Multiple sequence alignment - TraesCS6D01G237800

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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 TraesCS6D01G237800 chr6D 100.000 3224 0 0 1 3224 337080405 337077182 0.000000e+00 5954
1 TraesCS6D01G237800 chr6B 91.911 2831 93 48 288 3053 483331724 483334483 0.000000e+00 3834
2 TraesCS6D01G237800 chr6B 92.265 362 17 2 1 359 483331180 483331533 1.340000e-138 503
3 TraesCS6D01G237800 chr6B 93.143 175 11 1 3050 3224 483334697 483334870 4.130000e-64 255
4 TraesCS6D01G237800 chr6A 90.503 2306 100 54 987 3224 477517028 477514774 0.000000e+00 2935
5 TraesCS6D01G237800 chr6A 93.532 1005 32 12 1 988 477518047 477517059 0.000000e+00 1465


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 TraesCS6D01G237800 chr6D 337077182 337080405 3223 True 5954.000000 5954 100.000000 1 3224 1 chr6D.!!$R1 3223
1 TraesCS6D01G237800 chr6B 483331180 483334870 3690 False 1530.666667 3834 92.439667 1 3224 3 chr6B.!!$F1 3223
2 TraesCS6D01G237800 chr6A 477514774 477518047 3273 True 2200.000000 2935 92.017500 1 3224 2 chr6A.!!$R1 3223

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
985 1284 0.392060 CACTGCAGCTCTGGCATGTA 60.392 55.000 15.27 0.0 41.06 2.29 F
1263 1600 1.228154 AAACGGCAAGTGGGTCTCC 60.228 57.895 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2384 0.231790 GACCGTACGTAGCTAGCGAG 59.768 60.0 15.21 7.32 0.00 5.03 R
2922 3322 0.240678 TTGCCTATGCGCTTGTGTTG 59.759 50.0 9.73 0.00 41.78 3.33 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 74 1.899814 TCTAGTCCAACACAATCGGCT 59.100 47.619 0.00 0.00 0.00 5.52
109 110 1.308069 CCGGTCTGAAATGGCCACAG 61.308 60.000 8.16 12.12 0.00 3.66
110 111 1.885871 GGTCTGAAATGGCCACAGC 59.114 57.895 8.16 7.60 38.76 4.40
234 246 1.841663 GCGGACAAGAAAAGCGAGCA 61.842 55.000 0.00 0.00 0.00 4.26
244 256 2.959507 AAAGCGAGCAAACCAAAAGT 57.040 40.000 0.00 0.00 0.00 2.66
335 609 2.965462 CCGGCCGTATCTTTCGCC 60.965 66.667 26.12 0.00 0.00 5.54
601 880 1.944177 AGCCATACACACACTCTCCT 58.056 50.000 0.00 0.00 0.00 3.69
786 1075 1.590259 GCCGGATCTCACGCTTCTC 60.590 63.158 5.05 0.00 0.00 2.87
787 1076 1.066587 CCGGATCTCACGCTTCTCC 59.933 63.158 0.00 0.00 0.00 3.71
830 1125 1.428525 ACCTACCTACCTAGCCTAGCC 59.571 57.143 0.00 0.00 0.00 3.93
843 1138 1.406860 CCTAGCCCTCCTCTTCCAGC 61.407 65.000 0.00 0.00 0.00 4.85
870 1165 0.898326 TACTCTCTTCCCGCAGCACA 60.898 55.000 0.00 0.00 0.00 4.57
883 1182 4.312231 GCACACGCGCACACACAT 62.312 61.111 5.73 0.00 0.00 3.21
885 1184 3.345808 ACACGCGCACACACATCC 61.346 61.111 5.73 0.00 0.00 3.51
890 1189 3.027170 GCGCACACACATCCCGAAG 62.027 63.158 0.30 0.00 0.00 3.79
915 1214 1.926561 GGTACTTAACCGCTTACCCG 58.073 55.000 0.00 0.00 38.88 5.28
919 1218 2.248086 CTTAACCGCTTACCCGCCCT 62.248 60.000 0.00 0.00 0.00 5.19
985 1284 0.392060 CACTGCAGCTCTGGCATGTA 60.392 55.000 15.27 0.00 41.06 2.29
1140 1477 2.183555 CCGGTTCACCTAGGCGAC 59.816 66.667 9.30 4.92 0.00 5.19
1161 1498 4.612412 GTGGGGACAACGACGGCA 62.612 66.667 0.00 0.00 46.06 5.69
1263 1600 1.228154 AAACGGCAAGTGGGTCTCC 60.228 57.895 0.00 0.00 0.00 3.71
1399 1736 2.749839 TCAATTTCCCTGGCGCCG 60.750 61.111 23.90 16.52 0.00 6.46
1736 2073 4.052229 CTCCGACGAGTGGCCGTT 62.052 66.667 0.00 0.00 43.49 4.44
1789 2126 2.933573 ACCACGATCCCTAGTGAGTAG 58.066 52.381 0.00 0.00 40.56 2.57
1790 2127 2.241685 ACCACGATCCCTAGTGAGTAGT 59.758 50.000 0.00 0.00 40.56 2.73
1791 2128 3.457380 ACCACGATCCCTAGTGAGTAGTA 59.543 47.826 0.00 0.00 40.56 1.82
1805 2142 6.226787 AGTGAGTAGTATATTGCATTGGCTC 58.773 40.000 0.00 0.00 41.91 4.70
1882 2219 6.462552 ACTAAACCTAGTTAATCCGGAGTC 57.537 41.667 8.16 0.00 34.53 3.36
1945 2291 3.333804 TGGTATATATGCGTGTGCCATG 58.666 45.455 0.00 0.00 41.78 3.66
2036 2384 8.951954 ACGTCAGATTCGATATTATGTTCTAC 57.048 34.615 0.00 0.00 0.00 2.59
2037 2385 8.784994 ACGTCAGATTCGATATTATGTTCTACT 58.215 33.333 0.00 0.00 0.00 2.57
2038 2386 9.268255 CGTCAGATTCGATATTATGTTCTACTC 57.732 37.037 0.00 0.00 0.00 2.59
2127 2483 0.907486 ACTATGAGAGCAAGCAGGCA 59.093 50.000 2.37 0.00 35.83 4.75
2218 2579 9.893305 GACTAATGCATTGTAACTTTTGTAACT 57.107 29.630 22.27 0.00 0.00 2.24
2256 2617 3.985019 TGGCGGTGGATAAACTAAGAA 57.015 42.857 0.00 0.00 0.00 2.52
2269 2630 1.135083 ACTAAGAAGGATGCGGACGTG 60.135 52.381 0.00 0.00 0.00 4.49
2286 2647 4.320494 GGACGTGCATATGGATCCAATTTC 60.320 45.833 20.67 9.35 0.00 2.17
2306 2667 4.094830 TCCCTTTTCTTTAGTGGTGTCC 57.905 45.455 0.00 0.00 0.00 4.02
2652 3032 1.603678 GCTACGTCGGTTTCTCCAACA 60.604 52.381 0.00 0.00 37.07 3.33
2814 3194 8.623903 TCATATCTGTTCATACTTGATTTTGCC 58.376 33.333 0.00 0.00 0.00 4.52
2835 3223 3.380954 CCACATGCTGTATATGCCAACAA 59.619 43.478 0.00 0.00 0.00 2.83
2838 3226 6.238981 CCACATGCTGTATATGCCAACAATAA 60.239 38.462 0.00 0.00 0.00 1.40
2847 3235 9.073475 TGTATATGCCAACAATAACCCTATTTC 57.927 33.333 0.00 0.00 0.00 2.17
2851 3239 6.459923 TGCCAACAATAACCCTATTTCAAAC 58.540 36.000 0.00 0.00 0.00 2.93
2900 3298 8.349245 CACAACTTGGTGAAAACAGACATATAA 58.651 33.333 0.00 0.00 41.32 0.98
2901 3299 9.077885 ACAACTTGGTGAAAACAGACATATAAT 57.922 29.630 0.00 0.00 0.00 1.28
2902 3300 9.912634 CAACTTGGTGAAAACAGACATATAATT 57.087 29.630 0.00 0.00 0.00 1.40
2903 3301 9.912634 AACTTGGTGAAAACAGACATATAATTG 57.087 29.630 0.00 0.00 0.00 2.32
2922 3322 2.156098 TGGAATTTTCACAGGTACGCC 58.844 47.619 0.00 0.00 0.00 5.68
2926 3326 2.039818 TTTTCACAGGTACGCCAACA 57.960 45.000 0.00 0.00 37.19 3.33
2948 3348 1.033746 AGCGCATAGGCAAAGCACAT 61.034 50.000 11.47 0.00 41.24 3.21
3001 3406 5.789710 AAAGATACCAAATTGTCGTACCG 57.210 39.130 0.00 0.00 0.00 4.02
3003 3408 4.679662 AGATACCAAATTGTCGTACCGAG 58.320 43.478 0.00 0.00 36.23 4.63
3018 3431 4.514441 CGTACCGAGTACTCTACCATTGAT 59.486 45.833 20.34 0.00 36.93 2.57
3027 3440 7.680730 AGTACTCTACCATTGATTCAACAACT 58.319 34.615 0.15 0.00 32.50 3.16
3035 3448 5.916883 CCATTGATTCAACAACTCAGACAAC 59.083 40.000 0.15 0.00 32.50 3.32
3044 3457 7.546358 TCAACAACTCAGACAACAAAATGATT 58.454 30.769 0.00 0.00 0.00 2.57
3098 3728 1.943116 TTGCACTGCGCTGGTTTGTT 61.943 50.000 18.98 0.00 43.06 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 1.411246 CCGGGAGTTGACGAATATCCA 59.589 52.381 0.00 0.00 0.00 3.41
111 112 0.740868 CATATATCGGCGCCCTGTGG 60.741 60.000 23.46 6.36 0.00 4.17
112 113 1.361668 GCATATATCGGCGCCCTGTG 61.362 60.000 23.46 12.59 0.00 3.66
113 114 1.079127 GCATATATCGGCGCCCTGT 60.079 57.895 23.46 9.61 0.00 4.00
114 115 1.815421 GGCATATATCGGCGCCCTG 60.815 63.158 23.46 8.15 38.67 4.45
115 116 2.584608 GGCATATATCGGCGCCCT 59.415 61.111 23.46 11.53 38.67 5.19
116 117 2.890474 CGGCATATATCGGCGCCC 60.890 66.667 23.46 3.23 45.66 6.13
217 229 2.385315 GTTTGCTCGCTTTTCTTGTCC 58.615 47.619 0.00 0.00 0.00 4.02
234 246 1.691163 CCAGGTGGGGACTTTTGGTTT 60.691 52.381 0.00 0.00 0.00 3.27
335 609 4.202398 TGCTGATAATTTCTCTAGGGGCTG 60.202 45.833 0.00 0.00 0.00 4.85
491 766 1.044790 TCGGGATCGAGTTTACCCCC 61.045 60.000 0.00 0.00 40.88 5.40
601 880 1.522806 AGACCGCGTTGTTTGAGCA 60.523 52.632 4.92 0.00 0.00 4.26
665 946 1.585895 TCGGAGAAGAGAGGAGAGGA 58.414 55.000 0.00 0.00 0.00 3.71
666 947 2.229792 CATCGGAGAAGAGAGGAGAGG 58.770 57.143 0.00 0.00 43.58 3.69
786 1075 0.038159 AGAAACGCACGAGGAGAAGG 60.038 55.000 0.00 0.00 0.00 3.46
787 1076 1.457303 CAAGAAACGCACGAGGAGAAG 59.543 52.381 0.00 0.00 0.00 2.85
830 1125 0.987294 TCAAAGGCTGGAAGAGGAGG 59.013 55.000 0.00 0.00 34.07 4.30
843 1138 2.417515 GCGGGAAGAGAGTACTCAAAGG 60.418 54.545 24.44 8.02 44.79 3.11
890 1189 2.160853 GCGGTTAAGTACCCGTCGC 61.161 63.158 9.56 6.36 44.70 5.19
915 1214 2.830370 GCAGGTGTATGCCAGGGC 60.830 66.667 2.62 2.62 40.43 5.19
919 1218 2.745884 GCACGCAGGTGTATGCCA 60.746 61.111 0.00 0.00 46.13 4.92
985 1284 1.782752 AGCCATGTACCATTAGGGCAT 59.217 47.619 9.00 0.00 43.72 4.40
1017 1348 1.910772 AGCAGACGAGGAGGTTGCT 60.911 57.895 0.00 0.00 40.07 3.91
1140 1477 2.663852 GTCGTTGTCCCCACCGTG 60.664 66.667 0.00 0.00 0.00 4.94
1789 2126 5.756195 TGTCTTGAGCCAATGCAATATAC 57.244 39.130 0.00 0.00 41.13 1.47
1790 2127 6.063404 TCATGTCTTGAGCCAATGCAATATA 58.937 36.000 0.00 0.00 41.13 0.86
1791 2128 4.891168 TCATGTCTTGAGCCAATGCAATAT 59.109 37.500 0.00 0.00 41.13 1.28
1805 2142 2.274437 CTCACCGGTCATCATGTCTTG 58.726 52.381 2.59 0.00 0.00 3.02
1882 2219 2.030562 GCCGGGGTCCATGTATCG 59.969 66.667 2.18 0.00 0.00 2.92
1974 2320 8.624367 ACTATCTAGGTAGCGGCTATAATATG 57.376 38.462 13.60 2.71 0.00 1.78
2036 2384 0.231790 GACCGTACGTAGCTAGCGAG 59.768 60.000 15.21 7.32 0.00 5.03
2037 2385 0.460109 TGACCGTACGTAGCTAGCGA 60.460 55.000 15.21 0.00 0.00 4.93
2038 2386 0.585357 ATGACCGTACGTAGCTAGCG 59.415 55.000 15.21 12.26 0.00 4.26
2127 2483 3.851458 AGGAAGAAAAAGGTACGTGGT 57.149 42.857 0.00 0.00 0.00 4.16
2153 2509 7.495934 GCAATCCACTCGGCACTTTATATATAT 59.504 37.037 0.00 0.00 0.00 0.86
2177 2538 0.613572 TAGTCTCCCGGTGATGTGCA 60.614 55.000 0.00 0.00 0.00 4.57
2218 2579 7.415765 CCACCGCCAAATATTTTTATGTCTACA 60.416 37.037 0.00 0.00 0.00 2.74
2269 2630 5.813513 AAAGGGAAATTGGATCCATATGC 57.186 39.130 17.06 9.91 38.80 3.14
2286 2647 4.100279 AGGACACCACTAAAGAAAAGGG 57.900 45.455 0.00 0.00 0.00 3.95
2335 2696 1.677820 CGGCTAACTTCCCCAATTCGT 60.678 52.381 0.00 0.00 0.00 3.85
2696 3076 4.091365 CGTCGTTCAACAGCTCAATTATGA 59.909 41.667 0.00 0.00 0.00 2.15
2697 3077 4.326205 CGTCGTTCAACAGCTCAATTATG 58.674 43.478 0.00 0.00 0.00 1.90
2698 3078 3.370978 CCGTCGTTCAACAGCTCAATTAT 59.629 43.478 0.00 0.00 0.00 1.28
2699 3079 2.734606 CCGTCGTTCAACAGCTCAATTA 59.265 45.455 0.00 0.00 0.00 1.40
2700 3080 1.531149 CCGTCGTTCAACAGCTCAATT 59.469 47.619 0.00 0.00 0.00 2.32
2900 3298 3.192633 GGCGTACCTGTGAAAATTCCAAT 59.807 43.478 0.00 0.00 0.00 3.16
2901 3299 2.554893 GGCGTACCTGTGAAAATTCCAA 59.445 45.455 0.00 0.00 0.00 3.53
2902 3300 2.156098 GGCGTACCTGTGAAAATTCCA 58.844 47.619 0.00 0.00 0.00 3.53
2903 3301 2.156098 TGGCGTACCTGTGAAAATTCC 58.844 47.619 0.00 0.00 36.63 3.01
2922 3322 0.240678 TTGCCTATGCGCTTGTGTTG 59.759 50.000 9.73 0.00 41.78 3.33
2926 3326 1.243342 TGCTTTGCCTATGCGCTTGT 61.243 50.000 9.73 0.00 41.78 3.16
2932 3332 1.747355 AGTCATGTGCTTTGCCTATGC 59.253 47.619 0.00 0.00 38.26 3.14
2948 3348 4.094887 GCTTTTGCCAATTCGATCTAGTCA 59.905 41.667 0.00 0.00 40.15 3.41
3000 3405 6.330278 TGTTGAATCAATGGTAGAGTACTCG 58.670 40.000 17.07 1.44 34.09 4.18
3001 3406 7.819900 AGTTGTTGAATCAATGGTAGAGTACTC 59.180 37.037 15.41 15.41 0.00 2.59
3003 3408 7.602644 TGAGTTGTTGAATCAATGGTAGAGTAC 59.397 37.037 0.00 0.00 0.00 2.73
3018 3431 6.918626 TCATTTTGTTGTCTGAGTTGTTGAA 58.081 32.000 0.00 0.00 0.00 2.69
3027 3440 8.286800 CGTACCTAAAATCATTTTGTTGTCTGA 58.713 33.333 5.56 0.00 34.19 3.27
3044 3457 8.632906 TTTTTGGGATTTATGTCGTACCTAAA 57.367 30.769 0.00 0.00 0.00 1.85
3131 3761 7.661847 GCATGAGCCTACTTGGTATATAAAACT 59.338 37.037 0.00 0.00 38.35 2.66
3142 3772 0.391661 ACACGCATGAGCCTACTTGG 60.392 55.000 0.00 0.00 37.52 3.61
3144 3774 0.321671 ACACACGCATGAGCCTACTT 59.678 50.000 0.00 0.00 37.52 2.24


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

AutoCloner maintained by Alex Coulton.