Multiple sequence alignment - TraesCS1A01G313900

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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 TraesCS1A01G313900 chr1A 100.000 4437 0 0 1 4437 505484988 505480552 0.000000e+00 8194.0
1 TraesCS1A01G313900 chr1A 89.041 365 34 2 996 1360 505480935 505480577 8.750000e-122 448.0
2 TraesCS1A01G313900 chr1A 89.041 365 34 2 4054 4412 505483993 505483629 8.750000e-122 448.0
3 TraesCS1A01G313900 chr1A 95.968 248 10 0 1 248 41258345 41258592 1.920000e-108 403.0
4 TraesCS1A01G313900 chr1A 85.149 404 39 12 1220 1610 523757246 523756851 1.160000e-105 394.0
5 TraesCS1A01G313900 chr1A 88.201 339 19 11 1255 1585 552504549 552504874 6.960000e-103 385.0
6 TraesCS1A01G313900 chr1A 91.579 95 7 1 2272 2365 531647146 531647240 3.600000e-26 130.0
7 TraesCS1A01G313900 chr1D 92.654 1443 61 20 2427 3849 409527681 409526264 0.000000e+00 2036.0
8 TraesCS1A01G313900 chr1D 88.664 988 39 30 656 1611 409529395 409528449 0.000000e+00 1136.0
9 TraesCS1A01G313900 chr1D 91.262 515 17 16 3901 4410 409526181 409525690 0.000000e+00 676.0
10 TraesCS1A01G313900 chr1D 80.691 782 89 32 1523 2281 409528426 409527684 6.490000e-153 551.0
11 TraesCS1A01G313900 chr1D 89.385 358 32 2 1000 1357 409526042 409525691 3.150000e-121 446.0
12 TraesCS1A01G313900 chr1D 89.167 360 30 3 4054 4404 409529062 409528703 1.460000e-119 440.0
13 TraesCS1A01G313900 chr1D 87.071 379 25 7 292 656 258360846 258360478 1.490000e-109 407.0
14 TraesCS1A01G313900 chr1D 95.547 247 10 1 1 247 12486665 12486420 1.160000e-105 394.0
15 TraesCS1A01G313900 chr1D 77.537 601 93 28 2870 3437 409525322 409524731 1.540000e-84 324.0
16 TraesCS1A01G313900 chr1D 90.909 99 5 3 2267 2365 192809902 192809996 3.600000e-26 130.0
17 TraesCS1A01G313900 chr1D 94.203 69 3 1 2364 2431 407351158 407351090 2.180000e-18 104.0
18 TraesCS1A01G313900 chr1B 93.394 1211 59 14 2427 3626 551232499 551231299 0.000000e+00 1773.0
19 TraesCS1A01G313900 chr1B 91.024 947 25 21 738 1651 551234015 551233096 0.000000e+00 1223.0
20 TraesCS1A01G313900 chr1B 92.203 513 18 10 3909 4410 551230770 551230269 0.000000e+00 706.0
21 TraesCS1A01G313900 chr1B 88.976 508 27 15 1099 1585 39564955 39565454 6.350000e-168 601.0
22 TraesCS1A01G313900 chr1B 88.827 358 34 2 1000 1357 551230621 551230270 6.820000e-118 435.0
23 TraesCS1A01G313900 chr1B 88.140 371 32 3 4054 4412 551233769 551233399 8.820000e-117 431.0
24 TraesCS1A01G313900 chr1B 78.209 592 96 25 2870 3437 551229898 551229316 9.130000e-92 348.0
25 TraesCS1A01G313900 chr1B 85.075 268 25 4 4157 4409 39564955 39565222 4.400000e-65 259.0
26 TraesCS1A01G313900 chr1B 84.651 215 12 8 3638 3851 551231238 551231044 1.260000e-45 195.0
27 TraesCS1A01G313900 chr1B 95.455 66 3 0 2364 2429 22433831 22433766 6.070000e-19 106.0
28 TraesCS1A01G313900 chr1B 96.825 63 2 0 580 642 622949511 622949573 6.070000e-19 106.0
29 TraesCS1A01G313900 chr6A 88.845 502 30 14 1099 1585 595961327 595961817 1.060000e-165 593.0
30 TraesCS1A01G313900 chr6A 90.659 364 21 6 292 642 584509499 584509136 5.190000e-129 472.0
31 TraesCS1A01G313900 chr6A 95.968 248 6 2 1 244 528946745 528946498 2.490000e-107 399.0
32 TraesCS1A01G313900 chr6A 96.875 64 1 1 580 642 38946847 38946784 6.070000e-19 106.0
33 TraesCS1A01G313900 chr6A 100.000 32 0 0 243 274 584509532 584509501 4.790000e-05 60.2
34 TraesCS1A01G313900 chr3B 86.704 534 41 13 1099 1610 10181197 10181722 2.320000e-157 566.0
35 TraesCS1A01G313900 chr3B 95.918 245 10 0 1 245 768201329 768201085 8.940000e-107 398.0
36 TraesCS1A01G313900 chr3B 81.303 353 66 0 4057 4409 571602078 571602430 2.020000e-73 287.0
37 TraesCS1A01G313900 chr3B 83.704 270 25 8 4157 4409 10181197 10181464 2.060000e-58 237.0
38 TraesCS1A01G313900 chr3B 91.667 96 6 2 2270 2365 756059631 756059724 1.000000e-26 132.0
39 TraesCS1A01G313900 chr3B 96.875 64 1 1 580 642 131527921 131527984 6.070000e-19 106.0
40 TraesCS1A01G313900 chr6B 84.646 508 49 17 1099 1585 148312313 148311814 3.100000e-131 479.0
41 TraesCS1A01G313900 chr6B 95.492 244 11 0 1 244 489487608 489487365 1.500000e-104 390.0
42 TraesCS1A01G313900 chr6B 94.382 89 5 0 2277 2365 609097530 609097618 2.150000e-28 137.0
43 TraesCS1A01G313900 chr6B 89.041 73 4 4 571 642 131674655 131674724 2.200000e-13 87.9
44 TraesCS1A01G313900 chr2A 85.030 501 40 18 1099 1585 287751470 287751949 1.120000e-130 477.0
45 TraesCS1A01G313900 chr2A 95.547 247 7 1 1 247 79464591 79464349 4.160000e-105 392.0
46 TraesCS1A01G313900 chr2A 87.162 148 11 4 2135 2281 19648316 19648176 1.280000e-35 161.0
47 TraesCS1A01G313900 chr5B 96.327 245 7 2 1 244 551809230 551808987 6.910000e-108 401.0
48 TraesCS1A01G313900 chr5B 90.816 98 7 2 2269 2365 132614188 132614284 3.600000e-26 130.0
49 TraesCS1A01G313900 chr5B 87.778 90 9 2 2364 2452 550925113 550925201 2.180000e-18 104.0
50 TraesCS1A01G313900 chr5A 95.142 247 11 1 1 246 10833020 10832774 5.380000e-104 388.0
51 TraesCS1A01G313900 chr5A 94.253 87 5 0 2279 2365 6596313 6596227 2.780000e-27 134.0
52 TraesCS1A01G313900 chr2B 95.161 248 8 1 1 248 543165524 543165281 5.380000e-104 388.0
53 TraesCS1A01G313900 chr2B 74.771 872 174 38 2593 3437 699048592 699049444 2.540000e-92 350.0
54 TraesCS1A01G313900 chr2B 83.146 356 46 8 4057 4409 699039996 699040340 3.330000e-81 313.0
55 TraesCS1A01G313900 chr3A 84.488 361 50 6 1000 1360 574255302 574255656 7.060000e-93 351.0
56 TraesCS1A01G313900 chr3A 81.395 387 68 4 4024 4409 574255270 574255653 3.330000e-81 313.0
57 TraesCS1A01G313900 chr3A 85.714 224 16 11 1375 1585 678045161 678044941 5.780000e-54 222.0
58 TraesCS1A01G313900 chr3A 83.152 184 31 0 4229 4412 678053202 678053019 7.630000e-38 169.0
59 TraesCS1A01G313900 chr3D 81.586 353 65 0 4057 4409 435444004 435444356 4.340000e-75 292.0
60 TraesCS1A01G313900 chr3D 84.158 101 13 2 4262 4359 608304498 608304598 1.310000e-15 95.3
61 TraesCS1A01G313900 chr4A 96.386 83 3 0 2283 2365 575736535 575736453 2.150000e-28 137.0
62 TraesCS1A01G313900 chr4A 96.721 61 2 0 582 642 311258804 311258864 7.850000e-18 102.0
63 TraesCS1A01G313900 chr4A 86.364 88 5 7 560 642 636011332 636011247 6.110000e-14 89.8
64 TraesCS1A01G313900 chr2D 96.341 82 3 0 2284 2365 174430834 174430753 7.740000e-28 135.0
65 TraesCS1A01G313900 chr2D 95.238 63 3 0 582 644 180078198 180078260 2.820000e-17 100.0
66 TraesCS1A01G313900 chr7B 90.000 100 8 2 2286 2384 451446881 451446979 1.300000e-25 128.0
67 TraesCS1A01G313900 chr7B 84.694 98 12 2 4265 4359 458528451 458528548 1.310000e-15 95.3
68 TraesCS1A01G313900 chr4B 92.208 77 5 1 2364 2440 370917045 370916970 1.690000e-19 108.0
69 TraesCS1A01G313900 chr7D 94.203 69 4 0 2364 2432 92212915 92212983 6.070000e-19 106.0
70 TraesCS1A01G313900 chr7D 94.203 69 3 1 2364 2431 271541795 271541863 2.180000e-18 104.0
71 TraesCS1A01G313900 chr5D 95.455 66 3 0 2364 2429 222673166 222673231 6.070000e-19 106.0
72 TraesCS1A01G313900 chr5D 94.118 68 4 0 2364 2431 226705879 226705946 2.180000e-18 104.0
73 TraesCS1A01G313900 chr7A 92.105 76 3 3 2368 2441 547951709 547951783 2.180000e-18 104.0
74 TraesCS1A01G313900 chr7A 95.082 61 2 1 581 641 14414629 14414570 1.310000e-15 95.3


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 TraesCS1A01G313900 chr1A 505480552 505484988 4436 True 8194.000000 8194 100.000000 1 4437 1 chr1A.!!$R1 4436
1 TraesCS1A01G313900 chr1A 505480577 505483993 3416 True 448.000000 448 89.041000 996 4412 2 chr1A.!!$R3 3416
2 TraesCS1A01G313900 chr1D 409524731 409529395 4664 True 801.285714 2036 87.051429 656 4410 7 chr1D.!!$R4 3754
3 TraesCS1A01G313900 chr1B 551229316 551234015 4699 True 730.142857 1773 88.064000 738 4412 7 chr1B.!!$R2 3674
4 TraesCS1A01G313900 chr3B 10181197 10181722 525 False 401.500000 566 85.204000 1099 4409 2 chr3B.!!$F4 3310
5 TraesCS1A01G313900 chr2B 699048592 699049444 852 False 350.000000 350 74.771000 2593 3437 1 chr2B.!!$F2 844


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
371 372 0.032515 TTCCCTAGATCCAGACGGCA 60.033 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4414 4934 4.071961 TCCGAATGTCCAATCCTACATG 57.928 45.455 0.0 0.0 36.47 3.21 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)



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AutoCloner maintained by Alex Coulton.