Multiple sequence alignment - TraesCS7A01G480500

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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 TraesCS7A01G480500 chr7A 100.000 5387 0 0 1 5387 672782118 672787504 0 9949
1 TraesCS7A01G480500 chr7A 97.236 5391 139 8 1 5387 672815466 672820850 0 9121
2 TraesCS7A01G480500 chr7A 96.374 1572 56 1 1 1572 672803135 672804705 0 2586
3 TraesCS7A01G480500 chr7A 97.476 634 15 1 4754 5387 672805220 672805852 0 1081
4 TraesCS7A01G480500 chr7A 95.981 423 17 0 4965 5387 114547365 114546943 0 688
5 TraesCS7A01G480500 chr6A 95.612 3578 140 14 1398 4966 557900623 557904192 0 5722
6 TraesCS7A01G480500 chr6A 96.503 429 15 0 4959 5387 557907785 557908213 0 710
7 TraesCS7A01G480500 chr6A 95.338 429 20 0 4959 5387 40171298 40171726 0 682
8 TraesCS7A01G480500 chr1D 95.507 3583 135 19 1398 4966 259732261 259735831 0 5701
9 TraesCS7A01G480500 chr1D 95.428 3587 136 20 1398 4966 299671527 299675103 0 5690
10 TraesCS7A01G480500 chr1D 93.758 1570 82 4 1 1556 482464225 482465792 0 2342
11 TraesCS7A01G480500 chr4A 95.338 3582 146 12 1398 4966 573624840 573628413 0 5670
12 TraesCS7A01G480500 chr4A 95.223 3580 154 14 1398 4969 31822358 31818788 0 5648
13 TraesCS7A01G480500 chr7D 95.310 3582 146 17 1398 4966 13245309 13248881 0 5664
14 TraesCS7A01G480500 chr7D 95.177 3587 143 24 1398 4966 108580776 108584350 0 5638
15 TraesCS7A01G480500 chr7D 93.215 1577 84 16 1 1557 564926619 564925046 0 2298
16 TraesCS7A01G480500 chr7D 92.939 1572 82 6 1 1557 110029407 110030964 0 2261
17 TraesCS7A01G480500 chr7D 92.632 1588 85 17 1 1557 69767665 69769251 0 2255
18 TraesCS7A01G480500 chr7D 93.504 585 32 5 973 1557 26633165 26633743 0 865
19 TraesCS7A01G480500 chr6D 95.124 3589 145 20 1399 4966 54712170 54715749 0 5631
20 TraesCS7A01G480500 chr6D 90.488 3364 226 33 1 3330 300937527 300934224 0 4353
21 TraesCS7A01G480500 chr6D 93.953 1571 79 8 1 1557 365491479 365493047 0 2361
22 TraesCS7A01G480500 chr2A 93.571 1571 86 3 1 1557 770758914 770757345 0 2327
23 TraesCS7A01G480500 chr5D 93.511 1572 86 3 1 1557 551286058 551287628 0 2324
24 TraesCS7A01G480500 chr5D 95.578 995 43 1 1 995 408066869 408067862 0 1592
25 TraesCS7A01G480500 chr5D 95.804 429 18 0 4959 5387 408076540 408076968 0 693
26 TraesCS7A01G480500 chr3D 93.128 1557 69 7 1 1557 553629562 553631080 0 2248
27 TraesCS7A01G480500 chr3D 92.317 1588 90 13 1 1557 572934789 572933203 0 2228
28 TraesCS7A01G480500 chr5A 92.503 1574 71 6 1 1557 46181034 46179491 0 2209
29 TraesCS7A01G480500 chr5A 96.217 423 15 1 4965 5387 46176973 46176552 0 691
30 TraesCS7A01G480500 chr7B 91.908 1557 112 5 1 1557 470038061 470036519 0 2165
31 TraesCS7A01G480500 chrUn 91.023 1114 87 7 1187 2289 216257511 216258622 0 1491
32 TraesCS7A01G480500 chr3A 96.737 429 13 1 4959 5387 31906846 31907273 0 713
33 TraesCS7A01G480500 chr2D 95.981 423 17 0 4965 5387 608281135 608280713 0 688


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 TraesCS7A01G480500 chr7A 672782118 672787504 5386 False 9949.0 9949 100.0000 1 5387 1 chr7A.!!$F1 5386
1 TraesCS7A01G480500 chr7A 672815466 672820850 5384 False 9121.0 9121 97.2360 1 5387 1 chr7A.!!$F2 5386
2 TraesCS7A01G480500 chr7A 672803135 672805852 2717 False 1833.5 2586 96.9250 1 5387 2 chr7A.!!$F3 5386
3 TraesCS7A01G480500 chr6A 557900623 557908213 7590 False 3216.0 5722 96.0575 1398 5387 2 chr6A.!!$F2 3989
4 TraesCS7A01G480500 chr1D 259732261 259735831 3570 False 5701.0 5701 95.5070 1398 4966 1 chr1D.!!$F1 3568
5 TraesCS7A01G480500 chr1D 299671527 299675103 3576 False 5690.0 5690 95.4280 1398 4966 1 chr1D.!!$F2 3568
6 TraesCS7A01G480500 chr1D 482464225 482465792 1567 False 2342.0 2342 93.7580 1 1556 1 chr1D.!!$F3 1555
7 TraesCS7A01G480500 chr4A 573624840 573628413 3573 False 5670.0 5670 95.3380 1398 4966 1 chr4A.!!$F1 3568
8 TraesCS7A01G480500 chr4A 31818788 31822358 3570 True 5648.0 5648 95.2230 1398 4969 1 chr4A.!!$R1 3571
9 TraesCS7A01G480500 chr7D 13245309 13248881 3572 False 5664.0 5664 95.3100 1398 4966 1 chr7D.!!$F1 3568
10 TraesCS7A01G480500 chr7D 108580776 108584350 3574 False 5638.0 5638 95.1770 1398 4966 1 chr7D.!!$F4 3568
11 TraesCS7A01G480500 chr7D 564925046 564926619 1573 True 2298.0 2298 93.2150 1 1557 1 chr7D.!!$R1 1556
12 TraesCS7A01G480500 chr7D 110029407 110030964 1557 False 2261.0 2261 92.9390 1 1557 1 chr7D.!!$F5 1556
13 TraesCS7A01G480500 chr7D 69767665 69769251 1586 False 2255.0 2255 92.6320 1 1557 1 chr7D.!!$F3 1556
14 TraesCS7A01G480500 chr7D 26633165 26633743 578 False 865.0 865 93.5040 973 1557 1 chr7D.!!$F2 584
15 TraesCS7A01G480500 chr6D 54712170 54715749 3579 False 5631.0 5631 95.1240 1399 4966 1 chr6D.!!$F1 3567
16 TraesCS7A01G480500 chr6D 300934224 300937527 3303 True 4353.0 4353 90.4880 1 3330 1 chr6D.!!$R1 3329
17 TraesCS7A01G480500 chr6D 365491479 365493047 1568 False 2361.0 2361 93.9530 1 1557 1 chr6D.!!$F2 1556
18 TraesCS7A01G480500 chr2A 770757345 770758914 1569 True 2327.0 2327 93.5710 1 1557 1 chr2A.!!$R1 1556
19 TraesCS7A01G480500 chr5D 551286058 551287628 1570 False 2324.0 2324 93.5110 1 1557 1 chr5D.!!$F3 1556
20 TraesCS7A01G480500 chr5D 408066869 408067862 993 False 1592.0 1592 95.5780 1 995 1 chr5D.!!$F1 994
21 TraesCS7A01G480500 chr3D 553629562 553631080 1518 False 2248.0 2248 93.1280 1 1557 1 chr3D.!!$F1 1556
22 TraesCS7A01G480500 chr3D 572933203 572934789 1586 True 2228.0 2228 92.3170 1 1557 1 chr3D.!!$R1 1556
23 TraesCS7A01G480500 chr5A 46176552 46181034 4482 True 1450.0 2209 94.3600 1 5387 2 chr5A.!!$R1 5386
24 TraesCS7A01G480500 chr7B 470036519 470038061 1542 True 2165.0 2165 91.9080 1 1557 1 chr7B.!!$R1 1556
25 TraesCS7A01G480500 chrUn 216257511 216258622 1111 False 1491.0 1491 91.0230 1187 2289 1 chrUn.!!$F1 1102

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
234 240 0.322456 ATGCTAGGCACGCCAAAGAA 60.322 50.000 11.35 2.08 43.04 2.52 F
935 951 1.392589 CCATCCACAAATTCGAGGGG 58.607 55.000 0.00 0.00 0.00 4.79 F
1601 1803 0.454600 CGTACAGTACTGCACCCGAT 59.545 55.000 22.90 3.96 0.00 4.18 F
2425 2632 0.689412 GGTAGCTCCTCTGGCTCCTT 60.689 60.000 0.00 0.00 40.74 3.36 F
2834 3062 3.769844 CCAGTTGTATCCCACTACTCAGT 59.230 47.826 0.00 0.00 40.63 3.41 F
3775 4025 2.136298 TTGAGTGTTTGGTTCCAGCA 57.864 45.000 0.00 0.00 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1759 0.107800 ACTGGTGCTGCTGCTATCAG 60.108 55.000 17.00 19.8 43.16 2.90 R
1812 2019 3.450904 ACCAGAGCACACCTAGGATTTA 58.549 45.455 17.98 0.0 0.00 1.40 R
3110 3349 1.560505 GCCCACTTGATCCCAACAAT 58.439 50.000 0.00 0.0 0.00 2.71 R
3775 4025 0.184933 TGTGGCTTGCCTAAGGTGTT 59.815 50.000 13.18 0.0 34.40 3.32 R
4231 4487 1.079503 GGCCTGACACATTTCTCGAC 58.920 55.000 0.00 0.0 0.00 4.20 R
4858 5121 2.550606 GCCACAAACACGATGGTTCTAA 59.449 45.455 0.00 0.0 35.79 2.10 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
135 137 3.569701 CACCTAAACTCAAACCATGCACT 59.430 43.478 0.00 0.00 0.00 4.40
148 150 2.617788 CCATGCACTGTTAGCCAGGTTA 60.618 50.000 0.00 0.00 46.06 2.85
213 219 0.601558 CCTTCGACGAGTCCCTTCAA 59.398 55.000 0.00 0.00 0.00 2.69
234 240 0.322456 ATGCTAGGCACGCCAAAGAA 60.322 50.000 11.35 2.08 43.04 2.52
261 267 2.364632 GGCTACACATATTGCACACCA 58.635 47.619 0.00 0.00 0.00 4.17
706 712 3.758023 CTCCTAAATCATGGTTGTGCACA 59.242 43.478 17.42 17.42 0.00 4.57
726 732 5.215160 CACAATCGGGCTATTCATTTTAGC 58.785 41.667 0.00 0.00 41.08 3.09
743 749 7.870954 TCATTTTAGCGAGAAGTGAGAAGTTAA 59.129 33.333 0.00 0.00 0.00 2.01
935 951 1.392589 CCATCCACAAATTCGAGGGG 58.607 55.000 0.00 0.00 0.00 4.79
1202 1340 3.706373 GCCGGAGAAGGTGGCTCA 61.706 66.667 5.05 0.00 45.40 4.26
1237 1396 1.676678 GACTCCTCTGCCACGCCATA 61.677 60.000 0.00 0.00 0.00 2.74
1364 1565 2.958355 TCTATTTTTGGGCATGGCTAGC 59.042 45.455 19.78 6.04 0.00 3.42
1416 1617 6.598503 TCTGTACCTAGATTCGTTAGATCCA 58.401 40.000 0.00 0.00 0.00 3.41
1557 1759 5.469421 TCCAAAATGTGTTGATGCCAAATTC 59.531 36.000 0.00 0.00 33.49 2.17
1601 1803 0.454600 CGTACAGTACTGCACCCGAT 59.545 55.000 22.90 3.96 0.00 4.18
1663 1870 3.500448 TGAAACTATCCTTGCACACCA 57.500 42.857 0.00 0.00 0.00 4.17
1725 1932 2.118513 AGGTGTCTCCTCTGCCGT 59.881 61.111 0.00 0.00 44.42 5.68
1897 2104 2.871182 TCTTTGATCGATGGACTCCG 57.129 50.000 0.54 0.00 0.00 4.63
2053 2260 8.902806 CAAATATGTAGCTTGACCTTGGAATTA 58.097 33.333 0.00 0.00 0.00 1.40
2320 2527 5.012148 CCCAAGTATGAAATCCTAGATCCGT 59.988 44.000 0.00 0.00 0.00 4.69
2425 2632 0.689412 GGTAGCTCCTCTGGCTCCTT 60.689 60.000 0.00 0.00 40.74 3.36
2542 2749 7.339721 ACGAGAATGAAGAAGAGGTTAGTCATA 59.660 37.037 0.00 0.00 0.00 2.15
2549 2756 8.235230 TGAAGAAGAGGTTAGTCATATATCCCT 58.765 37.037 0.00 0.00 0.00 4.20
2551 2766 8.429237 AGAAGAGGTTAGTCATATATCCCTTG 57.571 38.462 0.00 0.00 0.00 3.61
2834 3062 3.769844 CCAGTTGTATCCCACTACTCAGT 59.230 47.826 0.00 0.00 40.63 3.41
2883 3111 6.421377 TCAAAAATGTCATCGATTCGTGAT 57.579 33.333 5.89 0.00 0.00 3.06
3347 3587 7.765360 CACAACTGGTGGCATAAATGATAAAAT 59.235 33.333 0.00 0.00 44.04 1.82
3434 3674 8.706322 ACTTTACCTAGAACATTGAATGGTTT 57.294 30.769 10.27 0.27 33.60 3.27
3575 3815 6.615264 TCACGAGCTATTTTATCTAGTCGT 57.385 37.500 0.00 0.00 35.43 4.34
3576 3816 6.656945 TCACGAGCTATTTTATCTAGTCGTC 58.343 40.000 0.00 0.00 34.17 4.20
3710 3960 9.594478 CTAAAGGTTGTTTGGTTAGTGAATTTT 57.406 29.630 0.00 0.00 0.00 1.82
3775 4025 2.136298 TTGAGTGTTTGGTTCCAGCA 57.864 45.000 0.00 0.00 0.00 4.41
4143 4399 6.428771 ACTTACGCAACATTTGGTACTACATT 59.571 34.615 0.00 0.00 0.00 2.71
4231 4487 1.302033 GAGCTGGACAGTGGTGTGG 60.302 63.158 0.00 0.00 36.88 4.17
4347 4609 1.648467 GCAGTCGGAACATCCCAAGC 61.648 60.000 0.00 0.00 31.13 4.01
4384 4646 0.250901 ACGCTTTCAGGGTGAAGCAT 60.251 50.000 8.56 0.00 40.09 3.79
4386 4648 1.538047 GCTTTCAGGGTGAAGCATGA 58.462 50.000 0.00 0.00 37.70 3.07
4536 4798 6.527722 GTGAACGTTTATGGTCGAACTATGTA 59.472 38.462 0.46 0.00 0.00 2.29
4845 5108 2.230660 AGTTTGCTGCCTAAGGTGTTC 58.769 47.619 0.00 0.00 0.00 3.18
4857 5120 5.297029 GCCTAAGGTGTTCATCCAAGTAATC 59.703 44.000 0.00 0.00 0.00 1.75
4858 5121 6.653989 CCTAAGGTGTTCATCCAAGTAATCT 58.346 40.000 0.00 0.00 0.00 2.40
4880 5143 0.665835 GAACCATCGTGTTTGTGGCA 59.334 50.000 0.00 0.00 36.47 4.92
5017 8880 5.116084 AATGGAATTGTAGCCTTGAGCTA 57.884 39.130 0.00 0.00 43.51 3.32
5137 9000 7.226918 TGTCTTTGATTTGTGTAAATACCGACA 59.773 33.333 0.00 0.00 36.66 4.35
5174 9037 6.658188 TTTAGTCAAAATTTTGGGACGGAT 57.342 33.333 26.45 8.91 38.66 4.18
5273 9136 2.613595 ACAAATGCATGCGATACGTGAT 59.386 40.909 14.09 0.00 37.49 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.066716 GTGGTTGTCTACGTGGCCATA 60.067 52.381 9.72 0.00 0.00 2.74
97 99 0.323360 GGTGGCTAGGTTTGCATGGA 60.323 55.000 0.00 0.00 0.00 3.41
135 137 1.775459 TGTGGGTTAACCTGGCTAACA 59.225 47.619 23.69 14.72 41.11 2.41
148 150 1.340991 GCTGGATGTATGGTGTGGGTT 60.341 52.381 0.00 0.00 0.00 4.11
213 219 1.140852 TCTTTGGCGTGCCTAGCATAT 59.859 47.619 12.84 0.00 41.91 1.78
234 240 1.663643 CAATATGTGTAGCCGCGTGTT 59.336 47.619 4.92 0.00 0.00 3.32
261 267 3.695060 ACTAGTGAATGACGTCGGATCTT 59.305 43.478 11.62 0.00 0.00 2.40
319 325 0.732880 CAACGAGCTAGTGTCCACCG 60.733 60.000 0.00 0.00 0.00 4.94
706 712 4.385825 TCGCTAAAATGAATAGCCCGATT 58.614 39.130 0.37 0.00 42.18 3.34
726 732 7.010183 TGTCAAAACTTAACTTCTCACTTCTCG 59.990 37.037 0.00 0.00 0.00 4.04
743 749 2.033299 CACGTCTTGCCATGTCAAAACT 59.967 45.455 0.00 0.00 0.00 2.66
935 951 1.079057 GAGGCGTGGGAGGAGAAAC 60.079 63.158 0.00 0.00 0.00 2.78
1202 1340 1.078848 GTCACCTGCTCCAGCGAAT 60.079 57.895 0.00 0.00 45.83 3.34
1237 1396 2.906458 CTGCGGAAGAGGAGGCAT 59.094 61.111 0.00 0.00 34.49 4.40
1364 1565 4.756084 AGATGGAAGAAAAGCAGAAACG 57.244 40.909 0.00 0.00 0.00 3.60
1416 1617 1.622312 GACCCGTCCTTGAAACCTACT 59.378 52.381 0.00 0.00 0.00 2.57
1557 1759 0.107800 ACTGGTGCTGCTGCTATCAG 60.108 55.000 17.00 19.80 43.16 2.90
1639 1846 3.441572 GTGTGCAAGGATAGTTTCATGCT 59.558 43.478 10.39 0.00 38.70 3.79
1663 1870 3.722101 AGCTACTAGGGCCCACATAAATT 59.278 43.478 27.56 2.06 0.00 1.82
1810 2017 4.288626 ACCAGAGCACACCTAGGATTTAAA 59.711 41.667 17.98 0.00 0.00 1.52
1812 2019 3.450904 ACCAGAGCACACCTAGGATTTA 58.549 45.455 17.98 0.00 0.00 1.40
2583 2810 4.602340 TGTACTGACCAGAGAAAACCTC 57.398 45.455 3.76 0.00 42.28 3.85
2853 3081 4.490743 TCGATGACATTTTTGAGCGACTA 58.509 39.130 0.00 0.00 0.00 2.59
2856 3084 4.492409 CGAATCGATGACATTTTTGAGCGA 60.492 41.667 0.00 0.00 0.00 4.93
2883 3111 8.570488 CATCTAATGGCATTTTGAGTAAGCATA 58.430 33.333 19.21 0.00 0.00 3.14
2931 3160 7.350744 TGGCATTATTGAGCAAACATCTAAT 57.649 32.000 0.00 0.00 0.00 1.73
3110 3349 1.560505 GCCCACTTGATCCCAACAAT 58.439 50.000 0.00 0.00 0.00 2.71
3423 3663 8.042515 CCCATCAATGTTTCTAAACCATTCAAT 58.957 33.333 3.27 0.00 38.11 2.57
3434 3674 2.652348 ACCCCACCCATCAATGTTTCTA 59.348 45.455 0.00 0.00 0.00 2.10
3483 3723 8.052141 TGGATATTGAAAGTCCACATGTTATCA 58.948 33.333 0.00 0.00 37.12 2.15
3706 3956 8.981659 CCTTAGGTATGGAAATCTTTGGAAAAT 58.018 33.333 0.00 0.00 0.00 1.82
3710 3960 6.652205 ACCTTAGGTATGGAAATCTTTGGA 57.348 37.500 0.15 0.00 32.11 3.53
3775 4025 0.184933 TGTGGCTTGCCTAAGGTGTT 59.815 50.000 13.18 0.00 34.40 3.32
4143 4399 3.376234 CGACATCGTCACTTAGGACCTAA 59.624 47.826 13.42 13.42 34.24 2.69
4231 4487 1.079503 GGCCTGACACATTTCTCGAC 58.920 55.000 0.00 0.00 0.00 4.20
4347 4609 1.600957 CGTAGCCATTCTTGATGCTGG 59.399 52.381 0.00 0.00 34.25 4.85
4384 4646 3.375922 TCAAGTACTCGACATACGCATCA 59.624 43.478 0.00 0.00 42.26 3.07
4386 4648 4.036380 TCATCAAGTACTCGACATACGCAT 59.964 41.667 0.00 0.00 42.26 4.73
4536 4798 3.257624 GCACCACTTAGTAGTACTGGTGT 59.742 47.826 27.36 15.61 43.13 4.16
4845 5108 6.986817 ACGATGGTTCTAAGATTACTTGGATG 59.013 38.462 0.00 0.00 41.76 3.51
4857 5120 3.364964 GCCACAAACACGATGGTTCTAAG 60.365 47.826 0.00 0.00 35.79 2.18
4858 5121 2.550606 GCCACAAACACGATGGTTCTAA 59.449 45.455 0.00 0.00 35.79 2.10
4880 5143 5.443283 ACTTTGTGATCATCATGTAGCCAT 58.557 37.500 0.00 0.00 0.00 4.40
5017 8880 4.574674 TTCCATCTACCAAGCTGAATGT 57.425 40.909 0.00 0.00 0.00 2.71
5078 8941 4.280174 GGACGGATGGAGTACTAAAGCATA 59.720 45.833 0.00 0.00 0.00 3.14
5273 9136 3.157087 TCTAGCCATGCATCGATAGTCA 58.843 45.455 14.88 0.00 37.40 3.41


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

AutoCloner maintained by Alex Coulton.