Multiple sequence alignment - TraesCS6B01G180400

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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 TraesCS6B01G180400 chr6B 100.000 2300 0 0 1 2300 200613115 200610816 0.000000e+00 4248
1 TraesCS6B01G180400 chr6B 86.501 363 46 3 599 959 538028663 538028302 1.660000e-106 396
2 TraesCS6B01G180400 chr6B 86.508 126 16 1 1577 1701 200611419 200611294 1.110000e-28 137
3 TraesCS6B01G180400 chr6B 86.508 126 16 1 1697 1822 200611539 200611415 1.110000e-28 137
4 TraesCS6B01G180400 chr5B 92.612 1719 108 12 600 2300 20046686 20044969 0.000000e+00 2453
5 TraesCS6B01G180400 chr5B 92.500 1720 103 16 597 2300 8170146 8168437 0.000000e+00 2438
6 TraesCS6B01G180400 chr5B 94.030 603 33 3 1 600 326657210 326657812 0.000000e+00 911
7 TraesCS6B01G180400 chr5B 93.729 606 28 9 1 600 434880961 434880360 0.000000e+00 900
8 TraesCS6B01G180400 chr5B 86.373 499 62 4 1714 2209 420194112 420194607 7.230000e-150 540
9 TraesCS6B01G180400 chr5B 91.262 309 20 6 1999 2300 8167128 8166820 4.570000e-112 414
10 TraesCS6B01G180400 chr5B 90.615 309 22 6 1999 2300 8167359 8167051 9.900000e-109 403
11 TraesCS6B01G180400 chr5B 90.615 309 22 6 1999 2300 8167590 8167282 9.900000e-109 403
12 TraesCS6B01G180400 chr5B 90.615 309 22 6 1999 2300 8168052 8167744 9.900000e-109 403
13 TraesCS6B01G180400 chr5B 87.607 234 29 0 599 832 199389942 199390175 2.910000e-69 272
14 TraesCS6B01G180400 chr4B 91.855 1240 54 11 998 2227 672120174 672118972 0.000000e+00 1687
15 TraesCS6B01G180400 chr4B 94.833 600 29 2 1 599 112873322 112873920 0.000000e+00 935
16 TraesCS6B01G180400 chr3B 94.850 602 28 3 1 600 447558622 447559222 0.000000e+00 937
17 TraesCS6B01G180400 chr3B 94.040 604 24 6 1 600 340848501 340847906 0.000000e+00 905
18 TraesCS6B01G180400 chr3B 85.806 465 63 3 1714 2175 770046359 770045895 7.380000e-135 490
19 TraesCS6B01G180400 chr3B 85.956 413 46 9 599 1008 342423227 342423630 4.540000e-117 431
20 TraesCS6B01G180400 chr3B 88.187 364 40 3 599 960 704976846 704976484 4.540000e-117 431
21 TraesCS6B01G180400 chr3B 88.085 235 28 0 598 832 22878759 22878525 1.740000e-71 279
22 TraesCS6B01G180400 chr2B 94.020 602 30 5 1 600 250892189 250892786 0.000000e+00 907
23 TraesCS6B01G180400 chr7B 94.020 602 28 3 1 600 519082304 519081709 0.000000e+00 905
24 TraesCS6B01G180400 chr7B 93.750 608 28 9 1 600 64932896 64933501 0.000000e+00 904
25 TraesCS6B01G180400 chr7B 93.688 602 35 3 1 600 424134357 424134957 0.000000e+00 898
26 TraesCS6B01G180400 chr7D 86.127 519 67 4 1714 2227 123250071 123249553 2.580000e-154 555
27 TraesCS6B01G180400 chr1B 85.397 541 61 7 1697 2227 535152051 535151519 1.550000e-151 545
28 TraesCS6B01G180400 chr1B 84.223 412 45 6 599 1008 213647 213254 1.290000e-102 383
29 TraesCS6B01G180400 chr1B 83.738 412 47 6 599 1008 196034 195641 2.790000e-99 372
30 TraesCS6B01G180400 chr2A 85.472 413 40 6 599 1008 762105893 762106288 1.640000e-111 412
31 TraesCS6B01G180400 chr7A 83.088 408 42 8 602 1008 671456547 671456166 1.690000e-91 346
32 TraesCS6B01G180400 chr7A 81.995 411 45 10 599 1008 347088260 347087878 2.850000e-84 322
33 TraesCS6B01G180400 chr1A 81.918 365 47 3 597 960 546173135 546173481 8.040000e-75 291


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 TraesCS6B01G180400 chr6B 200610816 200613115 2299 True 1507.333333 4248 91.005333 1 2300 3 chr6B.!!$R2 2299
1 TraesCS6B01G180400 chr5B 20044969 20046686 1717 True 2453.000000 2453 92.612000 600 2300 1 chr5B.!!$R1 1700
2 TraesCS6B01G180400 chr5B 326657210 326657812 602 False 911.000000 911 94.030000 1 600 1 chr5B.!!$F2 599
3 TraesCS6B01G180400 chr5B 434880360 434880961 601 True 900.000000 900 93.729000 1 600 1 chr5B.!!$R2 599
4 TraesCS6B01G180400 chr5B 8166820 8170146 3326 True 812.200000 2438 91.121400 597 2300 5 chr5B.!!$R3 1703
5 TraesCS6B01G180400 chr4B 672118972 672120174 1202 True 1687.000000 1687 91.855000 998 2227 1 chr4B.!!$R1 1229
6 TraesCS6B01G180400 chr4B 112873322 112873920 598 False 935.000000 935 94.833000 1 599 1 chr4B.!!$F1 598
7 TraesCS6B01G180400 chr3B 447558622 447559222 600 False 937.000000 937 94.850000 1 600 1 chr3B.!!$F2 599
8 TraesCS6B01G180400 chr3B 340847906 340848501 595 True 905.000000 905 94.040000 1 600 1 chr3B.!!$R2 599
9 TraesCS6B01G180400 chr2B 250892189 250892786 597 False 907.000000 907 94.020000 1 600 1 chr2B.!!$F1 599
10 TraesCS6B01G180400 chr7B 519081709 519082304 595 True 905.000000 905 94.020000 1 600 1 chr7B.!!$R1 599
11 TraesCS6B01G180400 chr7B 64932896 64933501 605 False 904.000000 904 93.750000 1 600 1 chr7B.!!$F1 599
12 TraesCS6B01G180400 chr7B 424134357 424134957 600 False 898.000000 898 93.688000 1 600 1 chr7B.!!$F2 599
13 TraesCS6B01G180400 chr7D 123249553 123250071 518 True 555.000000 555 86.127000 1714 2227 1 chr7D.!!$R1 513
14 TraesCS6B01G180400 chr1B 535151519 535152051 532 True 545.000000 545 85.397000 1697 2227 1 chr1B.!!$R3 530

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
910 927 0.777446 ACACACCAGCCCTAAACCAT 59.223 50.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 1994 1.781025 TTGGCACGTCCTTCGCAAAG 61.781 55.0 0.0 0.0 44.19 2.77 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
66 67 2.649816 ACCTAGGGCATTTTGAGGAAGT 59.350 45.455 14.81 0.00 0.00 3.01
354 366 1.340991 CCGACTTGTGGGGGAATCATT 60.341 52.381 0.00 0.00 0.00 2.57
356 368 1.478105 GACTTGTGGGGGAATCATTGC 59.522 52.381 0.00 0.00 0.00 3.56
357 369 1.077663 ACTTGTGGGGGAATCATTGCT 59.922 47.619 0.00 0.00 0.00 3.91
370 382 5.509163 GGAATCATTGCTTCCATCATCCTTG 60.509 44.000 13.19 0.00 41.55 3.61
573 587 6.032094 GTCAACTACATGATCATGCAAAAGG 58.968 40.000 31.17 18.11 42.39 3.11
657 671 4.410228 TCTCAGGCCATAAGCATTTCTAGT 59.590 41.667 5.01 0.00 46.50 2.57
679 693 4.624452 GTCGTTAGATCGCCACTTTTAGTT 59.376 41.667 0.00 0.00 0.00 2.24
688 702 4.082136 TCGCCACTTTTAGTTGTTTTTGGT 60.082 37.500 0.00 0.00 0.00 3.67
697 711 2.946990 AGTTGTTTTTGGTCGTCGGATT 59.053 40.909 0.00 0.00 0.00 3.01
699 713 2.290464 TGTTTTTGGTCGTCGGATTGT 58.710 42.857 0.00 0.00 0.00 2.71
718 732 6.314400 GGATTGTTGTTAGTCGCACCTAAATA 59.686 38.462 0.00 0.00 0.00 1.40
725 739 4.906065 AGTCGCACCTAAATATCGTACA 57.094 40.909 0.00 0.00 0.00 2.90
726 740 5.449107 AGTCGCACCTAAATATCGTACAT 57.551 39.130 0.00 0.00 0.00 2.29
756 770 4.082523 GCGGGTCAGGCTGCACTA 62.083 66.667 10.34 0.00 0.00 2.74
816 830 4.210331 GTCTGACATTCAATTGGGCCTAT 58.790 43.478 4.53 0.00 0.00 2.57
845 860 3.137360 ACTGGGCCTTTTCTATCATCCTC 59.863 47.826 4.53 0.00 0.00 3.71
857 872 2.738587 TCATCCTCGCCTTCTCTACT 57.261 50.000 0.00 0.00 0.00 2.57
877 893 1.270571 TGTCTATCCAACACAGCGCAA 60.271 47.619 11.47 0.00 0.00 4.85
879 895 2.076100 TCTATCCAACACAGCGCAAAG 58.924 47.619 11.47 0.64 0.00 2.77
897 914 2.719354 GGTGAAACGCCACACACC 59.281 61.111 0.00 0.00 44.23 4.16
910 927 0.777446 ACACACCAGCCCTAAACCAT 59.223 50.000 0.00 0.00 0.00 3.55
931 949 1.758440 TTCGCCACCTGCTCTGTTCT 61.758 55.000 0.00 0.00 38.05 3.01
940 958 1.373999 GCTCTGTTCTGACTGCGCT 60.374 57.895 9.73 0.00 34.04 5.92
1055 1078 2.280186 GCTAACCTCCATCGGCCG 60.280 66.667 22.12 22.12 0.00 6.13
1057 1080 4.215742 TAACCTCCATCGGCCGCG 62.216 66.667 23.51 14.33 0.00 6.46
1086 1109 1.573108 ACAACCAGATCGATCCAGGT 58.427 50.000 26.19 26.19 37.32 4.00
1114 1137 0.036022 GATGGCAGTCTATCCAGCCC 59.964 60.000 0.00 0.00 46.45 5.19
1149 1184 1.026718 GCAACAAGGGGATCAGTCGG 61.027 60.000 0.00 0.00 0.00 4.79
1154 1189 0.546747 AAGGGGATCAGTCGGTCCAA 60.547 55.000 0.00 0.00 36.19 3.53
1291 1326 7.223584 TCAAGATGTGGTCATTCTTCAGTTTA 58.776 34.615 0.00 0.00 34.06 2.01
1486 1530 3.495806 CCTTGTCCTGATGCCCTCTTATC 60.496 52.174 0.00 0.00 0.00 1.75
1523 1567 6.182627 ACATACAGATGATGTTCATGTTGGT 58.817 36.000 0.00 0.00 37.68 3.67
1549 1593 4.755411 TGTCAACTCATTTCGGTAGATCC 58.245 43.478 0.00 0.00 0.00 3.36
1617 1661 6.881602 GGTCAGAACCAAAAGAAGAGACATAT 59.118 38.462 0.00 0.00 45.68 1.78
1667 1711 8.467598 AGACGTGTGATGTTTACTTCTGTATAT 58.532 33.333 0.00 0.00 0.00 0.86
1807 1853 2.151202 GTGTTTCAGATTTGGAGCCGA 58.849 47.619 0.00 0.00 0.00 5.54
1812 1858 2.426522 TCAGATTTGGAGCCGAAACAG 58.573 47.619 0.00 0.00 0.00 3.16
1850 1896 6.306199 TGGTTACAGACTTACAGGTACACTA 58.694 40.000 0.00 0.00 0.00 2.74
1970 2021 0.110486 AGGACGTGCCAATGGTCTTT 59.890 50.000 2.38 0.00 40.02 2.52
2005 2057 1.228675 AAGGGCAGCCTTGAAGGTG 60.229 57.895 13.58 10.75 37.80 4.00
2093 2151 8.045507 TCTTCTGCCATAATCAGATATCATTCC 58.954 37.037 5.32 0.00 39.96 3.01
2250 3932 5.655090 TGAAGGTACTCGGATGATCAACTTA 59.345 40.000 0.00 0.00 38.49 2.24
2292 3975 6.816136 TGCTTGACCGATTATCTTCTCATTA 58.184 36.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 7.782049 TGTCACTTTCATATACTAGTGGGAAG 58.218 38.462 5.39 5.53 38.75 3.46
249 258 4.797933 GCCAAAGAAGCCCAACGAAATAAA 60.798 41.667 0.00 0.00 0.00 1.40
256 265 2.650778 GGCCAAAGAAGCCCAACG 59.349 61.111 0.00 0.00 45.16 4.10
292 304 9.500785 TTTATGAAAAATAAAAGAGGCCAAAGG 57.499 29.630 5.01 0.00 0.00 3.11
354 366 0.627451 AGGCAAGGATGATGGAAGCA 59.373 50.000 0.00 0.00 35.55 3.91
356 368 2.295885 GTGAGGCAAGGATGATGGAAG 58.704 52.381 0.00 0.00 0.00 3.46
357 369 1.634973 TGTGAGGCAAGGATGATGGAA 59.365 47.619 0.00 0.00 0.00 3.53
370 382 0.682209 AGCATTGTCCCATGTGAGGC 60.682 55.000 0.00 0.00 0.00 4.70
573 587 4.512944 ACACGCTCCATCATTGTCATATTC 59.487 41.667 0.00 0.00 0.00 1.75
645 659 4.740695 GCGATCTAACGACTAGAAATGCTT 59.259 41.667 0.00 0.00 40.12 3.91
657 671 4.445452 ACTAAAAGTGGCGATCTAACGA 57.555 40.909 0.00 0.00 35.09 3.85
679 693 2.290464 ACAATCCGACGACCAAAAACA 58.710 42.857 0.00 0.00 0.00 2.83
688 702 2.587956 CGACTAACAACAATCCGACGA 58.412 47.619 0.00 0.00 0.00 4.20
697 711 5.517411 CGATATTTAGGTGCGACTAACAACA 59.483 40.000 0.00 0.00 32.97 3.33
699 713 5.653507 ACGATATTTAGGTGCGACTAACAA 58.346 37.500 0.00 0.00 32.97 2.83
718 732 2.095869 CGAGTTAGCGCCTATGTACGAT 60.096 50.000 2.29 0.00 0.00 3.73
742 756 2.124942 GCCTAGTGCAGCCTGACC 60.125 66.667 0.00 0.00 40.77 4.02
845 860 3.215151 TGGATAGACAGTAGAGAAGGCG 58.785 50.000 0.00 0.00 0.00 5.52
857 872 0.320050 TGCGCTGTGTTGGATAGACA 59.680 50.000 9.73 0.00 0.00 3.41
877 893 1.077357 TGTGTGGCGTTTCACCCTT 60.077 52.632 0.00 0.00 36.87 3.95
879 895 2.719354 GTGTGTGGCGTTTCACCC 59.281 61.111 0.00 0.00 36.87 4.61
897 914 0.451783 GCGAACATGGTTTAGGGCTG 59.548 55.000 0.00 0.00 0.00 4.85
931 949 3.244281 ATGTCAGGCAGCGCAGTCA 62.244 57.895 11.47 0.00 0.00 3.41
1011 1034 2.595386 GGCAGCGATCGAATTGTTTTT 58.405 42.857 21.57 0.00 0.00 1.94
1057 1080 0.611714 ATCTGGTTGTACGGTGACCC 59.388 55.000 0.00 0.00 32.39 4.46
1064 1087 2.543861 CCTGGATCGATCTGGTTGTACG 60.544 54.545 23.96 3.63 0.00 3.67
1065 1088 2.431057 ACCTGGATCGATCTGGTTGTAC 59.569 50.000 26.42 10.99 32.72 2.90
1086 1109 2.824689 AGACTGCCATCTCTCTCTCA 57.175 50.000 0.00 0.00 0.00 3.27
1135 1170 0.546747 TTGGACCGACTGATCCCCTT 60.547 55.000 0.00 0.00 33.69 3.95
1149 1184 2.781595 ATCGCCTGTGTCGGTTGGAC 62.782 60.000 0.00 0.00 46.27 4.02
1154 1189 0.172803 GACTAATCGCCTGTGTCGGT 59.827 55.000 0.00 0.00 0.00 4.69
1523 1567 5.361427 TCTACCGAAATGAGTTGACAACAA 58.639 37.500 20.08 8.48 0.00 2.83
1549 1593 6.998968 AATAAACAGATCAGAAAGCTCCAG 57.001 37.500 0.00 0.00 0.00 3.86
1667 1711 3.407698 TCTGGCGCTAAATCTGAAACAA 58.592 40.909 7.64 0.00 0.00 2.83
1680 1724 3.253230 GCAAAAATATTGTTCTGGCGCT 58.747 40.909 7.64 0.00 0.00 5.92
1682 1726 4.033129 CCATGCAAAAATATTGTTCTGGCG 59.967 41.667 0.00 0.00 0.00 5.69
1812 1858 7.927048 AGTCTGTAACCAAAGACAAAACATAC 58.073 34.615 5.68 0.00 44.34 2.39
1943 1994 1.781025 TTGGCACGTCCTTCGCAAAG 61.781 55.000 0.00 0.00 44.19 2.77
1970 2021 6.365970 TGCCCTTGCTAATTAAAATTCCAA 57.634 33.333 0.00 0.00 38.71 3.53
2005 2057 3.557595 CCACAAGTTAAGATCATCCGAGC 59.442 47.826 0.00 0.00 0.00 5.03
2042 2096 2.093235 GGGAAGATACTGCAGTCAAGCT 60.093 50.000 25.56 12.61 34.99 3.74
2093 2151 7.080724 GGTTTATTTCTTTGACAAGCTCTCTG 58.919 38.462 0.00 0.00 0.00 3.35
2134 2193 8.464404 GTGGTCAGTATATAGGCATTCGTATAA 58.536 37.037 0.00 0.00 31.65 0.98
2140 2199 5.807520 CGATGTGGTCAGTATATAGGCATTC 59.192 44.000 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.