Multiple sequence alignment - TraesCS2D01G083800

Loading Multiple Alignment...

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 TraesCS2D01G083800 chr2D 100.000 2363 0 0 1 2363 36271261 36268899 0.000000e+00 4364.0
1 TraesCS2D01G083800 chr2D 81.834 567 60 21 167 703 36281673 36281120 1.000000e-118 436.0
2 TraesCS2D01G083800 chr2D 83.596 317 34 14 167 468 578601506 578601193 4.970000e-72 281.0
3 TraesCS2D01G083800 chr2D 86.243 189 21 2 1 188 36281870 36281686 1.430000e-47 200.0
4 TraesCS2D01G083800 chr2D 84.574 188 25 1 1 188 578601702 578601519 1.440000e-42 183.0
5 TraesCS2D01G083800 chr2D 100.000 34 0 0 1148 1181 36270081 36270048 1.960000e-06 63.9
6 TraesCS2D01G083800 chr2D 100.000 34 0 0 1181 1214 36270114 36270081 1.960000e-06 63.9
7 TraesCS2D01G083800 chr2B 94.635 1193 38 6 1 1180 60144142 60145321 0.000000e+00 1825.0
8 TraesCS2D01G083800 chr2B 93.220 1180 45 10 1 1173 59771929 59773080 0.000000e+00 1703.0
9 TraesCS2D01G083800 chr2B 89.583 480 29 14 1812 2289 59774207 59774667 7.270000e-165 590.0
10 TraesCS2D01G083800 chr2B 87.050 556 18 19 1812 2363 60146244 60146749 1.570000e-161 579.0
11 TraesCS2D01G083800 chr2B 88.913 469 42 5 1350 1816 59773701 59774161 9.480000e-159 569.0
12 TraesCS2D01G083800 chr2B 81.481 567 62 23 167 703 59759435 59759988 2.170000e-115 425.0
13 TraesCS2D01G083800 chr2B 88.417 259 23 3 1354 1612 60145850 60146101 2.950000e-79 305.0
14 TraesCS2D01G083800 chr2B 95.906 171 7 0 1181 1351 60145289 60145459 6.430000e-71 278.0
15 TraesCS2D01G083800 chr2B 86.772 189 20 2 1 188 59759238 59759422 3.080000e-49 206.0
16 TraesCS2D01G083800 chr2B 85.638 188 23 1 1 188 695580805 695580622 6.660000e-46 195.0
17 TraesCS2D01G083800 chr2B 96.703 91 3 0 1090 1180 59773082 59773172 4.070000e-33 152.0
18 TraesCS2D01G083800 chrUn 93.350 1188 44 8 1 1181 12899299 12900458 0.000000e+00 1724.0
19 TraesCS2D01G083800 chrUn 96.552 348 7 2 1181 1527 12900425 12900768 2.630000e-159 571.0
20 TraesCS2D01G083800 chrUn 82.092 564 45 21 1821 2363 12900975 12901503 4.670000e-117 431.0
21 TraesCS2D01G083800 chr2A 93.350 1188 44 8 1 1181 39717362 39718521 0.000000e+00 1724.0
22 TraesCS2D01G083800 chr2A 96.552 348 7 2 1181 1527 39718488 39718831 2.630000e-159 571.0
23 TraesCS2D01G083800 chr2A 82.092 564 45 21 1821 2363 39719038 39719566 4.670000e-117 431.0
24 TraesCS2D01G083800 chr2A 81.028 564 62 25 167 703 39706629 39707174 7.860000e-110 407.0
25 TraesCS2D01G083800 chr2A 87.281 228 20 4 167 386 716177688 716177462 3.900000e-63 252.0
26 TraesCS2D01G083800 chr2A 87.302 189 19 2 1 188 39706432 39706616 6.620000e-51 211.0
27 TraesCS2D01G083800 chr2A 85.638 188 23 1 1 188 716177884 716177701 6.660000e-46 195.0
28 TraesCS2D01G083800 chr5B 94.541 458 18 4 409 859 524380292 524379835 0.000000e+00 701.0
29 TraesCS2D01G083800 chr5B 93.820 356 15 4 409 757 199321945 199321590 1.610000e-146 529.0
30 TraesCS2D01G083800 chr5B 97.394 307 7 1 452 757 141599610 141599916 2.690000e-144 521.0
31 TraesCS2D01G083800 chr6B 97.068 307 8 1 452 757 250027771 250027465 1.250000e-142 516.0
32 TraesCS2D01G083800 chr3B 97.068 307 8 1 452 757 278405436 278405130 1.250000e-142 516.0
33 TraesCS2D01G083800 chr1D 86.702 188 21 1 1 188 467859699 467859516 3.080000e-49 206.0


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 TraesCS2D01G083800 chr2D 36268899 36271261 2362 True 1497.266667 4364 100.000000 1 2363 3 chr2D.!!$R1 2362
1 TraesCS2D01G083800 chr2D 36281120 36281870 750 True 318.000000 436 84.038500 1 703 2 chr2D.!!$R2 702
2 TraesCS2D01G083800 chr2D 578601193 578601702 509 True 232.000000 281 84.085000 1 468 2 chr2D.!!$R3 467
3 TraesCS2D01G083800 chr2B 59771929 59774667 2738 False 753.500000 1703 92.104750 1 2289 4 chr2B.!!$F2 2288
4 TraesCS2D01G083800 chr2B 60144142 60146749 2607 False 746.750000 1825 91.502000 1 2363 4 chr2B.!!$F3 2362
5 TraesCS2D01G083800 chr2B 59759238 59759988 750 False 315.500000 425 84.126500 1 703 2 chr2B.!!$F1 702
6 TraesCS2D01G083800 chrUn 12899299 12901503 2204 False 908.666667 1724 90.664667 1 2363 3 chrUn.!!$F1 2362
7 TraesCS2D01G083800 chr2A 39717362 39719566 2204 False 908.666667 1724 90.664667 1 2363 3 chr2A.!!$F2 2362
8 TraesCS2D01G083800 chr2A 39706432 39707174 742 False 309.000000 407 84.165000 1 703 2 chr2A.!!$F1 702

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
217 321 0.035056 CTGCCTCCCGGATTTCTTGT 60.035 55.0 0.73 0.0 0.0 3.16 F
938 1105 0.110486 AACGAACCTCAGCAACCCAT 59.890 50.0 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 1218 0.323629 TCCGAGAATTCCTTGCGGTT 59.676 50.0 19.45 0.0 42.4 4.44 R
2273 2968 1.994885 AATATGCCCAGTCCCCACCG 61.995 60.0 0.00 0.0 0.0 4.94 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
39 41 3.444916 CATGTTACAACTATCCGCGTCT 58.555 45.455 4.92 0.00 0.00 4.18
40 42 3.581024 TGTTACAACTATCCGCGTCTT 57.419 42.857 4.92 0.00 0.00 3.01
41 43 4.700268 TGTTACAACTATCCGCGTCTTA 57.300 40.909 4.92 0.00 0.00 2.10
42 44 5.058149 TGTTACAACTATCCGCGTCTTAA 57.942 39.130 4.92 0.00 0.00 1.85
67 69 2.590073 CTCACTCAAGTACGTCTGCAG 58.410 52.381 7.63 7.63 0.00 4.41
117 119 0.390340 AGCAGTAGTGTGATGTGCCG 60.390 55.000 0.00 0.00 34.56 5.69
150 152 3.899371 TGGTCTTGCCAGTGCCTA 58.101 55.556 0.00 0.00 43.61 3.93
217 321 0.035056 CTGCCTCCCGGATTTCTTGT 60.035 55.000 0.73 0.00 0.00 3.16
383 498 5.789512 GCACATAATTTTCCGCAAACATTTG 59.210 36.000 0.00 0.00 41.03 2.32
449 579 6.690194 AGACATAGGCTCAAATCAAATCAC 57.310 37.500 0.00 0.00 0.00 3.06
488 631 2.086054 AAGAACGCCAGAAGTAGCAG 57.914 50.000 0.00 0.00 0.00 4.24
515 676 4.407945 ACCATTCCCACAGTACTATGGTAC 59.592 45.833 18.79 11.19 42.79 3.34
866 1033 2.203280 CCCAACAGAACCCGCACA 60.203 61.111 0.00 0.00 0.00 4.57
917 1084 1.152830 ATCACCGCCCAAACCAACT 59.847 52.632 0.00 0.00 0.00 3.16
938 1105 0.110486 AACGAACCTCAGCAACCCAT 59.890 50.000 0.00 0.00 0.00 4.00
943 1110 0.773644 ACCTCAGCAACCCATTGTCT 59.226 50.000 0.00 0.00 38.17 3.41
1022 1189 1.473080 GGAGTCTCTGAAGCTGGATGC 60.473 57.143 0.00 0.00 43.29 3.91
1051 1218 2.545526 CTGCAGCGACAAAGAGAAGAAA 59.454 45.455 0.00 0.00 0.00 2.52
1088 1255 4.253685 TCGGATTTCTCCAAGCAAGTTAG 58.746 43.478 0.00 0.00 42.19 2.34
1206 1425 5.691305 GCTCATCTCTGCAATAGTTACTGAG 59.309 44.000 0.00 2.81 0.00 3.35
1213 1432 4.905429 TGCAATAGTTACTGAGCCAAGAA 58.095 39.130 0.00 0.00 0.00 2.52
1224 1443 0.622665 AGCCAAGAACAGATGAGGGG 59.377 55.000 0.00 0.00 0.00 4.79
1388 2007 3.254014 CTCAAACACCAAGCCCGCG 62.254 63.158 0.00 0.00 0.00 6.46
1643 2263 3.057596 GCTATCGACCTCATCCTCTTCAG 60.058 52.174 0.00 0.00 0.00 3.02
1652 2272 1.608717 ATCCTCTTCAGAAGCGCCGT 61.609 55.000 2.29 0.00 0.00 5.68
1654 2274 2.126463 TCTTCAGAAGCGCCGTCG 60.126 61.111 2.29 0.00 39.07 5.12
1701 2321 4.821589 CGTCTTCGGCAGCCTCCC 62.822 72.222 10.54 0.00 0.00 4.30
1703 2323 2.058595 GTCTTCGGCAGCCTCCCTA 61.059 63.158 10.54 0.00 0.00 3.53
1804 2424 2.433145 CGAAGCAAGCCTCAGCGA 60.433 61.111 0.00 0.00 46.67 4.93
1839 2516 3.372730 GGCCAAATGCAGCCGACA 61.373 61.111 0.00 0.00 43.89 4.35
2035 2716 3.164977 TGAACTGGCCGGTGACCA 61.165 61.111 20.54 14.04 35.40 4.02
2273 2968 2.299297 TCGAAGAAGTGGAAGGAAGGAC 59.701 50.000 0.00 0.00 0.00 3.85
2311 3019 1.518367 TCCCTCTCCCTCTCTCTCTC 58.482 60.000 0.00 0.00 0.00 3.20
2312 3020 0.108585 CCCTCTCCCTCTCTCTCTCG 59.891 65.000 0.00 0.00 0.00 4.04
2313 3021 0.837272 CCTCTCCCTCTCTCTCTCGT 59.163 60.000 0.00 0.00 0.00 4.18
2314 3022 1.202651 CCTCTCCCTCTCTCTCTCGTC 60.203 61.905 0.00 0.00 0.00 4.20
2315 3023 0.834612 TCTCCCTCTCTCTCTCGTCC 59.165 60.000 0.00 0.00 0.00 4.79
2316 3024 0.531974 CTCCCTCTCTCTCTCGTCCG 60.532 65.000 0.00 0.00 0.00 4.79
2317 3025 1.222387 CCCTCTCTCTCTCGTCCGT 59.778 63.158 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 7.310664 CAGACGTACTTGAGTGAGGTAATTAA 58.689 38.462 0.00 0.00 0.00 1.40
40 42 6.624423 GCAGACGTACTTGAGTGAGGTAATTA 60.624 42.308 0.00 0.00 0.00 1.40
41 43 5.710984 CAGACGTACTTGAGTGAGGTAATT 58.289 41.667 0.00 0.00 0.00 1.40
42 44 4.380655 GCAGACGTACTTGAGTGAGGTAAT 60.381 45.833 0.00 0.00 0.00 1.89
150 152 4.532521 AGTTGTACTGCTCTATGGTCCTTT 59.467 41.667 0.00 0.00 0.00 3.11
383 498 3.882888 TGACTGGTTGACCAAGATTGTTC 59.117 43.478 4.18 0.00 46.97 3.18
398 522 6.636454 TTCCTATCATTAAGGTTGACTGGT 57.364 37.500 0.00 0.00 35.48 4.00
399 523 7.938140 TTTTCCTATCATTAAGGTTGACTGG 57.062 36.000 0.00 0.00 35.48 4.00
488 631 5.820947 CCATAGTACTGTGGGAATGGTTTAC 59.179 44.000 26.62 0.00 38.09 2.01
515 676 8.768019 TGCGAACATAAATAGATGATCTCAAAG 58.232 33.333 0.00 0.00 0.00 2.77
866 1033 2.362120 GATGGGCTTGCCTGTGCT 60.362 61.111 11.71 0.00 38.71 4.40
917 1084 1.141254 TGGGTTGCTGAGGTTCGTTAA 59.859 47.619 0.00 0.00 0.00 2.01
938 1105 1.071699 GTCAGTTACAGGGCCAGACAA 59.928 52.381 6.18 0.00 0.00 3.18
943 1110 0.759959 TTTCGTCAGTTACAGGGCCA 59.240 50.000 6.18 0.00 0.00 5.36
1022 1189 0.662619 TTGTCGCTGCAGAGTTTTGG 59.337 50.000 20.43 0.00 0.00 3.28
1051 1218 0.323629 TCCGAGAATTCCTTGCGGTT 59.676 50.000 19.45 0.00 42.40 4.44
1206 1425 1.034292 GCCCCTCATCTGTTCTTGGC 61.034 60.000 0.00 0.00 0.00 4.52
1213 1432 0.329596 GGAGTTTGCCCCTCATCTGT 59.670 55.000 0.00 0.00 0.00 3.41
1224 1443 0.693049 TTCCAGGAGGAGGAGTTTGC 59.307 55.000 0.00 0.00 46.74 3.68
1388 2007 6.861055 TGAATTAAATTGGCTTCAGTTTCGTC 59.139 34.615 0.00 0.00 33.38 4.20
1624 2244 3.304911 TCTGAAGAGGATGAGGTCGAT 57.695 47.619 0.00 0.00 0.00 3.59
1630 2250 1.569708 GCGCTTCTGAAGAGGATGAG 58.430 55.000 21.06 4.01 0.00 2.90
1659 2279 3.770040 CGGAGATGCGGTGGGTGA 61.770 66.667 0.00 0.00 0.00 4.02
1978 2658 3.068064 TGATCAGGAGGACGCGCA 61.068 61.111 5.73 0.00 0.00 6.09
2249 2944 2.814280 TCCTTCCACTTCTTCGACAC 57.186 50.000 0.00 0.00 0.00 3.67
2261 2956 2.221299 CCCACCGTCCTTCCTTCCA 61.221 63.158 0.00 0.00 0.00 3.53
2273 2968 1.994885 AATATGCCCAGTCCCCACCG 61.995 60.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.