Multiple sequence alignment - TraesCS2B01G127300

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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 TraesCS2B01G127300 chr2B 100.000 2669 0 0 1 2669 95488192 95485524 0.000000e+00 4929
1 TraesCS2B01G127300 chr3D 95.582 2467 102 4 204 2669 349870558 349873018 0.000000e+00 3945
2 TraesCS2B01G127300 chr6B 94.229 1958 111 2 712 2669 164580056 164578101 0.000000e+00 2988
3 TraesCS2B01G127300 chr6B 92.847 713 46 1 1 713 164588661 164587954 0.000000e+00 1029
4 TraesCS2B01G127300 chr6B 98.684 76 1 0 2594 2669 474432263 474432338 4.630000e-28 135
5 TraesCS2B01G127300 chr7B 94.123 1174 69 0 763 1936 712830414 712829241 0.000000e+00 1786
6 TraesCS2B01G127300 chr7B 91.440 771 61 2 1 767 712832741 712831972 0.000000e+00 1053
7 TraesCS2B01G127300 chr7B 90.682 440 29 1 1963 2402 712829242 712828815 2.300000e-160 575
8 TraesCS2B01G127300 chr7B 96.296 270 10 0 2400 2669 712794218 712793949 6.780000e-121 444
9 TraesCS2B01G127300 chr5D 89.213 927 95 3 1743 2669 88498138 88499059 0.000000e+00 1153
10 TraesCS2B01G127300 chr7D 77.185 1350 298 10 1325 2669 461536900 461538244 0.000000e+00 778
11 TraesCS2B01G127300 chr3A 75.294 1360 287 28 1310 2662 552690603 552691920 2.940000e-169 604
12 TraesCS2B01G127300 chr6A 76.882 186 40 3 1213 1396 106069987 106069803 4.700000e-18 102


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 TraesCS2B01G127300 chr2B 95485524 95488192 2668 True 4929 4929 100.000000 1 2669 1 chr2B.!!$R1 2668
1 TraesCS2B01G127300 chr3D 349870558 349873018 2460 False 3945 3945 95.582000 204 2669 1 chr3D.!!$F1 2465
2 TraesCS2B01G127300 chr6B 164578101 164580056 1955 True 2988 2988 94.229000 712 2669 1 chr6B.!!$R1 1957
3 TraesCS2B01G127300 chr6B 164587954 164588661 707 True 1029 1029 92.847000 1 713 1 chr6B.!!$R2 712
4 TraesCS2B01G127300 chr7B 712828815 712832741 3926 True 1138 1786 92.081667 1 2402 3 chr7B.!!$R2 2401
5 TraesCS2B01G127300 chr5D 88498138 88499059 921 False 1153 1153 89.213000 1743 2669 1 chr5D.!!$F1 926
6 TraesCS2B01G127300 chr7D 461536900 461538244 1344 False 778 778 77.185000 1325 2669 1 chr7D.!!$F1 1344
7 TraesCS2B01G127300 chr3A 552690603 552691920 1317 False 604 604 75.294000 1310 2662 1 chr3A.!!$F1 1352

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
343 348 0.111639 AAAACACCGCCCCATACACT 59.888 50.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 3628 0.602106 CACTGCGCATGCCTATAGCT 60.602 55.0 12.24 0.0 44.23 3.32 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
39 40 2.265739 GCCGCCTCAGATGTGACA 59.734 61.111 0.00 0.00 0.00 3.58
90 91 1.599606 CTACTGACCTGCTGGACGCT 61.600 60.000 17.64 1.86 40.11 5.07
121 122 2.686835 GCTCTCAGGGTGCCCTCT 60.687 66.667 6.84 0.00 46.28 3.69
243 248 1.599606 GCCAGAGCTCTTCCTCGACA 61.600 60.000 15.27 0.00 36.95 4.35
278 283 3.752796 CGGATTCAAGCCGGAGTTA 57.247 52.632 6.07 0.00 44.87 2.24
307 312 3.000819 ATTGGCACCTCGTCCGGA 61.001 61.111 0.00 0.00 0.00 5.14
322 327 1.602237 CGGACAGCCTATTGGTGGT 59.398 57.895 0.00 0.00 46.86 4.16
338 343 1.906333 GGTGAAAACACCGCCCCAT 60.906 57.895 3.65 0.00 35.30 4.00
343 348 0.111639 AAAACACCGCCCCATACACT 59.888 50.000 0.00 0.00 0.00 3.55
417 422 3.380320 TCGTCAAGTTCAGAGACAGAACA 59.620 43.478 8.54 0.00 45.93 3.18
446 451 1.991230 GCCTCCTCAAAGGGCACTA 59.009 57.895 0.00 0.00 44.69 2.74
460 465 1.614317 GGCACTACAAGGTGGATTGCT 60.614 52.381 3.21 0.00 37.65 3.91
525 530 2.338620 CGGAACTGCACCTCGTCA 59.661 61.111 0.00 0.00 0.00 4.35
591 596 1.229428 CACATGCGGACAACAGAAGT 58.771 50.000 0.00 0.00 0.00 3.01
662 667 1.311859 GATGCAAGATCGATTGGCCA 58.688 50.000 0.00 0.00 0.00 5.36
693 698 0.378962 GCAGAGACAGACGCGACTAT 59.621 55.000 15.93 0.00 0.00 2.12
727 732 1.074319 TCGCCGTTGTCGTAATGAGC 61.074 55.000 0.00 0.00 35.01 4.26
782 2349 1.279025 ATACCATGGGCAACGGAGGT 61.279 55.000 18.09 0.00 37.95 3.85
955 2522 0.322816 GGCAGTCATCCCAGCTTCAA 60.323 55.000 0.00 0.00 0.00 2.69
961 2528 0.392193 CATCCCAGCTTCAAGTCGCT 60.392 55.000 0.00 0.00 36.83 4.93
1004 2571 4.933064 CTCGGCGAGGACGATGCC 62.933 72.222 28.52 0.00 44.17 4.40
1031 2598 0.616111 ACCCTGGAGACTCTTCGCAT 60.616 55.000 1.74 0.00 0.00 4.73
1033 2600 0.820226 CCTGGAGACTCTTCGCATCA 59.180 55.000 1.74 0.00 0.00 3.07
1055 2622 2.892425 GCGTGGCCATTCTCCTCG 60.892 66.667 9.72 7.07 41.79 4.63
1058 2625 2.688666 TGGCCATTCTCCTCGGCT 60.689 61.111 0.00 0.00 45.50 5.52
1124 2691 1.593787 CTCACAGCGACTGGGATGT 59.406 57.895 11.38 0.00 43.41 3.06
1128 2695 1.672030 CAGCGACTGGGATGTTGCA 60.672 57.895 9.19 0.00 46.74 4.08
1149 2716 1.685491 CCTACTTCCCCTACAGCGAGT 60.685 57.143 0.00 0.00 0.00 4.18
1268 2835 4.985538 TCTCCTCTATTTGTTGTTTGCCT 58.014 39.130 0.00 0.00 0.00 4.75
1353 2920 2.850130 ACGTTGGCTGGGGTGGTA 60.850 61.111 0.00 0.00 0.00 3.25
1483 3062 1.305046 GGGGAAGAGGTCACGGAGA 60.305 63.158 0.00 0.00 0.00 3.71
1493 3072 0.179171 GTCACGGAGAAAGCGATCGA 60.179 55.000 21.57 0.00 0.00 3.59
1583 3162 1.742761 CTGGATTGTGACCTTGCGAT 58.257 50.000 0.00 0.00 0.00 4.58
1747 3326 1.754803 CTACAGTCCTGATTGCCGGTA 59.245 52.381 1.90 0.00 0.00 4.02
1901 3480 3.181464 TGGAACGTGTGTGGACTGAATTA 60.181 43.478 0.00 0.00 0.00 1.40
1921 3500 1.906574 ACCCAAATAGAAGAGCCACGA 59.093 47.619 0.00 0.00 0.00 4.35
2049 3628 3.294493 GGTTTTGCTCAGCGCCCA 61.294 61.111 2.29 0.00 38.05 5.36
2080 3659 0.099436 GCGCAGTGGGATTTTGCTAG 59.901 55.000 12.03 0.00 35.73 3.42
2100 3681 4.581309 AGTGTGGGATGAAGATCATGTT 57.419 40.909 0.00 0.00 37.20 2.71
2226 3808 3.757745 AACAACCTCAAAGACGTGTTG 57.242 42.857 0.00 4.92 41.47 3.33
2272 3854 1.358152 ACCTTTGGGAGAACGATGGA 58.642 50.000 0.00 0.00 36.25 3.41
2277 3859 4.202357 CCTTTGGGAGAACGATGGATCATA 60.202 45.833 0.00 0.00 33.58 2.15
2303 3885 5.242171 CGGGTGACTTTAACCAAATTTACCT 59.758 40.000 0.00 0.00 39.65 3.08
2320 3902 3.515602 ACCTGGCAAGAGACAAGAATT 57.484 42.857 0.00 0.00 27.50 2.17
2496 4078 5.193527 TGAGGATTGGGATATCACCTTTGAA 59.806 40.000 1.61 0.00 34.61 2.69
2542 4124 2.568509 TCATCACTCTCTGACCATTGCA 59.431 45.455 0.00 0.00 0.00 4.08
2557 4139 2.743928 GCACACTTCTCCTGGCCG 60.744 66.667 0.00 0.00 0.00 6.13
2622 4205 1.379916 CTGGACCAACATGCCAGGA 59.620 57.895 8.10 0.00 44.24 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.175710 ACCTTGCGGGGACAACCT 61.176 61.111 1.64 0.00 40.03 3.50
278 283 0.607489 GTGCCAATCCTCAGCAGTGT 60.607 55.000 0.00 0.00 37.15 3.55
307 312 2.890945 GTTTTCACCACCAATAGGCTGT 59.109 45.455 0.00 0.00 39.06 4.40
322 327 0.110678 TGTATGGGGCGGTGTTTTCA 59.889 50.000 0.00 0.00 0.00 2.69
338 343 1.509463 CGGCTTGGACGCTAGTGTA 59.491 57.895 9.36 0.00 0.00 2.90
417 422 1.332889 TGAGGAGGCAGCGATGACAT 61.333 55.000 10.23 0.00 0.00 3.06
460 465 7.095144 GCATTTGAAACATGTGAATGGATTTCA 60.095 33.333 18.28 11.66 42.09 2.69
474 479 0.968405 ACTGCCGGCATTTGAAACAT 59.032 45.000 32.87 4.02 0.00 2.71
591 596 2.195727 TCAGAATGGTCACCATGGCTA 58.804 47.619 11.08 0.00 44.40 3.93
627 632 0.606401 CATCACGGTTGGCAGGAACT 60.606 55.000 0.00 0.00 43.88 3.01
693 698 0.593618 GGCGATCATCTCTAGCGTCA 59.406 55.000 0.00 0.00 0.00 4.35
699 704 1.002792 CGACAACGGCGATCATCTCTA 60.003 52.381 16.62 0.00 35.72 2.43
1004 2571 0.397254 AGTCTCCAGGGTGGGTATCG 60.397 60.000 0.00 0.00 38.32 2.92
1069 2636 2.154580 CGATGATGTCGCATGAAGTAGC 59.845 50.000 0.00 0.00 44.33 3.58
1124 2691 1.906574 CTGTAGGGGAAGTAGGTGCAA 59.093 52.381 0.00 0.00 0.00 4.08
1128 2695 0.333993 TCGCTGTAGGGGAAGTAGGT 59.666 55.000 0.00 0.00 33.87 3.08
1287 2854 1.912043 CTTGGAGAGGGTGATCTTGGT 59.088 52.381 0.00 0.00 0.00 3.67
1467 3034 1.673329 GCTTTCTCCGTGACCTCTTCC 60.673 57.143 0.00 0.00 0.00 3.46
1493 3072 1.612950 TGAACATTGCCACAAAGCGAT 59.387 42.857 0.00 0.00 37.34 4.58
1731 3310 1.496060 TCATACCGGCAATCAGGACT 58.504 50.000 0.00 0.00 0.00 3.85
1747 3326 2.821969 CAGCTACCAAAACCAGCTTCAT 59.178 45.455 0.00 0.00 42.95 2.57
1901 3480 1.906574 TCGTGGCTCTTCTATTTGGGT 59.093 47.619 0.00 0.00 0.00 4.51
1921 3500 5.923114 CAGACGTAGCAATAGTAGCATTGAT 59.077 40.000 0.00 0.00 38.01 2.57
1987 3566 2.895404 AGGAAGCAACAACAGCATCAAT 59.105 40.909 0.00 0.00 31.78 2.57
2049 3628 0.602106 CACTGCGCATGCCTATAGCT 60.602 55.000 12.24 0.00 44.23 3.32
2080 3659 3.310774 CGAACATGATCTTCATCCCACAC 59.689 47.826 0.00 0.00 34.28 3.82
2100 3681 1.144969 GGTGAACATTCTCAACGCGA 58.855 50.000 15.93 0.00 0.00 5.87
2226 3808 2.675348 CTCATCCTTCGGCTCTTGAAAC 59.325 50.000 0.00 0.00 0.00 2.78
2272 3854 3.199071 TGGTTAAAGTCACCCGCTATGAT 59.801 43.478 0.00 0.00 32.71 2.45
2277 3859 2.351706 TTTGGTTAAAGTCACCCGCT 57.648 45.000 0.00 0.00 32.71 5.52
2303 3885 4.464008 AGAACAATTCTTGTCTCTTGCCA 58.536 39.130 0.00 0.00 44.59 4.92
2320 3902 4.033019 CGACTACGATTCGCATTAGAACA 58.967 43.478 5.86 0.00 42.66 3.18
2331 3913 1.488527 GGGTGATGCGACTACGATTC 58.511 55.000 0.00 0.00 42.66 2.52
2416 3998 3.448660 GGGTTATTTTGCTCATTGCTCCT 59.551 43.478 0.00 0.00 43.37 3.69
2542 4124 0.904865 TCATCGGCCAGGAGAAGTGT 60.905 55.000 2.24 0.00 0.00 3.55
2557 4139 1.673665 GCCGAGGGCCATCATCATC 60.674 63.158 19.00 0.00 44.06 2.92
2622 4205 3.390639 CCTCTAGGATGACTTGCTGGAAT 59.609 47.826 0.00 0.00 32.94 3.01


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

AutoCloner maintained by Alex Coulton.