Multiple sequence alignment - TraesCS5D01G022300

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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 TraesCS5D01G022300 chr5D 100.000 3669 0 0 1 3669 15064502 15060834 0.000000e+00 6776
1 TraesCS5D01G022300 chr5D 92.598 3148 224 8 1 3145 447574092 447577233 0.000000e+00 4514
2 TraesCS5D01G022300 chr5D 92.156 3149 233 14 1 3145 414804699 414801561 0.000000e+00 4434
3 TraesCS5D01G022300 chr3D 92.789 3148 214 13 1 3144 155045911 155042773 0.000000e+00 4543
4 TraesCS5D01G022300 chr3D 96.505 515 15 2 3157 3669 43659762 43659249 0.000000e+00 848
5 TraesCS5D01G022300 chr7D 91.651 3150 247 15 1 3145 404524821 404521683 0.000000e+00 4346
6 TraesCS5D01G022300 chr7D 91.371 3152 257 14 1 3145 105133490 105136633 0.000000e+00 4300
7 TraesCS5D01G022300 chr6D 89.686 3151 305 18 1 3144 275511660 275508523 0.000000e+00 4000
8 TraesCS5D01G022300 chr6D 89.192 3155 311 26 1 3145 30846159 30849293 0.000000e+00 3910
9 TraesCS5D01G022300 chr1D 89.404 3152 313 21 1 3145 322235489 322232352 0.000000e+00 3951
10 TraesCS5D01G022300 chr1D 89.393 3149 315 18 5 3145 179844090 179847227 0.000000e+00 3947
11 TraesCS5D01G022300 chr6B 95.736 516 18 3 3157 3669 636588839 636588325 0.000000e+00 828
12 TraesCS5D01G022300 chr1B 93.045 532 18 3 3157 3669 648250730 648250199 0.000000e+00 760
13 TraesCS5D01G022300 chr2A 81.509 530 59 15 3154 3669 699445126 699445630 2.050000e-107 399
14 TraesCS5D01G022300 chr2A 85.028 354 29 8 3317 3669 699446497 699446827 4.540000e-89 339
15 TraesCS5D01G022300 chr7A 84.034 357 45 7 3316 3669 130787618 130787271 2.110000e-87 333


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 TraesCS5D01G022300 chr5D 15060834 15064502 3668 True 6776 6776 100.0000 1 3669 1 chr5D.!!$R1 3668
1 TraesCS5D01G022300 chr5D 447574092 447577233 3141 False 4514 4514 92.5980 1 3145 1 chr5D.!!$F1 3144
2 TraesCS5D01G022300 chr5D 414801561 414804699 3138 True 4434 4434 92.1560 1 3145 1 chr5D.!!$R2 3144
3 TraesCS5D01G022300 chr3D 155042773 155045911 3138 True 4543 4543 92.7890 1 3144 1 chr3D.!!$R2 3143
4 TraesCS5D01G022300 chr3D 43659249 43659762 513 True 848 848 96.5050 3157 3669 1 chr3D.!!$R1 512
5 TraesCS5D01G022300 chr7D 404521683 404524821 3138 True 4346 4346 91.6510 1 3145 1 chr7D.!!$R1 3144
6 TraesCS5D01G022300 chr7D 105133490 105136633 3143 False 4300 4300 91.3710 1 3145 1 chr7D.!!$F1 3144
7 TraesCS5D01G022300 chr6D 275508523 275511660 3137 True 4000 4000 89.6860 1 3144 1 chr6D.!!$R1 3143
8 TraesCS5D01G022300 chr6D 30846159 30849293 3134 False 3910 3910 89.1920 1 3145 1 chr6D.!!$F1 3144
9 TraesCS5D01G022300 chr1D 322232352 322235489 3137 True 3951 3951 89.4040 1 3145 1 chr1D.!!$R1 3144
10 TraesCS5D01G022300 chr1D 179844090 179847227 3137 False 3947 3947 89.3930 5 3145 1 chr1D.!!$F1 3140
11 TraesCS5D01G022300 chr6B 636588325 636588839 514 True 828 828 95.7360 3157 3669 1 chr6B.!!$R1 512
12 TraesCS5D01G022300 chr1B 648250199 648250730 531 True 760 760 93.0450 3157 3669 1 chr1B.!!$R1 512
13 TraesCS5D01G022300 chr2A 699445126 699446827 1701 False 369 399 83.2685 3154 3669 2 chr2A.!!$F1 515

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
355 357 0.037232 GTTCGAGTGGGGAAGGAGTG 60.037 60.0 0.0 0.0 0.00 3.51 F
1356 1367 0.035343 ATCCGAGTGACGAGAGGACA 60.035 55.0 0.0 0.0 45.77 4.02 F
2154 2168 1.198759 ACCAGGCAAGTATCCGTGGT 61.199 55.0 0.0 0.0 33.36 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1665 0.457853 GCGGCTGAATGTGTCGTCTA 60.458 55.000 0.0 0.0 0.00 2.59 R
2458 2474 2.134789 TACCCGAGTTAGAGGTGACC 57.865 55.000 0.0 0.0 35.02 4.02 R
3037 3055 2.688446 TGGGTGTACAAATGCAAAACGA 59.312 40.909 0.0 0.0 0.00 3.85 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
48 49 5.718801 TTAAGGTACATAAAGATGGGGCA 57.281 39.130 0.00 0.00 37.39 5.36
53 54 4.280929 GGTACATAAAGATGGGGCATTTCC 59.719 45.833 0.00 0.00 37.39 3.13
95 97 9.520515 AAGTGACATAAATGACCATTAAGTCTT 57.479 29.630 16.01 0.00 37.66 3.01
97 99 8.116753 GTGACATAAATGACCATTAAGTCTTCG 58.883 37.037 16.01 0.00 37.66 3.79
234 236 4.699257 GTGGATGATGCTATCCCTTGAATC 59.301 45.833 11.12 0.00 44.93 2.52
246 248 4.911390 TCCCTTGAATCCTTCTGACTTTC 58.089 43.478 0.00 0.00 0.00 2.62
271 273 1.219724 GATGTCCTAGGGGAGGGTGTA 59.780 57.143 9.46 0.00 46.70 2.90
294 296 1.789523 GTCAGGCCTATGACCCTACA 58.210 55.000 3.98 0.00 43.12 2.74
346 348 1.003718 GGTTCAGGGTTCGAGTGGG 60.004 63.158 0.00 0.00 0.00 4.61
355 357 0.037232 GTTCGAGTGGGGAAGGAGTG 60.037 60.000 0.00 0.00 0.00 3.51
512 518 5.795441 GCTTCGAGTGTTGATATGGAAAAAC 59.205 40.000 0.00 0.00 0.00 2.43
545 551 1.302271 CAGGTTGCTCTGCTGCTCA 60.302 57.895 0.00 0.00 0.00 4.26
562 569 2.941415 GCTCACGGATCTTGTGGGATTT 60.941 50.000 18.73 0.00 40.33 2.17
583 590 1.573829 AATTTTCAGGAAGCGCGCGA 61.574 50.000 37.18 13.97 0.00 5.87
695 702 0.322997 TGCGGGATTTGACGGGATTT 60.323 50.000 0.00 0.00 0.00 2.17
711 718 2.617021 GGATTTCTTGGACCCGCAAGTA 60.617 50.000 0.00 0.00 0.00 2.24
814 824 0.321653 GTTTCTCCACCGCATCCACT 60.322 55.000 0.00 0.00 0.00 4.00
829 839 3.377759 ACTTCTGCTCTCGGCGCT 61.378 61.111 7.64 0.00 45.43 5.92
1059 1069 0.249489 GACTGATTCCCCACGGATCG 60.249 60.000 0.00 0.00 38.24 3.69
1255 1265 0.888285 TGCATTCGTGTCCATGTGCA 60.888 50.000 0.00 0.00 39.94 4.57
1271 1281 2.627699 TGTGCAAGAATTTCCTGGGTTC 59.372 45.455 0.00 0.00 0.00 3.62
1293 1303 3.513209 ACCACACTGGGGTCTTTTG 57.487 52.632 0.00 0.00 43.37 2.44
1323 1334 1.982660 TCACCTGTCGTTCTCAGTCT 58.017 50.000 0.00 0.00 0.00 3.24
1324 1335 3.136009 TCACCTGTCGTTCTCAGTCTA 57.864 47.619 0.00 0.00 0.00 2.59
1356 1367 0.035343 ATCCGAGTGACGAGAGGACA 60.035 55.000 0.00 0.00 45.77 4.02
1376 1387 2.362736 ACATGTGATCCAGATGTGTGC 58.637 47.619 8.62 0.00 44.66 4.57
1406 1417 4.977739 TGGGATCCAAATGAGAGGTAAGAT 59.022 41.667 15.23 0.00 0.00 2.40
1456 1467 2.997315 TCAGAGGGTGGCAGTCGG 60.997 66.667 0.00 0.00 0.00 4.79
1469 1480 1.471119 CAGTCGGCCTGGTTCTACTA 58.529 55.000 0.00 0.00 37.54 1.82
1615 1627 1.733399 GTGGTCCAGCTCGTTCGTC 60.733 63.158 0.00 0.00 0.00 4.20
1653 1665 4.357325 TGGATCTGCTAGAAGTCTTCCTT 58.643 43.478 9.04 0.00 35.59 3.36
1710 1722 3.304829 TCTGATGTGGATGTATTCGGGA 58.695 45.455 0.00 0.00 0.00 5.14
1727 1739 2.296190 CGGGAATCGATGATACCACTCA 59.704 50.000 0.00 0.00 42.43 3.41
1993 2006 1.910772 AACGGAGAGCAGGAGCAGT 60.911 57.895 0.00 0.00 45.49 4.40
1999 2012 1.300542 GAGCAGGAGCAGTATCCGC 60.301 63.158 0.00 0.00 44.65 5.54
2138 2152 2.404923 TCCAAACAAACTCACGACCA 57.595 45.000 0.00 0.00 0.00 4.02
2154 2168 1.198759 ACCAGGCAAGTATCCGTGGT 61.199 55.000 0.00 0.00 33.36 4.16
2198 2212 1.222936 CCTCAAAGCGCCCTCAGAT 59.777 57.895 2.29 0.00 0.00 2.90
2200 2214 1.712977 CTCAAAGCGCCCTCAGATGC 61.713 60.000 2.29 0.00 0.00 3.91
2206 2220 2.739996 CGCCCTCAGATGCCTTCCT 61.740 63.158 0.00 0.00 0.00 3.36
2210 2224 1.202330 CCTCAGATGCCTTCCTCAGT 58.798 55.000 0.00 0.00 0.00 3.41
2231 2245 2.579738 GACTGAGAAGGCCCCGAC 59.420 66.667 0.00 0.00 0.00 4.79
2422 2438 1.561643 CTGCTACCTCTGGGACTTCA 58.438 55.000 0.00 0.00 36.25 3.02
2430 2446 2.503356 CCTCTGGGACTTCAGCTTACAT 59.497 50.000 0.00 0.00 34.91 2.29
2458 2474 1.594862 GACGAGGAAATGGAAGATGCG 59.405 52.381 0.00 0.00 0.00 4.73
2471 2487 1.853963 AGATGCGGTCACCTCTAACT 58.146 50.000 0.00 0.00 0.00 2.24
2486 2502 4.445162 CCTCTAACTCGGGTATGACTCTCT 60.445 50.000 0.00 0.00 0.00 3.10
2491 2507 8.435187 TCTAACTCGGGTATGACTCTCTTAATA 58.565 37.037 0.00 0.00 0.00 0.98
2497 2513 6.802348 CGGGTATGACTCTCTTAATATTGTCG 59.198 42.308 0.00 0.00 0.00 4.35
2587 2604 2.567169 TGTCATTGACCTTCCAGACGAT 59.433 45.455 14.05 0.00 0.00 3.73
2607 2624 2.887568 CGAGGATGTGCCGCTGAC 60.888 66.667 0.00 0.00 43.43 3.51
2721 2739 3.187227 CCAATCGGACTTCTGTGACTTTG 59.813 47.826 0.00 0.00 0.00 2.77
2723 2741 2.036387 TCGGACTTCTGTGACTTTGGA 58.964 47.619 0.00 0.00 0.00 3.53
2928 2946 1.559965 ATGCCAGCTCAGCTCTCCAA 61.560 55.000 0.00 0.00 36.40 3.53
2938 2956 2.039480 TCAGCTCTCCAAAGCAATGTCT 59.961 45.455 0.00 0.00 45.00 3.41
3026 3044 6.611236 TGAAAACTTTCCTTGAGGGATCTTTT 59.389 34.615 0.00 0.00 44.66 2.27
3037 3055 7.997803 CCTTGAGGGATCTTTTCTATCAATCTT 59.002 37.037 0.00 0.00 37.23 2.40
3310 4502 1.333636 CCCAAAGGCCCAACACACAA 61.334 55.000 0.00 0.00 0.00 3.33
3363 4590 2.898840 CAGCCGCAGCCATCGATT 60.899 61.111 0.00 0.00 41.25 3.34
3505 4732 1.568504 TCTAGCGGTTGAATCAGGGT 58.431 50.000 0.00 0.00 0.00 4.34
3562 4789 5.929697 ATGTCACTGGTATTATCGCAATG 57.070 39.130 0.00 0.00 0.00 2.82
3592 4836 5.583495 ACTCCGAGTAGATTTTTCAGATCG 58.417 41.667 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 7.554835 TCACTTATTATTGGCGTTACTGGAAAT 59.445 33.333 0.00 0.00 0.00 2.17
53 54 6.656314 TGTCACTTATTATTGGCGTTACTG 57.344 37.500 0.00 0.00 0.00 2.74
97 99 1.997606 CAACGGTCGGACATTTACTCC 59.002 52.381 10.76 0.00 0.00 3.85
234 236 2.289694 ACATCACCCGAAAGTCAGAAGG 60.290 50.000 0.00 0.00 0.00 3.46
246 248 1.075525 TCCCCTAGGACATCACCCG 60.076 63.158 11.48 0.00 37.19 5.28
294 296 7.310113 GGCTAATGATGAAGCTATGTACCTAGT 60.310 40.741 6.99 0.00 38.80 2.57
346 348 3.939592 CGGAAGTATTTTCCACTCCTTCC 59.060 47.826 6.73 0.00 42.81 3.46
355 357 7.148804 GCAAAAATTGAGTCGGAAGTATTTTCC 60.149 37.037 0.00 0.00 35.27 3.13
512 518 3.188048 GCAACCTGTCAGACTGAAGATTG 59.812 47.826 6.76 11.12 0.00 2.67
545 551 3.433306 TTCAAATCCCACAAGATCCGT 57.567 42.857 0.00 0.00 0.00 4.69
562 569 0.109781 GCGCGCTTCCTGAAAATTCA 60.110 50.000 26.67 0.00 35.57 2.57
695 702 0.321298 GCTTACTTGCGGGTCCAAGA 60.321 55.000 8.71 0.00 43.79 3.02
705 712 0.741221 CTCCCGAGTGGCTTACTTGC 60.741 60.000 4.06 0.00 40.53 4.01
711 718 1.545706 GGTCTTCTCCCGAGTGGCTT 61.546 60.000 0.00 0.00 0.00 4.35
744 751 2.597217 CAGAAAACCCCAGCCGCA 60.597 61.111 0.00 0.00 0.00 5.69
1255 1265 3.559384 GGTCGAGAACCCAGGAAATTCTT 60.559 47.826 0.00 0.00 42.85 2.52
1271 1281 2.657237 GACCCCAGTGTGGTCGAG 59.343 66.667 9.15 0.00 42.63 4.04
1290 1300 5.098893 CGACAGGTGAAAATGTGTTTCAAA 58.901 37.500 3.22 0.00 39.76 2.69
1293 1303 4.287238 ACGACAGGTGAAAATGTGTTTC 57.713 40.909 0.00 0.00 0.00 2.78
1323 1334 3.694072 CACTCGGATTGGCCTTTTTGATA 59.306 43.478 3.32 0.00 0.00 2.15
1324 1335 2.493278 CACTCGGATTGGCCTTTTTGAT 59.507 45.455 3.32 0.00 0.00 2.57
1356 1367 2.362736 GCACACATCTGGATCACATGT 58.637 47.619 0.00 0.00 0.00 3.21
1376 1387 1.064758 TCATTTGGATCCCAAGACCCG 60.065 52.381 9.90 0.00 44.84 5.28
1406 1417 4.591321 AGAATCATGGCTGGGAAAGTAA 57.409 40.909 0.00 0.00 0.00 2.24
1456 1467 3.007614 TGGTCTTTGTAGTAGAACCAGGC 59.992 47.826 0.00 0.00 0.00 4.85
1469 1480 1.371558 GGAGTCGGCTGGTCTTTGT 59.628 57.895 0.00 0.00 0.00 2.83
1615 1627 2.767445 CCATGCCAGTCACGCCATG 61.767 63.158 0.00 0.00 0.00 3.66
1653 1665 0.457853 GCGGCTGAATGTGTCGTCTA 60.458 55.000 0.00 0.00 0.00 2.59
1661 1673 1.878775 GCTTGAAGCGGCTGAATGT 59.121 52.632 1.81 0.00 0.00 2.71
1710 1722 4.835056 TGGATCTGAGTGGTATCATCGATT 59.165 41.667 0.00 0.00 0.00 3.34
1727 1739 1.872773 GACTTCCTCTGGGTGGATCT 58.127 55.000 0.00 0.00 33.09 2.75
1831 1844 4.330944 TGTCTGGTTCATACGAGTTGTT 57.669 40.909 0.00 0.00 32.51 2.83
1906 1919 5.924475 ACAAAAGTCAGTCGGTTGATAAG 57.076 39.130 0.00 0.00 0.00 1.73
1910 1923 2.940410 GGAACAAAAGTCAGTCGGTTGA 59.060 45.455 0.00 0.00 0.00 3.18
1993 2006 3.546543 CGCCTCCCCTTGCGGATA 61.547 66.667 0.00 0.00 46.65 2.59
2138 2152 2.679930 GCTTTACCACGGATACTTGCCT 60.680 50.000 0.00 0.00 33.76 4.75
2198 2212 2.922503 TCGGCACTGAGGAAGGCA 60.923 61.111 0.00 0.00 0.00 4.75
2200 2214 3.382111 AGTCGGCACTGAGGAAGG 58.618 61.111 0.00 0.00 0.00 3.46
2210 2224 3.706373 GGGCCTTCTCAGTCGGCA 61.706 66.667 0.84 0.00 45.53 5.69
2422 2438 4.160439 TCCTCGTCTTCATTCATGTAAGCT 59.840 41.667 0.00 0.00 0.00 3.74
2430 2446 4.551702 TCCATTTCCTCGTCTTCATTCA 57.448 40.909 0.00 0.00 0.00 2.57
2458 2474 2.134789 TACCCGAGTTAGAGGTGACC 57.865 55.000 0.00 0.00 35.02 4.02
2471 2487 7.308408 CGACAATATTAAGAGAGTCATACCCGA 60.308 40.741 0.00 0.00 0.00 5.14
2486 2502 6.256321 GGCCGAGAAAGTAACGACAATATTAA 59.744 38.462 0.00 0.00 0.00 1.40
2491 2507 2.344025 GGCCGAGAAAGTAACGACAAT 58.656 47.619 0.00 0.00 0.00 2.71
2497 2513 2.288729 ACAAAACGGCCGAGAAAGTAAC 59.711 45.455 35.90 0.00 0.00 2.50
2587 2604 3.381983 AGCGGCACATCCTCGTCA 61.382 61.111 1.45 0.00 0.00 4.35
2607 2624 2.939103 CTGTTTCTTCTTCCCATAGGCG 59.061 50.000 0.00 0.00 0.00 5.52
2754 2772 4.194720 GGAGTCTGCGCGGTCGAT 62.195 66.667 17.37 0.18 38.10 3.59
2928 2946 5.366768 TGATAAGCCTACCTAGACATTGCTT 59.633 40.000 0.00 0.00 40.37 3.91
2938 2956 3.220110 CAGTCGGTGATAAGCCTACCTA 58.780 50.000 0.00 0.00 32.28 3.08
2983 3001 7.630082 AGTTTTCAGGTAGCATATCCTAACAA 58.370 34.615 0.00 0.00 32.26 2.83
3026 3044 7.592938 ACAAATGCAAAACGAAGATTGATAGA 58.407 30.769 0.00 0.00 31.71 1.98
3037 3055 2.688446 TGGGTGTACAAATGCAAAACGA 59.312 40.909 0.00 0.00 0.00 3.85
3066 3084 4.893424 TTTACTCTGTGGCAAGTCAAAC 57.107 40.909 0.00 0.00 0.00 2.93
3080 3098 8.524487 AGTCGACTCAAGATACAAATTTACTCT 58.476 33.333 13.58 0.00 0.00 3.24
3151 3170 4.394712 GTGTCACCCCTGCCTCCG 62.395 72.222 0.00 0.00 0.00 4.63
3152 3171 4.035102 GGTGTCACCCCTGCCTCC 62.035 72.222 11.30 0.00 30.04 4.30
3188 3210 4.026804 CGAATACCTAGCGAACATTCACAC 60.027 45.833 0.00 0.00 0.00 3.82
3310 4502 5.104900 AGTTTCCTGATGCGTAGGTAGATTT 60.105 40.000 0.00 0.00 36.67 2.17
3363 4590 6.075984 ACCTAGGAAGAAAACTGACTACTCA 58.924 40.000 17.98 0.00 0.00 3.41
3505 4732 4.202233 TGCCAAAATCAGTTGATGAAGCAA 60.202 37.500 0.00 0.00 42.53 3.91
3541 4768 3.559655 GCATTGCGATAATACCAGTGACA 59.440 43.478 0.00 0.00 0.00 3.58
3562 4789 5.358298 AAAATCTACTCGGAGTTTGTTGC 57.642 39.130 16.95 0.00 33.25 4.17
3592 4836 6.491745 TGGACTAGTTCATCATATGTCTCTCC 59.508 42.308 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.