Multiple sequence alignment - TraesCS7B01G051800

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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 TraesCS7B01G051800 chr7B 100.000 4496 0 0 1 4496 54309918 54314413 0.000000e+00 8303
1 TraesCS7B01G051800 chr7D 94.462 3864 142 36 698 4496 98660402 98664258 0.000000e+00 5884
2 TraesCS7B01G051800 chr7D 94.522 712 37 2 1 711 98659676 98660386 0.000000e+00 1098
3 TraesCS7B01G051800 chr7A 95.989 3341 118 6 1170 4496 101219457 101222795 0.000000e+00 5413
4 TraesCS7B01G051800 chr7A 83.685 711 62 25 501 1174 101218732 101219425 4.940000e-174 621
5 TraesCS7B01G051800 chr7A 85.268 448 60 3 1 448 101218143 101218584 1.470000e-124 457
6 TraesCS7B01G051800 chr6D 93.602 2407 152 1 1170 3574 450648711 450651117 0.000000e+00 3591
7 TraesCS7B01G051800 chr6D 78.264 1279 195 52 1 1212 450647458 450648720 0.000000e+00 745
8 TraesCS7B01G051800 chr6D 93.902 82 4 1 3614 3695 450651116 450651196 6.110000e-24 122
9 TraesCS7B01G051800 chr6B 93.436 2407 156 1 1170 3574 684411037 684413443 0.000000e+00 3568
10 TraesCS7B01G051800 chr6B 87.363 364 33 8 860 1212 684410685 684411046 5.420000e-109 405
11 TraesCS7B01G051800 chr6B 93.902 82 4 1 3614 3695 684413442 684413522 6.110000e-24 122
12 TraesCS7B01G051800 chr6A 92.979 2407 167 1 1170 3574 596169442 596171848 0.000000e+00 3507
13 TraesCS7B01G051800 chr6A 87.055 309 32 5 911 1212 596169144 596169451 4.310000e-90 342
14 TraesCS7B01G051800 chr6A 95.122 82 3 1 3614 3695 596171847 596171927 1.310000e-25 128
15 TraesCS7B01G051800 chrUn 96.491 399 14 0 2091 2489 478902044 478901646 0.000000e+00 660


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 TraesCS7B01G051800 chr7B 54309918 54314413 4495 False 8303.000000 8303 100.000000 1 4496 1 chr7B.!!$F1 4495
1 TraesCS7B01G051800 chr7D 98659676 98664258 4582 False 3491.000000 5884 94.492000 1 4496 2 chr7D.!!$F1 4495
2 TraesCS7B01G051800 chr7A 101218143 101222795 4652 False 2163.666667 5413 88.314000 1 4496 3 chr7A.!!$F1 4495
3 TraesCS7B01G051800 chr6D 450647458 450651196 3738 False 1486.000000 3591 88.589333 1 3695 3 chr6D.!!$F1 3694
4 TraesCS7B01G051800 chr6B 684410685 684413522 2837 False 1365.000000 3568 91.567000 860 3695 3 chr6B.!!$F1 2835
5 TraesCS7B01G051800 chr6A 596169144 596171927 2783 False 1325.666667 3507 91.718667 911 3695 3 chr6A.!!$F1 2784

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
358 359 0.458669 CATGGGCTTGTCAAGGATGC 59.541 55.000 14.4 0.42 0.00 3.91 F
967 1154 1.221840 GGCGATCCTCCTGCTCAAA 59.778 57.895 0.0 0.00 0.00 2.69 F
2286 2512 0.703488 TTGGGAACATGGATGAGGCA 59.297 50.000 0.0 0.00 42.32 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 1561 0.817654 ACAGAACGCGGATGATCTCA 59.182 50.000 12.47 0.0 0.0 3.27 R
2801 3027 1.140312 AACTGTTGAAGCTCCCTGGA 58.860 50.000 0.00 0.0 0.0 3.86 R
4069 4297 1.005215 AGGAAGCCTCAAACATCTGGG 59.995 52.381 0.00 0.0 0.0 4.45 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
21 22 3.791320 TCACACAGATCTAGGGTTTCCT 58.209 45.455 0.00 0.00 46.96 3.36
33 34 2.087646 GGGTTTCCTCTAAAGCTGCAG 58.912 52.381 10.11 10.11 43.61 4.41
38 39 3.077617 CTCTAAAGCTGCAGAGGCC 57.922 57.895 20.43 0.00 40.13 5.19
60 61 3.215975 GTGGCTAGAAGTATCTCCTCGT 58.784 50.000 0.00 0.00 37.10 4.18
194 195 2.292267 CTCGCAAGCCCACTAATGAAT 58.708 47.619 0.00 0.00 37.18 2.57
209 210 4.895668 AATGAATCACCACAGCCAATTT 57.104 36.364 0.00 0.00 0.00 1.82
222 223 1.604278 GCCAATTTCAGGCGGATCTAC 59.396 52.381 0.00 0.00 43.15 2.59
230 231 1.909287 GGCGGATCTACCTCTCCCC 60.909 68.421 0.00 0.00 36.31 4.81
258 259 1.651240 CCTTGCCAGGTCATTGCTCG 61.651 60.000 0.00 0.00 35.06 5.03
358 359 0.458669 CATGGGCTTGTCAAGGATGC 59.541 55.000 14.40 0.42 0.00 3.91
416 417 4.156739 GTGCGAAGAATTTGGAAGAGGATT 59.843 41.667 0.00 0.00 28.96 3.01
584 684 7.978414 TCAAAGTGAACATGCAGACAAAAATAA 59.022 29.630 0.00 0.00 0.00 1.40
637 737 2.914059 ACTAAAATAAGCACGCCGGAT 58.086 42.857 5.05 0.00 0.00 4.18
719 849 6.042322 ACATAATGAATGGATGAATTGGTGGG 59.958 38.462 0.00 0.00 40.16 4.61
809 976 1.304891 CAATCCCCTCCCCCAAACTA 58.695 55.000 0.00 0.00 0.00 2.24
967 1154 1.221840 GGCGATCCTCCTGCTCAAA 59.778 57.895 0.00 0.00 0.00 2.69
1335 1561 2.025155 CATGACCTCGCTACCTACACT 58.975 52.381 0.00 0.00 0.00 3.55
1413 1639 3.219928 GAGATCCTCTCGCCGGCA 61.220 66.667 28.98 12.94 33.35 5.69
1446 1672 3.474570 GGCCCTGAGATCGTGCCT 61.475 66.667 0.00 0.00 39.05 4.75
1466 1692 3.134262 CCTCTCATGGATCAGCTCAGAAA 59.866 47.826 0.00 0.00 0.00 2.52
1617 1843 5.278266 GGCAGTTTTGACTTGCAACATACTA 60.278 40.000 0.00 0.00 35.91 1.82
1661 1887 4.504858 GGTGACTCGGAGATTGTTGTATT 58.495 43.478 12.86 0.00 33.89 1.89
1866 2092 1.204467 TGCGGAAAGATTGATTTGGCC 59.796 47.619 0.00 0.00 0.00 5.36
1914 2140 1.068352 AGGGGGTTCAAGTTGAGCCT 61.068 55.000 30.53 14.26 45.66 4.58
1944 2170 2.369983 ACATGGTAATGGATGGGCTG 57.630 50.000 0.00 0.00 38.19 4.85
2004 2230 1.600916 GAACAAGGCGAGGCAAGGT 60.601 57.895 0.00 0.00 0.00 3.50
2139 2365 2.919666 ATTGCCACATTGCGAGTTAC 57.080 45.000 0.00 0.00 0.00 2.50
2257 2483 7.874940 TCTGTATAACATTGCCATTTATGCTC 58.125 34.615 0.00 0.00 0.00 4.26
2286 2512 0.703488 TTGGGAACATGGATGAGGCA 59.297 50.000 0.00 0.00 42.32 4.75
2318 2544 3.176411 TGAGAGAAATGAAGGCTGAGGA 58.824 45.455 0.00 0.00 0.00 3.71
2372 2598 5.631026 CGTGATCAAGGGTTATTGTTTGAG 58.369 41.667 0.00 0.00 33.53 3.02
2466 2692 5.324409 ACATATAACATATTGGCCAGTGGG 58.676 41.667 11.69 5.23 37.18 4.61
2501 2727 3.564225 GGTCTTGTTACAGAGGTGTTTGG 59.436 47.826 0.00 0.00 38.19 3.28
2671 2897 8.094798 TGAAGTATTGTACAGTTCAATGGTTC 57.905 34.615 14.08 14.80 36.92 3.62
2801 3027 4.044065 TGACCTTTGTAGGGATGGAAATGT 59.956 41.667 0.00 0.00 46.58 2.71
2951 3177 1.067060 TGATATGGTTCAGCGAGGACG 59.933 52.381 0.00 0.00 42.93 4.79
3152 3378 2.159352 GCGTGAGTAAGGAGAGAAGGAC 60.159 54.545 0.00 0.00 0.00 3.85
3388 3614 4.476479 AGGGAGAAATAGAGAAGGCACAAT 59.524 41.667 0.00 0.00 0.00 2.71
3481 3707 2.648059 CCTTGAGGGAAAGGCAGTATG 58.352 52.381 0.00 0.00 40.37 2.39
3545 3773 6.176975 TCACGTCAGCAAGGTAATATTTTG 57.823 37.500 0.00 0.00 0.00 2.44
3570 3798 5.453567 AGTCACAAATTTACTGAAAGCCC 57.546 39.130 0.00 0.00 37.60 5.19
3580 3808 2.188817 ACTGAAAGCCCGGATCTAAGT 58.811 47.619 0.73 2.21 37.60 2.24
3617 3845 7.123098 TGCTTCCACTTGAATATGTGATGAAAT 59.877 33.333 0.00 0.00 34.77 2.17
3782 4010 9.180678 CAGAAGCATACTTGTTTAAAAATCGTT 57.819 29.630 0.00 0.00 35.82 3.85
3799 4027 4.681074 TCGTTCCAAGATATGCCATACA 57.319 40.909 0.00 0.00 0.00 2.29
3863 4091 4.351192 GTGAATGACAAACTTCACCACAC 58.649 43.478 8.59 0.00 43.42 3.82
3900 4128 7.920160 TGCATGACTTCATTAGTGTATGAAA 57.080 32.000 0.00 0.00 42.29 2.69
3902 4130 7.607607 TGCATGACTTCATTAGTGTATGAAACT 59.392 33.333 0.00 0.00 42.29 2.66
3990 4218 9.936759 GTTTTTCCCTTGGTAATATTGAAATGA 57.063 29.630 0.00 0.00 0.00 2.57
4080 4308 6.515272 ACTGCTTATAAACCCAGATGTTTG 57.485 37.500 12.02 0.00 38.79 2.93
4123 4352 2.490115 TGTTGCGTCAAACTGGAGTTTT 59.510 40.909 1.90 0.00 45.07 2.43
4124 4353 2.842208 TGCGTCAAACTGGAGTTTTG 57.158 45.000 1.90 0.00 45.07 2.44
4125 4354 1.202245 TGCGTCAAACTGGAGTTTTGC 60.202 47.619 1.90 7.70 45.07 3.68
4133 4362 4.853924 AACTGGAGTTTTGCTGTATTGG 57.146 40.909 0.00 0.00 33.93 3.16
4148 4377 5.447818 GCTGTATTGGACTTCATGCTTGTAC 60.448 44.000 0.00 0.00 0.00 2.90
4199 4428 6.285990 TGACTTATACTTTAAATCCTCGCCC 58.714 40.000 0.00 0.00 0.00 6.13
4201 4430 6.289064 ACTTATACTTTAAATCCTCGCCCTG 58.711 40.000 0.00 0.00 0.00 4.45
4221 4463 3.951680 CTGGTCTGTTAACCTGGTGTTTT 59.048 43.478 0.00 0.00 40.20 2.43
4233 4475 4.106663 ACCTGGTGTTTTTAGTTGGGGATA 59.893 41.667 0.00 0.00 0.00 2.59
4278 4520 7.121168 TCGAATTATTTCTGCTGAAAAGATGGT 59.879 33.333 20.69 7.65 44.22 3.55
4302 4544 2.358322 TCTTCCCTGTTTGGTTCCAC 57.642 50.000 0.00 0.00 0.00 4.02
4304 4546 2.158667 TCTTCCCTGTTTGGTTCCACTC 60.159 50.000 0.00 0.00 0.00 3.51
4309 4551 2.422597 CTGTTTGGTTCCACTCGCATA 58.577 47.619 0.00 0.00 0.00 3.14
4361 4603 3.793060 AGCCGTAGAGCTTGTGGT 58.207 55.556 0.00 0.00 41.41 4.16
4362 4604 1.293498 AGCCGTAGAGCTTGTGGTG 59.707 57.895 0.00 0.00 41.41 4.17
4374 4616 2.047179 GTGGTGGCTCCGGAAGTC 60.047 66.667 5.23 1.64 39.52 3.01
4375 4617 2.203788 TGGTGGCTCCGGAAGTCT 60.204 61.111 5.23 0.00 39.52 3.24
4390 4632 1.078848 GTCTTGGATGCGGCTGACT 60.079 57.895 0.00 0.00 0.00 3.41
4457 4699 4.347000 AGTCTTGGTGCAAGGTAGAACTAA 59.653 41.667 0.00 0.00 41.33 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.219124 CGGCCTCTGCAGCTTTAGA 59.781 57.895 9.47 0.00 40.13 2.10
33 34 1.000052 GATACTTCTAGCCACGGCCTC 60.000 57.143 3.95 0.00 43.17 4.70
37 38 2.554893 GAGGAGATACTTCTAGCCACGG 59.445 54.545 0.00 0.00 30.30 4.94
38 39 2.224549 CGAGGAGATACTTCTAGCCACG 59.775 54.545 0.00 0.00 30.30 4.94
60 61 2.552315 GTTTCCTTCTTGTTGGCATCGA 59.448 45.455 0.00 0.00 0.00 3.59
194 195 1.619654 CCTGAAATTGGCTGTGGTGA 58.380 50.000 0.00 0.00 0.00 4.02
209 210 0.178987 GGAGAGGTAGATCCGCCTGA 60.179 60.000 10.07 0.00 41.99 3.86
222 223 0.340208 AGGAGTTAGTGGGGGAGAGG 59.660 60.000 0.00 0.00 0.00 3.69
258 259 4.203618 GGCTCGTGAAGGCTAACC 57.796 61.111 0.00 0.00 46.82 2.85
416 417 4.703897 GGACAAATTCATCTCACCCGATA 58.296 43.478 0.00 0.00 0.00 2.92
458 505 8.368668 AGTTAATTTATCCCTACGAGAAGGATG 58.631 37.037 10.04 0.00 40.63 3.51
719 849 6.127703 GGGAGATTTTAGCCTGTCTTTTTACC 60.128 42.308 0.00 0.00 0.00 2.85
1137 1327 4.069232 CCGCTCGAGGTGGCTTCA 62.069 66.667 15.58 0.00 38.88 3.02
1335 1561 0.817654 ACAGAACGCGGATGATCTCA 59.182 50.000 12.47 0.00 0.00 3.27
1446 1672 4.028825 TCTTTCTGAGCTGATCCATGAGA 58.971 43.478 0.00 0.00 0.00 3.27
1617 1843 2.228343 GCTCTCAGCTGCAAATTTGAGT 59.772 45.455 22.31 0.00 38.45 3.41
1810 2036 7.119699 ACCGGTTATAAATGATGAGTATGCATG 59.880 37.037 10.16 0.00 0.00 4.06
1866 2092 5.349270 GCTGATCTCTTGCAGAATAGCATAG 59.651 44.000 0.00 0.00 45.19 2.23
1914 2140 7.833682 CCATCCATTACCATGTTATAAGCCATA 59.166 37.037 0.00 0.00 0.00 2.74
1944 2170 1.881973 TGCAGTCTCATTTCCTTGCAC 59.118 47.619 0.00 0.00 36.71 4.57
2139 2365 6.481954 AACTTCGTAAAGCATTGTAGAAGG 57.518 37.500 15.02 0.00 38.23 3.46
2257 2483 2.343101 CATGTTCCCAAGCTTGCAATG 58.657 47.619 21.43 13.97 0.00 2.82
2286 2512 7.327214 CCTTCATTTCTCTCAGTAGCTTAACT 58.673 38.462 0.00 0.00 0.00 2.24
2318 2544 4.285517 AGTGAATTCTGTCAGGTGTCAGAT 59.714 41.667 7.05 0.00 39.29 2.90
2372 2598 2.024414 GTGCATTTGGTACATCTCCCC 58.976 52.381 0.00 0.00 39.30 4.81
2400 2626 2.938869 GCCTTCAGCATCACTTCAAAC 58.061 47.619 0.00 0.00 42.97 2.93
2501 2727 1.338200 CCGCCATATGGTCTAGAAGGC 60.338 57.143 22.79 4.29 37.57 4.35
2671 2897 1.534595 GCCTGAATGCAAATAGCCACG 60.535 52.381 0.00 0.00 44.83 4.94
2801 3027 1.140312 AACTGTTGAAGCTCCCTGGA 58.860 50.000 0.00 0.00 0.00 3.86
2951 3177 9.973246 CAGTGTATACAATAACATCAACAGAAC 57.027 33.333 7.25 0.00 0.00 3.01
3135 3361 5.948842 AGATAGGTCCTTCTCTCCTTACTC 58.051 45.833 0.00 0.00 33.34 2.59
3152 3378 8.470805 TGTTCTGCTTTACTCTAAGAAGATAGG 58.529 37.037 0.00 0.00 39.12 2.57
3219 3445 4.493547 TCAATACGGTGTAAAAGGGTACG 58.506 43.478 0.00 0.00 0.00 3.67
3281 3507 4.380867 GCAACAATTCATCAAATCGTCCCT 60.381 41.667 0.00 0.00 0.00 4.20
3388 3614 9.231297 CCTGTCTACCATTTCTTCAAAAAGATA 57.769 33.333 0.00 0.00 41.12 1.98
3481 3707 5.032863 GCAGCAAAATCATACATGTCACTC 58.967 41.667 0.00 0.00 0.00 3.51
3545 3773 6.861572 GGGCTTTCAGTAAATTTGTGACTTAC 59.138 38.462 0.00 0.00 0.00 2.34
3589 3817 6.433716 TCATCACATATTCAAGTGGAAGCAAA 59.566 34.615 0.00 0.00 39.30 3.68
3776 4004 5.620206 TGTATGGCATATCTTGGAACGATT 58.380 37.500 10.92 0.00 0.00 3.34
3778 4006 4.343814 TCTGTATGGCATATCTTGGAACGA 59.656 41.667 10.92 0.00 0.00 3.85
3782 4010 6.470278 CATCTTCTGTATGGCATATCTTGGA 58.530 40.000 10.92 7.53 0.00 3.53
3799 4027 3.891977 TCTATACTTCGCCAGCATCTTCT 59.108 43.478 0.00 0.00 0.00 2.85
3863 4091 1.802960 GTCATGCATTATGCTCTCCCG 59.197 52.381 18.44 0.98 45.31 5.14
3958 4186 3.978460 CCAAGGGAAAAACGTTGGG 57.022 52.632 0.00 0.00 47.00 4.12
3960 4188 7.371936 TCAATATTACCAAGGGAAAAACGTTG 58.628 34.615 0.00 0.00 36.33 4.10
3990 4218 7.093377 TGGCTATCTATTGAACAATTTGGCTTT 60.093 33.333 5.37 0.00 32.50 3.51
3993 4221 6.147864 TGGCTATCTATTGAACAATTTGGC 57.852 37.500 5.37 5.38 32.50 4.52
4029 4257 7.452880 ACTTTGATCACTGCAATTAGCTTAA 57.547 32.000 0.00 0.00 45.94 1.85
4069 4297 1.005215 AGGAAGCCTCAAACATCTGGG 59.995 52.381 0.00 0.00 0.00 4.45
4080 4308 1.065126 AGCACATGGTAAGGAAGCCTC 60.065 52.381 0.00 0.00 30.89 4.70
4123 4352 3.354948 AGCATGAAGTCCAATACAGCA 57.645 42.857 0.00 0.00 0.00 4.41
4124 4353 3.441572 ACAAGCATGAAGTCCAATACAGC 59.558 43.478 0.00 0.00 0.00 4.40
4125 4354 5.877012 AGTACAAGCATGAAGTCCAATACAG 59.123 40.000 0.00 0.00 0.00 2.74
4133 4362 6.595716 AGGATTTACAGTACAAGCATGAAGTC 59.404 38.462 0.00 0.00 0.00 3.01
4148 4377 4.775236 AGCTTAGAGGCAAGGATTTACAG 58.225 43.478 0.00 0.00 34.17 2.74
4199 4428 2.930826 ACACCAGGTTAACAGACCAG 57.069 50.000 8.10 0.00 42.35 4.00
4201 4430 4.994907 AAAAACACCAGGTTAACAGACC 57.005 40.909 8.10 0.00 39.29 3.85
4221 4463 7.612633 GTGACCTTTGTAAATATCCCCAACTAA 59.387 37.037 0.00 0.00 0.00 2.24
4233 4475 6.642707 TTCGATTTGGTGACCTTTGTAAAT 57.357 33.333 2.11 0.00 0.00 1.40
4278 4520 4.079672 TGGAACCAAACAGGGAAGAACTTA 60.080 41.667 0.00 0.00 43.89 2.24
4302 4544 3.181482 ACACTCAGTCCTTGATATGCGAG 60.181 47.826 0.00 0.00 34.68 5.03
4304 4546 3.170791 ACACTCAGTCCTTGATATGCG 57.829 47.619 0.00 0.00 34.68 4.73
4309 4551 4.543590 ATCGAAACACTCAGTCCTTGAT 57.456 40.909 0.00 0.00 34.68 2.57
4361 4603 0.909610 ATCCAAGACTTCCGGAGCCA 60.910 55.000 3.34 0.00 30.84 4.75
4362 4604 0.462759 CATCCAAGACTTCCGGAGCC 60.463 60.000 3.34 0.00 30.84 4.70
4374 4616 0.461548 TCTAGTCAGCCGCATCCAAG 59.538 55.000 0.00 0.00 0.00 3.61
4375 4617 0.901827 TTCTAGTCAGCCGCATCCAA 59.098 50.000 0.00 0.00 0.00 3.53
4438 4680 5.043737 ACTTTAGTTCTACCTTGCACCAA 57.956 39.130 0.00 0.00 0.00 3.67
4457 4699 2.425668 ACGTAGTTTTGCAGCCAAACTT 59.574 40.909 25.18 8.97 37.78 2.66


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

AutoCloner maintained by Alex Coulton.