Multiple sequence alignment - TraesCS2A01G510500

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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 TraesCS2A01G510500 chr2A 100.000 2330 0 0 1 2330 735696437 735698766 0.000000e+00 4303.0
1 TraesCS2A01G510500 chr2A 83.657 361 49 4 15 369 735764790 735764434 4.800000e-87 331.0
2 TraesCS2A01G510500 chr1D 97.968 1624 29 4 708 2330 436606150 436604530 0.000000e+00 2813.0
3 TraesCS2A01G510500 chr1D 85.556 90 13 0 704 793 379836504 379836415 6.850000e-16 95.3
4 TraesCS2A01G510500 chr2B 94.820 946 46 3 1386 2330 391354662 391355605 0.000000e+00 1472.0
5 TraesCS2A01G510500 chr7B 94.220 917 22 9 1386 2295 730141906 730142798 0.000000e+00 1371.0
6 TraesCS2A01G510500 chr7B 91.738 581 30 6 828 1392 730140583 730141161 0.000000e+00 791.0
7 TraesCS2A01G510500 chr7B 87.429 525 54 8 1386 1908 708134031 708133517 5.540000e-166 593.0
8 TraesCS2A01G510500 chr7B 84.836 244 34 3 2089 2330 708133440 708133198 2.310000e-60 243.0
9 TraesCS2A01G510500 chr1B 94.111 917 23 9 1386 2295 614185937 614186829 0.000000e+00 1365.0
10 TraesCS2A01G510500 chr1B 91.146 576 25 9 828 1392 614184632 614185192 0.000000e+00 758.0
11 TraesCS2A01G510500 chr2D 92.351 706 38 3 4 709 603399135 603399824 0.000000e+00 990.0
12 TraesCS2A01G510500 chr2D 88.293 709 80 2 4 709 603499487 603500195 0.000000e+00 846.0
13 TraesCS2A01G510500 chr6A 95.392 586 25 2 1386 1970 566690212 566689628 0.000000e+00 931.0
14 TraesCS2A01G510500 chr6A 88.866 476 36 7 752 1214 566691697 566691226 9.340000e-159 569.0
15 TraesCS2A01G510500 chr6A 93.913 345 20 1 1048 1392 566691267 566690924 9.540000e-144 520.0
16 TraesCS2A01G510500 chr3D 91.079 695 45 9 708 1392 91975584 91976271 0.000000e+00 924.0
17 TraesCS2A01G510500 chr3D 90.593 691 49 7 708 1392 472313592 472314272 0.000000e+00 902.0
18 TraesCS2A01G510500 chr3D 92.941 510 21 6 1827 2330 91976637 91977137 0.000000e+00 728.0
19 TraesCS2A01G510500 chr3D 92.054 516 21 6 1827 2330 472314638 472315145 0.000000e+00 708.0
20 TraesCS2A01G510500 chr4D 90.072 695 49 10 708 1392 8130217 8130901 0.000000e+00 883.0
21 TraesCS2A01G510500 chr4D 95.238 147 7 0 1899 2045 8132380 8132526 1.390000e-57 233.0
22 TraesCS2A01G510500 chr6D 90.072 695 48 11 708 1392 23615864 23616547 0.000000e+00 881.0
23 TraesCS2A01G510500 chr6D 92.427 515 20 7 1827 2330 23616848 23617354 0.000000e+00 717.0
24 TraesCS2A01G510500 chr7D 92.941 510 22 5 1827 2330 524444166 524443665 0.000000e+00 730.0
25 TraesCS2A01G510500 chr7D 92.260 323 19 4 1072 1392 524444849 524444531 9.820000e-124 453.0
26 TraesCS2A01G510500 chr7D 92.265 181 9 4 708 884 524445356 524445177 3.840000e-63 252.0
27 TraesCS2A01G510500 chr7D 85.227 88 11 2 708 794 93953830 93953744 3.190000e-14 89.8
28 TraesCS2A01G510500 chr5B 87.452 526 49 11 1386 1908 334895397 334895908 7.170000e-165 590.0
29 TraesCS2A01G510500 chr3B 82.353 510 78 11 1396 1900 658390179 658389677 1.280000e-117 433.0
30 TraesCS2A01G510500 chr4B 81.481 513 76 15 1396 1900 175901661 175902162 1.000000e-108 403.0
31 TraesCS2A01G510500 chr7A 88.372 86 10 0 708 793 719572161 719572246 1.140000e-18 104.0
32 TraesCS2A01G510500 chr5A 89.873 79 8 0 708 786 225194250 225194328 4.100000e-18 102.0


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 TraesCS2A01G510500 chr2A 735696437 735698766 2329 False 4303.000000 4303 100.000000 1 2330 1 chr2A.!!$F1 2329
1 TraesCS2A01G510500 chr1D 436604530 436606150 1620 True 2813.000000 2813 97.968000 708 2330 1 chr1D.!!$R2 1622
2 TraesCS2A01G510500 chr2B 391354662 391355605 943 False 1472.000000 1472 94.820000 1386 2330 1 chr2B.!!$F1 944
3 TraesCS2A01G510500 chr7B 730140583 730142798 2215 False 1081.000000 1371 92.979000 828 2295 2 chr7B.!!$F1 1467
4 TraesCS2A01G510500 chr7B 708133198 708134031 833 True 418.000000 593 86.132500 1386 2330 2 chr7B.!!$R1 944
5 TraesCS2A01G510500 chr1B 614184632 614186829 2197 False 1061.500000 1365 92.628500 828 2295 2 chr1B.!!$F1 1467
6 TraesCS2A01G510500 chr2D 603399135 603399824 689 False 990.000000 990 92.351000 4 709 1 chr2D.!!$F1 705
7 TraesCS2A01G510500 chr2D 603499487 603500195 708 False 846.000000 846 88.293000 4 709 1 chr2D.!!$F2 705
8 TraesCS2A01G510500 chr6A 566689628 566691697 2069 True 673.333333 931 92.723667 752 1970 3 chr6A.!!$R1 1218
9 TraesCS2A01G510500 chr3D 91975584 91977137 1553 False 826.000000 924 92.010000 708 2330 2 chr3D.!!$F1 1622
10 TraesCS2A01G510500 chr3D 472313592 472315145 1553 False 805.000000 902 91.323500 708 2330 2 chr3D.!!$F2 1622
11 TraesCS2A01G510500 chr4D 8130217 8132526 2309 False 558.000000 883 92.655000 708 2045 2 chr4D.!!$F1 1337
12 TraesCS2A01G510500 chr6D 23615864 23617354 1490 False 799.000000 881 91.249500 708 2330 2 chr6D.!!$F1 1622
13 TraesCS2A01G510500 chr7D 524443665 524445356 1691 True 478.333333 730 92.488667 708 2330 3 chr7D.!!$R2 1622
14 TraesCS2A01G510500 chr5B 334895397 334895908 511 False 590.000000 590 87.452000 1386 1908 1 chr5B.!!$F1 522
15 TraesCS2A01G510500 chr3B 658389677 658390179 502 True 433.000000 433 82.353000 1396 1900 1 chr3B.!!$R1 504
16 TraesCS2A01G510500 chr4B 175901661 175902162 501 False 403.000000 403 81.481000 1396 1900 1 chr4B.!!$F1 504

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
43 44 0.818296 TGTAAGCGAGAGAGAAGGGC 59.182 55.000 0.0 0.0 0.0 5.19 F
749 764 2.106338 TGAGTTGGTGATGATGGTGTGT 59.894 45.455 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1037 1066 2.050918 GGGTAGGGGGAAGAAGAGATG 58.949 57.143 0.0 0.0 0.0 2.90 R
1799 3454 5.851177 CGATCACACACAACAAGGAAATAAC 59.149 40.000 0.0 0.0 0.0 1.89 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
43 44 0.818296 TGTAAGCGAGAGAGAAGGGC 59.182 55.000 0.00 0.00 0.00 5.19
59 60 3.637911 AGGGCCATGTTCATTACGTTA 57.362 42.857 6.18 0.00 0.00 3.18
106 107 3.645053 AGGGAGAGATATGGGTCATGT 57.355 47.619 0.00 0.00 0.00 3.21
124 125 9.497030 GGGTCATGTTTAATTTGTTTTGTTTTC 57.503 29.630 0.00 0.00 0.00 2.29
129 130 7.965045 TGTTTAATTTGTTTTGTTTTCTCCCG 58.035 30.769 0.00 0.00 0.00 5.14
130 131 7.817962 TGTTTAATTTGTTTTGTTTTCTCCCGA 59.182 29.630 0.00 0.00 0.00 5.14
156 157 2.205022 CCACATGTGAGGGACATTGT 57.795 50.000 27.46 0.00 43.20 2.71
170 171 4.892965 TTGTGCCCGTGCCAGCTT 62.893 61.111 0.00 0.00 36.33 3.74
193 194 5.502079 TCGAAGGTCATTTTAGGCCAAATA 58.498 37.500 5.01 0.00 0.00 1.40
272 273 9.614792 AATATAAGGGCAAAACTAAGTAGAGTG 57.385 33.333 0.00 0.00 0.00 3.51
295 296 9.569122 AGTGAAAAAGTAAGAGCAAACCTTATA 57.431 29.630 0.00 0.00 0.00 0.98
388 389 5.245531 CCATCACCTTTTGTCTGCTAGTAA 58.754 41.667 0.00 0.00 0.00 2.24
395 396 5.371115 TTTTGTCTGCTAGTAAATGCACC 57.629 39.130 0.00 0.00 35.20 5.01
399 400 4.163268 TGTCTGCTAGTAAATGCACCCATA 59.837 41.667 0.00 0.00 35.20 2.74
414 415 3.757493 CACCCATACGACTAGAGGGATAC 59.243 52.174 2.29 0.00 42.25 2.24
526 530 8.956426 TCCCTAAAAATAGAACATTTAGCAGTG 58.044 33.333 0.00 0.00 36.02 3.66
533 537 4.324267 AGAACATTTAGCAGTGGGTGTAC 58.676 43.478 0.00 0.00 0.00 2.90
616 620 7.624549 AGATTTTGCTATTTCTCAGGTGTCTA 58.375 34.615 0.00 0.00 0.00 2.59
727 742 7.939588 GGCCACATCTCTACTCCTATAAAATTT 59.060 37.037 0.00 0.00 0.00 1.82
749 764 2.106338 TGAGTTGGTGATGATGGTGTGT 59.894 45.455 0.00 0.00 0.00 3.72
824 839 3.539604 CCCCACTTCACATTTGCAAAAA 58.460 40.909 17.19 4.89 0.00 1.94
1037 1066 2.610859 TTCCCCCTCCTGCCTGTC 60.611 66.667 0.00 0.00 0.00 3.51
1064 1095 1.001248 TTCCCCCTACCCTGTCTCG 59.999 63.158 0.00 0.00 0.00 4.04
1132 1298 1.310933 GGTCGGCGACACCTCTTCTA 61.311 60.000 37.13 0.00 33.68 2.10
1384 1557 2.646175 GGCACTACCCACGAGCTCA 61.646 63.158 15.40 0.00 0.00 4.26
1393 2317 1.367471 CACGAGCTCAACTGTCCCA 59.633 57.895 15.40 0.00 0.00 4.37
1799 3454 4.301072 TTTCAGGTCAGACCCCAAATAG 57.699 45.455 16.72 0.00 39.75 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.748729 GGTCCCACACCACAAAACGA 60.749 55.000 0.00 0.00 45.98 3.85
1 2 1.731093 GGTCCCACACCACAAAACG 59.269 57.895 0.00 0.00 45.98 3.60
43 44 7.007905 CGGAAAAACATAACGTAATGAACATGG 59.992 37.037 0.00 0.00 0.00 3.66
59 60 1.076350 TGGGACCCATCGGAAAAACAT 59.924 47.619 9.95 0.00 0.00 2.71
106 107 7.009357 CGTCGGGAGAAAACAAAACAAATTAAA 59.991 33.333 0.00 0.00 42.89 1.52
129 130 1.079127 CTCACATGTGGGACCCGTC 60.079 63.158 21.75 2.09 31.13 4.79
130 131 2.592993 CCTCACATGTGGGACCCGT 61.593 63.158 27.64 0.00 31.13 5.28
170 171 3.426787 TTGGCCTAAAATGACCTTCGA 57.573 42.857 3.32 0.00 0.00 3.71
174 175 5.206905 AGGTATTTGGCCTAAAATGACCT 57.793 39.130 15.52 15.52 33.46 3.85
193 194 0.872881 CGTGTCGTTCGGTCAAAGGT 60.873 55.000 0.00 0.00 0.00 3.50
295 296 5.514500 TTGCCCTTAATGAGAACTTACCT 57.486 39.130 0.00 0.00 0.00 3.08
300 301 5.482006 GCATTTTTGCCCTTAATGAGAACT 58.518 37.500 0.00 0.00 32.36 3.01
388 389 2.365617 CCTCTAGTCGTATGGGTGCATT 59.634 50.000 0.00 0.00 0.00 3.56
395 396 3.436015 CACGTATCCCTCTAGTCGTATGG 59.564 52.174 0.00 0.00 0.00 2.74
399 400 1.307097 GCACGTATCCCTCTAGTCGT 58.693 55.000 0.00 0.00 0.00 4.34
414 415 0.457851 CCTCTTCTCCCTAGTGCACG 59.542 60.000 12.01 0.00 0.00 5.34
499 503 9.178758 ACTGCTAAATGTTCTATTTTTAGGGAG 57.821 33.333 0.00 0.00 34.82 4.30
516 520 2.910319 TGGAGTACACCCACTGCTAAAT 59.090 45.455 6.89 0.00 37.72 1.40
526 530 6.887626 TCAATTAAAACTTGGAGTACACCC 57.112 37.500 6.89 2.15 0.00 4.61
591 595 6.479884 AGACACCTGAGAAATAGCAAAATCT 58.520 36.000 0.00 0.00 0.00 2.40
593 597 8.635765 TTTAGACACCTGAGAAATAGCAAAAT 57.364 30.769 0.00 0.00 0.00 1.82
646 661 0.873312 CGACGAGCTCCATCATGGTG 60.873 60.000 8.47 1.79 39.03 4.17
647 662 1.439228 CGACGAGCTCCATCATGGT 59.561 57.895 8.47 0.00 39.03 3.55
648 663 1.300465 CCGACGAGCTCCATCATGG 60.300 63.158 8.47 0.00 39.43 3.66
651 666 0.466372 ATCTCCGACGAGCTCCATCA 60.466 55.000 8.47 0.00 35.94 3.07
654 669 2.180862 CGATCTCCGACGAGCTCCA 61.181 63.158 8.47 0.00 41.76 3.86
727 742 3.148412 CACACCATCATCACCAACTCAA 58.852 45.455 0.00 0.00 0.00 3.02
749 764 6.174720 AGGTCGAAAATTATAGATGGCAGA 57.825 37.500 0.00 0.00 0.00 4.26
824 839 3.264450 CAGGACATAGAGGACAAGGGTTT 59.736 47.826 0.00 0.00 0.00 3.27
1037 1066 2.050918 GGGTAGGGGGAAGAAGAGATG 58.949 57.143 0.00 0.00 0.00 2.90
1132 1298 3.884091 GCTTCTGCATCAAAGATGGAGAT 59.116 43.478 24.99 0.00 44.05 2.75
1366 1539 2.167398 TTGAGCTCGTGGGTAGTGCC 62.167 60.000 9.64 0.00 0.00 5.01
1384 1557 4.898861 TCCTTTTGCTTATTTGGGACAGTT 59.101 37.500 0.00 0.00 42.39 3.16
1393 2317 5.243954 GGAGTGGTCTTCCTTTTGCTTATTT 59.756 40.000 0.00 0.00 34.23 1.40
1799 3454 5.851177 CGATCACACACAACAAGGAAATAAC 59.149 40.000 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.