Multiple sequence alignment - TraesCS6A01G326400

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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 TraesCS6A01G326400 chr6A 100.000 3041 0 0 1 3041 559866029 559862989 0.000000e+00 5616.0
1 TraesCS6A01G326400 chr6D 93.714 2259 84 24 582 2786 414794529 414792275 0.000000e+00 3332.0
2 TraesCS6A01G326400 chr6D 92.327 782 35 7 1 762 414795305 414794529 0.000000e+00 1088.0
3 TraesCS6A01G326400 chr6D 93.436 259 15 2 2785 3041 414792243 414791985 1.710000e-102 383.0
4 TraesCS6A01G326400 chr6D 100.000 31 0 0 2721 2751 122690247 122690277 1.180000e-04 58.4
5 TraesCS6A01G326400 chr6B 96.137 1553 51 4 919 2462 625380716 625379164 0.000000e+00 2527.0
6 TraesCS6A01G326400 chr6B 91.927 929 51 8 1 914 625381714 625380795 0.000000e+00 1279.0
7 TraesCS6A01G326400 chr6B 93.133 466 17 5 2590 3041 625379047 625378583 0.000000e+00 669.0
8 TraesCS6A01G326400 chr3D 86.567 67 5 4 2720 2784 502894318 502894382 1.510000e-08 71.3
9 TraesCS6A01G326400 chr3D 84.848 66 6 4 2720 2784 27552579 27552517 2.530000e-06 63.9
10 TraesCS6A01G326400 chr3B 86.567 67 5 4 2720 2784 663979171 663979235 1.510000e-08 71.3
11 TraesCS6A01G326400 chrUn 84.375 64 8 1 2720 2781 263815761 263815824 9.100000e-06 62.1
12 TraesCS6A01G326400 chr3A 84.375 64 8 1 2720 2781 533619759 533619822 9.100000e-06 62.1
13 TraesCS6A01G326400 chr7B 97.059 34 1 0 2720 2753 314455109 314455076 1.180000e-04 58.4
14 TraesCS6A01G326400 chr2D 97.059 34 1 0 2720 2753 265947845 265947812 1.180000e-04 58.4


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 TraesCS6A01G326400 chr6A 559862989 559866029 3040 True 5616.000000 5616 100.000000 1 3041 1 chr6A.!!$R1 3040
1 TraesCS6A01G326400 chr6D 414791985 414795305 3320 True 1601.000000 3332 93.159000 1 3041 3 chr6D.!!$R1 3040
2 TraesCS6A01G326400 chr6B 625378583 625381714 3131 True 1491.666667 2527 93.732333 1 3041 3 chr6B.!!$R1 3040

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
245 247 0.546122 TTGTGACTTCTGGTGCCTGT 59.454 50.0 0.0 0.0 0.0 4.00 F
1071 1347 0.105964 CGCCGTATCCCATTCCTTCA 59.894 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1221 1497 0.322098 TTCCACACATGTAAGGGCGG 60.322 55.0 13.95 0.0 0.0 6.13 R
2488 2773 2.435533 TGTCCGTACGCACAATGTTA 57.564 45.0 10.13 0.0 0.0 2.41 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
100 102 5.026790 AGTCTTATCTGGCTCTTAGGTGTT 58.973 41.667 0.00 0.00 0.00 3.32
163 165 7.099266 TCATTATTTAATGCTCCTGGTTGTG 57.901 36.000 5.59 0.00 42.06 3.33
184 186 2.352715 GCCAGCGCCTTGTTTCTTTATT 60.353 45.455 2.29 0.00 0.00 1.40
185 187 3.860754 GCCAGCGCCTTGTTTCTTTATTT 60.861 43.478 2.29 0.00 0.00 1.40
186 188 4.617298 GCCAGCGCCTTGTTTCTTTATTTA 60.617 41.667 2.29 0.00 0.00 1.40
188 190 5.743872 CCAGCGCCTTGTTTCTTTATTTATC 59.256 40.000 2.29 0.00 0.00 1.75
189 191 6.404734 CCAGCGCCTTGTTTCTTTATTTATCT 60.405 38.462 2.29 0.00 0.00 1.98
190 192 6.470235 CAGCGCCTTGTTTCTTTATTTATCTG 59.530 38.462 2.29 0.00 0.00 2.90
191 193 5.230097 GCGCCTTGTTTCTTTATTTATCTGC 59.770 40.000 0.00 0.00 0.00 4.26
194 196 7.323420 GCCTTGTTTCTTTATTTATCTGCCTT 58.677 34.615 0.00 0.00 0.00 4.35
242 244 3.437049 GTCTATTTGTGACTTCTGGTGCC 59.563 47.826 0.00 0.00 0.00 5.01
245 247 0.546122 TTGTGACTTCTGGTGCCTGT 59.454 50.000 0.00 0.00 0.00 4.00
285 287 7.337689 CCATTCTTGTGGATCTGAAGTTTGATA 59.662 37.037 0.00 0.00 42.02 2.15
291 293 3.563390 GGATCTGAAGTTTGATAGCCTGC 59.437 47.826 0.00 0.00 0.00 4.85
292 294 2.621338 TCTGAAGTTTGATAGCCTGCG 58.379 47.619 0.00 0.00 0.00 5.18
293 295 1.063174 CTGAAGTTTGATAGCCTGCGC 59.937 52.381 0.00 0.00 0.00 6.09
324 338 3.369546 AAGCTGCAATTGTGTGGTAAC 57.630 42.857 7.40 0.00 0.00 2.50
331 345 3.296628 CAATTGTGTGGTAACGTTGCTC 58.703 45.455 16.07 10.07 42.51 4.26
334 348 1.937223 TGTGTGGTAACGTTGCTCAAG 59.063 47.619 16.07 0.00 42.51 3.02
356 372 7.736447 AAGAGTTTTCTTGTCTCAATCGAAT 57.264 32.000 0.00 0.00 42.04 3.34
361 377 5.536554 TTCTTGTCTCAATCGAATTCTGC 57.463 39.130 3.52 0.00 0.00 4.26
365 381 0.940126 CTCAATCGAATTCTGCGGGG 59.060 55.000 3.52 0.00 0.00 5.73
393 409 7.432252 GGTCGATTTGGTTATGAAAACATGATC 59.568 37.037 0.00 0.00 30.76 2.92
394 410 7.164171 GTCGATTTGGTTATGAAAACATGATCG 59.836 37.037 0.00 12.44 43.21 3.69
403 425 5.295431 TGAAAACATGATCGTTTGCCTAG 57.705 39.130 0.00 0.00 39.04 3.02
426 448 0.961019 TTGATGTGCTCCTTGGTTGC 59.039 50.000 0.00 0.00 0.00 4.17
459 481 5.048782 TGGCAATCTGTTGATACACTTTCAC 60.049 40.000 0.00 0.00 37.53 3.18
502 524 2.542766 ACTTGTGTGCTTTTGACACG 57.457 45.000 0.00 0.00 45.63 4.49
527 549 7.169982 CGATTCACAACCTTCTACATTATCTCC 59.830 40.741 0.00 0.00 0.00 3.71
613 635 6.315891 GGCTTGGCTTTGCATATTCATTTTTA 59.684 34.615 0.00 0.00 0.00 1.52
641 663 4.689062 AGGGTAGAACTTTCTCCTGATGA 58.311 43.478 0.00 0.00 38.70 2.92
798 1000 4.451774 GCAGAGAATATGCTGGATGAGTTC 59.548 45.833 0.00 0.00 40.59 3.01
802 1004 7.331440 CAGAGAATATGCTGGATGAGTTCATAC 59.669 40.741 0.00 0.00 36.57 2.39
835 1037 6.377996 CCCCTTCATATGACTTTGATTGTCAA 59.622 38.462 4.48 0.00 45.82 3.18
878 1080 7.654022 AGGGACTTTCTTTTGTTTGTTCATA 57.346 32.000 0.00 0.00 27.25 2.15
881 1083 9.325198 GGGACTTTCTTTTGTTTGTTCATATTT 57.675 29.630 0.00 0.00 0.00 1.40
892 1094 6.097554 TGTTTGTTCATATTTCTGGTGTGGTT 59.902 34.615 0.00 0.00 0.00 3.67
922 1198 5.694995 TCTCCCCTCCTTTATTTGCTATTG 58.305 41.667 0.00 0.00 0.00 1.90
937 1213 8.773033 ATTTGCTATTGATCCTCCTGTTTATT 57.227 30.769 0.00 0.00 0.00 1.40
941 1217 7.715249 TGCTATTGATCCTCCTGTTTATTGTAC 59.285 37.037 0.00 0.00 0.00 2.90
1071 1347 0.105964 CGCCGTATCCCATTCCTTCA 59.894 55.000 0.00 0.00 0.00 3.02
1083 1359 3.278574 CATTCCTTCATACCGCTGGAAA 58.721 45.455 1.50 0.00 39.77 3.13
1161 1437 2.355108 GGAAGATGCCAACTGCTCTGTA 60.355 50.000 0.00 0.00 42.00 2.74
1203 1479 1.069636 GCTGTGCTTCTCCTTTGTTCG 60.070 52.381 0.00 0.00 0.00 3.95
1221 1497 1.364626 CGTCTCATGACAAGGGCTGC 61.365 60.000 0.00 0.00 43.06 5.25
1440 1716 1.349067 GGTGGACTGTGGTAGAACCT 58.651 55.000 0.00 0.00 39.58 3.50
1452 1728 3.057033 TGGTAGAACCTGCTCGAAGTTAC 60.057 47.826 0.00 0.00 39.58 2.50
1458 1734 2.567615 ACCTGCTCGAAGTTACCTGAAT 59.432 45.455 0.00 0.00 0.00 2.57
1461 1737 2.280628 GCTCGAAGTTACCTGAATGGG 58.719 52.381 0.00 0.00 41.11 4.00
1578 1854 1.450312 GGAAGTGGATCCTGCCGTG 60.450 63.158 14.23 0.00 36.50 4.94
1809 2085 1.151668 GTCAAGTTGCTCAGCGACAT 58.848 50.000 19.71 4.07 44.70 3.06
1815 2091 1.344226 TTGCTCAGCGACATCGAACG 61.344 55.000 5.26 0.00 43.02 3.95
1938 2214 2.722487 GGCGACGACGAGGATGAT 59.278 61.111 12.29 0.00 42.66 2.45
2334 2615 2.139917 TGTGTTGGATACTGCGTTGTC 58.860 47.619 0.00 0.00 37.61 3.18
2338 2620 0.036765 TGGATACTGCGTTGTCCACC 60.037 55.000 0.00 0.00 35.91 4.61
2346 2628 3.009723 CTGCGTTGTCCACCTATTTCAT 58.990 45.455 0.00 0.00 0.00 2.57
2434 2719 4.093850 CAGACATGAGAACGATGAAATGCA 59.906 41.667 0.00 0.00 0.00 3.96
2437 2722 4.397103 ACATGAGAACGATGAAATGCACAT 59.603 37.500 0.00 0.00 0.00 3.21
2438 2723 4.604843 TGAGAACGATGAAATGCACATC 57.395 40.909 5.86 5.86 40.19 3.06
2488 2773 2.270434 TAGTGCTCCCTTCCTTCCAT 57.730 50.000 0.00 0.00 0.00 3.41
2503 2788 3.242284 CCTTCCATAACATTGTGCGTACG 60.242 47.826 11.84 11.84 0.00 3.67
2592 2899 4.420168 CGTCGGATTTTTAAACATGGCAT 58.580 39.130 0.00 0.00 0.00 4.40
2633 3003 4.961438 AACTGAACATGGCAAGGATTTT 57.039 36.364 0.00 0.00 0.00 1.82
2678 3048 7.039504 ACTGACATCAATTTGTAGCAAAATCCT 60.040 33.333 0.00 0.00 0.00 3.24
2757 3134 8.225603 AGTTTATGAAGCTTGACTTTTGAAGA 57.774 30.769 2.10 0.00 39.29 2.87
2758 3135 8.854117 AGTTTATGAAGCTTGACTTTTGAAGAT 58.146 29.630 2.10 0.00 39.29 2.40
2931 3346 4.737946 GCTCTACATGCTACGATTTCCAGT 60.738 45.833 0.00 0.00 0.00 4.00
2936 3351 4.811024 ACATGCTACGATTTCCAGTACATG 59.189 41.667 0.00 0.00 37.78 3.21
3003 3418 8.986477 ATAACAAATTAACAACAGATCAAGGC 57.014 30.769 0.00 0.00 0.00 4.35
3033 3448 4.443457 GCTCTACATGCTACTGATTTCCCA 60.443 45.833 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.364735 TCAGATCTGCCAGATTAGATGTGAA 59.635 40.000 18.36 0.00 45.21 3.18
135 137 9.037737 CAACCAGGAGCATTAAATAATGAAATG 57.962 33.333 15.53 8.45 44.40 2.32
163 165 0.596082 TAAAGAAACAAGGCGCTGGC 59.404 50.000 7.64 0.00 38.90 4.85
184 186 3.844211 AGTACAGTTGGGAAGGCAGATAA 59.156 43.478 0.00 0.00 0.00 1.75
185 187 3.450904 AGTACAGTTGGGAAGGCAGATA 58.549 45.455 0.00 0.00 0.00 1.98
186 188 2.269940 AGTACAGTTGGGAAGGCAGAT 58.730 47.619 0.00 0.00 0.00 2.90
188 190 2.154462 CAAGTACAGTTGGGAAGGCAG 58.846 52.381 0.00 0.00 0.00 4.85
189 191 1.202879 CCAAGTACAGTTGGGAAGGCA 60.203 52.381 7.80 0.00 43.02 4.75
190 192 1.073284 TCCAAGTACAGTTGGGAAGGC 59.927 52.381 14.43 0.00 46.24 4.35
191 193 3.610911 GATCCAAGTACAGTTGGGAAGG 58.389 50.000 14.43 0.00 46.24 3.46
194 196 1.913419 GGGATCCAAGTACAGTTGGGA 59.087 52.381 15.23 4.24 46.24 4.37
291 293 0.179205 GCAGCTTTACTCTTGCAGCG 60.179 55.000 0.00 0.00 37.35 5.18
292 294 0.877071 TGCAGCTTTACTCTTGCAGC 59.123 50.000 0.00 0.00 39.20 5.25
293 295 3.844577 ATTGCAGCTTTACTCTTGCAG 57.155 42.857 0.00 0.00 33.70 4.41
334 348 7.743838 CAGAATTCGATTGAGACAAGAAAACTC 59.256 37.037 0.00 0.00 0.00 3.01
344 360 1.594862 CCCGCAGAATTCGATTGAGAC 59.405 52.381 0.00 0.00 0.00 3.36
365 381 4.218852 TGTTTTCATAACCAAATCGACCCC 59.781 41.667 0.00 0.00 0.00 4.95
393 409 3.667960 GCACATCAACTTCTAGGCAAACG 60.668 47.826 0.00 0.00 0.00 3.60
394 410 3.503748 AGCACATCAACTTCTAGGCAAAC 59.496 43.478 0.00 0.00 0.00 2.93
403 425 2.508526 ACCAAGGAGCACATCAACTTC 58.491 47.619 0.00 0.00 0.00 3.01
426 448 8.785946 TGTATCAACAGATTGCCAATATACATG 58.214 33.333 4.96 0.00 35.63 3.21
502 524 7.169982 CGGAGATAATGTAGAAGGTTGTGAATC 59.830 40.741 0.00 0.00 0.00 2.52
527 549 5.111989 ACACATCATAGATCAAAGTCCACG 58.888 41.667 0.00 0.00 0.00 4.94
613 635 6.960542 TCAGGAGAAAGTTCTACCCTAGAAAT 59.039 38.462 0.00 0.00 45.56 2.17
641 663 4.723789 ACTGGGATCATACACTTCCAAGAT 59.276 41.667 0.00 0.00 34.66 2.40
798 1000 7.941238 AGTCATATGAAGGGGAAAATGAGTATG 59.059 37.037 7.07 0.00 0.00 2.39
802 1004 7.340232 TCAAAGTCATATGAAGGGGAAAATGAG 59.660 37.037 7.07 0.00 0.00 2.90
811 1013 7.395190 TTGACAATCAAAGTCATATGAAGGG 57.605 36.000 7.07 0.00 44.66 3.95
878 1080 4.288105 AGAGATCAGAACCACACCAGAAAT 59.712 41.667 0.00 0.00 0.00 2.17
881 1083 2.828520 GAGAGATCAGAACCACACCAGA 59.171 50.000 0.00 0.00 0.00 3.86
892 1094 4.841813 ATAAAGGAGGGGAGAGATCAGA 57.158 45.455 0.00 0.00 0.00 3.27
922 1198 7.009907 GTGTAACGTACAATAAACAGGAGGATC 59.990 40.741 0.00 0.00 40.93 3.36
937 1213 5.463286 CACCTCATAACAGTGTAACGTACA 58.537 41.667 0.00 0.00 45.86 2.90
941 1217 3.585862 AGCACCTCATAACAGTGTAACG 58.414 45.455 0.00 0.00 45.86 3.18
1083 1359 1.260544 GGTTGGCTCCTTTCATTGCT 58.739 50.000 0.00 0.00 0.00 3.91
1203 1479 1.028868 GGCAGCCCTTGTCATGAGAC 61.029 60.000 0.00 0.00 45.19 3.36
1221 1497 0.322098 TTCCACACATGTAAGGGCGG 60.322 55.000 13.95 0.00 0.00 6.13
1452 1728 3.766545 TGTTCTCCTTTTCCCATTCAGG 58.233 45.455 0.00 0.00 37.03 3.86
1458 1734 2.673775 TGCATGTTCTCCTTTTCCCA 57.326 45.000 0.00 0.00 0.00 4.37
1461 1737 3.508762 CTGCATGCATGTTCTCCTTTTC 58.491 45.455 26.79 7.53 0.00 2.29
1578 1854 1.205893 AGCGATCTCCACTTCTGTTCC 59.794 52.381 0.00 0.00 0.00 3.62
1755 2031 1.471119 TCAACCTCCGAGCGTTATCT 58.529 50.000 2.97 0.00 0.00 1.98
1809 2085 0.671796 TCTGGAGACTTTGCGTTCGA 59.328 50.000 0.00 0.00 0.00 3.71
1815 2091 2.224402 ACTTGGACTCTGGAGACTTTGC 60.224 50.000 4.49 0.00 0.00 3.68
2334 2615 6.271488 ACATGTCACAAATGAAATAGGTGG 57.729 37.500 0.00 0.00 36.31 4.61
2338 2620 6.690530 ACCCAACATGTCACAAATGAAATAG 58.309 36.000 0.00 0.00 36.31 1.73
2346 2628 8.258007 TGTATTTAAAACCCAACATGTCACAAA 58.742 29.630 0.00 0.00 0.00 2.83
2446 2731 4.431809 TGCCAAAATGTGCTGTATTATGC 58.568 39.130 0.00 0.00 0.00 3.14
2488 2773 2.435533 TGTCCGTACGCACAATGTTA 57.564 45.000 10.13 0.00 0.00 2.41
2503 2788 3.587797 TGGTCGAACTCTACAATGTCC 57.412 47.619 0.33 0.00 0.00 4.02
2552 2859 3.786048 CGACGCCAGATTTTTAGCATTTC 59.214 43.478 0.00 0.00 0.00 2.17
2613 2983 4.961438 AAAAATCCTTGCCATGTTCAGT 57.039 36.364 0.00 0.00 0.00 3.41
2757 3134 9.586732 TTCCATAATATAGCTGGCAAAGTTTAT 57.413 29.630 0.00 0.00 0.00 1.40
2758 3135 8.988546 TTCCATAATATAGCTGGCAAAGTTTA 57.011 30.769 0.00 0.00 0.00 2.01
2931 3346 9.612066 TTTTGAGCACATATGTAATCTCATGTA 57.388 29.630 23.60 13.53 32.37 2.29
3003 3418 5.354767 TCAGTAGCATGTAGAGCAAATGAG 58.645 41.667 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.