Multiple sequence alignment - TraesCS7B01G281500

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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 TraesCS7B01G281500 chr7B 100.000 2431 0 0 1 2431 515590560 515592990 0.000000e+00 4490.0
1 TraesCS7B01G281500 chr7B 94.814 1639 80 4 795 2431 575977294 575975659 0.000000e+00 2551.0
2 TraesCS7B01G281500 chr6B 96.034 1639 63 2 795 2431 671454189 671455827 0.000000e+00 2665.0
3 TraesCS7B01G281500 chr2D 95.729 1639 62 6 795 2431 645428945 645430577 0.000000e+00 2632.0
4 TraesCS7B01G281500 chr2D 96.110 797 25 2 1 797 598695048 598694258 0.000000e+00 1295.0
5 TraesCS7B01G281500 chr2D 94.421 717 37 3 858 1573 586830966 586831680 0.000000e+00 1099.0
6 TraesCS7B01G281500 chr3A 95.607 1639 68 3 795 2431 629105947 629107583 0.000000e+00 2625.0
7 TraesCS7B01G281500 chr5B 96.424 1426 48 3 1 1423 527732241 527733666 0.000000e+00 2348.0
8 TraesCS7B01G281500 chr5B 90.968 775 61 4 1 770 533554592 533555362 0.000000e+00 1035.0
9 TraesCS7B01G281500 chr5B 95.575 565 9 2 1868 2431 581252873 581252324 0.000000e+00 891.0
10 TraesCS7B01G281500 chr5B 91.429 210 18 0 1 210 510141064 510140855 3.060000e-74 289.0
11 TraesCS7B01G281500 chr5B 93.976 83 5 0 578 660 702376665 702376583 2.540000e-25 126.0
12 TraesCS7B01G281500 chr5B 100.000 33 0 0 765 797 533555370 533555402 7.260000e-06 62.1
13 TraesCS7B01G281500 chr1B 96.929 1335 39 2 1099 2431 665424813 665423479 0.000000e+00 2237.0
14 TraesCS7B01G281500 chr1B 92.241 1160 74 5 1286 2431 232329633 232330790 0.000000e+00 1629.0
15 TraesCS7B01G281500 chr4D 91.200 1500 84 16 858 2354 437505855 437507309 0.000000e+00 1995.0
16 TraesCS7B01G281500 chr7D 96.754 1140 33 3 1294 2431 41752456 41751319 0.000000e+00 1897.0
17 TraesCS7B01G281500 chr3B 95.479 1106 42 4 868 1972 749193609 749192511 0.000000e+00 1759.0
18 TraesCS7B01G281500 chr3B 90.328 641 56 4 1 641 183623819 183624453 0.000000e+00 835.0
19 TraesCS7B01G281500 chr3B 95.238 210 10 0 1 210 787978758 787978549 1.390000e-87 333.0
20 TraesCS7B01G281500 chr3B 100.000 33 0 0 765 797 183624650 183624682 7.260000e-06 62.1
21 TraesCS7B01G281500 chr4A 94.354 797 38 4 1 797 340238061 340237272 0.000000e+00 1216.0
22 TraesCS7B01G281500 chr1A 93.495 784 39 9 1 778 557595686 557594909 0.000000e+00 1155.0
23 TraesCS7B01G281500 chr1A 100.000 33 0 0 765 797 557594909 557594877 7.260000e-06 62.1
24 TraesCS7B01G281500 chr5D 94.625 707 33 4 1 703 480176512 480175807 0.000000e+00 1090.0
25 TraesCS7B01G281500 chr5D 92.500 200 11 4 462 660 550205487 550205683 1.420000e-72 283.0
26 TraesCS7B01G281500 chr5D 82.443 262 27 3 204 462 550205187 550205432 6.810000e-51 211.0
27 TraesCS7B01G281500 chr3D 94.003 717 41 2 858 1573 10933418 10932703 0.000000e+00 1085.0
28 TraesCS7B01G281500 chr3D 93.584 717 44 2 858 1573 588696155 588696870 0.000000e+00 1068.0
29 TraesCS7B01G281500 chr3D 90.361 83 5 2 680 759 25952286 25952368 3.310000e-19 106.0
30 TraesCS7B01G281500 chr2B 95.044 565 12 2 1868 2431 81564407 81564956 0.000000e+00 874.0


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 TraesCS7B01G281500 chr7B 515590560 515592990 2430 False 4490.00 4490 100.0000 1 2431 1 chr7B.!!$F1 2430
1 TraesCS7B01G281500 chr7B 575975659 575977294 1635 True 2551.00 2551 94.8140 795 2431 1 chr7B.!!$R1 1636
2 TraesCS7B01G281500 chr6B 671454189 671455827 1638 False 2665.00 2665 96.0340 795 2431 1 chr6B.!!$F1 1636
3 TraesCS7B01G281500 chr2D 645428945 645430577 1632 False 2632.00 2632 95.7290 795 2431 1 chr2D.!!$F2 1636
4 TraesCS7B01G281500 chr2D 598694258 598695048 790 True 1295.00 1295 96.1100 1 797 1 chr2D.!!$R1 796
5 TraesCS7B01G281500 chr2D 586830966 586831680 714 False 1099.00 1099 94.4210 858 1573 1 chr2D.!!$F1 715
6 TraesCS7B01G281500 chr3A 629105947 629107583 1636 False 2625.00 2625 95.6070 795 2431 1 chr3A.!!$F1 1636
7 TraesCS7B01G281500 chr5B 527732241 527733666 1425 False 2348.00 2348 96.4240 1 1423 1 chr5B.!!$F1 1422
8 TraesCS7B01G281500 chr5B 581252324 581252873 549 True 891.00 891 95.5750 1868 2431 1 chr5B.!!$R2 563
9 TraesCS7B01G281500 chr5B 533554592 533555402 810 False 548.55 1035 95.4840 1 797 2 chr5B.!!$F2 796
10 TraesCS7B01G281500 chr1B 665423479 665424813 1334 True 2237.00 2237 96.9290 1099 2431 1 chr1B.!!$R1 1332
11 TraesCS7B01G281500 chr1B 232329633 232330790 1157 False 1629.00 1629 92.2410 1286 2431 1 chr1B.!!$F1 1145
12 TraesCS7B01G281500 chr4D 437505855 437507309 1454 False 1995.00 1995 91.2000 858 2354 1 chr4D.!!$F1 1496
13 TraesCS7B01G281500 chr7D 41751319 41752456 1137 True 1897.00 1897 96.7540 1294 2431 1 chr7D.!!$R1 1137
14 TraesCS7B01G281500 chr3B 749192511 749193609 1098 True 1759.00 1759 95.4790 868 1972 1 chr3B.!!$R1 1104
15 TraesCS7B01G281500 chr3B 183623819 183624682 863 False 448.55 835 95.1640 1 797 2 chr3B.!!$F1 796
16 TraesCS7B01G281500 chr4A 340237272 340238061 789 True 1216.00 1216 94.3540 1 797 1 chr4A.!!$R1 796
17 TraesCS7B01G281500 chr1A 557594877 557595686 809 True 608.55 1155 96.7475 1 797 2 chr1A.!!$R1 796
18 TraesCS7B01G281500 chr5D 480175807 480176512 705 True 1090.00 1090 94.6250 1 703 1 chr5D.!!$R1 702
19 TraesCS7B01G281500 chr3D 10932703 10933418 715 True 1085.00 1085 94.0030 858 1573 1 chr3D.!!$R1 715
20 TraesCS7B01G281500 chr3D 588696155 588696870 715 False 1068.00 1068 93.5840 858 1573 1 chr3D.!!$F2 715
21 TraesCS7B01G281500 chr2B 81564407 81564956 549 False 874.00 874 95.0440 1868 2431 1 chr2B.!!$F1 563

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
408 411 1.214589 GGCTGAATGCTTGCACTGG 59.785 57.895 0.0 0.0 42.39 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1610 2.170397 TGCCACAACTCTGAACTCAAGA 59.83 45.455 0.0 0.0 0.0 3.02 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
44 45 3.117888 CCCATGTCAAGGTAGCCACTATT 60.118 47.826 0.00 0.00 0.00 1.73
116 117 1.591703 CAAGGGAGTAGCTCGTGCA 59.408 57.895 12.58 0.00 42.74 4.57
172 173 1.718757 CCGCTACTGCTGGATTTGGC 61.719 60.000 0.00 0.00 35.80 4.52
177 180 2.361104 TGCTGGATTTGGCGGGTC 60.361 61.111 0.00 0.00 0.00 4.46
333 336 4.454847 ACTGAATGTGTGAGCTGATTTCAG 59.545 41.667 12.84 12.84 46.40 3.02
375 378 2.163010 GTGTTCACTGGATGCATTCTGG 59.837 50.000 15.60 6.86 0.00 3.86
408 411 1.214589 GGCTGAATGCTTGCACTGG 59.785 57.895 0.00 0.00 42.39 4.00
476 479 7.272978 GGTCTCTGCTACATCTGGTAAATTAA 58.727 38.462 0.00 0.00 0.00 1.40
551 554 3.779444 TCTTGCTCCCTGTTAAGAGAGA 58.221 45.455 0.19 0.00 31.43 3.10
835 942 6.348498 GTTGGCCCATTATTGCTAGATTTTT 58.652 36.000 0.00 0.00 0.00 1.94
837 944 7.049799 TGGCCCATTATTGCTAGATTTTTAC 57.950 36.000 0.00 0.00 0.00 2.01
899 1006 6.968904 AGCATACAATTTTGCTCAAATAGTCG 59.031 34.615 2.26 0.00 45.83 4.18
959 1073 3.274288 GCTTGTTGCTAGCTGTAGGATT 58.726 45.455 17.23 0.00 38.95 3.01
963 1077 4.507710 TGTTGCTAGCTGTAGGATTTGAG 58.492 43.478 17.23 0.00 0.00 3.02
1009 1123 1.005450 GGCCAAGGGAAATGACTACCA 59.995 52.381 0.00 0.00 0.00 3.25
1132 1250 4.133820 CAACAACCTCTACAATGTCCACA 58.866 43.478 0.00 0.00 0.00 4.17
1148 1266 2.295349 TCCACACCTACAAGTTCTCGAC 59.705 50.000 0.00 0.00 0.00 4.20
1177 1296 5.699839 AGCTCTTTGCAGTATTTTTAACCG 58.300 37.500 0.00 0.00 45.94 4.44
1319 1438 0.762418 TGTCCACGACCAAGACCAAT 59.238 50.000 0.00 0.00 0.00 3.16
1491 1610 1.139058 ACGACTTGTCTGTGCTTCCTT 59.861 47.619 0.00 0.00 0.00 3.36
1654 1785 4.292186 AGGAAATGATAGGCGCATATGT 57.708 40.909 20.67 4.99 0.00 2.29
1739 1871 6.779117 AGTGTAATCAATCTCTTTTCATGCG 58.221 36.000 0.00 0.00 0.00 4.73
2222 2354 6.667848 TCATCCTCTTCACTGGAGTAACAATA 59.332 38.462 0.00 0.00 35.63 1.90
2405 2538 7.014711 GGATCTGGTTGAGTCTCTATGATGTTA 59.985 40.741 0.65 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.857052 CGAAATAGTGGCTACCTTGACA 58.143 45.455 0.00 0.00 0.00 3.58
44 45 1.351017 GATGGGGATAAGATGGGCGAA 59.649 52.381 0.00 0.00 0.00 4.70
116 117 0.752054 CAACAAACACATGCCCCAGT 59.248 50.000 0.00 0.00 0.00 4.00
177 180 1.454847 CCCTCTCTGGTCTCTCCCG 60.455 68.421 0.00 0.00 34.77 5.14
226 229 6.681729 ATTGAAGTACCTACCTTGAAGACA 57.318 37.500 0.00 0.00 0.00 3.41
333 336 2.810439 ACCAAGATCTCTGCTATCGC 57.190 50.000 0.00 0.00 0.00 4.58
614 619 0.037605 GTCCCGTCGTCCATCAAACT 60.038 55.000 0.00 0.00 0.00 2.66
835 942 2.108168 GTACAGAGCATCACCAGGGTA 58.892 52.381 0.00 0.00 37.82 3.69
837 944 1.198713 AGTACAGAGCATCACCAGGG 58.801 55.000 0.00 0.00 37.82 4.45
899 1006 7.872113 ATCCTACAGAATCAAGGAAACATTC 57.128 36.000 3.67 0.00 42.53 2.67
959 1073 5.237344 CACCAAAACAACAACCAAAACTCAA 59.763 36.000 0.00 0.00 0.00 3.02
963 1077 5.180304 ACATCACCAAAACAACAACCAAAAC 59.820 36.000 0.00 0.00 0.00 2.43
1132 1250 1.811359 CGGAGTCGAGAACTTGTAGGT 59.189 52.381 0.00 0.00 38.74 3.08
1148 1266 2.941453 TACTGCAAAGAGCTACGGAG 57.059 50.000 0.00 0.00 45.94 4.63
1177 1296 3.304293 GCAGAGACACTTGCAAACAAAAC 59.696 43.478 0.00 0.00 34.74 2.43
1482 1601 3.733337 TCTGAACTCAAGAAGGAAGCAC 58.267 45.455 0.00 0.00 0.00 4.40
1491 1610 2.170397 TGCCACAACTCTGAACTCAAGA 59.830 45.455 0.00 0.00 0.00 3.02
1654 1785 7.885922 TCAACAAACTGGGAAGCATAATAACTA 59.114 33.333 0.00 0.00 0.00 2.24
1713 1844 7.752239 CGCATGAAAAGAGATTGATTACACTTT 59.248 33.333 0.00 0.00 0.00 2.66
1732 1864 3.928992 GTCACTTCAGAAGATCGCATGAA 59.071 43.478 17.56 8.56 0.00 2.57
1739 1871 6.876257 ACATTTACTGGTCACTTCAGAAGATC 59.124 38.462 17.56 6.36 36.22 2.75
1982 2114 8.150945 TCAAAACTTAGCACTAGAAGATCAGTT 58.849 33.333 0.00 0.00 0.00 3.16
2222 2354 7.873505 GGAGACTATACAAGAGTTGTTTTGACT 59.126 37.037 0.00 0.00 42.22 3.41
2405 2538 6.535963 TGACATGACATGACACTAAGAGAT 57.464 37.500 22.19 0.00 30.39 2.75


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

AutoCloner maintained by Alex Coulton.