Multiple sequence alignment - TraesCS6B01G001800

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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 TraesCS6B01G001800 chr6B 100.000 1728 0 0 564 2291 1181829 1183556 0.000000e+00 3192
1 TraesCS6B01G001800 chr6B 90.000 350 29 4 921 1266 1654329 1654676 4.490000e-122 448
2 TraesCS6B01G001800 chr6B 100.000 210 0 0 1 210 1181266 1181475 2.760000e-104 388
3 TraesCS6B01G001800 chr6B 93.023 172 11 1 12 182 65428221 65428050 1.360000e-62 250
4 TraesCS6B01G001800 chr6B 81.333 225 26 10 1307 1517 704153263 704153485 3.910000e-38 169
5 TraesCS6B01G001800 chr6B 92.373 118 6 2 619 734 1654118 1654234 5.060000e-37 165
6 TraesCS6B01G001800 chr6B 81.560 141 17 2 967 1098 409717027 409716887 8.650000e-20 108
7 TraesCS6B01G001800 chr5B 96.628 1631 48 2 661 2291 517433230 517431607 0.000000e+00 2700
8 TraesCS6B01G001800 chr5B 91.163 215 11 2 1 207 517433837 517433623 3.730000e-73 285
9 TraesCS6B01G001800 chr3B 96.264 1017 27 2 1276 2291 785216173 785215167 0.000000e+00 1657
10 TraesCS6B01G001800 chr3B 95.202 667 32 0 612 1278 785216975 785216309 0.000000e+00 1055
11 TraesCS6B01G001800 chr3B 89.474 209 12 3 12 210 41469936 41469728 2.920000e-64 255
12 TraesCS6B01G001800 chr4B 95.972 1018 36 4 1276 2291 215240546 215239532 0.000000e+00 1648
13 TraesCS6B01G001800 chr4B 94.104 424 24 1 855 1278 215241104 215240682 0.000000e+00 643
14 TraesCS6B01G001800 chr4B 91.687 409 30 4 1884 2291 203234576 203234981 4.270000e-157 564
15 TraesCS6B01G001800 chr4B 85.082 429 32 10 855 1278 203233961 203234362 2.120000e-110 409
16 TraesCS6B01G001800 chr4B 94.231 208 10 2 653 860 215241270 215241065 1.320000e-82 316
17 TraesCS6B01G001800 chr4B 85.906 298 24 9 564 860 203233720 203234000 3.700000e-78 302
18 TraesCS6B01G001800 chr4B 92.994 157 11 0 35 191 215241978 215241822 1.770000e-56 230
19 TraesCS6B01G001800 chr5A 95.674 1017 39 2 1276 2291 450327513 450326501 0.000000e+00 1629
20 TraesCS6B01G001800 chr5A 95.047 424 15 2 855 1278 450328066 450327649 0.000000e+00 662
21 TraesCS6B01G001800 chr5A 94.615 260 9 5 601 860 450328281 450328027 4.590000e-107 398
22 TraesCS6B01G001800 chr5A 88.584 219 16 3 1 210 450328884 450328666 8.120000e-65 257
23 TraesCS6B01G001800 chr7A 95.580 1018 39 6 1276 2291 287666572 287665559 0.000000e+00 1626
24 TraesCS6B01G001800 chr7A 92.604 649 38 5 626 1274 287669004 287668366 0.000000e+00 924
25 TraesCS6B01G001800 chr7A 87.783 221 15 4 1 210 287669624 287669405 4.890000e-62 248
26 TraesCS6B01G001800 chr7A 86.977 215 12 4 12 210 125842407 125842193 6.370000e-56 228
27 TraesCS6B01G001800 chr6A 87.912 546 50 9 1313 1854 608790932 608791465 1.490000e-176 628
28 TraesCS6B01G001800 chr6A 93.939 165 6 4 615 779 32065027 32065187 1.760000e-61 246
29 TraesCS6B01G001800 chr6A 90.476 126 11 1 1737 1861 608677943 608678068 5.060000e-37 165
30 TraesCS6B01G001800 chr1B 90.884 362 28 3 921 1278 44998811 44998451 4.430000e-132 481
31 TraesCS6B01G001800 chr1B 91.935 186 13 2 713 896 81015700 81015515 2.260000e-65 259
32 TraesCS6B01G001800 chr1B 91.195 159 13 1 1999 2157 646282634 646282791 4.960000e-52 215
33 TraesCS6B01G001800 chrUn 90.608 362 29 3 921 1278 219180911 219181271 2.060000e-130 475
34 TraesCS6B01G001800 chr6D 86.068 323 37 5 1542 1861 461817682 461817999 7.840000e-90 340
35 TraesCS6B01G001800 chr6D 89.637 193 17 3 1279 1469 462023978 462024169 2.270000e-60 243
36 TraesCS6B01G001800 chr6D 82.239 259 29 12 1276 1519 461817360 461817616 8.290000e-50 207
37 TraesCS6B01G001800 chr2A 88.479 217 18 3 1 210 774250549 774250333 2.920000e-64 255
38 TraesCS6B01G001800 chr2A 91.463 164 13 1 2000 2163 343551245 343551407 8.240000e-55 224
39 TraesCS6B01G001800 chr3A 90.426 188 9 5 32 210 688811484 688811671 2.940000e-59 239
40 TraesCS6B01G001800 chr3A 89.865 148 8 7 586 730 688812165 688812308 1.400000e-42 183
41 TraesCS6B01G001800 chr3A 80.233 258 38 10 1386 1640 699315583 699315830 5.030000e-42 182
42 TraesCS6B01G001800 chr4A 90.854 164 14 1 2000 2163 467939022 467938860 3.830000e-53 219
43 TraesCS6B01G001800 chr2D 92.742 124 8 1 1884 2006 19879556 19879679 6.500000e-41 178
44 TraesCS6B01G001800 chr3D 78.378 259 41 11 1386 1640 564529013 564529260 1.100000e-33 154
45 TraesCS6B01G001800 chr7B 84.146 164 13 7 619 782 625592960 625592810 1.830000e-31 147


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 TraesCS6B01G001800 chr6B 1181266 1183556 2290 False 1790.000000 3192 100.000000 1 2291 2 chr6B.!!$F2 2290
1 TraesCS6B01G001800 chr6B 1654118 1654676 558 False 306.500000 448 91.186500 619 1266 2 chr6B.!!$F3 647
2 TraesCS6B01G001800 chr5B 517431607 517433837 2230 True 1492.500000 2700 93.895500 1 2291 2 chr5B.!!$R1 2290
3 TraesCS6B01G001800 chr3B 785215167 785216975 1808 True 1356.000000 1657 95.733000 612 2291 2 chr3B.!!$R2 1679
4 TraesCS6B01G001800 chr4B 215239532 215241978 2446 True 709.250000 1648 94.325250 35 2291 4 chr4B.!!$R1 2256
5 TraesCS6B01G001800 chr4B 203233720 203234981 1261 False 425.000000 564 87.558333 564 2291 3 chr4B.!!$F1 1727
6 TraesCS6B01G001800 chr5A 450326501 450328884 2383 True 736.500000 1629 93.480000 1 2291 4 chr5A.!!$R1 2290
7 TraesCS6B01G001800 chr7A 287665559 287669624 4065 True 932.666667 1626 91.989000 1 2291 3 chr7A.!!$R2 2290
8 TraesCS6B01G001800 chr6A 608790932 608791465 533 False 628.000000 628 87.912000 1313 1854 1 chr6A.!!$F3 541
9 TraesCS6B01G001800 chr6D 461817360 461817999 639 False 273.500000 340 84.153500 1276 1861 2 chr6D.!!$F2 585
10 TraesCS6B01G001800 chr3A 688811484 688812308 824 False 211.000000 239 90.145500 32 730 2 chr3A.!!$F2 698

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
819 1222 0.397675 AGGAGATCGAGGATGCCACA 60.398 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 4458 4.158394 ACAATCAGCAAATACATGTGACCC 59.842 41.667 9.11 0.0 0.0 4.46 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
99 108 2.032528 CACGCACCCACTCACCAT 59.967 61.111 0.00 0.00 0.00 3.55
164 173 2.507992 CTCACCTGCTCGCCGAAG 60.508 66.667 0.00 0.00 0.00 3.79
165 174 3.288308 CTCACCTGCTCGCCGAAGT 62.288 63.158 0.00 0.00 0.00 3.01
582 729 1.958205 CAGATCCAATCGCCCTCGC 60.958 63.158 0.00 0.00 35.26 5.03
659 1059 4.150454 CCCCTCTCTCCTCCGCCT 62.150 72.222 0.00 0.00 0.00 5.52
819 1222 0.397675 AGGAGATCGAGGATGCCACA 60.398 55.000 0.00 0.00 0.00 4.17
853 1256 2.071540 CTCTTTCTCATTGCGCTGTCA 58.928 47.619 9.73 0.00 0.00 3.58
871 1310 0.512952 CACGCGTTTTCCTTCTCCTG 59.487 55.000 10.22 0.00 0.00 3.86
881 1320 3.386768 TCCTTCTCCTGTTTCTCGTTG 57.613 47.619 0.00 0.00 0.00 4.10
886 1325 0.531974 TCCTGTTTCTCGTTGCGCTT 60.532 50.000 9.73 0.00 0.00 4.68
914 1401 2.756760 TCAAGTAGAATAACCCGACGCT 59.243 45.455 0.00 0.00 0.00 5.07
915 1402 2.858344 CAAGTAGAATAACCCGACGCTG 59.142 50.000 0.00 0.00 0.00 5.18
916 1403 2.372264 AGTAGAATAACCCGACGCTGA 58.628 47.619 0.00 0.00 0.00 4.26
917 1404 2.098770 AGTAGAATAACCCGACGCTGAC 59.901 50.000 0.00 0.00 0.00 3.51
919 1406 1.749609 GAATAACCCGACGCTGACGC 61.750 60.000 0.00 0.00 45.53 5.19
960 1453 0.967380 GTGGTTATGCTTGCAGGCCT 60.967 55.000 19.11 11.31 0.00 5.19
1266 1768 2.225791 CTGACGAGTTCGGATGCCCA 62.226 60.000 6.48 0.00 44.95 5.36
1346 3645 7.415206 GCCGTATCATTCAACCAGAAGTTTAAT 60.415 37.037 0.00 0.00 40.15 1.40
1404 3704 6.166984 TCAATGTTGGAAATAAACCTTGCA 57.833 33.333 0.00 0.00 34.84 4.08
1409 3709 3.766545 TGGAAATAAACCTTGCAGCTCT 58.233 40.909 0.00 0.00 0.00 4.09
1444 3745 4.163458 TCTGTAGGTTCAGTTTCAGGTGTT 59.837 41.667 0.00 0.00 36.85 3.32
1464 3765 6.756074 GGTGTTGTTTTCATCAGTTTCATCAA 59.244 34.615 0.00 0.00 31.27 2.57
1469 3779 7.499292 TGTTTTCATCAGTTTCATCAATTGGT 58.501 30.769 5.42 0.00 0.00 3.67
1488 3798 9.226606 CAATTGGTGGATTAGTTAGTTAGAACA 57.773 33.333 0.00 0.00 0.00 3.18
1551 3904 0.170561 GCCGGATATCGCATAGTCGT 59.829 55.000 5.05 0.00 37.59 4.34
1575 3928 2.106338 CCACAAGCCCCATTTCCTTTTT 59.894 45.455 0.00 0.00 0.00 1.94
1576 3929 3.326297 CCACAAGCCCCATTTCCTTTTTA 59.674 43.478 0.00 0.00 0.00 1.52
1734 4090 5.560953 GCCAATTGATATGCCGAAGACTTAC 60.561 44.000 7.12 0.00 0.00 2.34
1751 4107 6.850555 AGACTTACTCATTAGTCAACGGTAC 58.149 40.000 0.00 0.00 42.51 3.34
2041 4398 8.691661 ACTGTTTTGACATTAAGTGGATTACT 57.308 30.769 0.00 0.00 42.89 2.24
2101 4458 7.653713 TGCTTTAAACTAGTCTCACTTTCTCAG 59.346 37.037 0.00 0.00 0.00 3.35
2108 4465 2.365617 GTCTCACTTTCTCAGGGTCACA 59.634 50.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 75 4.682334 TGGGGTCTGCGGGTACGA 62.682 66.667 0.00 0.00 44.60 3.43
99 108 2.592287 GCGTGGGGTTTGGAACGA 60.592 61.111 0.00 0.00 38.27 3.85
182 202 1.700042 GCGATCTTGGTGGAGGGGAT 61.700 60.000 0.00 0.00 0.00 3.85
659 1059 2.203938 GTGGAGGGAGTGGGGTGA 60.204 66.667 0.00 0.00 0.00 4.02
819 1222 4.101119 TGAGAAAGAGGAGAAGGAAAACGT 59.899 41.667 0.00 0.00 0.00 3.99
853 1256 0.106149 ACAGGAGAAGGAAAACGCGT 59.894 50.000 5.58 5.58 0.00 6.01
871 1310 1.154654 CGGAAGCGCAACGAGAAAC 60.155 57.895 11.47 0.00 0.00 2.78
886 1325 3.514645 GGTTATTCTACTTGAACGCGGA 58.485 45.455 12.47 0.00 37.52 5.54
1266 1768 1.133792 CCAACTGAAGGTGACCTTGGT 60.134 52.381 23.60 16.68 44.82 3.67
1346 3645 5.730296 TTTGTTTCAAAAGGTTCACAGGA 57.270 34.783 0.00 0.00 0.00 3.86
1444 3745 7.438757 CACCAATTGATGAAACTGATGAAAACA 59.561 33.333 7.12 0.00 0.00 2.83
1488 3798 3.970640 AGCCTGCTAGCTAAACCTTCTAT 59.029 43.478 17.23 0.00 42.70 1.98
1734 4090 7.878477 TTTACTTGTACCGTTGACTAATGAG 57.122 36.000 0.00 0.00 0.00 2.90
1751 4107 5.973565 CAGTGGCTTCAGTTTCTTTTACTTG 59.026 40.000 0.00 0.00 0.00 3.16
1906 4263 4.395959 AGCAGTCAATATTTGGGCATTG 57.604 40.909 0.00 0.00 34.17 2.82
2041 4398 8.723311 CACCGAAATAGTACCAAACTGATTTAA 58.277 33.333 0.00 0.00 39.39 1.52
2101 4458 4.158394 ACAATCAGCAAATACATGTGACCC 59.842 41.667 9.11 0.00 0.00 4.46
2108 4465 9.807649 GAAAATCCTTACAATCAGCAAATACAT 57.192 29.630 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.