Multiple sequence alignment - TraesCS7D01G025600

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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 TraesCS7D01G025600 chr7D 100.000 2606 0 0 1 2606 12189530 12186925 0.000000e+00 4813.0
1 TraesCS7D01G025600 chr7D 82.702 977 159 10 735 1705 12125873 12126845 0.000000e+00 859.0
2 TraesCS7D01G025600 chr7D 82.830 961 156 9 751 1705 49233418 49232461 0.000000e+00 852.0
3 TraesCS7D01G025600 chr7D 93.810 420 11 4 2199 2604 35577893 35578311 3.680000e-173 617.0
4 TraesCS7D01G025600 chr7D 99.379 161 1 0 1856 2016 35577543 35577703 2.540000e-75 292.0
5 TraesCS7D01G025600 chr7D 93.878 147 9 0 2057 2203 35577696 35577842 3.380000e-54 222.0
6 TraesCS7D01G025600 chr7D 84.000 175 22 6 548 719 12188780 12188609 2.080000e-36 163.0
7 TraesCS7D01G025600 chr7D 84.000 175 22 6 751 922 12188983 12188812 2.080000e-36 163.0
8 TraesCS7D01G025600 chr7D 97.727 44 1 0 1740 1783 35577498 35577541 2.780000e-10 76.8
9 TraesCS7D01G025600 chr7A 96.040 1692 67 0 1 1692 11583135 11581444 0.000000e+00 2754.0
10 TraesCS7D01G025600 chr7A 88.059 1700 185 10 5 1688 11943324 11945021 0.000000e+00 1999.0
11 TraesCS7D01G025600 chr7A 88.901 955 102 4 737 1688 11844472 11845425 0.000000e+00 1173.0
12 TraesCS7D01G025600 chr7A 88.150 692 75 3 5 690 11843473 11844163 0.000000e+00 817.0
13 TraesCS7D01G025600 chr7A 93.436 518 22 6 1689 2203 734996443 734996951 0.000000e+00 758.0
14 TraesCS7D01G025600 chr7A 89.560 364 36 2 1327 1688 11891004 11891367 6.570000e-126 460.0
15 TraesCS7D01G025600 chr7A 86.946 429 16 9 2196 2606 734996996 734997402 1.840000e-121 446.0
16 TraesCS7D01G025600 chr7A 94.531 256 13 1 1 256 11659444 11659190 6.760000e-106 394.0
17 TraesCS7D01G025600 chr7A 96.316 190 7 0 1691 1880 734996257 734996446 1.950000e-81 313.0
18 TraesCS7D01G025600 chr7A 85.143 175 20 6 548 719 11582385 11582214 9.590000e-40 174.0
19 TraesCS7D01G025600 chr7A 84.571 175 21 6 751 922 11582588 11582417 4.460000e-38 169.0
20 TraesCS7D01G025600 chr7B 88.364 1693 185 10 7 1692 717029851 717028164 0.000000e+00 2025.0
21 TraesCS7D01G025600 chr7B 89.279 513 53 1 1182 1692 717052470 717051958 2.190000e-180 641.0
22 TraesCS7D01G025600 chr4A 92.080 947 70 5 749 1692 725859902 725860846 0.000000e+00 1328.0
23 TraesCS7D01G025600 chr4A 95.468 684 31 0 1 684 725858858 725859541 0.000000e+00 1092.0
24 TraesCS7D01G025600 chr3B 96.296 513 18 1 1691 2203 672611009 672610498 0.000000e+00 841.0
25 TraesCS7D01G025600 chr3B 95.437 526 20 3 1679 2203 206162594 206163116 0.000000e+00 835.0
26 TraesCS7D01G025600 chr3B 88.498 426 15 7 2199 2606 672610450 672610041 3.900000e-133 484.0
27 TraesCS7D01G025600 chr3B 86.374 433 24 8 2193 2606 206163158 206163574 8.560000e-120 440.0
28 TraesCS7D01G025600 chr1A 87.376 404 34 3 2220 2606 3833697 3834100 5.120000e-122 448.0
29 TraesCS7D01G025600 chr1A 87.597 387 31 6 1690 2076 3832987 3833356 1.430000e-117 433.0
30 TraesCS7D01G025600 chr1A 87.080 387 33 9 1690 2076 3828811 3829180 3.100000e-114 422.0
31 TraesCS7D01G025600 chr1A 90.152 132 11 1 2074 2203 3832005 3832136 1.240000e-38 171.0
32 TraesCS7D01G025600 chr2A 88.608 316 32 3 1761 2076 667946301 667945990 5.260000e-102 381.0
33 TraesCS7D01G025600 chr1D 88.652 141 15 1 1812 1952 456136247 456136386 1.240000e-38 171.0
34 TraesCS7D01G025600 chr1D 89.147 129 14 0 1690 1818 456134722 456134850 7.460000e-36 161.0


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 TraesCS7D01G025600 chr7D 12186925 12189530 2605 True 1713.000000 4813 89.333333 1 2606 3 chr7D.!!$R2 2605
1 TraesCS7D01G025600 chr7D 12125873 12126845 972 False 859.000000 859 82.702000 735 1705 1 chr7D.!!$F1 970
2 TraesCS7D01G025600 chr7D 49232461 49233418 957 True 852.000000 852 82.830000 751 1705 1 chr7D.!!$R1 954
3 TraesCS7D01G025600 chr7D 35577498 35578311 813 False 301.950000 617 96.198500 1740 2604 4 chr7D.!!$F2 864
4 TraesCS7D01G025600 chr7A 11943324 11945021 1697 False 1999.000000 1999 88.059000 5 1688 1 chr7A.!!$F2 1683
5 TraesCS7D01G025600 chr7A 11581444 11583135 1691 True 1032.333333 2754 88.584667 1 1692 3 chr7A.!!$R2 1691
6 TraesCS7D01G025600 chr7A 11843473 11845425 1952 False 995.000000 1173 88.525500 5 1688 2 chr7A.!!$F3 1683
7 TraesCS7D01G025600 chr7A 734996257 734997402 1145 False 505.666667 758 92.232667 1689 2606 3 chr7A.!!$F4 917
8 TraesCS7D01G025600 chr7B 717028164 717029851 1687 True 2025.000000 2025 88.364000 7 1692 1 chr7B.!!$R1 1685
9 TraesCS7D01G025600 chr7B 717051958 717052470 512 True 641.000000 641 89.279000 1182 1692 1 chr7B.!!$R2 510
10 TraesCS7D01G025600 chr4A 725858858 725860846 1988 False 1210.000000 1328 93.774000 1 1692 2 chr4A.!!$F1 1691
11 TraesCS7D01G025600 chr3B 672610041 672611009 968 True 662.500000 841 92.397000 1691 2606 2 chr3B.!!$R1 915
12 TraesCS7D01G025600 chr3B 206162594 206163574 980 False 637.500000 835 90.905500 1679 2606 2 chr3B.!!$F1 927
13 TraesCS7D01G025600 chr1A 3828811 3834100 5289 False 368.500000 448 88.051250 1690 2606 4 chr1A.!!$F1 916

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
843 1152 2.424601 CCATGACCAAGTTGCATACTGG 59.575 50.0 0.0 6.87 37.12 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 6384 1.396653 GACCTCATGGGCCTTCAATG 58.603 55.0 4.53 0.0 39.1 2.82 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
125 131 7.979444 AAATCGACTGTGATTTTTAGAAGGA 57.021 32.000 10.41 0.00 44.08 3.36
171 177 8.085296 GGTCTATCCTCTGTACAATAGTTGATG 58.915 40.741 10.62 0.00 0.00 3.07
428 436 8.659527 TCCAGATTTGACATATTAATGCTAGGA 58.340 33.333 0.00 0.00 36.50 2.94
710 719 6.275381 TCCCATACATCATATCCATCCAACTT 59.725 38.462 0.00 0.00 0.00 2.66
843 1152 2.424601 CCATGACCAAGTTGCATACTGG 59.575 50.000 0.00 6.87 37.12 4.00
1013 1327 4.142182 GCAACAATATATGGCACCAACACT 60.142 41.667 0.00 0.00 0.00 3.55
1022 1336 1.252904 GCACCAACACTGATGGCCAT 61.253 55.000 20.96 20.96 41.89 4.40
1080 1394 3.575351 GACCACGACGGCTCAAGCT 62.575 63.158 0.00 0.00 41.70 3.74
1103 1417 1.303561 GATCTGGTGGTGGCAAGCA 60.304 57.895 0.00 0.00 0.00 3.91
1119 1433 1.376683 GCACATGGCGACCAACCTA 60.377 57.895 0.00 0.00 36.95 3.08
1163 1477 5.056480 CGCAGAATTCAAGTACCCATATGA 58.944 41.667 8.44 0.00 0.00 2.15
1185 1499 5.013495 TGAAGATCCTGACACAGAGGAATTT 59.987 40.000 0.00 0.00 43.01 1.82
1193 1507 7.505585 TCCTGACACAGAGGAATTTTGTTTAAT 59.494 33.333 0.00 0.00 36.63 1.40
1214 1528 2.583441 CCCTCCAGTCGGACAAGCA 61.583 63.158 11.27 0.00 35.91 3.91
1290 1604 1.914798 AGGGGTCGAGTCACTACTACT 59.085 52.381 0.00 0.00 35.56 2.57
1432 1746 1.494721 TGATCAGGGATTACCAAGGCC 59.505 52.381 0.00 0.00 43.89 5.19
1654 1970 7.841915 TGTTTATCTGCGAGAAAATATGTCA 57.158 32.000 0.00 0.00 0.00 3.58
1783 2100 6.202954 CACTTTGACAGACGTCTAGGATTTTT 59.797 38.462 19.57 0.00 43.06 1.94
1891 6384 1.816679 GGTTAATCGGGCCGTGGAC 60.817 63.158 27.32 18.80 0.00 4.02
2065 6561 1.844357 CGTTGGCGAGATTACACTACG 59.156 52.381 0.00 0.00 41.33 3.51
2382 7101 3.125146 TCTCAGATCGCAATTTCCAAACG 59.875 43.478 0.00 0.00 0.00 3.60
2484 7210 2.230025 CCTGTGACACAACAACACCAAA 59.770 45.455 10.02 0.00 34.18 3.28
2485 7211 3.119173 CCTGTGACACAACAACACCAAAT 60.119 43.478 10.02 0.00 34.18 2.32
2487 7213 4.987832 TGTGACACAACAACACCAAATAC 58.012 39.130 5.62 0.00 34.18 1.89
2559 7301 2.420022 CGGTGTTGGATCCATGAACTTC 59.580 50.000 17.06 8.45 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 131 6.911308 AGACCTTTACAATAATGGTATGCCT 58.089 36.000 0.16 0.00 35.27 4.75
288 294 1.288350 GCACAACACATTGCTGCAAA 58.712 45.000 20.06 3.01 40.05 3.68
428 436 9.965902 ATAAAAGTTGATACTCAGTTTGGATCT 57.034 29.630 0.00 0.00 31.99 2.75
453 461 1.068333 GTGTCCAGCGAATGCACAAAT 60.068 47.619 0.00 0.00 46.23 2.32
669 678 7.880160 TGTATGGGAGGTTGAGATTTATTTG 57.120 36.000 0.00 0.00 0.00 2.32
843 1152 5.302360 TGCGTATAGTGGGGTTCATAAATC 58.698 41.667 0.00 0.00 0.00 2.17
1022 1336 3.876914 GACAATGGCGGAGAATACAATGA 59.123 43.478 0.00 0.00 0.00 2.57
1080 1394 2.905996 GCCACCACCAGATCCACCA 61.906 63.158 0.00 0.00 0.00 4.17
1103 1417 0.036388 CACTAGGTTGGTCGCCATGT 60.036 55.000 0.00 0.00 31.53 3.21
1106 1420 3.065306 CCACTAGGTTGGTCGCCA 58.935 61.111 0.00 0.00 0.00 5.69
1119 1433 0.679505 TCTTGCACGCTTCTACCACT 59.320 50.000 0.00 0.00 0.00 4.00
1143 1457 8.160106 GGATCTTCATATGGGTACTTGAATTCT 58.840 37.037 7.05 0.00 0.00 2.40
1144 1458 8.160106 AGGATCTTCATATGGGTACTTGAATTC 58.840 37.037 2.13 0.00 0.00 2.17
1145 1459 7.941238 CAGGATCTTCATATGGGTACTTGAATT 59.059 37.037 2.13 0.00 0.00 2.17
1163 1477 5.511386 AAATTCCTCTGTGTCAGGATCTT 57.489 39.130 0.00 0.00 39.91 2.40
1185 1499 3.558321 CCGACTGGAGGGTCATTAAACAA 60.558 47.826 0.00 0.00 37.49 2.83
1214 1528 1.003696 GGTCCTTAGCCTCAGTGCTTT 59.996 52.381 0.00 0.00 42.75 3.51
1290 1604 4.144297 ACATTTTCTTGACCTTGCTGCTA 58.856 39.130 0.00 0.00 0.00 3.49
1452 1766 3.572682 CCATCCAACGGACTAGCTGTATA 59.427 47.826 0.00 0.00 34.15 1.47
1722 2039 4.103153 AGAACTTCAAATCACTGTGGAGGA 59.897 41.667 8.11 0.00 0.00 3.71
1783 2100 2.609299 TTGGGGGATGACCGAGCA 60.609 61.111 0.00 0.00 41.60 4.26
1891 6384 1.396653 GACCTCATGGGCCTTCAATG 58.603 55.000 4.53 0.00 39.10 2.82
2038 6534 3.567478 ATCTCGCCAACGTGACGCA 62.567 57.895 4.25 0.00 43.76 5.24
2444 7168 3.665745 GGACACACCTGCAATCAAAAT 57.334 42.857 0.00 0.00 35.41 1.82
2484 7210 3.093057 TGGTCTGAGAGAGCACTGTAT 57.907 47.619 1.39 0.00 46.53 2.29
2485 7211 2.586648 TGGTCTGAGAGAGCACTGTA 57.413 50.000 1.39 0.00 46.53 2.74


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

AutoCloner maintained by Alex Coulton.