Multiple sequence alignment - TraesCS4A01G377600

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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 TraesCS4A01G377600 chr4A 100.000 3313 0 0 1518 4830 653074414 653077726 0.000000e+00 6119.0
1 TraesCS4A01G377600 chr4A 88.335 2486 263 13 1519 3977 654059646 654057161 0.000000e+00 2959.0
2 TraesCS4A01G377600 chr4A 88.305 2206 232 16 1519 3701 652815138 652817340 0.000000e+00 2621.0
3 TraesCS4A01G377600 chr4A 87.792 1671 164 22 2348 3986 653410937 653412599 0.000000e+00 1919.0
4 TraesCS4A01G377600 chr4A 100.000 1018 0 0 1 1018 653072897 653073914 0.000000e+00 1881.0
5 TraesCS4A01G377600 chr4A 88.113 816 85 4 1519 2325 653410138 653410950 0.000000e+00 959.0
6 TraesCS4A01G377600 chr4A 80.252 238 32 10 1595 1819 578387503 578387268 1.080000e-36 165.0
7 TraesCS4A01G377600 chr4A 91.209 91 0 5 3871 3954 573662592 573662681 3.050000e-22 117.0
8 TraesCS4A01G377600 chr4A 92.857 70 4 1 4090 4158 654053486 654053417 3.080000e-17 100.0
9 TraesCS4A01G377600 chr4A 87.692 65 2 2 3871 3930 597889007 597888944 2.410000e-08 71.3
10 TraesCS4A01G377600 chr7A 96.813 3357 53 14 1519 4830 45857669 45854322 0.000000e+00 5557.0
11 TraesCS4A01G377600 chr7A 87.634 2604 245 38 1519 4083 45982379 45979814 0.000000e+00 2953.0
12 TraesCS4A01G377600 chr7A 86.348 2571 282 40 1522 4050 46061938 46059395 0.000000e+00 2739.0
13 TraesCS4A01G377600 chr7A 86.300 2562 293 37 1519 4050 44821950 44824483 0.000000e+00 2734.0
14 TraesCS4A01G377600 chr7A 85.930 2580 255 58 1519 4050 44448246 44445727 0.000000e+00 2654.0
15 TraesCS4A01G377600 chr7A 85.770 2572 293 47 1522 4050 46100529 46097988 0.000000e+00 2654.0
16 TraesCS4A01G377600 chr7A 92.626 556 35 4 1 550 45859283 45858728 0.000000e+00 795.0
17 TraesCS4A01G377600 chr7A 89.575 259 13 6 547 796 45858228 45857975 2.810000e-82 316.0
18 TraesCS4A01G377600 chr7A 86.192 239 4 11 801 1018 45857918 45857688 1.050000e-56 231.0
19 TraesCS4A01G377600 chr7A 86.131 137 8 6 884 1018 44448401 44448274 2.340000e-28 137.0
20 TraesCS4A01G377600 chr7A 88.393 112 13 0 1 112 728624340 728624229 8.430000e-28 135.0
21 TraesCS4A01G377600 chr7A 79.535 215 17 12 4167 4354 45978636 45978422 1.410000e-25 128.0
22 TraesCS4A01G377600 chr7D 95.475 3337 86 16 1519 4830 43634547 43631251 0.000000e+00 5265.0
23 TraesCS4A01G377600 chr7D 88.497 1504 153 16 2345 3831 43637647 43636147 0.000000e+00 1801.0
24 TraesCS4A01G377600 chr7D 89.910 555 43 5 1 550 43635942 43635396 0.000000e+00 702.0
25 TraesCS4A01G377600 chr7D 87.576 491 61 0 1864 2354 43638414 43637924 1.950000e-158 569.0
26 TraesCS4A01G377600 chr7D 85.488 441 38 5 114 550 213813559 213813977 2.060000e-118 436.0
27 TraesCS4A01G377600 chr7D 87.675 357 35 3 1519 1869 43660542 43660189 1.620000e-109 407.0
28 TraesCS4A01G377600 chr7D 87.395 357 36 3 1519 1869 43681901 43681548 7.530000e-108 401.0
29 TraesCS4A01G377600 chr7D 92.400 250 6 5 547 796 43634917 43634681 1.290000e-90 344.0
30 TraesCS4A01G377600 chr7D 82.143 168 26 4 1598 1763 534634303 534634138 1.810000e-29 141.0
31 TraesCS4A01G377600 chr7D 88.393 112 12 1 1 112 250922857 250922747 3.030000e-27 134.0
32 TraesCS4A01G377600 chr7D 100.000 71 0 0 948 1018 43634636 43634566 1.090000e-26 132.0
33 TraesCS4A01G377600 chr4B 76.158 1619 287 62 1519 3068 36131707 36133295 0.000000e+00 760.0
34 TraesCS4A01G377600 chr4B 76.502 1515 273 55 1607 3060 36001545 36003037 0.000000e+00 749.0
35 TraesCS4A01G377600 chr4B 77.075 253 44 9 1519 1761 41846855 41846607 3.030000e-27 134.0
36 TraesCS4A01G377600 chr4B 90.426 94 1 5 3871 3957 41844255 41844163 3.050000e-22 117.0
37 TraesCS4A01G377600 chr3B 87.104 442 31 4 113 550 67074851 67075270 1.220000e-130 477.0
38 TraesCS4A01G377600 chr3B 81.524 525 63 18 35 550 109541269 109540770 7.530000e-108 401.0
39 TraesCS4A01G377600 chr3B 97.297 37 1 0 4460 4496 16132285 16132249 4.040000e-06 63.9
40 TraesCS4A01G377600 chr3D 86.878 442 32 14 113 550 418242764 418242345 5.660000e-129 472.0
41 TraesCS4A01G377600 chr3D 87.719 114 14 0 1 114 136395637 136395524 3.030000e-27 134.0
42 TraesCS4A01G377600 chr3D 91.667 48 2 2 4460 4506 11443780 11443734 1.120000e-06 65.8
43 TraesCS4A01G377600 chr2D 86.652 442 32 15 114 550 331438353 331438772 9.470000e-127 464.0
44 TraesCS4A01G377600 chr2D 86.364 440 35 3 114 550 192668512 192668929 1.580000e-124 457.0
45 TraesCS4A01G377600 chrUn 72.372 1817 379 79 1519 3254 52140490 52142264 1.220000e-125 460.0
46 TraesCS4A01G377600 chr5B 85.714 441 36 5 114 550 680282965 680282548 1.600000e-119 440.0
47 TraesCS4A01G377600 chr5B 85.169 445 35 6 114 550 4876248 4876669 1.240000e-115 427.0
48 TraesCS4A01G377600 chr1D 84.944 445 37 6 114 550 258530169 258529747 1.610000e-114 424.0
49 TraesCS4A01G377600 chr1D 84.354 441 43 15 114 550 135468801 135468383 4.500000e-110 409.0
50 TraesCS4A01G377600 chr1D 95.671 231 8 2 114 343 485675477 485675706 2.120000e-98 370.0
51 TraesCS4A01G377600 chr1A 81.818 539 63 19 18 549 287407805 287407295 2.080000e-113 420.0
52 TraesCS4A01G377600 chr1B 86.687 323 37 3 219 535 125359007 125358685 2.140000e-93 353.0
53 TraesCS4A01G377600 chr4D 84.409 186 23 2 1599 1778 24338168 24337983 1.380000e-40 178.0
54 TraesCS4A01G377600 chr4D 83.069 189 25 3 1596 1778 25155517 25155704 1.080000e-36 165.0
55 TraesCS4A01G377600 chr4D 78.715 249 39 9 1519 1757 5643029 5643273 2.330000e-33 154.0
56 TraesCS4A01G377600 chr4D 90.426 94 1 5 3871 3957 29412823 29412731 3.050000e-22 117.0
57 TraesCS4A01G377600 chr6B 77.778 252 42 9 1519 1760 625827541 625827788 5.040000e-30 143.0
58 TraesCS4A01G377600 chr6B 100.000 33 0 0 3871 3903 625883132 625883164 1.450000e-05 62.1
59 TraesCS4A01G377600 chr6D 88.288 111 13 0 2 112 384561780 384561670 3.030000e-27 134.0
60 TraesCS4A01G377600 chr3A 87.611 113 13 1 1 113 571164544 571164655 3.920000e-26 130.0


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 TraesCS4A01G377600 chr4A 653072897 653077726 4829 False 4000.000000 6119 100.000000 1 4830 2 chr4A.!!$F3 4829
1 TraesCS4A01G377600 chr4A 652815138 652817340 2202 False 2621.000000 2621 88.305000 1519 3701 1 chr4A.!!$F2 2182
2 TraesCS4A01G377600 chr4A 654053417 654059646 6229 True 1529.500000 2959 90.596000 1519 4158 2 chr4A.!!$R3 2639
3 TraesCS4A01G377600 chr4A 653410138 653412599 2461 False 1439.000000 1919 87.952500 1519 3986 2 chr4A.!!$F4 2467
4 TraesCS4A01G377600 chr7A 46059395 46061938 2543 True 2739.000000 2739 86.348000 1522 4050 1 chr7A.!!$R1 2528
5 TraesCS4A01G377600 chr7A 44821950 44824483 2533 False 2734.000000 2734 86.300000 1519 4050 1 chr7A.!!$F1 2531
6 TraesCS4A01G377600 chr7A 46097988 46100529 2541 True 2654.000000 2654 85.770000 1522 4050 1 chr7A.!!$R2 2528
7 TraesCS4A01G377600 chr7A 45854322 45859283 4961 True 1724.750000 5557 91.301500 1 4830 4 chr7A.!!$R5 4829
8 TraesCS4A01G377600 chr7A 45978422 45982379 3957 True 1540.500000 2953 83.584500 1519 4354 2 chr7A.!!$R6 2835
9 TraesCS4A01G377600 chr7A 44445727 44448401 2674 True 1395.500000 2654 86.030500 884 4050 2 chr7A.!!$R4 3166
10 TraesCS4A01G377600 chr7D 43631251 43638414 7163 True 1468.833333 5265 92.309667 1 4830 6 chr7D.!!$R5 4829
11 TraesCS4A01G377600 chr4B 36131707 36133295 1588 False 760.000000 760 76.158000 1519 3068 1 chr4B.!!$F2 1549
12 TraesCS4A01G377600 chr4B 36001545 36003037 1492 False 749.000000 749 76.502000 1607 3060 1 chr4B.!!$F1 1453
13 TraesCS4A01G377600 chrUn 52140490 52142264 1774 False 460.000000 460 72.372000 1519 3254 1 chrUn.!!$F1 1735
14 TraesCS4A01G377600 chr1A 287407295 287407805 510 True 420.000000 420 81.818000 18 549 1 chr1A.!!$R1 531

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
867 3912 0.105607 AACCCTATCTCGTCCTCCCC 60.106 60.000 0.0 0.0 0.00 4.81 F
868 3913 1.228925 CCCTATCTCGTCCTCCCCC 60.229 68.421 0.0 0.0 0.00 5.40 F
2193 5365 2.169978 CCTCTCAAGGCTGATGATGTCA 59.830 50.000 0.0 0.0 35.37 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 5315 0.670162 TGCTGCTGAAAAGAGTTGCC 59.330 50.0 0.00 0.0 0.0 4.52 R
2492 5704 2.497675 GTGGAGGTGCATCTTGAGAGTA 59.502 50.0 0.00 0.0 0.0 2.59 R
4030 8012 0.760572 ACAAGGCCAAGCAAGCAAAT 59.239 45.0 5.01 0.0 0.0 2.32 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
23 2497 1.675552 AACCGGATATGGCGGAAAAG 58.324 50.000 9.46 0.00 0.00 2.27
44 2518 5.441718 AGCCCTCTGATTTTATCTTCACA 57.558 39.130 0.00 0.00 0.00 3.58
58 2532 1.191489 TTCACAGCCCATCAGTCCGA 61.191 55.000 0.00 0.00 0.00 4.55
77 2551 2.816411 GACCCATATCCCATAGTCCGA 58.184 52.381 0.00 0.00 0.00 4.55
119 2593 1.912043 CAGGACTCCCTCAATGACCTT 59.088 52.381 0.00 0.00 42.02 3.50
120 2594 1.912043 AGGACTCCCTCAATGACCTTG 59.088 52.381 0.00 0.00 38.86 3.61
188 2662 9.911788 ATCAGAGGGGTATTAAATAGCATAATG 57.088 33.333 0.00 0.00 35.03 1.90
270 2744 3.006859 TCAACACTATGAGTCACCCACAG 59.993 47.826 0.00 0.00 0.00 3.66
337 2811 3.379452 ACTAGGGTTTGAGAGGAGATGG 58.621 50.000 0.00 0.00 0.00 3.51
340 2814 1.680249 GGGTTTGAGAGGAGATGGTGC 60.680 57.143 0.00 0.00 0.00 5.01
348 2822 1.222936 GGAGATGGTGCTGGGTCTG 59.777 63.158 0.00 0.00 0.00 3.51
386 2860 7.337436 TGCTGTTGAATATGTTGATGAAGATGA 59.663 33.333 0.00 0.00 0.00 2.92
417 2894 3.391774 AGATGAGAGGGTTGGTGATGAT 58.608 45.455 0.00 0.00 0.00 2.45
423 2900 3.118112 AGAGGGTTGGTGATGATGATGAC 60.118 47.826 0.00 0.00 0.00 3.06
439 2917 1.879575 TGACGATGATTTCCCCCTCT 58.120 50.000 0.00 0.00 0.00 3.69
460 2939 0.323542 GGAGAGAAGTCCCCTGACGA 60.324 60.000 0.00 0.00 46.51 4.20
474 2953 4.124351 ACGAAATCGCTCCGCCGA 62.124 61.111 2.15 0.00 44.43 5.54
501 2980 0.106015 AAGTGCTCCTGCCCAAGTTT 60.106 50.000 0.00 0.00 38.71 2.66
524 3003 2.183858 CTCGAGACGGCGACACTTCA 62.184 60.000 16.62 0.21 36.17 3.02
557 3539 8.100508 AGTAGTCTCCTTATTTTTGAAAGCAC 57.899 34.615 0.00 0.00 0.00 4.40
796 3786 2.350197 CGTGGGTCGGATTCGTAGATAC 60.350 54.545 0.00 0.00 37.69 2.24
823 3827 2.444256 CGCCCTTCCCCTTCCTAGG 61.444 68.421 0.82 0.82 41.60 3.02
864 3909 2.624364 GGAGAAACCCTATCTCGTCCTC 59.376 54.545 0.00 0.00 43.43 3.71
865 3910 2.624364 GAGAAACCCTATCTCGTCCTCC 59.376 54.545 0.00 0.00 34.50 4.30
866 3911 1.687660 GAAACCCTATCTCGTCCTCCC 59.312 57.143 0.00 0.00 0.00 4.30
867 3912 0.105607 AACCCTATCTCGTCCTCCCC 60.106 60.000 0.00 0.00 0.00 4.81
868 3913 1.228925 CCCTATCTCGTCCTCCCCC 60.229 68.421 0.00 0.00 0.00 5.40
2146 5315 2.297597 ACGACTTTCACCTTCTGGAGAG 59.702 50.000 0.00 0.00 34.54 3.20
2193 5365 2.169978 CCTCTCAAGGCTGATGATGTCA 59.830 50.000 0.00 0.00 35.37 3.58
2492 5704 1.889105 CGCCTGCGATTACCTGCAT 60.889 57.895 5.43 0.00 40.89 3.96
2527 5739 4.307432 CACCTCCACGGTATGATTCATAC 58.693 47.826 23.07 23.07 46.94 2.39
2943 6279 1.982938 GCTGGACACCCTCTACCGT 60.983 63.158 0.00 0.00 0.00 4.83
3223 6574 3.817084 TCAAAGATTGAACAGGTGCTGAG 59.183 43.478 0.00 0.00 36.59 3.35
3233 6584 1.278985 CAGGTGCTGAGGGATTACACA 59.721 52.381 0.00 0.00 32.44 3.72
3518 6887 1.687493 GACCTGCTGCCCTCTACCT 60.687 63.158 0.00 0.00 0.00 3.08
3583 6953 6.479990 CACGGCTGATTGACTTCTTATTATCA 59.520 38.462 0.00 0.00 0.00 2.15
3856 7226 5.304101 AGTGAGTCTGAGTGAATCTTCTGTT 59.696 40.000 0.00 0.00 40.15 3.16
4030 8012 1.908344 ATGCATGTGTGTGTGCCTAA 58.092 45.000 0.00 0.00 40.56 2.69
4054 8045 1.317613 CTTGCTTGGCCTTGTGTGTA 58.682 50.000 3.32 0.00 0.00 2.90
4083 8074 2.098117 GCTGCTATGGTTGTGATGAACC 59.902 50.000 0.00 0.00 45.06 3.62
4164 11981 0.541863 TTGCCCTGGCTAGCTAGTTC 59.458 55.000 24.56 16.23 42.51 3.01
4283 12127 2.159421 GCTAGTGACTGAACCGATCGAA 60.159 50.000 18.66 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 2478 0.818040 GCTTTTCCGCCATATCCGGT 60.818 55.000 0.00 0.00 45.71 5.28
23 2497 4.036144 GCTGTGAAGATAAAATCAGAGGGC 59.964 45.833 2.71 0.00 37.41 5.19
26 2500 5.188434 TGGGCTGTGAAGATAAAATCAGAG 58.812 41.667 0.00 0.00 39.30 3.35
27 2501 5.178096 TGGGCTGTGAAGATAAAATCAGA 57.822 39.130 0.00 0.00 0.00 3.27
28 2502 5.591472 TGATGGGCTGTGAAGATAAAATCAG 59.409 40.000 0.00 0.00 0.00 2.90
29 2503 5.508567 TGATGGGCTGTGAAGATAAAATCA 58.491 37.500 0.00 0.00 0.00 2.57
30 2504 5.591877 ACTGATGGGCTGTGAAGATAAAATC 59.408 40.000 0.00 0.00 0.00 2.17
31 2505 5.513233 ACTGATGGGCTGTGAAGATAAAAT 58.487 37.500 0.00 0.00 0.00 1.82
44 2518 3.083997 GGGTCGGACTGATGGGCT 61.084 66.667 8.23 0.00 0.00 5.19
58 2532 2.904434 GTTCGGACTATGGGATATGGGT 59.096 50.000 0.00 0.00 0.00 4.51
258 2732 1.053424 TTGGTACCTGTGGGTGACTC 58.947 55.000 14.36 0.00 46.75 3.36
270 2744 1.134491 CCGGAACCTCAGATTGGTACC 60.134 57.143 4.43 4.43 36.69 3.34
275 2749 3.328382 TTGTACCGGAACCTCAGATTG 57.672 47.619 9.46 0.00 0.00 2.67
337 2811 3.655810 CTCCGCTCAGACCCAGCAC 62.656 68.421 0.00 0.00 36.61 4.40
340 2814 1.440893 CATCTCCGCTCAGACCCAG 59.559 63.158 0.00 0.00 0.00 4.45
348 2822 1.078848 AACAGCACCATCTCCGCTC 60.079 57.895 0.00 0.00 32.48 5.03
417 2894 2.104792 GAGGGGGAAATCATCGTCATCA 59.895 50.000 0.00 0.00 0.00 3.07
423 2900 3.713902 CCAGAGGGGGAAATCATCG 57.286 57.895 0.00 0.00 0.00 3.84
445 2923 1.204941 CGATTTCGTCAGGGGACTTCT 59.795 52.381 0.00 0.00 42.05 2.85
474 2953 1.322442 GCAGGAGCACTTTTGTCCTT 58.678 50.000 0.00 0.00 38.75 3.36
486 2965 2.982744 GCGAAACTTGGGCAGGAGC 61.983 63.158 0.00 0.00 41.10 4.70
519 2998 3.447944 GGAGACTACTTTCGGGATGAAGT 59.552 47.826 0.00 0.00 37.99 3.01
524 3003 6.809976 AAATAAGGAGACTACTTTCGGGAT 57.190 37.500 4.95 0.00 42.68 3.85
796 3786 3.292492 AGGGGAAGGGCGTAATAAAAG 57.708 47.619 0.00 0.00 0.00 2.27
823 3827 0.924090 CGGAAAGTATCAGTGCGAGC 59.076 55.000 0.00 0.00 0.00 5.03
985 4059 3.344215 CATCAGCGGCGATCTGGC 61.344 66.667 12.98 0.00 40.44 4.85
986 4060 2.664185 CCATCAGCGGCGATCTGG 60.664 66.667 12.98 10.31 32.63 3.86
987 4061 3.344215 GCCATCAGCGGCGATCTG 61.344 66.667 12.98 9.95 43.52 2.90
1517 4599 2.846532 CAAGACACCAGCCCCCTT 59.153 61.111 0.00 0.00 0.00 3.95
2146 5315 0.670162 TGCTGCTGAAAAGAGTTGCC 59.330 50.000 0.00 0.00 0.00 4.52
2193 5365 3.492383 CGCAATATGCTGTCGATTTCTCT 59.508 43.478 0.43 0.00 42.25 3.10
2492 5704 2.497675 GTGGAGGTGCATCTTGAGAGTA 59.502 50.000 0.00 0.00 0.00 2.59
2943 6279 0.106769 TGCAGTTCACCCAGCTGAAA 60.107 50.000 17.39 0.76 31.90 2.69
3223 6574 2.143876 ATGCTGGGTTGTGTAATCCC 57.856 50.000 0.00 0.00 36.14 3.85
3518 6887 3.072476 GGGGCTTACCTGCATAGTCATAA 59.928 47.826 0.00 0.00 40.03 1.90
3583 6953 6.448006 GTTGAGTGAGACTACTACAACACAT 58.552 40.000 0.00 0.00 37.91 3.21
4030 8012 0.760572 ACAAGGCCAAGCAAGCAAAT 59.239 45.000 5.01 0.00 0.00 2.32
4054 8045 3.194116 CACAACCATAGCAGCCTGATTTT 59.806 43.478 0.00 0.00 0.00 1.82
4083 8074 3.313012 TTCTGGACAACATAGGTCACG 57.687 47.619 0.00 0.00 37.00 4.35
4088 11904 6.764308 ATGATGTTTTCTGGACAACATAGG 57.236 37.500 13.01 0.00 42.46 2.57
4164 11981 9.816354 TTTCAAAAATTCCCTGTAAGAAAAGAG 57.184 29.630 0.00 0.00 34.07 2.85
4270 12114 1.002366 CCTGCTTTCGATCGGTTCAG 58.998 55.000 16.41 15.83 0.00 3.02
4620 12470 2.162681 CATGAGTTTCTTTCCCCGCTT 58.837 47.619 0.00 0.00 0.00 4.68
4622 12472 1.821216 TCATGAGTTTCTTTCCCCGC 58.179 50.000 0.00 0.00 0.00 6.13
4623 12473 5.428253 TCTAATCATGAGTTTCTTTCCCCG 58.572 41.667 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.