Multiple sequence alignment - TraesCS3D01G037400

Loading Multiple Alignment...

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 TraesCS3D01G037400 chr3D 100.000 3411 0 0 1 3411 13552342 13555752 0.000000e+00 6300
1 TraesCS3D01G037400 chr3B 95.115 2395 69 16 1050 3411 19734547 19736926 0.000000e+00 3731
2 TraesCS3D01G037400 chr3B 95.095 734 21 10 330 1055 19733780 19734506 0.000000e+00 1142
3 TraesCS3D01G037400 chr3B 93.631 314 6 3 1 300 19733479 19733792 1.120000e-124 457
4 TraesCS3D01G037400 chr3A 92.181 1765 78 23 1042 2785 23476359 23474634 0.000000e+00 2440
5 TraesCS3D01G037400 chr3A 91.361 764 23 17 306 1055 23477137 23476403 0.000000e+00 1005
6 TraesCS3D01G037400 chr3A 94.531 640 24 7 2781 3411 23474586 23473949 0.000000e+00 977
7 TraesCS3D01G037400 chr3A 90.265 226 5 8 76 296 23477654 23477441 2.590000e-71 279
8 TraesCS3D01G037400 chr3A 94.118 85 4 1 1 84 23477756 23477672 9.940000e-26 128


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 TraesCS3D01G037400 chr3D 13552342 13555752 3410 False 6300.000000 6300 100.000000 1 3411 1 chr3D.!!$F1 3410
1 TraesCS3D01G037400 chr3B 19733479 19736926 3447 False 1776.666667 3731 94.613667 1 3411 3 chr3B.!!$F1 3410
2 TraesCS3D01G037400 chr3A 23473949 23477756 3807 True 965.800000 2440 92.491200 1 3411 5 chr3A.!!$R1 3410

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
291 325 0.179119 GCAATGCAATGCAGACTCCC 60.179 55.0 21.74 0.0 43.65 4.3 F
295 329 0.251354 TGCAATGCAGACTCCCTCTC 59.749 55.0 2.72 0.0 33.32 3.2 F
296 330 0.540923 GCAATGCAGACTCCCTCTCT 59.459 55.0 0.00 0.0 0.00 3.1 F
1441 1871 0.827925 TGGAGAGCTCAACGACCACT 60.828 55.0 17.77 0.0 0.00 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1466 1896 0.947180 TTCTTACTGGTTGCGTCGGC 60.947 55.0 0.00 0.00 40.52 5.54 R
1992 2426 1.135094 GAATCCTCCTCCCAGCATGA 58.865 55.0 0.00 0.00 39.69 3.07 R
2342 2787 2.224281 TGTAGTTGTGGTCTTCCTGCAG 60.224 50.0 6.78 6.78 34.23 4.41 R
3073 3579 0.947244 GAACCGGCCAGCTCATAATG 59.053 55.0 0.00 0.00 0.00 1.90 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
28 29 5.728471 ACCTATATACATGAGTGCAGATGC 58.272 41.667 0.00 0.00 42.50 3.91
243 277 7.974501 GTGCATAGTGACCTATATACATACACC 59.025 40.741 0.00 0.00 32.49 4.16
290 324 3.340727 GCAATGCAATGCAGACTCC 57.659 52.632 21.74 0.00 43.65 3.85
291 325 0.179119 GCAATGCAATGCAGACTCCC 60.179 55.000 21.74 0.00 43.65 4.30
292 326 1.471119 CAATGCAATGCAGACTCCCT 58.529 50.000 14.98 0.00 43.65 4.20
293 327 1.404391 CAATGCAATGCAGACTCCCTC 59.596 52.381 14.98 0.00 43.65 4.30
294 328 0.917533 ATGCAATGCAGACTCCCTCT 59.082 50.000 14.98 0.00 43.65 3.69
295 329 0.251354 TGCAATGCAGACTCCCTCTC 59.749 55.000 2.72 0.00 33.32 3.20
296 330 0.540923 GCAATGCAGACTCCCTCTCT 59.459 55.000 0.00 0.00 0.00 3.10
297 331 1.473080 GCAATGCAGACTCCCTCTCTC 60.473 57.143 0.00 0.00 0.00 3.20
298 332 2.109774 CAATGCAGACTCCCTCTCTCT 58.890 52.381 0.00 0.00 0.00 3.10
299 333 2.071778 ATGCAGACTCCCTCTCTCTC 57.928 55.000 0.00 0.00 0.00 3.20
300 334 0.998928 TGCAGACTCCCTCTCTCTCT 59.001 55.000 0.00 0.00 0.00 3.10
301 335 1.064758 TGCAGACTCCCTCTCTCTCTC 60.065 57.143 0.00 0.00 0.00 3.20
302 336 1.212935 GCAGACTCCCTCTCTCTCTCT 59.787 57.143 0.00 0.00 0.00 3.10
303 337 2.746472 GCAGACTCCCTCTCTCTCTCTC 60.746 59.091 0.00 0.00 0.00 3.20
304 338 2.774234 CAGACTCCCTCTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
363 697 4.079500 TCTCTAGGAGATGAAGAAGAGGCA 60.080 45.833 0.00 0.00 33.35 4.75
464 798 2.839324 CTTTCGCGCACACAGCATCC 62.839 60.000 8.75 0.00 46.13 3.51
483 817 2.986019 TCCTGAGAGAGGGATCTAGAGG 59.014 54.545 0.00 0.00 43.06 3.69
484 818 2.986019 CCTGAGAGAGGGATCTAGAGGA 59.014 54.545 0.00 0.00 38.36 3.71
485 819 3.009473 CCTGAGAGAGGGATCTAGAGGAG 59.991 56.522 0.00 0.00 38.36 3.69
679 1018 4.439253 ACACTTTAAGACAGCCTTTCCT 57.561 40.909 0.00 0.00 36.34 3.36
772 1130 9.502091 CAATAATACTAGTGCTACTCTCTCTCT 57.498 37.037 5.39 0.00 0.00 3.10
778 1136 2.172717 GTGCTACTCTCTCTCTCCCTCT 59.827 54.545 0.00 0.00 0.00 3.69
797 1157 4.442612 CCTCTCTCTCTCTCTGTCTCTCTG 60.443 54.167 0.00 0.00 0.00 3.35
799 1159 4.160439 TCTCTCTCTCTCTGTCTCTCTGTC 59.840 50.000 0.00 0.00 0.00 3.51
800 1160 4.096681 TCTCTCTCTCTGTCTCTCTGTCT 58.903 47.826 0.00 0.00 0.00 3.41
801 1161 4.160439 TCTCTCTCTCTGTCTCTCTGTCTC 59.840 50.000 0.00 0.00 0.00 3.36
802 1162 4.096681 TCTCTCTCTGTCTCTCTGTCTCT 58.903 47.826 0.00 0.00 0.00 3.10
803 1163 4.160439 TCTCTCTCTGTCTCTCTGTCTCTC 59.840 50.000 0.00 0.00 0.00 3.20
804 1164 4.096681 TCTCTCTGTCTCTCTGTCTCTCT 58.903 47.826 0.00 0.00 0.00 3.10
805 1165 4.160439 TCTCTCTGTCTCTCTGTCTCTCTC 59.840 50.000 0.00 0.00 0.00 3.20
806 1166 4.096681 TCTCTGTCTCTCTGTCTCTCTCT 58.903 47.826 0.00 0.00 0.00 3.10
807 1167 4.081476 TCTCTGTCTCTCTGTCTCTCTCTG 60.081 50.000 0.00 0.00 0.00 3.35
854 1214 4.314961 TGATGATGTACTGAACACACCAC 58.685 43.478 0.00 0.00 42.09 4.16
863 1223 2.366153 GAACACACCACCCCCACCAT 62.366 60.000 0.00 0.00 0.00 3.55
962 1324 4.217334 TGTTCAGTTGTTGCTGTTTCTTCA 59.783 37.500 0.00 0.00 37.70 3.02
1079 1498 4.997395 TGAAACACTATTCTCCTTGCTGTC 59.003 41.667 0.00 0.00 0.00 3.51
1393 1823 1.147817 AGCCCCTTGGACTTGAACAAT 59.852 47.619 0.00 0.00 0.00 2.71
1441 1871 0.827925 TGGAGAGCTCAACGACCACT 60.828 55.000 17.77 0.00 0.00 4.00
1494 1924 4.554723 CGCAACCAGTAAGAAACTCCAAAG 60.555 45.833 0.00 0.00 35.76 2.77
1524 1954 8.737168 ACTATTTCATTCGATTTGAAGATGGA 57.263 30.769 10.19 0.00 40.65 3.41
1707 2137 1.758936 CCAAGGCAAGCATCATCTGA 58.241 50.000 0.00 0.00 0.00 3.27
1728 2158 2.432510 ACAGATCACAACCCTAGCTAGC 59.567 50.000 15.74 6.62 0.00 3.42
1736 2166 4.401519 CACAACCCTAGCTAGCTGTTACTA 59.598 45.833 27.68 4.87 0.00 1.82
1737 2167 4.401837 ACAACCCTAGCTAGCTGTTACTAC 59.598 45.833 27.68 0.00 0.00 2.73
1738 2168 4.523168 ACCCTAGCTAGCTGTTACTACT 57.477 45.455 27.68 0.00 0.00 2.57
1927 2361 2.704190 TTAGGGTTTTTCCATGGCCA 57.296 45.000 8.56 8.56 38.11 5.36
1992 2426 3.005539 AGGCAGTGCTCCATCGGT 61.006 61.111 16.11 0.00 0.00 4.69
2654 3099 1.824852 GGTTTTATGGACTTGCCCCAG 59.175 52.381 0.00 0.00 37.08 4.45
2666 3111 3.181466 ACTTGCCCCAGTTGATGTTTTTC 60.181 43.478 0.00 0.00 0.00 2.29
2675 3120 7.086376 CCCAGTTGATGTTTTTCATTCTACTG 58.914 38.462 0.00 0.00 37.29 2.74
2697 3142 7.791029 ACTGTAAAATGTTTGAGAAATTGGGT 58.209 30.769 0.00 0.00 0.00 4.51
2699 3144 9.927668 CTGTAAAATGTTTGAGAAATTGGGTAT 57.072 29.630 0.00 0.00 0.00 2.73
2925 3431 6.983474 TTAGAATCGATCATTTTGCACTCA 57.017 33.333 0.00 0.00 0.00 3.41
2930 3436 4.820897 TCGATCATTTTGCACTCACTAGT 58.179 39.130 0.00 0.00 35.91 2.57
2968 3474 0.539986 TACCTGGAGACGGCAAATCC 59.460 55.000 0.00 0.00 34.42 3.01
3073 3579 4.923281 GTCAACCAATGTAAAGATGGCAAC 59.077 41.667 0.00 0.00 37.77 4.17
3138 3656 6.180472 CACTGAAGTACCCTTTGGATTATGT 58.820 40.000 0.00 0.00 34.81 2.29
3383 3910 2.922387 TGCATATTGTTTTGCGATGCAC 59.078 40.909 3.84 0.00 45.86 4.57
3384 3911 2.035508 GCATATTGTTTTGCGATGCACG 60.036 45.455 0.00 0.00 41.98 5.34
3395 3922 2.030335 TGCGATGCACGTACATTGATTC 59.970 45.455 18.53 3.24 44.60 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.404265 AAACATCACACATGCACACG 57.596 45.000 0.00 0.00 0.00 4.49
243 277 5.350914 GTGAATCTGATCTCTGTGTTTGAGG 59.649 44.000 0.00 0.00 32.78 3.86
287 321 3.312890 AGAGAGAGAGAGAGAGAGGGAG 58.687 54.545 0.00 0.00 0.00 4.30
288 322 3.051803 AGAGAGAGAGAGAGAGAGAGGGA 60.052 52.174 0.00 0.00 0.00 4.20
289 323 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
290 324 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
291 325 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
292 326 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
293 327 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
294 328 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
295 329 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
296 330 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
297 331 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
298 332 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
299 333 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
300 334 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
301 335 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
302 336 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
303 337 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
304 338 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
359 692 4.141733 GCTATCCTTTCTCTCTCTTTGCCT 60.142 45.833 0.00 0.00 0.00 4.75
363 697 6.013812 AGTGTTGCTATCCTTTCTCTCTCTTT 60.014 38.462 0.00 0.00 0.00 2.52
464 798 3.009473 CCTCCTCTAGATCCCTCTCTCAG 59.991 56.522 0.00 0.00 32.66 3.35
483 817 2.573369 TCTACATACACCGCTCTCCTC 58.427 52.381 0.00 0.00 0.00 3.71
484 818 2.730934 TCTACATACACCGCTCTCCT 57.269 50.000 0.00 0.00 0.00 3.69
485 819 2.623889 ACATCTACATACACCGCTCTCC 59.376 50.000 0.00 0.00 0.00 3.71
772 1130 2.771943 GAGACAGAGAGAGAGAGAGGGA 59.228 54.545 0.00 0.00 0.00 4.20
778 1136 4.096681 AGACAGAGAGACAGAGAGAGAGA 58.903 47.826 0.00 0.00 0.00 3.10
797 1157 2.554462 TGTGTACTGTGCAGAGAGAGAC 59.446 50.000 19.13 13.30 0.00 3.36
799 1159 2.294512 TGTGTGTACTGTGCAGAGAGAG 59.705 50.000 19.13 0.00 0.00 3.20
800 1160 2.034685 GTGTGTGTACTGTGCAGAGAGA 59.965 50.000 19.13 1.74 0.00 3.10
801 1161 2.035193 AGTGTGTGTACTGTGCAGAGAG 59.965 50.000 19.13 1.49 0.00 3.20
802 1162 2.031870 AGTGTGTGTACTGTGCAGAGA 58.968 47.619 19.13 0.00 0.00 3.10
803 1163 2.398498 GAGTGTGTGTACTGTGCAGAG 58.602 52.381 9.74 9.74 0.00 3.35
804 1164 1.068588 GGAGTGTGTGTACTGTGCAGA 59.931 52.381 6.17 0.00 0.00 4.26
805 1165 1.202521 TGGAGTGTGTGTACTGTGCAG 60.203 52.381 0.00 0.00 0.00 4.41
806 1166 0.827368 TGGAGTGTGTGTACTGTGCA 59.173 50.000 0.00 0.00 0.00 4.57
807 1167 1.217882 GTGGAGTGTGTGTACTGTGC 58.782 55.000 0.00 0.00 0.00 4.57
854 1214 1.133809 ATATCGGGTGATGGTGGGGG 61.134 60.000 0.00 0.00 35.99 5.40
863 1223 3.116862 GGGAGGGGATATATATCGGGTGA 60.117 52.174 15.06 0.00 33.52 4.02
962 1324 0.470833 AGAGCAGTGGTGTGAGAGGT 60.471 55.000 0.00 0.00 0.00 3.85
1038 1400 5.163205 TGTTTCAGAAGGGAAAGTGATGAGA 60.163 40.000 0.00 0.00 37.44 3.27
1079 1498 8.477256 AGAGAGAAGAGGATGAATAAACAAGAG 58.523 37.037 0.00 0.00 0.00 2.85
1247 1674 3.874392 GGCTGCACCAAACTATCAATT 57.126 42.857 0.50 0.00 38.86 2.32
1393 1823 2.439701 CCGTACTCCTCCGGCAGA 60.440 66.667 0.00 0.00 37.43 4.26
1466 1896 0.947180 TTCTTACTGGTTGCGTCGGC 60.947 55.000 0.00 0.00 40.52 5.54
1524 1954 6.546428 ACATGTTAGTACCTCTATGCAAGT 57.454 37.500 0.00 0.00 0.00 3.16
1707 2137 2.432510 GCTAGCTAGGGTTGTGATCTGT 59.567 50.000 22.10 0.00 0.00 3.41
1728 2158 6.166279 TGCATGGAAGAGAAAGTAGTAACAG 58.834 40.000 0.00 0.00 0.00 3.16
1736 2166 3.255149 CAGCTTTGCATGGAAGAGAAAGT 59.745 43.478 0.00 0.00 0.00 2.66
1737 2167 3.367087 CCAGCTTTGCATGGAAGAGAAAG 60.367 47.826 0.00 0.00 39.02 2.62
1738 2168 2.559668 CCAGCTTTGCATGGAAGAGAAA 59.440 45.455 0.00 0.00 39.02 2.52
1860 2294 1.374947 GGTAGGCAGTGCACCTCAA 59.625 57.895 18.61 0.00 38.81 3.02
1927 2361 5.363939 CAGAAGAGAAAGAAGTTCAGTGGT 58.636 41.667 5.50 0.00 38.86 4.16
1992 2426 1.135094 GAATCCTCCTCCCAGCATGA 58.865 55.000 0.00 0.00 39.69 3.07
2342 2787 2.224281 TGTAGTTGTGGTCTTCCTGCAG 60.224 50.000 6.78 6.78 34.23 4.41
2349 2794 2.548067 CCGAAGCTGTAGTTGTGGTCTT 60.548 50.000 0.00 0.00 0.00 3.01
2471 2916 9.357161 TCCAAAAACTTAACAGCCTATCTTAAA 57.643 29.630 0.00 0.00 0.00 1.52
2732 3179 7.121168 CCTGTTTTAACTGAGCCTTCATGAATA 59.879 37.037 8.96 0.00 31.68 1.75
2787 3289 9.722056 CTTTAGTTTCACATAAATATGCTCACC 57.278 33.333 0.36 0.00 37.19 4.02
2844 3349 9.524106 CGTTGACAGTGGAGTATTATTATGTTA 57.476 33.333 0.00 0.00 0.00 2.41
2862 3367 5.872617 TGATTATGGGTTTAGTCGTTGACAG 59.127 40.000 0.00 0.00 34.60 3.51
2899 3405 8.124823 TGAGTGCAAAATGATCGATTCTAATTC 58.875 33.333 0.00 0.00 0.00 2.17
2925 3431 9.372369 GTAGAGCAATTAAATGAAGTGACTAGT 57.628 33.333 0.00 0.00 35.03 2.57
2930 3436 6.599244 CCAGGTAGAGCAATTAAATGAAGTGA 59.401 38.462 0.00 0.00 35.03 3.41
2968 3474 1.013596 TTGACGGTCTTGTGCAACTG 58.986 50.000 9.88 0.00 38.04 3.16
3016 3522 5.572511 CCATGTCAAATCACGTTTAATGTGG 59.427 40.000 16.11 1.88 35.86 4.17
3073 3579 0.947244 GAACCGGCCAGCTCATAATG 59.053 55.000 0.00 0.00 0.00 1.90
3241 3765 5.679382 GCATACCAGAAATTAATGTGCTGCA 60.679 40.000 0.00 0.00 0.00 4.41
3383 3910 6.892310 TGTCTTGAGATGAATCAATGTACG 57.108 37.500 0.00 0.00 38.47 3.67
3384 3911 7.012138 AGCATGTCTTGAGATGAATCAATGTAC 59.988 37.037 11.25 0.00 38.47 2.90


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

AutoCloner maintained by Alex Coulton.