Multiple sequence alignment - TraesCS2B01G067900

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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 TraesCS2B01G067900 chr2B 100.000 3114 0 0 1 3114 34474468 34477581 0.000000e+00 5751.0
1 TraesCS2B01G067900 chr2B 94.067 2545 124 10 581 3114 34453556 34456084 0.000000e+00 3838.0
2 TraesCS2B01G067900 chr2B 93.690 2298 114 13 371 2658 34434148 34436424 0.000000e+00 3411.0
3 TraesCS2B01G067900 chr2B 97.044 778 23 0 931 1708 34539340 34540117 0.000000e+00 1310.0
4 TraesCS2B01G067900 chr2B 95.491 377 15 1 170 544 34453180 34453556 4.440000e-168 601.0
5 TraesCS2B01G067900 chr2B 95.213 376 16 1 171 544 34538708 34539083 7.440000e-166 593.0
6 TraesCS2B01G067900 chr2B 90.782 358 32 1 2299 2656 34542447 34542803 7.810000e-131 477.0
7 TraesCS2B01G067900 chr2B 95.802 262 11 0 581 842 34539083 34539344 1.030000e-114 424.0
8 TraesCS2B01G067900 chr2B 93.776 241 11 3 2876 3114 34441871 34442109 2.950000e-95 359.0
9 TraesCS2B01G067900 chr2B 91.279 172 15 0 2 173 34451218 34451389 5.190000e-58 235.0
10 TraesCS2B01G067900 chr2B 81.221 213 36 3 2887 3096 34418385 34418596 5.340000e-38 169.0
11 TraesCS2B01G067900 chr2B 97.059 68 2 0 1 68 34527296 34527363 7.060000e-22 115.0
12 TraesCS2B01G067900 chr2B 94.118 51 3 0 4 54 34295068 34295118 9.260000e-11 78.7
13 TraesCS2B01G067900 chrUn 89.085 1924 157 22 524 2433 210798586 210800470 0.000000e+00 2340.0
14 TraesCS2B01G067900 chrUn 88.958 1920 167 20 524 2433 154084220 154082336 0.000000e+00 2329.0
15 TraesCS2B01G067900 chrUn 88.929 1924 160 22 524 2433 146914020 146912136 0.000000e+00 2324.0
16 TraesCS2B01G067900 chrUn 88.641 1928 162 25 524 2433 146899048 146897160 0.000000e+00 2294.0
17 TraesCS2B01G067900 chrUn 87.838 1924 156 26 524 2433 147072564 147070705 0.000000e+00 2185.0
18 TraesCS2B01G067900 chrUn 92.552 1383 94 5 1736 3114 146950007 146951384 0.000000e+00 1975.0
19 TraesCS2B01G067900 chrUn 92.408 1383 96 5 1736 3114 233285055 233286432 0.000000e+00 1964.0
20 TraesCS2B01G067900 chrUn 90.789 1064 80 9 1371 2433 252346169 252347215 0.000000e+00 1406.0
21 TraesCS2B01G067900 chrUn 91.116 968 77 5 2151 3114 154145128 154144166 0.000000e+00 1303.0
22 TraesCS2B01G067900 chrUn 85.750 400 32 10 524 910 426721242 426721629 1.740000e-107 399.0
23 TraesCS2B01G067900 chr2A 89.033 1924 158 22 524 2433 22651280 22653164 0.000000e+00 2335.0
24 TraesCS2B01G067900 chr2A 88.981 1924 159 22 524 2433 22618898 22620782 0.000000e+00 2329.0
25 TraesCS2B01G067900 chr2A 88.929 1924 160 23 524 2433 22939668 22937784 0.000000e+00 2324.0
26 TraesCS2B01G067900 chr2A 92.769 1383 91 5 1736 3114 23288587 23289964 0.000000e+00 1991.0
27 TraesCS2B01G067900 chr2A 92.625 1383 93 5 1736 3114 23266524 23267901 0.000000e+00 1980.0
28 TraesCS2B01G067900 chr2A 92.213 1387 95 6 1736 3114 22838665 22837284 0.000000e+00 1951.0
29 TraesCS2B01G067900 chr2A 86.988 830 73 13 524 1340 22664723 22665530 0.000000e+00 902.0


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 TraesCS2B01G067900 chr2B 34474468 34477581 3113 False 5751 5751 100.000000 1 3114 1 chr2B.!!$F5 3113
1 TraesCS2B01G067900 chr2B 34434148 34436424 2276 False 3411 3411 93.690000 371 2658 1 chr2B.!!$F3 2287
2 TraesCS2B01G067900 chr2B 34451218 34456084 4866 False 1558 3838 93.612333 2 3114 3 chr2B.!!$F7 3112
3 TraesCS2B01G067900 chr2B 34538708 34542803 4095 False 701 1310 94.710250 171 2656 4 chr2B.!!$F8 2485
4 TraesCS2B01G067900 chrUn 210798586 210800470 1884 False 2340 2340 89.085000 524 2433 1 chrUn.!!$F2 1909
5 TraesCS2B01G067900 chrUn 154082336 154084220 1884 True 2329 2329 88.958000 524 2433 1 chrUn.!!$R4 1909
6 TraesCS2B01G067900 chrUn 146912136 146914020 1884 True 2324 2324 88.929000 524 2433 1 chrUn.!!$R2 1909
7 TraesCS2B01G067900 chrUn 146897160 146899048 1888 True 2294 2294 88.641000 524 2433 1 chrUn.!!$R1 1909
8 TraesCS2B01G067900 chrUn 147070705 147072564 1859 True 2185 2185 87.838000 524 2433 1 chrUn.!!$R3 1909
9 TraesCS2B01G067900 chrUn 146950007 146951384 1377 False 1975 1975 92.552000 1736 3114 1 chrUn.!!$F1 1378
10 TraesCS2B01G067900 chrUn 233285055 233286432 1377 False 1964 1964 92.408000 1736 3114 1 chrUn.!!$F3 1378
11 TraesCS2B01G067900 chrUn 252346169 252347215 1046 False 1406 1406 90.789000 1371 2433 1 chrUn.!!$F4 1062
12 TraesCS2B01G067900 chrUn 154144166 154145128 962 True 1303 1303 91.116000 2151 3114 1 chrUn.!!$R5 963
13 TraesCS2B01G067900 chr2A 22651280 22653164 1884 False 2335 2335 89.033000 524 2433 1 chr2A.!!$F2 1909
14 TraesCS2B01G067900 chr2A 22618898 22620782 1884 False 2329 2329 88.981000 524 2433 1 chr2A.!!$F1 1909
15 TraesCS2B01G067900 chr2A 22937784 22939668 1884 True 2324 2324 88.929000 524 2433 1 chr2A.!!$R2 1909
16 TraesCS2B01G067900 chr2A 23288587 23289964 1377 False 1991 1991 92.769000 1736 3114 1 chr2A.!!$F5 1378
17 TraesCS2B01G067900 chr2A 23266524 23267901 1377 False 1980 1980 92.625000 1736 3114 1 chr2A.!!$F4 1378
18 TraesCS2B01G067900 chr2A 22837284 22838665 1381 True 1951 1951 92.213000 1736 3114 1 chr2A.!!$R1 1378
19 TraesCS2B01G067900 chr2A 22664723 22665530 807 False 902 902 86.988000 524 1340 1 chr2A.!!$F3 816

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
198 1993 0.388659 CTGAGCTCGCTGGCTAGAAT 59.611 55.0 9.64 0.00 43.20 2.40 F
416 2211 0.598065 AAAAAGCAGCATGGGACGTC 59.402 50.0 7.13 7.13 35.86 4.34 F
1770 5293 0.178967 TGCAAGGCTGGATCCAACAA 60.179 50.0 17.00 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 2978 1.065358 TGAAAATCTCGAACCGACGC 58.935 50.000 0.0 0.0 0.0 5.19 R
1773 5296 1.112315 AAAGCCGGTGATGGTTGCAA 61.112 50.000 1.9 0.0 0.0 4.08 R
2585 6149 4.746535 TTGTCATCGCCTATCACCTTAA 57.253 40.909 0.0 0.0 0.0 1.85 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
31 32 3.131577 GGCAATGAAATCAGCTCCATGAA 59.868 43.478 0.00 0.00 31.76 2.57
34 35 5.221263 GCAATGAAATCAGCTCCATGAAGAT 60.221 40.000 0.00 0.00 31.76 2.40
56 57 8.110860 AGATGGTATATTTGGAAATAAAGGCG 57.889 34.615 0.00 0.00 34.79 5.52
59 60 6.263617 TGGTATATTTGGAAATAAAGGCGACC 59.736 38.462 0.00 0.00 34.79 4.79
78 79 9.623000 AGGCGACCTTTACTAAATATGTTTTAT 57.377 29.630 0.00 0.00 0.00 1.40
79 80 9.659830 GGCGACCTTTACTAAATATGTTTTATG 57.340 33.333 0.00 0.00 0.00 1.90
141 142 7.928167 AGAATCGATACATTTGTAAGAGCATCA 59.072 33.333 0.00 0.00 32.07 3.07
148 149 4.481930 TTTGTAAGAGCATCAACAACCG 57.518 40.909 0.00 0.00 41.10 4.44
156 157 1.401018 GCATCAACAACCGCAAGTACC 60.401 52.381 0.00 0.00 0.00 3.34
160 161 1.533731 CAACAACCGCAAGTACCGAAT 59.466 47.619 0.00 0.00 0.00 3.34
161 162 1.435577 ACAACCGCAAGTACCGAATC 58.564 50.000 0.00 0.00 0.00 2.52
198 1993 0.388659 CTGAGCTCGCTGGCTAGAAT 59.611 55.000 9.64 0.00 43.20 2.40
280 2075 2.962421 GCTCCAACCATCTAGTCTAGCT 59.038 50.000 1.60 0.00 0.00 3.32
303 2098 2.325583 TTGAATCGATACCTGCCCAC 57.674 50.000 0.00 0.00 0.00 4.61
314 2109 1.741770 CTGCCCACGCCTGTAGTTC 60.742 63.158 0.00 0.00 0.00 3.01
353 2148 8.406172 GAGAGTTCAATCTCAGTTGATACTTC 57.594 38.462 0.00 0.00 44.32 3.01
358 2153 8.865001 GTTCAATCTCAGTTGATACTTCTGTAC 58.135 37.037 0.00 0.00 37.88 2.90
369 2164 9.769093 GTTGATACTTCTGTACGCAAAATTATT 57.231 29.630 0.00 0.00 32.17 1.40
416 2211 0.598065 AAAAAGCAGCATGGGACGTC 59.402 50.000 7.13 7.13 35.86 4.34
466 2261 9.970395 CTTGTTGAATTGTATATGCCACATTAT 57.030 29.630 0.00 0.00 0.00 1.28
856 2670 2.960170 ACGCACCGTGTCTCCTAC 59.040 61.111 0.00 0.00 39.18 3.18
895 2709 8.807118 CATGACACTATATATACCACCAAGTCT 58.193 37.037 0.00 0.00 0.00 3.24
916 2730 4.119136 CTCATCCAACAAACCAAACCAAC 58.881 43.478 0.00 0.00 0.00 3.77
917 2731 3.515502 TCATCCAACAAACCAAACCAACA 59.484 39.130 0.00 0.00 0.00 3.33
918 2732 3.320673 TCCAACAAACCAAACCAACAC 57.679 42.857 0.00 0.00 0.00 3.32
919 2733 2.900546 TCCAACAAACCAAACCAACACT 59.099 40.909 0.00 0.00 0.00 3.55
920 2734 4.087182 TCCAACAAACCAAACCAACACTA 58.913 39.130 0.00 0.00 0.00 2.74
921 2735 4.712337 TCCAACAAACCAAACCAACACTAT 59.288 37.500 0.00 0.00 0.00 2.12
922 2736 5.892119 TCCAACAAACCAAACCAACACTATA 59.108 36.000 0.00 0.00 0.00 1.31
923 2737 6.551601 TCCAACAAACCAAACCAACACTATAT 59.448 34.615 0.00 0.00 0.00 0.86
924 2738 7.724506 TCCAACAAACCAAACCAACACTATATA 59.275 33.333 0.00 0.00 0.00 0.86
929 2743 9.997482 CAAACCAAACCAACACTATATATACAC 57.003 33.333 0.00 0.00 0.00 2.90
1377 3191 3.243035 TGAGTTTTGATGTTGTTCCAGCG 60.243 43.478 0.00 0.00 0.00 5.18
1603 3417 2.973945 ACCGGCAAGTTAATCTCACTC 58.026 47.619 0.00 0.00 0.00 3.51
1642 3456 3.667360 TGACTGTGATGTTCATGGTGAG 58.333 45.455 0.00 0.00 0.00 3.51
1770 5293 0.178967 TGCAAGGCTGGATCCAACAA 60.179 50.000 17.00 0.00 0.00 2.83
1773 5296 2.173519 CAAGGCTGGATCCAACAATGT 58.826 47.619 17.00 0.00 0.00 2.71
2017 5544 2.307496 AGAATTCATGGGGCACAACA 57.693 45.000 8.44 0.00 0.00 3.33
2368 5930 6.655078 AAACATTTGGCTATGTCAAGAGTT 57.345 33.333 6.34 0.00 37.76 3.01
2433 5996 8.038351 CGGGTCTTTTTGGTATTTATTGGAATT 58.962 33.333 0.00 0.00 0.00 2.17
2482 6045 5.551233 CATCCTACGGGTGATTTGTATCAT 58.449 41.667 0.00 0.00 42.49 2.45
2522 6086 5.812127 GCACTATTTCAATTGAACCAATCCC 59.188 40.000 20.35 3.67 32.43 3.85
2585 6149 4.235353 GCCTAACGCATGACACCTTATGT 61.235 47.826 0.00 0.00 40.47 2.29
2758 6322 5.523438 TTAGGCATTCCGTTTCAACTTTT 57.477 34.783 0.00 0.00 37.47 2.27
2773 6337 9.445786 GTTTCAACTTTTCGTATGAAATCAAGA 57.554 29.630 10.85 5.30 43.32 3.02
2838 6403 6.846350 CGAAGCACTTTTAGGATGAAAAGAT 58.154 36.000 13.93 0.00 45.41 2.40
2895 6461 8.974060 AAGTATTTATCATGTGGAACGGTAAT 57.026 30.769 0.00 0.00 42.39 1.89
3109 6678 4.589908 AGAATTGTACCACTGGAATCACC 58.410 43.478 0.71 0.00 39.54 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 7.942341 TCGCCTTTATTTCCAAATATACCATCT 59.058 33.333 0.00 0.00 31.47 2.90
34 35 6.263617 GGTCGCCTTTATTTCCAAATATACCA 59.736 38.462 0.00 0.00 31.47 3.25
78 79 9.202273 GGCATTTTAATTTACAAGTCATCAACA 57.798 29.630 0.00 0.00 0.00 3.33
79 80 8.372521 CGGCATTTTAATTTACAAGTCATCAAC 58.627 33.333 0.00 0.00 0.00 3.18
80 81 7.543868 CCGGCATTTTAATTTACAAGTCATCAA 59.456 33.333 0.00 0.00 0.00 2.57
91 92 7.393796 TCTTCTAACACCCGGCATTTTAATTTA 59.606 33.333 0.00 0.00 0.00 1.40
96 97 4.289238 TCTTCTAACACCCGGCATTTTA 57.711 40.909 0.00 0.00 0.00 1.52
102 103 1.134907 TCGATTCTTCTAACACCCGGC 60.135 52.381 0.00 0.00 0.00 6.13
141 142 1.802365 GATTCGGTACTTGCGGTTGTT 59.198 47.619 0.00 0.00 0.00 2.83
148 149 4.553668 GGGGGATTCGGTACTTGC 57.446 61.111 0.00 0.00 0.00 4.01
198 1993 0.918258 TATCAGCACCCAGGCATTCA 59.082 50.000 0.00 0.00 35.83 2.57
280 2075 3.452990 TGGGCAGGTATCGATTCAAACTA 59.547 43.478 1.71 0.00 0.00 2.24
303 2098 2.271800 GACATTGGAGAACTACAGGCG 58.728 52.381 0.00 0.00 0.00 5.52
314 2109 2.751166 ACTCTCAACCGACATTGGAG 57.249 50.000 0.00 0.00 35.09 3.86
353 2148 8.742554 AAGAAGGAAAATAATTTTGCGTACAG 57.257 30.769 0.00 0.00 44.45 2.74
358 2153 7.622048 GCAGGAAAGAAGGAAAATAATTTTGCG 60.622 37.037 0.00 0.00 44.45 4.85
369 2164 5.336531 CGTAGTCTAGCAGGAAAGAAGGAAA 60.337 44.000 0.00 0.00 0.00 3.13
407 2202 1.358152 TTCCCTTTCTGACGTCCCAT 58.642 50.000 14.12 0.00 0.00 4.00
416 2211 8.115490 AGAGTTGTATTGAAATTCCCTTTCTG 57.885 34.615 0.00 0.00 43.14 3.02
509 2306 1.002366 CAAGTAGGCGCTTGCTAGTG 58.998 55.000 11.11 2.58 39.26 2.74
895 2709 3.515502 TGTTGGTTTGGTTTGTTGGATGA 59.484 39.130 0.00 0.00 0.00 2.92
916 2730 7.331934 GGATGGCAAGTGTGTGTATATATAGTG 59.668 40.741 0.00 0.00 0.00 2.74
917 2731 7.235606 AGGATGGCAAGTGTGTGTATATATAGT 59.764 37.037 0.00 0.00 0.00 2.12
918 2732 7.615403 AGGATGGCAAGTGTGTGTATATATAG 58.385 38.462 0.00 0.00 0.00 1.31
919 2733 7.553504 AGGATGGCAAGTGTGTGTATATATA 57.446 36.000 0.00 0.00 0.00 0.86
920 2734 6.439636 AGGATGGCAAGTGTGTGTATATAT 57.560 37.500 0.00 0.00 0.00 0.86
921 2735 5.887214 AGGATGGCAAGTGTGTGTATATA 57.113 39.130 0.00 0.00 0.00 0.86
922 2736 4.778213 AGGATGGCAAGTGTGTGTATAT 57.222 40.909 0.00 0.00 0.00 0.86
923 2737 4.442893 GCTAGGATGGCAAGTGTGTGTATA 60.443 45.833 0.00 0.00 44.73 1.47
924 2738 3.682718 GCTAGGATGGCAAGTGTGTGTAT 60.683 47.826 0.00 0.00 44.73 2.29
1164 2978 1.065358 TGAAAATCTCGAACCGACGC 58.935 50.000 0.00 0.00 0.00 5.19
1377 3191 1.323271 TGGCTCTCCAGTCCATCGTC 61.323 60.000 0.00 0.00 37.47 4.20
1603 3417 2.805099 GTCAACCAACTCTTGCTCTGAG 59.195 50.000 0.00 0.00 37.55 3.35
1642 3456 2.203126 CCCTCGCAGCCTTGATCC 60.203 66.667 0.00 0.00 0.00 3.36
1770 5293 1.876497 GCCGGTGATGGTTGCAACAT 61.876 55.000 29.55 20.24 0.00 2.71
1773 5296 1.112315 AAAGCCGGTGATGGTTGCAA 61.112 50.000 1.90 0.00 0.00 4.08
2017 5544 2.242196 CAAGTACCCATTCTCACCCCAT 59.758 50.000 0.00 0.00 0.00 4.00
2405 5968 6.151480 TCCAATAAATACCAAAAAGACCCGAC 59.849 38.462 0.00 0.00 0.00 4.79
2433 5996 8.303876 GCCTCCAATTTTCAGTTAAGACATTAA 58.696 33.333 0.00 0.00 0.00 1.40
2510 6074 2.392662 TGTTGCAAGGGATTGGTTCAA 58.607 42.857 0.00 0.00 0.00 2.69
2515 6079 3.967332 AATCTTGTTGCAAGGGATTGG 57.033 42.857 15.90 0.00 0.00 3.16
2522 6086 6.044682 AGTTTCCTCAAAATCTTGTTGCAAG 58.955 36.000 0.00 2.71 33.94 4.01
2585 6149 4.746535 TTGTCATCGCCTATCACCTTAA 57.253 40.909 0.00 0.00 0.00 1.85
2599 6163 7.798596 ACATAATGATGTCTCCTTTGTCATC 57.201 36.000 0.00 0.00 43.01 2.92
2746 6310 7.830217 TGATTTCATACGAAAAGTTGAAACG 57.170 32.000 0.00 0.00 44.12 3.60
2793 6357 9.398170 GCTTCGCATACATATTTTGATTGTTAT 57.602 29.630 0.00 0.00 0.00 1.89
2794 6358 8.401709 TGCTTCGCATACATATTTTGATTGTTA 58.598 29.630 0.00 0.00 31.71 2.41


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

AutoCloner maintained by Alex Coulton.