Multiple sequence alignment - TraesCS7B01G400500

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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 TraesCS7B01G400500 chr7B 100.000 3967 0 0 1 3967 666686396 666682430 0.000000e+00 7326
1 TraesCS7B01G400500 chr7B 86.757 808 98 6 990 1788 677115616 677114809 0.000000e+00 891
2 TraesCS7B01G400500 chr7B 79.571 1165 160 46 1846 2970 677114687 677113561 0.000000e+00 761
3 TraesCS7B01G400500 chr7D 93.859 3159 156 22 1 3130 594985782 594988931 0.000000e+00 4724
4 TraesCS7B01G400500 chr7D 83.293 2083 229 71 967 2971 591806113 591804072 0.000000e+00 1808
5 TraesCS7B01G400500 chr7D 87.624 808 91 5 990 1788 598253130 598252323 0.000000e+00 929
6 TraesCS7B01G400500 chr7D 80.390 1178 148 48 1827 2970 598252217 598251089 0.000000e+00 819
7 TraesCS7B01G400500 chr7A 93.163 2618 135 19 529 3133 687952667 687955253 0.000000e+00 3803
8 TraesCS7B01G400500 chr7A 83.972 2034 210 66 989 2971 682892304 682890336 0.000000e+00 1844
9 TraesCS7B01G400500 chr7A 82.447 2011 262 53 990 2970 690532246 690534195 0.000000e+00 1674
10 TraesCS7B01G400500 chr7A 93.822 518 26 3 1 518 687951495 687952006 0.000000e+00 774
11 TraesCS7B01G400500 chr7A 85.644 202 24 4 323 523 687952095 687952292 1.440000e-49 207
12 TraesCS7B01G400500 chr7A 95.506 89 4 0 589 677 687952006 687952094 4.130000e-30 143
13 TraesCS7B01G400500 chr6A 97.002 834 24 1 3132 3964 73296232 73297065 0.000000e+00 1400
14 TraesCS7B01G400500 chr6A 94.139 836 48 1 3132 3967 77085037 77085871 0.000000e+00 1271
15 TraesCS7B01G400500 chr6A 92.773 844 60 1 3124 3967 34552637 34551795 0.000000e+00 1219
16 TraesCS7B01G400500 chr5B 96.651 836 28 0 3132 3967 576053570 576052735 0.000000e+00 1389
17 TraesCS7B01G400500 chr5B 86.442 1158 126 23 992 2123 584096528 584095376 0.000000e+00 1240
18 TraesCS7B01G400500 chr5B 90.528 834 76 3 3132 3964 31441217 31442048 0.000000e+00 1099
19 TraesCS7B01G400500 chr5B 96.916 616 19 0 3349 3964 707424835 707425450 0.000000e+00 1033
20 TraesCS7B01G400500 chr5B 88.189 254 27 3 2191 2443 584094842 584094591 2.320000e-77 300
21 TraesCS7B01G400500 chr4A 92.754 828 55 3 3138 3964 575691106 575691929 0.000000e+00 1192
22 TraesCS7B01G400500 chr5D 86.442 1099 122 20 1036 2118 476674009 476672922 0.000000e+00 1179
23 TraesCS7B01G400500 chr5D 77.187 846 123 41 2179 2975 476672812 476671988 2.830000e-116 429
24 TraesCS7B01G400500 chr4D 93.886 687 41 1 3281 3967 27578639 27577954 0.000000e+00 1035
25 TraesCS7B01G400500 chr4D 91.655 719 57 3 3129 3845 41918622 41917905 0.000000e+00 992
26 TraesCS7B01G400500 chr2A 97.568 329 7 1 3132 3460 699611967 699612294 2.680000e-156 562


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 TraesCS7B01G400500 chr7B 666682430 666686396 3966 True 7326.00 7326 100.00000 1 3967 1 chr7B.!!$R1 3966
1 TraesCS7B01G400500 chr7B 677113561 677115616 2055 True 826.00 891 83.16400 990 2970 2 chr7B.!!$R2 1980
2 TraesCS7B01G400500 chr7D 594985782 594988931 3149 False 4724.00 4724 93.85900 1 3130 1 chr7D.!!$F1 3129
3 TraesCS7B01G400500 chr7D 591804072 591806113 2041 True 1808.00 1808 83.29300 967 2971 1 chr7D.!!$R1 2004
4 TraesCS7B01G400500 chr7D 598251089 598253130 2041 True 874.00 929 84.00700 990 2970 2 chr7D.!!$R2 1980
5 TraesCS7B01G400500 chr7A 682890336 682892304 1968 True 1844.00 1844 83.97200 989 2971 1 chr7A.!!$R1 1982
6 TraesCS7B01G400500 chr7A 690532246 690534195 1949 False 1674.00 1674 82.44700 990 2970 1 chr7A.!!$F1 1980
7 TraesCS7B01G400500 chr7A 687951495 687955253 3758 False 1231.75 3803 92.03375 1 3133 4 chr7A.!!$F2 3132
8 TraesCS7B01G400500 chr6A 73296232 73297065 833 False 1400.00 1400 97.00200 3132 3964 1 chr6A.!!$F1 832
9 TraesCS7B01G400500 chr6A 77085037 77085871 834 False 1271.00 1271 94.13900 3132 3967 1 chr6A.!!$F2 835
10 TraesCS7B01G400500 chr6A 34551795 34552637 842 True 1219.00 1219 92.77300 3124 3967 1 chr6A.!!$R1 843
11 TraesCS7B01G400500 chr5B 576052735 576053570 835 True 1389.00 1389 96.65100 3132 3967 1 chr5B.!!$R1 835
12 TraesCS7B01G400500 chr5B 31441217 31442048 831 False 1099.00 1099 90.52800 3132 3964 1 chr5B.!!$F1 832
13 TraesCS7B01G400500 chr5B 707424835 707425450 615 False 1033.00 1033 96.91600 3349 3964 1 chr5B.!!$F2 615
14 TraesCS7B01G400500 chr5B 584094591 584096528 1937 True 770.00 1240 87.31550 992 2443 2 chr5B.!!$R2 1451
15 TraesCS7B01G400500 chr4A 575691106 575691929 823 False 1192.00 1192 92.75400 3138 3964 1 chr4A.!!$F1 826
16 TraesCS7B01G400500 chr5D 476671988 476674009 2021 True 804.00 1179 81.81450 1036 2975 2 chr5D.!!$R1 1939
17 TraesCS7B01G400500 chr4D 27577954 27578639 685 True 1035.00 1035 93.88600 3281 3967 1 chr4D.!!$R1 686
18 TraesCS7B01G400500 chr4D 41917905 41918622 717 True 992.00 992 91.65500 3129 3845 1 chr4D.!!$R2 716

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
26 27 0.322456 TTTGGGCCACTCAATCCTCG 60.322 55.0 5.23 0.0 0.00 4.63 F
784 1446 0.787908 CGTGCGTAAACATCGTTGCC 60.788 55.0 0.00 0.0 0.00 4.52 F
1641 2314 1.693627 CCACCGCAGTATCCTACTCT 58.306 55.0 0.00 0.0 36.76 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 2314 0.112218 ACAGTATGGCCAGGTTTGCA 59.888 50.0 13.05 0.00 43.62 4.08 R
2119 2916 0.179150 TTTGTTTGTGGAGTGCACGC 60.179 50.0 12.67 12.67 0.00 5.34 R
3495 4902 0.037139 TTTAAGAAGCGGCTACGGCA 60.037 50.0 1.35 0.00 41.36 5.69 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
26 27 0.322456 TTTGGGCCACTCAATCCTCG 60.322 55.000 5.23 0.00 0.00 4.63
66 67 4.301637 TCGCATCATCTAACGCTCTAAA 57.698 40.909 0.00 0.00 0.00 1.85
139 140 3.494251 GCAATGCAAAACCGTTCTCATTT 59.506 39.130 0.00 0.00 0.00 2.32
268 269 4.360563 ACGTTCTTATTGTGCCTAGATCG 58.639 43.478 0.00 0.00 36.45 3.69
479 485 1.418342 GCGCGCGAGATTACTTCCAA 61.418 55.000 37.18 0.00 0.00 3.53
497 503 4.583871 TCCAATATGTGTGTGTATGTGCA 58.416 39.130 0.00 0.00 0.00 4.57
506 512 3.566322 TGTGTGTATGTGCAAGGTTTACC 59.434 43.478 0.00 0.00 0.00 2.85
527 1183 3.365364 CCAGTCCTTTGTTTCGATCTTGC 60.365 47.826 0.00 0.00 0.00 4.01
576 1232 5.974751 TCAGGCACGTTTATTGAAAAAGAAC 59.025 36.000 0.00 0.00 0.00 3.01
669 1325 5.048504 CCAAGTAGCATTTCATGTTGTCTGT 60.049 40.000 0.00 0.00 0.00 3.41
743 1399 3.754850 TCTCACTGTCATCCAAGCAATTG 59.245 43.478 0.00 0.00 0.00 2.32
751 1407 4.096382 GTCATCCAAGCAATTGTAACCGAT 59.904 41.667 7.40 0.00 0.00 4.18
752 1408 4.096231 TCATCCAAGCAATTGTAACCGATG 59.904 41.667 7.40 11.50 0.00 3.84
753 1409 3.417101 TCCAAGCAATTGTAACCGATGT 58.583 40.909 7.40 0.00 0.00 3.06
778 1440 2.735134 ACTTTCCTCGTGCGTAAACATC 59.265 45.455 0.00 0.00 0.00 3.06
784 1446 0.787908 CGTGCGTAAACATCGTTGCC 60.788 55.000 0.00 0.00 0.00 4.52
855 1517 9.277565 CACGACCACTGAAAATTTTATAATCTG 57.722 33.333 2.75 0.00 0.00 2.90
1641 2314 1.693627 CCACCGCAGTATCCTACTCT 58.306 55.000 0.00 0.00 36.76 3.24
1786 2467 3.068590 GGCCATGATGGTTTGGTAAGATG 59.931 47.826 13.84 0.00 40.46 2.90
2128 2951 2.650163 CGTAAGGTAGCGTGCACTC 58.350 57.895 16.19 7.07 0.00 3.51
2141 2966 3.793801 GCGTGCACTCCACAAACAAAATA 60.794 43.478 16.19 0.00 44.91 1.40
2177 3025 1.347707 AGTGGTCTCGCTGATTTTCCA 59.652 47.619 0.00 0.00 31.64 3.53
2299 3594 0.537143 TGTTTGCCGGCTCAGTGATT 60.537 50.000 29.70 0.00 0.00 2.57
2517 3843 6.148976 AGTGACATGATCTTTGTCTGAACATG 59.851 38.462 21.89 10.82 44.68 3.21
2650 3980 2.543653 GCATTTGAACGGGATGGTATGC 60.544 50.000 0.00 0.00 0.00 3.14
2784 4153 1.869767 CAGTCTCACCAAGCTTGTGTC 59.130 52.381 24.35 15.27 0.00 3.67
2791 4160 0.445436 CCAAGCTTGTGTCGCTCATC 59.555 55.000 24.35 0.00 36.56 2.92
2931 4335 7.982761 TTGAATCAGGCAATTAAAGCAAAAT 57.017 28.000 5.74 0.00 0.00 1.82
2994 4398 3.494850 CCTATGGCGGGAACATTGT 57.505 52.632 0.00 0.00 0.00 2.71
3000 4404 4.817318 ATGGCGGGAACATTGTATTTTT 57.183 36.364 0.00 0.00 0.00 1.94
3026 4430 1.408422 GGTCAAACATGCAAGCGAAC 58.592 50.000 0.00 0.00 0.00 3.95
3368 4774 4.506654 GCATTCTTCATAAATTGCTGCTGG 59.493 41.667 0.00 0.00 0.00 4.85
3512 4919 1.141019 CTGCCGTAGCCGCTTCTTA 59.859 57.895 0.00 0.00 38.69 2.10
3580 4987 2.950309 TGGTCTCGAAGTATAGCACCTC 59.050 50.000 0.00 0.00 0.00 3.85
3615 5022 1.001487 CTGGCAATGTCGAAACTTGCA 60.001 47.619 21.92 11.84 45.44 4.08
3678 5085 4.574013 CAGCCATGTCTCCTAATTCTGTTC 59.426 45.833 0.00 0.00 0.00 3.18
3730 5137 1.303309 GAGTGCCGATATTGCTTGCT 58.697 50.000 0.00 0.00 0.00 3.91
3731 5138 1.672881 GAGTGCCGATATTGCTTGCTT 59.327 47.619 0.00 0.00 0.00 3.91
3747 5154 0.391661 GCTTCGATCTGGTTGGCTCA 60.392 55.000 0.00 0.00 0.00 4.26
3867 5275 9.793259 AATGACTTAGTTGGATTCTTAGACAAA 57.207 29.630 0.00 0.00 0.00 2.83
3915 5323 1.142667 TCTCTTTCCACCATGCACACA 59.857 47.619 0.00 0.00 0.00 3.72
3946 5354 1.597742 CGCTGCCATACCTAGCAAAT 58.402 50.000 0.00 0.00 38.82 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.122330 TGATGCGATTGACAATTGTAGTAAATC 58.878 33.333 11.95 15.72 0.00 2.17
93 94 2.416836 CGGTCTTTATGCACGAGGAGAA 60.417 50.000 0.00 0.00 0.00 2.87
129 130 5.457799 ACCGATGATTACGTAAATGAGAACG 59.542 40.000 12.81 11.16 44.47 3.95
139 140 5.775686 CCCTATTGAACCGATGATTACGTA 58.224 41.667 0.00 0.00 0.00 3.57
242 243 4.927425 TCTAGGCACAATAAGAACGTTGAC 59.073 41.667 5.00 0.00 0.00 3.18
268 269 6.256539 TCATTGAGAAAGTTCAGCATCGATAC 59.743 38.462 0.00 0.00 0.00 2.24
341 342 3.876914 GGCCAAACGATATGATGACTTCA 59.123 43.478 0.00 0.00 39.12 3.02
404 410 5.466728 GGTTTTGCCTTCATTTTTCCTCTTC 59.533 40.000 0.00 0.00 0.00 2.87
405 411 5.368145 GGTTTTGCCTTCATTTTTCCTCTT 58.632 37.500 0.00 0.00 0.00 2.85
465 471 6.535150 ACACACACATATTGGAAGTAATCTCG 59.465 38.462 0.00 0.00 0.00 4.04
466 472 7.849804 ACACACACATATTGGAAGTAATCTC 57.150 36.000 0.00 0.00 0.00 2.75
479 485 4.588899 ACCTTGCACATACACACACATAT 58.411 39.130 0.00 0.00 0.00 1.78
497 503 4.337274 CGAAACAAAGGACTGGTAAACCTT 59.663 41.667 0.02 0.00 44.53 3.50
506 512 3.365364 GGCAAGATCGAAACAAAGGACTG 60.365 47.826 0.00 0.00 0.00 3.51
527 1183 4.576463 AGCACGCCTTTTTCATTAGATAGG 59.424 41.667 0.00 0.00 0.00 2.57
576 1232 3.742433 ACCAGCGGATAGAGATTTGAG 57.258 47.619 1.50 0.00 0.00 3.02
584 1240 2.706890 GTTCCAAAACCAGCGGATAGA 58.293 47.619 1.50 0.00 0.00 1.98
669 1325 0.670546 GCGAGTAGTCCAAGCAGCAA 60.671 55.000 0.00 0.00 0.00 3.91
695 1351 7.772166 TGATGTGACTGATAAGTAGTAAGTGG 58.228 38.462 0.00 0.00 0.00 4.00
778 1440 4.020378 CGTTGGTTCGGGGCAACG 62.020 66.667 0.00 0.00 43.01 4.10
784 1446 1.635663 GCATCAGACGTTGGTTCGGG 61.636 60.000 0.00 0.00 34.94 5.14
855 1517 5.728255 CGTAGCAGATTACTATGTTTGCAC 58.272 41.667 0.00 0.00 34.17 4.57
985 1648 4.630644 TCTCCATTCTTGTCAGCTTCTT 57.369 40.909 0.00 0.00 0.00 2.52
986 1649 4.577875 CTTCTCCATTCTTGTCAGCTTCT 58.422 43.478 0.00 0.00 0.00 2.85
1038 1708 1.368969 CGTATTCTCGTCCCGCTCG 60.369 63.158 0.00 0.00 0.00 5.03
1348 2021 3.234730 GACGAGGGCGATGGGGAT 61.235 66.667 0.00 0.00 41.64 3.85
1641 2314 0.112218 ACAGTATGGCCAGGTTTGCA 59.888 50.000 13.05 0.00 43.62 4.08
1786 2467 5.308825 TCAGGAGAACTTGTTGAGGATTTC 58.691 41.667 0.00 0.00 0.00 2.17
1866 2616 3.816523 CACCATTCCAAGCTGCAAATTTT 59.183 39.130 1.02 0.00 0.00 1.82
2119 2916 0.179150 TTTGTTTGTGGAGTGCACGC 60.179 50.000 12.67 12.67 0.00 5.34
2141 2966 6.262049 CGAGACCACTCAGCATATATAGCTAT 59.738 42.308 11.77 11.77 41.14 2.97
2189 3480 4.563976 GGAAACGCGTGTACTGTATTGTAT 59.436 41.667 14.98 0.00 0.00 2.29
2191 3482 2.733026 GGAAACGCGTGTACTGTATTGT 59.267 45.455 14.98 0.00 0.00 2.71
2299 3594 5.294306 GCGTAGAGAAATCATTGTGATGGAA 59.706 40.000 0.00 0.00 37.15 3.53
2517 3843 3.384789 TCCATAGAGCACACCTGTATGTC 59.615 47.826 6.70 0.00 43.02 3.06
2650 3980 5.839262 TTAAAGTTCGTGCTGACATAGTG 57.161 39.130 0.00 0.00 0.00 2.74
2931 4335 6.098409 GGAAGAGAAGATCCTAACACCATGTA 59.902 42.308 0.00 0.00 32.75 2.29
3000 4404 0.957362 TGCATGTTTGACCGCATCAA 59.043 45.000 0.00 0.00 45.92 2.57
3026 4430 7.582435 AGCTATGTATATCGATTTGTTTCCG 57.418 36.000 1.71 0.00 0.00 4.30
3368 4774 1.468914 GAGGAAATTCGCTTGGACCAC 59.531 52.381 0.00 0.00 0.00 4.16
3495 4902 0.037139 TTTAAGAAGCGGCTACGGCA 60.037 50.000 1.35 0.00 41.36 5.69
3512 4919 4.888326 TGCAGCAATATCCCTTTTGTTT 57.112 36.364 0.00 0.00 0.00 2.83
3580 4987 2.816958 CAGTGGCACTGGCGCTAG 60.817 66.667 34.59 20.26 46.89 3.42
3678 5085 3.188048 ACTCAAGAGCGAAATTCAAGCAG 59.812 43.478 0.00 0.00 0.00 4.24
3730 5137 2.499693 TGTATGAGCCAACCAGATCGAA 59.500 45.455 0.00 0.00 0.00 3.71
3731 5138 2.101415 CTGTATGAGCCAACCAGATCGA 59.899 50.000 0.00 0.00 0.00 3.59
3747 5154 1.014044 CACACGGCGAGCAACTGTAT 61.014 55.000 16.62 0.00 0.00 2.29
3867 5275 1.903877 CGGTGATGGCTGACCTCCTT 61.904 60.000 0.00 0.00 36.63 3.36
3915 5323 1.750399 GGCAGCGGTGGTGAATGAT 60.750 57.895 17.54 0.00 32.22 2.45
3946 5354 0.396435 CAAGTACAGGAGGTGTGGCA 59.604 55.000 0.00 0.00 40.69 4.92


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

AutoCloner maintained by Alex Coulton.