Multiple sequence alignment - TraesCS4B01G297400

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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 TraesCS4B01G297400 chr4B 100.000 3392 0 0 1 3392 582826941 582830332 0.000000e+00 6264
1 TraesCS4B01G297400 chr4D 91.643 3470 157 57 1 3392 465760503 465763917 0.000000e+00 4678
2 TraesCS4B01G297400 chr4A 91.737 2856 104 29 598 3377 4797858 4795059 0.000000e+00 3845
3 TraesCS4B01G297400 chr4A 92.084 619 27 14 1 607 4818463 4817855 0.000000e+00 852
4 TraesCS4B01G297400 chr1D 86.780 295 34 4 90 379 204024353 204024059 1.170000e-84 324
5 TraesCS4B01G297400 chr1A 86.780 295 34 4 90 379 259049710 259049416 1.170000e-84 324
6 TraesCS4B01G297400 chr1B 85.763 295 37 4 90 379 299438317 299438023 1.180000e-79 307


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 TraesCS4B01G297400 chr4B 582826941 582830332 3391 False 6264 6264 100.000 1 3392 1 chr4B.!!$F1 3391
1 TraesCS4B01G297400 chr4D 465760503 465763917 3414 False 4678 4678 91.643 1 3392 1 chr4D.!!$F1 3391
2 TraesCS4B01G297400 chr4A 4795059 4797858 2799 True 3845 3845 91.737 598 3377 1 chr4A.!!$R1 2779
3 TraesCS4B01G297400 chr4A 4817855 4818463 608 True 852 852 92.084 1 607 1 chr4A.!!$R2 606

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
830 851 0.46362 GGGACTGGAGCACTCATCTC 59.536 60.0 0.0 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2495 2581 1.346395 TGAAACCTTCCTGCTCGCTTA 59.654 47.619 0.0 0.0 0.0 3.09 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
73 78 3.034721 TCGTGGGCTAAAGTTGTACTG 57.965 47.619 0.00 0.00 0.00 2.74
74 79 2.629137 TCGTGGGCTAAAGTTGTACTGA 59.371 45.455 0.00 0.00 0.00 3.41
132 139 1.002624 GGGCTCGTGGACCATTTCA 60.003 57.895 0.00 0.00 44.40 2.69
141 148 2.817844 GTGGACCATTTCAGGGTTGTAC 59.182 50.000 0.00 0.00 39.19 2.90
144 151 3.000727 GACCATTTCAGGGTTGTACGAG 58.999 50.000 0.00 0.00 39.19 4.18
168 175 2.515523 GGCGGCTGCATCATGAGT 60.516 61.111 21.31 0.00 45.35 3.41
180 187 1.550327 TCATGAGTTCCACGAGCTCT 58.450 50.000 12.85 0.00 39.92 4.09
420 427 2.278857 CTCGACGGAATGGCGAGG 60.279 66.667 12.16 0.00 45.54 4.63
421 428 3.064987 CTCGACGGAATGGCGAGGT 62.065 63.158 12.16 0.00 45.54 3.85
422 429 2.125673 CGACGGAATGGCGAGGTT 60.126 61.111 0.00 0.00 0.00 3.50
447 458 1.972198 CGTAGGAGTGGGAGTGCAA 59.028 57.895 0.00 0.00 0.00 4.08
523 539 2.436646 CCGCCCGGATATGCCATC 60.437 66.667 0.73 0.00 37.50 3.51
719 739 3.179048 GGCGAATAAGTGTTTCATTGGC 58.821 45.455 0.00 0.00 34.00 4.52
738 758 1.216710 CCGGTCCAGCTGAGTTCTC 59.783 63.158 17.39 0.00 0.00 2.87
803 824 3.071206 TCACTCTCTCGCCCTGGC 61.071 66.667 0.00 0.00 37.85 4.85
804 825 3.073735 CACTCTCTCGCCCTGGCT 61.074 66.667 6.60 0.00 39.32 4.75
805 826 3.073735 ACTCTCTCGCCCTGGCTG 61.074 66.667 6.60 0.24 39.32 4.85
808 829 4.463879 CTCTCGCCCTGGCTGTGG 62.464 72.222 6.60 0.00 39.32 4.17
816 837 3.644606 CTGGCTGTGGCTGGGACT 61.645 66.667 0.00 0.00 38.73 3.85
817 838 3.914579 CTGGCTGTGGCTGGGACTG 62.915 68.421 0.00 0.00 38.73 3.51
818 839 4.729918 GGCTGTGGCTGGGACTGG 62.730 72.222 0.00 0.00 38.73 4.00
819 840 3.640407 GCTGTGGCTGGGACTGGA 61.640 66.667 0.00 0.00 35.22 3.86
820 841 2.667418 CTGTGGCTGGGACTGGAG 59.333 66.667 0.00 0.00 0.00 3.86
821 842 3.618780 CTGTGGCTGGGACTGGAGC 62.619 68.421 0.00 0.00 34.23 4.70
822 843 3.640407 GTGGCTGGGACTGGAGCA 61.640 66.667 0.00 0.00 36.90 4.26
823 844 3.640407 TGGCTGGGACTGGAGCAC 61.640 66.667 0.00 0.00 36.90 4.40
824 845 3.325753 GGCTGGGACTGGAGCACT 61.326 66.667 0.00 0.00 36.90 4.40
825 846 2.267324 GCTGGGACTGGAGCACTC 59.733 66.667 0.00 0.00 35.15 3.51
826 847 2.587247 GCTGGGACTGGAGCACTCA 61.587 63.158 0.00 0.00 35.15 3.41
830 851 0.463620 GGGACTGGAGCACTCATCTC 59.536 60.000 0.00 0.00 0.00 2.75
964 994 5.180271 GGTGACCTCATACCATCGTTTTAA 58.820 41.667 0.00 0.00 36.94 1.52
974 1004 2.277084 CATCGTTTTAACCCTCTCCGG 58.723 52.381 0.00 0.00 0.00 5.14
1155 1185 3.479370 CGGAGCAAGAAGAAGCGG 58.521 61.111 0.00 0.00 35.48 5.52
1311 1341 2.671619 GCCAAGCCGCACAAGGTA 60.672 61.111 0.00 0.00 0.00 3.08
1356 1386 2.995872 GCTCTTCGAGGTCTGCCGT 61.996 63.158 0.00 0.00 40.50 5.68
1561 1591 0.846015 TCCTCATGATTTCCGGGCAT 59.154 50.000 0.00 0.00 0.00 4.40
1614 1644 0.473694 TGGTCACACTGGAGGATGGT 60.474 55.000 0.00 0.00 0.00 3.55
1706 1736 1.319614 GCCGGTAACACCAATGCCAT 61.320 55.000 1.90 0.00 38.47 4.40
1884 1914 1.600413 GCAGAGGCAAAAGGTTTGACG 60.600 52.381 4.93 0.00 40.72 4.35
1929 1959 3.197790 GCAGTCGCGGTGATGCAT 61.198 61.111 6.13 0.00 38.54 3.96
1946 1976 4.684484 TGCATGAGATACTGAGCTTCAT 57.316 40.909 0.00 0.00 0.00 2.57
1947 1977 4.377897 TGCATGAGATACTGAGCTTCATG 58.622 43.478 15.04 15.04 33.48 3.07
2154 2184 3.174779 GGTAAGGTGGAGAGAGAAGGTT 58.825 50.000 0.00 0.00 0.00 3.50
2227 2257 1.889170 AGTCGTCTGATTCTGAGCACA 59.111 47.619 0.00 0.00 0.00 4.57
2228 2258 2.495270 AGTCGTCTGATTCTGAGCACAT 59.505 45.455 0.00 0.00 0.00 3.21
2237 2267 4.514816 TGATTCTGAGCACATTTTGTTCGA 59.485 37.500 0.00 0.00 38.26 3.71
2260 2290 2.340337 CGAGCTCATCAACATGTGACA 58.660 47.619 15.40 0.00 39.72 3.58
2370 2430 4.202336 ACAGATGATGGTGAGATGGATGAC 60.202 45.833 0.00 0.00 0.00 3.06
2377 2437 1.070445 GAGATGGATGACGCTGGGG 59.930 63.158 0.00 0.00 0.00 4.96
2424 2484 4.943705 TGTTGAGATGGTTTTAGGAGATGC 59.056 41.667 0.00 0.00 0.00 3.91
2495 2581 8.571336 GCCTAACATAATGAACATTAAGCTCAT 58.429 33.333 10.58 0.00 36.90 2.90
2520 2606 3.535561 CGAGCAGGAAGGTTTCATATGT 58.464 45.455 1.90 0.00 0.00 2.29
2534 2620 6.151144 GGTTTCATATGTGAGCTTGTTTAGGT 59.849 38.462 1.90 0.00 35.39 3.08
2535 2621 7.309194 GGTTTCATATGTGAGCTTGTTTAGGTT 60.309 37.037 1.90 0.00 35.39 3.50
2538 2624 7.816640 TCATATGTGAGCTTGTTTAGGTTTTC 58.183 34.615 1.90 0.00 33.94 2.29
2625 2712 3.321968 ACGCTGCAGGATCTCATAACATA 59.678 43.478 17.12 0.00 0.00 2.29
2640 2727 5.309543 TCATAACATATACCCCCTGTCTTGG 59.690 44.000 0.00 0.00 0.00 3.61
2641 2728 3.431411 ACATATACCCCCTGTCTTGGA 57.569 47.619 0.00 0.00 0.00 3.53
2642 2729 3.954662 ACATATACCCCCTGTCTTGGAT 58.045 45.455 0.00 0.00 0.00 3.41
2701 2788 1.982958 AGGTGGACTTTGAATACCGGT 59.017 47.619 13.98 13.98 36.55 5.28
2772 2859 1.459450 GCCTTGCTTTCCACCGATAA 58.541 50.000 0.00 0.00 0.00 1.75
2780 2867 3.684413 GCTTTCCACCGATAAATCCCTCA 60.684 47.826 0.00 0.00 0.00 3.86
2853 2940 6.663734 AGACTTCAAGTAATTCTATTGGGGG 58.336 40.000 0.00 0.00 0.00 5.40
2867 2954 6.714278 TCTATTGGGGGTTACTCTTTACAAC 58.286 40.000 0.00 0.00 0.00 3.32
3070 3163 5.382618 AATTTGATCTCAACCAGACTTGC 57.617 39.130 0.00 0.00 35.28 4.01
3088 3181 3.241067 TGCCATAACAGACGTAAGGTC 57.759 47.619 0.00 0.00 46.45 3.85
3098 3191 3.027974 GACGTAAGGTCAGCCATATCC 57.972 52.381 0.00 0.00 45.36 2.59
3123 3216 1.135286 GCTGTAAAACTGCCTGCATCC 60.135 52.381 0.00 0.00 37.12 3.51
3141 3234 3.179443 TCCAGTGATAATTCCGTGCTC 57.821 47.619 0.00 0.00 0.00 4.26
3196 3289 5.290643 GCAGACACTAATGCTAAGTCTTCAG 59.709 44.000 0.00 0.00 37.45 3.02
3198 3291 6.529829 CAGACACTAATGCTAAGTCTTCAGTC 59.470 42.308 0.00 0.00 37.45 3.51
3242 3335 7.972832 TTCTACATTTCAACTTTATCCACGT 57.027 32.000 0.00 0.00 0.00 4.49
3350 3444 3.492137 CGTTGTGCCCTTATACCTCCTAC 60.492 52.174 0.00 0.00 0.00 3.18
3354 3448 4.347000 TGTGCCCTTATACCTCCTACAATC 59.653 45.833 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.403814 TGTTGGCGTCAAATGGGAAA 58.596 45.000 2.85 0.00 34.28 3.13
55 56 5.761165 TTTTCAGTACAACTTTAGCCCAC 57.239 39.130 0.00 0.00 0.00 4.61
132 139 1.590147 CTTCCGCTCGTACAACCCT 59.410 57.895 0.00 0.00 0.00 4.34
168 175 1.176619 TCACCGAAGAGCTCGTGGAA 61.177 55.000 23.22 11.39 46.65 3.53
419 426 0.391263 CACTCCTACGCTTCCCAACC 60.391 60.000 0.00 0.00 0.00 3.77
420 427 0.391263 CCACTCCTACGCTTCCCAAC 60.391 60.000 0.00 0.00 0.00 3.77
421 428 1.550130 CCCACTCCTACGCTTCCCAA 61.550 60.000 0.00 0.00 0.00 4.12
422 429 1.987855 CCCACTCCTACGCTTCCCA 60.988 63.158 0.00 0.00 0.00 4.37
447 458 0.977395 CACTCCCTTCCTTCGTCCTT 59.023 55.000 0.00 0.00 0.00 3.36
719 739 2.232298 GAGAACTCAGCTGGACCGGG 62.232 65.000 15.13 0.00 0.00 5.73
803 824 2.667418 CTCCAGTCCCAGCCACAG 59.333 66.667 0.00 0.00 0.00 3.66
804 825 3.640407 GCTCCAGTCCCAGCCACA 61.640 66.667 0.00 0.00 0.00 4.17
805 826 3.640407 TGCTCCAGTCCCAGCCAC 61.640 66.667 0.00 0.00 34.47 5.01
808 829 1.908340 ATGAGTGCTCCAGTCCCAGC 61.908 60.000 0.00 0.00 33.27 4.85
810 831 0.252421 AGATGAGTGCTCCAGTCCCA 60.252 55.000 0.00 0.00 33.27 4.37
811 832 0.463620 GAGATGAGTGCTCCAGTCCC 59.536 60.000 0.00 0.00 33.27 4.46
817 838 2.279120 CGCGGAGATGAGTGCTCC 60.279 66.667 0.00 0.00 46.74 4.70
818 839 2.279120 CCGCGGAGATGAGTGCTC 60.279 66.667 24.07 0.00 0.00 4.26
819 840 4.521062 GCCGCGGAGATGAGTGCT 62.521 66.667 33.48 0.00 0.00 4.40
946 976 4.777463 AGGGTTAAAACGATGGTATGAGG 58.223 43.478 0.00 0.00 0.00 3.86
974 1004 2.322830 GGTGCCGACGGAAAAGACC 61.323 63.158 20.50 10.60 0.00 3.85
1009 1039 2.719774 GGCATTTGCGCGAACAAGC 61.720 57.895 13.41 16.39 43.26 4.01
1011 1041 1.371512 CAGGCATTTGCGCGAACAA 60.372 52.632 13.41 1.72 43.26 2.83
1561 1591 1.454847 GGAACAAGTGCACCCACCA 60.455 57.895 14.63 0.00 43.09 4.17
1614 1644 3.391296 AGGAAACAAGCTCCAAGTAGTCA 59.609 43.478 0.00 0.00 35.20 3.41
1706 1736 3.585289 TCCTGGTGTACTAGCATTGGAAA 59.415 43.478 0.00 0.00 35.99 3.13
1884 1914 2.941720 GTCAAACTCATGAGATCCAGGC 59.058 50.000 29.27 11.25 0.00 4.85
1929 1959 4.467438 TCCAACATGAAGCTCAGTATCTCA 59.533 41.667 0.00 0.00 0.00 3.27
1946 1976 2.024176 TACCAGCCTCTTCTCCAACA 57.976 50.000 0.00 0.00 0.00 3.33
1947 1977 2.303311 AGTTACCAGCCTCTTCTCCAAC 59.697 50.000 0.00 0.00 0.00 3.77
2049 2079 2.461300 TCCCCCTCTCAGACACATAG 57.539 55.000 0.00 0.00 0.00 2.23
2131 2161 2.763448 CCTTCTCTCTCCACCTTACCAG 59.237 54.545 0.00 0.00 0.00 4.00
2154 2184 4.458295 CCTCTGTAACCAGTAAGTCGAAGA 59.542 45.833 0.00 0.00 39.82 2.87
2227 2257 2.076100 TGAGCTCGCATCGAACAAAAT 58.924 42.857 9.64 0.00 34.74 1.82
2228 2258 1.507562 TGAGCTCGCATCGAACAAAA 58.492 45.000 9.64 0.00 34.74 2.44
2237 2267 1.669265 CACATGTTGATGAGCTCGCAT 59.331 47.619 9.64 0.00 33.36 4.73
2260 2290 1.545841 TCGTCATCACTGCTACCACT 58.454 50.000 0.00 0.00 0.00 4.00
2424 2484 5.173664 TCACTGACTCTGCATAATCACTTG 58.826 41.667 0.00 0.00 0.00 3.16
2495 2581 1.346395 TGAAACCTTCCTGCTCGCTTA 59.654 47.619 0.00 0.00 0.00 3.09
2520 2606 4.340950 CCAAGGAAAACCTAAACAAGCTCA 59.659 41.667 0.00 0.00 0.00 4.26
2534 2620 4.151121 TCATCAACATCAGCCAAGGAAAA 58.849 39.130 0.00 0.00 0.00 2.29
2535 2621 3.765381 TCATCAACATCAGCCAAGGAAA 58.235 40.909 0.00 0.00 0.00 3.13
2538 2624 5.301045 ACAATATCATCAACATCAGCCAAGG 59.699 40.000 0.00 0.00 0.00 3.61
2625 2712 2.509964 GTTGATCCAAGACAGGGGGTAT 59.490 50.000 0.00 0.00 0.00 2.73
2640 2727 2.372264 ACAGCATCACCATGGTTGATC 58.628 47.619 16.84 14.08 38.76 2.92
2641 2728 2.494471 CAACAGCATCACCATGGTTGAT 59.506 45.455 16.84 17.96 38.76 2.57
2642 2729 1.887854 CAACAGCATCACCATGGTTGA 59.112 47.619 16.84 16.44 38.76 3.18
2701 2788 4.216708 TCAATGCCAATCATCCATGCTTA 58.783 39.130 0.00 0.00 33.40 3.09
2772 2859 2.357569 GCAGGACTGGAATTGAGGGATT 60.358 50.000 1.01 0.00 0.00 3.01
2780 2867 1.668826 TGGTAGGCAGGACTGGAATT 58.331 50.000 1.01 0.00 0.00 2.17
2853 2940 2.156310 CACCGGCGTTGTAAAGAGTAAC 59.844 50.000 6.01 0.00 0.00 2.50
2922 3015 9.040939 CCAAATACGTCAATACTGATACATGAA 57.959 33.333 0.00 0.00 33.05 2.57
3070 3163 3.187700 GCTGACCTTACGTCTGTTATGG 58.812 50.000 0.00 0.00 42.49 2.74
3098 3191 3.191162 TGCAGGCAGTTTTACAGCAATAG 59.809 43.478 0.00 0.00 31.72 1.73
3123 3216 5.755375 ACTAATGAGCACGGAATTATCACTG 59.245 40.000 0.00 0.00 0.00 3.66
3196 3289 8.950403 AGAAAAATAAGAAATACAAGTGCGAC 57.050 30.769 0.00 0.00 0.00 5.19
3198 3291 9.820229 TGTAGAAAAATAAGAAATACAAGTGCG 57.180 29.630 0.00 0.00 0.00 5.34
3350 3444 4.019174 ACAAATGCCCCTTCTGTAGATTG 58.981 43.478 0.00 0.00 0.00 2.67
3354 3448 5.418840 ACATTAACAAATGCCCCTTCTGTAG 59.581 40.000 0.00 0.00 33.57 2.74


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

AutoCloner maintained by Alex Coulton.