Multiple sequence alignment - TraesCS7A01G393400

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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 TraesCS7A01G393400 chr7A 100.000 2234 0 0 1 2234 571634013 571636246 0 4126
1 TraesCS7A01G393400 chr7A 95.133 2260 82 10 1 2234 638507638 638509895 0 3539
2 TraesCS7A01G393400 chr7A 95.002 2261 82 12 1 2234 708245651 708243395 0 3520
3 TraesCS7A01G393400 chrUn 95.263 2259 80 10 1 2234 171008312 171006056 0 3554
4 TraesCS7A01G393400 chr7D 95.253 2254 85 11 1 2234 382089825 382087574 0 3550
5 TraesCS7A01G393400 chr7D 94.949 2257 86 12 1 2234 626711169 626713420 0 3511
6 TraesCS7A01G393400 chr7D 94.849 2252 96 9 1 2234 307032624 307034873 0 3498
7 TraesCS7A01G393400 chr6B 95.177 2260 80 12 1 2234 596601832 596604088 0 3542
8 TraesCS7A01G393400 chr5B 94.914 2261 86 12 1 2234 567280022 567277764 0 3511
9 TraesCS7A01G393400 chr1A 95.011 2245 93 9 1 2229 94663915 94666156 0 3507
10 TraesCS7A01G393400 chr4D 94.900 2255 91 12 1 2234 123401545 123399294 0 3506
11 TraesCS7A01G393400 chr1B 94.774 2258 91 11 1 2234 672541248 672538994 0 3491
12 TraesCS7A01G393400 chr1D 94.718 2253 85 13 1 2234 275786563 275788800 0 3470
13 TraesCS7A01G393400 chr1D 95.055 1901 74 9 352 2234 212445900 212447798 0 2972


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 TraesCS7A01G393400 chr7A 571634013 571636246 2233 False 4126 4126 100.000 1 2234 1 chr7A.!!$F1 2233
1 TraesCS7A01G393400 chr7A 638507638 638509895 2257 False 3539 3539 95.133 1 2234 1 chr7A.!!$F2 2233
2 TraesCS7A01G393400 chr7A 708243395 708245651 2256 True 3520 3520 95.002 1 2234 1 chr7A.!!$R1 2233
3 TraesCS7A01G393400 chrUn 171006056 171008312 2256 True 3554 3554 95.263 1 2234 1 chrUn.!!$R1 2233
4 TraesCS7A01G393400 chr7D 382087574 382089825 2251 True 3550 3550 95.253 1 2234 1 chr7D.!!$R1 2233
5 TraesCS7A01G393400 chr7D 626711169 626713420 2251 False 3511 3511 94.949 1 2234 1 chr7D.!!$F2 2233
6 TraesCS7A01G393400 chr7D 307032624 307034873 2249 False 3498 3498 94.849 1 2234 1 chr7D.!!$F1 2233
7 TraesCS7A01G393400 chr6B 596601832 596604088 2256 False 3542 3542 95.177 1 2234 1 chr6B.!!$F1 2233
8 TraesCS7A01G393400 chr5B 567277764 567280022 2258 True 3511 3511 94.914 1 2234 1 chr5B.!!$R1 2233
9 TraesCS7A01G393400 chr1A 94663915 94666156 2241 False 3507 3507 95.011 1 2229 1 chr1A.!!$F1 2228
10 TraesCS7A01G393400 chr4D 123399294 123401545 2251 True 3506 3506 94.900 1 2234 1 chr4D.!!$R1 2233
11 TraesCS7A01G393400 chr1B 672538994 672541248 2254 True 3491 3491 94.774 1 2234 1 chr1B.!!$R1 2233
12 TraesCS7A01G393400 chr1D 275786563 275788800 2237 False 3470 3470 94.718 1 2234 1 chr1D.!!$F2 2233
13 TraesCS7A01G393400 chr1D 212445900 212447798 1898 False 2972 2972 95.055 352 2234 1 chr1D.!!$F1 1882

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
177 178 0.239879 GGCGCCGAGAAATTTTGACA 59.76 50.0 12.58 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 1771 1.147333 TTCCCCCTTTACCGGAAACA 58.853 50.0 9.46 0.0 32.73 2.83 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
51 52 3.696898 AGACGCATTCAAGTCGATCTAC 58.303 45.455 0.00 0.00 41.86 2.59
52 53 2.789893 GACGCATTCAAGTCGATCTACC 59.210 50.000 0.00 0.00 0.00 3.18
62 63 1.067142 GTCGATCTACCACAACCAGCA 60.067 52.381 0.00 0.00 0.00 4.41
64 65 1.337728 CGATCTACCACAACCAGCACA 60.338 52.381 0.00 0.00 0.00 4.57
177 178 0.239879 GGCGCCGAGAAATTTTGACA 59.760 50.000 12.58 0.00 0.00 3.58
181 182 3.564511 CGCCGAGAAATTTTGACATGTT 58.435 40.909 0.00 0.00 0.00 2.71
379 389 3.235200 AGGCGAACATCTAATCTAGGCT 58.765 45.455 0.00 0.00 0.00 4.58
452 462 6.833041 TGGATATTAAGGAAGCCGTATTTCA 58.167 36.000 0.00 0.00 0.00 2.69
505 515 2.809601 CCTCCTGCGGTCGTTTCG 60.810 66.667 0.00 0.00 0.00 3.46
539 549 1.263342 TGGCTTCCCTCAGCTCAGAG 61.263 60.000 0.00 0.00 39.97 3.35
625 635 4.115516 CTGAATGTCATCGGGTACTCTTG 58.884 47.826 0.00 0.00 0.00 3.02
628 638 1.822990 TGTCATCGGGTACTCTTGACC 59.177 52.381 17.96 0.00 36.68 4.02
634 644 0.252558 GGGTACTCTTGACCTCCCCA 60.253 60.000 0.00 0.00 37.13 4.96
707 717 2.966516 AGAGTGGACGAGAAAGAAAGGT 59.033 45.455 0.00 0.00 0.00 3.50
730 744 1.551452 TTTTATTGGAGCAACCCCCG 58.449 50.000 0.00 0.00 38.00 5.73
759 773 0.771127 CCCAGGAGTTCACTTTCCCA 59.229 55.000 0.00 0.00 33.83 4.37
766 780 5.032846 AGGAGTTCACTTTCCCATATGAGA 58.967 41.667 3.65 0.00 33.83 3.27
810 824 2.076863 GGAAGAGTCAAATGGTCACCG 58.923 52.381 0.00 0.00 0.00 4.94
862 876 4.052229 CGTCTGAGGGTTCGCCGT 62.052 66.667 0.00 0.00 38.45 5.68
939 953 2.688446 CACCTATCACTAGTCTTCGGCA 59.312 50.000 0.00 0.00 0.00 5.69
1106 1123 3.320826 GTGAGGTACAACAAGGCCATTTT 59.679 43.478 5.01 0.00 0.00 1.82
1143 1160 1.133790 GAGCCGTACATGGACGTTACT 59.866 52.381 27.88 21.18 41.31 2.24
1264 1281 5.222048 GCCCTAACCATCCTAAATATGGACA 60.222 44.000 9.02 0.00 45.77 4.02
1270 1287 6.385443 ACCATCCTAAATATGGACAGAGAGA 58.615 40.000 9.02 0.00 45.77 3.10
1298 1315 2.288025 TTTTCCGGGGTCCTCGAGG 61.288 63.158 26.32 26.32 0.00 4.63
1338 1355 2.569183 GACGCTAGGGAGTCTGTGT 58.431 57.895 14.59 0.00 38.83 3.72
1398 1415 4.344865 GAGCCTCCCGTTTGCCCA 62.345 66.667 0.00 0.00 0.00 5.36
1563 1580 2.688958 TCTAAGCGAGCCTCTAAAGACC 59.311 50.000 0.00 0.00 0.00 3.85
1584 1601 9.558133 AAGACCCTACTCCTACTTTAAACTTAT 57.442 33.333 0.00 0.00 0.00 1.73
1606 1623 9.331282 CTTATAGTCCGATTCTTCCAATTCTTT 57.669 33.333 0.00 0.00 0.00 2.52
1608 1625 4.631813 AGTCCGATTCTTCCAATTCTTTCG 59.368 41.667 0.00 0.00 0.00 3.46
1685 1702 2.435693 GCGGCTACTCTGGGATGGT 61.436 63.158 0.00 0.00 0.00 3.55
1686 1703 1.742768 CGGCTACTCTGGGATGGTC 59.257 63.158 0.00 0.00 0.00 4.02
1687 1704 1.742768 GGCTACTCTGGGATGGTCG 59.257 63.158 0.00 0.00 0.00 4.79
1688 1705 0.755698 GGCTACTCTGGGATGGTCGA 60.756 60.000 0.00 0.00 0.00 4.20
1691 1728 0.629596 TACTCTGGGATGGTCGAGGT 59.370 55.000 0.00 0.00 0.00 3.85
1697 1734 0.322546 GGGATGGTCGAGGTTTGCTT 60.323 55.000 0.00 0.00 0.00 3.91
1711 1748 3.636764 GGTTTGCTTCCTTTCTTCTGGAA 59.363 43.478 0.00 0.00 39.73 3.53
1724 1761 4.489737 TCTTCTGGAACTAAGGAAGGACA 58.510 43.478 0.00 0.00 36.71 4.02
1734 1771 0.772124 AGGAAGGACATGTGGGTGGT 60.772 55.000 1.15 0.00 0.00 4.16
1814 1851 1.964373 GGGTTGGCGTTGTGTCGAT 60.964 57.895 0.00 0.00 0.00 3.59
1857 1894 6.294787 GGCTAGAGGTAATTTCGATGATCTCA 60.295 42.308 0.00 0.00 0.00 3.27
1864 1901 1.326951 TTCGATGATCTCACCGGCCA 61.327 55.000 0.00 0.00 32.68 5.36
1865 1902 1.143838 CGATGATCTCACCGGCCAA 59.856 57.895 0.00 0.00 0.00 4.52
1904 1941 4.751060 TCGCAATAACAATAAGGAGACGT 58.249 39.130 0.00 0.00 0.00 4.34
1922 1959 0.108804 GTGGTGACGTCGTCATCCAT 60.109 55.000 32.76 1.62 44.63 3.41
1992 2031 4.333372 GGGCTTGGATTCGTTTCGTTTATA 59.667 41.667 0.00 0.00 0.00 0.98
2146 2186 4.175787 ACTACGTTCTAACTTGAGCAGG 57.824 45.455 0.00 0.00 0.00 4.85
2196 2236 0.617820 CACCACCCCTACTACTGCCT 60.618 60.000 0.00 0.00 0.00 4.75
2229 2269 0.178961 GGTGAGCTTTCCCCAAGGTT 60.179 55.000 0.00 0.00 43.58 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 8.621286 AGAAGAAAATGAAATACGAACAACTGT 58.379 29.630 0.00 0.00 0.00 3.55
64 65 9.665264 GAAGAAGAAAATGAAATACGAACAACT 57.335 29.630 0.00 0.00 0.00 3.16
134 135 6.315551 CGAGAGAAAGACGAGATTCAGTAAA 58.684 40.000 0.00 0.00 0.00 2.01
169 170 2.773487 TCGACCCGAACATGTCAAAAT 58.227 42.857 0.00 0.00 31.06 1.82
177 178 0.747255 CCTCTGATCGACCCGAACAT 59.253 55.000 0.00 0.00 37.94 2.71
181 182 1.374343 CGAACCTCTGATCGACCCGA 61.374 60.000 0.00 0.00 41.43 5.14
379 389 1.136305 CCTTCATAGAAAGGCGACCGA 59.864 52.381 0.00 0.00 39.47 4.69
452 462 2.363683 GCTTCTTGGAGCTGCTATTGT 58.636 47.619 6.82 0.00 39.57 2.71
505 515 0.610232 AGCCAGCCAATTGAGTCACC 60.610 55.000 7.12 0.00 0.00 4.02
564 574 0.404040 GGGCGGGGATAATCATTCCA 59.596 55.000 0.00 0.00 34.77 3.53
625 635 0.698818 ACAAGAATGGTGGGGAGGTC 59.301 55.000 0.00 0.00 0.00 3.85
628 638 2.041081 TGGTTACAAGAATGGTGGGGAG 59.959 50.000 0.00 0.00 0.00 4.30
634 644 4.202567 ACAGGTGATGGTTACAAGAATGGT 60.203 41.667 0.00 0.00 0.00 3.55
676 686 1.612442 GTCCACTCTAGGGGGTGCA 60.612 63.158 0.00 0.00 32.68 4.57
714 724 2.685534 CCCGGGGGTTGCTCCAATA 61.686 63.158 14.71 0.00 38.11 1.90
715 725 4.060667 CCCGGGGGTTGCTCCAAT 62.061 66.667 14.71 0.00 38.11 3.16
766 780 9.085645 TCCACTGACTTATATATGTACCGAATT 57.914 33.333 1.48 0.00 0.00 2.17
802 816 0.324368 ATCCTCAGTAGCGGTGACCA 60.324 55.000 1.11 0.00 0.00 4.02
810 824 2.753319 GGGGGAGATCCTCAGTAGC 58.247 63.158 0.22 0.00 38.61 3.58
835 849 1.341187 ACCCTCAGACGACCCTTCTAG 60.341 57.143 0.00 0.00 0.00 2.43
862 876 4.300189 GTGTAAGCACAACAATGAACCA 57.700 40.909 0.00 0.00 44.64 3.67
939 953 2.990740 TTGTGCAATAAACCCCTCCT 57.009 45.000 0.00 0.00 0.00 3.69
1106 1123 1.228337 TCCGTGAGAAGGTGGACGA 60.228 57.895 0.00 0.00 33.64 4.20
1132 1149 4.046938 CTGTATGAGCAGTAACGTCCAT 57.953 45.455 0.00 0.00 0.00 3.41
1264 1281 3.086282 GGAAAACTCGAGACCTCTCTCT 58.914 50.000 21.68 0.00 40.96 3.10
1270 1287 1.542187 CCCCGGAAAACTCGAGACCT 61.542 60.000 21.68 1.60 0.00 3.85
1298 1315 4.025015 TCTACTCGACCTAAAATGCGAC 57.975 45.455 0.00 0.00 0.00 5.19
1338 1355 1.619827 CTTGAAATGCCAAGGGAAGCA 59.380 47.619 0.00 0.00 44.45 3.91
1398 1415 3.962718 CTGGATGTTAAATGCCCCTTGAT 59.037 43.478 0.00 0.00 0.00 2.57
1412 1429 5.006386 GGACTGATTTTGTCTCTGGATGTT 58.994 41.667 0.00 0.00 35.04 2.71
1537 1554 1.398692 AGAGGCTCGCTTAGAAGGAG 58.601 55.000 9.22 4.36 0.00 3.69
1584 1601 5.810587 CGAAAGAATTGGAAGAATCGGACTA 59.189 40.000 0.00 0.00 0.00 2.59
1606 1623 5.179045 ACGAAGTTCTACTTTGTCTTCGA 57.821 39.130 24.83 0.00 46.95 3.71
1685 1702 2.930826 AGAAAGGAAGCAAACCTCGA 57.069 45.000 0.00 0.00 36.67 4.04
1686 1703 3.058639 CAGAAGAAAGGAAGCAAACCTCG 60.059 47.826 0.00 0.00 36.67 4.63
1687 1704 3.254411 CCAGAAGAAAGGAAGCAAACCTC 59.746 47.826 0.00 0.00 36.67 3.85
1688 1705 3.117512 TCCAGAAGAAAGGAAGCAAACCT 60.118 43.478 0.00 0.00 39.69 3.50
1691 1728 4.536765 AGTTCCAGAAGAAAGGAAGCAAA 58.463 39.130 0.00 0.00 44.08 3.68
1697 1734 5.013183 CCTTCCTTAGTTCCAGAAGAAAGGA 59.987 44.000 14.90 14.90 39.09 3.36
1711 1748 2.305927 CACCCACATGTCCTTCCTTAGT 59.694 50.000 0.00 0.00 0.00 2.24
1724 1761 1.228429 CCGGAAACACCACCCACAT 60.228 57.895 0.00 0.00 38.90 3.21
1734 1771 1.147333 TTCCCCCTTTACCGGAAACA 58.853 50.000 9.46 0.00 32.73 2.83
1771 1808 2.144078 TGGGGCACTTCGAAGGTCA 61.144 57.895 27.86 15.00 0.00 4.02
1857 1894 1.674322 CGAGGAACAATTGGCCGGT 60.674 57.895 10.83 0.00 0.00 5.28
1864 1901 2.346803 CGATGGTGACGAGGAACAATT 58.653 47.619 0.00 0.00 0.00 2.32
1865 1902 2.007049 GCGATGGTGACGAGGAACAAT 61.007 52.381 0.00 0.00 0.00 2.71
1904 1941 1.465794 TATGGATGACGACGTCACCA 58.534 50.000 33.82 33.82 45.65 4.17
1922 1959 6.241882 CCTTTGGGGTTTTCTTTTTCCTTA 57.758 37.500 0.00 0.00 0.00 2.69
2044 2084 6.033937 GCGATTGGCTTCACTTTAGATTTTTC 59.966 38.462 0.00 0.00 39.11 2.29
2146 2186 5.240121 AGATGTCAAATGCCACCAATTTTC 58.760 37.500 0.00 0.00 0.00 2.29
2196 2236 1.888512 GCTCACCAAAGCAGGATTTCA 59.111 47.619 0.00 0.00 42.05 2.69


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

AutoCloner maintained by Alex Coulton.