Multiple sequence alignment - TraesCS2B01G195900

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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 TraesCS2B01G195900 chr2B 100.000 2805 0 0 1 2805 173484268 173487072 0 5180
1 TraesCS2B01G195900 chr2D 92.742 2852 135 27 1 2805 120564383 120567209 0 4054
2 TraesCS2B01G195900 chr2A 92.013 2792 133 38 1 2739 124389917 124392671 0 3838


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 TraesCS2B01G195900 chr2B 173484268 173487072 2804 False 5180 5180 100.000 1 2805 1 chr2B.!!$F1 2804
1 TraesCS2B01G195900 chr2D 120564383 120567209 2826 False 4054 4054 92.742 1 2805 1 chr2D.!!$F1 2804
2 TraesCS2B01G195900 chr2A 124389917 124392671 2754 False 3838 3838 92.013 1 2739 1 chr2A.!!$F1 2738

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
962 979 0.10412 GGTTGCGGATTAATTGGGCC 59.896 55.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 2655 1.618837 TGCTGGAGCGAGAATATACCC 59.381 52.381 0.0 0.0 45.83 3.69 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
75 76 0.889994 TGTACGTCAATAGTGCCCGT 59.110 50.000 11.35 11.35 36.46 5.28
76 77 1.274596 GTACGTCAATAGTGCCCGTG 58.725 55.000 14.92 0.00 34.95 4.94
77 78 0.173935 TACGTCAATAGTGCCCGTGG 59.826 55.000 14.92 0.00 34.95 4.94
86 87 0.535102 AGTGCCCGTGGAGTTTCAAG 60.535 55.000 0.00 0.00 0.00 3.02
101 102 7.708752 TGGAGTTTCAAGCAATTTTTACGAAAT 59.291 29.630 0.00 0.00 0.00 2.17
134 135 7.383300 AGTGTAAACGTGAGGTTGAATAGTTAC 59.617 37.037 0.00 0.00 43.76 2.50
136 137 7.710044 TGTAAACGTGAGGTTGAATAGTTACAA 59.290 33.333 0.00 0.00 43.76 2.41
158 159 5.767816 AATCAAAGTTTGTGGGTACTCAC 57.232 39.130 19.42 19.42 38.09 3.51
186 187 2.592102 AATGATCCGCCAATATGCCT 57.408 45.000 0.00 0.00 0.00 4.75
200 201 0.749649 ATGCCTAGAGTTGCTCCTCG 59.250 55.000 0.00 0.00 36.56 4.63
214 215 3.512329 TGCTCCTCGATACCTAAACAACA 59.488 43.478 0.00 0.00 0.00 3.33
218 219 6.626623 GCTCCTCGATACCTAAACAACACTAA 60.627 42.308 0.00 0.00 0.00 2.24
220 221 7.844009 TCCTCGATACCTAAACAACACTAATT 58.156 34.615 0.00 0.00 0.00 1.40
260 261 9.182214 ACTACTTCGTGGACAATTTATAGTCTA 57.818 33.333 0.00 0.00 35.18 2.59
306 318 3.071479 TGACGCTTTATGAAACCTGGTC 58.929 45.455 0.00 0.00 0.00 4.02
329 341 2.102588 GGCCTACCGATAAGCTCAAAGA 59.897 50.000 0.00 0.00 0.00 2.52
388 400 9.918630 ATTTCAGATGATTTCGAGTGAATTTTT 57.081 25.926 0.00 0.00 33.20 1.94
593 609 4.331992 TGAGAGACAAACGAGATACTACCG 59.668 45.833 0.00 0.00 0.00 4.02
598 614 3.698040 ACAAACGAGATACTACCGGTGAT 59.302 43.478 19.93 7.86 0.00 3.06
599 615 4.883585 ACAAACGAGATACTACCGGTGATA 59.116 41.667 19.93 9.91 0.00 2.15
600 616 5.210715 CAAACGAGATACTACCGGTGATAC 58.789 45.833 19.93 4.92 0.00 2.24
727 744 3.938963 AGCATATGCCGGTAAATATTCCG 59.061 43.478 23.96 8.29 45.42 4.30
751 768 1.272760 ACGTCACCATCCTCTTCCTCT 60.273 52.381 0.00 0.00 0.00 3.69
752 769 1.827969 CGTCACCATCCTCTTCCTCTT 59.172 52.381 0.00 0.00 0.00 2.85
753 770 2.159170 CGTCACCATCCTCTTCCTCTTC 60.159 54.545 0.00 0.00 0.00 2.87
754 771 2.169561 GTCACCATCCTCTTCCTCTTCC 59.830 54.545 0.00 0.00 0.00 3.46
755 772 2.045047 TCACCATCCTCTTCCTCTTCCT 59.955 50.000 0.00 0.00 0.00 3.36
756 773 2.433970 CACCATCCTCTTCCTCTTCCTC 59.566 54.545 0.00 0.00 0.00 3.71
757 774 2.317594 ACCATCCTCTTCCTCTTCCTCT 59.682 50.000 0.00 0.00 0.00 3.69
758 775 2.965147 CCATCCTCTTCCTCTTCCTCTC 59.035 54.545 0.00 0.00 0.00 3.20
759 776 2.838637 TCCTCTTCCTCTTCCTCTCC 57.161 55.000 0.00 0.00 0.00 3.71
760 777 2.293246 TCCTCTTCCTCTTCCTCTCCT 58.707 52.381 0.00 0.00 0.00 3.69
793 810 2.483877 CCTCACTAACCACGTACGTACA 59.516 50.000 22.34 5.46 0.00 2.90
794 811 3.482786 CTCACTAACCACGTACGTACAC 58.517 50.000 22.34 2.17 0.00 2.90
796 813 1.250476 CTAACCACGTACGTACACGC 58.750 55.000 22.34 0.00 45.77 5.34
900 917 3.501828 TCGTAGATTGTTGTTGCATTGCT 59.498 39.130 10.49 0.00 0.00 3.91
962 979 0.104120 GGTTGCGGATTAATTGGGCC 59.896 55.000 0.00 0.00 0.00 5.80
1008 1025 4.533919 TGATTTGGACGCCATGAAATTT 57.466 36.364 0.00 0.00 31.53 1.82
1024 1041 4.648762 TGAAATTTGGAAAGTGGCTCAAGA 59.351 37.500 0.00 0.00 0.00 3.02
1194 1211 3.131933 AGGAGGAGTTCTTCATCATCACG 59.868 47.826 0.00 0.00 38.35 4.35
1204 1221 1.762370 TCATCATCACGCACAGGGTAT 59.238 47.619 0.00 0.00 0.00 2.73
1223 1240 2.162319 TGTGTTTGCGCTGATCACTA 57.838 45.000 9.73 2.16 0.00 2.74
1224 1241 2.068519 TGTGTTTGCGCTGATCACTAG 58.931 47.619 9.73 0.00 0.00 2.57
1226 1243 0.375106 GTTTGCGCTGATCACTAGCC 59.625 55.000 9.73 0.32 37.90 3.93
1227 1244 0.036483 TTTGCGCTGATCACTAGCCA 60.036 50.000 9.73 2.48 37.90 4.75
1228 1245 0.460811 TTGCGCTGATCACTAGCCAG 60.461 55.000 9.73 0.00 37.90 4.85
1229 1246 1.142748 GCGCTGATCACTAGCCAGT 59.857 57.895 0.00 0.00 37.90 4.00
1233 1250 1.805871 GCTGATCACTAGCCAGTCAGC 60.806 57.143 18.21 18.21 40.70 4.26
1271 1288 2.328473 CGCTGTGAATTTCTCTGACGA 58.672 47.619 8.87 0.00 0.00 4.20
1274 1291 4.562789 CGCTGTGAATTTCTCTGACGATTA 59.437 41.667 8.87 0.00 0.00 1.75
1275 1292 5.499334 CGCTGTGAATTTCTCTGACGATTAC 60.499 44.000 8.87 0.00 0.00 1.89
1278 1295 6.455647 TGTGAATTTCTCTGACGATTACTGT 58.544 36.000 0.00 0.00 0.00 3.55
1279 1296 6.929049 TGTGAATTTCTCTGACGATTACTGTT 59.071 34.615 0.00 0.00 0.00 3.16
1285 1302 8.433421 TTTCTCTGACGATTACTGTTTTCTTT 57.567 30.769 0.00 0.00 0.00 2.52
1289 1306 6.537301 TCTGACGATTACTGTTTTCTTTGTGT 59.463 34.615 0.00 0.00 0.00 3.72
1832 1854 1.612513 CCCATTCCCCGTCCAATGA 59.387 57.895 0.00 0.00 32.56 2.57
1833 1855 0.185901 CCCATTCCCCGTCCAATGAT 59.814 55.000 0.00 0.00 32.56 2.45
1991 2021 5.824904 AGGTGTGAGCATACAAATTCATC 57.175 39.130 0.00 0.00 31.36 2.92
1994 2024 5.822519 GGTGTGAGCATACAAATTCATCCTA 59.177 40.000 0.00 0.00 31.36 2.94
2072 2125 6.903883 ATTGAGTGCGTCGTAGAAAATTAT 57.096 33.333 0.00 0.00 39.69 1.28
2098 2151 6.121590 TCTAATTCAAACTGCCATGATGCTA 58.878 36.000 0.00 0.00 0.00 3.49
2101 2154 4.439305 TCAAACTGCCATGATGCTAAAC 57.561 40.909 0.00 0.00 0.00 2.01
2117 2170 9.421806 TGATGCTAAACAAAAATTATGGTTCTG 57.578 29.630 0.00 0.00 0.00 3.02
2170 2224 1.779221 CTCTGGCTCCTGATGAGTCT 58.221 55.000 0.00 0.00 46.32 3.24
2190 2244 2.922740 AGAGGTCAAGGCAAAACGTA 57.077 45.000 0.00 0.00 0.00 3.57
2197 2251 3.064271 GTCAAGGCAAAACGTACAACAGA 59.936 43.478 0.00 0.00 0.00 3.41
2218 2272 5.016173 AGAAAATTGATCGTTCCCCAATGA 58.984 37.500 0.00 0.00 31.62 2.57
2225 2279 5.556915 TGATCGTTCCCCAATGATTATACC 58.443 41.667 0.00 0.00 38.22 2.73
2234 2288 6.003950 CCCCAATGATTATACCGTTTCAGAT 58.996 40.000 0.00 0.00 0.00 2.90
2238 2292 9.450807 CCAATGATTATACCGTTTCAGATTTTC 57.549 33.333 0.00 0.00 0.00 2.29
2271 2325 7.165460 TCACGAGTTAATCCATTAGTCTGAA 57.835 36.000 0.00 0.00 0.00 3.02
2347 2401 5.928153 GTTTAGAGAAACAATTCCGTCAGG 58.072 41.667 0.00 0.00 43.80 3.86
2350 2404 2.814336 GAGAAACAATTCCGTCAGGCTT 59.186 45.455 0.00 0.00 36.12 4.35
2420 2475 2.262915 CGAAGCGGCCAGAAGACT 59.737 61.111 2.24 0.00 0.00 3.24
2421 2476 1.511305 CGAAGCGGCCAGAAGACTA 59.489 57.895 2.24 0.00 0.00 2.59
2498 2553 1.742268 GGTTGGAGATTCAGCAGCTTC 59.258 52.381 0.00 0.00 0.00 3.86
2599 2655 4.135306 CCCTCTCATGTTGGAAGATGATG 58.865 47.826 0.10 0.00 37.94 3.07
2610 2666 7.453393 TGTTGGAAGATGATGGGTATATTCTC 58.547 38.462 0.00 0.00 0.00 2.87
2618 2674 1.618837 TGGGTATATTCTCGCTCCAGC 59.381 52.381 0.00 0.00 37.78 4.85
2656 2712 2.108952 AGGTGCAAAGGAAGATGGACTT 59.891 45.455 0.00 0.00 42.03 3.01
2742 2798 1.604278 AGCAAGCCGAGTCTGTTTTTC 59.396 47.619 0.00 0.00 0.00 2.29
2749 2805 3.242944 GCCGAGTCTGTTTTTCTTTTTGC 59.757 43.478 0.00 0.00 0.00 3.68
2764 2820 8.447924 TTTCTTTTTGCATGATGGATGAAAAA 57.552 26.923 0.00 0.00 44.72 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 6.137794 TCGTAAAAATTGCTTGAAACTCCA 57.862 33.333 0.00 0.00 0.00 3.86
76 77 7.458038 TTTCGTAAAAATTGCTTGAAACTCC 57.542 32.000 0.00 0.00 0.00 3.85
77 78 9.914923 AAATTTCGTAAAAATTGCTTGAAACTC 57.085 25.926 0.00 0.00 30.94 3.01
101 102 7.208777 TCAACCTCACGTTTACACTATACAAA 58.791 34.615 0.00 0.00 29.93 2.83
134 135 5.977129 GTGAGTACCCACAAACTTTGATTTG 59.023 40.000 8.55 0.00 43.81 2.32
136 137 5.445964 AGTGAGTACCCACAAACTTTGATT 58.554 37.500 10.39 0.00 39.42 2.57
152 153 3.932710 GGATCATTTCGTGCAAGTGAGTA 59.067 43.478 0.00 0.00 34.45 2.59
158 159 0.248215 GGCGGATCATTTCGTGCAAG 60.248 55.000 0.00 0.00 0.00 4.01
186 187 3.579534 AGGTATCGAGGAGCAACTCTA 57.420 47.619 6.18 0.00 35.33 2.43
241 242 7.255569 TGTGTCTAGACTATAAATTGTCCACG 58.744 38.462 23.01 0.00 33.89 4.94
329 341 4.137116 TGTCCGCATACAAAGAAGCTAT 57.863 40.909 0.00 0.00 0.00 2.97
343 355 0.821301 TTTGACCAGCATTGTCCGCA 60.821 50.000 0.00 0.00 31.60 5.69
388 400 8.006298 AGAATTTGAACCTTGTATTCACACAA 57.994 30.769 0.00 0.00 35.82 3.33
420 432 8.331740 GGAAGATATTATCTCCATGAAATCCCA 58.668 37.037 6.65 0.00 39.08 4.37
608 624 5.350504 TTCTGCTCTGCTCTAGCTTAAAT 57.649 39.130 3.26 0.00 40.73 1.40
751 768 0.836400 AAGCGGTTGGAGGAGAGGAA 60.836 55.000 0.00 0.00 0.00 3.36
752 769 0.040646 TAAGCGGTTGGAGGAGAGGA 59.959 55.000 10.73 0.00 0.00 3.71
753 770 0.175989 GTAAGCGGTTGGAGGAGAGG 59.824 60.000 10.73 0.00 0.00 3.69
754 771 0.175989 GGTAAGCGGTTGGAGGAGAG 59.824 60.000 10.73 0.00 0.00 3.20
755 772 0.252103 AGGTAAGCGGTTGGAGGAGA 60.252 55.000 10.73 0.00 0.00 3.71
756 773 0.175989 GAGGTAAGCGGTTGGAGGAG 59.824 60.000 10.73 0.00 0.00 3.69
757 774 0.543410 TGAGGTAAGCGGTTGGAGGA 60.543 55.000 10.73 0.00 0.00 3.71
758 775 0.391263 GTGAGGTAAGCGGTTGGAGG 60.391 60.000 10.73 0.00 0.00 4.30
759 776 0.608640 AGTGAGGTAAGCGGTTGGAG 59.391 55.000 10.73 0.00 0.00 3.86
760 777 1.927487 TAGTGAGGTAAGCGGTTGGA 58.073 50.000 10.73 0.00 0.00 3.53
962 979 0.526524 GAGATCACCGACTGCCTTCG 60.527 60.000 0.00 0.00 38.80 3.79
1008 1025 0.250901 GCCTCTTGAGCCACTTTCCA 60.251 55.000 0.00 0.00 0.00 3.53
1024 1041 2.795110 GGCTCTGCTCGATCTGCCT 61.795 63.158 9.88 0.00 37.58 4.75
1138 1155 7.670344 AGAAGGCGTTGATCTTCTCGATCTG 62.670 48.000 0.00 0.00 44.30 2.90
1204 1221 2.068519 CTAGTGATCAGCGCAAACACA 58.931 47.619 19.96 7.79 34.47 3.72
1207 1224 0.375106 GGCTAGTGATCAGCGCAAAC 59.625 55.000 11.47 0.00 40.05 2.93
1209 1226 0.460811 CTGGCTAGTGATCAGCGCAA 60.461 55.000 11.47 0.00 40.05 4.85
1223 1240 2.357836 CATTGGGGCTGACTGGCT 59.642 61.111 5.87 0.00 41.48 4.75
1224 1241 2.757099 CCATTGGGGCTGACTGGC 60.757 66.667 0.00 0.00 40.96 4.85
1248 1265 2.071540 TCAGAGAAATTCACAGCGCAG 58.928 47.619 11.47 3.33 0.00 5.18
1252 1269 4.935885 AATCGTCAGAGAAATTCACAGC 57.064 40.909 0.00 0.00 0.00 4.40
1271 1288 7.976826 TCGTACAACACAAAGAAAACAGTAAT 58.023 30.769 0.00 0.00 0.00 1.89
1274 1291 5.672819 GCTCGTACAACACAAAGAAAACAGT 60.673 40.000 0.00 0.00 0.00 3.55
1275 1292 4.728608 GCTCGTACAACACAAAGAAAACAG 59.271 41.667 0.00 0.00 0.00 3.16
1278 1295 4.201871 CCTGCTCGTACAACACAAAGAAAA 60.202 41.667 0.00 0.00 0.00 2.29
1279 1296 3.311322 CCTGCTCGTACAACACAAAGAAA 59.689 43.478 0.00 0.00 0.00 2.52
1285 1302 0.319555 GCTCCTGCTCGTACAACACA 60.320 55.000 0.00 0.00 36.03 3.72
1468 1489 3.254060 GCGCTTGTCATACTTCTTGAGA 58.746 45.455 0.00 0.00 0.00 3.27
1971 2001 5.824904 AGGATGAATTTGTATGCTCACAC 57.175 39.130 0.00 0.00 0.00 3.82
2035 2065 4.337763 GCACTCAATTAGATTTGACGCTG 58.662 43.478 0.00 0.00 32.39 5.18
2049 2079 6.903883 ATAATTTTCTACGACGCACTCAAT 57.096 33.333 0.00 0.00 0.00 2.57
2072 2125 6.774170 AGCATCATGGCAGTTTGAATTAGATA 59.226 34.615 0.00 0.00 35.83 1.98
2133 2186 5.732810 GCCAGAGCTGAAAGAATTGCTAATC 60.733 44.000 0.00 0.00 35.76 1.75
2170 2224 2.922740 ACGTTTTGCCTTGACCTCTA 57.077 45.000 0.00 0.00 0.00 2.43
2190 2244 4.022329 GGGGAACGATCAATTTTCTGTTGT 60.022 41.667 0.00 0.00 0.00 3.32
2197 2251 5.937975 ATCATTGGGGAACGATCAATTTT 57.062 34.783 0.00 0.00 0.00 1.82
2218 2272 7.282450 GGTCTGGAAAATCTGAAACGGTATAAT 59.718 37.037 0.00 0.00 0.00 1.28
2225 2279 4.829064 TTGGTCTGGAAAATCTGAAACG 57.171 40.909 0.00 0.00 0.00 3.60
2234 2288 3.485463 ACTCGTGATTGGTCTGGAAAA 57.515 42.857 0.00 0.00 0.00 2.29
2238 2292 3.871594 GGATTAACTCGTGATTGGTCTGG 59.128 47.826 0.00 0.00 0.00 3.86
2271 2325 4.346127 TCCAGTCACATAGCATTATCAGCT 59.654 41.667 0.00 0.00 45.77 4.24
2414 2469 3.918591 TCGTCGCTTTTGATGTAGTCTTC 59.081 43.478 0.00 0.00 0.00 2.87
2420 2475 6.588756 AGTTTATCTTCGTCGCTTTTGATGTA 59.411 34.615 0.00 0.00 0.00 2.29
2421 2476 5.408604 AGTTTATCTTCGTCGCTTTTGATGT 59.591 36.000 0.00 0.00 0.00 3.06
2498 2553 4.916831 TCGCTGCAACAATTTTATGACAAG 59.083 37.500 0.00 0.00 0.00 3.16
2577 2633 3.920231 TCATCTTCCAACATGAGAGGG 57.080 47.619 0.00 0.00 0.00 4.30
2599 2655 1.618837 TGCTGGAGCGAGAATATACCC 59.381 52.381 0.00 0.00 45.83 3.69
2610 2666 2.990674 CTACCGTCGATGCTGGAGCG 62.991 65.000 0.00 0.00 45.83 5.03
2618 2674 2.547211 CACCTACTACCTACCGTCGATG 59.453 54.545 0.00 0.00 0.00 3.84
2742 2798 7.247728 CCATTTTTCATCCATCATGCAAAAAG 58.752 34.615 0.00 0.00 39.88 2.27
2749 2805 3.134985 TGGCCCATTTTTCATCCATCATG 59.865 43.478 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.