Multiple sequence alignment - TraesCS3B01G082500

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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 TraesCS3B01G082500 chr3B 100.000 3755 0 0 1 3755 52142682 52146436 0.000000e+00 6935
1 TraesCS3B01G082500 chr3B 96.956 2924 75 7 845 3755 52839624 52836702 0.000000e+00 4894
2 TraesCS3B01G082500 chr3B 82.469 2835 425 40 954 3744 51727000 51729806 0.000000e+00 2416
3 TraesCS3B01G082500 chr3B 87.615 2067 242 7 856 2913 52164490 52166551 0.000000e+00 2386
4 TraesCS3B01G082500 chr3B 81.947 2825 443 41 952 3729 52853759 52850955 0.000000e+00 2329
5 TraesCS3B01G082500 chr3B 82.061 2804 427 49 954 3708 52426286 52429062 0.000000e+00 2322
6 TraesCS3B01G082500 chr3B 82.570 2576 397 33 1009 3542 51947796 51950361 0.000000e+00 2222
7 TraesCS3B01G082500 chr3B 82.036 2633 416 37 952 3542 51228487 51231104 0.000000e+00 2189
8 TraesCS3B01G082500 chr3B 84.947 857 115 12 1 852 358655302 358654455 0.000000e+00 856
9 TraesCS3B01G082500 chr3A 95.657 2924 113 7 845 3755 41117647 41120569 0.000000e+00 4684
10 TraesCS3B01G082500 chr3A 81.797 2961 451 56 849 3755 40936231 40939157 0.000000e+00 2401
11 TraesCS3B01G082500 chr3A 81.831 2807 442 47 954 3714 41537184 41539968 0.000000e+00 2296
12 TraesCS3B01G082500 chr3A 78.129 1454 270 31 2340 3755 41624148 41625591 0.000000e+00 880
13 TraesCS3B01G082500 chr3D 82.522 2815 416 42 954 3714 30006656 30009448 0.000000e+00 2403
14 TraesCS3B01G082500 chr3D 84.482 2133 292 24 956 3070 29970797 29972908 0.000000e+00 2069
15 TraesCS3B01G082500 chr3D 94.333 847 45 3 845 1688 29978975 29979821 0.000000e+00 1295
16 TraesCS3B01G082500 chr1B 89.905 842 78 5 1 837 565170521 565171360 0.000000e+00 1077
17 TraesCS3B01G082500 chr2B 88.126 859 95 2 1 852 177449598 177448740 0.000000e+00 1014
18 TraesCS3B01G082500 chr2B 92.521 468 34 1 1 468 385038473 385038939 0.000000e+00 669
19 TraesCS3B01G082500 chr7B 87.368 855 102 4 1 852 653530551 653531402 0.000000e+00 976
20 TraesCS3B01G082500 chr7B 87.018 855 105 4 1 852 653462829 653463680 0.000000e+00 959
21 TraesCS3B01G082500 chr6B 87.108 861 96 11 1 850 70767006 70766150 0.000000e+00 961
22 TraesCS3B01G082500 chr6B 84.455 862 108 19 3 852 165438450 165439297 0.000000e+00 826
23 TraesCS3B01G082500 chr4B 87.093 860 98 12 1 852 306952610 306953464 0.000000e+00 961
24 TraesCS3B01G082500 chr4B 89.901 505 46 5 1 503 241676847 241676346 0.000000e+00 645
25 TraesCS3B01G082500 chr6D 84.496 774 100 18 1 765 34554755 34553993 0.000000e+00 747
26 TraesCS3B01G082500 chr5B 90.316 506 45 3 1 504 127742579 127743082 0.000000e+00 660
27 TraesCS3B01G082500 chr5B 78.846 208 41 3 3341 3547 292752949 292753154 1.820000e-28 137


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 TraesCS3B01G082500 chr3B 52142682 52146436 3754 False 6935 6935 100.000 1 3755 1 chr3B.!!$F4 3754
1 TraesCS3B01G082500 chr3B 52836702 52839624 2922 True 4894 4894 96.956 845 3755 1 chr3B.!!$R1 2910
2 TraesCS3B01G082500 chr3B 51727000 51729806 2806 False 2416 2416 82.469 954 3744 1 chr3B.!!$F2 2790
3 TraesCS3B01G082500 chr3B 52164490 52166551 2061 False 2386 2386 87.615 856 2913 1 chr3B.!!$F5 2057
4 TraesCS3B01G082500 chr3B 52850955 52853759 2804 True 2329 2329 81.947 952 3729 1 chr3B.!!$R2 2777
5 TraesCS3B01G082500 chr3B 52426286 52429062 2776 False 2322 2322 82.061 954 3708 1 chr3B.!!$F6 2754
6 TraesCS3B01G082500 chr3B 51947796 51950361 2565 False 2222 2222 82.570 1009 3542 1 chr3B.!!$F3 2533
7 TraesCS3B01G082500 chr3B 51228487 51231104 2617 False 2189 2189 82.036 952 3542 1 chr3B.!!$F1 2590
8 TraesCS3B01G082500 chr3B 358654455 358655302 847 True 856 856 84.947 1 852 1 chr3B.!!$R3 851
9 TraesCS3B01G082500 chr3A 41117647 41120569 2922 False 4684 4684 95.657 845 3755 1 chr3A.!!$F2 2910
10 TraesCS3B01G082500 chr3A 40936231 40939157 2926 False 2401 2401 81.797 849 3755 1 chr3A.!!$F1 2906
11 TraesCS3B01G082500 chr3A 41537184 41539968 2784 False 2296 2296 81.831 954 3714 1 chr3A.!!$F3 2760
12 TraesCS3B01G082500 chr3A 41624148 41625591 1443 False 880 880 78.129 2340 3755 1 chr3A.!!$F4 1415
13 TraesCS3B01G082500 chr3D 30006656 30009448 2792 False 2403 2403 82.522 954 3714 1 chr3D.!!$F3 2760
14 TraesCS3B01G082500 chr3D 29970797 29972908 2111 False 2069 2069 84.482 956 3070 1 chr3D.!!$F1 2114
15 TraesCS3B01G082500 chr3D 29978975 29979821 846 False 1295 1295 94.333 845 1688 1 chr3D.!!$F2 843
16 TraesCS3B01G082500 chr1B 565170521 565171360 839 False 1077 1077 89.905 1 837 1 chr1B.!!$F1 836
17 TraesCS3B01G082500 chr2B 177448740 177449598 858 True 1014 1014 88.126 1 852 1 chr2B.!!$R1 851
18 TraesCS3B01G082500 chr7B 653530551 653531402 851 False 976 976 87.368 1 852 1 chr7B.!!$F2 851
19 TraesCS3B01G082500 chr7B 653462829 653463680 851 False 959 959 87.018 1 852 1 chr7B.!!$F1 851
20 TraesCS3B01G082500 chr6B 70766150 70767006 856 True 961 961 87.108 1 850 1 chr6B.!!$R1 849
21 TraesCS3B01G082500 chr6B 165438450 165439297 847 False 826 826 84.455 3 852 1 chr6B.!!$F1 849
22 TraesCS3B01G082500 chr4B 306952610 306953464 854 False 961 961 87.093 1 852 1 chr4B.!!$F1 851
23 TraesCS3B01G082500 chr4B 241676346 241676847 501 True 645 645 89.901 1 503 1 chr4B.!!$R1 502
24 TraesCS3B01G082500 chr6D 34553993 34554755 762 True 747 747 84.496 1 765 1 chr6D.!!$R1 764
25 TraesCS3B01G082500 chr5B 127742579 127743082 503 False 660 660 90.316 1 504 1 chr5B.!!$F1 503

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
343 351 0.592637 TCCGACGCGAAGTTCAGTAA 59.407 50.000 15.93 0.0 0.00 2.24 F
504 518 1.652947 CACCCAGTGGTAGTTACCCT 58.347 55.000 8.74 0.6 45.57 4.34 F
930 960 2.614987 GCTTTTGGTTATTGCCATGCCA 60.615 45.455 0.00 0.0 38.48 4.92 F
2109 2156 0.529378 GTTGCCTCCCTCTTGCAATG 59.471 55.000 0.00 0.0 45.66 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1632 0.768622 TCCTCCGGTTCCAACAACAT 59.231 50.000 0.0 0.0 0.0 2.71 R
2109 2156 3.678548 CCAGAACACTAGCGGTAACTTTC 59.321 47.826 0.0 0.0 0.0 2.62 R
2417 2464 5.186198 CGTTATCTGGTTGGAGGAGATTTT 58.814 41.667 0.0 0.0 0.0 1.82 R
3294 3375 0.040958 CAGCGAAGACAAACAGGTGC 60.041 55.000 0.0 0.0 0.0 5.01 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
81 84 3.120060 ACGATATCTATCCAACGGCGTAC 60.120 47.826 15.20 0.00 0.00 3.67
100 103 3.683365 ACCATTTGCTTCATTCCAACC 57.317 42.857 0.00 0.00 0.00 3.77
340 348 0.856641 TTTTCCGACGCGAAGTTCAG 59.143 50.000 15.93 0.00 0.00 3.02
343 351 0.592637 TCCGACGCGAAGTTCAGTAA 59.407 50.000 15.93 0.00 0.00 2.24
363 373 3.533606 ATCTCTATTGCAGTGCTCGTT 57.466 42.857 17.60 0.90 0.00 3.85
456 466 7.828712 ACTAATATTAGCAGAATAGACCGTCC 58.171 38.462 20.24 0.00 34.09 4.79
504 518 1.652947 CACCCAGTGGTAGTTACCCT 58.347 55.000 8.74 0.60 45.57 4.34
506 520 3.381335 CACCCAGTGGTAGTTACCCTAT 58.619 50.000 8.74 0.00 45.57 2.57
775 804 6.965500 ACACGTACATACTCTCTATTTTGACG 59.035 38.462 0.00 0.00 0.00 4.35
785 814 8.289939 ACTCTCTATTTTGACGGATACTACAA 57.710 34.615 0.00 0.00 0.00 2.41
837 866 3.412386 ACCACTGCTTGTAGGAAACATC 58.588 45.455 0.00 0.00 38.10 3.06
845 874 5.012664 TGCTTGTAGGAAACATCTGTCCTAA 59.987 40.000 1.06 0.00 45.85 2.69
892 922 9.683069 CTCAATTCAAAGCATGTTAATATACCC 57.317 33.333 0.00 0.00 0.00 3.69
896 926 8.588290 TTCAAAGCATGTTAATATACCCTGTT 57.412 30.769 0.00 0.00 0.00 3.16
898 928 8.465999 TCAAAGCATGTTAATATACCCTGTTTG 58.534 33.333 0.00 0.00 0.00 2.93
911 941 5.869649 ACCCTGTTTGTTAATTTTCAGCT 57.130 34.783 0.00 0.00 0.00 4.24
930 960 2.614987 GCTTTTGGTTATTGCCATGCCA 60.615 45.455 0.00 0.00 38.48 4.92
1023 1058 5.138758 TGGGGAACATACTAGAAGCTCTA 57.861 43.478 0.00 0.00 0.00 2.43
1038 1073 2.692557 AGCTCTACTTCGATCATGTGCT 59.307 45.455 0.00 0.00 0.00 4.40
1289 1325 4.292306 ACTTCCTAACCACCCTTCATCATT 59.708 41.667 0.00 0.00 0.00 2.57
1344 1380 6.478512 TCAGTTTTCCCTTGCTTTTGTAAT 57.521 33.333 0.00 0.00 0.00 1.89
1363 1399 2.797074 TATTGGTTCACGTCGTGACA 57.203 45.000 26.95 19.35 42.60 3.58
1380 1416 3.063997 GTGACATTGCTGTTCGGATTAGG 59.936 47.826 0.00 0.00 35.14 2.69
1447 1483 7.561021 TTCTTAACATTCAACAGTAGTGCAA 57.439 32.000 0.00 0.00 0.00 4.08
1595 1632 4.989168 GGAAAAGAAGTCTTACAAGCTCGA 59.011 41.667 0.00 0.00 34.61 4.04
1638 1675 3.762288 TCGGTAAGACAACACTAGCTCAT 59.238 43.478 0.00 0.00 0.00 2.90
1700 1738 3.741249 TGCATGCATGGATTTGTGTTTT 58.259 36.364 27.34 0.00 0.00 2.43
2109 2156 0.529378 GTTGCCTCCCTCTTGCAATG 59.471 55.000 0.00 0.00 45.66 2.82
2140 2187 1.002430 CTAGTGTTCTGGCAAGCAGGA 59.998 52.381 0.00 0.00 0.00 3.86
2159 2206 5.525378 GCAGGAATCGAACAGATAATGAGTT 59.475 40.000 0.00 0.00 38.98 3.01
2202 2249 1.068055 GCTTGCTCCCAGAACATGTTG 60.068 52.381 17.58 2.75 0.00 3.33
2417 2464 7.612244 GGAGTACTACTATGAGCTAATCCATCA 59.388 40.741 0.00 0.00 0.00 3.07
2900 2957 3.067742 TCTTCCTTCGACGATATCCCAAC 59.932 47.826 0.00 0.00 0.00 3.77
2901 2958 2.380941 TCCTTCGACGATATCCCAACA 58.619 47.619 0.00 0.00 0.00 3.33
2930 2987 9.699703 ACAGTTTAAGATGTCTTAGTCTTCTTC 57.300 33.333 9.87 0.02 39.36 2.87
2960 3017 9.807649 CAAATATAAATGAAGTTCAGAAAGGGG 57.192 33.333 11.91 0.00 0.00 4.79
3011 3068 2.522193 GGTTTCCGGTTGGGGCAA 60.522 61.111 0.00 0.00 36.01 4.52
3048 3105 5.674525 TGATGTACAAGATGGATGGAAGTC 58.325 41.667 0.00 0.00 0.00 3.01
3110 3167 4.555906 CGTTGGTTAAATTGGAAAGAGCGT 60.556 41.667 0.00 0.00 0.00 5.07
3174 3234 3.655615 AGGACTAGTACTGGAGTGGAG 57.344 52.381 13.86 0.00 0.00 3.86
3281 3362 2.203877 TTGGTCGGCAGTACCCCT 60.204 61.111 0.00 0.00 36.06 4.79
3294 3375 3.197116 CAGTACCCCTACTGGTTTGGTAG 59.803 52.174 0.63 0.00 44.43 3.18
3347 3431 5.187186 ACCCTTAGAAATCTACGATGTGTGT 59.813 40.000 0.00 0.00 0.00 3.72
3363 3447 4.513442 TGTGTGTATCTTCCACCTATTGC 58.487 43.478 0.00 0.00 31.71 3.56
3436 3520 1.632589 AGGTTGGCCCTGAATTTGTC 58.367 50.000 0.00 0.00 44.08 3.18
3589 3678 1.640149 TGATGAAGGGGGAGCAAATGA 59.360 47.619 0.00 0.00 0.00 2.57
3626 3715 1.153086 GGACGATGCCCAATCTGCT 60.153 57.895 0.00 0.00 32.61 4.24
3670 3759 4.911514 TGGTAAGGTTGAAACTTGAAGC 57.088 40.909 5.59 0.00 0.00 3.86
3714 3803 1.009389 GCGACAACTTGGAGAGGACG 61.009 60.000 0.00 0.00 0.00 4.79
3732 3821 1.069204 ACGCTGTCAGCTTGAAGAAGA 59.931 47.619 22.13 0.00 39.60 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 84 3.592059 CTGGTTGGAATGAAGCAAATGG 58.408 45.455 0.00 0.00 33.14 3.16
130 136 3.356639 GATGACGAGTGGCAGCGGA 62.357 63.158 13.29 1.40 0.00 5.54
309 317 1.262151 GTCGGAAAAAGCTGCACGTAA 59.738 47.619 1.02 0.00 0.00 3.18
319 327 1.259507 TGAACTTCGCGTCGGAAAAAG 59.740 47.619 5.77 2.58 0.00 2.27
340 348 4.363999 ACGAGCACTGCAATAGAGATTAC 58.636 43.478 3.30 0.00 0.00 1.89
343 351 3.193263 CAACGAGCACTGCAATAGAGAT 58.807 45.455 3.30 0.00 0.00 2.75
363 373 2.624364 AGTGCACTGCATCATTTTGACA 59.376 40.909 20.97 0.00 41.91 3.58
468 482 3.596046 TGGGTGGTAGAATGGATTTTCCT 59.404 43.478 0.00 0.00 37.46 3.36
504 518 9.901172 ACCACGTGATAGTATATGAGACATATA 57.099 33.333 19.30 7.20 0.00 0.86
506 520 9.159364 GTACCACGTGATAGTATATGAGACATA 57.841 37.037 19.30 0.00 0.00 2.29
775 804 7.269724 GCGTTTTGTATGTTGTTTGTAGTATCC 59.730 37.037 0.00 0.00 0.00 2.59
785 814 4.987832 TCACTTGCGTTTTGTATGTTGTT 58.012 34.783 0.00 0.00 0.00 2.83
870 899 8.766994 ACAGGGTATATTAACATGCTTTGAAT 57.233 30.769 0.00 0.00 0.00 2.57
892 922 7.973601 ACCAAAAGCTGAAAATTAACAAACAG 58.026 30.769 0.00 0.00 0.00 3.16
898 928 8.015087 GGCAATAACCAAAAGCTGAAAATTAAC 58.985 33.333 0.00 0.00 0.00 2.01
911 941 3.777106 TTGGCATGGCAATAACCAAAA 57.223 38.095 29.00 5.47 44.65 2.44
930 960 5.069914 GGGTCAGGGTGACTTGTTTAATTTT 59.930 40.000 6.99 0.00 46.19 1.82
1023 1058 5.584253 ACTTACTAGCACATGATCGAAGT 57.416 39.130 0.00 3.01 0.00 3.01
1237 1273 2.235016 TCCTTTGCATTTAGCCACGTT 58.765 42.857 0.00 0.00 44.83 3.99
1289 1325 8.504812 TTTACATGCAGCTGATTTACTTGATA 57.495 30.769 20.43 1.30 0.00 2.15
1344 1380 2.797074 TGTCACGACGTGAACCAATA 57.203 45.000 30.68 11.31 44.49 1.90
1363 1399 2.421529 GGGTCCTAATCCGAACAGCAAT 60.422 50.000 0.00 0.00 0.00 3.56
1380 1416 6.710744 TGTTCTCTATCTTTTTGTTGAGGGTC 59.289 38.462 0.00 0.00 0.00 4.46
1595 1632 0.768622 TCCTCCGGTTCCAACAACAT 59.231 50.000 0.00 0.00 0.00 2.71
1700 1738 5.302059 AGAGTTACTTCACTGTAGTCTTGCA 59.698 40.000 0.00 0.00 0.00 4.08
2109 2156 3.678548 CCAGAACACTAGCGGTAACTTTC 59.321 47.826 0.00 0.00 0.00 2.62
2140 2187 9.831737 CTTTTTCAACTCATTATCTGTTCGATT 57.168 29.630 0.00 0.00 33.48 3.34
2417 2464 5.186198 CGTTATCTGGTTGGAGGAGATTTT 58.814 41.667 0.00 0.00 0.00 1.82
2673 2723 5.924825 GCAAAAATCTCTTGAACAATGCTCT 59.075 36.000 0.00 0.00 0.00 4.09
2900 2957 9.915629 AAGACTAAGACATCTTAAACTGTACTG 57.084 33.333 3.09 0.00 37.92 2.74
3011 3068 8.114331 TCTTGTACATCAGCATTTTCAATTCT 57.886 30.769 0.00 0.00 0.00 2.40
3048 3105 4.058124 TGACAAAGATGACAACTCTTCCG 58.942 43.478 0.00 0.00 31.83 4.30
3110 3167 9.366216 CGCCAATAATGTATTACTATAGCAAGA 57.634 33.333 0.00 0.00 0.00 3.02
3174 3234 8.710551 CAGTGCTAACATCTTCTGAATATGATC 58.289 37.037 18.96 7.92 0.00 2.92
3281 3362 2.051692 ACAGGTGCTACCAAACCAGTA 58.948 47.619 7.86 0.00 41.95 2.74
3294 3375 0.040958 CAGCGAAGACAAACAGGTGC 60.041 55.000 0.00 0.00 0.00 5.01
3347 3431 2.106511 GCTGGGCAATAGGTGGAAGATA 59.893 50.000 0.00 0.00 0.00 1.98
3363 3447 2.286365 TTTCAAGTTGGGTAGCTGGG 57.714 50.000 2.34 0.00 0.00 4.45
3436 3520 0.676782 GATCACCCTTCCCACAACCG 60.677 60.000 0.00 0.00 0.00 4.44
3542 3626 7.500227 TCAGCATCTTCTTCTTCTTTTTCTTCA 59.500 33.333 0.00 0.00 0.00 3.02
3556 3642 4.462133 CCCTTCATCATCAGCATCTTCTT 58.538 43.478 0.00 0.00 0.00 2.52
3589 3678 3.748568 GTCCTTTCGAATCTCAGCAACTT 59.251 43.478 0.00 0.00 0.00 2.66
3626 3715 5.986501 AACAAGGAAACAAACACAACCTA 57.013 34.783 0.00 0.00 0.00 3.08
3670 3759 2.486796 GCCCTCAGCTTTAAGCAGG 58.513 57.895 19.63 16.63 45.56 4.85
3714 3803 2.348059 CGATCTTCTTCAAGCTGACAGC 59.652 50.000 20.12 20.12 42.84 4.40


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

AutoCloner maintained by Alex Coulton.