Multiple sequence alignment - TraesCS7B01G100300

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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 TraesCS7B01G100300 chr7B 100.000 3579 0 0 1 3579 114938022 114941600 0.000000e+00 6610
1 TraesCS7B01G100300 chr7B 81.615 2328 364 40 554 2835 107821452 107823761 0.000000e+00 1869
2 TraesCS7B01G100300 chr7B 78.777 278 39 13 2364 2627 59179244 59178973 6.150000e-38 169
3 TraesCS7B01G100300 chr7D 93.821 3593 190 19 1 3579 152946459 152950033 0.000000e+00 5376
4 TraesCS7B01G100300 chr7D 82.446 1897 299 20 554 2425 143976361 143974474 0.000000e+00 1628
5 TraesCS7B01G100300 chr7D 79.328 387 50 17 2355 2722 101797803 101797428 9.930000e-61 244
6 TraesCS7B01G100300 chr7A 93.990 1847 99 4 590 2425 154062288 154064133 0.000000e+00 2785
7 TraesCS7B01G100300 chr7A 80.712 2333 385 47 554 2838 146024849 146027164 0.000000e+00 1755
8 TraesCS7B01G100300 chr7A 92.029 552 33 2 1 552 154061760 154062300 0.000000e+00 765
9 TraesCS7B01G100300 chr7A 91.339 508 39 3 3075 3579 154091214 154091719 0.000000e+00 689
10 TraesCS7B01G100300 chr7A 90.289 484 40 4 2475 2953 154064130 154064611 8.440000e-176 627
11 TraesCS7B01G100300 chrUn 79.530 2384 389 64 306 2621 29901757 29899405 0.000000e+00 1607
12 TraesCS7B01G100300 chrUn 81.129 1187 202 18 816 1990 29882697 29881521 0.000000e+00 931
13 TraesCS7B01G100300 chrUn 80.960 1187 204 18 816 1990 29884107 29882931 0.000000e+00 920
14 TraesCS7B01G100300 chr5A 79.892 2223 384 51 443 2621 706407154 706404951 0.000000e+00 1570
15 TraesCS7B01G100300 chr2D 81.855 744 128 7 2834 3573 506768990 506769730 1.410000e-173 619
16 TraesCS7B01G100300 chr2D 79.333 750 144 10 2835 3579 94198986 94198243 1.910000e-142 516
17 TraesCS7B01G100300 chr2A 81.994 722 126 4 2860 3579 553428698 553429417 8.500000e-171 610
18 TraesCS7B01G100300 chr2A 79.518 747 148 5 2835 3579 357176579 357175836 8.800000e-146 527
19 TraesCS7B01G100300 chr4D 81.342 745 127 8 2835 3576 338843536 338842801 2.380000e-166 595
20 TraesCS7B01G100300 chr4B 80.671 745 137 7 2835 3576 99494019 99493279 4.010000e-159 571
21 TraesCS7B01G100300 chr1A 80.000 745 131 16 2835 3571 328072900 328073634 5.260000e-148 534
22 TraesCS7B01G100300 chr3B 76.122 557 107 18 2158 2697 61896188 61895641 5.890000e-68 268
23 TraesCS7B01G100300 chr3D 75.510 245 58 1 2158 2400 39032182 39031938 6.280000e-23 119


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 TraesCS7B01G100300 chr7B 114938022 114941600 3578 False 6610.000000 6610 100.000000 1 3579 1 chr7B.!!$F2 3578
1 TraesCS7B01G100300 chr7B 107821452 107823761 2309 False 1869.000000 1869 81.615000 554 2835 1 chr7B.!!$F1 2281
2 TraesCS7B01G100300 chr7D 152946459 152950033 3574 False 5376.000000 5376 93.821000 1 3579 1 chr7D.!!$F1 3578
3 TraesCS7B01G100300 chr7D 143974474 143976361 1887 True 1628.000000 1628 82.446000 554 2425 1 chr7D.!!$R2 1871
4 TraesCS7B01G100300 chr7A 146024849 146027164 2315 False 1755.000000 1755 80.712000 554 2838 1 chr7A.!!$F1 2284
5 TraesCS7B01G100300 chr7A 154061760 154064611 2851 False 1392.333333 2785 92.102667 1 2953 3 chr7A.!!$F3 2952
6 TraesCS7B01G100300 chr7A 154091214 154091719 505 False 689.000000 689 91.339000 3075 3579 1 chr7A.!!$F2 504
7 TraesCS7B01G100300 chrUn 29899405 29901757 2352 True 1607.000000 1607 79.530000 306 2621 1 chrUn.!!$R1 2315
8 TraesCS7B01G100300 chrUn 29881521 29884107 2586 True 925.500000 931 81.044500 816 1990 2 chrUn.!!$R2 1174
9 TraesCS7B01G100300 chr5A 706404951 706407154 2203 True 1570.000000 1570 79.892000 443 2621 1 chr5A.!!$R1 2178
10 TraesCS7B01G100300 chr2D 506768990 506769730 740 False 619.000000 619 81.855000 2834 3573 1 chr2D.!!$F1 739
11 TraesCS7B01G100300 chr2D 94198243 94198986 743 True 516.000000 516 79.333000 2835 3579 1 chr2D.!!$R1 744
12 TraesCS7B01G100300 chr2A 553428698 553429417 719 False 610.000000 610 81.994000 2860 3579 1 chr2A.!!$F1 719
13 TraesCS7B01G100300 chr2A 357175836 357176579 743 True 527.000000 527 79.518000 2835 3579 1 chr2A.!!$R1 744
14 TraesCS7B01G100300 chr4D 338842801 338843536 735 True 595.000000 595 81.342000 2835 3576 1 chr4D.!!$R1 741
15 TraesCS7B01G100300 chr4B 99493279 99494019 740 True 571.000000 571 80.671000 2835 3576 1 chr4B.!!$R1 741
16 TraesCS7B01G100300 chr1A 328072900 328073634 734 False 534.000000 534 80.000000 2835 3571 1 chr1A.!!$F1 736
17 TraesCS7B01G100300 chr3B 61895641 61896188 547 True 268.000000 268 76.122000 2158 2697 1 chr3B.!!$R1 539

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
175 176 0.179000 AGATTGGTCGATCCTGGCAC 59.821 55.000 0.0 0.0 37.07 5.01 F
1201 1237 1.149854 AGGTTTCACCCAACGGACC 59.850 57.895 0.0 0.0 39.75 4.46 F
2271 3724 0.953727 CAACATGGGTATGGATGGCG 59.046 55.000 0.0 0.0 38.66 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 3224 0.679505 TCACCACCTTCTTCAGTCCG 59.320 55.000 0.00 0.0 0.0 4.79 R
2429 3883 1.345063 AAGAAAGCCAAGCAAGCCAT 58.655 45.000 0.00 0.0 0.0 4.40 R
3101 4601 1.885887 GGCATGCCTGTTGTTTCTGTA 59.114 47.619 29.98 0.0 0.0 2.74 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
69 70 2.597995 ACAAAACGCCCCCTTTTGT 58.402 47.368 7.72 7.72 43.72 2.83
108 109 2.187685 CACGCATAGCTGGAGGCA 59.812 61.111 0.00 0.00 44.79 4.75
175 176 0.179000 AGATTGGTCGATCCTGGCAC 59.821 55.000 0.00 0.00 37.07 5.01
318 319 5.755375 CACAGAGTGCAAATTATACCGATCT 59.245 40.000 0.00 0.00 0.00 2.75
347 348 2.905075 CATGCGGGAATTCAGTAGTGA 58.095 47.619 7.93 0.00 0.00 3.41
404 406 3.133721 CCAAAGGTGTTGTTTTCATGGGA 59.866 43.478 0.00 0.00 0.00 4.37
413 415 5.887598 TGTTGTTTTCATGGGAGGATAGATG 59.112 40.000 0.00 0.00 0.00 2.90
414 416 5.974156 TGTTTTCATGGGAGGATAGATGA 57.026 39.130 0.00 0.00 0.00 2.92
415 417 5.933617 TGTTTTCATGGGAGGATAGATGAG 58.066 41.667 0.00 0.00 0.00 2.90
416 418 5.667172 TGTTTTCATGGGAGGATAGATGAGA 59.333 40.000 0.00 0.00 0.00 3.27
417 419 6.183361 TGTTTTCATGGGAGGATAGATGAGAG 60.183 42.308 0.00 0.00 0.00 3.20
418 420 5.345307 TTCATGGGAGGATAGATGAGAGA 57.655 43.478 0.00 0.00 0.00 3.10
456 458 8.481314 AGATGTGATTGTTACTGACACTCATAT 58.519 33.333 7.94 7.94 45.82 1.78
484 487 6.070656 CCACCTTGTACCCATCATATTGAAT 58.929 40.000 0.00 0.00 0.00 2.57
664 679 6.852404 AGGGTGGAATGCATACATAGTAAAT 58.148 36.000 0.00 0.00 34.62 1.40
770 793 5.923684 TGACAAGAAACCAAAAGTGTTCAAC 59.076 36.000 0.00 0.00 0.00 3.18
788 811 2.811431 CAACCTGGCATGACGTTTCTTA 59.189 45.455 0.00 0.00 0.00 2.10
824 847 4.200447 ACCTAGCACCTATCACCACTAT 57.800 45.455 0.00 0.00 0.00 2.12
922 953 4.816392 TCGTATACATCCATCCATTTCCG 58.184 43.478 3.32 0.00 0.00 4.30
949 981 5.610398 AGAACAAATTAAACAAAGCCCCAG 58.390 37.500 0.00 0.00 0.00 4.45
1019 1051 2.698797 TCCTATTTAAGCACCTCCCTCG 59.301 50.000 0.00 0.00 0.00 4.63
1069 1101 8.004801 TCCTTCCATACATACAGACATCTCTAA 58.995 37.037 0.00 0.00 0.00 2.10
1076 1108 7.993821 ACATACAGACATCTCTAACATTTCG 57.006 36.000 0.00 0.00 0.00 3.46
1097 1130 1.357761 CCCCAATACTTGTTCCACCCT 59.642 52.381 0.00 0.00 0.00 4.34
1201 1237 1.149854 AGGTTTCACCCAACGGACC 59.850 57.895 0.00 0.00 39.75 4.46
1441 2887 4.006319 CACTGGAAAGGACAAGGAGATTC 58.994 47.826 0.00 0.00 0.00 2.52
1778 3224 5.918608 TGTAGAATCTTCCATAAGAGCACC 58.081 41.667 0.00 0.00 44.79 5.01
1798 3246 1.605712 CGGACTGAAGAAGGTGGTGAC 60.606 57.143 0.00 0.00 0.00 3.67
1814 3262 3.214328 GGTGACGCCTTCATATTCCATT 58.786 45.455 0.00 0.00 36.32 3.16
2249 3700 2.045561 TCTCCAGTGAGATCTCGTCC 57.954 55.000 17.76 8.30 42.73 4.79
2271 3724 0.953727 CAACATGGGTATGGATGGCG 59.046 55.000 0.00 0.00 38.66 5.69
2347 3800 6.767456 TGCACAAAATAATCTTCCACCAAAT 58.233 32.000 0.00 0.00 0.00 2.32
2429 3883 4.065088 GTCACAGGAGAGTTTGTATGCAA 58.935 43.478 0.00 0.00 0.00 4.08
2533 4006 4.766891 ACCTAGCTACATTTGCATGTGTTT 59.233 37.500 9.42 0.97 43.92 2.83
2547 4020 8.508800 TTGCATGTGTTTTTAAATACCTAACG 57.491 30.769 6.36 0.00 0.00 3.18
2671 4164 1.334869 GGAGTAGAATTTGGGCATGCG 59.665 52.381 12.44 0.00 0.00 4.73
2687 4180 0.681733 TGCGCCAATCTAGAGGGATC 59.318 55.000 15.57 7.50 0.00 3.36
2809 4303 4.807304 GTGGCTTTGATGATAAATGGCAAG 59.193 41.667 6.28 0.00 31.04 4.01
2924 4423 9.470399 TCTTACCACACAATACTTCTACATCTA 57.530 33.333 0.00 0.00 0.00 1.98
2940 4439 3.993081 ACATCTATAGCAATCTGAAGCGC 59.007 43.478 0.00 0.00 35.48 5.92
3080 4580 6.464222 AGTACCGATATCACATAAACCATGG 58.536 40.000 11.19 11.19 39.13 3.66
3087 4587 9.051679 CGATATCACATAAACCATGGTAGAAAA 57.948 33.333 20.12 2.27 39.13 2.29
3101 4601 6.200878 TGGTAGAAAAGACCTCCAATCTTT 57.799 37.500 0.00 0.00 46.07 2.52
3484 4992 9.283768 GGATGGAATTTAAACCACTTCAATTTT 57.716 29.630 0.00 0.00 39.06 1.82
3543 5052 9.757227 AAATGTAGCTACTATCTCAGAATCAAC 57.243 33.333 23.84 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 2.806745 GCTATGTGCTTATCTTGCGGGA 60.807 50.000 0.00 0.00 38.95 5.14
158 159 1.153369 CGTGCCAGGATCGACCAAT 60.153 57.895 0.00 0.00 42.04 3.16
175 176 5.461078 GTGTATTGGTGTAGGTAAGTATGCG 59.539 44.000 0.00 0.00 0.00 4.73
347 348 1.070289 GGTAAGGGCGCTAGTGCTAAT 59.930 52.381 26.36 15.04 36.97 1.73
404 406 6.326161 TCTCTCTCTCTCTCTCATCTATCCT 58.674 44.000 0.00 0.00 0.00 3.24
413 415 5.069648 TCACATCTCTCTCTCTCTCTCTCTC 59.930 48.000 0.00 0.00 0.00 3.20
414 416 4.964897 TCACATCTCTCTCTCTCTCTCTCT 59.035 45.833 0.00 0.00 0.00 3.10
415 417 5.282055 TCACATCTCTCTCTCTCTCTCTC 57.718 47.826 0.00 0.00 0.00 3.20
416 418 5.901413 ATCACATCTCTCTCTCTCTCTCT 57.099 43.478 0.00 0.00 0.00 3.10
417 419 5.824624 ACAATCACATCTCTCTCTCTCTCTC 59.175 44.000 0.00 0.00 0.00 3.20
418 420 5.759059 ACAATCACATCTCTCTCTCTCTCT 58.241 41.667 0.00 0.00 0.00 3.10
456 458 0.037590 GATGGGTACAAGGTGGTGCA 59.962 55.000 0.00 0.00 0.00 4.57
484 487 4.166725 ACAAGGAGATGGCTTTGATGGATA 59.833 41.667 0.00 0.00 0.00 2.59
562 567 8.621532 TTCCATCCTATGCAATCATAAACTAC 57.378 34.615 0.00 0.00 34.97 2.73
573 578 7.293828 TGGTTTACATATTCCATCCTATGCAA 58.706 34.615 0.00 0.00 0.00 4.08
664 679 5.162794 GTGATGCAAAGCAAACATATGTCA 58.837 37.500 9.23 0.26 43.62 3.58
770 793 2.972625 TCTAAGAAACGTCATGCCAGG 58.027 47.619 0.00 0.00 0.00 4.45
919 950 6.919115 GCTTTGTTTAATTTGTTCTTACCGGA 59.081 34.615 9.46 0.00 0.00 5.14
922 953 6.425721 GGGGCTTTGTTTAATTTGTTCTTACC 59.574 38.462 0.00 0.00 0.00 2.85
949 981 0.519077 CAGAGAAGCCTTGGCGTTTC 59.481 55.000 9.40 9.40 0.00 2.78
1041 1073 7.345653 AGAGATGTCTGTATGTATGGAAGGAAA 59.654 37.037 0.00 0.00 0.00 3.13
1097 1130 4.042934 AGGCTCTTTCTTAAAAGGGTGCTA 59.957 41.667 0.22 0.00 43.71 3.49
1201 1237 5.365021 AGGTAGAAGGTGATGATTTCCAG 57.635 43.478 0.00 0.00 0.00 3.86
1317 2763 3.736227 TGGTCCTTCTCCCCCATATTA 57.264 47.619 0.00 0.00 0.00 0.98
1441 2887 4.838152 CATGGTCGGCGGGTGGAG 62.838 72.222 7.21 0.00 0.00 3.86
1616 3062 4.219944 GGTTTGGAAATACCTTGGAAGACC 59.780 45.833 0.00 0.00 39.86 3.85
1718 3164 8.387813 TCCTCCTACCAACAAACATAAACTAAT 58.612 33.333 0.00 0.00 0.00 1.73
1730 3176 4.595781 ACAACATACTCCTCCTACCAACAA 59.404 41.667 0.00 0.00 0.00 2.83
1778 3224 0.679505 TCACCACCTTCTTCAGTCCG 59.320 55.000 0.00 0.00 0.00 4.79
1798 3246 2.862541 TGGGAATGGAATATGAAGGCG 58.137 47.619 0.00 0.00 0.00 5.52
2249 3700 2.221169 CCATCCATACCCATGTTGACG 58.779 52.381 0.00 0.00 0.00 4.35
2271 3724 6.595326 TCATTTGATCATCAGTAGTTCCACAC 59.405 38.462 0.00 0.00 0.00 3.82
2327 3780 9.309516 CTGATCATTTGGTGGAAGATTATTTTG 57.690 33.333 0.00 0.00 0.00 2.44
2389 3842 8.814931 TCCTGTGACCATGATGAAAATAAAATT 58.185 29.630 0.00 0.00 0.00 1.82
2413 3867 3.019564 AGCCATTGCATACAAACTCTCC 58.980 45.455 0.00 0.00 39.77 3.71
2429 3883 1.345063 AAGAAAGCCAAGCAAGCCAT 58.655 45.000 0.00 0.00 0.00 4.40
2533 4006 7.334671 TGCATGACACATCGTTAGGTATTTAAA 59.665 33.333 0.00 0.00 0.00 1.52
2547 4020 6.158598 AGGTTTAAAACATGCATGACACATC 58.841 36.000 32.75 15.49 0.00 3.06
2671 4164 2.614259 TGGAGATCCCTCTAGATTGGC 58.386 52.381 0.00 0.00 39.38 4.52
2699 4192 8.674263 AATCAAAGTGGACATAAGAGATCATC 57.326 34.615 0.00 0.00 0.00 2.92
2770 4264 7.453393 TCAAAGCCACTAGGATATAAATGGAG 58.547 38.462 0.00 0.00 36.89 3.86
2809 4303 4.580580 CCTTTTAGCACTTATGGGATGGAC 59.419 45.833 0.00 0.00 0.00 4.02
2857 4351 6.417191 TTCTTATAACTTGGATCGCAACAC 57.583 37.500 0.00 0.00 0.00 3.32
2924 4423 1.672881 GTTGGCGCTTCAGATTGCTAT 59.327 47.619 7.64 0.00 0.00 2.97
2933 4432 1.378531 GATACCATGTTGGCGCTTCA 58.621 50.000 7.64 4.67 42.67 3.02
3037 4537 7.341256 TCGGTACTCTTATAAGTGATGTTCCTT 59.659 37.037 18.87 0.00 0.00 3.36
3043 4543 9.776158 GTGATATCGGTACTCTTATAAGTGATG 57.224 37.037 18.87 8.24 0.00 3.07
3054 4554 6.971726 TGGTTTATGTGATATCGGTACTCT 57.028 37.500 0.00 0.00 0.00 3.24
3055 4555 6.590292 CCATGGTTTATGTGATATCGGTACTC 59.410 42.308 2.57 0.00 34.87 2.59
3080 4580 8.095169 TCTGTAAAGATTGGAGGTCTTTTCTAC 58.905 37.037 6.45 1.13 41.75 2.59
3087 4587 6.187727 TGTTTCTGTAAAGATTGGAGGTCT 57.812 37.500 0.00 0.00 0.00 3.85
3101 4601 1.885887 GGCATGCCTGTTGTTTCTGTA 59.114 47.619 29.98 0.00 0.00 2.74
3223 4727 9.516314 GCAATAGTTAAGGATTTATTGGTTGAC 57.484 33.333 5.54 0.00 35.23 3.18
3453 4961 3.093057 TGGTTTAAATTCCATCCACCCG 58.907 45.455 0.00 0.00 0.00 5.28
3484 4992 5.882000 ACTTGCTGCTCATGTTGATATTACA 59.118 36.000 0.00 0.00 29.82 2.41
3489 4997 3.941573 TCACTTGCTGCTCATGTTGATA 58.058 40.909 0.00 0.00 31.52 2.15
3543 5052 8.158169 TCATAAGCTTAGTGCAAAATATGGAG 57.842 34.615 12.54 0.00 45.94 3.86


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

AutoCloner maintained by Alex Coulton.