Multiple sequence alignment - TraesCS5A01G339500

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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 TraesCS5A01G339500 chr5A 100.000 2334 0 0 1 2334 546723831 546721498 0.000000e+00 4311
1 TraesCS5A01G339500 chr5A 90.956 1559 119 15 26 1572 546884012 546885560 0.000000e+00 2078
2 TraesCS5A01G339500 chr5A 95.346 752 19 3 1583 2334 241266226 241266961 0.000000e+00 1181
3 TraesCS5A01G339500 chr3B 99.070 753 7 0 1582 2334 13370905 13371657 0.000000e+00 1352
4 TraesCS5A01G339500 chr3B 96.615 325 9 2 1582 1905 708299266 708299589 2.640000e-149 538
5 TraesCS5A01G339500 chr3A 97.500 760 17 2 1576 2334 732869316 732868558 0.000000e+00 1297
6 TraesCS5A01G339500 chr3A 95.878 752 17 1 1583 2334 668578205 668577468 0.000000e+00 1205
7 TraesCS5A01G339500 chr4A 97.009 769 20 3 1568 2334 144633507 144634274 0.000000e+00 1290
8 TraesCS5A01G339500 chr2B 95.213 752 22 1 1583 2334 272466102 272465365 0.000000e+00 1177
9 TraesCS5A01G339500 chr2B 97.841 602 11 2 1582 2182 355568652 355568052 0.000000e+00 1038
10 TraesCS5A01G339500 chr2B 80.828 459 76 9 438 886 390813090 390812634 1.330000e-92 350
11 TraesCS5A01G339500 chr5B 89.631 839 64 15 759 1586 522498960 522499786 0.000000e+00 1046
12 TraesCS5A01G339500 chr5B 90.447 649 39 11 944 1584 521241486 521240853 0.000000e+00 833
13 TraesCS5A01G339500 chr5B 95.604 91 2 1 866 954 521242241 521242151 6.720000e-31 145
14 TraesCS5A01G339500 chr4B 98.003 601 11 1 1583 2182 621711906 621711306 0.000000e+00 1042
15 TraesCS5A01G339500 chr7B 97.793 589 13 0 1746 2334 100406324 100405736 0.000000e+00 1016
16 TraesCS5A01G339500 chr7B 82.593 856 118 26 55 886 534537291 534536443 0.000000e+00 726
17 TraesCS5A01G339500 chr5D 91.257 732 40 12 866 1584 431627563 431626843 0.000000e+00 976
18 TraesCS5A01G339500 chr5D 81.547 905 140 17 1 886 353295168 353294272 0.000000e+00 721
19 TraesCS5A01G339500 chr5D 90.702 527 46 3 204 728 431640165 431639640 0.000000e+00 699
20 TraesCS5A01G339500 chr5D 81.369 891 129 27 20 886 421490674 421491551 0.000000e+00 691
21 TraesCS5A01G339500 chr1A 81.718 908 124 17 13 886 572220746 572219847 0.000000e+00 719
22 TraesCS5A01G339500 chr4D 81.117 895 135 25 14 886 13250480 13251362 0.000000e+00 686
23 TraesCS5A01G339500 chr4D 79.934 907 135 37 14 889 47995490 47996380 7.080000e-175 623
24 TraesCS5A01G339500 chr2A 80.512 898 123 31 15 886 398856410 398857281 1.960000e-180 641
25 TraesCS5A01G339500 chr2A 80.401 898 124 31 15 886 398459163 398458292 9.100000e-179 636
26 TraesCS5A01G339500 chr2A 76.628 860 153 26 41 886 579443374 579442549 4.610000e-117 431
27 TraesCS5A01G339500 chr1D 80.688 756 111 26 15 752 40807659 40806921 2.620000e-154 555
28 TraesCS5A01G339500 chr1D 81.769 373 60 4 522 886 448221581 448221209 2.910000e-79 305
29 TraesCS5A01G339500 chr6A 86.131 274 37 1 614 886 45758898 45758625 6.310000e-76 294
30 TraesCS5A01G339500 chr1B 79.570 372 66 7 522 885 613525536 613525167 8.280000e-65 257


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 TraesCS5A01G339500 chr5A 546721498 546723831 2333 True 4311 4311 100.0000 1 2334 1 chr5A.!!$R1 2333
1 TraesCS5A01G339500 chr5A 546884012 546885560 1548 False 2078 2078 90.9560 26 1572 1 chr5A.!!$F2 1546
2 TraesCS5A01G339500 chr5A 241266226 241266961 735 False 1181 1181 95.3460 1583 2334 1 chr5A.!!$F1 751
3 TraesCS5A01G339500 chr3B 13370905 13371657 752 False 1352 1352 99.0700 1582 2334 1 chr3B.!!$F1 752
4 TraesCS5A01G339500 chr3A 732868558 732869316 758 True 1297 1297 97.5000 1576 2334 1 chr3A.!!$R2 758
5 TraesCS5A01G339500 chr3A 668577468 668578205 737 True 1205 1205 95.8780 1583 2334 1 chr3A.!!$R1 751
6 TraesCS5A01G339500 chr4A 144633507 144634274 767 False 1290 1290 97.0090 1568 2334 1 chr4A.!!$F1 766
7 TraesCS5A01G339500 chr2B 272465365 272466102 737 True 1177 1177 95.2130 1583 2334 1 chr2B.!!$R1 751
8 TraesCS5A01G339500 chr2B 355568052 355568652 600 True 1038 1038 97.8410 1582 2182 1 chr2B.!!$R2 600
9 TraesCS5A01G339500 chr5B 522498960 522499786 826 False 1046 1046 89.6310 759 1586 1 chr5B.!!$F1 827
10 TraesCS5A01G339500 chr5B 521240853 521242241 1388 True 489 833 93.0255 866 1584 2 chr5B.!!$R1 718
11 TraesCS5A01G339500 chr4B 621711306 621711906 600 True 1042 1042 98.0030 1583 2182 1 chr4B.!!$R1 599
12 TraesCS5A01G339500 chr7B 100405736 100406324 588 True 1016 1016 97.7930 1746 2334 1 chr7B.!!$R1 588
13 TraesCS5A01G339500 chr7B 534536443 534537291 848 True 726 726 82.5930 55 886 1 chr7B.!!$R2 831
14 TraesCS5A01G339500 chr5D 431626843 431627563 720 True 976 976 91.2570 866 1584 1 chr5D.!!$R2 718
15 TraesCS5A01G339500 chr5D 353294272 353295168 896 True 721 721 81.5470 1 886 1 chr5D.!!$R1 885
16 TraesCS5A01G339500 chr5D 431639640 431640165 525 True 699 699 90.7020 204 728 1 chr5D.!!$R3 524
17 TraesCS5A01G339500 chr5D 421490674 421491551 877 False 691 691 81.3690 20 886 1 chr5D.!!$F1 866
18 TraesCS5A01G339500 chr1A 572219847 572220746 899 True 719 719 81.7180 13 886 1 chr1A.!!$R1 873
19 TraesCS5A01G339500 chr4D 13250480 13251362 882 False 686 686 81.1170 14 886 1 chr4D.!!$F1 872
20 TraesCS5A01G339500 chr4D 47995490 47996380 890 False 623 623 79.9340 14 889 1 chr4D.!!$F2 875
21 TraesCS5A01G339500 chr2A 398856410 398857281 871 False 641 641 80.5120 15 886 1 chr2A.!!$F1 871
22 TraesCS5A01G339500 chr2A 398458292 398459163 871 True 636 636 80.4010 15 886 1 chr2A.!!$R1 871
23 TraesCS5A01G339500 chr2A 579442549 579443374 825 True 431 431 76.6280 41 886 1 chr2A.!!$R2 845
24 TraesCS5A01G339500 chr1D 40806921 40807659 738 True 555 555 80.6880 15 752 1 chr1D.!!$R1 737

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
701 797 1.571919 CCCGGTCAAAATCGAGCTAG 58.428 55.0 0.0 0.0 0.0 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 2393 9.621629 CGTCCATTAGGAGTAGAGATATAGATT 57.378 37.037 0.0 0.0 46.92 2.4 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
271 327 9.902684 TGACTTTCCAAAAATATAATACCCGTA 57.097 29.630 0.00 0.00 0.00 4.02
291 348 7.447238 ACCCGTAATATTTTGTAATGGATGGAG 59.553 37.037 0.00 0.00 0.00 3.86
340 398 6.969366 TGATGGAGTGTGTTTTGTTTCTATG 58.031 36.000 0.00 0.00 0.00 2.23
457 521 6.772233 TGACTGCATGTATTATATTGGTGCTT 59.228 34.615 0.00 0.00 32.67 3.91
485 552 6.515272 ATCACATGGTGACACTTATTTTCC 57.485 37.500 5.39 0.00 45.65 3.13
555 625 5.910637 TTGCTGCTGATTGATTTGAAAAC 57.089 34.783 0.00 0.00 0.00 2.43
562 632 5.914635 GCTGATTGATTTGAAAACTCGTTGA 59.085 36.000 0.00 0.00 0.00 3.18
696 792 2.435234 CGGCCCGGTCAAAATCGA 60.435 61.111 0.00 0.00 0.00 3.59
698 794 2.761195 GGCCCGGTCAAAATCGAGC 61.761 63.158 0.00 0.00 0.00 5.03
701 797 1.571919 CCCGGTCAAAATCGAGCTAG 58.428 55.000 0.00 0.00 0.00 3.42
840 957 4.990526 ACTCAATCTTCATTGGTGACCTT 58.009 39.130 2.11 0.00 40.08 3.50
859 978 4.463891 ACCTTAATTCAATGTGGGCTCTTG 59.536 41.667 0.00 0.00 0.00 3.02
985 1781 2.168496 TCGACTCCGTCCTCTCAAAAT 58.832 47.619 0.00 0.00 37.05 1.82
1045 1843 1.734477 CTCGTCGTGCTCACCCTTG 60.734 63.158 0.00 0.00 0.00 3.61
1109 1907 3.331889 TGCCCTTCTCTTTTCCATCTCTT 59.668 43.478 0.00 0.00 0.00 2.85
1118 1916 5.891198 TCTTTTCCATCTCTTTTCCATGGA 58.109 37.500 11.44 11.44 43.63 3.41
1154 1954 4.217118 GCTAATTGTGTCCATCCATCCATC 59.783 45.833 0.00 0.00 0.00 3.51
1155 1955 2.734755 TTGTGTCCATCCATCCATCC 57.265 50.000 0.00 0.00 0.00 3.51
1157 1957 2.137702 TGTGTCCATCCATCCATCCAT 58.862 47.619 0.00 0.00 0.00 3.41
1158 1958 2.158579 TGTGTCCATCCATCCATCCATG 60.159 50.000 0.00 0.00 0.00 3.66
1159 1959 2.107031 GTGTCCATCCATCCATCCATGA 59.893 50.000 0.00 0.00 0.00 3.07
1225 2025 2.424557 CTGATATGCATGGACTGGCTC 58.575 52.381 10.16 0.00 0.00 4.70
1324 2124 2.584835 ATTGCCACTGTACCATGTGT 57.415 45.000 9.02 0.00 32.76 3.72
1335 2135 8.038944 CCACTGTACCATGTGTTATAAGTAAGT 58.961 37.037 9.02 0.00 32.76 2.24
1342 2142 8.419442 ACCATGTGTTATAAGTAAGTACTAGGC 58.581 37.037 0.00 0.00 34.99 3.93
1348 2148 9.305555 TGTTATAAGTAAGTACTAGGCTATGGG 57.694 37.037 0.00 0.00 34.99 4.00
1349 2149 9.306777 GTTATAAGTAAGTACTAGGCTATGGGT 57.693 37.037 0.00 0.00 34.99 4.51
1352 2152 6.776887 AGTAAGTACTAGGCTATGGGTAGA 57.223 41.667 0.00 0.00 34.13 2.59
1355 2155 6.776887 AAGTACTAGGCTATGGGTAGAGTA 57.223 41.667 0.00 0.00 0.00 2.59
1362 2170 9.071334 ACTAGGCTATGGGTAGAGTAATAGTAT 57.929 37.037 0.00 0.00 0.00 2.12
1384 2192 9.331282 AGTATCTGCTAATAAATTGACAGTTCC 57.669 33.333 0.00 0.00 0.00 3.62
1444 2256 0.301987 GTTTCCGCTTGATCGCTAGC 59.698 55.000 4.06 4.06 39.12 3.42
1480 2292 5.048013 TGACCATGTTGTTGTGTTGTGTTTA 60.048 36.000 0.00 0.00 0.00 2.01
1481 2293 5.164954 ACCATGTTGTTGTGTTGTGTTTAC 58.835 37.500 0.00 0.00 0.00 2.01
1519 2336 6.321181 TGGTTGTATATTGGCTGAATTCTTCC 59.679 38.462 7.05 8.15 0.00 3.46
1559 2377 8.944138 CCCTATCTCTATATCCATCTCTACTCA 58.056 40.741 0.00 0.00 0.00 3.41
2039 2891 7.393234 TGGTAAGGTCATAACTCAGGAAATTTG 59.607 37.037 0.00 0.00 0.00 2.32
2096 2948 2.175499 CCCCAAAGGCTATCAATCCAGA 59.825 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
230 256 8.647143 TTGGAAAGTCAAATTTCTTTAGCTTG 57.353 30.769 0.00 0.00 38.86 4.01
284 341 6.263168 CACCCATCAAACTAAATACTCCATCC 59.737 42.308 0.00 0.00 0.00 3.51
291 348 4.862371 TCCCCACCCATCAAACTAAATAC 58.138 43.478 0.00 0.00 0.00 1.89
340 398 4.615912 GCCCATCAAATCACCGCATTATAC 60.616 45.833 0.00 0.00 0.00 1.47
485 552 1.995626 CACCCTCCCACCACCTAGG 60.996 68.421 7.41 7.41 45.67 3.02
562 632 3.768878 TGGTTTATGATTTTGACCGGGT 58.231 40.909 6.32 0.00 33.07 5.28
696 792 3.445008 TGAGGTCTTCAATGGTCTAGCT 58.555 45.455 0.00 0.00 31.34 3.32
840 957 6.267471 AGTTTTCAAGAGCCCACATTGAATTA 59.733 34.615 0.90 0.00 41.24 1.40
985 1781 2.354303 CCTCCATAGGTGCGTGTGTTTA 60.354 50.000 0.00 0.00 38.19 2.01
1013 1811 1.371595 GACGAGGAAGTAGAGAGCGT 58.628 55.000 0.00 0.00 0.00 5.07
1022 1820 1.286260 GTGAGCACGACGAGGAAGT 59.714 57.895 0.00 0.00 0.00 3.01
1071 1869 1.429148 GGCAAGGCAATCGAGTACCG 61.429 60.000 0.00 0.00 40.25 4.02
1109 1907 4.463891 GCAGGAGATCTTTTTCCATGGAAA 59.536 41.667 31.75 31.75 41.69 3.13
1118 1916 6.151817 GGACACAATTAGCAGGAGATCTTTTT 59.848 38.462 0.00 0.00 0.00 1.94
1154 1954 1.156736 ACGCGGAAAGAAACTCATGG 58.843 50.000 12.47 0.00 0.00 3.66
1155 1955 3.250744 TCTACGCGGAAAGAAACTCATG 58.749 45.455 12.47 0.00 0.00 3.07
1157 1957 2.555325 TCTCTACGCGGAAAGAAACTCA 59.445 45.455 12.47 0.00 0.00 3.41
1158 1958 3.119919 TCTCTCTACGCGGAAAGAAACTC 60.120 47.826 12.47 0.00 0.00 3.01
1159 1959 2.818432 TCTCTCTACGCGGAAAGAAACT 59.182 45.455 12.47 0.00 0.00 2.66
1295 2095 1.019673 CAGTGGCAATAGCGCTTGAT 58.980 50.000 18.68 0.00 43.41 2.57
1335 2135 8.460317 ACTATTACTCTACCCATAGCCTAGTA 57.540 38.462 0.00 0.00 0.00 1.82
1344 2144 9.998752 ATTAGCAGATACTATTACTCTACCCAT 57.001 33.333 0.00 0.00 0.00 4.00
1362 2170 7.611467 ACATGGAACTGTCAATTTATTAGCAGA 59.389 33.333 0.00 0.00 0.00 4.26
1384 2192 4.151867 CCATGAGCGATACAGATGAACATG 59.848 45.833 0.00 0.00 34.41 3.21
1444 2256 4.761739 ACAACATGGTCATCACACCTAAAG 59.238 41.667 0.00 0.00 37.34 1.85
1480 2292 0.038744 CAACCAAGGCATGAGAGGGT 59.961 55.000 0.00 0.00 0.00 4.34
1481 2293 0.038744 ACAACCAAGGCATGAGAGGG 59.961 55.000 0.00 0.00 0.00 4.30
1575 2393 9.621629 CGTCCATTAGGAGTAGAGATATAGATT 57.378 37.037 0.00 0.00 46.92 2.40


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

AutoCloner maintained by Alex Coulton.