Multiple sequence alignment - TraesCS4A01G345000

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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 TraesCS4A01G345000 chr4A 100.000 2550 0 0 1 2550 624732184 624734733 0.000000e+00 4710
1 TraesCS4A01G345000 chr4A 100.000 545 0 0 2640 3184 624734823 624735367 0.000000e+00 1007
2 TraesCS4A01G345000 chr4A 88.961 770 79 4 1346 2113 624747298 624748063 0.000000e+00 946
3 TraesCS4A01G345000 chr4A 81.656 1063 156 14 953 1986 24919618 24918566 0.000000e+00 846
4 TraesCS4A01G345000 chr4A 79.507 1298 182 48 722 1986 24935208 24936454 0.000000e+00 846
5 TraesCS4A01G345000 chr4A 85.607 535 38 21 722 1241 624746491 624747001 2.810000e-145 525
6 TraesCS4A01G345000 chr4A 88.050 159 19 0 365 523 26325396 26325238 4.190000e-44 189
7 TraesCS4A01G345000 chr1A 98.219 2246 28 7 315 2550 569378110 569375867 0.000000e+00 3916
8 TraesCS4A01G345000 chr1A 89.831 767 72 4 1349 2113 569355566 569354804 0.000000e+00 979
9 TraesCS4A01G345000 chr1A 98.438 512 8 0 2673 3184 569375733 569375222 0.000000e+00 902
10 TraesCS4A01G345000 chr1A 95.238 315 9 2 1 310 569378584 569378271 7.930000e-136 494
11 TraesCS4A01G345000 chr5D 90.668 2261 147 31 315 2548 544798334 544800557 0.000000e+00 2948
12 TraesCS4A01G345000 chr5D 89.233 808 75 8 1310 2113 544817245 544818044 0.000000e+00 1000
13 TraesCS4A01G345000 chr5D 87.194 531 38 17 722 1241 544816470 544816981 7.660000e-161 577
14 TraesCS4A01G345000 chr5D 90.120 415 37 4 2667 3080 544800843 544801254 1.300000e-148 536
15 TraesCS4A01G345000 chr5D 79.830 471 89 6 2693 3159 6822004 6822472 3.930000e-89 339
16 TraesCS4A01G345000 chr5B 88.355 1958 142 46 315 2247 687222974 687224870 0.000000e+00 2274
17 TraesCS4A01G345000 chr5B 89.391 1725 115 23 839 2548 687212504 687214175 0.000000e+00 2109
18 TraesCS4A01G345000 chr5B 87.995 808 78 12 1310 2113 687326390 687327182 0.000000e+00 937
19 TraesCS4A01G345000 chr5B 88.554 498 51 3 2680 3176 687233034 687233526 1.630000e-167 599
20 TraesCS4A01G345000 chr5B 86.549 565 32 20 721 1262 687325609 687326152 1.650000e-162 582
21 TraesCS4A01G345000 chr5B 87.406 532 31 16 722 1239 687259261 687259770 2.130000e-161 579
22 TraesCS4A01G345000 chr5B 85.102 490 34 16 781 1252 687342057 687342525 6.220000e-127 464
23 TraesCS4A01G345000 chr5B 86.364 308 28 6 1 301 687211629 687211929 1.100000e-84 324
24 TraesCS4A01G345000 chr5B 86.513 304 27 6 3 299 687222507 687222803 3.960000e-84 322
25 TraesCS4A01G345000 chr5B 89.189 259 23 3 315 572 687212092 687212346 5.130000e-83 318
26 TraesCS4A01G345000 chr5B 89.655 174 8 5 2358 2530 687232767 687232931 2.490000e-51 213
27 TraesCS4A01G345000 chr4B 83.834 1466 165 45 722 2149 547309113 547310544 0.000000e+00 1328
28 TraesCS4A01G345000 chr4B 76.051 547 73 40 724 1254 550488306 550487802 6.870000e-57 231
29 TraesCS4A01G345000 chr4B 89.726 146 15 0 378 523 547308350 547308495 1.510000e-43 187
30 TraesCS4A01G345000 chr4D 83.734 1457 153 43 722 2135 441255523 441256938 0.000000e+00 1301
31 TraesCS4A01G345000 chr4D 80.108 1297 174 50 724 1986 442223382 442222136 0.000000e+00 889
32 TraesCS4A01G345000 chrUn 100.000 390 0 0 1023 1412 480040813 480040424 0.000000e+00 721
33 TraesCS4A01G345000 chr5A 77.294 436 93 5 2727 3158 3133118 3132685 5.270000e-63 252
34 TraesCS4A01G345000 chr7B 81.230 309 46 8 1 301 145938480 145938176 4.100000e-59 239
35 TraesCS4A01G345000 chr2D 77.097 310 57 10 1 301 110631174 110630870 1.960000e-37 167
36 TraesCS4A01G345000 chr2A 76.699 309 61 8 1 301 106655702 106655397 9.140000e-36 161
37 TraesCS4A01G345000 chr2A 84.000 125 16 4 1 124 105679084 105679205 2.010000e-22 117
38 TraesCS4A01G345000 chr2B 77.917 240 50 3 1 239 159603225 159602988 2.560000e-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 TraesCS4A01G345000 chr4A 624732184 624735367 3183 False 2858.500000 4710 100.000000 1 3184 2 chr4A.!!$F2 3183
1 TraesCS4A01G345000 chr4A 24918566 24919618 1052 True 846.000000 846 81.656000 953 1986 1 chr4A.!!$R1 1033
2 TraesCS4A01G345000 chr4A 24935208 24936454 1246 False 846.000000 846 79.507000 722 1986 1 chr4A.!!$F1 1264
3 TraesCS4A01G345000 chr4A 624746491 624748063 1572 False 735.500000 946 87.284000 722 2113 2 chr4A.!!$F3 1391
4 TraesCS4A01G345000 chr1A 569375222 569378584 3362 True 1770.666667 3916 97.298333 1 3184 3 chr1A.!!$R2 3183
5 TraesCS4A01G345000 chr1A 569354804 569355566 762 True 979.000000 979 89.831000 1349 2113 1 chr1A.!!$R1 764
6 TraesCS4A01G345000 chr5D 544798334 544801254 2920 False 1742.000000 2948 90.394000 315 3080 2 chr5D.!!$F2 2765
7 TraesCS4A01G345000 chr5D 544816470 544818044 1574 False 788.500000 1000 88.213500 722 2113 2 chr5D.!!$F3 1391
8 TraesCS4A01G345000 chr5B 687222507 687224870 2363 False 1298.000000 2274 87.434000 3 2247 2 chr5B.!!$F4 2244
9 TraesCS4A01G345000 chr5B 687211629 687214175 2546 False 917.000000 2109 88.314667 1 2548 3 chr5B.!!$F3 2547
10 TraesCS4A01G345000 chr5B 687325609 687327182 1573 False 759.500000 937 87.272000 721 2113 2 chr5B.!!$F6 1392
11 TraesCS4A01G345000 chr5B 687259261 687259770 509 False 579.000000 579 87.406000 722 1239 1 chr5B.!!$F1 517
12 TraesCS4A01G345000 chr5B 687232767 687233526 759 False 406.000000 599 89.104500 2358 3176 2 chr5B.!!$F5 818
13 TraesCS4A01G345000 chr4B 547308350 547310544 2194 False 757.500000 1328 86.780000 378 2149 2 chr4B.!!$F1 1771
14 TraesCS4A01G345000 chr4B 550487802 550488306 504 True 231.000000 231 76.051000 724 1254 1 chr4B.!!$R1 530
15 TraesCS4A01G345000 chr4D 441255523 441256938 1415 False 1301.000000 1301 83.734000 722 2135 1 chr4D.!!$F1 1413
16 TraesCS4A01G345000 chr4D 442222136 442223382 1246 True 889.000000 889 80.108000 724 1986 1 chr4D.!!$R1 1262

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
272 280 0.386838 CCCAACCTACGGGTCGTATC 59.613 60.0 0.55 0.0 46.67 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 3205 4.145365 TGTGAAACGAGGGAGAGAAAAA 57.855 40.909 0.0 0.0 42.39 1.94 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
125 128 5.400066 TCTTGTGAGTTCATACGGATTCA 57.600 39.130 0.00 0.0 0.00 2.57
214 217 1.749063 GGATTTGGGGTTCCGTGATTC 59.251 52.381 0.00 0.0 35.24 2.52
272 280 0.386838 CCCAACCTACGGGTCGTATC 59.613 60.000 0.55 0.0 46.67 2.24
279 288 1.336125 CTACGGGTCGTATCCAACCTC 59.664 57.143 0.55 0.0 41.53 3.85
310 319 7.169476 GGTTAAAGATAGTTATCACGGCTTCTC 59.831 40.741 2.29 0.0 35.17 2.87
312 321 3.253677 AGATAGTTATCACGGCTTCTCGG 59.746 47.826 2.29 0.0 35.17 4.63
313 322 1.183549 AGTTATCACGGCTTCTCGGT 58.816 50.000 0.00 0.0 0.00 4.69
337 502 3.058639 GGTTGAATCAGTCAGCAGTGAAC 60.059 47.826 0.00 0.0 39.14 3.18
386 551 4.553756 AAGAAAACGCTGAAGACTTTCC 57.446 40.909 0.00 0.0 32.09 3.13
466 631 1.478631 TGGCTGACTCAGATGACGAT 58.521 50.000 10.45 0.0 32.44 3.73
610 786 6.352516 AGGCATAACTCAACTATGAAAGAGG 58.647 40.000 0.00 0.0 34.49 3.69
652 1009 1.145571 TTGGAGGTAGTTGGGCTTGT 58.854 50.000 0.00 0.0 0.00 3.16
663 1020 3.261137 AGTTGGGCTTGTAGTTAGAGACC 59.739 47.826 0.00 0.0 39.14 3.85
665 1022 1.136500 GGGCTTGTAGTTAGAGACCGG 59.864 57.143 0.00 0.0 0.00 5.28
670 1027 4.157472 GCTTGTAGTTAGAGACCGGTTAGT 59.843 45.833 9.42 0.0 0.00 2.24
988 1673 5.296780 CCTATTTAAGCATCACCATTGTCGT 59.703 40.000 0.00 0.0 0.00 4.34
2951 4165 0.039256 CCTTTGGATGTGTTGCACCG 60.039 55.000 0.00 0.0 32.73 4.94
2967 4181 4.110493 CGCGAGGATGGAGGAAAC 57.890 61.111 0.00 0.0 0.00 2.78
3164 4379 0.305922 GGTACACCGTCGTCCGATAG 59.694 60.000 0.00 0.0 39.56 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 66 4.345547 TCTCTCGGATCTCTAGCAGTCTTA 59.654 45.833 0.00 0.00 0.00 2.10
125 128 1.640917 TACCAAAGGCTCCTTCTCGT 58.359 50.000 1.05 1.82 34.84 4.18
214 217 1.291877 CTTCAACCCGCAGTCCGAAG 61.292 60.000 0.00 0.00 40.02 3.79
279 288 7.272948 GCCGTGATAACTATCTTTAACCTATCG 59.727 40.741 0.00 0.00 33.88 2.92
301 310 3.239253 AACCCACCGAGAAGCCGT 61.239 61.111 0.00 0.00 0.00 5.68
310 319 1.442769 CTGACTGATTCAACCCACCG 58.557 55.000 0.00 0.00 32.21 4.94
312 321 1.808945 CTGCTGACTGATTCAACCCAC 59.191 52.381 0.00 0.00 32.21 4.61
313 322 1.421268 ACTGCTGACTGATTCAACCCA 59.579 47.619 0.00 0.00 32.21 4.51
362 527 3.340337 AGTCTTCAGCGTTTTCTTTGC 57.660 42.857 0.00 0.00 0.00 3.68
386 551 4.202141 TGTCTTCAGCACAATTTTTGAGGG 60.202 41.667 0.00 0.00 0.00 4.30
466 631 8.440059 CGCAAGTACACATTAGTTTCTTAATCA 58.560 33.333 0.00 0.00 0.00 2.57
610 786 1.565156 TTGGAGCGCGTGATTCACAC 61.565 55.000 16.61 6.19 45.11 3.82
663 1020 8.445493 CCACCAACTAGTTAAAATTACTAACCG 58.555 37.037 8.04 0.00 30.88 4.44
665 1022 9.006839 AGCCACCAACTAGTTAAAATTACTAAC 57.993 33.333 8.04 3.28 0.00 2.34
670 1027 6.314400 CGCTAGCCACCAACTAGTTAAAATTA 59.686 38.462 8.04 0.00 39.48 1.40
771 1422 8.351461 GCTCTACTACCTCGTTTCTTAATATGT 58.649 37.037 0.00 0.00 0.00 2.29
846 1502 1.303888 ACATGGCTGCAACCTCCAG 60.304 57.895 7.82 0.00 32.78 3.86
988 1673 4.770010 GGGTTTGGTTGTGAGGAATGATTA 59.230 41.667 0.00 0.00 0.00 1.75
2217 3205 4.145365 TGTGAAACGAGGGAGAGAAAAA 57.855 40.909 0.00 0.00 42.39 1.94
2800 4014 2.281070 CAGTTCACCCTGCGCACT 60.281 61.111 5.66 0.00 0.00 4.40
2951 4165 1.521681 CCGTTTCCTCCATCCTCGC 60.522 63.158 0.00 0.00 0.00 5.03
2967 4181 4.831307 CTCTCCGTCGCCGTTCCG 62.831 72.222 0.00 0.00 0.00 4.30
3027 4241 1.554042 GACGTTGCACTACCACCACG 61.554 60.000 2.00 2.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.