Multiple sequence alignment - TraesCS4B01G125200

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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 TraesCS4B01G125200 chr4B 100.000 3183 0 0 1 3183 154114115 154110933 0.000000e+00 5879.0
1 TraesCS4B01G125200 chr4B 86.266 2665 309 38 474 3117 486848441 486845813 0.000000e+00 2841.0
2 TraesCS4B01G125200 chr2B 88.286 2783 282 33 395 3155 295832070 295834830 0.000000e+00 3293.0
3 TraesCS4B01G125200 chr2B 91.048 2033 163 14 1 2021 762705405 762707430 0.000000e+00 2728.0
4 TraesCS4B01G125200 chr2B 87.754 1576 184 8 450 2020 399402674 399401103 0.000000e+00 1832.0
5 TraesCS4B01G125200 chr2B 88.474 1501 158 9 530 2021 545612313 545610819 0.000000e+00 1799.0
6 TraesCS4B01G125200 chr2B 87.522 1138 115 19 2037 3155 570518829 570517700 0.000000e+00 1290.0
7 TraesCS4B01G125200 chr2B 87.522 1138 115 19 2037 3155 570604210 570603081 0.000000e+00 1290.0
8 TraesCS4B01G125200 chr2B 86.426 1164 125 25 2037 3183 337501588 337502735 0.000000e+00 1243.0
9 TraesCS4B01G125200 chr2B 88.443 1047 96 18 2047 3083 637508454 637507423 0.000000e+00 1240.0
10 TraesCS4B01G125200 chr2B 86.380 1116 126 21 2013 3118 724013002 724011903 0.000000e+00 1195.0
11 TraesCS4B01G125200 chr2B 96.599 588 20 0 7 594 318537780 318537193 0.000000e+00 976.0
12 TraesCS4B01G125200 chr2B 94.343 601 25 4 1 594 762709967 762710565 0.000000e+00 913.0
13 TraesCS4B01G125200 chr2B 96.530 317 11 0 13 329 286172386 286172070 2.810000e-145 525.0
14 TraesCS4B01G125200 chr2B 87.892 223 23 3 374 594 702959259 702959039 3.150000e-65 259.0
15 TraesCS4B01G125200 chr2B 76.555 209 29 14 389 594 405165933 405166124 2.610000e-16 97.1
16 TraesCS4B01G125200 chr6B 88.013 2753 262 38 400 3112 272298778 272296054 0.000000e+00 3193.0
17 TraesCS4B01G125200 chr6B 90.833 600 26 13 1 594 278346561 278347137 0.000000e+00 776.0
18 TraesCS4B01G125200 chr6B 91.837 294 19 4 7 298 190078236 190077946 3.820000e-109 405.0
19 TraesCS4B01G125200 chr3B 93.781 1817 94 13 1308 3118 40495746 40497549 0.000000e+00 2712.0
20 TraesCS4B01G125200 chr3B 83.671 2768 352 73 363 3083 289834737 289837451 0.000000e+00 2516.0
21 TraesCS4B01G125200 chr3B 90.839 1823 150 12 483 2295 261627211 261629026 0.000000e+00 2425.0
22 TraesCS4B01G125200 chr1B 89.941 2028 182 15 7 2021 387430935 387428917 0.000000e+00 2595.0
23 TraesCS4B01G125200 chr1B 93.782 595 25 6 7 594 387426778 387426189 0.000000e+00 883.0
24 TraesCS4B01G125200 chr7B 88.477 1970 207 17 344 2301 233948786 233950747 0.000000e+00 2362.0
25 TraesCS4B01G125200 chr4D 87.234 611 58 14 10 611 245557303 245556704 0.000000e+00 678.0


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 TraesCS4B01G125200 chr4B 154110933 154114115 3182 True 5879.0 5879 100.0000 1 3183 1 chr4B.!!$R1 3182
1 TraesCS4B01G125200 chr4B 486845813 486848441 2628 True 2841.0 2841 86.2660 474 3117 1 chr4B.!!$R2 2643
2 TraesCS4B01G125200 chr2B 295832070 295834830 2760 False 3293.0 3293 88.2860 395 3155 1 chr2B.!!$F1 2760
3 TraesCS4B01G125200 chr2B 399401103 399402674 1571 True 1832.0 1832 87.7540 450 2020 1 chr2B.!!$R3 1570
4 TraesCS4B01G125200 chr2B 762705405 762710565 5160 False 1820.5 2728 92.6955 1 2021 2 chr2B.!!$F4 2020
5 TraesCS4B01G125200 chr2B 545610819 545612313 1494 True 1799.0 1799 88.4740 530 2021 1 chr2B.!!$R4 1491
6 TraesCS4B01G125200 chr2B 570517700 570518829 1129 True 1290.0 1290 87.5220 2037 3155 1 chr2B.!!$R5 1118
7 TraesCS4B01G125200 chr2B 570603081 570604210 1129 True 1290.0 1290 87.5220 2037 3155 1 chr2B.!!$R6 1118
8 TraesCS4B01G125200 chr2B 337501588 337502735 1147 False 1243.0 1243 86.4260 2037 3183 1 chr2B.!!$F2 1146
9 TraesCS4B01G125200 chr2B 637507423 637508454 1031 True 1240.0 1240 88.4430 2047 3083 1 chr2B.!!$R7 1036
10 TraesCS4B01G125200 chr2B 724011903 724013002 1099 True 1195.0 1195 86.3800 2013 3118 1 chr2B.!!$R9 1105
11 TraesCS4B01G125200 chr2B 318537193 318537780 587 True 976.0 976 96.5990 7 594 1 chr2B.!!$R2 587
12 TraesCS4B01G125200 chr6B 272296054 272298778 2724 True 3193.0 3193 88.0130 400 3112 1 chr6B.!!$R2 2712
13 TraesCS4B01G125200 chr6B 278346561 278347137 576 False 776.0 776 90.8330 1 594 1 chr6B.!!$F1 593
14 TraesCS4B01G125200 chr3B 40495746 40497549 1803 False 2712.0 2712 93.7810 1308 3118 1 chr3B.!!$F1 1810
15 TraesCS4B01G125200 chr3B 289834737 289837451 2714 False 2516.0 2516 83.6710 363 3083 1 chr3B.!!$F3 2720
16 TraesCS4B01G125200 chr3B 261627211 261629026 1815 False 2425.0 2425 90.8390 483 2295 1 chr3B.!!$F2 1812
17 TraesCS4B01G125200 chr1B 387426189 387430935 4746 True 1739.0 2595 91.8615 7 2021 2 chr1B.!!$R1 2014
18 TraesCS4B01G125200 chr7B 233948786 233950747 1961 False 2362.0 2362 88.4770 344 2301 1 chr7B.!!$F1 1957
19 TraesCS4B01G125200 chr4D 245556704 245557303 599 True 678.0 678 87.2340 10 611 1 chr4D.!!$R1 601

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
533 566 1.486726 CCGCTGATTTCCTAGTCCCTT 59.513 52.381 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 2456 3.423154 GAAACAGCTCACCGGGCG 61.423 66.667 6.32 0.0 34.52 6.13 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
170 171 6.439375 TGTAACCTGAATCATGGTGTAGTACT 59.561 38.462 0.00 0.00 36.57 2.73
217 218 4.038763 TGTGTTCTGTAGTCCCTGTGTTAG 59.961 45.833 0.00 0.00 0.00 2.34
233 234 6.147164 CCTGTGTTAGTTACGTTCATGTGAAT 59.853 38.462 0.00 0.00 36.33 2.57
272 273 9.803315 GTGTTGTGATATATTTCTGTCTCTGTA 57.197 33.333 0.00 0.00 0.00 2.74
379 386 9.874215 GTTTTAGCGTCTCTAGTAAAACAAAAT 57.126 29.630 14.53 0.00 41.69 1.82
533 566 1.486726 CCGCTGATTTCCTAGTCCCTT 59.513 52.381 0.00 0.00 0.00 3.95
582 616 2.930455 GCGTAAAAACCCCGCTGTACTA 60.930 50.000 0.00 0.00 0.00 1.82
654 688 5.541101 TGTGTGAGGCTTTAGACTAGGTTTA 59.459 40.000 0.00 0.00 30.09 2.01
655 689 6.100668 GTGTGAGGCTTTAGACTAGGTTTAG 58.899 44.000 0.00 0.00 30.09 1.85
663 697 7.605309 GGCTTTAGACTAGGTTTAGCTTGTTTA 59.395 37.037 0.00 0.00 0.00 2.01
664 698 8.441608 GCTTTAGACTAGGTTTAGCTTGTTTAC 58.558 37.037 0.00 0.00 0.00 2.01
670 704 7.937649 ACTAGGTTTAGCTTGTTTACCTTTTG 58.062 34.615 0.00 0.00 39.76 2.44
673 707 5.233476 GGTTTAGCTTGTTTACCTTTTGTGC 59.767 40.000 0.00 0.00 0.00 4.57
674 708 5.845391 TTAGCTTGTTTACCTTTTGTGCT 57.155 34.783 0.00 0.00 0.00 4.40
675 709 4.736126 AGCTTGTTTACCTTTTGTGCTT 57.264 36.364 0.00 0.00 0.00 3.91
741 782 8.758715 CCAGTTATTTTCTCTTTCTTTGCTTTG 58.241 33.333 0.00 0.00 0.00 2.77
744 786 9.301153 GTTATTTTCTCTTTCTTTGCTTTGTCA 57.699 29.630 0.00 0.00 0.00 3.58
747 789 7.992180 TTTCTCTTTCTTTGCTTTGTCATTC 57.008 32.000 0.00 0.00 0.00 2.67
757 802 4.081406 TGCTTTGTCATTCTGCAGGTTAT 58.919 39.130 15.13 2.41 0.00 1.89
758 803 4.523943 TGCTTTGTCATTCTGCAGGTTATT 59.476 37.500 15.13 0.00 0.00 1.40
759 804 4.860907 GCTTTGTCATTCTGCAGGTTATTG 59.139 41.667 15.13 5.03 0.00 1.90
831 877 2.353579 ACAGTACAAACAGCACGGAAAC 59.646 45.455 0.00 0.00 0.00 2.78
841 887 3.746492 ACAGCACGGAAACTATTCAAGAC 59.254 43.478 0.00 0.00 37.29 3.01
865 911 8.970859 ACTTGATAAGTAAGATTTCCCATCAG 57.029 34.615 0.00 0.00 40.69 2.90
909 955 7.155328 CAGCGAGGTATAGTTTTTGAGGATAT 58.845 38.462 0.00 0.00 0.00 1.63
911 957 6.929606 GCGAGGTATAGTTTTTGAGGATATGT 59.070 38.462 0.00 0.00 0.00 2.29
926 972 8.291191 TGAGGATATGTCTAGCTCTTATGATG 57.709 38.462 0.00 0.00 0.00 3.07
1039 1085 2.041081 TCATCCTCCGGATTGTTTTGGT 59.959 45.455 3.57 0.00 39.79 3.67
1044 1090 4.013728 CCTCCGGATTGTTTTGGTATGAA 58.986 43.478 3.57 0.00 0.00 2.57
1061 1107 6.088824 GGTATGAACTTTTCTCAACAGCATG 58.911 40.000 0.00 0.00 46.00 4.06
1068 1114 1.746470 TCTCAACAGCATGGCTCATG 58.254 50.000 9.94 9.94 43.62 3.07
1098 1144 1.434188 TACTCATATGGGTGGCCTGG 58.566 55.000 18.87 0.00 0.00 4.45
1105 1151 1.814292 ATGGGTGGCCTGGAAACCAT 61.814 55.000 17.04 14.78 38.46 3.55
1111 1157 4.202631 GGGTGGCCTGGAAACCATAATATA 60.203 45.833 17.04 0.00 38.46 0.86
1143 1189 6.159398 AGGAATAACAACCCTGAGATCTCATT 59.841 38.462 25.30 17.17 39.13 2.57
1579 1646 1.357258 CGTCACATCCAGCTGAGCAC 61.357 60.000 17.39 4.61 0.00 4.40
1695 1762 5.879223 GTGATCAAGTTGGAGACTCATCATT 59.121 40.000 4.53 0.00 38.68 2.57
1722 1789 6.711645 ACTACTCTCGAAGAAGTACAAGAAGT 59.288 38.462 0.00 0.00 34.09 3.01
1753 1820 6.819284 AGATGAAGATGAAGAACCTGAGATC 58.181 40.000 0.00 0.00 0.00 2.75
2377 2495 7.275183 TGTTTCATGACCCATTCTGAGTATAG 58.725 38.462 0.00 0.00 0.00 1.31
2492 2613 5.463392 GTGCTTGATGAGAATATGCGAACTA 59.537 40.000 0.00 0.00 0.00 2.24
2622 2743 9.077885 ACTTAATCATTTTCTGCTTTTACCTCA 57.922 29.630 0.00 0.00 0.00 3.86
2674 2796 1.846007 TTTGTGCCAAGTGTGTTCCT 58.154 45.000 0.00 0.00 0.00 3.36
2675 2797 1.846007 TTGTGCCAAGTGTGTTCCTT 58.154 45.000 0.00 0.00 0.00 3.36
2712 2834 5.369699 ACCTAACCACTATGGATTAGCATGT 59.630 40.000 0.84 0.00 40.96 3.21
2767 2889 5.250313 AGACATGGAGAAGTGAAGATTCCTT 59.750 40.000 0.00 0.00 34.81 3.36
2793 2917 7.462109 TTTTGTGCTTATGTGTTGTTCATTC 57.538 32.000 0.00 0.00 0.00 2.67
2969 3099 1.958579 CTCGGGATCGGTGGTATGTTA 59.041 52.381 0.00 0.00 36.95 2.41
2983 3113 4.019681 TGGTATGTTACTTTGGGGAGACAG 60.020 45.833 0.00 0.00 0.00 3.51
3056 3192 2.905085 TCGGTGGTATGTTCCTTTGGTA 59.095 45.455 0.00 0.00 0.00 3.25
3135 3278 7.336679 CACAATGTTCCTGGTAATAAGTGATCA 59.663 37.037 0.00 0.00 0.00 2.92
3136 3279 7.888021 ACAATGTTCCTGGTAATAAGTGATCAA 59.112 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.375834 TCTGAATTTTACAGACTACACGTCAT 58.624 34.615 0.00 0.00 45.32 3.06
5 6 6.741109 TCTGAATTTTACAGACTACACGTCA 58.259 36.000 0.00 0.00 45.32 4.35
22 23 9.377312 GAAGCAAGTACTCTTAGAATCTGAATT 57.623 33.333 0.00 0.00 32.07 2.17
272 273 6.019108 ACAAAGGGGAAGAAAGAATGCTATT 58.981 36.000 0.00 0.00 0.00 1.73
533 566 3.507597 CGGATGTCGTGTTCTCCAA 57.492 52.632 0.00 0.00 0.00 3.53
582 616 3.118702 TGGCGCCAAAATGATCAATTGAT 60.119 39.130 30.74 20.85 37.51 2.57
654 688 4.736126 AAGCACAAAAGGTAAACAAGCT 57.264 36.364 0.00 0.00 37.60 3.74
655 689 8.757164 ATATAAAGCACAAAAGGTAAACAAGC 57.243 30.769 0.00 0.00 0.00 4.01
694 728 6.681541 ACTGGAATAAGGTTTAGGGGTTAGAT 59.318 38.462 0.00 0.00 0.00 1.98
712 746 8.864087 AGCAAAGAAAGAGAAAATAACTGGAAT 58.136 29.630 0.00 0.00 0.00 3.01
732 773 3.243636 ACCTGCAGAATGACAAAGCAAAG 60.244 43.478 17.39 0.00 39.69 2.77
736 777 4.708726 ATAACCTGCAGAATGACAAAGC 57.291 40.909 17.39 0.00 39.69 3.51
757 802 4.701651 AGCCATATCTGAGAAGATGCAA 57.298 40.909 0.00 0.00 0.00 4.08
758 803 4.701651 AAGCCATATCTGAGAAGATGCA 57.298 40.909 0.00 0.00 0.00 3.96
759 804 5.792741 AGTAAGCCATATCTGAGAAGATGC 58.207 41.667 2.99 0.00 0.00 3.91
813 859 5.049954 TGAATAGTTTCCGTGCTGTTTGTAC 60.050 40.000 0.00 0.00 0.00 2.90
841 887 8.970859 ACTGATGGGAAATCTTACTTATCAAG 57.029 34.615 0.00 0.00 0.00 3.02
865 911 3.185391 GCTGCCGAGCTAAATCATCTAAC 59.815 47.826 0.00 0.00 42.52 2.34
893 939 9.153479 AGAGCTAGACATATCCTCAAAAACTAT 57.847 33.333 0.00 0.00 0.00 2.12
909 955 8.187913 AGAATAAGCATCATAAGAGCTAGACA 57.812 34.615 0.00 0.00 37.70 3.41
911 957 9.746457 TCTAGAATAAGCATCATAAGAGCTAGA 57.254 33.333 0.00 0.00 37.70 2.43
926 972 4.632327 AAGGATGGCCTCTAGAATAAGC 57.368 45.455 3.32 0.00 46.28 3.09
1039 1085 5.335897 GCCATGCTGTTGAGAAAAGTTCATA 60.336 40.000 0.00 0.00 0.00 2.15
1044 1090 2.555757 GAGCCATGCTGTTGAGAAAAGT 59.444 45.455 0.00 0.00 39.88 2.66
1068 1114 6.042143 CACCCATATGAGTAATTGTTTTGGC 58.958 40.000 3.65 0.00 0.00 4.52
1111 1157 8.742125 TCTCAGGGTTGTTATTCCTATATGAT 57.258 34.615 0.00 0.00 0.00 2.45
1122 1168 6.319048 ACAATGAGATCTCAGGGTTGTTAT 57.681 37.500 26.61 12.61 43.61 1.89
1123 1169 5.762179 ACAATGAGATCTCAGGGTTGTTA 57.238 39.130 26.61 6.70 43.61 2.41
1143 1189 4.640201 GCATTGGATAACTAGAGGCAAACA 59.360 41.667 0.00 0.00 0.00 2.83
1683 1750 7.485418 TCGAGAGTAGTAAATGATGAGTCTC 57.515 40.000 0.00 0.00 34.58 3.36
1695 1762 8.613060 TTCTTGTACTTCTTCGAGAGTAGTAA 57.387 34.615 12.24 7.96 39.17 2.24
1722 1789 7.388776 CAGGTTCTTCATCTTCATCTACAACAA 59.611 37.037 0.00 0.00 0.00 2.83
1753 1820 5.072055 TCATGTATGACAATAGGCCAATGG 58.928 41.667 5.01 0.00 0.00 3.16
2340 2456 3.423154 GAAACAGCTCACCGGGCG 61.423 66.667 6.32 0.00 34.52 6.13
2377 2495 4.841443 TTCAGCATGTATCAATGGATGC 57.159 40.909 0.00 0.00 41.29 3.91
2492 2613 7.814107 CACTAGTTTACATGGCATTCAACAATT 59.186 33.333 0.00 0.00 0.00 2.32
2571 2692 8.529476 GTTTTCTAGTGTACTAGGGATTTGAGA 58.471 37.037 16.66 0.00 44.60 3.27
2626 2747 7.914427 ACATCTAAACATGGTGATCTAGGTA 57.086 36.000 0.00 0.00 0.00 3.08
2674 2796 4.518970 GTGGTTAGGTGATTGCTCTCAAAA 59.481 41.667 0.00 0.00 35.56 2.44
2675 2797 4.072131 GTGGTTAGGTGATTGCTCTCAAA 58.928 43.478 0.00 0.00 35.56 2.69
2712 2834 2.367567 GCTACCGATCCAGGGAACATAA 59.632 50.000 0.00 0.00 35.02 1.90
2927 3057 5.099042 GAACATGGTATACACCTGGTTCT 57.901 43.478 15.77 0.00 45.32 3.01
2969 3099 3.662759 TTTTGTCTGTCTCCCCAAAGT 57.337 42.857 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.