Multiple sequence alignment - TraesCS7A01G297000

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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 TraesCS7A01G297000 chr7A 100.000 2885 0 0 1 2885 397126837 397123953 0.000000e+00 5328
1 TraesCS7A01G297000 chr7B 98.186 1599 26 2 734 2330 355906775 355905178 0.000000e+00 2789
2 TraesCS7A01G297000 chr7B 92.922 664 45 2 2 663 264009636 264010299 0.000000e+00 965
3 TraesCS7A01G297000 chr7B 91.789 475 23 6 2339 2813 355904979 355904521 0.000000e+00 647
4 TraesCS7A01G297000 chr7B 90.909 88 7 1 664 750 355917118 355917031 1.820000e-22 117
5 TraesCS7A01G297000 chr7D 97.835 1478 28 3 664 2138 350094127 350095603 0.000000e+00 2549
6 TraesCS7A01G297000 chr7D 93.413 334 9 2 2339 2672 350095935 350096255 1.550000e-132 483
7 TraesCS7A01G297000 chr7D 92.105 228 8 3 2658 2885 350096404 350096621 2.160000e-81 313
8 TraesCS7A01G297000 chr7D 93.243 148 7 3 664 809 350093610 350093756 6.260000e-52 215
9 TraesCS7A01G297000 chr7D 84.021 194 29 2 471 663 8888754 8888946 4.910000e-43 185
10 TraesCS7A01G297000 chr7D 95.402 87 2 2 2257 2341 350095824 350095910 1.390000e-28 137
11 TraesCS7A01G297000 chr6D 76.605 701 142 19 1054 1743 440664273 440663584 1.630000e-97 366
12 TraesCS7A01G297000 chr6B 76.571 700 144 19 1054 1743 665716560 665715871 1.630000e-97 366
13 TraesCS7A01G297000 chr6A 76.143 700 147 18 1054 1743 588605062 588604373 1.650000e-92 350
14 TraesCS7A01G297000 chr3B 88.205 195 21 2 471 663 779290093 779290287 6.220000e-57 231
15 TraesCS7A01G297000 chr5B 87.310 197 24 1 474 669 631357243 631357047 1.040000e-54 224


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 TraesCS7A01G297000 chr7A 397123953 397126837 2884 True 5328.0 5328 100.0000 1 2885 1 chr7A.!!$R1 2884
1 TraesCS7A01G297000 chr7B 355904521 355906775 2254 True 1718.0 2789 94.9875 734 2813 2 chr7B.!!$R2 2079
2 TraesCS7A01G297000 chr7B 264009636 264010299 663 False 965.0 965 92.9220 2 663 1 chr7B.!!$F1 661
3 TraesCS7A01G297000 chr7D 350093610 350096621 3011 False 739.4 2549 94.3996 664 2885 5 chr7D.!!$F2 2221
4 TraesCS7A01G297000 chr6D 440663584 440664273 689 True 366.0 366 76.6050 1054 1743 1 chr6D.!!$R1 689
5 TraesCS7A01G297000 chr6B 665715871 665716560 689 True 366.0 366 76.5710 1054 1743 1 chr6B.!!$R1 689
6 TraesCS7A01G297000 chr6A 588604373 588605062 689 True 350.0 350 76.1430 1054 1743 1 chr6A.!!$R1 689

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
77 78 0.034670 ACAGGAAGGAAGCCAGATGC 60.035 55.0 0.0 0.0 41.71 3.91 F
275 276 0.179179 GTTGCTCGCCTTCAATCAGC 60.179 55.0 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1555 1.961277 GGCGGGCTTACCATCATCG 60.961 63.158 0.0 0.0 40.22 3.84 R
2148 2674 4.040952 ACACCTCTATATGAATGACTGGGC 59.959 45.833 0.0 0.0 0.00 5.36 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
30 31 7.903431 CCACATAATTAGTAGACAAAGCGAAAC 59.097 37.037 0.00 0.00 0.00 2.78
60 61 7.392494 AGATCAATCGTTAGACTAACTCACA 57.608 36.000 20.36 5.10 36.54 3.58
64 65 6.208007 TCAATCGTTAGACTAACTCACAGGAA 59.792 38.462 20.36 0.00 36.54 3.36
77 78 0.034670 ACAGGAAGGAAGCCAGATGC 60.035 55.000 0.00 0.00 41.71 3.91
89 90 2.288666 GCCAGATGCGGATCACTAAAA 58.711 47.619 19.67 0.00 0.00 1.52
133 134 2.849081 CGCACTACGGGTTGGATTT 58.151 52.632 0.00 0.00 38.44 2.17
167 168 1.209261 TCACAGTCAACAACCTGCTCA 59.791 47.619 0.00 0.00 0.00 4.26
174 175 0.185901 AACAACCTGCTCATGTGGGT 59.814 50.000 0.00 0.00 0.00 4.51
209 210 1.975363 GATGCTCGCAGTCAACAGCC 61.975 60.000 0.00 0.00 0.00 4.85
239 240 2.433436 GGGCCTTGTTAGTTGAATCGT 58.567 47.619 0.84 0.00 0.00 3.73
271 272 0.598065 GGTTGTTGCTCGCCTTCAAT 59.402 50.000 0.00 0.00 0.00 2.57
275 276 0.179179 GTTGCTCGCCTTCAATCAGC 60.179 55.000 0.00 0.00 0.00 4.26
292 293 2.982744 GCCGCTCCTGAAACCTTGC 61.983 63.158 0.00 0.00 0.00 4.01
321 322 6.891361 TCACCAGATTTAACCATTCATCACAT 59.109 34.615 0.00 0.00 0.00 3.21
363 364 8.951243 CGGATAATAGTGTCAGAGAATGAGATA 58.049 37.037 0.00 0.00 39.07 1.98
373 374 6.265196 GTCAGAGAATGAGATAGTCATGGAGT 59.735 42.308 0.00 0.00 45.89 3.85
386 387 3.320541 GTCATGGAGTAGAGAGGATGGTG 59.679 52.174 0.00 0.00 0.00 4.17
402 403 2.528127 TGGGAGGTTTCTCGGCCA 60.528 61.111 2.24 0.00 40.85 5.36
488 491 7.125792 AGACAATCTTCACGGAATACCTAAT 57.874 36.000 0.00 0.00 0.00 1.73
493 496 4.712829 TCTTCACGGAATACCTAATGTCCA 59.287 41.667 0.00 0.00 0.00 4.02
517 520 6.986817 CAGTGTTTGTATCGAGGAAGGATATT 59.013 38.462 0.00 0.00 0.00 1.28
538 541 3.290948 TGGGTTATGTGGGTAAGATGC 57.709 47.619 0.00 0.00 0.00 3.91
540 543 2.158871 GGGTTATGTGGGTAAGATGCGA 60.159 50.000 0.00 0.00 0.00 5.10
549 552 3.445518 TAAGATGCGAGCCTGGCGG 62.446 63.158 13.96 10.71 0.00 6.13
556 559 2.044946 GAGCCTGGCGGGATGTTT 60.045 61.111 18.84 0.00 37.23 2.83
559 562 2.700773 GCCTGGCGGGATGTTTCAC 61.701 63.158 18.84 0.00 37.23 3.18
562 565 0.523072 CTGGCGGGATGTTTCACAAG 59.477 55.000 0.00 0.00 0.00 3.16
565 568 1.523758 GCGGGATGTTTCACAAGTCT 58.476 50.000 0.00 0.00 0.00 3.24
569 572 3.476552 GGGATGTTTCACAAGTCTCACA 58.523 45.455 0.00 0.00 0.00 3.58
577 580 8.450578 TGTTTCACAAGTCTCACATATTTTCT 57.549 30.769 0.00 0.00 0.00 2.52
578 581 8.902806 TGTTTCACAAGTCTCACATATTTTCTT 58.097 29.630 0.00 0.00 0.00 2.52
587 590 7.118390 AGTCTCACATATTTTCTTTCTCAACCG 59.882 37.037 0.00 0.00 0.00 4.44
591 594 6.001460 ACATATTTTCTTTCTCAACCGTGGA 58.999 36.000 0.00 0.00 0.00 4.02
657 660 3.365265 GCCCGTTCCCACTTGCAG 61.365 66.667 0.00 0.00 0.00 4.41
663 666 1.153066 TTCCCACTTGCAGCGTGAA 60.153 52.632 16.91 4.60 34.35 3.18
664 667 0.537143 TTCCCACTTGCAGCGTGAAT 60.537 50.000 16.91 0.00 34.35 2.57
665 668 0.537143 TCCCACTTGCAGCGTGAATT 60.537 50.000 16.91 0.00 34.35 2.17
666 669 0.314935 CCCACTTGCAGCGTGAATTT 59.685 50.000 16.91 0.00 34.35 1.82
667 670 1.666888 CCCACTTGCAGCGTGAATTTC 60.667 52.381 16.91 0.00 34.35 2.17
668 671 1.001487 CCACTTGCAGCGTGAATTTCA 60.001 47.619 16.91 0.00 34.35 2.69
669 672 2.543445 CCACTTGCAGCGTGAATTTCAA 60.543 45.455 16.91 0.00 34.35 2.69
670 673 3.311106 CACTTGCAGCGTGAATTTCAAT 58.689 40.909 11.52 0.00 34.35 2.57
671 674 3.120616 CACTTGCAGCGTGAATTTCAATG 59.879 43.478 11.52 2.37 34.35 2.82
672 675 3.004629 ACTTGCAGCGTGAATTTCAATGA 59.995 39.130 0.00 0.00 0.00 2.57
673 676 3.639716 TGCAGCGTGAATTTCAATGAA 57.360 38.095 0.00 0.00 0.00 2.57
674 677 3.974912 TGCAGCGTGAATTTCAATGAAA 58.025 36.364 11.10 11.10 35.94 2.69
675 678 3.982701 TGCAGCGTGAATTTCAATGAAAG 59.017 39.130 14.10 1.47 34.92 2.62
861 1382 3.655211 CTGTGGGCCCCTGCTTCT 61.655 66.667 22.27 0.00 37.74 2.85
891 1412 6.101881 CCCCTTCCTCATCTTATTACTTTCCT 59.898 42.308 0.00 0.00 0.00 3.36
938 1461 1.553704 CGCAAACCCTAACCCTAGAGT 59.446 52.381 0.00 0.00 0.00 3.24
957 1480 4.214327 CGCTTCGCTCCTCCTCCC 62.214 72.222 0.00 0.00 0.00 4.30
976 1499 2.476199 CCCCAACAAGATCTCTCTCCT 58.524 52.381 0.00 0.00 0.00 3.69
1014 1537 3.716195 CCGATGTCTGCCCCACCA 61.716 66.667 0.00 0.00 0.00 4.17
1760 2286 2.357881 CTCGCTGCTGACCTTGCA 60.358 61.111 0.00 0.00 38.81 4.08
1768 2294 1.860484 GCTGACCTTGCAGTGCTTCC 61.860 60.000 17.60 1.91 38.17 3.46
2139 2665 6.594937 ACTGAAAATTGAACTGTTGTGCATTT 59.405 30.769 0.00 0.00 30.60 2.32
2218 2744 3.385755 GCCATATTGCCTTTCTGTGGAAT 59.614 43.478 0.00 0.00 0.00 3.01
2224 2750 4.524316 TGCCTTTCTGTGGAATTCAATG 57.476 40.909 7.93 0.00 0.00 2.82
2444 3264 4.227527 CCCCTTAATTACTGGGACTTGACT 59.772 45.833 19.31 0.00 43.47 3.41
2545 3377 6.091034 TGCTTTATTTCGCTAACGTATCACAA 59.909 34.615 0.00 0.00 41.18 3.33
2546 3378 6.957077 GCTTTATTTCGCTAACGTATCACAAA 59.043 34.615 0.00 0.00 41.18 2.83
2547 3379 7.638683 GCTTTATTTCGCTAACGTATCACAAAT 59.361 33.333 0.00 0.00 41.18 2.32
2549 3381 9.904647 TTTATTTCGCTAACGTATCACAAATAC 57.095 29.630 0.00 0.00 41.18 1.89
2550 3382 5.954434 TTCGCTAACGTATCACAAATACC 57.046 39.130 0.00 0.00 41.18 2.73
2551 3383 4.996344 TCGCTAACGTATCACAAATACCA 58.004 39.130 0.00 0.00 41.18 3.25
2552 3384 5.593968 TCGCTAACGTATCACAAATACCAT 58.406 37.500 0.00 0.00 41.18 3.55
2553 3385 6.044046 TCGCTAACGTATCACAAATACCATT 58.956 36.000 0.00 0.00 41.18 3.16
2554 3386 6.535865 TCGCTAACGTATCACAAATACCATTT 59.464 34.615 0.00 0.00 41.18 2.32
2555 3387 6.844279 CGCTAACGTATCACAAATACCATTTC 59.156 38.462 0.00 0.00 33.53 2.17
2556 3388 7.464844 CGCTAACGTATCACAAATACCATTTCA 60.465 37.037 0.00 0.00 33.53 2.69
2648 3480 6.598753 TCAAACCTACAGTTTTTCTCTTCG 57.401 37.500 0.00 0.00 46.79 3.79
2807 3802 1.478105 GCTTCTTTGGATTGCGGGATT 59.522 47.619 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.094881 GCTTTGTCTACTAATTATGTGGGCAA 59.905 38.462 11.52 11.52 38.40 4.52
7 8 8.869897 TCTGTTTCGCTTTGTCTACTAATTATG 58.130 33.333 0.00 0.00 0.00 1.90
60 61 1.222936 CGCATCTGGCTTCCTTCCT 59.777 57.895 0.00 0.00 41.67 3.36
64 65 1.340399 TGATCCGCATCTGGCTTCCT 61.340 55.000 0.00 0.00 41.67 3.36
77 78 7.359262 TGTGTTATGAAGTTTTAGTGATCCG 57.641 36.000 0.00 0.00 0.00 4.18
89 90 2.163010 GCATGCAGCTGTGTTATGAAGT 59.837 45.455 16.64 0.00 41.15 3.01
116 117 1.402325 GCAAAATCCAACCCGTAGTGC 60.402 52.381 0.00 0.00 0.00 4.40
124 125 4.219288 AGAATCACAGAGCAAAATCCAACC 59.781 41.667 0.00 0.00 0.00 3.77
167 168 3.136260 ACAAAGCAAAATCCAACCCACAT 59.864 39.130 0.00 0.00 0.00 3.21
174 175 4.309099 GAGCATCACAAAGCAAAATCCAA 58.691 39.130 0.00 0.00 33.17 3.53
209 210 3.437795 CAAGGCCCGCAAGAGCAG 61.438 66.667 0.00 0.00 42.27 4.24
215 216 0.179015 TCAACTAACAAGGCCCGCAA 60.179 50.000 0.00 0.00 0.00 4.85
239 240 0.892755 AACAACCGCGTCTAGGATCA 59.107 50.000 4.92 0.00 0.00 2.92
271 272 1.768684 AAGGTTTCAGGAGCGGCTGA 61.769 55.000 7.50 0.00 0.00 4.26
275 276 2.335712 GGCAAGGTTTCAGGAGCGG 61.336 63.158 0.00 0.00 0.00 5.52
292 293 2.483014 TGGTTAAATCTGGTGACCGG 57.517 50.000 3.42 3.42 33.07 5.28
337 338 7.208225 TCTCATTCTCTGACACTATTATCCG 57.792 40.000 0.00 0.00 0.00 4.18
349 350 6.372104 ACTCCATGACTATCTCATTCTCTGA 58.628 40.000 0.00 0.00 37.53 3.27
363 364 3.206412 ACCATCCTCTCTACTCCATGACT 59.794 47.826 0.00 0.00 0.00 3.41
373 374 1.319947 ACCTCCCACCATCCTCTCTA 58.680 55.000 0.00 0.00 0.00 2.43
386 387 1.452108 CATGGCCGAGAAACCTCCC 60.452 63.158 0.00 0.00 0.00 4.30
471 474 5.018539 TGGACATTAGGTATTCCGTGAAG 57.981 43.478 0.02 0.00 39.05 3.02
472 475 4.468510 ACTGGACATTAGGTATTCCGTGAA 59.531 41.667 0.02 0.00 39.05 3.18
477 480 5.944007 ACAAACACTGGACATTAGGTATTCC 59.056 40.000 0.00 0.00 0.00 3.01
488 491 2.894765 TCCTCGATACAAACACTGGACA 59.105 45.455 0.00 0.00 0.00 4.02
493 496 6.732896 ATATCCTTCCTCGATACAAACACT 57.267 37.500 0.00 0.00 0.00 3.55
517 520 3.626930 GCATCTTACCCACATAACCCAA 58.373 45.455 0.00 0.00 0.00 4.12
538 541 3.976701 AAACATCCCGCCAGGCTCG 62.977 63.158 10.54 0.00 35.76 5.03
540 543 2.044946 GAAACATCCCGCCAGGCT 60.045 61.111 10.54 0.00 35.76 4.58
556 559 8.908786 AGAAAGAAAATATGTGAGACTTGTGA 57.091 30.769 0.00 0.00 0.00 3.58
559 562 9.604626 GTTGAGAAAGAAAATATGTGAGACTTG 57.395 33.333 0.00 0.00 0.00 3.16
562 565 7.095187 ACGGTTGAGAAAGAAAATATGTGAGAC 60.095 37.037 0.00 0.00 0.00 3.36
565 568 6.072728 CCACGGTTGAGAAAGAAAATATGTGA 60.073 38.462 0.00 0.00 0.00 3.58
569 572 5.121768 CGTCCACGGTTGAGAAAGAAAATAT 59.878 40.000 0.00 0.00 35.37 1.28
577 580 0.249573 GGACGTCCACGGTTGAGAAA 60.250 55.000 29.75 0.00 44.95 2.52
578 581 1.364901 GGACGTCCACGGTTGAGAA 59.635 57.895 29.75 0.00 44.95 2.87
591 594 2.607635 GCATAATGTCATTCGTGGACGT 59.392 45.455 0.07 0.00 40.80 4.34
602 605 2.346766 ATCAAGCCCGCATAATGTCA 57.653 45.000 0.00 0.00 0.00 3.58
636 639 4.324991 AAGTGGGAACGGGCCGTC 62.325 66.667 34.23 23.96 39.99 4.79
657 660 9.862585 AAATTAAACTTTCATTGAAATTCACGC 57.137 25.926 12.04 0.00 30.85 5.34
729 732 2.138656 GAGGCGTAGTCACACCACGT 62.139 60.000 0.00 0.00 37.95 4.49
730 733 1.443872 GAGGCGTAGTCACACCACG 60.444 63.158 0.00 0.00 38.66 4.94
731 734 1.080025 GGAGGCGTAGTCACACCAC 60.080 63.158 0.00 0.00 28.47 4.16
732 735 1.532078 TGGAGGCGTAGTCACACCA 60.532 57.895 0.00 0.00 31.12 4.17
861 1382 0.253347 AAGATGAGGAAGGGGAGGCA 60.253 55.000 0.00 0.00 0.00 4.75
912 1433 1.543871 GGGTTAGGGTTTGCGAGACAA 60.544 52.381 0.00 0.00 36.13 3.18
957 1480 5.602145 AGATTAGGAGAGAGATCTTGTTGGG 59.398 44.000 0.00 0.00 0.00 4.12
976 1499 1.064758 AGCCGGTGCATCCAAAGATTA 60.065 47.619 1.90 0.00 41.13 1.75
1032 1555 1.961277 GGCGGGCTTACCATCATCG 60.961 63.158 0.00 0.00 40.22 3.84
1768 2294 4.996788 AATATGCCTCCTTCAGCTTTTG 57.003 40.909 0.00 0.00 0.00 2.44
2108 2634 6.092944 ACAACAGTTCAATTTTCAGTCGTACA 59.907 34.615 0.00 0.00 0.00 2.90
2110 2636 6.482835 CACAACAGTTCAATTTTCAGTCGTA 58.517 36.000 0.00 0.00 0.00 3.43
2148 2674 4.040952 ACACCTCTATATGAATGACTGGGC 59.959 45.833 0.00 0.00 0.00 5.36
2149 2675 5.305386 TGACACCTCTATATGAATGACTGGG 59.695 44.000 0.00 0.00 0.00 4.45
2224 2750 7.992180 AATCAACACAAACAATGAAGAGTTC 57.008 32.000 0.00 0.00 0.00 3.01
2390 3210 7.831193 AGTCAAATAGTGTTTATCTTGCAGGAT 59.169 33.333 16.26 16.26 0.00 3.24
2507 3327 6.251376 GCGAAATAAAGCAAGAAACTGGTATG 59.749 38.462 0.00 0.00 0.00 2.39
2551 3383 6.770746 ATCAAGCTCTGCATTTACTGAAAT 57.229 33.333 0.00 0.00 35.56 2.17
2552 3384 6.207221 TGAATCAAGCTCTGCATTTACTGAAA 59.793 34.615 0.00 0.00 0.00 2.69
2553 3385 5.706833 TGAATCAAGCTCTGCATTTACTGAA 59.293 36.000 0.00 0.00 0.00 3.02
2554 3386 5.247862 TGAATCAAGCTCTGCATTTACTGA 58.752 37.500 0.00 0.00 0.00 3.41
2555 3387 5.556355 TGAATCAAGCTCTGCATTTACTG 57.444 39.130 0.00 0.00 0.00 2.74
2556 3388 4.096081 GCTGAATCAAGCTCTGCATTTACT 59.904 41.667 0.00 0.00 40.20 2.24
2565 3397 2.758736 AGAACGCTGAATCAAGCTCT 57.241 45.000 0.00 0.00 41.24 4.09
2612 3444 8.319057 ACTGTAGGTTTGATATCAATGGAGTA 57.681 34.615 18.61 0.04 35.55 2.59
2648 3480 6.564873 GCAAACGATCTTATCTTATCACCTGC 60.565 42.308 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.