Multiple sequence alignment - TraesCS2A01G286600

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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 TraesCS2A01G286600 chr2A 100.000 2969 0 0 1 2969 486286729 486283761 0.000000e+00 5483.0
1 TraesCS2A01G286600 chr2A 94.625 986 43 3 1 986 448567721 448568696 0.000000e+00 1519.0
2 TraesCS2A01G286600 chr2A 94.124 987 51 3 1 986 473646390 473645410 0.000000e+00 1495.0
3 TraesCS2A01G286600 chr2A 95.238 63 3 0 2742 2804 643991429 643991491 1.880000e-17 100.0
4 TraesCS2A01G286600 chr2B 94.946 1939 55 19 1049 2969 429651533 429649620 0.000000e+00 2998.0
5 TraesCS2A01G286600 chr2D 95.282 1314 37 13 1058 2355 361278824 361277520 0.000000e+00 2060.0
6 TraesCS2A01G286600 chr2D 92.518 989 68 6 1 986 645854571 645853586 0.000000e+00 1411.0
7 TraesCS2A01G286600 chr2D 96.753 616 19 1 2355 2969 361277464 361276849 0.000000e+00 1026.0
8 TraesCS2A01G286600 chr2D 91.228 57 3 2 983 1038 361382677 361382622 3.170000e-10 76.8
9 TraesCS2A01G286600 chr5D 96.353 987 33 3 1 986 517367501 517368485 0.000000e+00 1620.0
10 TraesCS2A01G286600 chr7A 96.045 986 38 1 1 986 41452614 41451630 0.000000e+00 1604.0
11 TraesCS2A01G286600 chr7A 93.043 230 13 3 2742 2969 637270759 637270531 1.710000e-87 333.0
12 TraesCS2A01G286600 chr4D 95.943 986 37 2 1 986 461336375 461335393 0.000000e+00 1596.0
13 TraesCS2A01G286600 chr5A 95.745 987 39 3 1 986 547122440 547123424 0.000000e+00 1587.0
14 TraesCS2A01G286600 chr1B 95.418 982 40 3 6 984 669940258 669939279 0.000000e+00 1559.0
15 TraesCS2A01G286600 chr7B 92.014 864 64 5 124 986 667215727 667214868 0.000000e+00 1208.0
16 TraesCS2A01G286600 chr7B 95.238 63 3 0 2742 2804 557210580 557210642 1.880000e-17 100.0
17 TraesCS2A01G286600 chr3B 93.277 595 31 7 1844 2430 742324597 742325190 0.000000e+00 869.0
18 TraesCS2A01G286600 chr3B 92.793 222 14 2 2750 2969 769609971 769610192 1.330000e-83 320.0
19 TraesCS2A01G286600 chr4A 91.304 230 17 3 2742 2969 321983392 321983164 7.990000e-81 311.0
20 TraesCS2A01G286600 chr4A 95.238 63 3 0 2742 2804 24453574 24453636 1.880000e-17 100.0
21 TraesCS2A01G286600 chr4B 90.435 230 20 2 2742 2969 651056988 651057217 4.810000e-78 302.0


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 TraesCS2A01G286600 chr2A 486283761 486286729 2968 True 5483 5483 100.0000 1 2969 1 chr2A.!!$R2 2968
1 TraesCS2A01G286600 chr2A 448567721 448568696 975 False 1519 1519 94.6250 1 986 1 chr2A.!!$F1 985
2 TraesCS2A01G286600 chr2A 473645410 473646390 980 True 1495 1495 94.1240 1 986 1 chr2A.!!$R1 985
3 TraesCS2A01G286600 chr2B 429649620 429651533 1913 True 2998 2998 94.9460 1049 2969 1 chr2B.!!$R1 1920
4 TraesCS2A01G286600 chr2D 361276849 361278824 1975 True 1543 2060 96.0175 1058 2969 2 chr2D.!!$R3 1911
5 TraesCS2A01G286600 chr2D 645853586 645854571 985 True 1411 1411 92.5180 1 986 1 chr2D.!!$R2 985
6 TraesCS2A01G286600 chr5D 517367501 517368485 984 False 1620 1620 96.3530 1 986 1 chr5D.!!$F1 985
7 TraesCS2A01G286600 chr7A 41451630 41452614 984 True 1604 1604 96.0450 1 986 1 chr7A.!!$R1 985
8 TraesCS2A01G286600 chr4D 461335393 461336375 982 True 1596 1596 95.9430 1 986 1 chr4D.!!$R1 985
9 TraesCS2A01G286600 chr5A 547122440 547123424 984 False 1587 1587 95.7450 1 986 1 chr5A.!!$F1 985
10 TraesCS2A01G286600 chr1B 669939279 669940258 979 True 1559 1559 95.4180 6 984 1 chr1B.!!$R1 978
11 TraesCS2A01G286600 chr7B 667214868 667215727 859 True 1208 1208 92.0140 124 986 1 chr7B.!!$R1 862
12 TraesCS2A01G286600 chr3B 742324597 742325190 593 False 869 869 93.2770 1844 2430 1 chr3B.!!$F1 586

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
61 62 0.958382 GGTACAAGGGCAACATGCGA 60.958 55.000 0.0 0.0 46.21 5.10 F
460 462 1.026584 TTCATCATCGCCATGCCTTG 58.973 50.000 0.0 0.0 0.00 3.61 F
1543 1570 1.226323 CGACGAGGAAAGCGACGAT 60.226 57.895 0.0 0.0 46.35 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 1570 0.106469 CCTCCTCGTCATCCTCCTCA 60.106 60.000 0.0 0.0 0.00 3.86 R
1704 1731 0.824182 ATCGTCCTCGTCATCCTCCC 60.824 60.000 0.0 0.0 38.33 4.30 R
2387 2491 1.128692 GTACACGCCAGAAGATGCAAC 59.871 52.381 0.0 0.0 0.00 4.17 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
61 62 0.958382 GGTACAAGGGCAACATGCGA 60.958 55.000 0.00 0.00 46.21 5.10
88 89 1.207089 TGGGCGAGAAGATGAATCGTT 59.793 47.619 0.00 0.00 38.66 3.85
269 270 1.352622 TGGTGCTCTGGAGGGTTTGT 61.353 55.000 0.00 0.00 0.00 2.83
341 342 6.540189 AGGTGTCTTTGTGATTATCTATGCAC 59.460 38.462 0.00 0.00 0.00 4.57
379 380 4.656575 TGCTACAATTAGGCTGTATGGGTA 59.343 41.667 0.00 0.00 0.00 3.69
460 462 1.026584 TTCATCATCGCCATGCCTTG 58.973 50.000 0.00 0.00 0.00 3.61
518 521 8.762645 TCTCTCTGTTGATGGTTCTTATTGTAT 58.237 33.333 0.00 0.00 0.00 2.29
582 585 3.452627 ACAAGGGTGGTGTTATTTTTGCA 59.547 39.130 0.00 0.00 0.00 4.08
590 593 4.342378 TGGTGTTATTTTTGCAGCTTACCA 59.658 37.500 0.00 0.00 32.56 3.25
787 793 5.136828 TGGCAGAAATCAAAGGTTTACTGA 58.863 37.500 0.00 0.00 0.00 3.41
843 849 4.325741 CGTGATCAAAACAAAGTTGCACAA 59.674 37.500 0.00 0.00 0.00 3.33
866 872 9.573166 ACAATGCTTAGCAAATTATGGTAGATA 57.427 29.630 12.08 0.00 43.62 1.98
968 974 7.040062 TGTGAGTTTGGAATAAAACACCCTATG 60.040 37.037 2.97 0.00 41.56 2.23
1019 1025 9.941325 TTCCTTTCTATAAAAATACGGTACACA 57.059 29.630 0.00 0.00 0.00 3.72
1020 1026 9.941325 TCCTTTCTATAAAAATACGGTACACAA 57.059 29.630 0.00 0.00 0.00 3.33
1029 1035 8.561738 AAAAATACGGTACACAATTGATCTCT 57.438 30.769 13.59 0.00 0.00 3.10
1030 1036 9.661563 AAAAATACGGTACACAATTGATCTCTA 57.338 29.630 13.59 0.00 0.00 2.43
1031 1037 9.661563 AAAATACGGTACACAATTGATCTCTAA 57.338 29.630 13.59 0.00 0.00 2.10
1032 1038 9.661563 AAATACGGTACACAATTGATCTCTAAA 57.338 29.630 13.59 0.00 0.00 1.85
1033 1039 9.661563 AATACGGTACACAATTGATCTCTAAAA 57.338 29.630 13.59 0.00 0.00 1.52
1034 1040 7.972832 ACGGTACACAATTGATCTCTAAAAA 57.027 32.000 13.59 0.00 0.00 1.94
1228 1255 2.280321 ACGGTTTTACGCCACGCT 60.280 55.556 0.00 0.00 37.37 5.07
1389 1416 2.482296 AAGCGTAAGACGGACACCGG 62.482 60.000 14.50 0.00 45.80 5.28
1543 1570 1.226323 CGACGAGGAAAGCGACGAT 60.226 57.895 0.00 0.00 46.35 3.73
1585 1612 2.026879 GGAGATGGCGACGAGAGC 59.973 66.667 0.00 0.00 0.00 4.09
2027 2072 1.455383 CCGCAACCTTGGTCTTGCTT 61.455 55.000 12.76 0.00 40.59 3.91
2136 2181 3.492337 AGGTAGACATAGCTGTAGCCTC 58.508 50.000 0.00 0.00 43.38 4.70
2222 2270 3.191162 TGCTGTCCTTGTTTGATGCATAC 59.809 43.478 0.00 0.00 0.00 2.39
2272 2320 7.455638 ACTTAACCTTGTCCAGTTAGGTATACA 59.544 37.037 5.01 0.00 41.33 2.29
2387 2491 4.506758 CTTTAATTGGCCAGGGAACAATG 58.493 43.478 5.11 0.00 35.22 2.82
2402 2506 1.200716 ACAATGTTGCATCTTCTGGCG 59.799 47.619 0.00 0.00 0.00 5.69
2408 2512 0.735978 TGCATCTTCTGGCGTGTACG 60.736 55.000 0.00 0.00 43.27 3.67
2471 2575 7.517614 TCCTAACAGTGCATTTTTAATGTCA 57.482 32.000 0.00 0.00 0.00 3.58
2567 2671 2.903784 TCAGCTAGTTGCACCCTTTAGA 59.096 45.455 0.97 0.00 45.94 2.10
2683 2788 1.205893 CTCCTGTTACCCTGAGTGCTC 59.794 57.143 0.00 0.00 0.00 4.26
2804 2909 4.698583 AAAGCAGATCTGTTTGATGCTC 57.301 40.909 23.41 4.51 34.56 4.26
2806 2911 2.026542 AGCAGATCTGTTTGATGCTCCA 60.027 45.455 23.38 0.00 31.32 3.86
2895 3001 5.409826 GGGGATTTATCTCATAGAACTTGCG 59.590 44.000 0.00 0.00 0.00 4.85
2906 3012 5.693104 TCATAGAACTTGCGTTTTTAGTCGT 59.307 36.000 0.00 0.00 32.39 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.122779 GATTCCTCTCTAAGTTAGTTGCTAGTA 57.877 37.037 9.71 0.00 0.00 1.82
61 62 2.086869 CATCTTCTCGCCCACACATTT 58.913 47.619 0.00 0.00 0.00 2.32
88 89 7.093068 TGGGACAGACTAGTAAAGCATGAAATA 60.093 37.037 0.00 0.00 0.00 1.40
379 380 5.779241 TTACCTTTGATCACCTCTTCCAT 57.221 39.130 0.00 0.00 0.00 3.41
441 443 1.026584 CAAGGCATGGCGATGATGAA 58.973 50.000 18.95 0.00 0.00 2.57
518 521 2.659016 CTGCAGCTCCGTCTTCCA 59.341 61.111 0.00 0.00 0.00 3.53
582 585 4.094887 CAGTGATAAATGCGTTGGTAAGCT 59.905 41.667 0.00 0.00 0.00 3.74
590 593 5.220854 GCCTCATTACAGTGATAAATGCGTT 60.221 40.000 0.00 0.00 31.98 4.84
787 793 8.851541 TTAATACGAACAAACACCCTATTCTT 57.148 30.769 0.00 0.00 0.00 2.52
843 849 9.182214 CCATATCTACCATAATTTGCTAAGCAT 57.818 33.333 0.00 0.00 38.76 3.79
866 872 2.435805 CAGCACACAGTACTATCCCCAT 59.564 50.000 0.00 0.00 0.00 4.00
993 999 9.941325 TGTGTACCGTATTTTTATAGAAAGGAA 57.059 29.630 0.00 0.00 0.00 3.36
994 1000 9.941325 TTGTGTACCGTATTTTTATAGAAAGGA 57.059 29.630 0.00 0.00 0.00 3.36
1003 1009 9.661563 AGAGATCAATTGTGTACCGTATTTTTA 57.338 29.630 5.13 0.00 0.00 1.52
1004 1010 8.561738 AGAGATCAATTGTGTACCGTATTTTT 57.438 30.769 5.13 0.00 0.00 1.94
1005 1011 9.661563 TTAGAGATCAATTGTGTACCGTATTTT 57.338 29.630 5.13 0.00 0.00 1.82
1006 1012 9.661563 TTTAGAGATCAATTGTGTACCGTATTT 57.338 29.630 5.13 0.00 0.00 1.40
1007 1013 9.661563 TTTTAGAGATCAATTGTGTACCGTATT 57.338 29.630 5.13 0.00 0.00 1.89
1008 1014 9.661563 TTTTTAGAGATCAATTGTGTACCGTAT 57.338 29.630 5.13 0.00 0.00 3.06
1010 1016 7.972832 TTTTTAGAGATCAATTGTGTACCGT 57.027 32.000 5.13 0.00 0.00 4.83
1034 1040 7.730364 TTCGAGCTCTGAGTATTTTCTTTTT 57.270 32.000 12.85 0.00 0.00 1.94
1035 1041 7.730364 TTTCGAGCTCTGAGTATTTTCTTTT 57.270 32.000 12.85 0.00 0.00 2.27
1036 1042 7.657761 TCTTTTCGAGCTCTGAGTATTTTCTTT 59.342 33.333 12.85 0.00 0.00 2.52
1037 1043 7.155328 TCTTTTCGAGCTCTGAGTATTTTCTT 58.845 34.615 12.85 0.00 0.00 2.52
1038 1044 6.692486 TCTTTTCGAGCTCTGAGTATTTTCT 58.308 36.000 12.85 0.00 0.00 2.52
1039 1045 6.952935 TCTTTTCGAGCTCTGAGTATTTTC 57.047 37.500 12.85 0.00 0.00 2.29
1040 1046 7.442666 ACTTTCTTTTCGAGCTCTGAGTATTTT 59.557 33.333 12.85 0.00 0.00 1.82
1041 1047 6.931840 ACTTTCTTTTCGAGCTCTGAGTATTT 59.068 34.615 12.85 0.00 0.00 1.40
1042 1048 6.459923 ACTTTCTTTTCGAGCTCTGAGTATT 58.540 36.000 12.85 0.00 0.00 1.89
1043 1049 6.031751 ACTTTCTTTTCGAGCTCTGAGTAT 57.968 37.500 12.85 0.00 0.00 2.12
1044 1050 5.455056 ACTTTCTTTTCGAGCTCTGAGTA 57.545 39.130 12.85 1.04 0.00 2.59
1045 1051 4.329462 ACTTTCTTTTCGAGCTCTGAGT 57.671 40.909 12.85 1.36 0.00 3.41
1046 1052 4.509600 ACAACTTTCTTTTCGAGCTCTGAG 59.490 41.667 12.85 0.00 0.00 3.35
1047 1053 4.442706 ACAACTTTCTTTTCGAGCTCTGA 58.557 39.130 12.85 8.14 0.00 3.27
1120 1127 3.248602 GCTTCTGAGCCGGTAACATATTG 59.751 47.826 1.90 0.00 43.29 1.90
1205 1231 4.092652 GCGTAAAACCGTGGCCCG 62.093 66.667 0.00 2.96 0.00 6.13
1215 1241 0.389426 GGAGAGAGCGTGGCGTAAAA 60.389 55.000 0.00 0.00 0.00 1.52
1228 1255 3.550820 CGAGAGAAATGGAGAGGAGAGA 58.449 50.000 0.00 0.00 0.00 3.10
1389 1416 0.893727 GAGGGGAGAGATCTCGGAGC 60.894 65.000 16.97 8.02 43.76 4.70
1543 1570 0.106469 CCTCCTCGTCATCCTCCTCA 60.106 60.000 0.00 0.00 0.00 3.86
1585 1612 1.004277 GATCCTCGCATAAGCCGTCG 61.004 60.000 0.00 0.00 37.52 5.12
1704 1731 0.824182 ATCGTCCTCGTCATCCTCCC 60.824 60.000 0.00 0.00 38.33 4.30
1967 2006 5.238583 ACCAGCAGTGATACTTGTTTACTC 58.761 41.667 0.00 0.00 0.00 2.59
2222 2270 4.298332 CAACGGTTCCAGAAGAAAAATGG 58.702 43.478 0.00 0.00 35.85 3.16
2298 2346 5.883685 ATGCTCAGATATGACCTCAAGAA 57.116 39.130 0.00 0.00 0.00 2.52
2387 2491 1.128692 GTACACGCCAGAAGATGCAAC 59.871 52.381 0.00 0.00 0.00 4.17
2402 2506 2.428171 TGGCTTGGTCCTATACGTACAC 59.572 50.000 0.00 0.00 0.00 2.90
2408 2512 1.508256 ACCCTGGCTTGGTCCTATAC 58.492 55.000 0.00 0.00 0.00 1.47
2471 2575 8.767085 CAACACATCAAACAAATAAGAAAGCAT 58.233 29.630 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.