Multiple sequence alignment - TraesCS1B01G028700

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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 TraesCS1B01G028700 chr1B 100.000 6830 0 0 1 6830 13964202 13971031 0.000000e+00 12613.0
1 TraesCS1B01G028700 chr1B 98.489 1522 16 4 2772 4289 556661187 556659669 0.000000e+00 2676.0
2 TraesCS1B01G028700 chr1B 99.763 422 0 1 1785 2205 13967744 13968165 0.000000e+00 773.0
3 TraesCS1B01G028700 chr1B 99.289 422 2 1 1785 2205 556660413 556659992 0.000000e+00 761.0
4 TraesCS1B01G028700 chr1B 99.099 333 3 0 2474 2806 13968158 13968490 3.530000e-167 599.0
5 TraesCS1B01G028700 chr1B 98.799 333 2 1 2474 2806 556659999 556659669 5.900000e-165 592.0
6 TraesCS1B01G028700 chr1B 95.439 285 13 0 1 285 569704838 569705122 8.080000e-124 455.0
7 TraesCS1B01G028700 chr5B 99.119 1816 13 2 2474 4289 697005424 697007236 0.000000e+00 3262.0
8 TraesCS1B01G028700 chr5B 99.465 747 4 0 3543 4289 697005010 697005756 0.000000e+00 1358.0
9 TraesCS1B01G028700 chr5B 99.526 422 1 1 1785 2205 697005010 697005431 0.000000e+00 767.0
10 TraesCS1B01G028700 chr5B 99.526 422 1 1 1785 2205 697006492 697006913 0.000000e+00 767.0
11 TraesCS1B01G028700 chr5B 99.399 333 0 1 2474 2806 697006906 697007236 2.730000e-168 603.0
12 TraesCS1B01G028700 chr5B 95.017 301 11 3 2198 2498 451177109 451177405 2.880000e-128 470.0
13 TraesCS1B01G028700 chr5B 94.700 283 15 0 3 285 56592804 56593086 2.260000e-119 440.0
14 TraesCS1B01G028700 chr4A 98.789 1816 22 0 2474 4289 726804520 726806335 0.000000e+00 3232.0
15 TraesCS1B01G028700 chr4A 99.197 747 6 0 3543 4289 726804106 726804852 0.000000e+00 1347.0
16 TraesCS1B01G028700 chr4A 99.526 422 1 1 1785 2205 726804106 726804527 0.000000e+00 767.0
17 TraesCS1B01G028700 chr4A 98.815 422 4 1 1785 2205 726805589 726806010 0.000000e+00 750.0
18 TraesCS1B01G028700 chr4A 99.399 333 2 0 2474 2806 726806003 726806335 7.580000e-169 604.0
19 TraesCS1B01G028700 chr4A 87.847 288 35 0 3177 3464 705905766 705905479 8.490000e-89 339.0
20 TraesCS1B01G028700 chr4A 83.462 260 37 5 6355 6611 640611950 640612206 3.180000e-58 237.0
21 TraesCS1B01G028700 chr4A 83.333 258 37 6 6357 6611 656555847 656556101 4.120000e-57 233.0
22 TraesCS1B01G028700 chr3B 98.681 1820 21 2 2474 4292 623943009 623944826 0.000000e+00 3225.0
23 TraesCS1B01G028700 chr3B 85.706 1749 183 29 4297 6017 154439019 154440728 0.000000e+00 1783.0
24 TraesCS1B01G028700 chr3B 98.527 747 9 1 3543 4289 623942595 623943339 0.000000e+00 1317.0
25 TraesCS1B01G028700 chr3B 98.595 427 4 2 1780 2205 623942591 623943016 0.000000e+00 754.0
26 TraesCS1B01G028700 chr3B 98.815 422 4 1 1785 2205 623944076 623944497 0.000000e+00 750.0
27 TraesCS1B01G028700 chr3B 77.937 1396 161 74 481 1782 154437672 154439014 0.000000e+00 736.0
28 TraesCS1B01G028700 chr3B 99.700 333 1 0 2474 2806 623944490 623944822 1.630000e-170 610.0
29 TraesCS1B01G028700 chr3B 95.341 279 12 1 1 279 647231603 647231880 6.290000e-120 442.0
30 TraesCS1B01G028700 chr3B 84.556 259 32 8 6357 6611 199545418 199545164 4.090000e-62 250.0
31 TraesCS1B01G028700 chr3B 78.261 414 66 17 2624 3026 792724280 792724680 1.900000e-60 244.0
32 TraesCS1B01G028700 chr3B 94.828 58 3 0 350 407 154437632 154437575 2.620000e-14 91.6
33 TraesCS1B01G028700 chr3B 81.373 102 17 2 999 1099 810251036 810251136 1.580000e-11 82.4
34 TraesCS1B01G028700 chr3B 94.595 37 2 0 1065 1101 28699254 28699290 2.660000e-04 58.4
35 TraesCS1B01G028700 chr3B 94.595 37 2 0 1065 1101 823809284 823809320 2.660000e-04 58.4
36 TraesCS1B01G028700 chrUn 94.118 1615 81 8 4291 5893 96549742 96551354 0.000000e+00 2444.0
37 TraesCS1B01G028700 chrUn 89.104 1340 76 15 481 1784 96548440 96549745 0.000000e+00 1602.0
38 TraesCS1B01G028700 chrUn 99.059 744 7 0 3546 4289 181270282 181269539 0.000000e+00 1336.0
39 TraesCS1B01G028700 chrUn 96.791 748 17 2 3543 4289 104669849 104669108 0.000000e+00 1242.0
40 TraesCS1B01G028700 chrUn 99.045 419 3 1 1788 2205 181270282 181269864 0.000000e+00 750.0
41 TraesCS1B01G028700 chrUn 99.701 335 1 0 2474 2808 181269871 181269537 1.260000e-171 614.0
42 TraesCS1B01G028700 chrUn 87.395 119 9 1 5888 6006 96555081 96555193 1.550000e-26 132.0
43 TraesCS1B01G028700 chr1A 92.757 1643 100 10 4290 5914 10971416 10969775 0.000000e+00 2357.0
44 TraesCS1B01G028700 chr1A 86.832 1086 61 30 617 1656 10972546 10971497 0.000000e+00 1138.0
45 TraesCS1B01G028700 chr1A 89.241 158 17 0 481 638 10972751 10972594 1.500000e-46 198.0
46 TraesCS1B01G028700 chr1A 97.727 88 1 1 1697 1784 10971498 10971412 4.270000e-32 150.0
47 TraesCS1B01G028700 chr1A 83.486 109 15 2 3467 3572 44315092 44314984 1.570000e-16 99.0
48 TraesCS1B01G028700 chr1D 90.847 1464 90 27 4493 5928 9645684 9644237 0.000000e+00 1921.0
49 TraesCS1B01G028700 chr1D 87.520 625 42 23 607 1209 9646753 9646143 0.000000e+00 689.0
50 TraesCS1B01G028700 chr1D 92.453 265 19 1 4903 5167 9642495 9642232 1.800000e-100 377.0
51 TraesCS1B01G028700 chr1D 92.827 237 11 4 1201 1431 9645963 9645727 8.490000e-89 339.0
52 TraesCS1B01G028700 chr3D 86.070 1608 171 21 4290 5866 103789051 103790636 0.000000e+00 1679.0
53 TraesCS1B01G028700 chr3D 79.519 1372 146 60 481 1785 103787753 103789056 0.000000e+00 852.0
54 TraesCS1B01G028700 chr3D 86.819 349 44 1 3118 3464 500139670 500139322 8.310000e-104 388.0
55 TraesCS1B01G028700 chr3D 90.217 92 7 2 350 439 103667353 103667262 1.200000e-22 119.0
56 TraesCS1B01G028700 chr3D 78.947 95 20 0 1005 1099 603634715 603634621 1.590000e-06 65.8
57 TraesCS1B01G028700 chr3D 78.788 99 17 2 1005 1101 602449605 602449509 5.720000e-06 63.9
58 TraesCS1B01G028700 chr3A 85.081 1173 132 15 4797 5933 552539231 552538066 0.000000e+00 1157.0
59 TraesCS1B01G028700 chr3A 91.766 668 50 4 2733 3395 660004770 660004103 0.000000e+00 924.0
60 TraesCS1B01G028700 chr3A 91.467 668 52 4 2733 3395 660014867 660014200 0.000000e+00 913.0
61 TraesCS1B01G028700 chr3A 95.677 532 20 3 3345 3875 9487511 9488040 0.000000e+00 852.0
62 TraesCS1B01G028700 chr3A 85.579 527 51 8 4290 4805 552542761 552542249 4.690000e-146 529.0
63 TraesCS1B01G028700 chr3A 78.953 898 94 48 933 1785 552543603 552542756 2.180000e-144 523.0
64 TraesCS1B01G028700 chr3A 97.173 283 8 0 2199 2481 724060669 724060387 4.790000e-131 479.0
65 TraesCS1B01G028700 chr3A 80.492 569 93 15 6054 6616 518710369 518709813 2.950000e-113 420.0
66 TraesCS1B01G028700 chr3A 87.365 277 32 3 1 276 50966198 50966472 1.430000e-81 315.0
67 TraesCS1B01G028700 chr3A 84.291 261 35 5 6355 6612 747097723 747097980 4.090000e-62 250.0
68 TraesCS1B01G028700 chr3A 83.908 261 36 5 6355 6612 747137834 747138091 1.900000e-60 244.0
69 TraesCS1B01G028700 chr3A 83.525 261 37 5 6355 6612 747117855 747118112 8.850000e-59 239.0
70 TraesCS1B01G028700 chr3A 78.641 103 18 4 999 1099 732419297 732419397 1.590000e-06 65.8
71 TraesCS1B01G028700 chr7D 83.378 1131 122 44 2693 3787 277899251 277900351 0.000000e+00 987.0
72 TraesCS1B01G028700 chr2A 92.357 628 44 3 2771 3395 174035209 174035835 0.000000e+00 891.0
73 TraesCS1B01G028700 chr2A 98.540 274 4 0 2201 2474 650241299 650241026 1.030000e-132 484.0
74 TraesCS1B01G028700 chr2A 95.088 285 14 0 1 285 733425774 733426058 3.760000e-122 449.0
75 TraesCS1B01G028700 chr6B 97.193 285 8 0 1 285 27117982 27117698 3.700000e-132 483.0
76 TraesCS1B01G028700 chr6B 88.413 397 38 6 3178 3571 712477061 712476670 8.020000e-129 472.0
77 TraesCS1B01G028700 chr6B 95.439 285 13 0 2199 2483 49551605 49551321 8.080000e-124 455.0
78 TraesCS1B01G028700 chr6B 80.620 129 14 8 3484 3607 712477494 712477372 9.430000e-14 89.8
79 TraesCS1B01G028700 chr5A 97.491 279 7 0 2199 2477 650689305 650689583 1.720000e-130 477.0
80 TraesCS1B01G028700 chr5A 87.500 288 36 0 3174 3461 555170976 555171263 3.950000e-87 333.0
81 TraesCS1B01G028700 chr6D 96.491 285 10 0 1 285 106666825 106666541 8.020000e-129 472.0
82 TraesCS1B01G028700 chr7A 96.491 285 9 1 2194 2478 660936838 660936555 2.880000e-128 470.0
83 TraesCS1B01G028700 chr7A 82.437 279 40 9 6345 6620 26582877 26583149 1.150000e-57 235.0
84 TraesCS1B01G028700 chr2B 97.445 274 7 0 2201 2474 748596579 748596852 1.040000e-127 468.0
85 TraesCS1B01G028700 chr2B 83.525 261 36 6 6355 6612 115052015 115052271 3.180000e-58 237.0
86 TraesCS1B01G028700 chr2B 79.381 291 50 9 2693 2979 116257736 116257452 5.400000e-46 196.0
87 TraesCS1B01G028700 chr7B 96.085 281 9 1 2194 2474 81417492 81417770 2.250000e-124 457.0
88 TraesCS1B01G028700 chr4B 96.057 279 11 0 2199 2477 479214971 479214693 8.080000e-124 455.0
89 TraesCS1B01G028700 chr4B 93.684 285 16 1 1 285 424063294 424063012 6.330000e-115 425.0
90 TraesCS1B01G028700 chr5D 93.684 285 18 0 1 285 377296672 377296388 1.760000e-115 427.0
91 TraesCS1B01G028700 chr4D 83.333 258 38 5 6357 6612 302780375 302780629 4.120000e-57 233.0


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 TraesCS1B01G028700 chr1B 13964202 13971031 6829 False 4661.666667 12613 99.620667 1 6830 3 chr1B.!!$F2 6829
1 TraesCS1B01G028700 chr1B 556659669 556661187 1518 True 1343.000000 2676 98.859000 1785 4289 3 chr1B.!!$R1 2504
2 TraesCS1B01G028700 chr5B 697005010 697007236 2226 False 1351.400000 3262 99.407000 1785 4289 5 chr5B.!!$F3 2504
3 TraesCS1B01G028700 chr4A 726804106 726806335 2229 False 1340.000000 3232 99.145200 1785 4289 5 chr4A.!!$F3 2504
4 TraesCS1B01G028700 chr3B 623942591 623944826 2235 False 1331.200000 3225 98.863600 1780 4292 5 chr3B.!!$F7 2512
5 TraesCS1B01G028700 chr3B 154437672 154440728 3056 False 1259.500000 1783 81.821500 481 6017 2 chr3B.!!$F6 5536
6 TraesCS1B01G028700 chrUn 96548440 96555193 6753 False 1392.666667 2444 90.205667 481 6006 3 chrUn.!!$F1 5525
7 TraesCS1B01G028700 chrUn 104669108 104669849 741 True 1242.000000 1242 96.791000 3543 4289 1 chrUn.!!$R1 746
8 TraesCS1B01G028700 chrUn 181269537 181270282 745 True 900.000000 1336 99.268333 1788 4289 3 chrUn.!!$R2 2501
9 TraesCS1B01G028700 chr1A 10969775 10972751 2976 True 960.750000 2357 91.639250 481 5914 4 chr1A.!!$R2 5433
10 TraesCS1B01G028700 chr1D 9642232 9646753 4521 True 831.500000 1921 90.911750 607 5928 4 chr1D.!!$R1 5321
11 TraesCS1B01G028700 chr3D 103787753 103790636 2883 False 1265.500000 1679 82.794500 481 5866 2 chr3D.!!$F1 5385
12 TraesCS1B01G028700 chr3A 660004103 660004770 667 True 924.000000 924 91.766000 2733 3395 1 chr3A.!!$R2 662
13 TraesCS1B01G028700 chr3A 660014200 660014867 667 True 913.000000 913 91.467000 2733 3395 1 chr3A.!!$R3 662
14 TraesCS1B01G028700 chr3A 9487511 9488040 529 False 852.000000 852 95.677000 3345 3875 1 chr3A.!!$F1 530
15 TraesCS1B01G028700 chr3A 552538066 552543603 5537 True 736.333333 1157 83.204333 933 5933 3 chr3A.!!$R5 5000
16 TraesCS1B01G028700 chr3A 518709813 518710369 556 True 420.000000 420 80.492000 6054 6616 1 chr3A.!!$R1 562
17 TraesCS1B01G028700 chr7D 277899251 277900351 1100 False 987.000000 987 83.378000 2693 3787 1 chr7D.!!$F1 1094
18 TraesCS1B01G028700 chr2A 174035209 174035835 626 False 891.000000 891 92.357000 2771 3395 1 chr2A.!!$F1 624
19 TraesCS1B01G028700 chr6B 712476670 712477494 824 True 280.900000 472 84.516500 3178 3607 2 chr6B.!!$R3 429


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
461 462 0.039074 CGCAGTGTTCGTCTCCTCTT 60.039 55.000 0.00 0.00 0.00 2.85 F
474 475 0.104855 TCCTCTTTGATGCCGATCGG 59.895 55.000 30.03 30.03 38.57 4.18 F
475 476 0.104855 CCTCTTTGATGCCGATCGGA 59.895 55.000 37.64 21.99 37.50 4.55 F
1227 1541 0.109132 CTGTTGAAAGGAATGCCGGC 60.109 55.000 22.73 22.73 39.96 6.13 F
2208 2583 0.110295 TGTGTGCTGTTAGGGCATGT 59.890 50.000 0.00 0.00 41.86 3.21 F
2452 2827 1.005097 TCCTACGTGGCACTCCTAAGA 59.995 52.381 16.72 2.12 35.26 2.10 F
4106 4520 1.282157 GTGGTAGCCAAGGGAAGTGAT 59.718 52.381 0.00 0.00 34.18 3.06 F
4467 4894 1.021390 AAGAGCATCCCGTTCGCTTG 61.021 55.000 0.00 0.00 35.75 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2454 2829 0.332632 AGGGCATGTACAATGGTGCT 59.667 50.000 16.47 0.0 37.70 4.40 R
2470 2845 1.079127 CACACTCGGCCACTAAGGG 60.079 63.158 2.24 0.0 38.09 3.95 R
2471 2846 1.079127 CCACACTCGGCCACTAAGG 60.079 63.158 2.24 0.0 41.84 2.69 R
2987 3381 0.036732 GGCCTGTCACCATCTTGTCA 59.963 55.000 0.00 0.0 0.00 3.58 R
4106 4520 1.003118 AGACACGATAGCTTTGCCCAA 59.997 47.619 0.00 0.0 42.67 4.12 R
4443 4870 2.803492 GCGAACGGGATGCTCTTAAGAT 60.803 50.000 5.44 0.0 0.00 2.40 R
5116 8586 0.035439 TTGACCCGCCTCCAAATCTC 60.035 55.000 0.00 0.0 0.00 2.75 R
6036 13286 0.103026 TGACCATCGAGGCGATCTTG 59.897 55.000 0.00 0.0 45.19 3.02 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)



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

AutoCloner maintained by Alex Coulton.