Multiple sequence alignment - TraesCS7D01G378200

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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 TraesCS7D01G378200 chr7D 100.000 3114 0 0 1 3114 489302797 489299684 0.000000e+00 5751
1 TraesCS7D01G378200 chr7D 89.182 1100 91 6 667 1765 484071838 484070766 0.000000e+00 1347
2 TraesCS7D01G378200 chr7D 97.365 683 14 3 1 682 147376957 147376278 0.000000e+00 1158
3 TraesCS7D01G378200 chr7D 87.616 646 66 11 679 1320 535510771 535511406 0.000000e+00 737
4 TraesCS7D01G378200 chr7D 86.460 517 36 16 2596 3103 484069328 484068837 1.270000e-148 536
5 TraesCS7D01G378200 chr7B 94.674 1840 86 5 667 2504 517933563 517931734 0.000000e+00 2844
6 TraesCS7D01G378200 chr7B 88.259 1712 171 20 667 2367 509736844 509735152 0.000000e+00 2021
7 TraesCS7D01G378200 chr7B 85.870 644 81 7 680 1320 577201346 577201982 0.000000e+00 676
8 TraesCS7D01G378200 chr7B 86.932 528 41 13 2596 3114 509733452 509732944 4.510000e-158 568
9 TraesCS7D01G378200 chr7B 91.733 375 17 3 2744 3114 517931378 517931014 2.770000e-140 508
10 TraesCS7D01G378200 chr7B 93.865 326 12 2 2504 2829 517931696 517931379 4.670000e-133 484
11 TraesCS7D01G378200 chr6A 84.430 1657 198 32 674 2281 577723613 577721968 0.000000e+00 1576
12 TraesCS7D01G378200 chr6A 80.767 1591 238 33 799 2346 64679792 64678227 0.000000e+00 1181
13 TraesCS7D01G378200 chr6D 81.345 1710 242 48 667 2346 49182502 49184164 0.000000e+00 1319
14 TraesCS7D01G378200 chr6D 81.120 1589 235 36 799 2346 50604941 50606505 0.000000e+00 1212
15 TraesCS7D01G378200 chr6D 82.545 1375 194 20 933 2276 50179781 50181140 0.000000e+00 1168
16 TraesCS7D01G378200 chr6D 98.204 668 12 0 1 668 258541123 258541790 0.000000e+00 1168
17 TraesCS7D01G378200 chr7A 89.716 1021 94 7 667 1686 551542845 551541835 0.000000e+00 1293
18 TraesCS7D01G378200 chr7A 81.019 1707 255 41 667 2340 591023941 591025611 0.000000e+00 1293
19 TraesCS7D01G378200 chr7A 86.090 647 77 10 680 1320 615785854 615786493 0.000000e+00 684
20 TraesCS7D01G378200 chr7A 85.781 647 80 9 679 1320 616443991 616443352 0.000000e+00 675
21 TraesCS7D01G378200 chr7A 86.492 496 43 12 2627 3114 551540794 551540315 9.890000e-145 523
22 TraesCS7D01G378200 chrUn 80.830 1591 237 33 799 2346 277361152 277362717 0.000000e+00 1186
23 TraesCS7D01G378200 chr1D 98.353 668 11 0 1 668 189684119 189683452 0.000000e+00 1173
24 TraesCS7D01G378200 chr1D 98.353 668 9 2 1 668 402389840 402390505 0.000000e+00 1171
25 TraesCS7D01G378200 chr1D 98.071 674 12 1 1 673 402396846 402397519 0.000000e+00 1171
26 TraesCS7D01G378200 chr1D 98.065 672 12 1 1 672 188420178 188419508 0.000000e+00 1168
27 TraesCS7D01G378200 chr1D 98.060 670 13 0 1 670 119274439 119275108 0.000000e+00 1166
28 TraesCS7D01G378200 chr5D 98.204 668 12 0 1 668 526525518 526526185 0.000000e+00 1168
29 TraesCS7D01G378200 chr5D 77.419 248 31 24 2878 3107 394162948 394163188 1.170000e-24 124
30 TraesCS7D01G378200 chr3D 98.204 668 12 0 1 668 53456170 53455503 0.000000e+00 1168
31 TraesCS7D01G378200 chr6B 86.641 1033 129 3 1345 2369 649832149 649831118 0.000000e+00 1134
32 TraesCS7D01G378200 chr2D 85.285 666 75 14 667 1324 89468764 89469414 0.000000e+00 665
33 TraesCS7D01G378200 chr4A 81.890 254 19 14 2875 3107 30287257 30287010 4.100000e-44 189
34 TraesCS7D01G378200 chr4D 80.859 256 18 17 2875 3107 437818491 437818738 4.130000e-39 172
35 TraesCS7D01G378200 chr4B 80.315 254 23 12 2875 3107 540726082 540726329 1.920000e-37 167
36 TraesCS7D01G378200 chr5A 77.075 253 29 23 2878 3107 496134855 496135101 5.460000e-23 119
37 TraesCS7D01G378200 chr5B 75.889 253 32 23 2878 3107 474047591 474047837 5.490000e-18 102


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 TraesCS7D01G378200 chr7D 489299684 489302797 3113 True 5751.000000 5751 100.0000 1 3114 1 chr7D.!!$R2 3113
1 TraesCS7D01G378200 chr7D 147376278 147376957 679 True 1158.000000 1158 97.3650 1 682 1 chr7D.!!$R1 681
2 TraesCS7D01G378200 chr7D 484068837 484071838 3001 True 941.500000 1347 87.8210 667 3103 2 chr7D.!!$R3 2436
3 TraesCS7D01G378200 chr7D 535510771 535511406 635 False 737.000000 737 87.6160 679 1320 1 chr7D.!!$F1 641
4 TraesCS7D01G378200 chr7B 509732944 509736844 3900 True 1294.500000 2021 87.5955 667 3114 2 chr7B.!!$R1 2447
5 TraesCS7D01G378200 chr7B 517931014 517933563 2549 True 1278.666667 2844 93.4240 667 3114 3 chr7B.!!$R2 2447
6 TraesCS7D01G378200 chr7B 577201346 577201982 636 False 676.000000 676 85.8700 680 1320 1 chr7B.!!$F1 640
7 TraesCS7D01G378200 chr6A 577721968 577723613 1645 True 1576.000000 1576 84.4300 674 2281 1 chr6A.!!$R2 1607
8 TraesCS7D01G378200 chr6A 64678227 64679792 1565 True 1181.000000 1181 80.7670 799 2346 1 chr6A.!!$R1 1547
9 TraesCS7D01G378200 chr6D 49182502 49184164 1662 False 1319.000000 1319 81.3450 667 2346 1 chr6D.!!$F1 1679
10 TraesCS7D01G378200 chr6D 50604941 50606505 1564 False 1212.000000 1212 81.1200 799 2346 1 chr6D.!!$F3 1547
11 TraesCS7D01G378200 chr6D 50179781 50181140 1359 False 1168.000000 1168 82.5450 933 2276 1 chr6D.!!$F2 1343
12 TraesCS7D01G378200 chr6D 258541123 258541790 667 False 1168.000000 1168 98.2040 1 668 1 chr6D.!!$F4 667
13 TraesCS7D01G378200 chr7A 591023941 591025611 1670 False 1293.000000 1293 81.0190 667 2340 1 chr7A.!!$F1 1673
14 TraesCS7D01G378200 chr7A 551540315 551542845 2530 True 908.000000 1293 88.1040 667 3114 2 chr7A.!!$R2 2447
15 TraesCS7D01G378200 chr7A 615785854 615786493 639 False 684.000000 684 86.0900 680 1320 1 chr7A.!!$F2 640
16 TraesCS7D01G378200 chr7A 616443352 616443991 639 True 675.000000 675 85.7810 679 1320 1 chr7A.!!$R1 641
17 TraesCS7D01G378200 chrUn 277361152 277362717 1565 False 1186.000000 1186 80.8300 799 2346 1 chrUn.!!$F1 1547
18 TraesCS7D01G378200 chr1D 189683452 189684119 667 True 1173.000000 1173 98.3530 1 668 1 chr1D.!!$R2 667
19 TraesCS7D01G378200 chr1D 402389840 402390505 665 False 1171.000000 1171 98.3530 1 668 1 chr1D.!!$F2 667
20 TraesCS7D01G378200 chr1D 402396846 402397519 673 False 1171.000000 1171 98.0710 1 673 1 chr1D.!!$F3 672
21 TraesCS7D01G378200 chr1D 188419508 188420178 670 True 1168.000000 1168 98.0650 1 672 1 chr1D.!!$R1 671
22 TraesCS7D01G378200 chr1D 119274439 119275108 669 False 1166.000000 1166 98.0600 1 670 1 chr1D.!!$F1 669
23 TraesCS7D01G378200 chr5D 526525518 526526185 667 False 1168.000000 1168 98.2040 1 668 1 chr5D.!!$F2 667
24 TraesCS7D01G378200 chr3D 53455503 53456170 667 True 1168.000000 1168 98.2040 1 668 1 chr3D.!!$R1 667
25 TraesCS7D01G378200 chr6B 649831118 649832149 1031 True 1134.000000 1134 86.6410 1345 2369 1 chr6B.!!$R1 1024
26 TraesCS7D01G378200 chr2D 89468764 89469414 650 False 665.000000 665 85.2850 667 1324 1 chr2D.!!$F1 657

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
460 461 0.103208 GGGACGTCATCGAGCTGAAT 59.897 55.0 18.91 0.0 40.62 2.57 F
1368 1439 0.823356 GCCAAGCACAGGACAGGAAA 60.823 55.0 0.00 0.0 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 1776 1.076332 GTTACTCCGAACAAGCGCAT 58.924 50.0 11.47 0.0 0.0 4.73 R
2306 2406 2.279935 TCACCAATTAAACAGCCGGT 57.720 45.0 1.90 0.0 0.0 5.28 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
194 195 3.832237 CTCCACACTTGGTGCGCCT 62.832 63.158 18.96 0.00 46.50 5.52
460 461 0.103208 GGGACGTCATCGAGCTGAAT 59.897 55.000 18.91 0.00 40.62 2.57
536 537 2.421424 AGACGTACGACTACATCAACCC 59.579 50.000 24.41 0.00 0.00 4.11
751 757 6.688813 GCTAATCATTGAATCCGACTGAAAAC 59.311 38.462 0.00 0.00 0.00 2.43
752 758 5.567138 ATCATTGAATCCGACTGAAAACC 57.433 39.130 0.00 0.00 0.00 3.27
753 759 3.435327 TCATTGAATCCGACTGAAAACCG 59.565 43.478 0.00 0.00 0.00 4.44
760 767 2.165030 TCCGACTGAAAACCGTATCCTC 59.835 50.000 0.00 0.00 0.00 3.71
925 948 2.159028 TGATGATGCGTTCACCCGAATA 60.159 45.455 0.00 0.00 37.11 1.75
1053 1091 4.333926 GTCCCTCTTAGCATTGACATTGAC 59.666 45.833 1.52 0.00 0.00 3.18
1311 1358 4.620982 CAAGAAGGCCAAGGTTAACTTTG 58.379 43.478 20.39 20.39 37.29 2.77
1320 1367 5.533528 GCCAAGGTTAACTTTGTAGAGGAAA 59.466 40.000 23.91 0.00 37.29 3.13
1368 1439 0.823356 GCCAAGCACAGGACAGGAAA 60.823 55.000 0.00 0.00 0.00 3.13
1538 1609 9.929180 GCTCCTGTTATGAATATGTACTATGAA 57.071 33.333 0.00 0.00 0.00 2.57
1717 1791 1.328680 AGCTGAATATGCGCTTGTTCG 59.671 47.619 21.86 18.00 35.28 3.95
1753 1827 0.685097 TCAGTGGTGCCTCCTGTTAC 59.315 55.000 0.00 0.00 37.07 2.50
2024 2101 9.060347 TCATTACTCTGAAATATTTGCTCCATC 57.940 33.333 5.17 0.00 0.00 3.51
2189 2285 3.382546 GTGGCAGCCATTTATGATGAACT 59.617 43.478 19.75 0.00 35.28 3.01
2306 2406 7.520937 GCGTTTGATCACTTTTTCCCTTTAGTA 60.521 37.037 0.00 0.00 0.00 1.82
2405 4284 3.605634 CCGTCCATAAGATGTTTGGTCA 58.394 45.455 4.52 0.00 0.00 4.02
2410 4289 6.128035 CGTCCATAAGATGTTTGGTCATTTGA 60.128 38.462 4.52 0.00 0.00 2.69
2413 4292 9.473007 TCCATAAGATGTTTGGTCATTTGATAA 57.527 29.630 4.52 0.00 0.00 1.75
2466 4353 7.922278 ACGAACCGACTATTTTGCACTATAATA 59.078 33.333 0.00 0.00 0.00 0.98
2563 4496 1.281287 ACGAGACCAGACCTGCTACTA 59.719 52.381 0.00 0.00 0.00 1.82
2571 4504 3.181461 CCAGACCTGCTACTAATCTTGGG 60.181 52.174 0.00 0.00 0.00 4.12
2578 4511 6.157994 ACCTGCTACTAATCTTGGGATACAAA 59.842 38.462 0.00 0.00 38.91 2.83
2579 4512 6.483640 CCTGCTACTAATCTTGGGATACAAAC 59.516 42.308 0.00 0.00 38.91 2.93
2580 4513 7.195374 TGCTACTAATCTTGGGATACAAACT 57.805 36.000 0.00 0.00 38.91 2.66
2631 4614 4.101942 TCACGAAACAAAACACAAGCATC 58.898 39.130 0.00 0.00 0.00 3.91
2657 4640 3.393800 CGGCCGATCAATCAATCTACTT 58.606 45.455 24.07 0.00 0.00 2.24
2728 4720 2.679716 GAGTTGAGGCCCAGGCAT 59.320 61.111 11.50 2.35 44.11 4.40
2752 4744 0.115152 TCCACAGGCTCCTCTTCTGA 59.885 55.000 0.00 0.00 33.19 3.27
2797 4791 2.333014 GAAGTCAGCTCCACTTCGAAG 58.667 52.381 23.43 23.43 40.23 3.79
2834 4900 8.197439 ACTGAGGAGAACAAAATTTAAAACCAG 58.803 33.333 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.033405 CGGACTAGACCAAGGGGAGA 60.033 60.000 11.84 0.00 38.05 3.71
305 306 4.736473 TCGAGGTGTAATATGATGGAGGA 58.264 43.478 0.00 0.00 0.00 3.71
312 313 7.692460 ACGGTATTATCGAGGTGTAATATGA 57.308 36.000 2.82 0.00 0.00 2.15
460 461 1.611977 CACCTCCGAGTTCTACACACA 59.388 52.381 0.00 0.00 0.00 3.72
536 537 0.368907 CGGAAGCGTTATCACAACGG 59.631 55.000 11.06 0.00 43.25 4.44
751 757 2.600731 GATGCAGAATCGAGGATACGG 58.399 52.381 0.00 0.00 46.39 4.02
925 948 5.125356 TGAACACTGAAACATGATGTGTCT 58.875 37.500 16.14 0.00 41.14 3.41
1053 1091 4.201990 GCTTAAGTCATCTGCAATGGAAGG 60.202 45.833 4.02 0.00 0.00 3.46
1311 1358 5.599999 TCCTGAACTGCTATTTCCTCTAC 57.400 43.478 0.00 0.00 0.00 2.59
1320 1367 3.690460 CTTTGGGTTCCTGAACTGCTAT 58.310 45.455 9.68 0.00 40.94 2.97
1538 1609 1.756538 CCAAAAGTGTTGCTTCCCTGT 59.243 47.619 0.00 0.00 36.17 4.00
1603 1674 4.150359 GGAAATGAGAGCCATGGATGATT 58.850 43.478 18.40 4.23 35.24 2.57
1705 1776 1.076332 GTTACTCCGAACAAGCGCAT 58.924 50.000 11.47 0.00 0.00 4.73
1717 1791 4.557205 CACTGAGTTGTAGGTGTTACTCC 58.443 47.826 0.00 0.00 36.94 3.85
1753 1827 4.031089 CGAAATCGATAGCATCATTCTCCG 59.969 45.833 0.00 0.00 43.02 4.63
2306 2406 2.279935 TCACCAATTAAACAGCCGGT 57.720 45.000 1.90 0.00 0.00 5.28
2413 4292 7.173562 ACGAACGTGATAGCTAGAGAGATTAAT 59.826 37.037 0.00 0.00 0.00 1.40
2443 4330 9.998106 ATCTATTATAGTGCAAAATAGTCGGTT 57.002 29.630 14.25 1.31 35.58 4.44
2466 4353 7.715657 TGTTTACAGCAGAAATGAAACAATCT 58.284 30.769 0.00 0.00 34.74 2.40
2482 4369 2.364002 TCTGGGGCTTTTTGTTTACAGC 59.636 45.455 0.00 0.00 0.00 4.40
2563 4496 4.082245 CCGCAAAGTTTGTATCCCAAGATT 60.082 41.667 16.70 0.00 33.75 2.40
2571 4504 3.907894 TTCCACCGCAAAGTTTGTATC 57.092 42.857 16.70 0.00 0.00 2.24
2578 4511 4.142249 GGCTATTTATTTCCACCGCAAAGT 60.142 41.667 0.00 0.00 0.00 2.66
2579 4512 4.359706 GGCTATTTATTTCCACCGCAAAG 58.640 43.478 0.00 0.00 0.00 2.77
2580 4513 3.131400 GGGCTATTTATTTCCACCGCAAA 59.869 43.478 0.00 0.00 0.00 3.68
2631 4614 2.661866 GATTGATCGGCCGGTCGG 60.662 66.667 31.88 10.38 38.57 4.79
2657 4640 2.833943 TGCATGCTCCTTCTCAACTAGA 59.166 45.455 20.33 0.00 0.00 2.43
2728 4720 2.856760 AGAGGAGCCTGTGGATAGAA 57.143 50.000 0.00 0.00 0.00 2.10
2752 4744 3.173953 TGGTTGGATGATGCCTTTCTT 57.826 42.857 0.00 0.00 0.00 2.52
2797 4791 4.174762 GTTCTCCTCAGTATGGTTCGAAC 58.825 47.826 20.14 20.14 36.16 3.95
2834 4900 4.090498 GGTACGTACAAACTCGAAATGGTC 59.910 45.833 26.02 0.24 0.00 4.02


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

AutoCloner maintained by Alex Coulton.