Multiple sequence alignment - TraesCS1A01G241200

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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 TraesCS1A01G241200 chr1A 100.000 2585 0 0 1 2585 428868747 428866163 0.000000e+00 4774.0
1 TraesCS1A01G241200 chr1A 94.554 2589 117 15 2 2583 428860584 428858013 0.000000e+00 3978.0
2 TraesCS1A01G241200 chr1A 93.333 930 58 4 1 927 297467786 297466858 0.000000e+00 1371.0
3 TraesCS1A01G241200 chr1A 93.548 651 39 3 1005 1654 163668808 163669456 0.000000e+00 966.0
4 TraesCS1A01G241200 chr1A 91.244 651 54 3 1005 1654 163695624 163696272 0.000000e+00 883.0
5 TraesCS1A01G241200 chr1A 92.714 398 23 6 2191 2584 474637765 474638160 1.040000e-158 569.0
6 TraesCS1A01G241200 chr1A 92.208 77 6 0 1531 1607 250712630 250712554 2.720000e-20 110.0
7 TraesCS1A01G241200 chr7A 91.900 1889 138 10 1 1878 421521671 421523555 0.000000e+00 2627.0
8 TraesCS1A01G241200 chr7A 85.735 680 68 15 1924 2584 665083606 665082937 0.000000e+00 691.0
9 TraesCS1A01G241200 chr7A 93.333 405 21 6 2183 2584 168015591 168015190 6.160000e-166 593.0
10 TraesCS1A01G241200 chr5A 93.411 1457 84 8 1 1447 404296705 404298159 0.000000e+00 2148.0
11 TraesCS1A01G241200 chr5A 92.651 1456 96 7 1 1447 404289175 404290628 0.000000e+00 2085.0
12 TraesCS1A01G241200 chr5A 82.436 706 81 21 1905 2583 528761878 528761189 6.200000e-161 577.0
13 TraesCS1A01G241200 chr5A 92.763 304 20 2 1577 1878 286005962 286005659 3.050000e-119 438.0
14 TraesCS1A01G241200 chr5A 85.385 260 27 11 1708 1959 244299157 244298901 2.550000e-65 259.0
15 TraesCS1A01G241200 chr2A 92.060 1209 85 7 2 1201 258560994 258562200 0.000000e+00 1690.0
16 TraesCS1A01G241200 chr2A 92.314 1145 76 8 1 1134 388499478 388500621 0.000000e+00 1616.0
17 TraesCS1A01G241200 chr2A 91.965 1145 80 8 1 1134 388507595 388508738 0.000000e+00 1594.0
18 TraesCS1A01G241200 chr2A 91.460 644 53 2 1237 1878 258562199 258562842 0.000000e+00 883.0
19 TraesCS1A01G241200 chr2A 83.673 637 68 24 1971 2584 352050337 352050960 3.730000e-158 568.0
20 TraesCS1A01G241200 chr2A 85.934 455 35 11 690 1134 384096964 384097399 2.340000e-125 459.0
21 TraesCS1A01G241200 chr2A 92.208 308 21 3 1609 1915 407198168 407198473 1.420000e-117 433.0
22 TraesCS1A01G241200 chr2A 89.041 73 6 2 967 1038 369014824 369014753 3.540000e-14 89.8
23 TraesCS1A01G241200 chr3A 92.396 960 62 9 1 954 247355717 247354763 0.000000e+00 1358.0
24 TraesCS1A01G241200 chr3A 90.994 533 42 6 1005 1534 263711882 263712411 0.000000e+00 713.0
25 TraesCS1A01G241200 chr3A 90.789 532 45 4 1005 1534 263719912 263720441 0.000000e+00 708.0
26 TraesCS1A01G241200 chr3A 84.669 711 71 23 1872 2557 428550295 428549598 0.000000e+00 675.0
27 TraesCS1A01G241200 chr3A 93.284 402 22 5 2183 2581 574958645 574959044 2.870000e-164 588.0
28 TraesCS1A01G241200 chr3A 91.542 402 31 3 2183 2582 189884260 189884660 3.760000e-153 551.0
29 TraesCS1A01G241200 chr3A 81.124 747 79 39 1872 2584 316658062 316657344 2.260000e-150 542.0
30 TraesCS1A01G241200 chr3A 77.534 592 87 34 1949 2506 7605796 7605217 5.370000e-82 315.0
31 TraesCS1A01G241200 chr3A 77.409 602 88 36 1940 2506 308225149 308225737 5.370000e-82 315.0
32 TraesCS1A01G241200 chr6A 84.985 686 65 19 1924 2581 319229624 319230299 0.000000e+00 662.0
33 TraesCS1A01G241200 chr6A 85.690 580 58 15 2026 2584 435673743 435673168 2.870000e-164 588.0
34 TraesCS1A01G241200 chr6A 92.857 406 24 5 2183 2585 159640698 159640295 3.710000e-163 584.0
35 TraesCS1A01G241200 chr6A 85.282 496 62 11 2093 2583 107627163 107627652 3.840000e-138 501.0
36 TraesCS1A01G241200 chr6A 91.118 304 25 2 1577 1878 309634864 309634561 6.660000e-111 411.0
37 TraesCS1A01G241200 chr6A 90.523 306 25 3 1577 1878 309626807 309626502 4.010000e-108 401.0
38 TraesCS1A01G241200 chr4A 92.208 308 22 2 1609 1915 400451855 400451549 3.950000e-118 435.0
39 TraesCS1A01G241200 chr4A 77.647 595 86 35 1947 2506 407188489 407189071 4.150000e-83 318.0
40 TraesCS1A01G241200 chr2B 91.118 304 23 3 1577 1878 143536212 143535911 2.390000e-110 409.0


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 TraesCS1A01G241200 chr1A 428866163 428868747 2584 True 4774.0 4774 100.000 1 2585 1 chr1A.!!$R4 2584
1 TraesCS1A01G241200 chr1A 428858013 428860584 2571 True 3978.0 3978 94.554 2 2583 1 chr1A.!!$R3 2581
2 TraesCS1A01G241200 chr1A 297466858 297467786 928 True 1371.0 1371 93.333 1 927 1 chr1A.!!$R2 926
3 TraesCS1A01G241200 chr1A 163668808 163669456 648 False 966.0 966 93.548 1005 1654 1 chr1A.!!$F1 649
4 TraesCS1A01G241200 chr1A 163695624 163696272 648 False 883.0 883 91.244 1005 1654 1 chr1A.!!$F2 649
5 TraesCS1A01G241200 chr7A 421521671 421523555 1884 False 2627.0 2627 91.900 1 1878 1 chr7A.!!$F1 1877
6 TraesCS1A01G241200 chr7A 665082937 665083606 669 True 691.0 691 85.735 1924 2584 1 chr7A.!!$R2 660
7 TraesCS1A01G241200 chr5A 404296705 404298159 1454 False 2148.0 2148 93.411 1 1447 1 chr5A.!!$F2 1446
8 TraesCS1A01G241200 chr5A 404289175 404290628 1453 False 2085.0 2085 92.651 1 1447 1 chr5A.!!$F1 1446
9 TraesCS1A01G241200 chr5A 528761189 528761878 689 True 577.0 577 82.436 1905 2583 1 chr5A.!!$R3 678
10 TraesCS1A01G241200 chr2A 388499478 388500621 1143 False 1616.0 1616 92.314 1 1134 1 chr2A.!!$F3 1133
11 TraesCS1A01G241200 chr2A 388507595 388508738 1143 False 1594.0 1594 91.965 1 1134 1 chr2A.!!$F4 1133
12 TraesCS1A01G241200 chr2A 258560994 258562842 1848 False 1286.5 1690 91.760 2 1878 2 chr2A.!!$F6 1876
13 TraesCS1A01G241200 chr2A 352050337 352050960 623 False 568.0 568 83.673 1971 2584 1 chr2A.!!$F1 613
14 TraesCS1A01G241200 chr3A 247354763 247355717 954 True 1358.0 1358 92.396 1 954 1 chr3A.!!$R2 953
15 TraesCS1A01G241200 chr3A 263711882 263712411 529 False 713.0 713 90.994 1005 1534 1 chr3A.!!$F2 529
16 TraesCS1A01G241200 chr3A 263719912 263720441 529 False 708.0 708 90.789 1005 1534 1 chr3A.!!$F3 529
17 TraesCS1A01G241200 chr3A 428549598 428550295 697 True 675.0 675 84.669 1872 2557 1 chr3A.!!$R4 685
18 TraesCS1A01G241200 chr3A 316657344 316658062 718 True 542.0 542 81.124 1872 2584 1 chr3A.!!$R3 712
19 TraesCS1A01G241200 chr3A 7605217 7605796 579 True 315.0 315 77.534 1949 2506 1 chr3A.!!$R1 557
20 TraesCS1A01G241200 chr3A 308225149 308225737 588 False 315.0 315 77.409 1940 2506 1 chr3A.!!$F4 566
21 TraesCS1A01G241200 chr6A 319229624 319230299 675 False 662.0 662 84.985 1924 2581 1 chr6A.!!$F2 657
22 TraesCS1A01G241200 chr6A 435673168 435673743 575 True 588.0 588 85.690 2026 2584 1 chr6A.!!$R4 558
23 TraesCS1A01G241200 chr4A 407188489 407189071 582 False 318.0 318 77.647 1947 2506 1 chr4A.!!$F1 559

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
831 838 0.0982 CGTAGCCGTTCGAGTCATCA 59.902 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 1722 4.459089 GCGCGCCTCCTTCCTTCT 62.459 66.667 23.24 0.0 0.0 2.85 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
83 85 4.734370 GCAATTTGGTGCAACAACAATTTC 59.266 37.500 18.78 6.23 40.90 2.17
209 212 1.632589 GTGGAAAGAAAGGGTGCCAT 58.367 50.000 0.00 0.00 0.00 4.40
221 224 1.410648 GGGTGCCATGGTGATGAATCT 60.411 52.381 14.67 0.00 0.00 2.40
420 423 2.603110 CACGGTTCAACTCATACATCGG 59.397 50.000 0.00 0.00 0.00 4.18
485 488 1.933115 GCATGCGTTTCGGGTGGAAT 61.933 55.000 0.00 0.00 33.85 3.01
516 519 1.066430 TGGAAGTAGTCGTTCATGGGC 60.066 52.381 0.00 0.00 0.00 5.36
648 651 5.416083 TCGTCATCGAACTTGGTCAAATAT 58.584 37.500 0.00 0.00 43.34 1.28
675 678 0.877071 GGGTAGACGTTCACTCGACA 59.123 55.000 0.00 0.00 34.70 4.35
762 767 2.784356 TTCGGGGTCAACGACACGT 61.784 57.895 0.00 0.00 43.97 4.49
771 776 2.853594 GTCAACGACACGTAACTTGACA 59.146 45.455 16.42 0.00 40.93 3.58
780 787 2.288666 CGTAACTTGACATCCATGGGG 58.711 52.381 13.02 7.37 0.00 4.96
802 809 2.706636 CCGAGGGTCGACGGTATTA 58.293 57.895 9.92 0.00 43.74 0.98
831 838 0.098200 CGTAGCCGTTCGAGTCATCA 59.902 55.000 0.00 0.00 0.00 3.07
839 846 2.032302 CGTTCGAGTCATCAGTAGAGGG 59.968 54.545 0.00 0.00 0.00 4.30
878 886 1.211949 CCTTCGGGGTTGTCATGGTAT 59.788 52.381 0.00 0.00 0.00 2.73
965 977 1.936547 GCACTTGTCATCGAGGGAATC 59.063 52.381 0.00 0.00 30.25 2.52
979 991 3.813166 GAGGGAATCGTCTTGACAAAACA 59.187 43.478 1.59 0.00 0.00 2.83
992 1005 3.208594 GACAAAACAAAGGGGTACTCGT 58.791 45.455 0.00 0.00 0.00 4.18
1105 1121 0.039165 GGCAAAAGCCCTCGTTCAAG 60.039 55.000 0.00 0.00 0.00 3.02
1179 1195 3.788142 TGGAGAGGCCTATGGAAAAGAAT 59.212 43.478 3.53 0.00 37.63 2.40
1221 1237 2.096268 CGCTGCTCATTCGTTTGAAAGA 60.096 45.455 0.00 0.00 37.71 2.52
1261 1277 1.004560 CAGGCATCACAGACACCGT 60.005 57.895 0.00 0.00 0.00 4.83
1453 1470 1.767692 GGAGTTCCTGCTTGGGGAA 59.232 57.895 0.00 0.00 40.14 3.97
1518 1536 2.128507 GGGAGGCGACGAAGAGGAT 61.129 63.158 0.00 0.00 0.00 3.24
1672 1690 4.451150 CGGTAGCAGGAAGGCGCA 62.451 66.667 10.83 0.00 39.27 6.09
2004 2029 2.110011 GGGCTCTCTCTCCCTCTATCTT 59.890 54.545 0.00 0.00 39.46 2.40
2045 2076 9.467796 AGAAAGAAAAGAAAGAGAGGAAAGAAA 57.532 29.630 0.00 0.00 0.00 2.52
2046 2077 9.729023 GAAAGAAAAGAAAGAGAGGAAAGAAAG 57.271 33.333 0.00 0.00 0.00 2.62
2047 2078 9.467796 AAAGAAAAGAAAGAGAGGAAAGAAAGA 57.532 29.630 0.00 0.00 0.00 2.52
2048 2079 9.467796 AAGAAAAGAAAGAGAGGAAAGAAAGAA 57.532 29.630 0.00 0.00 0.00 2.52
2435 2501 6.220930 CCTCGGTTTAAATGGATCGAAGATA 58.779 40.000 0.00 0.00 45.12 1.98
2584 2656 0.176680 GAAGGCATCTGAAGCTCCGA 59.823 55.000 4.77 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 175 1.269174 CACCACGATGACAAAATGCCA 59.731 47.619 0.00 0.00 0.00 4.92
209 212 5.163488 GGCATCATTTTCAGATTCATCACCA 60.163 40.000 0.00 0.00 0.00 4.17
221 224 2.620585 TGTTGTCGTGGCATCATTTTCA 59.379 40.909 0.00 0.00 0.00 2.69
420 423 1.696832 GCTCGTGGACCGAATGCTTC 61.697 60.000 0.00 0.00 46.75 3.86
485 488 3.434641 CGACTACTTCCACTACGAACTCA 59.565 47.826 0.00 0.00 0.00 3.41
648 651 2.162208 GTGAACGTCTACCCACATCGTA 59.838 50.000 0.00 0.00 34.38 3.43
762 767 4.340617 GAAACCCCATGGATGTCAAGTTA 58.659 43.478 15.22 0.00 34.81 2.24
771 776 1.645402 CCCTCGGAAACCCCATGGAT 61.645 60.000 15.22 0.00 34.81 3.41
831 838 2.830651 ATCCGTCAAGTCCCTCTACT 57.169 50.000 0.00 0.00 0.00 2.57
872 880 2.092592 GTCCGAAGACCCCAAATACCAT 60.093 50.000 0.00 0.00 37.00 3.55
878 886 0.536460 GCAAGTCCGAAGACCCCAAA 60.536 55.000 0.00 0.00 44.72 3.28
965 977 2.425668 ACCCCTTTGTTTTGTCAAGACG 59.574 45.455 2.14 0.00 0.00 4.18
979 991 2.173143 TGGTTTTGACGAGTACCCCTTT 59.827 45.455 0.00 0.00 0.00 3.11
992 1005 3.146066 CCTCCGAAGAACATGGTTTTGA 58.854 45.455 0.00 0.00 0.00 2.69
1018 1031 3.582647 ACATGATGACCTGACAAGTACCA 59.417 43.478 0.00 0.00 0.00 3.25
1105 1121 3.479269 CGTCAAGTTCGAGCGCCC 61.479 66.667 2.29 0.00 0.00 6.13
1144 1160 2.541466 CCTCTCCAAGACCAGGTTACT 58.459 52.381 0.00 0.00 0.00 2.24
1221 1237 2.026641 TGCTGCTGCTGTTTTCTTTCT 58.973 42.857 17.00 0.00 40.48 2.52
1273 1289 3.257561 CATCTTCGGCCGTCTGCG 61.258 66.667 27.15 8.68 42.61 5.18
1704 1722 4.459089 GCGCGCCTCCTTCCTTCT 62.459 66.667 23.24 0.00 0.00 2.85
2186 2241 5.278061 ACACTTCTATAACCAAGCCCTAGA 58.722 41.667 0.00 0.00 0.00 2.43
2435 2501 6.887626 AACTCAACCAAATAAACCGTATGT 57.112 33.333 0.00 0.00 0.00 2.29
2515 2587 7.282675 TGAATTGTTTGGTTCTTTGCATTCATT 59.717 29.630 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.