Multiple sequence alignment - TraesCS7A01G030400

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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 TraesCS7A01G030400 chr7A 100.000 3199 0 0 1 3199 12312136 12308938 0.000000e+00 5908.0
1 TraesCS7A01G030400 chr7A 100.000 384 0 0 3442 3825 12308695 12308312 0.000000e+00 710.0
2 TraesCS7A01G030400 chr7A 97.931 145 2 1 3055 3199 214679663 214679806 2.280000e-62 250.0
3 TraesCS7A01G030400 chr7A 75.306 409 99 2 2230 2637 143079899 143080306 1.080000e-45 195.0
4 TraesCS7A01G030400 chr7A 100.000 28 0 0 1521 1548 12310455 12310428 7.000000e-03 52.8
5 TraesCS7A01G030400 chr7A 100.000 28 0 0 1682 1709 12310616 12310589 7.000000e-03 52.8
6 TraesCS7A01G030400 chr4A 99.083 1962 18 0 1087 3048 724853842 724855803 0.000000e+00 3524.0
7 TraesCS7A01G030400 chr4A 91.790 1145 49 19 1 1119 724852689 724853814 0.000000e+00 1552.0
8 TraesCS7A01G030400 chr4A 98.182 385 6 1 3442 3825 382432553 382432169 0.000000e+00 671.0
9 TraesCS7A01G030400 chr4A 98.674 377 5 0 3449 3825 550413590 550413214 0.000000e+00 669.0
10 TraesCS7A01G030400 chr4A 82.162 740 94 17 2244 2975 725319298 725318589 5.470000e-168 601.0
11 TraesCS7A01G030400 chr4A 87.719 456 45 7 2474 2928 724857143 724857588 4.380000e-144 521.0
12 TraesCS7A01G030400 chr4A 84.035 451 57 8 1688 2137 725319841 725319405 1.640000e-113 420.0
13 TraesCS7A01G030400 chr4A 85.093 322 48 0 1160 1481 725325005 725324684 2.850000e-86 329.0
14 TraesCS7A01G030400 chr4A 98.013 151 2 1 3049 3199 382432714 382432565 1.050000e-65 261.0
15 TraesCS7A01G030400 chr4A 100.000 28 0 0 1521 1548 724854437 724854464 7.000000e-03 52.8
16 TraesCS7A01G030400 chr7D 98.976 1367 11 1 1682 3048 12734828 12733465 0.000000e+00 2444.0
17 TraesCS7A01G030400 chr7D 94.994 799 24 5 1 799 12736638 12735856 0.000000e+00 1240.0
18 TraesCS7A01G030400 chr7D 92.491 799 11 7 790 1548 12735590 12734801 0.000000e+00 1098.0
19 TraesCS7A01G030400 chr7D 92.466 292 20 2 335 625 40665629 40665339 2.130000e-112 416.0
20 TraesCS7A01G030400 chr7D 99.265 136 1 0 1548 1683 203510420 203510285 2.950000e-61 246.0
21 TraesCS7A01G030400 chr7D 99.265 136 1 0 1548 1683 382060505 382060370 2.950000e-61 246.0
22 TraesCS7A01G030400 chr7D 98.561 139 2 0 1545 1683 626687404 626687542 2.950000e-61 246.0
23 TraesCS7A01G030400 chr7D 73.775 408 107 0 2230 2637 140846439 140846846 1.100000e-35 161.0
24 TraesCS7A01G030400 chr3B 100.000 384 0 0 3442 3825 197768960 197769343 0.000000e+00 710.0
25 TraesCS7A01G030400 chr3B 99.740 384 1 0 3442 3825 423541670 423541287 0.000000e+00 704.0
26 TraesCS7A01G030400 chr3B 98.438 384 6 0 3442 3825 828646456 828646073 0.000000e+00 676.0
27 TraesCS7A01G030400 chr3B 97.922 385 7 1 3442 3825 170762814 170762430 0.000000e+00 665.0
28 TraesCS7A01G030400 chr3B 98.750 160 1 1 3041 3199 423541844 423541685 2.250000e-72 283.0
29 TraesCS7A01G030400 chr3B 98.026 152 2 1 3048 3199 828646616 828646466 2.930000e-66 263.0
30 TraesCS7A01G030400 chr3B 96.203 158 4 2 3042 3199 170762978 170762823 1.360000e-64 257.0
31 TraesCS7A01G030400 chr7B 99.221 385 2 1 3442 3825 729447544 729447160 0.000000e+00 693.0
32 TraesCS7A01G030400 chr7B 95.000 160 5 3 3041 3199 620006814 620006657 8.210000e-62 248.0
33 TraesCS7A01G030400 chr7B 99.270 137 0 1 3048 3183 729447897 729447761 2.950000e-61 246.0
34 TraesCS7A01G030400 chr7B 73.311 592 137 16 2230 2816 104243989 104244564 8.380000e-47 198.0
35 TraesCS7A01G030400 chr7B 73.201 403 108 0 2230 2632 106128648 106129050 3.080000e-31 147.0
36 TraesCS7A01G030400 chr7B 71.838 593 139 15 2230 2816 103978351 103977781 1.110000e-30 145.0
37 TraesCS7A01G030400 chr5A 98.958 384 4 0 3442 3825 32716114 32715731 0.000000e+00 688.0
38 TraesCS7A01G030400 chr5A 87.109 256 21 6 81 325 329337608 329337862 2.910000e-71 279.0
39 TraesCS7A01G030400 chr5A 90.173 173 14 1 630 799 329337874 329338046 4.970000e-54 222.0
40 TraesCS7A01G030400 chr2B 98.429 382 5 1 3445 3825 762026713 762027094 0.000000e+00 671.0
41 TraesCS7A01G030400 chr2D 92.833 293 19 2 337 628 628164192 628163901 1.270000e-114 424.0
42 TraesCS7A01G030400 chr2D 93.056 288 18 2 339 625 142440460 142440746 1.640000e-113 420.0
43 TraesCS7A01G030400 chr2D 92.708 288 19 2 339 625 89336349 89336635 7.650000e-112 414.0
44 TraesCS7A01G030400 chr2D 91.919 297 22 2 337 632 444042979 444042684 7.650000e-112 414.0
45 TraesCS7A01G030400 chr4D 93.056 288 18 2 339 625 57816327 57816613 1.640000e-113 420.0
46 TraesCS7A01G030400 chr4D 92.708 288 19 2 339 625 509132927 509132641 7.650000e-112 414.0
47 TraesCS7A01G030400 chr6A 93.151 219 13 2 115 333 110350387 110350603 1.710000e-83 320.0
48 TraesCS7A01G030400 chr6A 90.230 174 14 1 630 800 110350608 110350781 1.380000e-54 224.0
49 TraesCS7A01G030400 chr5D 90.222 225 18 4 109 331 259922982 259923204 1.340000e-74 291.0
50 TraesCS7A01G030400 chr6B 91.080 213 18 1 119 331 717301071 717300860 1.740000e-73 287.0
51 TraesCS7A01G030400 chr6B 89.175 194 16 3 625 813 717300859 717300666 1.780000e-58 237.0
52 TraesCS7A01G030400 chr3A 90.233 215 20 1 114 328 17603678 17603465 2.910000e-71 279.0
53 TraesCS7A01G030400 chr3A 91.139 158 8 6 3043 3199 735244766 735244614 3.870000e-50 209.0
54 TraesCS7A01G030400 chr3A 87.283 173 12 8 641 808 17603459 17603292 5.040000e-44 189.0
55 TraesCS7A01G030400 chr5B 95.570 158 4 3 3042 3199 48715 48869 2.280000e-62 250.0
56 TraesCS7A01G030400 chrUn 99.265 136 1 0 1548 1683 189402910 189402775 2.950000e-61 246.0
57 TraesCS7A01G030400 chrUn 98.561 139 2 0 1545 1683 264054162 264054300 2.950000e-61 246.0
58 TraesCS7A01G030400 chrUn 98.561 139 2 0 1545 1683 266524066 266524204 2.950000e-61 246.0
59 TraesCS7A01G030400 chr6D 99.265 136 1 0 1548 1683 124527951 124527816 2.950000e-61 246.0
60 TraesCS7A01G030400 chr1B 98.561 139 2 0 1545 1683 638708824 638708962 2.950000e-61 246.0
61 TraesCS7A01G030400 chr4B 93.243 74 5 0 677 750 272067504 272067577 4.040000e-20 110.0


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 TraesCS7A01G030400 chr7A 12308312 12312136 3824 True 1680.90 5908 100.0000 1 3825 4 chr7A.!!$R1 3824
1 TraesCS7A01G030400 chr4A 724852689 724857588 4899 False 1412.45 3524 94.6480 1 3048 4 chr4A.!!$F1 3047
2 TraesCS7A01G030400 chr4A 725318589 725319841 1252 True 510.50 601 83.0985 1688 2975 2 chr4A.!!$R4 1287
3 TraesCS7A01G030400 chr4A 382432169 382432714 545 True 466.00 671 98.0975 3049 3825 2 chr4A.!!$R3 776
4 TraesCS7A01G030400 chr7D 12733465 12736638 3173 True 1594.00 2444 95.4870 1 3048 3 chr7D.!!$R4 3047
5 TraesCS7A01G030400 chr3B 423541287 423541844 557 True 493.50 704 99.2450 3041 3825 2 chr3B.!!$R2 784
6 TraesCS7A01G030400 chr3B 828646073 828646616 543 True 469.50 676 98.2320 3048 3825 2 chr3B.!!$R3 777
7 TraesCS7A01G030400 chr3B 170762430 170762978 548 True 461.00 665 97.0625 3042 3825 2 chr3B.!!$R1 783
8 TraesCS7A01G030400 chr7B 729447160 729447897 737 True 469.50 693 99.2455 3048 3825 2 chr7B.!!$R3 777

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
325 337 0.107800 ACAGCACTCCTGCAGCTATG 60.108 55.000 8.66 6.58 46.97 2.23 F
502 514 0.322456 TGAGAATGAAAGGTGGGCCG 60.322 55.000 0.00 0.00 40.50 6.13 F
510 522 2.303175 GAAAGGTGGGCCGCATAATAA 58.697 47.619 20.39 0.00 40.50 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1166 1558 1.045911 AGACTCCCTCGCCTTCATCC 61.046 60.000 0.00 0.00 0.0 3.51 R
1814 2206 2.095252 GCAGAGTTTCCGCGGTCTC 61.095 63.158 27.15 26.93 0.0 3.36 R
2945 3416 4.324267 ACCACTTAGCATACACCAAGAAC 58.676 43.478 0.00 0.00 0.0 3.01 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
117 118 2.584064 CTCATGGTGCCGTGCCTA 59.416 61.111 5.59 0.00 33.28 3.93
146 158 5.917447 GGATTTTCAGAGAAGTTGTTTGCTC 59.083 40.000 0.00 0.00 0.00 4.26
170 182 2.581354 CTGGGACTGAGGAAGCCG 59.419 66.667 0.00 0.00 0.00 5.52
172 184 3.003763 GGGACTGAGGAAGCCGGT 61.004 66.667 1.90 0.00 0.00 5.28
323 335 1.593787 GACAGCACTCCTGCAGCTA 59.406 57.895 8.66 0.00 46.97 3.32
324 336 0.177604 GACAGCACTCCTGCAGCTAT 59.822 55.000 8.66 0.00 46.97 2.97
325 337 0.107800 ACAGCACTCCTGCAGCTATG 60.108 55.000 8.66 6.58 46.97 2.23
326 338 0.814410 CAGCACTCCTGCAGCTATGG 60.814 60.000 8.66 0.00 46.97 2.74
327 339 1.222936 GCACTCCTGCAGCTATGGT 59.777 57.895 8.66 0.00 43.62 3.55
407 419 9.819267 AACTAGTATATTCTGTTTAGTTGGAGC 57.181 33.333 0.00 0.00 32.03 4.70
409 421 9.469807 CTAGTATATTCTGTTTAGTTGGAGCAG 57.530 37.037 0.00 0.00 0.00 4.24
435 447 3.748645 AGAGGAGAGAGAAGGTAAGCA 57.251 47.619 0.00 0.00 0.00 3.91
436 448 4.054359 AGAGGAGAGAGAAGGTAAGCAA 57.946 45.455 0.00 0.00 0.00 3.91
502 514 0.322456 TGAGAATGAAAGGTGGGCCG 60.322 55.000 0.00 0.00 40.50 6.13
510 522 2.303175 GAAAGGTGGGCCGCATAATAA 58.697 47.619 20.39 0.00 40.50 1.40
627 639 7.180946 TGGCTATACTATTAACCATGCTCTCAT 59.819 37.037 0.00 0.00 0.00 2.90
628 640 8.696374 GGCTATACTATTAACCATGCTCTCATA 58.304 37.037 0.00 0.00 0.00 2.15
635 647 9.935241 CTATTAACCATGCTCTCATAAGTACAT 57.065 33.333 0.00 0.00 0.00 2.29
700 712 4.021719 CAGGCTTCATCCAAACACATTTCT 60.022 41.667 0.00 0.00 0.00 2.52
703 715 5.406477 GGCTTCATCCAAACACATTTCTTTC 59.594 40.000 0.00 0.00 0.00 2.62
802 1094 5.526111 TGGACACAAAACAAACTAGCTCTAC 59.474 40.000 0.00 0.00 0.00 2.59
1166 1558 2.325583 TCCCTTGCGTATAAAGCCAG 57.674 50.000 0.00 0.00 0.00 4.85
1607 1999 2.391724 TTTGCCGGTCTGTCTGTCCC 62.392 60.000 1.90 0.00 0.00 4.46
1814 2206 1.604755 CCGAGGAGAAGGTCTACATCG 59.395 57.143 0.00 0.00 31.96 3.84
2426 2894 4.708726 AGCAGGATTAGCACAATTGAAC 57.291 40.909 13.59 3.29 0.00 3.18
2932 3403 7.564793 TGCTCTACTTATGTTATGATGTGGTT 58.435 34.615 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.601914 GGACGGCCATTTTGTCAACAC 60.602 52.381 0.00 0.00 34.32 3.32
84 85 0.031585 TGAGGACGTGAACCGAACTG 59.968 55.000 0.00 0.00 40.70 3.16
89 90 1.014044 CACCATGAGGACGTGAACCG 61.014 60.000 0.00 0.00 39.73 4.44
117 118 4.077822 CAACTTCTCTGAAAATCCAGGCT 58.922 43.478 0.00 0.00 34.99 4.58
146 158 1.185618 TCCTCAGTCCCAGGACAACG 61.186 60.000 18.77 7.04 46.76 4.10
170 182 1.139853 CTCAAGTATCCAGGCCAGACC 59.860 57.143 5.01 0.00 39.61 3.85
172 184 0.833287 GCTCAAGTATCCAGGCCAGA 59.167 55.000 5.01 0.45 0.00 3.86
323 335 4.410228 ACTTGCTCTGACATACCATACCAT 59.590 41.667 0.00 0.00 0.00 3.55
324 336 3.774766 ACTTGCTCTGACATACCATACCA 59.225 43.478 0.00 0.00 0.00 3.25
325 337 4.408182 ACTTGCTCTGACATACCATACC 57.592 45.455 0.00 0.00 0.00 2.73
396 408 4.221703 CCTCTTCTCTCTGCTCCAACTAAA 59.778 45.833 0.00 0.00 0.00 1.85
407 419 4.202441 CCTTCTCTCTCCTCTTCTCTCTG 58.798 52.174 0.00 0.00 0.00 3.35
409 421 4.236527 ACCTTCTCTCTCCTCTTCTCTC 57.763 50.000 0.00 0.00 0.00 3.20
545 557 8.961634 TCTACAGCCTATCTTATAGCTAACATG 58.038 37.037 0.00 0.00 33.33 3.21
551 563 9.707957 ATGTTATCTACAGCCTATCTTATAGCT 57.292 33.333 0.00 0.00 40.83 3.32
555 567 9.314133 TGACATGTTATCTACAGCCTATCTTAT 57.686 33.333 0.00 0.00 40.83 1.73
700 712 4.109675 GGCCAGGCTAGCCGGAAA 62.110 66.667 34.53 0.00 41.41 3.13
788 1080 9.368416 TGGATATAGATTGTAGAGCTAGTTTGT 57.632 33.333 0.00 0.00 28.18 2.83
802 1094 4.560128 CGTGAGTGGGTGGATATAGATTG 58.440 47.826 0.00 0.00 0.00 2.67
859 1151 0.846693 ATACTCTTGGTGGATGGGGC 59.153 55.000 0.00 0.00 0.00 5.80
1166 1558 1.045911 AGACTCCCTCGCCTTCATCC 61.046 60.000 0.00 0.00 0.00 3.51
1607 1999 3.557595 GGTCAGCGAGAGTTCATTATTGG 59.442 47.826 0.00 0.00 0.00 3.16
1814 2206 2.095252 GCAGAGTTTCCGCGGTCTC 61.095 63.158 27.15 26.93 0.00 3.36
2945 3416 4.324267 ACCACTTAGCATACACCAAGAAC 58.676 43.478 0.00 0.00 0.00 3.01
2947 3418 4.775780 AGTACCACTTAGCATACACCAAGA 59.224 41.667 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.