Multiple sequence alignment - TraesCS1A01G234800

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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 TraesCS1A01G234800 chr1A 100.000 3940 0 0 1 3940 412457414 412461353 0.000000e+00 7276.0
1 TraesCS1A01G234800 chr1A 92.453 53 2 2 2968 3020 35140796 35140846 1.520000e-09 75.0
2 TraesCS1A01G234800 chr1D 96.532 3979 91 16 1 3940 326284735 326288705 0.000000e+00 6540.0
3 TraesCS1A01G234800 chr1B 96.818 3488 70 15 1 3469 439844499 439847964 0.000000e+00 5788.0
4 TraesCS1A01G234800 chr1B 96.531 490 10 2 3453 3940 439848536 439849020 0.000000e+00 804.0
5 TraesCS1A01G234800 chr3B 96.000 50 2 0 2976 3025 597475713 597475664 9.070000e-12 82.4
6 TraesCS1A01G234800 chr3D 95.918 49 2 0 2974 3022 329605878 329605926 3.260000e-11 80.5
7 TraesCS1A01G234800 chr6D 94.231 52 2 1 2970 3021 10434412 10434362 1.170000e-10 78.7
8 TraesCS1A01G234800 chr4D 94.231 52 2 1 2976 3027 47511185 47511135 1.170000e-10 78.7
9 TraesCS1A01G234800 chr3A 92.593 54 2 2 2967 3020 677842644 677842695 4.220000e-10 76.8
10 TraesCS1A01G234800 chr3A 83.750 80 10 3 2976 3053 446317991 446317913 5.460000e-09 73.1


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 TraesCS1A01G234800 chr1A 412457414 412461353 3939 False 7276 7276 100.0000 1 3940 1 chr1A.!!$F2 3939
1 TraesCS1A01G234800 chr1D 326284735 326288705 3970 False 6540 6540 96.5320 1 3940 1 chr1D.!!$F1 3939
2 TraesCS1A01G234800 chr1B 439844499 439849020 4521 False 3296 5788 96.6745 1 3940 2 chr1B.!!$F1 3939

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
261 264 0.107312 CAGTCCCCCAGCATCTGAAG 60.107 60.000 0.00 0.00 32.44 3.02 F
728 739 0.883833 GAACCATTCCACCACTGCAG 59.116 55.000 13.48 13.48 0.00 4.41 F
896 907 1.003442 CCCTCCCTCCATCTCCACA 59.997 63.158 0.00 0.00 0.00 4.17 F
2311 2326 1.002659 CCACCGTCCTTATTCCACACA 59.997 52.381 0.00 0.00 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2208 2223 0.326264 AACCACTCAGGCCATCTGAC 59.674 55.000 5.01 0.0 46.71 3.51 R
2213 2228 2.450476 GAATTCAACCACTCAGGCCAT 58.550 47.619 5.01 0.0 43.14 4.40 R
2794 2822 0.534203 TTTCCACTCGGGTTCTGTGC 60.534 55.000 0.00 0.0 38.11 4.57 R
3451 3497 1.202989 TGTGGCTTCCTGCACCAATAA 60.203 47.619 0.00 0.0 45.15 1.40 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
127 129 7.432350 TTGCAACCACAAAATATCAAATTCC 57.568 32.000 0.00 0.00 0.00 3.01
151 153 5.689068 CAGAACTCAAAATGCTGAAAAGGAC 59.311 40.000 0.00 0.00 0.00 3.85
225 227 9.358872 GATATACATGTCTGCGAAAATAGATGA 57.641 33.333 0.00 0.00 0.00 2.92
261 264 0.107312 CAGTCCCCCAGCATCTGAAG 60.107 60.000 0.00 0.00 32.44 3.02
280 283 5.569355 TGAAGAAACATCTGGGAATAAGCA 58.431 37.500 0.00 0.00 0.00 3.91
323 326 1.872952 TGCTTGTCACTCACAAATCCG 59.127 47.619 0.00 0.00 44.71 4.18
387 390 7.161773 TCAATTGAATTTGAGGGATCAAGTC 57.838 36.000 5.45 0.00 35.47 3.01
431 434 4.319694 GGTTTGCCACTTGAATCAATTTGC 60.320 41.667 0.00 0.00 34.09 3.68
510 513 7.822822 AGGTACACAAGTTAAATATCTGTGTCC 59.177 37.037 13.41 13.63 39.36 4.02
511 514 7.604927 GGTACACAAGTTAAATATCTGTGTCCA 59.395 37.037 13.41 0.00 39.36 4.02
520 523 8.893727 GTTAAATATCTGTGTCCATTAACTGCT 58.106 33.333 0.00 0.00 32.09 4.24
552 556 4.630111 TCTTTGCCATGTCATTGTTTTCC 58.370 39.130 0.00 0.00 0.00 3.13
620 624 4.101274 AGAGCATACTGAGTGAATGCATCT 59.899 41.667 19.20 15.38 46.66 2.90
728 739 0.883833 GAACCATTCCACCACTGCAG 59.116 55.000 13.48 13.48 0.00 4.41
842 853 2.270205 CTACCTGCACCAGCCCAG 59.730 66.667 0.00 0.00 41.13 4.45
844 855 2.527951 CTACCTGCACCAGCCCAGAC 62.528 65.000 0.00 0.00 41.13 3.51
847 858 3.480679 CTGCACCAGCCCAGACACA 62.481 63.158 0.00 0.00 41.13 3.72
896 907 1.003442 CCCTCCCTCCATCTCCACA 59.997 63.158 0.00 0.00 0.00 4.17
984 996 7.346751 ACATCACCACTGAACTTGTTTATTT 57.653 32.000 0.00 0.00 0.00 1.40
1012 1027 4.397417 ACAGAAGAGCCATGAAGCAATTAC 59.603 41.667 0.00 0.00 34.23 1.89
1440 1455 7.772757 GGAGAACTCTGGATAAATGTCTTGAAT 59.227 37.037 1.86 0.00 0.00 2.57
2172 2187 3.233507 ACAGGTGAGCCAATGATTTGTT 58.766 40.909 0.00 0.00 37.19 2.83
2213 2228 7.851387 TGTTTGTGTATAAAGTGTTGTCAGA 57.149 32.000 0.00 0.00 0.00 3.27
2311 2326 1.002659 CCACCGTCCTTATTCCACACA 59.997 52.381 0.00 0.00 0.00 3.72
2580 2595 9.538508 TCAGAAACTCTTATACATCATGTCATG 57.461 33.333 6.47 6.47 0.00 3.07
2592 2607 7.707624 ACATCATGTCATGGTATTTTCAAGT 57.292 32.000 12.90 0.00 0.00 3.16
2593 2608 7.541162 ACATCATGTCATGGTATTTTCAAGTG 58.459 34.615 12.90 0.00 0.00 3.16
2594 2609 7.394077 ACATCATGTCATGGTATTTTCAAGTGA 59.606 33.333 12.90 0.00 0.00 3.41
2595 2610 7.757941 TCATGTCATGGTATTTTCAAGTGAA 57.242 32.000 12.90 0.00 0.00 3.18
2596 2611 8.352137 TCATGTCATGGTATTTTCAAGTGAAT 57.648 30.769 12.90 0.00 33.54 2.57
2597 2612 8.245491 TCATGTCATGGTATTTTCAAGTGAATG 58.755 33.333 12.90 0.00 33.54 2.67
2598 2613 7.757941 TGTCATGGTATTTTCAAGTGAATGA 57.242 32.000 0.00 0.00 33.54 2.57
2599 2614 8.352137 TGTCATGGTATTTTCAAGTGAATGAT 57.648 30.769 0.00 0.00 33.54 2.45
2600 2615 8.805175 TGTCATGGTATTTTCAAGTGAATGATT 58.195 29.630 0.00 0.00 33.54 2.57
2601 2616 9.294030 GTCATGGTATTTTCAAGTGAATGATTC 57.706 33.333 0.00 0.00 33.54 2.52
2643 2671 1.416401 ACAACCGAACATCAGTGGTCT 59.584 47.619 0.00 0.00 40.01 3.85
2794 2822 7.414540 GGTGAAGCAATATCTTCCAAACTACAG 60.415 40.741 2.61 0.00 41.23 2.74
2917 2945 7.721399 ACAGAGAATATTTCAAAAGACACCAGT 59.279 33.333 0.00 0.00 0.00 4.00
2956 2984 8.254508 GTCCTCATGAGAGTTTCTACTGTAAAT 58.745 37.037 24.62 0.00 40.40 1.40
2963 2991 9.653287 TGAGAGTTTCTACTGTAAATAATGTGG 57.347 33.333 0.00 0.00 33.84 4.17
3241 3279 6.270000 AGGATTATATCGGTCCATGAAACAGA 59.730 38.462 0.00 0.00 34.42 3.41
3274 3312 3.368843 GCACAAAGATAAAGCCATGCAAC 59.631 43.478 0.00 0.00 0.00 4.17
3352 3390 1.405661 GGGTAGAAAAGGCTGGTCTCG 60.406 57.143 3.63 0.00 0.00 4.04
3418 3464 6.155475 AGAGACCTGTATAGATGCAGAAAC 57.845 41.667 8.96 1.34 42.19 2.78
3576 4212 1.171308 CAGAAGGTGAATGGCCTGTG 58.829 55.000 3.32 0.00 36.30 3.66
3719 4355 8.713971 TCCACCATGAATATGATACTGTTTAGT 58.286 33.333 0.00 0.00 37.42 2.24
3846 4488 5.179555 GGGCTGGAGCTAATAATTCTAAACG 59.820 44.000 0.00 0.00 41.70 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.116940 AATCCCTTTGCCCACATGGT 59.883 50.000 0.00 0.00 36.04 3.55
67 68 3.011144 TGGATCACCTAGGCATTTTTCCA 59.989 43.478 9.30 10.19 37.04 3.53
127 129 5.689068 GTCCTTTTCAGCATTTTGAGTTCTG 59.311 40.000 0.00 0.00 0.00 3.02
225 227 3.817647 GGACTGTTTTCTGACTTCATGCT 59.182 43.478 0.00 0.00 0.00 3.79
261 264 8.169977 TGATAATGCTTATTCCCAGATGTTTC 57.830 34.615 0.00 0.00 0.00 2.78
280 283 7.883833 AGCATCTTGTTGAGCATATCTGATAAT 59.116 33.333 0.81 0.00 0.00 1.28
323 326 5.448360 GCCAAGATGTTATCTCTGTGCTTTC 60.448 44.000 0.00 0.00 39.08 2.62
431 434 7.282332 TGATCAAGTCATCAGATGGTACTAG 57.718 40.000 10.67 0.00 0.00 2.57
510 513 7.148853 GCAAAGATGAAACAGAAGCAGTTAATG 60.149 37.037 0.00 0.00 0.00 1.90
511 514 6.865205 GCAAAGATGAAACAGAAGCAGTTAAT 59.135 34.615 0.00 0.00 0.00 1.40
520 523 4.583907 TGACATGGCAAAGATGAAACAGAA 59.416 37.500 0.00 0.00 0.00 3.02
552 556 1.676967 GCACCTTGCCAGGGAGAAG 60.677 63.158 8.98 0.00 46.01 2.85
620 624 3.161866 GTGTATGGAGGAAGGGCAAAAA 58.838 45.455 0.00 0.00 0.00 1.94
657 668 4.632538 GCTTATGTTTTAAGCATCCCGT 57.367 40.909 11.43 0.00 46.61 5.28
728 739 8.953368 AGGAAAATTTGGATCAAAGATTATGC 57.047 30.769 0.00 0.00 36.76 3.14
842 853 4.020128 AGGAGAACTTGAAGGGTATGTGTC 60.020 45.833 0.00 0.00 0.00 3.67
844 855 4.559862 AGGAGAACTTGAAGGGTATGTG 57.440 45.455 0.00 0.00 0.00 3.21
847 858 7.834681 GGATTTAAAGGAGAACTTGAAGGGTAT 59.165 37.037 0.00 0.00 39.96 2.73
896 907 1.606531 GCAAGAGCAGAGGGATGGT 59.393 57.895 0.00 0.00 41.58 3.55
984 996 3.369892 GCTTCATGGCTCTTCTGTAGGAA 60.370 47.826 0.00 0.00 0.00 3.36
1054 1069 1.007271 CGTGCTCGGTTGTGACTCT 60.007 57.895 0.00 0.00 0.00 3.24
1167 1182 1.614241 GCGGGAAGCTGGAGAGGTTA 61.614 60.000 0.00 0.00 40.07 2.85
1440 1455 4.453136 GCCAAACCATACTTCAACGTCTTA 59.547 41.667 0.00 0.00 0.00 2.10
1613 1628 5.935945 TCTCCTAGTTGTTCAAATCAACCA 58.064 37.500 5.38 0.00 44.02 3.67
1814 1829 5.185454 AGTTGTCACAGATGTGTTCTTTCA 58.815 37.500 12.43 2.50 45.76 2.69
1927 1942 1.411977 CTGATCCTCGGTGAAGCTCAT 59.588 52.381 0.00 0.00 0.00 2.90
2172 2187 8.500753 ACACAAACATCTTTAGTAACACAAGA 57.499 30.769 0.00 0.00 0.00 3.02
2208 2223 0.326264 AACCACTCAGGCCATCTGAC 59.674 55.000 5.01 0.00 46.71 3.51
2213 2228 2.450476 GAATTCAACCACTCAGGCCAT 58.550 47.619 5.01 0.00 43.14 4.40
2245 2260 4.080129 AGTGCATGGATCTCCTGTAAACAT 60.080 41.667 0.00 0.00 36.82 2.71
2258 2273 5.600069 TGAGTTGAGATAGTAGTGCATGGAT 59.400 40.000 0.00 0.00 0.00 3.41
2311 2326 3.827302 AGAACTCCATGTAAGTGACGTCT 59.173 43.478 17.92 0.00 0.00 4.18
2548 2563 7.861629 TGATGTATAAGAGTTTCTGAATGGGT 58.138 34.615 0.00 0.00 0.00 4.51
2589 2604 7.544566 GCATGAAACAAGATGAATCATTCACTT 59.455 33.333 0.98 5.89 43.48 3.16
2590 2605 7.033791 GCATGAAACAAGATGAATCATTCACT 58.966 34.615 0.98 0.00 43.48 3.41
2591 2606 6.809689 TGCATGAAACAAGATGAATCATTCAC 59.190 34.615 0.98 0.00 43.48 3.18
2592 2607 6.926313 TGCATGAAACAAGATGAATCATTCA 58.074 32.000 1.59 1.59 45.01 2.57
2593 2608 7.255569 TCTGCATGAAACAAGATGAATCATTC 58.744 34.615 0.00 0.00 29.03 2.67
2594 2609 7.165460 TCTGCATGAAACAAGATGAATCATT 57.835 32.000 0.00 0.00 29.03 2.57
2595 2610 6.769134 TCTGCATGAAACAAGATGAATCAT 57.231 33.333 0.00 0.00 30.62 2.45
2596 2611 6.405397 CCATCTGCATGAAACAAGATGAATCA 60.405 38.462 17.29 0.00 36.28 2.57
2597 2612 5.977725 CCATCTGCATGAAACAAGATGAATC 59.022 40.000 17.29 0.00 36.28 2.52
2598 2613 5.163447 CCCATCTGCATGAAACAAGATGAAT 60.163 40.000 17.29 0.00 36.28 2.57
2599 2614 4.158949 CCCATCTGCATGAAACAAGATGAA 59.841 41.667 17.29 0.00 36.28 2.57
2600 2615 3.697542 CCCATCTGCATGAAACAAGATGA 59.302 43.478 17.29 0.00 36.28 2.92
2601 2616 3.697542 TCCCATCTGCATGAAACAAGATG 59.302 43.478 0.00 6.37 34.61 2.90
2643 2671 6.500751 AGGTAGAAAACTTCCTCATCTGGTAA 59.499 38.462 0.00 0.00 0.00 2.85
2794 2822 0.534203 TTTCCACTCGGGTTCTGTGC 60.534 55.000 0.00 0.00 38.11 4.57
2917 2945 2.391926 TGAGGACAAGGGTAGTGACA 57.608 50.000 0.00 0.00 0.00 3.58
3241 3279 6.403866 TTTATCTTTGTGCTGGAACAACAT 57.596 33.333 0.00 0.00 39.70 2.71
3249 3287 3.777478 CATGGCTTTATCTTTGTGCTGG 58.223 45.455 0.00 0.00 0.00 4.85
3274 3312 3.659786 TGGTTAGTGGTTCAGTTCATCG 58.340 45.455 0.00 0.00 0.00 3.84
3352 3390 3.615224 TTGTTAATCACCGGTCTACCC 57.385 47.619 2.59 0.00 0.00 3.69
3451 3497 1.202989 TGTGGCTTCCTGCACCAATAA 60.203 47.619 0.00 0.00 45.15 1.40
3634 4270 8.526667 TCAATCTACTCTAGTTAGATGCAACT 57.473 34.615 13.90 0.86 41.56 3.16
3636 4272 7.561722 ACCTCAATCTACTCTAGTTAGATGCAA 59.438 37.037 13.90 5.80 31.58 4.08
3719 4355 7.877003 TCAAGCTTTTAACGGACAATCATAAA 58.123 30.769 0.00 0.00 0.00 1.40
3731 4367 3.259064 TCGATCCCTCAAGCTTTTAACG 58.741 45.455 0.00 0.00 0.00 3.18
3846 4488 5.105351 CCATCCCTTTTCCACTTAATTGGAC 60.105 44.000 13.74 0.00 45.80 4.02
3900 4542 8.712363 GTTATTGACGTATATGCTGATGTGAAT 58.288 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.