Multiple sequence alignment - TraesCS2A01G472700

Loading Multiple Alignment...

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 TraesCS2A01G472700 chr2A 100.000 3095 0 0 1 3095 714206296 714209390 0.000000e+00 5716.0
1 TraesCS2A01G472700 chr2D 92.986 3037 141 37 83 3095 576190459 576193447 0.000000e+00 4362.0
2 TraesCS2A01G472700 chr2B 91.936 3063 162 50 26 3039 692161283 692164309 0.000000e+00 4209.0
3 TraesCS2A01G472700 chr2B 98.305 59 1 0 3037 3095 692164468 692164526 1.520000e-18 104.0
4 TraesCS2A01G472700 chr2B 80.263 76 15 0 1114 1189 690666757 690666682 1.200000e-04 58.4
5 TraesCS2A01G472700 chr6B 80.370 540 71 19 2215 2744 173816982 173817496 8.100000e-101 377.0
6 TraesCS2A01G472700 chr7B 78.172 536 65 30 2215 2747 171091135 171090649 8.390000e-76 294.0
7 TraesCS2A01G472700 chr1B 80.405 296 38 11 2215 2510 87189660 87189385 1.120000e-49 207.0
8 TraesCS2A01G472700 chr5D 82.101 257 31 7 2215 2471 181607417 181607176 4.050000e-49 206.0
9 TraesCS2A01G472700 chr4A 92.683 82 5 1 2230 2310 20573249 20573330 1.950000e-22 117.0


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 TraesCS2A01G472700 chr2A 714206296 714209390 3094 False 5716.0 5716 100.0000 1 3095 1 chr2A.!!$F1 3094
1 TraesCS2A01G472700 chr2D 576190459 576193447 2988 False 4362.0 4362 92.9860 83 3095 1 chr2D.!!$F1 3012
2 TraesCS2A01G472700 chr2B 692161283 692164526 3243 False 2156.5 4209 95.1205 26 3095 2 chr2B.!!$F1 3069
3 TraesCS2A01G472700 chr6B 173816982 173817496 514 False 377.0 377 80.3700 2215 2744 1 chr6B.!!$F1 529

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
294 336 0.523968 CGCAGGCCATTCGAATTGTG 60.524 55.000 8.21 7.29 0.0 3.33 F
668 730 1.154035 GGCAGGCAATTTCCGTTCG 60.154 57.895 0.00 0.00 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1560 0.169672 TCGAATTGGTCTCGACGTCC 59.830 55.000 10.58 0.0 40.25 4.79 R
2600 2677 1.808945 ACAATTCCTGCAAGAGAAGCG 59.191 47.619 0.00 0.0 34.07 4.68 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
22 23 4.248058 GTTACCGTACCACATATATGGCC 58.752 47.826 16.96 0.00 44.33 5.36
23 24 1.626825 ACCGTACCACATATATGGCCC 59.373 52.381 16.96 0.00 44.33 5.80
24 25 1.906574 CCGTACCACATATATGGCCCT 59.093 52.381 16.96 0.00 44.33 5.19
47 48 9.640952 CCCTTATTACCCTTCAAAAAGATATGA 57.359 33.333 0.00 0.00 34.14 2.15
54 55 6.890268 ACCCTTCAAAAAGATATGACCCTTAC 59.110 38.462 0.00 0.00 34.14 2.34
75 108 9.014297 CCTTACTAACATCAAATCCAGAACTTT 57.986 33.333 0.00 0.00 0.00 2.66
77 110 7.454260 ACTAACATCAAATCCAGAACTTTCC 57.546 36.000 0.00 0.00 0.00 3.13
78 111 5.728637 AACATCAAATCCAGAACTTTCCC 57.271 39.130 0.00 0.00 0.00 3.97
79 112 4.089361 ACATCAAATCCAGAACTTTCCCC 58.911 43.478 0.00 0.00 0.00 4.81
80 113 3.169512 TCAAATCCAGAACTTTCCCCC 57.830 47.619 0.00 0.00 0.00 5.40
81 114 2.448961 TCAAATCCAGAACTTTCCCCCA 59.551 45.455 0.00 0.00 0.00 4.96
82 115 3.116939 TCAAATCCAGAACTTTCCCCCAA 60.117 43.478 0.00 0.00 0.00 4.12
83 116 3.628832 AATCCAGAACTTTCCCCCAAA 57.371 42.857 0.00 0.00 0.00 3.28
84 117 3.628832 ATCCAGAACTTTCCCCCAAAA 57.371 42.857 0.00 0.00 0.00 2.44
85 118 3.406512 TCCAGAACTTTCCCCCAAAAA 57.593 42.857 0.00 0.00 0.00 1.94
144 177 8.825667 TTTGTTCTAGAAAACAATTATTGCCC 57.174 30.769 6.78 0.00 45.70 5.36
145 178 7.531857 TGTTCTAGAAAACAATTATTGCCCA 57.468 32.000 6.78 0.00 36.25 5.36
147 180 8.250332 TGTTCTAGAAAACAATTATTGCCCATC 58.750 33.333 6.78 0.00 36.25 3.51
152 185 6.213195 AGAAAACAATTATTGCCCATCCTCAA 59.787 34.615 4.68 0.00 0.00 3.02
157 193 6.667414 ACAATTATTGCCCATCCTCAAACTAA 59.333 34.615 4.68 0.00 0.00 2.24
173 209 7.858382 CCTCAAACTAATATAGACGTCACTGAG 59.142 40.741 19.50 9.23 0.00 3.35
174 210 8.277490 TCAAACTAATATAGACGTCACTGAGT 57.723 34.615 19.50 9.86 0.00 3.41
176 212 9.435802 CAAACTAATATAGACGTCACTGAGTAC 57.564 37.037 19.50 0.00 0.00 2.73
223 259 3.260884 TGCGGGGAAAGACATATCCTATC 59.739 47.826 0.00 0.00 35.95 2.08
260 298 4.737353 TCATGCATGCATTAATCGAGAC 57.263 40.909 30.32 0.00 33.90 3.36
267 305 5.641209 GCATGCATTAATCGAGACCTATCTT 59.359 40.000 14.21 0.00 34.34 2.40
279 318 5.508200 AGACCTATCTTCTAAAGACGCAG 57.492 43.478 0.00 0.00 41.01 5.18
286 325 2.024176 TCTAAAGACGCAGGCCATTC 57.976 50.000 5.01 0.00 0.00 2.67
294 336 0.523968 CGCAGGCCATTCGAATTGTG 60.524 55.000 8.21 7.29 0.00 3.33
325 367 8.450578 TGCATTAATTGTGTTTCTATCTAGGG 57.549 34.615 0.00 0.00 0.00 3.53
365 407 6.435904 CACCCTCCTATGGAAAGATACTCTAG 59.564 46.154 0.00 0.00 0.00 2.43
366 408 6.335850 ACCCTCCTATGGAAAGATACTCTAGA 59.664 42.308 0.00 0.00 0.00 2.43
486 548 4.717629 CGCACCGCAGAGACCGAA 62.718 66.667 0.00 0.00 0.00 4.30
541 603 2.185350 CTAGGAGCGCACCACCAG 59.815 66.667 26.04 15.02 0.00 4.00
609 671 1.304630 TCCCGGGCTTTAAAAGGGC 60.305 57.895 18.49 3.41 41.76 5.19
668 730 1.154035 GGCAGGCAATTTCCGTTCG 60.154 57.895 0.00 0.00 0.00 3.95
781 844 4.344865 GGCCCAGCTTCCCGTCAA 62.345 66.667 0.00 0.00 0.00 3.18
808 871 2.680370 GGGATTCACTTCCGCCCCT 61.680 63.158 0.00 0.00 36.58 4.79
815 878 3.162154 CTTCCGCCCCTACCTCCC 61.162 72.222 0.00 0.00 0.00 4.30
934 997 2.825836 CCCTGCAATGCCCTCGTC 60.826 66.667 1.53 0.00 0.00 4.20
938 1001 2.125512 GCAATGCCCTCGTCGACT 60.126 61.111 14.70 0.00 0.00 4.18
941 1004 1.982395 AATGCCCTCGTCGACTCCA 60.982 57.895 14.70 3.67 0.00 3.86
943 1006 4.500116 GCCCTCGTCGACTCCAGC 62.500 72.222 14.70 7.82 0.00 4.85
981 1044 2.332104 CTGATAATCATCGGCCTGTCG 58.668 52.381 0.00 0.00 33.51 4.35
1259 1328 2.657143 CTCCGCCTTCCTCTACTACTT 58.343 52.381 0.00 0.00 0.00 2.24
1269 1338 1.400846 CTCTACTACTTCAGCCGCGAA 59.599 52.381 8.23 0.00 0.00 4.70
1305 1374 2.115343 GGTTCACCCTCAACCTGATC 57.885 55.000 0.00 0.00 40.33 2.92
1344 1413 3.113043 GTCCCAGGTAACCAACTCCTAT 58.887 50.000 0.00 0.00 37.17 2.57
1414 1483 4.464244 AGTTCATCGAGAAGTCCAAGATCA 59.536 41.667 0.00 0.00 34.84 2.92
1491 1560 1.672356 CAAAGAGTCCCGCACCCAG 60.672 63.158 0.00 0.00 0.00 4.45
1560 1629 0.813184 ATTTCGGGAACATGCTGCAG 59.187 50.000 10.11 10.11 0.00 4.41
1674 1743 2.821810 GAGCTCTTTGGCCCGCTC 60.822 66.667 6.43 6.31 41.60 5.03
1707 1776 4.118410 CCACAGAGTGCATCAAGATAGAC 58.882 47.826 0.00 0.00 31.34 2.59
1764 1833 3.904339 ACTTCATCTACACAGACACCCTT 59.096 43.478 0.00 0.00 32.25 3.95
1785 1854 3.889815 TCCTGATAACTGCAAAGATGGG 58.110 45.455 0.00 0.00 0.00 4.00
1788 1857 4.706476 CCTGATAACTGCAAAGATGGGAAA 59.294 41.667 0.00 0.00 0.00 3.13
2134 2203 4.040829 CACCTTATCATGGACTGATAGGCA 59.959 45.833 0.00 0.00 45.36 4.75
2668 2746 8.383175 TGTTGACCCTTCATTCTCTTTACTAAT 58.617 33.333 0.00 0.00 0.00 1.73
2719 2798 6.071784 TCCACCTGAATCATTGTGAAAATCAG 60.072 38.462 12.71 10.97 36.38 2.90
2755 2834 7.437862 ACACAATTTTTACACATACAAAGGCAG 59.562 33.333 0.00 0.00 0.00 4.85
2765 2844 5.240623 CACATACAAAGGCAGAAACACCTTA 59.759 40.000 0.00 0.00 45.62 2.69
2766 2845 5.830991 ACATACAAAGGCAGAAACACCTTAA 59.169 36.000 0.00 0.00 45.62 1.85
2775 2854 8.910351 AGGCAGAAACACCTTAATAATATCTC 57.090 34.615 0.00 0.00 29.74 2.75
2875 2955 6.249192 TGTCCCACCATATTTTGTTGTATGA 58.751 36.000 0.00 0.00 31.48 2.15
2879 2959 7.068103 TCCCACCATATTTTGTTGTATGATCAC 59.932 37.037 0.00 0.00 31.48 3.06
2890 2970 4.167652 TGTATGATCACCATTGGCATGA 57.832 40.909 1.54 0.07 36.71 3.07
2911 2991 8.677300 GCATGAATATACCTCTTGAACAGAAAA 58.323 33.333 0.00 0.00 0.00 2.29
2944 3024 3.644738 TCTCTGCAGATGATCATAAGCCA 59.355 43.478 18.63 11.51 0.00 4.75
2986 3066 8.055279 TGAATCAGAAACATATTCCAGAAACC 57.945 34.615 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.248058 GGCCATATATGTGGTACGGTAAC 58.752 47.826 18.66 0.00 41.47 2.50
1 2 3.261390 GGGCCATATATGTGGTACGGTAA 59.739 47.826 18.66 0.00 41.47 2.85
2 3 2.833338 GGGCCATATATGTGGTACGGTA 59.167 50.000 18.66 0.00 41.47 4.02
4 5 1.906574 AGGGCCATATATGTGGTACGG 59.093 52.381 18.66 0.00 41.47 4.02
5 6 3.695830 AAGGGCCATATATGTGGTACG 57.304 47.619 18.66 0.00 41.47 3.67
6 7 7.052248 GGTAATAAGGGCCATATATGTGGTAC 58.948 42.308 18.66 12.23 41.47 3.34
7 8 6.159046 GGGTAATAAGGGCCATATATGTGGTA 59.841 42.308 18.66 4.92 41.47 3.25
8 9 5.044402 GGGTAATAAGGGCCATATATGTGGT 60.044 44.000 18.66 2.84 41.47 4.16
9 10 5.193728 AGGGTAATAAGGGCCATATATGTGG 59.806 44.000 13.91 13.91 42.35 4.17
10 11 6.327386 AGGGTAATAAGGGCCATATATGTG 57.673 41.667 6.18 4.67 0.00 3.21
11 12 6.507485 TGAAGGGTAATAAGGGCCATATATGT 59.493 38.462 6.18 0.00 0.00 2.29
12 13 6.969043 TGAAGGGTAATAAGGGCCATATATG 58.031 40.000 6.18 5.68 0.00 1.78
13 14 7.597850 TTGAAGGGTAATAAGGGCCATATAT 57.402 36.000 6.18 0.00 0.00 0.86
14 15 7.409408 TTTGAAGGGTAATAAGGGCCATATA 57.591 36.000 6.18 0.00 0.00 0.86
15 16 5.941146 TTGAAGGGTAATAAGGGCCATAT 57.059 39.130 6.18 0.00 0.00 1.78
16 17 5.735733 TTTGAAGGGTAATAAGGGCCATA 57.264 39.130 6.18 0.00 0.00 2.74
17 18 4.618378 TTTGAAGGGTAATAAGGGCCAT 57.382 40.909 6.18 0.00 0.00 4.40
18 19 4.405756 TTTTGAAGGGTAATAAGGGCCA 57.594 40.909 6.18 0.00 0.00 5.36
19 20 5.020795 TCTTTTTGAAGGGTAATAAGGGCC 58.979 41.667 0.00 0.00 0.00 5.80
20 21 6.791867 ATCTTTTTGAAGGGTAATAAGGGC 57.208 37.500 0.00 0.00 0.00 5.19
21 22 9.640952 TCATATCTTTTTGAAGGGTAATAAGGG 57.359 33.333 0.00 0.00 0.00 3.95
24 25 9.416284 GGGTCATATCTTTTTGAAGGGTAATAA 57.584 33.333 0.00 0.00 0.00 1.40
47 48 6.636454 TCTGGATTTGATGTTAGTAAGGGT 57.364 37.500 0.00 0.00 0.00 4.34
54 55 6.127619 GGGGAAAGTTCTGGATTTGATGTTAG 60.128 42.308 0.00 0.00 0.00 2.34
127 160 5.721000 TGAGGATGGGCAATAATTGTTTTCT 59.279 36.000 0.00 0.00 0.00 2.52
131 164 5.484998 AGTTTGAGGATGGGCAATAATTGTT 59.515 36.000 0.00 0.00 0.00 2.83
139 172 7.224297 GTCTATATTAGTTTGAGGATGGGCAA 58.776 38.462 0.00 0.00 0.00 4.52
142 175 6.994221 ACGTCTATATTAGTTTGAGGATGGG 58.006 40.000 0.00 0.00 0.00 4.00
143 176 7.595502 GTGACGTCTATATTAGTTTGAGGATGG 59.404 40.741 17.92 0.00 0.00 3.51
144 177 8.353684 AGTGACGTCTATATTAGTTTGAGGATG 58.646 37.037 17.92 0.00 0.00 3.51
145 178 8.353684 CAGTGACGTCTATATTAGTTTGAGGAT 58.646 37.037 17.92 0.00 0.00 3.24
147 180 7.704271 TCAGTGACGTCTATATTAGTTTGAGG 58.296 38.462 17.92 0.00 0.00 3.86
152 185 8.728337 TGTACTCAGTGACGTCTATATTAGTT 57.272 34.615 17.92 0.00 0.00 2.24
157 193 6.535540 AGGATGTACTCAGTGACGTCTATAT 58.464 40.000 17.92 3.27 33.04 0.86
176 212 9.656040 CAGAAAAAGATAGGATGAGATAGGATG 57.344 37.037 0.00 0.00 0.00 3.51
223 259 9.089601 TGCATGCATGATTAATTGTTTTTCTAG 57.910 29.630 30.64 0.00 0.00 2.43
241 279 3.748083 AGGTCTCGATTAATGCATGCAT 58.252 40.909 27.46 27.46 38.46 3.96
260 298 3.385577 GCCTGCGTCTTTAGAAGATAGG 58.614 50.000 10.06 10.06 40.18 2.57
267 305 1.739035 CGAATGGCCTGCGTCTTTAGA 60.739 52.381 3.32 0.00 0.00 2.10
279 318 1.742831 TGCTACACAATTCGAATGGCC 59.257 47.619 12.25 0.00 0.00 5.36
286 325 6.473131 ACAATTAATGCATGCTACACAATTCG 59.527 34.615 20.33 12.59 0.00 3.34
294 336 9.173939 GATAGAAACACAATTAATGCATGCTAC 57.826 33.333 20.33 0.00 0.00 3.58
325 367 2.427095 GAGGGTGCCCATTAATTGTGTC 59.573 50.000 10.26 0.00 38.92 3.67
365 407 2.061773 CTCGTGGGATAATGCATCGTC 58.938 52.381 0.00 0.76 34.12 4.20
366 408 1.686587 TCTCGTGGGATAATGCATCGT 59.313 47.619 0.00 0.00 34.12 3.73
482 544 0.179189 GGCTCGTGATTTGCTTTCGG 60.179 55.000 0.00 0.00 0.00 4.30
486 548 0.036732 TGGAGGCTCGTGATTTGCTT 59.963 50.000 8.69 0.00 0.00 3.91
525 587 4.082523 GCTGGTGGTGCGCTCCTA 62.083 66.667 27.24 12.48 0.00 2.94
609 671 1.020333 TCGGTTTTATTCCGCCCGTG 61.020 55.000 0.00 0.00 46.49 4.94
629 691 2.600470 GTCCAAACCCCTGCCACC 60.600 66.667 0.00 0.00 0.00 4.61
668 730 0.111832 AGAGGAAAACCCCGGAAACC 59.888 55.000 0.73 0.00 34.66 3.27
781 844 3.090532 GTGAATCCCCCTCCCGCT 61.091 66.667 0.00 0.00 0.00 5.52
787 850 2.680370 GGCGGAAGTGAATCCCCCT 61.680 63.158 0.00 0.00 35.00 4.79
789 852 2.124278 GGGCGGAAGTGAATCCCC 60.124 66.667 0.00 0.00 36.00 4.81
933 996 0.541998 TTTCTGGAGGCTGGAGTCGA 60.542 55.000 0.00 0.00 0.00 4.20
934 997 0.390472 GTTTCTGGAGGCTGGAGTCG 60.390 60.000 0.00 0.00 0.00 4.18
938 1001 2.231380 GGGGTTTCTGGAGGCTGGA 61.231 63.158 0.00 0.00 0.00 3.86
941 1004 1.925972 GGAGGGGTTTCTGGAGGCT 60.926 63.158 0.00 0.00 0.00 4.58
943 1006 2.990479 CGGAGGGGTTTCTGGAGG 59.010 66.667 0.00 0.00 0.00 4.30
981 1044 3.803162 GAAGGAGGAGCAGGGGGC 61.803 72.222 0.00 0.00 45.30 5.80
988 1051 1.225704 CACCCATGGAAGGAGGAGC 59.774 63.158 15.22 0.00 0.00 4.70
1259 1328 2.736995 CGTCCTTTTCGCGGCTGA 60.737 61.111 6.13 0.00 0.00 4.26
1269 1338 2.750350 CTGGCCCTGACGTCCTTT 59.250 61.111 14.12 0.00 0.00 3.11
1344 1413 3.430790 CCGGAGAGAATGTGTGCTTCATA 60.431 47.826 0.00 0.00 0.00 2.15
1414 1483 4.083862 GAGGAACGGCGAGCCCTT 62.084 66.667 16.62 3.14 0.00 3.95
1491 1560 0.169672 TCGAATTGGTCTCGACGTCC 59.830 55.000 10.58 0.00 40.25 4.79
1674 1743 2.095364 GCACTCTGTGGCATTTTCTCTG 60.095 50.000 0.00 0.00 33.64 3.35
1707 1776 4.108336 CGAATATCATAGGCTCCATGTCG 58.892 47.826 0.00 0.00 0.00 4.35
1764 1833 3.523157 TCCCATCTTTGCAGTTATCAGGA 59.477 43.478 0.00 0.00 0.00 3.86
2134 2203 6.726490 TCTGAACCAGAGTAAAACAGTACT 57.274 37.500 0.00 0.00 35.39 2.73
2536 2613 8.218488 AGAACTTTCTGGGAGTACTACATTTTT 58.782 33.333 7.57 0.00 35.89 1.94
2537 2614 7.746703 AGAACTTTCTGGGAGTACTACATTTT 58.253 34.615 7.57 0.00 35.89 1.82
2553 2630 5.632034 AAACTCCTGTACCAGAACTTTCT 57.368 39.130 0.00 0.00 38.25 2.52
2600 2677 1.808945 ACAATTCCTGCAAGAGAAGCG 59.191 47.619 0.00 0.00 34.07 4.68
2668 2746 1.248785 GGGCGGTACTCTCACTGTGA 61.249 60.000 10.50 10.50 0.00 3.58
2727 2806 9.418045 GCCTTTGTATGTGTAAAAATTGTGTAT 57.582 29.630 0.00 0.00 0.00 2.29
2857 2937 7.953005 TGGTGATCATACAACAAAATATGGT 57.047 32.000 0.00 0.00 34.39 3.55
2875 2955 5.895807 AGGTATATTCATGCCAATGGTGAT 58.104 37.500 0.00 0.00 39.29 3.06
2879 2959 6.005823 TCAAGAGGTATATTCATGCCAATGG 58.994 40.000 0.00 0.00 39.29 3.16
2911 2991 4.713814 TCATCTGCAGAGAAGTCATTACCT 59.286 41.667 22.96 0.00 0.00 3.08
2944 3024 7.274447 TCTGATTCATTTTTGCTGGTTCTTTT 58.726 30.769 0.00 0.00 0.00 2.27
2986 3066 6.573664 TCACTTGACAGGGAAACATTTATG 57.426 37.500 0.00 0.00 25.02 1.90


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

AutoCloner maintained by Alex Coulton.