Multiple sequence alignment - TraesCS7A01G389200

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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 TraesCS7A01G389200 chr7A 100.000 3564 0 0 1 3564 565441160 565437597 0.000000e+00 6582.0
1 TraesCS7A01G389200 chr7A 90.057 875 73 8 1216 2084 533581460 533582326 0.000000e+00 1122.0
2 TraesCS7A01G389200 chr7A 90.087 575 55 2 1 574 428640728 428640155 0.000000e+00 745.0
3 TraesCS7A01G389200 chr7A 81.188 202 29 8 644 838 299321251 299321450 1.710000e-33 154.0
4 TraesCS7A01G389200 chr7A 91.667 72 6 0 2084 2155 533585932 533586003 2.260000e-17 100.0
5 TraesCS7A01G389200 chr6A 99.028 2263 13 3 730 2992 68976739 68978992 0.000000e+00 4048.0
6 TraesCS7A01G389200 chr6A 99.154 591 4 1 2975 3564 68981416 68982006 0.000000e+00 1062.0
7 TraesCS7A01G389200 chr6A 90.625 576 49 5 1 574 478126951 478126379 0.000000e+00 760.0
8 TraesCS7A01G389200 chr6A 89.100 578 60 3 1 576 542840517 542839941 0.000000e+00 715.0
9 TraesCS7A01G389200 chr6A 96.923 130 4 0 646 775 68976611 68976740 5.990000e-53 219.0
10 TraesCS7A01G389200 chr6A 94.805 77 4 0 575 651 390968768 390968692 1.740000e-23 121.0
11 TraesCS7A01G389200 chr6A 81.967 122 19 3 647 767 592404033 592404152 2.260000e-17 100.0
12 TraesCS7A01G389200 chrUn 91.283 1021 58 7 2550 3563 297391446 297390450 0.000000e+00 1363.0
13 TraesCS7A01G389200 chrUn 91.283 1021 58 7 2550 3563 355898226 355899222 0.000000e+00 1363.0
14 TraesCS7A01G389200 chrUn 86.400 125 16 1 647 770 325797344 325797468 6.210000e-28 135.0
15 TraesCS7A01G389200 chr7D 92.447 940 60 5 1227 2160 467162330 467161396 0.000000e+00 1332.0
16 TraesCS7A01G389200 chr7D 92.742 248 16 1 2213 2460 467161392 467161147 1.220000e-94 357.0
17 TraesCS7A01G389200 chr7D 89.496 238 23 2 2720 2957 176564937 176564702 2.080000e-77 300.0
18 TraesCS7A01G389200 chr7D 85.664 286 27 5 2274 2553 467045104 467044827 4.500000e-74 289.0
19 TraesCS7A01G389200 chr7D 94.737 38 2 0 1090 1127 59674089 59674052 3.840000e-05 60.2
20 TraesCS7A01G389200 chr7B 90.423 804 59 7 1672 2460 490680524 490679724 0.000000e+00 1042.0
21 TraesCS7A01G389200 chr7B 92.202 436 29 2 1218 1653 490681523 490681093 2.350000e-171 612.0
22 TraesCS7A01G389200 chr7B 91.064 235 18 3 2720 2954 687561882 687562113 7.430000e-82 315.0
23 TraesCS7A01G389200 chr7B 86.400 125 16 1 647 770 709482574 709482450 6.210000e-28 135.0
24 TraesCS7A01G389200 chr5A 91.115 574 48 3 2 574 478491562 478490991 0.000000e+00 774.0
25 TraesCS7A01G389200 chr5A 96.104 77 3 0 575 651 56662533 56662609 3.740000e-25 126.0
26 TraesCS7A01G389200 chr5A 96.104 77 3 0 575 651 698917019 698916943 3.740000e-25 126.0
27 TraesCS7A01G389200 chr5A 94.805 77 4 0 575 651 70189386 70189310 1.740000e-23 121.0
28 TraesCS7A01G389200 chr5A 92.647 68 5 0 1061 1128 547793606 547793539 8.140000e-17 99.0
29 TraesCS7A01G389200 chr1D 90.543 571 51 3 1 569 296115383 296114814 0.000000e+00 752.0
30 TraesCS7A01G389200 chr1A 89.913 575 57 1 1 574 212373199 212372625 0.000000e+00 739.0
31 TraesCS7A01G389200 chr1A 94.387 481 27 0 877 1357 543393515 543393995 0.000000e+00 739.0
32 TraesCS7A01G389200 chr1A 96.460 339 11 1 2297 2634 543395601 543395939 3.110000e-155 558.0
33 TraesCS7A01G389200 chr1A 95.695 302 13 0 1310 1611 543395290 543395591 1.490000e-133 486.0
34 TraesCS7A01G389200 chr1A 99.153 118 1 0 2587 2704 543395939 543396056 2.790000e-51 213.0
35 TraesCS7A01G389200 chr1A 85.405 185 23 4 648 830 543392872 543393054 4.700000e-44 189.0
36 TraesCS7A01G389200 chr1A 80.833 120 20 3 649 767 576157896 576158013 1.360000e-14 91.6
37 TraesCS7A01G389200 chr1A 87.013 77 8 2 633 708 561613790 561613865 6.340000e-13 86.1
38 TraesCS7A01G389200 chr4A 89.637 579 56 4 2 578 567450492 567451068 0.000000e+00 734.0
39 TraesCS7A01G389200 chr4D 89.236 576 58 4 1 574 113925028 113925601 0.000000e+00 717.0
40 TraesCS7A01G389200 chr3A 86.371 653 80 8 1 650 404274325 404273679 0.000000e+00 704.0
41 TraesCS7A01G389200 chr5B 87.234 329 37 5 3237 3564 475697193 475697517 1.560000e-98 370.0
42 TraesCS7A01G389200 chr5B 94.805 77 4 0 575 651 335867349 335867425 1.740000e-23 121.0
43 TraesCS7A01G389200 chr5B 94.805 77 4 0 575 651 624684141 624684065 1.740000e-23 121.0
44 TraesCS7A01G389200 chr5B 94.805 77 4 0 575 651 628270354 628270278 1.740000e-23 121.0
45 TraesCS7A01G389200 chr2B 90.756 238 20 2 2720 2957 711202031 711201796 2.070000e-82 316.0
46 TraesCS7A01G389200 chr2B 83.333 216 28 8 687 898 409330080 409329869 3.630000e-45 193.0
47 TraesCS7A01G389200 chr2B 89.167 120 13 0 648 767 476575228 476575347 2.220000e-32 150.0
48 TraesCS7A01G389200 chr4B 90.638 235 20 2 2720 2954 241711293 241711525 9.610000e-81 311.0
49 TraesCS7A01G389200 chr6B 90.336 238 20 3 2720 2957 88829391 88829157 3.460000e-80 309.0
50 TraesCS7A01G389200 chr6B 76.224 286 46 12 647 928 155471510 155471777 8.030000e-27 132.0
51 TraesCS7A01G389200 chr3B 90.435 230 21 1 2720 2949 511057821 511057593 5.780000e-78 302.0
52 TraesCS7A01G389200 chr3B 79.787 188 30 7 713 898 10317837 10318018 2.890000e-26 130.0
53 TraesCS7A01G389200 chr3B 90.426 94 9 0 676 769 731268696 731268789 1.340000e-24 124.0
54 TraesCS7A01G389200 chr3D 80.087 231 22 9 648 865 501161924 501161705 2.220000e-32 150.0
55 TraesCS7A01G389200 chr5D 94.805 77 4 0 575 651 209822462 209822386 1.740000e-23 121.0
56 TraesCS7A01G389200 chr5D 92.308 39 3 0 1090 1128 220777917 220777879 4.970000e-04 56.5


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 TraesCS7A01G389200 chr7A 565437597 565441160 3563 True 6582.000000 6582 100.000000 1 3564 1 chr7A.!!$R2 3563
1 TraesCS7A01G389200 chr7A 428640155 428640728 573 True 745.000000 745 90.087000 1 574 1 chr7A.!!$R1 573
2 TraesCS7A01G389200 chr7A 533581460 533586003 4543 False 611.000000 1122 90.862000 1216 2155 2 chr7A.!!$F2 939
3 TraesCS7A01G389200 chr6A 68976611 68982006 5395 False 1776.333333 4048 98.368333 646 3564 3 chr6A.!!$F2 2918
4 TraesCS7A01G389200 chr6A 478126379 478126951 572 True 760.000000 760 90.625000 1 574 1 chr6A.!!$R2 573
5 TraesCS7A01G389200 chr6A 542839941 542840517 576 True 715.000000 715 89.100000 1 576 1 chr6A.!!$R3 575
6 TraesCS7A01G389200 chrUn 297390450 297391446 996 True 1363.000000 1363 91.283000 2550 3563 1 chrUn.!!$R1 1013
7 TraesCS7A01G389200 chrUn 355898226 355899222 996 False 1363.000000 1363 91.283000 2550 3563 1 chrUn.!!$F2 1013
8 TraesCS7A01G389200 chr7D 467161147 467162330 1183 True 844.500000 1332 92.594500 1227 2460 2 chr7D.!!$R4 1233
9 TraesCS7A01G389200 chr7B 490679724 490681523 1799 True 827.000000 1042 91.312500 1218 2460 2 chr7B.!!$R2 1242
10 TraesCS7A01G389200 chr5A 478490991 478491562 571 True 774.000000 774 91.115000 2 574 1 chr5A.!!$R2 572
11 TraesCS7A01G389200 chr1D 296114814 296115383 569 True 752.000000 752 90.543000 1 569 1 chr1D.!!$R1 568
12 TraesCS7A01G389200 chr1A 212372625 212373199 574 True 739.000000 739 89.913000 1 574 1 chr1A.!!$R1 573
13 TraesCS7A01G389200 chr1A 543392872 543396056 3184 False 437.000000 739 94.220000 648 2704 5 chr1A.!!$F3 2056
14 TraesCS7A01G389200 chr4A 567450492 567451068 576 False 734.000000 734 89.637000 2 578 1 chr4A.!!$F1 576
15 TraesCS7A01G389200 chr4D 113925028 113925601 573 False 717.000000 717 89.236000 1 574 1 chr4D.!!$F1 573
16 TraesCS7A01G389200 chr3A 404273679 404274325 646 True 704.000000 704 86.371000 1 650 1 chr3A.!!$R1 649

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
89 90 0.920664 TTTGACGCATAGATCGCACG 59.079 50.000 0.0 0.0 0.0 5.34 F
505 508 1.681780 CCCAATAGTGAACCGCCATGT 60.682 52.381 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1294 1756 5.005740 TGAGTTGAATGTCCTCCTGAAATG 58.994 41.667 0.0 0.0 0.00 2.32 R
3476 11949 2.325583 TTCGGTGATGGGTATCAAGC 57.674 50.000 0.0 0.0 44.49 4.01 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
26 27 1.672145 GGTCGAGCCAAGGTGACTAAC 60.672 57.143 2.39 0.0 42.68 2.34
89 90 0.920664 TTTGACGCATAGATCGCACG 59.079 50.000 0.00 0.0 0.00 5.34
250 251 2.793288 GGATTTTACCCAGGTTCGGA 57.207 50.000 0.00 0.0 0.00 4.55
463 466 6.434340 GTCTTTGTGGAATCCTCCTTGTATTT 59.566 38.462 0.00 0.0 42.94 1.40
505 508 1.681780 CCCAATAGTGAACCGCCATGT 60.682 52.381 0.00 0.0 0.00 3.21
601 605 5.989477 TCTTTGTGATGGGTTCGATCTTAT 58.011 37.500 0.00 0.0 0.00 1.73
602 606 5.817296 TCTTTGTGATGGGTTCGATCTTATG 59.183 40.000 0.00 0.0 0.00 1.90
614 618 3.643320 TCGATCTTATGGTGCTTGATCCT 59.357 43.478 0.00 0.0 32.36 3.24
620 624 5.425217 TCTTATGGTGCTTGATCCTAGTGAA 59.575 40.000 0.00 0.0 0.00 3.18
622 626 4.365514 TGGTGCTTGATCCTAGTGAAAA 57.634 40.909 0.00 0.0 0.00 2.29
683 687 3.118112 CCCTGAAGAACTCATAGGCACAT 60.118 47.826 0.00 0.0 32.14 3.21
767 815 5.163195 ACCGAGGGCATCTTAGTAATTTCAT 60.163 40.000 0.00 0.0 0.00 2.57
879 1341 4.787280 CCCCGCCTCCTCTCCTGT 62.787 72.222 0.00 0.0 0.00 4.00
1294 1756 2.312390 TGGCCCTTGAAACAACTAACC 58.688 47.619 0.00 0.0 0.00 2.85
2664 8688 8.014070 TGCCATTTCTGATATGACATCATTTT 57.986 30.769 9.31 0.0 37.76 1.82
3476 11949 7.962373 TGCACTTTAACTCAATTATTGTCGATG 59.038 33.333 4.77 0.0 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.936764 CATCTTCATCGACGGCTCGG 60.937 60.000 0.00 0.00 40.58 4.63
71 72 0.869880 CCGTGCGATCTATGCGTCAA 60.870 55.000 0.00 0.00 34.24 3.18
78 79 0.534427 TCGTCTCCCGTGCGATCTAT 60.534 55.000 0.00 0.00 37.94 1.98
89 90 4.555262 GATGAGAATTCAGATCGTCTCCC 58.445 47.826 8.44 1.86 36.49 4.30
362 364 1.202463 CCGAGGCCAGACTAGTCAATG 60.202 57.143 24.44 14.45 0.00 2.82
585 589 2.808543 GCACCATAAGATCGAACCCATC 59.191 50.000 0.00 0.00 0.00 3.51
586 590 2.439507 AGCACCATAAGATCGAACCCAT 59.560 45.455 0.00 0.00 0.00 4.00
601 605 4.365514 TTTTCACTAGGATCAAGCACCA 57.634 40.909 0.00 0.00 0.00 4.17
620 624 4.202493 ACATACGTGTAGGTTCCCCTTTTT 60.202 41.667 0.00 0.00 42.66 1.94
622 626 2.908351 ACATACGTGTAGGTTCCCCTTT 59.092 45.455 0.00 0.00 42.66 3.11
683 687 3.611674 TGACGTGGCTGGCTTCGA 61.612 61.111 20.48 0.00 0.00 3.71
1294 1756 5.005740 TGAGTTGAATGTCCTCCTGAAATG 58.994 41.667 0.00 0.00 0.00 2.32
3476 11949 2.325583 TTCGGTGATGGGTATCAAGC 57.674 50.000 0.00 0.00 44.49 4.01


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

AutoCloner maintained by Alex Coulton.