Multiple sequence alignment - TraesCS7D01G189300

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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 TraesCS7D01G189300 chr7D 100.000 2818 0 0 1 2818 142215307 142212490 0.000000e+00 5204
1 TraesCS7D01G189300 chr7D 93.972 1742 71 14 1079 2816 548186436 548184725 0.000000e+00 2604
2 TraesCS7D01G189300 chr7D 91.506 883 60 8 430 1302 544156025 544155148 0.000000e+00 1201
3 TraesCS7D01G189300 chr7D 96.302 622 21 1 2132 2751 544153965 544153344 0.000000e+00 1020
4 TraesCS7D01G189300 chr4D 92.558 1411 73 17 1 1408 410093576 410094957 0.000000e+00 1995
5 TraesCS7D01G189300 chr4D 97.720 307 7 0 2510 2816 410096393 410096699 1.920000e-146 529
6 TraesCS7D01G189300 chr4A 93.563 1305 77 4 1 1302 504677840 504676540 0.000000e+00 1938
7 TraesCS7D01G189300 chr3D 93.359 1310 72 9 1 1303 21770833 21769532 0.000000e+00 1923
8 TraesCS7D01G189300 chr3D 93.169 1098 64 5 1148 2244 596628824 596629911 0.000000e+00 1602
9 TraesCS7D01G189300 chr3D 96.785 622 19 1 2132 2753 21768367 21767747 0.000000e+00 1037
10 TraesCS7D01G189300 chr7A 92.765 1313 84 10 1 1308 675750775 675749469 0.000000e+00 1888
11 TraesCS7D01G189300 chr2D 91.480 1385 87 9 376 1754 291609651 291608292 0.000000e+00 1875
12 TraesCS7D01G189300 chr2D 95.591 1066 46 1 1750 2814 291597970 291596905 0.000000e+00 1707
13 TraesCS7D01G189300 chr6D 94.171 1098 57 4 1148 2244 322698090 322699181 0.000000e+00 1666
14 TraesCS7D01G189300 chr6D 93.733 1101 57 8 1148 2247 384196145 384195056 0.000000e+00 1640
15 TraesCS7D01G189300 chr6D 92.007 588 37 8 666 1245 67658270 67658855 0.000000e+00 817
16 TraesCS7D01G189300 chr6D 88.300 641 58 14 7 641 283305111 283304482 0.000000e+00 752
17 TraesCS7D01G189300 chr1D 93.625 1098 59 8 1148 2244 353181177 353182264 0.000000e+00 1629
18 TraesCS7D01G189300 chr1D 92.049 566 41 4 674 1236 408917434 408916870 0.000000e+00 793
19 TraesCS7D01G189300 chr2A 93.460 1101 65 5 1148 2247 722101983 722100889 0.000000e+00 1628
20 TraesCS7D01G189300 chr2A 88.995 418 25 8 2059 2465 656373139 656372732 5.420000e-137 497
21 TraesCS7D01G189300 chrUn 93.364 1100 65 5 1148 2246 102599765 102598673 0.000000e+00 1620
22 TraesCS7D01G189300 chr3B 93.279 1101 62 8 1148 2247 87708806 87707717 0.000000e+00 1613
23 TraesCS7D01G189300 chr1B 93.260 1098 66 5 1148 2244 39265301 39266391 0.000000e+00 1611
24 TraesCS7D01G189300 chr1B 92.486 905 61 3 1 898 659196381 659195477 0.000000e+00 1288
25 TraesCS7D01G189300 chr1B 95.185 623 27 3 2132 2753 659103298 659102678 0.000000e+00 981
26 TraesCS7D01G189300 chr1B 88.028 710 74 6 610 1308 659105039 659104330 0.000000e+00 830
27 TraesCS7D01G189300 chr1B 94.347 513 27 2 1 511 659105551 659105039 0.000000e+00 785
28 TraesCS7D01G189300 chr5B 95.981 622 24 1 2132 2753 89069299 89068679 0.000000e+00 1009
29 TraesCS7D01G189300 chr7B 95.491 621 26 2 2134 2753 130902364 130901745 0.000000e+00 990
30 TraesCS7D01G189300 chr7B 85.826 642 65 20 7 641 706375794 706375172 0.000000e+00 658
31 TraesCS7D01G189300 chr6A 93.056 648 34 6 1820 2465 291914478 291915116 0.000000e+00 937
32 TraesCS7D01G189300 chr6A 95.572 271 8 3 2487 2753 595723350 595723620 5.580000e-117 431
33 TraesCS7D01G189300 chr2B 85.429 652 66 21 1 641 91293330 91293963 0.000000e+00 651
34 TraesCS7D01G189300 chr3A 94.690 113 5 1 2705 2816 707589843 707589731 1.040000e-39 174
35 TraesCS7D01G189300 chr3A 96.154 78 3 0 2739 2816 667989131 667989208 8.190000e-26 128


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 TraesCS7D01G189300 chr7D 142212490 142215307 2817 True 5204.000000 5204 100.000 1 2818 1 chr7D.!!$R1 2817
1 TraesCS7D01G189300 chr7D 548184725 548186436 1711 True 2604.000000 2604 93.972 1079 2816 1 chr7D.!!$R2 1737
2 TraesCS7D01G189300 chr7D 544153344 544156025 2681 True 1110.500000 1201 93.904 430 2751 2 chr7D.!!$R3 2321
3 TraesCS7D01G189300 chr4D 410093576 410096699 3123 False 1262.000000 1995 95.139 1 2816 2 chr4D.!!$F1 2815
4 TraesCS7D01G189300 chr4A 504676540 504677840 1300 True 1938.000000 1938 93.563 1 1302 1 chr4A.!!$R1 1301
5 TraesCS7D01G189300 chr3D 596628824 596629911 1087 False 1602.000000 1602 93.169 1148 2244 1 chr3D.!!$F1 1096
6 TraesCS7D01G189300 chr3D 21767747 21770833 3086 True 1480.000000 1923 95.072 1 2753 2 chr3D.!!$R1 2752
7 TraesCS7D01G189300 chr7A 675749469 675750775 1306 True 1888.000000 1888 92.765 1 1308 1 chr7A.!!$R1 1307
8 TraesCS7D01G189300 chr2D 291608292 291609651 1359 True 1875.000000 1875 91.480 376 1754 1 chr2D.!!$R2 1378
9 TraesCS7D01G189300 chr2D 291596905 291597970 1065 True 1707.000000 1707 95.591 1750 2814 1 chr2D.!!$R1 1064
10 TraesCS7D01G189300 chr6D 322698090 322699181 1091 False 1666.000000 1666 94.171 1148 2244 1 chr6D.!!$F2 1096
11 TraesCS7D01G189300 chr6D 384195056 384196145 1089 True 1640.000000 1640 93.733 1148 2247 1 chr6D.!!$R2 1099
12 TraesCS7D01G189300 chr6D 67658270 67658855 585 False 817.000000 817 92.007 666 1245 1 chr6D.!!$F1 579
13 TraesCS7D01G189300 chr6D 283304482 283305111 629 True 752.000000 752 88.300 7 641 1 chr6D.!!$R1 634
14 TraesCS7D01G189300 chr1D 353181177 353182264 1087 False 1629.000000 1629 93.625 1148 2244 1 chr1D.!!$F1 1096
15 TraesCS7D01G189300 chr1D 408916870 408917434 564 True 793.000000 793 92.049 674 1236 1 chr1D.!!$R1 562
16 TraesCS7D01G189300 chr2A 722100889 722101983 1094 True 1628.000000 1628 93.460 1148 2247 1 chr2A.!!$R2 1099
17 TraesCS7D01G189300 chrUn 102598673 102599765 1092 True 1620.000000 1620 93.364 1148 2246 1 chrUn.!!$R1 1098
18 TraesCS7D01G189300 chr3B 87707717 87708806 1089 True 1613.000000 1613 93.279 1148 2247 1 chr3B.!!$R1 1099
19 TraesCS7D01G189300 chr1B 39265301 39266391 1090 False 1611.000000 1611 93.260 1148 2244 1 chr1B.!!$F1 1096
20 TraesCS7D01G189300 chr1B 659195477 659196381 904 True 1288.000000 1288 92.486 1 898 1 chr1B.!!$R1 897
21 TraesCS7D01G189300 chr1B 659102678 659105551 2873 True 865.333333 981 92.520 1 2753 3 chr1B.!!$R2 2752
22 TraesCS7D01G189300 chr5B 89068679 89069299 620 True 1009.000000 1009 95.981 2132 2753 1 chr5B.!!$R1 621
23 TraesCS7D01G189300 chr7B 130901745 130902364 619 True 990.000000 990 95.491 2134 2753 1 chr7B.!!$R1 619
24 TraesCS7D01G189300 chr7B 706375172 706375794 622 True 658.000000 658 85.826 7 641 1 chr7B.!!$R2 634
25 TraesCS7D01G189300 chr6A 291914478 291915116 638 False 937.000000 937 93.056 1820 2465 1 chr6A.!!$F1 645
26 TraesCS7D01G189300 chr2B 91293330 91293963 633 False 651.000000 651 85.429 1 641 1 chr2B.!!$F1 640

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
716 730 1.0756 GCTCTCTCTGCCCTACCCT 60.076 63.158 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2558 3982 0.250295 AAGCAAACTAGCAGCCGTGA 60.25 50.0 0.0 0.0 36.85 4.35 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
324 328 7.903431 GCTAATATGTTGAGTGTTTACCGAAAG 59.097 37.037 0.00 0.00 0.00 2.62
711 725 1.988956 CCACAGCTCTCTCTGCCCT 60.989 63.158 0.00 0.00 37.59 5.19
716 730 1.075600 GCTCTCTCTGCCCTACCCT 60.076 63.158 0.00 0.00 0.00 4.34
956 980 3.151022 GAGCCAGACGGGAGGAGG 61.151 72.222 0.00 0.00 40.01 4.30
1005 1033 2.192979 GCAAGGGGATCGATGGCA 59.807 61.111 0.54 0.00 0.00 4.92
1071 1100 2.762535 CCGAGTGGTTCATGTACCTT 57.237 50.000 20.70 10.27 39.04 3.50
1099 1128 2.430694 TGGACCACCTACATCTTCATCG 59.569 50.000 0.00 0.00 37.04 3.84
1110 1139 5.850557 ACATCTTCATCGTCTTCATCTCT 57.149 39.130 0.00 0.00 0.00 3.10
1136 1165 2.175715 TCCTCATCCTCTCCATCTTCGA 59.824 50.000 0.00 0.00 0.00 3.71
1144 1173 0.534412 CTCCATCTTCGACTGCACCT 59.466 55.000 0.00 0.00 0.00 4.00
1195 1225 2.125673 CTTCGTGGTACCCGCCTG 60.126 66.667 10.07 2.94 0.00 4.85
1260 1329 3.061322 TGGATCGTGTTTGTTTACCTCG 58.939 45.455 0.00 0.00 0.00 4.63
1264 1333 5.106830 GGATCGTGTTTGTTTACCTCGATTT 60.107 40.000 0.00 0.00 35.71 2.17
1265 1334 5.085636 TCGTGTTTGTTTACCTCGATTTG 57.914 39.130 0.00 0.00 0.00 2.32
1328 1865 1.472728 GGGGTGTAGATCGTTCGCATT 60.473 52.381 0.00 0.00 0.00 3.56
1358 1895 0.755698 TCGCCTCCCCTAGCTACAAG 60.756 60.000 0.00 0.00 0.00 3.16
1556 2773 0.608130 GTTGGCCCAACCTCAATTCC 59.392 55.000 16.01 0.00 38.30 3.01
1716 2934 3.244215 GGGAACTCCATTCGCTGATGATA 60.244 47.826 0.00 0.00 44.79 2.15
1801 3019 5.727515 GCAACAGAAAATTTCTTGTTGTGGC 60.728 40.000 29.14 21.04 43.15 5.01
1828 3046 8.554870 TCCTGTAGTCCTCTAAGTGTTATTCTA 58.445 37.037 0.00 0.00 0.00 2.10
1862 3080 6.857437 ATTAATACTGCTTTTGGGAGCTTT 57.143 33.333 0.00 0.00 43.11 3.51
1914 3132 3.575256 TGCACAAAGATTGATTCTGGCTT 59.425 39.130 0.00 0.00 33.93 4.35
1919 3137 5.159209 CAAAGATTGATTCTGGCTTGTCAC 58.841 41.667 0.00 0.00 33.93 3.67
2138 3555 3.824443 AGTAACTTAAACTTGGCGGCAAT 59.176 39.130 25.71 13.20 0.00 3.56
2143 3560 2.158561 AAACTTGGCGGCAATCTGGC 62.159 55.000 25.71 0.00 43.82 4.85
2558 3982 9.826574 TTAACTGTTAGTACAAGACATCAAGTT 57.173 29.630 0.00 0.00 32.92 2.66
2635 4059 3.513515 TGTGGATTTTAAGCATGGTTCCC 59.486 43.478 14.50 9.23 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.762407 TGGGTGTCAAAAGATTCGAGA 57.238 42.857 0.00 0.00 0.00 4.04
112 114 6.506500 TTTGTTGCAAAATTGGACAAATGT 57.493 29.167 0.00 0.00 30.94 2.71
292 295 7.944729 AAACACTCAACATATTAGCCTCATT 57.055 32.000 0.00 0.00 0.00 2.57
367 373 8.147058 ACCAATCAGAGTCTAGCTTATGTAATG 58.853 37.037 0.00 0.00 0.00 1.90
542 553 1.152652 TGGATCGGGGAGAGAGAGC 60.153 63.158 0.00 0.00 0.00 4.09
711 725 2.836667 CTGTGGGTAGGGTTTAGGGTA 58.163 52.381 0.00 0.00 0.00 3.69
716 730 1.984817 CGGCTGTGGGTAGGGTTTA 59.015 57.895 0.00 0.00 0.00 2.01
849 872 0.178950 CCCCTCTCGATCTGGATCCA 60.179 60.000 15.27 15.27 34.40 3.41
979 1007 3.341469 ATCCCCTTGCCCTACCGGA 62.341 63.158 9.46 0.00 0.00 5.14
1005 1033 1.738099 CGCCTGCACGTAGAGCTTT 60.738 57.895 0.00 0.00 46.38 3.51
1099 1128 2.499289 TGAGGAGCCAAGAGATGAAGAC 59.501 50.000 0.00 0.00 0.00 3.01
1110 1139 0.043183 TGGAGAGGATGAGGAGCCAA 59.957 55.000 0.00 0.00 0.00 4.52
1195 1225 2.367107 GAGGGAAGGGAGGGGGAC 60.367 72.222 0.00 0.00 0.00 4.46
1206 1239 1.076677 ACGTGTAAGAGAGGGAGGGAA 59.923 52.381 0.00 0.00 0.00 3.97
1260 1329 6.129194 GCAATCGAGGTAAACAAACACAAATC 60.129 38.462 0.00 0.00 0.00 2.17
1264 1333 3.880490 AGCAATCGAGGTAAACAAACACA 59.120 39.130 0.00 0.00 0.00 3.72
1265 1334 4.483476 AGCAATCGAGGTAAACAAACAC 57.517 40.909 0.00 0.00 0.00 3.32
1328 1865 2.754375 GAGGCGAAGGGTGGGAAA 59.246 61.111 0.00 0.00 0.00 3.13
1448 2665 9.933723 AAAGTAGCAAAAGAATGATTAAATGCT 57.066 25.926 10.58 10.58 44.35 3.79
1716 2934 7.421382 CCAAGTCAACCTATTATACATCCCCTT 60.421 40.741 0.00 0.00 0.00 3.95
1801 3019 7.558444 AGAATAACACTTAGAGGACTACAGGAG 59.442 40.741 0.00 0.00 0.00 3.69
1862 3080 1.070445 CCATGCTGTTCCTTGCCAAAA 59.930 47.619 0.00 0.00 0.00 2.44
1914 3132 9.936759 TGATGAATAAGTGTAGTATTTGTGACA 57.063 29.630 0.00 0.00 0.00 3.58
2138 3555 1.003118 ACAGCCAAGTATTTCGCCAGA 59.997 47.619 0.00 0.00 0.00 3.86
2143 3560 3.242091 CGTGATCACAGCCAAGTATTTCG 60.242 47.826 24.93 2.55 0.00 3.46
2144 3561 3.684788 ACGTGATCACAGCCAAGTATTTC 59.315 43.478 24.93 0.00 0.00 2.17
2558 3982 0.250295 AAGCAAACTAGCAGCCGTGA 60.250 50.000 0.00 0.00 36.85 4.35
2593 4017 6.667848 TCCACACCTACATATACATATCCCAG 59.332 42.308 0.00 0.00 0.00 4.45
2611 4035 4.494484 GAACCATGCTTAAAATCCACACC 58.506 43.478 0.00 0.00 0.00 4.16
2635 4059 7.090808 AGTGGTATGCACTTATCACATATACG 58.909 38.462 12.16 0.00 35.96 3.06


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

AutoCloner maintained by Alex Coulton.