Multiple sequence alignment - TraesCS1B01G391300

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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 TraesCS1B01G391300 chr1B 100.000 3984 0 0 1 3984 624667581 624663598 0.000000e+00 7358.0
1 TraesCS1B01G391300 chr1B 91.124 507 40 5 1 503 56132313 56132818 0.000000e+00 682.0
2 TraesCS1B01G391300 chr1B 95.122 82 4 0 3488 3569 624663985 624663904 3.230000e-26 130.0
3 TraesCS1B01G391300 chr1B 95.122 82 4 0 3597 3678 624664094 624664013 3.230000e-26 130.0
4 TraesCS1B01G391300 chr1B 97.297 37 1 0 2818 2854 624664693 624664657 3.320000e-06 63.9
5 TraesCS1B01G391300 chr1D 96.702 3153 70 10 1 3143 454171635 454168507 0.000000e+00 5216.0
6 TraesCS1B01G391300 chr1D 99.753 811 1 1 3175 3984 454168513 454167703 0.000000e+00 1485.0
7 TraesCS1B01G391300 chr1D 95.122 82 4 0 3488 3569 454168090 454168009 3.230000e-26 130.0
8 TraesCS1B01G391300 chr1D 95.122 82 4 0 3597 3678 454168199 454168118 3.230000e-26 130.0
9 TraesCS1B01G391300 chr1D 97.297 37 1 0 2818 2854 454168758 454168722 3.320000e-06 63.9
10 TraesCS1B01G391300 chr2B 89.565 1792 134 28 1059 2825 554720553 554722316 0.000000e+00 2224.0
11 TraesCS1B01G391300 chr2B 91.952 497 36 4 1 494 5440989 5441484 0.000000e+00 693.0
12 TraesCS1B01G391300 chr2B 91.549 497 39 3 1 494 5017480 5017976 0.000000e+00 682.0
13 TraesCS1B01G391300 chr2B 91.089 505 39 5 1 500 768457897 768457394 0.000000e+00 678.0
14 TraesCS1B01G391300 chr2B 90.965 487 34 7 3092 3569 42145981 42146466 0.000000e+00 647.0
15 TraesCS1B01G391300 chr2B 90.041 241 20 3 2858 3097 42145694 42145931 3.870000e-80 309.0
16 TraesCS1B01G391300 chr2B 87.719 228 19 6 3758 3984 42146483 42146702 1.420000e-64 257.0
17 TraesCS1B01G391300 chr2B 93.137 102 7 0 3594 3695 42146382 42146483 2.480000e-32 150.0
18 TraesCS1B01G391300 chr4A 86.052 1226 115 20 1608 2792 48299315 48300525 0.000000e+00 1266.0
19 TraesCS1B01G391300 chr4A 91.485 505 39 4 1 501 618919700 618919196 0.000000e+00 691.0
20 TraesCS1B01G391300 chr4D 85.614 994 104 10 1608 2565 415294103 415293113 0.000000e+00 1007.0
21 TraesCS1B01G391300 chr4D 93.860 228 12 2 2564 2791 415293009 415292784 3.810000e-90 342.0
22 TraesCS1B01G391300 chr6B 88.355 687 61 7 2142 2825 462685559 462684889 0.000000e+00 808.0
23 TraesCS1B01G391300 chr6B 94.430 377 18 2 1542 1916 462685934 462685559 9.600000e-161 577.0
24 TraesCS1B01G391300 chr6B 80.755 530 65 22 603 1131 252085509 252085016 2.910000e-101 379.0
25 TraesCS1B01G391300 chr6B 84.000 325 44 7 2284 2603 192915669 192915990 5.000000e-79 305.0
26 TraesCS1B01G391300 chr2D 92.475 505 33 5 1 500 199131858 199131354 0.000000e+00 717.0
27 TraesCS1B01G391300 chr2D 91.340 485 29 8 3092 3569 26767313 26767791 0.000000e+00 651.0
28 TraesCS1B01G391300 chr2D 90.041 241 20 3 2858 3097 26767026 26767263 3.870000e-80 309.0
29 TraesCS1B01G391300 chr2D 88.596 228 20 4 3758 3984 26767808 26768030 5.070000e-69 272.0
30 TraesCS1B01G391300 chr2D 92.157 102 8 0 3594 3695 26767707 26767808 1.150000e-30 145.0
31 TraesCS1B01G391300 chrUn 92.555 497 33 4 1 494 26663318 26663813 0.000000e+00 710.0
32 TraesCS1B01G391300 chr7B 90.927 507 38 7 1 502 746356031 746355528 0.000000e+00 675.0
33 TraesCS1B01G391300 chr7B 87.361 269 24 7 3717 3982 21254307 21254568 2.330000e-77 300.0
34 TraesCS1B01G391300 chr7B 81.395 129 19 4 1206 1331 68839887 68839761 2.530000e-17 100.0
35 TraesCS1B01G391300 chr7B 79.562 137 24 3 786 921 91779564 91779697 1.180000e-15 95.3
36 TraesCS1B01G391300 chr7B 95.918 49 2 0 3671 3719 21254200 21254248 3.300000e-11 80.5
37 TraesCS1B01G391300 chr2A 91.304 483 31 8 3092 3569 29098356 29098832 0.000000e+00 649.0
38 TraesCS1B01G391300 chr2A 87.216 352 37 7 2256 2603 32807487 32807140 1.040000e-105 394.0
39 TraesCS1B01G391300 chr2A 90.871 241 18 3 2858 3097 29098069 29098306 1.790000e-83 320.0
40 TraesCS1B01G391300 chr2A 87.719 228 22 4 3758 3984 29098849 29099071 1.100000e-65 261.0
41 TraesCS1B01G391300 chr4B 90.807 446 36 5 2347 2791 512164841 512164400 3.430000e-165 592.0
42 TraesCS1B01G391300 chr4B 87.056 479 53 4 1609 2078 512165576 512165098 2.110000e-147 532.0
43 TraesCS1B01G391300 chr5A 83.048 525 56 6 3460 3982 609634784 609634291 2.820000e-121 446.0
44 TraesCS1B01G391300 chr5A 88.043 368 37 2 3092 3459 609635213 609634853 2.840000e-116 429.0
45 TraesCS1B01G391300 chr5A 87.179 351 36 8 2258 2603 362401251 362400905 1.340000e-104 390.0
46 TraesCS1B01G391300 chr5A 86.722 241 27 4 2858 3097 609635499 609635263 3.050000e-66 263.0
47 TraesCS1B01G391300 chr7D 79.829 585 64 20 2013 2567 583281596 583281036 1.050000e-100 377.0
48 TraesCS1B01G391300 chr3A 92.578 256 16 3 3090 3344 108029006 108029259 8.140000e-97 364.0
49 TraesCS1B01G391300 chr3A 91.102 236 18 2 2859 3093 108028634 108028867 2.310000e-82 316.0
50 TraesCS1B01G391300 chr3A 89.627 241 21 3 2858 3097 611184864 611185101 1.800000e-78 303.0
51 TraesCS1B01G391300 chr3A 87.701 187 17 1 3092 3278 611185309 611185489 3.120000e-51 213.0
52 TraesCS1B01G391300 chr3A 97.222 36 1 0 2818 2853 108028662 108028697 1.200000e-05 62.1
53 TraesCS1B01G391300 chr3A 100.000 30 0 0 1059 1088 703420483 703420512 5.560000e-04 56.5
54 TraesCS1B01G391300 chr1A 92.460 252 15 2 3093 3344 537062876 537062629 1.360000e-94 357.0
55 TraesCS1B01G391300 chr1A 91.561 237 17 2 2858 3093 537063252 537063018 1.380000e-84 324.0
56 TraesCS1B01G391300 chr1A 84.921 126 16 3 935 1059 42510570 42510693 1.500000e-24 124.0
57 TraesCS1B01G391300 chr1A 97.222 36 1 0 2818 2853 537063223 537063188 1.200000e-05 62.1
58 TraesCS1B01G391300 chr5D 83.402 241 33 7 1185 1421 34040492 34040729 2.410000e-52 217.0
59 TraesCS1B01G391300 chr3D 84.127 126 17 3 935 1059 576612747 576612870 6.990000e-23 119.0
60 TraesCS1B01G391300 chr5B 92.000 50 2 2 2858 2907 651227674 651227627 7.140000e-08 69.4


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 TraesCS1B01G391300 chr1B 624663598 624667581 3983 True 1920.475000 7358 96.885250 1 3984 4 chr1B.!!$R1 3983
1 TraesCS1B01G391300 chr1B 56132313 56132818 505 False 682.000000 682 91.124000 1 503 1 chr1B.!!$F1 502
2 TraesCS1B01G391300 chr1D 454167703 454171635 3932 True 1404.980000 5216 96.799200 1 3984 5 chr1D.!!$R1 3983
3 TraesCS1B01G391300 chr2B 554720553 554722316 1763 False 2224.000000 2224 89.565000 1059 2825 1 chr2B.!!$F3 1766
4 TraesCS1B01G391300 chr2B 768457394 768457897 503 True 678.000000 678 91.089000 1 500 1 chr2B.!!$R1 499
5 TraesCS1B01G391300 chr2B 42145694 42146702 1008 False 340.750000 647 90.465500 2858 3984 4 chr2B.!!$F4 1126
6 TraesCS1B01G391300 chr4A 48299315 48300525 1210 False 1266.000000 1266 86.052000 1608 2792 1 chr4A.!!$F1 1184
7 TraesCS1B01G391300 chr4A 618919196 618919700 504 True 691.000000 691 91.485000 1 501 1 chr4A.!!$R1 500
8 TraesCS1B01G391300 chr4D 415292784 415294103 1319 True 674.500000 1007 89.737000 1608 2791 2 chr4D.!!$R1 1183
9 TraesCS1B01G391300 chr6B 462684889 462685934 1045 True 692.500000 808 91.392500 1542 2825 2 chr6B.!!$R2 1283
10 TraesCS1B01G391300 chr2D 199131354 199131858 504 True 717.000000 717 92.475000 1 500 1 chr2D.!!$R1 499
11 TraesCS1B01G391300 chr2D 26767026 26768030 1004 False 344.250000 651 90.533500 2858 3984 4 chr2D.!!$F1 1126
12 TraesCS1B01G391300 chr7B 746355528 746356031 503 True 675.000000 675 90.927000 1 502 1 chr7B.!!$R2 501
13 TraesCS1B01G391300 chr2A 29098069 29099071 1002 False 410.000000 649 89.964667 2858 3984 3 chr2A.!!$F1 1126
14 TraesCS1B01G391300 chr4B 512164400 512165576 1176 True 562.000000 592 88.931500 1609 2791 2 chr4B.!!$R1 1182
15 TraesCS1B01G391300 chr5A 609634291 609635499 1208 True 379.333333 446 85.937667 2858 3982 3 chr5A.!!$R2 1124
16 TraesCS1B01G391300 chr7D 583281036 583281596 560 True 377.000000 377 79.829000 2013 2567 1 chr7D.!!$R1 554
17 TraesCS1B01G391300 chr3A 611184864 611185489 625 False 258.000000 303 88.664000 2858 3278 2 chr3A.!!$F3 420
18 TraesCS1B01G391300 chr3A 108028634 108029259 625 False 247.366667 364 93.634000 2818 3344 3 chr3A.!!$F2 526
19 TraesCS1B01G391300 chr1A 537062629 537063252 623 True 247.700000 357 93.747667 2818 3344 3 chr1A.!!$R1 526

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
69 70 0.182775 GTGAGGGTCTGTTTGGTGGT 59.817 55.000 0.00 0.00 0.00 4.16 F
237 239 0.251165 GGAAACCCTTGGCAGCAGTA 60.251 55.000 0.00 0.00 0.00 2.74 F
388 390 0.306533 TCGGCGTTTGTTTCTCTTGC 59.693 50.000 6.85 0.00 0.00 4.01 F
429 431 0.657840 GAACGTGACTGTGCTGCTTT 59.342 50.000 0.00 0.00 0.00 3.51 F
910 917 1.648467 GCAATCTGGAGAACCGGTGC 61.648 60.000 8.52 5.95 42.77 5.01 F
1332 1345 1.906333 GAGAGGGAGAGGGATCGGC 60.906 68.421 0.00 0.00 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1021 1028 0.761802 GAGAAGCGGGGATCCTCAAT 59.238 55.000 13.38 0.0 0.00 2.57 R
1793 1822 1.406069 CCGGTCTTTGCATAGTCAGCT 60.406 52.381 4.00 0.0 0.00 4.24 R
2328 2399 5.989477 TCCTCCATAGGTGACAATTTACAG 58.011 41.667 0.00 0.0 44.09 2.74 R
2784 3008 2.653726 TGGATGATGTTGGCATGGTAC 58.346 47.619 0.00 0.0 35.07 3.34 R
2967 3191 2.972625 TGTTCTAGCACCTGAAATCGG 58.027 47.619 0.00 0.0 0.00 4.18 R
3390 3937 2.223409 CGAACGGAGTCATCAACCGATA 60.223 50.000 11.64 0.0 45.00 2.92 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
69 70 0.182775 GTGAGGGTCTGTTTGGTGGT 59.817 55.000 0.00 0.00 0.00 4.16
80 81 1.067295 TTTGGTGGTGAGCTCTGGAT 58.933 50.000 16.19 0.00 0.00 3.41
97 98 1.457346 GATTGCCTGAGTTGGAGGTG 58.543 55.000 0.00 0.00 32.60 4.00
236 238 1.531602 GGAAACCCTTGGCAGCAGT 60.532 57.895 0.00 0.00 0.00 4.40
237 239 0.251165 GGAAACCCTTGGCAGCAGTA 60.251 55.000 0.00 0.00 0.00 2.74
243 245 0.811616 CCTTGGCAGCAGTATCGTCC 60.812 60.000 0.00 0.00 0.00 4.79
388 390 0.306533 TCGGCGTTTGTTTCTCTTGC 59.693 50.000 6.85 0.00 0.00 4.01
412 414 9.434420 TGCATTTTCTCTTTCTTTTCTTTTGAA 57.566 25.926 0.00 0.00 36.52 2.69
429 431 0.657840 GAACGTGACTGTGCTGCTTT 59.342 50.000 0.00 0.00 0.00 3.51
436 439 2.518112 TGTGCTGCTTTCGCCCAA 60.518 55.556 0.00 0.00 34.43 4.12
438 441 3.294493 TGCTGCTTTCGCCCAACC 61.294 61.111 0.00 0.00 34.43 3.77
456 459 4.386761 CCAACCCCTATCATTGGATGTCTT 60.387 45.833 0.00 0.00 44.84 3.01
487 494 4.857509 TTTTATACAAAGCGGGCAAACT 57.142 36.364 0.00 0.00 0.00 2.66
540 547 2.482721 AGCCACGTCGATTTTACTTTGG 59.517 45.455 0.00 0.00 0.00 3.28
844 851 2.038837 ATCACGAGAGCGGACACGA 61.039 57.895 0.00 0.00 44.60 4.35
845 852 2.254703 ATCACGAGAGCGGACACGAC 62.255 60.000 0.00 0.00 44.60 4.34
846 853 2.976350 ACGAGAGCGGACACGACA 60.976 61.111 0.00 0.00 44.60 4.35
847 854 2.202362 CGAGAGCGGACACGACAG 60.202 66.667 0.00 0.00 44.60 3.51
848 855 2.505118 GAGAGCGGACACGACAGC 60.505 66.667 0.00 0.00 44.60 4.40
849 856 3.973267 GAGAGCGGACACGACAGCC 62.973 68.421 0.00 0.00 44.60 4.85
910 917 1.648467 GCAATCTGGAGAACCGGTGC 61.648 60.000 8.52 5.95 42.77 5.01
980 987 2.737376 GACGGCGTTGACCAGGAC 60.737 66.667 16.19 0.00 0.00 3.85
1030 1037 2.299867 GGAGAGGAGCTCATTGAGGATC 59.700 54.545 17.19 4.64 45.81 3.36
1251 1258 3.256960 GCCAGTTGTGGGGGAGGA 61.257 66.667 0.00 0.00 45.17 3.71
1332 1345 1.906333 GAGAGGGAGAGGGATCGGC 60.906 68.421 0.00 0.00 0.00 5.54
1386 1410 2.898705 CATCCGTTTCTCTCTCCCTTG 58.101 52.381 0.00 0.00 0.00 3.61
1497 1522 3.648067 CCAAGCCATCCAAGGATAGACTA 59.352 47.826 0.40 0.00 32.93 2.59
1510 1535 9.101325 CCAAGGATAGACTATATTTGGGTCTTA 57.899 37.037 20.20 0.00 40.29 2.10
1793 1822 4.570930 TCCAATATGCAAACTACACGACA 58.429 39.130 0.00 0.00 0.00 4.35
1976 2009 6.035975 GGGTGTTGAAAGTTGAAATTGAACAG 59.964 38.462 0.00 0.00 0.00 3.16
2098 2141 3.678056 TGCCGTTTCAACTGAGAGTAT 57.322 42.857 0.00 0.00 0.00 2.12
2576 2792 4.137116 TGAAGAAATATGTGCCTAGCGT 57.863 40.909 0.00 0.00 0.00 5.07
2784 3008 5.702622 CACTATGTGTGGTCAGTAATTCG 57.297 43.478 0.00 0.00 42.68 3.34
3390 3937 9.014297 AGCTACTTACTGTTTTATTTGAATGCT 57.986 29.630 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.099062 CGATGCTTCCAACGCTGC 59.901 61.111 0.00 0.00 30.59 5.25
69 70 0.540454 CTCAGGCAATCCAGAGCTCA 59.460 55.000 17.77 0.00 38.84 4.26
80 81 1.455849 CCACCTCCAACTCAGGCAA 59.544 57.895 0.00 0.00 33.84 4.52
97 98 1.346068 CAGAGATTTCTCCCGATCCCC 59.654 57.143 3.97 0.00 43.88 4.81
236 238 2.528743 GGACGCGACGAGGACGATA 61.529 63.158 15.93 0.00 42.66 2.92
237 239 3.873883 GGACGCGACGAGGACGAT 61.874 66.667 15.93 0.00 42.66 3.73
243 245 1.801913 CAAGAAGGGACGCGACGAG 60.802 63.158 15.93 0.00 0.00 4.18
331 333 1.340248 AGAAACGAAGAAGCCTCGTGA 59.660 47.619 0.00 0.00 40.16 4.35
388 390 9.891535 CGTTCAAAAGAAAAGAAAGAGAAAATG 57.108 29.630 0.00 0.00 0.00 2.32
412 414 1.490693 CGAAAGCAGCACAGTCACGT 61.491 55.000 0.00 0.00 0.00 4.49
429 431 0.182537 CAATGATAGGGGTTGGGCGA 59.817 55.000 0.00 0.00 0.00 5.54
436 439 3.139025 CCAAGACATCCAATGATAGGGGT 59.861 47.826 0.00 0.00 0.00 4.95
438 441 4.443978 ACCAAGACATCCAATGATAGGG 57.556 45.455 0.00 0.00 0.00 3.53
468 473 3.681593 AGAGTTTGCCCGCTTTGTATAA 58.318 40.909 0.00 0.00 0.00 0.98
482 487 4.507756 GCTGCTTTACCCAAAAAGAGTTTG 59.492 41.667 0.69 0.00 38.50 2.93
487 494 2.292292 GACGCTGCTTTACCCAAAAAGA 59.708 45.455 0.00 0.00 38.50 2.52
540 547 1.272781 CTCGCTCTCCAATCAACGAC 58.727 55.000 0.00 0.00 0.00 4.34
849 856 3.978723 CTCTGCTCTGCCCGTGACG 62.979 68.421 0.00 0.00 0.00 4.35
980 987 2.248724 CGAGGATCTACGACGGCG 59.751 66.667 10.39 10.39 44.79 6.46
988 995 0.952280 GACGGCATGACGAGGATCTA 59.048 55.000 31.27 0.00 37.61 1.98
1021 1028 0.761802 GAGAAGCGGGGATCCTCAAT 59.238 55.000 13.38 0.00 0.00 2.57
1048 1055 3.733960 CACCTCGCTCCGTCGTGA 61.734 66.667 0.00 0.00 32.22 4.35
1332 1345 3.696051 CACCATTCCACAACCCTATCTTG 59.304 47.826 0.00 0.00 0.00 3.02
1386 1410 2.096417 CGAGGTGAAAATCGTGTTGTCC 60.096 50.000 0.00 0.00 34.30 4.02
1655 1680 2.280628 GAGTCGTGCATAAAAGAGGGG 58.719 52.381 0.00 0.00 0.00 4.79
1793 1822 1.406069 CCGGTCTTTGCATAGTCAGCT 60.406 52.381 4.00 0.00 0.00 4.24
1991 2027 6.434340 GTGATTAATGTTCAACTCTTTCCCCT 59.566 38.462 0.00 0.00 0.00 4.79
2007 2043 7.222031 CCATGCACAAATTCAGAGTGATTAATG 59.778 37.037 0.00 0.00 35.33 1.90
2328 2399 5.989477 TCCTCCATAGGTGACAATTTACAG 58.011 41.667 0.00 0.00 44.09 2.74
2784 3008 2.653726 TGGATGATGTTGGCATGGTAC 58.346 47.619 0.00 0.00 35.07 3.34
2967 3191 2.972625 TGTTCTAGCACCTGAAATCGG 58.027 47.619 0.00 0.00 0.00 4.18
3028 3252 3.769300 TGATCCAGTTTCTTCGGAGATGA 59.231 43.478 0.00 0.00 38.98 2.92
3029 3253 4.128925 TGATCCAGTTTCTTCGGAGATG 57.871 45.455 0.00 0.00 35.04 2.90
3030 3254 4.826274 TTGATCCAGTTTCTTCGGAGAT 57.174 40.909 0.00 0.00 35.04 2.75
3177 3717 4.821260 ACTTGCACATATTGACAGAACACA 59.179 37.500 0.00 0.00 0.00 3.72
3390 3937 2.223409 CGAACGGAGTCATCAACCGATA 60.223 50.000 11.64 0.00 45.00 2.92


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

AutoCloner maintained by Alex Coulton.