Multiple sequence alignment - TraesCS2A01G464400

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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 TraesCS2A01G464400 chr2A 100.000 2294 0 0 1 2294 709849029 709851322 0.000000e+00 4237
1 TraesCS2A01G464400 chr2A 90.589 1392 81 23 1 1389 710091834 710093178 0.000000e+00 1799
2 TraesCS2A01G464400 chr2A 98.901 910 9 1 1383 2291 710093210 710094119 0.000000e+00 1624
3 TraesCS2A01G464400 chr2A 87.739 1362 136 13 951 2281 710035892 710037253 0.000000e+00 1561
4 TraesCS2A01G464400 chr2A 81.579 874 155 4 1421 2289 710206308 710207180 0.000000e+00 717
5 TraesCS2A01G464400 chr2B 92.863 1331 87 6 63 1389 683041765 683043091 0.000000e+00 1925
6 TraesCS2A01G464400 chr2B 97.582 910 21 1 1383 2291 683043123 683044032 0.000000e+00 1557
7 TraesCS2A01G464400 chr2B 88.938 904 94 4 1383 2281 683067830 683068732 0.000000e+00 1110
8 TraesCS2A01G464400 chr2B 86.156 874 115 5 1421 2289 683054274 683055146 0.000000e+00 939
9 TraesCS2A01G464400 chr2B 85.486 875 118 7 1421 2289 683128386 683129257 0.000000e+00 904
10 TraesCS2A01G464400 chr2B 89.463 484 47 3 910 1389 683067315 683067798 1.950000e-170 608
11 TraesCS2A01G464400 chr2B 88.667 450 45 5 910 1356 683127776 683128222 5.570000e-151 544
12 TraesCS2A01G464400 chr2B 87.302 441 51 4 951 1389 683053771 683054208 1.220000e-137 499
13 TraesCS2A01G464400 chr2B 84.187 449 67 3 903 1351 794696841 794696397 1.260000e-117 433
14 TraesCS2A01G464400 chr2D 87.225 1362 143 13 951 2281 571208678 571210039 0.000000e+00 1522
15 TraesCS2A01G464400 chr2D 88.379 1265 118 12 103 1356 571193947 571195193 0.000000e+00 1495
16 TraesCS2A01G464400 chr2D 85.046 876 112 12 1424 2286 571195366 571196235 0.000000e+00 874
17 TraesCS2A01G464400 chr2D 88.819 635 66 3 52 682 645480008 645479375 0.000000e+00 774
18 TraesCS2A01G464400 chr6B 89.606 635 61 3 52 682 149349680 149350313 0.000000e+00 802
19 TraesCS2A01G464400 chr6A 89.449 635 62 3 52 682 69497848 69497215 0.000000e+00 797
20 TraesCS2A01G464400 chr6A 88.661 635 66 4 52 682 402589990 402590622 0.000000e+00 769
21 TraesCS2A01G464400 chr6A 88.661 635 64 4 52 682 39895831 39895201 0.000000e+00 767
22 TraesCS2A01G464400 chr7A 88.819 635 66 3 52 682 476374090 476373457 0.000000e+00 774
23 TraesCS2A01G464400 chr7A 88.189 635 70 3 52 682 67885188 67885821 0.000000e+00 752
24 TraesCS2A01G464400 chr7D 88.540 637 63 8 52 682 271124821 271125453 0.000000e+00 763
25 TraesCS2A01G464400 chrUn 84.187 449 67 3 903 1351 332504373 332504817 1.260000e-117 433


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 TraesCS2A01G464400 chr2A 709849029 709851322 2293 False 4237.0 4237 100.0000 1 2294 1 chr2A.!!$F1 2293
1 TraesCS2A01G464400 chr2A 710091834 710094119 2285 False 1711.5 1799 94.7450 1 2291 2 chr2A.!!$F4 2290
2 TraesCS2A01G464400 chr2A 710035892 710037253 1361 False 1561.0 1561 87.7390 951 2281 1 chr2A.!!$F2 1330
3 TraesCS2A01G464400 chr2A 710206308 710207180 872 False 717.0 717 81.5790 1421 2289 1 chr2A.!!$F3 868
4 TraesCS2A01G464400 chr2B 683041765 683044032 2267 False 1741.0 1925 95.2225 63 2291 2 chr2B.!!$F1 2228
5 TraesCS2A01G464400 chr2B 683067315 683068732 1417 False 859.0 1110 89.2005 910 2281 2 chr2B.!!$F3 1371
6 TraesCS2A01G464400 chr2B 683127776 683129257 1481 False 724.0 904 87.0765 910 2289 2 chr2B.!!$F4 1379
7 TraesCS2A01G464400 chr2B 683053771 683055146 1375 False 719.0 939 86.7290 951 2289 2 chr2B.!!$F2 1338
8 TraesCS2A01G464400 chr2D 571208678 571210039 1361 False 1522.0 1522 87.2250 951 2281 1 chr2D.!!$F1 1330
9 TraesCS2A01G464400 chr2D 571193947 571196235 2288 False 1184.5 1495 86.7125 103 2286 2 chr2D.!!$F2 2183
10 TraesCS2A01G464400 chr2D 645479375 645480008 633 True 774.0 774 88.8190 52 682 1 chr2D.!!$R1 630
11 TraesCS2A01G464400 chr6B 149349680 149350313 633 False 802.0 802 89.6060 52 682 1 chr6B.!!$F1 630
12 TraesCS2A01G464400 chr6A 69497215 69497848 633 True 797.0 797 89.4490 52 682 1 chr6A.!!$R2 630
13 TraesCS2A01G464400 chr6A 402589990 402590622 632 False 769.0 769 88.6610 52 682 1 chr6A.!!$F1 630
14 TraesCS2A01G464400 chr6A 39895201 39895831 630 True 767.0 767 88.6610 52 682 1 chr6A.!!$R1 630
15 TraesCS2A01G464400 chr7A 476373457 476374090 633 True 774.0 774 88.8190 52 682 1 chr7A.!!$R1 630
16 TraesCS2A01G464400 chr7A 67885188 67885821 633 False 752.0 752 88.1890 52 682 1 chr7A.!!$F1 630
17 TraesCS2A01G464400 chr7D 271124821 271125453 632 False 763.0 763 88.5400 52 682 1 chr7D.!!$F1 630

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
45 46 0.251634 TCATACCAAGCGGATGTGCA 59.748 50.0 0.0 0.0 37.31 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 1911 3.964411 ACCCCCTTTACAGAATTGCTAC 58.036 45.455 0.0 0.0 0.0 3.58 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
24 25 2.301346 CTTGGCCAGATTACCCATGTC 58.699 52.381 5.11 0.00 0.00 3.06
26 27 0.846693 GGCCAGATTACCCATGTCCT 59.153 55.000 0.00 0.00 0.00 3.85
27 28 1.202818 GGCCAGATTACCCATGTCCTC 60.203 57.143 0.00 0.00 0.00 3.71
29 30 2.107204 GCCAGATTACCCATGTCCTCAT 59.893 50.000 0.00 0.00 34.21 2.90
36 37 1.212935 ACCCATGTCCTCATACCAAGC 59.787 52.381 0.00 0.00 32.47 4.01
45 46 0.251634 TCATACCAAGCGGATGTGCA 59.748 50.000 0.00 0.00 37.31 4.57
48 49 0.391130 TACCAAGCGGATGTGCAGTC 60.391 55.000 0.00 0.00 37.31 3.51
90 91 2.881513 TGAACATACAAAGCCGCTTCAA 59.118 40.909 5.98 0.00 0.00 2.69
130 131 2.576191 TGCTATGGTTCCTACTGCCTTT 59.424 45.455 0.00 0.00 0.00 3.11
138 148 7.023171 TGGTTCCTACTGCCTTTAGAATTTA 57.977 36.000 0.00 0.00 0.00 1.40
140 150 6.542735 GGTTCCTACTGCCTTTAGAATTTAGG 59.457 42.308 0.00 0.00 0.00 2.69
217 228 2.590575 AACCCGTGCAGTCGTTGG 60.591 61.111 0.00 0.00 0.00 3.77
230 241 4.329545 GTTGGCCCGGCTCTGTCA 62.330 66.667 9.86 0.00 0.00 3.58
247 258 0.668535 TCATAGATAGCTGCGCGTGT 59.331 50.000 8.43 0.00 0.00 4.49
272 284 9.061610 GTTCTACATACCAAAATTTTGTCGATG 57.938 33.333 25.25 23.71 36.45 3.84
317 330 5.469421 CCCTCAAGATCAAGCATCTCATTAC 59.531 44.000 0.00 0.00 41.47 1.89
320 333 7.254829 CCTCAAGATCAAGCATCTCATTACTTG 60.255 40.741 0.00 0.00 41.47 3.16
350 371 2.114616 TGCAAGGTTGTGGAAACCATT 58.885 42.857 9.76 0.00 42.69 3.16
407 428 3.113322 GACGTTGCGCATACTTATCAGA 58.887 45.455 12.75 0.00 0.00 3.27
454 475 9.566432 CTAATGAGGATTCAATTTAAGCCTAGT 57.434 33.333 9.11 0.00 45.10 2.57
465 486 4.569761 TTAAGCCTAGTGATAGCGTGAG 57.430 45.455 0.00 0.00 0.00 3.51
1223 1254 2.273449 GGCCCTGTCACTGGATGG 59.727 66.667 1.37 0.00 0.00 3.51
1291 1322 3.762288 TGACTACTACCGACTTGAGCAAT 59.238 43.478 0.00 0.00 0.00 3.56
1349 1380 9.171877 TGTTCCATTTTTATTGCTTTCAGTTTT 57.828 25.926 0.00 0.00 0.00 2.43
1385 1449 6.700520 GCGTAATATGTAACCAAGAGTAGCTT 59.299 38.462 0.00 0.00 37.29 3.74
2260 2413 3.336694 ACAGGGGTGGATGGATTAAACTT 59.663 43.478 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.550914 GGACATGGGTAATCTGGCCA 59.449 55.000 4.71 4.71 38.03 5.36
24 25 1.586422 CACATCCGCTTGGTATGAGG 58.414 55.000 0.00 0.00 0.00 3.86
26 27 0.251634 TGCACATCCGCTTGGTATGA 59.748 50.000 0.00 0.00 0.00 2.15
27 28 0.659427 CTGCACATCCGCTTGGTATG 59.341 55.000 0.00 0.00 0.00 2.39
29 30 0.391130 GACTGCACATCCGCTTGGTA 60.391 55.000 0.00 0.00 0.00 3.25
36 37 2.159043 AGATAACCAGACTGCACATCCG 60.159 50.000 0.00 0.00 0.00 4.18
45 46 5.600484 AGTTAGCATAGCAGATAACCAGACT 59.400 40.000 7.91 0.00 40.30 3.24
48 49 5.847304 TCAGTTAGCATAGCAGATAACCAG 58.153 41.667 7.91 3.42 40.30 4.00
156 166 4.533707 CCTAGAGATCCCAAATGGCTATCA 59.466 45.833 12.69 0.00 31.98 2.15
217 228 1.203523 CTATCTATGACAGAGCCGGGC 59.796 57.143 12.11 12.11 36.48 6.13
219 230 2.094803 CAGCTATCTATGACAGAGCCGG 60.095 54.545 0.00 0.00 36.48 6.13
247 258 8.240682 CCATCGACAAAATTTTGGTATGTAGAA 58.759 33.333 29.37 9.07 42.34 2.10
317 330 0.604578 CCTTGCACCCATCAACCAAG 59.395 55.000 0.00 0.00 34.26 3.61
320 333 0.318120 CAACCTTGCACCCATCAACC 59.682 55.000 0.00 0.00 0.00 3.77
350 371 8.058667 ACAAATTAATGAGATGCTTGATGTCA 57.941 30.769 1.76 0.00 38.64 3.58
388 409 4.263800 GTTTCTGATAAGTATGCGCAACG 58.736 43.478 17.11 0.79 0.00 4.10
407 428 7.972832 TTAGATACTTTGACGTTGATGGTTT 57.027 32.000 0.00 0.00 0.00 3.27
454 475 0.108186 CACAAGGGCTCACGCTATCA 60.108 55.000 0.00 0.00 38.30 2.15
465 486 1.000843 GGGACAAAACATCACAAGGGC 59.999 52.381 0.00 0.00 0.00 5.19
1223 1254 7.711846 TGAATCATAAAGTAGCTCTCTGAGAC 58.288 38.462 2.58 1.47 0.00 3.36
1291 1322 6.737720 ATATGAAGCACCTTCTGTGATCTA 57.262 37.500 6.54 0.00 44.38 1.98
1349 1380 9.610705 TGGTTACATATTACGCCTACATAAAAA 57.389 29.630 0.00 0.00 0.00 1.94
1389 1453 9.598517 ACAAAAGCTGAATTCAAAAAGATAACA 57.401 25.926 9.88 0.00 0.00 2.41
1764 1911 3.964411 ACCCCCTTTACAGAATTGCTAC 58.036 45.455 0.00 0.00 0.00 3.58
2260 2413 8.646900 ACTTTATTACTTTTCAATGGAGCCAAA 58.353 29.630 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.