Multiple sequence alignment - TraesCS3D01G491600

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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 TraesCS3D01G491600 chr3D 100.000 3620 0 0 1 3620 585380315 585376696 0.000000e+00 6685.0
1 TraesCS3D01G491600 chr3D 97.851 977 19 2 1 977 605498081 605499055 0.000000e+00 1687.0
2 TraesCS3D01G491600 chr3D 97.651 979 21 1 1 977 536162647 536163625 0.000000e+00 1679.0
3 TraesCS3D01G491600 chr3D 97.648 978 20 3 1 978 32597604 32596630 0.000000e+00 1676.0
4 TraesCS3D01G491600 chr3D 97.646 977 20 3 1 977 584657634 584656661 0.000000e+00 1674.0
5 TraesCS3D01G491600 chr3D 97.344 979 25 1 1 979 572566797 572567774 0.000000e+00 1663.0
6 TraesCS3D01G491600 chr3D 80.387 1239 216 22 1488 2706 23615690 23616921 0.000000e+00 917.0
7 TraesCS3D01G491600 chr3D 87.200 375 45 3 1026 1398 23615275 23615648 1.200000e-114 424.0
8 TraesCS3D01G491600 chr7D 98.078 2654 32 3 978 3620 16222217 16224862 0.000000e+00 4601.0
9 TraesCS3D01G491600 chr7D 83.942 274 32 10 2989 3253 26459700 26459970 6.000000e-63 252.0
10 TraesCS3D01G491600 chr7A 95.551 2630 90 12 978 3589 15038018 15040638 0.000000e+00 4183.0
11 TraesCS3D01G491600 chr4A 94.470 2188 99 7 978 3147 718857276 718859459 0.000000e+00 3350.0
12 TraesCS3D01G491600 chr4A 79.853 1767 304 35 978 2719 714339628 714341367 0.000000e+00 1243.0
13 TraesCS3D01G491600 chr4A 84.872 390 34 18 3198 3584 718859457 718859824 1.590000e-98 370.0
14 TraesCS3D01G491600 chr4A 97.059 34 1 0 1833 1866 718852330 718852297 1.400000e-04 58.4
15 TraesCS3D01G491600 chr5D 98.269 982 12 1 1 977 552112352 552111371 0.000000e+00 1714.0
16 TraesCS3D01G491600 chr5D 97.957 979 17 3 1 979 432920589 432921564 0.000000e+00 1694.0
17 TraesCS3D01G491600 chr1D 97.556 982 17 3 1 977 59043616 59044595 0.000000e+00 1674.0
18 TraesCS3D01G491600 chr4D 97.643 976 20 3 3 978 54304513 54305485 0.000000e+00 1672.0
19 TraesCS3D01G491600 chr3A 83.568 1138 162 16 1642 2761 7487592 7486462 0.000000e+00 1042.0
20 TraesCS3D01G491600 chr3A 87.834 674 78 4 978 1649 7498190 7497519 0.000000e+00 787.0
21 TraesCS3D01G491600 chr6D 73.515 842 186 29 985 1815 440645197 440646012 5.920000e-73 285.0
22 TraesCS3D01G491600 chr2B 72.563 831 184 40 989 1797 778468659 778467851 7.820000e-57 231.0
23 TraesCS3D01G491600 chr2A 72.099 767 186 25 986 1738 778587191 778587943 4.740000e-49 206.0


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 TraesCS3D01G491600 chr3D 585376696 585380315 3619 True 6685.0 6685 100.0000 1 3620 1 chr3D.!!$R3 3619
1 TraesCS3D01G491600 chr3D 605498081 605499055 974 False 1687.0 1687 97.8510 1 977 1 chr3D.!!$F3 976
2 TraesCS3D01G491600 chr3D 536162647 536163625 978 False 1679.0 1679 97.6510 1 977 1 chr3D.!!$F1 976
3 TraesCS3D01G491600 chr3D 32596630 32597604 974 True 1676.0 1676 97.6480 1 978 1 chr3D.!!$R1 977
4 TraesCS3D01G491600 chr3D 584656661 584657634 973 True 1674.0 1674 97.6460 1 977 1 chr3D.!!$R2 976
5 TraesCS3D01G491600 chr3D 572566797 572567774 977 False 1663.0 1663 97.3440 1 979 1 chr3D.!!$F2 978
6 TraesCS3D01G491600 chr3D 23615275 23616921 1646 False 670.5 917 83.7935 1026 2706 2 chr3D.!!$F4 1680
7 TraesCS3D01G491600 chr7D 16222217 16224862 2645 False 4601.0 4601 98.0780 978 3620 1 chr7D.!!$F1 2642
8 TraesCS3D01G491600 chr7A 15038018 15040638 2620 False 4183.0 4183 95.5510 978 3589 1 chr7A.!!$F1 2611
9 TraesCS3D01G491600 chr4A 718857276 718859824 2548 False 1860.0 3350 89.6710 978 3584 2 chr4A.!!$F2 2606
10 TraesCS3D01G491600 chr4A 714339628 714341367 1739 False 1243.0 1243 79.8530 978 2719 1 chr4A.!!$F1 1741
11 TraesCS3D01G491600 chr5D 552111371 552112352 981 True 1714.0 1714 98.2690 1 977 1 chr5D.!!$R1 976
12 TraesCS3D01G491600 chr5D 432920589 432921564 975 False 1694.0 1694 97.9570 1 979 1 chr5D.!!$F1 978
13 TraesCS3D01G491600 chr1D 59043616 59044595 979 False 1674.0 1674 97.5560 1 977 1 chr1D.!!$F1 976
14 TraesCS3D01G491600 chr4D 54304513 54305485 972 False 1672.0 1672 97.6430 3 978 1 chr4D.!!$F1 975
15 TraesCS3D01G491600 chr3A 7486462 7487592 1130 True 1042.0 1042 83.5680 1642 2761 1 chr3A.!!$R1 1119
16 TraesCS3D01G491600 chr3A 7497519 7498190 671 True 787.0 787 87.8340 978 1649 1 chr3A.!!$R2 671
17 TraesCS3D01G491600 chr6D 440645197 440646012 815 False 285.0 285 73.5150 985 1815 1 chr6D.!!$F1 830
18 TraesCS3D01G491600 chr2B 778467851 778468659 808 True 231.0 231 72.5630 989 1797 1 chr2B.!!$R1 808
19 TraesCS3D01G491600 chr2A 778587191 778587943 752 False 206.0 206 72.0990 986 1738 1 chr2A.!!$F1 752

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
35 36 0.173708 CCCACCTCGCTAGTTGAGAC 59.826 60.000 13.69 0.0 35.43 3.36 F
815 825 1.152922 GGTTTGTCCCACCAACCGA 60.153 57.895 0.00 0.0 34.04 4.69 F
905 915 2.364632 CGGGACCAATGCTCACATTAA 58.635 47.619 0.00 0.0 44.83 1.40 F
2233 2280 2.699954 CAGAACTTGTAGGCGACCAAT 58.300 47.619 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2004 0.676736 CTATCCTGCTCGGACCTTCC 59.323 60.000 0.00 0.0 46.80 3.46 R
2156 2203 0.252284 ACCGACCCAGTCTGGAATCT 60.252 55.000 21.23 0.0 40.96 2.40 R
2440 2487 3.285484 CAATGCTCTTATGCCAACCTCT 58.715 45.455 0.00 0.0 0.00 3.69 R
3411 3504 1.891150 ACACGAGACCCGAATAAGTGT 59.109 47.619 0.00 0.0 41.76 3.55 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
35 36 0.173708 CCCACCTCGCTAGTTGAGAC 59.826 60.000 13.69 0.00 35.43 3.36
734 744 2.917205 ACTAGGACCAGGCCTTTAGTT 58.083 47.619 0.00 0.00 39.50 2.24
815 825 1.152922 GGTTTGTCCCACCAACCGA 60.153 57.895 0.00 0.00 34.04 4.69
905 915 2.364632 CGGGACCAATGCTCACATTAA 58.635 47.619 0.00 0.00 44.83 1.40
907 917 3.243168 CGGGACCAATGCTCACATTAATG 60.243 47.826 14.01 14.01 44.83 1.90
999 1009 7.231317 AGTGTTTGTAGATCAATTGGTTCACAT 59.769 33.333 5.42 0.00 35.84 3.21
1324 1337 3.266510 TGATGCTTGAGGTCATGGTAC 57.733 47.619 0.00 0.00 0.00 3.34
1400 1413 4.513198 TGTCATATGATATCGTTCGCCA 57.487 40.909 9.02 0.00 0.00 5.69
1489 1524 6.484288 AGTGGAATGGTGAATGTTATCAAGA 58.516 36.000 0.00 0.00 0.00 3.02
1620 1655 3.744660 AGACTGCAAGGACCTAAACAAG 58.255 45.455 0.00 0.00 39.30 3.16
1969 2004 6.528423 GGAACGGATATTTGTCTATCTCGATG 59.472 42.308 0.00 0.00 31.75 3.84
2156 2203 7.939039 CCTTAGGTTTGCTGGATATATTTCTCA 59.061 37.037 0.00 0.00 0.00 3.27
2233 2280 2.699954 CAGAACTTGTAGGCGACCAAT 58.300 47.619 0.00 0.00 0.00 3.16
2241 2288 3.680490 TGTAGGCGACCAATCATTTGAA 58.320 40.909 0.00 0.00 34.60 2.69
2278 2325 2.818432 CCCATCCTGAATAGCATCTTGC 59.182 50.000 0.00 0.00 45.46 4.01
2308 2355 8.316214 AGGTGCATTTTTACATTGATGAAGATT 58.684 29.630 0.00 0.00 0.00 2.40
2440 2487 6.280855 TCGAGATACTTGAATTGGACTTCA 57.719 37.500 0.00 0.00 33.42 3.02
2862 2938 9.771534 AAGCACTCTAATAAAGATGGAGTAATC 57.228 33.333 0.00 0.00 35.79 1.75
2941 3017 4.991789 TTATGGTATGCATTAGCCCAGA 57.008 40.909 3.54 0.94 41.13 3.86
3181 3257 7.315890 TGAGCACTACCATCATCGATAATTAG 58.684 38.462 0.00 0.00 0.00 1.73
3526 3622 9.604626 GATAAACGTTAATAGAGCGTACATACT 57.395 33.333 0.00 0.00 37.92 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.799420 GCTTATAAACCACTCTCGAGCTG 59.201 47.826 7.81 5.25 0.00 4.24
734 744 0.397564 GGTTCCTACCACAAACCGGA 59.602 55.000 9.46 0.00 44.36 5.14
776 786 3.628646 GACCAATGGGCCACGCTCT 62.629 63.158 9.28 0.00 37.90 4.09
905 915 0.949105 GTTCAGTCACGAACCGGCAT 60.949 55.000 0.00 0.00 39.52 4.40
907 917 3.241177 GTTCAGTCACGAACCGGC 58.759 61.111 0.00 0.00 39.52 6.13
999 1009 1.279025 GGGCTGGGTTGGTCTCCATA 61.279 60.000 0.00 0.00 31.53 2.74
1277 1290 1.609580 GCACCGGACACAAATCCACTA 60.610 52.381 9.46 0.00 38.87 2.74
1292 1305 1.638388 AAGCATCATGTCGTGCACCG 61.638 55.000 12.15 6.81 43.63 4.94
1324 1337 7.210873 ACGAAGTTAGCCTCTATTGATTTAGG 58.789 38.462 0.00 0.00 37.78 2.69
1400 1413 1.514983 TGCATCATGGATGGAGAGGT 58.485 50.000 8.18 0.00 40.10 3.85
1489 1524 2.827604 CGTGCTTCGTGTTCATCCT 58.172 52.632 0.00 0.00 34.52 3.24
1620 1655 4.808558 TGCAAATGTACCTCAAATGCTTC 58.191 39.130 0.00 0.00 40.19 3.86
1969 2004 0.676736 CTATCCTGCTCGGACCTTCC 59.323 60.000 0.00 0.00 46.80 3.46
2156 2203 0.252284 ACCGACCCAGTCTGGAATCT 60.252 55.000 21.23 0.00 40.96 2.40
2278 2325 7.092079 TCATCAATGTAAAAATGCACCTGAAG 58.908 34.615 0.00 0.00 0.00 3.02
2330 2377 7.264947 TCTCATATTCTTGAGCATACGAAACA 58.735 34.615 0.00 0.00 42.37 2.83
2388 2435 5.306937 TGTCATGGAGTCTTCCTCAAAACTA 59.693 40.000 0.00 0.00 44.36 2.24
2440 2487 3.285484 CAATGCTCTTATGCCAACCTCT 58.715 45.455 0.00 0.00 0.00 3.69
3181 3257 7.096312 ACGAGATTGTACGTCTGTCTTTTTAAC 60.096 37.037 5.42 0.00 38.34 2.01
3411 3504 1.891150 ACACGAGACCCGAATAAGTGT 59.109 47.619 0.00 0.00 41.76 3.55
3526 3622 3.177228 CTCTCCTTCCTCTTCCCTTGAA 58.823 50.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.