Multiple sequence alignment - TraesCS7A01G426200

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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 TraesCS7A01G426200 chr7A 100.000 3832 0 0 1 3832 619255224 619251393 0.000000e+00 7077.0
1 TraesCS7A01G426200 chr7A 87.557 659 58 8 1248 1882 44414246 44414904 0.000000e+00 741.0
2 TraesCS7A01G426200 chr4A 97.143 3850 65 13 1 3832 2618992 2622814 0.000000e+00 6458.0
3 TraesCS7A01G426200 chr2A 96.879 3813 71 11 57 3832 724110539 724106738 0.000000e+00 6338.0
4 TraesCS7A01G426200 chr2A 79.598 348 66 5 853 1199 394015668 394016011 1.060000e-60 244.0
5 TraesCS7A01G426200 chrUn 96.934 3523 93 8 313 3832 69802951 69799441 0.000000e+00 5893.0
6 TraesCS7A01G426200 chrUn 92.308 169 13 0 3050 3218 357719428 357719596 1.380000e-59 241.0
7 TraesCS7A01G426200 chr6D 96.914 2106 47 5 1737 3832 292688383 292686286 0.000000e+00 3513.0
8 TraesCS7A01G426200 chr6D 95.710 746 18 5 998 1742 292711642 292710910 0.000000e+00 1188.0
9 TraesCS7A01G426200 chr6D 96.522 690 18 2 313 1001 292716045 292715361 0.000000e+00 1136.0
10 TraesCS7A01G426200 chr6D 92.355 484 34 3 710 1192 25484166 25483685 0.000000e+00 686.0
11 TraesCS7A01G426200 chr6D 81.831 710 84 24 2788 3469 46626277 46625585 4.330000e-154 555.0
12 TraesCS7A01G426200 chr6D 80.370 703 85 29 2788 3451 46813589 46812901 5.760000e-133 484.0
13 TraesCS7A01G426200 chr6D 81.328 241 35 2 3239 3469 46844590 46844350 1.820000e-43 187.0
14 TraesCS7A01G426200 chr5A 94.337 883 39 4 313 1193 568570794 568571667 0.000000e+00 1343.0
15 TraesCS7A01G426200 chr5A 94.957 694 32 3 1193 1885 568571704 568572395 0.000000e+00 1085.0
16 TraesCS7A01G426200 chr3A 96.522 690 22 2 1193 1880 31814759 31815448 0.000000e+00 1140.0
17 TraesCS7A01G426200 chr3A 94.190 327 18 1 869 1194 31814397 31814723 7.390000e-137 497.0
18 TraesCS7A01G426200 chr1B 95.245 694 30 3 1193 1885 643260340 643259649 0.000000e+00 1096.0
19 TraesCS7A01G426200 chr1B 93.804 694 27 4 1193 1885 550237914 550237236 0.000000e+00 1029.0
20 TraesCS7A01G426200 chr1B 96.800 250 8 0 734 983 643260998 643260749 5.920000e-113 418.0
21 TraesCS7A01G426200 chr1B 96.226 212 8 0 982 1193 643260588 643260377 7.880000e-92 348.0
22 TraesCS7A01G426200 chr6B 93.362 693 30 4 1194 1885 563878652 563877975 0.000000e+00 1011.0
23 TraesCS7A01G426200 chr6B 94.397 589 32 1 1897 2484 72318973 72318385 0.000000e+00 904.0
24 TraesCS7A01G426200 chr6B 94.237 590 32 2 1897 2484 72316180 72315591 0.000000e+00 900.0
25 TraesCS7A01G426200 chr6B 94.237 590 32 2 1897 2484 72324567 72323978 0.000000e+00 900.0
26 TraesCS7A01G426200 chr6B 94.369 586 32 1 1900 2484 72321763 72321178 0.000000e+00 898.0
27 TraesCS7A01G426200 chr6B 93.559 590 36 2 1897 2484 72327363 72326774 0.000000e+00 878.0
28 TraesCS7A01G426200 chr6B 92.654 422 20 3 3053 3473 72314343 72313932 7.090000e-167 597.0
29 TraesCS7A01G426200 chr6B 88.506 435 35 11 3053 3473 678828623 678828190 2.640000e-141 512.0
30 TraesCS7A01G426200 chr6B 95.305 213 8 2 2503 2713 53636665 53636877 1.710000e-88 337.0
31 TraesCS7A01G426200 chr7B 94.737 589 31 0 1896 2484 703575664 703576252 0.000000e+00 917.0
32 TraesCS7A01G426200 chr7B 94.353 425 23 1 3050 3473 703577491 703577915 0.000000e+00 651.0
33 TraesCS7A01G426200 chr7B 94.545 330 18 0 3475 3804 703579070 703579399 9.500000e-141 510.0
34 TraesCS7A01G426200 chr7B 82.979 94 10 5 3476 3568 276795238 276795326 3.170000e-11 80.5
35 TraesCS7A01G426200 chr7D 97.749 311 7 0 3 313 31376317 31376007 1.570000e-148 536.0
36 TraesCS7A01G426200 chr7D 93.151 219 15 0 2516 2734 495142123 495142341 4.780000e-84 322.0
37 TraesCS7A01G426200 chr3D 97.756 312 6 1 3 313 19412660 19412349 1.570000e-148 536.0
38 TraesCS7A01G426200 chr3D 91.414 198 17 0 3607 3804 468667992 468668189 4.880000e-69 272.0
39 TraesCS7A01G426200 chr5D 97.143 315 7 2 1 313 370304076 370303762 7.290000e-147 531.0
40 TraesCS7A01G426200 chr4D 88.220 382 42 3 314 694 509330107 509330486 1.620000e-123 453.0
41 TraesCS7A01G426200 chr4D 92.281 285 19 3 2491 2772 494791794 494791510 5.960000e-108 401.0
42 TraesCS7A01G426200 chr1D 98.760 242 3 0 72 313 423888940 423888699 7.610000e-117 431.0
43 TraesCS7A01G426200 chr1D 87.879 198 17 2 3607 3804 395033933 395034123 3.850000e-55 226.0
44 TraesCS7A01G426200 chr1D 85.789 190 24 2 318 507 112622165 112621979 8.400000e-47 198.0
45 TraesCS7A01G426200 chr2B 96.078 255 3 3 1 248 741450963 741451217 3.560000e-110 409.0
46 TraesCS7A01G426200 chr3B 95.968 248 4 2 1 248 792139943 792139702 7.710000e-107 398.0
47 TraesCS7A01G426200 chr3B 95.565 248 5 2 1 248 792102509 792102268 3.590000e-105 392.0
48 TraesCS7A01G426200 chr3B 98.507 67 1 0 247 313 792102072 792102006 6.720000e-23 119.0
49 TraesCS7A01G426200 chr3B 98.507 67 1 0 247 313 792177545 792177479 6.720000e-23 119.0
50 TraesCS7A01G426200 chr4B 92.937 269 16 2 2507 2772 577024787 577024519 4.640000e-104 388.0
51 TraesCS7A01G426200 chr1A 90.265 226 18 4 2499 2720 7692903 7692678 3.740000e-75 292.0
52 TraesCS7A01G426200 chr2D 90.256 195 18 1 3610 3804 27014545 27014352 1.770000e-63 254.0
53 TraesCS7A01G426200 chr2D 79.697 330 62 5 853 1181 324600272 324599947 2.300000e-57 233.0
54 TraesCS7A01G426200 chr2D 81.159 138 8 8 3565 3688 555112812 555112679 1.130000e-15 95.3
55 TraesCS7A01G426200 chr5B 98.507 67 1 0 247 313 43243947 43244013 6.720000e-23 119.0


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 TraesCS7A01G426200 chr7A 619251393 619255224 3831 True 7077.000000 7077 100.000000 1 3832 1 chr7A.!!$R1 3831
1 TraesCS7A01G426200 chr7A 44414246 44414904 658 False 741.000000 741 87.557000 1248 1882 1 chr7A.!!$F1 634
2 TraesCS7A01G426200 chr4A 2618992 2622814 3822 False 6458.000000 6458 97.143000 1 3832 1 chr4A.!!$F1 3831
3 TraesCS7A01G426200 chr2A 724106738 724110539 3801 True 6338.000000 6338 96.879000 57 3832 1 chr2A.!!$R1 3775
4 TraesCS7A01G426200 chrUn 69799441 69802951 3510 True 5893.000000 5893 96.934000 313 3832 1 chrUn.!!$R1 3519
5 TraesCS7A01G426200 chr6D 292686286 292688383 2097 True 3513.000000 3513 96.914000 1737 3832 1 chr6D.!!$R5 2095
6 TraesCS7A01G426200 chr6D 292710910 292716045 5135 True 1162.000000 1188 96.116000 313 1742 2 chr6D.!!$R6 1429
7 TraesCS7A01G426200 chr6D 46625585 46626277 692 True 555.000000 555 81.831000 2788 3469 1 chr6D.!!$R2 681
8 TraesCS7A01G426200 chr6D 46812901 46813589 688 True 484.000000 484 80.370000 2788 3451 1 chr6D.!!$R3 663
9 TraesCS7A01G426200 chr5A 568570794 568572395 1601 False 1214.000000 1343 94.647000 313 1885 2 chr5A.!!$F1 1572
10 TraesCS7A01G426200 chr3A 31814397 31815448 1051 False 818.500000 1140 95.356000 869 1880 2 chr3A.!!$F1 1011
11 TraesCS7A01G426200 chr1B 550237236 550237914 678 True 1029.000000 1029 93.804000 1193 1885 1 chr1B.!!$R1 692
12 TraesCS7A01G426200 chr1B 643259649 643260998 1349 True 620.666667 1096 96.090333 734 1885 3 chr1B.!!$R2 1151
13 TraesCS7A01G426200 chr6B 563877975 563878652 677 True 1011.000000 1011 93.362000 1194 1885 1 chr6B.!!$R1 691
14 TraesCS7A01G426200 chr6B 72313932 72327363 13431 True 846.166667 904 93.908833 1897 3473 6 chr6B.!!$R3 1576
15 TraesCS7A01G426200 chr7B 703575664 703579399 3735 False 692.666667 917 94.545000 1896 3804 3 chr7B.!!$F2 1908
16 TraesCS7A01G426200 chr3B 792102006 792102509 503 True 255.500000 392 97.036000 1 313 2 chr3B.!!$R3 312

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
247 260 1.301165 CCTTGCTTGGCTTGTTGGC 60.301 57.895 0.0 0.0 42.18 4.52 F
304 317 3.507162 TTCAGGAAGAGGTGAATGCAA 57.493 42.857 0.0 0.0 0.00 4.08 F
2097 6359 1.511318 CGGTTCCATTTGTGTGCCGA 61.511 55.000 0.0 0.0 40.04 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 6359 2.732658 GGAGGTTGTGGTCGACGT 59.267 61.111 9.92 0.0 0.0 4.34 R
2185 6471 2.807967 TGAAAGAGTCGGTGCTGAATTG 59.192 45.455 0.00 0.0 0.0 2.32 R
2898 19503 2.355837 GCGTGCTCCTTGTCGTCA 60.356 61.111 0.00 0.0 0.0 4.35 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
47 52 4.837421 CCTCCTACCCCCACCCCC 62.837 77.778 0.00 0.00 0.00 5.40
247 260 1.301165 CCTTGCTTGGCTTGTTGGC 60.301 57.895 0.00 0.00 42.18 4.52
304 317 3.507162 TTCAGGAAGAGGTGAATGCAA 57.493 42.857 0.00 0.00 0.00 4.08
383 396 4.478317 TGGATTCATTAGGTCTGGTTGGAT 59.522 41.667 0.00 0.00 0.00 3.41
921 948 9.265901 AGTATGCATGTAAATCTGTCTCAATAC 57.734 33.333 10.16 0.00 0.00 1.89
934 961 7.583625 TCTGTCTCAATACTAACTGATAGGGA 58.416 38.462 0.00 0.00 35.81 4.20
1054 4966 8.479689 TGGAAAACGACCATAAGATAGATAACA 58.520 33.333 0.00 0.00 32.03 2.41
1336 5286 7.864882 CGCTATCTCAGTGATATGGTTATATGG 59.135 40.741 1.40 0.00 37.07 2.74
1401 5367 8.958175 AAATATAACGAAGCGAAAATTGTTCA 57.042 26.923 0.00 0.00 0.00 3.18
1718 5960 4.212143 TCCACTCATGGCTGATATATGC 57.788 45.455 0.00 0.00 46.80 3.14
2097 6359 1.511318 CGGTTCCATTTGTGTGCCGA 61.511 55.000 0.00 0.00 40.04 5.54
2185 6471 6.800543 TCTCAACTCACTCTGCTTATATCAC 58.199 40.000 0.00 0.00 0.00 3.06
2339 15015 4.164221 TCTCAAGGACTTCCAAGAAGTTGT 59.836 41.667 11.07 0.02 38.89 3.32
2514 19116 0.478507 CTCTCTCTCCCTCTCCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
2832 19436 1.304547 AGCCTGCAGTCGGAGTAGT 60.305 57.895 13.81 0.00 0.00 2.73
2842 19447 3.928992 CAGTCGGAGTAGTACTGACGTAA 59.071 47.826 7.76 0.00 45.09 3.18
3174 19862 7.782049 AGATGATCGTACTTATGGAAACTCAA 58.218 34.615 0.00 0.00 0.00 3.02
3181 19869 5.904362 ACTTATGGAAACTCAAATGCCTC 57.096 39.130 0.00 0.00 0.00 4.70
3608 21471 2.629017 AGGGGAAGAATTGGCAATGT 57.371 45.000 14.47 4.07 0.00 2.71
3648 21511 4.768583 AGCAAGAGGAAGATGATGAGTTC 58.231 43.478 0.00 0.00 0.00 3.01
3725 21588 4.441792 CCCACCTTTGCCTTTATTATTGC 58.558 43.478 0.00 0.00 0.00 3.56
3816 21679 6.317642 AGTTTTCAAAAATTTAGGTTGTGGGC 59.682 34.615 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.457794 GGGTGGGGGTAGGAGGAA 59.542 66.667 0.00 0.0 0.00 3.36
47 52 0.325933 TGGAGCTCACCATGTTCAGG 59.674 55.000 17.19 0.0 34.77 3.86
240 253 1.005450 GATCCCAACCCTAGCCAACAA 59.995 52.381 0.00 0.0 0.00 2.83
241 254 0.623723 GATCCCAACCCTAGCCAACA 59.376 55.000 0.00 0.0 0.00 3.33
242 255 0.919710 AGATCCCAACCCTAGCCAAC 59.080 55.000 0.00 0.0 0.00 3.77
243 256 1.681229 AAGATCCCAACCCTAGCCAA 58.319 50.000 0.00 0.0 0.00 4.52
244 257 1.564348 GAAAGATCCCAACCCTAGCCA 59.436 52.381 0.00 0.0 0.00 4.75
245 258 1.847088 AGAAAGATCCCAACCCTAGCC 59.153 52.381 0.00 0.0 0.00 3.93
246 259 2.774809 AGAGAAAGATCCCAACCCTAGC 59.225 50.000 0.00 0.0 0.00 3.42
247 260 4.591072 CCTAGAGAAAGATCCCAACCCTAG 59.409 50.000 0.00 0.0 0.00 3.02
304 317 0.560688 AAACACCCCCAATGTCCTGT 59.439 50.000 0.00 0.0 0.00 4.00
696 723 4.228824 TGATATGTCTACAACCTACCCCC 58.771 47.826 0.00 0.0 0.00 5.40
697 724 4.283722 CCTGATATGTCTACAACCTACCCC 59.716 50.000 0.00 0.0 0.00 4.95
698 725 4.900054 ACCTGATATGTCTACAACCTACCC 59.100 45.833 0.00 0.0 0.00 3.69
699 726 5.221461 CCACCTGATATGTCTACAACCTACC 60.221 48.000 0.00 0.0 0.00 3.18
700 727 5.363005 ACCACCTGATATGTCTACAACCTAC 59.637 44.000 0.00 0.0 0.00 3.18
715 742 6.270231 ACTCTCTTTGTAACTAACCACCTGAT 59.730 38.462 0.00 0.0 0.00 2.90
921 948 7.711339 GGTCACATTAGTTTCCCTATCAGTTAG 59.289 40.741 0.00 0.0 0.00 2.34
934 961 6.183360 GCAAAACAAAACGGTCACATTAGTTT 60.183 34.615 0.00 0.0 38.30 2.66
1052 4964 8.906867 CCATAATAACCAAATCACTGAATCTGT 58.093 33.333 0.00 0.0 0.00 3.41
1054 4966 9.347240 CTCCATAATAACCAAATCACTGAATCT 57.653 33.333 0.00 0.0 0.00 2.40
1336 5286 2.941720 CAAATCCTCACTTCTAGCAGCC 59.058 50.000 0.00 0.0 0.00 4.85
1369 5319 5.459110 TCGCTTCGTTATATTTTCGCTTT 57.541 34.783 0.00 0.0 0.00 3.51
1401 5367 5.337788 AGAAGTACAACTCCCAGATCTCTT 58.662 41.667 0.00 0.0 0.00 2.85
1530 5496 6.360370 AGAGAACAAATAGTGCAGACCTTA 57.640 37.500 0.00 0.0 0.00 2.69
1718 5960 9.530633 GGTATATTTATCCAGCCTAAATACTCG 57.469 37.037 0.00 0.0 35.16 4.18
2097 6359 2.732658 GGAGGTTGTGGTCGACGT 59.267 61.111 9.92 0.0 0.00 4.34
2185 6471 2.807967 TGAAAGAGTCGGTGCTGAATTG 59.192 45.455 0.00 0.0 0.00 2.32
2514 19116 4.347876 TGTAGATGGAGAGAGAGAGAGAGG 59.652 50.000 0.00 0.0 0.00 3.69
2786 19390 2.979676 CCGCTGTTCTGCAAGCCA 60.980 61.111 2.60 0.0 0.00 4.75
2832 19436 5.050634 GTGTTCTGCAAATGTTACGTCAGTA 60.051 40.000 0.00 0.0 0.00 2.74
2842 19447 1.333619 GTGTCGGTGTTCTGCAAATGT 59.666 47.619 0.00 0.0 0.00 2.71
2898 19503 2.355837 GCGTGCTCCTTGTCGTCA 60.356 61.111 0.00 0.0 0.00 4.35
3174 19862 3.437795 GCAGCAGTGCGAGGCATT 61.438 61.111 19.86 0.0 41.91 3.56
3461 20170 4.894705 AGCAATTATAATCATGTGCCACCA 59.105 37.500 13.69 0.0 32.38 4.17
3608 21471 6.533730 TCTTGCTCTCTTCTCACCAATTTAA 58.466 36.000 0.00 0.0 0.00 1.52
3648 21511 4.768968 AGGAATCTGAACCTTTTCCATGTG 59.231 41.667 9.08 0.0 40.09 3.21
3725 21588 8.511604 AAAGAAGACCCATCAACATATTAGTG 57.488 34.615 0.00 0.0 0.00 2.74


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

AutoCloner maintained by Alex Coulton.