Multiple sequence alignment - TraesCS7D01G248000

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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 TraesCS7D01G248000 chr7D 100.000 6365 0 0 1 6365 219290533 219296897 0.000000e+00 11755
1 TraesCS7D01G248000 chr7A 96.491 6212 121 40 206 6364 231543666 231549833 0.000000e+00 10174
2 TraesCS7D01G248000 chr7A 92.453 212 8 4 1 210 231542032 231542237 4.830000e-76 296
3 TraesCS7D01G248000 chr7B 96.548 5504 150 22 602 6083 181039170 181033685 0.000000e+00 9075
4 TraesCS7D01G248000 chr7B 85.294 612 34 28 1 573 181040017 181039423 1.190000e-161 580
5 TraesCS7D01G248000 chr7B 94.245 278 12 1 6087 6364 181033583 181033310 7.630000e-114 422


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 TraesCS7D01G248000 chr7D 219290533 219296897 6364 False 11755 11755 100.000 1 6365 1 chr7D.!!$F1 6364
1 TraesCS7D01G248000 chr7A 231542032 231549833 7801 False 5235 10174 94.472 1 6364 2 chr7A.!!$F1 6363
2 TraesCS7D01G248000 chr7B 181033310 181040017 6707 True 3359 9075 92.029 1 6364 3 chr7B.!!$R1 6363


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
311 1759 0.030369 CGGCATCAGTCGTACTACCC 59.970 60.000 0.0 0.0 38.25 3.69 F
312 1760 0.030369 GGCATCAGTCGTACTACCCG 59.970 60.000 0.0 0.0 0.00 5.28 F
934 2661 0.032403 TCGTCCGTTTTGATCCGTGT 59.968 50.000 0.0 0.0 0.00 4.49 F
1272 3002 1.152599 CCACCACCATCACCACCAA 59.847 57.895 0.0 0.0 0.00 3.67 F
1871 3602 2.877168 CCAATGCTTATGGTCTCTCTGC 59.123 50.000 0.0 0.0 33.08 4.26 F
3856 5587 1.700186 GTTGGTGGGAGAAAGACCTCT 59.300 52.381 0.0 0.0 33.79 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 4038 1.003580 TGATGGAGGAGACTTTGCCAC 59.996 52.381 0.00 0.00 44.43 5.01 R
3038 4769 7.396540 AATTACCTGTCCATCTGAATTTGAC 57.603 36.000 0.00 0.00 0.00 3.18 R
3466 5197 2.028404 GCATGCATTCGTTTTTGCTAGC 59.972 45.455 14.21 8.10 39.60 3.42 R
3856 5587 1.838112 TACGGCCCTTAAGAACGAGA 58.162 50.000 16.49 5.19 0.00 4.04 R
4068 5799 1.403780 CCCGGTAAGTCAAAGGTCTCG 60.404 57.143 0.00 0.00 0.00 4.04 R
6311 8170 0.611714 AAGGCATCGTTTCCTACCGT 59.388 50.000 0.00 0.00 31.24 4.83 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
307 1755 1.139734 CAGCGGCATCAGTCGTACT 59.860 57.895 1.45 0.00 46.51 2.73
308 1756 0.380733 CAGCGGCATCAGTCGTACTA 59.619 55.000 1.45 0.00 46.51 1.82
309 1757 0.381089 AGCGGCATCAGTCGTACTAC 59.619 55.000 1.45 0.00 46.51 2.73
311 1759 0.030369 CGGCATCAGTCGTACTACCC 59.970 60.000 0.00 0.00 38.25 3.69
312 1760 0.030369 GGCATCAGTCGTACTACCCG 59.970 60.000 0.00 0.00 0.00 5.28
313 1761 0.594284 GCATCAGTCGTACTACCCGC 60.594 60.000 0.00 0.00 0.00 6.13
314 1762 0.736636 CATCAGTCGTACTACCCGCA 59.263 55.000 0.00 0.00 0.00 5.69
315 1763 0.737219 ATCAGTCGTACTACCCGCAC 59.263 55.000 0.00 0.00 0.00 5.34
316 1764 1.138247 CAGTCGTACTACCCGCACC 59.862 63.158 0.00 0.00 0.00 5.01
317 1765 1.303561 AGTCGTACTACCCGCACCA 60.304 57.895 0.00 0.00 0.00 4.17
318 1766 1.138247 GTCGTACTACCCGCACCAG 59.862 63.158 0.00 0.00 0.00 4.00
319 1767 2.202703 CGTACTACCCGCACCAGC 60.203 66.667 0.00 0.00 37.42 4.85
320 1768 2.975536 GTACTACCCGCACCAGCA 59.024 61.111 0.00 0.00 42.27 4.41
321 1769 1.447314 GTACTACCCGCACCAGCAC 60.447 63.158 0.00 0.00 42.27 4.40
322 1770 2.652095 TACTACCCGCACCAGCACC 61.652 63.158 0.00 0.00 42.27 5.01
323 1771 4.015406 CTACCCGCACCAGCACCA 62.015 66.667 0.00 0.00 42.27 4.17
324 1772 3.958147 CTACCCGCACCAGCACCAG 62.958 68.421 0.00 0.00 42.27 4.00
589 2083 4.142609 CTAGTTGAGCAGCTAATCCCAA 57.857 45.455 0.00 0.00 0.00 4.12
760 2478 1.534729 GCCGTTTCCACCATTTCTCT 58.465 50.000 0.00 0.00 0.00 3.10
799 2517 1.292223 CTCCTGTTTTCTCCGCGGA 59.708 57.895 29.03 29.03 0.00 5.54
893 2619 1.212616 CGACTGCTCCAATCGAATCC 58.787 55.000 0.00 0.00 38.10 3.01
899 2626 2.044806 CTCCAATCGAATCCCCCGCT 62.045 60.000 0.00 0.00 0.00 5.52
934 2661 0.032403 TCGTCCGTTTTGATCCGTGT 59.968 50.000 0.00 0.00 0.00 4.49
1140 2870 4.109675 CCGGAGAACGCCCCCATT 62.110 66.667 0.00 0.00 42.52 3.16
1272 3002 1.152599 CCACCACCATCACCACCAA 59.847 57.895 0.00 0.00 0.00 3.67
1790 3520 6.959639 TGATGCCACTTTTAGGGATTTATC 57.040 37.500 0.00 0.00 37.32 1.75
1856 3587 6.705863 AGAAATGGTTTCTCTATCCAATGC 57.294 37.500 0.00 0.00 46.62 3.56
1868 3599 6.210385 TCTCTATCCAATGCTTATGGTCTCTC 59.790 42.308 3.49 0.00 39.09 3.20
1871 3602 2.877168 CCAATGCTTATGGTCTCTCTGC 59.123 50.000 0.00 0.00 33.08 4.26
1992 3723 2.902423 AAGGCTTGCCGGACACAACA 62.902 55.000 5.05 0.00 0.00 3.33
2143 3874 3.264450 ACTTGATCCCCTACTGAACTTGG 59.736 47.826 0.00 0.00 0.00 3.61
2144 3875 3.199442 TGATCCCCTACTGAACTTGGA 57.801 47.619 0.00 0.00 0.00 3.53
2145 3876 3.736094 TGATCCCCTACTGAACTTGGAT 58.264 45.455 0.00 0.00 35.38 3.41
2146 3877 4.890988 TGATCCCCTACTGAACTTGGATA 58.109 43.478 0.00 0.00 32.91 2.59
2307 4038 5.883661 ACTCAATCAATAATGCAAACTCCG 58.116 37.500 0.00 0.00 0.00 4.63
3038 4769 3.251479 TCAGACCATTCTCCATCAACG 57.749 47.619 0.00 0.00 0.00 4.10
3070 4801 7.611770 TCAGATGGACAGGTAATTTATATCGG 58.388 38.462 0.00 0.00 0.00 4.18
3079 4810 5.001232 GGTAATTTATATCGGAGCTTGCCA 58.999 41.667 0.00 0.00 0.00 4.92
3466 5197 3.217599 TGAAGTAAGTCTGCTGCTACG 57.782 47.619 0.00 0.00 0.00 3.51
3856 5587 1.700186 GTTGGTGGGAGAAAGACCTCT 59.300 52.381 0.00 0.00 33.79 3.69
3975 5706 4.699257 GCTTGACCATTGACTCTGAATCTT 59.301 41.667 0.00 0.00 0.00 2.40
4068 5799 8.200792 GGTACCATATATGATGATTCAGGAGTC 58.799 40.741 14.54 0.00 34.73 3.36
4216 5947 9.891828 GTGATTACAACTTTGAATGTTCATACA 57.108 29.630 0.00 0.00 37.00 2.29
5537 7268 2.040545 TGGATAAAACCTTGCCGGAAGA 59.959 45.455 5.05 0.00 32.82 2.87
6093 7940 8.470657 TTTATAAATACAGTATGCAATGCCCA 57.529 30.769 1.53 0.00 42.53 5.36
6181 8028 1.434696 GGGCTTGTGATGCGAATGG 59.565 57.895 0.00 0.00 0.00 3.16
6311 8170 1.739196 GTGATCTGCACAGCTCGCA 60.739 57.895 9.52 7.12 46.91 5.10
6336 8195 1.654023 GGAAACGATGCCTTTCCCGG 61.654 60.000 0.00 0.00 40.59 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.512435 ACATGTGTAGTACGAGTATTCAAATAC 57.488 33.333 0.00 4.99 41.19 1.89
36 37 5.754782 TCATTATTGTACTTGGCCTGACAT 58.245 37.500 3.32 0.00 0.00 3.06
86 93 3.967335 CGCGATCGGGTCCTCCTC 61.967 72.222 22.77 0.00 0.00 3.71
293 1741 0.030369 CGGGTAGTACGACTGATGCC 59.970 60.000 6.07 0.00 0.00 4.40
307 1755 4.015406 CTGGTGCTGGTGCGGGTA 62.015 66.667 0.00 0.00 43.34 3.69
309 1757 4.015406 TACTGGTGCTGGTGCGGG 62.015 66.667 0.00 0.00 43.34 6.13
311 1759 2.742372 GGTACTGGTGCTGGTGCG 60.742 66.667 0.00 0.00 43.34 5.34
312 1760 1.672356 CTGGTACTGGTGCTGGTGC 60.672 63.158 0.00 0.00 40.20 5.01
313 1761 0.973632 TACTGGTACTGGTGCTGGTG 59.026 55.000 0.00 0.00 0.00 4.17
314 1762 0.974383 GTACTGGTACTGGTGCTGGT 59.026 55.000 3.89 0.00 33.45 4.00
315 1763 0.249398 GGTACTGGTACTGGTGCTGG 59.751 60.000 10.19 0.00 36.36 4.85
316 1764 0.973632 TGGTACTGGTACTGGTGCTG 59.026 55.000 10.19 0.00 36.36 4.41
317 1765 1.267121 CTGGTACTGGTACTGGTGCT 58.733 55.000 10.19 0.00 36.36 4.40
318 1766 0.974383 ACTGGTACTGGTACTGGTGC 59.026 55.000 10.19 0.00 36.36 5.01
319 1767 2.494870 GGTACTGGTACTGGTACTGGTG 59.505 54.545 19.84 2.61 37.93 4.17
320 1768 2.812658 GGTACTGGTACTGGTACTGGT 58.187 52.381 19.84 10.84 37.93 4.00
321 1769 1.747355 CGGTACTGGTACTGGTACTGG 59.253 57.143 20.04 13.05 39.18 4.00
322 1770 1.133790 GCGGTACTGGTACTGGTACTG 59.866 57.143 21.87 21.87 42.50 2.74
323 1771 1.467920 GCGGTACTGGTACTGGTACT 58.532 55.000 17.89 0.00 41.52 2.73
324 1772 0.457443 GGCGGTACTGGTACTGGTAC 59.543 60.000 17.89 15.45 41.52 3.34
325 1773 0.039472 TGGCGGTACTGGTACTGGTA 59.961 55.000 17.89 0.00 41.52 3.25
634 2347 1.440938 ATCGAGCCGAGACGAAGAGG 61.441 60.000 0.00 0.00 39.91 3.69
799 2517 3.023949 GCCTCACCTCATGTCGCCT 62.024 63.158 0.00 0.00 0.00 5.52
805 2523 0.609131 AAAACCCGCCTCACCTCATG 60.609 55.000 0.00 0.00 0.00 3.07
920 2647 1.924191 GCCACAACACGGATCAAAACG 60.924 52.381 0.00 0.00 0.00 3.60
1790 3520 1.586422 CAACCGGTGGCATCATAGAG 58.414 55.000 8.52 0.00 0.00 2.43
1856 3587 1.761784 AGCCTGCAGAGAGACCATAAG 59.238 52.381 17.39 0.00 0.00 1.73
1868 3599 1.174783 AAAATGCTCTCAGCCTGCAG 58.825 50.000 6.78 6.78 41.51 4.41
1871 3602 5.181748 AGTAACTAAAATGCTCTCAGCCTG 58.818 41.667 0.00 0.00 41.51 4.85
1992 3723 2.346365 GGTTTTCCTCCGCCGTCT 59.654 61.111 0.00 0.00 36.94 4.18
2143 3874 5.786401 ATCAACAAGTGAAAGAGCGTATC 57.214 39.130 0.00 0.00 40.50 2.24
2144 3875 6.560253 AAATCAACAAGTGAAAGAGCGTAT 57.440 33.333 0.00 0.00 40.50 3.06
2145 3876 7.485418 TTAAATCAACAAGTGAAAGAGCGTA 57.515 32.000 0.00 0.00 40.50 4.42
2146 3877 4.900635 AAATCAACAAGTGAAAGAGCGT 57.099 36.364 0.00 0.00 40.50 5.07
2307 4038 1.003580 TGATGGAGGAGACTTTGCCAC 59.996 52.381 0.00 0.00 44.43 5.01
3038 4769 7.396540 AATTACCTGTCCATCTGAATTTGAC 57.603 36.000 0.00 0.00 0.00 3.18
3070 4801 3.863142 ATCAACTGAAATGGCAAGCTC 57.137 42.857 0.00 0.00 0.00 4.09
3079 4810 6.209192 TGGCTTGTGACATAATCAACTGAAAT 59.791 34.615 0.00 0.00 39.72 2.17
3466 5197 2.028404 GCATGCATTCGTTTTTGCTAGC 59.972 45.455 14.21 8.10 39.60 3.42
3856 5587 1.838112 TACGGCCCTTAAGAACGAGA 58.162 50.000 16.49 5.19 0.00 4.04
4047 5778 7.914871 GTCTCGACTCCTGAATCATCATATATG 59.085 40.741 6.36 6.36 34.37 1.78
4068 5799 1.403780 CCCGGTAAGTCAAAGGTCTCG 60.404 57.143 0.00 0.00 0.00 4.04
4175 5906 6.614694 TGTAATCACCTTCCTAGTGCTAAA 57.385 37.500 0.00 0.00 35.14 1.85
4216 5947 2.158623 TGAACCTGTTCTCAACCTGCAT 60.159 45.455 11.03 0.00 40.14 3.96
5537 7268 7.353525 TGATTATCCCCACATATCAACACTTT 58.646 34.615 0.00 0.00 0.00 2.66
5757 7494 5.359576 AGATTCACACTTACACCAGCAAAAA 59.640 36.000 0.00 0.00 0.00 1.94
5864 7601 9.834628 CTAAACACAAGACAAAACAGTAAGAAA 57.165 29.630 0.00 0.00 0.00 2.52
5865 7602 9.221933 TCTAAACACAAGACAAAACAGTAAGAA 57.778 29.630 0.00 0.00 0.00 2.52
5866 7603 8.662141 GTCTAAACACAAGACAAAACAGTAAGA 58.338 33.333 0.00 0.00 42.43 2.10
6012 7760 3.081804 ACCCAGGCTTTCTATCAAAACG 58.918 45.455 0.00 0.00 0.00 3.60
6043 7792 2.991190 CAAGGAAATGCATGCACAGAAC 59.009 45.455 25.37 12.57 0.00 3.01
6093 7940 2.545526 CACGGAAGCGAATCAGCATAAT 59.454 45.455 0.00 0.00 40.15 1.28
6168 8015 1.102809 GGCATCCCATTCGCATCACA 61.103 55.000 0.00 0.00 0.00 3.58
6181 8028 3.514417 GGAAAAGCTCCGGCATCC 58.486 61.111 0.00 0.00 41.70 3.51
6272 8119 3.706373 TCTGGGTCCGGCTTCTGC 61.706 66.667 0.00 0.00 38.76 4.26
6273 8120 2.266055 GTCTGGGTCCGGCTTCTG 59.734 66.667 0.00 0.00 0.00 3.02
6311 8170 0.611714 AAGGCATCGTTTCCTACCGT 59.388 50.000 0.00 0.00 31.24 4.83



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

AutoCloner maintained by Alex Coulton.