Multiple sequence alignment - TraesCS7D01G160600

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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 TraesCS7D01G160600 chr7D 100.000 3630 0 0 1 3630 110889678 110893307 0.000000e+00 6704
1 TraesCS7D01G160600 chr7D 87.736 636 70 2 1 636 272267428 272266801 0.000000e+00 736
2 TraesCS7D01G160600 chr7B 94.113 3669 138 30 1 3630 69848649 69852278 0.000000e+00 5507
3 TraesCS7D01G160600 chr7B 93.977 3669 143 31 1 3630 69911921 69915550 0.000000e+00 5480
4 TraesCS7D01G160600 chr7B 93.324 3670 164 32 1 3630 69991806 69995434 0.000000e+00 5345
5 TraesCS7D01G160600 chr7B 94.561 3107 116 26 1 3091 70068304 70071373 0.000000e+00 4752
6 TraesCS7D01G160600 chr7B 92.632 3271 163 36 411 3630 70339171 70342414 0.000000e+00 4634
7 TraesCS7D01G160600 chr7B 93.207 2841 128 29 411 3214 70242982 70245794 0.000000e+00 4117
8 TraesCS7D01G160600 chr7B 95.943 419 14 3 3213 3630 70245955 70246371 0.000000e+00 676
9 TraesCS7D01G160600 chr7B 94.545 385 18 2 3247 3630 70071903 70072285 3.120000e-165 592
10 TraesCS7D01G160600 chr7B 94.328 335 19 0 88 422 70337295 70337629 6.950000e-142 514
11 TraesCS7D01G160600 chr7B 93.168 161 5 3 3094 3250 70071586 70071744 7.840000e-57 231
12 TraesCS7D01G160600 chr6B 93.980 3671 134 30 1 3630 548947705 548951329 0.000000e+00 5474
13 TraesCS7D01G160600 chr6B 93.934 3676 132 33 1 3630 549028217 549031847 0.000000e+00 5469
14 TraesCS7D01G160600 chr7A 94.804 3137 88 21 122 3217 116018003 116021105 0.000000e+00 4820
15 TraesCS7D01G160600 chr7A 95.000 420 21 0 3211 3630 116021536 116021955 0.000000e+00 660
16 TraesCS7D01G160600 chrUn 87.718 2988 242 68 738 3630 16657285 16660242 0.000000e+00 3369
17 TraesCS7D01G160600 chrUn 89.170 2373 185 48 775 3091 16612153 16614509 0.000000e+00 2892
18 TraesCS7D01G160600 chrUn 93.167 1566 86 15 1510 3065 379234394 379232840 0.000000e+00 2279
19 TraesCS7D01G160600 chrUn 92.631 1167 45 17 1 1157 426294004 426295139 0.000000e+00 1640
20 TraesCS7D01G160600 chr2D 85.741 1592 139 33 2103 3630 19848234 19846667 0.000000e+00 1602
21 TraesCS7D01G160600 chr2A 86.026 1467 127 35 2151 3551 20366556 20368010 0.000000e+00 1502
22 TraesCS7D01G160600 chr5B 89.857 631 56 2 1 631 116642573 116643195 0.000000e+00 804
23 TraesCS7D01G160600 chr5B 88.162 642 62 4 1 636 237115910 237115277 0.000000e+00 752
24 TraesCS7D01G160600 chr4D 88.785 642 58 8 1 636 354985266 354984633 0.000000e+00 774
25 TraesCS7D01G160600 chr3B 85.714 644 74 9 4 639 85804755 85804122 0.000000e+00 664


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 TraesCS7D01G160600 chr7D 110889678 110893307 3629 False 6704.000000 6704 100.000000 1 3630 1 chr7D.!!$F1 3629
1 TraesCS7D01G160600 chr7D 272266801 272267428 627 True 736.000000 736 87.736000 1 636 1 chr7D.!!$R1 635
2 TraesCS7D01G160600 chr7B 69848649 69852278 3629 False 5507.000000 5507 94.113000 1 3630 1 chr7B.!!$F1 3629
3 TraesCS7D01G160600 chr7B 69911921 69915550 3629 False 5480.000000 5480 93.977000 1 3630 1 chr7B.!!$F2 3629
4 TraesCS7D01G160600 chr7B 69991806 69995434 3628 False 5345.000000 5345 93.324000 1 3630 1 chr7B.!!$F3 3629
5 TraesCS7D01G160600 chr7B 70337295 70342414 5119 False 2574.000000 4634 93.480000 88 3630 2 chr7B.!!$F6 3542
6 TraesCS7D01G160600 chr7B 70242982 70246371 3389 False 2396.500000 4117 94.575000 411 3630 2 chr7B.!!$F5 3219
7 TraesCS7D01G160600 chr7B 70068304 70072285 3981 False 1858.333333 4752 94.091333 1 3630 3 chr7B.!!$F4 3629
8 TraesCS7D01G160600 chr6B 548947705 548951329 3624 False 5474.000000 5474 93.980000 1 3630 1 chr6B.!!$F1 3629
9 TraesCS7D01G160600 chr6B 549028217 549031847 3630 False 5469.000000 5469 93.934000 1 3630 1 chr6B.!!$F2 3629
10 TraesCS7D01G160600 chr7A 116018003 116021955 3952 False 2740.000000 4820 94.902000 122 3630 2 chr7A.!!$F1 3508
11 TraesCS7D01G160600 chrUn 16657285 16660242 2957 False 3369.000000 3369 87.718000 738 3630 1 chrUn.!!$F2 2892
12 TraesCS7D01G160600 chrUn 16612153 16614509 2356 False 2892.000000 2892 89.170000 775 3091 1 chrUn.!!$F1 2316
13 TraesCS7D01G160600 chrUn 379232840 379234394 1554 True 2279.000000 2279 93.167000 1510 3065 1 chrUn.!!$R1 1555
14 TraesCS7D01G160600 chrUn 426294004 426295139 1135 False 1640.000000 1640 92.631000 1 1157 1 chrUn.!!$F3 1156
15 TraesCS7D01G160600 chr2D 19846667 19848234 1567 True 1602.000000 1602 85.741000 2103 3630 1 chr2D.!!$R1 1527
16 TraesCS7D01G160600 chr2A 20366556 20368010 1454 False 1502.000000 1502 86.026000 2151 3551 1 chr2A.!!$F1 1400
17 TraesCS7D01G160600 chr5B 116642573 116643195 622 False 804.000000 804 89.857000 1 631 1 chr5B.!!$F1 630
18 TraesCS7D01G160600 chr5B 237115277 237115910 633 True 752.000000 752 88.162000 1 636 1 chr5B.!!$R1 635
19 TraesCS7D01G160600 chr4D 354984633 354985266 633 True 774.000000 774 88.785000 1 636 1 chr4D.!!$R1 635
20 TraesCS7D01G160600 chr3B 85804122 85804755 633 True 664.000000 664 85.714000 4 639 1 chr3B.!!$R1 635

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
736 2339 1.202698 GCGATCCTTTGGCTAGGTGAT 60.203 52.381 6.21 0.0 36.63 3.06 F
1290 2939 0.175989 GTTCTTCTACGGGCTCCCTG 59.824 60.000 3.11 0.0 35.68 4.45 F
2501 4190 0.174845 TGGTACAATCTTCGGCCTCG 59.825 55.000 0.00 0.0 31.92 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2482 4171 0.174845 CGAGGCCGAAGATTGTACCA 59.825 55.000 0.00 0.0 38.22 3.25 R
2573 4262 0.536460 ACGGCGTTTTTGGTGAGGAT 60.536 50.000 6.77 0.0 0.00 3.24 R
3391 6030 2.028748 GCTTGGTTGGATGTTGCTTCAT 60.029 45.455 0.00 0.0 0.00 2.57 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
163 164 6.609212 TGCATAGATAGTCCCTCCTAATCATC 59.391 42.308 0.00 0.00 0.00 2.92
177 179 7.129109 TCCTAATCATCTTGTGTTCGTTTTC 57.871 36.000 0.00 0.00 0.00 2.29
291 305 8.871629 TTGGACTTAATAATTAGCAGTTCCAA 57.128 30.769 13.01 13.01 0.00 3.53
320 334 9.589111 TGATATACTGTGCGAAAACACTTATTA 57.411 29.630 0.00 0.00 41.30 0.98
451 2018 3.896648 TTTCTTCTTACCTTGCAAGCG 57.103 42.857 21.43 15.97 0.00 4.68
581 2159 1.692121 CCTCTCCTTGATCTGGCTCCT 60.692 57.143 0.00 0.00 0.00 3.69
607 2207 2.286523 CCGTCTTGCTGTCCCTCCT 61.287 63.158 0.00 0.00 0.00 3.69
608 2208 1.216710 CGTCTTGCTGTCCCTCCTC 59.783 63.158 0.00 0.00 0.00 3.71
705 2308 2.963782 AGTTGTTACGTGGAAGAGGAGT 59.036 45.455 0.00 0.00 0.00 3.85
706 2309 4.147321 AGTTGTTACGTGGAAGAGGAGTA 58.853 43.478 0.00 0.00 0.00 2.59
707 2310 4.217983 AGTTGTTACGTGGAAGAGGAGTAG 59.782 45.833 0.00 0.00 0.00 2.57
708 2311 2.490903 TGTTACGTGGAAGAGGAGTAGC 59.509 50.000 0.00 0.00 0.00 3.58
709 2312 2.754002 GTTACGTGGAAGAGGAGTAGCT 59.246 50.000 0.00 0.00 0.00 3.32
736 2339 1.202698 GCGATCCTTTGGCTAGGTGAT 60.203 52.381 6.21 0.00 36.63 3.06
790 2398 2.512515 GCACGGCCAGAGATGGAC 60.513 66.667 2.24 0.00 0.00 4.02
819 2427 2.158475 AGGTCTGCACCCAAATCAGAAA 60.158 45.455 0.74 0.00 45.12 2.52
852 2461 5.221661 ACCCTTAACAATATCCTCATCGGAC 60.222 44.000 0.00 0.00 46.80 4.79
1096 2720 0.413832 TGTGTAAGCCCTCTCCTCCT 59.586 55.000 0.00 0.00 0.00 3.69
1097 2721 1.116308 GTGTAAGCCCTCTCCTCCTC 58.884 60.000 0.00 0.00 0.00 3.71
1098 2722 1.011595 TGTAAGCCCTCTCCTCCTCT 58.988 55.000 0.00 0.00 0.00 3.69
1290 2939 0.175989 GTTCTTCTACGGGCTCCCTG 59.824 60.000 3.11 0.00 35.68 4.45
1507 3163 0.258484 CCCTAACCCATGCCATGTGA 59.742 55.000 3.63 0.00 0.00 3.58
1728 3396 1.317431 TGGATCGTCGACCCGTGATT 61.317 55.000 10.58 0.00 0.00 2.57
1986 3661 3.553917 CGTGCCAAAACCCTGTTAAAAAG 59.446 43.478 0.00 0.00 0.00 2.27
2375 4059 5.690409 CACGGTATGTACATAGACATTGGAC 59.310 44.000 15.93 3.62 40.54 4.02
2447 4136 4.503007 CGTGGTTCGATCTAACTGTTATGG 59.497 45.833 9.70 0.00 42.86 2.74
2482 4171 1.075748 GCAGATCCCCAATGCCCTT 60.076 57.895 0.00 0.00 33.81 3.95
2501 4190 0.174845 TGGTACAATCTTCGGCCTCG 59.825 55.000 0.00 0.00 31.92 4.63
2573 4262 2.981977 GAACGTCGAACTGCCCACCA 62.982 60.000 0.00 0.00 0.00 4.17
2639 4328 3.829886 TTGAGAAATAAGCTTGGCGTG 57.170 42.857 9.86 0.00 0.00 5.34
2937 4644 5.984926 CAGTGTGTGATGGCTTTGTTAATTT 59.015 36.000 0.00 0.00 0.00 1.82
3062 4783 1.880027 GAACCTGGTGTGAGCGAAAAT 59.120 47.619 0.00 0.00 0.00 1.82
3065 4786 1.879380 CCTGGTGTGAGCGAAAATGAA 59.121 47.619 0.00 0.00 0.00 2.57
3151 5102 1.271856 TCTTGCGGGGAAGTATGACA 58.728 50.000 0.00 0.00 0.00 3.58
3301 5927 9.103861 GAAAAATGAGTTGAGTATAGGAAGAGG 57.896 37.037 0.00 0.00 0.00 3.69
3320 5946 6.185114 AGAGGCATGCTCAAATTAGATAGT 57.815 37.500 18.92 0.00 0.00 2.12
3407 6046 3.005684 TCCAACATGAAGCAACATCCAAC 59.994 43.478 0.00 0.00 0.00 3.77
3608 6256 6.956202 TTTGTTAGGTTTTGTTCCCGAATA 57.044 33.333 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 5.216566 TCTTGACAGAAAACGAACACAAG 57.783 39.130 0.00 0.00 36.06 3.16
177 179 7.400301 CAGAAATTCGATCTGAATCTTGACAG 58.600 38.462 8.54 0.00 46.65 3.51
267 281 9.474313 AATTGGAACTGCTAATTATTAAGTCCA 57.526 29.630 4.17 4.17 36.11 4.02
288 302 7.008266 GTGTTTTCGCACAGTATATCAAATTGG 59.992 37.037 0.00 0.00 39.07 3.16
291 305 7.377766 AGTGTTTTCGCACAGTATATCAAAT 57.622 32.000 0.00 0.00 41.52 2.32
320 334 6.753913 TTACATGAAGCTAGATTCCTGGAT 57.246 37.500 23.89 11.07 31.41 3.41
451 2018 2.271800 CTACTGTCTTCATCCAACGGC 58.728 52.381 0.00 0.00 0.00 5.68
538 2116 1.228063 ATAAGGATGGCAGCGGCAG 60.228 57.895 11.88 0.00 42.43 4.85
581 2159 1.595109 CAGCAAGACGGCACTGTGA 60.595 57.895 12.86 0.00 35.83 3.58
607 2207 1.153568 CAAGATCGAGGCAAGCCGA 60.154 57.895 5.28 0.45 41.95 5.54
608 2208 2.817423 GCAAGATCGAGGCAAGCCG 61.817 63.158 5.28 0.00 41.95 5.52
705 2308 0.470080 AAGGATCGCCCAGCTAGCTA 60.470 55.000 18.86 0.83 37.41 3.32
706 2309 1.341156 AAAGGATCGCCCAGCTAGCT 61.341 55.000 12.68 12.68 37.41 3.32
707 2310 1.147153 AAAGGATCGCCCAGCTAGC 59.853 57.895 6.62 6.62 37.41 3.42
708 2311 0.533755 CCAAAGGATCGCCCAGCTAG 60.534 60.000 0.00 0.00 37.41 3.42
709 2312 1.526887 CCAAAGGATCGCCCAGCTA 59.473 57.895 0.00 0.00 37.41 3.32
736 2339 2.151202 GCCGTGTCAATTTCTTCCTCA 58.849 47.619 0.00 0.00 0.00 3.86
790 2398 1.207089 TGGGTGCAGACCTTATCGAAG 59.793 52.381 8.68 0.00 42.66 3.79
819 2427 2.463047 TTGTTAAGGGTGGCCAAACT 57.537 45.000 7.24 5.65 0.00 2.66
852 2461 2.017049 CTTCGCCTTCCCCAAGTTATG 58.983 52.381 0.00 0.00 0.00 1.90
1096 2720 4.101585 ATGAATACATTGCCGAGAGGAAGA 59.898 41.667 0.00 0.00 42.44 2.87
1097 2721 4.212847 CATGAATACATTGCCGAGAGGAAG 59.787 45.833 0.00 0.00 42.44 3.46
1098 2722 4.129380 CATGAATACATTGCCGAGAGGAA 58.871 43.478 0.00 0.00 44.55 3.36
1290 2939 2.668550 GCTGTTGGGGTGGACGAC 60.669 66.667 0.00 0.00 0.00 4.34
1507 3163 3.274586 CTGCACGCACAGCACAGT 61.275 61.111 0.00 0.00 37.02 3.55
1728 3396 8.623030 ACTAACAAGTTAAAGCGGTTATCAAAA 58.377 29.630 0.00 0.00 0.00 2.44
1866 3539 9.436957 AGGTGTACTACTTAACAAATTGAGATG 57.563 33.333 0.00 0.00 0.00 2.90
1986 3661 5.007724 AGGTGAACAACTCAATTCGAACTTC 59.992 40.000 0.00 0.00 35.22 3.01
2447 4136 5.449725 GGATCTGCACAGAATTTAAAGAGGC 60.450 44.000 4.14 0.00 41.36 4.70
2482 4171 0.174845 CGAGGCCGAAGATTGTACCA 59.825 55.000 0.00 0.00 38.22 3.25
2501 4190 0.671251 CCGTAGAGGATCAGCTGGAC 59.329 60.000 15.13 8.16 45.00 4.02
2573 4262 0.536460 ACGGCGTTTTTGGTGAGGAT 60.536 50.000 6.77 0.00 0.00 3.24
2639 4328 7.667557 ACTCAAAATCTTTAGGGCTAAAAACC 58.332 34.615 0.00 0.00 34.95 3.27
2730 4428 8.514594 CACAAAATTAAAGGCAATCTCAGACTA 58.485 33.333 0.00 0.00 0.00 2.59
2804 4507 9.745018 ATAACTCAGCTGCATTGGTATTTATAT 57.255 29.630 9.47 0.00 0.00 0.86
2805 4508 9.219603 GATAACTCAGCTGCATTGGTATTTATA 57.780 33.333 9.47 0.00 0.00 0.98
2806 4509 7.175641 GGATAACTCAGCTGCATTGGTATTTAT 59.824 37.037 9.47 0.43 0.00 1.40
2942 4656 5.013547 ACAAACACATCGGGGATATTGAAA 58.986 37.500 0.00 0.00 0.00 2.69
2953 4667 5.963004 CCGAAACATAATACAAACACATCGG 59.037 40.000 0.00 0.00 38.92 4.18
3011 4729 3.099141 CACCAATAAGATGCCCTTTGGT 58.901 45.455 0.00 0.00 43.37 3.67
3062 4783 7.385752 CGGTAATTAGGTTAAGTCTGTGTTTCA 59.614 37.037 0.00 0.00 0.00 2.69
3065 4786 6.168389 CCGGTAATTAGGTTAAGTCTGTGTT 58.832 40.000 0.00 0.00 0.00 3.32
3133 5072 1.066143 AGTGTCATACTTCCCCGCAAG 60.066 52.381 0.00 0.00 35.67 4.01
3151 5102 8.814038 AAATATTTCTAGCATGGACTCAAAGT 57.186 30.769 0.00 0.00 0.00 2.66
3301 5927 5.049129 GGTGGACTATCTAATTTGAGCATGC 60.049 44.000 10.51 10.51 0.00 4.06
3344 5970 5.536497 AATGGAAAGGTCTGGGTTCTTAT 57.464 39.130 0.00 0.00 0.00 1.73
3391 6030 2.028748 GCTTGGTTGGATGTTGCTTCAT 60.029 45.455 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.