Multiple sequence alignment - TraesCS3D01G397200

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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 TraesCS3D01G397200 chr3D 100.000 2895 0 0 1 2895 511727795 511724901 0.000000e+00 5347
1 TraesCS3D01G397200 chr3D 82.895 304 48 4 1100 1401 47493584 47493885 1.320000e-68 270
2 TraesCS3D01G397200 chr3B 94.426 2081 61 19 1 2057 674064472 674062423 0.000000e+00 3149
3 TraesCS3D01G397200 chr3B 88.348 575 29 15 2084 2636 674062434 674061876 0.000000e+00 656
4 TraesCS3D01G397200 chr3B 89.062 256 14 5 2638 2883 674061790 674061539 3.620000e-79 305
5 TraesCS3D01G397200 chr3B 82.566 304 49 4 1100 1401 74294229 74294530 6.150000e-67 265
6 TraesCS3D01G397200 chr3A 93.265 1960 78 21 973 2895 647755639 647753697 0.000000e+00 2839
7 TraesCS3D01G397200 chr3A 91.787 901 45 18 1 884 647756522 647755634 0.000000e+00 1227
8 TraesCS3D01G397200 chr3A 82.895 304 48 4 1100 1401 59532234 59532535 1.320000e-68 270
9 TraesCS3D01G397200 chr1B 89.059 393 40 2 1039 1428 475470184 475469792 4.340000e-133 484
10 TraesCS3D01G397200 chr1D 92.727 330 24 0 1099 1428 353557696 353557367 7.260000e-131 477
11 TraesCS3D01G397200 chr1A 88.295 393 43 2 1039 1428 453523585 453523193 4.370000e-128 468
12 TraesCS3D01G397200 chr4B 92.469 239 15 1 1545 1783 37400109 37399874 3.570000e-89 339
13 TraesCS3D01G397200 chr4B 84.351 262 37 3 1109 1368 77651297 77651556 1.330000e-63 254
14 TraesCS3D01G397200 chr2B 96.154 130 5 0 1651 1780 728932995 728933124 2.260000e-51 213


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 TraesCS3D01G397200 chr3D 511724901 511727795 2894 True 5347 5347 100.000 1 2895 1 chr3D.!!$R1 2894
1 TraesCS3D01G397200 chr3B 674061539 674064472 2933 True 1370 3149 90.612 1 2883 3 chr3B.!!$R1 2882
2 TraesCS3D01G397200 chr3A 647753697 647756522 2825 True 2033 2839 92.526 1 2895 2 chr3A.!!$R1 2894

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
339 345 0.33812 CCTCACTTCTCCCTCTCCCT 59.662 60.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2125 0.162082 GCGCACACGTAACGAATCAA 59.838 50.0 0.3 0.0 42.83 2.57 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
56 57 7.279536 ACATAATGATCATGGATACGATTGAGC 59.720 37.037 9.46 0.00 42.51 4.26
108 109 8.139989 CCAATCAGTATTCTTTCATTCCATTCC 58.860 37.037 0.00 0.00 0.00 3.01
115 116 4.996793 TCTTTCATTCCATTCCCTCACAA 58.003 39.130 0.00 0.00 0.00 3.33
116 117 5.392995 TCTTTCATTCCATTCCCTCACAAA 58.607 37.500 0.00 0.00 0.00 2.83
223 225 6.156083 TCAAATTCCATTCATTTAACCTCCCC 59.844 38.462 0.00 0.00 0.00 4.81
280 283 2.367567 TCCCCTTCCTCGCAACATATAC 59.632 50.000 0.00 0.00 0.00 1.47
281 284 2.404215 CCCTTCCTCGCAACATATACG 58.596 52.381 0.00 0.00 0.00 3.06
337 343 1.687996 CCTCCTCACTTCTCCCTCTCC 60.688 61.905 0.00 0.00 0.00 3.71
339 345 0.338120 CCTCACTTCTCCCTCTCCCT 59.662 60.000 0.00 0.00 0.00 4.20
343 349 1.006519 CACTTCTCCCTCTCCCTCTCA 59.993 57.143 0.00 0.00 0.00 3.27
344 350 1.936631 ACTTCTCCCTCTCCCTCTCAT 59.063 52.381 0.00 0.00 0.00 2.90
345 351 2.317594 ACTTCTCCCTCTCCCTCTCATT 59.682 50.000 0.00 0.00 0.00 2.57
347 353 1.219213 TCTCCCTCTCCCTCTCATTCC 59.781 57.143 0.00 0.00 0.00 3.01
348 354 1.220236 CTCCCTCTCCCTCTCATTCCT 59.780 57.143 0.00 0.00 0.00 3.36
349 355 1.062581 TCCCTCTCCCTCTCATTCCTG 60.063 57.143 0.00 0.00 0.00 3.86
350 356 1.343884 CCCTCTCCCTCTCATTCCTGT 60.344 57.143 0.00 0.00 0.00 4.00
584 607 4.903045 TCCTTTCTTTTATCCACTCGGT 57.097 40.909 0.00 0.00 0.00 4.69
653 679 2.028748 GTCCCAGTTAACTACGCTTCCA 60.029 50.000 8.04 0.00 0.00 3.53
777 803 6.911250 TCTAATTTATGGGAGATGCGAGTA 57.089 37.500 0.00 0.00 0.00 2.59
884 910 3.293337 TCTGGTTATACGCTGCTTCCTA 58.707 45.455 0.00 0.00 0.00 2.94
920 946 3.844577 TCTAGCTTCCTGACAACGTAC 57.155 47.619 0.00 0.00 0.00 3.67
939 967 6.102663 ACGTACAGATTTCATGGAAGAAGAG 58.897 40.000 0.00 0.00 0.00 2.85
945 973 2.084610 TCATGGAAGAAGAGCACACG 57.915 50.000 0.00 0.00 0.00 4.49
946 974 1.618343 TCATGGAAGAAGAGCACACGA 59.382 47.619 0.00 0.00 0.00 4.35
947 975 1.728971 CATGGAAGAAGAGCACACGAC 59.271 52.381 0.00 0.00 0.00 4.34
949 977 1.618640 GGAAGAAGAGCACACGACGC 61.619 60.000 0.00 0.00 0.00 5.19
950 978 1.935065 GAAGAAGAGCACACGACGCG 61.935 60.000 3.53 3.53 0.00 6.01
951 979 2.402282 AAGAAGAGCACACGACGCGA 62.402 55.000 15.93 0.00 0.00 5.87
952 980 2.429236 AAGAGCACACGACGCGAG 60.429 61.111 15.93 9.24 0.00 5.03
953 981 2.781750 GAAGAGCACACGACGCGAGA 62.782 60.000 15.93 0.00 0.00 4.04
954 982 2.788172 AAGAGCACACGACGCGAGAG 62.788 60.000 15.93 7.72 0.00 3.20
978 1006 1.416401 TCTCACCTTTCGTGCTTCCTT 59.584 47.619 0.00 0.00 42.69 3.36
981 1009 2.616842 TCACCTTTCGTGCTTCCTTTTC 59.383 45.455 0.00 0.00 42.69 2.29
1459 1487 0.247814 CATTTGCATCACGCTCGTCC 60.248 55.000 0.00 0.00 43.06 4.79
1690 1718 0.400213 TCGGGCAAGACCATCAGTTT 59.600 50.000 0.00 0.00 42.05 2.66
1720 1748 1.693062 CAGATGCTGTCCAGGAGCTAT 59.307 52.381 6.26 0.00 43.62 2.97
1780 1808 0.380024 GCTACGAGTTCGGGTACTCC 59.620 60.000 6.48 0.00 44.95 3.85
1831 1859 4.148825 GGTCTCGGCATGCTCGGT 62.149 66.667 18.92 0.00 0.00 4.69
2066 2100 1.117150 ATGTTGATGATTGGCTGCCC 58.883 50.000 17.53 0.72 0.00 5.36
2072 2106 1.000938 GATGATTGGCTGCCCGATTTC 60.001 52.381 17.53 6.37 35.24 2.17
2073 2107 0.034186 TGATTGGCTGCCCGATTTCT 60.034 50.000 17.53 0.00 35.24 2.52
2079 2113 1.401905 GGCTGCCCGATTTCTTTGTAG 59.598 52.381 7.66 0.00 0.00 2.74
2080 2114 2.084546 GCTGCCCGATTTCTTTGTAGT 58.915 47.619 0.00 0.00 0.00 2.73
2081 2115 3.267483 GCTGCCCGATTTCTTTGTAGTA 58.733 45.455 0.00 0.00 0.00 1.82
2082 2116 3.309954 GCTGCCCGATTTCTTTGTAGTAG 59.690 47.826 0.00 0.00 0.00 2.57
2083 2117 4.504858 CTGCCCGATTTCTTTGTAGTAGT 58.495 43.478 0.00 0.00 0.00 2.73
2087 2121 6.537301 TGCCCGATTTCTTTGTAGTAGTAATG 59.463 38.462 0.00 0.00 0.00 1.90
2088 2122 6.511282 GCCCGATTTCTTTGTAGTAGTAATGC 60.511 42.308 0.00 0.00 0.00 3.56
2091 2125 7.277981 CCGATTTCTTTGTAGTAGTAATGCTGT 59.722 37.037 0.00 0.00 0.00 4.40
2156 2190 3.667166 GCGCACTGTTTAGCTTTTACTCC 60.667 47.826 0.30 0.00 0.00 3.85
2235 2269 0.899019 TAGGAGTACATGCACGCCAA 59.101 50.000 19.60 0.00 40.53 4.52
2274 2310 2.604046 ATATGGTGCTCTTGGTCGAC 57.396 50.000 7.13 7.13 0.00 4.20
2315 2351 5.491070 TCTGTTTCATACATGACCTCTTGG 58.509 41.667 0.00 0.00 36.36 3.61
2454 2505 2.857483 TCAGCAGGTAGAGCTAGCTAG 58.143 52.381 19.38 16.84 41.45 3.42
2522 2587 3.974871 TCATGTCTACTATTGCGCGTA 57.025 42.857 8.43 0.00 0.00 4.42
2545 2610 8.548721 CGTACATCTCTTTTTCAAGTTAAGTGT 58.451 33.333 0.00 0.00 0.00 3.55
2548 2613 9.614792 ACATCTCTTTTTCAAGTTAAGTGTACT 57.385 29.630 0.00 0.00 0.00 2.73
2550 2615 8.658499 TCTCTTTTTCAAGTTAAGTGTACTCC 57.342 34.615 0.00 0.00 0.00 3.85
2572 2637 8.657712 ACTCCTAAGTGGTAAGACAAATTAAGT 58.342 33.333 0.00 0.00 33.32 2.24
2609 2674 6.500041 AGCTAAAATGGCGCGAATAATAAAA 58.500 32.000 12.10 0.00 34.52 1.52
2610 2675 6.636850 AGCTAAAATGGCGCGAATAATAAAAG 59.363 34.615 12.10 0.00 34.52 2.27
2636 2701 5.885230 TTAGCATTGATCTTTCCAGTGTG 57.115 39.130 0.00 0.00 0.00 3.82
2704 2853 1.001487 CATGAACAGTTTGGCGCTGAA 60.001 47.619 7.64 0.00 37.40 3.02
2750 2899 6.151480 TGTTGTCATATTCAACAGTGATGCAT 59.849 34.615 15.15 0.00 46.35 3.96
2751 2900 6.762702 TGTCATATTCAACAGTGATGCATT 57.237 33.333 0.00 0.00 32.48 3.56
2794 2943 8.804204 GGGCATTAAGCTAGTCTTCTACTATAA 58.196 37.037 3.17 0.00 44.79 0.98
2795 2944 9.849166 GGCATTAAGCTAGTCTTCTACTATAAG 57.151 37.037 3.17 0.00 44.79 1.73
2886 3045 1.066071 GGCAGTAACAGTTCCCTCTCC 60.066 57.143 0.00 0.00 0.00 3.71
2889 3048 3.514309 GCAGTAACAGTTCCCTCTCCTAA 59.486 47.826 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.645059 TGTTTTGTGTAAAATTTCAGTTCATGA 57.355 25.926 0.00 0.00 38.01 3.07
56 57 2.480932 CCGAGGTCAGTGTGATCATCTG 60.481 54.545 18.61 18.61 27.47 2.90
108 109 4.335416 AGAGAGAGAGAGAGTTTGTGAGG 58.665 47.826 0.00 0.00 0.00 3.86
115 116 5.276440 AGAGAGAGAGAGAGAGAGAGAGTT 58.724 45.833 0.00 0.00 0.00 3.01
116 117 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
223 225 1.396653 GATGGATGTTGGCTTGGGAG 58.603 55.000 0.00 0.00 0.00 4.30
280 283 0.670546 AAAGATGGTGAGGTGCGTCG 60.671 55.000 0.00 0.00 0.00 5.12
281 284 1.079503 GAAAGATGGTGAGGTGCGTC 58.920 55.000 0.00 0.00 0.00 5.19
347 353 2.550978 CTGCGGATTTACCCTGTACAG 58.449 52.381 16.34 16.34 34.64 2.74
348 354 1.208535 CCTGCGGATTTACCCTGTACA 59.791 52.381 0.00 0.00 34.64 2.90
349 355 1.474498 CCCTGCGGATTTACCCTGTAC 60.474 57.143 0.00 0.00 34.64 2.90
350 356 0.834612 CCCTGCGGATTTACCCTGTA 59.165 55.000 0.00 0.00 34.64 2.74
518 541 2.193248 GGTGGATGGCTGCCTACC 59.807 66.667 21.03 21.26 0.00 3.18
543 566 1.540267 AGAGAAGCTATCGGATCCGG 58.460 55.000 32.79 18.59 40.25 5.14
555 578 6.657117 AGTGGATAAAAGAAAGGAAGAGAAGC 59.343 38.462 0.00 0.00 0.00 3.86
584 607 3.697190 AAGCAAGGGGAGAGAGATAGA 57.303 47.619 0.00 0.00 0.00 1.98
653 679 2.105766 GCCTTTCTTGGATCAATGGCT 58.894 47.619 11.18 0.00 36.52 4.75
764 790 3.997021 CCAAATATGTACTCGCATCTCCC 59.003 47.826 0.00 0.00 0.00 4.30
777 803 8.677148 AGCACGAGAAAATATACCAAATATGT 57.323 30.769 0.00 0.00 0.00 2.29
797 823 2.505866 GAACGATGCCTAAAAAGCACG 58.494 47.619 0.00 0.00 44.40 5.34
884 910 3.390639 AGCTAGATGCAAGCATAGAACCT 59.609 43.478 11.29 3.20 45.94 3.50
920 946 4.698780 TGTGCTCTTCTTCCATGAAATCTG 59.301 41.667 0.00 0.00 0.00 2.90
951 979 1.343069 ACGAAAGGTGAGAAGGCTCT 58.657 50.000 0.00 0.00 41.84 4.09
952 980 3.917072 ACGAAAGGTGAGAAGGCTC 57.083 52.632 0.00 0.00 41.67 4.70
978 1006 2.066262 CTTCGCGCCTACTGAAAGAAA 58.934 47.619 0.00 0.00 37.43 2.52
981 1009 0.108804 TCCTTCGCGCCTACTGAAAG 60.109 55.000 0.00 0.00 42.29 2.62
1452 1480 3.247006 TGGTAAAGAAGATGGACGAGC 57.753 47.619 0.00 0.00 0.00 5.03
1459 1487 5.164012 GCGATGATCGATGGTAAAGAAGATG 60.164 44.000 20.25 0.00 43.74 2.90
1612 1640 1.298859 GCCCGACGTTGATGAAGCTT 61.299 55.000 3.74 0.00 0.00 3.74
1831 1859 1.289066 CTTCAGGAACGACGAGCCA 59.711 57.895 0.00 0.00 0.00 4.75
1838 1866 4.388499 GCCGGGCTTCAGGAACGA 62.388 66.667 12.87 0.00 0.00 3.85
2066 2100 8.186178 ACAGCATTACTACTACAAAGAAATCG 57.814 34.615 0.00 0.00 0.00 3.34
2072 2106 8.110612 CGAATCAACAGCATTACTACTACAAAG 58.889 37.037 0.00 0.00 0.00 2.77
2073 2107 7.601130 ACGAATCAACAGCATTACTACTACAAA 59.399 33.333 0.00 0.00 0.00 2.83
2079 2113 6.034256 ACGTAACGAATCAACAGCATTACTAC 59.966 38.462 0.00 0.00 0.00 2.73
2080 2114 6.034150 CACGTAACGAATCAACAGCATTACTA 59.966 38.462 0.00 0.00 0.00 1.82
2081 2115 4.927425 ACGTAACGAATCAACAGCATTACT 59.073 37.500 0.00 0.00 0.00 2.24
2082 2116 5.013236 CACGTAACGAATCAACAGCATTAC 58.987 41.667 0.00 0.00 0.00 1.89
2083 2117 4.687018 ACACGTAACGAATCAACAGCATTA 59.313 37.500 0.00 0.00 0.00 1.90
2087 2121 2.822827 CACACGTAACGAATCAACAGC 58.177 47.619 0.00 0.00 0.00 4.40
2088 2122 2.717595 CGCACACGTAACGAATCAACAG 60.718 50.000 0.00 0.00 33.53 3.16
2091 2125 0.162082 GCGCACACGTAACGAATCAA 59.838 50.000 0.30 0.00 42.83 2.57
2156 2190 3.687212 TGCATGGACACTAACAATAACCG 59.313 43.478 0.00 0.00 0.00 4.44
2454 2505 1.671054 TGTTTAGGTCGCAGCTGGC 60.671 57.895 17.12 6.97 39.90 4.85
2456 2507 0.320771 AGGTGTTTAGGTCGCAGCTG 60.321 55.000 10.11 10.11 39.17 4.24
2522 2587 9.614792 AGTACACTTAACTTGAAAAAGAGATGT 57.385 29.630 0.00 0.00 0.00 3.06
2546 2611 8.657712 ACTTAATTTGTCTTACCACTTAGGAGT 58.342 33.333 0.00 0.00 41.22 3.85
2547 2612 8.936864 CACTTAATTTGTCTTACCACTTAGGAG 58.063 37.037 0.00 0.00 41.22 3.69
2548 2613 7.389607 GCACTTAATTTGTCTTACCACTTAGGA 59.610 37.037 0.00 0.00 41.22 2.94
2549 2614 7.174253 TGCACTTAATTTGTCTTACCACTTAGG 59.826 37.037 0.00 0.00 45.67 2.69
2550 2615 8.094798 TGCACTTAATTTGTCTTACCACTTAG 57.905 34.615 0.00 0.00 0.00 2.18
2572 2637 5.472148 CCATTTTAGCTCATTCTTGTTGCA 58.528 37.500 0.00 0.00 0.00 4.08
2609 2674 7.395489 ACACTGGAAAGATCAATGCTAATTTCT 59.605 33.333 0.00 0.00 0.00 2.52
2610 2675 7.487189 CACACTGGAAAGATCAATGCTAATTTC 59.513 37.037 0.00 0.00 0.00 2.17
2636 2701 4.273724 ACAGTTTTCTTCTTCTTCGAAGCC 59.726 41.667 20.56 0.00 40.11 4.35
2750 2899 2.224257 GCCCAAACTGCTGAAATTGGAA 60.224 45.455 20.35 0.00 44.01 3.53
2751 2900 1.344114 GCCCAAACTGCTGAAATTGGA 59.656 47.619 20.35 0.00 44.01 3.53
2814 2973 8.425577 AGTTTATACAGAGAATGAAATGGACG 57.574 34.615 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.