Multiple sequence alignment - TraesCS7A01G179900

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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 TraesCS7A01G179900 chr7A 100.000 3134 0 0 1 3134 134490245 134493378 0.000000e+00 5788.0
1 TraesCS7A01G179900 chr7B 92.205 3156 179 34 2 3134 97191189 97194300 0.000000e+00 4403.0
2 TraesCS7A01G179900 chr7D 95.331 2677 85 13 467 3134 135356821 135359466 0.000000e+00 4215.0
3 TraesCS7A01G179900 chr7D 95.704 419 12 4 3 421 135356152 135356564 0.000000e+00 669.0
4 TraesCS7A01G179900 chr7D 95.902 244 3 2 984 1220 135356809 135356566 3.790000e-104 388.0
5 TraesCS7A01G179900 chr6B 75.390 833 147 46 997 1795 613610169 613610977 1.790000e-92 350.0
6 TraesCS7A01G179900 chr6B 78.238 386 75 7 1418 1798 614127916 614128297 4.040000e-59 239.0
7 TraesCS7A01G179900 chr6A 79.016 386 72 7 1418 1798 554716446 554716827 4.010000e-64 255.0
8 TraesCS7A01G179900 chr6D 78.497 386 74 7 1418 1798 409288380 409288761 8.680000e-61 244.0
9 TraesCS7A01G179900 chr6D 78.442 385 74 6 1419 1798 408945987 408946367 3.120000e-60 243.0
10 TraesCS7A01G179900 chr3A 80.315 127 21 4 1225 1349 330698437 330698561 3.330000e-15 93.5
11 TraesCS7A01G179900 chr1D 92.188 64 5 0 747 810 118475725 118475662 1.200000e-14 91.6
12 TraesCS7A01G179900 chr1B 77.966 118 26 0 1420 1537 615744798 615744681 1.210000e-09 75.0
13 TraesCS7A01G179900 chr1A 81.609 87 16 0 1441 1527 545009086 545009000 4.340000e-09 73.1


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 TraesCS7A01G179900 chr7A 134490245 134493378 3133 False 5788 5788 100.0000 1 3134 1 chr7A.!!$F1 3133
1 TraesCS7A01G179900 chr7B 97191189 97194300 3111 False 4403 4403 92.2050 2 3134 1 chr7B.!!$F1 3132
2 TraesCS7A01G179900 chr7D 135356152 135359466 3314 False 2442 4215 95.5175 3 3134 2 chr7D.!!$F1 3131
3 TraesCS7A01G179900 chr6B 613610169 613610977 808 False 350 350 75.3900 997 1795 1 chr6B.!!$F1 798

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
70 71 1.315981 TTGGCGTTGTCCAGCAAACA 61.316 50.000 0.00 0.00 39.03 2.83 F
106 107 1.770658 TCCAATCCTGTATCCTGCTGG 59.229 52.381 2.58 2.58 0.00 4.85 F
1912 2235 0.881118 CAACATCAACCCGGGTTCAG 59.119 55.000 36.32 27.69 36.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1114 1358 0.984230 CCAGCAAGTTGAGGTAGGGA 59.016 55.000 7.16 0.0 0.00 4.20 R
1918 2241 1.000060 CTGCCCACTGGTTTCAACATG 60.000 52.381 0.00 0.0 0.00 3.21 R
2897 3226 1.211457 CCTGCTCTAAGGCAAGGACAT 59.789 52.381 0.00 0.0 41.94 3.06 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
41 42 1.954382 CATGATCTGGGCTTCACCATG 59.046 52.381 0.00 0.00 40.36 3.66
70 71 1.315981 TTGGCGTTGTCCAGCAAACA 61.316 50.000 0.00 0.00 39.03 2.83
106 107 1.770658 TCCAATCCTGTATCCTGCTGG 59.229 52.381 2.58 2.58 0.00 4.85
137 138 7.785033 TGATGTAGCTTCACTGAATAATCTGA 58.215 34.615 0.00 0.00 0.00 3.27
315 316 9.416794 CAGTAAGGAAACATAGAGTATGCATAG 57.583 37.037 6.67 0.00 39.79 2.23
348 349 7.474190 ACAAATGCAATTTTTCAAGTCAAAGG 58.526 30.769 0.00 0.00 46.10 3.11
414 416 3.287867 AACCATACAGGCTTCAGATGG 57.712 47.619 10.63 10.63 43.14 3.51
449 686 8.469309 AAATATGGACCATCAGTTATTCAAGG 57.531 34.615 11.17 0.00 0.00 3.61
450 687 4.235079 TGGACCATCAGTTATTCAAGGG 57.765 45.455 0.00 0.00 0.00 3.95
451 688 3.849574 TGGACCATCAGTTATTCAAGGGA 59.150 43.478 0.00 0.00 0.00 4.20
452 689 4.290985 TGGACCATCAGTTATTCAAGGGAA 59.709 41.667 0.00 0.00 37.45 3.97
453 690 5.222233 TGGACCATCAGTTATTCAAGGGAAA 60.222 40.000 0.00 0.00 36.43 3.13
454 691 5.125578 GGACCATCAGTTATTCAAGGGAAAC 59.874 44.000 0.00 0.00 36.43 2.78
470 707 4.577834 GGAAACCCTTTTTCGTCATTCA 57.422 40.909 0.00 0.00 0.00 2.57
471 708 4.939271 GGAAACCCTTTTTCGTCATTCAA 58.061 39.130 0.00 0.00 0.00 2.69
481 718 9.740239 CCTTTTTCGTCATTCAATATCATGATT 57.260 29.630 14.65 0.00 32.07 2.57
496 733 9.491675 AATATCATGATTGTTCAAAAGCAAACA 57.508 25.926 14.65 0.00 34.96 2.83
1114 1358 1.284111 TGGCCATGGAAGCTGGAGAT 61.284 55.000 18.40 0.00 35.70 2.75
1713 2036 1.077644 CTCTGCAGCCTCCATTGCT 60.078 57.895 9.47 0.00 40.87 3.91
1849 2172 1.078143 GACTTAGCAGGGCAGGTGG 60.078 63.158 0.00 0.00 0.00 4.61
1870 2193 2.715046 CTCAGAACCAAATGCCTAGCA 58.285 47.619 0.00 0.00 44.86 3.49
1912 2235 0.881118 CAACATCAACCCGGGTTCAG 59.119 55.000 36.32 27.69 36.00 3.02
1918 2241 1.279846 TCAACCCGGGTTCAGATAACC 59.720 52.381 36.32 0.00 36.00 2.85
1934 2257 4.766891 AGATAACCATGTTGAAACCAGTGG 59.233 41.667 7.91 7.91 33.69 4.00
1959 2282 1.270907 ACCGCAGTGAGGAAGAGAAT 58.729 50.000 20.81 0.00 0.00 2.40
1961 2284 2.832129 ACCGCAGTGAGGAAGAGAATAA 59.168 45.455 20.81 0.00 0.00 1.40
1976 2299 5.072741 AGAGAATAACAGCAAGAAAAGGCA 58.927 37.500 0.00 0.00 0.00 4.75
2019 2342 0.738762 CACCTCTCACTGACATGGCG 60.739 60.000 0.00 0.00 0.00 5.69
2034 2357 1.737735 GGCGGCTTCCAACATTTGC 60.738 57.895 0.00 0.00 0.00 3.68
2067 2390 2.586635 TCAAACTGCGACGGCGTT 60.587 55.556 16.19 0.00 44.10 4.84
2091 2414 0.179040 GTCCGTTTCCCAGTTGGTCA 60.179 55.000 0.00 0.00 34.77 4.02
2444 2770 6.183309 AGTTGCTCGAAAATAGGTCATTTC 57.817 37.500 0.00 0.00 35.74 2.17
2481 2807 3.653344 TGGTGCGATGATATAGCTTGAC 58.347 45.455 0.00 0.00 0.00 3.18
2495 2821 0.229753 CTTGACTGACAACACGCGTC 59.770 55.000 9.86 0.00 34.56 5.19
2532 2860 0.471971 ACTGCTACCACACCAGAGGT 60.472 55.000 0.00 0.00 41.81 3.85
2541 2869 3.033909 CCACACCAGAGGTCATCTATCA 58.966 50.000 0.00 0.00 36.10 2.15
2542 2870 3.645212 CCACACCAGAGGTCATCTATCAT 59.355 47.826 0.00 0.00 36.10 2.45
2549 2877 8.575589 CACCAGAGGTCATCTATCATATATAGC 58.424 40.741 0.00 0.00 36.10 2.97
2609 2938 9.415544 CTTTATGCAGCTTCTAAATGTTTTTCT 57.584 29.630 0.00 0.00 0.00 2.52
2695 3024 7.096763 GCGAAAAATAAAACTAAAAGCACGAGT 60.097 33.333 0.00 0.00 0.00 4.18
2779 3108 4.821805 CCAACAGTGACTGAAAACTGGTAT 59.178 41.667 20.97 0.00 42.41 2.73
2793 3122 8.573035 TGAAAACTGGTATGAATTACAGGAAAC 58.427 33.333 0.00 0.00 31.99 2.78
2796 3125 7.016153 ACTGGTATGAATTACAGGAAACTCA 57.984 36.000 0.00 0.00 40.21 3.41
2820 3149 5.067674 ACAAACAGCTAGCTGAAAAACATGA 59.932 36.000 43.42 0.00 46.30 3.07
2821 3150 5.368256 AACAGCTAGCTGAAAAACATGAG 57.632 39.130 43.42 18.51 46.30 2.90
2823 3152 4.005650 CAGCTAGCTGAAAAACATGAGGA 58.994 43.478 36.47 0.00 46.30 3.71
2865 3194 8.814038 AAACATAAGCTTCTATGAAGGATTGT 57.186 30.769 14.73 0.00 34.07 2.71
2870 3199 5.994250 AGCTTCTATGAAGGATTGTTAGCA 58.006 37.500 9.04 0.00 0.00 3.49
2896 3225 0.321122 CTTCCTGTCAGGGTCAGCAC 60.321 60.000 19.11 0.00 35.59 4.40
2897 3226 1.053835 TTCCTGTCAGGGTCAGCACA 61.054 55.000 19.11 0.00 35.59 4.57
2938 3267 3.389983 GGTAAAAGTTTGCCCCCTTTTCT 59.610 43.478 7.37 0.00 40.39 2.52
2967 3296 6.438763 AGAAATTGACTCCGAAAACATGTTC 58.561 36.000 12.39 0.00 0.00 3.18
2969 3298 5.613358 ATTGACTCCGAAAACATGTTCTC 57.387 39.130 12.39 6.70 0.00 2.87
2973 3302 4.451900 ACTCCGAAAACATGTTCTCAAGT 58.548 39.130 12.39 10.85 0.00 3.16
2997 3326 4.941263 GGTAGCAACCTAACATCAACATCA 59.059 41.667 0.00 0.00 43.08 3.07
2999 3328 5.376854 AGCAACCTAACATCAACATCAAC 57.623 39.130 0.00 0.00 0.00 3.18
3032 3361 6.644592 TGTGTGCTTATATGCTTTCCAAAAAC 59.355 34.615 11.48 0.00 0.00 2.43
3105 3434 6.099341 CCAATTACTCCACTTGCAAAATACC 58.901 40.000 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.473235 GTCACTTGTTCGCTCTGAGTTC 59.527 50.000 6.53 0.00 0.00 3.01
41 42 2.540973 GGACAACGCCAAGTTCTGAAAC 60.541 50.000 0.00 0.00 42.02 2.78
70 71 4.262164 GGATTGGACAAACAGCTGAACAAT 60.262 41.667 23.35 18.45 32.77 2.71
106 107 2.928757 CAGTGAAGCTACATCAGAGTGC 59.071 50.000 0.00 0.00 0.00 4.40
137 138 2.478894 GCGTAGTGGCGTATAATGCATT 59.521 45.455 17.56 17.56 0.00 3.56
309 310 2.094078 GCATTTGTTGGGCTTCTATGCA 60.094 45.455 0.00 0.00 37.45 3.96
315 316 4.834357 AAAATTGCATTTGTTGGGCTTC 57.166 36.364 0.00 0.00 31.77 3.86
348 349 7.329717 CGGGTGATAGAGCTTAATTTCAGTATC 59.670 40.741 0.00 0.00 0.00 2.24
371 372 0.688487 TGGAACAGAAGGTAACCGGG 59.312 55.000 6.32 0.00 37.17 5.73
448 685 3.319689 TGAATGACGAAAAAGGGTTTCCC 59.680 43.478 0.00 0.00 45.90 3.97
449 686 4.577834 TGAATGACGAAAAAGGGTTTCC 57.422 40.909 0.00 0.00 0.00 3.13
450 687 8.026607 TGATATTGAATGACGAAAAAGGGTTTC 58.973 33.333 0.00 0.00 0.00 2.78
451 688 7.891561 TGATATTGAATGACGAAAAAGGGTTT 58.108 30.769 0.00 0.00 0.00 3.27
452 689 7.461182 TGATATTGAATGACGAAAAAGGGTT 57.539 32.000 0.00 0.00 0.00 4.11
453 690 7.339212 TCATGATATTGAATGACGAAAAAGGGT 59.661 33.333 0.00 0.00 0.00 4.34
454 691 7.706159 TCATGATATTGAATGACGAAAAAGGG 58.294 34.615 0.00 0.00 0.00 3.95
455 692 9.740239 AATCATGATATTGAATGACGAAAAAGG 57.260 29.630 9.04 0.00 35.71 3.11
459 696 9.720667 GAACAATCATGATATTGAATGACGAAA 57.279 29.630 9.04 0.00 38.84 3.46
460 697 8.891720 TGAACAATCATGATATTGAATGACGAA 58.108 29.630 9.04 0.00 38.84 3.85
461 698 8.436046 TGAACAATCATGATATTGAATGACGA 57.564 30.769 9.04 0.00 38.84 4.20
462 699 9.505995 TTTGAACAATCATGATATTGAATGACG 57.494 29.630 9.04 0.00 38.84 4.35
466 703 9.878667 TGCTTTTGAACAATCATGATATTGAAT 57.121 25.926 9.04 0.70 38.84 2.57
467 704 9.708092 TTGCTTTTGAACAATCATGATATTGAA 57.292 25.926 9.04 4.65 38.84 2.69
468 705 9.708092 TTTGCTTTTGAACAATCATGATATTGA 57.292 25.926 9.04 0.00 38.84 2.57
469 706 9.749490 GTTTGCTTTTGAACAATCATGATATTG 57.251 29.630 9.04 8.07 41.65 1.90
470 707 9.491675 TGTTTGCTTTTGAACAATCATGATATT 57.508 25.926 9.04 6.73 34.96 1.28
471 708 9.491675 TTGTTTGCTTTTGAACAATCATGATAT 57.508 25.926 9.04 0.00 39.92 1.63
481 718 6.571605 TCATGAGATTGTTTGCTTTTGAACA 58.428 32.000 0.00 0.00 34.22 3.18
519 756 5.233050 CGCTTGGTTCTGTTAGATGTAGATG 59.767 44.000 0.00 0.00 0.00 2.90
759 997 6.292381 CGTTCACTTTATGGTAGATAGCTTGC 60.292 42.308 0.00 0.00 0.00 4.01
1114 1358 0.984230 CCAGCAAGTTGAGGTAGGGA 59.016 55.000 7.16 0.00 0.00 4.20
1636 1959 2.033141 TGTCTGAGCTTGCAGCCC 59.967 61.111 4.77 0.00 43.77 5.19
1713 2036 3.329889 CTGGTAGTGGGGCTGGCA 61.330 66.667 2.88 0.00 0.00 4.92
1820 2143 2.105477 CCTGCTAAGTCTATGCCACCAT 59.895 50.000 0.00 0.00 35.44 3.55
1849 2172 1.403323 GCTAGGCATTTGGTTCTGAGC 59.597 52.381 0.00 0.00 0.00 4.26
1870 2193 5.245751 TGCCAATTGTGTGATCAAAGGTAAT 59.754 36.000 4.43 0.00 32.76 1.89
1881 2204 3.492309 GGTTGATGTTGCCAATTGTGTGA 60.492 43.478 4.43 0.00 0.00 3.58
1912 2235 4.082245 CCCACTGGTTTCAACATGGTTATC 60.082 45.833 0.00 0.00 0.00 1.75
1918 2241 1.000060 CTGCCCACTGGTTTCAACATG 60.000 52.381 0.00 0.00 0.00 3.21
1952 2275 5.536161 TGCCTTTTCTTGCTGTTATTCTCTT 59.464 36.000 0.00 0.00 0.00 2.85
1959 2282 4.644685 AGAAACTGCCTTTTCTTGCTGTTA 59.355 37.500 7.09 0.00 45.17 2.41
1961 2284 3.026694 AGAAACTGCCTTTTCTTGCTGT 58.973 40.909 4.24 0.00 42.09 4.40
1976 2299 5.455469 GGAAGGGAGTTTTCAGAGAGAAACT 60.455 44.000 1.50 1.50 45.48 2.66
2019 2342 3.261580 GGTATTGCAAATGTTGGAAGCC 58.738 45.455 1.71 2.93 44.23 4.35
2034 2357 4.012374 AGTTTGAGGTGCTGATGGTATTG 58.988 43.478 0.00 0.00 0.00 1.90
2067 2390 2.564062 CCAACTGGGAAACGGACTACTA 59.436 50.000 0.00 0.00 40.01 1.82
2091 2414 6.347696 CAGCTCTTCATCAAGTAGGATTTCT 58.652 40.000 0.00 0.00 0.00 2.52
2444 2770 3.845775 CGCACCATTTGTATCAAAGTTCG 59.154 43.478 1.67 0.00 0.00 3.95
2448 2774 5.233957 TCATCGCACCATTTGTATCAAAG 57.766 39.130 1.67 0.00 0.00 2.77
2481 2807 0.927537 TCTTTGACGCGTGTTGTCAG 59.072 50.000 20.70 3.64 46.17 3.51
2495 2821 3.914364 GCAGTGAGCGGTATTTTTCTTTG 59.086 43.478 0.00 0.00 0.00 2.77
2549 2877 8.507470 GGCAACTTTTCTTTATGTTAGTTCTG 57.493 34.615 0.00 0.00 0.00 3.02
2603 2932 7.455641 TCACCAAACAGTACTTCAAGAAAAA 57.544 32.000 0.00 0.00 0.00 1.94
2609 2938 7.297936 TCTAGATCACCAAACAGTACTTCAA 57.702 36.000 0.00 0.00 0.00 2.69
2688 3017 2.611518 ACTTCTTCTGCATACTCGTGC 58.388 47.619 0.00 0.00 45.25 5.34
2695 3024 6.054941 TGACTCAACAAACTTCTTCTGCATA 58.945 36.000 0.00 0.00 0.00 3.14
2779 3108 6.459573 GCTGTTTGTGAGTTTCCTGTAATTCA 60.460 38.462 0.00 0.00 0.00 2.57
2793 3122 4.818534 TTTTCAGCTAGCTGTTTGTGAG 57.181 40.909 36.99 15.29 43.96 3.51
2796 3125 4.981806 TGTTTTTCAGCTAGCTGTTTGT 57.018 36.364 36.99 5.29 43.96 2.83
2896 3225 2.286872 CTGCTCTAAGGCAAGGACATG 58.713 52.381 0.00 0.00 41.94 3.21
2897 3226 1.211457 CCTGCTCTAAGGCAAGGACAT 59.789 52.381 0.00 0.00 41.94 3.06
2938 3267 5.358442 TGTTTTCGGAGTCAATTTCTTGGAA 59.642 36.000 0.00 0.00 32.95 3.53
2999 3328 7.488187 AAGCATATAAGCACACATCTTAGTG 57.512 36.000 2.37 0.00 44.93 2.74
3105 3434 9.249457 TGATGAATCTGTTATACTCTTAAAGCG 57.751 33.333 0.00 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.