Multiple sequence alignment - TraesCS3D01G319900

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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 TraesCS3D01G319900 chr3D 100.000 3173 0 0 1 3173 433420376 433423548 0.000000e+00 5860.0
1 TraesCS3D01G319900 chr3D 94.040 755 41 3 2420 3173 490979873 490979122 0.000000e+00 1142.0
2 TraesCS3D01G319900 chr3D 100.000 32 0 0 1 32 374938455 374938424 3.420000e-05 60.2
3 TraesCS3D01G319900 chr3A 90.724 2404 172 25 40 2419 571795028 571797404 0.000000e+00 3157.0
4 TraesCS3D01G319900 chr3A 100.000 32 0 0 1 32 497618921 497618890 3.420000e-05 60.2
5 TraesCS3D01G319900 chr3B 89.474 2337 169 34 114 2419 566182136 566184426 0.000000e+00 2881.0
6 TraesCS3D01G319900 chr2D 98.276 754 13 0 2420 3173 8995941 8996694 0.000000e+00 1321.0
7 TraesCS3D01G319900 chr2D 98.361 732 12 0 2417 3148 8999726 9000457 0.000000e+00 1286.0
8 TraesCS3D01G319900 chr7D 97.497 759 18 1 2416 3173 53416663 53417421 0.000000e+00 1295.0
9 TraesCS3D01G319900 chr7D 94.063 758 40 4 2417 3173 520369664 520370417 0.000000e+00 1146.0
10 TraesCS3D01G319900 chr1D 95.503 756 34 0 2417 3172 91905681 91906436 0.000000e+00 1208.0
11 TraesCS3D01G319900 chr1D 95.503 756 33 1 2418 3172 91901361 91902116 0.000000e+00 1206.0
12 TraesCS3D01G319900 chr6D 94.848 757 33 4 2420 3173 394249261 394248508 0.000000e+00 1177.0
13 TraesCS3D01G319900 chr6D 94.368 728 37 3 2447 3173 394253321 394252597 0.000000e+00 1114.0
14 TraesCS3D01G319900 chr7A 100.000 46 0 0 2419 2464 105446371 105446326 5.640000e-13 86.1
15 TraesCS3D01G319900 chr5D 87.719 57 7 0 806 862 128550369 128550313 2.040000e-07 67.6
16 TraesCS3D01G319900 chr5D 100.000 30 0 0 1 30 298688745 298688774 4.420000e-04 56.5
17 TraesCS3D01G319900 chr1B 100.000 32 0 0 1 32 645254136 645254167 3.420000e-05 60.2
18 TraesCS3D01G319900 chr1A 100.000 32 0 0 1 32 576320959 576320990 3.420000e-05 60.2


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 TraesCS3D01G319900 chr3D 433420376 433423548 3172 False 5860.0 5860 100.0000 1 3173 1 chr3D.!!$F1 3172
1 TraesCS3D01G319900 chr3D 490979122 490979873 751 True 1142.0 1142 94.0400 2420 3173 1 chr3D.!!$R2 753
2 TraesCS3D01G319900 chr3A 571795028 571797404 2376 False 3157.0 3157 90.7240 40 2419 1 chr3A.!!$F1 2379
3 TraesCS3D01G319900 chr3B 566182136 566184426 2290 False 2881.0 2881 89.4740 114 2419 1 chr3B.!!$F1 2305
4 TraesCS3D01G319900 chr2D 8995941 9000457 4516 False 1303.5 1321 98.3185 2417 3173 2 chr2D.!!$F1 756
5 TraesCS3D01G319900 chr7D 53416663 53417421 758 False 1295.0 1295 97.4970 2416 3173 1 chr7D.!!$F1 757
6 TraesCS3D01G319900 chr7D 520369664 520370417 753 False 1146.0 1146 94.0630 2417 3173 1 chr7D.!!$F2 756
7 TraesCS3D01G319900 chr1D 91901361 91906436 5075 False 1207.0 1208 95.5030 2417 3172 2 chr1D.!!$F1 755
8 TraesCS3D01G319900 chr6D 394248508 394253321 4813 True 1145.5 1177 94.6080 2420 3173 2 chr6D.!!$R1 753


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
529 537 0.034896 GGGAGACTTGCTGGAAACGA 59.965 55.0 0.00 0.00 0.00 3.85 F
626 634 0.108804 CTGCAACCGACGGTGATAGT 60.109 55.0 22.53 0.19 35.34 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2181 0.107643 GCAATGCCTCCTCTACCTCC 59.892 60.000 0.0 0.0 0.0 4.30 R
2362 2399 2.143122 GTTGAACTGCGACATCTTCCA 58.857 47.619 0.0 0.0 0.0 3.53 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
26 27 2.746277 GCCAGGCGTAACAGGGTG 60.746 66.667 0.00 0.00 0.00 4.61
29 30 0.322322 CCAGGCGTAACAGGGTGTTA 59.678 55.000 0.00 0.00 41.45 2.41
43 44 4.152402 CAGGGTGTTACATCGAGTCTTTTG 59.848 45.833 0.00 0.00 0.00 2.44
53 54 5.357032 ACATCGAGTCTTTTGTTTTGAAGGT 59.643 36.000 0.00 0.00 0.00 3.50
55 56 4.938832 TCGAGTCTTTTGTTTTGAAGGTCA 59.061 37.500 0.00 0.00 0.00 4.02
79 83 3.249320 CGATCATCACCACTTGCATAAGG 59.751 47.826 0.00 0.00 38.26 2.69
82 86 3.010027 TCATCACCACTTGCATAAGGGAA 59.990 43.478 0.00 0.00 39.81 3.97
84 88 4.046286 TCACCACTTGCATAAGGGAATT 57.954 40.909 0.00 0.00 39.81 2.17
88 92 6.071616 TCACCACTTGCATAAGGGAATTAAAC 60.072 38.462 0.00 0.00 39.81 2.01
89 93 5.777732 ACCACTTGCATAAGGGAATTAAACA 59.222 36.000 0.00 0.00 39.81 2.83
139 143 7.773224 TCAATCCCTACAATTTTATGTCATCGT 59.227 33.333 0.00 0.00 34.75 3.73
182 187 4.405358 AGACCTTGATGCACTTTGGAAAAA 59.595 37.500 0.00 0.00 0.00 1.94
230 235 2.619074 GGCTCTTGTAGTGGCCTTGAAT 60.619 50.000 3.32 0.00 41.20 2.57
234 239 2.969821 TGTAGTGGCCTTGAATTGGT 57.030 45.000 3.32 0.00 0.00 3.67
258 263 0.830648 CCGATGTTGAGGCCCTAGAA 59.169 55.000 0.00 0.00 0.00 2.10
280 285 4.393155 CCGGTGCTGTAGCTGGCA 62.393 66.667 5.38 1.05 42.66 4.92
291 296 0.680921 TAGCTGGCAAAGGGTCATGC 60.681 55.000 0.00 0.00 41.82 4.06
296 301 1.588082 GCAAAGGGTCATGCTGTGG 59.412 57.895 0.00 0.00 39.46 4.17
365 370 1.877637 CTTGAACCATGACCACGACA 58.122 50.000 0.00 0.00 0.00 4.35
379 384 2.469826 CACGACAAGCTACAACAGTGA 58.530 47.619 0.00 0.00 0.00 3.41
387 392 1.359848 CTACAACAGTGATCACGGCC 58.640 55.000 23.58 0.00 36.20 6.13
449 457 1.683441 GAGTTGGAACCGGGACCAT 59.317 57.895 19.70 8.49 36.02 3.55
459 467 1.075525 CGGGACCATAGGGGAGTCA 60.076 63.158 0.00 0.00 41.15 3.41
527 535 0.609406 GGGGGAGACTTGCTGGAAAC 60.609 60.000 0.00 0.00 0.00 2.78
529 537 0.034896 GGGAGACTTGCTGGAAACGA 59.965 55.000 0.00 0.00 0.00 3.85
531 539 1.540363 GGAGACTTGCTGGAAACGACA 60.540 52.381 0.00 0.00 0.00 4.35
578 586 4.980805 GGTGCTGCAACGGTCCGA 62.981 66.667 20.51 0.00 0.00 4.55
622 630 3.858868 GAGCTGCAACCGACGGTGA 62.859 63.158 22.53 6.89 35.34 4.02
623 631 2.742372 GCTGCAACCGACGGTGAT 60.742 61.111 22.53 2.02 35.34 3.06
626 634 0.108804 CTGCAACCGACGGTGATAGT 60.109 55.000 22.53 0.19 35.34 2.12
644 653 1.974875 TCGAGAGGGCGCTACAACA 60.975 57.895 7.64 0.00 0.00 3.33
660 669 4.007644 CACTGGTGCTGCCGAGGA 62.008 66.667 0.00 0.00 41.21 3.71
668 677 2.109126 GCTGCCGAGGACATCAACC 61.109 63.158 0.00 0.00 0.00 3.77
669 678 1.296392 CTGCCGAGGACATCAACCA 59.704 57.895 0.00 0.00 0.00 3.67
681 692 3.943034 CAACCAACGAACGCGGCA 61.943 61.111 12.47 0.00 43.17 5.69
799 826 1.125633 TAGGGAATCCAACGGCTACC 58.874 55.000 0.09 0.00 34.83 3.18
800 827 1.153025 GGGAATCCAACGGCTACCC 60.153 63.158 0.09 0.00 0.00 3.69
1896 1932 0.669318 CGAAGCGGCTGTACAAGGAA 60.669 55.000 1.81 0.00 0.00 3.36
1980 2016 1.680338 AGGCTGGCGATTTTGATACC 58.320 50.000 0.00 0.00 0.00 2.73
2121 2157 8.874744 TCATTGAGAAGATGAAGGAGAAATTT 57.125 30.769 0.00 0.00 30.96 1.82
2127 2163 5.379706 AGATGAAGGAGAAATTTCCGGAT 57.620 39.130 14.61 0.00 42.29 4.18
2145 2181 2.373502 GGATAGGGATGAAGGGTGGAAG 59.626 54.545 0.00 0.00 0.00 3.46
2204 2240 6.369065 CACTCACAGGTATTGTTTTCCTACTC 59.631 42.308 0.00 0.00 38.16 2.59
2230 2267 8.826710 CACTGTTCTTAGAAACAATTACACAGA 58.173 33.333 10.61 0.00 38.60 3.41
2240 2277 9.480053 AGAAACAATTACACAGATTCAATTTGG 57.520 29.630 0.00 0.00 0.00 3.28
2241 2278 9.474920 GAAACAATTACACAGATTCAATTTGGA 57.525 29.630 0.00 0.00 0.00 3.53
2243 2280 9.829507 AACAATTACACAGATTCAATTTGGAAA 57.170 25.926 0.00 0.00 0.00 3.13
2244 2281 9.829507 ACAATTACACAGATTCAATTTGGAAAA 57.170 25.926 0.00 0.00 0.00 2.29
2289 2326 6.595326 TGTCTGAGTATCTTGTTTGGCTTATG 59.405 38.462 0.00 0.00 34.92 1.90
2291 2328 5.815581 TGAGTATCTTGTTTGGCTTATGGT 58.184 37.500 0.00 0.00 34.92 3.55
2293 2330 7.398829 TGAGTATCTTGTTTGGCTTATGGTAA 58.601 34.615 0.00 0.00 34.92 2.85
2294 2331 7.885922 TGAGTATCTTGTTTGGCTTATGGTAAA 59.114 33.333 0.00 0.00 34.92 2.01
2295 2332 8.051901 AGTATCTTGTTTGGCTTATGGTAAAC 57.948 34.615 0.00 0.00 34.51 2.01
2296 2333 5.715434 TCTTGTTTGGCTTATGGTAAACC 57.285 39.130 0.00 0.00 33.33 3.27
2297 2334 5.390387 TCTTGTTTGGCTTATGGTAAACCT 58.610 37.500 0.02 0.00 36.82 3.50
2298 2335 5.242838 TCTTGTTTGGCTTATGGTAAACCTG 59.757 40.000 0.02 0.00 36.82 4.00
2300 2337 2.889170 TGGCTTATGGTAAACCTGCA 57.111 45.000 0.02 0.00 36.82 4.41
2301 2338 3.162147 TGGCTTATGGTAAACCTGCAA 57.838 42.857 0.02 0.00 36.82 4.08
2302 2339 3.707316 TGGCTTATGGTAAACCTGCAAT 58.293 40.909 0.02 0.00 36.82 3.56
2313 2350 6.435591 TGGTAAACCTGCAATATTTCACATGA 59.564 34.615 0.00 0.00 36.82 3.07
2362 2399 9.618890 ATGCATTATACAAGTTGTTCTACATCT 57.381 29.630 14.90 0.00 29.96 2.90
3035 4944 2.995547 GGTGTTGGGTCGGGCTAT 59.004 61.111 0.00 0.00 0.00 2.97
3040 4949 1.117150 GTTGGGTCGGGCTATAGTCA 58.883 55.000 6.69 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.322322 TAACACCCTGTTACGCCTGG 59.678 55.000 0.00 0.00 41.45 4.45
11 12 3.919163 TAACACCCTGTTACGCCTG 57.081 52.632 0.00 0.00 41.45 4.85
17 18 4.084287 AGACTCGATGTAACACCCTGTTA 58.916 43.478 0.00 0.00 41.45 2.41
20 21 3.594603 AAGACTCGATGTAACACCCTG 57.405 47.619 0.00 0.00 0.00 4.45
21 22 4.202326 ACAAAAGACTCGATGTAACACCCT 60.202 41.667 0.00 0.00 0.00 4.34
26 27 7.376072 CCTTCAAAACAAAAGACTCGATGTAAC 59.624 37.037 0.00 0.00 0.00 2.50
29 30 5.357032 ACCTTCAAAACAAAAGACTCGATGT 59.643 36.000 0.00 0.00 0.00 3.06
31 32 5.588648 TGACCTTCAAAACAAAAGACTCGAT 59.411 36.000 0.00 0.00 0.00 3.59
32 33 4.938832 TGACCTTCAAAACAAAAGACTCGA 59.061 37.500 0.00 0.00 0.00 4.04
33 34 5.229921 TGACCTTCAAAACAAAAGACTCG 57.770 39.130 0.00 0.00 0.00 4.18
35 36 4.438744 CGCTGACCTTCAAAACAAAAGACT 60.439 41.667 0.00 0.00 0.00 3.24
37 38 3.692101 TCGCTGACCTTCAAAACAAAAGA 59.308 39.130 0.00 0.00 0.00 2.52
43 44 3.436704 TGATGATCGCTGACCTTCAAAAC 59.563 43.478 0.00 0.00 0.00 2.43
53 54 2.008543 GCAAGTGGTGATGATCGCTGA 61.009 52.381 5.91 0.00 0.00 4.26
55 56 0.036105 TGCAAGTGGTGATGATCGCT 60.036 50.000 5.91 0.00 0.00 4.93
106 110 9.878599 CATAAAATTGTAGGGATTGATACGTTC 57.121 33.333 0.00 0.00 0.00 3.95
149 154 7.054491 AGTGCATCAAGGTCTTTAATGTTTT 57.946 32.000 0.00 0.00 0.00 2.43
183 188 9.293404 CCTACAGATATTCACATCCAATCATTT 57.707 33.333 0.00 0.00 0.00 2.32
203 208 1.134670 GCCACTACAAGAGCCCTACAG 60.135 57.143 0.00 0.00 0.00 2.74
230 235 0.888736 CTCAACATCGGCACCACCAA 60.889 55.000 0.00 0.00 39.03 3.67
234 239 2.359850 GCCTCAACATCGGCACCA 60.360 61.111 0.00 0.00 45.59 4.17
258 263 0.176680 CAGCTACAGCACCGGAGAAT 59.823 55.000 9.46 0.00 45.16 2.40
280 285 1.607467 GCCCACAGCATGACCCTTT 60.607 57.895 0.00 0.00 42.97 3.11
365 370 2.688507 CCGTGATCACTGTTGTAGCTT 58.311 47.619 22.95 0.00 0.00 3.74
379 384 2.045926 GTTCCAGCTGGCCGTGAT 60.046 61.111 28.91 0.00 34.44 3.06
405 410 0.781787 TTCGTCGTTGCAACATCTCG 59.218 50.000 28.01 22.84 0.00 4.04
412 417 1.632120 GTCGTGTTCGTCGTTGCAA 59.368 52.632 0.00 0.00 38.33 4.08
449 457 0.832135 GCATCCCGATGACTCCCCTA 60.832 60.000 8.89 0.00 41.20 3.53
527 535 3.076258 TAGCCGCCATCACCTGTCG 62.076 63.158 0.00 0.00 0.00 4.35
529 537 1.626356 ATGTAGCCGCCATCACCTGT 61.626 55.000 0.00 0.00 0.00 4.00
531 539 1.337384 TGATGTAGCCGCCATCACCT 61.337 55.000 7.89 0.00 42.73 4.00
574 582 0.245266 TTCGTAGCTTGTGCATCGGA 59.755 50.000 0.00 0.00 42.74 4.55
576 584 1.067693 TGTTCGTAGCTTGTGCATCG 58.932 50.000 0.00 0.00 42.74 3.84
578 586 2.217750 TGTTGTTCGTAGCTTGTGCAT 58.782 42.857 0.00 0.00 42.74 3.96
582 590 2.066262 CGGATGTTGTTCGTAGCTTGT 58.934 47.619 0.00 0.00 0.00 3.16
622 630 0.179026 TGTAGCGCCCTCTCGACTAT 60.179 55.000 2.29 0.00 0.00 2.12
623 631 0.393402 TTGTAGCGCCCTCTCGACTA 60.393 55.000 2.29 0.00 0.00 2.59
626 634 1.974875 TGTTGTAGCGCCCTCTCGA 60.975 57.895 2.29 0.00 0.00 4.04
644 653 4.008933 GTCCTCGGCAGCACCAGT 62.009 66.667 0.00 0.00 39.03 4.00
660 669 1.567537 CGCGTTCGTTGGTTGATGT 59.432 52.632 0.00 0.00 0.00 3.06
700 711 1.081892 CGCTTCTCCTCCAATGTGTG 58.918 55.000 0.00 0.00 0.00 3.82
701 712 0.674895 GCGCTTCTCCTCCAATGTGT 60.675 55.000 0.00 0.00 0.00 3.72
763 774 2.421073 CCCTATCGATCCAACGCGTATA 59.579 50.000 14.46 3.56 0.00 1.47
765 776 0.594602 CCCTATCGATCCAACGCGTA 59.405 55.000 14.46 0.00 0.00 4.42
766 777 1.105167 TCCCTATCGATCCAACGCGT 61.105 55.000 5.58 5.58 0.00 6.01
773 784 2.353803 CCGTTGGATTCCCTATCGATCC 60.354 54.545 0.00 0.00 39.81 3.36
799 826 0.740737 GCCATTTGATCTGGGTTCGG 59.259 55.000 1.97 0.00 34.16 4.30
800 827 1.755179 AGCCATTTGATCTGGGTTCG 58.245 50.000 0.00 0.00 41.61 3.95
1068 1104 0.551131 AAGGGTTGAGGATGGAGGCT 60.551 55.000 0.00 0.00 0.00 4.58
1539 1575 2.425592 CTTGTGGTGCCGGACTCA 59.574 61.111 5.05 0.00 0.00 3.41
1724 1760 1.549950 GCCCCTGAACCCTTGAATTGA 60.550 52.381 0.00 0.00 0.00 2.57
1729 1765 1.774217 ACAGCCCCTGAACCCTTGA 60.774 57.895 0.00 0.00 35.18 3.02
1854 1890 1.640670 TCCTCCAAATCCCCTTCCTTG 59.359 52.381 0.00 0.00 0.00 3.61
1896 1932 1.149923 ACAAGCCCCTTCTTTCCCATT 59.850 47.619 0.00 0.00 0.00 3.16
1980 2016 2.872245 CTCATTGTATACACCAAGGGCG 59.128 50.000 4.68 0.00 0.00 6.13
2082 2118 2.357009 CTCAATGATCCCTTTTGCCTCG 59.643 50.000 0.00 0.00 0.00 4.63
2121 2157 0.566176 ACCCTTCATCCCTATCCGGA 59.434 55.000 6.61 6.61 36.02 5.14
2127 2163 1.368203 TCCTTCCACCCTTCATCCCTA 59.632 52.381 0.00 0.00 0.00 3.53
2145 2181 0.107643 GCAATGCCTCCTCTACCTCC 59.892 60.000 0.00 0.00 0.00 4.30
2204 2240 8.826710 TCTGTGTAATTGTTTCTAAGAACAGTG 58.173 33.333 0.00 0.00 40.33 3.66
2243 2280 9.347240 CAGACATCCCTATTCTCAAATTGTATT 57.653 33.333 0.00 0.00 0.00 1.89
2244 2281 8.717717 TCAGACATCCCTATTCTCAAATTGTAT 58.282 33.333 0.00 0.00 0.00 2.29
2246 2283 6.962182 TCAGACATCCCTATTCTCAAATTGT 58.038 36.000 0.00 0.00 0.00 2.71
2261 2298 4.333926 GCCAAACAAGATACTCAGACATCC 59.666 45.833 0.00 0.00 0.00 3.51
2289 2326 6.751888 GTCATGTGAAATATTGCAGGTTTACC 59.248 38.462 0.00 0.00 0.00 2.85
2291 2328 7.459795 TGTCATGTGAAATATTGCAGGTTTA 57.540 32.000 0.00 0.00 0.00 2.01
2293 2330 5.981088 TGTCATGTGAAATATTGCAGGTT 57.019 34.783 0.00 0.00 0.00 3.50
2294 2331 7.643569 TTATGTCATGTGAAATATTGCAGGT 57.356 32.000 0.00 0.00 0.00 4.00
2295 2332 7.436080 GGTTTATGTCATGTGAAATATTGCAGG 59.564 37.037 0.00 0.00 0.00 4.85
2296 2333 8.192774 AGGTTTATGTCATGTGAAATATTGCAG 58.807 33.333 0.00 0.00 0.00 4.41
2297 2334 7.975058 CAGGTTTATGTCATGTGAAATATTGCA 59.025 33.333 0.00 0.00 0.00 4.08
2298 2335 7.043192 GCAGGTTTATGTCATGTGAAATATTGC 60.043 37.037 0.00 0.00 0.00 3.56
2300 2337 8.065473 TGCAGGTTTATGTCATGTGAAATATT 57.935 30.769 0.00 0.00 0.00 1.28
2301 2338 7.643569 TGCAGGTTTATGTCATGTGAAATAT 57.356 32.000 0.00 0.00 0.00 1.28
2302 2339 7.459795 TTGCAGGTTTATGTCATGTGAAATA 57.540 32.000 0.00 0.00 0.00 1.40
2313 2350 7.706179 GCATATTGTAACATTGCAGGTTTATGT 59.294 33.333 10.56 3.35 34.14 2.29
2362 2399 2.143122 GTTGAACTGCGACATCTTCCA 58.857 47.619 0.00 0.00 0.00 3.53



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

AutoCloner maintained by Alex Coulton.