Multiple sequence alignment - TraesCS4A01G152000

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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 TraesCS4A01G152000 chr4A 100.000 2414 0 0 1 2414 309285417 309287830 0.000000e+00 4458
1 TraesCS4A01G152000 chr4A 97.416 658 16 1 1 658 349250294 349249638 0.000000e+00 1120
2 TraesCS4A01G152000 chr4A 94.038 520 17 6 1908 2414 665560767 665560249 0.000000e+00 776
3 TraesCS4A01G152000 chr4A 88.591 149 5 3 1899 2035 117984607 117984755 1.150000e-38 171
4 TraesCS4A01G152000 chr1D 95.544 1773 66 4 654 2414 254480118 254478347 0.000000e+00 2824
5 TraesCS4A01G152000 chr1D 94.279 1783 77 6 654 2414 180352608 180354387 0.000000e+00 2704
6 TraesCS4A01G152000 chr1D 92.157 1785 98 16 654 2414 244211829 244210063 0.000000e+00 2483
7 TraesCS4A01G152000 chr1D 91.942 1787 102 12 651 2414 244791789 244790022 0.000000e+00 2464
8 TraesCS4A01G152000 chr5D 95.177 1783 63 6 654 2414 6233110 6234891 0.000000e+00 2795
9 TraesCS4A01G152000 chr5D 94.755 1430 52 6 654 2061 483804638 483806066 0.000000e+00 2204
10 TraesCS4A01G152000 chr3B 95.064 1783 64 7 654 2414 201496141 201494361 0.000000e+00 2784
11 TraesCS4A01G152000 chr7A 91.545 1786 123 9 651 2414 352293672 352295451 0.000000e+00 2436
12 TraesCS4A01G152000 chr7A 98.018 656 13 0 1 656 363052199 363051544 0.000000e+00 1140
13 TraesCS4A01G152000 chr7A 97.432 662 16 1 1 661 202060036 202060697 0.000000e+00 1127
14 TraesCS4A01G152000 chrUn 95.438 1337 50 3 654 1980 386522601 386523936 0.000000e+00 2121
15 TraesCS4A01G152000 chrUn 97.419 930 24 0 1485 2414 397678311 397677382 0.000000e+00 1585
16 TraesCS4A01G152000 chrUn 95.358 991 34 3 654 1634 407032533 407031545 0.000000e+00 1565
17 TraesCS4A01G152000 chr6D 93.106 1175 67 6 654 1818 210722214 210723384 0.000000e+00 1709
18 TraesCS4A01G152000 chr6D 97.321 112 3 0 892 1003 150790264 150790153 8.810000e-45 191
19 TraesCS4A01G152000 chr6D 90.299 134 3 1 833 956 3650268 3650401 1.480000e-37 167
20 TraesCS4A01G152000 chr6D 98.795 83 1 0 887 969 346731570 346731488 5.380000e-32 148
21 TraesCS4A01G152000 chr1A 95.179 809 25 4 1619 2414 554444322 554445129 0.000000e+00 1266
22 TraesCS4A01G152000 chr1A 98.179 659 11 1 1 658 355227553 355228211 0.000000e+00 1149
23 TraesCS4A01G152000 chr1A 97.859 654 14 0 1 654 498745463 498746116 0.000000e+00 1131
24 TraesCS4A01G152000 chr1A 97.269 659 17 1 1 658 498731111 498731769 0.000000e+00 1116
25 TraesCS4A01G152000 chr2B 93.214 781 34 3 654 1424 474937989 474937218 0.000000e+00 1131
26 TraesCS4A01G152000 chr2A 97.856 653 14 0 1 653 578306693 578307345 0.000000e+00 1129
27 TraesCS4A01G152000 chr6A 97.703 653 15 0 1 653 322658048 322657396 0.000000e+00 1123
28 TraesCS4A01G152000 chr6A 97.416 658 17 0 1 658 322669401 322668744 0.000000e+00 1122
29 TraesCS4A01G152000 chr2D 94.860 681 24 2 654 1324 643856481 643855802 0.000000e+00 1053
30 TraesCS4A01G152000 chr2D 94.912 452 12 2 654 1095 359631756 359632206 0.000000e+00 697


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 TraesCS4A01G152000 chr4A 309285417 309287830 2413 False 4458 4458 100.000 1 2414 1 chr4A.!!$F2 2413
1 TraesCS4A01G152000 chr4A 349249638 349250294 656 True 1120 1120 97.416 1 658 1 chr4A.!!$R1 657
2 TraesCS4A01G152000 chr4A 665560249 665560767 518 True 776 776 94.038 1908 2414 1 chr4A.!!$R2 506
3 TraesCS4A01G152000 chr1D 254478347 254480118 1771 True 2824 2824 95.544 654 2414 1 chr1D.!!$R3 1760
4 TraesCS4A01G152000 chr1D 180352608 180354387 1779 False 2704 2704 94.279 654 2414 1 chr1D.!!$F1 1760
5 TraesCS4A01G152000 chr1D 244210063 244211829 1766 True 2483 2483 92.157 654 2414 1 chr1D.!!$R1 1760
6 TraesCS4A01G152000 chr1D 244790022 244791789 1767 True 2464 2464 91.942 651 2414 1 chr1D.!!$R2 1763
7 TraesCS4A01G152000 chr5D 6233110 6234891 1781 False 2795 2795 95.177 654 2414 1 chr5D.!!$F1 1760
8 TraesCS4A01G152000 chr5D 483804638 483806066 1428 False 2204 2204 94.755 654 2061 1 chr5D.!!$F2 1407
9 TraesCS4A01G152000 chr3B 201494361 201496141 1780 True 2784 2784 95.064 654 2414 1 chr3B.!!$R1 1760
10 TraesCS4A01G152000 chr7A 352293672 352295451 1779 False 2436 2436 91.545 651 2414 1 chr7A.!!$F2 1763
11 TraesCS4A01G152000 chr7A 363051544 363052199 655 True 1140 1140 98.018 1 656 1 chr7A.!!$R1 655
12 TraesCS4A01G152000 chr7A 202060036 202060697 661 False 1127 1127 97.432 1 661 1 chr7A.!!$F1 660
13 TraesCS4A01G152000 chrUn 386522601 386523936 1335 False 2121 2121 95.438 654 1980 1 chrUn.!!$F1 1326
14 TraesCS4A01G152000 chrUn 397677382 397678311 929 True 1585 1585 97.419 1485 2414 1 chrUn.!!$R1 929
15 TraesCS4A01G152000 chrUn 407031545 407032533 988 True 1565 1565 95.358 654 1634 1 chrUn.!!$R2 980
16 TraesCS4A01G152000 chr6D 210722214 210723384 1170 False 1709 1709 93.106 654 1818 1 chr6D.!!$F2 1164
17 TraesCS4A01G152000 chr1A 554444322 554445129 807 False 1266 1266 95.179 1619 2414 1 chr1A.!!$F4 795
18 TraesCS4A01G152000 chr1A 355227553 355228211 658 False 1149 1149 98.179 1 658 1 chr1A.!!$F1 657
19 TraesCS4A01G152000 chr1A 498745463 498746116 653 False 1131 1131 97.859 1 654 1 chr1A.!!$F3 653
20 TraesCS4A01G152000 chr1A 498731111 498731769 658 False 1116 1116 97.269 1 658 1 chr1A.!!$F2 657
21 TraesCS4A01G152000 chr2B 474937218 474937989 771 True 1131 1131 93.214 654 1424 1 chr2B.!!$R1 770
22 TraesCS4A01G152000 chr2A 578306693 578307345 652 False 1129 1129 97.856 1 653 1 chr2A.!!$F1 652
23 TraesCS4A01G152000 chr6A 322657396 322658048 652 True 1123 1123 97.703 1 653 1 chr6A.!!$R1 652
24 TraesCS4A01G152000 chr6A 322668744 322669401 657 True 1122 1122 97.416 1 658 1 chr6A.!!$R2 657
25 TraesCS4A01G152000 chr2D 643855802 643856481 679 True 1053 1053 94.860 654 1324 1 chr2D.!!$R1 670

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
882 887 3.568007 TGTTGCTCTTGCGGAAACTATTT 59.432 39.13 0.0 0.0 43.34 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1854 0.455972 GCATTGGCGCACGTGTAAAT 60.456 50.0 18.38 9.06 0.0 1.4 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
358 359 6.958767 TCATCCTTCCTTTCCCTTTACTTAG 58.041 40.000 0.00 0.00 0.00 2.18
580 581 6.198591 GGTCTATTTCTATCGTTTGTCTTCGG 59.801 42.308 0.00 0.00 0.00 4.30
582 583 7.166142 GTCTATTTCTATCGTTTGTCTTCGGAG 59.834 40.741 0.00 0.00 0.00 4.63
720 723 8.260270 ACTTTACAACGTTACAAAGAACTTCT 57.740 30.769 27.48 11.18 33.29 2.85
839 842 3.791353 CGTTCTTTGTGGCAGAAGTTTTC 59.209 43.478 9.57 0.00 30.72 2.29
882 887 3.568007 TGTTGCTCTTGCGGAAACTATTT 59.432 39.130 0.00 0.00 43.34 1.40
1066 1081 5.048782 TGGGATTGTGAAGTGAAAGAAATCG 60.049 40.000 0.00 0.00 0.00 3.34
1126 1141 1.933765 ACCAGGCCCCCATTAATACAA 59.066 47.619 0.00 0.00 0.00 2.41
1161 1176 4.385754 GGTCCTTTGAGAATATGCCTCCTT 60.386 45.833 3.71 0.00 0.00 3.36
1165 1180 6.069673 TCCTTTGAGAATATGCCTCCTTAACA 60.070 38.462 3.71 0.00 0.00 2.41
1179 1194 5.047590 CCTCCTTAACAACCAATGGTTAACC 60.048 44.000 18.29 18.27 45.01 2.85
1188 1203 2.348660 CAATGGTTAACCGCGGTTCTA 58.651 47.619 44.24 30.39 39.31 2.10
1194 1209 1.477553 TAACCGCGGTTCTATGGAGT 58.522 50.000 44.24 22.14 39.31 3.85
1218 1233 8.665685 AGTGGTTTTGCGAGAATAGTTAATAAG 58.334 33.333 0.00 0.00 0.00 1.73
1223 1238 8.644318 TTTGCGAGAATAGTTAATAAGGAGAC 57.356 34.615 0.00 0.00 0.00 3.36
1290 1305 2.030451 GGAAGAAGCTCAAAAGGCACTG 60.030 50.000 0.00 0.00 40.86 3.66
1324 1339 6.091441 CGAAGCTAACTTGAATAAAGCTGAGT 59.909 38.462 0.00 0.00 42.49 3.41
1329 1344 7.117812 GCTAACTTGAATAAAGCTGAGTGTACA 59.882 37.037 0.00 0.00 39.76 2.90
1395 1411 2.002586 CGAATCGAGGCTGTCAATTGT 58.997 47.619 5.13 0.00 0.00 2.71
1424 1440 4.467082 CCCATCCAATTGAAGACAATCCAA 59.533 41.667 7.12 0.00 44.67 3.53
1427 1443 6.127281 CCATCCAATTGAAGACAATCCAATGA 60.127 38.462 7.12 0.00 44.67 2.57
1490 1506 9.937175 GAAAAAGTTATTAGATAGCAAAGCGAT 57.063 29.630 0.00 0.00 0.00 4.58
1594 1610 7.425224 AGCAATACTCTAACCACTGAGTTAT 57.575 36.000 0.00 0.00 42.67 1.89
1684 1700 4.137116 AGCAATACCGCTCTGTTATTGA 57.863 40.909 5.03 0.00 37.91 2.57
1818 1835 8.288812 AGATATCTCTGATAAGGGCTATAGCTT 58.711 37.037 23.53 13.69 41.70 3.74
1831 1848 5.002516 GGCTATAGCTTAGTTCGGTAGAGA 58.997 45.833 23.53 0.00 41.70 3.10
1837 1854 4.765856 AGCTTAGTTCGGTAGAGAAACTCA 59.234 41.667 0.00 0.00 32.06 3.41
1963 1980 5.929415 GGAGAATAGTAGCCTGACAAATAGC 59.071 44.000 0.00 0.00 0.00 2.97
2016 2069 6.966534 AATAGAACCCTTATGGATTTGCTG 57.033 37.500 0.00 0.00 38.00 4.41
2035 2088 7.490962 TTGCTGGTTGATAAGGTAAATATCG 57.509 36.000 0.00 0.00 33.38 2.92
2190 2243 6.718294 AGGTTGATTTAATTTAGACCGGAGT 58.282 36.000 9.46 0.00 0.00 3.85
2300 2354 4.202503 GGGAGCCATCTCATTATCTTTCCA 60.203 45.833 0.00 0.00 41.13 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
164 165 1.768870 CCTCACCGTATTCCCCTTGAT 59.231 52.381 0.00 0.00 0.00 2.57
358 359 2.639065 TGACTTCACAAGGACCAACAC 58.361 47.619 0.00 0.00 0.00 3.32
580 581 5.444663 AAGTCTTCAAAACATGGAAGCTC 57.555 39.130 0.00 0.00 40.20 4.09
582 583 5.591099 TGAAAGTCTTCAAAACATGGAAGC 58.409 37.500 0.00 0.00 38.65 3.86
796 799 2.939103 GGCTGTGATAAGAAACGCTCAT 59.061 45.455 0.00 0.00 0.00 2.90
815 818 0.040067 CTTCTGCCACAAAGAACGGC 60.040 55.000 0.00 0.00 46.43 5.68
1110 1125 3.026707 ACTGTTGTATTAATGGGGGCC 57.973 47.619 0.00 0.00 0.00 5.80
1126 1141 5.529289 TCTCAAAGGACCCATATCTACTGT 58.471 41.667 0.00 0.00 0.00 3.55
1161 1176 2.225963 CGCGGTTAACCATTGGTTGTTA 59.774 45.455 27.66 12.31 46.35 2.41
1179 1194 0.108329 AACCACTCCATAGAACCGCG 60.108 55.000 0.00 0.00 0.00 6.46
1188 1203 2.270352 TTCTCGCAAAACCACTCCAT 57.730 45.000 0.00 0.00 0.00 3.41
1194 1209 7.825270 TCCTTATTAACTATTCTCGCAAAACCA 59.175 33.333 0.00 0.00 0.00 3.67
1313 1328 8.299570 CCAAATCTTTTGTACACTCAGCTTTAT 58.700 33.333 0.00 0.00 0.00 1.40
1324 1339 5.066634 TCGCTTCAACCAAATCTTTTGTACA 59.933 36.000 0.00 0.00 0.00 2.90
1329 1344 4.051237 GCTTCGCTTCAACCAAATCTTTT 58.949 39.130 0.00 0.00 0.00 2.27
1395 1411 4.231658 TGTCTTCAATTGGATGGGGGAATA 59.768 41.667 5.42 0.00 0.00 1.75
1594 1610 5.184864 CCTTTGTGGTGATAAATTGCCTACA 59.815 40.000 0.00 0.00 0.00 2.74
1818 1835 8.025445 GTGTAAATGAGTTTCTCTACCGAACTA 58.975 37.037 0.00 0.00 0.00 2.24
1831 1848 1.069500 GGCGCACGTGTAAATGAGTTT 60.069 47.619 18.38 0.00 0.00 2.66
1837 1854 0.455972 GCATTGGCGCACGTGTAAAT 60.456 50.000 18.38 9.06 0.00 1.40
1945 1962 2.364324 CCGGCTATTTGTCAGGCTACTA 59.636 50.000 0.00 0.00 36.48 1.82
1963 1980 1.276421 ACCTGAATCAGACTGAACCGG 59.724 52.381 12.53 13.89 32.44 5.28
2016 2069 7.333672 GTGGGATCGATATTTACCTTATCAACC 59.666 40.741 0.00 0.00 0.00 3.77
2035 2088 2.224305 ACGCCTAGCATTTAGTGGGATC 60.224 50.000 0.00 0.00 0.00 3.36
2190 2243 5.590818 AGGATTACCTTGACTTAGGTCTGA 58.409 41.667 6.54 0.00 45.44 3.27
2257 2310 4.219070 TCCCTGTGCTCTGATTGATTTTTG 59.781 41.667 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.