Multiple sequence alignment - TraesCS1A01G198500

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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 TraesCS1A01G198500 chr1A 100.000 3435 0 0 1 3435 356476949 356473515 0.000000e+00 6344
1 TraesCS1A01G198500 chr1B 92.016 3006 157 43 1 2942 387309083 387306097 0.000000e+00 4145
2 TraesCS1A01G198500 chr1B 97.143 490 13 1 2946 3435 387306056 387305568 0.000000e+00 826
3 TraesCS1A01G198500 chr1D 92.772 2850 131 33 1 2806 285058203 285055385 0.000000e+00 4052
4 TraesCS1A01G198500 chr1D 98.776 490 5 1 2946 3435 285055250 285054762 0.000000e+00 870
5 TraesCS1A01G198500 chr1D 92.593 108 6 1 2840 2947 285055391 285055286 1.650000e-33 154
6 TraesCS1A01G198500 chr1D 85.965 114 13 2 2801 2912 285055578 285055466 6.020000e-23 119


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 TraesCS1A01G198500 chr1A 356473515 356476949 3434 True 6344.00 6344 100.0000 1 3435 1 chr1A.!!$R1 3434
1 TraesCS1A01G198500 chr1B 387305568 387309083 3515 True 2485.50 4145 94.5795 1 3435 2 chr1B.!!$R1 3434
2 TraesCS1A01G198500 chr1D 285054762 285058203 3441 True 1298.75 4052 92.5265 1 3435 4 chr1D.!!$R1 3434

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
323 340 0.034380 TCCTCTACCACTAGCTGCGT 60.034 55.0 0.00 0.00 0.00 5.24 F
927 955 0.677098 ACTGGCAGCTGCATCTCTTG 60.677 55.0 37.63 20.42 44.36 3.02 F
2185 2234 0.467384 CCATCCTGATGCCGAAGAGT 59.533 55.0 1.49 0.00 37.49 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 1639 0.895530 TGGTCTCGTCTAAAGGCTGG 59.104 55.000 0.00 0.0 0.0 4.85 R
2325 2374 0.250901 TGAGCTCCCAGTTTTCAGGC 60.251 55.000 12.15 0.0 0.0 4.85 R
3102 3216 3.068873 GTCCTCTTGAGGCTGTCGATTAT 59.931 47.826 11.61 0.0 0.0 1.28 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
81 82 1.278238 CGTTTCCCTGTCTACGCATC 58.722 55.000 0.00 0.00 0.00 3.91
156 163 2.838693 GAGTCGCCTCCTACCCCC 60.839 72.222 0.00 0.00 0.00 5.40
165 172 4.188511 CCTACCCCCTCCCCCTCC 62.189 77.778 0.00 0.00 0.00 4.30
166 173 3.043404 CTACCCCCTCCCCCTCCT 61.043 72.222 0.00 0.00 0.00 3.69
167 174 3.040814 TACCCCCTCCCCCTCCTC 61.041 72.222 0.00 0.00 0.00 3.71
183 193 1.840635 TCCTCGTCTCTCCTCATCTCA 59.159 52.381 0.00 0.00 0.00 3.27
220 231 2.226437 CGACCACACCAAAAATCCAGAG 59.774 50.000 0.00 0.00 0.00 3.35
222 233 1.273327 CCACACCAAAAATCCAGAGCC 59.727 52.381 0.00 0.00 0.00 4.70
249 265 4.200283 CCTCGCCTCCTCGTCTGC 62.200 72.222 0.00 0.00 0.00 4.26
250 266 4.200283 CTCGCCTCCTCGTCTGCC 62.200 72.222 0.00 0.00 0.00 4.85
251 267 4.742649 TCGCCTCCTCGTCTGCCT 62.743 66.667 0.00 0.00 0.00 4.75
310 326 1.710996 CCTCTCTCCCGCCTCCTCTA 61.711 65.000 0.00 0.00 0.00 2.43
311 327 0.536460 CTCTCTCCCGCCTCCTCTAC 60.536 65.000 0.00 0.00 0.00 2.59
323 340 0.034380 TCCTCTACCACTAGCTGCGT 60.034 55.000 0.00 0.00 0.00 5.24
366 383 2.094752 GGACGGATTGGTTGATTGGTTG 60.095 50.000 0.00 0.00 0.00 3.77
374 391 1.547372 GGTTGATTGGTTGCTCTGCAT 59.453 47.619 0.00 0.00 38.76 3.96
383 400 2.223433 GGTTGCTCTGCATGATTAGCAC 60.223 50.000 13.74 10.00 44.19 4.40
385 402 0.950116 GCTCTGCATGATTAGCACCC 59.050 55.000 0.00 0.00 37.02 4.61
420 438 2.242408 ATTTGGGAGGATGGGTGGCC 62.242 60.000 0.00 0.00 0.00 5.36
441 459 1.087771 GGCCGGTCGATTCGTTGATT 61.088 55.000 1.90 0.00 0.00 2.57
454 474 1.098050 GTTGATTGCCCTGCGAGATT 58.902 50.000 0.00 0.00 0.00 2.40
457 477 2.997980 TGATTGCCCTGCGAGATTAAA 58.002 42.857 0.00 0.00 0.00 1.52
458 478 2.682856 TGATTGCCCTGCGAGATTAAAC 59.317 45.455 0.00 0.00 0.00 2.01
459 479 2.192664 TTGCCCTGCGAGATTAAACA 57.807 45.000 0.00 0.00 0.00 2.83
460 480 2.418368 TGCCCTGCGAGATTAAACAT 57.582 45.000 0.00 0.00 0.00 2.71
461 481 2.288666 TGCCCTGCGAGATTAAACATC 58.711 47.619 0.00 0.00 0.00 3.06
536 556 3.815757 GCCCCTATCATTTCCCCTGATTC 60.816 52.174 0.00 0.00 35.12 2.52
636 657 4.942852 AGAAGATGAAAGAGCCGATACTG 58.057 43.478 0.00 0.00 0.00 2.74
669 695 4.293648 GGTTGCGGGTTGGTTGGC 62.294 66.667 0.00 0.00 0.00 4.52
687 713 1.154016 CGGGTCTCTGTGTAGTGCG 60.154 63.158 0.00 0.00 0.00 5.34
694 720 4.046462 GTCTCTGTGTAGTGCGTGTTTTA 58.954 43.478 0.00 0.00 0.00 1.52
695 721 4.684703 GTCTCTGTGTAGTGCGTGTTTTAT 59.315 41.667 0.00 0.00 0.00 1.40
703 729 6.091713 GTGTAGTGCGTGTTTTATTAGGTGAT 59.908 38.462 0.00 0.00 0.00 3.06
778 804 1.238439 CAATCCGACCATATGCACCC 58.762 55.000 0.00 0.00 0.00 4.61
858 884 5.654603 TTCTGTCGGTGCTAAAGAAGATA 57.345 39.130 0.00 0.00 0.00 1.98
859 885 4.995124 TCTGTCGGTGCTAAAGAAGATAC 58.005 43.478 0.00 0.00 0.00 2.24
866 894 8.880750 GTCGGTGCTAAAGAAGATACTTTTATT 58.119 33.333 0.00 0.00 40.09 1.40
890 918 7.268199 TGATTTCATAAGTTCTGATCATGGC 57.732 36.000 0.00 0.00 0.00 4.40
891 919 5.739752 TTTCATAAGTTCTGATCATGGCG 57.260 39.130 0.00 0.00 0.00 5.69
896 924 1.146930 TTCTGATCATGGCGCTCCC 59.853 57.895 7.64 0.00 0.00 4.30
927 955 0.677098 ACTGGCAGCTGCATCTCTTG 60.677 55.000 37.63 20.42 44.36 3.02
1144 1173 4.961730 CCTTGACATCCATTAATTTCCCCA 59.038 41.667 0.00 0.00 0.00 4.96
1257 1286 2.281484 GTGAAGGCAACCGGAGCA 60.281 61.111 21.55 2.36 37.17 4.26
1350 1379 1.801178 GTTCCACTTTCAGAAGGAGCG 59.199 52.381 0.00 0.00 37.19 5.03
1384 1413 4.729918 AGCCTCTGCCAAAGCCCG 62.730 66.667 0.00 0.00 38.69 6.13
1434 1463 1.753649 GCAGCTACCATCAGTCTCTCA 59.246 52.381 0.00 0.00 0.00 3.27
1537 1566 3.181433 CCTCCCCCAGGTAATTATGGTTC 60.181 52.174 4.74 0.00 37.53 3.62
1575 1611 9.807649 GTGCATTTGTTCTATCCTTCAAATTAT 57.192 29.630 0.00 0.00 38.08 1.28
1602 1639 9.612620 CATCCTTGTGTTAGAAAGTTTCATTAC 57.387 33.333 17.65 11.78 0.00 1.89
1614 1661 6.819397 AAGTTTCATTACCAGCCTTTAGAC 57.181 37.500 0.00 0.00 0.00 2.59
1622 1669 1.134965 CCAGCCTTTAGACGAGACCAG 60.135 57.143 0.00 0.00 0.00 4.00
1691 1738 9.778993 CTTCACATGATATTTTTGAACTACCAG 57.221 33.333 0.00 0.00 0.00 4.00
1693 1740 8.946085 TCACATGATATTTTTGAACTACCAGAC 58.054 33.333 0.00 0.00 0.00 3.51
1778 1827 6.916360 TCATTTACCTGATTTTGCTTTCCT 57.084 33.333 0.00 0.00 0.00 3.36
1954 2003 4.007644 CTGACGTGCCCTCCTGCA 62.008 66.667 0.00 0.00 39.37 4.41
2095 2144 1.222936 CATCTGGAGGGAGCACACC 59.777 63.158 0.00 0.00 0.00 4.16
2185 2234 0.467384 CCATCCTGATGCCGAAGAGT 59.533 55.000 1.49 0.00 37.49 3.24
2212 2261 1.131638 CCCTTACCATAGCTGCCTCA 58.868 55.000 0.00 0.00 0.00 3.86
2325 2374 3.071580 GGATTGAAGCTCCGGTGAG 57.928 57.895 7.92 0.00 41.84 3.51
2371 2420 4.154347 CAGCTCTGGGACCCGCTC 62.154 72.222 8.34 0.00 0.00 5.03
2380 2429 4.222847 GACCCGCTCGGCCTTAGG 62.223 72.222 0.00 0.00 33.26 2.69
2391 2440 4.637771 CCTTAGGGTCAAAGGCGG 57.362 61.111 0.00 0.00 37.30 6.13
2398 2447 2.665185 GTCAAAGGCGGCGTGTCT 60.665 61.111 9.37 0.80 0.00 3.41
2402 2451 3.469863 AAAGGCGGCGTGTCTCCAA 62.470 57.895 9.37 0.00 0.00 3.53
2485 2534 7.201644 CGGCTGTGATAATTGTATCAAGAGTTT 60.202 37.037 0.00 0.00 46.05 2.66
2592 2644 5.701029 GGTGCAATCAATAAATTTCACCG 57.299 39.130 0.00 0.00 41.08 4.94
2713 2773 3.234353 TCCCAACATACCAAATGCAACA 58.766 40.909 0.00 0.00 0.00 3.33
2719 2779 3.261390 ACATACCAAATGCAACAGCCAAT 59.739 39.130 0.00 0.00 0.00 3.16
2722 2788 3.929094 ACCAAATGCAACAGCCAATTAG 58.071 40.909 0.00 0.00 0.00 1.73
2724 2790 4.526262 ACCAAATGCAACAGCCAATTAGTA 59.474 37.500 0.00 0.00 0.00 1.82
2725 2791 5.104374 CCAAATGCAACAGCCAATTAGTAG 58.896 41.667 0.00 0.00 0.00 2.57
2731 2797 6.674066 TGCAACAGCCAATTAGTAGTAAAAC 58.326 36.000 0.00 0.00 0.00 2.43
2780 2849 1.660575 GCAGTTGCTTGCTGTGCAG 60.661 57.895 0.00 0.00 40.61 4.41
2788 2866 2.821378 TGCTTGCTGTGCAGAATACATT 59.179 40.909 3.02 0.00 40.61 2.71
2870 2948 2.095461 TGCCAAAACACAACAGCTACA 58.905 42.857 0.00 0.00 0.00 2.74
2943 3021 4.574421 TCATCTTTGTTTGACGAAAGCTCA 59.426 37.500 0.00 0.00 0.00 4.26
3102 3216 1.141665 CACGCTGTCGATGATCCCA 59.858 57.895 0.00 0.00 39.41 4.37
3417 3531 2.635714 CTCACCAGCTGCATTACATCA 58.364 47.619 8.66 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.092921 TGTGTTGTGACTCGGCCAAC 61.093 55.000 2.24 0.00 39.08 3.77
25 26 2.365582 GTTTGACCCTGTGTTGTGACT 58.634 47.619 0.00 0.00 0.00 3.41
32 33 0.179029 CGGAAGGTTTGACCCTGTGT 60.179 55.000 0.00 0.00 39.75 3.72
81 82 2.345760 GGTTGGCACCCATCAGCAG 61.346 63.158 0.00 0.00 37.03 4.24
150 157 3.040814 GAGGAGGGGGAGGGGGTA 61.041 72.222 0.00 0.00 0.00 3.69
153 160 4.862823 GACGAGGAGGGGGAGGGG 62.863 77.778 0.00 0.00 0.00 4.79
156 163 1.152839 GAGAGACGAGGAGGGGGAG 60.153 68.421 0.00 0.00 0.00 4.30
165 172 1.946768 GGTGAGATGAGGAGAGACGAG 59.053 57.143 0.00 0.00 0.00 4.18
166 173 1.562008 AGGTGAGATGAGGAGAGACGA 59.438 52.381 0.00 0.00 0.00 4.20
167 174 1.675483 CAGGTGAGATGAGGAGAGACG 59.325 57.143 0.00 0.00 0.00 4.18
183 193 1.832608 TCGTGTGGAGAGCACAGGT 60.833 57.895 0.00 0.00 38.90 4.00
249 265 3.535962 GCGCAGGAGAGGAGGAGG 61.536 72.222 0.30 0.00 0.00 4.30
250 266 2.015227 GAAGCGCAGGAGAGGAGGAG 62.015 65.000 11.47 0.00 0.00 3.69
251 267 2.038007 AAGCGCAGGAGAGGAGGA 59.962 61.111 11.47 0.00 0.00 3.71
310 326 0.246635 AATTCGACGCAGCTAGTGGT 59.753 50.000 0.00 0.00 0.00 4.16
311 327 0.924090 GAATTCGACGCAGCTAGTGG 59.076 55.000 0.00 0.00 0.00 4.00
366 383 0.950116 GGGTGCTAATCATGCAGAGC 59.050 55.000 0.00 5.81 41.41 4.09
420 438 4.807039 AACGAATCGACCGGCCCG 62.807 66.667 10.55 5.81 0.00 6.13
441 459 2.092968 AGATGTTTAATCTCGCAGGGCA 60.093 45.455 0.00 0.00 0.00 5.36
636 657 3.014623 GCAACCACCCCTGTTACTAATC 58.985 50.000 0.00 0.00 0.00 1.75
669 695 1.154016 CGCACTACACAGAGACCCG 60.154 63.158 0.00 0.00 0.00 5.28
687 713 9.916397 CATCGAACTAATCACCTAATAAAACAC 57.084 33.333 0.00 0.00 0.00 3.32
694 720 7.348080 TGAGTCATCGAACTAATCACCTAAT 57.652 36.000 0.00 0.00 0.00 1.73
695 721 6.769134 TGAGTCATCGAACTAATCACCTAA 57.231 37.500 0.00 0.00 0.00 2.69
703 729 5.400066 TGGTGATTGAGTCATCGAACTAA 57.600 39.130 0.00 0.00 41.06 2.24
752 778 3.540617 CATATGGTCGGATTGGTTGACA 58.459 45.455 0.00 0.00 34.32 3.58
778 804 7.636150 ACAGTCTGATTAAATTTCATCCCTG 57.364 36.000 6.91 12.91 0.00 4.45
866 894 6.017687 CGCCATGATCAGAACTTATGAAATCA 60.018 38.462 0.09 0.00 0.00 2.57
901 929 2.959484 GCAGCTGCCAGTCACCCTA 61.959 63.158 28.76 0.00 34.31 3.53
905 933 1.367599 GAGATGCAGCTGCCAGTCAC 61.368 60.000 34.64 22.69 41.18 3.67
906 934 1.078637 GAGATGCAGCTGCCAGTCA 60.079 57.895 34.64 17.30 41.18 3.41
909 937 2.099143 CAAGAGATGCAGCTGCCAG 58.901 57.895 34.64 13.08 41.18 4.85
927 955 3.999663 GAGATGGTATATGCCAGAACTGC 59.000 47.826 17.97 7.88 42.47 4.40
962 990 1.618345 CCTAGCCTGTGAGGTGAGAGT 60.618 57.143 0.00 0.00 37.80 3.24
1144 1173 2.537633 TGGTAAGGACATACCGGAGT 57.462 50.000 9.46 2.96 46.94 3.85
1224 1253 4.094887 GCCTTCACGAGCAGAAAATGATAA 59.905 41.667 0.00 0.00 0.00 1.75
1257 1286 4.202212 CCGTCTTCAAAAATTGGACCCTTT 60.202 41.667 0.00 0.00 0.00 3.11
1350 1379 4.397417 AGAGGCTTCTCAATATGTGCAAAC 59.603 41.667 0.00 0.00 39.91 2.93
1384 1413 2.760650 CCAAGGGGTTAAATTCTGGAGC 59.239 50.000 0.00 0.00 0.00 4.70
1389 1418 2.179427 GCTGCCAAGGGGTTAAATTCT 58.821 47.619 0.00 0.00 36.17 2.40
1434 1463 2.716217 CTGAAAAAGCCTCCGAATCCT 58.284 47.619 0.00 0.00 0.00 3.24
1537 1566 2.554032 ACAAATGCACGAGGAAAAGAGG 59.446 45.455 0.00 0.00 0.00 3.69
1575 1611 8.463930 AATGAAACTTTCTAACACAAGGATGA 57.536 30.769 3.22 0.00 0.00 2.92
1592 1629 4.935808 CGTCTAAAGGCTGGTAATGAAACT 59.064 41.667 0.00 0.00 0.00 2.66
1602 1639 0.895530 TGGTCTCGTCTAAAGGCTGG 59.104 55.000 0.00 0.00 0.00 4.85
1691 1738 5.064707 TGCTCGTTTTAATAAGCTCCATGTC 59.935 40.000 0.00 0.00 35.76 3.06
1693 1740 5.484173 TGCTCGTTTTAATAAGCTCCATG 57.516 39.130 0.00 0.00 35.76 3.66
1741 1790 3.132646 GGTAAATGAATGGCATGCTCCAA 59.867 43.478 18.92 1.32 39.96 3.53
1778 1827 5.774690 ACTGGCCTTTATTCTGAAATGACAA 59.225 36.000 3.32 0.00 0.00 3.18
1918 1967 1.037579 GTTTCATACCAGCTGGGGGC 61.038 60.000 35.42 14.55 42.91 5.80
1954 2003 2.339712 GCACGGGCAGCAACAATT 59.660 55.556 3.77 0.00 40.72 2.32
2062 2111 2.426024 CCAGATGCCAAGAGGAACATTG 59.574 50.000 0.00 0.00 36.89 2.82
2095 2144 3.044986 CCATTGCACTGAAAACTTCGTG 58.955 45.455 5.49 6.87 37.30 4.35
2185 2234 3.437624 ATGGTAAGGGCCATGGCA 58.562 55.556 36.56 16.15 46.63 4.92
2212 2261 6.015918 TGAACCAATTGTCTGACCCAATATT 58.984 36.000 5.17 0.00 32.40 1.28
2325 2374 0.250901 TGAGCTCCCAGTTTTCAGGC 60.251 55.000 12.15 0.00 0.00 4.85
2371 2420 4.637771 CCTTTGACCCTAAGGCCG 57.362 61.111 0.00 0.00 36.08 6.13
2377 2426 3.315949 ACGCCGCCTTTGACCCTA 61.316 61.111 0.00 0.00 0.00 3.53
2380 2429 3.723348 GACACGCCGCCTTTGACC 61.723 66.667 0.00 0.00 0.00 4.02
2402 2451 1.450211 CAACAGTCGGAACCAGGGT 59.550 57.895 0.00 0.00 0.00 4.34
2452 2501 1.714899 ATTATCACAGCCGCCGCAAC 61.715 55.000 0.00 0.00 37.52 4.17
2504 2553 8.783093 TCCTTTACAAGACACAATAACAATGAG 58.217 33.333 0.00 0.00 0.00 2.90
2592 2644 4.112634 GCAAAGAAGAAACCAAAGGACAC 58.887 43.478 0.00 0.00 0.00 3.67
2713 2773 8.459911 AACACTTGTTTTACTACTAATTGGCT 57.540 30.769 0.00 0.00 33.93 4.75
2724 2790 9.968870 TCAAAAGTTTGTAACACTTGTTTTACT 57.031 25.926 0.00 0.00 39.18 2.24
2725 2791 9.998381 GTCAAAAGTTTGTAACACTTGTTTTAC 57.002 29.630 0.00 0.00 39.18 2.01
2780 2849 2.981140 GCTAGCCTCGTCGAATGTATTC 59.019 50.000 2.29 0.00 0.00 1.75
2788 2866 0.393402 TAACCAGCTAGCCTCGTCGA 60.393 55.000 12.13 0.00 0.00 4.20
2816 2894 5.695816 GCAAATGAAAGCACATGGAACTTAA 59.304 36.000 0.00 0.00 0.00 1.85
2819 2897 3.322828 AGCAAATGAAAGCACATGGAACT 59.677 39.130 0.00 0.00 0.00 3.01
2870 2948 1.000385 CGTTGCATTTGGTGTGATGGT 60.000 47.619 0.00 0.00 0.00 3.55
2943 3021 8.343168 ACGATGAGATATACTAAAGCTAGCTT 57.657 34.615 24.42 24.42 37.98 3.74
2947 3025 7.337184 CCCAGACGATGAGATATACTAAAGCTA 59.663 40.741 0.00 0.00 0.00 3.32
2949 3027 6.151312 TCCCAGACGATGAGATATACTAAAGC 59.849 42.308 0.00 0.00 0.00 3.51
2950 3028 7.175119 TGTCCCAGACGATGAGATATACTAAAG 59.825 40.741 0.00 0.00 34.95 1.85
2951 3029 7.002276 TGTCCCAGACGATGAGATATACTAAA 58.998 38.462 0.00 0.00 34.95 1.85
3102 3216 3.068873 GTCCTCTTGAGGCTGTCGATTAT 59.931 47.826 11.61 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.