Multiple sequence alignment - TraesCS2B01G265500

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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 TraesCS2B01G265500 chr2B 100.000 3738 0 0 1 3738 357719300 357715563 0.000000e+00 6903.0
1 TraesCS2B01G265500 chr2B 96.927 3742 106 8 1 3738 357345073 357341337 0.000000e+00 6264.0
2 TraesCS2B01G265500 chr2B 96.893 354 11 0 2665 3018 357229986 357230339 8.940000e-166 593.0
3 TraesCS2B01G265500 chr2B 98.387 62 1 0 3340 3401 717210005 717209944 3.950000e-20 110.0
4 TraesCS2B01G265500 chr2B 100.000 58 0 0 1 58 391149024 391149081 1.420000e-19 108.0
5 TraesCS2B01G265500 chr2B 100.000 58 0 0 1 58 391221023 391220966 1.420000e-19 108.0
6 TraesCS2B01G265500 chr2B 96.364 55 2 0 3185 3239 716494942 716494888 1.430000e-14 91.6
7 TraesCS2B01G265500 chr3B 97.275 2202 55 4 327 2527 39816436 39818633 0.000000e+00 3729.0
8 TraesCS2B01G265500 chr3B 96.730 2202 67 4 326 2527 173888429 173890625 0.000000e+00 3663.0
9 TraesCS2B01G265500 chr3B 100.000 58 0 0 1 58 797546611 797546554 1.420000e-19 108.0
10 TraesCS2B01G265500 chr3B 100.000 57 0 0 1 57 759909008 759909064 5.110000e-19 106.0
11 TraesCS2B01G265500 chr7A 97.273 2200 49 3 329 2527 211291971 211294160 0.000000e+00 3720.0
12 TraesCS2B01G265500 chr7A 96.857 350 11 0 3389 3738 4948026 4947677 1.500000e-163 586.0
13 TraesCS2B01G265500 chr5A 97.096 2204 58 6 327 2527 534933459 534935659 0.000000e+00 3711.0
14 TraesCS2B01G265500 chr5A 97.036 1923 55 2 606 2527 647029609 647031530 0.000000e+00 3234.0
15 TraesCS2B01G265500 chr5A 96.286 350 13 0 3389 3738 667817599 667817948 3.240000e-160 575.0
16 TraesCS2B01G265500 chr5A 96.275 349 13 0 3390 3738 614341828 614342176 1.160000e-159 573.0
17 TraesCS2B01G265500 chr6B 97.090 2199 63 1 329 2527 625641516 625639319 0.000000e+00 3705.0
18 TraesCS2B01G265500 chr6B 95.436 723 26 3 327 1047 215728827 215728110 0.000000e+00 1146.0
19 TraesCS2B01G265500 chr6B 96.000 350 12 1 3389 3738 388299872 388300219 5.420000e-158 568.0
20 TraesCS2B01G265500 chr6B 95.965 347 14 0 3389 3735 388182645 388182991 7.010000e-157 564.0
21 TraesCS2B01G265500 chr6B 95.714 350 15 0 3389 3738 388241469 388241818 7.010000e-157 564.0
22 TraesCS2B01G265500 chr6B 85.632 174 16 5 3154 3326 309903369 309903204 1.380000e-39 174.0
23 TraesCS2B01G265500 chr7B 95.506 2203 77 11 327 2527 139542520 139540338 0.000000e+00 3500.0
24 TraesCS2B01G265500 chr7B 96.286 350 13 0 3389 3738 47133479 47133130 3.240000e-160 575.0
25 TraesCS2B01G265500 chr7B 100.000 58 0 0 1 58 54044956 54044899 1.420000e-19 108.0
26 TraesCS2B01G265500 chr7D 98.430 1592 23 2 937 2527 579030028 579031618 0.000000e+00 2800.0
27 TraesCS2B01G265500 chr7D 95.312 64 1 2 1 62 601284183 601284246 2.380000e-17 100.0
28 TraesCS2B01G265500 chr7D 95.312 64 1 2 1 62 601314001 601313938 2.380000e-17 100.0
29 TraesCS2B01G265500 chrUn 98.487 1586 24 0 942 2527 86478354 86479939 0.000000e+00 2796.0
30 TraesCS2B01G265500 chrUn 98.367 1592 25 1 937 2527 221548123 221546532 0.000000e+00 2795.0
31 TraesCS2B01G265500 chrUn 95.699 93 3 1 2513 2604 209405282 209405374 8.360000e-32 148.0
32 TraesCS2B01G265500 chrUn 97.701 87 1 1 2519 2604 267893020 267892934 8.360000e-32 148.0
33 TraesCS2B01G265500 chrUn 97.701 87 1 1 2519 2604 378214589 378214503 8.360000e-32 148.0
34 TraesCS2B01G265500 chrUn 95.699 93 3 1 2513 2604 438448670 438448762 8.360000e-32 148.0
35 TraesCS2B01G265500 chrUn 100.000 58 0 0 1 58 171012508 171012565 1.420000e-19 108.0
36 TraesCS2B01G265500 chr5B 94.012 668 36 2 2416 3083 446667433 446668096 0.000000e+00 1009.0
37 TraesCS2B01G265500 chr2D 95.775 497 15 2 3247 3738 200912614 200912119 0.000000e+00 797.0
38 TraesCS2B01G265500 chr1B 96.479 142 5 0 2508 2649 551768867 551769008 6.240000e-58 235.0
39 TraesCS2B01G265500 chr6D 85.632 174 15 7 3154 3326 163709673 163709509 1.380000e-39 174.0
40 TraesCS2B01G265500 chr6D 97.701 87 1 1 2519 2604 283199259 283199173 8.360000e-32 148.0
41 TraesCS2B01G265500 chr1D 97.701 87 1 1 2519 2604 212440695 212440609 8.360000e-32 148.0
42 TraesCS2B01G265500 chr6A 97.143 70 2 0 3313 3382 117581002 117581071 6.560000e-23 119.0


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 TraesCS2B01G265500 chr2B 357715563 357719300 3737 True 6903 6903 100.000 1 3738 1 chr2B.!!$R2 3737
1 TraesCS2B01G265500 chr2B 357341337 357345073 3736 True 6264 6264 96.927 1 3738 1 chr2B.!!$R1 3737
2 TraesCS2B01G265500 chr3B 39816436 39818633 2197 False 3729 3729 97.275 327 2527 1 chr3B.!!$F1 2200
3 TraesCS2B01G265500 chr3B 173888429 173890625 2196 False 3663 3663 96.730 326 2527 1 chr3B.!!$F2 2201
4 TraesCS2B01G265500 chr7A 211291971 211294160 2189 False 3720 3720 97.273 329 2527 1 chr7A.!!$F1 2198
5 TraesCS2B01G265500 chr5A 534933459 534935659 2200 False 3711 3711 97.096 327 2527 1 chr5A.!!$F1 2200
6 TraesCS2B01G265500 chr5A 647029609 647031530 1921 False 3234 3234 97.036 606 2527 1 chr5A.!!$F3 1921
7 TraesCS2B01G265500 chr6B 625639319 625641516 2197 True 3705 3705 97.090 329 2527 1 chr6B.!!$R3 2198
8 TraesCS2B01G265500 chr6B 215728110 215728827 717 True 1146 1146 95.436 327 1047 1 chr6B.!!$R1 720
9 TraesCS2B01G265500 chr7B 139540338 139542520 2182 True 3500 3500 95.506 327 2527 1 chr7B.!!$R3 2200
10 TraesCS2B01G265500 chr7D 579030028 579031618 1590 False 2800 2800 98.430 937 2527 1 chr7D.!!$F1 1590
11 TraesCS2B01G265500 chrUn 86478354 86479939 1585 False 2796 2796 98.487 942 2527 1 chrUn.!!$F1 1585
12 TraesCS2B01G265500 chrUn 221546532 221548123 1591 True 2795 2795 98.367 937 2527 1 chrUn.!!$R1 1590
13 TraesCS2B01G265500 chr5B 446667433 446668096 663 False 1009 1009 94.012 2416 3083 1 chr5B.!!$F1 667

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
376 377 0.343372 TCAAGACCCCCAGGCTCTAT 59.657 55.000 0.0 0.0 36.11 1.98 F
1582 1588 2.033372 TGTGGTCCGTTCTAGTGACAA 58.967 47.619 0.0 0.0 0.00 3.18 F
2062 2069 0.693622 TTTGTTCACCATAGGCGGGA 59.306 50.000 0.0 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 1990 3.035055 TGTATCGAACCTCCCCACATA 57.965 47.619 0.0 0.0 0.00 2.29 R
2699 2707 0.458543 CACTGCTGTAGCCGTCGAAT 60.459 55.000 0.8 0.0 41.18 3.34 R
3208 3218 0.494095 ACCCACTCTCCTTTCCCTCT 59.506 55.000 0.0 0.0 0.00 3.69 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
243 244 7.716799 TTATTGATGTAAAGGCCACTTCATT 57.283 32.000 5.01 7.71 35.41 2.57
376 377 0.343372 TCAAGACCCCCAGGCTCTAT 59.657 55.000 0.00 0.00 36.11 1.98
404 405 3.847671 AGCAGGGCTAAACTTCTATCC 57.152 47.619 0.00 0.00 36.99 2.59
420 421 3.943381 TCTATCCGAGTCTTTACGAGCAA 59.057 43.478 0.00 0.00 0.00 3.91
639 642 2.738964 GCTTCGTTCCTATCTGGACCAC 60.739 54.545 0.00 0.00 46.14 4.16
1447 1453 2.680339 GGAGGAGCAGTTGATTTAGCAC 59.320 50.000 0.00 0.00 0.00 4.40
1582 1588 2.033372 TGTGGTCCGTTCTAGTGACAA 58.967 47.619 0.00 0.00 0.00 3.18
1811 1817 2.894763 TCAAGAAAACCGGTCTTCGA 57.105 45.000 14.84 4.67 42.43 3.71
1983 1990 7.103641 TCAAAATCTTTAGTTGGATCGCTACT 58.896 34.615 4.39 4.39 0.00 2.57
2058 2065 5.643379 TCATCTTTTTGTTCACCATAGGC 57.357 39.130 0.00 0.00 0.00 3.93
2062 2069 0.693622 TTTGTTCACCATAGGCGGGA 59.306 50.000 0.00 0.00 0.00 5.14
2068 2075 1.133294 TCACCATAGGCGGGATCACTA 60.133 52.381 0.00 0.00 0.00 2.74
2182 2190 4.509600 CCGTTTTTGCTTTATTTGCTGGAA 59.490 37.500 0.00 0.00 0.00 3.53
2222 2230 6.766467 GGTAAAATCTTTGGTCGGACATATCT 59.234 38.462 10.76 0.00 0.00 1.98
2621 2629 6.568869 TCAAATCGTTTCTTGTTTGGATTGT 58.431 32.000 0.00 0.00 33.55 2.71
2771 2779 2.009774 CGAAAGAATTCTCCGTGCCAT 58.990 47.619 8.78 0.00 33.17 4.40
2926 2934 5.837770 AGAATGGGATCTTGATGCTATCA 57.162 39.130 2.00 0.00 37.55 2.15
2938 2946 6.915544 TTGATGCTATCAATCTCAGTCAAC 57.084 37.500 7.27 0.00 43.84 3.18
2971 2980 5.830799 AATCAAAAGATGGAAAAAGCCCT 57.169 34.783 0.00 0.00 0.00 5.19
3047 3056 6.521151 AAGCAAACTCTTCCCATAAATCTG 57.479 37.500 0.00 0.00 0.00 2.90
3063 3072 5.352700 AAATCTGCCCAATCCCCAATATA 57.647 39.130 0.00 0.00 0.00 0.86
3198 3208 4.494484 GCCAGGTAGCTTTGGTTTTATTG 58.506 43.478 11.73 0.00 36.81 1.90
3208 3218 6.041523 AGCTTTGGTTTTATTGCTTCTGGTTA 59.958 34.615 0.00 0.00 0.00 2.85
3235 3245 0.983378 AGGAGAGTGGGTATGTGGGC 60.983 60.000 0.00 0.00 0.00 5.36
3270 3280 5.932303 TGTGCAAAGGTTATCACTTCTCTAC 59.068 40.000 0.00 0.00 0.00 2.59
3279 3289 6.388278 GTTATCACTTCTCTACGGAGTGTTT 58.612 40.000 0.00 0.00 45.73 2.83
3356 3366 3.003378 GGCATGGCGAGATTTTACTTACC 59.997 47.826 2.41 0.00 0.00 2.85
3358 3368 4.024809 GCATGGCGAGATTTTACTTACCTC 60.025 45.833 0.00 0.00 0.00 3.85
3406 3416 1.148273 GGGAGCGGCAATGATACCA 59.852 57.895 1.45 0.00 0.00 3.25
3409 3419 1.498865 GAGCGGCAATGATACCACCG 61.499 60.000 1.45 0.00 46.50 4.94
3543 3553 6.890979 GGAAATGCTGCTTCCTTTCTATAT 57.109 37.500 12.09 0.00 39.49 0.86
3721 3731 2.893489 AGATGTGCCAAAGAGGTTTTCC 59.107 45.455 0.00 0.00 40.61 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
324 325 4.282496 GGAGAGTGATCAGAAAGGAGGTA 58.718 47.826 0.00 0.00 0.00 3.08
404 405 3.109619 GGATCTTGCTCGTAAAGACTCG 58.890 50.000 0.00 0.00 36.52 4.18
420 421 0.398098 ACGTAACCCATCCCGGATCT 60.398 55.000 0.73 0.00 36.56 2.75
639 642 4.614284 GTGAAAGAATCAGTTGCGTGAATG 59.386 41.667 0.00 0.00 39.19 2.67
741 744 1.400530 CCGCCTTAAGGAGATCCCGT 61.401 60.000 26.21 0.00 40.87 5.28
879 882 8.862091 TTTCTAATTCCCTTCTAAGATCCTCT 57.138 34.615 0.00 0.00 0.00 3.69
998 1004 6.061441 AGCCATCGAACCATATTTGTCATTA 58.939 36.000 0.00 0.00 0.00 1.90
1397 1403 3.371166 GCTGGTAATACCACTTAAGGGCA 60.371 47.826 8.27 0.00 44.79 5.36
1582 1588 9.326413 CGGAAGTGATAATAAAAGTAGGAATGT 57.674 33.333 0.00 0.00 0.00 2.71
1983 1990 3.035055 TGTATCGAACCTCCCCACATA 57.965 47.619 0.00 0.00 0.00 2.29
2068 2075 6.609616 AGCCTAGAGTTTGCTAGAACTATTCT 59.390 38.462 0.00 0.00 39.84 2.40
2182 2190 9.555411 AAAGATTTTACCCACCCAATAGTAAAT 57.445 29.630 0.00 0.00 35.32 1.40
2222 2230 6.432403 AATGGATTTGGCCTAAAGTTTCAA 57.568 33.333 3.32 0.00 0.00 2.69
2557 2565 2.229062 TCTGAGTTGTGAGTAAGCGGAG 59.771 50.000 0.00 0.00 0.00 4.63
2621 2629 1.557832 AGGTATTTGCTACGGCCTTCA 59.442 47.619 0.00 0.00 37.74 3.02
2699 2707 0.458543 CACTGCTGTAGCCGTCGAAT 60.459 55.000 0.80 0.00 41.18 3.34
2717 2725 1.059098 CATCCAATCCGAGGGATCCA 58.941 55.000 15.23 0.00 42.27 3.41
2811 2819 1.201429 CCACTACCTGGGAAGCCAGT 61.201 60.000 0.00 0.00 36.18 4.00
2971 2980 0.645496 TGGGGGTTATCCAGCTCCTA 59.355 55.000 0.00 0.00 45.06 2.94
3124 3133 6.576662 AATGAATCCTACACTACGATCGAT 57.423 37.500 24.34 8.79 0.00 3.59
3125 3134 7.500720 TTAATGAATCCTACACTACGATCGA 57.499 36.000 24.34 4.52 0.00 3.59
3126 3135 8.383264 GATTAATGAATCCTACACTACGATCG 57.617 38.462 14.88 14.88 36.24 3.69
3198 3208 2.572104 TCCTTTCCCTCTAACCAGAAGC 59.428 50.000 0.00 0.00 0.00 3.86
3208 3218 0.494095 ACCCACTCTCCTTTCCCTCT 59.506 55.000 0.00 0.00 0.00 3.69
3235 3245 4.376340 ACCTTTGCACAAGTGAAAGAAG 57.624 40.909 18.24 6.30 33.57 2.85
3321 3331 2.085118 CCATGCCATGGGGTGATTTA 57.915 50.000 16.33 0.00 46.86 1.40
3356 3366 9.311916 CAACTCCAATCTCTGAACTATTTAGAG 57.688 37.037 4.42 4.42 39.38 2.43
3358 3368 9.311916 CTCAACTCCAATCTCTGAACTATTTAG 57.688 37.037 0.00 0.00 0.00 1.85
3406 3416 0.835276 GGTACTTATTCCTGGCCGGT 59.165 55.000 11.58 0.00 0.00 5.28
3409 3419 3.263681 GGGATAGGTACTTATTCCTGGCC 59.736 52.174 13.90 0.00 41.75 5.36
3444 3454 4.384940 ACACCAGCTTCTCTTCTCTTTTC 58.615 43.478 0.00 0.00 0.00 2.29
3543 3553 6.432162 ACATCTCTTCAAAGCAAGAATTAGCA 59.568 34.615 0.00 0.00 31.86 3.49
3649 3659 2.503356 ACTCATGTCTTCCAGGGCTTAG 59.497 50.000 0.00 0.00 0.00 2.18
3678 3688 9.227490 CATCTTTCGTGATCTAGTTAACAGTAG 57.773 37.037 8.61 2.04 0.00 2.57
3680 3690 7.542477 CACATCTTTCGTGATCTAGTTAACAGT 59.458 37.037 8.61 0.00 36.43 3.55
3695 3705 2.154462 CCTCTTTGGCACATCTTTCGT 58.846 47.619 0.00 0.00 39.30 3.85


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

AutoCloner maintained by Alex Coulton.