Multiple sequence alignment - TraesCS2D01G124400

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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 TraesCS2D01G124400 chr2D 100.000 3097 0 0 1 3097 72724159 72727255 0.000000e+00 5720.0
1 TraesCS2D01G124400 chr2D 95.641 1124 32 7 978 2091 72482706 72483822 0.000000e+00 1788.0
2 TraesCS2D01G124400 chr2D 94.833 600 25 3 2499 3096 72484498 72485093 0.000000e+00 931.0
3 TraesCS2D01G124400 chr2D 85.194 797 90 11 129 904 512454754 512453965 0.000000e+00 793.0
4 TraesCS2D01G124400 chr2D 94.861 467 12 4 2089 2545 72484037 72484501 0.000000e+00 719.0
5 TraesCS2D01G124400 chr2B 94.883 1192 44 13 904 2088 110033284 110034465 0.000000e+00 1847.0
6 TraesCS2D01G124400 chr2B 95.388 1019 33 4 2089 3097 110034684 110035698 0.000000e+00 1609.0
7 TraesCS2D01G124400 chr2B 94.444 90 4 1 11 100 618997425 618997337 1.500000e-28 137.0
8 TraesCS2D01G124400 chr5D 89.024 902 86 5 11 910 489175288 489174398 0.000000e+00 1105.0
9 TraesCS2D01G124400 chr3A 87.762 907 102 6 8 910 537152 538053 0.000000e+00 1051.0
10 TraesCS2D01G124400 chr7D 87.862 898 91 8 11 904 99421066 99420183 0.000000e+00 1038.0
11 TraesCS2D01G124400 chr7D 84.724 923 100 15 13 905 271756472 271757383 0.000000e+00 885.0
12 TraesCS2D01G124400 chrUn 84.378 1101 108 28 996 2086 108925231 108924185 0.000000e+00 1022.0
13 TraesCS2D01G124400 chrUn 86.871 556 71 2 1532 2086 108957046 108956492 3.390000e-174 621.0
14 TraesCS2D01G124400 chrUn 90.794 315 27 2 2089 2402 108923964 108923651 1.330000e-113 420.0
15 TraesCS2D01G124400 chrUn 82.562 281 45 3 998 1274 108957798 108957518 8.580000e-61 244.0
16 TraesCS2D01G124400 chr7A 85.479 909 104 13 8 901 324941064 324941959 0.000000e+00 922.0
17 TraesCS2D01G124400 chr4A 85.275 910 109 11 1 904 626544265 626545155 0.000000e+00 915.0
18 TraesCS2D01G124400 chr6B 84.516 930 112 21 1 904 207772701 207773624 0.000000e+00 891.0
19 TraesCS2D01G124400 chr6B 78.750 240 39 11 1596 1832 578505745 578505515 1.920000e-32 150.0
20 TraesCS2D01G124400 chr6B 75.556 315 58 17 1596 1904 578483122 578482821 1.500000e-28 137.0
21 TraesCS2D01G124400 chr7B 84.838 897 99 16 1 877 584275497 584276376 0.000000e+00 869.0
22 TraesCS2D01G124400 chr1B 83.662 912 114 13 11 904 642487072 642486178 0.000000e+00 826.0
23 TraesCS2D01G124400 chr5A 83.568 925 104 18 1 904 690020624 690019727 0.000000e+00 822.0
24 TraesCS2D01G124400 chr5A 82.434 871 104 19 8 877 1823145 1823967 0.000000e+00 715.0
25 TraesCS2D01G124400 chr5A 83.570 633 79 10 998 1620 704584600 704585217 1.250000e-158 569.0
26 TraesCS2D01G124400 chr5A 78.075 935 169 23 1163 2091 704553385 704552481 2.700000e-155 558.0
27 TraesCS2D01G124400 chr5A 81.222 442 72 5 1503 1939 704589858 704590293 2.290000e-91 346.0
28 TraesCS2D01G124400 chr5A 93.567 171 9 2 2794 2963 704589625 704589794 1.430000e-63 254.0
29 TraesCS2D01G124400 chr3B 85.484 744 82 8 155 896 53551343 53550624 0.000000e+00 752.0
30 TraesCS2D01G124400 chr3D 81.550 916 126 19 1 904 505052513 505053397 0.000000e+00 715.0
31 TraesCS2D01G124400 chr3D 81.561 884 130 18 1 872 92738398 92737536 0.000000e+00 699.0
32 TraesCS2D01G124400 chr3D 75.329 304 67 7 1678 1977 610412556 610412855 4.160000e-29 139.0
33 TraesCS2D01G124400 chr6A 77.551 931 149 42 1 899 121663705 121664607 9.910000e-140 507.0
34 TraesCS2D01G124400 chr4B 86.353 447 61 0 1645 2091 664791589 664791143 3.590000e-134 488.0
35 TraesCS2D01G124400 chr4B 81.073 354 53 7 999 1339 664792464 664792112 1.420000e-68 270.0
36 TraesCS2D01G124400 chr6D 82.288 271 35 9 1 268 408940328 408940068 4.020000e-54 222.0
37 TraesCS2D01G124400 chr1D 83.673 98 11 5 13 107 218271319 218271414 1.530000e-13 87.9


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 TraesCS2D01G124400 chr2D 72724159 72727255 3096 False 5720.0 5720 100.000000 1 3097 1 chr2D.!!$F1 3096
1 TraesCS2D01G124400 chr2D 72482706 72485093 2387 False 1146.0 1788 95.111667 978 3096 3 chr2D.!!$F2 2118
2 TraesCS2D01G124400 chr2D 512453965 512454754 789 True 793.0 793 85.194000 129 904 1 chr2D.!!$R1 775
3 TraesCS2D01G124400 chr2B 110033284 110035698 2414 False 1728.0 1847 95.135500 904 3097 2 chr2B.!!$F1 2193
4 TraesCS2D01G124400 chr5D 489174398 489175288 890 True 1105.0 1105 89.024000 11 910 1 chr5D.!!$R1 899
5 TraesCS2D01G124400 chr3A 537152 538053 901 False 1051.0 1051 87.762000 8 910 1 chr3A.!!$F1 902
6 TraesCS2D01G124400 chr7D 99420183 99421066 883 True 1038.0 1038 87.862000 11 904 1 chr7D.!!$R1 893
7 TraesCS2D01G124400 chr7D 271756472 271757383 911 False 885.0 885 84.724000 13 905 1 chr7D.!!$F1 892
8 TraesCS2D01G124400 chrUn 108923651 108925231 1580 True 721.0 1022 87.586000 996 2402 2 chrUn.!!$R1 1406
9 TraesCS2D01G124400 chrUn 108956492 108957798 1306 True 432.5 621 84.716500 998 2086 2 chrUn.!!$R2 1088
10 TraesCS2D01G124400 chr7A 324941064 324941959 895 False 922.0 922 85.479000 8 901 1 chr7A.!!$F1 893
11 TraesCS2D01G124400 chr4A 626544265 626545155 890 False 915.0 915 85.275000 1 904 1 chr4A.!!$F1 903
12 TraesCS2D01G124400 chr6B 207772701 207773624 923 False 891.0 891 84.516000 1 904 1 chr6B.!!$F1 903
13 TraesCS2D01G124400 chr7B 584275497 584276376 879 False 869.0 869 84.838000 1 877 1 chr7B.!!$F1 876
14 TraesCS2D01G124400 chr1B 642486178 642487072 894 True 826.0 826 83.662000 11 904 1 chr1B.!!$R1 893
15 TraesCS2D01G124400 chr5A 690019727 690020624 897 True 822.0 822 83.568000 1 904 1 chr5A.!!$R1 903
16 TraesCS2D01G124400 chr5A 1823145 1823967 822 False 715.0 715 82.434000 8 877 1 chr5A.!!$F1 869
17 TraesCS2D01G124400 chr5A 704584600 704585217 617 False 569.0 569 83.570000 998 1620 1 chr5A.!!$F2 622
18 TraesCS2D01G124400 chr5A 704552481 704553385 904 True 558.0 558 78.075000 1163 2091 1 chr5A.!!$R2 928
19 TraesCS2D01G124400 chr5A 704589625 704590293 668 False 300.0 346 87.394500 1503 2963 2 chr5A.!!$F3 1460
20 TraesCS2D01G124400 chr3B 53550624 53551343 719 True 752.0 752 85.484000 155 896 1 chr3B.!!$R1 741
21 TraesCS2D01G124400 chr3D 505052513 505053397 884 False 715.0 715 81.550000 1 904 1 chr3D.!!$F1 903
22 TraesCS2D01G124400 chr3D 92737536 92738398 862 True 699.0 699 81.561000 1 872 1 chr3D.!!$R1 871
23 TraesCS2D01G124400 chr6A 121663705 121664607 902 False 507.0 507 77.551000 1 899 1 chr6A.!!$F1 898
24 TraesCS2D01G124400 chr4B 664791143 664792464 1321 True 379.0 488 83.713000 999 2091 2 chr4B.!!$R1 1092

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
877 1082 0.523335 GCGGTGATTTTAAGCCTGCG 60.523 55.0 0.0 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 3314 0.687354 CACCTAAGCCACCTGACACT 59.313 55.0 0.0 0.0 0.0 3.55 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
72 93 4.975132 CCATGGACGGCAATGGTA 57.025 55.556 17.53 0.00 38.85 3.25
73 94 2.706636 CCATGGACGGCAATGGTAG 58.293 57.895 17.53 0.00 38.85 3.18
117 157 2.181777 GACGCGCCAGATCTGACA 59.818 61.111 24.62 0.00 0.00 3.58
245 286 2.654079 CCACGCCTTCTCCTGCTCT 61.654 63.158 0.00 0.00 0.00 4.09
277 352 3.274586 CTCATCCGTGGGCGCATG 61.275 66.667 15.70 15.70 37.60 4.06
348 433 1.964448 CGCACCATAGAGCCCGATA 59.036 57.895 0.00 0.00 0.00 2.92
457 549 1.730451 GCGAGGGAGCAGTAGGAGAC 61.730 65.000 0.00 0.00 37.05 3.36
673 805 2.813754 TGAGCTCAATTTGGTGTACTGC 59.186 45.455 15.67 0.00 0.00 4.40
692 824 3.399105 TACGGTAGCGTAGGCCCGA 62.399 63.158 25.20 10.89 43.88 5.14
694 826 2.832201 GGTAGCGTAGGCCCGACT 60.832 66.667 5.51 4.87 41.24 4.18
695 827 2.421399 GGTAGCGTAGGCCCGACTT 61.421 63.158 5.51 0.00 41.24 3.01
696 828 1.103398 GGTAGCGTAGGCCCGACTTA 61.103 60.000 5.51 0.00 41.24 2.24
711 844 2.797087 CGACTTATTAGCTCCCGCGAAA 60.797 50.000 8.23 0.00 42.32 3.46
806 1009 4.137849 GCTTTTGCTTCAATTTCTTGCC 57.862 40.909 0.00 0.00 43.35 4.52
824 1028 6.342111 TCTTGCCCGAAACAAGTTTTTAAAT 58.658 32.000 10.48 0.00 43.97 1.40
877 1082 0.523335 GCGGTGATTTTAAGCCTGCG 60.523 55.000 0.00 0.00 0.00 5.18
910 1115 0.783579 GCGAACTGTAAACGGCGTTA 59.216 50.000 27.05 9.79 0.00 3.18
911 1116 1.192090 GCGAACTGTAAACGGCGTTAA 59.808 47.619 27.05 13.61 0.00 2.01
912 1117 2.719688 GCGAACTGTAAACGGCGTTAAG 60.720 50.000 27.05 23.51 0.00 1.85
933 1138 2.417719 CAAGGTTTGCTAGAGACGCTT 58.582 47.619 0.00 0.00 0.00 4.68
951 1156 7.384477 AGACGCTTTAACTAGGTACAAAATCT 58.616 34.615 0.00 0.00 0.00 2.40
1042 1253 1.829096 GACGACCTCCTAGGCCTCC 60.829 68.421 9.68 0.00 39.63 4.30
1403 1841 1.623973 GCTTCTACAACCACGACGGC 61.624 60.000 0.00 0.00 39.03 5.68
1442 1883 1.374252 GTGCACAGGACACGGGTAG 60.374 63.158 13.17 0.00 0.00 3.18
1577 2059 0.974383 AGGAGTACACCCCGTTCAAG 59.026 55.000 5.63 0.00 0.00 3.02
1610 2092 1.984570 CAGCTCCTTCCCCGACAGA 60.985 63.158 0.00 0.00 0.00 3.41
1811 2547 0.042581 TGACCCCTGATGACCAGCTA 59.957 55.000 0.00 0.00 41.57 3.32
2081 2817 3.089284 TGTGGAGAGCGACTTAGATGAA 58.911 45.455 0.00 0.00 0.00 2.57
2091 3263 4.556233 CGACTTAGATGAAGACCAACACA 58.444 43.478 0.00 0.00 38.65 3.72
2136 3308 1.576451 ATTTCAGCGCACGCACATGA 61.576 50.000 18.24 9.48 44.88 3.07
2142 3314 2.567569 GCACGCACATGATTGCCA 59.432 55.556 0.00 0.00 39.53 4.92
2466 3640 3.238108 ACACTCAAGTCTAAGATGCCG 57.762 47.619 0.00 0.00 0.00 5.69
2586 3809 7.264221 TGCTTTTACTTTCACATTGTTCACAT 58.736 30.769 0.00 0.00 0.00 3.21
2658 3881 1.938577 CGGCTTTCATGATCTCCTGTG 59.061 52.381 0.00 0.00 0.00 3.66
2700 3925 3.625764 CGACACTATTACAAACCCATGGG 59.374 47.826 30.23 30.23 42.03 4.00
2834 4059 4.618920 TGATCAGGATCATGACATCAGG 57.381 45.455 13.05 0.00 42.42 3.86
2873 4098 8.989980 GTGTAAAATAGGAACCTATGCAGTATC 58.010 37.037 13.26 3.60 39.03 2.24
2971 4196 0.035056 AACCCTCATCTGCCTTTCCG 60.035 55.000 0.00 0.00 0.00 4.30
2987 4212 1.456518 CCGCTGGATCTCTGAGGGA 60.457 63.158 4.59 0.00 32.25 4.20
3032 4257 7.504926 ACATAGTTGTTACCTCCCAATCTAA 57.495 36.000 0.00 0.00 29.55 2.10
3041 4266 2.017049 CTCCCAATCTAAAAGGGCACG 58.983 52.381 0.00 0.00 42.52 5.34
3053 4278 2.663196 GGCACGCACCTCTTACCT 59.337 61.111 0.00 0.00 0.00 3.08
3077 4302 4.580868 TGGTGGTTTTCTGAATATACGCA 58.419 39.130 0.00 0.00 0.00 5.24
3084 4309 2.039418 TCTGAATATACGCAGCAGGGT 58.961 47.619 3.87 3.87 43.95 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 86 0.250467 CATCCCCGGAGCTACCATTG 60.250 60.000 0.73 0.00 38.90 2.82
66 87 0.399949 TCATCCCCGGAGCTACCATT 60.400 55.000 0.73 0.00 38.90 3.16
67 88 0.833834 CTCATCCCCGGAGCTACCAT 60.834 60.000 0.73 0.00 38.90 3.55
68 89 1.457643 CTCATCCCCGGAGCTACCA 60.458 63.158 0.73 0.00 38.90 3.25
69 90 2.210711 CCTCATCCCCGGAGCTACC 61.211 68.421 0.73 0.00 0.00 3.18
70 91 2.873525 GCCTCATCCCCGGAGCTAC 61.874 68.421 0.73 0.00 0.00 3.58
71 92 2.524394 GCCTCATCCCCGGAGCTA 60.524 66.667 0.73 0.00 0.00 3.32
145 185 2.266055 GGCTACCGCTGTTGAGCT 59.734 61.111 3.48 0.00 43.77 4.09
235 276 2.650116 GCGGACCAAGAGCAGGAGA 61.650 63.158 0.00 0.00 0.00 3.71
291 366 1.677552 GCTCCCTCTTCACCGGAAA 59.322 57.895 9.46 0.25 31.35 3.13
371 456 2.703430 AGGTAATCCTCGGGCCCT 59.297 61.111 22.43 1.26 40.58 5.19
450 542 0.663688 GATGCGCTCTTCGTCTCCTA 59.336 55.000 9.73 0.00 41.07 2.94
496 589 2.920912 ACGCCCGTCTGGAGGAAA 60.921 61.111 0.00 0.00 38.44 3.13
633 764 4.554363 CGGAGCTCGTGCGGTAGG 62.554 72.222 7.83 0.00 45.42 3.18
806 1009 9.411169 CCGTAAAAATTTAAAAACTTGTTTCGG 57.589 29.630 6.61 6.61 0.00 4.30
824 1028 4.727677 ACCTGTATCCAAACCCGTAAAAA 58.272 39.130 0.00 0.00 0.00 1.94
913 1118 2.086054 AGCGTCTCTAGCAAACCTTG 57.914 50.000 0.00 0.00 37.01 3.61
914 1119 2.841442 AAGCGTCTCTAGCAAACCTT 57.159 45.000 0.00 0.00 37.01 3.50
915 1120 2.841442 AAAGCGTCTCTAGCAAACCT 57.159 45.000 0.00 0.00 37.01 3.50
916 1121 3.995048 AGTTAAAGCGTCTCTAGCAAACC 59.005 43.478 0.00 0.00 37.01 3.27
917 1122 5.288952 CCTAGTTAAAGCGTCTCTAGCAAAC 59.711 44.000 0.00 0.00 37.01 2.93
918 1123 5.047519 ACCTAGTTAAAGCGTCTCTAGCAAA 60.048 40.000 0.00 0.00 37.01 3.68
919 1124 4.461781 ACCTAGTTAAAGCGTCTCTAGCAA 59.538 41.667 0.00 0.00 37.01 3.91
920 1125 4.015084 ACCTAGTTAAAGCGTCTCTAGCA 58.985 43.478 0.00 0.00 37.01 3.49
921 1126 4.635833 ACCTAGTTAAAGCGTCTCTAGC 57.364 45.455 0.00 0.00 0.00 3.42
922 1127 6.674694 TGTACCTAGTTAAAGCGTCTCTAG 57.325 41.667 0.00 0.00 0.00 2.43
972 1177 7.262048 ACGTTGGATGAATAGTTTGTTTGTTT 58.738 30.769 0.00 0.00 0.00 2.83
973 1178 6.801575 ACGTTGGATGAATAGTTTGTTTGTT 58.198 32.000 0.00 0.00 0.00 2.83
974 1179 6.038825 TGACGTTGGATGAATAGTTTGTTTGT 59.961 34.615 0.00 0.00 0.00 2.83
975 1180 6.434596 TGACGTTGGATGAATAGTTTGTTTG 58.565 36.000 0.00 0.00 0.00 2.93
1403 1841 5.976534 GCACTCTCTGATGTAAGTGTAGATG 59.023 44.000 0.00 0.00 40.92 2.90
1499 1941 8.568794 TCCGTACATACATTAGATCAAGAAGAG 58.431 37.037 0.00 0.00 0.00 2.85
1555 2037 1.823169 GAACGGGGTGTACTCCTGCA 61.823 60.000 13.44 0.00 34.06 4.41
1577 2059 1.154150 GCTGTTGATGTTGGAGCGC 60.154 57.895 0.00 0.00 0.00 5.92
1610 2092 2.764314 GGAGCCAACGCATCGCAAT 61.764 57.895 0.00 0.00 37.52 3.56
1682 2408 5.703130 AGAGAAAGGATTGTGCAAGAAGTAC 59.297 40.000 0.00 0.00 0.00 2.73
1811 2547 5.123820 CCAATTGTTGGTCATGATAACGACT 59.876 40.000 14.44 5.07 45.93 4.18
2091 3263 3.881089 CCTCAAAAACCTCCAACTTACGT 59.119 43.478 0.00 0.00 0.00 3.57
2136 3308 4.828409 CCACCTGACACTGGCAAT 57.172 55.556 0.00 0.00 0.00 3.56
2142 3314 0.687354 CACCTAAGCCACCTGACACT 59.313 55.000 0.00 0.00 0.00 3.55
2466 3640 9.520204 CATAGGATGTGGAAAAATCAACATAAC 57.480 33.333 0.00 0.00 0.00 1.89
2502 3684 4.622740 GTGTTAAGGAGCATTTGCAATGAC 59.377 41.667 0.00 0.00 45.16 3.06
2586 3809 0.770499 TCTTGGTGGTGAATCTGCCA 59.230 50.000 0.00 0.00 0.00 4.92
2658 3881 0.874390 TGATCTTGCACTTTGGCGTC 59.126 50.000 0.00 0.00 36.28 5.19
2700 3925 4.363138 CCCTCTTCAGAAACACAAAAAGC 58.637 43.478 0.00 0.00 0.00 3.51
2834 4059 4.568152 ATTTTACACAAGGTCTGCACAC 57.432 40.909 0.00 0.00 0.00 3.82
2883 4108 6.183360 CCTTCCCATGATAAATTTGGTGACTC 60.183 42.308 0.00 0.00 0.00 3.36
2971 4196 0.035176 GCATCCCTCAGAGATCCAGC 59.965 60.000 0.00 0.00 0.00 4.85
2987 4212 2.867109 ACCAAAGTACTCAGCAGCAT 57.133 45.000 0.00 0.00 0.00 3.79
3032 4257 0.605589 GTAAGAGGTGCGTGCCCTTT 60.606 55.000 3.84 0.00 30.60 3.11
3053 4278 6.350103 TGCGTATATTCAGAAAACCACCATA 58.650 36.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.