Multiple sequence alignment - TraesCS3A01G419200

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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 TraesCS3A01G419200 chr3A 100.000 3617 0 0 1 3617 661474238 661470622 0.000000e+00 6680
1 TraesCS3A01G419200 chr3D 93.308 3691 111 49 1 3617 526975476 526971848 0.000000e+00 5323
2 TraesCS3A01G419200 chr3B 93.684 2090 92 22 1 2063 696329081 696327005 0.000000e+00 3092
3 TraesCS3A01G419200 chr3B 92.593 1539 59 32 2113 3617 696327007 696325490 0.000000e+00 2159
4 TraesCS3A01G419200 chr7D 92.943 581 40 1 1 581 496314726 496314147 0.000000e+00 845
5 TraesCS3A01G419200 chr7B 92.662 477 28 6 1533 2006 312023748 312024220 0.000000e+00 680
6 TraesCS3A01G419200 chr7B 92.453 477 31 5 1533 2006 311927073 311927547 0.000000e+00 676
7 TraesCS3A01G419200 chr7B 96.094 128 5 0 948 1075 312023623 312023750 3.660000e-50 209
8 TraesCS3A01G419200 chr7B 95.312 128 6 0 948 1075 311926948 311927075 1.700000e-48 204


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 TraesCS3A01G419200 chr3A 661470622 661474238 3616 True 6680.0 6680 100.0000 1 3617 1 chr3A.!!$R1 3616
1 TraesCS3A01G419200 chr3D 526971848 526975476 3628 True 5323.0 5323 93.3080 1 3617 1 chr3D.!!$R1 3616
2 TraesCS3A01G419200 chr3B 696325490 696329081 3591 True 2625.5 3092 93.1385 1 3617 2 chr3B.!!$R1 3616
3 TraesCS3A01G419200 chr7D 496314147 496314726 579 True 845.0 845 92.9430 1 581 1 chr7D.!!$R1 580
4 TraesCS3A01G419200 chr7B 312023623 312024220 597 False 444.5 680 94.3780 948 2006 2 chr7B.!!$F2 1058
5 TraesCS3A01G419200 chr7B 311926948 311927547 599 False 440.0 676 93.8825 948 2006 2 chr7B.!!$F1 1058

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
607 625 0.251653 TCACTTCCGGCTCCAGTAGT 60.252 55.0 0.0 0.0 0.0 2.73 F
1399 1444 0.321671 ACATCACAACACCCTCCTCG 59.678 55.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 1526 2.653702 GCTCCGCAGTCTCTGTGT 59.346 61.111 9.01 0.0 39.99 3.72 R
3030 3122 0.741221 CAAGCCGAGCTACCTCAACC 60.741 60.000 0.00 0.0 38.25 3.77 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
165 166 2.764128 GGGAGGAGGCCACGATCA 60.764 66.667 5.01 0.00 0.00 2.92
607 625 0.251653 TCACTTCCGGCTCCAGTAGT 60.252 55.000 0.00 0.00 0.00 2.73
630 648 4.504916 CGGCTCGGTCCAGCTCAG 62.505 72.222 11.55 3.02 39.58 3.35
631 649 4.828925 GGCTCGGTCCAGCTCAGC 62.829 72.222 11.55 0.00 39.58 4.26
712 732 2.897350 GGATCCTGGAAAGGCGCG 60.897 66.667 3.84 0.00 0.00 6.86
867 888 3.711782 CCCCCTTCCCTCCCTCCT 61.712 72.222 0.00 0.00 0.00 3.69
868 889 2.461637 CCCCTTCCCTCCCTCCTT 59.538 66.667 0.00 0.00 0.00 3.36
869 890 1.694525 CCCCTTCCCTCCCTCCTTC 60.695 68.421 0.00 0.00 0.00 3.46
870 891 1.694525 CCCTTCCCTCCCTCCTTCC 60.695 68.421 0.00 0.00 0.00 3.46
871 892 1.694525 CCTTCCCTCCCTCCTTCCC 60.695 68.421 0.00 0.00 0.00 3.97
872 893 1.398234 CTTCCCTCCCTCCTTCCCT 59.602 63.158 0.00 0.00 0.00 4.20
873 894 0.692756 CTTCCCTCCCTCCTTCCCTC 60.693 65.000 0.00 0.00 0.00 4.30
874 895 2.040359 CCCTCCCTCCTTCCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
1142 1168 3.255725 TCGACAAGGTAATTAACTGCCG 58.744 45.455 3.17 8.24 0.00 5.69
1145 1171 4.331717 CGACAAGGTAATTAACTGCCGATT 59.668 41.667 3.17 0.00 0.00 3.34
1151 1177 7.730364 AGGTAATTAACTGCCGATTAATCAG 57.270 36.000 15.57 8.43 32.31 2.90
1152 1178 7.280356 AGGTAATTAACTGCCGATTAATCAGT 58.720 34.615 15.57 9.04 42.28 3.41
1153 1179 7.226720 AGGTAATTAACTGCCGATTAATCAGTG 59.773 37.037 15.57 4.54 40.54 3.66
1154 1180 7.225931 GGTAATTAACTGCCGATTAATCAGTGA 59.774 37.037 15.57 0.00 40.54 3.41
1155 1181 7.807977 AATTAACTGCCGATTAATCAGTGAT 57.192 32.000 15.57 0.00 40.54 3.06
1156 1182 7.807977 ATTAACTGCCGATTAATCAGTGATT 57.192 32.000 21.57 21.57 40.54 2.57
1157 1183 8.902540 ATTAACTGCCGATTAATCAGTGATTA 57.097 30.769 19.51 19.51 40.54 1.75
1158 1184 8.725405 TTAACTGCCGATTAATCAGTGATTAA 57.275 30.769 30.83 30.83 44.88 1.40
1196 1233 2.091541 TCGTTTCCTTCCATGCCATTC 58.908 47.619 0.00 0.00 0.00 2.67
1202 1239 3.559069 TCCTTCCATGCCATTCATTCTC 58.441 45.455 0.00 0.00 31.79 2.87
1263 1307 3.820467 TCTGGCAGTTGAATTGATTCGTT 59.180 39.130 15.27 0.00 39.62 3.85
1265 1309 3.057596 TGGCAGTTGAATTGATTCGTTCC 60.058 43.478 0.00 0.00 39.62 3.62
1267 1311 4.406943 GCAGTTGAATTGATTCGTTCCTC 58.593 43.478 0.00 0.00 39.62 3.71
1268 1312 4.083324 GCAGTTGAATTGATTCGTTCCTCA 60.083 41.667 0.00 0.00 39.62 3.86
1269 1313 5.392380 GCAGTTGAATTGATTCGTTCCTCAT 60.392 40.000 0.00 0.00 39.62 2.90
1270 1314 6.025896 CAGTTGAATTGATTCGTTCCTCATG 58.974 40.000 0.00 0.00 39.62 3.07
1271 1315 4.621068 TGAATTGATTCGTTCCTCATGC 57.379 40.909 0.00 0.00 39.62 4.06
1289 1333 3.306917 TGCGATCCTCGTTTGTTTCTA 57.693 42.857 0.00 0.00 42.81 2.10
1291 1336 3.430895 TGCGATCCTCGTTTGTTTCTAAC 59.569 43.478 0.00 0.00 42.81 2.34
1388 1433 2.301870 AGCTCGGAGGTTAACATCACAA 59.698 45.455 20.75 5.62 0.00 3.33
1393 1438 2.817844 GGAGGTTAACATCACAACACCC 59.182 50.000 20.75 0.00 0.00 4.61
1395 1440 3.751518 AGGTTAACATCACAACACCCTC 58.248 45.455 8.10 0.00 0.00 4.30
1397 1442 3.497942 GGTTAACATCACAACACCCTCCT 60.498 47.826 8.10 0.00 0.00 3.69
1399 1444 0.321671 ACATCACAACACCCTCCTCG 59.678 55.000 0.00 0.00 0.00 4.63
1400 1445 1.021390 CATCACAACACCCTCCTCGC 61.021 60.000 0.00 0.00 0.00 5.03
1402 1447 4.003788 ACAACACCCTCCTCGCCG 62.004 66.667 0.00 0.00 0.00 6.46
1430 1475 4.022503 GCCTGCTTTCTTGATCTCAACTTT 60.023 41.667 0.00 0.00 0.00 2.66
1481 1526 3.253188 CGGCTCTGAAATTGTTTGAGGAA 59.747 43.478 0.00 0.00 0.00 3.36
1721 1772 0.465705 AGAGGTGACACCACACACAG 59.534 55.000 26.30 0.00 44.93 3.66
1757 1809 8.811017 TGATCACTCCTCCTAATATCATTCTTC 58.189 37.037 0.00 0.00 0.00 2.87
1759 1811 8.187913 TCACTCCTCCTAATATCATTCTTCAG 57.812 38.462 0.00 0.00 0.00 3.02
1782 1834 5.035443 GCTGGTTGTTAGATCGTACTAGTG 58.965 45.833 5.39 0.00 0.00 2.74
1861 1917 3.673338 TGTTGAAGTGACATCGATCGTTC 59.327 43.478 15.94 9.96 0.00 3.95
1899 1955 9.918630 CCACAGTAAATGATTCTCTGAAATTTT 57.081 29.630 13.60 0.00 0.00 1.82
1975 2032 8.677148 ACATTTTAGATAACGTAATGGCATCT 57.323 30.769 0.00 0.00 32.04 2.90
1976 2033 9.772973 ACATTTTAGATAACGTAATGGCATCTA 57.227 29.630 0.00 0.00 32.04 1.98
1979 2036 9.826574 TTTTAGATAACGTAATGGCATCTAACT 57.173 29.630 0.00 0.00 37.72 2.24
1980 2037 8.812147 TTAGATAACGTAATGGCATCTAACTG 57.188 34.615 0.00 0.13 34.74 3.16
1981 2038 7.050970 AGATAACGTAATGGCATCTAACTGA 57.949 36.000 0.00 0.00 0.00 3.41
2000 2059 9.198475 CTAACTGACCTATTTCCTTAAGGAGTA 57.802 37.037 23.11 18.09 46.36 2.59
2049 2123 6.491745 TCCTGGATCTGACATCTGTATAAGAC 59.508 42.308 0.00 0.00 37.88 3.01
2181 2258 9.559732 CCTAATCATATGTGGATTTTGTAGTGA 57.440 33.333 1.90 0.00 36.45 3.41
2516 2595 6.428465 TCGATTAACCACTTCTGCAATTAACA 59.572 34.615 0.00 0.00 0.00 2.41
2547 2627 9.541143 TTTTCTTTCCATTTCCAGTTTATTGAC 57.459 29.630 0.00 0.00 0.00 3.18
2581 2661 6.532988 AGAACTACTTGGAGATGAGTTACC 57.467 41.667 0.00 0.00 30.66 2.85
2990 3072 7.602517 TTCAGAGCTTAATTACTGCTTCTTC 57.397 36.000 11.89 2.58 37.16 2.87
2991 3073 6.109359 TCAGAGCTTAATTACTGCTTCTTCC 58.891 40.000 11.89 2.09 37.16 3.46
2992 3074 5.006165 CAGAGCTTAATTACTGCTTCTTCCG 59.994 44.000 11.89 0.00 37.16 4.30
3030 3122 2.582052 TGGCAGTTAAACCAAGTGAGG 58.418 47.619 0.00 0.00 39.58 3.86
3097 3189 0.957395 CGTCTTTGGCTGCCATGTCT 60.957 55.000 24.03 0.00 31.53 3.41
3128 3220 1.591158 GTGCGTCTCAAGTTGTTTCGA 59.409 47.619 15.73 0.00 0.00 3.71
3158 3250 0.671781 GCGTTGCTCTCACTGGATGT 60.672 55.000 0.00 0.00 0.00 3.06
3215 3307 2.028112 TCACTAGGTGGTTGACTGATGC 60.028 50.000 0.00 0.00 33.87 3.91
3377 3470 1.470098 GACTTGACTTGCGCCATCATT 59.530 47.619 4.18 0.00 0.00 2.57
3382 3475 0.392461 ACTTGCGCCATCATTACCGT 60.392 50.000 4.18 0.00 0.00 4.83
3483 3576 5.816258 TGGTATCTTCGTGTTGTTTGTAACA 59.184 36.000 0.00 0.00 40.21 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 160 4.514577 CGCCGCCTCCTTGATCGT 62.515 66.667 0.00 0.00 0.00 3.73
162 163 3.854669 CTCCGCCGCCTCCTTGAT 61.855 66.667 0.00 0.00 0.00 2.57
712 732 1.747745 CCGAATCCAAACCCCCGAC 60.748 63.158 0.00 0.00 0.00 4.79
1157 1183 8.813282 GGAAACGAACAAAACAAATCACTAATT 58.187 29.630 0.00 0.00 0.00 1.40
1158 1184 8.194769 AGGAAACGAACAAAACAAATCACTAAT 58.805 29.630 0.00 0.00 0.00 1.73
1159 1185 7.540299 AGGAAACGAACAAAACAAATCACTAA 58.460 30.769 0.00 0.00 0.00 2.24
1160 1186 7.090953 AGGAAACGAACAAAACAAATCACTA 57.909 32.000 0.00 0.00 0.00 2.74
1161 1187 5.961272 AGGAAACGAACAAAACAAATCACT 58.039 33.333 0.00 0.00 0.00 3.41
1196 1233 5.570589 GCATTGAAGAAAGTTTCCGAGAATG 59.429 40.000 12.05 14.53 0.00 2.67
1202 1239 4.488126 TCAGCATTGAAGAAAGTTTCCG 57.512 40.909 12.05 0.00 0.00 4.30
1356 1401 1.871126 CTCCGAGCTGCTCTGTGTCA 61.871 60.000 25.59 4.31 0.00 3.58
1399 1444 3.435186 GAAAGCAGGCAGGTCGGC 61.435 66.667 0.00 0.00 41.61 5.54
1400 1445 1.302832 AAGAAAGCAGGCAGGTCGG 60.303 57.895 0.00 0.00 0.00 4.79
1402 1447 1.742268 GATCAAGAAAGCAGGCAGGTC 59.258 52.381 0.00 0.00 0.00 3.85
1406 1451 2.816087 GTTGAGATCAAGAAAGCAGGCA 59.184 45.455 0.00 0.00 36.39 4.75
1481 1526 2.653702 GCTCCGCAGTCTCTGTGT 59.346 61.111 9.01 0.00 39.99 3.72
1721 1772 3.265791 GAGGAGTGATCATGTTGGTGTC 58.734 50.000 0.00 0.00 0.00 3.67
1757 1809 4.111375 AGTACGATCTAACAACCAGCTG 57.889 45.455 6.78 6.78 0.00 4.24
1759 1811 5.035443 CACTAGTACGATCTAACAACCAGC 58.965 45.833 0.00 0.00 0.00 4.85
1782 1834 9.539825 TTCATTTGATCTAGAATCTACTTCTGC 57.460 33.333 0.00 0.00 44.12 4.26
1861 1917 4.599047 TTTACTGTGGCATTCAAAAGGG 57.401 40.909 0.00 0.00 0.00 3.95
1899 1955 3.572642 TGTTCCTGAAGAGTACCACAGA 58.427 45.455 0.00 0.00 32.90 3.41
1964 2021 7.173390 GGAAATAGGTCAGTTAGATGCCATTAC 59.827 40.741 0.00 0.00 0.00 1.89
1975 2032 9.725206 ATACTCCTTAAGGAAATAGGTCAGTTA 57.275 33.333 24.31 4.52 44.91 2.24
1976 2033 6.954352 ACTCCTTAAGGAAATAGGTCAGTT 57.046 37.500 24.31 0.00 44.91 3.16
2000 2059 8.860088 GGAGGGAAATGTAGTGCAAATTAATAT 58.140 33.333 0.00 0.00 0.00 1.28
2049 2123 4.498009 GGGGATATTGTGTCAATTTCAGCG 60.498 45.833 12.28 0.00 0.00 5.18
2203 2280 8.664079 AGCCTATTTATGTACCAGATGATCTTT 58.336 33.333 0.00 0.00 0.00 2.52
2221 2298 5.420104 AGAGCACAGCAAATTAAGCCTATTT 59.580 36.000 0.00 0.00 0.00 1.40
2262 2339 4.141914 GGGAACATCGGATCAACTACTTCT 60.142 45.833 0.00 0.00 0.00 2.85
2547 2627 4.526970 CAAGTAGTTCTTGCCATCATCG 57.473 45.455 0.00 0.00 45.37 3.84
2581 2661 5.181748 CCAGTCCTTCCTAATCTCAAAGTG 58.818 45.833 0.00 0.00 0.00 3.16
2990 3072 4.621034 GCCAAGAATATTTTCACAACACGG 59.379 41.667 0.00 0.00 34.08 4.94
2991 3073 5.218885 TGCCAAGAATATTTTCACAACACG 58.781 37.500 0.00 0.00 34.08 4.49
2992 3074 6.215845 ACTGCCAAGAATATTTTCACAACAC 58.784 36.000 0.00 0.00 34.08 3.32
3030 3122 0.741221 CAAGCCGAGCTACCTCAACC 60.741 60.000 0.00 0.00 38.25 3.77
3035 3127 0.977395 AAAGACAAGCCGAGCTACCT 59.023 50.000 0.00 0.00 38.25 3.08
3097 3189 4.400109 GACGCACGCGAGACCTCA 62.400 66.667 19.66 0.00 42.83 3.86
3128 3220 0.951040 GAGCAACGCCAACTAGTGCT 60.951 55.000 0.00 0.00 0.00 4.40
3158 3250 2.743538 CTACGGCAGCAGCAGCAA 60.744 61.111 12.41 0.00 45.49 3.91
3215 3307 1.219522 ACCTCAAGAAAACGGCGTCG 61.220 55.000 15.17 8.42 43.02 5.12
3260 3352 2.202440 CACCGACGCTACCACTCG 60.202 66.667 0.00 0.00 0.00 4.18
3261 3353 2.488087 AAGCACCGACGCTACCACTC 62.488 60.000 0.00 0.00 42.89 3.51
3398 3491 1.066573 CGGATCACTCTCCTTGCAAGT 60.067 52.381 24.35 3.73 32.77 3.16
3464 3557 5.640357 AGAACTGTTACAAACAACACGAAGA 59.360 36.000 0.00 0.00 41.61 2.87
3513 3630 2.754946 TTGACGGCGAACCTAAAGAT 57.245 45.000 16.62 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.