Multiple sequence alignment - TraesCS1B01G232600

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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 TraesCS1B01G232600 chr1B 100.000 3320 0 0 1 3320 418069181 418072500 0.000000e+00 6131
1 TraesCS1B01G232600 chr1B 85.065 154 19 2 2764 2913 442177117 442177270 1.600000e-33 154
2 TraesCS1B01G232600 chr1A 94.260 3345 134 27 1 3320 387833692 387837003 0.000000e+00 5060
3 TraesCS1B01G232600 chr1D 95.333 2507 92 13 1 2493 308453926 308456421 0.000000e+00 3958
4 TraesCS1B01G232600 chr1D 92.094 721 37 5 2573 3282 308456591 308457302 0.000000e+00 998
5 TraesCS1B01G232600 chr1D 98.333 60 1 0 2488 2547 308456532 308456591 4.530000e-19 106
6 TraesCS1B01G232600 chr2D 84.810 158 17 4 2761 2912 88290054 88290210 5.740000e-33 152
7 TraesCS1B01G232600 chr7D 84.076 157 21 2 2759 2911 197927005 197927161 7.420000e-32 148
8 TraesCS1B01G232600 chr7D 83.636 165 17 4 2762 2916 42644592 42644756 2.670000e-31 147
9 TraesCS1B01G232600 chr7A 84.076 157 21 2 2759 2911 206959856 206960012 7.420000e-32 148
10 TraesCS1B01G232600 chr7A 83.648 159 22 3 2762 2916 41966360 41966518 2.670000e-31 147
11 TraesCS1B01G232600 chr2B 84.076 157 18 4 2762 2912 141562170 141562325 9.600000e-31 145


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 TraesCS1B01G232600 chr1B 418069181 418072500 3319 False 6131.000000 6131 100.000000 1 3320 1 chr1B.!!$F1 3319
1 TraesCS1B01G232600 chr1A 387833692 387837003 3311 False 5060.000000 5060 94.260000 1 3320 1 chr1A.!!$F1 3319
2 TraesCS1B01G232600 chr1D 308453926 308457302 3376 False 1687.333333 3958 95.253333 1 3282 3 chr1D.!!$F1 3281

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
485 494 0.034896 GCACTTCCTCCGGACTTTCA 59.965 55.0 0.00 0.0 0.00 2.69 F
505 514 0.248094 TAATGCTCGTGCTCTCGTCG 60.248 55.0 11.19 0.0 40.48 5.12 F
1228 1257 0.826062 GGCATTGACATTTCCCCCTG 59.174 55.0 0.00 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 1469 0.460284 GGAGCGTGTCGACATCCATT 60.460 55.000 25.08 10.32 0.0 3.16 R
2108 2137 1.451927 GATGATCCGCCCAACAGCA 60.452 57.895 0.00 0.00 0.0 4.41 R
2688 2854 0.179000 AGAACGGCTAGCAAGGATGG 59.821 55.000 18.24 0.00 0.0 3.51 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
48 52 2.559668 TCTTCTTCTTGCATTTGCCTGG 59.440 45.455 0.00 0.00 41.18 4.45
130 139 2.703007 GAGGATCATGAAGCTGTACCCT 59.297 50.000 0.00 0.00 33.17 4.34
196 205 4.039092 GGGCTGCTGAGGCTCCAA 62.039 66.667 12.86 0.00 44.36 3.53
206 215 2.283821 GGCTCCAATGCCCAACCA 60.284 61.111 0.00 0.00 46.82 3.67
259 268 1.154263 GTTCGACACCGACTCCTCG 60.154 63.158 0.00 0.00 45.50 4.63
336 345 2.203126 GCTCGGCATCCCCAAGAG 60.203 66.667 0.00 0.00 0.00 2.85
430 439 4.247380 CCCTCCATGGCGAGCCTC 62.247 72.222 15.75 0.00 36.94 4.70
481 490 2.344203 CGAGCACTTCCTCCGGACT 61.344 63.158 0.00 0.00 0.00 3.85
485 494 0.034896 GCACTTCCTCCGGACTTTCA 59.965 55.000 0.00 0.00 0.00 2.69
505 514 0.248094 TAATGCTCGTGCTCTCGTCG 60.248 55.000 11.19 0.00 40.48 5.12
616 625 0.877071 AATTCGTTGTGGAGCAGCTG 59.123 50.000 10.11 10.11 0.00 4.24
735 756 9.736414 CAAGGAATATGAATGAATCCTACAGAT 57.264 33.333 0.00 0.00 39.56 2.90
791 816 8.493547 GTCTAACACGTTTAGTTTTATCTTGCT 58.506 33.333 13.52 0.00 0.00 3.91
792 817 9.695526 TCTAACACGTTTAGTTTTATCTTGCTA 57.304 29.630 13.52 0.00 0.00 3.49
920 945 5.491070 TCGAGATGGACATGAAGAACAATT 58.509 37.500 0.00 0.00 0.00 2.32
940 965 6.200854 ACAATTGTTCTTTCGGAAAATGCTTC 59.799 34.615 4.92 0.00 35.51 3.86
966 991 7.224949 CGTAAGTTCTTCTCTTGGAGTTTTTCT 59.775 37.037 0.00 0.00 0.00 2.52
1025 1051 1.941294 CATCCTCTGCATCTGCTTCAC 59.059 52.381 3.53 0.00 42.66 3.18
1228 1257 0.826062 GGCATTGACATTTCCCCCTG 59.174 55.000 0.00 0.00 0.00 4.45
1253 1282 3.182967 TGATTTTGTGTGTTTTGACGCC 58.817 40.909 0.00 0.00 0.00 5.68
1311 1340 3.221771 TGCAGGTAATCTTTGTGCAAGT 58.778 40.909 0.00 0.00 41.05 3.16
1316 1345 6.349280 GCAGGTAATCTTTGTGCAAGTATCAA 60.349 38.462 0.00 0.00 34.18 2.57
1317 1346 7.592938 CAGGTAATCTTTGTGCAAGTATCAAA 58.407 34.615 0.00 0.00 33.66 2.69
1440 1469 2.301583 TGTGGAGAATGATGGTGACGAA 59.698 45.455 0.00 0.00 0.00 3.85
1633 1662 2.218953 TCGTTCTCGACAAAACAGCT 57.781 45.000 0.00 0.00 41.35 4.24
1704 1733 3.022406 ACCTAGAGATGTAACGACCACC 58.978 50.000 0.00 0.00 0.00 4.61
1766 1795 2.874014 TGATGGAGTGAACCAATGCAA 58.126 42.857 0.00 0.00 43.47 4.08
1803 1832 1.007964 CGCAAAACCAACATCGCCA 60.008 52.632 0.00 0.00 0.00 5.69
1970 1999 3.677190 ACATGTAAACGTCGCAAAACA 57.323 38.095 0.00 0.00 0.00 2.83
2108 2137 1.147824 CGATCCAGCCTTCCAGCAT 59.852 57.895 0.00 0.00 34.23 3.79
2128 2157 0.106708 GCTGTTGGGCGGATCATCTA 59.893 55.000 0.00 0.00 0.00 1.98
2211 2240 4.479619 CTGCTATCAACTTTGTTGAAGGC 58.520 43.478 21.67 21.67 39.79 4.35
2259 2288 2.474816 GAAAGTTCAGACAGCGAGTGT 58.525 47.619 0.00 0.00 44.49 3.55
2261 2290 3.728076 AAGTTCAGACAGCGAGTGTAA 57.272 42.857 0.00 0.00 40.56 2.41
2455 2484 7.296628 TGCATTTCCTTTTATGTTTAGGTGT 57.703 32.000 0.00 0.00 0.00 4.16
2555 2720 7.332182 AGCTTAGCTGATAAGTTGTACAGAAAC 59.668 37.037 5.70 0.00 42.57 2.78
2617 2782 0.977395 CCTTCCACTTCCTCCTTCGT 59.023 55.000 0.00 0.00 0.00 3.85
2625 2790 0.951558 TTCCTCCTTCGTTTTGCTGC 59.048 50.000 0.00 0.00 0.00 5.25
2661 2827 6.927294 AGTTCTTTTTCTTGTCATCGTTCT 57.073 33.333 0.00 0.00 0.00 3.01
2688 2854 8.662141 TGAACTAAGAGGATAAAACATTTACGC 58.338 33.333 0.00 0.00 0.00 4.42
3006 3181 2.292845 TGCGTTTGAGCATGATTTGACA 59.707 40.909 0.00 0.00 42.92 3.58
3008 3183 3.302434 GCGTTTGAGCATGATTTGACATG 59.698 43.478 0.00 0.00 46.96 3.21
3030 3205 7.997223 ACATGATCACATATGTTCTCTTCCATT 59.003 33.333 5.37 0.00 34.00 3.16
3031 3206 7.797038 TGATCACATATGTTCTCTTCCATTG 57.203 36.000 5.37 0.00 0.00 2.82
3132 3316 3.702548 TGAGAATCCAATTGAAGCCATGG 59.297 43.478 7.63 7.63 0.00 3.66
3133 3317 3.703052 GAGAATCCAATTGAAGCCATGGT 59.297 43.478 14.67 0.00 34.50 3.55
3134 3318 4.870636 AGAATCCAATTGAAGCCATGGTA 58.129 39.130 14.67 0.00 34.50 3.25
3135 3319 5.271598 AGAATCCAATTGAAGCCATGGTAA 58.728 37.500 14.67 4.54 34.50 2.85
3136 3320 5.721000 AGAATCCAATTGAAGCCATGGTAAA 59.279 36.000 14.67 3.36 34.50 2.01
3137 3321 4.799564 TCCAATTGAAGCCATGGTAAAC 57.200 40.909 14.67 3.64 34.50 2.01
3138 3322 4.415596 TCCAATTGAAGCCATGGTAAACT 58.584 39.130 14.67 0.00 34.50 2.66
3139 3323 5.575157 TCCAATTGAAGCCATGGTAAACTA 58.425 37.500 14.67 0.68 34.50 2.24
3140 3324 6.194235 TCCAATTGAAGCCATGGTAAACTAT 58.806 36.000 14.67 2.99 34.50 2.12
3167 3353 9.049523 GTATAATCTTCATCATTTCAGCACAGA 57.950 33.333 0.00 0.00 0.00 3.41
3168 3354 6.829229 AATCTTCATCATTTCAGCACAGAA 57.171 33.333 0.00 0.00 0.00 3.02
3261 3451 2.034558 GCTTGTAGTGTTTGCATGTGGT 59.965 45.455 0.00 0.00 0.00 4.16
3269 3462 0.039035 TTTGCATGTGGTACTCCCCC 59.961 55.000 0.00 0.00 0.00 5.40
3290 3483 2.716217 GGTTTCTGAACTATGCTGGCT 58.284 47.619 0.00 0.00 36.03 4.75
3293 3486 3.423539 TTCTGAACTATGCTGGCTTGT 57.576 42.857 0.00 0.00 0.00 3.16
3294 3487 4.551702 TTCTGAACTATGCTGGCTTGTA 57.448 40.909 0.00 0.00 0.00 2.41
3295 3488 3.861840 TCTGAACTATGCTGGCTTGTAC 58.138 45.455 0.00 0.00 0.00 2.90
3310 3503 7.489757 GCTGGCTTGTACTACTATAATATGAGC 59.510 40.741 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.109323 GCAGCTGGGTGAGGTTTTGT 61.109 55.000 17.12 0.00 0.00 2.83
48 52 4.335594 CCTGGATTGGGATTTCTCGTTAAC 59.664 45.833 0.00 0.00 0.00 2.01
76 85 2.121963 TGCCTGAGACCCTGGGTT 60.122 61.111 21.59 10.05 35.25 4.11
196 205 4.839706 GCGGGGATGGTTGGGCAT 62.840 66.667 0.00 0.00 0.00 4.40
259 268 3.866582 CCGGGGATGACCAGCTCC 61.867 72.222 0.00 0.00 42.91 4.70
278 287 3.090532 GACGGGAATCCTGCCCCT 61.091 66.667 8.27 0.00 42.92 4.79
430 439 2.662006 TCAGCTTGATGGACTTCTCG 57.338 50.000 0.00 0.00 0.00 4.04
481 490 2.860136 CGAGAGCACGAGCATTATGAAA 59.140 45.455 7.77 0.00 45.49 2.69
485 494 1.598183 CGACGAGAGCACGAGCATTAT 60.598 52.381 7.77 0.00 45.49 1.28
505 514 2.266055 CTGGTCGGGCAGAGGAAC 59.734 66.667 0.00 0.00 0.00 3.62
616 625 1.157585 GGGAAGAAACGCACTTCTCC 58.842 55.000 13.59 10.46 42.07 3.71
661 670 4.326826 TCACCACAAGATAGAAAAGGCAG 58.673 43.478 0.00 0.00 0.00 4.85
667 676 5.645067 CAGAATGCTCACCACAAGATAGAAA 59.355 40.000 0.00 0.00 0.00 2.52
735 756 6.862608 CAGTGTGCAGTGCAGATAAAATAAAA 59.137 34.615 20.42 0.00 40.08 1.52
749 770 5.119279 GTGTTAGACTATTCAGTGTGCAGTG 59.881 44.000 0.00 0.80 34.21 3.66
791 816 9.872721 CGAGTCTAGGTACAGAATCTGTATATA 57.127 37.037 23.90 17.77 46.56 0.86
792 817 7.334921 GCGAGTCTAGGTACAGAATCTGTATAT 59.665 40.741 23.90 17.62 46.56 0.86
920 945 3.314080 ACGAAGCATTTTCCGAAAGAACA 59.686 39.130 0.00 0.00 32.95 3.18
940 965 6.846325 AAAACTCCAAGAGAAGAACTTACG 57.154 37.500 0.00 0.00 33.32 3.18
993 1019 4.700700 TGCAGAGGATGATCATAACAGTG 58.299 43.478 8.54 7.47 0.00 3.66
1025 1051 3.185594 CCTTTTCAACTGCATGCAACATG 59.814 43.478 22.88 19.22 0.00 3.21
1074 1100 1.227556 ACTTGAACTTGACGCGCCT 60.228 52.632 5.73 0.00 0.00 5.52
1228 1257 6.344032 GCGTCAAAACACACAAAATCATTAC 58.656 36.000 0.00 0.00 0.00 1.89
1253 1282 4.323104 CCTCCTTCTTCTACAGACAAAGGG 60.323 50.000 14.48 8.43 36.95 3.95
1311 1340 1.876714 GGCGAGCGCGTCTTTGATA 60.877 57.895 12.44 0.00 43.06 2.15
1316 1345 4.664677 ACTTGGCGAGCGCGTCTT 62.665 61.111 16.92 0.00 43.87 3.01
1317 1346 4.664677 AACTTGGCGAGCGCGTCT 62.665 61.111 16.92 5.17 43.87 4.18
1440 1469 0.460284 GGAGCGTGTCGACATCCATT 60.460 55.000 25.08 10.32 0.00 3.16
1633 1662 2.177394 TTGCTGCTATTCCGTGTCAA 57.823 45.000 0.00 0.00 0.00 3.18
1704 1733 3.947196 TGGAATCATCATTTCCTGAACCG 59.053 43.478 4.28 0.00 42.63 4.44
1766 1795 3.249799 TGCGACATTTTCATGTTCTTCGT 59.750 39.130 0.00 0.00 44.22 3.85
1803 1832 5.266788 ACCATCACATCCTCATCAACATTT 58.733 37.500 0.00 0.00 0.00 2.32
1810 1839 4.130118 GTTGGTACCATCACATCCTCATC 58.870 47.826 17.17 0.00 0.00 2.92
1889 1918 5.533903 CCCTCTGGAATATCTGAACCATTTG 59.466 44.000 0.00 0.00 0.00 2.32
1970 1999 2.026641 CATGACCGCTGGATGGATTTT 58.973 47.619 1.50 0.00 0.00 1.82
2108 2137 1.451927 GATGATCCGCCCAACAGCA 60.452 57.895 0.00 0.00 0.00 4.41
2128 2157 4.216902 CACATTATCATCCAACGCCATCAT 59.783 41.667 0.00 0.00 0.00 2.45
2211 2240 5.049405 GGTACTCAAATCAACAACAGGAGTG 60.049 44.000 0.00 0.00 35.85 3.51
2339 2368 6.460781 TGCTTCATTTTTCTTCATCAGCATT 58.539 32.000 0.00 0.00 29.93 3.56
2492 2657 9.587772 GCTACTTGTCTCTTCTTCATGTAAATA 57.412 33.333 0.00 0.00 0.00 1.40
2493 2658 8.317679 AGCTACTTGTCTCTTCTTCATGTAAAT 58.682 33.333 0.00 0.00 0.00 1.40
2494 2659 7.671302 AGCTACTTGTCTCTTCTTCATGTAAA 58.329 34.615 0.00 0.00 0.00 2.01
2495 2660 7.039714 TGAGCTACTTGTCTCTTCTTCATGTAA 60.040 37.037 0.00 0.00 0.00 2.41
2496 2661 6.434340 TGAGCTACTTGTCTCTTCTTCATGTA 59.566 38.462 0.00 0.00 0.00 2.29
2497 2662 5.244851 TGAGCTACTTGTCTCTTCTTCATGT 59.755 40.000 0.00 0.00 0.00 3.21
2498 2663 5.718146 TGAGCTACTTGTCTCTTCTTCATG 58.282 41.667 0.00 0.00 0.00 3.07
2499 2664 5.991933 TGAGCTACTTGTCTCTTCTTCAT 57.008 39.130 0.00 0.00 0.00 2.57
2500 2665 5.777802 CTTGAGCTACTTGTCTCTTCTTCA 58.222 41.667 0.00 0.00 0.00 3.02
2501 2666 4.625311 GCTTGAGCTACTTGTCTCTTCTTC 59.375 45.833 0.00 0.00 38.21 2.87
2502 2667 4.565022 GCTTGAGCTACTTGTCTCTTCTT 58.435 43.478 0.00 0.00 38.21 2.52
2503 2668 4.186856 GCTTGAGCTACTTGTCTCTTCT 57.813 45.455 0.00 0.00 38.21 2.85
2530 2695 7.457060 GTTTCTGTACAACTTATCAGCTAAGC 58.543 38.462 0.00 0.00 40.53 3.09
2555 2720 0.306228 TGCCGTTCAAACATGACACG 59.694 50.000 0.00 0.00 0.00 4.49
2617 2782 8.802267 AGAACTTGGTTAAATATAGCAGCAAAA 58.198 29.630 0.00 0.00 0.00 2.44
2688 2854 0.179000 AGAACGGCTAGCAAGGATGG 59.821 55.000 18.24 0.00 0.00 3.51
2832 3002 3.878086 AGACGCATAGTGTGTTTGTTG 57.122 42.857 0.00 0.00 41.77 3.33
3006 3181 7.997223 ACAATGGAAGAGAACATATGTGATCAT 59.003 33.333 9.63 3.64 38.00 2.45
3008 3183 7.798596 ACAATGGAAGAGAACATATGTGATC 57.201 36.000 9.63 10.48 0.00 2.92
3030 3205 3.309961 TGCAGTTTTCTGTGCAAAACA 57.690 38.095 12.85 0.00 46.53 2.83
3139 3323 9.346005 TGTGCTGAAATGATGAAGATTATACAT 57.654 29.630 0.00 0.00 0.00 2.29
3140 3324 8.735692 TGTGCTGAAATGATGAAGATTATACA 57.264 30.769 0.00 0.00 0.00 2.29
3164 3350 1.893544 CCAGCTAGGCATCCATTCTG 58.106 55.000 0.00 0.00 0.00 3.02
3261 3451 0.978907 GTTCAGAAACCGGGGGAGTA 59.021 55.000 6.32 0.00 0.00 2.59
3269 3462 1.398390 GCCAGCATAGTTCAGAAACCG 59.602 52.381 0.00 0.00 35.92 4.44


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

AutoCloner maintained by Alex Coulton.