Multiple sequence alignment - TraesCS7A01G008200

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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 TraesCS7A01G008200 chr7A 100.000 2603 0 0 1 2603 3635737 3633135 0.000000e+00 4807
1 TraesCS7A01G008200 chr7A 93.791 612 24 9 974 1583 2002640 2002041 0.000000e+00 907
2 TraesCS7A01G008200 chr7A 97.740 177 4 0 694 870 610448569 610448745 3.250000e-79 305
3 TraesCS7A01G008200 chr7A 87.678 211 25 1 2143 2353 3211518 3211309 7.200000e-61 244
4 TraesCS7A01G008200 chr7A 87.204 211 23 3 2143 2353 2000247 2000041 1.200000e-58 237
5 TraesCS7A01G008200 chr7A 87.500 96 9 3 1626 1721 21000736 21000644 9.850000e-20 108
6 TraesCS7A01G008200 chr7D 95.051 687 33 1 1 686 2360598 2359912 0.000000e+00 1079
7 TraesCS7A01G008200 chr7D 91.242 628 45 3 893 1517 2359913 2359293 0.000000e+00 846
8 TraesCS7A01G008200 chr7D 88.889 216 23 1 2143 2358 3903282 3903496 5.520000e-67 265
9 TraesCS7A01G008200 chr7D 85.526 228 25 7 1901 2123 396452204 396452428 5.600000e-57 231
10 TraesCS7A01G008200 chr7D 87.245 196 21 4 1584 1779 636913786 636913977 1.210000e-53 220
11 TraesCS7A01G008200 chr7D 87.097 186 21 2 2183 2366 2568865 2568681 9.440000e-50 207
12 TraesCS7A01G008200 chr4A 90.043 693 64 5 1 690 740924550 740925240 0.000000e+00 893
13 TraesCS7A01G008200 chr4A 88.809 697 46 13 871 1546 740926665 740927350 0.000000e+00 826
14 TraesCS7A01G008200 chr4A 90.053 563 44 5 985 1546 740268864 740269415 0.000000e+00 719
15 TraesCS7A01G008200 chr4A 89.876 563 42 6 985 1546 740303017 740303565 0.000000e+00 710
16 TraesCS7A01G008200 chr4A 89.698 563 46 5 985 1546 740346269 740346820 0.000000e+00 708
17 TraesCS7A01G008200 chr4A 89.591 538 46 4 985 1518 741588189 741588720 0.000000e+00 675
18 TraesCS7A01G008200 chr4A 89.259 540 52 2 988 1527 740022760 740022227 0.000000e+00 671
19 TraesCS7A01G008200 chr4A 87.831 567 53 9 988 1545 741491248 741490689 0.000000e+00 651
20 TraesCS7A01G008200 chr4A 86.957 207 26 1 2143 2349 740929353 740929558 5.600000e-57 231
21 TraesCS7A01G008200 chr4A 87.500 96 9 2 1626 1721 669455990 669456082 9.850000e-20 108
22 TraesCS7A01G008200 chr1D 82.051 507 64 13 1 504 247538300 247537818 8.670000e-110 407
23 TraesCS7A01G008200 chr1D 81.818 440 71 7 1 436 204803791 204803357 6.850000e-96 361
24 TraesCS7A01G008200 chr1D 79.592 441 65 15 1 436 204800647 204800227 2.530000e-75 292
25 TraesCS7A01G008200 chr1D 80.688 378 67 6 1 374 217103945 217104320 3.280000e-74 289
26 TraesCS7A01G008200 chr2A 96.791 187 5 1 695 881 778800746 778800561 6.990000e-81 311
27 TraesCS7A01G008200 chr2A 75.381 394 85 11 38 429 445713339 445712956 2.060000e-41 180
28 TraesCS7A01G008200 chr1A 98.286 175 3 0 696 870 572357491 572357665 9.050000e-80 307
29 TraesCS7A01G008200 chr1A 97.175 177 5 0 697 873 508278235 508278059 1.510000e-77 300
30 TraesCS7A01G008200 chr1A 97.175 177 5 0 697 873 508305561 508305385 1.510000e-77 300
31 TraesCS7A01G008200 chr1A 97.175 177 5 0 697 873 508310445 508310269 1.510000e-77 300
32 TraesCS7A01G008200 chr1A 97.175 177 5 0 697 873 508337159 508336983 1.510000e-77 300
33 TraesCS7A01G008200 chr1A 82.258 248 34 9 1901 2144 520561475 520561234 3.400000e-49 206
34 TraesCS7A01G008200 chr1A 85.950 121 14 2 2257 2375 459273228 459273347 2.720000e-25 126
35 TraesCS7A01G008200 chr2B 94.737 190 10 0 690 879 634243147 634243336 1.960000e-76 296
36 TraesCS7A01G008200 chr5A 96.111 180 7 0 695 874 547238945 547238766 7.040000e-76 294
37 TraesCS7A01G008200 chr6D 85.294 272 40 0 1 272 327634122 327633851 5.480000e-72 281
38 TraesCS7A01G008200 chr6D 82.996 247 29 10 1904 2144 340467965 340467726 7.300000e-51 211
39 TraesCS7A01G008200 chr6D 86.179 123 13 3 2256 2375 392273231 392273110 2.100000e-26 130
40 TraesCS7A01G008200 chr6A 85.463 227 28 5 1901 2123 514705116 514704891 5.600000e-57 231
41 TraesCS7A01G008200 chr6A 85.366 123 14 3 2256 2375 538097836 538097715 9.780000e-25 124
42 TraesCS7A01G008200 chr2D 85.202 223 31 2 1903 2123 566250507 566250729 7.250000e-56 228
43 TraesCS7A01G008200 chr4D 84.545 220 32 2 1906 2123 255811228 255811447 1.570000e-52 217
44 TraesCS7A01G008200 chr7B 84.141 227 31 5 1901 2123 313691030 313690805 5.640000e-52 215
45 TraesCS7A01G008200 chr7B 84.305 223 30 5 1904 2123 40342898 40342678 2.030000e-51 213
46 TraesCS7A01G008200 chr7B 82.353 170 16 7 1615 1773 648467787 648467953 4.520000e-28 135
47 TraesCS7A01G008200 chr7B 86.441 118 13 2 2260 2375 437669566 437669682 2.720000e-25 126
48 TraesCS7A01G008200 chr3B 84.234 222 33 2 1904 2123 682655380 682655601 5.640000e-52 215
49 TraesCS7A01G008200 chr3B 83.085 201 18 9 1584 1773 41642069 41641874 4.460000e-38 169
50 TraesCS7A01G008200 chr3B 84.756 164 18 6 1584 1747 747567273 747567429 9.640000e-35 158
51 TraesCS7A01G008200 chr3B 82.955 176 26 2 1598 1773 800981783 800981954 3.470000e-34 156
52 TraesCS7A01G008200 chr3B 76.757 185 37 4 1595 1777 144220209 144220029 5.930000e-17 99
53 TraesCS7A01G008200 chr6B 76.334 431 73 18 1 431 491619451 491619050 1.220000e-48 204
54 TraesCS7A01G008200 chr1B 83.163 196 29 4 1584 1779 595784410 595784219 2.660000e-40 176
55 TraesCS7A01G008200 chr1B 83.085 201 19 5 1584 1773 453196654 453196458 4.460000e-38 169
56 TraesCS7A01G008200 chr1B 82.587 201 20 5 1584 1773 78820134 78819938 2.070000e-36 163
57 TraesCS7A01G008200 chrUn 87.500 96 9 2 1626 1721 296652201 296652109 9.850000e-20 108


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 TraesCS7A01G008200 chr7A 3633135 3635737 2602 True 4807.0 4807 100.0000 1 2603 1 chr7A.!!$R2 2602
1 TraesCS7A01G008200 chr7A 2000041 2002640 2599 True 572.0 907 90.4975 974 2353 2 chr7A.!!$R4 1379
2 TraesCS7A01G008200 chr7D 2359293 2360598 1305 True 962.5 1079 93.1465 1 1517 2 chr7D.!!$R2 1516
3 TraesCS7A01G008200 chr4A 740268864 740269415 551 False 719.0 719 90.0530 985 1546 1 chr4A.!!$F2 561
4 TraesCS7A01G008200 chr4A 740303017 740303565 548 False 710.0 710 89.8760 985 1546 1 chr4A.!!$F3 561
5 TraesCS7A01G008200 chr4A 740346269 740346820 551 False 708.0 708 89.6980 985 1546 1 chr4A.!!$F4 561
6 TraesCS7A01G008200 chr4A 741588189 741588720 531 False 675.0 675 89.5910 985 1518 1 chr4A.!!$F5 533
7 TraesCS7A01G008200 chr4A 740022227 740022760 533 True 671.0 671 89.2590 988 1527 1 chr4A.!!$R1 539
8 TraesCS7A01G008200 chr4A 741490689 741491248 559 True 651.0 651 87.8310 988 1545 1 chr4A.!!$R2 557
9 TraesCS7A01G008200 chr4A 740924550 740929558 5008 False 650.0 893 88.6030 1 2349 3 chr4A.!!$F6 2348
10 TraesCS7A01G008200 chr1D 204800227 204803791 3564 True 326.5 361 80.7050 1 436 2 chr1D.!!$R2 435


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
800 1313 0.098025 GTGTGTGTTGACGTGGGTTG 59.902 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2455 8758 0.037605 AATCTTGTGTCCGACCGGTC 60.038 55.0 25.28 25.28 36.47 4.79 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)



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AutoCloner maintained by Alex Coulton.