Multiple sequence alignment - TraesCS2A01G234600

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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 TraesCS2A01G234600 chr2A 100.000 7204 0 0 1 7204 284799909 284807112 0.000000e+00 13304
1 TraesCS2A01G234600 chr2A 97.421 7212 171 13 1 7204 685104323 685097119 0.000000e+00 12273
2 TraesCS2A01G234600 chr2A 96.992 7215 186 20 1 7204 572969920 572962726 0.000000e+00 12092
3 TraesCS2A01G234600 chr2A 96.589 7211 217 19 1 7204 716654162 716646974 0.000000e+00 11926
4 TraesCS2A01G234600 chr2A 88.817 2763 251 31 1 2752 160674569 160671854 0.000000e+00 3338
5 TraesCS2A01G234600 chr2A 86.599 2761 254 62 1 2747 116997464 116994806 0.000000e+00 2942
6 TraesCS2A01G234600 chr2A 94.937 79 3 1 1 79 266689725 266689802 9.810000e-24 122
7 TraesCS2A01G234600 chr2A 94.937 79 3 1 1 79 270198858 270198781 9.810000e-24 122
8 TraesCS2A01G234600 chr2A 94.937 79 3 1 1 79 270226837 270226914 9.810000e-24 122
9 TraesCS2A01G234600 chr2A 89.744 78 8 0 1 78 369287047 369287124 4.600000e-17 100
10 TraesCS2A01G234600 chr5A 97.102 7211 186 16 1 7204 465654121 465661315 0.000000e+00 12137
11 TraesCS2A01G234600 chr5A 96.980 7219 194 20 1 7204 34943374 34936165 0.000000e+00 12102
12 TraesCS2A01G234600 chr5A 96.852 7212 201 17 1 7204 541976901 541984094 0.000000e+00 12037
13 TraesCS2A01G234600 chr3A 96.812 7215 186 18 1 7204 662010409 662003228 0.000000e+00 12009
14 TraesCS2A01G234600 chr3A 96.659 7213 217 16 1 7204 554827440 554834637 0.000000e+00 11963
15 TraesCS2A01G234600 chr1A 97.462 6344 152 8 864 7204 70944907 70938570 0.000000e+00 10815


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 TraesCS2A01G234600 chr2A 284799909 284807112 7203 False 13304 13304 100.000 1 7204 1 chr2A.!!$F3 7203
1 TraesCS2A01G234600 chr2A 685097119 685104323 7204 True 12273 12273 97.421 1 7204 1 chr2A.!!$R5 7203
2 TraesCS2A01G234600 chr2A 572962726 572969920 7194 True 12092 12092 96.992 1 7204 1 chr2A.!!$R4 7203
3 TraesCS2A01G234600 chr2A 716646974 716654162 7188 True 11926 11926 96.589 1 7204 1 chr2A.!!$R6 7203
4 TraesCS2A01G234600 chr2A 160671854 160674569 2715 True 3338 3338 88.817 1 2752 1 chr2A.!!$R2 2751
5 TraesCS2A01G234600 chr2A 116994806 116997464 2658 True 2942 2942 86.599 1 2747 1 chr2A.!!$R1 2746
6 TraesCS2A01G234600 chr5A 465654121 465661315 7194 False 12137 12137 97.102 1 7204 1 chr5A.!!$F1 7203
7 TraesCS2A01G234600 chr5A 34936165 34943374 7209 True 12102 12102 96.980 1 7204 1 chr5A.!!$R1 7203
8 TraesCS2A01G234600 chr5A 541976901 541984094 7193 False 12037 12037 96.852 1 7204 1 chr5A.!!$F2 7203
9 TraesCS2A01G234600 chr3A 662003228 662010409 7181 True 12009 12009 96.812 1 7204 1 chr3A.!!$R1 7203
10 TraesCS2A01G234600 chr3A 554827440 554834637 7197 False 11963 11963 96.659 1 7204 1 chr3A.!!$F1 7203
11 TraesCS2A01G234600 chr1A 70938570 70944907 6337 True 10815 10815 97.462 864 7204 1 chr1A.!!$R1 6340

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
566 576 0.836400 AGACCTCCACCAACACCGAT 60.836 55.000 0.00 0.0 0.00 4.18 F
1191 1211 0.467384 AGGCCAATGAGGTGATCTCG 59.533 55.000 5.01 0.0 45.32 4.04 F
2036 2066 1.672030 CCTGACCGACATGCTGCAA 60.672 57.895 6.36 0.0 0.00 4.08 F
2295 2328 2.666190 GCGAGCTGCCAGACAACA 60.666 61.111 0.00 0.0 37.76 3.33 F
3276 3320 3.155167 GTTCGGAGCCCCCTCGAT 61.155 66.667 0.00 0.0 39.06 3.59 F
4514 4563 2.249309 CCACGACGCACTGCAAAG 59.751 61.111 1.11 0.0 0.00 2.77 F
4748 4799 0.105593 AAGCGTCATCATGCCGAGAT 59.894 50.000 0.00 0.0 34.73 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2295 2328 1.681538 ACTCCTGCGTACTCGATGAT 58.318 50.000 0.00 0.0 39.71 2.45 R
3161 3199 1.429299 TCTCTCTCTTGACCTGTGGGA 59.571 52.381 0.00 0.0 36.25 4.37 R
3969 4017 0.699981 TAACTTAGGTTGGGGGTGGC 59.300 55.000 0.00 0.0 36.92 5.01 R
4364 4413 0.247736 ATCCCACTTGCACGTCTCTC 59.752 55.000 0.00 0.0 0.00 3.20 R
4748 4799 0.033504 GTTGCTCCTCTTGTCCGACA 59.966 55.000 0.00 0.0 0.00 4.35 R
5836 5894 0.321564 CCGCTTGTCACCTCCAATGA 60.322 55.000 0.00 0.0 0.00 2.57 R
6449 6507 2.911509 TGTTGCGTGGCAGCCATT 60.912 55.556 19.75 0.0 40.61 3.16 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
144 146 4.265893 TGTCAACCAGTAACTCAGCAAAA 58.734 39.130 0.00 0.00 0.00 2.44
484 493 4.994907 TTAGCACCACACATAGTATCGT 57.005 40.909 0.00 0.00 0.00 3.73
566 576 0.836400 AGACCTCCACCAACACCGAT 60.836 55.000 0.00 0.00 0.00 4.18
604 614 5.545723 AGTGGGATAAGCAGCTGATAAGTAT 59.454 40.000 20.43 6.08 0.00 2.12
766 777 2.747443 TTCTTCCACGCCACCACCA 61.747 57.895 0.00 0.00 0.00 4.17
1006 1026 2.360191 GGAGGAAGGCCATGGCAA 59.640 61.111 36.56 0.00 44.11 4.52
1101 1121 1.134901 CGAGAAGCGCGACTACACT 59.865 57.895 12.10 7.34 0.00 3.55
1177 1197 2.281484 GCGAACCAGACAAGGCCA 60.281 61.111 5.01 0.00 0.00 5.36
1191 1211 0.467384 AGGCCAATGAGGTGATCTCG 59.533 55.000 5.01 0.00 45.32 4.04
1236 1256 2.558795 CAGGATTCGTAGGATCATCGGT 59.441 50.000 0.00 0.00 0.00 4.69
1290 1310 2.434843 CCAGATGGCGGCAGTCCTA 61.435 63.158 19.29 0.00 0.00 2.94
1538 1563 7.952671 TGAACCTGATACACTGGATTACTATC 58.047 38.462 0.00 0.00 40.23 2.08
2036 2066 1.672030 CCTGACCGACATGCTGCAA 60.672 57.895 6.36 0.00 0.00 4.08
2093 2123 3.990092 TGAAAGCGACAAAGAGAAGCTA 58.010 40.909 0.00 0.00 37.15 3.32
2295 2328 2.666190 GCGAGCTGCCAGACAACA 60.666 61.111 0.00 0.00 37.76 3.33
2412 2445 3.193056 GGAGGCTAACAACTTCTACGACT 59.807 47.826 0.00 0.00 0.00 4.18
2422 2455 5.718607 ACAACTTCTACGACTACCCCTATTT 59.281 40.000 0.00 0.00 0.00 1.40
2555 2589 4.319046 CCAGTATGATTATGTCGTGCTTGC 60.319 45.833 0.00 0.00 39.69 4.01
2717 2752 5.736358 CGTTGCTCTAAAGTACTAGTTACGG 59.264 44.000 0.00 0.00 35.61 4.02
2862 2897 6.603599 TGCACTATCAGTACAACTCAGTCTAT 59.396 38.462 0.00 0.00 0.00 1.98
2929 2965 8.641499 TGAGAATAATCACAAAAACAAACACC 57.359 30.769 0.00 0.00 0.00 4.16
2942 2978 3.860641 ACAAACACCAAAAAGAAGGCAG 58.139 40.909 0.00 0.00 0.00 4.85
3018 3055 7.990886 ACAAAAAGTATGAGTCCAAGTTACTGA 59.009 33.333 0.00 0.00 0.00 3.41
3161 3199 4.296729 AGGACCCGTCGACCAGGT 62.297 66.667 21.57 21.57 36.31 4.00
3276 3320 3.155167 GTTCGGAGCCCCCTCGAT 61.155 66.667 0.00 0.00 39.06 3.59
3419 3463 5.594317 CCAAATAAGCCCAGCTATACAAACT 59.406 40.000 0.00 0.00 38.25 2.66
3466 3510 6.966435 AACCACAAGAAAAATGTTTGTCAG 57.034 33.333 0.00 0.00 33.06 3.51
3969 4017 4.569162 TGCTCGTAAAATAATCTCAACCCG 59.431 41.667 0.00 0.00 0.00 5.28
4364 4413 3.880047 AAATGCCATCATCACAACCAG 57.120 42.857 0.00 0.00 31.27 4.00
4403 4452 7.715249 GTGGGATTTAGCAGATCATAAGTACAA 59.285 37.037 0.00 0.00 0.00 2.41
4459 4508 5.613329 ACATTTGTCTTGGACGGTTAGTTA 58.387 37.500 0.00 0.00 34.95 2.24
4467 4516 2.502538 TGGACGGTTAGTTATTCCAGGG 59.497 50.000 0.00 0.00 0.00 4.45
4514 4563 2.249309 CCACGACGCACTGCAAAG 59.751 61.111 1.11 0.00 0.00 2.77
4575 4624 2.508928 CTCCCACACACCACCGTT 59.491 61.111 0.00 0.00 0.00 4.44
4722 4773 4.424711 GCCATGGCGGAGGAACCA 62.425 66.667 23.48 0.00 41.06 3.67
4748 4799 0.105593 AAGCGTCATCATGCCGAGAT 59.894 50.000 0.00 0.00 34.73 2.75
4793 4844 2.125431 CATTAACGTCCCCGGCGT 60.125 61.111 6.01 0.00 45.07 5.68
4838 4889 1.415672 AAAGGGGTTGAGCTCCACGA 61.416 55.000 12.15 0.00 41.40 4.35
4888 4939 1.070786 GAACCAGACAAGGCCGACA 59.929 57.895 0.00 0.00 0.00 4.35
4922 4973 4.161295 CAGGATGAAGGGCGGCGA 62.161 66.667 12.98 0.00 39.69 5.54
4943 4994 2.688446 ACTTGTATCCGAGCTTCATCGA 59.312 45.455 0.00 0.00 45.56 3.59
5150 5206 8.788806 CCCAACTAGATGAACTACTATAGTCTG 58.211 40.741 9.12 6.47 38.26 3.51
5462 5519 8.213679 ACAAAGATGTATCAAGCACTGGTATAT 58.786 33.333 0.00 0.00 38.24 0.86
5507 5564 8.225603 AGAAAACTAAACTTGAATCAAGCAGA 57.774 30.769 21.69 6.97 44.43 4.26
5836 5894 8.729805 AAATTGTACACATTTGTTGGTTTCAT 57.270 26.923 12.33 0.00 37.15 2.57
6068 6126 0.764271 TGCCAGACAACCTCATCACA 59.236 50.000 0.00 0.00 0.00 3.58
6212 6270 2.417586 TGAAGATGCATGAAAGTCTGCG 59.582 45.455 2.46 0.00 41.32 5.18
6277 6335 9.965824 CCTTAGTATTGTTGTTTCAGATTTGTT 57.034 29.630 0.00 0.00 0.00 2.83
6417 6475 6.096001 AGCTTCCTATTTTGTTCATCCATCAC 59.904 38.462 0.00 0.00 0.00 3.06
6601 6661 8.687292 TTAGACATGAACGGTAGTACTATCAT 57.313 34.615 13.53 11.49 0.00 2.45
6964 7029 6.263168 GTGCTAGGATTATACCAAACATTGCT 59.737 38.462 0.00 0.00 0.00 3.91
7093 7160 7.711846 ACTAGCATCAAACAACACAAACAATA 58.288 30.769 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.636150 AATAATAATGTCACTGCTTCAGCTT 57.364 32.000 0.00 0.00 42.66 3.74
15 16 7.636150 AAATAATAATGTCACTGCTTCAGCT 57.364 32.000 0.00 0.00 42.66 4.24
484 493 7.444792 AGTGTAATTGAACGTACCAAATACCAA 59.555 33.333 18.29 5.95 32.01 3.67
566 576 2.179547 CCACTTGCACGTGTCAGCA 61.180 57.895 20.52 5.71 39.32 4.41
604 614 4.556104 GCACCGATTCGTATAGTCAAGCTA 60.556 45.833 5.20 0.00 0.00 3.32
1006 1026 1.600916 GCTTGGCAGACGGTTCCTT 60.601 57.895 0.00 0.00 0.00 3.36
1101 1121 3.867216 GCTTAACCCCTTTGAGCGTTCTA 60.867 47.826 0.00 0.00 37.11 2.10
1177 1197 1.686052 GAGCCTCGAGATCACCTCATT 59.314 52.381 15.71 0.00 42.06 2.57
1191 1211 0.107752 CAAGCTTCCTCCAGAGCCTC 60.108 60.000 0.00 0.00 0.00 4.70
1290 1310 2.287915 GAGTTCGTCAATGCACAACTGT 59.712 45.455 0.00 0.00 0.00 3.55
1730 1755 8.657074 TGTTGAAATAGGATAACATAGAACCG 57.343 34.615 0.00 0.00 0.00 4.44
1764 1789 5.549347 TGTTCCGCATTGGTACTAGTTTAA 58.451 37.500 0.00 0.00 38.74 1.52
2036 2066 4.805192 GCAAATGTGAACAACTTGTCATGT 59.195 37.500 0.00 0.00 0.00 3.21
2093 2123 3.430374 CGATCTCCATACCGGACAACTTT 60.430 47.826 9.46 0.00 39.64 2.66
2115 2145 1.804748 GTCGATGAACTTGTTGGGGTC 59.195 52.381 0.00 0.00 0.00 4.46
2295 2328 1.681538 ACTCCTGCGTACTCGATGAT 58.318 50.000 0.00 0.00 39.71 2.45
2412 2445 3.047857 CCGTAAAGGGGAAATAGGGGTA 58.952 50.000 0.00 0.00 35.97 3.69
2555 2589 9.180678 GACATAACTAAACTTGTTCAAACATGG 57.819 33.333 11.89 4.86 38.95 3.66
2717 2752 3.602390 ACGTTGTGTGATTAGTTGCAC 57.398 42.857 0.00 0.00 35.63 4.57
2862 2897 5.648178 TTCAGAACTATGGTACTTGCGTA 57.352 39.130 0.00 0.00 0.00 4.42
2929 2965 6.757947 TCATTTGAGTTTCTGCCTTCTTTTTG 59.242 34.615 0.00 0.00 0.00 2.44
3018 3055 7.963532 TGTTTGAATCTAGTACTTGACTCCTT 58.036 34.615 12.15 2.62 39.81 3.36
3161 3199 1.429299 TCTCTCTCTTGACCTGTGGGA 59.571 52.381 0.00 0.00 36.25 4.37
3247 3291 3.370209 GGGCTCCGAACCTGTTTATAAGT 60.370 47.826 0.00 0.00 0.00 2.24
3276 3320 1.551883 GGTTTAGTCCCACCTCGCTAA 59.448 52.381 0.00 0.00 0.00 3.09
3419 3463 1.354101 TTTCTTTGTCCCGCCCTCTA 58.646 50.000 0.00 0.00 0.00 2.43
3969 4017 0.699981 TAACTTAGGTTGGGGGTGGC 59.300 55.000 0.00 0.00 36.92 5.01
4364 4413 0.247736 ATCCCACTTGCACGTCTCTC 59.752 55.000 0.00 0.00 0.00 3.20
4403 4452 4.752101 GTGCACTGATTAGTCTTGTCAAGT 59.248 41.667 10.32 0.00 34.07 3.16
4748 4799 0.033504 GTTGCTCCTCTTGTCCGACA 59.966 55.000 0.00 0.00 0.00 4.35
4793 4844 1.080772 CTGGTGTACTCGCGCTTCA 60.081 57.895 5.56 0.00 0.00 3.02
4838 4889 0.820871 GATCTCCAGCGTCTCCTTGT 59.179 55.000 0.00 0.00 0.00 3.16
4922 4973 2.688446 TCGATGAAGCTCGGATACAAGT 59.312 45.455 0.00 0.00 39.13 3.16
4943 4994 2.631062 TCGGTGTACTCCACATCAACTT 59.369 45.455 14.09 0.00 46.44 2.66
5150 5206 5.810587 ACATGTAATCGTGTATCCACTTCAC 59.189 40.000 0.00 0.00 41.37 3.18
5189 5245 5.192927 TCCACTTCACAGTTTCAGAAATGT 58.807 37.500 0.00 2.49 44.15 2.71
5507 5564 6.737720 TTACCAGAGTCAATGATAGATGCT 57.262 37.500 0.00 0.00 0.00 3.79
5836 5894 0.321564 CCGCTTGTCACCTCCAATGA 60.322 55.000 0.00 0.00 0.00 2.57
6212 6270 5.240844 AGGTAGCTGGTTCAACATAACAAAC 59.759 40.000 0.00 0.00 0.00 2.93
6277 6335 5.038033 GGTTCAACATAACGAAAGCAAACA 58.962 37.500 0.00 0.00 0.00 2.83
6417 6475 6.927294 ACTTCAACCTACTTCAACTTCAAG 57.073 37.500 0.00 0.00 0.00 3.02
6449 6507 2.911509 TGTTGCGTGGCAGCCATT 60.912 55.556 19.75 0.00 40.61 3.16
6506 6564 6.459923 AGTCTGCCACTTTTGTTTGTTTTTA 58.540 32.000 0.00 0.00 26.56 1.52
6516 6574 5.179555 GTCCTTAGTTAGTCTGCCACTTTTG 59.820 44.000 0.00 0.00 36.43 2.44
6964 7029 1.140312 AGGCTGTGGTTCTTCTCCAA 58.860 50.000 0.00 0.00 36.68 3.53
7026 7092 6.494842 TCTTGTGATTTTTCTCTTTTGTCGG 58.505 36.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.