Multiple sequence alignment - TraesCS7B01G304100

Loading Multiple Alignment...

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 TraesCS7B01G304100 chr7B 100.000 3486 0 0 1 3486 544880151 544883636 0.000000e+00 6438.0
1 TraesCS7B01G304100 chr7B 95.684 1923 49 15 578 2492 544981824 544983720 0.000000e+00 3061.0
2 TraesCS7B01G304100 chr7B 97.852 1769 32 6 727 2492 545975549 545973784 0.000000e+00 3051.0
3 TraesCS7B01G304100 chr7B 94.970 338 15 1 3149 3486 97964645 97964980 2.380000e-146 529.0
4 TraesCS7B01G304100 chr7B 87.410 278 26 6 2724 2999 55837671 55837401 9.400000e-81 311.0
5 TraesCS7B01G304100 chr7D 94.911 2653 95 16 1 2644 513310955 513313576 0.000000e+00 4115.0
6 TraesCS7B01G304100 chr7D 92.882 1714 77 18 772 2478 514092143 514093818 0.000000e+00 2447.0
7 TraesCS7B01G304100 chr7D 94.213 864 28 6 772 1632 515238206 515237362 0.000000e+00 1299.0
8 TraesCS7B01G304100 chr7D 93.981 864 30 6 772 1632 515222000 515221156 0.000000e+00 1288.0
9 TraesCS7B01G304100 chr7D 96.144 752 29 0 1727 2478 515236979 515236228 0.000000e+00 1229.0
10 TraesCS7B01G304100 chr7D 95.878 752 31 0 1727 2478 515220773 515220022 0.000000e+00 1218.0
11 TraesCS7B01G304100 chr7D 87.156 763 64 15 2723 3473 73175826 73176566 0.000000e+00 835.0
12 TraesCS7B01G304100 chr7A 92.334 2009 109 22 738 2726 586693952 586691969 0.000000e+00 2815.0
13 TraesCS7B01G304100 chr7A 91.864 1942 112 27 560 2476 588740887 588738967 0.000000e+00 2669.0
14 TraesCS7B01G304100 chr7A 93.053 1497 59 19 986 2476 587518483 587519940 0.000000e+00 2146.0
15 TraesCS7B01G304100 chr7A 88.518 749 59 12 1 722 586694687 586693939 0.000000e+00 881.0
16 TraesCS7B01G304100 chr7A 92.516 481 29 6 519 994 588751018 588750540 0.000000e+00 682.0
17 TraesCS7B01G304100 chr7A 89.080 348 26 8 519 856 587518120 587518465 4.160000e-114 422.0
18 TraesCS7B01G304100 chr7A 79.296 483 80 17 3 472 588748602 588748127 1.560000e-83 320.0
19 TraesCS7B01G304100 chr7A 89.516 124 11 2 1 122 586918917 586918794 4.660000e-34 156.0
20 TraesCS7B01G304100 chr7A 91.228 114 10 0 1 114 586933926 586933813 4.660000e-34 156.0
21 TraesCS7B01G304100 chr5B 93.659 757 43 4 2727 3480 42140388 42141142 0.000000e+00 1127.0
22 TraesCS7B01G304100 chr1B 93.351 767 38 5 2723 3486 278474445 278475201 0.000000e+00 1122.0
23 TraesCS7B01G304100 chr1B 96.386 332 10 1 3155 3486 537326966 537326637 2.370000e-151 545.0
24 TraesCS7B01G304100 chr1B 89.222 334 28 7 2944 3276 192222855 192223181 9.010000e-111 411.0
25 TraesCS7B01G304100 chr4B 91.349 786 40 6 2727 3486 371980098 371979315 0.000000e+00 1050.0
26 TraesCS7B01G304100 chr5D 88.393 560 42 15 2727 3270 410638473 410639025 0.000000e+00 652.0
27 TraesCS7B01G304100 chr6D 86.528 527 36 16 2950 3473 412486243 412485749 6.580000e-152 547.0
28 TraesCS7B01G304100 chr6B 95.783 332 12 2 3155 3486 134484564 134484235 5.120000e-148 534.0
29 TraesCS7B01G304100 chr1A 94.970 338 15 1 3149 3486 528075938 528076273 2.380000e-146 529.0
30 TraesCS7B01G304100 chr2A 94.379 338 17 1 3149 3486 391355330 391355665 5.160000e-143 518.0
31 TraesCS7B01G304100 chr2A 84.540 511 53 11 2968 3473 686297720 686298209 1.880000e-132 483.0
32 TraesCS7B01G304100 chr3B 88.889 279 22 6 2723 2999 675570296 675570025 5.580000e-88 335.0
33 TraesCS7B01G304100 chr3B 89.091 275 21 6 2727 2999 482003145 482003412 2.010000e-87 333.0
34 TraesCS7B01G304100 chr2B 85.512 283 27 10 2717 2999 583524051 583523783 2.050000e-72 283.0
35 TraesCS7B01G304100 chr3A 80.000 90 12 6 118 203 44821452 44821539 1.040000e-05 62.1


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 TraesCS7B01G304100 chr7B 544880151 544883636 3485 False 6438 6438 100.0000 1 3486 1 chr7B.!!$F2 3485
1 TraesCS7B01G304100 chr7B 544981824 544983720 1896 False 3061 3061 95.6840 578 2492 1 chr7B.!!$F3 1914
2 TraesCS7B01G304100 chr7B 545973784 545975549 1765 True 3051 3051 97.8520 727 2492 1 chr7B.!!$R2 1765
3 TraesCS7B01G304100 chr7D 513310955 513313576 2621 False 4115 4115 94.9110 1 2644 1 chr7D.!!$F2 2643
4 TraesCS7B01G304100 chr7D 514092143 514093818 1675 False 2447 2447 92.8820 772 2478 1 chr7D.!!$F3 1706
5 TraesCS7B01G304100 chr7D 515236228 515238206 1978 True 1264 1299 95.1785 772 2478 2 chr7D.!!$R2 1706
6 TraesCS7B01G304100 chr7D 515220022 515222000 1978 True 1253 1288 94.9295 772 2478 2 chr7D.!!$R1 1706
7 TraesCS7B01G304100 chr7D 73175826 73176566 740 False 835 835 87.1560 2723 3473 1 chr7D.!!$F1 750
8 TraesCS7B01G304100 chr7A 588738967 588740887 1920 True 2669 2669 91.8640 560 2476 1 chr7A.!!$R3 1916
9 TraesCS7B01G304100 chr7A 586691969 586694687 2718 True 1848 2815 90.4260 1 2726 2 chr7A.!!$R4 2725
10 TraesCS7B01G304100 chr7A 587518120 587519940 1820 False 1284 2146 91.0665 519 2476 2 chr7A.!!$F1 1957
11 TraesCS7B01G304100 chr7A 588748127 588751018 2891 True 501 682 85.9060 3 994 2 chr7A.!!$R5 991
12 TraesCS7B01G304100 chr5B 42140388 42141142 754 False 1127 1127 93.6590 2727 3480 1 chr5B.!!$F1 753
13 TraesCS7B01G304100 chr1B 278474445 278475201 756 False 1122 1122 93.3510 2723 3486 1 chr1B.!!$F2 763
14 TraesCS7B01G304100 chr4B 371979315 371980098 783 True 1050 1050 91.3490 2727 3486 1 chr4B.!!$R1 759
15 TraesCS7B01G304100 chr5D 410638473 410639025 552 False 652 652 88.3930 2727 3270 1 chr5D.!!$F1 543

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
853 911 2.741486 TAGCCGGCAACCACAACCTC 62.741 60.0 31.54 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2663 4450 0.540923 GGATCAAGTGGCTCTGAGCT 59.459 55.0 27.09 7.31 41.99 4.09 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
540 566 7.446769 AGGTGAACCTTTTTAAAAACACAACT 58.553 30.769 22.95 17.65 46.09 3.16
698 730 5.399727 GGGATGAAATATTGGGGAGGTGTTA 60.400 44.000 0.00 0.00 0.00 2.41
717 766 6.295123 GGTGTTATATCCCATGTACGAGATGT 60.295 42.308 0.00 0.00 0.00 3.06
853 911 2.741486 TAGCCGGCAACCACAACCTC 62.741 60.000 31.54 0.00 0.00 3.85
867 925 4.389687 CCACAACCTCAAAATAGCAAATGC 59.610 41.667 0.00 0.00 42.49 3.56
948 1007 5.305585 CGATGTGTATATAAGGTTGGGCTT 58.694 41.667 0.00 0.00 0.00 4.35
1018 1473 4.321601 CCAAAATGGCGTTGAGGAACATTA 60.322 41.667 4.82 0.00 32.03 1.90
1032 1487 6.602009 TGAGGAACATTACGATGAGAGTCTTA 59.398 38.462 0.00 0.00 36.73 2.10
1969 2970 2.696125 ATCTCCATTGGCCCCGGT 60.696 61.111 0.00 0.00 0.00 5.28
2073 3074 0.243907 AAGGACGTGACCGACATCAG 59.756 55.000 0.00 0.00 37.88 2.90
2492 4263 1.647545 ATGCGACGCCTGAACCATTG 61.648 55.000 18.69 0.00 0.00 2.82
2495 4266 1.796796 GACGCCTGAACCATTGCTC 59.203 57.895 0.00 0.00 0.00 4.26
2503 4274 0.035820 GAACCATTGCTCCCACGGTA 60.036 55.000 0.00 0.00 0.00 4.02
2517 4288 4.159135 TCCCACGGTAGAAGAGATAACAAC 59.841 45.833 0.00 0.00 0.00 3.32
2522 4293 4.380233 CGGTAGAAGAGATAACAACACCGT 60.380 45.833 0.00 0.00 41.02 4.83
2523 4294 4.863131 GGTAGAAGAGATAACAACACCGTG 59.137 45.833 0.00 0.00 0.00 4.94
2546 4317 3.121929 AGGCACTCTCCTTCCATCTTA 57.878 47.619 0.00 0.00 30.82 2.10
2551 4322 0.744874 TCTCCTTCCATCTTACGCGG 59.255 55.000 12.47 0.00 0.00 6.46
2589 4360 5.217393 TCGGTATGTAGATTTTCGAATCCG 58.783 41.667 0.00 0.00 35.35 4.18
2593 4364 1.859080 GTAGATTTTCGAATCCGCGCT 59.141 47.619 5.56 0.00 35.37 5.92
2644 4415 4.468868 AGGTTGACCGCTTACCTTTATACT 59.531 41.667 0.00 0.00 39.19 2.12
2663 4450 9.984190 TTTATACTCAAATATATGTACGTGCCA 57.016 29.630 0.00 0.00 0.00 4.92
2668 4455 4.600692 AATATATGTACGTGCCAGCTCA 57.399 40.909 0.00 0.00 0.00 4.26
2695 4482 7.293073 AGCCACTTGATCCATATACTTTTGAT 58.707 34.615 0.00 0.00 0.00 2.57
2705 4492 7.424803 TCCATATACTTTTGATGATTTTGGCG 58.575 34.615 0.00 0.00 0.00 5.69
2708 4495 9.086336 CATATACTTTTGATGATTTTGGCGTTT 57.914 29.630 0.00 0.00 0.00 3.60
2832 4619 1.804151 CCGGCTGAAGAAAACGATTCA 59.196 47.619 0.00 0.00 34.41 2.57
2842 4629 6.884295 TGAAGAAAACGATTCACCCTATCATT 59.116 34.615 8.09 0.00 30.67 2.57
2855 4642 3.243771 CCCTATCATTTTCTACCTCGCGT 60.244 47.826 5.77 0.00 0.00 6.01
2946 4740 0.978146 CCCCTGGTCGTCCTCATCTT 60.978 60.000 0.00 0.00 34.23 2.40
2959 4762 1.515088 CATCTTCGTGCTCGTCGCT 60.515 57.895 8.17 0.00 40.11 4.93
3109 4922 2.279851 CCACGGTGTTGTGCTCGA 60.280 61.111 7.45 0.00 38.55 4.04
3127 4940 1.799181 CGAAGCATCACCGGTAGTCAG 60.799 57.143 6.87 0.00 0.00 3.51
3131 4944 0.807667 CATCACCGGTAGTCAGCAGC 60.808 60.000 6.87 0.00 0.00 5.25
3174 4991 5.526506 GATTTCCAGCAAATCTAATGGCT 57.473 39.130 1.73 0.00 45.02 4.75
3290 5130 1.746220 AGTGCGGTTGTAGCAAAAACA 59.254 42.857 0.00 0.00 46.97 2.83
3394 5234 4.634199 CTGGTTCCAGCAAAAATGACATT 58.366 39.130 5.89 0.00 0.00 2.71
3407 5247 0.605319 TGACATTGTCGCAGGTTCCC 60.605 55.000 11.97 0.00 34.95 3.97
3473 5313 3.559238 TCTGCGGAATGAAGCTTTTTC 57.441 42.857 0.00 7.45 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 125 9.590451 CCATCATGCACTTATGAAAAGTTTATT 57.410 29.630 6.38 0.00 40.21 1.40
325 326 2.330231 AAATGTTCATCGTGCGGTTG 57.670 45.000 0.00 0.00 0.00 3.77
328 330 2.276201 TCCTAAATGTTCATCGTGCGG 58.724 47.619 0.00 0.00 0.00 5.69
329 331 4.536364 ATTCCTAAATGTTCATCGTGCG 57.464 40.909 0.00 0.00 0.00 5.34
517 543 9.194271 TGTAGTTGTGTTTTTAAAAAGGTTCAC 57.806 29.630 13.58 16.47 0.00 3.18
698 730 5.265191 AGCTACATCTCGTACATGGGATAT 58.735 41.667 0.00 0.00 0.00 1.63
853 911 2.348971 TGCATGCGCATTTGCTATTTTG 59.651 40.909 29.90 15.21 45.36 2.44
888 946 7.148689 GGACAAGTGTTCGTCTTAATTATTCGT 60.149 37.037 0.00 0.00 32.57 3.85
948 1007 0.478072 TTTCAGGCCAGGAGCTTCAA 59.522 50.000 5.01 0.00 43.05 2.69
1018 1473 3.957497 AGGAGCAATAAGACTCTCATCGT 59.043 43.478 0.00 0.00 33.29 3.73
1032 1487 3.650950 ACCACCGCCAGGAGCAAT 61.651 61.111 0.00 0.00 44.04 3.56
1083 1538 1.406614 CCATCTGCGCTCTCCTTCTTT 60.407 52.381 9.73 0.00 0.00 2.52
1135 1620 3.525545 GTCGTACTCCCCGCCCTC 61.526 72.222 0.00 0.00 0.00 4.30
1205 1690 3.458044 TCTCTCTCCTTCAGCACCTAA 57.542 47.619 0.00 0.00 0.00 2.69
1644 2334 1.714366 GAATGCGCGCACGAATACG 60.714 57.895 39.05 0.00 36.15 3.06
1762 2763 4.148079 TGATAGAGATGCCTTCGATGAGT 58.852 43.478 0.00 0.00 0.00 3.41
1969 2970 2.618241 GCTGATGTTGACTTGTGTGGAA 59.382 45.455 0.00 0.00 0.00 3.53
2073 3074 2.127609 GCACGCAGTTCTTGACGC 60.128 61.111 0.00 0.00 41.61 5.19
2492 4263 1.404843 ATCTCTTCTACCGTGGGAGC 58.595 55.000 0.00 0.00 0.00 4.70
2495 4266 4.081862 TGTTGTTATCTCTTCTACCGTGGG 60.082 45.833 0.00 0.00 0.00 4.61
2503 4274 4.523173 TCTCACGGTGTTGTTATCTCTTCT 59.477 41.667 8.17 0.00 0.00 2.85
2546 4317 1.812571 AGAAAAGAAATCATGCCGCGT 59.187 42.857 4.92 0.00 0.00 6.01
2551 4322 6.124088 ACATACCGAGAAAAGAAATCATGC 57.876 37.500 0.00 0.00 0.00 4.06
2610 4381 2.742589 GCGGTCAACCTAGGAAGAAAAG 59.257 50.000 17.98 8.27 0.00 2.27
2644 4415 4.956085 AGCTGGCACGTACATATATTTGA 58.044 39.130 0.00 0.00 0.00 2.69
2663 4450 0.540923 GGATCAAGTGGCTCTGAGCT 59.459 55.000 27.09 7.31 41.99 4.09
2668 4455 6.506538 AAAGTATATGGATCAAGTGGCTCT 57.493 37.500 0.00 0.00 0.00 4.09
2695 4482 7.492669 TCAAAAGACAAATAAACGCCAAAATCA 59.507 29.630 0.00 0.00 0.00 2.57
2703 4490 7.068955 CCCAAAATCAAAAGACAAATAAACGC 58.931 34.615 0.00 0.00 0.00 4.84
2705 4492 7.924940 TGCCCAAAATCAAAAGACAAATAAAC 58.075 30.769 0.00 0.00 0.00 2.01
2708 4495 6.201806 CGTTGCCCAAAATCAAAAGACAAATA 59.798 34.615 0.00 0.00 0.00 1.40
2781 4568 2.202610 CGCGCTCAGATCCAACGA 60.203 61.111 5.56 0.00 0.00 3.85
2832 4619 3.243771 CGCGAGGTAGAAAATGATAGGGT 60.244 47.826 0.00 0.00 0.00 4.34
3109 4922 0.108138 GCTGACTACCGGTGATGCTT 60.108 55.000 19.93 0.00 0.00 3.91
3174 4991 2.545532 CGCAGAATTTTTGCTGGAACCA 60.546 45.455 9.87 0.00 39.38 3.67
3242 5082 0.324091 CTGCTGGAAGGGGCTTCATT 60.324 55.000 0.00 0.00 41.77 2.57
3243 5083 1.210204 TCTGCTGGAAGGGGCTTCAT 61.210 55.000 0.00 0.00 41.77 2.57
3251 5091 4.553323 CACTGAATTTTTCTGCTGGAAGG 58.447 43.478 0.00 0.00 35.16 3.46
3307 5147 4.430765 CGGCGAGCTACAACCGGT 62.431 66.667 0.00 0.00 41.95 5.28
3407 5247 4.442073 CGAGAAAGCTTCAACCAAAATGTG 59.558 41.667 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.