Multiple sequence alignment - TraesCS1A01G019200

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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 TraesCS1A01G019200 chr1A 100.000 3585 0 0 1 3585 9645000 9641416 0.000000e+00 6621.0
1 TraesCS1A01G019200 chr1D 92.911 3583 177 32 51 3584 7950199 7946645 0.000000e+00 5138.0
2 TraesCS1A01G019200 chr1D 96.000 50 2 0 1 50 7950890 7950841 8.250000e-12 82.4
3 TraesCS1A01G019200 chr1B 91.802 3574 218 29 48 3584 10206702 10203167 0.000000e+00 4907.0
4 TraesCS1A01G019200 chr1B 82.768 383 41 7 168 527 132902706 132902326 5.780000e-83 318.0
5 TraesCS1A01G019200 chr1B 80.051 391 49 14 162 527 114573850 114574236 2.740000e-66 263.0
6 TraesCS1A01G019200 chr3A 85.590 687 60 19 334 996 740265796 740265125 0.000000e+00 684.0
7 TraesCS1A01G019200 chr3B 82.195 410 60 8 582 980 13893699 13893292 1.230000e-89 340.0
8 TraesCS1A01G019200 chr6B 81.818 385 45 7 166 527 114045589 114045971 2.090000e-77 300.0
9 TraesCS1A01G019200 chr7B 81.606 386 41 11 168 527 663439399 663439018 3.500000e-75 292.0
10 TraesCS1A01G019200 chr4B 80.256 390 50 14 162 527 619902086 619902472 5.900000e-68 268.0
11 TraesCS1A01G019200 chr4B 79.070 258 32 8 292 527 619895347 619895090 1.330000e-34 158.0
12 TraesCS1A01G019200 chr2B 79.692 389 54 9 162 527 284074909 284075295 1.280000e-64 257.0
13 TraesCS1A01G019200 chr5B 84.444 225 25 7 162 378 30594608 30594830 2.800000e-51 213.0


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 TraesCS1A01G019200 chr1A 9641416 9645000 3584 True 6621.0 6621 100.0000 1 3585 1 chr1A.!!$R1 3584
1 TraesCS1A01G019200 chr1D 7946645 7950890 4245 True 2610.2 5138 94.4555 1 3584 2 chr1D.!!$R1 3583
2 TraesCS1A01G019200 chr1B 10203167 10206702 3535 True 4907.0 4907 91.8020 48 3584 1 chr1B.!!$R1 3536
3 TraesCS1A01G019200 chr3A 740265125 740265796 671 True 684.0 684 85.5900 334 996 1 chr3A.!!$R1 662

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
259 917 0.340208 CCTGGTTAGTCTCTCCCCCT 59.66 60.0 0.00 0.0 0.00 4.79 F
1074 1770 0.250209 CAGTGCAGCAGTCTGGTTCT 60.25 55.0 0.65 0.0 40.65 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2659 0.898320 AACTCACATCTGACGGGAGG 59.102 55.0 7.98 0.0 0.0 4.30 R
2804 3518 0.877071 GGCACCACACAATGACAGAG 59.123 55.0 0.00 0.0 0.0 3.35 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
45 46 0.936297 GTCGCTGGCTGCACAAAAAG 60.936 55.000 16.76 0.00 43.06 2.27
58 700 1.541588 ACAAAAAGAAGATGCCCTCGC 59.458 47.619 0.00 0.00 0.00 5.03
82 724 2.198304 ATCCCGAAAGTGCCCCTGTC 62.198 60.000 0.00 0.00 0.00 3.51
255 913 1.487300 GACCCCTGGTTAGTCTCTCC 58.513 60.000 0.00 0.00 35.25 3.71
257 915 0.691413 CCCCTGGTTAGTCTCTCCCC 60.691 65.000 0.00 0.00 0.00 4.81
259 917 0.340208 CCTGGTTAGTCTCTCCCCCT 59.660 60.000 0.00 0.00 0.00 4.79
262 920 0.398806 GGTTAGTCTCTCCCCCTCCC 60.399 65.000 0.00 0.00 0.00 4.30
264 922 1.600763 TTAGTCTCTCCCCCTCCCCC 61.601 65.000 0.00 0.00 0.00 5.40
278 936 3.532155 CCCCCTCTCTCTTCCGCG 61.532 72.222 0.00 0.00 0.00 6.46
280 938 4.560856 CCCTCTCTCTTCCGCGCG 62.561 72.222 25.67 25.67 0.00 6.86
325 990 2.884894 CCTAGGGTTAGGTGTTAGCG 57.115 55.000 0.00 0.00 41.42 4.26
429 1114 3.349006 CTTGTCACGCGGCTGCTT 61.349 61.111 17.03 2.40 39.65 3.91
454 1139 2.119801 TGAAGCCAATCTGAAGCCTC 57.880 50.000 0.00 0.00 0.00 4.70
455 1140 1.012841 GAAGCCAATCTGAAGCCTCG 58.987 55.000 0.00 0.00 0.00 4.63
497 1183 3.636282 AAACAACGCAGTGGGAATTAC 57.364 42.857 14.98 0.00 45.00 1.89
573 1259 3.735237 TTCAGTCAGTCTCCTGTGAAC 57.265 47.619 0.00 0.00 39.82 3.18
584 1270 0.689623 CCTGTGAACCAGAGCTTCCT 59.310 55.000 0.00 0.00 44.49 3.36
597 1283 3.852578 AGAGCTTCCTAATCCTTTGGGAA 59.147 43.478 3.91 3.91 46.69 3.97
716 1406 7.754924 GGTGTGTATCATCGAAAACAAATCAAT 59.245 33.333 0.00 0.00 0.00 2.57
835 1525 1.680338 ATTTCTGCCTGTAATCGCCC 58.320 50.000 0.00 0.00 0.00 6.13
841 1531 3.644265 TCTGCCTGTAATCGCCCTATAAA 59.356 43.478 0.00 0.00 0.00 1.40
875 1565 5.883673 AGTTTGTTTGCTGGTACTGACTTTA 59.116 36.000 0.00 0.00 0.00 1.85
967 1662 9.862371 GTTAAAGAGTGATTCAGTGATAGAGAA 57.138 33.333 0.00 0.00 0.00 2.87
987 1682 1.416401 ACAGAACAGGTGGTAGTGGTG 59.584 52.381 0.00 0.00 0.00 4.17
1020 1716 1.298667 GTACCGTGGTGGGCTTGAT 59.701 57.895 0.72 0.00 44.64 2.57
1056 1752 2.347490 GCCTTGGAGCCGTTCTCA 59.653 61.111 4.63 0.00 43.70 3.27
1074 1770 0.250209 CAGTGCAGCAGTCTGGTTCT 60.250 55.000 0.65 0.00 40.65 3.01
1078 1774 1.071987 CAGCAGTCTGGTTCTGGCA 59.928 57.895 0.65 0.00 36.68 4.92
1110 1806 2.972505 ACGGCGGTGAAAGTGCAG 60.973 61.111 13.24 0.00 0.00 4.41
1171 1867 0.677098 CAGCCAGAGTCAGCATGCTT 60.677 55.000 19.98 3.07 34.76 3.91
1182 1878 2.789917 CATGCTTCGCAGAGTGCC 59.210 61.111 0.00 0.00 43.65 5.01
1215 1911 2.034687 GGGCAAGAAGCTGCTGGA 59.965 61.111 0.00 0.00 44.79 3.86
1347 2043 4.474303 TGGGAATGCCATTGATAGGATT 57.526 40.909 0.00 0.00 35.15 3.01
1496 2192 2.029649 GCCTGATGTTTGATGCACTTGT 60.030 45.455 0.00 0.00 0.00 3.16
1604 2318 4.483476 AACTCAATAGACAACGGTTTGC 57.517 40.909 0.00 0.00 36.00 3.68
1706 2420 8.482852 AATGGCAGGATTATAGCTGTAAAATT 57.517 30.769 7.03 0.00 0.00 1.82
1845 2559 6.035112 GCAAACGAGAGATTAACTAAGGACAG 59.965 42.308 0.00 0.00 0.00 3.51
2050 2764 4.332543 CGCTATGGTGTTAGCAAATCAGAA 59.667 41.667 4.54 0.00 43.92 3.02
2069 2783 5.593909 TCAGAAGTGCCATTGAAGAGAAAAA 59.406 36.000 0.00 0.00 0.00 1.94
2145 2859 0.959553 AGACCGTCGAAGAGAAGCAA 59.040 50.000 0.00 0.00 36.95 3.91
2148 2862 2.135933 ACCGTCGAAGAGAAGCAAAAG 58.864 47.619 0.00 0.00 36.95 2.27
2173 2887 5.679894 GCGGAGAGTGTCATTTAGAGATCAA 60.680 44.000 0.00 0.00 0.00 2.57
2239 2953 3.885297 CAGATGTTGAAACTGAACCAGGT 59.115 43.478 0.00 0.00 35.51 4.00
2296 3010 4.762956 GTACGAGTCTCTTGTACAGGTT 57.237 45.455 17.37 0.00 45.62 3.50
2470 3184 1.578215 AACTGGGCTCATCATGGGCT 61.578 55.000 10.02 0.00 45.01 5.19
2601 3315 7.081976 GGCGACTAGTTATTTTGTCACATTTT 58.918 34.615 0.00 0.00 0.00 1.82
2780 3494 1.488393 TGCGATCATGGGGATTGTACA 59.512 47.619 0.00 0.00 39.30 2.90
2781 3495 2.092699 TGCGATCATGGGGATTGTACAA 60.093 45.455 11.41 11.41 39.30 2.41
2784 3498 3.002246 CGATCATGGGGATTGTACAAACG 59.998 47.826 13.23 0.00 36.00 3.60
2803 3517 2.094675 CGATGTTGCCCCATTTCTTCT 58.905 47.619 0.00 0.00 0.00 2.85
2804 3518 2.098117 CGATGTTGCCCCATTTCTTCTC 59.902 50.000 0.00 0.00 0.00 2.87
2832 3546 0.533308 TGTGTGGTGCCGTTAACTCC 60.533 55.000 3.71 2.10 0.00 3.85
2904 3618 6.673154 CATTATGATGCACTCTCTTGTTGA 57.327 37.500 0.00 0.00 0.00 3.18
3005 3725 4.801330 TCATGTTCGTCTGGTCAAGTAT 57.199 40.909 0.00 0.00 0.00 2.12
3062 3785 5.351465 CACATGTCATAAGTGTGGTAAGTCC 59.649 44.000 0.00 0.00 39.54 3.85
3080 3803 1.272490 TCCTGTCTCTAGTTTGTGGCG 59.728 52.381 0.00 0.00 0.00 5.69
3143 3866 4.349930 TCCTGTTTTGCCTCTACTTTAGGT 59.650 41.667 0.00 0.00 36.43 3.08
3176 3899 9.753674 AATATGTAAGGAGTGATTTTTCTTCCA 57.246 29.630 0.00 0.00 0.00 3.53
3241 3966 2.915869 TGGTCCCCTGTTTCTCATAGT 58.084 47.619 0.00 0.00 0.00 2.12
3260 3985 3.665675 CTCCCTCCCGTTCAAGCCG 62.666 68.421 0.00 0.00 0.00 5.52
3262 3987 2.652095 CCCTCCCGTTCAAGCCGTA 61.652 63.158 0.00 0.00 0.00 4.02
3321 4046 6.931281 AGTTAACCATCATGATCCTGTTATCG 59.069 38.462 4.86 0.00 0.00 2.92
3352 4077 1.992557 TGAAGGCCCAAGTCCTTATGT 59.007 47.619 0.00 0.00 43.54 2.29
3353 4078 3.186283 TGAAGGCCCAAGTCCTTATGTA 58.814 45.455 0.00 0.00 43.54 2.29
3354 4079 3.785887 TGAAGGCCCAAGTCCTTATGTAT 59.214 43.478 0.00 0.00 43.54 2.29
3391 4116 2.806945 TCCACCATCCAATCCTTGTC 57.193 50.000 0.00 0.00 0.00 3.18
3419 4144 8.630054 AAGTATGTTGAAACTGCATAAGGTTA 57.370 30.769 0.00 0.00 35.31 2.85
3458 4183 3.399440 AGCCTAACTAGCATGCATCTC 57.601 47.619 21.98 0.23 0.00 2.75
3460 4185 2.038295 GCCTAACTAGCATGCATCTCCT 59.962 50.000 21.98 0.00 0.00 3.69
3505 4230 8.706322 ACTTGGTATTTTGACTTAGTTTGGAT 57.294 30.769 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.389059 CAGCGACAATCTCTATGTCCG 58.611 52.381 1.45 0.00 43.34 4.79
45 46 0.815615 ATTTCGGCGAGGGCATCTTC 60.816 55.000 10.46 0.00 42.47 2.87
58 700 1.654023 GGGCACTTTCGGGATTTCGG 61.654 60.000 0.00 0.00 0.00 4.30
82 724 1.200020 GCTCGTTTTGGTCAATCTGGG 59.800 52.381 0.00 0.00 0.00 4.45
246 904 2.019272 GGGGGAGGGGGAGAGACTA 61.019 68.421 0.00 0.00 0.00 2.59
262 920 4.214327 GCGCGGAAGAGAGAGGGG 62.214 72.222 8.83 0.00 0.00 4.79
414 1080 3.807631 AAGAAGCAGCCGCGTGACA 62.808 57.895 4.92 0.00 45.49 3.58
429 1114 3.755378 GCTTCAGATTGGCTTCAAGAAGA 59.245 43.478 13.70 0.00 40.79 2.87
443 1128 5.091261 ACTATTTTCACGAGGCTTCAGAT 57.909 39.130 0.00 0.00 0.00 2.90
447 1132 6.757010 TGAATCTACTATTTTCACGAGGCTTC 59.243 38.462 0.00 0.00 0.00 3.86
484 1170 4.695217 TTGAATTCGTAATTCCCACTGC 57.305 40.909 13.93 0.00 45.23 4.40
532 1218 0.173708 GGTAGAGTTGGCGAGTGAGG 59.826 60.000 0.00 0.00 0.00 3.86
573 1259 3.549794 CCAAAGGATTAGGAAGCTCTGG 58.450 50.000 0.00 0.00 0.00 3.86
584 1270 4.178956 GGGCTGTATTCCCAAAGGATTA 57.821 45.455 0.00 0.00 43.54 1.75
597 1283 0.182061 CTGTGATGGCTGGGCTGTAT 59.818 55.000 0.00 0.00 0.00 2.29
716 1406 1.525197 CTTTGACTCAAACGCGCTACA 59.475 47.619 5.73 0.00 0.00 2.74
835 1525 9.862585 GCAAACAAACTTTCAACCAATTTATAG 57.137 29.630 0.00 0.00 0.00 1.31
841 1531 4.635324 CCAGCAAACAAACTTTCAACCAAT 59.365 37.500 0.00 0.00 0.00 3.16
875 1565 3.323774 TCCCCTACAGACGGATTACAT 57.676 47.619 0.00 0.00 0.00 2.29
967 1662 1.416401 CACCACTACCACCTGTTCTGT 59.584 52.381 0.00 0.00 0.00 3.41
987 1682 1.614413 CGGTACATCTCCCCTAAGCTC 59.386 57.143 0.00 0.00 0.00 4.09
1056 1752 0.250209 CAGAACCAGACTGCTGCACT 60.250 55.000 0.00 0.00 40.91 4.40
1110 1806 3.455469 GGCACCAATGGAGCTGGC 61.455 66.667 20.36 10.17 39.22 4.85
1230 1926 2.203280 CCACCAAACTGCGTCCCA 60.203 61.111 0.00 0.00 0.00 4.37
1347 2043 6.753913 ATATGCCTCTTCTTGTCCAGATTA 57.246 37.500 0.00 0.00 0.00 1.75
1395 2091 3.584406 ACTGATGGTCCAAGACAATCTCA 59.416 43.478 12.21 0.00 41.97 3.27
1496 2192 1.677576 ACTCGTACGTCCAACTGAACA 59.322 47.619 16.05 0.00 0.00 3.18
1604 2318 3.565482 AGCACAATATTCCATTACAGGCG 59.435 43.478 0.00 0.00 0.00 5.52
1837 2551 2.054799 AGTTCAACAGGGCTGTCCTTA 58.945 47.619 0.00 0.00 45.47 2.69
1845 2559 2.223805 CCAACTTCAAGTTCAACAGGGC 60.224 50.000 0.00 0.00 36.03 5.19
1945 2659 0.898320 AACTCACATCTGACGGGAGG 59.102 55.000 7.98 0.00 0.00 4.30
2050 2764 5.595952 AGAACTTTTTCTCTTCAATGGCACT 59.404 36.000 0.00 0.00 37.55 4.40
2069 2783 2.026449 CAGAAGCATCCCCAGAAGAACT 60.026 50.000 0.00 0.00 0.00 3.01
2134 2848 1.466558 CTCCGCCTTTTGCTTCTCTTC 59.533 52.381 0.00 0.00 38.05 2.87
2145 2859 2.568623 AAATGACACTCTCCGCCTTT 57.431 45.000 0.00 0.00 0.00 3.11
2148 2862 2.427453 TCTCTAAATGACACTCTCCGCC 59.573 50.000 0.00 0.00 0.00 6.13
2173 2887 3.054802 CCTGAATAAGCTCTCCACCAACT 60.055 47.826 0.00 0.00 0.00 3.16
2239 2953 1.142870 CCTTCCTTCACACCAACTGGA 59.857 52.381 1.86 0.00 38.94 3.86
2296 3010 6.442541 TCCTTTCCTTTTGGTATGACAGTA 57.557 37.500 0.00 0.00 41.38 2.74
2470 3184 4.104579 TCTGGCTGGCCATCTGATTTATAA 59.895 41.667 15.04 0.00 46.15 0.98
2601 3315 6.109156 TCAAGGCAATTCACTACTAACTGA 57.891 37.500 0.00 0.00 0.00 3.41
2752 3466 1.608590 CCCCATGATCGCAACCATAAC 59.391 52.381 0.00 0.00 0.00 1.89
2780 3494 2.247358 AGAAATGGGGCAACATCGTTT 58.753 42.857 0.00 0.00 34.60 3.60
2781 3495 1.923356 AGAAATGGGGCAACATCGTT 58.077 45.000 0.00 0.00 39.74 3.85
2784 3498 3.359950 AGAGAAGAAATGGGGCAACATC 58.640 45.455 0.00 0.00 39.74 3.06
2803 3517 1.543208 GGCACCACACAATGACAGAGA 60.543 52.381 0.00 0.00 0.00 3.10
2804 3518 0.877071 GGCACCACACAATGACAGAG 59.123 55.000 0.00 0.00 0.00 3.35
2832 3546 1.075536 AGAAACCAGGGCAGGGTAAAG 59.924 52.381 0.00 0.00 37.77 1.85
3062 3785 2.440539 ACGCCACAAACTAGAGACAG 57.559 50.000 0.00 0.00 0.00 3.51
3111 3834 3.860641 AGGCAAAACAGGACAAACAAAG 58.139 40.909 0.00 0.00 0.00 2.77
3120 3843 4.349930 ACCTAAAGTAGAGGCAAAACAGGA 59.650 41.667 0.00 0.00 37.63 3.86
3143 3866 4.562767 TCACTCCTTACATATTAGGGGCA 58.437 43.478 0.00 0.00 35.28 5.36
3191 3914 8.768501 AGGTGATTTCCTTATTTTATCTTCCC 57.231 34.615 0.00 0.00 33.52 3.97
3241 3966 2.291043 GGCTTGAACGGGAGGGAGA 61.291 63.158 0.00 0.00 0.00 3.71
3260 3985 3.005897 TGCAGAAAGAGTCCAGACAGTAC 59.994 47.826 0.00 0.00 0.00 2.73
3262 3987 2.042464 TGCAGAAAGAGTCCAGACAGT 58.958 47.619 0.00 0.00 0.00 3.55
3321 4046 4.280929 ACTTGGGCCTTCATTCAAAAGTAC 59.719 41.667 4.53 0.00 0.00 2.73
3354 4079 9.739276 GATGGTGGAATACTATCAAATGGATAA 57.261 33.333 0.00 0.00 44.23 1.75
3391 4116 4.685169 ATGCAGTTTCAACATACTTCCG 57.315 40.909 0.00 0.00 0.00 4.30
3458 4183 1.741706 CAAGCAATGGTCACTAGCAGG 59.258 52.381 0.00 0.00 36.36 4.85
3460 4185 1.825090 CCAAGCAATGGTCACTAGCA 58.175 50.000 0.54 0.00 44.85 3.49


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

AutoCloner maintained by Alex Coulton.