Multiple sequence alignment - TraesCS5A01G401200

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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 TraesCS5A01G401200 chr5A 100.000 2993 0 0 1 2993 594082956 594079964 0.000000e+00 5528
1 TraesCS5A01G401200 chr5B 89.914 3034 134 69 27 2993 581831027 581828099 0.000000e+00 3749
2 TraesCS5A01G401200 chr5D 91.507 1825 56 37 596 2353 474815182 474813390 0.000000e+00 2420
3 TraesCS5A01G401200 chr5D 90.112 627 30 18 1 611 474815808 474815198 0.000000e+00 785
4 TraesCS5A01G401200 chr5D 90.702 484 17 12 2515 2993 474813145 474812685 1.180000e-173 619


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 TraesCS5A01G401200 chr5A 594079964 594082956 2992 True 5528.000000 5528 100.000000 1 2993 1 chr5A.!!$R1 2992
1 TraesCS5A01G401200 chr5B 581828099 581831027 2928 True 3749.000000 3749 89.914000 27 2993 1 chr5B.!!$R1 2966
2 TraesCS5A01G401200 chr5D 474812685 474815808 3123 True 1274.666667 2420 90.773667 1 2993 3 chr5D.!!$R1 2992

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
554 574 0.442699 GAACGAACCGTCCAATGAGC 59.557 55.0 0.0 0.0 39.99 4.26 F
779 839 0.459237 CCTCACTAGCTCCACTTGCG 60.459 60.0 0.0 0.0 35.28 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1802 1.078143 GATGGAGCACCTGTGGACC 60.078 63.158 0.71 0.0 37.04 4.46 R
2619 2873 0.243907 TGAGTACACTTCTCCGCTGC 59.756 55.000 0.00 0.0 0.00 5.25 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
25 26 0.747283 CCTGCTGCAGAAGATCCACC 60.747 60.000 30.10 0.00 32.44 4.61
29 30 2.011046 GCTGCAGAAGATCCACCACTC 61.011 57.143 20.43 0.00 0.00 3.51
33 34 1.277273 CAGAAGATCCACCACTCTGCA 59.723 52.381 0.00 0.00 0.00 4.41
35 36 0.617413 AAGATCCACCACTCTGCAGG 59.383 55.000 15.13 7.28 0.00 4.85
65 67 2.504244 CGACGGACGGAAGCTCAC 60.504 66.667 0.00 0.00 38.46 3.51
136 138 1.827399 ATCTTCCAAGCACGTCCGGT 61.827 55.000 0.00 0.00 0.00 5.28
138 140 1.005867 TTCCAAGCACGTCCGGTAC 60.006 57.895 0.00 0.00 0.00 3.34
233 235 0.739112 CCTCCAGAAGAAGCACGAGC 60.739 60.000 0.00 0.00 42.56 5.03
286 288 1.208259 CCAAACGCTGGCTTTGTTTC 58.792 50.000 12.59 0.00 38.76 2.78
309 317 1.228956 ACCACTACCGTAGCCACCA 60.229 57.895 5.42 0.00 0.00 4.17
312 320 1.986210 ACTACCGTAGCCACCACCC 60.986 63.158 5.42 0.00 0.00 4.61
313 321 2.684655 TACCGTAGCCACCACCCC 60.685 66.667 0.00 0.00 0.00 4.95
316 324 3.782443 CGTAGCCACCACCCCCTC 61.782 72.222 0.00 0.00 0.00 4.30
317 325 2.609610 GTAGCCACCACCCCCTCA 60.610 66.667 0.00 0.00 0.00 3.86
318 326 2.001269 GTAGCCACCACCCCCTCAT 61.001 63.158 0.00 0.00 0.00 2.90
342 350 3.017265 GACCCACTGTCATTTTGCTTG 57.983 47.619 0.00 0.00 43.85 4.01
344 352 1.068895 CCCACTGTCATTTTGCTTGCA 59.931 47.619 0.00 0.00 0.00 4.08
345 353 2.129607 CCACTGTCATTTTGCTTGCAC 58.870 47.619 0.00 0.00 0.00 4.57
346 354 2.223876 CCACTGTCATTTTGCTTGCACT 60.224 45.455 0.00 0.00 0.00 4.40
347 355 3.047796 CACTGTCATTTTGCTTGCACTC 58.952 45.455 0.00 0.00 0.00 3.51
348 356 2.954318 ACTGTCATTTTGCTTGCACTCT 59.046 40.909 0.00 0.00 0.00 3.24
349 357 4.023792 CACTGTCATTTTGCTTGCACTCTA 60.024 41.667 0.00 0.00 0.00 2.43
350 358 4.023707 ACTGTCATTTTGCTTGCACTCTAC 60.024 41.667 0.00 0.00 0.00 2.59
526 545 6.417327 GCACTACGTATATATAGCGTCGAAT 58.583 40.000 17.68 0.00 39.64 3.34
527 546 6.904011 GCACTACGTATATATAGCGTCGAATT 59.096 38.462 17.68 0.00 39.64 2.17
554 574 0.442699 GAACGAACCGTCCAATGAGC 59.557 55.000 0.00 0.00 39.99 4.26
603 623 3.000724 GCAGCTCGAGCAGTAAACTAATG 59.999 47.826 36.87 22.84 45.16 1.90
668 724 3.257561 CGGCGACCGCTTCTCATG 61.258 66.667 14.25 0.00 41.17 3.07
669 725 3.567797 GGCGACCGCTTCTCATGC 61.568 66.667 14.25 0.00 41.60 4.06
670 726 2.815211 GCGACCGCTTCTCATGCA 60.815 61.111 7.19 0.00 38.26 3.96
758 818 4.866224 CCACCACACACACCCGCA 62.866 66.667 0.00 0.00 0.00 5.69
759 819 2.826287 CACCACACACACCCGCAA 60.826 61.111 0.00 0.00 0.00 4.85
760 820 2.826738 ACCACACACACCCGCAAC 60.827 61.111 0.00 0.00 0.00 4.17
779 839 0.459237 CCTCACTAGCTCCACTTGCG 60.459 60.000 0.00 0.00 35.28 4.85
786 846 3.429141 CTCCACTTGCGCTGCCTG 61.429 66.667 9.73 0.00 0.00 4.85
877 952 1.772156 TCCACCACCCACCACATCA 60.772 57.895 0.00 0.00 0.00 3.07
1065 1162 1.441732 GCCCCCACCGCTTTATAACG 61.442 60.000 0.00 0.00 0.00 3.18
1158 1265 3.730761 CTCAGCCACCGCACAAGC 61.731 66.667 0.00 0.00 37.52 4.01
1159 1266 4.560743 TCAGCCACCGCACAAGCA 62.561 61.111 0.00 0.00 42.27 3.91
1160 1267 3.594775 CAGCCACCGCACAAGCAA 61.595 61.111 0.00 0.00 42.27 3.91
1254 1376 2.108566 CTGATCCCGGAGCAGCAG 59.891 66.667 19.43 7.27 39.19 4.24
1453 1575 4.421479 CGCAGCCGGAGTCGTTCT 62.421 66.667 5.05 0.00 33.95 3.01
1488 1610 1.284982 CCGAGTTCAAGTGCTCCGTG 61.285 60.000 0.00 0.00 0.00 4.94
1938 2063 0.460987 GCAAGATGTGGGAGGACGAG 60.461 60.000 0.00 0.00 0.00 4.18
1974 2099 1.746991 CCTCGCCTTCAAGAAGCCC 60.747 63.158 4.30 0.00 37.11 5.19
1996 2121 1.220206 CTTCTCACCGCCTGAGCAT 59.780 57.895 3.94 0.00 45.64 3.79
1999 2124 0.395724 TCTCACCGCCTGAGCATCTA 60.396 55.000 3.94 0.00 45.64 1.98
2026 2151 1.735386 CTGCATGGATCCCATCGATC 58.265 55.000 9.90 0.00 43.15 3.69
2071 2201 2.878406 AGTCCAGTGGTGAAATTCGTTG 59.122 45.455 9.54 0.00 0.00 4.10
2124 2254 4.517952 ACAGATTGAGTGAGTGAGTGAG 57.482 45.455 0.00 0.00 0.00 3.51
2125 2255 3.894427 ACAGATTGAGTGAGTGAGTGAGT 59.106 43.478 0.00 0.00 0.00 3.41
2126 2256 5.073428 ACAGATTGAGTGAGTGAGTGAGTA 58.927 41.667 0.00 0.00 0.00 2.59
2127 2257 5.536538 ACAGATTGAGTGAGTGAGTGAGTAA 59.463 40.000 0.00 0.00 0.00 2.24
2128 2258 6.210385 ACAGATTGAGTGAGTGAGTGAGTAAT 59.790 38.462 0.00 0.00 0.00 1.89
2129 2259 7.394641 ACAGATTGAGTGAGTGAGTGAGTAATA 59.605 37.037 0.00 0.00 0.00 0.98
2130 2260 7.700234 CAGATTGAGTGAGTGAGTGAGTAATAC 59.300 40.741 0.00 0.00 0.00 1.89
2365 2517 6.897259 ATTGGAATTGATGAAAATTCTGCG 57.103 33.333 8.96 0.00 43.25 5.18
2417 2569 5.401550 TCGATGAAACTTCAAATGATTGGC 58.598 37.500 0.00 0.00 41.13 4.52
2454 2606 3.472283 TTCCCTTTGCGTACACTGTAA 57.528 42.857 0.00 0.00 0.00 2.41
2471 2724 6.821665 ACACTGTAATAACTTGTATTCGCCAT 59.178 34.615 0.00 0.00 0.00 4.40
2543 2797 6.136541 ACTGTAACTTGCAAGAAGGAAAAG 57.863 37.500 32.50 19.50 0.00 2.27
2553 2807 4.134563 CAAGAAGGAAAAGGAGACGGAAA 58.865 43.478 0.00 0.00 0.00 3.13
2559 2813 3.260128 GGAAAAGGAGACGGAAACCTCTA 59.740 47.826 0.00 0.00 33.16 2.43
2614 2868 2.558378 TGATCAGTTCATAGCAGCAGC 58.442 47.619 0.00 0.00 42.56 5.25
2615 2869 2.093341 TGATCAGTTCATAGCAGCAGCA 60.093 45.455 3.17 0.00 45.49 4.41
2616 2870 2.019948 TCAGTTCATAGCAGCAGCAG 57.980 50.000 3.17 0.00 45.49 4.24
2617 2871 1.015109 CAGTTCATAGCAGCAGCAGG 58.985 55.000 3.17 0.00 45.49 4.85
2618 2872 0.907486 AGTTCATAGCAGCAGCAGGA 59.093 50.000 3.17 0.00 45.49 3.86
2619 2873 1.134461 AGTTCATAGCAGCAGCAGGAG 60.134 52.381 3.17 0.00 45.49 3.69
2620 2874 0.463295 TTCATAGCAGCAGCAGGAGC 60.463 55.000 3.17 0.00 45.49 4.70
2648 2902 1.329256 AGTGTACTCAACCTCGCACT 58.671 50.000 0.00 0.00 33.05 4.40
2657 2911 2.105128 CCTCGCACTGACCGATCC 59.895 66.667 0.00 0.00 33.83 3.36
2659 2913 1.439228 CTCGCACTGACCGATCCAT 59.561 57.895 0.00 0.00 33.83 3.41
2712 2967 0.917259 GCGTGACGTGATTAGCTCTG 59.083 55.000 6.91 0.00 0.00 3.35
2763 3018 0.251386 TGTTTAGCCGGGGAATTGCA 60.251 50.000 2.18 0.00 0.00 4.08
2780 3035 1.712081 CAGCGTGACATGTGCTAGC 59.288 57.895 8.10 8.10 37.15 3.42
2781 3036 0.738762 CAGCGTGACATGTGCTAGCT 60.739 55.000 17.23 5.96 37.15 3.32
2782 3037 0.817654 AGCGTGACATGTGCTAGCTA 59.182 50.000 17.23 5.45 37.15 3.32
2783 3038 1.202348 AGCGTGACATGTGCTAGCTAG 60.202 52.381 16.84 16.84 37.15 3.42
2807 3062 3.537580 AGCTAGAAGGAGACTACGACTG 58.462 50.000 0.00 0.00 42.68 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.673665 GAGTTGGCCCTGCAGAGTG 60.674 63.158 17.39 4.27 0.00 3.51
29 30 2.435586 CTCGAGTTGGCCCTGCAG 60.436 66.667 6.78 6.78 0.00 4.41
51 53 2.125912 CCTGTGAGCTTCCGTCCG 60.126 66.667 0.00 0.00 0.00 4.79
136 138 2.918802 AGACCACGCAACCGGGTA 60.919 61.111 6.32 0.00 37.88 3.69
138 140 4.308458 TCAGACCACGCAACCGGG 62.308 66.667 6.32 0.00 39.22 5.73
163 165 0.672711 GACCCGGTAACAAGTCAGCC 60.673 60.000 0.00 0.00 37.99 4.85
286 288 1.153628 GCTACGGTAGTGGTGCTGG 60.154 63.158 16.05 0.00 0.00 4.85
309 317 0.114364 GTGGGTCAAAATGAGGGGGT 59.886 55.000 0.00 0.00 0.00 4.95
312 320 2.162681 GACAGTGGGTCAAAATGAGGG 58.837 52.381 0.00 0.00 46.19 4.30
340 348 1.278127 GTTAGGGCCAGTAGAGTGCAA 59.722 52.381 6.18 0.00 0.00 4.08
342 350 0.902531 TGTTAGGGCCAGTAGAGTGC 59.097 55.000 6.18 0.00 0.00 4.40
344 352 3.450904 TGATTGTTAGGGCCAGTAGAGT 58.549 45.455 6.18 0.00 0.00 3.24
345 353 4.487714 TTGATTGTTAGGGCCAGTAGAG 57.512 45.455 6.18 0.00 0.00 2.43
346 354 4.566907 GGTTTGATTGTTAGGGCCAGTAGA 60.567 45.833 6.18 0.00 0.00 2.59
347 355 3.694566 GGTTTGATTGTTAGGGCCAGTAG 59.305 47.826 6.18 0.00 0.00 2.57
348 356 3.692690 GGTTTGATTGTTAGGGCCAGTA 58.307 45.455 6.18 0.00 0.00 2.74
349 357 2.525368 GGTTTGATTGTTAGGGCCAGT 58.475 47.619 6.18 0.00 0.00 4.00
350 358 1.472480 CGGTTTGATTGTTAGGGCCAG 59.528 52.381 6.18 0.00 0.00 4.85
394 405 1.702401 TGAAACATCTAGGGTGGTGCA 59.298 47.619 0.00 0.00 0.00 4.57
395 406 2.084546 GTGAAACATCTAGGGTGGTGC 58.915 52.381 0.00 0.00 36.32 5.01
396 407 2.028476 TCGTGAAACATCTAGGGTGGTG 60.028 50.000 0.00 0.00 35.74 4.17
397 408 2.253610 TCGTGAAACATCTAGGGTGGT 58.746 47.619 0.00 0.00 35.74 4.16
500 519 3.933031 ACGCTATATATACGTAGTGCGC 58.067 45.455 17.00 0.00 45.73 6.09
526 545 3.881688 TGGACGGTTCGTTCCAAAATAAA 59.118 39.130 8.39 0.00 41.37 1.40
527 546 3.474600 TGGACGGTTCGTTCCAAAATAA 58.525 40.909 8.39 0.00 41.37 1.40
554 574 0.719465 GTGCGTATTTGACCCTCACG 59.281 55.000 0.00 0.00 35.78 4.35
603 623 2.472934 CGCTAACGCCGTTTCCAC 59.527 61.111 8.19 0.00 0.00 4.02
664 720 2.261361 CGGACCGACTGTGCATGA 59.739 61.111 8.64 0.00 34.43 3.07
666 722 4.002506 TGCGGACCGACTGTGCAT 62.003 61.111 20.50 0.00 34.43 3.96
667 723 4.961511 GTGCGGACCGACTGTGCA 62.962 66.667 20.50 0.92 34.43 4.57
668 724 4.664677 AGTGCGGACCGACTGTGC 62.665 66.667 20.50 0.00 0.00 4.57
669 725 2.734723 CAGTGCGGACCGACTGTG 60.735 66.667 25.66 12.59 33.71 3.66
670 726 2.910479 TCAGTGCGGACCGACTGT 60.910 61.111 29.24 8.82 36.84 3.55
757 817 2.693069 CAAGTGGAGCTAGTGAGGTTG 58.307 52.381 0.00 0.00 32.11 3.77
758 818 1.002544 GCAAGTGGAGCTAGTGAGGTT 59.997 52.381 0.00 0.00 32.11 3.50
759 819 0.610687 GCAAGTGGAGCTAGTGAGGT 59.389 55.000 0.00 0.00 35.63 3.85
760 820 0.459237 CGCAAGTGGAGCTAGTGAGG 60.459 60.000 0.00 0.00 0.00 3.86
779 839 4.736896 GCAAGCAAGGCAGGCAGC 62.737 66.667 0.00 0.00 44.65 5.25
877 952 0.923358 TGTGGGTCACTTGGGTTCTT 59.077 50.000 0.00 0.00 35.11 2.52
976 1069 3.838795 GTGGTCGATCGTGCGCAC 61.839 66.667 30.42 30.42 0.00 5.34
1065 1162 1.594310 GGAGTGGTGGAGTGAGAGC 59.406 63.158 0.00 0.00 0.00 4.09
1332 1454 2.262774 ATCGCTTCCTCTTGGCCCAG 62.263 60.000 0.00 0.00 0.00 4.45
1488 1610 2.970974 GCTGAAGGACTTGCCGCAC 61.971 63.158 0.00 0.00 43.43 5.34
1680 1802 1.078143 GATGGAGCACCTGTGGACC 60.078 63.158 0.71 0.00 37.04 4.46
1938 2063 3.791586 GGGCTCTGCACCTCCTCC 61.792 72.222 0.00 0.00 0.00 4.30
2026 2151 2.965147 ACTGGACCAAAAACTTGGATGG 59.035 45.455 10.80 0.00 44.82 3.51
2027 2152 3.005791 GGACTGGACCAAAAACTTGGATG 59.994 47.826 10.80 1.12 44.82 3.51
2028 2153 3.230976 GGACTGGACCAAAAACTTGGAT 58.769 45.455 10.80 0.00 44.82 3.41
2071 2201 7.169140 AGCAGAACAAATTTAACCAAACGAATC 59.831 33.333 0.00 0.00 0.00 2.52
2125 2255 9.458727 GGCTACTGGAGTATGTATGTAGTATTA 57.541 37.037 0.00 0.00 32.50 0.98
2126 2256 7.948447 TGGCTACTGGAGTATGTATGTAGTATT 59.052 37.037 0.00 0.00 32.50 1.89
2127 2257 7.467650 TGGCTACTGGAGTATGTATGTAGTAT 58.532 38.462 0.00 0.00 32.50 2.12
2128 2258 6.844829 TGGCTACTGGAGTATGTATGTAGTA 58.155 40.000 0.00 0.00 32.50 1.82
2129 2259 5.702266 TGGCTACTGGAGTATGTATGTAGT 58.298 41.667 0.00 0.00 32.50 2.73
2130 2260 6.842437 ATGGCTACTGGAGTATGTATGTAG 57.158 41.667 0.00 0.00 0.00 2.74
2355 2507 7.656707 ATTGATAAAACAAGCGCAGAATTTT 57.343 28.000 11.47 12.93 33.22 1.82
2365 2517 8.424731 CACCGAAGTTAAATTGATAAAACAAGC 58.575 33.333 0.00 0.00 33.22 4.01
2417 2569 2.618053 GGAATACACGTGGGAGAACTG 58.382 52.381 21.57 0.00 0.00 3.16
2454 2606 5.680619 TCCTTCATGGCGAATACAAGTTAT 58.319 37.500 0.00 0.00 35.26 1.89
2471 2724 2.054799 AGTTACAGCAGGGTTCCTTCA 58.945 47.619 0.00 0.00 0.00 3.02
2543 2797 2.824341 TGAAGTAGAGGTTTCCGTCTCC 59.176 50.000 0.00 0.00 37.10 3.71
2594 2848 2.093341 TGCTGCTGCTATGAACTGATCA 60.093 45.455 17.00 0.00 40.46 2.92
2595 2849 2.544686 CTGCTGCTGCTATGAACTGATC 59.455 50.000 17.00 0.00 40.48 2.92
2596 2850 2.562635 CTGCTGCTGCTATGAACTGAT 58.437 47.619 17.00 0.00 40.48 2.90
2614 2868 1.447489 CACTTCTCCGCTGCTCCTG 60.447 63.158 0.00 0.00 0.00 3.86
2615 2869 0.612174 TACACTTCTCCGCTGCTCCT 60.612 55.000 0.00 0.00 0.00 3.69
2616 2870 0.458716 GTACACTTCTCCGCTGCTCC 60.459 60.000 0.00 0.00 0.00 4.70
2617 2871 0.528470 AGTACACTTCTCCGCTGCTC 59.472 55.000 0.00 0.00 0.00 4.26
2618 2872 0.528470 GAGTACACTTCTCCGCTGCT 59.472 55.000 0.00 0.00 0.00 4.24
2619 2873 0.243907 TGAGTACACTTCTCCGCTGC 59.756 55.000 0.00 0.00 0.00 5.25
2620 2874 2.329379 GTTGAGTACACTTCTCCGCTG 58.671 52.381 0.00 0.00 0.00 5.18
2657 2911 2.969238 CTTGCTAGGCGGCCGATG 60.969 66.667 33.48 15.87 0.00 3.84
2659 2913 4.143333 GTCTTGCTAGGCGGCCGA 62.143 66.667 33.48 7.20 0.00 5.54
2712 2967 5.468746 TGGAATCGGATTTGATTATTCGTCC 59.531 40.000 4.47 0.00 38.65 4.79
2763 3018 0.817654 TAGCTAGCACATGTCACGCT 59.182 50.000 18.83 13.11 39.80 5.07
2780 3035 4.927425 CGTAGTCTCCTTCTAGCTAGCTAG 59.073 50.000 36.20 36.20 45.38 3.42
2781 3036 4.588106 TCGTAGTCTCCTTCTAGCTAGCTA 59.412 45.833 22.85 22.85 0.00 3.32
2782 3037 3.388676 TCGTAGTCTCCTTCTAGCTAGCT 59.611 47.826 23.12 23.12 0.00 3.32
2783 3038 3.495753 GTCGTAGTCTCCTTCTAGCTAGC 59.504 52.174 16.35 6.62 0.00 3.42
2807 3062 2.033194 GCCAGCGGTGTCTTGTACC 61.033 63.158 14.40 0.00 34.81 3.34
2891 3149 2.736531 GCAAGTTGGGCTGGGTTG 59.263 61.111 4.75 0.00 0.00 3.77
2892 3150 2.524148 GGCAAGTTGGGCTGGGTT 60.524 61.111 4.75 0.00 0.00 4.11
2893 3151 4.974721 CGGCAAGTTGGGCTGGGT 62.975 66.667 4.75 0.00 33.98 4.51


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

AutoCloner maintained by Alex Coulton.