Multiple sequence alignment - TraesCS2B01G086100

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 TraesCS2B01G086100 chr2B 100.000 5350 0 0 1 5350 47814527 47819876 0.000000e+00 9880
1 TraesCS2B01G086100 chr2B 98.501 5137 59 2 232 5350 47743105 47748241 0.000000e+00 9044
2 TraesCS2B01G086100 chr2B 98.455 4984 58 3 385 5350 47772944 47777926 0.000000e+00 8759
3 TraesCS2B01G086100 chr2B 98.051 3335 45 3 1861 5177 47718259 47721591 0.000000e+00 5781
4 TraesCS2B01G086100 chr2B 98.402 3004 30 2 2192 5177 47697620 47700623 0.000000e+00 5265
5 TraesCS2B01G086100 chr2B 98.043 1380 24 2 1861 3240 47691873 47693249 0.000000e+00 2396
6 TraesCS2B01G086100 chr2B 97.889 900 18 1 761 1660 47683927 47684825 0.000000e+00 1555
7 TraesCS2B01G086100 chr2B 97.889 900 18 1 761 1660 47709606 47710504 0.000000e+00 1555
8 TraesCS2B01G086100 chr2B 99.138 232 2 0 1 232 47682807 47683038 8.290000e-113 418
9 TraesCS2B01G086100 chr2B 99.138 232 2 0 1 232 47707884 47708115 8.290000e-113 418
10 TraesCS2B01G086100 chr2B 98.707 232 3 0 1 232 47742497 47742728 3.860000e-111 412
11 TraesCS2B01G086100 chr2B 98.707 232 3 0 1 232 47770237 47770468 3.860000e-111 412
12 TraesCS2B01G086100 chr2B 97.938 97 2 0 1655 1751 47691781 47691877 9.220000e-38 169
13 TraesCS2B01G086100 chr2B 97.938 97 2 0 1655 1751 47718167 47718263 9.220000e-38 169
14 TraesCS2B01G086100 chr2B 95.522 67 3 0 5284 5350 796269596 796269530 2.040000e-19 108
15 TraesCS2B01G086100 chr2D 93.429 1674 90 7 2738 4393 29686647 29688318 0.000000e+00 2464
16 TraesCS2B01G086100 chr2D 90.119 840 60 11 1861 2680 29685820 29686656 0.000000e+00 1070
17 TraesCS2B01G086100 chr2D 87.013 847 68 15 919 1751 29685006 29685824 0.000000e+00 917
18 TraesCS2B01G086100 chr2D 77.990 836 158 18 3546 4359 29531869 29531038 8.000000e-138 501
19 TraesCS2B01G086100 chr2D 84.410 449 60 6 231 669 638385787 638386235 2.960000e-117 433
20 TraesCS2B01G086100 chr2D 96.667 120 3 1 1747 1865 630017807 630017926 1.180000e-46 198
21 TraesCS2B01G086100 chrUn 97.715 1269 12 1 3926 5177 344072828 344071560 0.000000e+00 2167
22 TraesCS2B01G086100 chrUn 97.715 1269 12 1 3926 5177 344119251 344120519 0.000000e+00 2167
23 TraesCS2B01G086100 chrUn 96.064 1245 35 5 429 1660 406624538 406625781 0.000000e+00 2015
24 TraesCS2B01G086100 chrUn 98.707 232 3 0 1 232 392616792 392617023 3.860000e-111 412
25 TraesCS2B01G086100 chr2A 89.730 1704 137 18 2718 4401 31897862 31899547 0.000000e+00 2143
26 TraesCS2B01G086100 chr2A 89.042 1086 70 25 686 1751 31896100 31897156 0.000000e+00 1301
27 TraesCS2B01G086100 chr2A 86.906 695 65 7 4520 5192 31899603 31900293 0.000000e+00 756
28 TraesCS2B01G086100 chr2A 87.613 444 55 0 1001 1444 31836618 31836175 2.860000e-142 516
29 TraesCS2B01G086100 chr7A 78.405 1116 208 25 3261 4359 725231392 725230293 0.000000e+00 695
30 TraesCS2B01G086100 chr7A 78.175 504 91 15 3261 3752 725311233 725310737 2.420000e-78 303
31 TraesCS2B01G086100 chr1D 87.529 425 52 1 997 1420 100839000 100838576 1.730000e-134 490
32 TraesCS2B01G086100 chr1D 84.009 469 63 9 231 688 375353154 375352687 1.770000e-119 440
33 TraesCS2B01G086100 chr4D 84.764 466 61 5 231 687 99207150 99207614 4.880000e-125 459
34 TraesCS2B01G086100 chr4D 88.525 122 13 1 2580 2701 259497252 259497372 4.320000e-31 147
35 TraesCS2B01G086100 chr5D 84.368 467 62 5 233 688 520111239 520111705 1.060000e-121 448
36 TraesCS2B01G086100 chr5D 83.547 468 65 6 230 686 485603781 485603315 1.380000e-115 427
37 TraesCS2B01G086100 chr1A 84.335 466 60 10 232 686 584525799 584526262 1.370000e-120 444
38 TraesCS2B01G086100 chr1A 95.522 67 3 0 5284 5350 153661307 153661241 2.040000e-19 108
39 TraesCS2B01G086100 chr5A 83.795 469 64 8 231 688 11092316 11092783 8.230000e-118 435
40 TraesCS2B01G086100 chr5A 97.458 118 2 1 1748 1864 706439026 706438909 3.270000e-47 200
41 TraesCS2B01G086100 chr5A 95.522 67 3 0 5284 5350 117632235 117632301 2.040000e-19 108
42 TraesCS2B01G086100 chr5A 95.522 67 3 0 5284 5350 273726585 273726651 2.040000e-19 108
43 TraesCS2B01G086100 chr4A 95.455 132 2 3 1748 1878 252658956 252658828 1.950000e-49 207
44 TraesCS2B01G086100 chr7B 97.458 118 2 1 1748 1864 692308705 692308822 3.270000e-47 200
45 TraesCS2B01G086100 chr3B 93.382 136 7 2 1748 1882 667390003 667390137 3.270000e-47 200
46 TraesCS2B01G086100 chr6A 95.238 126 5 1 1740 1864 296983554 296983679 1.180000e-46 198
47 TraesCS2B01G086100 chr6A 94.574 129 4 2 1748 1873 395248887 395249015 4.230000e-46 196
48 TraesCS2B01G086100 chr6D 90.678 118 9 2 2588 2704 90111256 90111140 7.170000e-34 156
49 TraesCS2B01G086100 chr6D 88.430 121 13 1 2584 2703 302113754 302113634 1.550000e-30 145
50 TraesCS2B01G086100 chr5B 97.015 67 2 0 5284 5350 318089692 318089626 4.380000e-21 113
51 TraesCS2B01G086100 chr6B 95.522 67 3 0 5284 5350 280621022 280620956 2.040000e-19 108
52 TraesCS2B01G086100 chr1B 95.522 67 3 0 5284 5350 525804868 525804934 2.040000e-19 108


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 TraesCS2B01G086100 chr2B 47814527 47819876 5349 False 9880.000000 9880 100.000000 1 5350 1 chr2B.!!$F2 5349
1 TraesCS2B01G086100 chr2B 47697620 47700623 3003 False 5265.000000 5265 98.402000 2192 5177 1 chr2B.!!$F1 2985
2 TraesCS2B01G086100 chr2B 47742497 47748241 5744 False 4728.000000 9044 98.604000 1 5350 2 chr2B.!!$F7 5349
3 TraesCS2B01G086100 chr2B 47770237 47777926 7689 False 4585.500000 8759 98.581000 1 5350 2 chr2B.!!$F8 5349
4 TraesCS2B01G086100 chr2B 47718167 47721591 3424 False 2975.000000 5781 97.994500 1655 5177 2 chr2B.!!$F6 3522
5 TraesCS2B01G086100 chr2B 47691781 47693249 1468 False 1282.500000 2396 97.990500 1655 3240 2 chr2B.!!$F4 1585
6 TraesCS2B01G086100 chr2B 47682807 47684825 2018 False 986.500000 1555 98.513500 1 1660 2 chr2B.!!$F3 1659
7 TraesCS2B01G086100 chr2B 47707884 47710504 2620 False 986.500000 1555 98.513500 1 1660 2 chr2B.!!$F5 1659
8 TraesCS2B01G086100 chr2D 29685006 29688318 3312 False 1483.666667 2464 90.187000 919 4393 3 chr2D.!!$F3 3474
9 TraesCS2B01G086100 chr2D 29531038 29531869 831 True 501.000000 501 77.990000 3546 4359 1 chr2D.!!$R1 813
10 TraesCS2B01G086100 chrUn 344071560 344072828 1268 True 2167.000000 2167 97.715000 3926 5177 1 chrUn.!!$R1 1251
11 TraesCS2B01G086100 chrUn 344119251 344120519 1268 False 2167.000000 2167 97.715000 3926 5177 1 chrUn.!!$F1 1251
12 TraesCS2B01G086100 chrUn 406624538 406625781 1243 False 2015.000000 2015 96.064000 429 1660 1 chrUn.!!$F3 1231
13 TraesCS2B01G086100 chr2A 31896100 31900293 4193 False 1400.000000 2143 88.559333 686 5192 3 chr2A.!!$F1 4506
14 TraesCS2B01G086100 chr7A 725230293 725231392 1099 True 695.000000 695 78.405000 3261 4359 1 chr7A.!!$R1 1098

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
533 2859 0.395173 AAGTTGTGTCCGGCTTTGGT 60.395 50.000 0.00 0.0 0.00 3.67 F
978 3899 1.105167 TGAGTCCGTGACACCGTCTT 61.105 55.000 0.00 0.0 34.60 3.01 F
1529 4450 1.672356 ACCATTGGTGCGCTCAGAC 60.672 57.895 7.76 0.0 32.98 3.51 F
2626 5854 2.568623 ACTTGTCGCTCAAAGGGATT 57.431 45.000 0.00 0.0 39.44 3.01 F
3428 6660 2.503895 AGGCTTTCTCCTCAACATGG 57.496 50.000 0.00 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 4836 0.108615 CTGAAGGCTAGTGGTCACCG 60.109 60.000 0.00 0.0 0.00 4.94 R
2037 4972 3.066190 CGACTACCGGTGGGAGCA 61.066 66.667 23.02 0.0 36.97 4.26 R
3428 6660 1.540267 TGGAGTCAAGACAGTAGCGAC 59.460 52.381 2.72 0.0 0.00 5.19 R
3430 6662 1.542030 AGTGGAGTCAAGACAGTAGCG 59.458 52.381 2.72 0.0 0.00 4.26 R
5106 8406 1.880340 CTCTTCCGTCAGCGATGGC 60.880 63.158 0.00 0.0 38.52 4.40 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
193 194 2.003937 TCTGCCGGCCATATAGTACA 57.996 50.000 26.77 0.00 0.00 2.90
240 618 0.456221 CGGAAGAGAGCGGCTTCTTA 59.544 55.000 19.93 0.00 41.11 2.10
510 2836 5.367302 GACTACTTCCCGACTGTCTACTAT 58.633 45.833 6.21 0.00 0.00 2.12
533 2859 0.395173 AAGTTGTGTCCGGCTTTGGT 60.395 50.000 0.00 0.00 0.00 3.67
977 3898 1.527611 TGAGTCCGTGACACCGTCT 60.528 57.895 0.00 0.00 34.60 4.18
978 3899 1.105167 TGAGTCCGTGACACCGTCTT 61.105 55.000 0.00 0.00 34.60 3.01
1529 4450 1.672356 ACCATTGGTGCGCTCAGAC 60.672 57.895 7.76 0.00 32.98 3.51
1744 4678 4.703645 TCTGACTTCAAGTGATACTCCG 57.296 45.455 0.00 0.00 0.00 4.63
1902 4836 8.316640 TCTTTGAAGTTCTAGATTGAAGCTTC 57.683 34.615 19.89 19.89 36.21 3.86
1904 4838 5.171476 TGAAGTTCTAGATTGAAGCTTCGG 58.829 41.667 21.11 7.34 37.16 4.30
2281 5488 8.999895 ACCACCTATTTAGTTATGTAGGATGTT 58.000 33.333 4.43 0.00 37.67 2.71
2626 5854 2.568623 ACTTGTCGCTCAAAGGGATT 57.431 45.000 0.00 0.00 39.44 3.01
3428 6660 2.503895 AGGCTTTCTCCTCAACATGG 57.496 50.000 0.00 0.00 0.00 3.66
3430 6662 2.087646 GGCTTTCTCCTCAACATGGTC 58.912 52.381 0.00 0.00 0.00 4.02
3975 7249 6.852664 AGTTTGAACGTCTTGATTTTGAAGT 58.147 32.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 194 8.523658 GTGGAAAGCTATTCTGAAGGTAAAAAT 58.476 33.333 0.00 0.0 0.00 1.82
332 710 0.319469 CACCAACCAAATCCCGCAAC 60.319 55.000 0.00 0.0 0.00 4.17
510 2836 2.335316 AAGCCGGACACAACTTGTTA 57.665 45.000 5.05 0.0 39.17 2.41
533 2859 3.107601 CACCTTCATCACTCCTCCCTTA 58.892 50.000 0.00 0.0 0.00 2.69
977 3898 1.937223 CTGACCTTGTTGTGTGCGTAA 59.063 47.619 0.00 0.0 0.00 3.18
978 3899 1.577468 CTGACCTTGTTGTGTGCGTA 58.423 50.000 0.00 0.0 0.00 4.42
1432 4353 0.328450 TGGGCCCTTACCTCCATGAT 60.328 55.000 25.70 0.0 0.00 2.45
1529 4450 2.601398 CGACAGTGCAGTGTGCTGG 61.601 63.158 31.24 13.5 45.31 4.85
1744 4678 2.413142 CCGGACGGAGGGAGTACAC 61.413 68.421 4.40 0.0 37.50 2.90
1902 4836 0.108615 CTGAAGGCTAGTGGTCACCG 60.109 60.000 0.00 0.0 0.00 4.94
1904 4838 3.196685 AGATTCTGAAGGCTAGTGGTCAC 59.803 47.826 0.00 0.0 0.00 3.67
2037 4972 3.066190 CGACTACCGGTGGGAGCA 61.066 66.667 23.02 0.0 36.97 4.26
2281 5488 5.507077 GTGTTGTTCGATTGTAAAAGCTGA 58.493 37.500 0.00 0.0 0.00 4.26
3154 6386 8.246180 AGACAATGACACATTTAATAAAGCAGG 58.754 33.333 0.00 0.0 0.00 4.85
3182 6414 7.519927 TGTAACCCAAGACTTTATAACCAAGT 58.480 34.615 0.00 0.0 37.18 3.16
3428 6660 1.540267 TGGAGTCAAGACAGTAGCGAC 59.460 52.381 2.72 0.0 0.00 5.19
3430 6662 1.542030 AGTGGAGTCAAGACAGTAGCG 59.458 52.381 2.72 0.0 0.00 4.26
5106 8406 1.880340 CTCTTCCGTCAGCGATGGC 60.880 63.158 0.00 0.0 38.52 4.40


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

AutoCloner maintained by Alex Coulton.