Multiple sequence alignment - TraesCS2B01G103100

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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 TraesCS2B01G103100 chr2B 100.000 4005 0 0 1 4005 64069480 64073484 0.000000e+00 7396
1 TraesCS2B01G103100 chr2B 94.312 3200 104 33 1 3175 63854101 63857247 0.000000e+00 4830
2 TraesCS2B01G103100 chr2B 97.165 1517 35 3 908 2416 64206809 64205293 0.000000e+00 2556
3 TraesCS2B01G103100 chr2B 97.295 1331 23 4 2687 4005 64205315 64203986 0.000000e+00 2246
4 TraesCS2B01G103100 chr2B 98.460 844 7 1 3168 4005 63858298 63859141 0.000000e+00 1482
5 TraesCS2B01G103100 chr2B 89.196 833 37 17 2 826 64207849 64207062 0.000000e+00 990
6 TraesCS2B01G103100 chr2B 93.633 534 29 3 3477 4005 64203604 64203071 0.000000e+00 793
7 TraesCS2B01G103100 chr2B 84.161 745 93 19 908 1642 64230283 64229554 0.000000e+00 699
8 TraesCS2B01G103100 chr2B 83.984 743 92 21 922 1654 63845270 63845995 0.000000e+00 688
9 TraesCS2B01G103100 chr2B 89.286 308 28 4 959 1262 63821995 63822301 8.120000e-102 381
10 TraesCS2B01G103100 chr2B 79.292 565 82 24 2788 3329 64228750 64228198 2.940000e-96 363
11 TraesCS2B01G103100 chr2B 81.336 434 61 11 1286 1704 63827964 63828392 6.410000e-88 335
12 TraesCS2B01G103100 chr2B 83.969 262 34 7 2407 2666 790214263 790214008 1.110000e-60 244
13 TraesCS2B01G103100 chr2B 83.908 261 30 7 2755 3009 63837975 63838229 5.170000e-59 239
14 TraesCS2B01G103100 chr2A 90.309 1620 111 21 813 2416 41644325 41642736 0.000000e+00 2080
15 TraesCS2B01G103100 chr2A 91.109 1046 70 15 2687 3718 41642758 41641722 0.000000e+00 1395
16 TraesCS2B01G103100 chr2A 85.271 258 30 5 2755 3008 41652429 41652176 3.970000e-65 259
17 TraesCS2B01G103100 chr2D 89.344 1098 88 18 1329 2415 36932249 36931170 0.000000e+00 1352
18 TraesCS2B01G103100 chr2D 83.301 1527 178 38 908 2405 37022938 37021460 0.000000e+00 1336
19 TraesCS2B01G103100 chr2D 89.698 893 64 15 3087 3968 36930951 36930076 0.000000e+00 1114
20 TraesCS2B01G103100 chr2D 83.875 769 96 19 959 1704 37045788 37045025 0.000000e+00 708
21 TraesCS2B01G103100 chr2D 92.653 490 25 7 850 1331 36998555 36998069 0.000000e+00 695
22 TraesCS2B01G103100 chr2D 84.875 681 83 13 2728 3395 37021422 37020749 0.000000e+00 669
23 TraesCS2B01G103100 chr2D 82.668 802 78 30 1 770 36999354 36998582 0.000000e+00 654
24 TraesCS2B01G103100 chr2D 83.599 628 79 19 1025 1642 37031318 37030705 5.810000e-158 568
25 TraesCS2B01G103100 chr2D 79.428 559 86 21 2788 3329 37030243 37029697 6.320000e-98 368
26 TraesCS2B01G103100 chr2D 90.393 229 17 4 2687 2911 36931190 36930963 3.030000e-76 296
27 TraesCS2B01G103100 chr2D 83.846 260 30 7 2755 3008 37043906 37043653 1.860000e-58 237
28 TraesCS2B01G103100 chr3D 91.756 279 17 3 2410 2686 40004746 40004472 2.260000e-102 383
29 TraesCS2B01G103100 chr7B 88.811 286 27 4 2405 2686 667195460 667195744 2.960000e-91 346
30 TraesCS2B01G103100 chr7B 88.929 280 28 3 2409 2686 587481281 587481559 3.830000e-90 342
31 TraesCS2B01G103100 chr6A 87.544 281 22 7 2407 2686 593423963 593424231 3.010000e-81 313
32 TraesCS2B01G103100 chr1B 90.625 224 13 3 2410 2631 686927134 686927351 1.410000e-74 291
33 TraesCS2B01G103100 chrUn 85.034 294 33 9 2409 2697 296164676 296164963 5.060000e-74 289
34 TraesCS2B01G103100 chrUn 85.034 294 33 9 2409 2697 296174860 296175147 5.060000e-74 289


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 TraesCS2B01G103100 chr2B 64069480 64073484 4004 False 7396.000000 7396 100.000000 1 4005 1 chr2B.!!$F5 4004
1 TraesCS2B01G103100 chr2B 63854101 63859141 5040 False 3156.000000 4830 96.386000 1 4005 2 chr2B.!!$F6 4004
2 TraesCS2B01G103100 chr2B 64203071 64207849 4778 True 1646.250000 2556 94.322250 2 4005 4 chr2B.!!$R2 4003
3 TraesCS2B01G103100 chr2B 63845270 63845995 725 False 688.000000 688 83.984000 922 1654 1 chr2B.!!$F4 732
4 TraesCS2B01G103100 chr2B 64228198 64230283 2085 True 531.000000 699 81.726500 908 3329 2 chr2B.!!$R3 2421
5 TraesCS2B01G103100 chr2A 41641722 41644325 2603 True 1737.500000 2080 90.709000 813 3718 2 chr2A.!!$R2 2905
6 TraesCS2B01G103100 chr2D 37020749 37022938 2189 True 1002.500000 1336 84.088000 908 3395 2 chr2D.!!$R3 2487
7 TraesCS2B01G103100 chr2D 36930076 36932249 2173 True 920.666667 1352 89.811667 1329 3968 3 chr2D.!!$R1 2639
8 TraesCS2B01G103100 chr2D 36998069 36999354 1285 True 674.500000 695 87.660500 1 1331 2 chr2D.!!$R2 1330
9 TraesCS2B01G103100 chr2D 37043653 37045788 2135 True 472.500000 708 83.860500 959 3008 2 chr2D.!!$R5 2049
10 TraesCS2B01G103100 chr2D 37029697 37031318 1621 True 468.000000 568 81.513500 1025 3329 2 chr2D.!!$R4 2304

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
440 471 1.007238 AGGTCTTAGCTAGAGGTGCCA 59.993 52.381 0.0 0.0 32.23 4.92 F
1175 1470 0.108329 ATGCGTACCCTTCTTCCACG 60.108 55.000 0.0 0.0 35.78 4.94 F
2476 3312 1.134401 CACTCACCCCTATGAACGCAT 60.134 52.381 0.0 0.0 38.54 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1690 1.077787 GGCCCGTGGATCATCAACA 60.078 57.895 0.00 0.0 0.00 3.33 R
2499 3335 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.0 35.32 4.40 R
3465 5462 3.009143 ACTTGGCTCTTGGTAACCCTAAG 59.991 47.826 0.00 0.0 0.00 2.18 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
96 97 9.528018 TCTTGAAAAATGTTAATGGACTTCAAC 57.472 29.630 0.00 0.00 30.64 3.18
255 257 5.126061 CGGAGGACATGAAGGAAATCAAATT 59.874 40.000 0.00 0.00 32.06 1.82
265 267 7.816640 TGAAGGAAATCAAATTAGAAAGACGG 58.183 34.615 0.00 0.00 0.00 4.79
384 408 5.687166 TTGTACCATTTAGTCTCCGGAAT 57.313 39.130 5.23 0.00 0.00 3.01
390 414 5.186198 CCATTTAGTCTCCGGAATGTTTCT 58.814 41.667 5.23 0.48 0.00 2.52
391 415 5.065218 CCATTTAGTCTCCGGAATGTTTCTG 59.935 44.000 5.23 0.00 35.78 3.02
400 431 4.274950 TCCGGAATGTTTCTGAAGTTCAAC 59.725 41.667 0.00 3.19 38.34 3.18
408 439 5.123186 TGTTTCTGAAGTTCAACGTTGATGT 59.877 36.000 30.10 17.94 37.00 3.06
440 471 1.007238 AGGTCTTAGCTAGAGGTGCCA 59.993 52.381 0.00 0.00 32.23 4.92
505 545 7.147143 TCATAATTTAGTTTGTGGCGCTTTA 57.853 32.000 7.64 0.00 0.00 1.85
631 692 5.277601 TGCGAACAAACTATTAGCACTTC 57.722 39.130 0.00 0.00 33.48 3.01
801 863 3.791973 TGCTAAAAACCACCTTGTGTG 57.208 42.857 0.00 0.00 45.01 3.82
803 865 3.119316 TGCTAAAAACCACCTTGTGTGTG 60.119 43.478 0.00 0.00 43.85 3.82
828 910 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
1175 1470 0.108329 ATGCGTACCCTTCTTCCACG 60.108 55.000 0.00 0.00 35.78 4.94
1283 1588 5.947228 TCTTCCTGCTTTTGAGTGTATTG 57.053 39.130 0.00 0.00 0.00 1.90
1284 1589 5.620206 TCTTCCTGCTTTTGAGTGTATTGA 58.380 37.500 0.00 0.00 0.00 2.57
1285 1590 5.470098 TCTTCCTGCTTTTGAGTGTATTGAC 59.530 40.000 0.00 0.00 0.00 3.18
1286 1591 4.973168 TCCTGCTTTTGAGTGTATTGACT 58.027 39.130 0.00 0.00 0.00 3.41
1306 1613 1.280998 TCCCTTCGGATTTCCACTTCC 59.719 52.381 0.00 0.00 35.14 3.46
1383 1690 6.095860 ACATTGCAGCATATACAATCAAGTGT 59.904 34.615 0.00 0.00 31.82 3.55
1517 1824 4.034285 AGAAAATTCCCATTCCGAGTGT 57.966 40.909 0.00 0.00 0.00 3.55
2071 2524 1.671328 TCGCCATTCTAGACGACTCTG 59.329 52.381 0.00 0.00 0.00 3.35
2436 3272 4.450976 TGAGCATCAGTACAAACACAAGT 58.549 39.130 0.00 0.00 42.56 3.16
2476 3312 1.134401 CACTCACCCCTATGAACGCAT 60.134 52.381 0.00 0.00 38.54 4.73
2499 3335 1.046472 CGCACACCCTACCCCTATGA 61.046 60.000 0.00 0.00 0.00 2.15
2500 3336 0.759346 GCACACCCTACCCCTATGAG 59.241 60.000 0.00 0.00 0.00 2.90
2519 3355 0.963355 GCACCTCCGAGAGACTGAGT 60.963 60.000 0.00 0.00 0.00 3.41
2542 3378 8.830201 AGTCAGCATATCATCTTGAGATTTAC 57.170 34.615 0.00 0.00 31.21 2.01
2566 3402 0.635009 CCACCTACCTCCTCCCACTA 59.365 60.000 0.00 0.00 0.00 2.74
2576 3412 1.017387 CCTCCCACTAAAAGCGCATC 58.983 55.000 11.47 0.00 0.00 3.91
2593 3429 2.689983 GCATCACCGGAAATCCTGAAAT 59.310 45.455 9.46 0.00 0.00 2.17
2616 3452 0.471191 TCCAGGAATGATGCGAGCAT 59.529 50.000 10.66 10.66 39.69 3.79
2669 3506 4.098654 CCACTGTCTACCTAACCATCTCAG 59.901 50.000 0.00 0.00 0.00 3.35
2678 3515 0.773644 AACCATCTCAGCCACAGGTT 59.226 50.000 0.00 0.00 34.72 3.50
2735 3580 3.800506 GTGCGTATCCATAGCGTTTACTT 59.199 43.478 0.00 0.00 0.00 2.24
2736 3581 4.977963 GTGCGTATCCATAGCGTTTACTTA 59.022 41.667 0.00 0.00 0.00 2.24
2737 3582 5.459762 GTGCGTATCCATAGCGTTTACTTAA 59.540 40.000 0.00 0.00 0.00 1.85
2738 3583 5.688621 TGCGTATCCATAGCGTTTACTTAAG 59.311 40.000 0.00 0.00 0.00 1.85
2739 3584 5.118203 GCGTATCCATAGCGTTTACTTAAGG 59.882 44.000 7.53 0.00 0.00 2.69
2741 3586 6.698766 CGTATCCATAGCGTTTACTTAAGGTT 59.301 38.462 7.53 0.00 0.00 3.50
2742 3587 6.920569 ATCCATAGCGTTTACTTAAGGTTG 57.079 37.500 7.53 0.00 0.00 3.77
2743 3588 5.180271 TCCATAGCGTTTACTTAAGGTTGG 58.820 41.667 7.53 0.97 0.00 3.77
2744 3589 4.334481 CCATAGCGTTTACTTAAGGTTGGG 59.666 45.833 7.53 0.00 0.00 4.12
2745 3590 3.775261 AGCGTTTACTTAAGGTTGGGA 57.225 42.857 7.53 0.00 0.00 4.37
2746 3591 4.089408 AGCGTTTACTTAAGGTTGGGAA 57.911 40.909 7.53 0.00 0.00 3.97
2747 3592 4.463070 AGCGTTTACTTAAGGTTGGGAAA 58.537 39.130 7.53 0.00 0.00 3.13
2748 3593 4.888823 AGCGTTTACTTAAGGTTGGGAAAA 59.111 37.500 7.53 0.00 0.00 2.29
2749 3594 5.009310 AGCGTTTACTTAAGGTTGGGAAAAG 59.991 40.000 7.53 1.79 0.00 2.27
2750 3595 5.008911 GCGTTTACTTAAGGTTGGGAAAAGA 59.991 40.000 7.53 0.00 0.00 2.52
2796 3705 5.948992 AGAACCTTGCAATCTAGTTTCAC 57.051 39.130 0.00 0.00 0.00 3.18
3096 4022 7.814107 TGTTTGAAGAAAGTTCCATTGATATGC 59.186 33.333 0.00 0.00 0.00 3.14
3465 5462 4.494410 GCAAAATGAAATAACCGCGTAGAC 59.506 41.667 4.92 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 6.677913 AGTCCATTAACATTTTTCAAGACCG 58.322 36.000 0.00 0.00 0.00 4.79
240 242 7.574967 GCCGTCTTTCTAATTTGATTTCCTTCA 60.575 37.037 0.00 0.00 0.00 3.02
255 257 1.530323 GCTTTTGGGCCGTCTTTCTA 58.470 50.000 0.00 0.00 0.00 2.10
265 267 1.946768 GGTTTTTGAAGGCTTTTGGGC 59.053 47.619 0.00 0.00 41.20 5.36
384 408 5.123186 ACATCAACGTTGAACTTCAGAAACA 59.877 36.000 32.69 7.48 41.13 2.83
390 414 4.951254 TCCTACATCAACGTTGAACTTCA 58.049 39.130 32.69 15.90 41.13 3.02
391 415 4.989168 ACTCCTACATCAACGTTGAACTTC 59.011 41.667 32.69 0.00 41.13 3.01
400 431 3.679980 CCTTGACAACTCCTACATCAACG 59.320 47.826 0.00 0.00 0.00 4.10
408 439 4.417437 AGCTAAGACCTTGACAACTCCTA 58.583 43.478 0.00 0.00 0.00 2.94
505 545 1.202651 GGGCTGCCACTATACAACGAT 60.203 52.381 22.05 0.00 0.00 3.73
535 595 0.178924 AATATTCATGGGGCCCAGGC 60.179 55.000 31.85 6.89 36.75 4.85
537 597 4.676109 TCATTAATATTCATGGGGCCCAG 58.324 43.478 31.98 21.84 36.75 4.45
639 701 1.674359 AGCTCACTCGACTCGATGAT 58.326 50.000 0.62 0.00 34.61 2.45
781 843 3.791973 CACACAAGGTGGTTTTTAGCA 57.208 42.857 1.07 0.00 44.04 3.49
794 856 1.535028 ACACACACACACACACACAAG 59.465 47.619 0.00 0.00 0.00 3.16
797 859 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
801 863 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
803 865 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
844 926 0.040781 AATAAACACACACACGCGCC 60.041 50.000 5.73 0.00 0.00 6.53
846 928 4.377911 TCTTAATAAACACACACACGCG 57.622 40.909 3.53 3.53 0.00 6.01
848 930 7.348956 TCATGTTCTTAATAAACACACACACG 58.651 34.615 5.88 0.00 39.29 4.49
1175 1470 2.484889 AGACGTGAACTTTCTCCTTGC 58.515 47.619 0.00 0.00 0.00 4.01
1383 1690 1.077787 GGCCCGTGGATCATCAACA 60.078 57.895 0.00 0.00 0.00 3.33
1517 1824 6.167685 CCTTTCATTGATGCCAAGAATTCAA 58.832 36.000 8.44 0.00 35.48 2.69
2414 3250 4.273235 CACTTGTGTTTGTACTGATGCTCA 59.727 41.667 0.00 0.00 0.00 4.26
2428 3264 3.370978 GCGTGTATATGAGCACTTGTGTT 59.629 43.478 2.61 0.00 33.78 3.32
2476 3312 2.285024 GGGGTAGGGTGTGCGTGTA 61.285 63.158 0.00 0.00 0.00 2.90
2499 3335 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.00 35.32 4.40
2500 3336 0.963355 ACTCAGTCTCTCGGAGGTGC 60.963 60.000 4.96 0.00 41.46 5.01
2519 3355 7.661040 TCGTAAATCTCAAGATGATATGCTGA 58.339 34.615 0.00 0.00 34.49 4.26
2542 3378 1.677637 GGAGGAGGTAGGTGGCTTCG 61.678 65.000 0.00 0.00 0.00 3.79
2566 3402 0.887933 ATTTCCGGTGATGCGCTTTT 59.112 45.000 9.73 0.00 0.00 2.27
2576 3412 5.359576 TGGATTTATTTCAGGATTTCCGGTG 59.640 40.000 0.00 0.00 42.08 4.94
2593 3429 3.141398 GCTCGCATCATTCCTGGATTTA 58.859 45.455 0.00 0.00 0.00 1.40
2616 3452 2.584835 CCACCAGGGTTCAAATCTGA 57.415 50.000 0.00 0.00 0.00 3.27
2654 3491 2.766263 CTGTGGCTGAGATGGTTAGGTA 59.234 50.000 0.00 0.00 0.00 3.08
2678 3515 4.340617 AAAGAATTCTTATGGGCGAACCA 58.659 39.130 20.76 1.56 44.51 3.67
2796 3705 4.410883 TGTAGTAGGTATGTCAATTGGGGG 59.589 45.833 5.42 0.00 0.00 5.40
3096 4022 6.992123 TCAATAACTATGCCCATGTTGAGTAG 59.008 38.462 0.00 0.00 0.00 2.57
3381 5378 8.913487 TCGAGACTATACATGATTAGTGGTTA 57.087 34.615 14.26 0.15 0.00 2.85
3465 5462 3.009143 ACTTGGCTCTTGGTAACCCTAAG 59.991 47.826 0.00 0.00 0.00 2.18


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

AutoCloner maintained by Alex Coulton.