Multiple sequence alignment - TraesCS6D01G177900

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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 TraesCS6D01G177900 chr6D 100.000 2346 0 0 1 2346 182941599 182939254 0 4333
1 TraesCS6D01G177900 chr6D 95.092 2343 112 2 7 2346 124524162 124521820 0 3687
2 TraesCS6D01G177900 chr7D 95.019 2349 112 3 1 2346 382056721 382054375 0 3685
3 TraesCS6D01G177900 chr7D 94.891 2349 115 3 1 2346 203549759 203552105 0 3668
4 TraesCS6D01G177900 chr7D 94.891 2349 115 3 1 2346 381967122 381969468 0 3668
5 TraesCS6D01G177900 chr7D 94.851 2350 115 5 1 2346 381930644 381928297 0 3664
6 TraesCS6D01G177900 chr7D 94.849 2349 116 3 1 2346 203506636 203504290 0 3663
7 TraesCS6D01G177900 chr7A 94.934 2349 114 3 1 2346 4966398 4964052 0 3674
8 TraesCS6D01G177900 chrUn 94.891 2349 115 3 1 2346 189399126 189396780 0 3668
9 TraesCS6D01G177900 chrUn 94.764 2349 118 3 1 2346 171050371 171048025 0 3651


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 TraesCS6D01G177900 chr6D 182939254 182941599 2345 True 4333 4333 100.000 1 2346 1 chr6D.!!$R2 2345
1 TraesCS6D01G177900 chr6D 124521820 124524162 2342 True 3687 3687 95.092 7 2346 1 chr6D.!!$R1 2339
2 TraesCS6D01G177900 chr7D 382054375 382056721 2346 True 3685 3685 95.019 1 2346 1 chr7D.!!$R3 2345
3 TraesCS6D01G177900 chr7D 203549759 203552105 2346 False 3668 3668 94.891 1 2346 1 chr7D.!!$F1 2345
4 TraesCS6D01G177900 chr7D 381967122 381969468 2346 False 3668 3668 94.891 1 2346 1 chr7D.!!$F2 2345
5 TraesCS6D01G177900 chr7D 381928297 381930644 2347 True 3664 3664 94.851 1 2346 1 chr7D.!!$R2 2345
6 TraesCS6D01G177900 chr7D 203504290 203506636 2346 True 3663 3663 94.849 1 2346 1 chr7D.!!$R1 2345
7 TraesCS6D01G177900 chr7A 4964052 4966398 2346 True 3674 3674 94.934 1 2346 1 chr7A.!!$R1 2345
8 TraesCS6D01G177900 chrUn 189396780 189399126 2346 True 3668 3668 94.891 1 2346 1 chrUn.!!$R2 2345
9 TraesCS6D01G177900 chrUn 171048025 171050371 2346 True 3651 3651 94.764 1 2346 1 chrUn.!!$R1 2345

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
249 251 0.179032 TTGAAGCAGGGCGAGACAAA 60.179 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 1486 1.136305 TGGTGCTAGGAATGACTACGC 59.864 52.381 0.0 0.0 0.0 4.42 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
83 84 9.610705 CTAATACTATGCAGGCTCATCAAATAT 57.389 33.333 0.00 0.00 0.00 1.28
85 86 5.872963 ACTATGCAGGCTCATCAAATATCA 58.127 37.500 0.00 0.00 0.00 2.15
88 89 5.294734 TGCAGGCTCATCAAATATCACTA 57.705 39.130 0.00 0.00 0.00 2.74
110 111 8.950210 CACTATTGAGCTTTCTTTAGGATTTGA 58.050 33.333 0.00 0.00 0.00 2.69
143 144 1.135024 GGTAGATTCCCACGCGTTACA 60.135 52.381 10.22 0.00 0.00 2.41
152 153 1.521234 ACGCGTTACACACCCGTTT 60.521 52.632 5.58 0.00 0.00 3.60
189 190 3.950397 ACTATTCCGATTCCAGCAAACA 58.050 40.909 0.00 0.00 0.00 2.83
208 210 1.275291 CAGAGGCCGTTAGGTCAAAGA 59.725 52.381 0.00 0.00 46.92 2.52
217 219 1.171308 TAGGTCAAAGACGTAGCGCT 58.829 50.000 17.26 17.26 32.77 5.92
218 220 1.171308 AGGTCAAAGACGTAGCGCTA 58.829 50.000 14.45 14.45 32.65 4.26
220 222 1.135460 GGTCAAAGACGTAGCGCTAGT 60.135 52.381 19.48 17.45 32.65 2.57
224 226 2.322355 AAGACGTAGCGCTAGTCCTA 57.678 50.000 28.17 7.21 35.65 2.94
249 251 0.179032 TTGAAGCAGGGCGAGACAAA 60.179 50.000 0.00 0.00 0.00 2.83
262 264 4.441634 GGCGAGACAAATTTAGCTAGGAGA 60.442 45.833 0.00 0.00 0.00 3.71
264 266 5.651530 CGAGACAAATTTAGCTAGGAGACA 58.348 41.667 0.00 0.00 0.00 3.41
275 277 3.056465 AGCTAGGAGACACTTTTCCTTCG 60.056 47.826 0.00 0.00 40.96 3.79
301 303 1.673920 GCTCCCTGAAAACAACGTTCA 59.326 47.619 0.00 0.00 33.97 3.18
316 318 4.829064 ACGTTCAACTTGCATGTGTTAT 57.171 36.364 5.94 0.00 0.00 1.89
348 350 0.321671 CGTTCCTTCTGAGCCAGGAA 59.678 55.000 8.42 8.42 45.32 3.36
359 361 2.147150 GAGCCAGGAACAAACTCAGAC 58.853 52.381 0.00 0.00 0.00 3.51
381 383 0.685097 TGACTATGATTAGGCGGGGC 59.315 55.000 0.00 0.00 36.10 5.80
382 384 0.977395 GACTATGATTAGGCGGGGCT 59.023 55.000 0.00 0.00 0.00 5.19
389 391 1.351350 GATTAGGCGGGGCTAGGATTT 59.649 52.381 2.11 0.00 0.00 2.17
425 427 1.761784 AGGTCATGAGCCTGATGAGTC 59.238 52.381 20.92 0.00 34.56 3.36
445 447 0.468648 GACCAATTCCTCTACCCCGG 59.531 60.000 0.00 0.00 0.00 5.73
456 458 0.912968 CTACCCCGGTTCTTCCCCTT 60.913 60.000 0.00 0.00 0.00 3.95
482 484 6.858941 TCTTTCTTTCCCTCTTCCCATAAAA 58.141 36.000 0.00 0.00 0.00 1.52
556 558 3.888930 TCCAAAACTACAAGCAAGGGAAG 59.111 43.478 0.00 0.00 0.00 3.46
664 668 5.125417 CCTGAATTAAGGGAATGCGAGAAAA 59.875 40.000 0.00 0.00 33.28 2.29
703 707 4.734917 TCAAAACAAAACAAACGGACGAT 58.265 34.783 0.00 0.00 0.00 3.73
713 717 3.930848 ACAAACGGACGATTGAATCCTAC 59.069 43.478 19.14 0.00 33.11 3.18
742 746 5.779529 AATTCTTTTGAGAAGAGCTTGCA 57.220 34.783 0.00 0.00 0.00 4.08
821 827 2.620585 GACCAGCAAATCCATTAGAGCC 59.379 50.000 0.00 0.00 0.00 4.70
918 924 0.752054 CCAAAGCCAACAAGCCTTCA 59.248 50.000 0.00 0.00 0.00 3.02
1000 1006 2.027561 ACGCATTAGCCAGTAGAAACCA 60.028 45.455 0.00 0.00 37.52 3.67
1004 1010 2.710096 TAGCCAGTAGAAACCATGCC 57.290 50.000 0.00 0.00 0.00 4.40
1007 1013 1.656652 CCAGTAGAAACCATGCCTCG 58.343 55.000 0.00 0.00 0.00 4.63
1009 1015 2.158900 CCAGTAGAAACCATGCCTCGAT 60.159 50.000 0.00 0.00 0.00 3.59
1013 1019 3.845781 AGAAACCATGCCTCGATGTAT 57.154 42.857 0.00 0.00 0.00 2.29
1020 1026 5.240891 ACCATGCCTCGATGTATATTCTTG 58.759 41.667 0.00 0.00 0.00 3.02
1062 1068 5.784023 TGGATCCAGGTACCTCAACTATTA 58.216 41.667 12.84 0.00 0.00 0.98
1170 1176 6.554982 ACATTCCTAGTATGCTCCACTCATTA 59.445 38.462 0.00 0.00 0.00 1.90
1174 1180 7.238710 TCCTAGTATGCTCCACTCATTATACA 58.761 38.462 0.00 0.00 0.00 2.29
1190 1196 2.897271 TACACCAAGCACCCAATCAT 57.103 45.000 0.00 0.00 0.00 2.45
1218 1224 8.970020 GGATCAGAATCACACTCTAGATCATAT 58.030 37.037 0.00 0.00 33.62 1.78
1226 1232 8.525290 TCACACTCTAGATCATATCTTTCACA 57.475 34.615 0.00 0.00 40.76 3.58
1242 1248 5.714806 TCTTTCACAAAAGAAAAGGACAGGT 59.285 36.000 0.00 0.00 46.09 4.00
1246 1252 4.580580 CACAAAAGAAAAGGACAGGTAGCT 59.419 41.667 0.00 0.00 0.00 3.32
1291 1297 3.996363 CTCTTCACACCGTCAATCAATCA 59.004 43.478 0.00 0.00 0.00 2.57
1377 1383 6.721318 AGAAAGATCTTGGGCACAAATACTA 58.279 36.000 9.17 0.00 35.89 1.82
1488 1494 5.664457 AGAATGATTTCTCATGCGTAGTCA 58.336 37.500 0.00 0.00 41.72 3.41
1496 1502 3.004839 TCTCATGCGTAGTCATTCCTAGC 59.995 47.826 0.00 0.00 0.00 3.42
1563 1569 0.099436 GGCATACTTCCTGCGCTTTG 59.901 55.000 9.73 0.00 40.59 2.77
1629 1635 7.523052 GCCCCTCGCAATAAATATGTAAATTCA 60.523 37.037 0.00 0.00 37.47 2.57
1754 1761 1.743958 CCTTTCTCTGCAGCATTGGAG 59.256 52.381 9.47 0.00 43.49 3.86
1780 1787 0.906066 TCGGGCTTGGCATAGTTACA 59.094 50.000 0.00 0.00 0.00 2.41
1795 1802 4.532314 AGTTACAAGGTTCCCGTTCTAG 57.468 45.455 0.00 0.00 0.00 2.43
1822 1829 6.667558 ACTAACACTAACTGAAGCTAACCT 57.332 37.500 0.00 0.00 0.00 3.50
1840 1847 4.363991 ACCTGAAGCTTTCTTCTCATGT 57.636 40.909 0.00 0.00 46.81 3.21
1853 1860 4.774200 TCTTCTCATGTGACTCTTGGATCA 59.226 41.667 0.00 0.00 0.00 2.92
1891 1898 2.954753 GACCACGGCTGAAACTGCG 61.955 63.158 0.00 0.00 0.00 5.18
1897 1904 2.042831 GGCTGAAACTGCGAGGCAT 61.043 57.895 0.00 0.00 38.13 4.40
1925 1932 7.414266 ACTAAAAGCTTTTATCAGGGATTCCT 58.586 34.615 27.35 4.06 36.60 3.36
1954 1961 7.114529 GTCAAACGACTACCATACATAGCATAC 59.885 40.741 0.00 0.00 0.00 2.39
2001 2008 2.628178 AGAAGACTGGATGTGAACACGA 59.372 45.455 0.00 0.00 0.00 4.35
2026 2033 1.203050 ACATTGGCTATGTATGGGGCC 60.203 52.381 12.87 0.00 45.62 5.80
2039 2046 1.279025 TGGGGCCCTCACTAATCACC 61.279 60.000 25.93 0.00 0.00 4.02
2075 2082 7.992754 ACAACTAGCAGAAAGAAAGATGAAT 57.007 32.000 0.00 0.00 0.00 2.57
2251 2258 9.206690 CTTCTATTCTATATCAAGATAGGGGCA 57.793 37.037 0.00 0.00 31.37 5.36
2305 2312 1.271926 GGTTCTACCACACAAGGGCAT 60.272 52.381 0.00 0.00 38.42 4.40
2311 2318 1.133513 ACCACACAAGGGCATCTTTCA 60.134 47.619 0.00 0.00 32.41 2.69
2326 2333 7.311297 GGGCATCTTTCATAGTCCAGGATTATA 60.311 40.741 4.18 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.485394 TCATGCTTAGCTGGTGTTTTCA 58.515 40.909 5.60 0.00 0.00 2.69
9 10 1.066605 GCCAATCATGCTTAGCTGGTG 59.933 52.381 5.60 2.25 0.00 4.17
50 51 6.326583 TGAGCCTGCATAGTATTAGGTAGTTT 59.673 38.462 10.48 0.00 32.85 2.66
83 84 8.950210 CAAATCCTAAAGAAAGCTCAATAGTGA 58.050 33.333 0.00 0.00 0.00 3.41
85 86 8.951243 GTCAAATCCTAAAGAAAGCTCAATAGT 58.049 33.333 0.00 0.00 0.00 2.12
88 89 6.153510 GGGTCAAATCCTAAAGAAAGCTCAAT 59.846 38.462 0.00 0.00 0.00 2.57
101 102 3.934068 GAACAGTTCGGGTCAAATCCTA 58.066 45.455 0.00 0.00 0.00 2.94
125 126 1.545136 TGTGTAACGCGTGGGAATCTA 59.455 47.619 14.98 0.00 42.39 1.98
143 144 0.968393 ACAAAGTGGCAAACGGGTGT 60.968 50.000 0.00 0.00 0.00 4.16
152 153 4.518970 GGAATAGTTGAGAACAAAGTGGCA 59.481 41.667 0.00 0.00 37.77 4.92
189 190 1.275573 GTCTTTGACCTAACGGCCTCT 59.724 52.381 0.00 0.00 0.00 3.69
208 210 3.399440 ACTATAGGACTAGCGCTACGT 57.601 47.619 14.45 15.51 0.00 3.57
217 219 5.396436 GCCCTGCTTCAAAACTATAGGACTA 60.396 44.000 4.43 0.00 0.00 2.59
218 220 4.626529 GCCCTGCTTCAAAACTATAGGACT 60.627 45.833 4.43 0.00 0.00 3.85
220 222 3.681594 CGCCCTGCTTCAAAACTATAGGA 60.682 47.826 4.43 0.00 0.00 2.94
224 226 2.027192 TCTCGCCCTGCTTCAAAACTAT 60.027 45.455 0.00 0.00 0.00 2.12
249 251 6.628644 AGGAAAAGTGTCTCCTAGCTAAAT 57.371 37.500 0.00 0.00 40.42 1.40
275 277 1.979155 GTTTTCAGGGAGCTGGGCC 60.979 63.158 0.00 0.00 0.00 5.80
287 289 3.902150 TGCAAGTTGAACGTTGTTTTCA 58.098 36.364 5.00 0.00 0.00 2.69
323 325 1.142778 GCTCAGAAGGAACGCTAGCG 61.143 60.000 34.27 34.27 46.03 4.26
348 350 9.429359 CTAATCATAGTCAAAGTCTGAGTTTGT 57.571 33.333 27.96 17.43 39.07 2.83
359 361 3.403038 CCCCGCCTAATCATAGTCAAAG 58.597 50.000 0.00 0.00 0.00 2.77
381 383 4.213564 AGACTGCAGGTTCAAATCCTAG 57.786 45.455 19.93 0.00 33.54 3.02
382 384 4.041567 TGAAGACTGCAGGTTCAAATCCTA 59.958 41.667 24.04 6.24 33.54 2.94
425 427 0.104304 CGGGGTAGAGGAATTGGTCG 59.896 60.000 0.00 0.00 0.00 4.79
445 447 5.652891 GGGAAAGAAAGATAAGGGGAAGAAC 59.347 44.000 0.00 0.00 0.00 3.01
456 458 7.765149 TTATGGGAAGAGGGAAAGAAAGATA 57.235 36.000 0.00 0.00 0.00 1.98
482 484 6.671779 AGAGTGGTTAGGAGAGAGAATCAATT 59.328 38.462 0.00 0.00 37.82 2.32
526 528 6.325919 TGCTTGTAGTTTTGGATCGATTTT 57.674 33.333 0.00 0.00 0.00 1.82
527 529 5.957842 TGCTTGTAGTTTTGGATCGATTT 57.042 34.783 0.00 0.00 0.00 2.17
677 681 6.805271 TCGTCCGTTTGTTTTGTTTTGAATTA 59.195 30.769 0.00 0.00 0.00 1.40
703 707 9.243637 CAAAAGAATTTCGTTTGTAGGATTCAA 57.756 29.630 22.04 0.00 39.73 2.69
713 717 6.914757 AGCTCTTCTCAAAAGAATTTCGTTTG 59.085 34.615 23.47 23.47 43.77 2.93
742 746 6.963322 AGGTGATTTTTCTAGAAGCATAGGT 58.037 36.000 5.12 0.00 0.00 3.08
776 780 5.627182 ATGATGACCAAGTAGAAGCATCT 57.373 39.130 0.00 0.00 39.82 2.90
821 827 4.389077 GGACACTACCATCAAAGAAAGACG 59.611 45.833 0.00 0.00 0.00 4.18
918 924 7.118971 GCTTAGATGATGAAACAACTTCTGAGT 59.881 37.037 13.29 0.00 37.87 3.41
987 993 1.383523 GAGGCATGGTTTCTACTGGC 58.616 55.000 0.00 0.00 34.65 4.85
1000 1006 4.898320 TGCAAGAATATACATCGAGGCAT 58.102 39.130 0.00 0.00 0.00 4.40
1004 1010 7.041848 TCCAAACATGCAAGAATATACATCGAG 60.042 37.037 0.00 0.00 0.00 4.04
1007 1013 7.934457 ACTCCAAACATGCAAGAATATACATC 58.066 34.615 0.00 0.00 0.00 3.06
1009 1015 7.701539 AACTCCAAACATGCAAGAATATACA 57.298 32.000 0.00 0.00 0.00 2.29
1013 1019 6.815089 ACAAAACTCCAAACATGCAAGAATA 58.185 32.000 0.00 0.00 0.00 1.75
1020 1026 3.068024 TCCAGACAAAACTCCAAACATGC 59.932 43.478 0.00 0.00 0.00 4.06
1077 1083 5.661759 ACTAGAAAGAGGGAATACCGATGTT 59.338 40.000 0.00 0.00 46.96 2.71
1082 1088 3.321396 GGGACTAGAAAGAGGGAATACCG 59.679 52.174 0.00 0.00 46.96 4.02
1145 1151 4.290093 TGAGTGGAGCATACTAGGAATGT 58.710 43.478 8.59 0.00 0.00 2.71
1170 1176 2.897271 TGATTGGGTGCTTGGTGTAT 57.103 45.000 0.00 0.00 0.00 2.29
1174 1180 2.980541 CCATGATTGGGTGCTTGGT 58.019 52.632 0.00 0.00 39.56 3.67
1190 1196 4.871822 TCTAGAGTGTGATTCTGATCCCA 58.128 43.478 0.00 0.00 0.00 4.37
1226 1232 3.570125 GCAGCTACCTGTCCTTTTCTTTT 59.430 43.478 0.00 0.00 41.26 2.27
1242 1248 7.193717 GGAGATCTTCCTTTAGCAGCAGCTA 62.194 48.000 6.74 6.74 45.89 3.32
1246 1252 2.840038 TGGAGATCTTCCTTTAGCAGCA 59.160 45.455 0.00 0.00 46.92 4.41
1274 1280 4.191544 AGGTATGATTGATTGACGGTGTG 58.808 43.478 0.00 0.00 0.00 3.82
1277 1283 7.386851 CCTATAAGGTATGATTGATTGACGGT 58.613 38.462 0.00 0.00 0.00 4.83
1352 1358 5.649831 AGTATTTGTGCCCAAGATCTTTCTC 59.350 40.000 4.86 0.00 0.00 2.87
1377 1383 7.441157 TGAATCTATGTCTTTCGTGAAAAGTGT 59.559 33.333 0.00 0.00 44.07 3.55
1478 1484 2.224066 GGTGCTAGGAATGACTACGCAT 60.224 50.000 0.00 0.00 33.22 4.73
1480 1486 1.136305 TGGTGCTAGGAATGACTACGC 59.864 52.381 0.00 0.00 0.00 4.42
1488 1494 3.624777 CTGTTGGAATGGTGCTAGGAAT 58.375 45.455 0.00 0.00 0.00 3.01
1496 1502 1.747355 GAGCATCCTGTTGGAATGGTG 59.253 52.381 0.00 0.00 46.80 4.17
1563 1569 7.233348 AGGATGAAGACTGATTTAGATCCTCTC 59.767 40.741 0.00 0.00 34.62 3.20
1629 1635 6.308766 CGAAAATCTCTGAATTTCGGCAAAAT 59.691 34.615 17.52 0.00 45.39 1.82
1633 1639 4.340894 CGAAAATCTCTGAATTTCGGCA 57.659 40.909 17.52 0.00 45.39 5.69
1706 1712 7.817910 TGGGTAAAAGAAGGTCTTTATCCTA 57.182 36.000 16.46 11.65 45.19 2.94
1780 1787 6.041979 TGTTAGTTAACTAGAACGGGAACCTT 59.958 38.462 14.73 0.00 41.10 3.50
1795 1802 8.706936 GGTTAGCTTCAGTTAGTGTTAGTTAAC 58.293 37.037 15.46 15.46 36.31 2.01
1840 1847 4.074970 GCCTCTTTTTGATCCAAGAGTCA 58.925 43.478 18.29 0.00 43.14 3.41
1853 1860 1.613836 CAGTCCAGCAGCCTCTTTTT 58.386 50.000 0.00 0.00 0.00 1.94
1891 1898 4.790765 AAAAGCTTTTAGTCCATGCCTC 57.209 40.909 22.70 0.00 0.00 4.70
1897 1904 6.134535 TCCCTGATAAAAGCTTTTAGTCCA 57.865 37.500 29.69 24.50 36.22 4.02
2001 2008 2.550855 CCATACATAGCCAATGTCCGCT 60.551 50.000 5.61 0.00 46.15 5.52
2039 2046 8.547967 TTTCTGCTAGTTGTTTCCTACTAATG 57.452 34.615 0.00 0.00 30.29 1.90
2045 2052 7.506114 TCTTTCTTTCTGCTAGTTGTTTCCTA 58.494 34.615 0.00 0.00 0.00 2.94
2075 2082 1.141657 AGAGCAAGGAGTGAAAGTGCA 59.858 47.619 0.00 0.00 37.68 4.57
2251 2258 0.108138 GCGGTCAGCCAAGTACTGAT 60.108 55.000 0.00 0.00 45.40 2.90


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

AutoCloner maintained by Alex Coulton.