Multiple sequence alignment - TraesCS4B01G126100

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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 TraesCS4B01G126100 chr4B 100.000 2640 0 0 1 2640 159345893 159348532 0.000000e+00 4876
1 TraesCS4B01G126100 chr6D 95.015 2668 102 11 1 2640 384292288 384289624 0.000000e+00 4161
2 TraesCS4B01G126100 chr6D 88.835 1030 93 10 1262 2275 210881629 210882652 0.000000e+00 1245
3 TraesCS4B01G126100 chr2B 94.853 2662 114 9 1 2640 241245572 241248232 0.000000e+00 4135
4 TraesCS4B01G126100 chr2B 88.668 2312 203 31 1 2275 609289288 609286999 0.000000e+00 2763
5 TraesCS4B01G126100 chr2B 88.676 2296 212 17 1 2275 282448241 282450509 0.000000e+00 2756
6 TraesCS4B01G126100 chr2B 90.657 1156 72 17 826 1952 57159289 57158141 0.000000e+00 1504
7 TraesCS4B01G126100 chr1A 90.509 2297 179 19 2 2275 520852853 520855133 0.000000e+00 2998
8 TraesCS4B01G126100 chr3A 90.096 2302 183 22 2 2275 703931813 703929529 0.000000e+00 2946
9 TraesCS4B01G126100 chr6A 90.043 2300 179 26 2 2275 425737603 425739878 0.000000e+00 2933
10 TraesCS4B01G126100 chr6A 95.410 915 40 2 1727 2640 391444170 391445083 0.000000e+00 1456
11 TraesCS4B01G126100 chr6A 91.049 648 41 8 1098 1729 391427872 391428518 0.000000e+00 859
12 TraesCS4B01G126100 chr7A 88.171 2012 182 37 308 2275 299381037 299379038 0.000000e+00 2346
13 TraesCS4B01G126100 chr3B 90.415 1158 74 20 826 1952 795066634 795067785 0.000000e+00 1489
14 TraesCS4B01G126100 chr3B 92.950 922 50 4 4 916 145897417 145896502 0.000000e+00 1328
15 TraesCS4B01G126100 chr3B 85.340 191 28 0 2450 2640 780604298 780604488 5.760000e-47 198
16 TraesCS4B01G126100 chr6B 90.398 1156 75 17 826 1952 168771144 168772292 0.000000e+00 1487
17 TraesCS4B01G126100 chr5A 92.973 925 50 4 1 916 543950929 543951847 0.000000e+00 1334
18 TraesCS4B01G126100 chr5A 85.484 186 24 2 2457 2640 144288747 144288931 9.640000e-45 191
19 TraesCS4B01G126100 chr5B 92.017 927 50 6 1 916 239332842 239331929 0.000000e+00 1280
20 TraesCS4B01G126100 chr2D 90.256 975 71 13 610 1563 650754425 650753454 0.000000e+00 1253
21 TraesCS4B01G126100 chr2A 90.166 966 77 9 610 1560 779969558 779970520 0.000000e+00 1242


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 TraesCS4B01G126100 chr4B 159345893 159348532 2639 False 4876 4876 100.000 1 2640 1 chr4B.!!$F1 2639
1 TraesCS4B01G126100 chr6D 384289624 384292288 2664 True 4161 4161 95.015 1 2640 1 chr6D.!!$R1 2639
2 TraesCS4B01G126100 chr6D 210881629 210882652 1023 False 1245 1245 88.835 1262 2275 1 chr6D.!!$F1 1013
3 TraesCS4B01G126100 chr2B 241245572 241248232 2660 False 4135 4135 94.853 1 2640 1 chr2B.!!$F1 2639
4 TraesCS4B01G126100 chr2B 609286999 609289288 2289 True 2763 2763 88.668 1 2275 1 chr2B.!!$R2 2274
5 TraesCS4B01G126100 chr2B 282448241 282450509 2268 False 2756 2756 88.676 1 2275 1 chr2B.!!$F2 2274
6 TraesCS4B01G126100 chr2B 57158141 57159289 1148 True 1504 1504 90.657 826 1952 1 chr2B.!!$R1 1126
7 TraesCS4B01G126100 chr1A 520852853 520855133 2280 False 2998 2998 90.509 2 2275 1 chr1A.!!$F1 2273
8 TraesCS4B01G126100 chr3A 703929529 703931813 2284 True 2946 2946 90.096 2 2275 1 chr3A.!!$R1 2273
9 TraesCS4B01G126100 chr6A 425737603 425739878 2275 False 2933 2933 90.043 2 2275 1 chr6A.!!$F3 2273
10 TraesCS4B01G126100 chr6A 391444170 391445083 913 False 1456 1456 95.410 1727 2640 1 chr6A.!!$F2 913
11 TraesCS4B01G126100 chr6A 391427872 391428518 646 False 859 859 91.049 1098 1729 1 chr6A.!!$F1 631
12 TraesCS4B01G126100 chr7A 299379038 299381037 1999 True 2346 2346 88.171 308 2275 1 chr7A.!!$R1 1967
13 TraesCS4B01G126100 chr3B 795066634 795067785 1151 False 1489 1489 90.415 826 1952 1 chr3B.!!$F2 1126
14 TraesCS4B01G126100 chr3B 145896502 145897417 915 True 1328 1328 92.950 4 916 1 chr3B.!!$R1 912
15 TraesCS4B01G126100 chr6B 168771144 168772292 1148 False 1487 1487 90.398 826 1952 1 chr6B.!!$F1 1126
16 TraesCS4B01G126100 chr5A 543950929 543951847 918 False 1334 1334 92.973 1 916 1 chr5A.!!$F2 915
17 TraesCS4B01G126100 chr5B 239331929 239332842 913 True 1280 1280 92.017 1 916 1 chr5B.!!$R1 915
18 TraesCS4B01G126100 chr2D 650753454 650754425 971 True 1253 1253 90.256 610 1563 1 chr2D.!!$R1 953
19 TraesCS4B01G126100 chr2A 779969558 779970520 962 False 1242 1242 90.166 610 1560 1 chr2A.!!$F1 950

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
938 1038 1.275291 TCGCCAGGAACTTGAAGTAGG 59.725 52.381 0.0 0.02 34.6 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2360 2524 0.320374 TTCAACGTCTCGCCCTCATT 59.68 50.0 0.0 0.0 0.0 2.57 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
224 228 8.387190 TCTTATAGCAGATCAAAATCATGGTG 57.613 34.615 0.00 0.00 34.07 4.17
259 276 5.363562 AGATCAGAATCATGGTTGTGCTA 57.636 39.130 10.91 0.00 34.07 3.49
381 404 8.441312 AAGCTGTGTCAATTTTTCATCAATTT 57.559 26.923 0.00 0.00 0.00 1.82
451 539 3.698040 AGATTGGTTGACTTGGATCATGC 59.302 43.478 0.00 0.00 0.00 4.06
806 896 4.921515 GCGGCGAGATAACAATACTGATTA 59.078 41.667 12.98 0.00 0.00 1.75
876 971 4.581077 TTGTTGCTAATGTGTTCATGCA 57.419 36.364 0.00 0.00 33.29 3.96
938 1038 1.275291 TCGCCAGGAACTTGAAGTAGG 59.725 52.381 0.00 0.02 34.60 3.18
1090 1190 4.932146 TGAGCTCTTTTACCAAAACAAGC 58.068 39.130 16.19 6.14 35.70 4.01
1126 1226 7.600375 TGTCTAAAATTGCAACTCAAAAACACA 59.400 29.630 0.00 0.00 38.34 3.72
1231 1352 3.699038 GACTATTGCAGAGAGAGTGACCT 59.301 47.826 4.81 0.00 0.00 3.85
1244 1365 4.798882 AGAGTGACCTATTCTCGAGGATT 58.201 43.478 12.49 0.00 37.53 3.01
1306 1443 5.132312 AGCACCTACACTGTAGGTCTATCTA 59.868 44.000 30.64 0.00 45.55 1.98
1316 1453 8.908903 CACTGTAGGTCTATCTATTCAGTTTCT 58.091 37.037 0.00 0.00 33.54 2.52
1499 1642 3.257127 GCCTCCTTTCGCTATATCAGAGT 59.743 47.826 0.00 0.00 0.00 3.24
1505 1648 6.980978 TCCTTTCGCTATATCAGAGTTGAAAG 59.019 38.462 4.79 4.79 37.77 2.62
1571 1715 6.320164 ACTTACATGGCTTTTCTGTACAAACA 59.680 34.615 0.00 0.00 0.00 2.83
1574 1718 5.810074 ACATGGCTTTTCTGTACAAACAAAC 59.190 36.000 0.00 0.00 34.49 2.93
1575 1719 5.652994 TGGCTTTTCTGTACAAACAAACT 57.347 34.783 0.00 0.00 34.49 2.66
1578 1722 7.603651 TGGCTTTTCTGTACAAACAAACTTTA 58.396 30.769 0.00 0.00 34.49 1.85
1579 1723 8.254508 TGGCTTTTCTGTACAAACAAACTTTAT 58.745 29.630 0.00 0.00 34.49 1.40
1580 1724 8.752254 GGCTTTTCTGTACAAACAAACTTTATC 58.248 33.333 0.00 0.00 34.49 1.75
1630 1789 2.049063 GAGCAGGCTGACGACGTT 60.049 61.111 20.86 0.00 0.00 3.99
1757 1916 0.179100 CGACGCAGGGTTCATCATCT 60.179 55.000 0.00 0.00 0.00 2.90
1795 1954 2.744202 CAAAGTGATCCACCTTTCCTCG 59.256 50.000 0.00 0.00 34.49 4.63
1952 2113 6.650120 AGCGGATCTTTCAAGGTTAATTAGA 58.350 36.000 0.00 0.00 0.00 2.10
2063 2225 1.660560 CCAGAATTGCCAGGCCTTCG 61.661 60.000 9.64 0.00 0.00 3.79
2064 2226 0.677731 CAGAATTGCCAGGCCTTCGA 60.678 55.000 9.64 0.00 0.00 3.71
2119 2281 3.057315 CAGGTGACTTTCCATGCGATTTT 60.057 43.478 0.00 0.00 40.21 1.82
2349 2513 2.484287 AATGGCTGAACAGGGGACGG 62.484 60.000 3.99 0.00 0.00 4.79
2360 2524 2.372074 GGGGACGGCCAGGATTACA 61.372 63.158 11.00 0.00 35.15 2.41
2407 2571 1.095228 CGGCAACTGTGACCACAACT 61.095 55.000 4.30 0.00 41.33 3.16
2409 2573 1.094785 GCAACTGTGACCACAACTGT 58.905 50.000 4.30 0.00 41.33 3.55
2489 2653 0.107410 TTGTGTTTCTGTCCAGCCGT 60.107 50.000 0.00 0.00 0.00 5.68
2520 2684 3.004951 CAGCTCCCATTCCAGCCT 58.995 61.111 0.00 0.00 36.17 4.58
2529 2693 2.061061 CCATTCCAGCCTATCCCTTCT 58.939 52.381 0.00 0.00 0.00 2.85
2551 2715 1.882989 GAGCCTTCAGGTGAGCGAGT 61.883 60.000 0.00 0.00 37.57 4.18
2566 2730 2.567615 AGCGAGTAACTTCCATTCCACT 59.432 45.455 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 125 0.734889 AGCAAAGCCATGTATGCGTC 59.265 50.000 0.00 0.00 43.39 5.19
153 155 3.068732 CAGAGTTCAGACTTCACCAGTGA 59.931 47.826 0.00 0.00 35.01 3.41
163 165 8.057536 AGTTCGTAATATTCAGAGTTCAGACT 57.942 34.615 0.00 0.00 39.32 3.24
259 276 4.229123 CCATCATGAGGCCCCTATAGAATT 59.771 45.833 0.00 0.00 0.00 2.17
493 581 6.312918 TCAACTTGTATCTTCAAATACGAGCC 59.687 38.462 10.01 0.00 43.27 4.70
675 763 8.762645 TGATCTCAGAAACAATTAGGTGAGTAT 58.237 33.333 0.00 0.00 34.35 2.12
876 971 8.529424 TTTCAGCATATCAAAATCTGAGGAAT 57.471 30.769 0.00 0.00 37.52 3.01
938 1038 6.509418 TTATGTTGCTAAAATCCTCACACC 57.491 37.500 0.00 0.00 0.00 4.16
1090 1190 9.683069 AGTTGCAATTTTAGACAAATGAACTAG 57.317 29.630 0.59 0.00 0.00 2.57
1231 1352 8.750298 ACTCAAAGACTAAAATCCTCGAGAATA 58.250 33.333 15.71 0.00 0.00 1.75
1244 1365 7.360861 CCATTTGATGCGTACTCAAAGACTAAA 60.361 37.037 12.57 0.76 43.63 1.85
1445 1587 5.048991 CGGTGTGCAGATACCTTAAACTTTT 60.049 40.000 11.62 0.00 34.77 2.27
1499 1642 6.811253 AACGTATACTGAATTGGCTTTCAA 57.189 33.333 0.56 0.00 40.01 2.69
1505 1648 6.755141 TCTTCTGTAACGTATACTGAATTGGC 59.245 38.462 19.75 0.00 35.74 4.52
1571 1715 6.716628 TCAAGTCATGAGCCTTGATAAAGTTT 59.283 34.615 19.55 0.00 41.47 2.66
1574 1718 5.645067 TGTCAAGTCATGAGCCTTGATAAAG 59.355 40.000 23.85 3.36 46.20 1.85
1575 1719 5.559770 TGTCAAGTCATGAGCCTTGATAAA 58.440 37.500 23.85 14.24 46.20 1.40
1578 1722 3.262660 TCTGTCAAGTCATGAGCCTTGAT 59.737 43.478 23.85 0.00 46.20 2.57
1579 1723 2.634453 TCTGTCAAGTCATGAGCCTTGA 59.366 45.455 19.55 19.55 43.47 3.02
1580 1724 3.049708 TCTGTCAAGTCATGAGCCTTG 57.950 47.619 16.31 16.31 39.19 3.61
1583 1727 4.005650 TGATTTCTGTCAAGTCATGAGCC 58.994 43.478 0.00 0.00 39.19 4.70
1630 1789 1.541310 CGGTGGGGCTTCAGTAGACA 61.541 60.000 0.00 0.00 31.29 3.41
1724 1883 3.419759 GTCGGCGCGTTGACCATT 61.420 61.111 18.25 0.00 0.00 3.16
1757 1916 3.133362 ACTTTGGTTACCTGACGAAGACA 59.867 43.478 2.07 0.00 0.00 3.41
1795 1954 8.896744 TCACAATAAAATGGATCTGATGAGAAC 58.103 33.333 0.00 0.00 0.00 3.01
1992 2153 4.835678 TGTGAGTGCAACATGATACTGAT 58.164 39.130 0.00 0.00 41.43 2.90
2063 2225 7.589221 GCAGCATATGAACTTATAGCAAAAGTC 59.411 37.037 6.97 0.00 36.17 3.01
2064 2226 7.284034 AGCAGCATATGAACTTATAGCAAAAGT 59.716 33.333 6.97 0.00 38.82 2.66
2276 2440 7.229907 CACCATTTACCCTTAGTTAACAGTGTT 59.770 37.037 14.05 14.05 0.00 3.32
2349 2513 1.322442 GCCCTCATTGTAATCCTGGC 58.678 55.000 0.00 0.00 0.00 4.85
2360 2524 0.320374 TTCAACGTCTCGCCCTCATT 59.680 50.000 0.00 0.00 0.00 2.57
2407 2571 3.938334 CCATGGTCGATGTTAATGTCACA 59.062 43.478 2.57 0.00 0.00 3.58
2409 2573 3.198853 TCCCATGGTCGATGTTAATGTCA 59.801 43.478 11.73 0.00 0.00 3.58
2413 2577 2.806745 CGCTCCCATGGTCGATGTTAAT 60.807 50.000 11.73 0.00 0.00 1.40
2520 2684 3.438668 CCTGAAGGCTCCTAGAAGGGATA 60.439 52.174 0.00 0.00 35.59 2.59
2529 2693 1.323271 CGCTCACCTGAAGGCTCCTA 61.323 60.000 0.00 0.00 39.32 2.94
2551 2715 4.041567 TCTGCTTCAGTGGAATGGAAGTTA 59.958 41.667 0.00 0.00 40.06 2.24
2566 2730 3.449018 GGAACCTCTAGATGTCTGCTTCA 59.551 47.826 0.78 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.