Multiple sequence alignment - TraesCS7A01G525100

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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 TraesCS7A01G525100 chr7A 100.000 2791 0 0 332 3122 707800032 707802822 0.000000e+00 5155.0
1 TraesCS7A01G525100 chr7A 98.305 2537 37 5 332 2864 710504151 710501617 0.000000e+00 4442.0
2 TraesCS7A01G525100 chr7A 95.094 1223 34 6 864 2066 710803630 710804846 0.000000e+00 1903.0
3 TraesCS7A01G525100 chr7A 91.504 1177 70 7 864 2011 707545866 707544691 0.000000e+00 1592.0
4 TraesCS7A01G525100 chr7A 92.266 1099 76 6 919 2011 710480039 710478944 0.000000e+00 1550.0
5 TraesCS7A01G525100 chr7A 92.059 1020 71 3 982 1991 707497519 707496500 0.000000e+00 1426.0
6 TraesCS7A01G525100 chr7A 93.729 877 51 2 1139 2011 707520349 707519473 0.000000e+00 1312.0
7 TraesCS7A01G525100 chr7A 92.308 481 29 5 2074 2548 707496093 707495615 0.000000e+00 676.0
8 TraesCS7A01G525100 chr7A 90.761 368 31 2 2074 2438 710805274 710805641 3.620000e-134 488.0
9 TraesCS7A01G525100 chr7A 99.213 254 2 0 2869 3122 710501177 710500924 2.840000e-125 459.0
10 TraesCS7A01G525100 chr7A 100.000 204 0 0 1 204 707799701 707799904 8.170000e-101 377.0
11 TraesCS7A01G525100 chr7A 98.529 204 3 0 1 204 710504376 710504173 8.230000e-96 361.0
12 TraesCS7A01G525100 chr7A 95.217 230 7 2 612 841 710803416 710803641 8.230000e-96 361.0
13 TraesCS7A01G525100 chr7A 92.742 248 16 2 2617 2863 576204187 576203941 1.060000e-94 357.0
14 TraesCS7A01G525100 chr7A 89.695 262 10 12 2869 3122 61758775 61759027 5.020000e-83 318.0
15 TraesCS7A01G525100 chr7A 82.993 294 32 8 332 611 734524876 734524587 1.860000e-62 250.0
16 TraesCS7A01G525100 chr7A 89.333 150 5 5 612 760 707546021 707545882 8.900000e-41 178.0
17 TraesCS7A01G525100 chr7A 92.793 111 7 1 2438 2548 710805804 710805913 3.220000e-35 159.0
18 TraesCS7A01G525100 chr7A 94.595 74 4 0 616 689 710480275 710480202 7.080000e-22 115.0
19 TraesCS7A01G525100 chr7A 94.286 70 4 0 772 841 710480178 710480109 1.180000e-19 108.0
20 TraesCS7A01G525100 chr7D 93.491 1229 51 7 864 2069 614795244 614794022 0.000000e+00 1799.0
21 TraesCS7A01G525100 chr7D 93.831 1151 47 7 864 1991 614728951 614727802 0.000000e+00 1711.0
22 TraesCS7A01G525100 chr7D 93.069 202 14 0 3 204 104614383 104614584 2.350000e-76 296.0
23 TraesCS7A01G525100 chr7D 93.085 188 12 1 611 797 614823169 614822982 1.100000e-69 274.0
24 TraesCS7A01G525100 chr7D 92.513 187 13 1 612 797 614757859 614757673 1.850000e-67 267.0
25 TraesCS7A01G525100 chr7D 83.553 304 26 9 333 613 104614604 104614906 2.390000e-66 263.0
26 TraesCS7A01G525100 chr7D 94.410 161 8 1 611 770 614802648 614802488 2.400000e-61 246.0
27 TraesCS7A01G525100 chr7D 86.310 168 23 0 334 501 18055181 18055014 1.910000e-42 183.0
28 TraesCS7A01G525100 chr7D 90.164 122 7 3 864 981 614815768 614815648 1.500000e-33 154.0
29 TraesCS7A01G525100 chr7D 94.828 58 3 0 784 841 614728997 614728940 1.190000e-14 91.6
30 TraesCS7A01G525100 chr7D 94.828 58 3 0 784 841 614795290 614795233 1.190000e-14 91.6
31 TraesCS7A01G525100 chr7D 93.103 58 4 0 784 841 614815814 614815757 5.550000e-13 86.1
32 TraesCS7A01G525100 chrUn 90.994 1177 76 7 864 2011 298697583 298696408 0.000000e+00 1559.0
33 TraesCS7A01G525100 chrUn 90.646 898 54 16 864 1732 427480112 427481008 0.000000e+00 1166.0
34 TraesCS7A01G525100 chrUn 91.684 481 32 5 2074 2548 298699674 298699196 0.000000e+00 660.0
35 TraesCS7A01G525100 chrUn 93.061 245 16 1 2620 2863 70918163 70918407 1.060000e-94 357.0
36 TraesCS7A01G525100 chrUn 89.844 256 16 8 2869 3122 316992404 316992651 1.400000e-83 320.0
37 TraesCS7A01G525100 chrUn 84.502 271 15 15 864 1108 384585490 384585759 3.110000e-60 243.0
38 TraesCS7A01G525100 chrUn 89.333 150 5 5 612 760 384585335 384585474 8.900000e-41 178.0
39 TraesCS7A01G525100 chrUn 89.333 150 5 5 612 760 427479957 427480096 8.900000e-41 178.0
40 TraesCS7A01G525100 chrUn 86.842 114 4 5 648 760 298697702 298697599 1.970000e-22 117.0
41 TraesCS7A01G525100 chrUn 95.652 46 2 0 796 841 298697617 298697572 1.200000e-09 75.0
42 TraesCS7A01G525100 chrUn 95.652 46 2 0 796 841 384585456 384585501 1.200000e-09 75.0
43 TraesCS7A01G525100 chrUn 95.652 46 2 0 796 841 427480078 427480123 1.200000e-09 75.0
44 TraesCS7A01G525100 chr5A 94.309 246 13 1 2619 2863 494873777 494873532 2.940000e-100 375.0
45 TraesCS7A01G525100 chr5A 93.496 246 15 1 2619 2863 556404948 556404703 6.360000e-97 364.0
46 TraesCS7A01G525100 chr4A 92.969 256 12 4 2869 3122 631404760 631404509 4.920000e-98 368.0
47 TraesCS7A01G525100 chr3A 93.227 251 16 1 2614 2863 15954084 15954334 4.920000e-98 368.0
48 TraesCS7A01G525100 chr3A 92.742 248 16 2 2617 2863 31600411 31600657 1.060000e-94 357.0
49 TraesCS7A01G525100 chr3A 91.154 260 12 5 2869 3122 704116026 704115772 2.980000e-90 342.0
50 TraesCS7A01G525100 chr1A 93.469 245 15 1 2620 2863 29086398 29086154 2.290000e-96 363.0
51 TraesCS7A01G525100 chr1A 91.829 257 19 2 2612 2867 22448844 22449099 1.060000e-94 357.0
52 TraesCS7A01G525100 chr3D 91.016 256 11 8 2869 3120 556834059 556834306 4.990000e-88 335.0
53 TraesCS7A01G525100 chr3D 86.477 281 26 7 332 611 601827859 601828128 6.550000e-77 298.0
54 TraesCS7A01G525100 chr2B 90.234 256 16 7 2869 3122 565207766 565207518 3.000000e-85 326.0
55 TraesCS7A01G525100 chr2B 93.069 202 14 0 3 204 484892291 484892090 2.350000e-76 296.0
56 TraesCS7A01G525100 chr2A 89.844 256 13 8 2869 3122 97261925 97262169 1.810000e-82 316.0
57 TraesCS7A01G525100 chr1D 89.494 257 17 8 2869 3122 470773924 470774173 1.810000e-82 316.0
58 TraesCS7A01G525100 chr1D 86.598 291 24 6 332 609 13100283 13099995 1.090000e-79 307.0
59 TraesCS7A01G525100 chr1D 92.079 202 16 0 3 204 453641529 453641328 5.100000e-73 285.0
60 TraesCS7A01G525100 chr4D 91.781 219 17 1 332 550 491506280 491506497 1.410000e-78 303.0
61 TraesCS7A01G525100 chr4D 93.069 202 13 1 3 204 12109002 12109202 8.470000e-76 294.0
62 TraesCS7A01G525100 chr4D 92.574 202 15 0 3 204 491506058 491506259 1.100000e-74 291.0
63 TraesCS7A01G525100 chr1B 92.195 205 12 2 3 204 587057493 587057290 1.420000e-73 287.0
64 TraesCS7A01G525100 chr1B 92.195 205 12 2 3 204 587079878 587079675 1.420000e-73 287.0
65 TraesCS7A01G525100 chr6A 92.079 202 16 0 3 204 572169672 572169471 5.100000e-73 285.0
66 TraesCS7A01G525100 chr6A 85.000 240 21 4 385 611 14674019 14673782 2.420000e-56 230.0
67 TraesCS7A01G525100 chr2D 84.122 296 30 7 332 613 619227885 619227593 1.430000e-68 270.0
68 TraesCS7A01G525100 chr2D 83.959 293 32 4 332 611 472143830 472144120 1.850000e-67 267.0
69 TraesCS7A01G525100 chr5D 83.673 294 31 6 332 611 497368080 497367790 8.590000e-66 261.0
70 TraesCS7A01G525100 chr6B 84.064 251 23 9 373 609 621113808 621114055 3.130000e-55 226.0
71 TraesCS7A01G525100 chr7B 86.400 125 13 3 489 611 748392165 748392043 1.950000e-27 134.0


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 TraesCS7A01G525100 chr7A 707799701 707802822 3121 False 2766.00 5155 100.000000 1 3122 2 chr7A.!!$F2 3121
1 TraesCS7A01G525100 chr7A 710500924 710504376 3452 True 1754.00 4442 98.682333 1 3122 3 chr7A.!!$R7 3121
2 TraesCS7A01G525100 chr7A 707519473 707520349 876 True 1312.00 1312 93.729000 1139 2011 1 chr7A.!!$R2 872
3 TraesCS7A01G525100 chr7A 707495615 707497519 1904 True 1051.00 1426 92.183500 982 2548 2 chr7A.!!$R4 1566
4 TraesCS7A01G525100 chr7A 707544691 707546021 1330 True 885.00 1592 90.418500 612 2011 2 chr7A.!!$R5 1399
5 TraesCS7A01G525100 chr7A 710803416 710805913 2497 False 727.75 1903 93.466250 612 2548 4 chr7A.!!$F3 1936
6 TraesCS7A01G525100 chr7A 710478944 710480275 1331 True 591.00 1550 93.715667 616 2011 3 chr7A.!!$R6 1395
7 TraesCS7A01G525100 chr7D 614794022 614795290 1268 True 945.30 1799 94.159500 784 2069 2 chr7D.!!$R6 1285
8 TraesCS7A01G525100 chr7D 614727802 614728997 1195 True 901.30 1711 94.329500 784 1991 2 chr7D.!!$R5 1207
9 TraesCS7A01G525100 chr7D 104614383 104614906 523 False 279.50 296 88.311000 3 613 2 chr7D.!!$F1 610
10 TraesCS7A01G525100 chrUn 298696408 298699674 3266 True 602.75 1559 91.293000 648 2548 4 chrUn.!!$R1 1900
11 TraesCS7A01G525100 chrUn 427479957 427481008 1051 False 473.00 1166 91.877000 612 1732 3 chrUn.!!$F4 1120

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
574 575 0.928451 GTTCTTGTGTTTCACGCGCC 60.928 55.000 5.73 0.0 37.14 6.53 F
575 576 1.369839 TTCTTGTGTTTCACGCGCCA 61.370 50.000 5.73 0.0 37.14 5.69 F
1426 2804 2.308570 AGATTAACCATCCAGTGCACCA 59.691 45.455 14.63 0.0 31.20 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 3139 0.107643 TGTGCGTCATCTTGTGGGAA 59.892 50.000 0.0 0.0 0.0 3.97 R
1932 3349 1.217779 GAGCAGAGGAGTGAGCACC 59.782 63.158 0.0 0.0 0.0 5.01 R
2806 4813 0.542333 TGGTTTGAGACACAACCCGA 59.458 50.000 0.0 0.0 42.8 5.14 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
451 452 5.887214 ACAATACATGTATACCCTCAGCA 57.113 39.130 18.56 0.00 41.63 4.41
557 558 4.359706 GTTTTTGACAAATCTCAGCCGTT 58.640 39.130 0.50 0.00 0.00 4.44
558 559 3.896648 TTTGACAAATCTCAGCCGTTC 57.103 42.857 0.00 0.00 0.00 3.95
574 575 0.928451 GTTCTTGTGTTTCACGCGCC 60.928 55.000 5.73 0.00 37.14 6.53
575 576 1.369839 TTCTTGTGTTTCACGCGCCA 61.370 50.000 5.73 0.00 37.14 5.69
1418 2796 2.419990 CCAGCGACAGATTAACCATCCA 60.420 50.000 0.00 0.00 31.20 3.41
1426 2804 2.308570 AGATTAACCATCCAGTGCACCA 59.691 45.455 14.63 0.00 31.20 4.17
1482 2860 2.417933 CCTGCTCGGAATCTTGTTCAAG 59.582 50.000 6.24 6.24 33.16 3.02
1810 3191 5.462405 GTGACAACGATGACTTCTTCTACT 58.538 41.667 0.00 0.00 0.00 2.57
1932 3349 0.023732 CAACGTGTAGCAGCGAATCG 59.976 55.000 0.00 0.00 0.00 3.34
2182 4022 0.680280 CTTCGACGGGGAAGGAGAGA 60.680 60.000 9.20 0.00 39.76 3.10
2240 4082 4.660938 GGTCAAAGCTGGCCCGGT 62.661 66.667 0.00 0.00 41.98 5.28
2379 4221 6.039941 AGTCCAATGTTGTAAATCAAACCGAA 59.960 34.615 0.00 0.00 37.81 4.30
2666 4672 6.992715 AGTCACAGGGTAATATTCACATTAGC 59.007 38.462 0.00 0.00 37.88 3.09
2697 4703 2.445427 TCACGAACCGGGACTAATGTA 58.555 47.619 6.32 0.00 32.99 2.29
2734 4740 1.537348 CGTGCGGCTAAGGCATTAGTA 60.537 52.381 18.55 1.96 43.19 1.82
2758 4764 3.591023 GGTTCACCTGAGCTCTTTAGTC 58.409 50.000 16.19 0.43 0.00 2.59
2806 4813 0.107654 GGTGCGATGCCCTTTAGTCT 60.108 55.000 0.00 0.00 0.00 3.24
2864 4871 3.604875 TTAGTCCCGGTTTGAGACATC 57.395 47.619 9.96 0.00 32.82 3.06
2865 4872 1.645710 AGTCCCGGTTTGAGACATCT 58.354 50.000 9.96 0.00 32.82 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
451 452 4.157105 GCACCGGTCCAATTACTTTTGTAT 59.843 41.667 2.59 0.00 34.49 2.29
557 558 1.369839 TTGGCGCGTGAAACACAAGA 61.370 50.000 8.43 0.00 35.74 3.02
558 559 0.929824 CTTGGCGCGTGAAACACAAG 60.930 55.000 8.43 2.61 35.74 3.16
574 575 2.742372 CCCCCGACTGAACGCTTG 60.742 66.667 0.00 0.00 0.00 4.01
644 646 2.818274 GAGCTGTTAACCCGGGCG 60.818 66.667 24.08 3.04 0.00 6.13
645 647 2.437895 GGAGCTGTTAACCCGGGC 60.438 66.667 24.08 4.22 0.00 6.13
647 649 1.921869 ATGGGGAGCTGTTAACCCGG 61.922 60.000 2.48 0.00 46.38 5.73
648 650 0.463833 GATGGGGAGCTGTTAACCCG 60.464 60.000 2.48 0.00 46.38 5.28
650 652 2.755103 CAAAGATGGGGAGCTGTTAACC 59.245 50.000 2.48 0.00 0.00 2.85
651 653 2.164422 GCAAAGATGGGGAGCTGTTAAC 59.836 50.000 0.00 0.00 0.00 2.01
1418 2796 1.612726 GCTTCTTCTCCATGGTGCACT 60.613 52.381 17.98 0.00 0.00 4.40
1426 2804 0.990374 ACCTGCTGCTTCTTCTCCAT 59.010 50.000 0.00 0.00 0.00 3.41
1758 3139 0.107643 TGTGCGTCATCTTGTGGGAA 59.892 50.000 0.00 0.00 0.00 3.97
1764 3145 1.726248 TCGAATGTGTGCGTCATCTTG 59.274 47.619 0.00 0.00 0.00 3.02
1810 3191 7.856398 CGACGTTCTTCTAATTTGCTCTAGATA 59.144 37.037 0.00 0.00 0.00 1.98
1932 3349 1.217779 GAGCAGAGGAGTGAGCACC 59.782 63.158 0.00 0.00 0.00 5.01
2379 4221 5.794894 ACATTTCACTCTCGAACTAACCAT 58.205 37.500 0.00 0.00 0.00 3.55
2394 4236 8.926715 AGTAAAGAGAAAAACCAACATTTCAC 57.073 30.769 0.00 0.00 37.87 3.18
2666 4672 1.666872 GTTCGTGACTGAACCGGGG 60.667 63.158 6.32 0.00 41.88 5.73
2697 4703 1.674322 CGAACCGGGACCAATGCTT 60.674 57.895 6.32 0.00 0.00 3.91
2734 4740 1.122019 AAGAGCTCAGGTGAACCGGT 61.122 55.000 17.77 0.00 42.08 5.28
2758 4764 0.785979 CGGTTCGTGTCTTAAACGGG 59.214 55.000 0.00 0.00 41.34 5.28
2806 4813 0.542333 TGGTTTGAGACACAACCCGA 59.458 50.000 0.00 0.00 42.80 5.14


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

AutoCloner maintained by Alex Coulton.