Multiple sequence alignment - TraesCS2B01G056600

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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 TraesCS2B01G056600 chr2B 100.000 3210 0 0 1 3210 27621658 27618449 0.000000e+00 5928.0
1 TraesCS2B01G056600 chr2B 94.831 2844 108 14 363 3199 27585042 27582231 0.000000e+00 4401.0
2 TraesCS2B01G056600 chr2B 86.375 1622 199 14 1141 2752 27546846 27545237 0.000000e+00 1751.0
3 TraesCS2B01G056600 chr2B 86.450 369 34 11 285 649 27548494 27548138 1.080000e-104 390.0
4 TraesCS2B01G056600 chr2B 88.889 126 13 1 1 125 27585165 27585040 1.540000e-33 154.0
5 TraesCS2B01G056600 chr2B 92.771 83 5 1 5 86 27548578 27548496 5.630000e-23 119.0
6 TraesCS2B01G056600 chr2A 87.403 2699 256 41 120 2753 17416249 17413570 0.000000e+00 3024.0
7 TraesCS2B01G056600 chr2A 91.679 2067 148 8 1141 3199 17427378 17425328 0.000000e+00 2843.0
8 TraesCS2B01G056600 chr2A 83.817 2138 263 40 674 2753 17536728 17534616 0.000000e+00 1954.0
9 TraesCS2B01G056600 chr2A 86.128 1622 207 10 1141 2752 17551562 17549949 0.000000e+00 1733.0
10 TraesCS2B01G056600 chr2A 85.642 1588 195 18 1180 2752 17505122 17503553 0.000000e+00 1639.0
11 TraesCS2B01G056600 chr2A 81.211 2065 281 48 765 2752 17544018 17541984 0.000000e+00 1565.0
12 TraesCS2B01G056600 chr2A 89.671 881 85 1 2319 3199 17599601 17598727 0.000000e+00 1118.0
13 TraesCS2B01G056600 chr2A 82.968 593 61 22 99 666 17506220 17505643 1.720000e-137 499.0
14 TraesCS2B01G056600 chr2A 88.949 371 31 6 121 483 17538221 17537853 1.760000e-122 449.0
15 TraesCS2B01G056600 chr2A 88.926 298 33 0 2902 3199 17503439 17503142 5.060000e-98 368.0
16 TraesCS2B01G056600 chr2A 88.926 298 32 1 2902 3199 17549835 17549539 1.820000e-97 366.0
17 TraesCS2B01G056600 chr2A 83.820 377 43 15 299 671 17553763 17553401 3.070000e-90 342.0
18 TraesCS2B01G056600 chr2A 87.291 299 36 2 2902 3199 17475282 17474985 1.100000e-89 340.0
19 TraesCS2B01G056600 chr2A 81.922 437 46 18 79 490 17428393 17427965 3.970000e-89 339.0
20 TraesCS2B01G056600 chr2A 89.820 167 14 3 106 270 17553991 17553826 9.020000e-51 211.0
21 TraesCS2B01G056600 chr2A 88.750 160 14 2 507 666 17536942 17536787 3.270000e-45 193.0
22 TraesCS2B01G056600 chr2A 86.391 169 20 3 923 1090 17505328 17505162 7.070000e-42 182.0
23 TraesCS2B01G056600 chr2A 92.754 69 4 1 5 72 703288186 703288118 7.330000e-17 99.0
24 TraesCS2B01G056600 chr2D 86.340 1735 206 13 1032 2753 15474392 15472676 0.000000e+00 1862.0
25 TraesCS2B01G056600 chr2D 84.924 1718 208 27 838 2525 15460561 15458865 0.000000e+00 1690.0
26 TraesCS2B01G056600 chr2D 81.954 870 144 8 2320 3187 15517291 15516433 0.000000e+00 725.0
27 TraesCS2B01G056600 chr2D 87.234 376 34 4 295 670 15466335 15465974 1.780000e-112 416.0
28 TraesCS2B01G056600 chr2D 89.761 293 30 0 2907 3199 15506865 15506573 3.020000e-100 375.0
29 TraesCS2B01G056600 chr2D 88.814 295 33 0 2905 3199 15472560 15472266 2.350000e-96 363.0
30 TraesCS2B01G056600 chr2D 86.306 314 34 4 353 666 15456576 15456272 1.850000e-87 333.0
31 TraesCS2B01G056600 chr2D 88.608 158 13 3 106 258 15495467 15495310 1.520000e-43 187.0
32 TraesCS2B01G056600 chr1D 96.923 65 2 0 1 65 299894938 299895002 3.390000e-20 110.0
33 TraesCS2B01G056600 chr7D 98.361 61 1 0 5 65 148116770 148116710 1.220000e-19 108.0
34 TraesCS2B01G056600 chr7B 94.286 70 3 1 5 73 745413183 745413114 4.380000e-19 106.0
35 TraesCS2B01G056600 chr5D 94.203 69 4 0 5 73 550371080 550371012 4.380000e-19 106.0
36 TraesCS2B01G056600 chr1A 95.385 65 3 0 1 65 474387537 474387473 1.580000e-18 104.0
37 TraesCS2B01G056600 chr4A 91.667 72 3 3 1 70 546550669 546550739 2.640000e-16 97.1


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 TraesCS2B01G056600 chr2B 27618449 27621658 3209 True 5928.000000 5928 100.00000 1 3210 1 chr2B.!!$R1 3209
1 TraesCS2B01G056600 chr2B 27582231 27585165 2934 True 2277.500000 4401 91.86000 1 3199 2 chr2B.!!$R3 3198
2 TraesCS2B01G056600 chr2B 27545237 27548578 3341 True 753.333333 1751 88.53200 5 2752 3 chr2B.!!$R2 2747
3 TraesCS2B01G056600 chr2A 17413570 17416249 2679 True 3024.000000 3024 87.40300 120 2753 1 chr2A.!!$R1 2633
4 TraesCS2B01G056600 chr2A 17425328 17428393 3065 True 1591.000000 2843 86.80050 79 3199 2 chr2A.!!$R5 3120
5 TraesCS2B01G056600 chr2A 17598727 17599601 874 True 1118.000000 1118 89.67100 2319 3199 1 chr2A.!!$R3 880
6 TraesCS2B01G056600 chr2A 17534616 17544018 9402 True 1040.250000 1954 85.68175 121 2753 4 chr2A.!!$R7 2632
7 TraesCS2B01G056600 chr2A 17503142 17506220 3078 True 672.000000 1639 85.98175 99 3199 4 chr2A.!!$R6 3100
8 TraesCS2B01G056600 chr2A 17549539 17553991 4452 True 663.000000 1733 87.17350 106 3199 4 chr2A.!!$R8 3093
9 TraesCS2B01G056600 chr2D 15472266 15474392 2126 True 1112.500000 1862 87.57700 1032 3199 2 chr2D.!!$R6 2167
10 TraesCS2B01G056600 chr2D 15456272 15460561 4289 True 1011.500000 1690 85.61500 353 2525 2 chr2D.!!$R5 2172
11 TraesCS2B01G056600 chr2D 15516433 15517291 858 True 725.000000 725 81.95400 2320 3187 1 chr2D.!!$R4 867

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
433 6176 1.066914 CTGCTTCTCAAGACTGACGC 58.933 55.00 0.0 0.0 0.0 5.19 F
487 6230 3.255395 TGACGGAATGACATGCAACAAAT 59.745 39.13 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1472 10293 1.877680 CGCGGATGCTCCAAATCCATA 60.878 52.381 0.0 0.0 43.33 2.74 R
2388 11244 2.198827 TGGAACATGCCAACTGGTAG 57.801 50.000 0.0 0.0 34.31 3.18 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
86 88 4.788617 AGATACCTCCCTACAACATGGTTT 59.211 41.667 0.00 0.00 0.00 3.27
92 94 5.050126 TCCCTACAACATGGTTTACAACA 57.950 39.130 0.00 0.00 0.00 3.33
135 5813 1.227853 GTGAGGTTGCCCTGACGTT 60.228 57.895 0.00 0.00 42.86 3.99
200 5882 1.227943 GCACCACTGAACTGGCTCA 60.228 57.895 0.00 0.00 34.20 4.26
215 5898 6.869206 ACTGGCTCAGTTTTCTATTACCTA 57.131 37.500 2.38 0.00 42.59 3.08
277 6004 4.858935 TGATGTTTTTAACAGTCTGCAGC 58.141 39.130 9.47 4.26 45.95 5.25
336 6064 7.603404 GCAATTTTTGGCTATATGATAATGGCA 59.397 33.333 0.00 0.00 35.22 4.92
433 6176 1.066914 CTGCTTCTCAAGACTGACGC 58.933 55.000 0.00 0.00 0.00 5.19
448 6191 3.948473 ACTGACGCGATATAGCCTGATAT 59.052 43.478 15.93 0.00 0.00 1.63
449 6192 5.123936 ACTGACGCGATATAGCCTGATATA 58.876 41.667 15.93 0.00 0.00 0.86
450 6193 5.589050 ACTGACGCGATATAGCCTGATATAA 59.411 40.000 15.93 0.00 0.00 0.98
487 6230 3.255395 TGACGGAATGACATGCAACAAAT 59.745 39.130 0.00 0.00 0.00 2.32
491 6234 6.219473 ACGGAATGACATGCAACAAATTAAA 58.781 32.000 0.00 0.00 0.00 1.52
492 6235 6.365789 ACGGAATGACATGCAACAAATTAAAG 59.634 34.615 0.00 0.00 0.00 1.85
493 6236 6.365789 CGGAATGACATGCAACAAATTAAAGT 59.634 34.615 0.00 0.00 0.00 2.66
494 6237 7.512297 GGAATGACATGCAACAAATTAAAGTG 58.488 34.615 0.00 0.00 0.00 3.16
699 9278 5.312079 AGCAAAGCTACATCCATATTCCTC 58.688 41.667 0.00 0.00 36.99 3.71
821 9408 7.083875 ACCAACCTGAATCAATTTGTATACG 57.916 36.000 0.00 0.00 0.00 3.06
900 9487 7.823745 AGTGAGGAATGATGTTAACTTGTTT 57.176 32.000 7.22 0.00 0.00 2.83
902 9489 9.003658 AGTGAGGAATGATGTTAACTTGTTTAG 57.996 33.333 7.22 0.00 0.00 1.85
1087 9722 6.210185 TCCTACTTCGGTTTCTTTAGCTACTT 59.790 38.462 0.00 0.00 0.00 2.24
1203 10001 9.349713 AGTTATCACTCACTTCCATGTTTTTAA 57.650 29.630 0.00 0.00 0.00 1.52
1235 10033 6.863126 CACTTGGTCCTTGCTTTAATTTGTAG 59.137 38.462 0.00 0.00 0.00 2.74
1472 10293 2.503356 CTGATCTACTTCAAGGGCTGGT 59.497 50.000 0.00 0.00 0.00 4.00
2061 10900 7.274468 CGATGATATAAGCCACAAGATAGTCAC 59.726 40.741 0.00 0.00 0.00 3.67
2363 11219 5.183969 TCATTCTTCCTTTCTGCAGATGAG 58.816 41.667 19.04 17.60 0.00 2.90
2388 11244 6.751888 GCCACCAAGAAATACAACATCAATAC 59.248 38.462 0.00 0.00 0.00 1.89
2390 11246 9.173021 CCACCAAGAAATACAACATCAATACTA 57.827 33.333 0.00 0.00 0.00 1.82
2456 11312 3.679502 TGTTACATCTGTCTCATTGCACG 59.320 43.478 0.00 0.00 0.00 5.34
2525 11381 0.392863 TCCATCTGGACCATTGCACG 60.393 55.000 0.00 0.00 39.78 5.34
2543 11399 3.796717 GCACGAATATCACAGACGATGAA 59.203 43.478 0.00 0.00 0.00 2.57
2571 11427 3.640498 TCCAAGCCACAATGAAAACATGA 59.360 39.130 0.00 0.00 0.00 3.07
2594 11450 5.393866 ACATGTTTCCAGAAGTTATGGGTT 58.606 37.500 16.37 0.00 38.44 4.11
3069 11934 1.873591 CAGTGAAAACCCTTGACCTCG 59.126 52.381 0.00 0.00 0.00 4.63
3075 11940 1.657804 AACCCTTGACCTCGGAGAAT 58.342 50.000 6.58 0.00 34.09 2.40
3096 11961 3.876309 TGGAAGCTCCAAACCTAAAGT 57.124 42.857 2.78 0.00 45.00 2.66
3099 11964 3.889538 GGAAGCTCCAAACCTAAAGTGTT 59.110 43.478 0.00 0.00 36.28 3.32
3104 11969 6.303839 AGCTCCAAACCTAAAGTGTTTCATA 58.696 36.000 0.00 0.00 33.82 2.15
3117 11982 0.038021 TTTCATACTGCTGGGCTGCA 59.962 50.000 0.50 5.71 41.05 4.41
3166 12031 2.618709 CGGAAGATAAAAGGACATGGGC 59.381 50.000 0.00 0.00 0.00 5.36
3167 12032 2.618709 GGAAGATAAAAGGACATGGGCG 59.381 50.000 0.00 0.00 0.00 6.13
3199 12064 0.448990 CACATCAGCACCGTCCAATG 59.551 55.000 0.00 0.00 0.00 2.82
3200 12065 0.324614 ACATCAGCACCGTCCAATGA 59.675 50.000 0.00 0.00 0.00 2.57
3201 12066 0.729116 CATCAGCACCGTCCAATGAC 59.271 55.000 0.00 0.00 38.18 3.06
3202 12067 0.324614 ATCAGCACCGTCCAATGACA 59.675 50.000 0.00 0.00 41.85 3.58
3203 12068 0.320683 TCAGCACCGTCCAATGACAG 60.321 55.000 0.00 0.00 41.85 3.51
3204 12069 1.672356 AGCACCGTCCAATGACAGC 60.672 57.895 0.00 0.00 41.85 4.40
3205 12070 1.672356 GCACCGTCCAATGACAGCT 60.672 57.895 0.00 0.00 41.85 4.24
3206 12071 1.237285 GCACCGTCCAATGACAGCTT 61.237 55.000 0.00 0.00 41.85 3.74
3209 12074 1.361668 CCGTCCAATGACAGCTTCCG 61.362 60.000 0.00 0.00 41.85 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 5.489637 TGTAAACCATGTTGTAGGGAGGTAT 59.510 40.000 0.00 0.00 33.45 2.73
92 94 2.037772 AGTCAAGCCAACGTCTTCTGAT 59.962 45.455 0.00 0.00 0.00 2.90
135 5813 1.312371 GGCCGCCTCATTACTTTGCA 61.312 55.000 0.71 0.00 0.00 4.08
158 5836 0.454600 CCACATGTCTGCTTCCATGC 59.545 55.000 0.00 0.00 41.69 4.06
215 5898 7.148035 ACCGTTGTTGTAAAATTAAACCTGACT 60.148 33.333 0.00 0.00 0.00 3.41
277 6004 7.981142 ACCACATATTTTTACCATAGTTGTCG 58.019 34.615 0.00 0.00 0.00 4.35
448 6191 8.670135 CATTCCGTCACATAACCAAGTTATTTA 58.330 33.333 0.00 0.00 36.70 1.40
449 6192 7.392113 TCATTCCGTCACATAACCAAGTTATTT 59.608 33.333 0.00 0.00 36.70 1.40
450 6193 6.882140 TCATTCCGTCACATAACCAAGTTATT 59.118 34.615 0.00 0.00 36.70 1.40
463 6206 1.535028 GTTGCATGTCATTCCGTCACA 59.465 47.619 0.00 0.00 0.00 3.58
464 6207 1.535028 TGTTGCATGTCATTCCGTCAC 59.465 47.619 0.00 0.00 0.00 3.67
471 6214 7.710044 TGTCACTTTAATTTGTTGCATGTCATT 59.290 29.630 0.00 0.00 0.00 2.57
699 9278 6.965592 ATGCAGACATGTGCCTTGAGTAGG 62.966 50.000 1.15 0.00 43.28 3.18
821 9408 9.771534 AGAAGGATTTTACTAATCTGCAGATAC 57.228 33.333 28.92 5.95 33.73 2.24
837 9424 6.472887 TCGTACAGATTTGGAGAAGGATTTT 58.527 36.000 0.00 0.00 0.00 1.82
840 9427 4.712337 ACTCGTACAGATTTGGAGAAGGAT 59.288 41.667 0.00 0.00 0.00 3.24
877 9464 8.784043 ACTAAACAAGTTAACATCATTCCTCAC 58.216 33.333 8.61 0.00 33.35 3.51
900 9487 6.697641 AATTCCTTCCTTTCCTACACACTA 57.302 37.500 0.00 0.00 0.00 2.74
902 9489 6.264518 TGAAAATTCCTTCCTTTCCTACACAC 59.735 38.462 0.00 0.00 0.00 3.82
1014 9645 5.447778 AGATCAAGGTGAGTGATGGATTT 57.552 39.130 0.00 0.00 35.84 2.17
1087 9722 7.681939 AAAAATCAAGATCCAAGTTACGCTA 57.318 32.000 0.00 0.00 0.00 4.26
1472 10293 1.877680 CGCGGATGCTCCAAATCCATA 60.878 52.381 0.00 0.00 43.33 2.74
2363 11219 4.782019 TGATGTTGTATTTCTTGGTGGC 57.218 40.909 0.00 0.00 0.00 5.01
2388 11244 2.198827 TGGAACATGCCAACTGGTAG 57.801 50.000 0.00 0.00 34.31 3.18
2390 11246 3.529948 TTGGAACATGCCAACTGGT 57.470 47.368 1.02 0.00 42.75 4.00
2456 11312 2.489722 GGGAGGAGATGCAAAACTGAAC 59.510 50.000 0.00 0.00 0.00 3.18
2525 11381 5.284864 TGCTCTTCATCGTCTGTGATATTC 58.715 41.667 0.00 0.00 0.00 1.75
2543 11399 1.005097 TCATTGTGGCTTGGATGCTCT 59.995 47.619 0.00 0.00 0.00 4.09
2571 11427 4.998051 ACCCATAACTTCTGGAAACATGT 58.002 39.130 0.00 0.00 41.51 3.21
2594 11450 6.012858 ACCAATCTGTATACCTCAAAACCAGA 60.013 38.462 0.00 0.00 0.00 3.86
2799 11664 1.131883 GTTGAGGAGTGATGCACATGC 59.868 52.381 0.00 0.00 36.74 4.06
2800 11665 2.708051 AGTTGAGGAGTGATGCACATG 58.292 47.619 0.00 0.00 36.74 3.21
2801 11666 3.079578 CAAGTTGAGGAGTGATGCACAT 58.920 45.455 0.00 0.00 36.74 3.21
2802 11667 2.158769 ACAAGTTGAGGAGTGATGCACA 60.159 45.455 10.54 0.00 36.74 4.57
2803 11668 2.481952 GACAAGTTGAGGAGTGATGCAC 59.518 50.000 10.54 0.00 34.10 4.57
3092 11957 2.558359 GCCCAGCAGTATGAAACACTTT 59.442 45.455 0.00 0.00 39.69 2.66
3096 11961 1.825090 CAGCCCAGCAGTATGAAACA 58.175 50.000 0.00 0.00 39.69 2.83
3099 11964 0.038021 TTGCAGCCCAGCAGTATGAA 59.962 50.000 0.00 0.00 46.54 2.57
3104 11969 1.602888 CTTCTTGCAGCCCAGCAGT 60.603 57.895 0.00 0.00 46.54 4.40
3117 11982 4.516698 CCATAATATTGCACGGAGCTTCTT 59.483 41.667 0.00 0.00 45.94 2.52
3166 12031 1.872952 TGATGTGCAACTTCTCCAACG 59.127 47.619 0.00 0.00 41.21 4.10
3167 12032 2.351157 GCTGATGTGCAACTTCTCCAAC 60.351 50.000 0.00 0.00 41.21 3.77


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

AutoCloner maintained by Alex Coulton.