Multiple sequence alignment - TraesCS2A01G228200

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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 TraesCS2A01G228200 chr2A 100.000 3522 0 0 1 3522 249738556 249742077 0 6505
1 TraesCS2A01G228200 chr2D 98.717 1325 16 1 1477 2800 250617020 250618344 0 2351
2 TraesCS2A01G228200 chr2D 95.548 831 25 6 660 1482 250610989 250611815 0 1319
3 TraesCS2A01G228200 chr7A 96.694 726 20 2 2800 3522 94461731 94462455 0 1205
4 TraesCS2A01G228200 chr7A 94.595 666 36 0 1 666 200269005 200268340 0 1031
5 TraesCS2A01G228200 chr7A 94.394 660 37 0 4 663 89521768 89521109 0 1014
6 TraesCS2A01G228200 chr1A 96.685 724 18 4 2804 3522 540654766 540654044 0 1199
7 TraesCS2A01G228200 chr1A 96.676 722 21 2 2804 3522 309743611 309744332 0 1197
8 TraesCS2A01G228200 chr1A 95.188 665 31 1 4 668 436659411 436658748 0 1050
9 TraesCS2A01G228200 chr4A 94.744 723 35 2 2803 3522 436449900 436449178 0 1122
10 TraesCS2A01G228200 chr4A 95.324 663 31 0 1 663 578021428 578022090 0 1053
11 TraesCS2A01G228200 chr6A 96.682 663 22 0 1 663 14225667 14225005 0 1103
12 TraesCS2A01G228200 chr6A 96.112 643 23 2 21 663 14231255 14230615 0 1048
13 TraesCS2A01G228200 chr6A 94.611 668 34 2 1 668 591225485 591224820 0 1033
14 TraesCS2A01G228200 chr5A 94.199 724 37 3 2804 3522 264085102 264085825 0 1099
15 TraesCS2A01G228200 chr6B 93.793 725 41 2 2801 3522 714113066 714113789 0 1086
16 TraesCS2A01G228200 chr6B 93.629 722 42 2 2804 3522 714095251 714095971 0 1075
17 TraesCS2A01G228200 chr5B 93.620 721 45 1 2803 3522 225539871 225539151 0 1075
18 TraesCS2A01G228200 chr7B 93.611 720 44 2 2804 3522 648055431 648054713 0 1074
19 TraesCS2A01G228200 chr3A 95.324 663 31 0 1 663 150222981 150223643 0 1053
20 TraesCS2A01G228200 chr3A 94.461 668 36 1 1 668 700597855 700597189 0 1027


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 TraesCS2A01G228200 chr2A 249738556 249742077 3521 False 6505 6505 100.000 1 3522 1 chr2A.!!$F1 3521
1 TraesCS2A01G228200 chr2D 250617020 250618344 1324 False 2351 2351 98.717 1477 2800 1 chr2D.!!$F2 1323
2 TraesCS2A01G228200 chr2D 250610989 250611815 826 False 1319 1319 95.548 660 1482 1 chr2D.!!$F1 822
3 TraesCS2A01G228200 chr7A 94461731 94462455 724 False 1205 1205 96.694 2800 3522 1 chr7A.!!$F1 722
4 TraesCS2A01G228200 chr7A 200268340 200269005 665 True 1031 1031 94.595 1 666 1 chr7A.!!$R2 665
5 TraesCS2A01G228200 chr7A 89521109 89521768 659 True 1014 1014 94.394 4 663 1 chr7A.!!$R1 659
6 TraesCS2A01G228200 chr1A 540654044 540654766 722 True 1199 1199 96.685 2804 3522 1 chr1A.!!$R2 718
7 TraesCS2A01G228200 chr1A 309743611 309744332 721 False 1197 1197 96.676 2804 3522 1 chr1A.!!$F1 718
8 TraesCS2A01G228200 chr1A 436658748 436659411 663 True 1050 1050 95.188 4 668 1 chr1A.!!$R1 664
9 TraesCS2A01G228200 chr4A 436449178 436449900 722 True 1122 1122 94.744 2803 3522 1 chr4A.!!$R1 719
10 TraesCS2A01G228200 chr4A 578021428 578022090 662 False 1053 1053 95.324 1 663 1 chr4A.!!$F1 662
11 TraesCS2A01G228200 chr6A 14225005 14225667 662 True 1103 1103 96.682 1 663 1 chr6A.!!$R1 662
12 TraesCS2A01G228200 chr6A 14230615 14231255 640 True 1048 1048 96.112 21 663 1 chr6A.!!$R2 642
13 TraesCS2A01G228200 chr6A 591224820 591225485 665 True 1033 1033 94.611 1 668 1 chr6A.!!$R3 667
14 TraesCS2A01G228200 chr5A 264085102 264085825 723 False 1099 1099 94.199 2804 3522 1 chr5A.!!$F1 718
15 TraesCS2A01G228200 chr6B 714113066 714113789 723 False 1086 1086 93.793 2801 3522 1 chr6B.!!$F2 721
16 TraesCS2A01G228200 chr6B 714095251 714095971 720 False 1075 1075 93.629 2804 3522 1 chr6B.!!$F1 718
17 TraesCS2A01G228200 chr5B 225539151 225539871 720 True 1075 1075 93.620 2803 3522 1 chr5B.!!$R1 719
18 TraesCS2A01G228200 chr7B 648054713 648055431 718 True 1074 1074 93.611 2804 3522 1 chr7B.!!$R1 718
19 TraesCS2A01G228200 chr3A 150222981 150223643 662 False 1053 1053 95.324 1 663 1 chr3A.!!$F1 662
20 TraesCS2A01G228200 chr3A 700597189 700597855 666 True 1027 1027 94.461 1 668 1 chr3A.!!$R1 667

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
796 797 0.254747 CCAAGGTTCGAAGGCCCATA 59.745 55.0 0.0 0.0 0.0 2.74 F
1195 1204 0.463654 AAGAGTTCGCTGGTTGTGCA 60.464 50.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 1691 0.514255 CAGGATATGCAATGACGGCG 59.486 55.0 4.80 4.8 0.0 6.46 R
2787 2797 1.909700 ACCAATTGATGACGGCAAGT 58.090 45.0 7.12 0.0 0.0 3.16 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
304 305 1.138247 CCGACGACTACTTTCCCGG 59.862 63.158 0.00 0.00 0.00 5.73
348 349 1.366854 CGACCTCCTCGACGACATGA 61.367 60.000 0.00 0.00 46.14 3.07
366 367 4.778415 CAGGCGAGGACACCGACG 62.778 72.222 0.00 0.00 40.56 5.12
679 680 7.945033 TTCCAACACTATTCTTTTTGCAATC 57.055 32.000 0.00 0.00 0.00 2.67
685 686 9.683069 AACACTATTCTTTTTGCAATCTAAGTG 57.317 29.630 0.00 10.43 36.43 3.16
796 797 0.254747 CCAAGGTTCGAAGGCCCATA 59.745 55.000 0.00 0.00 0.00 2.74
811 812 0.525761 CCATACAAAGTGGCCCGTTG 59.474 55.000 14.90 14.90 38.35 4.10
826 827 3.616219 CCCGTTGAGTCCATATCCAAAA 58.384 45.455 0.00 0.00 0.00 2.44
827 828 4.013728 CCCGTTGAGTCCATATCCAAAAA 58.986 43.478 0.00 0.00 0.00 1.94
828 829 4.644685 CCCGTTGAGTCCATATCCAAAAAT 59.355 41.667 0.00 0.00 0.00 1.82
829 830 5.825679 CCCGTTGAGTCCATATCCAAAAATA 59.174 40.000 0.00 0.00 0.00 1.40
830 831 6.320164 CCCGTTGAGTCCATATCCAAAAATAA 59.680 38.462 0.00 0.00 0.00 1.40
832 833 9.062524 CCGTTGAGTCCATATCCAAAAATAATA 57.937 33.333 0.00 0.00 0.00 0.98
833 834 9.878599 CGTTGAGTCCATATCCAAAAATAATAC 57.121 33.333 0.00 0.00 0.00 1.89
835 836 8.934023 TGAGTCCATATCCAAAAATAATACCC 57.066 34.615 0.00 0.00 0.00 3.69
841 850 2.944349 TCCAAAAATAATACCCCGTCGC 59.056 45.455 0.00 0.00 0.00 5.19
932 941 8.309163 TCATTTTCATTTTCATTTTCGGAAGG 57.691 30.769 0.00 0.00 0.00 3.46
1085 1094 0.976073 TGACCACCGAATCCCTCTCC 60.976 60.000 0.00 0.00 0.00 3.71
1108 1117 7.319646 TCCTTATTCCCAACAATTCGAAATTG 58.680 34.615 0.00 10.01 35.29 2.32
1164 1173 8.761575 AAACGCATCAATCTGTGATTATTTTT 57.238 26.923 0.00 0.00 45.13 1.94
1195 1204 0.463654 AAGAGTTCGCTGGTTGTGCA 60.464 50.000 0.00 0.00 0.00 4.57
1235 1244 4.769345 TGGGGCACAGAATTTTTCTTTT 57.231 36.364 0.00 0.00 38.11 2.27
1295 1304 0.676466 CCATGTAAACTGGCAGCGGA 60.676 55.000 15.89 0.00 0.00 5.54
1351 1360 1.731720 GGGATCGAGGCATATCAAGC 58.268 55.000 0.00 0.00 0.00 4.01
1432 1441 5.825593 TTTTCTCTGGGTGTGAATCTAGT 57.174 39.130 0.00 0.00 0.00 2.57
1438 1447 3.708631 CTGGGTGTGAATCTAGTCCATCT 59.291 47.826 0.00 0.00 0.00 2.90
1581 1590 3.003793 GCTTTCCTCCTGTTCTGTTTGAC 59.996 47.826 0.00 0.00 0.00 3.18
1662 1671 5.615289 AGATTGGCTACATTGCTAACCTAG 58.385 41.667 0.00 0.00 36.31 3.02
1682 1691 0.961019 TGCAAAACCAGTGAGGCATC 59.039 50.000 0.00 0.00 43.14 3.91
2372 2381 0.687354 AGAGATGGAACGTGCCAAGT 59.313 50.000 21.97 9.90 42.16 3.16
2373 2382 1.072331 AGAGATGGAACGTGCCAAGTT 59.928 47.619 21.97 8.05 42.16 2.66
2413 2422 2.380410 GCAAGCAGCAATGCAGTGC 61.380 57.895 30.52 30.52 44.79 4.40
2565 2574 9.770097 CTCTGCACTATATCTCTTTCCATAAAA 57.230 33.333 0.00 0.00 0.00 1.52
2587 2596 8.707938 AAAATATTTTTGCCTTGCTCAGATAC 57.292 30.769 7.64 0.00 0.00 2.24
2734 2744 8.600625 TGCGTAATGTCACAAATTAGATAAGAC 58.399 33.333 0.00 0.00 0.00 3.01
2787 2797 8.898761 ACATGACATATTTATTTCCTACGCAAA 58.101 29.630 0.00 0.00 0.00 3.68
3087 3103 1.218844 AATACTAATGCCCGGTGGGT 58.781 50.000 0.00 0.00 46.51 4.51
3284 3302 0.969917 TGTGCCTGCAACACCTTTGT 60.970 50.000 14.98 0.00 37.22 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 2.041206 GAGGCCTATTGTCCCGACCC 62.041 65.000 4.42 0.00 0.00 4.46
299 300 2.986306 GAAGAAGTCGTCGCCGGGA 61.986 63.158 2.18 0.00 33.95 5.14
304 305 2.506438 CGGGGAAGAAGTCGTCGC 60.506 66.667 3.27 3.27 36.78 5.19
348 349 3.681835 GTCGGTGTCCTCGCCTGT 61.682 66.667 0.00 0.00 41.65 4.00
366 367 2.359230 AGAAGCGCTGGACTTGGC 60.359 61.111 12.58 0.00 0.00 4.52
796 797 0.818040 GACTCAACGGGCCACTTTGT 60.818 55.000 4.39 0.00 0.00 2.83
811 812 7.120726 CGGGGTATTATTTTTGGATATGGACTC 59.879 40.741 0.00 0.00 0.00 3.36
908 917 7.017055 GCCTTCCGAAAATGAAAATGAAAATG 58.983 34.615 0.00 0.00 0.00 2.32
932 941 2.145536 TCGGAGGAAAGGTAAAAACGC 58.854 47.619 0.00 0.00 0.00 4.84
1041 1050 2.031012 TTGAGCTGGTCAGTGGCG 59.969 61.111 9.70 0.00 36.21 5.69
1085 1094 6.035975 GCCAATTTCGAATTGTTGGGAATAAG 59.964 38.462 25.83 9.86 41.05 1.73
1108 1117 1.959042 CATGATACAGTCCACCTGCC 58.041 55.000 0.00 0.00 45.68 4.85
1295 1304 4.751767 TGAGAACCAAAACAAAGCCAAT 57.248 36.364 0.00 0.00 0.00 3.16
1351 1360 4.213564 AGCAAATCTAGACCTTCCACAG 57.786 45.455 0.00 0.00 0.00 3.66
1432 1441 0.467106 CAGAGAGGCCTCGAGATGGA 60.467 60.000 26.95 0.00 44.08 3.41
1438 1447 0.539669 TGTCAACAGAGAGGCCTCGA 60.540 55.000 26.95 14.10 44.08 4.04
1543 1552 3.006752 GGAAAGCACCCACATTTGATCAA 59.993 43.478 3.38 3.38 0.00 2.57
1581 1590 7.582435 TGACAAGTCTTCTTCGCTTAAATAG 57.418 36.000 1.53 0.00 0.00 1.73
1662 1671 0.675633 ATGCCTCACTGGTTTTGCAC 59.324 50.000 0.00 0.00 38.35 4.57
1682 1691 0.514255 CAGGATATGCAATGACGGCG 59.486 55.000 4.80 4.80 0.00 6.46
2372 2381 5.580297 GCTTGTTTCCTGATTTTGTGAACAA 59.420 36.000 0.00 0.00 0.00 2.83
2373 2382 5.108517 GCTTGTTTCCTGATTTTGTGAACA 58.891 37.500 0.00 0.00 0.00 3.18
2413 2422 6.022163 TCGTAGTACCTTTTCCTCTTCAAG 57.978 41.667 0.00 0.00 0.00 3.02
2565 2574 5.590259 ACGTATCTGAGCAAGGCAAAAATAT 59.410 36.000 0.00 0.00 0.00 1.28
2566 2575 4.941263 ACGTATCTGAGCAAGGCAAAAATA 59.059 37.500 0.00 0.00 0.00 1.40
2587 2596 6.373779 ACAATGCTCTTTTCACAAGATTACG 58.626 36.000 0.00 0.00 0.00 3.18
2710 2720 9.314321 AGGTCTTATCTAATTTGTGACATTACG 57.686 33.333 0.00 0.00 0.00 3.18
2734 2744 7.696453 CCAAATATAGTAAAAAGACAACGCAGG 59.304 37.037 0.00 0.00 0.00 4.85
2787 2797 1.909700 ACCAATTGATGACGGCAAGT 58.090 45.000 7.12 0.00 0.00 3.16
2794 2804 4.409247 ACCCTAGTCCTACCAATTGATGAC 59.591 45.833 7.12 7.63 0.00 3.06
3087 3103 5.386924 GGCTTGGTCTATACTAGGAAGAGA 58.613 45.833 0.00 0.00 0.00 3.10
3264 3282 0.175302 CAAAGGTGTTGCAGGCACAA 59.825 50.000 20.15 0.00 38.51 3.33
3284 3302 0.324614 TCGCATTCTTCCAGAGCCAA 59.675 50.000 0.00 0.00 0.00 4.52
3417 3435 2.111251 GGGAAGGTGGCCTATCGC 59.889 66.667 3.32 1.56 31.13 4.58


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

AutoCloner maintained by Alex Coulton.