Multiple sequence alignment - TraesCS5A01G034700

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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 TraesCS5A01G034700 chr5A 100.000 2941 0 0 1 2941 32146027 32148967 0.000000e+00 5432.0
1 TraesCS5A01G034700 chr5A 96.824 1228 11 15 917 2123 30689642 30688422 0.000000e+00 2026.0
2 TraesCS5A01G034700 chr5A 93.333 570 30 7 406 971 30690204 30689639 0.000000e+00 835.0
3 TraesCS5A01G034700 chr5A 97.549 408 8 2 1 408 30701485 30701080 0.000000e+00 697.0
4 TraesCS5A01G034700 chr5A 79.346 581 101 11 1274 1843 31094028 31093456 9.880000e-105 390.0
5 TraesCS5A01G034700 chr5A 78.674 558 95 19 139 686 31296687 31297230 1.680000e-92 350.0
6 TraesCS5A01G034700 chr5A 78.674 558 94 18 139 686 31095326 31094784 6.030000e-92 348.0
7 TraesCS5A01G034700 chr5A 77.551 343 69 8 1477 1815 536970922 536971260 1.790000e-47 200.0
8 TraesCS5A01G034700 chr5A 97.727 88 2 0 2086 2173 30688431 30688344 5.080000e-33 152.0
9 TraesCS5A01G034700 chr5A 77.578 223 35 8 139 358 31318079 31318289 1.430000e-23 121.0
10 TraesCS5A01G034700 chr5A 93.590 78 5 0 817 894 30127839 30127916 1.850000e-22 117.0
11 TraesCS5A01G034700 chr5A 94.366 71 4 0 2012 2082 30705351 30705281 3.100000e-20 110.0
12 TraesCS5A01G034700 chr5D 88.082 1074 48 16 811 1862 43048453 43049468 0.000000e+00 1201.0
13 TraesCS5A01G034700 chr5D 92.991 214 15 0 1 214 43047404 43047617 2.200000e-81 313.0
14 TraesCS5A01G034700 chr5D 76.608 342 74 6 1477 1815 423474601 423474939 1.800000e-42 183.0
15 TraesCS5A01G034700 chr1A 90.347 777 60 8 2171 2941 587921731 587922498 0.000000e+00 1005.0
16 TraesCS5A01G034700 chr1A 90.190 683 54 8 2264 2941 513640604 513641278 0.000000e+00 878.0
17 TraesCS5A01G034700 chr1A 86.100 777 79 14 2173 2941 587945114 587945869 0.000000e+00 809.0
18 TraesCS5A01G034700 chr5B 93.436 518 24 2 1497 2004 38680401 38680918 0.000000e+00 760.0
19 TraesCS5A01G034700 chr5B 84.663 802 78 17 15 816 38652649 38653405 0.000000e+00 758.0
20 TraesCS5A01G034700 chr5B 81.583 619 38 20 875 1464 38679835 38680406 2.690000e-120 442.0
21 TraesCS5A01G034700 chr5B 78.538 424 76 8 139 557 38565074 38565487 6.250000e-67 265.0
22 TraesCS5A01G034700 chr5B 75.938 453 60 21 17 467 37794004 37793599 1.390000e-43 187.0
23 TraesCS5A01G034700 chr5B 76.471 340 78 2 1477 1815 511292688 511293026 1.800000e-42 183.0
24 TraesCS5A01G034700 chr5B 74.834 453 65 23 17 467 38563827 38564232 3.030000e-35 159.0
25 TraesCS5A01G034700 chr5B 85.714 119 16 1 2173 2291 11547386 11547503 1.110000e-24 124.0
26 TraesCS5A01G034700 chr5B 96.825 63 2 0 2011 2073 38680950 38681012 4.010000e-19 106.0
27 TraesCS5A01G034700 chr5B 90.000 60 6 0 907 966 38728327 38728386 8.740000e-11 78.7
28 TraesCS5A01G034700 chr6B 83.565 791 97 18 2164 2941 52156435 52157205 0.000000e+00 710.0
29 TraesCS5A01G034700 chr6B 80.971 783 117 20 2174 2941 586525969 586525204 2.520000e-165 592.0
30 TraesCS5A01G034700 chr3A 83.162 778 91 26 2175 2941 741116777 741116029 0.000000e+00 675.0
31 TraesCS5A01G034700 chr3A 85.489 634 78 6 2321 2941 19185967 19185335 0.000000e+00 649.0
32 TraesCS5A01G034700 chr3A 80.892 785 120 19 2172 2941 625234490 625233721 2.520000e-165 592.0
33 TraesCS5A01G034700 chr3A 83.701 589 61 21 2173 2749 22392301 22392866 9.340000e-145 523.0
34 TraesCS5A01G034700 chr1B 81.519 790 113 22 2169 2941 441997601 441996828 1.160000e-173 619.0
35 TraesCS5A01G034700 chr1B 79.146 820 105 38 1188 1970 554695160 554694370 9.410000e-140 507.0
36 TraesCS5A01G034700 chr1B 78.046 788 117 31 2173 2937 661050681 661049927 2.080000e-121 446.0
37 TraesCS5A01G034700 chr2B 81.234 794 115 22 2163 2941 31594436 31593662 6.970000e-171 610.0
38 TraesCS5A01G034700 chr7A 81.354 783 114 20 2174 2941 681575362 681576127 2.510000e-170 608.0
39 TraesCS5A01G034700 chr7A 81.298 786 113 22 2173 2941 660472558 660471790 9.010000e-170 606.0
40 TraesCS5A01G034700 chr7A 80.779 796 124 18 2161 2941 721562737 721563518 1.950000e-166 595.0
41 TraesCS5A01G034700 chr4B 80.971 783 119 19 2173 2941 30854628 30855394 7.020000e-166 593.0
42 TraesCS5A01G034700 chr4B 78.233 634 117 13 2321 2937 106489626 106490255 1.280000e-103 387.0
43 TraesCS5A01G034700 chr7B 81.210 777 103 27 2175 2937 702467194 702466447 1.170000e-163 586.0
44 TraesCS5A01G034700 chr3B 80.563 782 117 17 2173 2941 762628847 762629606 1.180000e-158 569.0
45 TraesCS5A01G034700 chr2D 85.556 270 35 4 1548 1815 118854240 118853973 2.230000e-71 279.0
46 TraesCS5A01G034700 chr2A 85.600 125 10 7 2170 2291 31615208 31615327 1.110000e-24 124.0
47 TraesCS5A01G034700 chr1D 87.879 66 3 3 2011 2075 411508443 411508382 4.070000e-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 TraesCS5A01G034700 chr5A 32146027 32148967 2940 False 5432.000000 5432 100.000000 1 2941 1 chr5A.!!$F4 2940
1 TraesCS5A01G034700 chr5A 30688344 30690204 1860 True 1004.333333 2026 95.961333 406 2173 3 chr5A.!!$R1 1767
2 TraesCS5A01G034700 chr5A 30701080 30705351 4271 True 403.500000 697 95.957500 1 2082 2 chr5A.!!$R2 2081
3 TraesCS5A01G034700 chr5A 31093456 31095326 1870 True 369.000000 390 79.010000 139 1843 2 chr5A.!!$R3 1704
4 TraesCS5A01G034700 chr5A 31296687 31297230 543 False 350.000000 350 78.674000 139 686 1 chr5A.!!$F2 547
5 TraesCS5A01G034700 chr5D 43047404 43049468 2064 False 757.000000 1201 90.536500 1 1862 2 chr5D.!!$F2 1861
6 TraesCS5A01G034700 chr1A 587921731 587922498 767 False 1005.000000 1005 90.347000 2171 2941 1 chr1A.!!$F2 770
7 TraesCS5A01G034700 chr1A 513640604 513641278 674 False 878.000000 878 90.190000 2264 2941 1 chr1A.!!$F1 677
8 TraesCS5A01G034700 chr1A 587945114 587945869 755 False 809.000000 809 86.100000 2173 2941 1 chr1A.!!$F3 768
9 TraesCS5A01G034700 chr5B 38652649 38653405 756 False 758.000000 758 84.663000 15 816 1 chr5B.!!$F2 801
10 TraesCS5A01G034700 chr5B 38679835 38681012 1177 False 436.000000 760 90.614667 875 2073 3 chr5B.!!$F6 1198
11 TraesCS5A01G034700 chr5B 38563827 38565487 1660 False 212.000000 265 76.686000 17 557 2 chr5B.!!$F5 540
12 TraesCS5A01G034700 chr6B 52156435 52157205 770 False 710.000000 710 83.565000 2164 2941 1 chr6B.!!$F1 777
13 TraesCS5A01G034700 chr6B 586525204 586525969 765 True 592.000000 592 80.971000 2174 2941 1 chr6B.!!$R1 767
14 TraesCS5A01G034700 chr3A 741116029 741116777 748 True 675.000000 675 83.162000 2175 2941 1 chr3A.!!$R3 766
15 TraesCS5A01G034700 chr3A 19185335 19185967 632 True 649.000000 649 85.489000 2321 2941 1 chr3A.!!$R1 620
16 TraesCS5A01G034700 chr3A 625233721 625234490 769 True 592.000000 592 80.892000 2172 2941 1 chr3A.!!$R2 769
17 TraesCS5A01G034700 chr3A 22392301 22392866 565 False 523.000000 523 83.701000 2173 2749 1 chr3A.!!$F1 576
18 TraesCS5A01G034700 chr1B 441996828 441997601 773 True 619.000000 619 81.519000 2169 2941 1 chr1B.!!$R1 772
19 TraesCS5A01G034700 chr1B 554694370 554695160 790 True 507.000000 507 79.146000 1188 1970 1 chr1B.!!$R2 782
20 TraesCS5A01G034700 chr1B 661049927 661050681 754 True 446.000000 446 78.046000 2173 2937 1 chr1B.!!$R3 764
21 TraesCS5A01G034700 chr2B 31593662 31594436 774 True 610.000000 610 81.234000 2163 2941 1 chr2B.!!$R1 778
22 TraesCS5A01G034700 chr7A 681575362 681576127 765 False 608.000000 608 81.354000 2174 2941 1 chr7A.!!$F1 767
23 TraesCS5A01G034700 chr7A 660471790 660472558 768 True 606.000000 606 81.298000 2173 2941 1 chr7A.!!$R1 768
24 TraesCS5A01G034700 chr7A 721562737 721563518 781 False 595.000000 595 80.779000 2161 2941 1 chr7A.!!$F2 780
25 TraesCS5A01G034700 chr4B 30854628 30855394 766 False 593.000000 593 80.971000 2173 2941 1 chr4B.!!$F1 768
26 TraesCS5A01G034700 chr4B 106489626 106490255 629 False 387.000000 387 78.233000 2321 2937 1 chr4B.!!$F2 616
27 TraesCS5A01G034700 chr7B 702466447 702467194 747 True 586.000000 586 81.210000 2175 2937 1 chr7B.!!$R1 762
28 TraesCS5A01G034700 chr3B 762628847 762629606 759 False 569.000000 569 80.563000 2173 2941 1 chr3B.!!$F1 768

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
680 5726 0.106335 TTGGCACCCGTCGTTAAGAA 59.894 50.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2485 8267 1.002087 CCGGCAGGAGTTCACTTAGTT 59.998 52.381 0.0 0.0 41.02 2.24 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
428 5434 7.148474 GGACACGCTTTTCAAGTAGATGATAAA 60.148 37.037 0.00 0.00 0.00 1.40
525 5533 1.740585 CGTGAAAAACCCAGTGTCACA 59.259 47.619 5.62 0.00 38.80 3.58
531 5539 3.806949 AAACCCAGTGTCACATGGTAT 57.193 42.857 14.67 5.34 34.58 2.73
632 5643 9.158233 CAATGAAATGATTTGCCTAAAATGTCT 57.842 29.630 0.00 0.00 38.64 3.41
680 5726 0.106335 TTGGCACCCGTCGTTAAGAA 59.894 50.000 0.00 0.00 0.00 2.52
725 5782 4.734920 AAAATGACCGCGCGCGTG 62.735 61.111 45.51 37.57 37.81 5.34
736 5793 0.573521 GCGCGCGTGTAGCTAAAATA 59.426 50.000 32.35 0.00 45.59 1.40
775 5832 0.594602 GCATGTCATGTGTGTGCTGT 59.405 50.000 14.26 0.00 33.25 4.40
1003 6545 2.055689 CTCCAGGCTCCAACACCACA 62.056 60.000 0.00 0.00 0.00 4.17
1005 6547 1.898574 CAGGCTCCAACACCACACC 60.899 63.158 0.00 0.00 0.00 4.16
1006 6548 2.194597 GGCTCCAACACCACACCA 59.805 61.111 0.00 0.00 0.00 4.17
1016 6559 0.037326 CACCACACCATAGTCACGCT 60.037 55.000 0.00 0.00 0.00 5.07
1017 6560 1.203758 CACCACACCATAGTCACGCTA 59.796 52.381 0.00 0.00 0.00 4.26
1019 6562 1.202417 CCACACCATAGTCACGCTAGG 60.202 57.143 0.00 0.00 32.45 3.02
1262 6860 1.035923 CGCCTCTTCCTCATCTGCTA 58.964 55.000 0.00 0.00 0.00 3.49
2154 7901 3.070446 TGGTCGTCTTTGATACAGTGGTT 59.930 43.478 0.00 0.00 0.00 3.67
2193 7940 1.698506 TTTTTCAACCGGGCTCACAT 58.301 45.000 6.32 0.00 0.00 3.21
2269 8026 4.394729 TGTCTAAAAGCCCAAACCACTAG 58.605 43.478 0.00 0.00 0.00 2.57
2270 8027 4.141344 TGTCTAAAAGCCCAAACCACTAGT 60.141 41.667 0.00 0.00 0.00 2.57
2296 8053 4.927267 AACAGAATGGAAGATACCACCA 57.073 40.909 0.00 0.00 43.62 4.17
2299 8056 3.054434 CAGAATGGAAGATACCACCACCA 60.054 47.826 0.00 0.00 43.03 4.17
2396 8159 1.123928 GATCCTGGAACGGACCATCT 58.876 55.000 0.00 0.00 39.34 2.90
2453 8232 2.200899 CAGCCCAACGAAAACAAAAGG 58.799 47.619 0.00 0.00 0.00 3.11
2454 8233 1.828595 AGCCCAACGAAAACAAAAGGT 59.171 42.857 0.00 0.00 0.00 3.50
2464 8243 5.773176 ACGAAAACAAAAGGTCCAGGATAAT 59.227 36.000 0.00 0.00 0.00 1.28
2471 8253 9.574516 AACAAAAGGTCCAGGATAATATATGAC 57.425 33.333 0.00 0.00 0.00 3.06
2485 8267 8.887036 ATAATATATGACGACAAACTTCTGCA 57.113 30.769 0.00 0.00 0.00 4.41
2492 8274 4.189231 ACGACAAACTTCTGCAACTAAGT 58.811 39.130 3.56 3.56 37.54 2.24
2498 8280 5.993106 AACTTCTGCAACTAAGTGAACTC 57.007 39.130 8.94 0.00 36.12 3.01
2504 8286 2.069273 CAACTAAGTGAACTCCTGCCG 58.931 52.381 0.00 0.00 0.00 5.69
2553 8335 1.455849 CCAGTGGGGAACAGCAAGA 59.544 57.895 0.00 0.00 40.01 3.02
2569 8353 3.488090 GAAAAGGGACCGAGCGCG 61.488 66.667 0.00 0.00 37.24 6.86
2581 8373 1.521681 GAGCGCGGACTAGCCAATT 60.522 57.895 8.83 0.00 35.94 2.32
2643 8435 0.900182 TGAGATCTGTCCACCAGCGT 60.900 55.000 0.00 0.00 41.25 5.07
2803 8595 6.811253 TCAAATGTAACTTTATTGCGGAGT 57.189 33.333 0.00 0.00 0.00 3.85
2812 8604 2.552599 TATTGCGGAGTGTCCAAACA 57.447 45.000 0.00 0.00 35.91 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 3874 5.707298 TCTCTTCTGAACACATGGAAAATCC 59.293 40.000 0.00 0.00 36.96 3.01
77 3944 9.857656 GCCTAACCCTAAACTATAAACCTTAAT 57.142 33.333 0.00 0.00 0.00 1.40
428 5434 4.586001 AGTTTTGCATTGTCATCTTGACCT 59.414 37.500 5.27 0.00 46.40 3.85
441 5447 2.172293 TGGGGCTTCAAAGTTTTGCATT 59.828 40.909 0.00 0.00 38.05 3.56
447 5453 2.833943 GGATGATGGGGCTTCAAAGTTT 59.166 45.455 0.00 0.00 0.00 2.66
449 5455 1.358787 TGGATGATGGGGCTTCAAAGT 59.641 47.619 0.00 0.00 0.00 2.66
548 5556 4.868171 CGTTAGCTGATGCAACCTTAACTA 59.132 41.667 0.00 0.00 42.74 2.24
619 5630 5.817816 GCTAGCTTCTAAGACATTTTAGGCA 59.182 40.000 7.70 0.00 32.66 4.75
621 5632 9.771534 ATAAGCTAGCTTCTAAGACATTTTAGG 57.228 33.333 32.51 0.00 37.47 2.69
657 5702 1.015085 TAACGACGGGTGCCAAATCG 61.015 55.000 0.00 6.50 38.71 3.34
680 5726 5.086104 AGCGTGATTTCTAGTAACACCAT 57.914 39.130 0.00 0.00 0.00 3.55
1003 6545 1.400737 GTCCCTAGCGTGACTATGGT 58.599 55.000 0.00 0.00 37.76 3.55
1005 6547 1.338337 CTGGTCCCTAGCGTGACTATG 59.662 57.143 5.59 0.00 0.00 2.23
1006 6548 1.063867 ACTGGTCCCTAGCGTGACTAT 60.064 52.381 5.59 0.00 0.00 2.12
1016 6559 2.512896 CCTACTCCTGTACTGGTCCCTA 59.487 54.545 17.42 0.00 0.00 3.53
1017 6560 1.288335 CCTACTCCTGTACTGGTCCCT 59.712 57.143 17.42 2.95 0.00 4.20
1019 6562 1.287146 TCCCTACTCCTGTACTGGTCC 59.713 57.143 17.42 0.00 0.00 4.46
1020 6563 2.822707 TCCCTACTCCTGTACTGGTC 57.177 55.000 17.42 0.00 0.00 4.02
1021 6564 2.888911 GCTTCCCTACTCCTGTACTGGT 60.889 54.545 17.42 3.20 0.00 4.00
1023 6566 2.457598 TGCTTCCCTACTCCTGTACTG 58.542 52.381 0.00 0.00 0.00 2.74
2131 7878 3.254060 CCACTGTATCAAAGACGACCAG 58.746 50.000 0.00 0.00 0.00 4.00
2193 7940 6.376864 TGATTGCGAAATTAATGGAAAGGAGA 59.623 34.615 0.00 0.00 0.00 3.71
2269 8026 6.535508 GTGGTATCTTCCATTCTGTTAGTGAC 59.464 42.308 0.00 0.00 39.81 3.67
2270 8027 6.351881 GGTGGTATCTTCCATTCTGTTAGTGA 60.352 42.308 0.00 0.00 39.81 3.41
2308 8065 8.450578 TTTTCAGTCTCATTTAGCTCTCAAAA 57.549 30.769 0.00 0.00 0.00 2.44
2309 8066 7.173907 CCTTTTCAGTCTCATTTAGCTCTCAAA 59.826 37.037 0.00 0.00 0.00 2.69
2310 8067 6.652481 CCTTTTCAGTCTCATTTAGCTCTCAA 59.348 38.462 0.00 0.00 0.00 3.02
2311 8068 6.169094 CCTTTTCAGTCTCATTTAGCTCTCA 58.831 40.000 0.00 0.00 0.00 3.27
2312 8069 5.584251 CCCTTTTCAGTCTCATTTAGCTCTC 59.416 44.000 0.00 0.00 0.00 3.20
2313 8070 5.495640 CCCTTTTCAGTCTCATTTAGCTCT 58.504 41.667 0.00 0.00 0.00 4.09
2314 8071 4.637977 CCCCTTTTCAGTCTCATTTAGCTC 59.362 45.833 0.00 0.00 0.00 4.09
2318 8076 4.567747 GCTCCCCCTTTTCAGTCTCATTTA 60.568 45.833 0.00 0.00 0.00 1.40
2453 8232 8.088981 AGTTTGTCGTCATATATTATCCTGGAC 58.911 37.037 0.00 0.00 0.00 4.02
2454 8233 8.190326 AGTTTGTCGTCATATATTATCCTGGA 57.810 34.615 0.00 0.00 0.00 3.86
2464 8243 6.163476 AGTTGCAGAAGTTTGTCGTCATATA 58.837 36.000 0.00 0.00 0.00 0.86
2470 8252 4.034048 CACTTAGTTGCAGAAGTTTGTCGT 59.966 41.667 7.73 0.00 33.60 4.34
2471 8253 4.270084 TCACTTAGTTGCAGAAGTTTGTCG 59.730 41.667 7.73 0.00 33.60 4.35
2485 8267 1.002087 CCGGCAGGAGTTCACTTAGTT 59.998 52.381 0.00 0.00 41.02 2.24
2498 8280 1.379527 GGTTTATGTCTTCCGGCAGG 58.620 55.000 0.00 0.00 39.46 4.85
2504 8286 1.379527 CCGCTGGGTTTATGTCTTCC 58.620 55.000 0.00 0.00 0.00 3.46
2569 8353 1.685180 GGGGTCCAAATTGGCTAGTCC 60.685 57.143 7.24 4.08 37.47 3.85
2581 8373 1.573108 GAGACAGAGATGGGGTCCAA 58.427 55.000 0.00 0.00 36.95 3.53
2741 8533 2.503895 CCTCTGGAGGCTGTTTTCAT 57.496 50.000 3.52 0.00 42.44 2.57
2803 8595 0.774276 TATGCTGGGGTGTTTGGACA 59.226 50.000 0.00 0.00 0.00 4.02
2812 8604 0.324552 TTGCTGCAATATGCTGGGGT 60.325 50.000 11.69 0.00 45.31 4.95
2875 8667 1.448540 GCAGAGCTTCGCTTGGCTA 60.449 57.895 1.29 0.00 39.88 3.93


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

AutoCloner maintained by Alex Coulton.