Multiple sequence alignment - TraesCS7A01G556900

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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 TraesCS7A01G556900 chr7A 100.000 3098 0 0 801 3898 727858366 727861463 0.000000e+00 5722.0
1 TraesCS7A01G556900 chr7A 100.000 447 0 0 1 447 727857566 727858012 0.000000e+00 826.0
2 TraesCS7A01G556900 chrUn 94.934 3099 110 12 818 3898 93957624 93960693 0.000000e+00 4809.0
3 TraesCS7A01G556900 chrUn 91.852 405 24 3 45 445 93957100 93957499 1.220000e-154 556.0
4 TraesCS7A01G556900 chr7D 94.000 3100 103 12 818 3898 568457466 568460501 0.000000e+00 4617.0
5 TraesCS7A01G556900 chr7D 100.000 44 0 0 5 48 568456915 568456958 8.980000e-12 82.4
6 TraesCS7A01G556900 chr1D 95.840 2620 84 6 818 3419 66758798 66761410 0.000000e+00 4211.0
7 TraesCS7A01G556900 chr1D 95.699 558 22 2 818 1375 370167843 370168398 0.000000e+00 896.0
8 TraesCS7A01G556900 chr1D 92.793 444 28 2 5 447 370167275 370167715 1.180000e-179 640.0
9 TraesCS7A01G556900 chr1D 90.315 444 25 8 5 444 66758229 66758658 2.030000e-157 566.0
10 TraesCS7A01G556900 chr3D 95.840 2620 81 6 818 3419 21935290 21937899 0.000000e+00 4209.0
11 TraesCS7A01G556900 chr3D 91.441 444 25 4 5 447 21930960 21931391 7.210000e-167 597.0
12 TraesCS7A01G556900 chr2A 92.987 2467 135 8 818 3266 268560829 268558383 0.000000e+00 3563.0
13 TraesCS7A01G556900 chr2A 92.805 1765 69 21 2129 3891 772915046 772916754 0.000000e+00 2503.0
14 TraesCS7A01G556900 chr2A 92.414 435 32 1 818 1251 469875664 469876098 1.540000e-173 619.0
15 TraesCS7A01G556900 chr2A 89.435 407 31 5 45 447 268561356 268560958 1.620000e-138 503.0
16 TraesCS7A01G556900 chr2B 93.641 2296 89 17 1621 3898 71029553 71031809 0.000000e+00 3378.0
17 TraesCS7A01G556900 chr2B 94.758 1488 67 6 2413 3898 12732646 12734124 0.000000e+00 2305.0
18 TraesCS7A01G556900 chr2B 92.571 1575 65 12 2319 3891 60459859 60458335 0.000000e+00 2213.0
19 TraesCS7A01G556900 chr2B 93.157 1096 45 7 2796 3891 56097576 56098641 0.000000e+00 1581.0
20 TraesCS7A01G556900 chr2B 92.727 1100 45 10 2796 3891 752987597 752986529 0.000000e+00 1555.0
21 TraesCS7A01G556900 chr2B 90.675 1126 45 28 2796 3891 69400389 69401484 0.000000e+00 1443.0
22 TraesCS7A01G556900 chr2B 95.958 866 31 2 1621 2486 398111910 398112771 0.000000e+00 1402.0
23 TraesCS7A01G556900 chr2B 85.906 1192 82 34 2729 3898 490588239 490587112 0.000000e+00 1192.0
24 TraesCS7A01G556900 chr2B 90.545 275 9 5 3104 3369 275507156 275506890 8.020000e-92 348.0
25 TraesCS7A01G556900 chr2B 92.920 226 15 1 54 278 16377254 16377029 1.040000e-85 327.0
26 TraesCS7A01G556900 chr2B 98.734 79 0 1 1255 1333 12709209 12709286 5.250000e-29 139.0
27 TraesCS7A01G556900 chr2B 97.826 46 1 0 6 51 736899370 736899325 3.230000e-11 80.5
28 TraesCS7A01G556900 chr7B 95.569 1941 70 8 1562 3499 123397817 123399744 0.000000e+00 3094.0
29 TraesCS7A01G556900 chr7B 92.693 739 48 6 818 1556 123385788 123386520 0.000000e+00 1061.0
30 TraesCS7A01G556900 chr3B 93.506 1771 71 16 2129 3891 75640339 75638605 0.000000e+00 2593.0
31 TraesCS7A01G556900 chr3B 93.488 1766 73 14 2129 3892 484501178 484499453 0.000000e+00 2586.0
32 TraesCS7A01G556900 chr1B 93.310 1136 63 6 2763 3898 513974161 513975283 0.000000e+00 1664.0
33 TraesCS7A01G556900 chr1B 96.000 75 3 0 1255 1329 513973321 513973395 5.290000e-24 122.0
34 TraesCS7A01G556900 chr5B 93.169 1098 43 11 2796 3891 665599054 665597987 0.000000e+00 1583.0
35 TraesCS7A01G556900 chr5B 92.910 818 36 8 1345 2144 589128209 589127396 0.000000e+00 1170.0
36 TraesCS7A01G556900 chr5B 92.364 275 20 1 5 278 517326105 517326379 1.310000e-104 390.0
37 TraesCS7A01G556900 chr5B 87.500 184 14 6 241 418 589128950 589128770 1.840000e-48 204.0
38 TraesCS7A01G556900 chr5D 86.587 835 70 27 1340 2144 480714270 480713448 0.000000e+00 883.0
39 TraesCS7A01G556900 chr5A 87.113 776 67 20 1340 2097 599813663 599812903 0.000000e+00 848.0
40 TraesCS7A01G556900 chr1A 92.644 435 31 1 818 1251 343962633 343963067 3.310000e-175 625.0
41 TraesCS7A01G556900 chr1A 92.220 437 23 4 5 435 425126157 425126588 3.330000e-170 608.0
42 TraesCS7A01G556900 chr3A 92.446 278 15 2 5 281 51811823 51811551 3.650000e-105 392.0
43 TraesCS7A01G556900 chr6A 100.000 43 0 0 6 48 429226409 429226451 3.230000e-11 80.5


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 TraesCS7A01G556900 chr7A 727857566 727861463 3897 False 3274.0 5722 100.0000 1 3898 2 chr7A.!!$F1 3897
1 TraesCS7A01G556900 chrUn 93957100 93960693 3593 False 2682.5 4809 93.3930 45 3898 2 chrUn.!!$F1 3853
2 TraesCS7A01G556900 chr7D 568456915 568460501 3586 False 2349.7 4617 97.0000 5 3898 2 chr7D.!!$F1 3893
3 TraesCS7A01G556900 chr1D 66758229 66761410 3181 False 2388.5 4211 93.0775 5 3419 2 chr1D.!!$F1 3414
4 TraesCS7A01G556900 chr1D 370167275 370168398 1123 False 768.0 896 94.2460 5 1375 2 chr1D.!!$F2 1370
5 TraesCS7A01G556900 chr3D 21930960 21937899 6939 False 2403.0 4209 93.6405 5 3419 2 chr3D.!!$F1 3414
6 TraesCS7A01G556900 chr2A 772915046 772916754 1708 False 2503.0 2503 92.8050 2129 3891 1 chr2A.!!$F2 1762
7 TraesCS7A01G556900 chr2A 268558383 268561356 2973 True 2033.0 3563 91.2110 45 3266 2 chr2A.!!$R1 3221
8 TraesCS7A01G556900 chr2B 71029553 71031809 2256 False 3378.0 3378 93.6410 1621 3898 1 chr2B.!!$F5 2277
9 TraesCS7A01G556900 chr2B 12732646 12734124 1478 False 2305.0 2305 94.7580 2413 3898 1 chr2B.!!$F2 1485
10 TraesCS7A01G556900 chr2B 60458335 60459859 1524 True 2213.0 2213 92.5710 2319 3891 1 chr2B.!!$R2 1572
11 TraesCS7A01G556900 chr2B 56097576 56098641 1065 False 1581.0 1581 93.1570 2796 3891 1 chr2B.!!$F3 1095
12 TraesCS7A01G556900 chr2B 752986529 752987597 1068 True 1555.0 1555 92.7270 2796 3891 1 chr2B.!!$R6 1095
13 TraesCS7A01G556900 chr2B 69400389 69401484 1095 False 1443.0 1443 90.6750 2796 3891 1 chr2B.!!$F4 1095
14 TraesCS7A01G556900 chr2B 398111910 398112771 861 False 1402.0 1402 95.9580 1621 2486 1 chr2B.!!$F6 865
15 TraesCS7A01G556900 chr2B 490587112 490588239 1127 True 1192.0 1192 85.9060 2729 3898 1 chr2B.!!$R4 1169
16 TraesCS7A01G556900 chr7B 123397817 123399744 1927 False 3094.0 3094 95.5690 1562 3499 1 chr7B.!!$F2 1937
17 TraesCS7A01G556900 chr7B 123385788 123386520 732 False 1061.0 1061 92.6930 818 1556 1 chr7B.!!$F1 738
18 TraesCS7A01G556900 chr3B 75638605 75640339 1734 True 2593.0 2593 93.5060 2129 3891 1 chr3B.!!$R1 1762
19 TraesCS7A01G556900 chr3B 484499453 484501178 1725 True 2586.0 2586 93.4880 2129 3892 1 chr3B.!!$R2 1763
20 TraesCS7A01G556900 chr1B 513973321 513975283 1962 False 893.0 1664 94.6550 1255 3898 2 chr1B.!!$F1 2643
21 TraesCS7A01G556900 chr5B 665597987 665599054 1067 True 1583.0 1583 93.1690 2796 3891 1 chr5B.!!$R1 1095
22 TraesCS7A01G556900 chr5B 589127396 589128950 1554 True 687.0 1170 90.2050 241 2144 2 chr5B.!!$R2 1903
23 TraesCS7A01G556900 chr5D 480713448 480714270 822 True 883.0 883 86.5870 1340 2144 1 chr5D.!!$R1 804
24 TraesCS7A01G556900 chr5A 599812903 599813663 760 True 848.0 848 87.1130 1340 2097 1 chr5A.!!$R1 757

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
74 111 1.065854 CAACAAAACCAACCAGCCCAA 60.066 47.619 0.00 0.0 0.00 4.12 F
414 479 1.133450 TCACTATCCCCTCTTCCTCCG 60.133 57.143 0.00 0.0 0.00 4.63 F
1138 5002 1.304547 CTCCGAGGAGACCACCACT 60.305 63.158 13.69 0.0 44.53 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1077 4941 0.802494 CTTGCGGTACTTTTGCGGAT 59.198 50.000 0.00 0.00 0.00 4.18 R
2212 6122 0.336737 ACGAGGAATCAGAGGGAGGT 59.663 55.000 0.00 0.00 0.00 3.85 R
3096 7071 4.798344 CTGCTCCAGGCTGGCCAG 62.798 72.222 29.34 29.34 42.39 4.85 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
58 95 3.099841 TGGCCTCACCACCCAACA 61.100 61.111 3.32 0.00 46.36 3.33
74 111 1.065854 CAACAAAACCAACCAGCCCAA 60.066 47.619 0.00 0.00 0.00 4.12
81 118 1.437160 CAACCAGCCCAACACACAC 59.563 57.895 0.00 0.00 0.00 3.82
181 220 2.236223 CTGGCGACTGCATCCACTCT 62.236 60.000 0.00 0.00 45.35 3.24
414 479 1.133450 TCACTATCCCCTCTTCCTCCG 60.133 57.143 0.00 0.00 0.00 4.63
435 500 2.037847 GTGCCCCCAAATCCAGCT 59.962 61.111 0.00 0.00 0.00 4.24
1032 4896 2.600769 ACGAGGAGTCCGGCAAGT 60.601 61.111 2.76 0.00 0.00 3.16
1077 4941 2.202919 CCGTCATGCTCGCCATCA 60.203 61.111 4.94 0.00 29.71 3.07
1084 4948 2.896854 GCTCGCCATCATCCGCAA 60.897 61.111 0.00 0.00 0.00 4.85
1113 4977 1.398958 AAGATGGAGGAGAGGCTCGC 61.399 60.000 10.01 10.01 0.00 5.03
1138 5002 1.304547 CTCCGAGGAGACCACCACT 60.305 63.158 13.69 0.00 44.53 4.00
1161 5025 1.818642 GTCAAGCAGATGCAGGAGTT 58.181 50.000 7.68 0.00 45.16 3.01
1603 5493 6.011122 ACAAATAAATCCAGAGGAGCATCT 57.989 37.500 0.00 0.00 34.05 2.90
1604 5494 7.141758 ACAAATAAATCCAGAGGAGCATCTA 57.858 36.000 0.00 0.00 34.05 1.98
1633 5527 2.849294 TGTGGGGCTTTTATTTTGCC 57.151 45.000 0.00 0.00 45.42 4.52
1685 5579 3.702548 ACATGGGTCAATTGTGATGGATG 59.297 43.478 5.13 4.73 35.80 3.51
1863 5770 4.088634 TGGAGGCATCAGCTTTTACATTT 58.911 39.130 0.00 0.00 41.70 2.32
2212 6122 3.389329 GCATCTTGTCTTCATCTCCCCTA 59.611 47.826 0.00 0.00 0.00 3.53
2449 6376 5.984233 TGTTTACTGTAAGACTTGCTGTG 57.016 39.130 20.76 7.66 37.43 3.66
2472 6399 4.972514 AGCAAGGCTTGAGTAATTTAGC 57.027 40.909 30.45 10.89 33.89 3.09
2719 6651 4.000325 TGATGCTGTTAACAACATAGCGT 59.000 39.130 21.32 15.77 41.26 5.07
2723 6655 5.209240 TGCTGTTAACAACATAGCGTTTTC 58.791 37.500 10.03 0.00 41.26 2.29
2816 6748 6.204688 TCGTTGCTGTTCTCTTTTTCATATGT 59.795 34.615 1.90 0.00 0.00 2.29
2996 6943 4.846779 TGTGGATTCTTGTTTTGGTAGC 57.153 40.909 0.00 0.00 0.00 3.58
3096 7071 6.806751 TGCTTATCCAGTAGTATCAGTCAAC 58.193 40.000 0.00 0.00 0.00 3.18
3185 7160 7.175104 AGAAAATTAGACCAGCTGTCCATTTA 58.825 34.615 13.81 0.00 45.68 1.40
3190 7165 3.019564 GACCAGCTGTCCATTTATTGCT 58.980 45.455 13.81 0.00 38.09 3.91
3238 7222 5.506686 TGTGCTAGAGACATGCTACTTAG 57.493 43.478 0.00 0.00 0.00 2.18
3493 7479 9.457110 CAAAAGTATATGCAAAGTTTGTGTGTA 57.543 29.630 16.70 6.20 0.00 2.90
3495 7481 9.624697 AAAGTATATGCAAAGTTTGTGTGTATG 57.375 29.630 16.70 0.00 0.00 2.39
3496 7482 8.335532 AGTATATGCAAAGTTTGTGTGTATGT 57.664 30.769 16.70 5.74 0.00 2.29
3619 7615 8.023021 TCTCTTTGAATGTGCAGGTAGTATAT 57.977 34.615 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 95 0.539518 GTGTTGGGCTGGTTGGTTTT 59.460 50.000 0.00 0.00 0.00 2.43
74 111 1.335132 AACGAGGTGAGGGTGTGTGT 61.335 55.000 0.00 0.00 0.00 3.72
170 209 4.783621 GGCGGCAGAGTGGATGCA 62.784 66.667 3.07 0.00 45.68 3.96
197 236 2.766229 GGAGGGGAGAGGAGTGGC 60.766 72.222 0.00 0.00 0.00 5.01
201 240 2.612251 GAGGGGAGGGGAGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
202 241 3.036959 GGAGGGGAGGGGAGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
203 242 4.179599 GGGAGGGGAGGGGAGAGG 62.180 77.778 0.00 0.00 0.00 3.69
204 243 4.179599 GGGGAGGGGAGGGGAGAG 62.180 77.778 0.00 0.00 0.00 3.20
205 244 4.761304 AGGGGAGGGGAGGGGAGA 62.761 72.222 0.00 0.00 0.00 3.71
379 444 0.764369 AGTGAGGTGGTGGAGAAGCA 60.764 55.000 0.00 0.00 0.00 3.91
414 479 3.076916 GGATTTGGGGGCACAGGC 61.077 66.667 0.00 0.00 40.13 4.85
886 4623 1.228769 AGTGTCGTGGCTAGGGTCA 60.229 57.895 0.00 0.00 0.00 4.02
1077 4941 0.802494 CTTGCGGTACTTTTGCGGAT 59.198 50.000 0.00 0.00 0.00 4.18
1084 4948 1.906574 TCCTCCATCTTGCGGTACTTT 59.093 47.619 0.00 0.00 0.00 2.66
1138 5002 2.032376 TGCATCTGCTTGACGCCA 59.968 55.556 3.53 0.00 42.66 5.69
1161 5025 1.533033 TGGAACAGGAGAGTGCCGA 60.533 57.895 0.00 0.00 40.38 5.54
1603 5493 3.825908 AAGCCCCACAAAGGAAAGATA 57.174 42.857 0.00 0.00 41.22 1.98
1604 5494 2.702270 AAGCCCCACAAAGGAAAGAT 57.298 45.000 0.00 0.00 41.22 2.40
1633 5527 4.497473 TGGAAGTAAAATGACCTTTGCG 57.503 40.909 0.00 0.00 0.00 4.85
1685 5579 2.887152 GTGGGCCAATGGATACTTCATC 59.113 50.000 8.40 0.00 37.61 2.92
1863 5770 6.304356 CACTTGCTTGTGTGAGAAATTCTA 57.696 37.500 0.00 0.00 36.38 2.10
2212 6122 0.336737 ACGAGGAATCAGAGGGAGGT 59.663 55.000 0.00 0.00 0.00 3.85
2449 6376 5.502544 CGCTAAATTACTCAAGCCTTGCTAC 60.503 44.000 0.00 0.00 38.25 3.58
2472 6399 8.738199 TCAGTTGAAACTAAAGATGTAGTACG 57.262 34.615 0.00 0.00 37.08 3.67
2549 6479 7.201974 GGCTCCATTTGTAACTATAGTACTCCA 60.202 40.741 5.65 0.00 0.00 3.86
2701 6633 5.449304 AGAAAACGCTATGTTGTTAACAGC 58.551 37.500 14.87 14.87 45.95 4.40
2816 6748 5.715434 TCACACACATAACAGTAGCACTA 57.285 39.130 0.00 0.00 0.00 2.74
2996 6943 7.411157 GCATTTTACTCATAGCAAAGCAAACTG 60.411 37.037 0.00 0.00 0.00 3.16
3096 7071 4.798344 CTGCTCCAGGCTGGCCAG 62.798 72.222 29.34 29.34 42.39 4.85
3372 7356 1.876156 CAGCAGGGAGAAACAGTGAAC 59.124 52.381 0.00 0.00 0.00 3.18
3485 7469 5.476091 TCACTGGATACACATACACACAA 57.524 39.130 0.00 0.00 46.17 3.33
3493 7479 4.880120 CAGATTTGCTCACTGGATACACAT 59.120 41.667 0.00 0.00 46.17 3.21
3494 7480 4.256110 CAGATTTGCTCACTGGATACACA 58.744 43.478 0.00 0.00 46.17 3.72
3495 7481 4.256920 ACAGATTTGCTCACTGGATACAC 58.743 43.478 0.00 0.00 46.17 2.90
3782 7790 5.643777 AGCAGGATGTACACAAGAATACAAC 59.356 40.000 0.00 0.00 39.31 3.32


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

AutoCloner maintained by Alex Coulton.