Multiple sequence alignment - TraesCS4B01G151400

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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 TraesCS4B01G151400 chr4B 100.000 2321 0 0 1 2321 243183415 243181095 0.000000e+00 4287.0
1 TraesCS4B01G151400 chr4B 95.607 1525 45 10 124 1633 361733687 361732170 0.000000e+00 2425.0
2 TraesCS4B01G151400 chr4B 92.145 1604 85 19 64 1629 221191667 221193267 0.000000e+00 2226.0
3 TraesCS4B01G151400 chr4B 97.688 692 15 1 1630 2321 361732137 361731447 0.000000e+00 1188.0
4 TraesCS4B01G151400 chr4B 90.571 350 32 1 64 412 564156392 564156741 1.620000e-126 462.0
5 TraesCS4B01G151400 chr5B 96.966 1582 30 10 64 1630 706039877 706041455 0.000000e+00 2639.0
6 TraesCS4B01G151400 chr2A 95.954 1582 39 11 64 1630 492833561 492835132 0.000000e+00 2543.0
7 TraesCS4B01G151400 chr2A 96.642 685 19 3 1630 2310 492835168 492835852 0.000000e+00 1134.0
8 TraesCS4B01G151400 chr2A 92.405 79 1 4 1 75 402915850 402915773 8.770000e-20 108.0
9 TraesCS4B01G151400 chr2A 95.312 64 3 0 1 64 173786038 173786101 4.080000e-18 102.0
10 TraesCS4B01G151400 chr2A 94.118 68 1 3 1 68 49223865 49223929 1.470000e-17 100.0
11 TraesCS4B01G151400 chr3B 95.712 1586 48 11 64 1633 124768962 124767381 0.000000e+00 2534.0
12 TraesCS4B01G151400 chr3B 97.050 644 15 4 1681 2321 124767214 124766572 0.000000e+00 1081.0
13 TraesCS4B01G151400 chr3B 91.819 709 38 8 1633 2321 254908096 254907388 0.000000e+00 970.0
14 TraesCS4B01G151400 chr4A 95.839 1538 44 11 64 1585 90386786 90385253 0.000000e+00 2468.0
15 TraesCS4B01G151400 chr4A 96.584 644 18 4 1681 2321 90384948 90384306 0.000000e+00 1064.0
16 TraesCS4B01G151400 chr4A 90.789 76 2 5 1 76 306316207 306316277 1.900000e-16 97.1
17 TraesCS4B01G151400 chr1B 90.971 1462 79 23 220 1629 91886723 91885263 0.000000e+00 1919.0
18 TraesCS4B01G151400 chr1B 96.825 63 0 1 1 63 405713075 405713015 1.130000e-18 104.0
19 TraesCS4B01G151400 chr1B 96.774 62 1 1 1 62 599631885 599631945 4.080000e-18 102.0
20 TraesCS4B01G151400 chr1B 96.774 62 1 1 1 62 599703095 599703155 4.080000e-18 102.0
21 TraesCS4B01G151400 chr6D 93.301 1254 51 17 405 1628 352345986 352347236 0.000000e+00 1820.0
22 TraesCS4B01G151400 chr6D 92.368 1271 54 20 405 1633 59751323 59750054 0.000000e+00 1770.0
23 TraesCS4B01G151400 chr6D 91.230 1049 50 11 624 1630 173910678 173911726 0.000000e+00 1389.0
24 TraesCS4B01G151400 chr6D 93.750 704 30 7 1632 2321 59750019 59749316 0.000000e+00 1044.0
25 TraesCS4B01G151400 chr6D 93.626 706 31 6 1630 2321 263996743 263996038 0.000000e+00 1042.0
26 TraesCS4B01G151400 chr6D 93.475 705 32 7 1630 2321 352347275 352347978 0.000000e+00 1035.0
27 TraesCS4B01G151400 chr5D 92.937 1260 53 15 405 1630 61458850 61460107 0.000000e+00 1801.0
28 TraesCS4B01G151400 chr5D 93.759 705 31 7 1630 2321 61460143 61460847 0.000000e+00 1046.0
29 TraesCS4B01G151400 chr2D 93.343 706 31 8 1630 2321 540175052 540175755 0.000000e+00 1029.0
30 TraesCS4B01G151400 chr4D 90.250 800 35 18 405 1165 313007162 313007957 0.000000e+00 1005.0
31 TraesCS4B01G151400 chr1D 93.990 599 31 4 1036 1630 47377844 47378441 0.000000e+00 902.0
32 TraesCS4B01G151400 chr3D 91.143 350 30 1 64 412 562561592 562561941 7.510000e-130 473.0
33 TraesCS4B01G151400 chr1A 96.774 62 1 1 1 62 74004355 74004295 4.080000e-18 102.0
34 TraesCS4B01G151400 chr5A 92.958 71 1 4 1 69 626254805 626254737 1.470000e-17 100.0


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 TraesCS4B01G151400 chr4B 243181095 243183415 2320 True 4287.0 4287 100.0000 1 2321 1 chr4B.!!$R1 2320
1 TraesCS4B01G151400 chr4B 221191667 221193267 1600 False 2226.0 2226 92.1450 64 1629 1 chr4B.!!$F1 1565
2 TraesCS4B01G151400 chr4B 361731447 361733687 2240 True 1806.5 2425 96.6475 124 2321 2 chr4B.!!$R2 2197
3 TraesCS4B01G151400 chr5B 706039877 706041455 1578 False 2639.0 2639 96.9660 64 1630 1 chr5B.!!$F1 1566
4 TraesCS4B01G151400 chr2A 492833561 492835852 2291 False 1838.5 2543 96.2980 64 2310 2 chr2A.!!$F3 2246
5 TraesCS4B01G151400 chr3B 124766572 124768962 2390 True 1807.5 2534 96.3810 64 2321 2 chr3B.!!$R2 2257
6 TraesCS4B01G151400 chr3B 254907388 254908096 708 True 970.0 970 91.8190 1633 2321 1 chr3B.!!$R1 688
7 TraesCS4B01G151400 chr4A 90384306 90386786 2480 True 1766.0 2468 96.2115 64 2321 2 chr4A.!!$R1 2257
8 TraesCS4B01G151400 chr1B 91885263 91886723 1460 True 1919.0 1919 90.9710 220 1629 1 chr1B.!!$R1 1409
9 TraesCS4B01G151400 chr6D 352345986 352347978 1992 False 1427.5 1820 93.3880 405 2321 2 chr6D.!!$F2 1916
10 TraesCS4B01G151400 chr6D 59749316 59751323 2007 True 1407.0 1770 93.0590 405 2321 2 chr6D.!!$R2 1916
11 TraesCS4B01G151400 chr6D 173910678 173911726 1048 False 1389.0 1389 91.2300 624 1630 1 chr6D.!!$F1 1006
12 TraesCS4B01G151400 chr6D 263996038 263996743 705 True 1042.0 1042 93.6260 1630 2321 1 chr6D.!!$R1 691
13 TraesCS4B01G151400 chr5D 61458850 61460847 1997 False 1423.5 1801 93.3480 405 2321 2 chr5D.!!$F1 1916
14 TraesCS4B01G151400 chr2D 540175052 540175755 703 False 1029.0 1029 93.3430 1630 2321 1 chr2D.!!$F1 691
15 TraesCS4B01G151400 chr4D 313007162 313007957 795 False 1005.0 1005 90.2500 405 1165 1 chr4D.!!$F1 760
16 TraesCS4B01G151400 chr1D 47377844 47378441 597 False 902.0 902 93.9900 1036 1630 1 chr1D.!!$F1 594

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
611 618 1.08437 GTCCCCATCGCTTCAAGTCG 61.084 60.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2541 1.505353 GCATTGTCCTCACTGCTGC 59.495 57.895 0.0 0.0 43.66 5.25 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
23 24 5.827326 AAGGGTTTCATATCTAGCCTACC 57.173 43.478 0.00 0.0 38.75 3.18
24 25 4.168883 AGGGTTTCATATCTAGCCTACCC 58.831 47.826 0.00 0.0 43.42 3.69
25 26 3.263681 GGGTTTCATATCTAGCCTACCCC 59.736 52.174 0.00 0.0 38.39 4.95
26 27 3.908103 GGTTTCATATCTAGCCTACCCCA 59.092 47.826 0.00 0.0 0.00 4.96
27 28 4.349930 GGTTTCATATCTAGCCTACCCCAA 59.650 45.833 0.00 0.0 0.00 4.12
28 29 5.306394 GTTTCATATCTAGCCTACCCCAAC 58.694 45.833 0.00 0.0 0.00 3.77
29 30 4.487282 TCATATCTAGCCTACCCCAACT 57.513 45.455 0.00 0.0 0.00 3.16
30 31 4.827789 TCATATCTAGCCTACCCCAACTT 58.172 43.478 0.00 0.0 0.00 2.66
31 32 4.593206 TCATATCTAGCCTACCCCAACTTG 59.407 45.833 0.00 0.0 0.00 3.16
32 33 2.337359 TCTAGCCTACCCCAACTTGT 57.663 50.000 0.00 0.0 0.00 3.16
33 34 2.627933 TCTAGCCTACCCCAACTTGTT 58.372 47.619 0.00 0.0 0.00 2.83
34 35 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.0 0.00 2.83
35 36 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.0 34.63 2.93
47 48 5.213891 CAACTTGTTTGGGATAAAAGGCT 57.786 39.130 0.00 0.0 0.00 4.58
48 49 5.610398 CAACTTGTTTGGGATAAAAGGCTT 58.390 37.500 0.00 0.0 0.00 4.35
49 50 5.468540 ACTTGTTTGGGATAAAAGGCTTC 57.531 39.130 0.00 0.0 0.00 3.86
50 51 4.022329 ACTTGTTTGGGATAAAAGGCTTCG 60.022 41.667 0.00 0.0 0.00 3.79
51 52 3.492337 TGTTTGGGATAAAAGGCTTCGT 58.508 40.909 0.00 0.0 0.00 3.85
52 53 4.653868 TGTTTGGGATAAAAGGCTTCGTA 58.346 39.130 0.00 0.0 0.00 3.43
53 54 5.071370 TGTTTGGGATAAAAGGCTTCGTAA 58.929 37.500 0.00 0.0 0.00 3.18
54 55 5.712917 TGTTTGGGATAAAAGGCTTCGTAAT 59.287 36.000 0.00 0.0 0.00 1.89
55 56 5.828299 TTGGGATAAAAGGCTTCGTAATG 57.172 39.130 0.00 0.0 0.00 1.90
56 57 5.105567 TGGGATAAAAGGCTTCGTAATGA 57.894 39.130 0.00 0.0 0.00 2.57
57 58 4.879545 TGGGATAAAAGGCTTCGTAATGAC 59.120 41.667 0.00 0.0 0.00 3.06
344 345 7.807977 ACGATTAACAATTTCATGGCTATCT 57.192 32.000 0.00 0.0 0.00 1.98
376 377 3.894759 ACAGACATCATTGGCATTAGCT 58.105 40.909 0.00 0.0 41.70 3.32
404 405 1.610363 TGCGTTAAATGCCCTGTTGA 58.390 45.000 0.00 0.0 0.00 3.18
450 451 7.538334 TGTGAAGATGCTTATTGTTTCATTTCG 59.462 33.333 0.00 0.0 0.00 3.46
451 452 7.750458 GTGAAGATGCTTATTGTTTCATTTCGA 59.250 33.333 0.00 0.0 0.00 3.71
611 618 1.084370 GTCCCCATCGCTTCAAGTCG 61.084 60.000 0.00 0.0 0.00 4.18
755 762 4.804868 ACCATTACAAAATGCAGCATGA 57.195 36.364 9.18 0.0 41.06 3.07
810 817 6.327104 TGGCATTTAATTATTCTCCTGGCATT 59.673 34.615 0.00 0.0 33.69 3.56
811 818 7.147514 TGGCATTTAATTATTCTCCTGGCATTT 60.148 33.333 0.00 0.0 33.69 2.32
812 819 8.367156 GGCATTTAATTATTCTCCTGGCATTTA 58.633 33.333 0.00 0.0 0.00 1.40
986 1010 1.153647 CAAGATCACGGTGCGGCTA 60.154 57.895 2.51 0.0 0.00 3.93
1159 1233 3.310774 CGTACGTTCCCTCTTTCGATCTA 59.689 47.826 7.22 0.0 0.00 1.98
1426 1506 9.705103 ATATGGGCTGATACATTGCTAAATTAT 57.295 29.630 0.00 0.0 0.00 1.28
2110 2466 1.957177 CATAGCTGAGGGACGAGCTTA 59.043 52.381 0.00 0.0 43.15 3.09
2185 2541 1.001641 CTTGTGAAGGGCTCAGGGG 60.002 63.158 0.00 0.0 33.60 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.597940 GGGTAGGCTAGATATGAAACCCTT 59.402 45.833 8.73 0.00 41.75 3.95
2 3 4.168883 GGGTAGGCTAGATATGAAACCCT 58.831 47.826 8.73 0.00 41.75 4.34
3 4 3.263681 GGGGTAGGCTAGATATGAAACCC 59.736 52.174 7.65 7.65 43.82 4.11
4 5 3.908103 TGGGGTAGGCTAGATATGAAACC 59.092 47.826 0.00 0.00 0.00 3.27
5 6 5.071923 AGTTGGGGTAGGCTAGATATGAAAC 59.928 44.000 0.00 0.00 0.00 2.78
6 7 5.224441 AGTTGGGGTAGGCTAGATATGAAA 58.776 41.667 0.00 0.00 0.00 2.69
7 8 4.827789 AGTTGGGGTAGGCTAGATATGAA 58.172 43.478 0.00 0.00 0.00 2.57
8 9 4.487282 AGTTGGGGTAGGCTAGATATGA 57.513 45.455 0.00 0.00 0.00 2.15
9 10 4.348168 ACAAGTTGGGGTAGGCTAGATATG 59.652 45.833 7.96 0.00 0.00 1.78
10 11 4.567857 ACAAGTTGGGGTAGGCTAGATAT 58.432 43.478 7.96 0.00 0.00 1.63
11 12 4.003584 ACAAGTTGGGGTAGGCTAGATA 57.996 45.455 7.96 0.00 0.00 1.98
12 13 2.846950 ACAAGTTGGGGTAGGCTAGAT 58.153 47.619 7.96 0.00 0.00 1.98
13 14 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
14 15 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
15 16 3.149005 CAAACAAGTTGGGGTAGGCTA 57.851 47.619 7.96 0.00 33.18 3.93
16 17 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
25 26 5.213891 AGCCTTTTATCCCAAACAAGTTG 57.786 39.130 0.00 0.00 36.94 3.16
26 27 5.508994 CGAAGCCTTTTATCCCAAACAAGTT 60.509 40.000 0.00 0.00 0.00 2.66
27 28 4.022329 CGAAGCCTTTTATCCCAAACAAGT 60.022 41.667 0.00 0.00 0.00 3.16
28 29 4.022329 ACGAAGCCTTTTATCCCAAACAAG 60.022 41.667 0.00 0.00 0.00 3.16
29 30 3.892588 ACGAAGCCTTTTATCCCAAACAA 59.107 39.130 0.00 0.00 0.00 2.83
30 31 3.492337 ACGAAGCCTTTTATCCCAAACA 58.508 40.909 0.00 0.00 0.00 2.83
31 32 5.632244 TTACGAAGCCTTTTATCCCAAAC 57.368 39.130 0.00 0.00 0.00 2.93
32 33 5.946972 TCATTACGAAGCCTTTTATCCCAAA 59.053 36.000 0.00 0.00 0.00 3.28
33 34 5.355910 GTCATTACGAAGCCTTTTATCCCAA 59.644 40.000 0.00 0.00 0.00 4.12
34 35 4.879545 GTCATTACGAAGCCTTTTATCCCA 59.120 41.667 0.00 0.00 0.00 4.37
35 36 5.419760 GTCATTACGAAGCCTTTTATCCC 57.580 43.478 0.00 0.00 0.00 3.85
50 51 7.865889 TCATCACCATAGTCATTACGTCATTAC 59.134 37.037 0.00 0.00 0.00 1.89
51 52 7.865889 GTCATCACCATAGTCATTACGTCATTA 59.134 37.037 0.00 0.00 0.00 1.90
52 53 6.701841 GTCATCACCATAGTCATTACGTCATT 59.298 38.462 0.00 0.00 0.00 2.57
53 54 6.183360 TGTCATCACCATAGTCATTACGTCAT 60.183 38.462 0.00 0.00 0.00 3.06
54 55 5.126384 TGTCATCACCATAGTCATTACGTCA 59.874 40.000 0.00 0.00 0.00 4.35
55 56 5.588240 TGTCATCACCATAGTCATTACGTC 58.412 41.667 0.00 0.00 0.00 4.34
56 57 5.359860 TCTGTCATCACCATAGTCATTACGT 59.640 40.000 0.00 0.00 0.00 3.57
57 58 5.831997 TCTGTCATCACCATAGTCATTACG 58.168 41.667 0.00 0.00 0.00 3.18
58 59 6.219473 CCTCTGTCATCACCATAGTCATTAC 58.781 44.000 0.00 0.00 0.00 1.89
59 60 5.305386 CCCTCTGTCATCACCATAGTCATTA 59.695 44.000 0.00 0.00 0.00 1.90
60 61 4.102210 CCCTCTGTCATCACCATAGTCATT 59.898 45.833 0.00 0.00 0.00 2.57
61 62 3.645212 CCCTCTGTCATCACCATAGTCAT 59.355 47.826 0.00 0.00 0.00 3.06
62 63 3.033909 CCCTCTGTCATCACCATAGTCA 58.966 50.000 0.00 0.00 0.00 3.41
253 254 9.933723 AATTGTTGAAGCAAGCTATTATCTTTT 57.066 25.926 0.00 0.00 0.00 2.27
344 345 6.514870 GCCAATGATGTCTGTTTCTTACACAA 60.515 38.462 0.00 0.00 32.10 3.33
404 405 5.828328 TCACAATAGGACTACATCACTCGAT 59.172 40.000 0.00 0.00 0.00 3.59
916 937 1.402456 GCTTCACGACGTACATCACCT 60.402 52.381 0.00 0.00 0.00 4.00
986 1010 2.049888 GCCCATAGCTGAGCTTCTTT 57.950 50.000 14.14 0.00 40.44 2.52
1468 1552 2.040278 AGGAGAGCCATTGTAGCACAAA 59.960 45.455 5.94 0.00 41.96 2.83
1686 1944 6.425114 AGACATATCAGATTGCAACGTATTCC 59.575 38.462 0.00 0.00 0.00 3.01
2110 2466 5.794894 CTTTACACATGACCCTCAGTTACT 58.205 41.667 0.00 0.00 0.00 2.24
2185 2541 1.505353 GCATTGTCCTCACTGCTGC 59.495 57.895 0.00 0.00 43.66 5.25
2234 2590 6.710295 AGTATCACATGAGTGTTTACTTGCAA 59.290 34.615 0.00 0.00 46.01 4.08
2264 2630 5.300792 CACCACCTTTGTACTAACAACCAAT 59.699 40.000 0.00 0.00 45.18 3.16


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

AutoCloner maintained by Alex Coulton.