Multiple sequence alignment - TraesCS2A01G273300

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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 TraesCS2A01G273300 chr2A 100.000 4028 0 0 1 4028 447911477 447907450 0.000000e+00 7439.0
1 TraesCS2A01G273300 chr2D 96.829 3248 85 7 476 3716 337393249 337396485 0.000000e+00 5411.0
2 TraesCS2A01G273300 chr2D 92.082 341 8 6 3707 4028 337397367 337397707 2.840000e-126 462.0
3 TraesCS2A01G273300 chr2B 96.663 2907 81 7 594 3492 404747286 404744388 0.000000e+00 4817.0
4 TraesCS2A01G273300 chr2B 95.024 422 13 5 3614 4028 404744216 404743796 0.000000e+00 656.0
5 TraesCS2A01G273300 chr2B 91.515 330 22 3 286 613 404759426 404759101 2.210000e-122 449.0
6 TraesCS2A01G273300 chr2B 89.474 285 30 0 1 285 404760015 404759731 1.060000e-95 361.0
7 TraesCS2A01G273300 chr2B 89.655 58 5 1 3491 3547 404744264 404744207 5.580000e-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 TraesCS2A01G273300 chr2A 447907450 447911477 4027 True 7439.0 7439 100.000000 1 4028 1 chr2A.!!$R1 4027
1 TraesCS2A01G273300 chr2D 337393249 337397707 4458 False 2936.5 5411 94.455500 476 4028 2 chr2D.!!$F1 3552
2 TraesCS2A01G273300 chr2B 404743796 404747286 3490 True 1848.7 4817 93.780667 594 4028 3 chr2B.!!$R1 3434
3 TraesCS2A01G273300 chr2B 404759101 404760015 914 True 405.0 449 90.494500 1 613 2 chr2B.!!$R2 612

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
197 198 0.106967 GACCTCCTTGGCCAGATTCC 60.107 60.0 5.11 0.0 40.22 3.01 F
270 271 0.179202 CGAACATTCGCAATCGGCAA 60.179 50.0 0.37 0.0 44.26 4.52 F
278 279 0.519519 CGCAATCGGCAACCACTTTA 59.480 50.0 0.00 0.0 45.17 1.85 F
446 753 0.670854 GGAGTGTTCGCTGGGAGTTC 60.671 60.0 0.00 0.0 0.00 3.01 F
1251 1560 0.858139 AGTCCCTCCTCCTCTCCCTT 60.858 60.0 0.00 0.0 0.00 3.95 F
1654 1963 1.335132 GCTTGGTCTCACCGGGGATA 61.335 60.0 6.99 0.0 42.58 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1312 1621 1.153823 CATCGACGGACTCGGCTTT 60.154 57.895 0.00 0.00 43.49 3.51 R
1316 1625 1.374343 TTCCTCATCGACGGACTCGG 61.374 60.000 0.00 0.00 43.16 4.63 R
1546 1855 1.558756 CTTGAGCTCCTCCACCTCATT 59.441 52.381 12.15 0.00 35.72 2.57 R
1654 1963 1.759445 CTCCACCTCCTCGTCATCATT 59.241 52.381 0.00 0.00 0.00 2.57 R
2769 3085 1.404717 GCATCAGAGAAGCTTCGACCA 60.405 52.381 20.43 7.19 0.00 4.02 R
3444 3760 1.073763 ACTGCAACAGCCTGGTATCAA 59.926 47.619 0.00 0.00 34.37 2.57 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
32 33 8.213679 AGACTGTAATCTTATGCAATACCACAT 58.786 33.333 0.00 0.00 0.00 3.21
43 44 6.493189 TGCAATACCACATACCTCAGATTA 57.507 37.500 0.00 0.00 0.00 1.75
52 53 5.030147 ACATACCTCAGATTAGTGAACCCA 58.970 41.667 0.00 0.00 0.00 4.51
56 57 3.200825 CCTCAGATTAGTGAACCCACCAT 59.799 47.826 0.00 0.00 44.22 3.55
60 61 6.591935 TCAGATTAGTGAACCCACCATATTC 58.408 40.000 0.00 0.00 44.22 1.75
61 62 5.765182 CAGATTAGTGAACCCACCATATTCC 59.235 44.000 0.00 0.00 44.22 3.01
64 65 2.647299 AGTGAACCCACCATATTCCACA 59.353 45.455 0.00 0.00 44.22 4.17
74 75 6.550854 CCCACCATATTCCACAATGAGTAAAT 59.449 38.462 0.00 0.00 0.00 1.40
107 108 6.822442 TGAAATAACTAGGGTCGCATATTCA 58.178 36.000 0.00 0.00 0.00 2.57
111 112 7.956328 ATAACTAGGGTCGCATATTCATAGA 57.044 36.000 0.00 0.00 0.00 1.98
117 118 7.246171 AGGGTCGCATATTCATAGAAGTATT 57.754 36.000 0.00 0.00 0.00 1.89
118 119 7.680730 AGGGTCGCATATTCATAGAAGTATTT 58.319 34.615 0.00 0.00 0.00 1.40
153 154 4.819769 CACCCGAATTGAACCATGAAAAT 58.180 39.130 0.00 0.00 0.00 1.82
197 198 0.106967 GACCTCCTTGGCCAGATTCC 60.107 60.000 5.11 0.00 40.22 3.01
198 199 0.846427 ACCTCCTTGGCCAGATTCCA 60.846 55.000 5.11 0.00 40.22 3.53
205 206 0.896923 TGGCCAGATTCCATGCAAAC 59.103 50.000 0.00 0.00 0.00 2.93
207 208 1.188863 GCCAGATTCCATGCAAACCT 58.811 50.000 0.00 0.00 0.00 3.50
210 211 2.165030 CCAGATTCCATGCAAACCTCAC 59.835 50.000 0.00 0.00 0.00 3.51
217 218 2.163010 CCATGCAAACCTCACATCAGAC 59.837 50.000 0.00 0.00 0.00 3.51
252 253 4.888038 GGCTAAACCCCTTATTTGTACG 57.112 45.455 0.00 0.00 0.00 3.67
253 254 4.516323 GGCTAAACCCCTTATTTGTACGA 58.484 43.478 0.00 0.00 0.00 3.43
270 271 0.179202 CGAACATTCGCAATCGGCAA 60.179 50.000 0.37 0.00 44.26 4.52
278 279 0.519519 CGCAATCGGCAACCACTTTA 59.480 50.000 0.00 0.00 45.17 1.85
282 283 3.189702 GCAATCGGCAACCACTTTACTTA 59.810 43.478 0.00 0.00 43.97 2.24
313 618 4.621034 GGATGACATTTGCGAACGATTTTT 59.379 37.500 0.00 0.00 0.00 1.94
359 664 5.468072 GGTGATAATGTTCAGACTAGCATGG 59.532 44.000 0.00 0.00 0.00 3.66
427 734 0.874175 TCGCGATCAAACGGCTATGG 60.874 55.000 3.71 0.00 0.00 2.74
435 742 1.737793 CAAACGGCTATGGGAGTGTTC 59.262 52.381 0.00 0.00 0.00 3.18
443 750 1.903877 ATGGGAGTGTTCGCTGGGAG 61.904 60.000 0.00 0.00 37.19 4.30
446 753 0.670854 GGAGTGTTCGCTGGGAGTTC 60.671 60.000 0.00 0.00 0.00 3.01
461 768 3.230976 GGAGTTCCTTCCCAACAAATGT 58.769 45.455 0.00 0.00 0.00 2.71
463 770 4.100963 GGAGTTCCTTCCCAACAAATGTTT 59.899 41.667 0.00 0.00 35.83 2.83
466 773 2.103941 TCCTTCCCAACAAATGTTTGCC 59.896 45.455 5.44 0.00 41.79 4.52
468 775 2.906691 TCCCAACAAATGTTTGCCAG 57.093 45.000 5.44 0.00 41.79 4.85
521 828 1.237285 CGCGATCATTTCCCATCCCC 61.237 60.000 0.00 0.00 0.00 4.81
634 942 1.147473 GGTTTTGCCAAATGAAGCGG 58.853 50.000 0.00 0.00 37.17 5.52
1251 1560 0.858139 AGTCCCTCCTCCTCTCCCTT 60.858 60.000 0.00 0.00 0.00 3.95
1316 1625 4.803908 CGAGGGGGAGGGCAAAGC 62.804 72.222 0.00 0.00 0.00 3.51
1546 1855 2.490217 GCTGCGCCTTCTACGAGA 59.510 61.111 4.18 0.00 0.00 4.04
1654 1963 1.335132 GCTTGGTCTCACCGGGGATA 61.335 60.000 6.99 0.00 42.58 2.59
1729 2038 1.435408 GCCAAGCTCTTCCAGATCGC 61.435 60.000 0.00 0.00 0.00 4.58
1752 2061 2.222027 GATAAGAATGCGGGGGTTCAG 58.778 52.381 0.00 0.00 0.00 3.02
2215 2524 4.034975 GCAGACTGCAGATGGAGAAATAAC 59.965 45.833 23.35 0.00 44.26 1.89
2291 2600 9.449550 TTTTCTATTGCGATAAACATAATGCTG 57.550 29.630 0.00 0.00 0.00 4.41
2302 2611 6.956299 AAACATAATGCTGCAAATCTGTTC 57.044 33.333 6.36 0.00 0.00 3.18
2331 2640 9.064706 ACTTCTCCTGATTGCTGATAATTATTG 57.935 33.333 0.00 0.00 0.00 1.90
2394 2703 3.118542 GTTTGCCTAAATGCTGCTATGC 58.881 45.455 0.00 0.00 0.00 3.14
2453 2762 3.503748 GCTTTGAGTTCACATGCTACCTT 59.496 43.478 0.00 0.00 0.00 3.50
2644 2954 7.558444 CCCCTATTGTATTTTGGCTGTACTTTA 59.442 37.037 0.00 0.00 0.00 1.85
2672 2982 3.423749 TCACCAGCATGACATGTTGAAT 58.576 40.909 27.93 15.74 43.17 2.57
2678 2988 5.589855 CCAGCATGACATGTTGAATACCTAA 59.410 40.000 27.93 0.00 43.17 2.69
2737 3048 8.352942 AGAATCATTTGAAACTGGTACTGAAAC 58.647 33.333 0.00 0.00 0.00 2.78
2769 3085 4.079787 TCCTATGCAGTTAAAGGCCTGATT 60.080 41.667 5.69 0.00 0.00 2.57
2863 3179 2.030946 GGGAAAAGTCTGAATGCGATCG 59.969 50.000 11.69 11.69 0.00 3.69
2883 3199 3.044986 CGAAGGTGCACAAAACAAGATG 58.955 45.455 20.43 0.00 0.00 2.90
2900 3216 1.248785 ATGAGGCTTGCAGCAAGTGG 61.249 55.000 31.26 12.19 44.75 4.00
2913 3229 1.887956 GCAAGTGGAAGGAGGCAATCA 60.888 52.381 0.00 0.00 0.00 2.57
3040 3356 7.872113 AAGAAAAGCTAGGTATGAATGGAAG 57.128 36.000 0.00 0.00 0.00 3.46
3088 3404 0.099968 CATTTCTGATGGTGCCGCAG 59.900 55.000 0.00 5.02 0.00 5.18
3358 3674 9.923143 AGCGCACTACAGATAATATTGTTTATA 57.077 29.630 11.47 0.00 0.00 0.98
3444 3760 6.691754 TTGATTATGATACCGTGTTGCAAT 57.308 33.333 0.59 0.00 0.00 3.56
3459 3775 2.806434 TGCAATTGATACCAGGCTGTT 58.194 42.857 14.43 0.60 0.00 3.16
3503 3944 6.703165 ACTTACTTTAACTAGTTGGGTTCACG 59.297 38.462 18.56 3.47 0.00 4.35
3504 3945 5.280654 ACTTTAACTAGTTGGGTTCACGA 57.719 39.130 18.56 0.00 0.00 4.35
3505 3946 5.052481 ACTTTAACTAGTTGGGTTCACGAC 58.948 41.667 18.56 0.00 0.00 4.34
3648 4090 3.641434 AGGCACATAGTTGCTGAATCT 57.359 42.857 0.00 0.00 42.56 2.40
3718 5051 6.239148 TATCTGGAGATCAGTGTTATGCACTC 60.239 42.308 0.00 0.00 44.44 3.51
3763 5096 8.614994 AGTTCTTGAAACAAAACAATAAGTCG 57.385 30.769 0.00 0.00 0.00 4.18
3774 5107 8.185505 ACAAAACAATAAGTCGTGTATGTTTGT 58.814 29.630 2.84 0.00 28.86 2.83
3816 5161 0.824109 TCACTGGTTGGCTATCCTCG 59.176 55.000 0.00 0.00 0.00 4.63
3882 5227 9.933723 CCTTTCAGAAATTTGGTATCTTTGATT 57.066 29.630 0.00 0.00 0.00 2.57
3936 5281 5.880054 CGTAAGGTTCCATTGTCATTCTT 57.120 39.130 0.00 0.00 0.00 2.52
3938 5283 7.372451 CGTAAGGTTCCATTGTCATTCTTTA 57.628 36.000 0.00 0.00 0.00 1.85
3939 5284 7.464358 CGTAAGGTTCCATTGTCATTCTTTAG 58.536 38.462 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.786178 TGTGGTATTGCATAAGATTACAGTC 57.214 36.000 0.00 0.00 0.00 3.51
32 33 3.773119 GGTGGGTTCACTAATCTGAGGTA 59.227 47.826 0.00 0.00 43.17 3.08
43 44 2.647299 TGTGGAATATGGTGGGTTCACT 59.353 45.455 0.00 0.00 43.17 3.41
52 53 8.906867 CAAGATTTACTCATTGTGGAATATGGT 58.093 33.333 0.00 0.00 0.00 3.55
74 75 7.656137 GCGACCCTAGTTATTTCATAATCAAGA 59.344 37.037 0.00 0.00 0.00 3.02
107 108 7.500559 GTGCTTGGGAGATTGAAATACTTCTAT 59.499 37.037 0.00 0.00 32.33 1.98
111 112 4.706962 GGTGCTTGGGAGATTGAAATACTT 59.293 41.667 0.00 0.00 0.00 2.24
117 118 0.322456 CGGGTGCTTGGGAGATTGAA 60.322 55.000 0.00 0.00 0.00 2.69
118 119 1.198094 TCGGGTGCTTGGGAGATTGA 61.198 55.000 0.00 0.00 0.00 2.57
153 154 7.341512 TCCATTGGTGCAATAATGAAGACAATA 59.658 33.333 20.07 0.00 36.61 1.90
164 165 2.311542 AGGAGGTCCATTGGTGCAATAA 59.688 45.455 1.86 0.00 38.89 1.40
166 167 0.706433 AGGAGGTCCATTGGTGCAAT 59.294 50.000 1.86 0.00 38.89 3.56
171 172 1.384191 GCCAAGGAGGTCCATTGGT 59.616 57.895 19.82 0.00 41.85 3.67
197 198 3.079578 AGTCTGATGTGAGGTTTGCATG 58.920 45.455 0.00 0.00 0.00 4.06
198 199 3.430042 AGTCTGATGTGAGGTTTGCAT 57.570 42.857 0.00 0.00 0.00 3.96
205 206 4.248859 CAACCTTGTAGTCTGATGTGAGG 58.751 47.826 0.00 0.00 0.00 3.86
207 208 4.955811 ACAACCTTGTAGTCTGATGTGA 57.044 40.909 0.00 0.00 40.16 3.58
210 211 3.753272 CCCAACAACCTTGTAGTCTGATG 59.247 47.826 0.00 0.00 41.31 3.07
217 218 3.254903 GGTTTAGCCCAACAACCTTGTAG 59.745 47.826 0.00 0.00 41.31 2.74
252 253 1.259316 GTTGCCGATTGCGAATGTTC 58.741 50.000 0.00 0.00 45.60 3.18
253 254 0.109319 GGTTGCCGATTGCGAATGTT 60.109 50.000 0.00 0.00 45.60 2.71
260 261 1.539827 AGTAAAGTGGTTGCCGATTGC 59.460 47.619 0.00 0.00 41.77 3.56
278 279 6.058183 GCAAATGTCATCCTCCACTATAAGT 58.942 40.000 0.00 0.00 0.00 2.24
282 283 3.134623 TCGCAAATGTCATCCTCCACTAT 59.865 43.478 0.00 0.00 0.00 2.12
332 637 4.811557 GCTAGTCTGAACATTATCACCCAC 59.188 45.833 0.00 0.00 0.00 4.61
333 638 4.469586 TGCTAGTCTGAACATTATCACCCA 59.530 41.667 0.00 0.00 0.00 4.51
340 645 5.428253 GAACCCATGCTAGTCTGAACATTA 58.572 41.667 0.00 0.00 0.00 1.90
419 726 1.883084 GCGAACACTCCCATAGCCG 60.883 63.158 0.00 0.00 0.00 5.52
427 734 0.670854 GAACTCCCAGCGAACACTCC 60.671 60.000 0.00 0.00 0.00 3.85
435 742 2.269241 GGGAAGGAACTCCCAGCG 59.731 66.667 3.70 0.00 29.81 5.18
443 750 3.559655 GCAAACATTTGTTGGGAAGGAAC 59.440 43.478 6.24 0.00 40.24 3.62
446 753 2.158842 TGGCAAACATTTGTTGGGAAGG 60.159 45.455 6.24 0.00 40.24 3.46
459 766 4.215399 GTCAGTAATGCTAACTGGCAAACA 59.785 41.667 11.66 0.00 46.47 2.83
466 773 2.279136 GCGACGTCAGTAATGCTAACTG 59.721 50.000 17.16 7.17 44.66 3.16
468 775 1.252015 CGCGACGTCAGTAATGCTAAC 59.748 52.381 17.16 0.00 0.00 2.34
634 942 1.124462 CTGTCAAGCTATACGCGAGC 58.876 55.000 15.93 12.43 45.59 5.03
949 1258 2.281553 GATTCCCCCGCCGATTCC 60.282 66.667 0.00 0.00 0.00 3.01
1310 1619 3.479269 CGACGGACTCGGCTTTGC 61.479 66.667 0.00 0.00 43.49 3.68
1312 1621 1.153823 CATCGACGGACTCGGCTTT 60.154 57.895 0.00 0.00 43.49 3.51
1316 1625 1.374343 TTCCTCATCGACGGACTCGG 61.374 60.000 0.00 0.00 43.16 4.63
1546 1855 1.558756 CTTGAGCTCCTCCACCTCATT 59.441 52.381 12.15 0.00 35.72 2.57
1654 1963 1.759445 CTCCACCTCCTCGTCATCATT 59.241 52.381 0.00 0.00 0.00 2.57
1729 2038 2.348411 ACCCCCGCATTCTTATCAAG 57.652 50.000 0.00 0.00 0.00 3.02
1752 2061 4.526970 TGAAGACAGAATTATTCCCAGGC 58.473 43.478 0.78 0.00 0.00 4.85
1788 2097 4.012895 ACTTGTTGGCGCGCGAAG 62.013 61.111 37.18 28.17 0.00 3.79
2078 2387 3.077556 CTAGCCGCCCACTGTCCT 61.078 66.667 0.00 0.00 0.00 3.85
2215 2524 8.988064 ATAGTATAGCAAATATCAACCGAGTG 57.012 34.615 0.00 0.00 0.00 3.51
2291 2600 4.092091 CAGGAGAAGTACGAACAGATTTGC 59.908 45.833 0.00 0.00 0.00 3.68
2302 2611 3.510388 TCAGCAATCAGGAGAAGTACG 57.490 47.619 0.00 0.00 0.00 3.67
2331 2640 8.964476 TGAACCTAGATCAATAAAGATCCAAC 57.036 34.615 0.00 0.00 44.32 3.77
2453 2762 5.689514 CCAGTTGACAAAACGAAATTATGCA 59.310 36.000 0.00 0.00 0.00 3.96
2644 2954 5.012239 ACATGTCATGCTGGTGAAATAACT 58.988 37.500 12.91 0.00 0.00 2.24
2705 3016 5.069516 ACCAGTTTCAAATGATTCTGCAACT 59.930 36.000 0.00 1.69 0.00 3.16
2737 3048 6.259608 CCTTTAACTGCATAGGAACATCTCAG 59.740 42.308 0.00 0.00 0.00 3.35
2769 3085 1.404717 GCATCAGAGAAGCTTCGACCA 60.405 52.381 20.43 7.19 0.00 4.02
2863 3179 4.293415 CTCATCTTGTTTTGTGCACCTTC 58.707 43.478 15.69 3.00 0.00 3.46
2900 3216 4.439289 GCAACTGTAATGATTGCCTCCTTC 60.439 45.833 0.00 0.00 42.32 3.46
2913 3229 6.360370 TCCTCTAAGAGTTGCAACTGTAAT 57.640 37.500 35.67 19.97 39.88 1.89
3088 3404 3.838244 TGCCTAGGTATGTTGTGATCC 57.162 47.619 11.31 0.00 0.00 3.36
3268 3584 5.291971 CATCTCCCCAAAAGAAACAAACAG 58.708 41.667 0.00 0.00 0.00 3.16
3414 3730 4.687948 CACGGTATCATAATCAAGCTCTGG 59.312 45.833 0.00 0.00 0.00 3.86
3444 3760 1.073763 ACTGCAACAGCCTGGTATCAA 59.926 47.619 0.00 0.00 34.37 2.57
3459 3775 2.689471 AGTTCTGCAAAATGACACTGCA 59.311 40.909 8.07 8.07 43.54 4.41
3503 3944 1.680735 TCCATTGTGCAAAGTGTGGTC 59.319 47.619 0.00 0.00 0.00 4.02
3504 3945 1.408702 GTCCATTGTGCAAAGTGTGGT 59.591 47.619 0.00 0.00 0.00 4.16
3505 3946 1.682854 AGTCCATTGTGCAAAGTGTGG 59.317 47.619 0.00 0.00 0.00 4.17
3507 3948 3.550820 TGTAGTCCATTGTGCAAAGTGT 58.449 40.909 0.00 0.00 0.00 3.55
3763 5096 6.801862 GCTAAGGTCATGAAACAAACATACAC 59.198 38.462 0.00 0.00 0.00 2.90
3774 5107 4.826733 ACACACAATGCTAAGGTCATGAAA 59.173 37.500 0.00 0.00 0.00 2.69
3816 5161 0.387565 ATCCAAACCAAACACCACGC 59.612 50.000 0.00 0.00 0.00 5.34
3913 5258 4.261801 AGAATGACAATGGAACCTTACGG 58.738 43.478 0.00 0.00 0.00 4.02
3997 5349 4.246458 AGATACTTTGCCAAGAGAACGAC 58.754 43.478 4.25 0.00 33.72 4.34


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

AutoCloner maintained by Alex Coulton.