Multiple sequence alignment - TraesCS2B01G611200

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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 TraesCS2B01G611200 chr2B 100.000 2387 0 0 1 2387 790611918 790614304 0.000000e+00 4409
1 TraesCS2B01G611200 chr2B 86.283 1582 172 24 699 2246 790623440 790625010 0.000000e+00 1677
2 TraesCS2B01G611200 chr2B 83.929 616 82 14 7 611 563040756 563041365 7.400000e-160 573
3 TraesCS2B01G611200 chr2B 78.039 255 45 9 7 256 23240009 23239761 1.480000e-32 150
4 TraesCS2B01G611200 chr2D 97.705 1699 34 4 691 2386 644975966 644974270 0.000000e+00 2916
5 TraesCS2B01G611200 chr2D 86.181 1592 169 26 697 2255 644924648 644923075 0.000000e+00 1674
6 TraesCS2B01G611200 chr2D 94.369 1030 56 2 691 1719 644981459 644980431 0.000000e+00 1580
7 TraesCS2B01G611200 chr2D 95.146 618 20 2 4 611 644976979 644976362 0.000000e+00 966
8 TraesCS2B01G611200 chr2D 93.344 631 22 3 1 611 644982485 644981855 0.000000e+00 915
9 TraesCS2B01G611200 chr2D 82.632 570 75 16 12 576 196435670 196435120 1.280000e-132 483
10 TraesCS2B01G611200 chr2D 74.548 774 150 35 814 1546 579511275 579510508 6.450000e-76 294
11 TraesCS2B01G611200 chr2A 97.023 1310 30 4 1079 2386 770343037 770341735 0.000000e+00 2194
12 TraesCS2B01G611200 chr2A 86.996 1438 171 14 698 2126 770291159 770289729 0.000000e+00 1605
13 TraesCS2B01G611200 chr2A 96.446 619 14 1 1 611 770345916 770345298 0.000000e+00 1014
14 TraesCS2B01G611200 chr2A 80.303 792 123 17 764 1536 770023744 770022967 3.440000e-158 568
15 TraesCS2B01G611200 chr2A 96.886 289 8 1 691 978 770343322 770343034 1.280000e-132 483
16 TraesCS2B01G611200 chr2A 79.777 539 73 15 1 539 508049474 508049976 2.260000e-95 359
17 TraesCS2B01G611200 chr3B 91.452 1357 112 4 691 2044 48668763 48667408 0.000000e+00 1860
18 TraesCS2B01G611200 chr3B 88.800 125 12 2 2264 2386 48667010 48666886 4.110000e-33 152
19 TraesCS2B01G611200 chr7D 82.696 601 87 13 16 611 124874637 124874049 3.520000e-143 518
20 TraesCS2B01G611200 chr1A 83.978 543 77 10 2 539 63873971 63873434 1.640000e-141 512
21 TraesCS2B01G611200 chr6D 83.299 485 64 11 104 583 225216528 225216056 4.710000e-117 431
22 TraesCS2B01G611200 chr1B 80.944 551 93 11 42 586 289286290 289285746 2.190000e-115 425


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 TraesCS2B01G611200 chr2B 790611918 790614304 2386 False 4409.000000 4409 100.000 1 2387 1 chr2B.!!$F2 2386
1 TraesCS2B01G611200 chr2B 790623440 790625010 1570 False 1677.000000 1677 86.283 699 2246 1 chr2B.!!$F3 1547
2 TraesCS2B01G611200 chr2B 563040756 563041365 609 False 573.000000 573 83.929 7 611 1 chr2B.!!$F1 604
3 TraesCS2B01G611200 chr2D 644923075 644924648 1573 True 1674.000000 1674 86.181 697 2255 1 chr2D.!!$R3 1558
4 TraesCS2B01G611200 chr2D 644974270 644982485 8215 True 1594.250000 2916 95.141 1 2386 4 chr2D.!!$R4 2385
5 TraesCS2B01G611200 chr2D 196435120 196435670 550 True 483.000000 483 82.632 12 576 1 chr2D.!!$R1 564
6 TraesCS2B01G611200 chr2D 579510508 579511275 767 True 294.000000 294 74.548 814 1546 1 chr2D.!!$R2 732
7 TraesCS2B01G611200 chr2A 770289729 770291159 1430 True 1605.000000 1605 86.996 698 2126 1 chr2A.!!$R2 1428
8 TraesCS2B01G611200 chr2A 770341735 770345916 4181 True 1230.333333 2194 96.785 1 2386 3 chr2A.!!$R3 2385
9 TraesCS2B01G611200 chr2A 770022967 770023744 777 True 568.000000 568 80.303 764 1536 1 chr2A.!!$R1 772
10 TraesCS2B01G611200 chr2A 508049474 508049976 502 False 359.000000 359 79.777 1 539 1 chr2A.!!$F1 538
11 TraesCS2B01G611200 chr3B 48666886 48668763 1877 True 1006.000000 1860 90.126 691 2386 2 chr3B.!!$R1 1695
12 TraesCS2B01G611200 chr7D 124874049 124874637 588 True 518.000000 518 82.696 16 611 1 chr7D.!!$R1 595
13 TraesCS2B01G611200 chr1A 63873434 63873971 537 True 512.000000 512 83.978 2 539 1 chr1A.!!$R1 537
14 TraesCS2B01G611200 chr1B 289285746 289286290 544 True 425.000000 425 80.944 42 586 1 chr1B.!!$R1 544

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
624 6185 0.943673 TGATGTTCACCAAGCACGTG 59.056 50.0 12.28 12.28 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2328 10146 0.317269 GAAGACGACGACAACCACGA 60.317 55.0 0.0 0.0 34.7 4.35 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
297 5836 9.896263 TTCACCGTGGTTAATTACTAAAAATTC 57.104 29.630 0.00 0.00 31.63 2.17
611 6172 6.604396 TCTGCTGATGTTATCCATTTGATGTT 59.396 34.615 0.00 0.00 34.76 2.71
612 6173 6.798482 TGCTGATGTTATCCATTTGATGTTC 58.202 36.000 0.00 0.00 34.76 3.18
613 6174 6.377712 TGCTGATGTTATCCATTTGATGTTCA 59.622 34.615 0.00 0.00 34.76 3.18
614 6175 6.694411 GCTGATGTTATCCATTTGATGTTCAC 59.306 38.462 0.00 0.00 34.76 3.18
615 6176 7.099266 TGATGTTATCCATTTGATGTTCACC 57.901 36.000 0.00 0.00 34.76 4.02
618 6179 6.923012 TGTTATCCATTTGATGTTCACCAAG 58.077 36.000 0.00 0.00 34.76 3.61
619 6180 3.940209 TCCATTTGATGTTCACCAAGC 57.060 42.857 0.00 0.00 0.00 4.01
620 6181 3.229293 TCCATTTGATGTTCACCAAGCA 58.771 40.909 0.00 0.00 0.00 3.91
621 6182 3.005684 TCCATTTGATGTTCACCAAGCAC 59.994 43.478 0.00 0.00 0.00 4.40
622 6183 2.772568 TTTGATGTTCACCAAGCACG 57.227 45.000 0.00 0.00 0.00 5.34
623 6184 1.674359 TTGATGTTCACCAAGCACGT 58.326 45.000 0.00 0.00 0.00 4.49
624 6185 0.943673 TGATGTTCACCAAGCACGTG 59.056 50.000 12.28 12.28 0.00 4.49
626 6187 1.333619 GATGTTCACCAAGCACGTGTT 59.666 47.619 18.38 8.60 32.86 3.32
628 6189 2.357075 TGTTCACCAAGCACGTGTTAA 58.643 42.857 18.38 0.00 32.86 2.01
629 6190 2.096174 TGTTCACCAAGCACGTGTTAAC 59.904 45.455 18.38 12.19 32.86 2.01
630 6191 2.025589 TCACCAAGCACGTGTTAACA 57.974 45.000 18.38 3.59 32.86 2.41
631 6192 2.357075 TCACCAAGCACGTGTTAACAA 58.643 42.857 18.38 0.00 32.86 2.83
632 6193 2.747989 TCACCAAGCACGTGTTAACAAA 59.252 40.909 18.38 0.00 32.86 2.83
633 6194 2.849473 CACCAAGCACGTGTTAACAAAC 59.151 45.455 18.38 0.00 0.00 2.93
634 6195 2.750712 ACCAAGCACGTGTTAACAAACT 59.249 40.909 18.38 2.61 0.00 2.66
635 6196 3.181504 ACCAAGCACGTGTTAACAAACTC 60.182 43.478 18.38 0.00 0.00 3.01
636 6197 3.026349 CAAGCACGTGTTAACAAACTCG 58.974 45.455 18.38 12.03 42.98 4.18
639 6647 2.029486 GCACGTGTTAACAAACTCGTCA 59.971 45.455 18.38 0.00 46.70 4.35
642 6650 3.180980 ACGTGTTAACAAACTCGTCATCG 59.819 43.478 10.51 8.02 45.84 3.84
646 6654 5.175491 GTGTTAACAAACTCGTCATCGGTTA 59.825 40.000 10.51 0.00 37.69 2.85
650 6658 3.124636 ACAAACTCGTCATCGGTTATTGC 59.875 43.478 0.00 0.00 37.69 3.56
651 6659 2.961526 ACTCGTCATCGGTTATTGCT 57.038 45.000 0.00 0.00 37.69 3.91
653 6661 3.703420 ACTCGTCATCGGTTATTGCTAC 58.297 45.455 0.00 0.00 37.69 3.58
668 6676 7.096312 GGTTATTGCTACCGAAGTTATTAGTCG 60.096 40.741 0.00 0.00 34.58 4.18
721 8178 9.120538 GGCTATGAAATACAACCATCTAGAAAA 57.879 33.333 0.00 0.00 0.00 2.29
956 8419 2.374184 CAACTCACCAAAGTCCCACAA 58.626 47.619 0.00 0.00 0.00 3.33
1024 8618 1.967779 GGACATCTAGCTTCCTCCTCC 59.032 57.143 0.00 0.00 0.00 4.30
1045 8639 2.743664 CTCATCATTGTTGCGTTCCTCA 59.256 45.455 0.00 0.00 0.00 3.86
1046 8640 2.743664 TCATCATTGTTGCGTTCCTCAG 59.256 45.455 0.00 0.00 0.00 3.35
1168 8762 1.421268 ACCAACACATCCAAGAGCTCA 59.579 47.619 17.77 0.00 0.00 4.26
1169 8763 2.040813 ACCAACACATCCAAGAGCTCAT 59.959 45.455 17.77 0.00 0.00 2.90
1540 9148 8.457261 ACTTGACAATGATAAGAGCAGAAAATC 58.543 33.333 7.87 0.00 0.00 2.17
1870 9482 5.431765 GAGTGGACTTAATGTGATGGTGAT 58.568 41.667 0.00 0.00 0.00 3.06
1893 9505 8.235230 TGATGGAGGAGAGTAATTAGAGGTTAT 58.765 37.037 0.00 0.00 0.00 1.89
2379 10197 2.124403 CATGGGGTGAGCTCAGGC 60.124 66.667 18.89 6.18 39.06 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.949856 ACAAATTTGAGTCACTGACCTTGT 59.050 37.500 24.64 4.20 32.18 3.16
297 5836 5.463061 GCAAATTTTATGAATGGATCGTGGG 59.537 40.000 0.00 0.00 0.00 4.61
611 6172 2.025589 TGTTAACACGTGCTTGGTGA 57.974 45.000 17.22 0.00 38.73 4.02
612 6173 2.834574 TTGTTAACACGTGCTTGGTG 57.165 45.000 17.22 0.00 41.15 4.17
613 6174 2.750712 AGTTTGTTAACACGTGCTTGGT 59.249 40.909 17.22 0.00 36.70 3.67
614 6175 3.359654 GAGTTTGTTAACACGTGCTTGG 58.640 45.455 17.22 0.00 36.70 3.61
615 6176 3.026349 CGAGTTTGTTAACACGTGCTTG 58.974 45.455 17.22 1.86 41.45 4.01
622 6183 3.492011 ACCGATGACGAGTTTGTTAACAC 59.508 43.478 8.07 0.00 42.66 3.32
623 6184 3.719924 ACCGATGACGAGTTTGTTAACA 58.280 40.909 3.59 3.59 42.66 2.41
624 6185 4.720530 AACCGATGACGAGTTTGTTAAC 57.279 40.909 0.00 0.00 42.66 2.01
626 6187 5.163933 GCAATAACCGATGACGAGTTTGTTA 60.164 40.000 0.00 0.00 42.66 2.41
628 6189 3.124636 GCAATAACCGATGACGAGTTTGT 59.875 43.478 0.00 0.00 42.66 2.83
629 6190 3.370978 AGCAATAACCGATGACGAGTTTG 59.629 43.478 0.00 0.00 42.66 2.93
630 6191 3.596214 AGCAATAACCGATGACGAGTTT 58.404 40.909 0.00 0.00 42.66 2.66
631 6192 3.247006 AGCAATAACCGATGACGAGTT 57.753 42.857 0.00 0.00 42.66 3.01
632 6193 2.961526 AGCAATAACCGATGACGAGT 57.038 45.000 0.00 0.00 42.66 4.18
633 6194 3.050619 GGTAGCAATAACCGATGACGAG 58.949 50.000 0.00 0.00 42.66 4.18
634 6195 3.088194 GGTAGCAATAACCGATGACGA 57.912 47.619 0.00 0.00 42.66 4.20
642 6650 7.096312 CGACTAATAACTTCGGTAGCAATAACC 60.096 40.741 0.00 0.00 0.00 2.85
646 6654 5.287226 CCGACTAATAACTTCGGTAGCAAT 58.713 41.667 1.03 0.00 45.95 3.56
681 8005 3.423749 TCATAGCCGGGTATCGTCATAA 58.576 45.455 23.08 0.00 37.11 1.90
682 8006 3.076079 TCATAGCCGGGTATCGTCATA 57.924 47.619 23.08 0.00 37.11 2.15
685 8009 2.806608 TTTCATAGCCGGGTATCGTC 57.193 50.000 23.08 0.00 37.11 4.20
686 8010 3.575256 TGTATTTCATAGCCGGGTATCGT 59.425 43.478 23.08 11.52 37.11 3.73
687 8011 4.182693 TGTATTTCATAGCCGGGTATCG 57.817 45.455 23.08 17.47 38.88 2.92
689 8013 4.103469 TGGTTGTATTTCATAGCCGGGTAT 59.897 41.667 20.40 20.40 0.00 2.73
732 8189 8.579682 TTGACCTACTTAAACTTAGAAACGTC 57.420 34.615 0.00 0.00 0.00 4.34
956 8419 8.798975 TGGGGTTCTATATCTTGAGATAGTTT 57.201 34.615 10.77 0.00 40.04 2.66
1024 8618 2.743664 TGAGGAACGCAACAATGATGAG 59.256 45.455 0.00 0.00 33.41 2.90
1168 8762 0.329931 TCCAACACCGCCCAATGTAT 59.670 50.000 0.00 0.00 0.00 2.29
1169 8763 0.322098 CTCCAACACCGCCCAATGTA 60.322 55.000 0.00 0.00 0.00 2.29
1462 9058 1.331756 CATGGCAACGCAAGAGGATAC 59.668 52.381 0.00 0.00 43.62 2.24
1870 9482 7.592736 TGATAACCTCTAATTACTCTCCTCCA 58.407 38.462 0.00 0.00 0.00 3.86
1893 9505 6.415206 ACACTAAGCCTAAACACTAACTGA 57.585 37.500 0.00 0.00 0.00 3.41
2328 10146 0.317269 GAAGACGACGACAACCACGA 60.317 55.000 0.00 0.00 34.70 4.35


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

AutoCloner maintained by Alex Coulton.