Multiple sequence alignment - TraesCS7D01G043700

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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 TraesCS7D01G043700 chr7D 100.000 5138 0 0 1 5138 22532175 22527038 0.000000e+00 9489.0
1 TraesCS7D01G043700 chr7D 90.625 96 4 4 4994 5085 536314598 536314692 6.990000e-24 122.0
2 TraesCS7D01G043700 chr4A 91.683 2621 183 25 1977 4587 705180497 705177902 0.000000e+00 3600.0
3 TraesCS7D01G043700 chr4A 89.758 537 34 5 987 1507 705181413 705180882 0.000000e+00 667.0
4 TraesCS7D01G043700 chr4A 88.194 288 24 4 1547 1826 705180802 705180517 8.240000e-88 335.0
5 TraesCS7D01G043700 chr4A 78.272 382 52 15 996 1354 705227669 705227296 3.120000e-52 217.0
6 TraesCS7D01G043700 chr7A 89.121 2868 206 48 1547 4384 22920497 22917706 0.000000e+00 3470.0
7 TraesCS7D01G043700 chr7A 99.594 986 4 0 1 986 275272783 275273768 0.000000e+00 1799.0
8 TraesCS7D01G043700 chr7A 82.175 561 36 26 987 1525 22921074 22920556 1.710000e-114 424.0
9 TraesCS7D01G043700 chr7A 89.333 150 8 4 4994 5135 80542375 80542524 1.140000e-41 182.0
10 TraesCS7D01G043700 chr7A 93.684 95 5 1 4873 4967 80541907 80542000 1.930000e-29 141.0
11 TraesCS7D01G043700 chr7A 100.000 28 0 0 4967 4994 46960745 46960772 9.000000e-03 52.8
12 TraesCS7D01G043700 chr7A 100.000 28 0 0 4967 4994 47496734 47496707 9.000000e-03 52.8
13 TraesCS7D01G043700 chr2A 100.000 986 0 0 1 986 277143627 277142642 0.000000e+00 1821.0
14 TraesCS7D01G043700 chr6A 99.493 987 5 0 1 987 70917705 70918691 0.000000e+00 1796.0
15 TraesCS7D01G043700 chr6A 94.615 260 11 3 733 991 70916247 70915990 2.880000e-107 399.0
16 TraesCS7D01G043700 chr4B 99.291 987 7 0 1 987 53488749 53487763 0.000000e+00 1784.0
17 TraesCS7D01G043700 chr4B 88.816 152 7 6 4994 5135 653948641 653948792 1.470000e-40 178.0
18 TraesCS7D01G043700 chr6D 98.783 986 2 2 1 986 29737637 29736662 0.000000e+00 1746.0
19 TraesCS7D01G043700 chr6D 91.289 551 46 2 1887 2437 288466461 288467009 0.000000e+00 750.0
20 TraesCS7D01G043700 chr6D 88.144 388 35 7 2490 2876 288467007 288467384 7.850000e-123 451.0
21 TraesCS7D01G043700 chr2B 92.922 989 56 7 1 985 748143901 748144879 0.000000e+00 1426.0
22 TraesCS7D01G043700 chr2B 87.500 992 109 11 1887 2876 645134002 645133024 0.000000e+00 1131.0
23 TraesCS7D01G043700 chr2B 95.745 141 6 0 157 297 37643070 37643210 1.440000e-55 228.0
24 TraesCS7D01G043700 chr2B 97.436 39 1 0 138 176 37643078 37643116 3.320000e-07 67.6
25 TraesCS7D01G043700 chr5D 89.909 991 87 9 1887 2876 462796512 462795534 0.000000e+00 1264.0
26 TraesCS7D01G043700 chr5D 83.203 1024 118 26 1 984 479790558 479789549 0.000000e+00 889.0
27 TraesCS7D01G043700 chrUn 98.693 612 1 1 375 986 244517334 244516730 0.000000e+00 1079.0
28 TraesCS7D01G043700 chr5A 94.158 582 33 1 405 986 421252040 421252620 0.000000e+00 885.0
29 TraesCS7D01G043700 chr5A 89.474 152 5 8 4994 5135 670189077 670188927 1.140000e-41 182.0
30 TraesCS7D01G043700 chr5A 100.000 28 0 0 4445 4472 276637578 276637605 9.000000e-03 52.8
31 TraesCS7D01G043700 chr3D 90.877 559 49 2 1887 2445 283966779 283966223 0.000000e+00 749.0
32 TraesCS7D01G043700 chr3D 94.041 386 15 5 4589 4969 603305278 603304896 3.450000e-161 579.0
33 TraesCS7D01G043700 chr3D 88.462 286 22 7 2507 2791 283966214 283965939 8.240000e-88 335.0
34 TraesCS7D01G043700 chr3D 93.377 151 4 2 4994 5138 603304459 603304309 8.660000e-53 219.0
35 TraesCS7D01G043700 chr2D 93.005 386 19 5 4589 4969 294540915 294541297 1.620000e-154 556.0
36 TraesCS7D01G043700 chr2D 93.919 148 3 2 4994 5135 294541734 294541881 8.660000e-53 219.0
37 TraesCS7D01G043700 chr2D 82.558 86 12 3 4491 4575 630044571 630044654 7.140000e-09 73.1
38 TraesCS7D01G043700 chr2D 81.176 85 13 3 4491 4574 629976833 629976915 1.190000e-06 65.8
39 TraesCS7D01G043700 chr3A 91.799 378 27 4 4589 4965 187274279 187274653 1.640000e-144 523.0
40 TraesCS7D01G043700 chr3A 93.243 148 4 2 4994 5135 187287509 187287656 4.030000e-51 213.0
41 TraesCS7D01G043700 chr3A 81.081 148 15 7 4994 5135 340909603 340909463 7.040000e-19 106.0
42 TraesCS7D01G043700 chr7B 91.078 269 22 2 4589 4857 22835371 22835637 3.780000e-96 363.0
43 TraesCS7D01G043700 chr7B 90.476 273 24 2 4589 4861 22899273 22899543 4.890000e-95 359.0
44 TraesCS7D01G043700 chr7B 90.110 273 25 2 4589 4861 22711686 22711956 2.280000e-93 353.0
45 TraesCS7D01G043700 chr7B 90.262 267 23 3 4589 4855 22714739 22715002 3.810000e-91 346.0
46 TraesCS7D01G043700 chr7B 89.744 273 25 3 4589 4861 22791375 22791644 3.810000e-91 346.0
47 TraesCS7D01G043700 chr7B 89.377 273 27 2 4589 4861 22968624 22968894 4.930000e-90 342.0
48 TraesCS7D01G043700 chr7B 94.737 95 4 1 4873 4967 22670310 22670403 4.150000e-31 147.0
49 TraesCS7D01G043700 chr7B 93.684 95 5 1 4873 4967 22674256 22674349 1.930000e-29 141.0
50 TraesCS7D01G043700 chr7B 94.565 92 4 1 4876 4967 22791737 22791827 1.930000e-29 141.0
51 TraesCS7D01G043700 chr7B 93.684 95 5 1 4873 4967 22895048 22895141 1.930000e-29 141.0
52 TraesCS7D01G043700 chr7B 92.632 95 6 1 4873 4967 22713578 22713671 8.970000e-28 135.0
53 TraesCS7D01G043700 chr4D 92.000 150 6 5 4994 5138 362702222 362702074 6.740000e-49 206.0
54 TraesCS7D01G043700 chr4D 90.789 152 3 9 4994 5135 488423903 488424053 5.250000e-45 193.0
55 TraesCS7D01G043700 chr4D 82.308 130 18 3 4447 4575 64357323 64357198 1.960000e-19 108.0
56 TraesCS7D01G043700 chr4D 100.000 30 0 0 4542 4571 47990528 47990557 7.190000e-04 56.5
57 TraesCS7D01G043700 chr1A 91.429 105 9 0 165 269 440923549 440923445 1.490000e-30 145.0
58 TraesCS7D01G043700 chr1A 93.617 47 2 1 4530 4575 267144016 267143970 9.230000e-08 69.4
59 TraesCS7D01G043700 chr1D 86.154 130 13 3 4447 4575 211684202 211684077 8.970000e-28 135.0
60 TraesCS7D01G043700 chr5B 90.323 93 9 0 166 258 587477594 587477502 6.990000e-24 122.0


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 TraesCS7D01G043700 chr7D 22527038 22532175 5137 True 9489.0 9489 100.000000 1 5138 1 chr7D.!!$R1 5137
1 TraesCS7D01G043700 chr4A 705177902 705181413 3511 True 1534.0 3600 89.878333 987 4587 3 chr4A.!!$R2 3600
2 TraesCS7D01G043700 chr7A 22917706 22921074 3368 True 1947.0 3470 85.648000 987 4384 2 chr7A.!!$R2 3397
3 TraesCS7D01G043700 chr7A 275272783 275273768 985 False 1799.0 1799 99.594000 1 986 1 chr7A.!!$F2 985
4 TraesCS7D01G043700 chr2A 277142642 277143627 985 True 1821.0 1821 100.000000 1 986 1 chr2A.!!$R1 985
5 TraesCS7D01G043700 chr6A 70917705 70918691 986 False 1796.0 1796 99.493000 1 987 1 chr6A.!!$F1 986
6 TraesCS7D01G043700 chr4B 53487763 53488749 986 True 1784.0 1784 99.291000 1 987 1 chr4B.!!$R1 986
7 TraesCS7D01G043700 chr6D 29736662 29737637 975 True 1746.0 1746 98.783000 1 986 1 chr6D.!!$R1 985
8 TraesCS7D01G043700 chr6D 288466461 288467384 923 False 600.5 750 89.716500 1887 2876 2 chr6D.!!$F1 989
9 TraesCS7D01G043700 chr2B 748143901 748144879 978 False 1426.0 1426 92.922000 1 985 1 chr2B.!!$F1 984
10 TraesCS7D01G043700 chr2B 645133024 645134002 978 True 1131.0 1131 87.500000 1887 2876 1 chr2B.!!$R1 989
11 TraesCS7D01G043700 chr5D 462795534 462796512 978 True 1264.0 1264 89.909000 1887 2876 1 chr5D.!!$R1 989
12 TraesCS7D01G043700 chr5D 479789549 479790558 1009 True 889.0 889 83.203000 1 984 1 chr5D.!!$R2 983
13 TraesCS7D01G043700 chrUn 244516730 244517334 604 True 1079.0 1079 98.693000 375 986 1 chrUn.!!$R1 611
14 TraesCS7D01G043700 chr5A 421252040 421252620 580 False 885.0 885 94.158000 405 986 1 chr5A.!!$F2 581
15 TraesCS7D01G043700 chr3D 283965939 283966779 840 True 542.0 749 89.669500 1887 2791 2 chr3D.!!$R1 904
16 TraesCS7D01G043700 chr3D 603304309 603305278 969 True 399.0 579 93.709000 4589 5138 2 chr3D.!!$R2 549
17 TraesCS7D01G043700 chr2D 294540915 294541881 966 False 387.5 556 93.462000 4589 5135 2 chr2D.!!$F3 546
18 TraesCS7D01G043700 chr7B 22711686 22715002 3316 False 278.0 353 91.001333 4589 4967 3 chr7B.!!$F6 378


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
1093 1180 2.180017 GCGACTCGGCGAGGTAAA 59.820 61.111 36.81 2.29 33.35 2.01 F
1538 1647 0.031616 GTCTGGGGACTCCTCCATCT 60.032 60.000 5.91 0.00 38.52 2.90 F
1539 1648 0.263172 TCTGGGGACTCCTCCATCTC 59.737 60.000 5.91 0.00 38.52 2.75 F
1729 1875 0.592637 CGTTGCTGTCTGGCATGAAA 59.407 50.000 0.00 0.00 42.09 2.69 F
3273 3522 0.031616 AAAAAGGAGGCAACCCACCA 60.032 50.000 0.00 0.00 43.67 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2693 2915 0.606401 TTGCAGGCCAGTTAGACAGC 60.606 55.000 5.01 0.0 0.00 4.40 R
2916 3160 0.888619 CTTGCGGTACAGAGGAGACA 59.111 55.000 0.00 0.0 0.00 3.41 R
3273 3522 1.153086 GCTCATTGCCTCGTGGGAT 60.153 57.895 5.54 0.0 37.23 3.85 R
3330 3579 1.339631 CCACTCATTGCCCGGTAAGAA 60.340 52.381 0.00 0.0 0.00 2.52 R
4363 4621 0.108396 TGCACACACTGCCTGTACAT 59.892 50.000 0.00 0.0 46.51 2.29 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)



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AutoCloner maintained by Alex Coulton.