Multiple sequence alignment - TraesCS7B01G299400

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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 TraesCS7B01G299400 chr7B 100.000 2972 0 0 1 2972 536560127 536563098 0.000000e+00 5489.0
1 TraesCS7B01G299400 chr7B 80.431 557 86 18 786 1340 536357394 536357929 1.280000e-108 403.0
2 TraesCS7B01G299400 chr7D 95.361 2975 128 9 1 2972 508318324 508321291 0.000000e+00 4721.0
3 TraesCS7B01G299400 chr7D 77.273 198 41 3 13 210 58781695 58781502 2.420000e-21 113.0
4 TraesCS7B01G299400 chr7D 86.842 76 10 0 797 872 508275851 508275776 5.280000e-13 86.1
5 TraesCS7B01G299400 chr7A 94.013 2973 164 10 1 2972 578573520 578576479 0.000000e+00 4492.0
6 TraesCS7B01G299400 chr7A 93.586 1637 101 3 1059 2694 578325710 578327343 0.000000e+00 2438.0
7 TraesCS7B01G299400 chr7A 80.131 609 110 10 779 1382 578237908 578237306 7.560000e-121 444.0
8 TraesCS7B01G299400 chr7A 95.018 281 14 0 2692 2972 578338167 578338447 2.720000e-120 442.0
9 TraesCS7B01G299400 chr7A 82.222 495 78 9 824 1312 578236793 578237283 4.580000e-113 418.0
10 TraesCS7B01G299400 chr7A 77.404 208 39 5 13 218 252709859 252709658 1.870000e-22 117.0
11 TraesCS7B01G299400 chr1D 86.764 1987 203 26 291 2268 79172283 79174218 0.000000e+00 2158.0
12 TraesCS7B01G299400 chr1D 88.402 707 82 0 2266 2972 79309779 79310485 0.000000e+00 852.0
13 TraesCS7B01G299400 chr1D 77.181 149 26 6 77 225 478027655 478027515 2.460000e-11 80.5
14 TraesCS7B01G299400 chr1B 84.535 2095 231 50 178 2252 10127814 10125793 0.000000e+00 1988.0
15 TraesCS7B01G299400 chr1B 85.635 1448 195 8 1529 2972 130425115 130426553 0.000000e+00 1509.0
16 TraesCS7B01G299400 chr1B 85.912 937 119 6 601 1533 130422454 130423381 0.000000e+00 987.0
17 TraesCS7B01G299400 chr1B 87.367 657 77 6 2317 2972 10125792 10125141 0.000000e+00 749.0
18 TraesCS7B01G299400 chr1B 90.411 292 26 2 292 582 130366688 130366978 1.670000e-102 383.0
19 TraesCS7B01G299400 chr1B 79.433 141 25 3 1 137 47628913 47629053 2.440000e-16 97.1
20 TraesCS7B01G299400 chr2A 88.720 1055 113 3 1444 2494 103506051 103504999 0.000000e+00 1284.0
21 TraesCS7B01G299400 chr2A 90.821 414 35 2 2559 2972 103504999 103504589 4.330000e-153 551.0
22 TraesCS7B01G299400 chr1A 87.305 835 83 10 291 1119 98024759 98025576 0.000000e+00 933.0
23 TraesCS7B01G299400 chr1A 86.283 678 85 7 2298 2972 98222883 98223555 0.000000e+00 730.0
24 TraesCS7B01G299400 chr1A 85.384 691 93 7 1167 1855 98025852 98026536 0.000000e+00 710.0
25 TraesCS7B01G299400 chr1A 85.652 460 58 5 1845 2300 98182752 98183207 7.450000e-131 477.0
26 TraesCS7B01G299400 chr2D 77.778 225 46 2 1 225 101690617 101690837 5.170000e-28 135.0
27 TraesCS7B01G299400 chr4D 83.217 143 21 3 13 154 62711469 62711329 8.650000e-26 128.0
28 TraesCS7B01G299400 chr4D 82.353 136 17 4 92 226 505996745 505996874 8.710000e-21 111.0
29 TraesCS7B01G299400 chr5D 77.419 186 32 7 41 225 42921446 42921270 5.240000e-18 102.0
30 TraesCS7B01G299400 chrUn 76.774 155 33 3 1 154 20102956 20103108 1.900000e-12 84.2
31 TraesCS7B01G299400 chr6D 87.302 63 8 0 2751 2813 441868890 441868828 4.110000e-09 73.1


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 TraesCS7B01G299400 chr7B 536560127 536563098 2971 False 5489.0 5489 100.0000 1 2972 1 chr7B.!!$F2 2971
1 TraesCS7B01G299400 chr7B 536357394 536357929 535 False 403.0 403 80.4310 786 1340 1 chr7B.!!$F1 554
2 TraesCS7B01G299400 chr7D 508318324 508321291 2967 False 4721.0 4721 95.3610 1 2972 1 chr7D.!!$F1 2971
3 TraesCS7B01G299400 chr7A 578573520 578576479 2959 False 4492.0 4492 94.0130 1 2972 1 chr7A.!!$F4 2971
4 TraesCS7B01G299400 chr7A 578325710 578327343 1633 False 2438.0 2438 93.5860 1059 2694 1 chr7A.!!$F2 1635
5 TraesCS7B01G299400 chr7A 578237306 578237908 602 True 444.0 444 80.1310 779 1382 1 chr7A.!!$R2 603
6 TraesCS7B01G299400 chr1D 79172283 79174218 1935 False 2158.0 2158 86.7640 291 2268 1 chr1D.!!$F1 1977
7 TraesCS7B01G299400 chr1D 79309779 79310485 706 False 852.0 852 88.4020 2266 2972 1 chr1D.!!$F2 706
8 TraesCS7B01G299400 chr1B 10125141 10127814 2673 True 1368.5 1988 85.9510 178 2972 2 chr1B.!!$R1 2794
9 TraesCS7B01G299400 chr1B 130422454 130426553 4099 False 1248.0 1509 85.7735 601 2972 2 chr1B.!!$F3 2371
10 TraesCS7B01G299400 chr2A 103504589 103506051 1462 True 917.5 1284 89.7705 1444 2972 2 chr2A.!!$R1 1528
11 TraesCS7B01G299400 chr1A 98024759 98026536 1777 False 821.5 933 86.3445 291 1855 2 chr1A.!!$F3 1564
12 TraesCS7B01G299400 chr1A 98222883 98223555 672 False 730.0 730 86.2830 2298 2972 1 chr1A.!!$F2 674

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
174 175 0.782384 CGCGTGCGTTTATAGGGATC 59.218 55.0 6.00 0.0 34.35 3.36 F
917 945 1.198713 GGTCTCTTGGCTGATCCTCA 58.801 55.0 0.00 0.0 35.26 3.86 F
1486 1745 0.679960 AATTAGCGGCCAACCACCTC 60.680 55.0 2.24 0.0 34.57 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1086 1116 0.036875 CCAACTCCTCCGCCTTCTTT 59.963 55.000 0.0 0.0 0.00 2.52 R
1941 3976 3.181433 GGGGGAAAGGACTTGAAGAAGAA 60.181 47.826 0.0 0.0 32.98 2.52 R
2542 4587 3.489180 AGTCCGAAACTATCACTGTCG 57.511 47.619 0.0 0.0 36.07 4.35 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
34 35 2.264794 GGCCTTCCGACGATGTGT 59.735 61.111 0.00 0.00 0.00 3.72
51 52 3.181329 TGTGTGTTATGTGGGAGGAGAT 58.819 45.455 0.00 0.00 0.00 2.75
124 125 1.019278 GTGCCGGCTCATTTTCTCGA 61.019 55.000 29.70 0.00 0.00 4.04
172 173 1.879430 GCGCGTGCGTTTATAGGGA 60.879 57.895 16.27 0.00 42.09 4.20
174 175 0.782384 CGCGTGCGTTTATAGGGATC 59.218 55.000 6.00 0.00 34.35 3.36
176 177 2.206750 GCGTGCGTTTATAGGGATCAA 58.793 47.619 0.00 0.00 0.00 2.57
244 247 4.584638 AAGTACCCATAATTCTGGCACA 57.415 40.909 4.33 0.00 34.77 4.57
289 292 1.409427 CTGCGCTACCTAGCTTAACCT 59.591 52.381 9.73 0.00 46.85 3.50
305 308 8.329203 AGCTTAACCTGACATCTAAAGAAAAG 57.671 34.615 0.00 0.00 0.00 2.27
357 360 4.566545 TTATTGCCTTGGAATGTATGCG 57.433 40.909 0.00 0.00 0.00 4.73
362 365 1.321474 CTTGGAATGTATGCGGCCAT 58.679 50.000 2.24 0.00 35.44 4.40
363 366 2.503331 CTTGGAATGTATGCGGCCATA 58.497 47.619 2.24 0.00 32.85 2.74
365 368 3.153369 TGGAATGTATGCGGCCATAAT 57.847 42.857 2.24 0.00 35.79 1.28
367 370 4.657013 TGGAATGTATGCGGCCATAATTA 58.343 39.130 2.24 0.00 35.79 1.40
368 371 4.457603 TGGAATGTATGCGGCCATAATTAC 59.542 41.667 2.24 0.00 35.79 1.89
369 372 4.436852 GGAATGTATGCGGCCATAATTACG 60.437 45.833 2.24 0.00 35.79 3.18
512 519 3.210358 ACCAATCGGTTTAATTGCGTG 57.790 42.857 0.00 0.00 46.31 5.34
628 643 3.969981 GGTTACAATTGAACGTCGTTTGG 59.030 43.478 13.59 0.00 0.00 3.28
917 945 1.198713 GGTCTCTTGGCTGATCCTCA 58.801 55.000 0.00 0.00 35.26 3.86
1458 1717 2.001803 CCAGAGCATGGGGGAAAGA 58.998 57.895 0.00 0.00 46.36 2.52
1486 1745 0.679960 AATTAGCGGCCAACCACCTC 60.680 55.000 2.24 0.00 34.57 3.85
1552 3548 2.092968 GGGTCTCCAGCAATGTATCACA 60.093 50.000 0.00 0.00 0.00 3.58
1554 3550 2.604914 GTCTCCAGCAATGTATCACACG 59.395 50.000 0.00 0.00 0.00 4.49
1594 3590 1.548269 TCACCGACTACATGCACATGA 59.452 47.619 17.19 0.86 41.20 3.07
1700 3735 1.492176 AGCATCACCAGTTCCCTATGG 59.508 52.381 0.00 0.00 42.60 2.74
1771 3806 4.540824 GCAACAACAAGAGGATTCACTTC 58.459 43.478 0.00 0.00 0.00 3.01
1941 3976 2.188994 GGCGCTGATCCTGAAGCT 59.811 61.111 7.64 0.00 37.27 3.74
1981 4016 2.291540 CCCCCAATGTAAGCAAGGAGAA 60.292 50.000 0.00 0.00 0.00 2.87
2287 4330 4.990543 GCTAGATGCGCACAACATATAA 57.009 40.909 14.90 0.00 0.00 0.98
2392 4435 3.802948 ATCCGATGACTACACCTTCAC 57.197 47.619 0.00 0.00 0.00 3.18
2401 4444 4.251268 GACTACACCTTCACCCATGTTAC 58.749 47.826 0.00 0.00 0.00 2.50
2520 4565 0.324943 CAACCACGAGTCCTCCCAAT 59.675 55.000 0.00 0.00 0.00 3.16
2542 4587 3.878778 ACCTAACATGTGAGCAATCCTC 58.121 45.455 4.45 0.00 41.15 3.71
2587 4633 6.815089 AGAGAATAAGTCATCTTCGCTTCAT 58.185 36.000 0.00 0.00 35.36 2.57
2589 4635 8.081633 AGAGAATAAGTCATCTTCGCTTCATAG 58.918 37.037 0.00 0.00 35.36 2.23
2651 4697 6.277044 AGACCTAGGATAGAATCTTAGAGCCT 59.723 42.308 17.98 0.00 42.77 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.825593 GGAATATCTCCTCCCACATAACA 57.174 43.478 0.00 0.00 41.61 2.41
124 125 4.206244 ACTCTATCCCTATGAGCACCTT 57.794 45.455 0.00 0.00 0.00 3.50
172 173 6.420903 GCTCATACATACACACATACGTTGAT 59.579 38.462 0.00 0.00 0.00 2.57
174 175 5.518487 TGCTCATACATACACACATACGTTG 59.482 40.000 0.00 0.00 0.00 4.10
176 177 5.257082 TGCTCATACATACACACATACGT 57.743 39.130 0.00 0.00 0.00 3.57
229 232 9.248291 GTAAATATTTGTGTGCCAGAATTATGG 57.752 33.333 14.99 14.99 43.72 2.74
240 243 9.781834 TTGCTATAGTTGTAAATATTTGTGTGC 57.218 29.630 11.05 4.04 0.00 4.57
289 292 4.041198 ACCGACCCTTTTCTTTAGATGTCA 59.959 41.667 0.00 0.00 0.00 3.58
305 308 3.764218 TCTAGAAGATATGGACCGACCC 58.236 50.000 0.00 0.00 38.00 4.46
357 360 6.127952 TGGTAACTGAAAACGTAATTATGGCC 60.128 38.462 9.46 0.00 37.61 5.36
363 366 8.788806 TGATTCATGGTAACTGAAAACGTAATT 58.211 29.630 0.00 0.00 36.30 1.40
365 368 7.442969 AGTGATTCATGGTAACTGAAAACGTAA 59.557 33.333 0.00 0.00 36.30 3.18
367 370 5.763204 AGTGATTCATGGTAACTGAAAACGT 59.237 36.000 0.00 0.00 36.30 3.99
368 371 6.079763 CAGTGATTCATGGTAACTGAAAACG 58.920 40.000 9.67 0.00 40.54 3.60
369 372 6.381801 CCAGTGATTCATGGTAACTGAAAAC 58.618 40.000 14.62 1.11 40.54 2.43
808 827 8.259411 AGGTGCTTCATAAATGCATCATTAAAA 58.741 29.630 0.00 0.00 39.99 1.52
917 945 9.740710 GCAATAAGGGTGGATAGATTTATAGTT 57.259 33.333 0.00 0.00 0.00 2.24
1086 1116 0.036875 CCAACTCCTCCGCCTTCTTT 59.963 55.000 0.00 0.00 0.00 2.52
1458 1717 3.951775 TGGCCGCTAATTTTTGTGATT 57.048 38.095 0.00 0.00 0.00 2.57
1486 1745 3.041469 GCTCCTGGGGCTGGAAGAG 62.041 68.421 12.38 0.00 34.07 2.85
1554 3550 4.175337 TATGGAGCTGGCGGTGGC 62.175 66.667 0.00 0.00 38.90 5.01
1700 3735 2.430465 CCATATCCATGCCACTAGTGC 58.570 52.381 17.86 13.07 0.00 4.40
1771 3806 3.899980 TCTCCTCCATACCTCATCATGTG 59.100 47.826 0.00 0.00 0.00 3.21
1835 3870 5.010922 ACAATGCTTGTGTTGGTGTCATTAT 59.989 36.000 1.44 0.00 43.48 1.28
1941 3976 3.181433 GGGGGAAAGGACTTGAAGAAGAA 60.181 47.826 0.00 0.00 32.98 2.52
2009 4052 4.397420 AGCACAACCAAGATTACATGTCA 58.603 39.130 0.00 0.00 0.00 3.58
2040 4083 7.707464 TGCAATGACTAAATGAAATATGCTTGG 59.293 33.333 0.00 0.00 0.00 3.61
2190 4233 7.094975 CGTCAAGGGTCAACAAAAACTATCATA 60.095 37.037 0.00 0.00 0.00 2.15
2287 4330 9.892130 CACTTTCCTAGAACTATGGTAGATTTT 57.108 33.333 0.00 0.00 0.00 1.82
2349 4392 5.576563 TGGTCCTCCATTTCTTGAAGTTA 57.423 39.130 0.00 0.00 39.03 2.24
2392 4435 4.828829 AGGAGTTCTTTACGTAACATGGG 58.171 43.478 7.70 0.00 0.00 4.00
2401 4444 9.543018 GATGTGATTTTTAAGGAGTTCTTTACG 57.457 33.333 0.00 0.00 36.93 3.18
2520 4565 4.441495 CGAGGATTGCTCACATGTTAGGTA 60.441 45.833 9.05 0.00 0.00 3.08
2542 4587 3.489180 AGTCCGAAACTATCACTGTCG 57.511 47.619 0.00 0.00 36.07 4.35
2587 4633 5.265989 ACTCCCACTTTTTGGTTGTTTCTA 58.734 37.500 0.00 0.00 45.25 2.10
2589 4635 4.430007 GACTCCCACTTTTTGGTTGTTTC 58.570 43.478 0.00 0.00 45.25 2.78
2737 4783 3.881688 CGAGATTGGCATGGAGAGAAATT 59.118 43.478 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.