Multiple sequence alignment - TraesCS5B01G074100

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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 TraesCS5B01G074100 chr5B 100.000 3818 0 0 517 4334 87987839 87991656 0.000000e+00 7051
1 TraesCS5B01G074100 chr5B 100.000 212 0 0 1 212 87987323 87987534 4.060000e-105 392
2 TraesCS5B01G074100 chr5A 96.482 3326 111 4 517 3838 74730677 74734000 0.000000e+00 5489
3 TraesCS5B01G074100 chr5A 94.181 464 24 2 3869 4331 74734001 74734462 0.000000e+00 704
4 TraesCS5B01G074100 chr5A 94.118 119 1 3 83 196 74730531 74730648 4.450000e-40 176
5 TraesCS5B01G074100 chr5A 89.773 88 6 2 5 91 74728692 74728777 4.580000e-20 110
6 TraesCS5B01G074100 chr5D 96.944 3240 97 2 517 3755 78130984 78134222 0.000000e+00 5433
7 TraesCS5B01G074100 chr5D 88.344 163 18 1 3746 3907 78136140 78136302 1.230000e-45 195
8 TraesCS5B01G074100 chr5D 91.156 147 5 4 56 196 78130806 78130950 4.420000e-45 193


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 TraesCS5B01G074100 chr5B 87987323 87991656 4333 False 3721.500000 7051 100.0000 1 4334 2 chr5B.!!$F1 4333
1 TraesCS5B01G074100 chr5A 74728692 74734462 5770 False 1619.750000 5489 93.6385 5 4331 4 chr5A.!!$F1 4326
2 TraesCS5B01G074100 chr5D 78130806 78136302 5496 False 1940.333333 5433 92.1480 56 3907 3 chr5D.!!$F1 3851

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
756 2525 0.94805 ACTCCATCCTCCTCTCCCAT 59.052 55.0 0.0 0.0 0.0 4.00 F
1650 3419 0.59660 TTCGTTGTGCTCTGTCGGAC 60.597 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 4106 0.250901 GAGCTTTGGCAGTCTTCCCA 60.251 55.0 0.0 0.0 41.7 4.37 R
3586 5359 0.108662 CAGCACCGTCATACAGAGCA 60.109 55.0 0.0 0.0 0.0 4.26 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
20 21 1.950216 GCCTAAGCAGAGTAAATGGCC 59.050 52.381 0.00 0.00 39.53 5.36
21 22 2.683742 GCCTAAGCAGAGTAAATGGCCA 60.684 50.000 8.56 8.56 39.53 5.36
22 23 3.209410 CCTAAGCAGAGTAAATGGCCAG 58.791 50.000 13.05 0.00 0.00 4.85
23 24 1.467920 AAGCAGAGTAAATGGCCAGC 58.532 50.000 13.05 6.38 0.00 4.85
70 72 6.177610 AGACTGACTAACCACAAGTTCAAAA 58.822 36.000 0.00 0.00 40.05 2.44
176 1941 3.823330 CGTTCCTCCTCCGACCCG 61.823 72.222 0.00 0.00 0.00 5.28
177 1942 4.144703 GTTCCTCCTCCGACCCGC 62.145 72.222 0.00 0.00 0.00 6.13
178 1943 4.689549 TTCCTCCTCCGACCCGCA 62.690 66.667 0.00 0.00 0.00 5.69
756 2525 0.948050 ACTCCATCCTCCTCTCCCAT 59.052 55.000 0.00 0.00 0.00 4.00
942 2711 3.343421 GCCGTCACCGTCAACACC 61.343 66.667 0.00 0.00 0.00 4.16
969 2738 4.479993 GCGCTCTGCAGGGATGGT 62.480 66.667 20.53 0.00 45.45 3.55
1030 2799 3.728373 GCGGGGGAATCCACAGGT 61.728 66.667 3.02 0.00 35.77 4.00
1218 2987 1.079819 ACGGAACATGCTGGAGACG 60.080 57.895 0.00 0.00 0.00 4.18
1515 3284 1.918293 ACGGAGGGGCAATGAGTCA 60.918 57.895 0.00 0.00 0.00 3.41
1542 3311 0.722676 TATTGGGGGAGGTGGTCTCT 59.277 55.000 0.00 0.00 42.10 3.10
1650 3419 0.596600 TTCGTTGTGCTCTGTCGGAC 60.597 55.000 0.00 0.00 0.00 4.79
1674 3443 2.238646 TCATACTCCCAATGGTGTCACC 59.761 50.000 15.64 15.64 39.11 4.02
1737 3506 1.141657 GATGGGGCAGAGCAGATGTTA 59.858 52.381 0.00 0.00 0.00 2.41
1759 3528 9.713684 TGTTATTGGAAATGGAGGATAAATCTT 57.286 29.630 0.00 0.00 0.00 2.40
2012 3781 2.170166 TGATTTGCTGGTGAATGGTCC 58.830 47.619 0.00 0.00 0.00 4.46
2025 3794 2.899303 ATGGTCCGAGGAAAAATGGT 57.101 45.000 0.00 0.00 0.00 3.55
2250 4019 2.356069 GCTTGGGAAATCTAAGGAAGCG 59.644 50.000 0.00 0.00 0.00 4.68
2371 4140 4.637977 CCAAAGCTCTAAAACTCCTCCATC 59.362 45.833 0.00 0.00 0.00 3.51
2375 4144 5.880901 AGCTCTAAAACTCCTCCATCAAAA 58.119 37.500 0.00 0.00 0.00 2.44
2445 4214 1.687563 CGGGTCTTTTTGAGGTTGGT 58.312 50.000 0.00 0.00 0.00 3.67
2718 4487 0.038166 GAGGAATTGCCCCAGACACA 59.962 55.000 0.00 0.00 37.37 3.72
2902 4671 4.213694 CAGATAAGGTGCTGAATGAGATGC 59.786 45.833 0.00 0.00 34.06 3.91
2958 4727 2.691526 TGACATACTGGTCACGGGATAC 59.308 50.000 0.00 0.00 42.56 2.24
2990 4759 2.475864 GCAACAAAATCGAAGCAATGCA 59.524 40.909 8.35 0.00 0.00 3.96
3027 4796 1.819288 GTGGCTAAAGGCTTTCTTCCC 59.181 52.381 17.13 12.49 41.69 3.97
3052 4821 3.618594 AGTAAGCACATACAATGCACTCG 59.381 43.478 0.00 0.00 45.92 4.18
3147 4916 1.064463 CCACCCACATCCTGCACTTAT 60.064 52.381 0.00 0.00 0.00 1.73
3372 5141 2.977914 TCTCATCTACCAAGCAAGCAC 58.022 47.619 0.00 0.00 0.00 4.40
3555 5328 5.854431 ATGTTGTTGTTGTGGTGTTTTTC 57.146 34.783 0.00 0.00 0.00 2.29
3772 7472 9.549509 TTTTATTTGTATTGCTAGTTGCTAACG 57.450 29.630 0.00 0.00 43.37 3.18
3791 7491 6.093082 GCTAACGTATTCCTTTGTGGTATGTT 59.907 38.462 0.00 0.00 33.65 2.71
3792 7492 6.887626 AACGTATTCCTTTGTGGTATGTTT 57.112 33.333 0.00 0.00 37.07 2.83
3840 7540 1.805254 CTTGCTTTCCAGATGGCCG 59.195 57.895 0.00 0.00 34.44 6.13
3856 7556 1.810151 GGCCGCATTTCTGTAACAGAA 59.190 47.619 0.00 0.00 46.93 3.02
3912 7613 9.023962 TGAACCTTGTCAAAATTATTATCAGCT 57.976 29.630 0.00 0.00 0.00 4.24
3914 7615 9.643693 AACCTTGTCAAAATTATTATCAGCTTG 57.356 29.630 0.00 0.00 0.00 4.01
3929 7630 3.513119 TCAGCTTGTCAGTGAAGAGCTAT 59.487 43.478 23.59 7.69 41.43 2.97
3950 7651 2.168521 TCCTTCATTCGTAAGGAGCAGG 59.831 50.000 0.43 2.20 45.97 4.85
3987 7688 0.739813 ATTGGCTACCGCTCGTGTTC 60.740 55.000 0.00 0.00 36.09 3.18
3999 7700 2.128035 CTCGTGTTCTCCTTGTGTCAC 58.872 52.381 0.00 0.00 0.00 3.67
4001 7702 0.582005 GTGTTCTCCTTGTGTCACGC 59.418 55.000 0.00 0.00 0.00 5.34
4005 7706 0.240145 TCTCCTTGTGTCACGCTACG 59.760 55.000 0.00 0.00 0.00 3.51
4012 7713 0.776451 GTGTCACGCTACGTTGTGAG 59.224 55.000 17.24 9.46 45.08 3.51
4021 7722 2.287668 GCTACGTTGTGAGTCTGACAGT 60.288 50.000 10.88 0.00 0.00 3.55
4024 7725 2.286831 ACGTTGTGAGTCTGACAGTACG 60.287 50.000 13.07 13.07 34.11 3.67
4081 7782 4.561606 GCAAGCAGCAGATTTCATTTACAG 59.438 41.667 0.00 0.00 44.79 2.74
4107 7808 8.725148 GCCAGGTGATTATTATGAAGTTAGATG 58.275 37.037 0.00 0.00 0.00 2.90
4124 7825 7.196331 AGTTAGATGCACTTTGTTTTCTGAAC 58.804 34.615 0.00 0.00 0.00 3.18
4129 7830 3.786048 GCACTTTGTTTTCTGAACACTCG 59.214 43.478 8.04 0.27 0.00 4.18
4131 7832 5.446741 GCACTTTGTTTTCTGAACACTCGTA 60.447 40.000 8.04 0.00 0.00 3.43
4189 7891 8.593679 TCATCAAACTACTACTCTTGGAATTGA 58.406 33.333 0.00 0.00 0.00 2.57
4269 7971 8.059461 TCCTCTCTGTTTGTGTAGGATCTAATA 58.941 37.037 0.00 0.00 0.00 0.98
4274 7976 7.124298 TCTGTTTGTGTAGGATCTAATACAGCT 59.876 37.037 0.00 0.00 32.76 4.24
4295 7997 3.425162 AGGCTTCTGACGGAGAAAATT 57.575 42.857 1.38 0.00 40.33 1.82
4296 7998 3.077359 AGGCTTCTGACGGAGAAAATTG 58.923 45.455 1.38 0.00 40.33 2.32
4331 8033 1.005630 CTATACTCTGCCCAGCCGC 60.006 63.158 0.00 0.00 0.00 6.53
4332 8034 1.748329 CTATACTCTGCCCAGCCGCA 61.748 60.000 0.00 0.00 37.19 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.950216 GGCCATTTACTCTGCTTAGGC 59.050 52.381 0.00 0.00 40.08 3.93
1 2 3.209410 CTGGCCATTTACTCTGCTTAGG 58.791 50.000 5.51 0.00 0.00 2.69
2 3 2.615912 GCTGGCCATTTACTCTGCTTAG 59.384 50.000 5.51 0.00 0.00 2.18
3 4 2.643551 GCTGGCCATTTACTCTGCTTA 58.356 47.619 5.51 0.00 0.00 3.09
21 22 1.378514 AATGAAATCGGCCGTGGCT 60.379 52.632 27.15 8.35 41.60 4.75
22 23 1.226660 CAATGAAATCGGCCGTGGC 60.227 57.895 27.15 13.64 41.06 5.01
23 24 1.433064 CCAATGAAATCGGCCGTGG 59.567 57.895 27.15 19.60 0.00 4.94
25 26 2.414785 GCCCAATGAAATCGGCCGT 61.415 57.895 27.15 10.00 36.06 5.68
26 27 0.817634 TAGCCCAATGAAATCGGCCG 60.818 55.000 22.12 22.12 41.33 6.13
27 28 1.338020 CTTAGCCCAATGAAATCGGCC 59.662 52.381 0.00 0.00 41.33 6.13
28 29 2.033424 GTCTTAGCCCAATGAAATCGGC 59.967 50.000 0.00 0.00 40.86 5.54
29 30 3.313526 CAGTCTTAGCCCAATGAAATCGG 59.686 47.826 0.00 0.00 0.00 4.18
30 31 4.034510 GTCAGTCTTAGCCCAATGAAATCG 59.965 45.833 0.00 0.00 0.00 3.34
70 72 6.110707 TCGTGGTTAGTCAGTCTTTTTCTTT 58.889 36.000 0.00 0.00 0.00 2.52
73 75 5.978934 TTCGTGGTTAGTCAGTCTTTTTC 57.021 39.130 0.00 0.00 0.00 2.29
176 1941 2.740055 CGGCCTGTGAGTGAGTGC 60.740 66.667 0.00 0.00 0.00 4.40
177 1942 2.047844 CCGGCCTGTGAGTGAGTG 60.048 66.667 0.00 0.00 0.00 3.51
178 1943 4.008933 GCCGGCCTGTGAGTGAGT 62.009 66.667 18.11 0.00 0.00 3.41
723 2492 1.682684 GGAGTTGAGGGAGAGCGGA 60.683 63.158 0.00 0.00 0.00 5.54
1030 2799 1.724148 TTCCAGCCCACCACATCCAA 61.724 55.000 0.00 0.00 0.00 3.53
1189 2958 1.028330 ATGTTCCGTGCAGCATCAGG 61.028 55.000 0.00 3.05 0.00 3.86
1218 2987 3.782443 ACGCCGTCCCCCTTCATC 61.782 66.667 0.00 0.00 0.00 2.92
1515 3284 0.981277 CCTCCCCCAATAGACCGTGT 60.981 60.000 0.00 0.00 0.00 4.49
1542 3311 3.054434 CCAAATCCATGACCACACCTCTA 60.054 47.826 0.00 0.00 0.00 2.43
1650 3419 4.336433 GTGACACCATTGGGAGTATGATTG 59.664 45.833 7.78 0.00 38.18 2.67
1674 3443 6.092396 AGAGTGCATCGATTAGTACGGTATAG 59.908 42.308 0.00 0.00 0.00 1.31
1737 3506 8.416329 CGAAAAGATTTATCCTCCATTTCCAAT 58.584 33.333 0.00 0.00 0.00 3.16
1759 3528 5.984926 AGAACGTAACTACATTTGGACGAAA 59.015 36.000 0.00 0.00 34.54 3.46
1836 3605 6.410157 CCCTTTCCTTCATCTTCCTCATGTAT 60.410 42.308 0.00 0.00 0.00 2.29
2012 3781 5.417580 TCCTCCATTTTACCATTTTTCCTCG 59.582 40.000 0.00 0.00 0.00 4.63
2025 3794 4.032960 TGCTTCAGCTTCCTCCATTTTA 57.967 40.909 0.00 0.00 42.66 1.52
2066 3835 1.536284 GGTCTAGCAGCATACCACGTC 60.536 57.143 0.00 0.00 32.04 4.34
2250 4019 7.894376 TTGCATCTCTTTCAAAATTGATTCC 57.106 32.000 0.00 0.00 37.00 3.01
2337 4106 0.250901 GAGCTTTGGCAGTCTTCCCA 60.251 55.000 0.00 0.00 41.70 4.37
2371 4140 6.349694 GGCTTTATGGAACTCCTCTTCTTTTG 60.350 42.308 0.00 0.00 36.82 2.44
2375 4144 3.118592 CGGCTTTATGGAACTCCTCTTCT 60.119 47.826 0.00 0.00 36.82 2.85
2445 4214 0.959553 ACTTCGCCTTCTCGACAGAA 59.040 50.000 0.00 0.00 38.30 3.02
2560 4329 9.168451 CATCCATTCATGAATTTCCAAAATCAA 57.832 29.630 18.41 0.00 32.14 2.57
2718 4487 8.195436 CCAAGAATTAGAGCATTGAATGTGATT 58.805 33.333 7.05 0.00 0.00 2.57
2902 4671 2.791170 GCTCAATGCCCCTTCTCTG 58.209 57.895 0.00 0.00 35.15 3.35
2958 4727 4.266502 TCGATTTTGTTGCTTTGTTTTCCG 59.733 37.500 0.00 0.00 0.00 4.30
2990 4759 4.151883 AGCCACCATTTCACAATACAACT 58.848 39.130 0.00 0.00 0.00 3.16
3027 4796 5.702865 AGTGCATTGTATGTGCTTACTTTG 58.297 37.500 0.00 0.00 42.92 2.77
3147 4916 4.525996 CCCATCCACACACAAGAATATCA 58.474 43.478 0.00 0.00 0.00 2.15
3434 5203 2.568956 TCTGCCAGTAGCTTCTTGTCAT 59.431 45.455 0.00 0.00 44.23 3.06
3466 5235 3.181465 CCAGACACACTTACAGGTGACTT 60.181 47.826 0.00 0.00 40.21 3.01
3586 5359 0.108662 CAGCACCGTCATACAGAGCA 60.109 55.000 0.00 0.00 0.00 4.26
3856 7556 4.634883 CAGATTGCAGCTTATTGTGACTCT 59.365 41.667 0.00 0.00 0.00 3.24
3862 7562 5.184479 ACATGAACAGATTGCAGCTTATTGT 59.816 36.000 0.00 0.00 0.00 2.71
3863 7563 5.515270 CACATGAACAGATTGCAGCTTATTG 59.485 40.000 0.00 0.00 0.00 1.90
3864 7564 5.416639 TCACATGAACAGATTGCAGCTTATT 59.583 36.000 0.00 0.00 0.00 1.40
3866 7566 4.325972 TCACATGAACAGATTGCAGCTTA 58.674 39.130 0.00 0.00 0.00 3.09
3867 7567 3.151554 TCACATGAACAGATTGCAGCTT 58.848 40.909 0.00 0.00 0.00 3.74
3912 7613 4.528206 TGAAGGATAGCTCTTCACTGACAA 59.472 41.667 11.27 0.00 43.70 3.18
3914 7615 4.727507 TGAAGGATAGCTCTTCACTGAC 57.272 45.455 11.27 1.49 43.70 3.51
3950 7651 6.681777 AGCCAATAATTTCAGAAACTCACAC 58.318 36.000 0.00 0.00 0.00 3.82
3987 7688 0.039437 ACGTAGCGTGACACAAGGAG 60.039 55.000 6.37 0.00 39.18 3.69
3999 7700 1.328439 GTCAGACTCACAACGTAGCG 58.672 55.000 0.00 0.00 0.00 4.26
4001 7702 3.627732 ACTGTCAGACTCACAACGTAG 57.372 47.619 6.91 0.00 0.00 3.51
4005 7706 3.556513 CTCGTACTGTCAGACTCACAAC 58.443 50.000 6.91 0.00 0.00 3.32
4012 7713 1.202582 ACATGCCTCGTACTGTCAGAC 59.797 52.381 6.91 0.00 0.00 3.51
4071 7772 8.849168 CATAATAATCACCTGGCTGTAAATGAA 58.151 33.333 0.00 0.00 0.00 2.57
4081 7782 8.725148 CATCTAACTTCATAATAATCACCTGGC 58.275 37.037 0.00 0.00 0.00 4.85
4107 7808 3.786048 CGAGTGTTCAGAAAACAAAGTGC 59.214 43.478 6.24 0.00 31.20 4.40
4115 7816 4.446385 CCACGAATACGAGTGTTCAGAAAA 59.554 41.667 12.04 0.00 42.66 2.29
4124 7825 4.208355 CAAAACAACCACGAATACGAGTG 58.792 43.478 0.00 0.00 42.66 3.51
4129 7830 6.635166 AAAACACAAAACAACCACGAATAC 57.365 33.333 0.00 0.00 0.00 1.89
4131 7832 6.391537 AGTAAAACACAAAACAACCACGAAT 58.608 32.000 0.00 0.00 0.00 3.34
4237 7939 6.013379 TCCTACACAAACAGAGAGGATGAAAT 60.013 38.462 0.00 0.00 0.00 2.17
4269 7971 0.612174 TCCGTCAGAAGCCTAGCTGT 60.612 55.000 0.00 0.00 39.62 4.40
4274 7976 4.253685 CAATTTTCTCCGTCAGAAGCCTA 58.746 43.478 0.00 0.00 42.37 3.93
4295 7997 1.986413 GGAGAAGAAGCCTCCTGCA 59.014 57.895 0.00 0.00 45.18 4.41
4296 7998 4.952704 GGAGAAGAAGCCTCCTGC 57.047 61.111 0.00 0.00 45.18 4.85
4313 8015 1.005630 GCGGCTGGGCAGAGTATAG 60.006 63.158 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.