Multiple sequence alignment - TraesCS7D01G532700

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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 TraesCS7D01G532700 chr7D 100.000 3792 0 0 1 3792 626379924 626376133 0.000000e+00 7003.0
1 TraesCS7D01G532700 chr7D 91.935 310 9 8 295 588 443546248 443545939 1.630000e-113 420.0
2 TraesCS7D01G532700 chr7D 88.276 145 9 6 764 905 140797769 140797908 2.340000e-37 167.0
3 TraesCS7D01G532700 chr7D 98.592 71 1 0 295 365 105979268 105979338 3.980000e-25 126.0
4 TraesCS7D01G532700 chr7D 98.592 71 1 0 295 365 513239723 513239653 3.980000e-25 126.0
5 TraesCS7D01G532700 chr7D 83.333 72 10 2 1605 1675 632329314 632329384 8.790000e-07 65.8
6 TraesCS7D01G532700 chr7A 98.298 2526 37 4 1268 3792 721920990 721918470 0.000000e+00 4421.0
7 TraesCS7D01G532700 chr7A 95.743 1151 21 10 146 1290 721922282 721921154 0.000000e+00 1829.0
8 TraesCS7D01G532700 chr7A 91.971 137 10 1 3 138 148252217 148252353 1.390000e-44 191.0
9 TraesCS7D01G532700 chr7A 87.943 141 14 1 1620 1757 44439612 44439472 3.030000e-36 163.0
10 TraesCS7D01G532700 chr7B 97.507 2286 37 4 900 3183 726156532 726154265 0.000000e+00 3888.0
11 TraesCS7D01G532700 chr7B 93.045 762 31 10 152 905 726157615 726156868 0.000000e+00 1094.0
12 TraesCS7D01G532700 chr7B 96.644 596 16 4 3199 3792 726154279 726153686 0.000000e+00 987.0
13 TraesCS7D01G532700 chr7B 92.754 138 10 0 1 138 726159685 726159548 2.310000e-47 200.0
14 TraesCS7D01G532700 chr7B 93.130 131 9 0 8 138 289163720 289163590 3.870000e-45 193.0
15 TraesCS7D01G532700 chr5D 92.048 2012 118 17 1788 3792 44701011 44699035 0.000000e+00 2791.0
16 TraesCS7D01G532700 chr5D 94.109 1426 57 8 1761 3183 87541509 87540108 0.000000e+00 2143.0
17 TraesCS7D01G532700 chr5D 93.899 1426 57 11 1761 3183 122061081 122059683 0.000000e+00 2124.0
18 TraesCS7D01G532700 chr5D 85.909 809 61 29 2994 3792 44633233 44632468 0.000000e+00 813.0
19 TraesCS7D01G532700 chr5D 86.202 645 50 16 987 1600 44701673 44701037 0.000000e+00 662.0
20 TraesCS7D01G532700 chr5D 89.686 446 36 8 3199 3638 87540122 87539681 9.200000e-156 560.0
21 TraesCS7D01G532700 chr5D 88.170 448 35 10 3205 3638 122059691 122059248 5.620000e-143 518.0
22 TraesCS7D01G532700 chr5D 88.411 302 17 4 1301 1602 122061361 122061078 7.800000e-92 348.0
23 TraesCS7D01G532700 chr5D 87.417 302 20 7 1301 1602 87541789 87541506 7.850000e-87 331.0
24 TraesCS7D01G532700 chr5D 92.568 148 11 0 1606 1753 213480658 213480805 2.970000e-51 213.0
25 TraesCS7D01G532700 chr5D 93.893 131 7 1 8 138 269869555 269869426 2.990000e-46 196.0
26 TraesCS7D01G532700 chr5D 91.549 142 12 0 1617 1758 325957613 325957472 2.990000e-46 196.0
27 TraesCS7D01G532700 chr5D 92.029 138 10 1 1 138 269962730 269962594 3.870000e-45 193.0
28 TraesCS7D01G532700 chr5D 81.333 225 24 10 154 365 565660625 565660406 2.340000e-37 167.0
29 TraesCS7D01G532700 chr5D 97.368 38 1 0 1605 1642 541589820 541589783 8.790000e-07 65.8
30 TraesCS7D01G532700 chr5B 91.456 1779 115 12 1758 3531 44467206 44465460 0.000000e+00 2409.0
31 TraesCS7D01G532700 chr5B 87.402 635 54 8 985 1600 44467829 44467202 0.000000e+00 706.0
32 TraesCS7D01G532700 chr5B 89.057 265 24 5 3530 3792 44465305 44465044 1.310000e-84 324.0
33 TraesCS7D01G532700 chr5B 86.897 145 11 6 764 905 346108595 346108734 5.070000e-34 156.0
34 TraesCS7D01G532700 chr5B 86.747 83 8 3 1605 1687 352309042 352308963 5.220000e-14 89.8
35 TraesCS7D01G532700 chr5A 95.863 1426 45 6 1758 3181 35195430 35194017 0.000000e+00 2294.0
36 TraesCS7D01G532700 chr5A 92.707 1426 74 11 1761 3183 80511425 80510027 0.000000e+00 2030.0
37 TraesCS7D01G532700 chr5A 91.579 1330 64 13 1860 3183 121720859 121719572 0.000000e+00 1792.0
38 TraesCS7D01G532700 chr5A 92.469 717 28 9 900 1602 35196128 35195424 0.000000e+00 1002.0
39 TraesCS7D01G532700 chr5A 87.960 598 40 13 3199 3792 35194029 35193460 0.000000e+00 676.0
40 TraesCS7D01G532700 chr5A 88.248 451 38 8 3199 3638 80510041 80509595 3.360000e-145 525.0
41 TraesCS7D01G532700 chr5A 88.248 451 37 9 3199 3638 121719586 121719141 3.360000e-145 525.0
42 TraesCS7D01G532700 chr5A 87.417 302 20 4 1301 1602 80511705 80511422 7.850000e-87 331.0
43 TraesCS7D01G532700 chr5A 86.469 303 22 8 1301 1602 121721326 121721042 7.910000e-82 315.0
44 TraesCS7D01G532700 chr5A 95.213 188 8 1 1761 1947 121721045 121720858 2.860000e-76 296.0
45 TraesCS7D01G532700 chr5A 91.892 148 12 0 1606 1753 277726503 277726650 1.380000e-49 207.0
46 TraesCS7D01G532700 chr5A 93.130 131 9 0 8 138 547329431 547329301 3.870000e-45 193.0
47 TraesCS7D01G532700 chr5A 91.971 137 9 2 3 138 412105341 412105476 1.390000e-44 191.0
48 TraesCS7D01G532700 chr5A 87.586 145 10 6 764 905 598303004 598303143 1.090000e-35 161.0
49 TraesCS7D01G532700 chr1D 84.344 511 43 19 310 791 145883725 145884227 2.060000e-127 466.0
50 TraesCS7D01G532700 chr1D 83.023 483 42 23 339 791 82977078 82976606 5.900000e-108 401.0
51 TraesCS7D01G532700 chr1D 98.592 71 1 0 295 365 90270985 90271055 3.980000e-25 126.0
52 TraesCS7D01G532700 chr3A 84.633 449 45 16 356 791 25771841 25772278 3.500000e-115 425.0
53 TraesCS7D01G532700 chr3D 91.909 309 10 3 295 588 550608799 550608491 5.860000e-113 418.0
54 TraesCS7D01G532700 chr3D 91.549 142 11 1 1605 1746 479627402 479627542 1.070000e-45 195.0
55 TraesCS7D01G532700 chr4A 91.290 310 11 2 295 588 722721577 722721886 3.530000e-110 409.0
56 TraesCS7D01G532700 chr6D 91.262 309 12 1 295 588 412531996 412532304 1.270000e-109 407.0
57 TraesCS7D01G532700 chr6D 92.254 142 10 1 1605 1746 126435289 126435149 2.310000e-47 200.0
58 TraesCS7D01G532700 chr1A 85.132 417 40 10 391 793 580063974 580064382 1.270000e-109 407.0
59 TraesCS7D01G532700 chr4D 83.125 480 45 23 339 791 182471483 182471013 4.560000e-109 405.0
60 TraesCS7D01G532700 chr4D 98.592 71 1 0 295 365 495261206 495261136 3.980000e-25 126.0
61 TraesCS7D01G532700 chr2D 91.205 307 11 4 298 588 385100039 385100345 1.640000e-108 403.0
62 TraesCS7D01G532700 chr2D 83.709 399 32 20 416 791 616873951 616874339 2.800000e-91 346.0
63 TraesCS7D01G532700 chr6B 83.660 459 41 20 356 791 609194469 609194022 5.900000e-108 401.0
64 TraesCS7D01G532700 chr6B 90.845 142 12 1 1605 1746 224871822 224871682 5.000000e-44 189.0
65 TraesCS7D01G532700 chr6B 96.939 98 2 1 808 905 57748447 57748543 3.030000e-36 163.0
66 TraesCS7D01G532700 chr6B 87.586 145 10 6 764 905 132427470 132427609 1.090000e-35 161.0
67 TraesCS7D01G532700 chr6B 84.397 141 22 0 1617 1757 24927411 24927551 5.110000e-29 139.0
68 TraesCS7D01G532700 chr2A 90.939 309 12 9 295 588 2157102 2157409 5.900000e-108 401.0
69 TraesCS7D01G532700 chr2A 92.208 154 10 1 1605 1758 615288053 615287902 2.290000e-52 217.0
70 TraesCS7D01G532700 chr2A 91.971 137 10 1 3 138 768102081 768102217 1.390000e-44 191.0
71 TraesCS7D01G532700 chr4B 77.919 394 58 26 529 905 603094411 603094030 6.380000e-53 219.0
72 TraesCS7D01G532700 chr6A 93.893 131 8 0 8 138 600261025 600261155 8.310000e-47 198.0
73 TraesCS7D01G532700 chr6A 85.915 142 9 8 1605 1746 546479486 546479616 1.420000e-29 141.0
74 TraesCS7D01G532700 chr2B 88.276 145 9 6 764 905 439355002 439355141 2.340000e-37 167.0
75 TraesCS7D01G532700 chr1B 88.889 135 12 1 1627 1758 230030551 230030417 3.030000e-36 163.0


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 TraesCS7D01G532700 chr7D 626376133 626379924 3791 True 7003.000000 7003 100.000000 1 3792 1 chr7D.!!$R3 3791
1 TraesCS7D01G532700 chr7A 721918470 721922282 3812 True 3125.000000 4421 97.020500 146 3792 2 chr7A.!!$R2 3646
2 TraesCS7D01G532700 chr7B 726153686 726159685 5999 True 1542.250000 3888 94.987500 1 3792 4 chr7B.!!$R2 3791
3 TraesCS7D01G532700 chr5D 44699035 44701673 2638 True 1726.500000 2791 89.125000 987 3792 2 chr5D.!!$R7 2805
4 TraesCS7D01G532700 chr5D 87539681 87541789 2108 True 1011.333333 2143 90.404000 1301 3638 3 chr5D.!!$R8 2337
5 TraesCS7D01G532700 chr5D 122059248 122061361 2113 True 996.666667 2124 90.160000 1301 3638 3 chr5D.!!$R9 2337
6 TraesCS7D01G532700 chr5D 44632468 44633233 765 True 813.000000 813 85.909000 2994 3792 1 chr5D.!!$R1 798
7 TraesCS7D01G532700 chr5B 44465044 44467829 2785 True 1146.333333 2409 89.305000 985 3792 3 chr5B.!!$R2 2807
8 TraesCS7D01G532700 chr5A 35193460 35196128 2668 True 1324.000000 2294 92.097333 900 3792 3 chr5A.!!$R2 2892
9 TraesCS7D01G532700 chr5A 80509595 80511705 2110 True 962.000000 2030 89.457333 1301 3638 3 chr5A.!!$R3 2337
10 TraesCS7D01G532700 chr5A 121719141 121721326 2185 True 732.000000 1792 90.377250 1301 3638 4 chr5A.!!$R4 2337
11 TraesCS7D01G532700 chr1D 145883725 145884227 502 False 466.000000 466 84.344000 310 791 1 chr1D.!!$F2 481

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
217 2137 1.356059 TGCCCCTATTGCAACAGGTTA 59.644 47.619 22.02 5.46 35.40 2.85 F
919 3224 2.322355 ACTGAGAATGATTGCCTCCG 57.678 50.000 0.00 0.00 0.00 4.63 F
1708 4236 5.180117 TCGCTAGTCGACACTAAGTTTAGTT 59.820 40.000 19.50 0.00 41.03 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 4045 3.242446 GCTGCGAGCTTAAGGTATCAAAC 60.242 47.826 7.26 0.91 38.45 2.93 R
1930 4546 5.454045 CCCTAGGTCCTGAAATAGAAAGAGC 60.454 48.000 8.29 0.00 0.00 4.09 R
3265 5934 1.351017 TGGCCCAGGTCTAAAACTGAG 59.649 52.381 0.00 0.00 36.86 3.35 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
82 83 6.785337 TTTCTATGAAACGTGGAGGATAGA 57.215 37.500 0.00 0.00 0.00 1.98
85 86 7.361457 TCTATGAAACGTGGAGGATAGAAAT 57.639 36.000 0.00 0.00 0.00 2.17
99 100 9.898152 GGAGGATAGAAATAATTCCTTCATAGG 57.102 37.037 0.00 0.00 38.71 2.57
138 139 3.910989 ACAAACCAAAGGGCTCTAAAGT 58.089 40.909 0.00 0.00 37.90 2.66
139 140 3.636764 ACAAACCAAAGGGCTCTAAAGTG 59.363 43.478 0.00 0.00 37.90 3.16
140 141 1.911057 ACCAAAGGGCTCTAAAGTGC 58.089 50.000 0.00 0.00 37.90 4.40
143 144 3.073946 ACCAAAGGGCTCTAAAGTGCTTA 59.926 43.478 0.00 0.00 37.90 3.09
174 2094 3.126453 AGGATTTTGGCTAGTCCCTCAT 58.874 45.455 0.00 0.00 0.00 2.90
175 2095 3.137360 AGGATTTTGGCTAGTCCCTCATC 59.863 47.826 0.00 0.00 0.00 2.92
176 2096 3.117888 GGATTTTGGCTAGTCCCTCATCA 60.118 47.826 0.00 0.00 0.00 3.07
217 2137 1.356059 TGCCCCTATTGCAACAGGTTA 59.644 47.619 22.02 5.46 35.40 2.85
508 2462 2.811317 CGTCCCGAAGCTGCAGAC 60.811 66.667 20.43 9.11 0.00 3.51
622 2577 5.587388 AACTTTGTTGCATAGATGGATGG 57.413 39.130 0.00 0.00 0.00 3.51
652 2607 4.763793 GTGTCAATTGGATAGATGGATGGG 59.236 45.833 5.42 0.00 0.00 4.00
724 2688 7.543947 TCTTGTTGATATTGTCAGTGCTATG 57.456 36.000 0.00 0.00 38.29 2.23
735 2699 4.959839 TGTCAGTGCTATGTATTGGTCCTA 59.040 41.667 0.00 0.00 0.00 2.94
741 2705 5.934625 GTGCTATGTATTGGTCCTATTCCTG 59.065 44.000 0.00 0.00 0.00 3.86
919 3224 2.322355 ACTGAGAATGATTGCCTCCG 57.678 50.000 0.00 0.00 0.00 4.63
1280 3605 7.537715 TGCCTATTTGTGTTTGTTATCTGATG 58.462 34.615 0.00 0.00 0.00 3.07
1706 4234 5.213913 TCGCTAGTCGACACTAAGTTTAG 57.786 43.478 19.50 8.93 43.16 1.85
1708 4236 5.180117 TCGCTAGTCGACACTAAGTTTAGTT 59.820 40.000 19.50 0.00 41.03 2.24
2895 5519 2.009051 CGCTGCAGATCAATTGGTACA 58.991 47.619 20.43 0.00 0.00 2.90
3182 5820 8.749026 AGTCTCATTTGATTTTATCTGCATCT 57.251 30.769 0.00 0.00 0.00 2.90
3183 5821 9.186837 AGTCTCATTTGATTTTATCTGCATCTT 57.813 29.630 0.00 0.00 0.00 2.40
3184 5822 9.798994 GTCTCATTTGATTTTATCTGCATCTTT 57.201 29.630 0.00 0.00 0.00 2.52
3330 6007 8.085296 CACTTGACTTGAGAAGTACAGTTAGAT 58.915 37.037 0.00 0.00 43.03 1.98
3556 6407 5.358298 AAAAAGATCACTCGCAGTTTACC 57.642 39.130 0.00 0.00 0.00 2.85
3705 6557 2.289010 GGGGAGAAACATTGGCAAACAG 60.289 50.000 3.01 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.905713 AAATAAACATTAGCCTAGACTCAATGA 57.094 29.630 12.01 0.00 32.29 2.57
110 111 4.291249 AGAGCCCTTTGGTTTGTAGGAATA 59.709 41.667 0.00 0.00 0.00 1.75
118 119 3.552890 GCACTTTAGAGCCCTTTGGTTTG 60.553 47.826 0.00 0.00 0.00 2.93
138 139 7.342799 AGCCAAAATCCTCAAATTCTATAAGCA 59.657 33.333 0.00 0.00 0.00 3.91
139 140 7.720442 AGCCAAAATCCTCAAATTCTATAAGC 58.280 34.615 0.00 0.00 0.00 3.09
143 144 7.503902 GGACTAGCCAAAATCCTCAAATTCTAT 59.496 37.037 0.00 0.00 36.34 1.98
174 2094 7.415206 GGCACTCTGTTAACTCTTTTCTTTTGA 60.415 37.037 7.22 0.00 0.00 2.69
175 2095 6.693113 GGCACTCTGTTAACTCTTTTCTTTTG 59.307 38.462 7.22 0.00 0.00 2.44
176 2096 6.183360 GGGCACTCTGTTAACTCTTTTCTTTT 60.183 38.462 7.22 0.00 0.00 2.27
217 2137 2.491693 CGGTGGCATTCTTGTGGTAATT 59.508 45.455 0.00 0.00 0.00 1.40
508 2462 0.326048 AGGAGTGGAGGACTGGATGG 60.326 60.000 0.00 0.00 33.83 3.51
622 2577 6.091849 CCATCTATCCAATTGACACATCGATC 59.908 42.308 7.12 0.00 0.00 3.69
724 2688 7.112779 CCAATATCCAGGAATAGGACCAATAC 58.887 42.308 0.00 0.00 38.13 1.89
735 2699 6.575244 TTCACAGTACCAATATCCAGGAAT 57.425 37.500 0.00 0.00 0.00 3.01
741 2705 6.543831 AGCAAAGATTCACAGTACCAATATCC 59.456 38.462 0.00 0.00 0.00 2.59
806 2771 4.641541 TCACCATTCTCACATTAGCATTGG 59.358 41.667 0.00 0.00 0.00 3.16
1280 3605 5.590663 AGACAGAGAAAGAAACAAAGGGAAC 59.409 40.000 0.00 0.00 0.00 3.62
1519 4045 3.242446 GCTGCGAGCTTAAGGTATCAAAC 60.242 47.826 7.26 0.91 38.45 2.93
1930 4546 5.454045 CCCTAGGTCCTGAAATAGAAAGAGC 60.454 48.000 8.29 0.00 0.00 4.09
2895 5519 7.212274 ACAGCAAATAAAAGTTCAAGAAGCAT 58.788 30.769 0.00 0.00 0.00 3.79
3186 5824 9.545105 AGATGCAGATAAAATTGTTCACAAAAA 57.455 25.926 0.00 0.00 39.55 1.94
3187 5825 8.980610 CAGATGCAGATAAAATTGTTCACAAAA 58.019 29.630 0.00 0.00 39.55 2.44
3188 5826 8.143193 ACAGATGCAGATAAAATTGTTCACAAA 58.857 29.630 0.00 0.00 39.55 2.83
3189 5827 7.660112 ACAGATGCAGATAAAATTGTTCACAA 58.340 30.769 0.00 0.00 40.51 3.33
3190 5828 7.218228 ACAGATGCAGATAAAATTGTTCACA 57.782 32.000 0.00 0.00 0.00 3.58
3191 5829 8.236586 TGTACAGATGCAGATAAAATTGTTCAC 58.763 33.333 0.00 0.00 0.00 3.18
3192 5830 8.334263 TGTACAGATGCAGATAAAATTGTTCA 57.666 30.769 0.00 0.00 0.00 3.18
3193 5831 9.793252 ATTGTACAGATGCAGATAAAATTGTTC 57.207 29.630 0.00 0.00 0.00 3.18
3199 5837 9.612066 TCACATATTGTACAGATGCAGATAAAA 57.388 29.630 15.99 0.00 0.00 1.52
3200 5838 9.783081 ATCACATATTGTACAGATGCAGATAAA 57.217 29.630 15.99 0.00 0.00 1.40
3201 5839 9.211485 CATCACATATTGTACAGATGCAGATAA 57.789 33.333 15.99 0.00 26.94 1.75
3202 5840 8.370182 ACATCACATATTGTACAGATGCAGATA 58.630 33.333 16.33 2.87 33.91 1.98
3203 5841 7.222161 ACATCACATATTGTACAGATGCAGAT 58.778 34.615 16.33 15.79 33.91 2.90
3204 5842 6.585416 ACATCACATATTGTACAGATGCAGA 58.415 36.000 16.33 14.68 33.91 4.26
3205 5843 6.856135 ACATCACATATTGTACAGATGCAG 57.144 37.500 16.33 11.16 33.91 4.41
3206 5844 7.442062 CCTAACATCACATATTGTACAGATGCA 59.558 37.037 16.33 0.00 33.91 3.96
3207 5845 7.095060 CCCTAACATCACATATTGTACAGATGC 60.095 40.741 16.33 0.00 33.91 3.91
3208 5846 8.150296 TCCCTAACATCACATATTGTACAGATG 58.850 37.037 15.31 15.31 35.60 2.90
3209 5847 8.150945 GTCCCTAACATCACATATTGTACAGAT 58.849 37.037 0.00 0.00 0.00 2.90
3210 5848 7.497595 GTCCCTAACATCACATATTGTACAGA 58.502 38.462 0.00 0.00 0.00 3.41
3265 5934 1.351017 TGGCCCAGGTCTAAAACTGAG 59.649 52.381 0.00 0.00 36.86 3.35
3330 6007 8.055181 ACTAGAGATGCCAATCAAAGGAAATAA 58.945 33.333 0.00 0.00 35.03 1.40
3462 6154 5.179742 TGTTGGTAAACTGCAAACCGTATAG 59.820 40.000 0.00 0.00 37.19 1.31
3642 6494 9.076596 GCAGTGTTTTCCATATCTTATTTGAAC 57.923 33.333 0.00 0.00 0.00 3.18
3705 6557 3.983344 CACAGATGCAAACAAAAGCCTAC 59.017 43.478 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.