Multiple sequence alignment - TraesCS6B01G428200

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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 TraesCS6B01G428200 chr6B 100.000 1801 0 0 1 1801 696346264 696344464 0.000000e+00 3326
1 TraesCS6B01G428200 chr6B 92.585 971 67 3 831 1801 696251380 696250415 0.000000e+00 1389
2 TraesCS6B01G428200 chr6B 86.930 811 102 3 991 1801 696179058 696178252 0.000000e+00 907
3 TraesCS6B01G428200 chr6B 85.732 813 108 8 991 1801 696152504 696151698 0.000000e+00 852
4 TraesCS6B01G428200 chr6B 100.000 342 0 0 2183 2524 696344082 696343741 1.270000e-177 632
5 TraesCS6B01G428200 chr6B 92.135 178 12 2 650 826 696251738 696251562 1.500000e-62 250
6 TraesCS6B01G428200 chr6B 88.038 209 17 7 574 776 696244454 696244248 9.020000e-60 241
7 TraesCS6B01G428200 chr6A 91.392 848 65 2 954 1801 604610915 604610076 0.000000e+00 1155
8 TraesCS6B01G428200 chr6A 84.052 232 29 6 574 797 604618468 604618237 1.520000e-52 217
9 TraesCS6B01G428200 chr6A 96.154 130 4 1 831 959 604618053 604617924 7.070000e-51 211
10 TraesCS6B01G428200 chr6D 87.680 974 104 6 829 1801 458060454 458059496 0.000000e+00 1120
11 TraesCS6B01G428200 chr6D 88.395 810 93 1 991 1800 458028985 458028177 0.000000e+00 974
12 TraesCS6B01G428200 chr6D 87.546 811 97 2 991 1801 457699966 457699160 0.000000e+00 935
13 TraesCS6B01G428200 chr6D 85.802 810 111 2 991 1800 458019432 458018627 0.000000e+00 856
14 TraesCS6B01G428200 chr6D 86.545 602 78 1 987 1588 458050125 458049527 0.000000e+00 660
15 TraesCS6B01G428200 chr6D 89.796 343 27 5 2187 2524 457698794 457698455 1.390000e-117 433
16 TraesCS6B01G428200 chr6D 85.575 409 49 3 1402 1801 458012794 458012387 1.080000e-113 420
17 TraesCS6B01G428200 chr6D 82.000 250 18 12 574 797 458029605 458029357 1.190000e-43 187
18 TraesCS6B01G428200 chr6D 83.744 203 15 8 574 759 458061139 458060938 2.580000e-40 176
19 TraesCS6B01G428200 chr6D 89.051 137 9 3 831 965 458029109 458028977 5.590000e-37 165
20 TraesCS6B01G428200 chr6D 83.065 124 11 7 848 965 457700077 457699958 1.240000e-18 104
21 TraesCS6B01G428200 chr7A 99.825 573 1 0 1 573 291801588 291801016 0.000000e+00 1053
22 TraesCS6B01G428200 chr7A 98.953 573 6 0 1 573 403942236 403941664 0.000000e+00 1026
23 TraesCS6B01G428200 chr7B 99.129 574 5 0 1 574 695449319 695449892 0.000000e+00 1033
24 TraesCS6B01G428200 chr7B 98.780 574 6 1 1 574 654249319 654248747 0.000000e+00 1020
25 TraesCS6B01G428200 chr4A 98.957 575 5 1 1 575 629117797 629118370 0.000000e+00 1027
26 TraesCS6B01G428200 chr5A 98.606 574 8 0 1 574 665654307 665654880 0.000000e+00 1016
27 TraesCS6B01G428200 chr3A 98.432 574 9 0 1 574 648239985 648239412 0.000000e+00 1011
28 TraesCS6B01G428200 chr4B 98.087 575 11 0 1 575 662785121 662785695 0.000000e+00 1002
29 TraesCS6B01G428200 chr3D 91.349 578 43 5 1 574 319860901 319861475 0.000000e+00 784


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 TraesCS6B01G428200 chr6B 696343741 696346264 2523 True 1979.000000 3326 100.000000 1 2524 2 chr6B.!!$R5 2523
1 TraesCS6B01G428200 chr6B 696178252 696179058 806 True 907.000000 907 86.930000 991 1801 1 chr6B.!!$R2 810
2 TraesCS6B01G428200 chr6B 696151698 696152504 806 True 852.000000 852 85.732000 991 1801 1 chr6B.!!$R1 810
3 TraesCS6B01G428200 chr6B 696250415 696251738 1323 True 819.500000 1389 92.360000 650 1801 2 chr6B.!!$R4 1151
4 TraesCS6B01G428200 chr6A 604610076 604610915 839 True 1155.000000 1155 91.392000 954 1801 1 chr6A.!!$R1 847
5 TraesCS6B01G428200 chr6A 604617924 604618468 544 True 214.000000 217 90.103000 574 959 2 chr6A.!!$R2 385
6 TraesCS6B01G428200 chr6D 458018627 458019432 805 True 856.000000 856 85.802000 991 1800 1 chr6D.!!$R2 809
7 TraesCS6B01G428200 chr6D 458049527 458050125 598 True 660.000000 660 86.545000 987 1588 1 chr6D.!!$R3 601
8 TraesCS6B01G428200 chr6D 458059496 458061139 1643 True 648.000000 1120 85.712000 574 1801 2 chr6D.!!$R6 1227
9 TraesCS6B01G428200 chr6D 457698455 457700077 1622 True 490.666667 935 86.802333 848 2524 3 chr6D.!!$R4 1676
10 TraesCS6B01G428200 chr6D 458028177 458029605 1428 True 442.000000 974 86.482000 574 1800 3 chr6D.!!$R5 1226
11 TraesCS6B01G428200 chr7A 291801016 291801588 572 True 1053.000000 1053 99.825000 1 573 1 chr7A.!!$R1 572
12 TraesCS6B01G428200 chr7A 403941664 403942236 572 True 1026.000000 1026 98.953000 1 573 1 chr7A.!!$R2 572
13 TraesCS6B01G428200 chr7B 695449319 695449892 573 False 1033.000000 1033 99.129000 1 574 1 chr7B.!!$F1 573
14 TraesCS6B01G428200 chr7B 654248747 654249319 572 True 1020.000000 1020 98.780000 1 574 1 chr7B.!!$R1 573
15 TraesCS6B01G428200 chr4A 629117797 629118370 573 False 1027.000000 1027 98.957000 1 575 1 chr4A.!!$F1 574
16 TraesCS6B01G428200 chr5A 665654307 665654880 573 False 1016.000000 1016 98.606000 1 574 1 chr5A.!!$F1 573
17 TraesCS6B01G428200 chr3A 648239412 648239985 573 True 1011.000000 1011 98.432000 1 574 1 chr3A.!!$R1 573
18 TraesCS6B01G428200 chr4B 662785121 662785695 574 False 1002.000000 1002 98.087000 1 575 1 chr4B.!!$F1 574
19 TraesCS6B01G428200 chr3D 319860901 319861475 574 False 784.000000 784 91.349000 1 574 1 chr3D.!!$F1 573

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
736 766 1.528129 GCAGTAGGACAGCAAAGCTT 58.472 50.0 0.0 0.0 36.4 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 2097 0.393808 GCCCTTGGATCTTGCGGTAA 60.394 55.0 0.0 0.0 0.0 2.85 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
599 604 3.207265 TGGTTGCGTGCATCCTAATAT 57.793 42.857 19.58 0.00 36.89 1.28
600 605 4.344359 TGGTTGCGTGCATCCTAATATA 57.656 40.909 19.58 0.00 36.89 0.86
613 621 8.363390 TGCATCCTAATATACAGACTTTCAGAG 58.637 37.037 0.00 0.00 0.00 3.35
648 669 1.758862 ACTTATACGGCTACACCCACC 59.241 52.381 0.00 0.00 33.26 4.61
698 719 4.701651 TCAATGATCGTTCAAATCTTGGCT 59.298 37.500 0.00 0.00 34.96 4.75
736 766 1.528129 GCAGTAGGACAGCAAAGCTT 58.472 50.000 0.00 0.00 36.40 3.74
799 1025 7.157347 TGATATGACAAGAGGTGAGATAATGC 58.843 38.462 0.00 0.00 0.00 3.56
808 1034 3.894427 AGGTGAGATAATGCGTGAGAGAT 59.106 43.478 0.00 0.00 0.00 2.75
826 1054 8.229137 GTGAGAGATGCATATTTATCTTTGAGC 58.771 37.037 0.00 0.00 33.97 4.26
1045 1507 1.973812 GTCTTGGGTTCCCTGCTGC 60.974 63.158 9.43 0.00 0.00 5.25
1273 1735 2.820178 TCCACCAGCTCAGTAATGAGA 58.180 47.619 23.65 0.00 38.13 3.27
1412 1877 7.122055 TCTCAAGCAGGTAAAAGAGTTGAAAAA 59.878 33.333 0.00 0.00 0.00 1.94
1485 1950 3.793492 GCTTGTCTGCTCTTTTTGTTGAC 59.207 43.478 0.00 0.00 0.00 3.18
1543 2008 0.461339 CCTTGCCAATTGGATGCTGC 60.461 55.000 29.02 11.73 37.39 5.25
1558 2023 5.221303 TGGATGCTGCAAGATAAAAATAGCC 60.221 40.000 6.36 0.00 34.07 3.93
1559 2024 4.291540 TGCTGCAAGATAAAAATAGCCG 57.708 40.909 0.00 0.00 34.07 5.52
1562 2027 4.202010 GCTGCAAGATAAAAATAGCCGGAA 60.202 41.667 5.05 0.00 34.07 4.30
1566 2031 5.515270 GCAAGATAAAAATAGCCGGAACAAC 59.485 40.000 5.05 0.00 0.00 3.32
1571 2036 2.799126 AATAGCCGGAACAACCATCA 57.201 45.000 5.05 0.00 38.90 3.07
1584 2049 0.473755 ACCATCACAAGGTGCTGTCA 59.526 50.000 0.00 0.00 38.13 3.58
1611 2076 1.524008 GCTTCGGTGGGTTGGGAAAG 61.524 60.000 0.00 0.00 0.00 2.62
1613 2078 0.774908 TTCGGTGGGTTGGGAAAGAT 59.225 50.000 0.00 0.00 0.00 2.40
1632 2097 2.526873 ACACTGGCGAGGGAGGTT 60.527 61.111 4.44 0.00 0.00 3.50
1689 2154 1.942677 TTGTCTCGGTCTCGCAAAAA 58.057 45.000 0.00 0.00 36.13 1.94
1697 2162 2.542824 CGGTCTCGCAAAAACCAAATGT 60.543 45.455 0.00 0.00 32.35 2.71
1706 2171 8.202745 TCGCAAAAACCAAATGTTAAAGAAAT 57.797 26.923 0.00 0.00 35.67 2.17
1767 2232 7.661847 GGAAGATTTTATGGAAGGTATCGACAT 59.338 37.037 0.00 0.00 0.00 3.06
1768 2233 9.706691 GAAGATTTTATGGAAGGTATCGACATA 57.293 33.333 0.00 0.00 0.00 2.29
1770 2235 9.877178 AGATTTTATGGAAGGTATCGACATATC 57.123 33.333 0.00 0.00 0.00 1.63
2217 2682 8.217111 TGCATATGGGTTAAAGATTAGTGATGA 58.783 33.333 4.56 0.00 0.00 2.92
2268 2733 7.257722 CCGAACCTTTAAAGCATGAATAACAT 58.742 34.615 9.86 0.00 40.17 2.71
2288 2753 5.625150 ACATAGTGATTCATTCTAAGGGCC 58.375 41.667 0.00 0.00 0.00 5.80
2290 2755 4.162040 AGTGATTCATTCTAAGGGCCAG 57.838 45.455 6.18 0.00 0.00 4.85
2320 2785 7.773690 GTCCAAAGAACCTCCATTAGCTTTATA 59.226 37.037 0.00 0.00 0.00 0.98
2329 2794 8.289544 ACCTCCATTAGCTTTATATTTCCCTTT 58.710 33.333 0.00 0.00 0.00 3.11
2331 2796 8.706322 TCCATTAGCTTTATATTTCCCTTTCC 57.294 34.615 0.00 0.00 0.00 3.13
2333 2798 7.447238 CCATTAGCTTTATATTTCCCTTTCCGA 59.553 37.037 0.00 0.00 0.00 4.55
2340 2805 8.638629 TTTATATTTCCCTTTCCGAAGAAACA 57.361 30.769 0.00 0.00 37.07 2.83
2356 2821 4.962155 AGAAACAATCTTCCGAGTCTGTT 58.038 39.130 0.00 0.00 33.39 3.16
2377 2842 4.743057 TGATCTCATCAACTACCCACTG 57.257 45.455 0.00 0.00 36.11 3.66
2395 2860 4.487948 CACTGTGGTTATTTGATGCAAGG 58.512 43.478 0.00 0.00 0.00 3.61
2481 2947 0.608308 GAAACCCAAGGAGAACCCGG 60.608 60.000 0.00 0.00 40.87 5.73
2484 2950 0.474273 ACCCAAGGAGAACCCGGTAA 60.474 55.000 0.00 0.00 40.87 2.85
2509 2979 5.564550 ACATTTAGCATCAGAAGAACTGGT 58.435 37.500 0.00 0.00 45.76 4.00
2515 2985 5.486526 AGCATCAGAAGAACTGGTAGAAAG 58.513 41.667 0.00 0.00 45.76 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.606313 CCAAAACGATGCCCCCAGT 60.606 57.895 0.00 0.00 0.00 4.00
584 589 4.810790 AGTCTGTATATTAGGATGCACGC 58.189 43.478 0.00 0.00 0.00 5.34
585 590 6.923508 TGAAAGTCTGTATATTAGGATGCACG 59.076 38.462 0.00 0.00 0.00 5.34
600 605 7.923414 AAAAGTTGTAACTCTGAAAGTCTGT 57.077 32.000 0.00 0.00 38.57 3.41
613 621 8.498358 AGCCGTATAAGTTGTAAAAGTTGTAAC 58.502 33.333 0.00 0.00 0.00 2.50
616 624 7.656948 TGTAGCCGTATAAGTTGTAAAAGTTGT 59.343 33.333 0.00 0.00 0.00 3.32
731 761 6.857437 AAAGGCAGTGGAATAATTAAGCTT 57.143 33.333 3.48 3.48 0.00 3.74
732 762 6.665248 AGAAAAGGCAGTGGAATAATTAAGCT 59.335 34.615 0.00 0.00 0.00 3.74
736 766 5.951747 AGCAGAAAAGGCAGTGGAATAATTA 59.048 36.000 0.00 0.00 0.00 1.40
799 1025 8.302965 TCAAAGATAAATATGCATCTCTCACG 57.697 34.615 0.19 0.00 31.10 4.35
855 1310 4.868314 ATAATGGGGTTCGTACTAGCTC 57.132 45.455 0.00 0.00 0.00 4.09
982 1444 6.883756 ACCTCCATTGATCTCTCTTCTTTTTC 59.116 38.462 0.00 0.00 0.00 2.29
1045 1507 2.966309 GCAAACCGGTGAGCTTCCG 61.966 63.158 20.75 19.74 46.49 4.30
1412 1877 9.105844 AGGTAATATCATCCAGCTTGTAACTAT 57.894 33.333 0.00 0.00 0.00 2.12
1485 1950 2.908073 GCCCACAAGGTGTGCTTCG 61.908 63.158 2.77 0.00 46.51 3.79
1543 2008 6.033966 GGTTGTTCCGGCTATTTTTATCTTG 58.966 40.000 0.00 0.00 0.00 3.02
1558 2023 1.266718 CACCTTGTGATGGTTGTTCCG 59.733 52.381 0.00 0.00 35.71 4.30
1559 2024 1.000274 GCACCTTGTGATGGTTGTTCC 60.000 52.381 0.00 0.00 35.23 3.62
1562 2027 1.321474 CAGCACCTTGTGATGGTTGT 58.679 50.000 4.64 0.00 44.80 3.32
1571 2036 2.101249 CCAACAATTGACAGCACCTTGT 59.899 45.455 13.59 0.00 33.76 3.16
1584 2049 0.469144 ACCCACCGAAGCCAACAATT 60.469 50.000 0.00 0.00 0.00 2.32
1611 2076 1.142748 CTCCCTCGCCAGTGTCATC 59.857 63.158 0.00 0.00 0.00 2.92
1613 2078 2.997315 CCTCCCTCGCCAGTGTCA 60.997 66.667 0.00 0.00 0.00 3.58
1632 2097 0.393808 GCCCTTGGATCTTGCGGTAA 60.394 55.000 0.00 0.00 0.00 2.85
1706 2171 5.829924 GCTGGGAGATCAAATCCTTCATAAA 59.170 40.000 0.00 0.00 37.01 1.40
1767 2232 5.767665 CCAATACATTTGGGTTCATCCGATA 59.232 40.000 0.00 0.00 35.96 2.92
1768 2233 4.584325 CCAATACATTTGGGTTCATCCGAT 59.416 41.667 0.00 0.00 35.96 4.18
1770 2235 4.305989 CCAATACATTTGGGTTCATCCG 57.694 45.455 0.00 0.00 35.96 4.18
2238 2703 3.713826 TGCTTTAAAGGTTCGGGAGAT 57.286 42.857 16.78 0.00 39.57 2.75
2243 2708 6.616947 TGTTATTCATGCTTTAAAGGTTCGG 58.383 36.000 16.78 0.00 0.00 4.30
2244 2709 9.438291 CTATGTTATTCATGCTTTAAAGGTTCG 57.562 33.333 16.78 0.00 37.91 3.95
2268 2733 4.721776 ACTGGCCCTTAGAATGAATCACTA 59.278 41.667 0.00 0.00 0.00 2.74
2274 2739 4.079253 GACAAACTGGCCCTTAGAATGAA 58.921 43.478 0.00 0.00 0.00 2.57
2288 2753 3.287222 TGGAGGTTCTTTGGACAAACTG 58.713 45.455 0.00 0.00 0.00 3.16
2290 2755 4.937201 AATGGAGGTTCTTTGGACAAAC 57.063 40.909 0.00 0.00 0.00 2.93
2320 2785 5.775195 AGATTGTTTCTTCGGAAAGGGAAAT 59.225 36.000 6.84 0.00 43.56 2.17
2340 2805 4.464244 TGAGATCAACAGACTCGGAAGATT 59.536 41.667 0.00 0.00 40.84 2.40
2345 2810 3.356290 TGATGAGATCAACAGACTCGGA 58.644 45.455 0.00 0.00 36.11 4.55
2356 2821 4.081476 CACAGTGGGTAGTTGATGAGATCA 60.081 45.833 0.00 0.00 37.55 2.92
2372 2837 4.487948 CTTGCATCAAATAACCACAGTGG 58.512 43.478 18.93 18.93 45.02 4.00
2377 2842 3.591196 TGCCTTGCATCAAATAACCAC 57.409 42.857 0.00 0.00 31.71 4.16
2418 2883 9.372369 CCTCTCTCTTACTAAATAGGTTTTGTG 57.628 37.037 0.00 0.00 35.45 3.33
2467 2933 2.156917 GTTTTACCGGGTTCTCCTTGG 58.843 52.381 4.31 0.00 36.05 3.61
2481 2947 9.334693 CAGTTCTTCTGATGCTAAATGTTTTAC 57.665 33.333 0.00 0.00 46.27 2.01
2484 2950 6.491403 ACCAGTTCTTCTGATGCTAAATGTTT 59.509 34.615 0.00 0.00 46.27 2.83


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

AutoCloner maintained by Alex Coulton.