Multiple sequence alignment - TraesCS4B01G150100

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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 TraesCS4B01G150100 chr4B 100.000 2535 0 0 1 2535 229929600 229932134 0.000000e+00 4682
1 TraesCS4B01G150100 chr6B 88.745 2550 251 26 1 2535 2556067 2558595 0.000000e+00 3086
2 TraesCS4B01G150100 chr7A 87.508 1545 132 20 1 1534 673777788 673779282 0.000000e+00 1727
3 TraesCS4B01G150100 chr7A 91.989 749 53 5 1781 2528 458388841 458388099 0.000000e+00 1044
4 TraesCS4B01G150100 chr7A 93.258 178 12 0 1553 1730 673779344 673779521 1.930000e-66 263
5 TraesCS4B01G150100 chr1B 86.396 1551 164 24 1 1534 596882716 596881196 0.000000e+00 1652
6 TraesCS4B01G150100 chr1B 89.647 821 75 5 1722 2535 596880856 596880039 0.000000e+00 1037
7 TraesCS4B01G150100 chr5A 86.018 1552 138 43 1 1534 81310900 81312390 0.000000e+00 1591
8 TraesCS4B01G150100 chr5A 92.746 193 11 2 1342 1534 81312865 81313054 2.480000e-70 276
9 TraesCS4B01G150100 chr5A 93.714 175 11 0 1553 1727 81313116 81313290 1.930000e-66 263
10 TraesCS4B01G150100 chr5A 92.000 175 14 0 1553 1727 81312452 81312626 1.950000e-61 246
11 TraesCS4B01G150100 chr2A 88.085 1133 109 15 82 1195 374122743 374123868 0.000000e+00 1321
12 TraesCS4B01G150100 chr2A 87.612 670 64 11 1 656 588638854 588639518 0.000000e+00 760
13 TraesCS4B01G150100 chr2A 89.456 294 21 6 1722 2008 316950831 316950541 1.850000e-96 363
14 TraesCS4B01G150100 chr1D 92.072 782 51 4 1760 2535 308872022 308871246 0.000000e+00 1090
15 TraesCS4B01G150100 chr1D 94.699 698 34 2 1783 2479 319795949 319795254 0.000000e+00 1081
16 TraesCS4B01G150100 chr7D 94.444 702 32 3 1780 2480 48000691 48001386 0.000000e+00 1074
17 TraesCS4B01G150100 chr7D 87.482 703 64 13 1 698 157756877 157757560 0.000000e+00 789
18 TraesCS4B01G150100 chr3D 94.017 702 36 3 1780 2480 181944094 181943398 0.000000e+00 1059
19 TraesCS4B01G150100 chr4D 93.875 702 39 3 1780 2480 17109322 17108624 0.000000e+00 1055
20 TraesCS4B01G150100 chr5B 90.698 731 56 4 1118 1842 592640753 592640029 0.000000e+00 963
21 TraesCS4B01G150100 chr5B 86.957 713 79 11 411 1123 592650110 592649412 0.000000e+00 789
22 TraesCS4B01G150100 chr5B 87.934 605 54 12 941 1531 586816084 586816683 0.000000e+00 695
23 TraesCS4B01G150100 chr1A 85.637 926 107 18 28 933 193531291 193530372 0.000000e+00 950
24 TraesCS4B01G150100 chr5D 89.182 721 68 9 1 716 289585894 289585179 0.000000e+00 891
25 TraesCS4B01G150100 chr5D 88.167 600 56 9 940 1531 478957094 478957686 0.000000e+00 701
26 TraesCS4B01G150100 chr7B 93.836 584 35 1 1953 2535 695980519 695979936 0.000000e+00 878
27 TraesCS4B01G150100 chr7B 87.286 700 75 10 1 689 645438683 645437987 0.000000e+00 787
28 TraesCS4B01G150100 chr3B 87.240 674 72 12 1 662 726668520 726667849 0.000000e+00 756
29 TraesCS4B01G150100 chr3A 86.919 688 65 16 9 690 612615110 612614442 0.000000e+00 749


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 TraesCS4B01G150100 chr4B 229929600 229932134 2534 False 4682.0 4682 100.0000 1 2535 1 chr4B.!!$F1 2534
1 TraesCS4B01G150100 chr6B 2556067 2558595 2528 False 3086.0 3086 88.7450 1 2535 1 chr6B.!!$F1 2534
2 TraesCS4B01G150100 chr7A 458388099 458388841 742 True 1044.0 1044 91.9890 1781 2528 1 chr7A.!!$R1 747
3 TraesCS4B01G150100 chr7A 673777788 673779521 1733 False 995.0 1727 90.3830 1 1730 2 chr7A.!!$F1 1729
4 TraesCS4B01G150100 chr1B 596880039 596882716 2677 True 1344.5 1652 88.0215 1 2535 2 chr1B.!!$R1 2534
5 TraesCS4B01G150100 chr5A 81310900 81313290 2390 False 594.0 1591 91.1195 1 1727 4 chr5A.!!$F1 1726
6 TraesCS4B01G150100 chr2A 374122743 374123868 1125 False 1321.0 1321 88.0850 82 1195 1 chr2A.!!$F1 1113
7 TraesCS4B01G150100 chr2A 588638854 588639518 664 False 760.0 760 87.6120 1 656 1 chr2A.!!$F2 655
8 TraesCS4B01G150100 chr1D 308871246 308872022 776 True 1090.0 1090 92.0720 1760 2535 1 chr1D.!!$R1 775
9 TraesCS4B01G150100 chr1D 319795254 319795949 695 True 1081.0 1081 94.6990 1783 2479 1 chr1D.!!$R2 696
10 TraesCS4B01G150100 chr7D 48000691 48001386 695 False 1074.0 1074 94.4440 1780 2480 1 chr7D.!!$F1 700
11 TraesCS4B01G150100 chr7D 157756877 157757560 683 False 789.0 789 87.4820 1 698 1 chr7D.!!$F2 697
12 TraesCS4B01G150100 chr3D 181943398 181944094 696 True 1059.0 1059 94.0170 1780 2480 1 chr3D.!!$R1 700
13 TraesCS4B01G150100 chr4D 17108624 17109322 698 True 1055.0 1055 93.8750 1780 2480 1 chr4D.!!$R1 700
14 TraesCS4B01G150100 chr5B 592640029 592640753 724 True 963.0 963 90.6980 1118 1842 1 chr5B.!!$R1 724
15 TraesCS4B01G150100 chr5B 592649412 592650110 698 True 789.0 789 86.9570 411 1123 1 chr5B.!!$R2 712
16 TraesCS4B01G150100 chr5B 586816084 586816683 599 False 695.0 695 87.9340 941 1531 1 chr5B.!!$F1 590
17 TraesCS4B01G150100 chr1A 193530372 193531291 919 True 950.0 950 85.6370 28 933 1 chr1A.!!$R1 905
18 TraesCS4B01G150100 chr5D 289585179 289585894 715 True 891.0 891 89.1820 1 716 1 chr5D.!!$R1 715
19 TraesCS4B01G150100 chr5D 478957094 478957686 592 False 701.0 701 88.1670 940 1531 1 chr5D.!!$F1 591
20 TraesCS4B01G150100 chr7B 695979936 695980519 583 True 878.0 878 93.8360 1953 2535 1 chr7B.!!$R2 582
21 TraesCS4B01G150100 chr7B 645437987 645438683 696 True 787.0 787 87.2860 1 689 1 chr7B.!!$R1 688
22 TraesCS4B01G150100 chr3B 726667849 726668520 671 True 756.0 756 87.2400 1 662 1 chr3B.!!$R1 661
23 TraesCS4B01G150100 chr3A 612614442 612615110 668 True 749.0 749 86.9190 9 690 1 chr3A.!!$R1 681

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
630 684 0.107214 GCTCAAATCCCATCGACCCA 60.107 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 2672 0.250945 TTGGCCACAAACAGCGGATA 60.251 50.0 3.88 0.0 32.66 2.59 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
107 118 3.797865 GCAGCTGCAGTTCAAATTTGACT 60.798 43.478 33.36 16.55 41.59 3.41
146 157 6.212235 TCAGCGAAAATTTATCTTTTGCACA 58.788 32.000 9.53 0.00 43.04 4.57
393 410 2.908688 ATTTGTGTGGTGCCCTTTTC 57.091 45.000 0.00 0.00 0.00 2.29
487 506 4.642885 AGTTTCCGAACCAATCAAAACTCA 59.357 37.500 0.00 0.00 38.40 3.41
547 570 4.723285 CCATCCATATCTCCATCCCACATA 59.277 45.833 0.00 0.00 0.00 2.29
630 684 0.107214 GCTCAAATCCCATCGACCCA 60.107 55.000 0.00 0.00 0.00 4.51
710 801 2.919856 CGCCCTCTCCCGATCCAT 60.920 66.667 0.00 0.00 0.00 3.41
728 819 2.444388 CCATTCCTCCATCTCATTCCCA 59.556 50.000 0.00 0.00 0.00 4.37
746 837 1.544724 CATCGTCCAAACCCACCAAT 58.455 50.000 0.00 0.00 0.00 3.16
751 852 0.251564 TCCAAACCCACCAATGCGAT 60.252 50.000 0.00 0.00 0.00 4.58
848 954 1.217244 CTACCACCACCACCTACGC 59.783 63.158 0.00 0.00 0.00 4.42
928 1034 0.558712 ATCCCTACGCTCCTTCCTCT 59.441 55.000 0.00 0.00 0.00 3.69
982 1097 1.156095 CCCCTTCCCCAAAAGCAGT 59.844 57.895 0.00 0.00 0.00 4.40
1106 1223 2.285368 ATGTCCTCCTCCGCCCAA 60.285 61.111 0.00 0.00 0.00 4.12
1167 1295 3.501349 TCTCTTCTATCCCCTGATTCGG 58.499 50.000 0.00 0.00 32.18 4.30
1170 1298 2.767644 TCTATCCCCTGATTCGGTCA 57.232 50.000 0.00 0.00 35.05 4.02
1225 1353 1.143305 GATTGATGATGACGCCTCGG 58.857 55.000 0.00 0.00 0.00 4.63
1258 1386 2.616510 CCAAGTGGGAGAAGATCACCAC 60.617 54.545 13.22 13.22 43.89 4.16
1275 1404 3.087253 CCATGGGGCCGTCACCTA 61.087 66.667 2.85 0.00 0.00 3.08
1283 1412 2.280552 GCCGTCACCTACACCCTCA 61.281 63.158 0.00 0.00 0.00 3.86
1324 1453 3.728373 GGCCACCCCCACTTCGAT 61.728 66.667 0.00 0.00 0.00 3.59
1401 1534 3.181442 TGACCCGGGTCTAATTTGTTTCA 60.181 43.478 44.64 24.29 44.80 2.69
1441 1574 1.774110 ACCTGCACATCCACAACAAA 58.226 45.000 0.00 0.00 0.00 2.83
1614 1791 8.958119 TCTAGGTATATGGTGTGTTTCATTTC 57.042 34.615 0.00 0.00 0.00 2.17
1618 1795 9.747898 AGGTATATGGTGTGTTTCATTTCTTAA 57.252 29.630 0.00 0.00 0.00 1.85
1656 1833 7.929245 TGTACACAGCTCACTAAAATACTGAAA 59.071 33.333 0.00 0.00 0.00 2.69
1679 1856 9.358872 GAAAAATGTTAATGATTCAGTCCTTCC 57.641 33.333 0.00 0.00 0.00 3.46
1732 2133 0.322975 TTCTCCTTCACCTGCTGCTC 59.677 55.000 0.00 0.00 0.00 4.26
1741 2142 0.042731 ACCTGCTGCTCCTAACCCTA 59.957 55.000 0.00 0.00 0.00 3.53
1748 2149 3.622455 GCTGCTCCTAACCCTATTGTTGT 60.622 47.826 0.00 0.00 0.00 3.32
1750 2151 4.331968 TGCTCCTAACCCTATTGTTGTTG 58.668 43.478 0.00 0.00 0.00 3.33
1758 2161 7.990886 CCTAACCCTATTGTTGTTGCTCTATTA 59.009 37.037 0.00 0.00 0.00 0.98
1778 2181 3.060615 GCACCTCCTGCTGCTTGG 61.061 66.667 0.00 3.48 43.33 3.61
1785 2193 1.745864 CCTGCTGCTTGGCTCTGAG 60.746 63.158 0.00 0.00 0.00 3.35
1921 2329 3.173965 CTCTGAAGTCTGAACCCCCTAA 58.826 50.000 0.00 0.00 0.00 2.69
1928 2336 0.034186 CTGAACCCCCTAATGCTGCA 60.034 55.000 4.13 4.13 0.00 4.41
1955 2363 7.336475 TGCTCTCTCTCCCTATCTATTTCTA 57.664 40.000 0.00 0.00 0.00 2.10
2049 2459 7.327214 ACTTGTGATGTGTGGTTTTAAATTGT 58.673 30.769 0.00 0.00 0.00 2.71
2180 2590 3.694072 AGTGCTTGTGTTAGCTTTGTTCA 59.306 39.130 0.00 0.00 41.76 3.18
2228 2638 1.442769 ACTTGTGTTAGCCGAGCATG 58.557 50.000 0.00 0.00 0.00 4.06
2248 2658 1.874231 GATCGCTGATCGTCTAGTCCA 59.126 52.381 3.41 0.00 39.67 4.02
2262 2672 4.339814 GTCTAGTCCACGAGGAGAAATGAT 59.660 45.833 0.21 0.00 46.92 2.45
2278 2688 1.378531 TGATATCCGCTGTTTGTGGC 58.621 50.000 0.00 0.00 45.61 5.01
2319 2998 0.176680 CAGCCGATCACCTAGTTGCT 59.823 55.000 0.00 0.00 0.00 3.91
2345 3025 2.715749 TACTGCTGTGCTATGCCATT 57.284 45.000 6.48 0.00 0.00 3.16
2429 3109 2.099756 GGAATTGTTATGCAGGAGCCAC 59.900 50.000 0.00 0.00 41.13 5.01
2430 3110 2.512692 ATTGTTATGCAGGAGCCACA 57.487 45.000 0.00 0.00 41.13 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 73 5.098211 GCTGCCTCATAGTTTGCTTTTTAG 58.902 41.667 0.00 0.00 0.00 1.85
142 153 3.350833 AGATTTGATCCACCTCTTGTGC 58.649 45.455 0.00 0.00 44.01 4.57
146 157 6.015940 GTGTCAAAAGATTTGATCCACCTCTT 60.016 38.462 8.59 0.00 0.00 2.85
320 335 8.637986 GGATAAGGACCAATTTGTATGCATTTA 58.362 33.333 3.54 0.00 0.00 1.40
487 506 2.487805 CCATGTCATCAATCCGTGGGAT 60.488 50.000 0.00 0.00 45.46 3.85
547 570 9.552695 TGTTTCTATAGATAGATGGATGGATGT 57.447 33.333 2.58 0.00 39.02 3.06
572 602 4.884164 GGTGGGGTTATCTCTTCTTCATTG 59.116 45.833 0.00 0.00 0.00 2.82
579 611 1.913419 TGTGGGTGGGGTTATCTCTTC 59.087 52.381 0.00 0.00 0.00 2.87
657 730 2.919856 CGGCGAGGAGATGGGGAT 60.920 66.667 0.00 0.00 0.00 3.85
698 781 0.264657 TGGAGGAATGGATCGGGAGA 59.735 55.000 0.00 0.00 46.90 3.71
710 801 2.369860 CGATGGGAATGAGATGGAGGAA 59.630 50.000 0.00 0.00 0.00 3.36
728 819 1.544724 CATTGGTGGGTTTGGACGAT 58.455 50.000 0.00 0.00 0.00 3.73
848 954 2.373502 GGATTTAGGAGGGATCAGGTGG 59.626 54.545 0.00 0.00 0.00 4.61
928 1034 2.203112 GCTCGCTGCCATGGATGA 60.203 61.111 18.40 5.70 35.15 2.92
1167 1295 4.442705 CAAATACACGTCAAACGACTGAC 58.557 43.478 6.48 10.39 46.05 3.51
1170 1298 2.803956 CCCAAATACACGTCAAACGACT 59.196 45.455 6.48 0.00 46.05 4.18
1225 1353 2.768527 TCCCACTTGGACATCTCATCTC 59.231 50.000 0.00 0.00 38.61 2.75
1258 1386 3.087253 TAGGTGACGGCCCCATGG 61.087 66.667 4.14 4.14 0.00 3.66
1283 1412 4.115199 GAGGTTCCAGGCCGCCAT 62.115 66.667 13.15 0.00 0.00 4.40
1324 1453 2.435938 GATTTGACCGGCGGCTCA 60.436 61.111 28.71 24.41 0.00 4.26
1338 1467 5.807520 CGAAATATAGCATAGGCACGAGATT 59.192 40.000 0.67 0.00 44.61 2.40
1391 1524 3.186119 CCTGCAACACGTGAAACAAATT 58.814 40.909 25.01 0.19 35.74 1.82
1401 1534 2.032071 GGTAGGCCTGCAACACGT 59.968 61.111 23.21 0.00 0.00 4.49
1614 1791 8.721478 AGCTGTGTACAGTTGAATACAATTAAG 58.279 33.333 13.08 0.00 45.45 1.85
1618 1795 6.147821 GTGAGCTGTGTACAGTTGAATACAAT 59.852 38.462 13.08 0.00 45.45 2.71
1622 1799 5.468540 AGTGAGCTGTGTACAGTTGAATA 57.531 39.130 13.08 0.00 45.45 1.75
1628 1805 6.868864 CAGTATTTTAGTGAGCTGTGTACAGT 59.131 38.462 13.08 1.12 45.45 3.55
1656 1833 6.381133 GGGGAAGGACTGAATCATTAACATTT 59.619 38.462 0.00 0.00 29.49 2.32
1679 1856 4.856607 GAGGACTCGCGCGAAGGG 62.857 72.222 33.99 23.99 46.11 3.95
1709 1886 1.558756 CAGCAGGTGAAGGAGAAGGAT 59.441 52.381 0.00 0.00 0.00 3.24
1732 2133 4.589908 AGAGCAACAACAATAGGGTTAGG 58.410 43.478 0.00 0.00 0.00 2.69
1741 2142 5.106157 GGTGCAGTAATAGAGCAACAACAAT 60.106 40.000 0.00 0.00 44.99 2.71
1748 2149 3.107601 AGGAGGTGCAGTAATAGAGCAA 58.892 45.455 0.00 0.00 40.35 3.91
1750 2151 3.104843 CAGGAGGTGCAGTAATAGAGC 57.895 52.381 0.00 0.00 0.00 4.09
1778 2181 2.933056 GCAGGTTTAGTGGACTCAGAGC 60.933 54.545 0.00 0.00 0.00 4.09
1785 2193 1.807142 GAAGCAGCAGGTTTAGTGGAC 59.193 52.381 0.00 0.00 35.19 4.02
1921 2329 1.153329 GAGAGAGCAGCTGCAGCAT 60.153 57.895 38.24 24.39 45.16 3.79
1928 2336 1.782752 AGATAGGGAGAGAGAGCAGCT 59.217 52.381 0.00 0.00 0.00 4.24
1955 2363 8.821686 TGAATTACAGAGAAAGAGAGAGAGAT 57.178 34.615 0.00 0.00 0.00 2.75
2049 2459 3.940852 CCATGATTCAGTTCACGGATCAA 59.059 43.478 0.00 0.00 30.50 2.57
2228 2638 1.874231 TGGACTAGACGATCAGCGATC 59.126 52.381 0.00 8.05 44.57 3.69
2248 2658 2.894126 AGCGGATATCATTTCTCCTCGT 59.106 45.455 4.83 0.00 0.00 4.18
2262 2672 0.250945 TTGGCCACAAACAGCGGATA 60.251 50.000 3.88 0.00 32.66 2.59
2278 2688 7.649306 GGCTGTAAATATAGCAAAGTGAATTGG 59.351 37.037 10.70 0.00 41.52 3.16
2319 2998 5.417266 TGGCATAGCACAGCAGTAAATAAAA 59.583 36.000 0.00 0.00 0.00 1.52
2429 3109 1.001378 CCTTTGCCGAAGTCAAACCTG 60.001 52.381 0.00 0.00 27.34 4.00
2430 3110 1.318576 CCTTTGCCGAAGTCAAACCT 58.681 50.000 0.00 0.00 27.34 3.50
2462 3142 1.299850 GGCCAAAACAAGGACACGC 60.300 57.895 0.00 0.00 33.02 5.34
2466 3146 1.248486 GAGGAGGCCAAAACAAGGAC 58.752 55.000 5.01 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.