Multiple sequence alignment - TraesCS6B01G409100

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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 TraesCS6B01G409100 chr6B 100.000 3347 0 0 1 3347 683370664 683374010 0.000000e+00 6181.0
1 TraesCS6B01G409100 chr6B 97.379 1297 31 1 1 1294 683316049 683317345 0.000000e+00 2204.0
2 TraesCS6B01G409100 chr6B 97.677 1076 23 2 1873 2948 683317379 683318452 0.000000e+00 1847.0
3 TraesCS6B01G409100 chr6B 90.465 430 31 3 995 1418 705881148 705880723 2.920000e-155 558.0
4 TraesCS6B01G409100 chr6B 94.199 362 21 0 1 362 683308214 683308575 1.360000e-153 553.0
5 TraesCS6B01G409100 chr6B 97.021 235 5 1 2973 3205 683319298 683319532 8.700000e-106 394.0
6 TraesCS6B01G409100 chr6B 96.970 33 1 0 2600 2632 683318008 683318040 4.670000e-04 56.5
7 TraesCS6B01G409100 chr2A 91.771 2151 81 28 462 2585 38614998 38612917 0.000000e+00 2904.0
8 TraesCS6B01G409100 chr2D 93.156 1388 58 15 1508 2868 605386712 605385335 0.000000e+00 2002.0
9 TraesCS6B01G409100 chr2D 93.317 793 26 10 731 1514 605387720 605386946 0.000000e+00 1146.0
10 TraesCS6B01G409100 chr2D 88.736 364 37 3 1 362 119179764 119180125 3.060000e-120 442.0
11 TraesCS6B01G409100 chr2D 89.922 258 21 3 2971 3225 514349503 514349758 8.950000e-86 327.0
12 TraesCS6B01G409100 chr2D 95.322 171 7 1 398 567 605388122 605387952 1.530000e-68 270.0
13 TraesCS6B01G409100 chr2D 89.524 105 5 4 595 699 605387816 605387718 9.750000e-26 128.0
14 TraesCS6B01G409100 chr2D 93.902 82 5 0 2867 2948 93593504 93593423 1.260000e-24 124.0
15 TraesCS6B01G409100 chr2D 91.463 82 7 0 2867 2948 41467794 41467713 2.730000e-21 113.0
16 TraesCS6B01G409100 chr5D 89.968 1585 97 22 837 2378 32810129 32811694 0.000000e+00 1989.0
17 TraesCS6B01G409100 chr5D 84.525 769 98 9 1578 2336 32699292 32698535 0.000000e+00 741.0
18 TraesCS6B01G409100 chr5D 85.300 483 50 13 844 1326 32709636 32709175 2.340000e-131 479.0
19 TraesCS6B01G409100 chr5D 95.327 107 4 1 2330 2435 42032711 42032605 5.740000e-38 169.0
20 TraesCS6B01G409100 chr5A 89.577 1583 102 25 837 2386 21418642 21420194 0.000000e+00 1951.0
21 TraesCS6B01G409100 chr5A 84.414 1604 162 44 827 2392 21415083 21413530 0.000000e+00 1496.0
22 TraesCS6B01G409100 chr7D 93.287 432 21 5 995 1418 500956170 500956601 6.090000e-177 630.0
23 TraesCS6B01G409100 chr7D 89.807 363 36 1 1 362 565591372 565591734 6.540000e-127 464.0
24 TraesCS6B01G409100 chr7D 88.372 387 30 9 2971 3347 11014286 11014667 5.090000e-123 451.0
25 TraesCS6B01G409100 chr7D 88.920 361 39 1 3 362 565575524 565575884 8.520000e-121 444.0
26 TraesCS6B01G409100 chr7D 88.705 363 37 4 1 362 228774288 228774647 1.100000e-119 440.0
27 TraesCS6B01G409100 chr7D 95.217 230 8 2 3119 3347 235462974 235463201 8.830000e-96 361.0
28 TraesCS6B01G409100 chr6D 96.032 378 12 2 2971 3347 382560263 382559888 2.210000e-171 612.0
29 TraesCS6B01G409100 chr6D 88.076 369 37 5 1 365 243369803 243369438 6.630000e-117 431.0
30 TraesCS6B01G409100 chr1D 94.709 378 17 2 2971 3347 192421551 192421926 4.810000e-163 584.0
31 TraesCS6B01G409100 chr1D 90.000 380 31 5 2971 3347 34531259 34530884 5.020000e-133 484.0
32 TraesCS6B01G409100 chr1D 88.736 364 38 3 1 362 314231637 314231999 3.060000e-120 442.0
33 TraesCS6B01G409100 chr1D 93.902 82 3 1 2867 2948 192420831 192420910 4.530000e-24 122.0
34 TraesCS6B01G409100 chr3B 75.336 1338 233 55 1081 2354 79979184 79980488 1.360000e-153 553.0
35 TraesCS6B01G409100 chr3B 74.257 1414 265 57 1078 2424 126302784 126301403 1.390000e-138 503.0
36 TraesCS6B01G409100 chr3B 74.410 805 131 43 1085 1826 126299443 126298651 3.290000e-70 276.0
37 TraesCS6B01G409100 chr4A 89.952 418 35 4 1001 1412 275447605 275448021 1.770000e-147 532.0
38 TraesCS6B01G409100 chr4A 92.424 66 4 1 2803 2868 725275644 725275708 3.560000e-15 93.5
39 TraesCS6B01G409100 chr3A 74.644 1404 253 66 1079 2420 94183438 94182076 2.960000e-145 525.0
40 TraesCS6B01G409100 chr3A 74.464 1120 201 56 1274 2338 94107021 94108110 4.020000e-109 405.0
41 TraesCS6B01G409100 chr3A 93.333 75 5 0 2874 2948 730419917 730419843 9.820000e-21 111.0
42 TraesCS6B01G409100 chr3A 96.491 57 2 0 2805 2861 38029818 38029762 9.890000e-16 95.3
43 TraesCS6B01G409100 chr3D 74.527 1374 260 58 1078 2396 50425054 50426392 1.780000e-142 516.0
44 TraesCS6B01G409100 chr3D 89.817 383 33 5 2966 3344 87489357 87489737 1.400000e-133 486.0
45 TraesCS6B01G409100 chr3D 88.624 378 33 6 2971 3343 21599570 21599198 5.090000e-123 451.0
46 TraesCS6B01G409100 chr3D 74.343 495 94 19 1542 2018 80600738 80600259 2.650000e-41 180.0
47 TraesCS6B01G409100 chr3D 73.596 534 106 23 1504 2018 80916905 80916388 4.440000e-39 172.0
48 TraesCS6B01G409100 chr4D 90.634 363 31 3 1 362 400458130 400458490 2.340000e-131 479.0
49 TraesCS6B01G409100 chr4D 89.433 388 30 6 2966 3347 401644823 401645205 2.340000e-131 479.0
50 TraesCS6B01G409100 chr5B 89.676 339 29 2 1165 1497 24105037 24104699 8.580000e-116 427.0
51 TraesCS6B01G409100 chr5B 96.281 242 7 1 3106 3347 382951902 382951663 2.420000e-106 396.0
52 TraesCS6B01G409100 chr5B 85.564 381 41 8 1583 1960 24104641 24104272 1.460000e-103 387.0
53 TraesCS6B01G409100 chr5B 83.117 308 33 11 850 1157 24106647 24106359 2.560000e-66 263.0
54 TraesCS6B01G409100 chr5B 82.353 221 34 5 2164 2383 24104276 24104060 1.590000e-43 187.0
55 TraesCS6B01G409100 chr2B 94.048 84 5 0 2865 2948 415364635 415364718 9.750000e-26 128.0
56 TraesCS6B01G409100 chr1A 91.463 82 7 0 2867 2948 497485608 497485527 2.730000e-21 113.0
57 TraesCS6B01G409100 chr1A 93.333 75 5 0 2874 2948 12786536 12786462 9.820000e-21 111.0
58 TraesCS6B01G409100 chr1A 93.939 66 3 1 2803 2868 576632065 576632001 7.640000e-17 99.0
59 TraesCS6B01G409100 chr7A 93.333 75 5 0 2874 2948 511450396 511450322 9.820000e-21 111.0
60 TraesCS6B01G409100 chr7A 96.491 57 2 0 2805 2861 480985722 480985778 9.890000e-16 95.3
61 TraesCS6B01G409100 chr7A 92.424 66 4 1 2803 2868 536709658 536709722 3.560000e-15 93.5
62 TraesCS6B01G409100 chr6A 93.939 66 4 0 2803 2868 8396050 8396115 2.120000e-17 100.0


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 TraesCS6B01G409100 chr6B 683370664 683374010 3346 False 6181.000 6181 100.00000 1 3347 1 chr6B.!!$F2 3346
1 TraesCS6B01G409100 chr6B 683316049 683319532 3483 False 1125.375 2204 97.26175 1 3205 4 chr6B.!!$F3 3204
2 TraesCS6B01G409100 chr2A 38612917 38614998 2081 True 2904.000 2904 91.77100 462 2585 1 chr2A.!!$R1 2123
3 TraesCS6B01G409100 chr2D 605385335 605388122 2787 True 886.500 2002 92.82975 398 2868 4 chr2D.!!$R3 2470
4 TraesCS6B01G409100 chr5D 32810129 32811694 1565 False 1989.000 1989 89.96800 837 2378 1 chr5D.!!$F1 1541
5 TraesCS6B01G409100 chr5D 32698535 32699292 757 True 741.000 741 84.52500 1578 2336 1 chr5D.!!$R1 758
6 TraesCS6B01G409100 chr5A 21418642 21420194 1552 False 1951.000 1951 89.57700 837 2386 1 chr5A.!!$F1 1549
7 TraesCS6B01G409100 chr5A 21413530 21415083 1553 True 1496.000 1496 84.41400 827 2392 1 chr5A.!!$R1 1565
8 TraesCS6B01G409100 chr1D 192420831 192421926 1095 False 353.000 584 94.30550 2867 3347 2 chr1D.!!$F2 480
9 TraesCS6B01G409100 chr3B 79979184 79980488 1304 False 553.000 553 75.33600 1081 2354 1 chr3B.!!$F1 1273
10 TraesCS6B01G409100 chr3B 126298651 126302784 4133 True 389.500 503 74.33350 1078 2424 2 chr3B.!!$R1 1346
11 TraesCS6B01G409100 chr3A 94182076 94183438 1362 True 525.000 525 74.64400 1079 2420 1 chr3A.!!$R2 1341
12 TraesCS6B01G409100 chr3A 94107021 94108110 1089 False 405.000 405 74.46400 1274 2338 1 chr3A.!!$F1 1064
13 TraesCS6B01G409100 chr3D 50425054 50426392 1338 False 516.000 516 74.52700 1078 2396 1 chr3D.!!$F1 1318
14 TraesCS6B01G409100 chr5B 24104060 24106647 2587 True 316.000 427 85.17750 850 2383 4 chr5B.!!$R2 1533

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
291 292 0.529992 GTCCTACTATGTGTGGCCGC 60.53 60.0 10.11 10.11 0.00 6.53 F
1736 3517 0.039911 AGGTTCTCCTACTGCCTCGT 59.96 55.0 0.00 0.00 43.12 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 4011 0.886563 CCGAACCCTCGTACTTCACT 59.113 55.000 0.0 0.0 43.87 3.41 R
2642 4478 4.051922 GACTCGCTTTTCGACATATGGAT 58.948 43.478 7.8 0.0 43.16 3.41 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
112 113 2.594592 GCTCGCCCTGTTGGTGTT 60.595 61.111 0.00 0.00 45.41 3.32
204 205 2.930562 ACCTCGCCCCTTTGCTCT 60.931 61.111 0.00 0.00 0.00 4.09
242 243 3.568007 GGCATTGTCTTGGTTGTCTTGTA 59.432 43.478 0.00 0.00 0.00 2.41
257 258 2.891580 TCTTGTACTTCGGCTTCTCTGT 59.108 45.455 0.00 0.00 0.00 3.41
269 270 1.544825 TTCTCTGTGGCTTCCCTCCG 61.545 60.000 0.00 0.00 0.00 4.63
277 278 1.684734 GCTTCCCTCCGTGGTCCTA 60.685 63.158 0.00 0.00 0.00 2.94
291 292 0.529992 GTCCTACTATGTGTGGCCGC 60.530 60.000 10.11 10.11 0.00 6.53
328 329 0.887387 GCCCGTGCACAAGTAAAGGA 60.887 55.000 18.64 0.00 37.47 3.36
336 337 5.273944 GTGCACAAGTAAAGGAGTCAAAAG 58.726 41.667 13.17 0.00 0.00 2.27
337 338 4.338118 TGCACAAGTAAAGGAGTCAAAAGG 59.662 41.667 0.00 0.00 0.00 3.11
344 345 1.734655 AGGAGTCAAAAGGAGAGCCA 58.265 50.000 0.00 0.00 36.29 4.75
356 357 4.538746 AGGAGAGCCACTACTTTTGTAC 57.461 45.455 0.00 0.00 36.13 2.90
359 360 3.995048 GAGAGCCACTACTTTTGTACACC 59.005 47.826 0.00 0.00 0.00 4.16
362 363 3.007614 AGCCACTACTTTTGTACACCGAT 59.992 43.478 0.00 0.00 0.00 4.18
365 366 5.472148 CCACTACTTTTGTACACCGATACA 58.528 41.667 0.00 0.00 33.18 2.29
377 378 1.135721 ACCGATACAGAACCTTACGGC 59.864 52.381 0.00 0.00 42.09 5.68
556 558 5.049818 GGATCAGTCGGCTTAATTTGATCTG 60.050 44.000 12.59 0.00 40.28 2.90
646 774 7.095229 CGTTTCTGAAAGGTCTAATGTTGATGA 60.095 37.037 13.21 0.00 0.00 2.92
728 856 4.034510 CCACTCGAATGCTTCATCCTAAAC 59.965 45.833 0.00 0.00 0.00 2.01
1338 2806 1.153489 CCTCGTGTGGCTCAGATGG 60.153 63.158 0.00 0.00 0.00 3.51
1464 2954 2.994995 TCGTGCCACTCGGTCCAT 60.995 61.111 0.00 0.00 33.28 3.41
1476 2966 2.606587 GGTCCATGGCACCTCCTGT 61.607 63.158 20.17 0.00 35.26 4.00
1644 3425 2.104253 CGCCAACTTCGCCGGTTAT 61.104 57.895 1.90 0.00 0.00 1.89
1736 3517 0.039911 AGGTTCTCCTACTGCCTCGT 59.960 55.000 0.00 0.00 43.12 4.18
1875 3662 1.004745 ACAGTCGAAATCATGGCCCTT 59.995 47.619 0.00 0.00 0.00 3.95
2196 4008 2.616330 CGTGTGCTTGGCCATCGTT 61.616 57.895 6.09 0.00 0.00 3.85
2199 4011 1.971167 GTGCTTGGCCATCGTTCCA 60.971 57.895 6.09 0.00 0.00 3.53
2532 4358 3.713826 TCCTCCCTGTAACATCCAAAC 57.286 47.619 0.00 0.00 0.00 2.93
2633 4469 4.884164 CCTCCCTGTAACATCCAAATTCTC 59.116 45.833 0.00 0.00 0.00 2.87
2679 4515 5.386958 AGCGAGTCTACATAGAAACAACA 57.613 39.130 0.00 0.00 33.47 3.33
2745 4703 7.952671 TCTCGCATCTTACTTTCTAACCATAT 58.047 34.615 0.00 0.00 0.00 1.78
2894 4862 3.892740 ATGCCCGTGCGTTGCTACA 62.893 57.895 0.00 0.00 41.78 2.74
2963 4931 9.056005 ACATGCACATTACTATGTTATAAGGTG 57.944 33.333 0.00 4.83 42.29 4.00
3230 6770 6.698380 TCCTTCTTGGACTTAATCACACTAC 58.302 40.000 0.00 0.00 40.56 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 3.927481 GAGCCACCCTTGAGCCCAC 62.927 68.421 0.00 0.00 0.00 4.61
156 157 1.982073 GCAAGATTCTTGTCGGGGCG 61.982 60.000 23.66 0.83 0.00 6.13
162 163 1.032114 CCCCCGGCAAGATTCTTGTC 61.032 60.000 23.66 21.40 0.00 3.18
163 164 1.000896 CCCCCGGCAAGATTCTTGT 60.001 57.895 23.66 0.00 0.00 3.16
204 205 3.719268 ATGCCAAGGTCAGATACACAA 57.281 42.857 0.00 0.00 0.00 3.33
242 243 1.004440 GCCACAGAGAAGCCGAAGT 60.004 57.895 0.00 0.00 0.00 3.01
257 258 3.319198 GACCACGGAGGGAAGCCA 61.319 66.667 1.11 0.00 43.89 4.75
269 270 1.134491 GGCCACACATAGTAGGACCAC 60.134 57.143 0.00 0.00 0.00 4.16
291 292 4.796231 AGTTAGAGCCACGCGCCG 62.796 66.667 5.73 0.00 38.78 6.46
328 329 3.243724 AGTAGTGGCTCTCCTTTTGACT 58.756 45.455 0.00 0.00 0.00 3.41
336 337 3.995048 GTGTACAAAAGTAGTGGCTCTCC 59.005 47.826 0.00 0.00 0.00 3.71
337 338 3.995048 GGTGTACAAAAGTAGTGGCTCTC 59.005 47.826 0.00 0.00 0.00 3.20
344 345 6.579666 TCTGTATCGGTGTACAAAAGTAGT 57.420 37.500 0.00 0.00 34.41 2.73
353 354 4.346129 CGTAAGGTTCTGTATCGGTGTAC 58.654 47.826 0.00 0.00 0.00 2.90
646 774 5.584251 CCGCCAGCCAAAAATAAATAAATGT 59.416 36.000 0.00 0.00 0.00 2.71
1338 2806 1.149148 GAGAAGCAGAACCGTTGGTC 58.851 55.000 0.00 0.00 33.12 4.02
1476 2966 2.377628 GACACAAGGAGGTGGCGTCA 62.378 60.000 0.00 0.00 43.08 4.35
1584 3356 3.429141 CTGGGCACTTGCAGCTCG 61.429 66.667 3.15 0.00 44.36 5.03
1585 3357 2.033141 TCTGGGCACTTGCAGCTC 59.967 61.111 3.15 0.00 44.36 4.09
1736 3517 1.153706 GCGTCGCTTAAGTAGGGCA 60.154 57.895 10.68 0.00 36.78 5.36
1875 3662 2.241281 TGATCGAGTTCCCAACCCTA 57.759 50.000 0.00 0.00 0.00 3.53
2196 4008 1.891150 GAACCCTCGTACTTCACTGGA 59.109 52.381 0.00 0.00 0.00 3.86
2199 4011 0.886563 CCGAACCCTCGTACTTCACT 59.113 55.000 0.00 0.00 43.87 3.41
2532 4358 4.213059 GCTTCTTGTCCTTGTTCTCTTGAG 59.787 45.833 0.00 0.00 0.00 3.02
2633 4469 8.375465 GCTTTTCGACATATGGATTTTTCTTTG 58.625 33.333 7.80 0.00 0.00 2.77
2642 4478 4.051922 GACTCGCTTTTCGACATATGGAT 58.948 43.478 7.80 0.00 43.16 3.41
2745 4703 7.692460 ACATGAATCTTTGCTGTCTAAATCA 57.308 32.000 0.00 0.00 0.00 2.57
3206 6746 5.825593 AGTGTGATTAAGTCCAAGAAGGA 57.174 39.130 0.00 0.00 46.75 3.36
3218 6758 6.509656 ACAGAACGTGAAGTAGTGTGATTAA 58.490 36.000 0.00 0.00 30.38 1.40


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

AutoCloner maintained by Alex Coulton.