Multiple sequence alignment - TraesCS5A01G413100

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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 TraesCS5A01G413100 chr5A 100.000 3229 0 0 1 3229 601603421 601606649 0.000000e+00 5963
1 TraesCS5A01G413100 chr5A 85.484 1054 104 28 1282 2298 611980237 611979196 0.000000e+00 1053
2 TraesCS5A01G413100 chr6A 96.649 2208 48 8 1026 3229 203220229 203222414 0.000000e+00 3644
3 TraesCS5A01G413100 chr6A 91.137 1038 54 15 1 1034 203217657 203218660 0.000000e+00 1373
4 TraesCS5A01G413100 chr7A 93.226 1683 75 13 1282 2932 213100610 213102285 0.000000e+00 2440
5 TraesCS5A01G413100 chr7A 89.774 1281 77 18 3 1281 213099227 213100455 0.000000e+00 1591
6 TraesCS5A01G413100 chr7A 93.493 292 14 4 2943 3229 213102269 213102560 2.300000e-116 429
7 TraesCS5A01G413100 chr1B 92.705 1686 85 12 1282 2932 299551276 299549594 0.000000e+00 2398
8 TraesCS5A01G413100 chr1B 89.289 1167 89 23 124 1281 299552570 299551431 0.000000e+00 1430
9 TraesCS5A01G413100 chr1B 93.793 290 15 3 2943 3229 299549610 299549321 1.780000e-117 433
10 TraesCS5A01G413100 chr2B 92.632 1683 87 15 1282 2932 270743744 270742067 0.000000e+00 2386
11 TraesCS5A01G413100 chr2B 92.616 1395 66 12 1571 2930 406111686 406110294 0.000000e+00 1971
12 TraesCS5A01G413100 chr2B 89.453 1280 93 22 3 1281 270745138 270743900 0.000000e+00 1578
13 TraesCS5A01G413100 chr2B 90.990 1121 76 17 169 1281 406113195 406112092 0.000000e+00 1487
14 TraesCS5A01G413100 chr2B 94.464 289 14 2 2943 3229 406110308 406110020 8.220000e-121 444
15 TraesCS5A01G413100 chr2B 93.772 289 16 2 2943 3229 270742083 270741795 1.780000e-117 433
16 TraesCS5A01G413100 chr2B 94.340 106 6 0 3 108 406113306 406113201 2.580000e-36 163
17 TraesCS5A01G413100 chr2B 88.889 108 12 0 994 1101 733161788 733161895 2.020000e-27 134
18 TraesCS5A01G413100 chr7B 90.178 1517 106 22 1453 2932 433800077 433801587 0.000000e+00 1936
19 TraesCS5A01G413100 chr7B 89.848 591 40 6 1615 2188 289452902 289453489 0.000000e+00 741
20 TraesCS5A01G413100 chr7B 88.542 288 23 3 2943 3229 433801571 433801849 1.110000e-89 340
21 TraesCS5A01G413100 chr7B 76.547 307 38 6 3 309 304529431 304529159 1.560000e-28 137
22 TraesCS5A01G413100 chr5B 89.394 1518 114 24 1453 2932 106270984 106272492 0.000000e+00 1868
23 TraesCS5A01G413100 chr5B 89.273 289 29 2 2943 3229 106272476 106272764 8.520000e-96 361
24 TraesCS5A01G413100 chr3A 89.211 1520 116 20 1453 2932 282154337 282155848 0.000000e+00 1855
25 TraesCS5A01G413100 chr3A 89.273 289 29 2 2943 3229 282155832 282156120 8.520000e-96 361
26 TraesCS5A01G413100 chr5D 85.606 1056 102 27 1282 2298 441571388 441570344 0.000000e+00 1062
27 TraesCS5A01G413100 chr7D 85.333 1050 107 30 1282 2298 44718957 44717922 0.000000e+00 1042
28 TraesCS5A01G413100 chr6B 89.788 754 54 9 1453 2188 84994426 84995174 0.000000e+00 944
29 TraesCS5A01G413100 chr6B 89.431 123 11 1 3 123 605770612 605770490 1.550000e-33 154
30 TraesCS5A01G413100 chr2D 88.226 637 55 7 1739 2360 376351357 376351988 0.000000e+00 743
31 TraesCS5A01G413100 chr1A 83.901 764 78 21 1331 2059 538399897 538400650 0.000000e+00 688
32 TraesCS5A01G413100 chr6D 86.653 472 55 7 2464 2932 420229285 420228819 1.720000e-142 516
33 TraesCS5A01G413100 chr4B 87.356 348 35 7 1282 1624 564151802 564152145 1.090000e-104 390
34 TraesCS5A01G413100 chr4B 89.130 92 9 1 346 436 66633484 66633393 2.630000e-21 113
35 TraesCS5A01G413100 chr4B 84.404 109 17 0 3 111 66633850 66633742 1.220000e-19 108
36 TraesCS5A01G413100 chr4D 88.596 114 7 4 994 1101 451038015 451038128 2.020000e-27 134
37 TraesCS5A01G413100 chr4A 83.871 124 13 5 985 1101 15920395 15920272 9.470000e-21 111
38 TraesCS5A01G413100 chr3D 82.609 138 12 7 970 1101 562558986 562559117 9.470000e-21 111


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 TraesCS5A01G413100 chr5A 601603421 601606649 3228 False 5963.000000 5963 100.000000 1 3229 1 chr5A.!!$F1 3228
1 TraesCS5A01G413100 chr5A 611979196 611980237 1041 True 1053.000000 1053 85.484000 1282 2298 1 chr5A.!!$R1 1016
2 TraesCS5A01G413100 chr6A 203217657 203222414 4757 False 2508.500000 3644 93.893000 1 3229 2 chr6A.!!$F1 3228
3 TraesCS5A01G413100 chr7A 213099227 213102560 3333 False 1486.666667 2440 92.164333 3 3229 3 chr7A.!!$F1 3226
4 TraesCS5A01G413100 chr1B 299549321 299552570 3249 True 1420.333333 2398 91.929000 124 3229 3 chr1B.!!$R1 3105
5 TraesCS5A01G413100 chr2B 270741795 270745138 3343 True 1465.666667 2386 91.952333 3 3229 3 chr2B.!!$R1 3226
6 TraesCS5A01G413100 chr2B 406110020 406113306 3286 True 1016.250000 1971 93.102500 3 3229 4 chr2B.!!$R2 3226
7 TraesCS5A01G413100 chr7B 433800077 433801849 1772 False 1138.000000 1936 89.360000 1453 3229 2 chr7B.!!$F2 1776
8 TraesCS5A01G413100 chr7B 289452902 289453489 587 False 741.000000 741 89.848000 1615 2188 1 chr7B.!!$F1 573
9 TraesCS5A01G413100 chr5B 106270984 106272764 1780 False 1114.500000 1868 89.333500 1453 3229 2 chr5B.!!$F1 1776
10 TraesCS5A01G413100 chr3A 282154337 282156120 1783 False 1108.000000 1855 89.242000 1453 3229 2 chr3A.!!$F1 1776
11 TraesCS5A01G413100 chr5D 441570344 441571388 1044 True 1062.000000 1062 85.606000 1282 2298 1 chr5D.!!$R1 1016
12 TraesCS5A01G413100 chr7D 44717922 44718957 1035 True 1042.000000 1042 85.333000 1282 2298 1 chr7D.!!$R1 1016
13 TraesCS5A01G413100 chr6B 84994426 84995174 748 False 944.000000 944 89.788000 1453 2188 1 chr6B.!!$F1 735
14 TraesCS5A01G413100 chr2D 376351357 376351988 631 False 743.000000 743 88.226000 1739 2360 1 chr2D.!!$F1 621
15 TraesCS5A01G413100 chr1A 538399897 538400650 753 False 688.000000 688 83.901000 1331 2059 1 chr1A.!!$F1 728

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
807 824 0.462789 AGGGTCAACAGTCGTCGTTT 59.537 50.000 0.00 0.0 0.00 3.60 F
866 883 1.590259 GTGGCTCGATCCGCTTCTC 60.590 63.158 11.54 0.0 33.93 2.87 F
1329 3094 1.640149 TCCTTTCCAGGATTGCCATGA 59.360 47.619 0.00 0.0 45.20 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 3602 1.378514 CACCATCCAAAGTCCCCCG 60.379 63.158 0.0 0.0 0.0 5.73 R
1829 3680 1.677217 GGTGAATCTCAGTGTCCAGCC 60.677 57.143 0.0 0.0 0.0 4.85 R
2411 4302 5.188434 TGGCTTCTCTTATTGGATTGACAG 58.812 41.667 0.0 0.0 0.0 3.51 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
31 32 5.238650 TGGATCTTCTTTGGTTCTCGTTTTC 59.761 40.000 0.00 0.0 0.00 2.29
40 41 0.528033 TTCTCGTTTTCACCGTGCGA 60.528 50.000 0.00 0.0 0.00 5.10
73 74 1.841302 GACCATGACCTGTGGGCTCA 61.841 60.000 0.00 0.0 41.77 4.26
117 118 2.951458 CCTTTTTCGGGCACGGAC 59.049 61.111 9.32 0.0 41.39 4.79
118 119 2.554272 CTTTTTCGGGCACGGACG 59.446 61.111 9.32 0.0 41.39 4.79
119 120 2.961669 CTTTTTCGGGCACGGACGG 61.962 63.158 9.32 0.0 41.39 4.79
259 260 2.434331 GCTGCAGGTGGGGTTGTA 59.566 61.111 17.12 0.0 0.00 2.41
484 487 2.122167 GCCTCGTCATCCCTCTCGT 61.122 63.158 0.00 0.0 0.00 4.18
495 498 1.075698 TCCCTCTCGTTGTCCTCTCTT 59.924 52.381 0.00 0.0 0.00 2.85
515 518 2.128729 GGCATAGCCCTCTTCGTCT 58.871 57.895 0.00 0.0 44.06 4.18
679 690 1.491668 GGAGAGGGAAGGAAGGAGAC 58.508 60.000 0.00 0.0 0.00 3.36
722 739 4.946646 AGAGAAGATGAGAGGGAAAGACT 58.053 43.478 0.00 0.0 0.00 3.24
779 796 4.373116 GAGGGAGGCGCGACAACA 62.373 66.667 17.71 0.0 0.00 3.33
787 804 1.130613 GCGCGACAACAGACATGAC 59.869 57.895 12.10 0.0 0.00 3.06
802 819 1.048601 ATGACAGGGTCAACAGTCGT 58.951 50.000 2.87 0.0 45.96 4.34
807 824 0.462789 AGGGTCAACAGTCGTCGTTT 59.537 50.000 0.00 0.0 0.00 3.60
866 883 1.590259 GTGGCTCGATCCGCTTCTC 60.590 63.158 11.54 0.0 33.93 2.87
1037 2631 2.264794 CTACGCTCCGCAACCCTT 59.735 61.111 0.00 0.0 0.00 3.95
1103 2697 1.661463 TGCCTTCACCTCCTCTCATT 58.339 50.000 0.00 0.0 0.00 2.57
1329 3094 1.640149 TCCTTTCCAGGATTGCCATGA 59.360 47.619 0.00 0.0 45.20 3.07
1496 3278 5.401972 TGCACGATTGATGATTTTGTTTGAC 59.598 36.000 0.00 0.0 0.00 3.18
1753 3602 2.281345 AGTCTGTGTGCTGCTGCC 60.281 61.111 13.47 5.2 38.71 4.85
1829 3680 4.758674 TGGCTTCAAGAAGAATGAGAAGTG 59.241 41.667 13.70 0.0 40.79 3.16
2206 4087 2.236146 AGGTTCATGCTACCATTCGTGA 59.764 45.455 16.23 0.0 38.16 4.35
2504 4405 6.364568 TCAGTATGCAGTAATGGCTATCAT 57.635 37.500 0.00 0.0 34.57 2.45
2506 4407 7.226441 TCAGTATGCAGTAATGGCTATCATTT 58.774 34.615 0.00 0.0 40.59 2.32
2918 4825 5.842328 TCCCCTGTTTTCTTCTACTACAAGA 59.158 40.000 0.00 0.0 0.00 3.02
2919 4826 6.014499 TCCCCTGTTTTCTTCTACTACAAGAG 60.014 42.308 0.00 0.0 31.48 2.85
2920 4827 6.239629 CCCCTGTTTTCTTCTACTACAAGAGT 60.240 42.308 0.00 0.0 42.69 3.24
2921 4828 7.217906 CCCTGTTTTCTTCTACTACAAGAGTT 58.782 38.462 0.00 0.0 39.81 3.01
2922 4829 7.385478 CCCTGTTTTCTTCTACTACAAGAGTTC 59.615 40.741 0.00 0.0 39.81 3.01
2923 4830 8.145122 CCTGTTTTCTTCTACTACAAGAGTTCT 58.855 37.037 0.00 0.0 39.81 3.01
3185 5119 3.780804 TGCTGTATTAGTGGTGTTGGT 57.219 42.857 0.00 0.0 0.00 3.67
3187 5121 5.230323 TGCTGTATTAGTGGTGTTGGTTA 57.770 39.130 0.00 0.0 0.00 2.85
3188 5122 5.242434 TGCTGTATTAGTGGTGTTGGTTAG 58.758 41.667 0.00 0.0 0.00 2.34
3190 5124 5.350640 GCTGTATTAGTGGTGTTGGTTAGAC 59.649 44.000 0.00 0.0 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.096174 CACGGTGAAAACGAGAACCAAA 59.904 45.455 0.74 0.00 32.69 3.28
31 32 1.406219 CGAGAACTCATCGCACGGTG 61.406 60.000 3.15 3.15 32.81 4.94
40 41 1.134580 CATGGTCTGCCGAGAACTCAT 60.135 52.381 2.78 0.00 36.79 2.90
255 256 2.027561 CACGGGACCAAGGAGAATACAA 60.028 50.000 0.00 0.00 0.00 2.41
259 260 1.299976 GCACGGGACCAAGGAGAAT 59.700 57.895 0.00 0.00 0.00 2.40
531 538 2.611800 TCCATCACCTGCTGGGCT 60.612 61.111 14.82 0.00 39.10 5.19
532 539 2.124403 CTCCATCACCTGCTGGGC 60.124 66.667 14.82 0.00 39.10 5.36
533 540 2.593978 CCTCCATCACCTGCTGGG 59.406 66.667 14.82 4.64 41.89 4.45
534 541 2.124403 GCCTCCATCACCTGCTGG 60.124 66.667 8.29 8.29 39.83 4.85
535 542 2.513204 CGCCTCCATCACCTGCTG 60.513 66.667 0.00 0.00 0.00 4.41
536 543 4.479993 GCGCCTCCATCACCTGCT 62.480 66.667 0.00 0.00 0.00 4.24
722 739 1.018840 TCCCTCCTCTCCTTCCATCA 58.981 55.000 0.00 0.00 0.00 3.07
779 796 2.037772 GACTGTTGACCCTGTCATGTCT 59.962 50.000 13.36 0.00 42.40 3.41
787 804 0.249322 AACGACGACTGTTGACCCTG 60.249 55.000 0.00 0.00 33.40 4.45
866 883 1.231221 CTCCTCGTAGGTCCTGATCG 58.769 60.000 0.00 4.22 36.53 3.69
1037 2631 1.118965 TCTGCTGTGTCGGGAAGGAA 61.119 55.000 0.00 0.00 0.00 3.36
1329 3094 2.106566 AGCACTACAGTAGCAGCTCAT 58.893 47.619 18.07 2.41 36.20 2.90
1534 3317 9.661563 TCTTGTATTTCGATGTTTACCAACTAT 57.338 29.630 0.00 0.00 33.58 2.12
1753 3602 1.378514 CACCATCCAAAGTCCCCCG 60.379 63.158 0.00 0.00 0.00 5.73
1829 3680 1.677217 GGTGAATCTCAGTGTCCAGCC 60.677 57.143 0.00 0.00 0.00 4.85
2020 3901 6.860023 CCTGCTTCAGAAATAAGAACAAAGTG 59.140 38.462 0.00 0.00 32.44 3.16
2206 4087 6.041979 GGTTTATTTTGCCATGGTAGGATCAT 59.958 38.462 14.67 0.55 0.00 2.45
2411 4302 5.188434 TGGCTTCTCTTATTGGATTGACAG 58.812 41.667 0.00 0.00 0.00 3.51
2506 4407 9.383519 GAATGGACTACATGAGTATGAGAAAAA 57.616 33.333 0.00 0.00 40.44 1.94
2932 4839 8.940397 AATCATTAGAACTCTTCCCTCAAAAA 57.060 30.769 0.00 0.00 0.00 1.94
2933 4840 8.796475 CAAATCATTAGAACTCTTCCCTCAAAA 58.204 33.333 0.00 0.00 0.00 2.44
2934 4841 7.944554 ACAAATCATTAGAACTCTTCCCTCAAA 59.055 33.333 0.00 0.00 0.00 2.69
2935 4842 7.461749 ACAAATCATTAGAACTCTTCCCTCAA 58.538 34.615 0.00 0.00 0.00 3.02
2936 4843 7.020827 ACAAATCATTAGAACTCTTCCCTCA 57.979 36.000 0.00 0.00 0.00 3.86
2937 4844 8.261522 AGTACAAATCATTAGAACTCTTCCCTC 58.738 37.037 0.00 0.00 0.00 4.30
2938 4845 8.043710 CAGTACAAATCATTAGAACTCTTCCCT 58.956 37.037 0.00 0.00 0.00 4.20
2939 4846 7.824779 ACAGTACAAATCATTAGAACTCTTCCC 59.175 37.037 0.00 0.00 0.00 3.97
2940 4847 8.779354 ACAGTACAAATCATTAGAACTCTTCC 57.221 34.615 0.00 0.00 0.00 3.46
2943 4850 9.003658 CCAAACAGTACAAATCATTAGAACTCT 57.996 33.333 0.00 0.00 0.00 3.24
2944 4851 7.750903 GCCAAACAGTACAAATCATTAGAACTC 59.249 37.037 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.