Multiple sequence alignment - TraesCS7D01G274200

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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 TraesCS7D01G274200 chr7D 100.000 2873 0 0 1 2873 264072380 264075252 0.000000e+00 5306
1 TraesCS7D01G274200 chr7D 96.034 580 20 3 2296 2873 548107795 548108373 0.000000e+00 941
2 TraesCS7D01G274200 chr7D 96.014 577 22 1 2297 2873 77443253 77442678 0.000000e+00 937
3 TraesCS7D01G274200 chr7D 81.053 665 102 16 1364 2013 264082494 264083149 2.550000e-140 508
4 TraesCS7D01G274200 chr7D 74.672 916 184 27 1118 2014 264311927 264312813 2.100000e-96 363
5 TraesCS7D01G274200 chr7B 95.494 2330 82 14 3 2309 244423827 244426156 0.000000e+00 3699
6 TraesCS7D01G274200 chr7B 78.117 754 142 15 1136 1880 244635902 244636641 9.380000e-125 457
7 TraesCS7D01G274200 chr7A 96.797 2092 61 3 3 2091 287549723 287551811 0.000000e+00 3487
8 TraesCS7D01G274200 chr7A 77.112 651 121 19 1379 2014 287805446 287806083 4.550000e-93 351
9 TraesCS7D01G274200 chr7A 96.296 135 3 2 2177 2309 287551810 287551944 1.340000e-53 220
10 TraesCS7D01G274200 chr2D 97.345 565 14 1 2310 2873 15833558 15834122 0.000000e+00 959
11 TraesCS7D01G274200 chr4D 97.173 566 15 1 2309 2873 352521631 352521066 0.000000e+00 955
12 TraesCS7D01G274200 chr5D 97.168 565 13 2 2310 2873 7471815 7472377 0.000000e+00 952
13 TraesCS7D01G274200 chr3D 96.842 570 13 4 2306 2873 553346972 553346406 0.000000e+00 948
14 TraesCS7D01G274200 chr3D 96.454 564 16 3 2311 2873 416196712 416197272 0.000000e+00 928
15 TraesCS7D01G274200 chr1D 96.814 565 16 2 2310 2873 460759467 460760030 0.000000e+00 942
16 TraesCS7D01G274200 chr1D 96.460 565 19 1 2310 2873 101587184 101587748 0.000000e+00 931
17 TraesCS7D01G274200 chr3B 78.796 731 132 16 1158 1879 780315854 780315138 1.210000e-128 470
18 TraesCS7D01G274200 chr3B 78.796 731 132 16 1158 1879 780321228 780320512 1.210000e-128 470
19 TraesCS7D01G274200 chr3B 78.796 731 132 16 1158 1879 780325833 780325117 1.210000e-128 470
20 TraesCS7D01G274200 chr6A 75.817 918 181 30 1116 2017 34390516 34389624 7.360000e-116 427
21 TraesCS7D01G274200 chr6B 77.702 731 138 18 1158 1881 62633904 62633192 9.520000e-115 424
22 TraesCS7D01G274200 chrUn 75.515 874 175 25 1136 1993 101984016 101983166 2.680000e-105 392


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 TraesCS7D01G274200 chr7D 264072380 264075252 2872 False 5306.0 5306 100.0000 1 2873 1 chr7D.!!$F1 2872
1 TraesCS7D01G274200 chr7D 548107795 548108373 578 False 941.0 941 96.0340 2296 2873 1 chr7D.!!$F4 577
2 TraesCS7D01G274200 chr7D 77442678 77443253 575 True 937.0 937 96.0140 2297 2873 1 chr7D.!!$R1 576
3 TraesCS7D01G274200 chr7D 264082494 264083149 655 False 508.0 508 81.0530 1364 2013 1 chr7D.!!$F2 649
4 TraesCS7D01G274200 chr7D 264311927 264312813 886 False 363.0 363 74.6720 1118 2014 1 chr7D.!!$F3 896
5 TraesCS7D01G274200 chr7B 244423827 244426156 2329 False 3699.0 3699 95.4940 3 2309 1 chr7B.!!$F1 2306
6 TraesCS7D01G274200 chr7B 244635902 244636641 739 False 457.0 457 78.1170 1136 1880 1 chr7B.!!$F2 744
7 TraesCS7D01G274200 chr7A 287549723 287551944 2221 False 1853.5 3487 96.5465 3 2309 2 chr7A.!!$F2 2306
8 TraesCS7D01G274200 chr7A 287805446 287806083 637 False 351.0 351 77.1120 1379 2014 1 chr7A.!!$F1 635
9 TraesCS7D01G274200 chr2D 15833558 15834122 564 False 959.0 959 97.3450 2310 2873 1 chr2D.!!$F1 563
10 TraesCS7D01G274200 chr4D 352521066 352521631 565 True 955.0 955 97.1730 2309 2873 1 chr4D.!!$R1 564
11 TraesCS7D01G274200 chr5D 7471815 7472377 562 False 952.0 952 97.1680 2310 2873 1 chr5D.!!$F1 563
12 TraesCS7D01G274200 chr3D 553346406 553346972 566 True 948.0 948 96.8420 2306 2873 1 chr3D.!!$R1 567
13 TraesCS7D01G274200 chr3D 416196712 416197272 560 False 928.0 928 96.4540 2311 2873 1 chr3D.!!$F1 562
14 TraesCS7D01G274200 chr1D 460759467 460760030 563 False 942.0 942 96.8140 2310 2873 1 chr1D.!!$F2 563
15 TraesCS7D01G274200 chr1D 101587184 101587748 564 False 931.0 931 96.4600 2310 2873 1 chr1D.!!$F1 563
16 TraesCS7D01G274200 chr3B 780315138 780315854 716 True 470.0 470 78.7960 1158 1879 1 chr3B.!!$R1 721
17 TraesCS7D01G274200 chr3B 780320512 780325833 5321 True 470.0 470 78.7960 1158 1879 2 chr3B.!!$R2 721
18 TraesCS7D01G274200 chr6A 34389624 34390516 892 True 427.0 427 75.8170 1116 2017 1 chr6A.!!$R1 901
19 TraesCS7D01G274200 chr6B 62633192 62633904 712 True 424.0 424 77.7020 1158 1881 1 chr6B.!!$R1 723
20 TraesCS7D01G274200 chrUn 101983166 101984016 850 True 392.0 392 75.5150 1136 1993 1 chrUn.!!$R1 857

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
982 985 0.392193 AGAACCTTGATCGGCAGCAG 60.392 55.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 6699 0.527565 CAAGATCCGGCAAACAAGGG 59.472 55.0 0.0 0.0 0.0 3.95 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
42 43 4.507710 TGACAAGCCATCTAAAGCTGTAG 58.492 43.478 4.35 4.35 39.87 2.74
200 202 4.557205 GACGGATCGCTGAAATAGGTTAT 58.443 43.478 0.00 0.00 0.00 1.89
212 214 9.555727 GCTGAAATAGGTTATGTAGGAATTGTA 57.444 33.333 0.00 0.00 0.00 2.41
229 231 6.594547 GGAATTGTAAAGTCAACTCCTCCTAC 59.405 42.308 0.63 0.00 43.89 3.18
236 238 3.097614 GTCAACTCCTCCTACCTAGCAA 58.902 50.000 0.00 0.00 0.00 3.91
285 287 4.038271 TCCTCCTCATTTTGCTTCATGT 57.962 40.909 0.00 0.00 0.00 3.21
388 390 4.712476 AGCCTCATATGCTCAACTAAAGG 58.288 43.478 0.00 0.00 32.41 3.11
394 396 7.284034 CCTCATATGCTCAACTAAAGGTCATTT 59.716 37.037 0.00 0.00 34.72 2.32
413 415 3.764237 TTCGGCAGTAAGGAAGAAACT 57.236 42.857 0.00 0.00 0.00 2.66
414 416 3.040147 TCGGCAGTAAGGAAGAAACTG 57.960 47.619 0.00 0.00 42.80 3.16
605 607 9.454585 TCGTCGGTACAATTACTTAATATGAAG 57.545 33.333 0.00 0.00 0.00 3.02
606 608 9.454585 CGTCGGTACAATTACTTAATATGAAGA 57.545 33.333 6.84 0.00 0.00 2.87
690 692 3.664107 TGTACAGTGGATCTTGCTCAAC 58.336 45.455 0.00 0.00 0.00 3.18
709 711 0.676466 CGCCACCTAAACATGCCAGA 60.676 55.000 0.00 0.00 0.00 3.86
710 712 1.767759 GCCACCTAAACATGCCAGAT 58.232 50.000 0.00 0.00 0.00 2.90
982 985 0.392193 AGAACCTTGATCGGCAGCAG 60.392 55.000 0.00 0.00 0.00 4.24
1234 3260 3.260884 TGAGGCGGAAGTACAAGAAGATT 59.739 43.478 0.00 0.00 0.00 2.40
1281 3310 5.133221 TCTTCATCTATCACCATCGAGACA 58.867 41.667 0.00 0.00 0.00 3.41
1298 3327 2.361483 AATGTGCGATGGCCTGCA 60.361 55.556 12.86 12.86 38.85 4.41
1330 3359 1.893137 ACATCTACGGTGCTGTTGAGA 59.107 47.619 0.00 0.00 0.00 3.27
1604 6227 3.896317 AGGCGACTTCAGACAAGAC 57.104 52.632 0.00 0.00 37.44 3.01
1801 6430 4.411540 AGTGCAATATCAGGGATCTTGAGT 59.588 41.667 8.09 0.00 30.86 3.41
1884 6513 3.500448 AGCTCATAGATCTCCACGAGA 57.500 47.619 0.00 0.00 43.20 4.04
1913 6542 8.156165 TGTCACTCATATCATGTTATTGGCATA 58.844 33.333 0.00 0.00 0.00 3.14
1914 6543 9.170734 GTCACTCATATCATGTTATTGGCATAT 57.829 33.333 0.00 0.00 0.00 1.78
2036 6676 3.245048 GTGCCCGCAATATATTTTTGTGC 59.755 43.478 0.00 0.00 34.13 4.57
2059 6699 6.371548 TGCTGTCATAATAGTTTGGTTGAGAC 59.628 38.462 0.00 0.00 0.00 3.36
2064 6704 6.884295 TCATAATAGTTTGGTTGAGACCCTTG 59.116 38.462 0.00 0.00 45.92 3.61
2071 6711 0.310854 GTTGAGACCCTTGTTTGCCG 59.689 55.000 0.00 0.00 0.00 5.69
2091 6731 3.119990 CCGGATCTTGTTTTGCGTACATT 60.120 43.478 0.00 0.00 0.00 2.71
2104 6744 5.203060 TGCGTACATTATACATGCCAGTA 57.797 39.130 0.00 0.00 0.00 2.74
2105 6745 4.986034 TGCGTACATTATACATGCCAGTAC 59.014 41.667 0.00 0.00 0.00 2.73
2126 6766 5.659048 ACGAAGTCAGAAAAAGCTTGTAG 57.341 39.130 0.00 0.00 29.74 2.74
2268 6932 9.077885 ACTGCAGAAAAACTAAATCTCCATTTA 57.922 29.630 23.35 0.00 33.95 1.40
2383 7048 1.716028 AAAAGGAAGGAGCCACCCGT 61.716 55.000 0.00 0.00 40.05 5.28
2457 7126 3.314331 CACTCTGCTGTCCCCCGT 61.314 66.667 0.00 0.00 0.00 5.28
2829 7501 5.186996 AGCAACTGTCATAACAAAACCAG 57.813 39.130 0.00 0.00 34.24 4.00
2854 7526 7.716998 AGTCGATTGTCCTAATAAATCAAGCAT 59.283 33.333 0.00 0.00 31.88 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.818141 TTGTCAACTCTTGTCTAGATTGTTAG 57.182 34.615 0.00 0.00 30.92 2.34
42 43 2.334946 TGGGCACGAAATGAGCTGC 61.335 57.895 0.00 0.00 34.26 5.25
212 214 3.770388 GCTAGGTAGGAGGAGTTGACTTT 59.230 47.826 0.00 0.00 0.00 2.66
229 231 4.515191 TGCTTCTTTGTTGTACTTGCTAGG 59.485 41.667 0.00 0.00 0.00 3.02
236 238 4.705023 ACCTTGTTGCTTCTTTGTTGTACT 59.295 37.500 0.00 0.00 0.00 2.73
285 287 2.079170 TGGATCAAAACAGGTGGCAA 57.921 45.000 0.00 0.00 0.00 4.52
326 328 4.501559 CCATTATTTGCAGCAAAGTCATCG 59.498 41.667 24.39 11.12 36.76 3.84
388 390 3.596214 TCTTCCTTACTGCCGAAATGAC 58.404 45.455 0.00 0.00 0.00 3.06
394 396 2.631062 TCAGTTTCTTCCTTACTGCCGA 59.369 45.455 0.00 0.00 39.24 5.54
562 564 4.677378 CCGACGAATTTGCAATGTGTTTTA 59.323 37.500 0.00 0.00 0.00 1.52
605 607 7.384932 CCTTCTTTTTGGGTTTTGTATGTCATC 59.615 37.037 0.00 0.00 0.00 2.92
606 608 7.216494 CCTTCTTTTTGGGTTTTGTATGTCAT 58.784 34.615 0.00 0.00 0.00 3.06
690 692 0.676466 TCTGGCATGTTTAGGTGGCG 60.676 55.000 0.00 0.00 43.15 5.69
795 798 1.001641 GCTGGATCCTGGTGCAAGT 60.002 57.895 19.23 0.00 0.00 3.16
947 950 0.986527 TTCTTGATCTGGGAGCAGCA 59.013 50.000 0.00 0.00 0.00 4.41
982 985 7.225341 GGGAATCATGAAATTTTGTATTCCAGC 59.775 37.037 23.04 12.26 41.64 4.85
1234 3260 1.694150 ACTTGTCTCTAGGCTGTGCAA 59.306 47.619 0.00 0.00 0.00 4.08
1266 3292 3.457234 GCACATTGTCTCGATGGTGATA 58.543 45.455 0.00 0.00 30.00 2.15
1281 3310 2.361483 TGCAGGCCATCGCACATT 60.361 55.556 5.01 0.00 36.38 2.71
1298 3327 2.028130 CGTAGATGTCTCCAAGCCTCT 58.972 52.381 0.00 0.00 0.00 3.69
1330 3359 2.097825 GCTTGGCAACTGGATGATCTT 58.902 47.619 0.00 0.00 37.61 2.40
1596 6207 0.320374 TTCCGCAATCCGTCTTGTCT 59.680 50.000 0.00 0.00 34.38 3.41
1604 6227 0.744414 ACTGACCATTCCGCAATCCG 60.744 55.000 0.00 0.00 0.00 4.18
1700 6323 4.291249 TGGAAACTAGGGATTGTTTAGGCT 59.709 41.667 0.00 0.00 36.64 4.58
1784 6413 4.560739 TCCACACTCAAGATCCCTGATAT 58.439 43.478 0.00 0.00 0.00 1.63
1801 6430 1.002430 GAACAGATGTCCTGCTCCACA 59.998 52.381 0.00 0.00 46.81 4.17
1884 6513 7.012704 GCCAATAACATGATATGAGTGACAAGT 59.987 37.037 0.00 0.00 0.00 3.16
2036 6676 7.308782 GGTCTCAACCAAACTATTATGACAG 57.691 40.000 0.00 0.00 45.68 3.51
2059 6699 0.527565 CAAGATCCGGCAAACAAGGG 59.472 55.000 0.00 0.00 0.00 3.95
2064 6704 1.792367 GCAAAACAAGATCCGGCAAAC 59.208 47.619 0.00 0.00 0.00 2.93
2071 6711 7.690228 TGTATAATGTACGCAAAACAAGATCC 58.310 34.615 0.00 0.00 0.00 3.36
2091 6731 4.885325 TCTGACTTCGTACTGGCATGTATA 59.115 41.667 0.00 0.00 0.00 1.47
2104 6744 5.116882 ACTACAAGCTTTTTCTGACTTCGT 58.883 37.500 0.00 0.00 0.00 3.85
2105 6745 5.659048 ACTACAAGCTTTTTCTGACTTCG 57.341 39.130 0.00 0.00 0.00 3.79
2166 6829 4.025730 CAGCGACACTTCATAAATATGCGT 60.026 41.667 0.00 0.00 33.76 5.24
2167 6830 4.025730 ACAGCGACACTTCATAAATATGCG 60.026 41.667 0.00 0.00 33.76 4.73
2168 6831 5.409643 ACAGCGACACTTCATAAATATGC 57.590 39.130 0.00 0.00 33.76 3.14
2169 6832 9.935682 AAATAACAGCGACACTTCATAAATATG 57.064 29.630 0.00 0.00 35.04 1.78
2170 6833 9.935682 CAAATAACAGCGACACTTCATAAATAT 57.064 29.630 0.00 0.00 0.00 1.28
2292 6957 8.715088 AGCCACGTCCGAAATTATTTTATATAC 58.285 33.333 0.00 0.00 0.00 1.47
2585 7254 5.932883 GGGATCTAGTTTTGAAGAACTCGTT 59.067 40.000 0.00 0.00 40.24 3.85
2681 7352 5.880332 AGACAAACAAGAAGAGTTGCTTACA 59.120 36.000 0.00 0.00 36.83 2.41
2829 7501 7.246674 TGCTTGATTTATTAGGACAATCGAC 57.753 36.000 0.00 0.00 30.69 4.20


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

AutoCloner maintained by Alex Coulton.