Multiple sequence alignment - TraesCS1A01G350700

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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 TraesCS1A01G350700 chr1A 100.000 4454 0 0 1 4454 535433360 535428907 0.000000e+00 8226.0
1 TraesCS1A01G350700 chr1A 93.750 1056 39 14 930 1976 551511830 551512867 0.000000e+00 1559.0
2 TraesCS1A01G350700 chr1A 88.543 611 58 8 1594 2199 592318248 592317645 0.000000e+00 730.0
3 TraesCS1A01G350700 chr1A 94.681 376 15 5 569 940 551510917 551511291 2.990000e-161 579.0
4 TraesCS1A01G350700 chr1A 95.980 199 6 2 2002 2199 551512854 551513051 5.560000e-84 322.0
5 TraesCS1A01G350700 chr5A 98.211 3800 58 5 30 3828 680337685 680341475 0.000000e+00 6632.0
6 TraesCS1A01G350700 chr5A 98.889 360 4 0 4095 4454 680341773 680342132 1.040000e-180 643.0
7 TraesCS1A01G350700 chr2A 98.227 2481 37 4 1 2474 187940067 187942547 0.000000e+00 4331.0
8 TraesCS1A01G350700 chr2A 98.514 1346 20 0 2499 3844 187942540 187943885 0.000000e+00 2375.0
9 TraesCS1A01G350700 chr2A 96.975 562 10 3 3894 4454 187943884 187944439 0.000000e+00 937.0
10 TraesCS1A01G350700 chr2A 94.222 225 11 1 1977 2199 547265807 547265583 4.270000e-90 342.0
11 TraesCS1A01G350700 chr2A 94.222 225 11 1 1977 2199 642933963 642933739 4.270000e-90 342.0
12 TraesCS1A01G350700 chr2A 83.908 261 31 3 4166 4419 125129469 125129725 5.760000e-59 239.0
13 TraesCS1A01G350700 chr2A 90.164 122 12 0 4306 4427 12623264 12623385 4.610000e-35 159.0
14 TraesCS1A01G350700 chr2A 92.308 52 3 1 549 599 547265900 547265849 6.180000e-09 73.1
15 TraesCS1A01G350700 chr2A 92.308 52 3 1 549 599 642934056 642934005 6.180000e-09 73.1
16 TraesCS1A01G350700 chr1B 87.707 1326 117 24 886 2186 687073847 687072543 0.000000e+00 1504.0
17 TraesCS1A01G350700 chr1B 90.295 711 52 14 2197 2902 58449893 58449195 0.000000e+00 915.0
18 TraesCS1A01G350700 chr1B 93.224 428 25 4 570 995 602227749 602228174 1.050000e-175 627.0
19 TraesCS1A01G350700 chr1B 95.575 226 9 1 552 777 650490008 650489784 1.180000e-95 361.0
20 TraesCS1A01G350700 chr1D 84.182 1296 147 33 900 2186 493937415 493936169 0.000000e+00 1205.0
21 TraesCS1A01G350700 chr1D 94.118 340 18 2 2604 2942 99655519 99655181 2.380000e-142 516.0
22 TraesCS1A01G350700 chr1D 93.731 335 19 2 2609 2942 465937980 465937647 6.650000e-138 501.0
23 TraesCS1A01G350700 chr1D 96.000 275 10 1 2938 3212 465937510 465937237 3.160000e-121 446.0
24 TraesCS1A01G350700 chr1D 94.505 273 11 1 127 395 423889617 423889345 6.890000e-113 418.0
25 TraesCS1A01G350700 chr1D 93.907 279 12 2 2938 3212 99655044 99654767 2.480000e-112 416.0
26 TraesCS1A01G350700 chr1D 94.615 130 5 2 1 128 4551869 4551740 2.720000e-47 200.0
27 TraesCS1A01G350700 chr1D 92.727 55 4 0 2145 2199 493936255 493936201 3.690000e-11 80.5
28 TraesCS1A01G350700 chrUn 94.430 395 19 2 2548 2942 41122129 41122520 4.930000e-169 604.0
29 TraesCS1A01G350700 chrUn 95.440 307 12 1 2938 3242 41122665 41122971 5.180000e-134 488.0
30 TraesCS1A01G350700 chrUn 95.378 238 8 3 2196 2432 41121687 41121922 4.210000e-100 375.0
31 TraesCS1A01G350700 chrUn 95.946 74 3 0 3239 3312 41122944 41123017 2.180000e-23 121.0
32 TraesCS1A01G350700 chr7D 94.330 388 20 2 2556 2942 531995020 531995406 1.070000e-165 593.0
33 TraesCS1A01G350700 chr7D 95.636 275 11 1 2938 3212 531995543 531995816 1.470000e-119 440.0
34 TraesCS1A01G350700 chr7D 87.187 359 24 11 2197 2555 531994582 531994918 5.400000e-104 388.0
35 TraesCS1A01G350700 chr7D 84.255 235 24 6 4202 4427 47263099 47262869 2.700000e-52 217.0
36 TraesCS1A01G350700 chr7D 81.757 148 19 4 4152 4299 106645233 106645372 2.810000e-22 117.0
37 TraesCS1A01G350700 chr2B 89.197 361 30 5 2197 2555 429138409 429138762 4.090000e-120 442.0
38 TraesCS1A01G350700 chr2B 93.885 278 13 1 124 397 741450635 741450912 2.480000e-112 416.0
39 TraesCS1A01G350700 chr2B 87.921 356 17 6 2548 2902 429138864 429139194 3.230000e-106 396.0
40 TraesCS1A01G350700 chr2B 95.455 220 10 0 558 777 190231373 190231154 7.090000e-93 351.0
41 TraesCS1A01G350700 chr2B 82.310 277 39 5 4141 4411 174344207 174344479 9.630000e-57 231.0
42 TraesCS1A01G350700 chr2B 92.424 132 5 2 2 128 381372900 381373031 2.740000e-42 183.0
43 TraesCS1A01G350700 chr3B 88.643 361 31 6 2197 2555 31459167 31458815 8.850000e-117 431.0
44 TraesCS1A01G350700 chr3B 94.545 275 11 3 127 397 792140268 792139994 5.330000e-114 422.0
45 TraesCS1A01G350700 chr3B 93.455 275 14 1 127 397 792102834 792102560 5.360000e-109 405.0
46 TraesCS1A01G350700 chr3B 93.939 264 13 2 2548 2811 31458713 31458453 3.230000e-106 396.0
47 TraesCS1A01G350700 chr3B 97.260 146 4 0 398 543 351293196 351293341 9.570000e-62 248.0
48 TraesCS1A01G350700 chr3B 89.394 198 17 4 4135 4331 813797343 813797149 3.440000e-61 246.0
49 TraesCS1A01G350700 chr3B 96.575 146 5 0 398 543 792177996 792177851 4.450000e-60 243.0
50 TraesCS1A01G350700 chr3B 95.890 146 6 0 398 543 792139962 792139817 2.070000e-58 237.0
51 TraesCS1A01G350700 chr3B 95.205 146 7 0 398 543 792102528 792102383 9.630000e-57 231.0
52 TraesCS1A01G350700 chr3B 95.082 61 3 0 3182 3242 751095574 751095514 3.670000e-16 97.1
53 TraesCS1A01G350700 chr7A 94.891 274 14 0 124 397 38529656 38529929 3.180000e-116 429.0
54 TraesCS1A01G350700 chr7A 90.789 152 8 1 398 543 619255243 619255092 9.770000e-47 198.0
55 TraesCS1A01G350700 chr7A 93.750 128 8 0 1 128 686264753 686264880 4.550000e-45 193.0
56 TraesCS1A01G350700 chr7A 91.667 132 6 3 1 128 34221177 34221307 1.270000e-40 178.0
57 TraesCS1A01G350700 chr5D 94.585 277 12 1 124 397 469798072 469798348 4.120000e-115 425.0
58 TraesCS1A01G350700 chr5D 90.909 154 6 1 398 543 370304095 370303942 2.720000e-47 200.0
59 TraesCS1A01G350700 chr4D 94.545 275 11 1 127 397 28441361 28441087 5.330000e-114 422.0
60 TraesCS1A01G350700 chr6B 97.235 217 6 0 558 774 422698728 422698944 7.040000e-98 368.0
61 TraesCS1A01G350700 chr6B 97.110 173 4 1 569 741 332443851 332443680 1.570000e-74 291.0
62 TraesCS1A01G350700 chr6B 96.951 164 4 1 2208 2370 101217626 101217789 1.580000e-69 274.0
63 TraesCS1A01G350700 chr6B 95.312 128 5 1 1 128 710292139 710292013 7.550000e-48 202.0
64 TraesCS1A01G350700 chr5B 96.532 173 5 1 569 741 497373831 497373660 7.290000e-73 285.0
65 TraesCS1A01G350700 chr5B 89.474 152 11 5 4 152 588640767 588640618 2.120000e-43 187.0
66 TraesCS1A01G350700 chr5B 94.872 78 4 0 3235 3312 533439404 533439327 6.050000e-24 122.0
67 TraesCS1A01G350700 chr4B 94.220 173 9 1 2197 2369 605511903 605512074 3.420000e-66 263.0
68 TraesCS1A01G350700 chr2D 83.165 297 38 7 4130 4419 120972171 120972462 1.230000e-65 261.0
69 TraesCS1A01G350700 chr3D 91.503 153 6 1 398 543 19412681 19412529 2.100000e-48 204.0
70 TraesCS1A01G350700 chr3D 91.250 80 7 0 2938 3017 545247738 545247817 4.710000e-20 110.0
71 TraesCS1A01G350700 chr3A 93.893 131 5 1 1 128 11848319 11848449 1.260000e-45 195.0
72 TraesCS1A01G350700 chr7B 90.909 121 9 1 4301 4419 713856232 713856112 1.280000e-35 161.0
73 TraesCS1A01G350700 chr6D 90.756 119 11 0 4301 4419 69409779 69409661 4.610000e-35 159.0


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 TraesCS1A01G350700 chr1A 535428907 535433360 4453 True 8226.000000 8226 100.000000 1 4454 1 chr1A.!!$R1 4453
1 TraesCS1A01G350700 chr1A 551510917 551513051 2134 False 820.000000 1559 94.803667 569 2199 3 chr1A.!!$F1 1630
2 TraesCS1A01G350700 chr1A 592317645 592318248 603 True 730.000000 730 88.543000 1594 2199 1 chr1A.!!$R2 605
3 TraesCS1A01G350700 chr5A 680337685 680342132 4447 False 3637.500000 6632 98.550000 30 4454 2 chr5A.!!$F1 4424
4 TraesCS1A01G350700 chr2A 187940067 187944439 4372 False 2547.666667 4331 97.905333 1 4454 3 chr2A.!!$F3 4453
5 TraesCS1A01G350700 chr1B 687072543 687073847 1304 True 1504.000000 1504 87.707000 886 2186 1 chr1B.!!$R3 1300
6 TraesCS1A01G350700 chr1B 58449195 58449893 698 True 915.000000 915 90.295000 2197 2902 1 chr1B.!!$R1 705
7 TraesCS1A01G350700 chr1D 493936169 493937415 1246 True 642.750000 1205 88.454500 900 2199 2 chr1D.!!$R5 1299
8 TraesCS1A01G350700 chr1D 465937237 465937980 743 True 473.500000 501 94.865500 2609 3212 2 chr1D.!!$R4 603
9 TraesCS1A01G350700 chr1D 99654767 99655519 752 True 466.000000 516 94.012500 2604 3212 2 chr1D.!!$R3 608
10 TraesCS1A01G350700 chrUn 41121687 41123017 1330 False 397.000000 604 95.298500 2196 3312 4 chrUn.!!$F1 1116
11 TraesCS1A01G350700 chr7D 531994582 531995816 1234 False 473.666667 593 92.384333 2197 3212 3 chr7D.!!$F2 1015
12 TraesCS1A01G350700 chr2B 429138409 429139194 785 False 419.000000 442 88.559000 2197 2902 2 chr2B.!!$F4 705
13 TraesCS1A01G350700 chr3B 31458453 31459167 714 True 413.500000 431 91.291000 2197 2811 2 chr3B.!!$R4 614

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
456 461 1.002242 CTCCTCCCTCCTCCTACCCT 61.002 65.000 0.00 0.0 0.00 4.34 F
1276 1846 1.080025 GGACCCCGAAACGAGTCAG 60.080 63.158 13.04 0.0 33.76 3.51 F
2451 3070 0.321475 TGATGAGCGGCACACATGAA 60.321 50.000 1.29 0.0 0.00 2.57 F
2476 3095 1.321474 ATGGTTCTGCACACACAAGG 58.679 50.000 0.00 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1493 2084 0.327924 ACACCCTTTCATCGGCATCA 59.672 50.000 0.0 0.0 0.00 3.07 R
2482 3101 0.107752 TGTGTGTGTGCAGAGAAGCA 60.108 50.000 0.0 0.0 43.35 3.91 R
3282 4205 2.031495 ACTTGAGGCAGAGGGTTACT 57.969 50.000 0.0 0.0 0.00 2.24 R
3937 4861 3.244422 ACCGAGGTAAAAGAAGTGATGCA 60.244 43.478 0.0 0.0 0.00 3.96 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
378 383 4.961511 GGTCACGCAGGTGCACGA 62.962 66.667 11.45 0.00 44.03 4.35
456 461 1.002242 CTCCTCCCTCCTCCTACCCT 61.002 65.000 0.00 0.00 0.00 4.34
1276 1846 1.080025 GGACCCCGAAACGAGTCAG 60.080 63.158 13.04 0.00 33.76 3.51
1287 1858 4.576879 GAAACGAGTCAGGGGAGTTTATT 58.423 43.478 0.00 0.00 35.48 1.40
1693 2286 3.384789 ACGAAGCCTTGAGATATGCACTA 59.615 43.478 0.00 0.00 0.00 2.74
1694 2287 4.141937 ACGAAGCCTTGAGATATGCACTAA 60.142 41.667 0.00 0.00 0.00 2.24
2028 2624 2.157738 ACTGCTCTTTCTTGACATGCC 58.842 47.619 0.00 0.00 0.00 4.40
2039 2635 1.737838 TGACATGCCGAACCTGAATC 58.262 50.000 0.00 0.00 0.00 2.52
2451 3070 0.321475 TGATGAGCGGCACACATGAA 60.321 50.000 1.29 0.00 0.00 2.57
2458 3077 1.401552 GCGGCACACATGAACACATAT 59.598 47.619 0.00 0.00 0.00 1.78
2467 3086 4.156373 CACATGAACACATATGGTTCTGCA 59.844 41.667 24.83 14.10 43.84 4.41
2468 3087 4.156556 ACATGAACACATATGGTTCTGCAC 59.843 41.667 24.83 10.07 43.84 4.57
2473 3092 2.813172 CACATATGGTTCTGCACACACA 59.187 45.455 7.80 0.00 0.00 3.72
2474 3093 3.252944 CACATATGGTTCTGCACACACAA 59.747 43.478 7.80 0.00 0.00 3.33
2476 3095 1.321474 ATGGTTCTGCACACACAAGG 58.679 50.000 0.00 0.00 0.00 3.61
2981 3898 9.802039 ACCAACCTACAATTTTTACTCATTCTA 57.198 29.630 0.00 0.00 0.00 2.10
3282 4205 2.106477 TGCCAGCAACGATGTTGATA 57.894 45.000 11.06 0.00 39.90 2.15
3369 4292 2.617274 GGCGAACCTTGTGTCTGCC 61.617 63.158 0.00 0.00 39.20 4.85
3409 4332 3.627577 GGCTATTGTGTGTGGTGGAATAG 59.372 47.826 0.00 0.00 32.18 1.73
3423 4346 8.204160 TGTGGTGGAATAGAGTCAAGTTATATG 58.796 37.037 0.00 0.00 0.00 1.78
3476 4399 7.936496 AATCAAAAACAAGAAAACACCCAAT 57.064 28.000 0.00 0.00 0.00 3.16
3833 4756 5.412594 CGCATACCATCTAAAATATGCAGGT 59.587 40.000 13.70 0.00 46.70 4.00
3842 4765 9.853555 CATCTAAAATATGCAGGTAAAAACACA 57.146 29.630 0.00 0.00 0.00 3.72
3844 4767 9.906660 TCTAAAATATGCAGGTAAAAACACAAG 57.093 29.630 0.00 0.00 0.00 3.16
3845 4768 9.906660 CTAAAATATGCAGGTAAAAACACAAGA 57.093 29.630 0.00 0.00 0.00 3.02
3937 4861 8.307483 CCCACTCAGATATAATATTTCTCACGT 58.693 37.037 0.00 0.00 0.00 4.49
3976 4900 1.392510 CGGTAGTAGAAAAACAGCGGC 59.607 52.381 0.00 0.00 0.00 6.53
4008 4932 7.061752 ACGCTCTCACTTATTTTTGTACATC 57.938 36.000 0.00 0.00 0.00 3.06
4081 5005 4.386350 TCACAAGCGCATGAATCATTTTTG 59.614 37.500 20.91 7.83 0.00 2.44
4119 5073 3.786368 TGTCCATCACAGGATCAAACA 57.214 42.857 0.00 0.00 40.42 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
378 383 4.070552 GAGGAGCAGGGACGCGTT 62.071 66.667 15.53 0.00 36.85 4.84
456 461 1.194781 GGAGCTCACCAGGTTCAGGA 61.195 60.000 17.19 0.00 0.00 3.86
701 709 5.203528 AGACCAGTGCAATAAGCCATTAAT 58.796 37.500 0.00 0.00 44.83 1.40
1493 2084 0.327924 ACACCCTTTCATCGGCATCA 59.672 50.000 0.00 0.00 0.00 3.07
1551 2142 2.033299 ACACAAACGTTGAGGCTGAATG 59.967 45.455 0.00 4.27 0.00 2.67
1693 2286 3.977999 TGATATGGAGGTACCCGGAAATT 59.022 43.478 8.74 0.00 38.00 1.82
1694 2287 3.583086 CTGATATGGAGGTACCCGGAAAT 59.417 47.826 8.74 0.00 38.00 2.17
2028 2624 5.586243 ACTTGATTACATGGATTCAGGTTCG 59.414 40.000 10.83 0.01 38.88 3.95
2451 3070 2.813754 GTGTGTGCAGAACCATATGTGT 59.186 45.455 1.24 0.00 0.00 3.72
2458 3077 0.254462 TCCTTGTGTGTGCAGAACCA 59.746 50.000 0.00 0.00 0.00 3.67
2473 3092 2.936202 TGCAGAGAAGCAAGTTTCCTT 58.064 42.857 0.00 0.00 42.46 3.36
2474 3093 2.645838 TGCAGAGAAGCAAGTTTCCT 57.354 45.000 0.00 0.00 42.46 3.36
2482 3101 0.107752 TGTGTGTGTGCAGAGAAGCA 60.108 50.000 0.00 0.00 43.35 3.91
2483 3102 0.305922 GTGTGTGTGTGCAGAGAAGC 59.694 55.000 0.00 0.00 0.00 3.86
2485 3104 1.338579 TGTGTGTGTGTGTGCAGAGAA 60.339 47.619 0.00 0.00 0.00 2.87
2486 3105 0.248843 TGTGTGTGTGTGTGCAGAGA 59.751 50.000 0.00 0.00 0.00 3.10
2487 3106 0.374758 GTGTGTGTGTGTGTGCAGAG 59.625 55.000 0.00 0.00 0.00 3.35
2488 3107 0.321122 TGTGTGTGTGTGTGTGCAGA 60.321 50.000 0.00 0.00 0.00 4.26
2489 3108 0.179192 GTGTGTGTGTGTGTGTGCAG 60.179 55.000 0.00 0.00 0.00 4.41
2490 3109 0.886490 TGTGTGTGTGTGTGTGTGCA 60.886 50.000 0.00 0.00 0.00 4.57
2491 3110 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
2859 3626 9.154847 GCATGCTGATAGTGTTATTATCATGTA 57.845 33.333 11.37 0.00 37.03 2.29
2981 3898 5.047377 GTGGGTGTTCACATGGTCATTTTAT 60.047 40.000 0.00 0.00 37.57 1.40
3091 4008 7.830099 AGGAGGGCTAATTGAAAAATATGAG 57.170 36.000 0.00 0.00 0.00 2.90
3282 4205 2.031495 ACTTGAGGCAGAGGGTTACT 57.969 50.000 0.00 0.00 0.00 2.24
3369 4292 3.525537 AGCCACTAAACTCATCGATGTG 58.474 45.455 24.09 23.20 0.00 3.21
3409 4332 9.209175 GGGTATTGTGATCATATAACTTGACTC 57.791 37.037 0.00 0.00 0.00 3.36
3476 4399 6.429692 CCGCCATGTGGAAGACATAATAATAA 59.570 38.462 2.55 0.00 43.96 1.40
3888 4811 9.369672 TGGGTTTACCTGTATTGATTTTAACTT 57.630 29.630 0.00 0.00 41.11 2.66
3889 4812 8.799367 GTGGGTTTACCTGTATTGATTTTAACT 58.201 33.333 0.00 0.00 41.11 2.24
3890 4813 8.799367 AGTGGGTTTACCTGTATTGATTTTAAC 58.201 33.333 0.00 0.00 41.11 2.01
3891 4814 8.943594 AGTGGGTTTACCTGTATTGATTTTAA 57.056 30.769 0.00 0.00 41.11 1.52
3892 4815 8.164733 TGAGTGGGTTTACCTGTATTGATTTTA 58.835 33.333 0.00 0.00 41.11 1.52
3937 4861 3.244422 ACCGAGGTAAAAGAAGTGATGCA 60.244 43.478 0.00 0.00 0.00 3.96
3976 4900 4.732285 ATAAGTGAGAGCGTTGTGTTTG 57.268 40.909 0.00 0.00 0.00 2.93
4119 5073 7.031372 CACTTATGCAATAGAACACAAATGCT 58.969 34.615 5.53 0.00 34.97 3.79
4219 5173 7.502120 ACAGGATTCATGATGTTATACTTGC 57.498 36.000 5.16 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.