Multiple sequence alignment - TraesCS7D01G554500

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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 TraesCS7D01G554500 chr7D 100.000 2600 0 0 1 2600 638345181 638342582 0.000000e+00 4802
1 TraesCS7D01G554500 chr7D 87.883 751 68 11 857 1606 638354732 638354004 0.000000e+00 861
2 TraesCS7D01G554500 chr7D 82.637 455 52 8 1752 2190 638352367 638351924 6.790000e-101 377
3 TraesCS7D01G554500 chr7D 91.011 267 22 2 2188 2454 638351813 638351549 2.460000e-95 359
4 TraesCS7D01G554500 chr7D 87.805 123 7 3 1647 1767 638354007 638353891 1.250000e-28 137
5 TraesCS7D01G554500 chr7A 93.435 1569 81 11 1031 2598 727710385 727711932 0.000000e+00 2307
6 TraesCS7D01G554500 chr7A 94.785 1323 62 2 1278 2600 727597231 727598546 0.000000e+00 2054
7 TraesCS7D01G554500 chr7A 86.383 1645 177 24 1 1630 727582744 727584356 0.000000e+00 1753
8 TraesCS7D01G554500 chr7A 86.196 1304 132 23 1 1284 727585946 727587221 0.000000e+00 1367
9 TraesCS7D01G554500 chr7A 90.849 754 65 4 877 1630 727580703 727581452 0.000000e+00 1007
10 TraesCS7D01G554500 chr7A 83.898 1093 125 29 1 1071 727579636 727580699 0.000000e+00 996
11 TraesCS7D01G554500 chr7A 84.036 664 74 13 5 656 727709344 727709987 6.150000e-171 610
12 TraesCS7D01G554500 chr7A 90.431 209 9 7 653 858 727710099 727710299 5.520000e-67 265
13 TraesCS7D01G554500 chr7A 77.059 510 69 17 1122 1595 727692489 727692986 1.540000e-62 250
14 TraesCS7D01G554500 chr7B 87.760 1732 140 27 1 1717 734365154 734366828 0.000000e+00 1958
15 TraesCS7D01G554500 chr7B 93.043 460 32 0 1731 2190 734366925 734367384 0.000000e+00 673
16 TraesCS7D01G554500 chr7B 94.891 411 20 1 2190 2600 734368491 734368900 2.180000e-180 641
17 TraesCS7D01G554500 chr7B 77.778 648 105 28 998 1614 734379435 734380074 1.900000e-96 363


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 TraesCS7D01G554500 chr7D 638342582 638345181 2599 True 4802.000000 4802 100.000000 1 2600 1 chr7D.!!$R1 2599
1 TraesCS7D01G554500 chr7D 638351549 638354732 3183 True 433.500000 861 87.334000 857 2454 4 chr7D.!!$R2 1597
2 TraesCS7D01G554500 chr7A 727597231 727598546 1315 False 2054.000000 2054 94.785000 1278 2600 1 chr7A.!!$F1 1322
3 TraesCS7D01G554500 chr7A 727579636 727587221 7585 False 1280.750000 1753 86.831500 1 1630 4 chr7A.!!$F3 1629
4 TraesCS7D01G554500 chr7A 727709344 727711932 2588 False 1060.666667 2307 89.300667 5 2598 3 chr7A.!!$F4 2593
5 TraesCS7D01G554500 chr7B 734365154 734368900 3746 False 1090.666667 1958 91.898000 1 2600 3 chr7B.!!$F2 2599
6 TraesCS7D01G554500 chr7B 734379435 734380074 639 False 363.000000 363 77.778000 998 1614 1 chr7B.!!$F1 616

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
36 37 0.109723 GTAGTGGCACCCTTCACCAA 59.89 55.0 15.27 0.0 34.63 3.67 F
694 853 0.249741 ACCACTCGGTACAACAGTGC 60.25 55.0 10.97 0.0 46.71 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1970 0.909133 TGCTATCTCCACCACCAGCA 60.909 55.0 0.00 0.0 36.72 4.41 R
2146 8762 0.037697 CGTTCAATCTCCACCGGTCA 60.038 55.0 2.59 0.0 0.00 4.02 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
35 36 1.057275 TGTAGTGGCACCCTTCACCA 61.057 55.000 15.27 0.00 34.67 4.17
36 37 0.109723 GTAGTGGCACCCTTCACCAA 59.890 55.000 15.27 0.00 34.63 3.67
45 46 4.306600 GCACCCTTCACCAATGTAAAAAG 58.693 43.478 0.00 0.00 0.00 2.27
50 51 6.183360 ACCCTTCACCAATGTAAAAAGGAAAG 60.183 38.462 0.00 0.00 0.00 2.62
111 112 0.486879 TGTTGAAAAGGGGCCTGGAT 59.513 50.000 0.84 0.00 0.00 3.41
114 115 0.783206 TGAAAAGGGGCCTGGATTCA 59.217 50.000 0.84 6.59 0.00 2.57
133 135 5.371115 TTCAACCTATTTTTCCGCTTCAG 57.629 39.130 0.00 0.00 0.00 3.02
137 139 3.435671 ACCTATTTTTCCGCTTCAGTTCG 59.564 43.478 0.00 0.00 0.00 3.95
156 158 9.100554 TCAGTTCGAAATAAGAAAAGTACACAA 57.899 29.630 0.00 0.00 0.00 3.33
157 159 9.155053 CAGTTCGAAATAAGAAAAGTACACAAC 57.845 33.333 0.00 0.00 0.00 3.32
158 160 8.885722 AGTTCGAAATAAGAAAAGTACACAACA 58.114 29.630 0.00 0.00 0.00 3.33
204 206 4.620723 TCTGTCCCCTTACATGTCTACAT 58.379 43.478 0.00 0.00 36.96 2.29
246 249 2.095853 GCATGTACACATTGAACCCTCG 59.904 50.000 0.00 0.00 33.61 4.63
257 260 2.557317 TGAACCCTCGTTTGTCTGTTC 58.443 47.619 0.00 0.00 34.25 3.18
266 269 3.002246 TCGTTTGTCTGTTCATGCAGTTC 59.998 43.478 0.00 0.00 37.70 3.01
271 274 3.181462 TGTCTGTTCATGCAGTTCTGTCT 60.181 43.478 0.00 0.00 37.70 3.41
312 316 6.323482 CACAAACATATAATTGGTGGGGATGA 59.677 38.462 5.07 0.00 0.00 2.92
357 373 7.604657 AGAAGAAGAAGAGAAAGTTGGTCTA 57.395 36.000 0.00 0.00 0.00 2.59
363 379 7.659652 AGAAGAGAAAGTTGGTCTAAATTCG 57.340 36.000 0.00 0.00 0.00 3.34
401 417 1.227380 CGCCCTCATTTCCTCCTCG 60.227 63.158 0.00 0.00 0.00 4.63
423 439 3.867600 GCATATGAGCGGACATCCTGAAT 60.868 47.826 6.97 0.00 0.00 2.57
425 441 2.890808 TGAGCGGACATCCTGAATAC 57.109 50.000 0.00 0.00 0.00 1.89
529 546 6.490040 ACATATGGAAAGGATTTAATGTCCCG 59.510 38.462 7.80 0.00 39.27 5.14
533 550 4.457466 GAAAGGATTTAATGTCCCGGCTA 58.543 43.478 0.00 0.00 39.27 3.93
535 552 3.314693 AGGATTTAATGTCCCGGCTAGA 58.685 45.455 0.00 0.00 36.36 2.43
536 553 3.325135 AGGATTTAATGTCCCGGCTAGAG 59.675 47.826 0.00 0.00 36.36 2.43
537 554 3.323979 GGATTTAATGTCCCGGCTAGAGA 59.676 47.826 0.00 0.00 0.00 3.10
557 577 6.064717 AGAGACTCTTAGCACCACAATTTTT 58.935 36.000 0.00 0.00 0.00 1.94
607 651 4.617223 GCTAAAGCGTGTTTCATCTTTTCC 59.383 41.667 0.00 0.00 31.92 3.13
615 659 5.619086 CGTGTTTCATCTTTTCCCACATACC 60.619 44.000 0.00 0.00 0.00 2.73
627 671 0.796312 CACATACCGTGGTTCACTGC 59.204 55.000 0.00 0.00 42.34 4.40
636 680 2.417719 GTGGTTCACTGCTTGGTCTAG 58.582 52.381 0.00 0.00 0.00 2.43
682 841 3.057526 TCACAACTGATCACTACCACTCG 60.058 47.826 0.00 0.00 0.00 4.18
694 853 0.249741 ACCACTCGGTACAACAGTGC 60.250 55.000 10.97 0.00 46.71 4.40
740 902 7.458397 TGGACAAATATCCTTCCATGTATACC 58.542 38.462 0.00 0.00 39.75 2.73
741 903 6.594159 GGACAAATATCCTTCCATGTATACCG 59.406 42.308 0.00 0.00 35.68 4.02
742 904 6.472887 ACAAATATCCTTCCATGTATACCGG 58.527 40.000 0.00 0.00 0.00 5.28
746 908 1.351017 CCTTCCATGTATACCGGCCAT 59.649 52.381 0.00 0.00 0.00 4.40
836 999 2.757099 CCCGTACCGCCACTACCT 60.757 66.667 0.00 0.00 0.00 3.08
845 1008 2.505982 CCACTACCTCATGGCCCG 59.494 66.667 0.00 0.00 36.63 6.13
847 1010 3.480133 ACTACCTCATGGCCCGGC 61.480 66.667 0.00 0.00 36.63 6.13
848 1011 4.609018 CTACCTCATGGCCCGGCG 62.609 72.222 0.00 0.00 36.63 6.46
851 1014 4.169696 CCTCATGGCCCGGCGTTA 62.170 66.667 6.01 0.00 0.00 3.18
853 1016 4.476752 TCATGGCCCGGCGTTACC 62.477 66.667 6.01 4.49 0.00 2.85
854 1017 4.483243 CATGGCCCGGCGTTACCT 62.483 66.667 6.01 0.00 35.61 3.08
875 1045 2.671070 CACTGGTCCTTCCGCCAT 59.329 61.111 0.00 0.00 39.52 4.40
982 1159 2.559440 CTCTTAGCCACCAGAGCATTC 58.441 52.381 0.00 0.00 30.45 2.67
986 1163 2.989639 CCACCAGAGCATTCCGGA 59.010 61.111 0.00 0.00 0.00 5.14
987 1164 1.450312 CCACCAGAGCATTCCGGAC 60.450 63.158 1.83 0.00 0.00 4.79
1010 1187 0.884704 AACAAGACCATGCGCGTTCT 60.885 50.000 8.43 0.00 0.00 3.01
1251 1634 1.296715 CAGTTCCTCCTCCAACCCG 59.703 63.158 0.00 0.00 0.00 5.28
1286 1669 3.738982 TCAAGAAGAAGGCAATTGACGA 58.261 40.909 10.34 0.00 0.00 4.20
1797 6893 8.608844 TCATTTTCTTCAACTTCCTCTACTTC 57.391 34.615 0.00 0.00 0.00 3.01
1971 7081 3.583806 TGCTTGAACAAATTATTGGGCG 58.416 40.909 0.00 0.00 41.01 6.13
1977 7087 7.148490 GCTTGAACAAATTATTGGGCGTAAATT 60.148 33.333 0.00 0.00 41.01 1.82
2224 10615 1.142667 TGCAGGACAACAATCCACTGA 59.857 47.619 0.00 0.00 41.73 3.41
2346 10737 4.746115 GTCTACGACATAGTCTCGACATCT 59.254 45.833 0.00 0.00 35.08 2.90
2529 10920 2.866762 AGAAACACTCACGAAAGACTGC 59.133 45.455 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.107831 GTGAAGGGTGCCACTACACA 59.892 55.000 0.00 0.00 42.55 3.72
20 21 0.827507 ACATTGGTGAAGGGTGCCAC 60.828 55.000 0.00 0.00 31.19 5.01
111 112 4.825085 ACTGAAGCGGAAAAATAGGTTGAA 59.175 37.500 0.00 0.00 0.00 2.69
114 115 4.083484 CGAACTGAAGCGGAAAAATAGGTT 60.083 41.667 0.00 0.00 0.00 3.50
133 135 8.940924 GTGTTGTGTACTTTTCTTATTTCGAAC 58.059 33.333 0.00 0.00 0.00 3.95
204 206 4.124238 GCCAAACACTGTACTGTTGTCTA 58.876 43.478 2.16 0.00 34.50 2.59
212 214 3.813166 GTGTACATGCCAAACACTGTACT 59.187 43.478 0.00 0.00 40.33 2.73
214 216 3.809905 TGTGTACATGCCAAACACTGTA 58.190 40.909 17.04 0.00 43.09 2.74
246 249 4.201950 ACAGAACTGCATGAACAGACAAAC 60.202 41.667 7.27 0.00 40.25 2.93
257 260 5.048921 ACAATTTGAGAGACAGAACTGCATG 60.049 40.000 2.79 0.00 0.00 4.06
266 269 4.450419 GTGTCTGGACAATTTGAGAGACAG 59.550 45.833 20.22 13.00 43.77 3.51
271 274 4.946772 TGTTTGTGTCTGGACAATTTGAGA 59.053 37.500 2.79 0.00 43.77 3.27
347 363 5.181245 CACCATGTCGAATTTAGACCAACTT 59.819 40.000 7.12 0.00 37.80 2.66
349 365 4.693566 TCACCATGTCGAATTTAGACCAAC 59.306 41.667 7.12 0.00 37.80 3.77
357 373 2.744202 GACAGCTCACCATGTCGAATTT 59.256 45.455 0.00 0.00 36.76 1.82
363 379 0.037326 TTCGGACAGCTCACCATGTC 60.037 55.000 6.53 0.35 44.10 3.06
401 417 1.001293 TCAGGATGTCCGCTCATATGC 59.999 52.381 0.00 0.00 42.08 3.14
423 439 4.466370 AGACTCCCAAATCGTCTTCATGTA 59.534 41.667 0.00 0.00 34.55 2.29
425 441 3.620374 CAGACTCCCAAATCGTCTTCATG 59.380 47.826 0.00 0.00 35.95 3.07
529 546 2.100087 GTGGTGCTAAGAGTCTCTAGCC 59.900 54.545 21.45 15.76 34.87 3.93
533 550 4.899352 AATTGTGGTGCTAAGAGTCTCT 57.101 40.909 0.00 0.00 0.00 3.10
557 577 7.334421 ACTTTTCGATCTTGCTATGCTCTAAAA 59.666 33.333 0.00 0.00 0.00 1.52
560 580 5.750547 CACTTTTCGATCTTGCTATGCTCTA 59.249 40.000 0.00 0.00 0.00 2.43
561 581 4.569966 CACTTTTCGATCTTGCTATGCTCT 59.430 41.667 0.00 0.00 0.00 4.09
562 582 4.784710 GCACTTTTCGATCTTGCTATGCTC 60.785 45.833 0.00 0.00 0.00 4.26
572 598 3.123621 CACGCTTTAGCACTTTTCGATCT 59.876 43.478 2.29 0.00 42.21 2.75
577 621 4.347813 TGAAACACGCTTTAGCACTTTTC 58.652 39.130 2.29 7.13 42.21 2.29
615 659 0.532862 AGACCAAGCAGTGAACCACG 60.533 55.000 0.00 0.00 39.64 4.94
648 692 8.993121 AGTGATCAGTTGTGAAAATAGTAACTG 58.007 33.333 0.00 0.00 45.78 3.16
682 841 1.272807 TCTAGGGGCACTGTTGTACC 58.727 55.000 0.00 0.00 0.00 3.34
694 853 0.695347 GCCAATCCAGGATCTAGGGG 59.305 60.000 1.11 1.36 0.00 4.79
737 899 1.221293 CCGTTTGGTATGGCCGGTA 59.779 57.895 1.90 0.00 41.21 4.02
738 900 1.917336 ATCCGTTTGGTATGGCCGGT 61.917 55.000 1.90 0.00 41.21 5.28
739 901 0.107081 TATCCGTTTGGTATGGCCGG 59.893 55.000 0.00 0.00 41.21 6.13
740 902 1.956297 TTATCCGTTTGGTATGGCCG 58.044 50.000 0.00 0.00 41.21 6.13
741 903 4.648651 ACTATTATCCGTTTGGTATGGCC 58.351 43.478 0.00 0.00 36.30 5.36
742 904 6.225318 TGTACTATTATCCGTTTGGTATGGC 58.775 40.000 0.00 0.00 36.30 4.40
746 908 7.542890 TCGTTTGTACTATTATCCGTTTGGTA 58.457 34.615 0.00 0.00 36.30 3.25
836 999 4.476752 GGTAACGCCGGGCCATGA 62.477 66.667 14.55 0.00 0.00 3.07
842 1005 3.708544 TGGGAAGGTAACGCCGGG 61.709 66.667 2.18 0.00 43.70 5.73
845 1008 1.376812 CCAGTGGGAAGGTAACGCC 60.377 63.158 0.00 0.00 38.05 5.68
847 1010 0.036671 GGACCAGTGGGAAGGTAACG 60.037 60.000 15.21 0.00 38.50 3.18
848 1011 1.359168 AGGACCAGTGGGAAGGTAAC 58.641 55.000 15.21 0.00 38.50 2.50
850 1013 1.652947 GAAGGACCAGTGGGAAGGTA 58.347 55.000 15.21 0.00 38.50 3.08
851 1014 1.134438 GGAAGGACCAGTGGGAAGGT 61.134 60.000 15.21 0.00 41.83 3.50
853 1016 1.296715 CGGAAGGACCAGTGGGAAG 59.703 63.158 15.21 0.00 38.90 3.46
854 1017 2.890766 GCGGAAGGACCAGTGGGAA 61.891 63.158 15.21 0.00 38.90 3.97
875 1045 1.855295 TTATAGCGTCAGTGGGGTGA 58.145 50.000 0.00 0.00 0.00 4.02
982 1159 0.320421 ATGGTCTTGTTGTCGTCCGG 60.320 55.000 0.00 0.00 0.00 5.14
986 1163 1.841663 GCGCATGGTCTTGTTGTCGT 61.842 55.000 0.30 0.00 0.00 4.34
987 1164 1.154413 GCGCATGGTCTTGTTGTCG 60.154 57.895 0.30 0.00 0.00 4.35
1010 1187 3.695606 GGTGCAGGACTCTCGCCA 61.696 66.667 0.00 0.00 0.00 5.69
1075 1446 2.033141 CTGTGGTGAGGCAGGTGG 59.967 66.667 0.00 0.00 0.00 4.61
1077 1448 2.756042 TTGCTGTGGTGAGGCAGGT 61.756 57.895 0.00 0.00 37.28 4.00
1286 1669 3.547787 AAGGAGACGGTGGGGAGCT 62.548 63.158 0.00 0.00 0.00 4.09
1311 1694 2.345991 GGCTGTGGTGAAGCGGTA 59.654 61.111 0.00 0.00 41.78 4.02
1566 1970 0.909133 TGCTATCTCCACCACCAGCA 60.909 55.000 0.00 0.00 36.72 4.41
1797 6893 4.461992 ACAACGACTCATTTACCAAACG 57.538 40.909 0.00 0.00 0.00 3.60
1971 7081 5.470845 AGCTATTGTCGCACTCAATTTAC 57.529 39.130 0.00 0.00 36.92 2.01
1977 7087 7.279981 ACATATTAAAAGCTATTGTCGCACTCA 59.720 33.333 0.00 0.00 0.00 3.41
2069 7180 9.601971 GAGACTAAAAACGTAATTTGTTGCATA 57.398 29.630 8.95 0.00 0.00 3.14
2083 7194 6.968131 TGATTCAGATGGAGACTAAAAACG 57.032 37.500 0.00 0.00 0.00 3.60
2146 8762 0.037697 CGTTCAATCTCCACCGGTCA 60.038 55.000 2.59 0.00 0.00 4.02
2224 10615 3.875727 CTGCGGATTCATGACTTCTGATT 59.124 43.478 14.96 0.00 0.00 2.57
2529 10920 8.627208 ATCAAAATCCTAGCTACCAACATATG 57.373 34.615 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.