Multiple sequence alignment - TraesCS1A01G155900

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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 TraesCS1A01G155900 chr1A 100.000 1788 0 0 1 1788 276322725 276324512 0.000000e+00 3302.0
1 TraesCS1A01G155900 chr1A 100.000 1537 0 0 2496 4032 276325220 276326756 0.000000e+00 2839.0
2 TraesCS1A01G155900 chr1A 94.762 1661 67 12 1 1657 464427424 464425780 0.000000e+00 2567.0
3 TraesCS1A01G155900 chr1A 82.163 527 73 14 1139 1654 488967334 488967850 2.230000e-117 433.0
4 TraesCS1A01G155900 chr1A 80.315 254 38 8 1332 1579 75516633 75516880 8.900000e-42 182.0
5 TraesCS1A01G155900 chr4A 97.080 1541 29 7 2496 4032 203316245 203314717 0.000000e+00 2582.0
6 TraesCS1A01G155900 chr4A 84.980 253 36 2 617 868 603207982 603207731 5.170000e-64 255.0
7 TraesCS1A01G155900 chr4A 94.776 134 5 2 1656 1788 203317116 203316984 1.470000e-49 207.0
8 TraesCS1A01G155900 chr4A 86.486 111 9 3 2794 2902 153057095 153056989 2.550000e-22 117.0
9 TraesCS1A01G155900 chr5D 95.265 1436 47 10 1 1430 192752532 192751112 0.000000e+00 2255.0
10 TraesCS1A01G155900 chr7A 93.614 1378 72 7 284 1657 337833580 337832215 0.000000e+00 2043.0
11 TraesCS1A01G155900 chr7A 84.556 900 120 16 1 893 512889464 512888577 0.000000e+00 874.0
12 TraesCS1A01G155900 chr7A 95.517 290 9 4 1 289 337842689 337842403 1.020000e-125 460.0
13 TraesCS1A01G155900 chr7A 84.980 253 36 2 617 868 224165242 224165493 5.170000e-64 255.0
14 TraesCS1A01G155900 chr7A 90.667 75 6 1 1656 1730 347382380 347382453 9.220000e-17 99.0
15 TraesCS1A01G155900 chr4B 85.984 899 108 16 1 893 341932884 341931998 0.000000e+00 946.0
16 TraesCS1A01G155900 chr4B 87.879 297 30 4 3190 3483 266385081 266384788 1.070000e-90 344.0
17 TraesCS1A01G155900 chr4B 82.548 361 42 5 2537 2887 277555483 277555832 8.470000e-77 298.0
18 TraesCS1A01G155900 chr4B 90.647 139 6 3 2795 2930 168308592 168308726 1.150000e-40 178.0
19 TraesCS1A01G155900 chr4B 90.076 131 10 3 3355 3484 457870456 457870328 2.490000e-37 167.0
20 TraesCS1A01G155900 chr4B 89.209 139 8 3 2795 2930 550378131 550377997 2.490000e-37 167.0
21 TraesCS1A01G155900 chr4B 80.392 204 25 5 2821 3023 266385269 266385080 1.510000e-29 141.0
22 TraesCS1A01G155900 chr4B 92.105 76 3 3 1656 1730 120004977 120005050 1.980000e-18 104.0
23 TraesCS1A01G155900 chr4B 87.059 85 8 3 1656 1740 329081198 329081279 4.290000e-15 93.5
24 TraesCS1A01G155900 chr6D 85.078 898 116 15 1 893 242112424 242111540 0.000000e+00 900.0
25 TraesCS1A01G155900 chr6D 84.934 531 48 14 1139 1657 109724333 109723823 3.600000e-140 508.0
26 TraesCS1A01G155900 chr3A 84.710 896 117 16 1 890 146689733 146690614 0.000000e+00 878.0
27 TraesCS1A01G155900 chr3A 88.073 109 9 2 2795 2902 509941968 509941863 4.230000e-25 126.0
28 TraesCS1A01G155900 chr3A 92.000 75 5 1 2499 2572 300804283 300804209 1.980000e-18 104.0
29 TraesCS1A01G155900 chr3A 86.316 95 10 3 1656 1748 503347636 503347729 2.560000e-17 100.0
30 TraesCS1A01G155900 chr6B 91.877 554 30 9 3489 4032 399434592 399434044 0.000000e+00 760.0
31 TraesCS1A01G155900 chr6B 91.636 550 35 9 3489 4032 311202010 311201466 0.000000e+00 750.0
32 TraesCS1A01G155900 chr6B 80.159 378 35 20 2919 3265 44110554 44110186 3.110000e-61 246.0
33 TraesCS1A01G155900 chr6B 96.825 63 2 0 1667 1729 131284885 131284947 5.510000e-19 106.0
34 TraesCS1A01G155900 chr3B 91.833 551 28 7 3489 4032 426091627 426092167 0.000000e+00 752.0
35 TraesCS1A01G155900 chr3B 90.710 549 36 8 3489 4032 628827228 628826690 0.000000e+00 717.0
36 TraesCS1A01G155900 chr3B 88.410 371 39 4 3122 3489 679524408 679524039 1.030000e-120 444.0
37 TraesCS1A01G155900 chr3B 90.667 75 6 1 1656 1730 410851255 410851182 9.220000e-17 99.0
38 TraesCS1A01G155900 chr2B 90.676 547 34 12 3489 4028 556034827 556034291 0.000000e+00 712.0
39 TraesCS1A01G155900 chr2B 89.258 391 28 10 3646 4032 107588431 107588811 1.010000e-130 477.0
40 TraesCS1A01G155900 chr2B 85.027 374 46 10 3122 3489 402156046 402155677 4.920000e-99 372.0
41 TraesCS1A01G155900 chr7B 90.631 523 23 16 3517 4032 213489767 213490270 0.000000e+00 671.0
42 TraesCS1A01G155900 chr7B 90.580 138 7 3 2795 2930 547021042 547021175 1.150000e-40 178.0
43 TraesCS1A01G155900 chr7B 94.505 91 4 1 2496 2585 115703526 115703616 5.430000e-29 139.0
44 TraesCS1A01G155900 chr2D 90.535 486 40 3 3001 3484 172545989 172546470 4.390000e-179 638.0
45 TraesCS1A01G155900 chr2D 86.712 444 35 9 2537 2968 172545558 172545989 4.720000e-129 472.0
46 TraesCS1A01G155900 chr2D 90.265 113 6 5 2496 2605 163363270 163363160 4.200000e-30 143.0
47 TraesCS1A01G155900 chr3D 91.441 444 23 10 3597 4032 255239880 255239444 2.680000e-166 595.0
48 TraesCS1A01G155900 chr3D 90.496 242 17 4 3489 3724 255241363 255241122 8.410000e-82 315.0
49 TraesCS1A01G155900 chr3D 90.964 166 15 0 1492 1657 191039223 191039388 1.460000e-54 224.0
50 TraesCS1A01G155900 chr6A 83.815 519 63 15 1146 1654 128192599 128193106 1.310000e-129 473.0
51 TraesCS1A01G155900 chr6A 83.208 530 67 14 1139 1657 291447189 291446671 2.190000e-127 466.0
52 TraesCS1A01G155900 chr6A 80.070 286 32 11 2940 3200 25641725 25641440 5.320000e-44 189.0
53 TraesCS1A01G155900 chr6A 78.977 176 28 5 989 1162 162237461 162237629 1.180000e-20 111.0
54 TraesCS1A01G155900 chr5B 85.459 392 33 4 3122 3489 326997175 326997566 1.760000e-103 387.0
55 TraesCS1A01G155900 chr5B 91.061 179 11 2 3489 3665 345839599 345839774 1.870000e-58 237.0
56 TraesCS1A01G155900 chrUn 88.350 309 33 1 1139 1444 93045824 93046132 6.370000e-98 368.0
57 TraesCS1A01G155900 chrUn 81.638 354 28 18 2940 3265 94828289 94827945 4.000000e-65 259.0
58 TraesCS1A01G155900 chrUn 79.268 328 39 13 1332 1657 122476200 122476500 6.830000e-48 202.0
59 TraesCS1A01G155900 chrUn 81.780 236 14 5 1354 1579 475254753 475254969 1.930000e-38 171.0
60 TraesCS1A01G155900 chr1B 93.407 91 5 1 2496 2585 479647362 479647452 2.530000e-27 134.0
61 TraesCS1A01G155900 chr1B 90.411 73 5 2 1656 1728 246864018 246864088 1.190000e-15 95.3
62 TraesCS1A01G155900 chr5A 91.026 78 6 1 2496 2572 703029617 703029694 1.980000e-18 104.0
63 TraesCS1A01G155900 chr2A 90.667 75 6 1 1657 1731 284781462 284781535 9.220000e-17 99.0


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 TraesCS1A01G155900 chr1A 276322725 276326756 4031 False 3070.5 3302 100.0000 1 4032 2 chr1A.!!$F3 4031
1 TraesCS1A01G155900 chr1A 464425780 464427424 1644 True 2567.0 2567 94.7620 1 1657 1 chr1A.!!$R1 1656
2 TraesCS1A01G155900 chr1A 488967334 488967850 516 False 433.0 433 82.1630 1139 1654 1 chr1A.!!$F2 515
3 TraesCS1A01G155900 chr4A 203314717 203317116 2399 True 1394.5 2582 95.9280 1656 4032 2 chr4A.!!$R3 2376
4 TraesCS1A01G155900 chr5D 192751112 192752532 1420 True 2255.0 2255 95.2650 1 1430 1 chr5D.!!$R1 1429
5 TraesCS1A01G155900 chr7A 337832215 337833580 1365 True 2043.0 2043 93.6140 284 1657 1 chr7A.!!$R1 1373
6 TraesCS1A01G155900 chr7A 512888577 512889464 887 True 874.0 874 84.5560 1 893 1 chr7A.!!$R3 892
7 TraesCS1A01G155900 chr4B 341931998 341932884 886 True 946.0 946 85.9840 1 893 1 chr4B.!!$R1 892
8 TraesCS1A01G155900 chr6D 242111540 242112424 884 True 900.0 900 85.0780 1 893 1 chr6D.!!$R2 892
9 TraesCS1A01G155900 chr6D 109723823 109724333 510 True 508.0 508 84.9340 1139 1657 1 chr6D.!!$R1 518
10 TraesCS1A01G155900 chr3A 146689733 146690614 881 False 878.0 878 84.7100 1 890 1 chr3A.!!$F1 889
11 TraesCS1A01G155900 chr6B 399434044 399434592 548 True 760.0 760 91.8770 3489 4032 1 chr6B.!!$R3 543
12 TraesCS1A01G155900 chr6B 311201466 311202010 544 True 750.0 750 91.6360 3489 4032 1 chr6B.!!$R2 543
13 TraesCS1A01G155900 chr3B 426091627 426092167 540 False 752.0 752 91.8330 3489 4032 1 chr3B.!!$F1 543
14 TraesCS1A01G155900 chr3B 628826690 628827228 538 True 717.0 717 90.7100 3489 4032 1 chr3B.!!$R2 543
15 TraesCS1A01G155900 chr2B 556034291 556034827 536 True 712.0 712 90.6760 3489 4028 1 chr2B.!!$R2 539
16 TraesCS1A01G155900 chr7B 213489767 213490270 503 False 671.0 671 90.6310 3517 4032 1 chr7B.!!$F2 515
17 TraesCS1A01G155900 chr2D 172545558 172546470 912 False 555.0 638 88.6235 2537 3484 2 chr2D.!!$F1 947
18 TraesCS1A01G155900 chr3D 255239444 255241363 1919 True 455.0 595 90.9685 3489 4032 2 chr3D.!!$R1 543
19 TraesCS1A01G155900 chr6A 128192599 128193106 507 False 473.0 473 83.8150 1146 1654 1 chr6A.!!$F1 508
20 TraesCS1A01G155900 chr6A 291446671 291447189 518 True 466.0 466 83.2080 1139 1657 1 chr6A.!!$R2 518

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
995 1007 1.586028 GCTGAATCAAAGGCGGCAA 59.414 52.632 13.08 0.0 34.17 4.52 F
1039 1051 0.769873 CATCATGGAGGAAGAGGGGG 59.230 60.000 0.00 0.0 0.00 5.40 F
2818 2905 1.026718 CGAAGATCAACTGCACCCCC 61.027 60.000 0.00 0.0 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2793 2880 0.659957 GCAGTTGATCTTCGATGGGC 59.340 55.000 0.00 0.00 0.00 5.36 R
2992 3080 1.743252 CTTGGCGAGCTTCTGGTCC 60.743 63.158 0.00 0.00 37.40 4.46 R
3734 5211 7.601886 TCGATGTCCATACAAATTTGCAAAAAT 59.398 29.630 17.19 5.45 39.58 1.82 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
24 25 2.483013 GGTAGCATTGTATCTGGCACGA 60.483 50.000 0.00 0.00 0.00 4.35
725 730 1.899142 TGATCGTCCCTGTGACAATGA 59.101 47.619 0.00 0.00 44.71 2.57
775 781 4.563580 GCTCTTTTCCCCCTTTTTGATTCC 60.564 45.833 0.00 0.00 0.00 3.01
995 1007 1.586028 GCTGAATCAAAGGCGGCAA 59.414 52.632 13.08 0.00 34.17 4.52
1039 1051 0.769873 CATCATGGAGGAAGAGGGGG 59.230 60.000 0.00 0.00 0.00 5.40
1050 1062 1.617947 AAGAGGGGGCGACAGTGATC 61.618 60.000 0.00 0.00 0.00 2.92
1077 1090 4.996434 GCGTGGTGGCACTGCTCT 62.996 66.667 18.45 0.00 0.00 4.09
1091 1104 4.994471 CTCTGCACAGTGGCGCCA 62.994 66.667 29.03 29.03 36.28 5.69
1186 1199 1.415672 AAGGAGGAAGGCCACGACAA 61.416 55.000 5.01 0.00 36.29 3.18
1447 1463 3.577313 GGCTGCTTCGGCCGATTC 61.577 66.667 31.56 23.10 46.48 2.52
1528 1568 4.881440 GCTGGATCGGGCATGGCA 62.881 66.667 22.06 0.94 0.00 4.92
1607 1652 1.380524 TTTCTTTTGCACCGGTTCGA 58.619 45.000 2.97 0.00 0.00 3.71
1608 1653 1.380524 TTCTTTTGCACCGGTTCGAA 58.619 45.000 2.97 2.64 0.00 3.71
1637 1682 4.645136 CCAATCGCTACCTATATAGAGGCA 59.355 45.833 13.49 0.00 40.65 4.75
1659 1704 4.101585 CAGCTGTGATCCAAATACCTAGGA 59.898 45.833 17.98 0.00 35.59 2.94
1663 1708 4.350816 TGTGATCCAAATACCTAGGATGGG 59.649 45.833 17.98 8.39 45.72 4.00
1679 1724 8.532819 CCTAGGATGGGTCTATTCTAATAACAC 58.467 40.741 1.05 0.00 0.00 3.32
1681 1726 7.082972 AGGATGGGTCTATTCTAATAACACCT 58.917 38.462 9.05 0.00 30.14 4.00
1682 1727 7.235812 AGGATGGGTCTATTCTAATAACACCTC 59.764 40.741 9.05 3.96 30.14 3.85
1748 1793 4.446413 ATCCGAACACCCCGCGAC 62.446 66.667 8.23 0.00 0.00 5.19
1770 1815 4.796231 CGCGCGCTAGAACCCACT 62.796 66.667 30.48 0.00 0.00 4.00
2517 2593 2.630580 CCCCTCACTCTACCTCAATAGC 59.369 54.545 0.00 0.00 0.00 2.97
2793 2880 3.803082 CGCCGGCAGATGTGTTGG 61.803 66.667 28.98 0.98 0.00 3.77
2818 2905 1.026718 CGAAGATCAACTGCACCCCC 61.027 60.000 0.00 0.00 0.00 5.40
3262 3351 6.112734 TCATCCATGGTGTAGATGTTGTTAC 58.887 40.000 12.58 0.00 38.79 2.50
3470 3560 1.216064 TGGAAGGTCCCATCCATCAG 58.784 55.000 6.19 0.00 38.67 2.90
3554 3647 2.048023 CGATGGCCATGGTGTGCTT 61.048 57.895 26.56 0.00 0.00 3.91
3555 3648 1.597797 CGATGGCCATGGTGTGCTTT 61.598 55.000 26.56 0.00 0.00 3.51
3556 3649 0.609662 GATGGCCATGGTGTGCTTTT 59.390 50.000 26.56 0.00 0.00 2.27
4028 5517 3.432252 CGACATAGGTTGTGGTTCACTTC 59.568 47.826 0.00 0.00 39.18 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.842052 TGGTAGTCGTGCCAGATACA 58.158 50.000 0.00 0.00 32.64 2.29
24 25 8.621286 CAATTTGTTTCTTTGTCTACTGGTAGT 58.379 33.333 7.52 0.00 34.84 2.73
491 495 1.407299 CCGGATGTCTCTTGGATGCAA 60.407 52.381 0.00 0.00 0.00 4.08
812 819 5.927030 TGCAATTTAGAGATGTTGACGTTC 58.073 37.500 0.00 0.00 0.00 3.95
973 985 1.678635 CGCCTTTGATTCAGCCCCA 60.679 57.895 0.00 0.00 0.00 4.96
995 1007 1.919600 GCCCTCTTCCTCCATGCTGT 61.920 60.000 0.00 0.00 0.00 4.40
1039 1051 1.204941 ACAACCTAGGATCACTGTCGC 59.795 52.381 17.98 0.00 0.00 5.19
1050 1062 1.671054 CCACCACGCACAACCTAGG 60.671 63.158 7.41 7.41 0.00 3.02
1167 1180 1.415672 TTGTCGTGGCCTTCCTCCTT 61.416 55.000 3.32 0.00 0.00 3.36
1186 1199 1.344763 CCCACGACCTTCTTTCTCTGT 59.655 52.381 0.00 0.00 0.00 3.41
1460 1476 4.752879 ATGCCGTCCCGAACACCG 62.753 66.667 0.00 0.00 38.18 4.94
1461 1477 2.818274 GATGCCGTCCCGAACACC 60.818 66.667 0.00 0.00 0.00 4.16
1479 1495 1.057275 CCTCCCCTAGCTTCTTCCCC 61.057 65.000 0.00 0.00 0.00 4.81
1590 1633 1.380524 TTTCGAACCGGTGCAAAAGA 58.619 45.000 14.51 0.00 0.00 2.52
1607 1652 8.426489 TCTATATAGGTAGCGATTGGTTGTTTT 58.574 33.333 9.89 0.00 0.00 2.43
1608 1653 7.959175 TCTATATAGGTAGCGATTGGTTGTTT 58.041 34.615 9.89 0.00 0.00 2.83
1637 1682 4.298626 TCCTAGGTATTTGGATCACAGCT 58.701 43.478 9.08 0.00 0.00 4.24
1659 1704 8.568617 AAGAGGTGTTATTAGAATAGACCCAT 57.431 34.615 8.11 0.00 30.86 4.00
2511 2587 1.429148 GGTTGAGGACGCGGCTATTG 61.429 60.000 13.91 0.00 0.00 1.90
2620 2696 2.892852 TGCCCAAGTGGAATCTGAAAAG 59.107 45.455 0.00 0.00 37.39 2.27
2793 2880 0.659957 GCAGTTGATCTTCGATGGGC 59.340 55.000 0.00 0.00 0.00 5.36
2875 2963 2.186160 CACTTTGGACTGCACGGCA 61.186 57.895 0.00 0.00 36.92 5.69
2992 3080 1.743252 CTTGGCGAGCTTCTGGTCC 60.743 63.158 0.00 0.00 37.40 4.46
3262 3351 3.257561 CCCGTCGCGAGATTGCAG 61.258 66.667 10.24 0.00 45.19 4.41
3470 3560 7.431960 TCGCATGTATGAAAAATATGCAAGAAC 59.568 33.333 0.00 0.00 43.10 3.01
3734 5211 7.601886 TCGATGTCCATACAAATTTGCAAAAAT 59.398 29.630 17.19 5.45 39.58 1.82


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

AutoCloner maintained by Alex Coulton.