Multiple sequence alignment - TraesCS7A01G093100

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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 TraesCS7A01G093100 chr7A 100.000 1917 0 0 1 1917 56656989 56658905 0.000000e+00 3541.0
1 TraesCS7A01G093100 chr7A 96.123 748 25 3 1 745 56711812 56712558 0.000000e+00 1218.0
2 TraesCS7A01G093100 chr7A 81.760 1250 110 60 499 1659 56430175 56431395 0.000000e+00 937.0
3 TraesCS7A01G093100 chr7A 88.113 673 44 17 1253 1891 56738817 56739487 0.000000e+00 767.0
4 TraesCS7A01G093100 chr7A 99.667 300 1 0 1618 1917 56712593 56712892 1.390000e-152 549.0
5 TraesCS7A01G093100 chr7A 100.000 284 0 0 2365 2648 56659353 56659636 2.330000e-145 525.0
6 TraesCS7A01G093100 chr7A 97.535 284 7 0 2365 2648 56712908 56713191 1.100000e-133 486.0
7 TraesCS7A01G093100 chr7A 90.584 308 16 7 957 1252 56738455 56738761 1.910000e-106 396.0
8 TraesCS7A01G093100 chr7A 80.000 420 41 29 972 1361 55922664 55923070 1.210000e-68 270.0
9 TraesCS7A01G093100 chr7A 95.122 41 2 0 966 1006 56423604 56423644 6.120000e-07 65.8
10 TraesCS7A01G093100 chr7A 87.931 58 2 2 909 961 56982120 56982177 2.200000e-06 63.9
11 TraesCS7A01G093100 chr4A 90.278 720 45 13 957 1659 668323443 668324154 0.000000e+00 918.0
12 TraesCS7A01G093100 chr4A 87.019 701 63 17 971 1651 668305991 668306683 0.000000e+00 765.0
13 TraesCS7A01G093100 chr4A 84.805 691 61 32 959 1618 668287870 668288547 0.000000e+00 654.0
14 TraesCS7A01G093100 chr4A 86.705 519 54 11 1105 1618 668336965 668337473 1.780000e-156 562.0
15 TraesCS7A01G093100 chr4A 80.218 733 86 39 971 1654 668318934 668319656 1.830000e-136 496.0
16 TraesCS7A01G093100 chr4A 89.655 261 26 1 2388 2648 668324829 668325088 5.460000e-87 331.0
17 TraesCS7A01G093100 chr4A 81.979 283 31 9 596 877 668323104 668323367 3.430000e-54 222.0
18 TraesCS7A01G093100 chr4A 83.491 212 18 9 1704 1905 668324277 668324481 5.820000e-42 182.0
19 TraesCS7A01G093100 chr4A 76.547 307 56 10 372 671 714093276 714092979 1.270000e-33 154.0
20 TraesCS7A01G093100 chr4A 79.695 197 24 14 1704 1887 668359465 668359658 7.690000e-26 128.0
21 TraesCS7A01G093100 chr4A 88.889 72 5 3 1712 1781 668337650 668337720 4.700000e-13 86.1
22 TraesCS7A01G093100 chr4A 82.796 93 11 5 971 1061 668336799 668336888 7.860000e-11 78.7
23 TraesCS7A01G093100 chr4A 88.710 62 2 5 1723 1781 668365492 668365551 1.320000e-08 71.3
24 TraesCS7A01G093100 chr7D 82.613 972 84 45 957 1869 53577520 53578465 0.000000e+00 780.0
25 TraesCS7A01G093100 chr7D 85.870 736 48 23 1202 1905 53705013 53705724 0.000000e+00 732.0
26 TraesCS7A01G093100 chr7D 81.997 711 84 31 971 1654 53606047 53606740 4.950000e-157 564.0
27 TraesCS7A01G093100 chr7D 88.153 287 29 4 2367 2648 53712542 53712828 1.170000e-88 337.0
28 TraesCS7A01G093100 chr7D 79.423 520 64 27 1127 1618 53708076 53708580 7.070000e-86 327.0
29 TraesCS7A01G093100 chr7D 95.135 185 9 0 2365 2549 53705723 53705907 2.580000e-75 292.0
30 TraesCS7A01G093100 chr7D 78.935 432 45 27 545 939 53577043 53577465 4.380000e-63 252.0
31 TraesCS7A01G093100 chr7D 83.571 280 24 8 957 1215 53703325 53703603 2.630000e-60 243.0
32 TraesCS7A01G093100 chr7D 92.308 156 10 2 1221 1376 53711804 53711957 1.230000e-53 220.0
33 TraesCS7A01G093100 chr7D 78.676 272 29 17 1099 1361 53699868 53700119 1.270000e-33 154.0
34 TraesCS7A01G093100 chr7D 85.714 119 10 5 1790 1907 53631837 53631949 4.630000e-23 119.0
35 TraesCS7A01G093100 chr7D 89.796 49 3 1 971 1017 53699703 53699751 7.910000e-06 62.1
36 TraesCS7A01G093100 chr2A 81.271 299 45 10 372 662 618941 618646 5.700000e-57 231.0
37 TraesCS7A01G093100 chr1A 78.896 308 55 10 369 671 518771904 518772206 1.610000e-47 200.0
38 TraesCS7A01G093100 chr5A 78.966 290 52 9 369 656 702083988 702084270 3.480000e-44 189.0
39 TraesCS7A01G093100 chr5A 76.849 311 62 7 372 673 546102382 546102073 1.630000e-37 167.0
40 TraesCS7A01G093100 chr1B 77.023 309 58 12 377 677 565568684 565568381 5.860000e-37 165.0
41 TraesCS7A01G093100 chr4D 76.547 307 61 10 372 671 69660975 69660673 9.810000e-35 158.0
42 TraesCS7A01G093100 chr3B 76.452 310 60 10 369 671 17957081 17957384 3.530000e-34 156.0
43 TraesCS7A01G093100 chr6D 76.254 299 53 16 369 662 469096683 469096398 2.750000e-30 143.0
44 TraesCS7A01G093100 chr6A 75.841 327 54 10 368 670 176348038 176348363 2.750000e-30 143.0
45 TraesCS7A01G093100 chr1D 87.912 91 8 3 1 90 486314368 486314456 1.300000e-18 104.0
46 TraesCS7A01G093100 chr3D 83.838 99 15 1 1 98 281000344 281000246 2.810000e-15 93.5
47 TraesCS7A01G093100 chr2D 81.818 99 15 3 1 98 508079156 508079060 2.180000e-11 80.5


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 TraesCS7A01G093100 chr7A 56656989 56659636 2647 False 2033.000000 3541 100.0000 1 2648 2 chr7A.!!$F5 2647
1 TraesCS7A01G093100 chr7A 56430175 56431395 1220 False 937.000000 937 81.7600 499 1659 1 chr7A.!!$F3 1160
2 TraesCS7A01G093100 chr7A 56711812 56713191 1379 False 751.000000 1218 97.7750 1 2648 3 chr7A.!!$F6 2647
3 TraesCS7A01G093100 chr7A 56738455 56739487 1032 False 581.500000 767 89.3485 957 1891 2 chr7A.!!$F7 934
4 TraesCS7A01G093100 chr4A 668305991 668306683 692 False 765.000000 765 87.0190 971 1651 1 chr4A.!!$F2 680
5 TraesCS7A01G093100 chr4A 668287870 668288547 677 False 654.000000 654 84.8050 959 1618 1 chr4A.!!$F1 659
6 TraesCS7A01G093100 chr4A 668318934 668325088 6154 False 429.800000 918 85.1242 596 2648 5 chr4A.!!$F5 2052
7 TraesCS7A01G093100 chr4A 668336799 668337720 921 False 242.266667 562 86.1300 971 1781 3 chr4A.!!$F6 810
8 TraesCS7A01G093100 chr7D 53606047 53606740 693 False 564.000000 564 81.9970 971 1654 1 chr7D.!!$F1 683
9 TraesCS7A01G093100 chr7D 53577043 53578465 1422 False 516.000000 780 80.7740 545 1869 2 chr7D.!!$F3 1324
10 TraesCS7A01G093100 chr7D 53699703 53712828 13125 False 295.887500 732 86.6165 957 2648 8 chr7D.!!$F4 1691

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
828 4447 0.108804 CGAGCACATGGTCCTACGTT 60.109 55.0 0.0 0.0 39.23 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2498 14683 1.358152 CACCTCCAACCTAACCAGGA 58.642 55.0 0.0 0.0 45.91 3.86 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
102 103 5.852827 AGAAGCCAAATTGAATTTCCGAAA 58.147 33.333 0.00 0.00 0.00 3.46
170 171 7.973402 AGCCCCAAATTACAAAAAGATTACTT 58.027 30.769 0.00 0.00 38.05 2.24
387 389 3.401033 TTCTCTTCATGAAGGCGTTGA 57.599 42.857 30.33 18.74 38.88 3.18
402 404 3.436704 GGCGTTGATGTTGAAGAATCTCA 59.563 43.478 0.00 0.00 0.00 3.27
442 444 2.163010 GAGATGGTTTGTGCTGACATGG 59.837 50.000 0.00 0.00 30.13 3.66
489 491 8.919661 GTGTGGATTTGATCTTTTCAGATTTTC 58.080 33.333 0.00 0.00 40.14 2.29
513 515 8.821147 TCTTTTCGTGTTTAGACATAGCTTTA 57.179 30.769 0.00 0.00 38.23 1.85
539 541 7.775093 AGTCTTATATGACTTTGCTATTTGCCA 59.225 33.333 13.99 0.00 44.01 4.92
782 4378 1.492319 CGTCGCCAACAAAACGGAGA 61.492 55.000 0.00 0.00 0.00 3.71
785 4381 1.285950 GCCAACAAAACGGAGAGCC 59.714 57.895 0.00 0.00 0.00 4.70
801 4397 3.051210 CCCGCAGACAGACACTGA 58.949 61.111 5.76 0.00 37.54 3.41
802 4398 1.373497 CCCGCAGACAGACACTGAC 60.373 63.158 5.76 0.00 37.54 3.51
803 4399 1.662608 CCGCAGACAGACACTGACT 59.337 57.895 5.76 2.07 37.00 3.41
804 4400 0.387878 CCGCAGACAGACACTGACTC 60.388 60.000 5.76 0.00 34.66 3.36
806 4402 0.676184 GCAGACAGACACTGACTCCA 59.324 55.000 5.76 0.00 34.66 3.86
810 4406 0.955178 ACAGACACTGACTCCACTCG 59.045 55.000 5.76 0.00 35.18 4.18
811 4407 1.239347 CAGACACTGACTCCACTCGA 58.761 55.000 0.00 0.00 32.44 4.04
819 4415 0.459237 GACTCCACTCGAGCACATGG 60.459 60.000 13.61 12.93 43.01 3.66
828 4447 0.108804 CGAGCACATGGTCCTACGTT 60.109 55.000 0.00 0.00 39.23 3.99
844 4463 2.523015 ACGTTTTATCCTACGCACGAG 58.477 47.619 0.00 0.00 41.24 4.18
884 4503 3.488423 GGATCGATCCATGCCCCT 58.512 61.111 34.65 0.00 46.38 4.79
885 4504 1.002868 GGATCGATCCATGCCCCTG 60.003 63.158 34.65 0.00 46.38 4.45
886 4505 1.673665 GATCGATCCATGCCCCTGC 60.674 63.158 14.76 0.00 38.26 4.85
887 4506 3.201707 ATCGATCCATGCCCCTGCC 62.202 63.158 0.00 0.00 36.33 4.85
1042 4719 1.210538 TGCTCTGCCCATCTCATCTT 58.789 50.000 0.00 0.00 0.00 2.40
1072 4780 7.918033 CACATTCACTCAACTGATACTACTAGG 59.082 40.741 0.00 0.00 0.00 3.02
1079 4787 6.599445 TCAACTGATACTACTAGGTAGTCCC 58.401 44.000 12.74 7.67 44.86 4.46
1101 4837 1.852633 TCCTTCGGATCTCTTGCTCA 58.147 50.000 0.00 0.00 0.00 4.26
1150 4886 3.443925 CTCGACCAGAGGCTCGCA 61.444 66.667 9.22 0.00 43.20 5.10
1410 6660 8.155510 AGTTCATAGCACATATCTCATGAATGT 58.844 33.333 5.80 5.80 35.53 2.71
1430 6689 3.253188 TGTGTTGCCTGTAATTTCAGCTC 59.747 43.478 6.56 2.00 34.47 4.09
1532 6791 1.141019 GGCCTACTTCATCGTCGCA 59.859 57.895 0.00 0.00 0.00 5.10
2422 14604 7.442364 CCTCACACTCTAAATCTTTTGAGACAA 59.558 37.037 17.15 0.00 40.77 3.18
2439 14624 5.951148 TGAGACAATTTATTGGATGCCTTGA 59.049 36.000 7.33 0.00 41.96 3.02
2498 14683 2.921834 TTCTGTACTAGTGGAGCCCT 57.078 50.000 5.39 0.00 0.00 5.19
2596 14783 2.665649 ATCACATCCGCGTGTAAGAA 57.334 45.000 4.92 0.00 38.12 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 6.582677 TTCGGAAATTCAATTTGGCTTCTA 57.417 33.333 0.00 0.00 31.47 2.10
116 117 6.398918 ACACGCACTCTATTCTCATTTTACT 58.601 36.000 0.00 0.00 0.00 2.24
170 171 2.039216 TCACGTAGATTTGGGGCTTGAA 59.961 45.455 0.00 0.00 0.00 2.69
356 358 8.703336 GCCTTCATGAAGAGAAAATGTTTTTAC 58.297 33.333 32.49 5.62 40.79 2.01
387 389 6.718454 ACAAGGACAATGAGATTCTTCAACAT 59.282 34.615 0.00 0.00 0.00 2.71
402 404 5.241403 TCTCATTACACCACAAGGACAAT 57.759 39.130 0.00 0.00 38.69 2.71
442 444 5.105997 ACACCCGACAATCTACAGTAGTAAC 60.106 44.000 7.50 0.00 0.00 2.50
489 491 8.709646 ACTAAAGCTATGTCTAAACACGAAAAG 58.290 33.333 0.00 0.00 38.48 2.27
539 541 4.096382 CCAACTTCTACACACAAAACAGCT 59.904 41.667 0.00 0.00 0.00 4.24
782 4378 2.919856 AGTGTCTGTCTGCGGGCT 60.920 61.111 0.00 0.00 0.00 5.19
785 4381 0.387878 GAGTCAGTGTCTGTCTGCGG 60.388 60.000 0.00 0.00 30.81 5.69
801 4397 1.188219 ACCATGTGCTCGAGTGGAGT 61.188 55.000 22.67 7.74 45.03 3.85
802 4398 0.459237 GACCATGTGCTCGAGTGGAG 60.459 60.000 22.67 7.17 46.06 3.86
803 4399 1.591703 GACCATGTGCTCGAGTGGA 59.408 57.895 22.67 4.56 35.69 4.02
804 4400 1.448540 GGACCATGTGCTCGAGTGG 60.449 63.158 15.13 15.70 37.74 4.00
806 4402 0.818296 GTAGGACCATGTGCTCGAGT 59.182 55.000 15.13 0.00 35.47 4.18
810 4406 2.094762 AAACGTAGGACCATGTGCTC 57.905 50.000 0.00 0.00 35.47 4.26
811 4407 2.561478 AAAACGTAGGACCATGTGCT 57.439 45.000 0.00 0.00 38.00 4.40
819 4415 3.793492 GTGCGTAGGATAAAACGTAGGAC 59.207 47.826 0.00 0.00 41.10 3.85
828 4447 1.796253 CGTGCTCGTGCGTAGGATAAA 60.796 52.381 4.84 0.00 43.34 1.40
882 4501 1.766461 ACCGGATAAGAGGGGCAGG 60.766 63.158 9.46 0.00 0.00 4.85
883 4502 1.447643 CACCGGATAAGAGGGGCAG 59.552 63.158 9.46 0.00 0.00 4.85
884 4503 3.642078 CACCGGATAAGAGGGGCA 58.358 61.111 9.46 0.00 0.00 5.36
886 4505 1.048724 TCTGCACCGGATAAGAGGGG 61.049 60.000 9.46 0.00 0.00 4.79
887 4506 0.390860 CTCTGCACCGGATAAGAGGG 59.609 60.000 9.46 0.00 33.91 4.30
949 4582 2.430367 GGCAGGAAGACCGTGGTT 59.570 61.111 0.00 0.00 41.83 3.67
950 4583 3.637273 GGGCAGGAAGACCGTGGT 61.637 66.667 0.00 0.00 41.83 4.16
1042 4719 7.468141 AGTATCAGTTGAGTGAATGTGAGTA 57.532 36.000 0.00 0.00 0.00 2.59
1168 4904 1.300971 GGCCGGAACCGTTACCTTTC 61.301 60.000 5.05 0.00 37.81 2.62
1410 6660 2.483877 CGAGCTGAAATTACAGGCAACA 59.516 45.455 0.00 0.00 38.22 3.33
1414 6664 0.026803 CGCGAGCTGAAATTACAGGC 59.973 55.000 0.00 0.00 38.22 4.85
1430 6689 4.862092 AGCATCCTCACGCTCGCG 62.862 66.667 10.06 10.06 46.03 5.87
1532 6791 2.630889 TGGAGAGGATGGTCTTGTCT 57.369 50.000 0.00 0.00 0.00 3.41
2391 14573 4.464069 AGATTTAGAGTGTGAGGTCAGC 57.536 45.455 0.00 0.00 0.00 4.26
2422 14604 8.206189 CCTTATTTGTCAAGGCATCCAATAAAT 58.794 33.333 0.00 0.00 36.41 1.40
2439 14624 8.815912 ACTGCTAAATTTTCCATCCTTATTTGT 58.184 29.630 0.00 0.00 0.00 2.83
2498 14683 1.358152 CACCTCCAACCTAACCAGGA 58.642 55.000 0.00 0.00 45.91 3.86
2596 14783 7.504574 TCATTCTTTGGAATATCTCACATGCAT 59.495 33.333 0.00 0.00 39.87 3.96


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

AutoCloner maintained by Alex Coulton.