Multiple sequence alignment - TraesCS3D01G420800

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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 TraesCS3D01G420800 chr3D 100.000 3555 0 0 1 3555 532991190 532994744 0.000000e+00 6565
1 TraesCS3D01G420800 chr3D 90.245 2122 181 18 792 2893 533375448 533377563 0.000000e+00 2748
2 TraesCS3D01G420800 chr3D 90.240 2121 181 17 792 2893 533393218 533395331 0.000000e+00 2747
3 TraesCS3D01G420800 chr3D 90.089 2129 175 24 792 2893 533315109 533317228 0.000000e+00 2730
4 TraesCS3D01G420800 chr3D 88.610 1554 145 22 1356 2893 533411069 533412606 0.000000e+00 1860
5 TraesCS3D01G420800 chr3D 97.345 791 19 2 1 789 532981576 532982366 0.000000e+00 1343
6 TraesCS3D01G420800 chr3D 91.995 762 50 11 34 789 24829159 24829915 0.000000e+00 1059
7 TraesCS3D01G420800 chr3D 87.562 812 70 19 1 789 187508478 187509281 0.000000e+00 911
8 TraesCS3D01G420800 chr3D 87.300 811 73 17 1 789 187498823 187499625 0.000000e+00 900
9 TraesCS3D01G420800 chr3D 86.253 822 77 24 1 792 148893696 148892881 0.000000e+00 859
10 TraesCS3D01G420800 chr3D 88.837 645 63 5 883 1519 533410397 533411040 0.000000e+00 784
11 TraesCS3D01G420800 chr3D 89.247 372 33 2 3191 3555 533317488 533317859 3.230000e-125 459
12 TraesCS3D01G420800 chr3D 89.086 339 26 4 3227 3555 533413350 533413687 9.190000e-111 411
13 TraesCS3D01G420800 chr3D 91.603 262 20 2 2987 3247 533412605 533412865 9.380000e-96 361
14 TraesCS3D01G420800 chr3D 91.905 210 14 3 2987 3193 533317227 533317436 1.250000e-74 291
15 TraesCS3D01G420800 chr3D 89.595 173 16 2 3022 3192 533377578 533377750 5.980000e-53 219
16 TraesCS3D01G420800 chr3D 89.595 173 16 2 3022 3192 533395346 533395518 5.980000e-53 219
17 TraesCS3D01G420800 chr3A 92.513 2431 142 17 1140 3555 668985957 668988362 0.000000e+00 3445
18 TraesCS3D01G420800 chr3A 92.431 2431 145 15 1140 3555 668990301 668992707 0.000000e+00 3434
19 TraesCS3D01G420800 chr3A 92.368 2437 141 16 1140 3555 668981606 668984018 0.000000e+00 3428
20 TraesCS3D01G420800 chr3A 92.338 2310 134 17 792 3091 668818122 668820398 0.000000e+00 3245
21 TraesCS3D01G420800 chr3A 93.333 2115 119 12 792 2893 668867847 668869952 0.000000e+00 3105
22 TraesCS3D01G420800 chr3A 88.751 1209 96 13 1356 2553 669054771 669055950 0.000000e+00 1443
23 TraesCS3D01G420800 chr3A 88.764 712 66 9 818 1519 669054035 669054742 0.000000e+00 859
24 TraesCS3D01G420800 chr3A 89.626 588 41 5 2987 3555 669056380 669056966 0.000000e+00 730
25 TraesCS3D01G420800 chr3A 92.291 467 28 3 3096 3555 668820710 668821175 0.000000e+00 656
26 TraesCS3D01G420800 chr3A 87.675 357 38 3 792 1144 668924752 668925106 9.190000e-111 411
27 TraesCS3D01G420800 chr3B 87.307 2009 165 37 790 2766 705185290 705187240 0.000000e+00 2215
28 TraesCS3D01G420800 chr3B 92.412 369 19 5 3193 3555 705187465 705187830 5.260000e-143 518
29 TraesCS3D01G420800 chr4D 91.542 804 47 11 1 789 408228410 408227613 0.000000e+00 1088
30 TraesCS3D01G420800 chr4D 91.429 805 48 14 1 789 197790035 197790834 0.000000e+00 1085
31 TraesCS3D01G420800 chr4D 91.213 808 48 13 1 792 408238523 408237723 0.000000e+00 1077
32 TraesCS3D01G420800 chr4D 91.045 804 52 11 1 789 22166764 22165966 0.000000e+00 1068
33 TraesCS3D01G420800 chr4D 94.118 102 6 0 2890 2991 323929571 323929672 4.750000e-34 156
34 TraesCS3D01G420800 chr4D 87.903 124 12 3 2882 3005 482704105 482704225 3.700000e-30 143
35 TraesCS3D01G420800 chr6D 91.047 793 61 8 1 789 102297516 102298302 0.000000e+00 1062
36 TraesCS3D01G420800 chr6D 90.542 793 65 8 1 789 102307330 102308116 0.000000e+00 1040
37 TraesCS3D01G420800 chr6D 87.176 811 76 15 1 789 186938530 186939334 0.000000e+00 896
38 TraesCS3D01G420800 chr6D 87.160 810 74 16 1 789 180968105 180968905 0.000000e+00 893
39 TraesCS3D01G420800 chr6D 86.436 811 77 19 1 789 180958389 180959188 0.000000e+00 857
40 TraesCS3D01G420800 chr7D 92.026 765 45 12 34 789 100411746 100410989 0.000000e+00 1061
41 TraesCS3D01G420800 chr5B 95.000 100 5 0 2891 2990 57129965 57130064 1.320000e-34 158
42 TraesCS3D01G420800 chr2B 92.035 113 8 1 2882 2993 464611187 464611075 1.320000e-34 158
43 TraesCS3D01G420800 chr2B 94.949 99 5 0 2891 2989 31426070 31425972 4.750000e-34 156


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 TraesCS3D01G420800 chr3D 532991190 532994744 3554 False 6565.000000 6565 100.000000 1 3555 1 chr3D.!!$F5 3554
1 TraesCS3D01G420800 chr3D 533375448 533377750 2302 False 1483.500000 2748 89.920000 792 3192 2 chr3D.!!$F7 2400
2 TraesCS3D01G420800 chr3D 533393218 533395518 2300 False 1483.000000 2747 89.917500 792 3192 2 chr3D.!!$F8 2400
3 TraesCS3D01G420800 chr3D 532981576 532982366 790 False 1343.000000 1343 97.345000 1 789 1 chr3D.!!$F4 788
4 TraesCS3D01G420800 chr3D 533315109 533317859 2750 False 1160.000000 2730 90.413667 792 3555 3 chr3D.!!$F6 2763
5 TraesCS3D01G420800 chr3D 24829159 24829915 756 False 1059.000000 1059 91.995000 34 789 1 chr3D.!!$F1 755
6 TraesCS3D01G420800 chr3D 187508478 187509281 803 False 911.000000 911 87.562000 1 789 1 chr3D.!!$F3 788
7 TraesCS3D01G420800 chr3D 187498823 187499625 802 False 900.000000 900 87.300000 1 789 1 chr3D.!!$F2 788
8 TraesCS3D01G420800 chr3D 148892881 148893696 815 True 859.000000 859 86.253000 1 792 1 chr3D.!!$R1 791
9 TraesCS3D01G420800 chr3D 533410397 533413687 3290 False 854.000000 1860 89.534000 883 3555 4 chr3D.!!$F9 2672
10 TraesCS3D01G420800 chr3A 668981606 668992707 11101 False 3435.666667 3445 92.437333 1140 3555 3 chr3A.!!$F4 2415
11 TraesCS3D01G420800 chr3A 668867847 668869952 2105 False 3105.000000 3105 93.333000 792 2893 1 chr3A.!!$F1 2101
12 TraesCS3D01G420800 chr3A 668818122 668821175 3053 False 1950.500000 3245 92.314500 792 3555 2 chr3A.!!$F3 2763
13 TraesCS3D01G420800 chr3A 669054035 669056966 2931 False 1010.666667 1443 89.047000 818 3555 3 chr3A.!!$F5 2737
14 TraesCS3D01G420800 chr3B 705185290 705187830 2540 False 1366.500000 2215 89.859500 790 3555 2 chr3B.!!$F1 2765
15 TraesCS3D01G420800 chr4D 408227613 408228410 797 True 1088.000000 1088 91.542000 1 789 1 chr4D.!!$R2 788
16 TraesCS3D01G420800 chr4D 197790035 197790834 799 False 1085.000000 1085 91.429000 1 789 1 chr4D.!!$F1 788
17 TraesCS3D01G420800 chr4D 408237723 408238523 800 True 1077.000000 1077 91.213000 1 792 1 chr4D.!!$R3 791
18 TraesCS3D01G420800 chr4D 22165966 22166764 798 True 1068.000000 1068 91.045000 1 789 1 chr4D.!!$R1 788
19 TraesCS3D01G420800 chr6D 102297516 102298302 786 False 1062.000000 1062 91.047000 1 789 1 chr6D.!!$F1 788
20 TraesCS3D01G420800 chr6D 102307330 102308116 786 False 1040.000000 1040 90.542000 1 789 1 chr6D.!!$F2 788
21 TraesCS3D01G420800 chr6D 186938530 186939334 804 False 896.000000 896 87.176000 1 789 1 chr6D.!!$F5 788
22 TraesCS3D01G420800 chr6D 180968105 180968905 800 False 893.000000 893 87.160000 1 789 1 chr6D.!!$F4 788
23 TraesCS3D01G420800 chr6D 180958389 180959188 799 False 857.000000 857 86.436000 1 789 1 chr6D.!!$F3 788
24 TraesCS3D01G420800 chr7D 100410989 100411746 757 True 1061.000000 1061 92.026000 34 789 1 chr7D.!!$R1 755

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
804 871 1.001641 ACACCATTGCTGCCTCTCC 60.002 57.895 0.0 0.0 0.00 3.71 F
935 1011 1.147817 AGGCAACCAAGTCCATTTCCT 59.852 47.619 0.0 0.0 37.17 3.36 F
2195 6874 1.134995 CCAGTCTGCATCAACGAGCTA 60.135 52.381 0.0 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 6470 0.625849 ATGGTCAGGCAAACTAGGGG 59.374 55.0 0.0 0.0 0.00 4.79 R
2533 7213 0.657840 CGAATTCCCACGAGAATGGC 59.342 55.0 0.0 0.0 38.55 4.40 R
3341 13390 0.106918 TGTCAAACTTTCCCAGCCGT 60.107 50.0 0.0 0.0 0.00 5.68 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
79 109 3.459145 TGAAGGTGTTCGACGAAATGAA 58.541 40.909 12.67 0.00 35.17 2.57
120 151 2.360475 GGAGCTGGGACTTGGTGC 60.360 66.667 0.00 0.00 0.00 5.01
224 255 3.964031 TGGCAAATAAGGTCCAAACTTGT 59.036 39.130 0.00 0.00 0.00 3.16
636 687 2.446435 ACATGAGATGAAAAACCCCCG 58.554 47.619 0.00 0.00 0.00 5.73
804 871 1.001641 ACACCATTGCTGCCTCTCC 60.002 57.895 0.00 0.00 0.00 3.71
878 945 5.707495 AGAAAATACCCAACCAAGGTGTTA 58.293 37.500 0.00 0.00 37.70 2.41
880 947 4.734843 AATACCCAACCAAGGTGTTACT 57.265 40.909 0.00 0.00 37.00 2.24
881 948 4.734843 ATACCCAACCAAGGTGTTACTT 57.265 40.909 0.00 0.00 38.36 2.24
935 1011 1.147817 AGGCAACCAAGTCCATTTCCT 59.852 47.619 0.00 0.00 37.17 3.36
936 1012 1.546029 GGCAACCAAGTCCATTTCCTC 59.454 52.381 0.00 0.00 0.00 3.71
986 1069 7.264221 AGTGATGTGAGTTGTTGATATCTCTC 58.736 38.462 3.98 5.23 0.00 3.20
1020 1103 6.239317 GGCAGATGGAGTACTATAACATGACA 60.239 42.308 0.00 0.00 0.00 3.58
1062 1145 4.731961 GCAATGATGTTTGCTATCAAGACG 59.268 41.667 2.08 0.00 46.66 4.18
1113 1196 7.533900 CGACAAAATGAACAATCGTTAAGACAT 59.466 33.333 0.00 0.00 34.75 3.06
1222 1309 1.672030 GGCAATGTTGGCCCTTTGC 60.672 57.895 18.48 18.48 46.85 3.68
1557 1845 9.632807 GATGACTGAGATTAGTTGGATATGTAC 57.367 37.037 0.00 0.00 0.00 2.90
1646 6286 6.071840 AGCTTGTAACAAACACCACTGTTTTA 60.072 34.615 0.00 0.00 46.55 1.52
1694 6334 2.105477 AGCCATGCATCCACTAAGTAGG 59.895 50.000 0.00 0.00 0.00 3.18
1744 6386 9.515226 AGTAAAATGCTAACCTGAAAGATGTAA 57.485 29.630 0.00 0.00 34.07 2.41
1749 6391 7.534085 TGCTAACCTGAAAGATGTAATTACG 57.466 36.000 10.92 0.00 34.07 3.18
1984 6633 3.687200 GTCCAACAACAACCTGTTAACG 58.313 45.455 0.26 0.00 38.77 3.18
1993 6642 4.382291 ACAACCTGTTAACGCACAATCTA 58.618 39.130 0.26 0.00 0.00 1.98
2021 6676 3.258372 ACGTGAAGCCAACAGATTCTCTA 59.742 43.478 0.00 0.00 0.00 2.43
2051 6706 5.654650 ACTCTAGACTGTGCTACTGCTTTAT 59.345 40.000 0.00 0.00 40.48 1.40
2189 6868 1.310933 CCTGCCCAGTCTGCATCAAC 61.311 60.000 0.00 0.00 38.22 3.18
2195 6874 1.134995 CCAGTCTGCATCAACGAGCTA 60.135 52.381 0.00 0.00 0.00 3.32
2282 6961 2.743636 TTCAGAAGAAGTGCCCTACG 57.256 50.000 0.00 0.00 0.00 3.51
2565 7335 3.252215 TGGGAATTCGAAACATGTGTCAC 59.748 43.478 16.28 0.00 0.00 3.67
2749 11870 6.239829 CCATAGAGCCCTAAAAGACATCAGAT 60.240 42.308 0.00 0.00 0.00 2.90
2785 11906 3.575687 CCAATTGAGATTAGGCCCAATCC 59.424 47.826 18.88 11.65 35.85 3.01
2804 11925 7.787424 CCCAATCCCCCTTAAAAGACATAATTA 59.213 37.037 0.00 0.00 0.00 1.40
2910 12036 7.850935 TTATATACTCCCTCCGTCTCAAAAT 57.149 36.000 0.00 0.00 0.00 1.82
2983 12109 5.186198 AGACATTTATTTTGAGACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
3035 12161 3.162068 GCCGTCGCTAATATCTTCTACG 58.838 50.000 0.00 0.00 0.00 3.51
3083 12209 1.115467 ATGTGCGTTGGTTTTTGGGA 58.885 45.000 0.00 0.00 0.00 4.37
3341 13390 0.899019 TTACGAGCACATGGTGGCTA 59.101 50.000 8.51 0.00 41.22 3.93
3416 13469 1.178534 TAAGGCAAGCAGGGTGTTGC 61.179 55.000 0.00 0.00 46.88 4.17
3448 13501 6.674419 AGGTTCATAGGACCAGAAATCTAGTT 59.326 38.462 0.00 0.00 39.71 2.24
3450 13503 7.364762 GGTTCATAGGACCAGAAATCTAGTTGA 60.365 40.741 0.00 0.00 37.14 3.18
3464 13517 3.701542 TCTAGTTGAGATGCGAACTGGAT 59.298 43.478 0.00 0.00 35.48 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 151 1.021390 GGTGCATTGAGAGGTCACCG 61.021 60.000 0.00 0.00 37.96 4.94
224 255 9.486497 TTCAAATAATTCAAATTGTGCTTGCTA 57.514 25.926 0.00 0.00 0.00 3.49
403 434 9.640952 CTCCCCATAAGTTTTCTTCCATTTATA 57.359 33.333 0.00 0.00 40.91 0.98
636 687 3.503748 CCCAAGACTTGATTGTTGGTCTC 59.496 47.826 16.99 0.00 38.23 3.36
830 897 4.530857 ATTTCCTCGAGCCGCCCG 62.531 66.667 6.99 0.00 0.00 6.13
831 898 2.589159 GATTTCCTCGAGCCGCCC 60.589 66.667 6.99 0.00 0.00 6.13
935 1011 6.080648 ACGGTAATACTTCATATCTTGCGA 57.919 37.500 0.00 0.00 0.00 5.10
936 1012 6.764877 AACGGTAATACTTCATATCTTGCG 57.235 37.500 0.00 0.00 0.00 4.85
946 1022 7.758528 ACTCACATCACTAAACGGTAATACTTC 59.241 37.037 0.00 0.00 0.00 3.01
949 1025 7.330208 ACAACTCACATCACTAAACGGTAATAC 59.670 37.037 0.00 0.00 0.00 1.89
986 1069 2.173519 ACTCCATCTGCCCAAACAATG 58.826 47.619 0.00 0.00 0.00 2.82
1062 1145 1.067142 TGTCGGTTCTGAGCCATGTAC 60.067 52.381 11.24 3.87 0.00 2.90
1113 1196 2.422939 AGCCAGGGGAAGATGCTATA 57.577 50.000 0.00 0.00 0.00 1.31
1222 1309 2.996249 ACCATGTCTGCACTAGATGG 57.004 50.000 15.46 15.46 40.14 3.51
1406 1497 7.887996 AATTTACAACATAATTGGTGCACAG 57.112 32.000 20.43 1.46 44.88 3.66
1469 1564 5.163248 TGGTGAGTCCTTGAACATGTCTAAA 60.163 40.000 0.00 0.00 37.07 1.85
1484 1772 1.135199 CATTGCTGCAATGGTGAGTCC 60.135 52.381 36.01 0.00 45.03 3.85
1564 1852 2.247635 TCCTAGGCTAGAAGTCCCACAT 59.752 50.000 22.99 0.00 0.00 3.21
1615 6255 6.152154 AGTGGTGTTTGTTACAAGCTAAGTTT 59.848 34.615 12.72 0.00 38.80 2.66
1646 6286 3.261643 TCTGAACACACATGCTGGACTAT 59.738 43.478 0.00 0.00 0.00 2.12
1744 6386 7.780745 TGAATATGGGTAAATTGTTCCCGTAAT 59.219 33.333 14.59 9.29 43.39 1.89
1749 6391 9.533831 AGATATGAATATGGGTAAATTGTTCCC 57.466 33.333 6.06 6.06 41.41 3.97
1823 6469 0.770557 TGGTCAGGCAAACTAGGGGT 60.771 55.000 0.00 0.00 0.00 4.95
1824 6470 0.625849 ATGGTCAGGCAAACTAGGGG 59.374 55.000 0.00 0.00 0.00 4.79
1945 6594 1.596727 GACGCTCCAGAAAGATCATGC 59.403 52.381 0.00 0.00 0.00 4.06
1984 6633 4.026475 GCTTCACGTGTATCTAGATTGTGC 60.026 45.833 16.51 8.09 0.00 4.57
1993 6642 2.299013 TCTGTTGGCTTCACGTGTATCT 59.701 45.455 16.51 0.00 0.00 1.98
2021 6676 7.504238 AGCAGTAGCACAGTCTAGAGTTATTAT 59.496 37.037 0.00 0.00 45.49 1.28
2189 6868 2.095314 AGATGATGCATCGACTAGCTCG 60.095 50.000 21.34 8.00 44.67 5.03
2282 6961 1.248785 TGGTCAGCCTCCTACGACAC 61.249 60.000 0.00 0.00 35.27 3.67
2364 7043 3.271250 GGTGTTGATGCTCCACCAT 57.729 52.632 3.28 0.00 46.33 3.55
2533 7213 0.657840 CGAATTCCCACGAGAATGGC 59.342 55.000 0.00 0.00 38.55 4.40
2565 7335 4.154015 TCTTTGCAGATGTTCACAATACCG 59.846 41.667 0.00 0.00 0.00 4.02
2804 11925 3.073062 AGGCAAGTAGTGTGAGGAAACAT 59.927 43.478 0.00 0.00 31.49 2.71
2910 12036 8.726870 AAGTTGTACTAAGCTTGAAACACTTA 57.273 30.769 9.86 0.00 0.00 2.24
2965 12091 4.903045 ACTCCCTCCGTCTCAAAATAAA 57.097 40.909 0.00 0.00 0.00 1.40
2974 12100 2.304761 TGCAAAAATACTCCCTCCGTCT 59.695 45.455 0.00 0.00 0.00 4.18
2978 12104 3.631250 TGGATGCAAAAATACTCCCTCC 58.369 45.455 0.00 0.00 0.00 4.30
2983 12109 6.455360 TCTTGGATGGATGCAAAAATACTC 57.545 37.500 0.00 0.00 37.67 2.59
3115 12552 8.455682 GGTCAATAGATCCGAATGTAAAAACAA 58.544 33.333 0.00 0.00 0.00 2.83
3117 12554 7.981142 TGGTCAATAGATCCGAATGTAAAAAC 58.019 34.615 0.00 0.00 0.00 2.43
3341 13390 0.106918 TGTCAAACTTTCCCAGCCGT 60.107 50.000 0.00 0.00 0.00 5.68
3416 13469 4.956700 TCTGGTCCTATGAACCTACTTCAG 59.043 45.833 0.00 0.00 42.36 3.02
3448 13501 2.481969 GCTACATCCAGTTCGCATCTCA 60.482 50.000 0.00 0.00 0.00 3.27
3450 13503 1.759445 AGCTACATCCAGTTCGCATCT 59.241 47.619 0.00 0.00 0.00 2.90
3464 13517 7.724305 AAGAAAACTAATCGTTTGAGCTACA 57.276 32.000 0.00 0.00 44.77 2.74


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

AutoCloner maintained by Alex Coulton.