Multiple sequence alignment - TraesCS7D01G070400

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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 TraesCS7D01G070400 chr7D 100.000 2497 0 0 1 2497 41366846 41364350 0.000000e+00 4612.0
1 TraesCS7D01G070400 chr7D 96.887 1510 31 6 1 1498 41258587 41260092 0.000000e+00 2514.0
2 TraesCS7D01G070400 chr7D 94.616 1616 71 12 887 2497 41325313 41326917 0.000000e+00 2488.0
3 TraesCS7D01G070400 chr7D 89.277 802 62 7 480 1270 41274844 41275632 0.000000e+00 983.0
4 TraesCS7D01G070400 chr7D 85.934 391 36 9 455 838 41306750 41307128 1.390000e-107 399.0
5 TraesCS7D01G070400 chr7D 85.233 386 43 8 4 382 41274231 41274609 3.900000e-103 385.0
6 TraesCS7D01G070400 chr7D 84.496 387 50 7 4 382 41302604 41302988 8.430000e-100 374.0
7 TraesCS7D01G070400 chr7D 80.967 331 35 9 605 916 41273000 41273321 1.150000e-58 237.0
8 TraesCS7D01G070400 chr7D 95.050 101 5 0 1568 1668 473596182 473596282 2.570000e-35 159.0
9 TraesCS7D01G070400 chr7D 87.200 125 11 2 462 581 41274712 41274836 1.200000e-28 137.0
10 TraesCS7D01G070400 chr7D 74.877 406 48 20 453 836 41344168 41343795 4.330000e-28 135.0
11 TraesCS7D01G070400 chr7D 90.909 66 5 1 1366 1430 41431269 41431334 1.230000e-13 87.9
12 TraesCS7D01G070400 chr7D 91.803 61 5 0 1368 1428 41343221 41343161 4.430000e-13 86.1
13 TraesCS7D01G070400 chr7A 89.929 844 42 15 475 1303 40694881 40695696 0.000000e+00 1048.0
14 TraesCS7D01G070400 chr7A 79.418 481 70 14 1 478 40693268 40693722 1.860000e-81 313.0
15 TraesCS7D01G070400 chr7A 79.762 336 52 13 8 334 543963396 543963724 1.930000e-56 230.0
16 TraesCS7D01G070400 chr7A 79.730 148 26 3 232 377 551535313 551535168 1.220000e-18 104.0
17 TraesCS7D01G070400 chr7A 86.486 74 8 1 190 263 719491270 719491199 2.060000e-11 80.5
18 TraesCS7D01G070400 chr4A 85.413 1042 65 40 287 1303 648132815 648133794 0.000000e+00 1002.0
19 TraesCS7D01G070400 chr4A 84.908 762 60 25 585 1303 648260572 648261321 0.000000e+00 719.0
20 TraesCS7D01G070400 chr4A 90.782 499 37 5 1007 1498 648654189 648654685 0.000000e+00 658.0
21 TraesCS7D01G070400 chr4A 88.998 409 45 0 2089 2497 708656485 708656893 7.970000e-140 507.0
22 TraesCS7D01G070400 chr4A 88.824 340 38 0 962 1301 648337292 648337631 3.840000e-113 418.0
23 TraesCS7D01G070400 chr4A 93.023 129 9 0 1725 1853 648407125 648407253 3.280000e-44 189.0
24 TraesCS7D01G070400 chr4A 86.585 164 16 2 1368 1528 648582733 648582893 2.550000e-40 176.0
25 TraesCS7D01G070400 chr4A 87.261 157 15 3 1378 1530 648671985 648672140 9.180000e-40 174.0
26 TraesCS7D01G070400 chr4A 82.090 201 18 8 1368 1558 648337748 648337940 3.330000e-34 156.0
27 TraesCS7D01G070400 chr4A 90.179 112 10 1 450 560 648328159 648328270 7.200000e-31 145.0
28 TraesCS7D01G070400 chr4A 97.101 69 2 0 1785 1853 648290956 648291024 1.570000e-22 117.0
29 TraesCS7D01G070400 chr4A 87.879 99 12 0 450 548 648312213 648312311 1.570000e-22 117.0
30 TraesCS7D01G070400 chr4A 84.545 110 13 2 590 699 648335570 648335675 3.400000e-19 106.0
31 TraesCS7D01G070400 chrUn 85.370 540 45 16 765 1283 48835683 48836209 1.700000e-146 529.0
32 TraesCS7D01G070400 chrUn 90.244 123 11 1 1732 1853 48826879 48827001 2.570000e-35 159.0
33 TraesCS7D01G070400 chr7B 88.264 409 48 0 2089 2497 615784940 615785348 8.030000e-135 490.0
34 TraesCS7D01G070400 chr7B 92.381 105 8 0 1564 1668 13756196 13756092 1.550000e-32 150.0
35 TraesCS7D01G070400 chr7B 91.429 105 9 0 1564 1668 388787865 388787761 7.200000e-31 145.0
36 TraesCS7D01G070400 chr6D 87.531 409 50 1 2089 2497 435299447 435299040 2.910000e-129 472.0
37 TraesCS7D01G070400 chr6D 87.073 410 51 2 2089 2497 446813694 446813286 1.750000e-126 462.0
38 TraesCS7D01G070400 chr6D 77.564 156 31 4 202 357 455299107 455298956 9.510000e-15 91.6
39 TraesCS7D01G070400 chr6D 84.810 79 12 0 75 153 389915625 389915547 2.060000e-11 80.5
40 TraesCS7D01G070400 chr3B 87.286 409 52 0 2089 2497 99673826 99673418 3.760000e-128 468.0
41 TraesCS7D01G070400 chr2B 87.286 409 52 0 2089 2497 29220202 29220610 3.760000e-128 468.0
42 TraesCS7D01G070400 chr2B 86.640 247 29 4 1853 2098 120242590 120242347 1.140000e-68 270.0
43 TraesCS7D01G070400 chr2B 84.064 251 34 6 1851 2098 770313588 770313835 1.150000e-58 237.0
44 TraesCS7D01G070400 chr2B 92.308 104 8 0 1564 1667 458623246 458623143 5.560000e-32 148.0
45 TraesCS7D01G070400 chr2B 78.723 141 29 1 39 179 257528074 257527935 2.640000e-15 93.5
46 TraesCS7D01G070400 chr6B 87.042 409 53 0 2089 2497 131733364 131732956 1.750000e-126 462.0
47 TraesCS7D01G070400 chr6B 91.429 105 9 0 1564 1668 233991958 233992062 7.200000e-31 145.0
48 TraesCS7D01G070400 chr5B 86.797 409 54 0 2089 2497 560004018 560003610 8.140000e-125 457.0
49 TraesCS7D01G070400 chr1D 76.455 378 72 12 6 375 437838409 437838777 3.280000e-44 189.0
50 TraesCS7D01G070400 chr2D 94.231 104 6 0 1568 1671 382198253 382198150 2.570000e-35 159.0
51 TraesCS7D01G070400 chr2D 94.845 97 5 0 1571 1667 98693597 98693501 4.300000e-33 152.0
52 TraesCS7D01G070400 chr1A 89.474 114 8 1 1555 1668 351606750 351606859 9.310000e-30 141.0
53 TraesCS7D01G070400 chr5A 80.435 138 20 5 232 369 75367203 75367073 5.680000e-17 99.0
54 TraesCS7D01G070400 chr5A 75.909 220 34 9 224 439 574781715 574781511 7.350000e-16 95.3
55 TraesCS7D01G070400 chr4D 76.871 147 32 2 39 185 38143610 38143754 5.720000e-12 82.4
56 TraesCS7D01G070400 chr3A 77.165 127 26 3 232 358 576657600 576657477 1.240000e-08 71.3
57 TraesCS7D01G070400 chr4B 82.895 76 13 0 75 150 55637053 55637128 4.460000e-08 69.4


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 TraesCS7D01G070400 chr7D 41364350 41366846 2496 True 4612.000000 4612 100.00000 1 2497 1 chr7D.!!$R1 2496
1 TraesCS7D01G070400 chr7D 41258587 41260092 1505 False 2514.000000 2514 96.88700 1 1498 1 chr7D.!!$F1 1497
2 TraesCS7D01G070400 chr7D 41325313 41326917 1604 False 2488.000000 2488 94.61600 887 2497 1 chr7D.!!$F2 1610
3 TraesCS7D01G070400 chr7D 41273000 41275632 2632 False 435.500000 983 85.66925 4 1270 4 chr7D.!!$F5 1266
4 TraesCS7D01G070400 chr7D 41302604 41307128 4524 False 386.500000 399 85.21500 4 838 2 chr7D.!!$F6 834
5 TraesCS7D01G070400 chr7A 40693268 40695696 2428 False 680.500000 1048 84.67350 1 1303 2 chr7A.!!$F2 1302
6 TraesCS7D01G070400 chr4A 648132815 648133794 979 False 1002.000000 1002 85.41300 287 1303 1 chr4A.!!$F1 1016
7 TraesCS7D01G070400 chr4A 648260572 648261321 749 False 719.000000 719 84.90800 585 1303 1 chr4A.!!$F2 718
8 TraesCS7D01G070400 chr4A 648335570 648337940 2370 False 226.666667 418 85.15300 590 1558 3 chr4A.!!$F11 968
9 TraesCS7D01G070400 chrUn 48835683 48836209 526 False 529.000000 529 85.37000 765 1283 1 chrUn.!!$F2 518

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
369 1607 6.479972 TCCAACTACTTTATGGATCACGAT 57.52 37.5 0.0 0.0 38.3 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1541 9359 0.108186 TACATGCGCCAGGTTCTGAG 60.108 55.0 4.18 0.0 32.44 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
369 1607 6.479972 TCCAACTACTTTATGGATCACGAT 57.520 37.500 0.00 0.00 38.30 3.73
1541 9359 2.859165 TGGTGGGAATCACTCAGAAC 57.141 50.000 0.00 0.00 45.38 3.01
1582 9400 9.614792 ATGTAATTATTTTGTACTCCCTCTGTC 57.385 33.333 0.00 0.00 0.00 3.51
1583 9401 8.044908 TGTAATTATTTTGTACTCCCTCTGTCC 58.955 37.037 0.00 0.00 0.00 4.02
1601 9419 7.119846 CCTCTGTCCCAAAATAAGTGTCTTAAG 59.880 40.741 0.00 0.00 0.00 1.85
1602 9420 6.430000 TCTGTCCCAAAATAAGTGTCTTAAGC 59.570 38.462 0.00 0.00 0.00 3.09
1635 9453 9.944663 CAACTTTGTACTAGAGTTAATGCAAAA 57.055 29.630 0.00 0.00 32.69 2.44
1656 9474 9.860898 GCAAAATTGAGACACTTATTTTAGGAT 57.139 29.630 0.00 0.00 31.14 3.24
1664 9482 6.100424 AGACACTTATTTTAGGATGGAGGGAG 59.900 42.308 0.00 0.00 0.00 4.30
1756 9574 5.371526 AGGGACAATGCATATCAGTACTTG 58.628 41.667 0.00 0.00 0.00 3.16
1856 9674 8.491152 CAATTTAGATGCTTCAGGAGTATAACG 58.509 37.037 2.07 0.00 30.14 3.18
1869 9687 6.653740 CAGGAGTATAACGAAAAAGGGTTTCT 59.346 38.462 0.00 0.00 0.00 2.52
1883 9701 3.118371 AGGGTTTCTCCGCCTTGTATTAG 60.118 47.826 0.00 0.00 37.00 1.73
1890 9708 4.130118 CTCCGCCTTGTATTAGAAAGCAT 58.870 43.478 0.00 0.00 0.00 3.79
1899 9717 5.924356 TGTATTAGAAAGCATCCATCCGAA 58.076 37.500 0.00 0.00 0.00 4.30
1904 9722 3.826157 AGAAAGCATCCATCCGAAACAAA 59.174 39.130 0.00 0.00 0.00 2.83
1924 9742 5.605488 ACAAATAACGATAGGTACCTGGGAT 59.395 40.000 25.33 10.21 43.95 3.85
1932 9750 0.181350 GGTACCTGGGATGGAAGCAG 59.819 60.000 4.06 0.00 0.00 4.24
1950 9768 2.730715 GCAGCACAGTCACGTTCAAAAA 60.731 45.455 0.00 0.00 0.00 1.94
2013 9832 1.782023 CGGATCGACAAAAACGCGAAG 60.782 52.381 15.93 0.00 37.60 3.79
2061 9880 4.900154 CTCACCAAGCTCCGAGAC 57.100 61.111 0.00 0.00 0.00 3.36
2209 10028 3.530910 CTCGCCACCAAACCGACCT 62.531 63.158 0.00 0.00 0.00 3.85
2242 10061 1.508632 ACACGGTCATGAAGTTTCCG 58.491 50.000 17.44 17.44 45.53 4.30
2352 10171 2.997897 GCTCCACCTCCACCGTCT 60.998 66.667 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 1388 9.590088 CGTACAAAGTATTAAAAGTTGGAACTC 57.410 33.333 0.00 0.00 38.57 3.01
369 1607 2.046023 CCTGACTGCCCGATTGCA 60.046 61.111 0.00 0.00 39.37 4.08
662 6945 1.411493 GGCGTCGATGGAGTTCGTTC 61.411 60.000 6.79 0.00 40.03 3.95
663 6946 1.445582 GGCGTCGATGGAGTTCGTT 60.446 57.895 6.79 0.00 40.03 3.85
664 6947 2.181021 GGCGTCGATGGAGTTCGT 59.819 61.111 6.79 0.00 40.03 3.85
665 6948 2.949678 CGGCGTCGATGGAGTTCG 60.950 66.667 1.44 0.00 40.46 3.95
1541 9359 0.108186 TACATGCGCCAGGTTCTGAG 60.108 55.000 4.18 0.00 32.44 3.35
1582 9400 8.336801 ACTAAGCTTAAGACACTTATTTTGGG 57.663 34.615 6.67 0.00 0.00 4.12
1628 9446 9.643693 CCTAAAATAAGTGTCTCAATTTTGCAT 57.356 29.630 0.00 0.00 34.37 3.96
1630 9448 9.860898 ATCCTAAAATAAGTGTCTCAATTTTGC 57.139 29.630 0.00 0.00 34.37 3.68
1635 9453 7.995488 CCTCCATCCTAAAATAAGTGTCTCAAT 59.005 37.037 0.00 0.00 0.00 2.57
1640 9458 6.126739 ACTCCCTCCATCCTAAAATAAGTGTC 60.127 42.308 0.00 0.00 0.00 3.67
1652 9470 2.319438 AGAAAGGTACTCCCTCCATCCT 59.681 50.000 0.00 0.00 45.47 3.24
1656 9474 3.323775 ACAAAGAAAGGTACTCCCTCCA 58.676 45.455 0.00 0.00 45.47 3.86
1664 9482 7.327032 CGTTAGGTACACTACAAAGAAAGGTAC 59.673 40.741 0.00 0.00 0.00 3.34
1672 9490 4.083324 TCGGACGTTAGGTACACTACAAAG 60.083 45.833 0.00 0.00 0.00 2.77
1673 9491 3.818210 TCGGACGTTAGGTACACTACAAA 59.182 43.478 0.00 0.00 0.00 2.83
1674 9492 3.407698 TCGGACGTTAGGTACACTACAA 58.592 45.455 0.00 0.00 0.00 2.41
1675 9493 3.052455 TCGGACGTTAGGTACACTACA 57.948 47.619 0.00 0.00 0.00 2.74
1856 9674 1.617322 AGGCGGAGAAACCCTTTTTC 58.383 50.000 0.00 0.00 34.64 2.29
1869 9687 3.620427 TGCTTTCTAATACAAGGCGGA 57.380 42.857 0.00 0.00 0.00 5.54
1883 9701 3.848272 TTGTTTCGGATGGATGCTTTC 57.152 42.857 0.00 0.00 0.00 2.62
1890 9708 5.756347 CCTATCGTTATTTGTTTCGGATGGA 59.244 40.000 0.00 0.00 0.00 3.41
1899 9717 5.426185 TCCCAGGTACCTATCGTTATTTGTT 59.574 40.000 15.80 0.00 0.00 2.83
1904 9722 4.094476 CCATCCCAGGTACCTATCGTTAT 58.906 47.826 15.80 0.00 0.00 1.89
1924 9742 1.595109 CGTGACTGTGCTGCTTCCA 60.595 57.895 0.00 0.00 0.00 3.53
2061 9880 2.280186 GATACCGGCGCTTGGGAG 60.280 66.667 20.58 1.49 0.00 4.30
2126 9945 3.340789 GGCTTGACCAACACCGAC 58.659 61.111 0.00 0.00 38.86 4.79
2151 9970 1.596496 AGGTTGGGATCGGGAGAAAT 58.404 50.000 0.00 0.00 45.37 2.17
2242 10061 4.251760 CTGTGGTGAGACAGCGTC 57.748 61.111 0.00 1.15 37.16 5.19


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

AutoCloner maintained by Alex Coulton.