Multiple sequence alignment - TraesCS2B01G536800

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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 TraesCS2B01G536800 chr2B 100.000 2549 0 0 1 2549 732224837 732222289 0.000000e+00 4708
1 TraesCS2B01G536800 chr2B 98.925 93 1 0 1 93 732024316 732024224 1.570000e-37 167
2 TraesCS2B01G536800 chr2B 100.000 86 0 0 1 86 578135693 578135778 2.620000e-35 159
3 TraesCS2B01G536800 chr2D 97.058 2549 71 4 4 2549 602009826 602007279 0.000000e+00 4289
4 TraesCS2B01G536800 chr4B 87.621 2278 225 29 303 2549 654126317 654124066 0.000000e+00 2591
5 TraesCS2B01G536800 chr4B 87.049 1498 147 24 108 1561 654131805 654130311 0.000000e+00 1648
6 TraesCS2B01G536800 chr4B 88.247 987 104 5 326 1303 638988392 638987409 0.000000e+00 1170
7 TraesCS2B01G536800 chr4B 81.159 1242 180 34 1323 2538 638987314 638986101 0.000000e+00 948
8 TraesCS2B01G536800 chr4B 83.929 504 76 4 2049 2549 654129278 654128777 6.380000e-131 477
9 TraesCS2B01G536800 chr4B 77.503 849 149 28 330 1166 431795281 431796099 2.970000e-129 472
10 TraesCS2B01G536800 chr4B 88.557 201 23 0 1550 1750 654129765 654129565 7.040000e-61 244
11 TraesCS2B01G536800 chr5A 87.299 2244 238 27 276 2490 691814132 691811907 0.000000e+00 2521
12 TraesCS2B01G536800 chr5A 87.110 993 110 6 326 1303 678082356 678083345 0.000000e+00 1109
13 TraesCS2B01G536800 chr5A 82.463 1226 183 23 1323 2533 678083440 678084648 0.000000e+00 1044
14 TraesCS2B01G536800 chr5A 85.455 165 20 1 108 268 691814348 691814184 4.360000e-38 169
15 TraesCS2B01G536800 chr4D 87.714 993 104 7 326 1303 497667535 497666546 0.000000e+00 1142
16 TraesCS2B01G536800 chr4D 81.818 1232 190 26 1323 2538 497666451 497665238 0.000000e+00 1003
17 TraesCS2B01G536800 chr4D 75.663 867 142 55 325 1164 631004 630180 4.010000e-98 368
18 TraesCS2B01G536800 chr4A 82.456 1140 171 22 108 1236 731002619 731003740 0.000000e+00 970
19 TraesCS2B01G536800 chr5B 81.730 925 139 19 325 1234 6918243 6919152 0.000000e+00 745
20 TraesCS2B01G536800 chr5B 98.864 88 1 0 1 88 473868824 473868737 9.440000e-35 158
21 TraesCS2B01G536800 chr3B 98.837 86 1 0 1 86 213706399 213706314 1.220000e-33 154
22 TraesCS2B01G536800 chr3B 98.837 86 1 0 1 86 671522875 671522790 1.220000e-33 154
23 TraesCS2B01G536800 chr7A 95.238 84 4 0 2 85 158193849 158193932 1.590000e-27 134


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 TraesCS2B01G536800 chr2B 732222289 732224837 2548 True 4708.0 4708 100.0000 1 2549 1 chr2B.!!$R2 2548
1 TraesCS2B01G536800 chr2D 602007279 602009826 2547 True 4289.0 4289 97.0580 4 2549 1 chr2D.!!$R1 2545
2 TraesCS2B01G536800 chr4B 654124066 654131805 7739 True 1240.0 2591 86.7890 108 2549 4 chr4B.!!$R2 2441
3 TraesCS2B01G536800 chr4B 638986101 638988392 2291 True 1059.0 1170 84.7030 326 2538 2 chr4B.!!$R1 2212
4 TraesCS2B01G536800 chr4B 431795281 431796099 818 False 472.0 472 77.5030 330 1166 1 chr4B.!!$F1 836
5 TraesCS2B01G536800 chr5A 691811907 691814348 2441 True 1345.0 2521 86.3770 108 2490 2 chr5A.!!$R1 2382
6 TraesCS2B01G536800 chr5A 678082356 678084648 2292 False 1076.5 1109 84.7865 326 2533 2 chr5A.!!$F1 2207
7 TraesCS2B01G536800 chr4D 497665238 497667535 2297 True 1072.5 1142 84.7660 326 2538 2 chr4D.!!$R2 2212
8 TraesCS2B01G536800 chr4D 630180 631004 824 True 368.0 368 75.6630 325 1164 1 chr4D.!!$R1 839
9 TraesCS2B01G536800 chr4A 731002619 731003740 1121 False 970.0 970 82.4560 108 1236 1 chr4A.!!$F1 1128
10 TraesCS2B01G536800 chr5B 6918243 6919152 909 False 745.0 745 81.7300 325 1234 1 chr5B.!!$F1 909

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
70 71 0.040958 CGTCAAGTTTGAGCACCAGC 60.041 55.0 0.0 0.0 37.98 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 7379 0.745486 TCTATCGCCTCAACGTCGGA 60.745 55.0 0.0 0.0 0.0 4.55 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 5.297547 AGCACCAGTTATATGTATTCCACG 58.702 41.667 0.00 0.00 0.00 4.94
31 32 8.335356 CCAGTTATATGTATTCCACGAGTTTTG 58.665 37.037 0.00 0.00 0.00 2.44
36 37 1.981256 ATTCCACGAGTTTTGGCACT 58.019 45.000 0.00 0.00 33.71 4.40
40 41 2.875933 TCCACGAGTTTTGGCACTAAAG 59.124 45.455 0.00 0.00 33.71 1.85
60 61 4.287238 AGTGATTTTTCGCGTCAAGTTT 57.713 36.364 5.77 0.00 0.00 2.66
61 62 4.035017 AGTGATTTTTCGCGTCAAGTTTG 58.965 39.130 5.77 0.00 0.00 2.93
62 63 4.032355 GTGATTTTTCGCGTCAAGTTTGA 58.968 39.130 5.77 0.00 34.20 2.69
63 64 4.144731 GTGATTTTTCGCGTCAAGTTTGAG 59.855 41.667 5.77 0.00 37.98 3.02
68 69 1.771073 CGCGTCAAGTTTGAGCACCA 61.771 55.000 0.00 0.00 37.98 4.17
70 71 0.040958 CGTCAAGTTTGAGCACCAGC 60.041 55.000 0.00 0.00 37.98 4.85
84 85 2.094762 ACCAGCGGTGTAATTGACTC 57.905 50.000 14.40 0.00 32.98 3.36
85 86 1.623811 ACCAGCGGTGTAATTGACTCT 59.376 47.619 14.40 0.00 32.98 3.24
148 150 2.239654 GGTTCAGATGATTCAGGGACCA 59.760 50.000 7.86 0.00 0.00 4.02
256 264 2.079158 CGACATTGGTCATGCTCAAGT 58.921 47.619 6.67 5.31 44.54 3.16
307 360 0.247974 CGGTACCATGTCGTCGAGTC 60.248 60.000 13.54 0.00 0.00 3.36
420 473 1.302033 CAGGCACTTCTCAGCGGTT 60.302 57.895 0.00 0.00 34.60 4.44
1212 6527 1.141881 GGCCTTGATCTTCGCGAGA 59.858 57.895 9.59 9.85 39.13 4.04
1244 6559 0.179086 TTCGTGCTCACACTCTGCAA 60.179 50.000 0.69 0.00 45.10 4.08
1250 6565 2.281070 CACACTCTGCAACCCGCT 60.281 61.111 0.00 0.00 43.06 5.52
1317 6632 1.805254 GGAGCCGCTGTACTTCGTA 59.195 57.895 0.00 0.00 0.00 3.43
1473 6869 4.857509 AATCTCTAGCCCGTTCAGTATC 57.142 45.455 0.00 0.00 0.00 2.24
1485 6881 0.755698 TCAGTATCCCACCTCCGCTC 60.756 60.000 0.00 0.00 0.00 5.03
1616 7018 1.136329 AGGTCTGGAGTGCCAATGGT 61.136 55.000 0.00 0.00 45.41 3.55
1705 7107 2.439883 GGAGGCGGACGAGGTAGT 60.440 66.667 0.00 0.00 0.00 2.73
1815 7217 1.812686 GCTGGGTCTGGTACACGACA 61.813 60.000 13.58 0.00 37.92 4.35
1818 7220 1.183549 GGGTCTGGTACACGACATCT 58.816 55.000 13.58 0.00 37.92 2.90
1867 7269 3.119814 CGATGAATCGTAGATGATCGGGT 60.120 47.826 4.53 0.00 45.12 5.28
1917 7322 1.153086 GGCGTCGTAGAGGTAGGGA 60.153 63.158 0.00 0.00 45.16 4.20
1974 7379 2.169810 AATGGTCACCTTGGGCCCT 61.170 57.895 25.70 0.00 0.00 5.19
2052 7457 4.308458 TTCACCACGGCTCCCACG 62.308 66.667 0.00 0.00 37.36 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.294356 TCGTGGAATACATATAACTGGTGC 58.706 41.667 0.00 0.00 0.00 5.01
4 5 6.726490 ACTCGTGGAATACATATAACTGGT 57.274 37.500 0.00 0.00 0.00 4.00
6 7 8.335356 CCAAAACTCGTGGAATACATATAACTG 58.665 37.037 0.00 0.00 38.54 3.16
7 8 7.012044 GCCAAAACTCGTGGAATACATATAACT 59.988 37.037 0.00 0.00 38.54 2.24
8 9 7.130269 GCCAAAACTCGTGGAATACATATAAC 58.870 38.462 0.00 0.00 38.54 1.89
9 10 6.824196 TGCCAAAACTCGTGGAATACATATAA 59.176 34.615 0.00 0.00 38.54 0.98
10 11 6.259167 GTGCCAAAACTCGTGGAATACATATA 59.741 38.462 0.00 0.00 38.54 0.86
11 12 5.065988 GTGCCAAAACTCGTGGAATACATAT 59.934 40.000 0.00 0.00 38.54 1.78
12 13 4.393680 GTGCCAAAACTCGTGGAATACATA 59.606 41.667 0.00 0.00 38.54 2.29
19 20 2.623878 TTAGTGCCAAAACTCGTGGA 57.376 45.000 0.00 0.00 38.54 4.02
22 23 3.537580 TCACTTTAGTGCCAAAACTCGT 58.462 40.909 5.00 0.00 45.25 4.18
24 25 7.305993 CGAAAAATCACTTTAGTGCCAAAACTC 60.306 37.037 5.00 0.00 45.25 3.01
31 32 2.908626 CGCGAAAAATCACTTTAGTGCC 59.091 45.455 0.00 0.00 45.25 5.01
36 37 5.412526 ACTTGACGCGAAAAATCACTTTA 57.587 34.783 15.93 0.00 0.00 1.85
40 41 4.032355 TCAAACTTGACGCGAAAAATCAC 58.968 39.130 15.93 0.00 31.01 3.06
43 44 3.042887 GCTCAAACTTGACGCGAAAAAT 58.957 40.909 15.93 0.00 32.90 1.82
50 51 0.040958 CTGGTGCTCAAACTTGACGC 60.041 55.000 6.83 6.83 34.29 5.19
53 54 1.165907 CCGCTGGTGCTCAAACTTGA 61.166 55.000 0.00 0.00 36.97 3.02
54 55 1.283793 CCGCTGGTGCTCAAACTTG 59.716 57.895 0.00 0.00 36.97 3.16
148 150 5.821995 CACCAATTGAACATTTTCCTTTGGT 59.178 36.000 16.64 16.64 46.66 3.67
256 264 0.963225 TTGTTGATGGACGAGACCGA 59.037 50.000 0.00 0.00 39.50 4.69
321 374 1.209019 CTACAGCTGCAGGAGACCAAT 59.791 52.381 17.12 0.00 0.00 3.16
999 6314 1.672356 GCACCTGGTGTCGCTCATT 60.672 57.895 26.48 0.00 35.75 2.57
1120 6435 2.048503 GTACAAGGGCGTGCTCGT 60.049 61.111 10.18 0.00 39.49 4.18
1212 6527 2.047844 ACGAAGCTGCACATCGCT 60.048 55.556 18.07 3.47 43.06 4.93
1250 6565 1.158466 TCCAGAGAGGGCAAGACCA 59.842 57.895 0.00 0.00 42.05 4.02
1473 6869 1.377333 GAAAAGGAGCGGAGGTGGG 60.377 63.158 0.00 0.00 39.88 4.61
1485 6881 2.380410 CGGCTGGTCGTCGAAAAGG 61.380 63.158 0.00 0.00 45.36 3.11
1616 7018 0.796870 CAACGTCTACATCGCGCAGA 60.797 55.000 8.75 6.27 0.00 4.26
1974 7379 0.745486 TCTATCGCCTCAACGTCGGA 60.745 55.000 0.00 0.00 0.00 4.55
2052 7457 1.591863 GAATAGCTCCGTGACGCCC 60.592 63.158 0.00 0.00 0.00 6.13
2254 7671 2.169091 CGCGCGCTTCAACGTTTA 59.831 55.556 30.48 0.00 34.88 2.01


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

AutoCloner maintained by Alex Coulton.