Multiple sequence alignment - TraesCS3D01G318500

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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 TraesCS3D01G318500 chr3D 100.000 3197 0 0 1 3197 432142355 432139159 0.000000e+00 5904.0
1 TraesCS3D01G318500 chr3B 92.975 2548 107 22 6 2513 564343691 564341176 0.000000e+00 3648.0
2 TraesCS3D01G318500 chr3B 94.388 695 31 4 2511 3197 564340896 564340202 0.000000e+00 1061.0
3 TraesCS3D01G318500 chr3B 84.615 143 19 3 3054 3194 564340556 564340415 4.300000e-29 139.0
4 TraesCS3D01G318500 chr3A 89.761 2598 153 36 156 2667 569641741 569639171 0.000000e+00 3219.0
5 TraesCS3D01G318500 chr7D 84.375 64 10 0 3129 3192 469858335 469858272 2.660000e-06 63.9


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 TraesCS3D01G318500 chr3D 432139159 432142355 3196 True 5904 5904 100.000000 1 3197 1 chr3D.!!$R1 3196
1 TraesCS3D01G318500 chr3B 564340202 564343691 3489 True 1616 3648 90.659333 6 3197 3 chr3B.!!$R1 3191
2 TraesCS3D01G318500 chr3A 569639171 569641741 2570 True 3219 3219 89.761000 156 2667 1 chr3A.!!$R1 2511

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
314 335 0.547712 ACTACCCCTGGTCAGCACAT 60.548 55.0 0.0 0.0 37.09 3.21 F
1319 1389 0.606401 CCTGAACTGGATGCGTGGTT 60.606 55.0 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 1648 0.250597 AGGCGGTTTGGTCAGGTAAC 60.251 55.0 0.0 0.0 0.0 2.50 R
2994 3378 0.178903 TCTAGCCACCCCACTTCACT 60.179 55.0 0.0 0.0 0.0 3.41 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
39 40 8.888579 AGTCACAAAATCTTATACCTATTCCG 57.111 34.615 0.00 0.00 0.00 4.30
40 41 8.483758 AGTCACAAAATCTTATACCTATTCCGT 58.516 33.333 0.00 0.00 0.00 4.69
63 64 8.092687 CCGTGTAACATAATAAATAGGTAGCCT 58.907 37.037 0.00 0.00 35.74 4.58
64 65 9.136952 CGTGTAACATAATAAATAGGTAGCCTC 57.863 37.037 0.00 0.00 35.74 4.70
74 75 9.566432 AATAAATAGGTAGCCTCTTCTTGATTG 57.434 33.333 0.00 0.00 34.61 2.67
80 81 5.065346 GGTAGCCTCTTCTTGATTGCTAAAC 59.935 44.000 0.00 0.00 36.98 2.01
94 95 9.820229 TTGATTGCTAAACTAAATTGTAACTCG 57.180 29.630 0.00 0.00 0.00 4.18
112 113 4.398319 ACTCGATTCAACCAAGGACATTT 58.602 39.130 0.00 0.00 0.00 2.32
133 134 6.773976 TTTCCCTCCAGCATACAAATAAAG 57.226 37.500 0.00 0.00 0.00 1.85
140 141 7.556275 CCTCCAGCATACAAATAAAGTAAGGAA 59.444 37.037 0.00 0.00 0.00 3.36
163 164 0.908910 ATCAAGTATGGTGGCCGTCA 59.091 50.000 0.00 0.00 0.00 4.35
168 169 1.559682 AGTATGGTGGCCGTCAGATTT 59.440 47.619 0.00 0.00 0.00 2.17
171 172 2.107950 TGGTGGCCGTCAGATTTTAG 57.892 50.000 0.00 0.00 0.00 1.85
172 173 1.626321 TGGTGGCCGTCAGATTTTAGA 59.374 47.619 0.00 0.00 0.00 2.10
174 175 2.418976 GGTGGCCGTCAGATTTTAGAAC 59.581 50.000 0.00 0.00 0.00 3.01
218 219 5.116882 ACTGTACTTTGACCTTGACAAGTC 58.883 41.667 14.03 11.41 0.00 3.01
260 261 2.496817 CGGCAGGTGGAGTAGCTC 59.503 66.667 0.00 0.00 34.17 4.09
272 273 2.597520 GAGTAGCTCACCACGAAGAAC 58.402 52.381 0.00 0.00 0.00 3.01
273 274 2.229302 GAGTAGCTCACCACGAAGAACT 59.771 50.000 0.00 0.00 0.00 3.01
314 335 0.547712 ACTACCCCTGGTCAGCACAT 60.548 55.000 0.00 0.00 37.09 3.21
397 418 5.997129 TCATTTTCCATTAGATGCTCGCATA 59.003 36.000 4.10 0.00 36.70 3.14
491 512 2.002586 TGTGCAGAAAAGCTATCTCGC 58.997 47.619 12.67 12.67 34.99 5.03
613 638 3.403558 GCCCCCTGGTCCAGTCTC 61.404 72.222 17.85 0.49 0.00 3.36
614 639 2.122729 CCCCCTGGTCCAGTCTCA 59.877 66.667 17.85 0.00 0.00 3.27
652 678 3.694043 AATGGGGGAATTTTTGTTCCG 57.306 42.857 0.06 0.00 46.97 4.30
660 686 3.981416 GGAATTTTTGTTCCGTTCTGCTC 59.019 43.478 0.00 0.00 38.41 4.26
877 937 1.129058 TAATCTCCTTCCCCTTCCGC 58.871 55.000 0.00 0.00 0.00 5.54
920 981 3.512680 CCGAGATAGTTTCAACGCTTCT 58.487 45.455 0.00 0.00 0.00 2.85
965 1030 1.300620 CCAAGCAACCTCGTCGACA 60.301 57.895 17.16 1.87 0.00 4.35
1131 1196 2.668550 AAGACGTGCCCGAAAGCC 60.669 61.111 0.00 0.00 37.88 4.35
1287 1357 2.049767 TGCACGAGCCGTCTGGATA 61.050 57.895 1.39 0.00 38.32 2.59
1319 1389 0.606401 CCTGAACTGGATGCGTGGTT 60.606 55.000 0.00 0.00 0.00 3.67
1520 1590 2.389962 TGCCGTGTACCTGGTAATTC 57.610 50.000 8.40 0.00 0.00 2.17
1593 1666 4.499188 GCTTTCTTGTTACCTGACCAAACC 60.499 45.833 0.00 0.00 0.00 3.27
1669 1746 4.059459 GCAAGGTGTCGTCGTGCG 62.059 66.667 0.00 0.00 43.01 5.34
1719 1796 0.889186 ACGCCAACATTGTGGACCTC 60.889 55.000 8.80 0.00 41.65 3.85
1881 1958 2.048597 CTGGACAAGGCGTACGCA 60.049 61.111 37.99 17.43 44.11 5.24
2004 2081 1.301244 CGTGCTCAGCAACAGGACT 60.301 57.895 0.00 0.00 41.47 3.85
2007 2084 0.319728 TGCTCAGCAACAGGACTCTC 59.680 55.000 0.00 0.00 34.76 3.20
2243 2320 2.127232 GGTGGCTTGGTGCAAGTGT 61.127 57.895 0.00 0.00 42.77 3.55
2420 2506 2.589014 CTTTGAGATTTGGCGAGTTGC 58.411 47.619 0.00 0.00 45.38 4.17
2671 3050 6.012858 TCAACCTCCAAGCCTATTTTTCTCTA 60.013 38.462 0.00 0.00 0.00 2.43
2678 3057 6.887002 CCAAGCCTATTTTTCTCTAGGAAAGT 59.113 38.462 0.00 4.05 43.68 2.66
2714 3093 1.291184 TGAGAATGAACAGTGCCGCG 61.291 55.000 0.00 0.00 0.00 6.46
2795 3174 2.359975 CCTCCAACCACCGCCTTC 60.360 66.667 0.00 0.00 0.00 3.46
2841 3221 0.110509 CGTTTTCTCGTCGTCTCCGA 60.111 55.000 0.00 0.00 41.73 4.55
2870 3250 3.839432 CTTCTCCTCGGCGTCCCC 61.839 72.222 6.85 0.00 0.00 4.81
2871 3251 4.377760 TTCTCCTCGGCGTCCCCT 62.378 66.667 6.85 0.00 0.00 4.79
2872 3252 2.905935 CTTCTCCTCGGCGTCCCCTA 62.906 65.000 6.85 0.00 0.00 3.53
2876 3260 3.458163 CTCGGCGTCCCCTAGCAA 61.458 66.667 6.85 0.00 34.54 3.91
2882 3266 2.187163 GTCCCCTAGCAACGCTCC 59.813 66.667 0.00 0.00 40.44 4.70
2891 3275 3.000080 GCAACGCTCCTTCGTGTCG 62.000 63.158 0.00 0.00 42.46 4.35
2906 3290 1.890510 GTCGTTCCCGGCAACAAGT 60.891 57.895 9.37 0.00 38.92 3.16
2913 3297 0.885596 CCCGGCAACAAGTAAACCGA 60.886 55.000 0.00 0.00 46.71 4.69
2938 3322 1.001269 TCGGAGTCGGATCCACTGT 60.001 57.895 18.06 0.00 39.53 3.55
2949 3333 2.482796 ATCCACTGTTCGCCATGCCA 62.483 55.000 0.00 0.00 0.00 4.92
2994 3378 1.151810 AGCTTGGGGACAGAGGGAA 60.152 57.895 0.00 0.00 44.54 3.97
3011 3395 0.690762 GAAGTGAAGTGGGGTGGCTA 59.309 55.000 0.00 0.00 0.00 3.93
3026 3410 1.902508 TGGCTAGAGTTTGGTCCAGAG 59.097 52.381 0.00 0.00 0.00 3.35
3067 3451 1.605712 CCAAGACGACGCTTTCTCCTT 60.606 52.381 0.00 0.00 0.00 3.36
3078 3462 1.823169 TTTCTCCTTGACGTCCCCGG 61.823 60.000 14.12 10.63 38.78 5.73
3150 3536 2.512515 GTCTGATCCACTGCCCGC 60.513 66.667 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.326413 CGGAATAGGTATAAGATTTTGTGACTT 57.674 33.333 0.00 0.00 0.00 3.01
14 15 8.483758 ACGGAATAGGTATAAGATTTTGTGACT 58.516 33.333 0.00 0.00 0.00 3.41
16 17 8.262227 ACACGGAATAGGTATAAGATTTTGTGA 58.738 33.333 0.00 0.00 0.00 3.58
17 18 8.433421 ACACGGAATAGGTATAAGATTTTGTG 57.567 34.615 0.00 0.00 0.00 3.33
56 57 3.274095 AGCAATCAAGAAGAGGCTACC 57.726 47.619 0.00 0.00 38.57 3.18
68 69 9.820229 CGAGTTACAATTTAGTTTAGCAATCAA 57.180 29.630 0.00 0.00 0.00 2.57
80 81 7.962918 CCTTGGTTGAATCGAGTTACAATTTAG 59.037 37.037 0.00 0.00 0.00 1.85
92 93 3.756434 GGAAATGTCCTTGGTTGAATCGA 59.244 43.478 0.00 0.00 41.24 3.59
94 95 4.089361 AGGGAAATGTCCTTGGTTGAATC 58.911 43.478 0.82 0.00 44.28 2.52
97 98 2.225017 GGAGGGAAATGTCCTTGGTTGA 60.225 50.000 0.82 0.00 44.28 3.18
112 113 5.450818 ACTTTATTTGTATGCTGGAGGGA 57.549 39.130 0.00 0.00 0.00 4.20
133 134 6.625081 GCCACCATACTTGATTTGTTCCTTAC 60.625 42.308 0.00 0.00 0.00 2.34
140 141 2.091541 CGGCCACCATACTTGATTTGT 58.908 47.619 2.24 0.00 0.00 2.83
152 153 1.626321 TCTAAAATCTGACGGCCACCA 59.374 47.619 2.24 0.00 0.00 4.17
153 154 2.396590 TCTAAAATCTGACGGCCACC 57.603 50.000 2.24 0.00 0.00 4.61
154 155 3.125316 CAGTTCTAAAATCTGACGGCCAC 59.875 47.826 2.24 0.00 0.00 5.01
189 190 6.047231 GTCAAGGTCAAAGTACAGTACTGTT 58.953 40.000 32.15 14.04 41.83 3.16
194 195 6.229936 ACTTGTCAAGGTCAAAGTACAGTA 57.770 37.500 16.85 0.00 0.00 2.74
200 201 3.933861 AGGACTTGTCAAGGTCAAAGT 57.066 42.857 16.85 0.00 34.49 2.66
218 219 0.094046 CGCCGTTTACGCAAACTAGG 59.906 55.000 9.47 5.43 41.62 3.02
260 261 1.732259 GGCATACAGTTCTTCGTGGTG 59.268 52.381 0.00 0.00 0.00 4.17
314 335 4.651778 CATTTTAACTGGTCTCTGGTGGA 58.348 43.478 0.00 0.00 0.00 4.02
397 418 3.384668 CGATCGATGCATTTGTAGAGGT 58.615 45.455 10.26 0.00 0.00 3.85
425 446 7.067372 GGCAGTGCATATATGAAGGCAATATTA 59.933 37.037 18.61 0.00 38.10 0.98
429 450 3.508793 GGCAGTGCATATATGAAGGCAAT 59.491 43.478 18.61 3.47 38.10 3.56
513 538 2.052237 CACTTGTCAACGCACGCC 60.052 61.111 0.00 0.00 0.00 5.68
555 580 2.927580 TTCCGCGTCTGGACTGGAC 61.928 63.158 4.92 0.00 37.89 4.02
612 637 1.810853 CACGCGGCACATGAGATGA 60.811 57.895 12.47 0.00 0.00 2.92
613 638 1.360931 TTCACGCGGCACATGAGATG 61.361 55.000 12.47 0.00 0.00 2.90
614 639 0.673333 TTTCACGCGGCACATGAGAT 60.673 50.000 12.47 0.00 0.00 2.75
877 937 4.452733 GGGTCAGCCGGGAACTCG 62.453 72.222 2.18 0.00 34.97 4.18
897 957 1.204941 AGCGTTGAAACTATCTCGGCT 59.795 47.619 0.00 0.00 0.00 5.52
898 958 1.641577 AGCGTTGAAACTATCTCGGC 58.358 50.000 0.00 0.00 0.00 5.54
899 959 3.512680 AGAAGCGTTGAAACTATCTCGG 58.487 45.455 0.00 0.00 0.00 4.63
900 960 4.621460 TCAAGAAGCGTTGAAACTATCTCG 59.379 41.667 0.00 0.00 33.41 4.04
901 961 5.445275 GCTCAAGAAGCGTTGAAACTATCTC 60.445 44.000 1.64 0.00 42.21 2.75
902 962 4.390297 GCTCAAGAAGCGTTGAAACTATCT 59.610 41.667 1.64 0.00 42.21 1.98
926 987 1.671742 GTGACGAGGGGAAGCAGAA 59.328 57.895 0.00 0.00 0.00 3.02
927 988 2.636412 CGTGACGAGGGGAAGCAGA 61.636 63.158 0.00 0.00 0.00 4.26
965 1030 1.404315 GGAACAGAGCCGAATCGAGTT 60.404 52.381 3.36 0.78 0.00 3.01
1275 1345 2.017049 GCAAAACATATCCAGACGGCT 58.983 47.619 0.00 0.00 0.00 5.52
1284 1354 7.029563 CCAGTTCAGGTTAAGCAAAACATATC 58.970 38.462 18.43 0.00 0.00 1.63
1287 1357 4.892934 TCCAGTTCAGGTTAAGCAAAACAT 59.107 37.500 18.43 6.62 0.00 2.71
1412 1482 1.064803 CTTGATCCTCTCGACCTCGTG 59.935 57.143 0.00 0.00 40.80 4.35
1501 1571 1.624312 TGAATTACCAGGTACACGGCA 59.376 47.619 0.00 0.00 0.00 5.69
1520 1590 2.704572 GGGGGATTATCGATCTGCTTG 58.295 52.381 0.00 0.00 35.02 4.01
1542 1612 0.399454 ATCCATGGAGCCGATGAAGG 59.601 55.000 21.33 0.00 0.00 3.46
1543 1613 2.267174 AATCCATGGAGCCGATGAAG 57.733 50.000 21.33 0.00 0.00 3.02
1545 1615 2.173356 AGAAAATCCATGGAGCCGATGA 59.827 45.455 21.33 0.00 0.00 2.92
1546 1616 2.551459 GAGAAAATCCATGGAGCCGATG 59.449 50.000 21.33 0.00 0.00 3.84
1547 1617 2.173356 TGAGAAAATCCATGGAGCCGAT 59.827 45.455 21.33 5.92 0.00 4.18
1548 1618 1.559219 TGAGAAAATCCATGGAGCCGA 59.441 47.619 21.33 0.00 0.00 5.54
1549 1619 2.042686 TGAGAAAATCCATGGAGCCG 57.957 50.000 21.33 0.00 0.00 5.52
1550 1620 2.100418 GCTTGAGAAAATCCATGGAGCC 59.900 50.000 21.33 8.78 0.00 4.70
1551 1621 3.022406 AGCTTGAGAAAATCCATGGAGC 58.978 45.455 21.33 14.13 0.00 4.70
1578 1648 0.250597 AGGCGGTTTGGTCAGGTAAC 60.251 55.000 0.00 0.00 0.00 2.50
1582 1652 2.359975 GGAGGCGGTTTGGTCAGG 60.360 66.667 0.00 0.00 0.00 3.86
1593 1666 1.376037 GGTCTGGAACAAGGAGGCG 60.376 63.158 0.00 0.00 38.70 5.52
1669 1746 2.868787 GTCGTTCTCGGCGTCGAC 60.869 66.667 8.66 22.93 43.81 4.20
1719 1796 2.724977 TCACGCTGAAGTAGGTCTTG 57.275 50.000 0.00 0.00 36.40 3.02
1761 1838 3.680786 CTCCCCGACAGCACGACA 61.681 66.667 0.00 0.00 35.09 4.35
1931 2008 3.561120 TTGGGGTCCATGTCCACGC 62.561 63.158 6.53 1.89 31.53 5.34
2375 2461 4.310769 CACTCGGTCAAGAACAAAGAGAT 58.689 43.478 0.00 0.00 32.90 2.75
2671 3050 4.950205 TTTACCGAGAAGTGACTTTCCT 57.050 40.909 0.00 0.00 0.00 3.36
2678 3057 7.158697 TCATTCTCATTTTTACCGAGAAGTGA 58.841 34.615 7.12 7.79 46.01 3.41
2740 3119 4.738998 CCCCACATGAGGCGGCAA 62.739 66.667 13.08 0.00 0.00 4.52
2748 3127 2.609299 TCGGAAGGCCCCACATGA 60.609 61.111 0.00 0.00 0.00 3.07
2750 3129 2.933287 TGTCGGAAGGCCCCACAT 60.933 61.111 0.00 0.00 32.11 3.21
2841 3221 4.719369 GAGAAGCGTCGCCGTGGT 62.719 66.667 14.86 0.00 36.15 4.16
2870 3250 0.388649 ACACGAAGGAGCGTTGCTAG 60.389 55.000 0.00 0.00 43.59 3.42
2871 3251 0.388134 GACACGAAGGAGCGTTGCTA 60.388 55.000 0.00 0.00 43.59 3.49
2872 3252 1.664965 GACACGAAGGAGCGTTGCT 60.665 57.895 0.00 0.00 43.59 3.91
2876 3260 1.371389 GAACGACACGAAGGAGCGT 60.371 57.895 0.00 0.00 46.88 5.07
2891 3275 1.001048 GGTTTACTTGTTGCCGGGAAC 60.001 52.381 29.91 29.91 0.00 3.62
2913 3297 1.271163 GGATCCGACTCCGAGATCTCT 60.271 57.143 20.26 1.25 39.83 3.10
2938 3322 2.266070 CCTTCTTTGGCATGGCGAA 58.734 52.632 19.99 19.99 0.00 4.70
2949 3333 2.162681 CAATGAACTCCGGCCTTCTTT 58.837 47.619 0.00 1.49 0.00 2.52
2958 3342 2.009042 GCTCCTGTCCAATGAACTCCG 61.009 57.143 0.00 0.00 0.00 4.63
2994 3378 0.178903 TCTAGCCACCCCACTTCACT 60.179 55.000 0.00 0.00 0.00 3.41
3026 3410 4.041198 TGGTATTTTCATCCCTATCCGTCC 59.959 45.833 0.00 0.00 0.00 4.79
3030 3414 5.701290 CGTCTTGGTATTTTCATCCCTATCC 59.299 44.000 0.00 0.00 0.00 2.59
3078 3462 2.347731 CAAGAAGAAGAACTACCGGGC 58.652 52.381 6.32 0.00 0.00 6.13
3121 3507 2.159382 GGATCAGACTCCGAGATCTCC 58.841 57.143 17.13 2.52 38.51 3.71
3167 3553 1.016653 GCTCCTGTCAAGCGAACTCC 61.017 60.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.