Multiple sequence alignment - TraesCS3B01G360000

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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 TraesCS3B01G360000 chr3B 100.000 2416 0 0 1 2416 571810742 571813157 0.000000e+00 4462.0
1 TraesCS3B01G360000 chr3B 100.000 28 0 0 2378 2405 188248151 188248178 4.000000e-03 52.8
2 TraesCS3B01G360000 chr3D 94.808 2427 109 10 1 2416 436043571 436045991 0.000000e+00 3768.0
3 TraesCS3B01G360000 chr3D 93.493 2428 141 12 1 2416 436162785 436165207 0.000000e+00 3592.0
4 TraesCS3B01G360000 chr3D 76.667 150 29 6 2269 2414 427443555 427443702 7.160000e-11 78.7
5 TraesCS3B01G360000 chr3A 93.822 2428 128 14 1 2416 574865315 574867732 0.000000e+00 3633.0
6 TraesCS3B01G360000 chr5B 81.081 111 17 4 2308 2416 312276698 312276590 4.280000e-13 86.1
7 TraesCS3B01G360000 chr6D 80.000 95 16 3 192 285 447846449 447846541 1.550000e-07 67.6


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 TraesCS3B01G360000 chr3B 571810742 571813157 2415 False 4462 4462 100.000 1 2416 1 chr3B.!!$F2 2415
1 TraesCS3B01G360000 chr3D 436043571 436045991 2420 False 3768 3768 94.808 1 2416 1 chr3D.!!$F2 2415
2 TraesCS3B01G360000 chr3D 436162785 436165207 2422 False 3592 3592 93.493 1 2416 1 chr3D.!!$F3 2415
3 TraesCS3B01G360000 chr3A 574865315 574867732 2417 False 3633 3633 93.822 1 2416 1 chr3A.!!$F1 2415

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
223 224 0.384309 TTAGCTACGTGAGGATGGCG 59.616 55.0 0.00 0.0 0.00 5.69 F
1086 1093 0.036671 CCGTCGACCTAAAAGGGCTT 60.037 55.0 10.58 0.0 42.96 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1186 1193 0.179020 TTGGTGACCTTGGAGCACAG 60.179 55.0 2.11 0.0 34.33 3.66 R
2249 2263 1.102978 AACAGAGCAACCAAAGCGTT 58.897 45.0 0.00 0.0 37.01 4.84 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 4.826274 TGAATAGACCTGAAGAACCTGG 57.174 45.455 0.00 0.00 0.00 4.45
89 90 3.054139 AGAAATGCTAATCTCACTGCCCA 60.054 43.478 0.00 0.00 0.00 5.36
92 93 2.121948 TGCTAATCTCACTGCCCAGAT 58.878 47.619 1.69 0.00 0.00 2.90
143 144 7.711339 CCACTGTAGAAGTAAATATTGGACTCC 59.289 40.741 4.24 0.00 36.83 3.85
151 152 7.902920 AGTAAATATTGGACTCCGGTAAGTA 57.097 36.000 0.00 0.00 0.00 2.24
223 224 0.384309 TTAGCTACGTGAGGATGGCG 59.616 55.000 0.00 0.00 0.00 5.69
272 274 5.516090 TGTGCTTCAGTTTATTTTTCGACC 58.484 37.500 0.00 0.00 0.00 4.79
289 291 1.662122 GACCGAAACTTGTCGTGTGTT 59.338 47.619 0.00 0.00 39.43 3.32
325 327 3.159472 TCTTTGCATGACTGGAATTGCT 58.841 40.909 0.00 0.00 36.10 3.91
355 358 4.624364 CAGTGCCGGAGTGCCACA 62.624 66.667 5.05 0.00 0.00 4.17
386 389 5.867716 ACGTGTGTCACTTATCATTTAGGTC 59.132 40.000 4.27 0.00 31.34 3.85
503 506 1.971481 ATATGCTGCAAATGCCTCGA 58.029 45.000 6.36 0.00 41.18 4.04
601 604 6.519679 AAATAGCTGCATTTGTTGAGATGA 57.480 33.333 1.02 0.00 0.00 2.92
627 630 5.176774 TCAGTACAACAAACATAAGTGCTCG 59.823 40.000 0.00 0.00 0.00 5.03
669 672 4.158384 CAGAATGGACGGTTGAAATTTCG 58.842 43.478 13.34 4.70 0.00 3.46
713 716 6.801862 GGAATATATATGCAACGGAACAAAGC 59.198 38.462 3.03 0.00 0.00 3.51
749 752 3.192844 ACACGTGTCTACATAGGAACCAG 59.807 47.826 17.22 0.00 0.00 4.00
800 803 4.327357 GCATGTGTGTACATCTGTCTACAC 59.673 45.833 16.72 16.72 45.53 2.90
837 843 1.880027 GACACTTGTCAATCACCACCC 59.120 52.381 4.43 0.00 44.18 4.61
840 846 1.214175 ACTTGTCAATCACCACCCACA 59.786 47.619 0.00 0.00 0.00 4.17
936 942 1.949525 CAGAGGACAACCACACCAAAG 59.050 52.381 0.00 0.00 38.94 2.77
951 958 5.006746 CACACCAAAGAACACAACTCTAGAC 59.993 44.000 0.00 0.00 0.00 2.59
1015 1022 7.871853 AGTAGTAGTTATGGCAAAACACTTTG 58.128 34.615 0.00 0.00 44.11 2.77
1086 1093 0.036671 CCGTCGACCTAAAAGGGCTT 60.037 55.000 10.58 0.00 42.96 4.35
1089 1096 3.528532 CGTCGACCTAAAAGGGCTTATT 58.471 45.455 10.58 0.00 42.96 1.40
1092 1099 2.870411 CGACCTAAAAGGGCTTATTCGG 59.130 50.000 0.00 0.00 42.96 4.30
1103 1110 1.810151 GCTTATTCGGGAGTGCAAACA 59.190 47.619 0.00 0.00 0.00 2.83
1140 1147 1.134371 GCGAGCCCAAAGATAACTCCT 60.134 52.381 0.00 0.00 0.00 3.69
1177 1184 4.170468 AGTGTGGTTCAGAAGGTCAATT 57.830 40.909 0.00 0.00 0.00 2.32
1186 1193 0.521735 GAAGGTCAATTCACCGTGCC 59.478 55.000 0.00 0.00 41.90 5.01
1259 1266 5.126545 AGGTTGTGTATGTCGCTGATTACTA 59.873 40.000 0.00 0.00 0.00 1.82
1317 1324 6.967199 GCAGTAAGTGTTATATTTTGAGCCAC 59.033 38.462 0.00 0.00 0.00 5.01
1330 1337 4.739587 TTGAGCCACGTATTATGTACCA 57.260 40.909 0.00 0.00 0.00 3.25
1407 1414 3.591527 AGGTTACCATGTCCCATCTCAAA 59.408 43.478 3.51 0.00 0.00 2.69
1554 1562 2.258286 GAATGTGGCCGGTTGTGC 59.742 61.111 1.90 0.00 0.00 4.57
1649 1657 5.491323 TTTGTTTGGTCCTTTTCTGGTTT 57.509 34.783 0.00 0.00 0.00 3.27
1691 1699 6.991531 TGAATGGGGATTGAAAACAAGAAAAG 59.008 34.615 0.00 0.00 0.00 2.27
1702 1710 9.500785 TTGAAAACAAGAAAAGGAAATCTTTGT 57.499 25.926 0.00 0.00 44.30 2.83
1705 1713 8.707938 AAACAAGAAAAGGAAATCTTTGTCAG 57.292 30.769 0.00 0.00 44.30 3.51
1749 1757 8.258007 ACTATTCGATGATAAGTCCTTTGTGAA 58.742 33.333 0.00 0.00 0.00 3.18
1751 1759 6.968131 TCGATGATAAGTCCTTTGTGAAAG 57.032 37.500 0.00 0.00 38.24 2.62
1858 1866 1.247567 AAACTGGATTGGTGCTTCGG 58.752 50.000 0.00 0.00 0.00 4.30
1968 1980 7.722363 TGCCTCGATCTTTATTAATAGTGTGA 58.278 34.615 0.00 0.00 0.00 3.58
2019 2031 7.572814 TGGATGTGTCTGGATGAATAAATGTA 58.427 34.615 0.00 0.00 0.00 2.29
2079 2093 8.848474 ATACAACAAAAGTAAGTGCTCATAGT 57.152 30.769 0.00 0.00 0.00 2.12
2081 2095 7.417612 ACAACAAAAGTAAGTGCTCATAGTTG 58.582 34.615 0.00 0.00 37.89 3.16
2109 2123 4.396357 AGACAAACCCAATGGACCATTA 57.604 40.909 19.41 0.00 32.35 1.90
2136 2150 1.372872 GTGAATTGGTGTTGGCGCC 60.373 57.895 22.73 22.73 45.23 6.53
2191 2205 3.181455 TGCTAGTGTTGATGAAGTGGTGT 60.181 43.478 0.00 0.00 0.00 4.16
2243 2257 2.265739 GAGCACTCGGACCATGCA 59.734 61.111 13.30 0.00 41.97 3.96
2249 2263 2.837498 CACTCGGACCATGCATCATAA 58.163 47.619 0.00 0.00 0.00 1.90
2285 2300 4.954875 TCTGTTGAATTTTCGCCCAAAAT 58.045 34.783 0.00 0.00 45.15 1.82
2366 2381 6.316140 TGTTCATTCCTGCACATCAATAGTAC 59.684 38.462 0.00 0.00 0.00 2.73
2374 2389 4.155826 TGCACATCAATAGTACCAACAAGC 59.844 41.667 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.593933 CGCAATGGCAATATTTGGTGC 59.406 47.619 0.00 0.00 41.24 5.01
72 73 1.571955 TCTGGGCAGTGAGATTAGCA 58.428 50.000 0.00 0.00 0.00 3.49
92 93 9.817809 GGAGTACATATTTGTATTTCTGACTCA 57.182 33.333 12.26 0.00 40.35 3.41
143 144 6.003720 CGTATCTTACGTGTGGTACTTACCG 61.004 48.000 0.00 2.26 46.57 4.02
208 209 2.225068 AAATCGCCATCCTCACGTAG 57.775 50.000 0.00 0.00 0.00 3.51
213 214 2.917933 CCAACTAAATCGCCATCCTCA 58.082 47.619 0.00 0.00 0.00 3.86
223 224 2.094078 TGCCATGCTTGCCAACTAAATC 60.094 45.455 0.00 0.00 0.00 2.17
272 274 3.548668 TCAGTAACACACGACAAGTTTCG 59.451 43.478 0.00 6.08 44.87 3.46
289 291 7.884257 TCATGCAAAGATGACAAATTTCAGTA 58.116 30.769 0.00 0.00 0.00 2.74
325 327 3.319689 TCCGGCACTGACATTATTCGATA 59.680 43.478 0.00 0.00 0.00 2.92
601 604 6.055588 AGCACTTATGTTTGTTGTACTGACT 58.944 36.000 0.00 0.00 0.00 3.41
627 630 7.421530 TTCTGTTTGTCTTATAGTCAACTGC 57.578 36.000 0.00 0.00 0.00 4.40
692 695 6.094186 TGTTGCTTTGTTCCGTTGCATATATA 59.906 34.615 0.00 0.00 33.50 0.86
705 708 5.064707 TGTCTACACTTCTGTTGCTTTGTTC 59.935 40.000 0.00 0.00 0.00 3.18
713 716 3.444916 ACACGTGTCTACACTTCTGTTG 58.555 45.455 17.22 2.27 44.34 3.33
800 803 2.468040 GTGTCACGACTTCTGTTTCTCG 59.532 50.000 0.00 0.00 0.00 4.04
840 846 9.547279 AGGGAAAATAATTACTTCAATCAAGGT 57.453 29.630 10.00 0.00 36.26 3.50
936 942 9.909644 TTAGATGTTAAGTCTAGAGTTGTGTTC 57.090 33.333 20.93 12.83 30.45 3.18
951 958 6.547880 TGGCTACCTCTCTCTTAGATGTTAAG 59.452 42.308 0.00 0.00 35.10 1.85
1015 1022 1.269778 GGCAAGAACCAAGAGCAAACC 60.270 52.381 0.00 0.00 0.00 3.27
1086 1093 5.065859 CACATATTGTTTGCACTCCCGAATA 59.934 40.000 0.00 0.00 0.00 1.75
1089 1096 2.746904 CACATATTGTTTGCACTCCCGA 59.253 45.455 0.00 0.00 0.00 5.14
1092 1099 5.314923 ACATCACATATTGTTTGCACTCC 57.685 39.130 0.00 0.00 0.00 3.85
1103 1110 2.872245 CTCGCGGGAAACATCACATATT 59.128 45.455 0.00 0.00 0.00 1.28
1140 1147 2.799978 CACACTACAACATGCACTCGAA 59.200 45.455 0.00 0.00 0.00 3.71
1186 1193 0.179020 TTGGTGACCTTGGAGCACAG 60.179 55.000 2.11 0.00 34.33 3.66
1259 1266 3.490348 CCAGGTTTGAGTGGATTCTTGT 58.510 45.455 0.00 0.00 35.67 3.16
1317 1324 9.955208 TGACAAGTATTAGTGGTACATAATACG 57.045 33.333 18.97 13.13 42.70 3.06
1330 1337 9.049523 CATGCATAGTTCATGACAAGTATTAGT 57.950 33.333 0.00 0.00 42.84 2.24
1372 1379 7.259290 ACATGGTAACCTGCGAAAATATTAG 57.741 36.000 0.00 0.00 35.32 1.73
1407 1414 4.920640 ACGAAACATCCATCTATCGTCT 57.079 40.909 0.00 0.00 39.03 4.18
1649 1657 6.465948 CCCATTCACATTCAAAGGAATCAAA 58.534 36.000 0.00 0.00 41.78 2.69
1728 1736 6.368791 CACTTTCACAAAGGACTTATCATCGA 59.631 38.462 0.00 0.00 42.82 3.59
1749 1757 5.751990 GCAAGCATATACTTACCGTACACTT 59.248 40.000 0.00 0.00 0.00 3.16
1751 1759 5.045215 TGCAAGCATATACTTACCGTACAC 58.955 41.667 0.00 0.00 0.00 2.90
1842 1850 1.338674 TGTACCGAAGCACCAATCCAG 60.339 52.381 0.00 0.00 0.00 3.86
1846 1854 2.290008 TGATGTGTACCGAAGCACCAAT 60.290 45.455 0.00 0.00 34.94 3.16
2049 2061 8.462811 TGAGCACTTACTTTTGTTGTATTGAAA 58.537 29.630 0.00 0.00 0.00 2.69
2050 2062 7.990917 TGAGCACTTACTTTTGTTGTATTGAA 58.009 30.769 0.00 0.00 0.00 2.69
2054 2066 8.848474 ACTATGAGCACTTACTTTTGTTGTAT 57.152 30.769 0.00 0.00 0.00 2.29
2060 2072 7.426929 AGTCAACTATGAGCACTTACTTTTG 57.573 36.000 0.00 0.00 35.88 2.44
2063 2075 7.228314 TGTAGTCAACTATGAGCACTTACTT 57.772 36.000 0.00 0.00 35.88 2.24
2064 2076 6.835819 TGTAGTCAACTATGAGCACTTACT 57.164 37.500 0.00 0.00 35.88 2.24
2065 2077 7.273815 GTCTTGTAGTCAACTATGAGCACTTAC 59.726 40.741 0.00 0.00 35.88 2.34
2066 2078 7.039993 TGTCTTGTAGTCAACTATGAGCACTTA 60.040 37.037 0.00 0.00 35.88 2.24
2079 2093 4.582656 CCATTGGGTTTGTCTTGTAGTCAA 59.417 41.667 0.00 0.00 0.00 3.18
2081 2095 4.215613 GTCCATTGGGTTTGTCTTGTAGTC 59.784 45.833 2.09 0.00 34.93 2.59
2109 2123 4.280677 CCAACACCAATTCACAACCATACT 59.719 41.667 0.00 0.00 0.00 2.12
2199 2213 6.733160 GGTCATACCTATGGTCATACCACGT 61.733 48.000 0.00 1.26 42.87 4.49
2243 2257 3.758554 AGAGCAACCAAAGCGTTTATGAT 59.241 39.130 0.00 0.00 37.01 2.45
2249 2263 1.102978 AACAGAGCAACCAAAGCGTT 58.897 45.000 0.00 0.00 37.01 4.84
2285 2300 4.041567 TGAAGTCATTTGGAGCTACTTCCA 59.958 41.667 16.74 4.78 45.34 3.53
2316 2331 6.923199 ATGGAAGAAAACCAATCAACATCT 57.077 33.333 0.00 0.00 40.93 2.90
2366 2381 4.273480 TCGAGAAAGAAGAAAGCTTGTTGG 59.727 41.667 0.00 0.00 37.64 3.77


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

AutoCloner maintained by Alex Coulton.