Multiple sequence alignment - TraesCS2A01G576200

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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 TraesCS2A01G576200 chr2A 100.000 2303 0 0 1 2303 770344031 770341729 0.000000e+00 4253
1 TraesCS2A01G576200 chr2A 85.985 1056 132 14 995 2041 770290777 770289729 0.000000e+00 1116
2 TraesCS2A01G576200 chr2A 89.399 283 28 2 717 998 770291159 770290878 2.810000e-94 355
3 TraesCS2A01G576200 chr2A 80.087 462 83 5 1000 1452 770023428 770022967 3.670000e-88 335
4 TraesCS2A01G576200 chr2D 97.568 1316 23 3 995 2303 644975577 644974264 0.000000e+00 2244
5 TraesCS2A01G576200 chr2D 84.615 1209 129 27 995 2164 644924265 644923075 0.000000e+00 1149
6 TraesCS2A01G576200 chr2D 96.880 641 19 1 995 1635 644981070 644980431 0.000000e+00 1072
7 TraesCS2A01G576200 chr2D 96.220 291 11 0 708 998 644975968 644975678 5.760000e-131 477
8 TraesCS2A01G576200 chr2D 92.096 291 23 0 708 998 644981461 644981171 5.920000e-111 411
9 TraesCS2A01G576200 chr2D 90.106 283 28 0 716 998 644924648 644924366 3.610000e-98 368
10 TraesCS2A01G576200 chr2D 77.590 473 94 10 1000 1462 579510978 579510508 2.250000e-70 276
11 TraesCS2A01G576200 chr2B 96.960 1316 31 4 995 2303 790612996 790614309 0.000000e+00 2200
12 TraesCS2A01G576200 chr2B 85.179 1201 129 25 995 2155 790623819 790625010 0.000000e+00 1186
13 TraesCS2A01G576200 chr2B 96.886 289 8 1 710 998 790612608 790612895 1.240000e-132 483
14 TraesCS2A01G576200 chr2B 88.968 281 29 1 718 998 790623440 790623718 1.690000e-91 346
15 TraesCS2A01G576200 chr3B 91.529 968 79 3 995 1959 48668375 48667408 0.000000e+00 1330
16 TraesCS2A01G576200 chr3B 92.123 292 20 3 708 998 48668765 48668476 2.130000e-110 409
17 TraesCS2A01G576200 chr1D 96.615 709 21 3 1 708 372654448 372655154 0.000000e+00 1173
18 TraesCS2A01G576200 chr5D 96.469 708 25 0 1 708 456655070 456654363 0.000000e+00 1170
19 TraesCS2A01G576200 chr5D 96.469 708 23 2 1 708 15031898 15031193 0.000000e+00 1168
20 TraesCS2A01G576200 chr4D 96.224 715 24 3 1 715 337950728 337950017 0.000000e+00 1168
21 TraesCS2A01G576200 chr4D 96.213 713 25 2 1 712 390800055 390800766 0.000000e+00 1166
22 TraesCS2A01G576200 chr4D 96.343 711 23 3 1 709 404627305 404626596 0.000000e+00 1166
23 TraesCS2A01G576200 chr4D 96.084 715 24 4 1 714 351830123 351829412 0.000000e+00 1162
24 TraesCS2A01G576200 chr3D 96.333 709 24 2 1 708 586977481 586978188 0.000000e+00 1164
25 TraesCS2A01G576200 chr7D 96.328 708 25 1 1 708 44392979 44393685 0.000000e+00 1162


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 TraesCS2A01G576200 chr2A 770341729 770344031 2302 True 4253.0 4253 100.0000 1 2303 1 chr2A.!!$R2 2302
1 TraesCS2A01G576200 chr2A 770289729 770291159 1430 True 735.5 1116 87.6920 717 2041 2 chr2A.!!$R3 1324
2 TraesCS2A01G576200 chr2D 644974264 644975968 1704 True 1360.5 2244 96.8940 708 2303 2 chr2D.!!$R3 1595
3 TraesCS2A01G576200 chr2D 644923075 644924648 1573 True 758.5 1149 87.3605 716 2164 2 chr2D.!!$R2 1448
4 TraesCS2A01G576200 chr2D 644980431 644981461 1030 True 741.5 1072 94.4880 708 1635 2 chr2D.!!$R4 927
5 TraesCS2A01G576200 chr2B 790612608 790614309 1701 False 1341.5 2200 96.9230 710 2303 2 chr2B.!!$F1 1593
6 TraesCS2A01G576200 chr2B 790623440 790625010 1570 False 766.0 1186 87.0735 718 2155 2 chr2B.!!$F2 1437
7 TraesCS2A01G576200 chr3B 48667408 48668765 1357 True 869.5 1330 91.8260 708 1959 2 chr3B.!!$R1 1251
8 TraesCS2A01G576200 chr1D 372654448 372655154 706 False 1173.0 1173 96.6150 1 708 1 chr1D.!!$F1 707
9 TraesCS2A01G576200 chr5D 456654363 456655070 707 True 1170.0 1170 96.4690 1 708 1 chr5D.!!$R2 707
10 TraesCS2A01G576200 chr5D 15031193 15031898 705 True 1168.0 1168 96.4690 1 708 1 chr5D.!!$R1 707
11 TraesCS2A01G576200 chr4D 337950017 337950728 711 True 1168.0 1168 96.2240 1 715 1 chr4D.!!$R1 714
12 TraesCS2A01G576200 chr4D 390800055 390800766 711 False 1166.0 1166 96.2130 1 712 1 chr4D.!!$F1 711
13 TraesCS2A01G576200 chr4D 404626596 404627305 709 True 1166.0 1166 96.3430 1 709 1 chr4D.!!$R3 708
14 TraesCS2A01G576200 chr4D 351829412 351830123 711 True 1162.0 1162 96.0840 1 714 1 chr4D.!!$R2 713
15 TraesCS2A01G576200 chr3D 586977481 586978188 707 False 1164.0 1164 96.3330 1 708 1 chr3D.!!$F1 707
16 TraesCS2A01G576200 chr7D 44392979 44393685 706 False 1162.0 1162 96.3280 1 708 1 chr7D.!!$F1 707

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
35 36 1.066071 TCGGTCTCAACAAACACACCA 60.066 47.619 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
1842 1962 0.381801 GTGTCACCCAGCAAACACAG 59.618 55.0 0.0 0.0 41.24 3.66 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
35 36 1.066071 TCGGTCTCAACAAACACACCA 60.066 47.619 0.00 0.00 0.00 4.17
121 122 6.351711 CCAAAGAGAGAGAAGAAGCCATCTAA 60.352 42.308 0.00 0.00 37.42 2.10
139 141 7.256547 GCCATCTAACTAATAACTATGGACCCA 60.257 40.741 0.00 0.00 35.48 4.51
265 267 2.634940 CAAGATGGGATCTCACGGGTAT 59.365 50.000 0.00 0.00 39.08 2.73
453 457 1.197036 GTTGCTTTCTTGACGTAGGGC 59.803 52.381 0.00 0.00 0.00 5.19
532 536 4.491924 CGTTTGGACTCCGTTTGATATTCG 60.492 45.833 0.00 0.00 0.00 3.34
758 764 9.820229 TCTAGAAAGCATGTATTTAAACGTTTG 57.180 29.630 23.46 5.89 0.00 2.93
950 958 4.447290 TCACTTGTTTTGGATCGACTCAA 58.553 39.130 0.00 0.00 0.00 3.02
970 978 4.097741 TCAAATCACCAACTCACCAAAGTG 59.902 41.667 0.00 0.00 46.00 3.16
1441 1557 6.881065 AGCATACATCTACAACTTGACAATGT 59.119 34.615 0.00 0.45 0.00 2.71
1567 1684 7.745620 TTAGCACTAGATCGATCATTCTACA 57.254 36.000 26.47 4.80 0.00 2.74
1811 1931 5.241285 GGAGGAGAGTAATTAGAGGTTACCG 59.759 48.000 0.00 0.00 33.55 4.02
1842 1962 2.112190 AGGCTTAGTGTTAGAGGGCTC 58.888 52.381 0.00 0.00 0.00 4.70
2028 2175 1.656652 TTTCCTAGCGAGCAATGAGC 58.343 50.000 0.00 0.00 46.19 4.26
2261 2415 1.530013 GGTTCTCGTCGTCTTCCCCA 61.530 60.000 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 6.903340 ACCTTTGGGTCCATAGTTATTAGT 57.097 37.500 6.69 0.00 43.38 2.24
139 141 7.070322 TGTGTGAGTAGTTTACCTAAGACCTTT 59.930 37.037 0.00 0.00 0.00 3.11
147 149 6.183360 CCGATGATGTGTGAGTAGTTTACCTA 60.183 42.308 0.00 0.00 0.00 3.08
265 267 2.047655 CACCGCCGCAACCTTCTA 60.048 61.111 0.00 0.00 0.00 2.10
412 415 2.128507 GGAGAGCACGAGGTAGGGG 61.129 68.421 0.00 0.00 0.00 4.79
453 457 0.176680 CGTGATCCAGAGGACTTGGG 59.823 60.000 0.00 0.00 32.98 4.12
532 536 6.080406 CCTATTTCAGAGTTTCGCAGAAAAC 58.920 40.000 5.51 2.52 45.90 2.43
584 589 3.723325 TGGGACTAACCTATTAACCGGT 58.277 45.455 0.00 0.00 38.98 5.28
696 702 1.964552 CCGGGTAGTGATACGTCTCT 58.035 55.000 0.00 0.00 33.16 3.10
950 958 2.362077 GCACTTTGGTGAGTTGGTGATT 59.638 45.455 0.00 0.00 45.61 2.57
998 1110 4.086457 GTTCCACAATTGGTTACCCATCT 58.914 43.478 10.83 0.00 44.35 2.90
1441 1557 6.959639 AGTTGTTCCATTTTCTGCTCTTAA 57.040 33.333 0.00 0.00 0.00 1.85
1507 1623 4.944962 TTCATGACTCTTTGGTATTGCG 57.055 40.909 0.00 0.00 0.00 4.85
1567 1684 3.365472 GGAAACCATCCCACTGCTTATT 58.635 45.455 0.00 0.00 43.00 1.40
1811 1931 7.381323 TCTAACACTAAGCCTAAACACTAACC 58.619 38.462 0.00 0.00 0.00 2.85
1842 1962 0.381801 GTGTCACCCAGCAAACACAG 59.618 55.000 0.00 0.00 41.24 3.66
2028 2175 8.952278 TGGTTTTGCATATTAACTAACTACCTG 58.048 33.333 0.00 0.00 0.00 4.00
2175 2329 3.134471 AGGGGAAGGCTATGGATTTTCT 58.866 45.455 0.00 0.00 0.00 2.52
2239 2393 0.597072 GGAAGACGACGAGAACCACT 59.403 55.000 0.00 0.00 0.00 4.00
2246 2400 1.676746 TATCTGGGGAAGACGACGAG 58.323 55.000 0.00 0.00 37.88 4.18


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

AutoCloner maintained by Alex Coulton.