6.72 0.00 0.00 5.01
573 881 5.471456 GCTTGAGTGAAGAAAGGAAGAATGA 59.529 40.000 0.00 0.00 32.82 2.57
699 1008 1.077429 AAATGAGAGGAAGGCCGCC 60.077 57.895 0.00 0.00 39.96 6.13
709 1018 0.394899 GGAGGGGGTGCAAATGAGAG 60.395 60.000 0.00 0.00 0.00 3.20
762 1071 2.134287 GGAGGCAGGCACGGAGATA 61.134 63.158 0.00 0.00 0.00 1.98
763 1072 3.474570 GGAGGCAGGCACGGAGAT 61.475 66.667 0.00 0.00 0.00 2.75
805 1116 5.932661 CTTTGCTTACAGAAAGGAGCTAAC 58.067 41.667 0.00 0.00 36.82 2.34
930 1249 1.212490 CCACGCACGCAATCCATTT 59.788 52.632 0.00 0.00 0.00 2.32
931 1250 1.922135 GACCACGCACGCAATCCATT 61.922 55.000 0.00 0.00 0.00 3.16
965 1284 3.256136 AGGACGCTATATCGAAAAGGAGG 59.744 47.826 2.48 0.00 0.00 4.30
987 1306 4.746535 AGCATGCATCCATGATTTTCAA 57.253 36.364 21.98 0.00 45.15 2.69
995 1314 5.184287 TGGATAACATAAGCATGCATCCATG 59.816 40.000 22.87 18.93 44.43 3.66
996 1315 5.326900 TGGATAACATAAGCATGCATCCAT 58.673 37.500 22.87 8.16 44.43 3.41
997 1316 4.520111 GTGGATAACATAAGCATGCATCCA 59.480 41.667 22.87 22.87 45.70 3.41
998 1317 4.520111 TGTGGATAACATAAGCATGCATCC 59.480 41.667 21.98 20.26 42.35 3.51
999 1318 5.694231 TGTGGATAACATAAGCATGCATC 57.306 39.130 21.98 11.69 35.39 3.91
1003 1322 4.577693 ACAGCTGTGGATAACATAAGCATG 59.422 41.667 20.97 0.00 41.51 4.06
1036 1355 0.465097 CTCGGATCAATGGCCTTGCT 60.465 55.000 3.32 0.00 34.66 3.91
1080 1399 2.588877 GTGATCATCCGCCCCGTG 60.589 66.667 0.00 0.00 0.00 4.94
1104 1423 2.045926 ATGGCACCCTGAAGCGTC 60.046 61.111 0.00 0.00 0.00 5.19
1227 1546 0.915364 AGGCCTGATCACCTTCTTCC 59.085 55.000 3.11 0.00 29.74 3.46
1242 1561 0.988678 AAGGGGTCTCCATGTAGGCC 60.989 60.000 0.00 0.00 40.78 5.19
1335 1654 7.202016 TCAGAGTTCGAACAATTAAGCAAAT 57.798 32.000 28.78 4.53 0.00 2.32
1351 1670 7.039313 AGGTTATTTTTGGTGTTCAGAGTTC 57.961 36.000 0.00 0.00 0.00 3.01
1366 1685 6.040504 GTGGGTTCTCAACTTGAGGTTATTTT 59.959 38.462 17.12 0.00 44.39 1.82
1405 1724 4.281688 CCTGTTCCATTGTTTGAAGATGGT 59.718 41.667 0.00 0.00 40.89 3.55
1559 1885 4.201685 CGATTCAACCGACACAAGGATAAC 60.202 45.833 0.00 0.00 0.00 1.89
1590 1918 2.730934 AGGGCAGTCGAGTCTACATA 57.269 50.000 0.00 0.00 0.00 2.29
1598 1926 4.380550 GGGAAAAATAAAAGGGCAGTCGAG 60.381 45.833 0.00 0.00 0.00 4.04
1649 1978 7.430992 ACGAACTAGTTCAAATAAAACCTCC 57.569 36.000 29.95 4.13 39.46 4.30
1767 2100 2.218603 TCTTTCTGGTTTCCGTTGAGC 58.781 47.619 0.00 0.00 0.00 4.26
1997 2330 1.420138 AGGCCCTTCTCAGACGAAAAA 59.580 47.619 0.00 0.00 0.00 1.94
2058 2391 0.721718 GATTCGCTGGTGTTTCTCCG 59.278 55.000 0.00 0.00 0.00 4.63
2094 2427 3.147553 TGATCACCGATTTGGGAAACA 57.852 42.857 0.00 0.00 44.64 2.83
2105 2438 1.153309 CCAGCAGCATGATCACCGA 60.153 57.895 0.00 0.00 39.69 4.69
2268 2620 1.350351 AGCAGAGCCATCAACTGAAGT 59.650 47.619 0.00 0.00 34.07 3.01
2531 2883 2.365617 CAGACCTGGTGTTGACTGTACT 59.634 50.000 2.82 0.00 0.00 2.73
2585 2969 9.533253 AAAACCTTACATTCTGATTGAAACTTG 57.467 29.630 6.56 0.00 38.29 3.16
2726 3110 1.884579 CATTCTCCTTGTGCAGCTTGT 59.115 47.619 0.00 0.00 0.00 3.16
2877 3264 8.033038 GTCAAGTGTGTTGTTCCTACTATATGA 58.967 37.037 0.00 0.00 0.00 2.15
2884 3271 4.873827 TCAAGTCAAGTGTGTTGTTCCTAC 59.126 41.667 0.00 0.00 0.00 3.18
2906 3293 4.869297 CACTTCTCATCTCCATGACTTGTC 59.131 45.833 0.00 0.00 33.80 3.18
2960 3347 1.075536 ACTTGCCTAGGGGGTTTCTTG 59.924 52.381 11.72 0.00 37.43 3.02
2967 3354 1.201429 ACTCACACTTGCCTAGGGGG 61.201 60.000 11.72 0.00 38.36 5.40
2968 3355 0.036010 CACTCACACTTGCCTAGGGG 60.036 60.000 11.72 0.00 0.00 4.79
3045 3432 1.414919 AGACGTTTTAGTGCCTGGTGA 59.585 47.619 0.00 0.00 0.00 4.02
3246 3645 8.817100 TCACTATGTTGTAGCTCAATTTTATCG 58.183 33.333 0.00 0.00 38.38 2.92
3270 3669 4.067896 CCAGCTTAAGAGTGCTTTTCTCA 58.932 43.478 6.67 0.00 37.44 3.27
3278 3684 1.090728 GAAGGCCAGCTTAAGAGTGC 58.909 55.000 5.01 4.37 0.00 4.40
3297 3703 1.826054 TGGCTTTCCAACGGGTGTG 60.826 57.895 0.00 0.00 39.99 3.82
3298 3704 1.826487 GTGGCTTTCCAACGGGTGT 60.826 57.895 0.00 0.00 45.53 4.16
3299 3705 2.903547 CGTGGCTTTCCAACGGGTG 61.904 63.158 0.00 0.00 45.53 4.61
3300 3706 2.593436 CGTGGCTTTCCAACGGGT 60.593 61.111 0.00 0.00 45.53 5.28
3519 3926 6.662414 TCCGTAGAATTGAAACTTATGCTG 57.338 37.500 0.00 0.00 0.00 4.41
3542 3949 8.871125 TCTCTGAAACTCTTATCTTACACCTTT 58.129 33.333 0.00 0.00 0.00 3.11
3544 3951 7.672239 ACTCTCTGAAACTCTTATCTTACACCT 59.328 37.037 0.00 0.00 0.00 4.00
3577 3985 3.477530 GCCTTGTGGTCAGTACTTTCTT 58.522 45.455 0.00 0.00 35.27 2.52
3678 4096 5.408880 TCAATAATCAGTACCACGTTGGA 57.591 39.130 10.46 0.00 40.96 3.53
3679 4097 6.315144 TGATTCAATAATCAGTACCACGTTGG 59.685 38.462 2.92 2.92 45.17 3.77


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

AutoCloner maintained by Alex Coulton.