Multiple sequence alignment - TraesCS4B01G147900

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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 TraesCS4B01G147900 chr4B 100.000 3368 0 0 1 3368 211099983 211096616 0 6220
1 TraesCS4B01G147900 chr6B 96.083 3370 122 4 5 3368 42183838 42180473 0 5483
2 TraesCS4B01G147900 chr6B 95.699 3371 129 8 5 3368 536423341 536419980 0 5408
3 TraesCS4B01G147900 chr6B 93.746 1407 74 11 5 1404 85662846 85664245 0 2098
4 TraesCS4B01G147900 chr2B 95.371 3370 139 6 5 3368 293242771 293246129 0 5343
5 TraesCS4B01G147900 chr2B 95.909 1882 65 5 1493 3368 317054190 317052315 0 3038
6 TraesCS4B01G147900 chr3B 95.138 3373 143 11 5 3368 649105550 649102190 0 5301
7 TraesCS4B01G147900 chr3B 95.319 3162 132 7 5 3159 572150988 572147836 0 5005
8 TraesCS4B01G147900 chr3B 95.864 2563 91 6 813 3368 664732515 664729961 0 4132
9 TraesCS4B01G147900 chr3B 93.929 1400 81 3 5 1404 545972550 545971155 0 2111
10 TraesCS4B01G147900 chr1B 94.926 3370 153 7 5 3368 84525605 84522248 0 5260
11 TraesCS4B01G147900 chr7B 95.696 1882 68 6 1493 3368 300043095 300044969 0 3014
12 TraesCS4B01G147900 chr7B 94.460 1408 67 8 5 1404 300041537 300042941 0 2158


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 TraesCS4B01G147900 chr4B 211096616 211099983 3367 True 6220 6220 100.000 1 3368 1 chr4B.!!$R1 3367
1 TraesCS4B01G147900 chr6B 42180473 42183838 3365 True 5483 5483 96.083 5 3368 1 chr6B.!!$R1 3363
2 TraesCS4B01G147900 chr6B 536419980 536423341 3361 True 5408 5408 95.699 5 3368 1 chr6B.!!$R2 3363
3 TraesCS4B01G147900 chr6B 85662846 85664245 1399 False 2098 2098 93.746 5 1404 1 chr6B.!!$F1 1399
4 TraesCS4B01G147900 chr2B 293242771 293246129 3358 False 5343 5343 95.371 5 3368 1 chr2B.!!$F1 3363
5 TraesCS4B01G147900 chr2B 317052315 317054190 1875 True 3038 3038 95.909 1493 3368 1 chr2B.!!$R1 1875
6 TraesCS4B01G147900 chr3B 649102190 649105550 3360 True 5301 5301 95.138 5 3368 1 chr3B.!!$R3 3363
7 TraesCS4B01G147900 chr3B 572147836 572150988 3152 True 5005 5005 95.319 5 3159 1 chr3B.!!$R2 3154
8 TraesCS4B01G147900 chr3B 664729961 664732515 2554 True 4132 4132 95.864 813 3368 1 chr3B.!!$R4 2555
9 TraesCS4B01G147900 chr3B 545971155 545972550 1395 True 2111 2111 93.929 5 1404 1 chr3B.!!$R1 1399
10 TraesCS4B01G147900 chr1B 84522248 84525605 3357 True 5260 5260 94.926 5 3368 1 chr1B.!!$R1 3363
11 TraesCS4B01G147900 chr7B 300041537 300044969 3432 False 2586 3014 95.078 5 3368 2 chr7B.!!$F1 3363

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
919 933 0.247736 CTCTCCCTCGTTCCCACAAG 59.752 60.0 0.00 0.00 0.0 3.16 F
2082 2163 1.437625 TCATCGACATTCAGCGCAAA 58.562 45.0 11.47 3.45 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 2387 0.521291 CCGCTCTTTCGCAAATTCCA 59.479 50.000 0.0 0.00 0.00 3.53 R
3086 3176 4.284550 TTGACCTGTGGGCCCTGC 62.285 66.667 25.7 16.63 35.63 4.85 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
291 295 0.693767 AGCTATGCCTTCTCCTGCCT 60.694 55.000 0.00 0.00 0.00 4.75
300 304 1.839994 CTTCTCCTGCCTGTCCCAATA 59.160 52.381 0.00 0.00 0.00 1.90
480 486 4.383010 CCATTAGCACCACACATAGTCTCA 60.383 45.833 0.00 0.00 0.00 3.27
498 504 4.992951 GTCTCACTGGTAATTGGTACGTTT 59.007 41.667 0.00 0.00 33.01 3.60
501 507 7.171337 GTCTCACTGGTAATTGGTACGTTTAAA 59.829 37.037 0.00 0.00 33.01 1.52
600 606 3.812053 GTGGGATAAGCAGCTGATAAGTG 59.188 47.826 20.43 0.00 0.00 3.16
603 609 4.070716 GGATAAGCAGCTGATAAGTGCAT 58.929 43.478 20.43 0.00 39.80 3.96
680 686 0.671472 GCAAGTGGGATTTTGCAGGC 60.671 55.000 4.48 0.00 46.72 4.85
695 701 2.503765 TGCAGGCCATAAGTACAGCTTA 59.496 45.455 5.01 0.00 43.13 3.09
717 723 7.171678 GCTTAACAAGACTAGTCAGTTCAACAT 59.828 37.037 26.88 12.48 34.21 2.71
753 759 3.947910 TTGGACGGTTAGTTCTTCGAT 57.052 42.857 0.00 0.00 0.00 3.59
827 840 2.660802 CCCCACGACCACTACACC 59.339 66.667 0.00 0.00 0.00 4.16
877 890 3.342627 CCGTCGGCGCACTGAAAA 61.343 61.111 10.83 0.00 36.67 2.29
878 891 2.629210 CGTCGGCGCACTGAAAAA 59.371 55.556 10.83 0.00 31.36 1.94
919 933 0.247736 CTCTCCCTCGTTCCCACAAG 59.752 60.000 0.00 0.00 0.00 3.16
985 999 2.157738 CTCTCTCCAAAGCCCAAAGTG 58.842 52.381 0.00 0.00 0.00 3.16
1008 1022 3.969250 GACGAAGGCCATGGCGGAA 62.969 63.158 29.90 0.00 43.06 4.30
1080 1094 2.182825 CTCGTCGACATTAAAGTCCCG 58.817 52.381 17.16 7.93 35.07 5.14
1217 1231 2.672996 GAGGAAGCTTGGCGGCAA 60.673 61.111 24.02 24.02 34.17 4.52
1368 1382 4.019411 TGGTGAGCAATCCTACTCATTTGA 60.019 41.667 0.00 0.00 44.29 2.69
1375 1389 4.574674 ATCCTACTCATTTGACCTGCAA 57.425 40.909 0.00 0.00 33.88 4.08
1619 1698 8.976986 AGTGAAGTATTTTCTGAAATTGATGC 57.023 30.769 3.31 0.00 36.82 3.91
1744 1823 9.760660 GAACATACAACATTGACTGAAACTATC 57.239 33.333 0.00 0.00 0.00 2.08
1774 1853 6.697395 TCCAAGAAGAAGAATAACATGACGA 58.303 36.000 0.00 0.00 0.00 4.20
1871 1950 5.794894 ACTACTTCGTGGATTCATCACTTT 58.205 37.500 0.00 0.00 33.31 2.66
1878 1959 6.367421 TCGTGGATTCATCACTTTTAAAACG 58.633 36.000 0.00 0.00 33.31 3.60
2082 2163 1.437625 TCATCGACATTCAGCGCAAA 58.562 45.000 11.47 3.45 0.00 3.68
2243 2324 2.161808 CAGACAACCTCATCGAGTACGT 59.838 50.000 0.00 0.00 40.69 3.57
2274 2355 2.202336 TACGCCGCGTACAAGTCG 60.202 61.111 21.35 0.16 41.54 4.18
2306 2387 2.555325 TCGACTACGTCACAGATGGTTT 59.445 45.455 0.00 0.00 40.69 3.27
2519 2600 8.731605 TGTTTGAACAAGTTTAGTTATGTCACA 58.268 29.630 0.00 0.00 35.67 3.58
2784 2868 6.744993 CGCTACTATGAATGCACTATCAGTAG 59.255 42.308 16.58 16.58 32.07 2.57
2833 2917 5.440610 AGTTCTGAAAATGACACCAGAAGT 58.559 37.500 0.00 0.00 43.62 3.01
2955 3039 6.803154 AAAAGTATCAGTCCAAGTTACTGC 57.197 37.500 1.50 0.00 43.30 4.40
3034 3124 6.542370 GCCCTAACAATGCTAGATACTTGAAA 59.458 38.462 0.00 0.00 0.00 2.69
3042 3132 4.342378 TGCTAGATACTTGAAATCGAGCCT 59.658 41.667 13.28 0.00 45.83 4.58
3160 3250 4.039245 TCAGGTAAGTGTTCAGAGGAGTTG 59.961 45.833 0.00 0.00 0.00 3.16
3202 3292 2.419574 GCTTATAAACAGGTCCGGAGCA 60.420 50.000 33.52 14.61 0.00 4.26
3255 3345 2.728015 CACGCGCACGACACACTA 60.728 61.111 5.73 0.00 43.93 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.106351 TGCTTCAGCGGGCAGAAAAA 61.106 50.000 0.25 0.00 45.83 1.94
3 4 1.528076 TGCTTCAGCGGGCAGAAAA 60.528 52.632 0.25 0.00 45.83 2.29
291 295 6.440647 ACTGATAGTCTTTCTGTATTGGGACA 59.559 38.462 1.79 0.00 0.00 4.02
457 463 4.122776 GAGACTATGTGTGGTGCTAATGG 58.877 47.826 0.00 0.00 0.00 3.16
480 486 6.541641 TGTGTTTAAACGTACCAATTACCAGT 59.458 34.615 13.45 0.00 0.00 4.00
498 504 4.819630 GGACTGGTGATTGAAGTGTGTTTA 59.180 41.667 0.00 0.00 0.00 2.01
501 507 2.806745 CGGACTGGTGATTGAAGTGTGT 60.807 50.000 0.00 0.00 0.00 3.72
600 606 4.051922 ACCGATTCGAATAGTCAAGATGC 58.948 43.478 11.38 0.00 0.00 3.91
603 609 3.444916 GCACCGATTCGAATAGTCAAGA 58.555 45.455 11.38 0.00 0.00 3.02
680 686 8.251721 ACTAGTCTTGTTAAGCTGTACTTATGG 58.748 37.037 0.00 0.00 40.55 2.74
695 701 8.958119 TTAATGTTGAACTGACTAGTCTTGTT 57.042 30.769 24.35 24.35 35.69 2.83
717 723 8.959705 AACCGTCCAATTTAAATGGTTTTTAA 57.040 26.923 12.01 0.00 38.79 1.52
781 787 3.947841 GCAGTGCGTCGTGGCAAA 61.948 61.111 0.00 0.00 45.93 3.68
877 890 7.678171 AGAGTTGGAATACAATGGGGTATTTTT 59.322 33.333 0.00 0.00 42.43 1.94
878 891 7.189087 AGAGTTGGAATACAATGGGGTATTTT 58.811 34.615 0.00 0.00 42.43 1.82
899 913 0.471211 TTGTGGGAACGAGGGAGAGT 60.471 55.000 0.00 0.00 0.00 3.24
1035 1049 0.250597 TCCTCTTGTCCGACGTCTCA 60.251 55.000 14.70 7.38 0.00 3.27
1217 1231 0.100146 GCCGACGATCCTACGAAACT 59.900 55.000 0.00 0.00 37.03 2.66
1289 1303 1.565156 TTCATCGACGCACAACTGCC 61.565 55.000 0.00 0.00 40.73 4.85
1305 1319 1.765904 TGGTACACCAAGCAGAGTTCA 59.234 47.619 0.00 0.00 44.35 3.18
1368 1382 2.387757 ACAGACAAACCATTTGCAGGT 58.612 42.857 1.23 0.00 44.39 4.00
1612 1691 9.853555 TTCTTACGAAAATAACATTGCATCAAT 57.146 25.926 0.00 0.00 34.04 2.57
1641 1720 5.297029 AGTGCTTCACAAAGTCCTTAGTTTC 59.703 40.000 0.00 0.00 36.74 2.78
1655 1734 1.065491 ACACAGAACCAGTGCTTCACA 60.065 47.619 1.16 0.00 40.59 3.58
1856 1935 8.476925 GTTTCGTTTTAAAAGTGATGAATCCAC 58.523 33.333 0.00 0.00 34.89 4.02
2102 2183 5.068723 TCAGTCAAGGAGTCGTACTCTTTTT 59.931 40.000 12.62 5.26 41.00 1.94
2243 2324 1.731433 GGCGTACGCATCCAGTCCTA 61.731 60.000 37.99 0.00 44.11 2.94
2274 2355 3.146618 ACGTAGTCGATCATGAACCAC 57.853 47.619 0.00 0.00 29.74 4.16
2306 2387 0.521291 CCGCTCTTTCGCAAATTCCA 59.479 50.000 0.00 0.00 0.00 3.53
2597 2678 7.607991 ACGTTCCATTCAGAAGATACTTTTCAT 59.392 33.333 0.00 0.00 0.00 2.57
2607 2689 3.057019 CGACAACGTTCCATTCAGAAGA 58.943 45.455 0.00 0.00 34.56 2.87
2740 2824 0.924090 GCTTACGGACTGATGCTTCG 59.076 55.000 0.00 0.00 0.00 3.79
2784 2868 5.052304 CGATACTTGCGTGTAGACTGATTTC 60.052 44.000 0.00 0.00 0.00 2.17
2787 2871 3.377485 ACGATACTTGCGTGTAGACTGAT 59.623 43.478 0.00 0.00 40.94 2.90
2808 2892 6.483640 ACTTCTGGTGTCATTTTCAGAACTAC 59.516 38.462 0.00 0.00 40.13 2.73
2955 3039 7.496529 TTGTTTGTTTGAATCTAGACTCCTG 57.503 36.000 0.00 0.00 0.00 3.86
3008 3098 5.130311 TCAAGTATCTAGCATTGTTAGGGCA 59.870 40.000 7.57 0.00 0.00 5.36
3014 3104 7.254590 GCTCGATTTCAAGTATCTAGCATTGTT 60.255 37.037 0.00 0.00 39.38 2.83
3086 3176 4.284550 TTGACCTGTGGGCCCTGC 62.285 66.667 25.70 16.63 35.63 4.85


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

AutoCloner maintained by Alex Coulton.