Multiple sequence alignment - TraesCS7D01G119400

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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 TraesCS7D01G119400 chr7D 100.000 2642 0 0 1 2642 74132320 74134961 0 4879
1 TraesCS7D01G119400 chrUn 96.157 2628 99 2 1 2627 229310391 229307765 0 4292
2 TraesCS7D01G119400 chrUn 96.158 2629 98 3 1 2627 274341446 274338819 0 4292
3 TraesCS7D01G119400 chrUn 96.157 2628 99 2 1 2627 291535276 291537902 0 4292
4 TraesCS7D01G119400 chrUn 96.119 2628 100 2 1 2627 199874660 199877286 0 4287
5 TraesCS7D01G119400 chrUn 96.119 2628 99 3 1 2627 67501172 67498547 0 4285
6 TraesCS7D01G119400 chrUn 96.081 2628 100 3 1 2627 245705904 245708529 0 4279
7 TraesCS7D01G119400 chrUn 96.043 2628 102 2 1 2627 237311545 237314171 0 4276
8 TraesCS7D01G119400 chrUn 96.005 2628 103 2 1 2627 199904580 199907206 0 4270
9 TraesCS7D01G119400 chr1B 96.081 2628 99 3 1 2627 544593533 544596157 0 4279


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 TraesCS7D01G119400 chr7D 74132320 74134961 2641 False 4879 4879 100.000 1 2642 1 chr7D.!!$F1 2641
1 TraesCS7D01G119400 chrUn 229307765 229310391 2626 True 4292 4292 96.157 1 2627 1 chrUn.!!$R2 2626
2 TraesCS7D01G119400 chrUn 274338819 274341446 2627 True 4292 4292 96.158 1 2627 1 chrUn.!!$R3 2626
3 TraesCS7D01G119400 chrUn 291535276 291537902 2626 False 4292 4292 96.157 1 2627 1 chrUn.!!$F5 2626
4 TraesCS7D01G119400 chrUn 199874660 199877286 2626 False 4287 4287 96.119 1 2627 1 chrUn.!!$F1 2626
5 TraesCS7D01G119400 chrUn 67498547 67501172 2625 True 4285 4285 96.119 1 2627 1 chrUn.!!$R1 2626
6 TraesCS7D01G119400 chrUn 245705904 245708529 2625 False 4279 4279 96.081 1 2627 1 chrUn.!!$F4 2626
7 TraesCS7D01G119400 chrUn 237311545 237314171 2626 False 4276 4276 96.043 1 2627 1 chrUn.!!$F3 2626
8 TraesCS7D01G119400 chrUn 199904580 199907206 2626 False 4270 4270 96.005 1 2627 1 chrUn.!!$F2 2626
9 TraesCS7D01G119400 chr1B 544593533 544596157 2624 False 4279 4279 96.081 1 2627 1 chr1B.!!$F1 2626

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
431 432 0.107831 TTGGTAAGCAGAACTGGCGT 59.892 50.0 3.99 0.0 36.08 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 1909 0.03759 TTTAACAGATGTGCCGCCCT 59.962 50.0 0.0 0.0 0.0 5.19 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
67 68 3.008375 CCTGATCTTCTGTGAAGGGTTCA 59.992 47.826 7.37 7.52 37.33 3.18
72 73 4.451900 TCTTCTGTGAAGGGTTCAAGTTC 58.548 43.478 7.37 0.00 42.15 3.01
78 79 2.224523 TGAAGGGTTCAAGTTCGAGCAT 60.225 45.455 1.01 0.00 36.59 3.79
179 180 1.865865 ACTGACGTGCAAATCGTTCT 58.134 45.000 0.00 0.00 41.64 3.01
204 205 2.105993 GACTTGGGTATAGGGGCGAAAT 59.894 50.000 0.00 0.00 0.00 2.17
289 290 6.924060 CCATTACGAGTTCTATCAGGTAAAGG 59.076 42.308 0.00 0.00 0.00 3.11
338 339 3.508793 ACGTCCTCGACCTATTCTCAAAA 59.491 43.478 0.00 0.00 40.62 2.44
431 432 0.107831 TTGGTAAGCAGAACTGGCGT 59.892 50.000 3.99 0.00 36.08 5.68
487 488 0.457853 CTGCGCGCTAACCTAGAACA 60.458 55.000 33.29 5.84 0.00 3.18
531 532 1.003355 CAGCAGGACGGTGGTCATT 60.003 57.895 0.00 0.00 45.28 2.57
574 575 1.961793 GTGTAACAACTCACCTGCCA 58.038 50.000 0.00 0.00 36.32 4.92
601 602 0.923358 TAGCCCCGAAAATGGATGGT 59.077 50.000 0.00 0.00 0.00 3.55
692 693 2.679996 GCTGCAAAACCCGGGGAT 60.680 61.111 27.92 10.91 0.00 3.85
693 694 3.005540 GCTGCAAAACCCGGGGATG 62.006 63.158 27.92 20.83 0.00 3.51
694 695 1.606313 CTGCAAAACCCGGGGATGT 60.606 57.895 27.92 5.21 0.00 3.06
728 729 1.660355 GGCCGTCGATGCAGATCTA 59.340 57.895 11.36 0.00 0.00 1.98
738 739 3.319405 CGATGCAGATCTAGGTGGTAGTT 59.681 47.826 0.00 0.00 0.00 2.24
748 749 7.716998 AGATCTAGGTGGTAGTTGCAAATATTG 59.283 37.037 10.15 0.00 0.00 1.90
901 902 1.064979 GGGTTAAGATTTCCCGAGCCA 60.065 52.381 0.00 0.00 0.00 4.75
918 919 1.302431 CAGGATGTGGCGGTTGACA 60.302 57.895 0.00 0.00 0.00 3.58
932 933 2.129607 GTTGACAGCGACGTTAGGAAA 58.870 47.619 0.00 0.00 0.00 3.13
935 936 2.230508 TGACAGCGACGTTAGGAAATCT 59.769 45.455 0.00 0.00 0.00 2.40
983 984 7.390718 GGGAAGAGTTATCTTTTCTGCTTAACA 59.609 37.037 4.59 0.00 45.98 2.41
1087 1088 4.128388 CCGGCGGCCCATGAAAAC 62.128 66.667 15.42 0.00 0.00 2.43
1113 1114 2.192608 GACCGAGTACCGTTCACGCT 62.193 60.000 0.00 0.00 38.18 5.07
1154 1155 2.123589 TCAGGTCTCCAAGGTGAACAA 58.876 47.619 8.73 0.00 0.00 2.83
1156 1157 1.843851 AGGTCTCCAAGGTGAACAACA 59.156 47.619 8.73 0.00 0.00 3.33
1200 1201 1.864711 CAAGAGAAGTCGGCAAAACGA 59.135 47.619 0.00 0.00 41.13 3.85
1235 1236 2.291217 GGAAAAGGATTGGCTCTGAGGT 60.291 50.000 6.83 0.00 0.00 3.85
1395 1396 2.141535 AACAGTCGACTCAGAACTGC 57.858 50.000 16.96 0.00 32.16 4.40
1624 1625 2.940514 TGAGATTCCCACTGTCCCTA 57.059 50.000 0.00 0.00 0.00 3.53
1685 1686 0.179045 CGGAATCAGCGGGGAAAGAT 60.179 55.000 0.00 0.00 0.00 2.40
1727 1728 5.470368 TCTAGTCCGACTTTGTGAAATGAG 58.530 41.667 6.31 0.00 0.00 2.90
1728 1729 2.808543 AGTCCGACTTTGTGAAATGAGC 59.191 45.455 0.00 0.00 0.00 4.26
1888 1891 0.768622 TCCGGGTGGAAGACATTGTT 59.231 50.000 0.00 0.00 42.85 2.83
1906 1909 1.631898 GTTAGGTGGGGAGTTTGGCTA 59.368 52.381 0.00 0.00 0.00 3.93
1932 1935 5.221048 GGCGGCACATCTGTTAAAAGATAAT 60.221 40.000 7.86 0.00 35.09 1.28
2013 2017 6.566197 AAAGCTCGTTTGATTCTGATTTCT 57.434 33.333 0.00 0.00 0.00 2.52
2021 2025 7.484007 TCGTTTGATTCTGATTTCTAGTACGAC 59.516 37.037 0.00 0.00 0.00 4.34
2038 2042 2.288579 ACGACTATGAACCGTGAAAGCA 60.289 45.455 0.00 0.00 35.02 3.91
2071 2075 7.394816 TCAATCCTTTAGATCTTCGGAGTTTT 58.605 34.615 0.00 0.00 32.47 2.43
2134 2138 1.902918 TGGCAGCCAAGCGTTCATT 60.903 52.632 13.33 0.00 34.64 2.57
2170 2174 1.880675 GATCCTTCGATGTCGGCTCTA 59.119 52.381 2.25 0.00 40.29 2.43
2178 2182 2.095668 CGATGTCGGCTCTACCTATCAC 60.096 54.545 0.00 0.00 35.61 3.06
2280 2284 7.016858 AGACAGGTTTGTTTTACCCTACTGATA 59.983 37.037 0.00 0.00 37.76 2.15
2296 2300 1.679153 TGATAACAGTGCCGCGATAGA 59.321 47.619 8.23 0.00 39.76 1.98
2355 2359 1.169661 TTGGTCATCGCGCTTGGTTT 61.170 50.000 5.56 0.00 0.00 3.27
2360 2364 2.655001 GTCATCGCGCTTGGTTTAAAAC 59.345 45.455 5.56 0.00 0.00 2.43
2406 2410 2.550978 CGGATTATGACTGAACGCCTT 58.449 47.619 0.00 0.00 0.00 4.35
2436 2440 1.811266 CCAAGCTAGCATGCGACGT 60.811 57.895 18.83 0.93 38.13 4.34
2585 2589 1.006281 TGGGCTGAATCCTTTGCAGAT 59.994 47.619 0.00 0.00 0.00 2.90
2622 2626 0.811281 GGGCATTGTAAGTGGCAGAC 59.189 55.000 0.00 0.00 43.28 3.51
2633 2637 2.512515 GGCAGACTGGCACGATCC 60.513 66.667 23.18 0.66 43.14 3.36
2634 2638 2.265739 GCAGACTGGCACGATCCA 59.734 61.111 4.26 0.00 34.42 3.41
2635 2639 2.103042 GCAGACTGGCACGATCCAC 61.103 63.158 4.26 0.00 31.74 4.02
2636 2640 1.593787 CAGACTGGCACGATCCACT 59.406 57.895 0.00 0.00 31.74 4.00
2637 2641 0.738762 CAGACTGGCACGATCCACTG 60.739 60.000 0.00 0.00 31.74 3.66
2638 2642 0.900182 AGACTGGCACGATCCACTGA 60.900 55.000 0.00 0.00 31.74 3.41
2639 2643 0.459237 GACTGGCACGATCCACTGAG 60.459 60.000 0.00 0.00 31.74 3.35
2640 2644 0.900182 ACTGGCACGATCCACTGAGA 60.900 55.000 0.00 0.00 31.74 3.27
2641 2645 0.247460 CTGGCACGATCCACTGAGAA 59.753 55.000 0.00 0.00 31.74 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.616111 ACAGAAGATCAGGGTCGGCT 60.616 55.000 0.00 0.00 0.00 5.52
67 68 1.016130 CGACAGGCATGCTCGAACTT 61.016 55.000 19.73 0.00 34.17 2.66
72 73 4.147449 TCCCGACAGGCATGCTCG 62.147 66.667 18.92 18.41 35.76 5.03
179 180 2.124411 GCCCCTATACCCAAGTCAGAA 58.876 52.381 0.00 0.00 0.00 3.02
204 205 6.430308 CCAGCTACTAGATGGTTCGATTAGTA 59.570 42.308 11.67 0.00 46.23 1.82
289 290 2.298163 CCCCAATGCCTCTAATCATTGC 59.702 50.000 8.87 0.00 44.83 3.56
338 339 4.320202 CCGCGCCATGCTAACTATTTAAAT 60.320 41.667 0.00 5.89 43.27 1.40
348 349 3.809775 GCAACCGCGCCATGCTAA 61.810 61.111 17.94 0.00 43.27 3.09
431 432 1.376683 CTTCCGGTTCATCCCGCAA 60.377 57.895 0.00 0.00 46.71 4.85
462 463 3.047877 GTTAGCGCGCAGTTGGGT 61.048 61.111 35.10 13.45 0.00 4.51
531 532 2.494471 TCCTTAGCGGATTTCGACTTCA 59.506 45.455 0.00 0.00 42.43 3.02
574 575 3.447229 CCATTTTCGGGGCTAGTTGATTT 59.553 43.478 0.00 0.00 0.00 2.17
614 615 4.360405 GATGGCCGGGTGTGGGTT 62.360 66.667 2.18 0.00 0.00 4.11
728 729 6.909550 TTTCAATATTTGCAACTACCACCT 57.090 33.333 0.00 0.00 0.00 4.00
738 739 9.761504 TTCAAAGTTCTCATTTCAATATTTGCA 57.238 25.926 0.00 0.00 0.00 4.08
748 749 3.502211 TCGGCCTTCAAAGTTCTCATTTC 59.498 43.478 0.00 0.00 0.00 2.17
797 798 1.677518 CGGCTTACCCATGTGCAAGTA 60.678 52.381 0.00 0.00 0.00 2.24
834 835 1.153429 GCGCTATCTGTCGGGGTTT 60.153 57.895 0.00 0.00 0.00 3.27
842 843 4.616592 CGTGATCGCGCTATCTGT 57.383 55.556 20.95 0.00 0.00 3.41
901 902 1.003355 CTGTCAACCGCCACATCCT 60.003 57.895 0.00 0.00 0.00 3.24
918 919 1.822990 TCCAGATTTCCTAACGTCGCT 59.177 47.619 0.00 0.00 0.00 4.93
983 984 2.777960 TTTCCAGGGTTGGCAGGCT 61.778 57.895 0.00 0.00 44.63 4.58
1013 1014 1.002533 GGCCACTGGACCCTACCTA 59.997 63.158 0.00 0.00 0.00 3.08
1119 1120 3.898123 AGACCTGATGCGGTTATGAGTAT 59.102 43.478 0.00 0.00 37.42 2.12
1154 1155 2.307496 TTGTTCCATTGGCCAGATGT 57.693 45.000 19.84 2.57 0.00 3.06
1156 1157 2.823959 ACATTGTTCCATTGGCCAGAT 58.176 42.857 5.11 0.00 0.00 2.90
1184 1185 1.804748 GGATTCGTTTTGCCGACTTCT 59.195 47.619 0.00 0.00 36.42 2.85
1270 1271 2.586079 CGAGCAATCCGCCGACAT 60.586 61.111 0.00 0.00 44.04 3.06
1624 1625 3.704566 TGTGGTTTCGCTGGATAGTAGAT 59.295 43.478 0.00 0.00 0.00 1.98
1685 1686 1.070758 GAGTCAAGCTCAACAGGGTCA 59.929 52.381 0.00 0.00 43.58 4.02
1727 1728 3.068873 CCACTTATCCTACACCTCTCAGC 59.931 52.174 0.00 0.00 0.00 4.26
1728 1729 3.639094 CCCACTTATCCTACACCTCTCAG 59.361 52.174 0.00 0.00 0.00 3.35
1875 1878 2.041081 CCCCACCTAACAATGTCTTCCA 59.959 50.000 0.00 0.00 0.00 3.53
1888 1891 1.580059 CTAGCCAAACTCCCCACCTA 58.420 55.000 0.00 0.00 0.00 3.08
1906 1909 0.037590 TTTAACAGATGTGCCGCCCT 59.962 50.000 0.00 0.00 0.00 5.19
1932 1935 3.027412 GAGCTCATCTTAGGACACCTCA 58.973 50.000 9.40 0.00 34.61 3.86
1986 1990 6.801539 ATCAGAATCAAACGAGCTTTTACA 57.198 33.333 0.00 0.00 0.00 2.41
2013 2017 5.674569 GCTTTCACGGTTCATAGTCGTACTA 60.675 44.000 0.00 0.00 35.23 1.82
2021 2025 2.223340 GCCATGCTTTCACGGTTCATAG 60.223 50.000 0.00 0.00 0.00 2.23
2024 2028 0.537143 AGCCATGCTTTCACGGTTCA 60.537 50.000 0.00 0.00 33.89 3.18
2038 2042 7.605691 CGAAGATCTAAAGGATTGATAAGCCAT 59.394 37.037 0.00 0.00 40.13 4.40
2043 2047 8.251383 ACTCCGAAGATCTAAAGGATTGATAA 57.749 34.615 12.38 0.00 34.33 1.75
2048 2052 9.384764 CTTAAAACTCCGAAGATCTAAAGGATT 57.615 33.333 12.38 6.25 34.33 3.01
2071 2075 6.420913 AACTTTTCTGACACCTCTAGCTTA 57.579 37.500 0.00 0.00 0.00 3.09
2134 2138 1.334599 GGATCAAAAAGCAACGTCGCA 60.335 47.619 0.00 0.00 0.00 5.10
2227 2231 1.672145 GGTCTAAACCCAGCTCACGTC 60.672 57.143 0.00 0.00 39.93 4.34
2280 2284 2.024176 ATTTCTATCGCGGCACTGTT 57.976 45.000 6.13 0.00 0.00 3.16
2287 2291 4.369182 ACTAGGTTGAATTTCTATCGCGG 58.631 43.478 6.13 0.00 0.00 6.46
2296 2300 6.396450 GTTCCTCTCGTACTAGGTTGAATTT 58.604 40.000 0.00 0.00 34.30 1.82
2355 2359 1.717194 CTTCGCGCCACTAGGTTTTA 58.283 50.000 0.00 0.00 37.19 1.52
2360 2364 1.589196 GTAGCTTCGCGCCACTAGG 60.589 63.158 0.00 0.00 40.39 3.02
2362 2366 2.493030 GGTAGCTTCGCGCCACTA 59.507 61.111 0.00 0.00 40.39 2.74
2406 2410 5.420725 TGCTAGCTTGGATTCTGACTTAA 57.579 39.130 17.23 0.00 0.00 1.85
2459 2463 3.315949 AAGCGCCCCTAACGTGGA 61.316 61.111 2.29 0.00 0.00 4.02
2534 2538 0.037447 GAAGGGAGCTTCAAGGCAGT 59.963 55.000 0.00 0.00 33.80 4.40
2536 2540 1.380302 GGAAGGGAGCTTCAAGGCA 59.620 57.895 0.00 0.00 35.19 4.75
2541 2545 1.374947 CGTTGGGAAGGGAGCTTCA 59.625 57.895 0.00 0.00 35.19 3.02
2585 2589 1.469595 CCCCGTCGCGTATTTAAGTCA 60.470 52.381 5.77 0.00 0.00 3.41
2622 2626 0.247460 TTCTCAGTGGATCGTGCCAG 59.753 55.000 0.00 0.00 38.95 4.85


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

AutoCloner maintained by Alex Coulton.