Multiple sequence alignment - TraesCS2B01G486100

Loading Multiple Alignment...

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 TraesCS2B01G486100 chr2B 100.000 5924 0 0 1 5924 683042955 683048878 0.000000e+00 10940
1 TraesCS2B01G486100 chr2B 85.855 5274 660 51 1 5223 683067662 683072900 0.000000e+00 5528
2 TraesCS2B01G486100 chr2B 84.408 2001 291 14 1 1990 683054073 683056063 0.000000e+00 1947
3 TraesCS2B01G486100 chr2B 84.727 1794 259 11 207 1990 683128386 683130174 0.000000e+00 1781
4 TraesCS2B01G486100 chr2B 87.843 1456 166 8 2019 3470 683056128 683057576 0.000000e+00 1698
5 TraesCS2B01G486100 chr2B 81.523 2035 314 35 3238 5233 794691206 794689195 0.000000e+00 1618
6 TraesCS2B01G486100 chr2B 81.523 2035 314 35 3238 5233 794800107 794798096 0.000000e+00 1618
7 TraesCS2B01G486100 chr2B 83.324 1751 249 28 3498 5223 683057571 683059303 0.000000e+00 1576
8 TraesCS2B01G486100 chr2B 86.818 1100 135 6 2000 3093 683130214 683131309 0.000000e+00 1219
9 TraesCS2B01G486100 chr2B 82.353 119 21 0 4986 5104 683074161 683074279 2.920000e-18 104
10 TraesCS2B01G486100 chr2D 92.265 5740 396 31 210 5924 571195366 571201082 0.000000e+00 8096
11 TraesCS2B01G486100 chr2D 89.384 3099 305 14 1 3096 571208980 571212057 0.000000e+00 3879
12 TraesCS2B01G486100 chr2D 84.501 2897 403 32 224 3093 571443443 571446320 0.000000e+00 2820
13 TraesCS2B01G486100 chr2D 79.601 2755 434 73 3096 5767 571212084 571214793 0.000000e+00 1857
14 TraesCS2B01G486100 chr2D 81.379 2132 351 34 3115 5221 571530171 571532281 0.000000e+00 1696
15 TraesCS2B01G486100 chr2A 90.516 5082 400 42 1 5037 710093042 710098086 0.000000e+00 6639
16 TraesCS2B01G486100 chr2A 93.261 3324 175 26 2632 5924 709858411 709861716 0.000000e+00 4852
17 TraesCS2B01G486100 chr2A 95.304 2470 102 7 169 2637 709850411 709852867 0.000000e+00 3906
18 TraesCS2B01G486100 chr2A 89.287 3099 308 14 1 3096 710036194 710039271 0.000000e+00 3862
19 TraesCS2B01G486100 chr2A 82.481 1975 322 14 3096 5059 710039298 710041259 0.000000e+00 1709
20 TraesCS2B01G486100 chr2A 87.398 1476 173 10 2000 3470 710189963 710191430 0.000000e+00 1683
21 TraesCS2B01G486100 chr2A 94.891 137 7 0 1 137 709850281 709850417 1.290000e-51 215
22 TraesCS2B01G486100 chr6A 86.360 1107 141 8 1995 3096 617078703 617079804 0.000000e+00 1199


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 TraesCS2B01G486100 chr2B 683042955 683048878 5923 False 10940.000000 10940 100.000000 1 5924 1 chr2B.!!$F1 5923
1 TraesCS2B01G486100 chr2B 683067662 683074279 6617 False 2816.000000 5528 84.104000 1 5223 2 chr2B.!!$F3 5222
2 TraesCS2B01G486100 chr2B 683054073 683059303 5230 False 1740.333333 1947 85.191667 1 5223 3 chr2B.!!$F2 5222
3 TraesCS2B01G486100 chr2B 794689195 794691206 2011 True 1618.000000 1618 81.523000 3238 5233 1 chr2B.!!$R1 1995
4 TraesCS2B01G486100 chr2B 794798096 794800107 2011 True 1618.000000 1618 81.523000 3238 5233 1 chr2B.!!$R2 1995
5 TraesCS2B01G486100 chr2B 683128386 683131309 2923 False 1500.000000 1781 85.772500 207 3093 2 chr2B.!!$F4 2886
6 TraesCS2B01G486100 chr2D 571195366 571201082 5716 False 8096.000000 8096 92.265000 210 5924 1 chr2D.!!$F1 5714
7 TraesCS2B01G486100 chr2D 571208980 571214793 5813 False 2868.000000 3879 84.492500 1 5767 2 chr2D.!!$F4 5766
8 TraesCS2B01G486100 chr2D 571443443 571446320 2877 False 2820.000000 2820 84.501000 224 3093 1 chr2D.!!$F2 2869
9 TraesCS2B01G486100 chr2D 571530171 571532281 2110 False 1696.000000 1696 81.379000 3115 5221 1 chr2D.!!$F3 2106
10 TraesCS2B01G486100 chr2A 710093042 710098086 5044 False 6639.000000 6639 90.516000 1 5037 1 chr2A.!!$F2 5036
11 TraesCS2B01G486100 chr2A 709858411 709861716 3305 False 4852.000000 4852 93.261000 2632 5924 1 chr2A.!!$F1 3292
12 TraesCS2B01G486100 chr2A 710036194 710041259 5065 False 2785.500000 3862 85.884000 1 5059 2 chr2A.!!$F5 5058
13 TraesCS2B01G486100 chr2A 709850281 709852867 2586 False 2060.500000 3906 95.097500 1 2637 2 chr2A.!!$F4 2636
14 TraesCS2B01G486100 chr2A 710189963 710191430 1467 False 1683.000000 1683 87.398000 2000 3470 1 chr2A.!!$F3 1470
15 TraesCS2B01G486100 chr6A 617078703 617079804 1101 False 1199.000000 1199 86.360000 1995 3096 1 chr6A.!!$F1 1101

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
778 789 1.382629 GGCAGTGGTGGTATTGGGT 59.617 57.895 0.0 0.0 0.00 4.51 F
1668 1683 1.676006 GTATTGGCAGGGATGGTTTCG 59.324 52.381 0.0 0.0 0.00 3.46 F
2505 2562 0.798776 CAACCTGGCTTTCTAGTGCG 59.201 55.000 0.0 0.0 0.00 5.34 F
3701 3818 0.615331 GTGATGACCTCAGCCCAAGA 59.385 55.000 0.0 0.0 33.51 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2229 0.721718 GAGAGGTCATTTTGCCGACG 59.278 55.0 0.00 0.0 32.74 5.12 R
2998 3058 1.100510 CCAACATGCAGGTCCATCAG 58.899 55.0 3.65 0.0 0.00 2.90 R
3861 3978 0.034756 CACCCACCAACGATGAGACA 59.965 55.0 0.00 0.0 0.00 3.41 R
5088 5236 1.757574 CACAAAATGTGCTGGTGACG 58.242 50.0 0.00 0.0 41.89 4.35 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
67 68 6.506500 CACAGAAGGTGCTTCATATTTCTT 57.493 37.500 0.00 0.00 42.37 2.52
75 76 8.409358 AGGTGCTTCATATTTCTTTACTGTTT 57.591 30.769 0.00 0.00 0.00 2.83
179 181 8.442632 TCAGATTATCTCTTGCTTAATTGTGG 57.557 34.615 0.00 0.00 29.16 4.17
192 197 8.729805 TGCTTAATTGTGGTCTTTTTGAATTT 57.270 26.923 0.00 0.00 0.00 1.82
348 356 5.955959 TGCTCCTACTGGTACTAATCTTGAA 59.044 40.000 0.00 0.00 34.23 2.69
490 498 2.223433 GCTCATTGTAACATGCTGCCTC 60.223 50.000 0.00 0.00 0.00 4.70
555 563 5.658634 AGTGACTCTTCTATGCAGTAATGGA 59.341 40.000 0.00 0.00 0.00 3.41
778 789 1.382629 GGCAGTGGTGGTATTGGGT 59.617 57.895 0.00 0.00 0.00 4.51
800 811 3.372954 AGACGACGCTTGTTAGATATGC 58.627 45.455 0.00 0.00 0.00 3.14
1231 1246 3.958147 AACCGCGAGCACCATCCTG 62.958 63.158 8.23 0.00 0.00 3.86
1330 1345 4.941657 TCTGAGCACAGATGTTAGCTATG 58.058 43.478 10.01 0.00 46.55 2.23
1668 1683 1.676006 GTATTGGCAGGGATGGTTTCG 59.324 52.381 0.00 0.00 0.00 3.46
2148 2205 2.486982 GCGCCATCTTATTGCTCATGAT 59.513 45.455 0.00 0.00 0.00 2.45
2162 2219 3.379372 GCTCATGATAAAGTGCACCATGT 59.621 43.478 23.57 9.87 36.79 3.21
2163 2220 4.732647 GCTCATGATAAAGTGCACCATGTG 60.733 45.833 23.57 22.23 36.79 3.21
2167 2224 6.999871 TCATGATAAAGTGCACCATGTGATAT 59.000 34.615 23.57 10.12 36.79 1.63
2172 2229 5.443185 AAGTGCACCATGTGATATATTGC 57.557 39.130 14.63 0.00 35.23 3.56
2279 2336 2.977914 TGAGCTTGTATCACTTGGAGC 58.022 47.619 0.00 0.00 0.00 4.70
2321 2378 1.826096 GACTAAAGAAGAGGCGAGGGT 59.174 52.381 0.00 0.00 0.00 4.34
2505 2562 0.798776 CAACCTGGCTTTCTAGTGCG 59.201 55.000 0.00 0.00 0.00 5.34
2532 2589 5.506708 TCAGTTACCTCACTGCAGATACTA 58.493 41.667 23.35 0.00 43.51 1.82
2931 2991 8.185505 TGTAAATTGTTGGACACTTACTTTGAC 58.814 33.333 10.88 0.00 0.00 3.18
3017 3077 1.100510 CTGATGGACCTGCATGTTGG 58.899 55.000 0.00 0.00 0.00 3.77
3136 3250 1.681793 GGCCATCTAGTCTGCGTAGAA 59.318 52.381 4.26 0.00 34.01 2.10
3235 3349 1.671379 GGAGTTCCGGGACTTGCAC 60.671 63.158 18.86 3.45 0.00 4.57
3351 3465 9.305925 GGCATAAGATTGTTTCAAATAAGAAGG 57.694 33.333 0.00 0.00 0.00 3.46
3507 3624 3.259633 AAGCAGCCTTGTCCTCCCG 62.260 63.158 0.00 0.00 0.00 5.14
3604 3721 5.814705 CAGTCCCTTGAGAAGTTGCTATTAG 59.185 44.000 0.00 0.00 0.00 1.73
3628 3745 4.508584 GGGGGTGTCCTCAGATAAAGTTTT 60.509 45.833 0.00 0.00 32.39 2.43
3700 3817 0.617413 AGTGATGACCTCAGCCCAAG 59.383 55.000 0.00 0.00 33.51 3.61
3701 3818 0.615331 GTGATGACCTCAGCCCAAGA 59.385 55.000 0.00 0.00 33.51 3.02
3702 3819 1.211457 GTGATGACCTCAGCCCAAGAT 59.789 52.381 0.00 0.00 33.51 2.40
3703 3820 1.487976 TGATGACCTCAGCCCAAGATC 59.512 52.381 0.00 0.00 0.00 2.75
3704 3821 1.487976 GATGACCTCAGCCCAAGATCA 59.512 52.381 0.00 0.00 0.00 2.92
3705 3822 0.907486 TGACCTCAGCCCAAGATCAG 59.093 55.000 0.00 0.00 0.00 2.90
3831 3948 6.948886 ACTCTACAAGATTCACCTCTCTTACA 59.051 38.462 0.00 0.00 30.70 2.41
3894 4011 2.225727 GGTGGGTGAAACGAAAGATGAC 59.774 50.000 0.00 0.00 38.12 3.06
3903 4020 3.604875 ACGAAAGATGACGGTACCATT 57.395 42.857 13.54 0.00 0.00 3.16
3911 4031 3.686916 TGACGGTACCATTGATGTTGA 57.313 42.857 13.54 0.00 0.00 3.18
3941 4061 4.141733 CCCACCATCACTTGAAAACCTTTT 60.142 41.667 0.00 0.00 0.00 2.27
3999 4119 2.585900 TCCTCAAGGCCTTCTCTACCTA 59.414 50.000 17.29 0.00 32.08 3.08
4044 4164 3.199677 CCCGTGTTTGAAGTCTGTACAA 58.800 45.455 0.00 0.00 0.00 2.41
4235 4355 6.548993 GGGAATCAAATTCAGCTATTTCCTCT 59.451 38.462 2.42 0.00 41.03 3.69
4260 4380 7.216494 TGTCACTTGATAAACTTGAGATCACA 58.784 34.615 0.00 0.00 29.44 3.58
5088 5236 3.138304 TGTACACATTTCTGCACTCACC 58.862 45.455 0.00 0.00 0.00 4.02
5318 5515 5.488341 TCCTGATTAGCTTTGTTAGTGGAC 58.512 41.667 0.00 0.00 0.00 4.02
5608 5878 7.781548 TTAAATTGGCTCGTACTTCCTATTC 57.218 36.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
348 356 3.776969 TGGATGAAGACACATAGCTTCCT 59.223 43.478 0.00 0.00 39.73 3.36
536 544 8.557864 CAGAATTTCCATTACTGCATAGAAGAG 58.442 37.037 0.00 0.00 0.00 2.85
555 563 5.711698 TGAAGAACCCCCTTTACAGAATTT 58.288 37.500 0.00 0.00 0.00 1.82
778 789 4.035909 TGCATATCTAACAAGCGTCGTCTA 59.964 41.667 0.00 0.00 0.00 2.59
983 997 7.325660 TCATCCATTACAAGCAGAAATCTTC 57.674 36.000 0.00 0.00 0.00 2.87
1231 1246 5.146010 TGTTTCCCAATAGATTGCAAACC 57.854 39.130 1.71 0.00 36.48 3.27
1330 1345 0.716108 CGAACTGTCGTCCAATGCTC 59.284 55.000 0.00 0.00 42.53 4.26
1668 1683 7.383572 CCATCTATAGTAGCACACTCATTTGAC 59.616 40.741 0.00 0.00 38.80 3.18
2148 2205 6.293353 CGCAATATATCACATGGTGCACTTTA 60.293 38.462 17.98 4.06 32.98 1.85
2172 2229 0.721718 GAGAGGTCATTTTGCCGACG 59.278 55.000 0.00 0.00 32.74 5.12
2279 2336 7.701445 AGTCTTCACATTTTCAAGTTGAGAAG 58.299 34.615 17.78 17.78 38.57 2.85
2321 2378 0.754587 TTTGTGTGTCAGCATGGCCA 60.755 50.000 8.56 8.56 42.68 5.36
2532 2589 3.107402 TCCTTGCACTCCTCTAGATGT 57.893 47.619 0.00 0.00 0.00 3.06
2582 2642 3.636153 ATGTCAGCTTCCTAAGGGAAC 57.364 47.619 0.00 0.00 45.72 3.62
2679 2739 6.478129 TCCATAAGAACCGGTACATTTTTCT 58.522 36.000 8.00 1.22 0.00 2.52
2735 2795 1.734465 GTTGAGGGCAGTTCTTGATCG 59.266 52.381 0.00 0.00 0.00 3.69
2907 2967 8.282455 TGTCAAAGTAAGTGTCCAACAATTTA 57.718 30.769 0.00 0.00 37.58 1.40
2931 2991 2.734606 CCAGTTGCTGCAACATCATTTG 59.265 45.455 37.75 27.43 45.66 2.32
2998 3058 1.100510 CCAACATGCAGGTCCATCAG 58.899 55.000 3.65 0.00 0.00 2.90
3017 3077 3.745458 CAGAGAAGGAACTGAAACTCTGC 59.255 47.826 0.00 0.00 41.73 4.26
3136 3250 3.899360 CAAGGGCAATCATGGATGGTAAT 59.101 43.478 0.00 0.00 0.00 1.89
3267 3381 5.798132 AGCACACTCAACTCATTAGATTCA 58.202 37.500 0.00 0.00 0.00 2.57
3351 3465 6.169094 TGAAAGAGAGATCAGATTTGGACAC 58.831 40.000 0.00 0.00 0.00 3.67
3507 3624 6.369890 TGCTAATGTTGACAGATTTGAGAGAC 59.630 38.462 0.00 0.00 0.00 3.36
3628 3745 7.330946 CGTTTCTGTAGGTTGACTGATTGATAA 59.669 37.037 0.00 0.00 0.00 1.75
3700 3817 7.701078 CAGTTTCAATTCATGTTCATCCTGATC 59.299 37.037 0.00 0.00 0.00 2.92
3701 3818 7.544622 CAGTTTCAATTCATGTTCATCCTGAT 58.455 34.615 0.00 0.00 0.00 2.90
3702 3819 6.570957 GCAGTTTCAATTCATGTTCATCCTGA 60.571 38.462 0.00 0.00 0.00 3.86
3703 3820 5.575606 GCAGTTTCAATTCATGTTCATCCTG 59.424 40.000 0.00 0.00 0.00 3.86
3704 3821 5.337009 GGCAGTTTCAATTCATGTTCATCCT 60.337 40.000 0.00 0.00 0.00 3.24
3705 3822 4.866486 GGCAGTTTCAATTCATGTTCATCC 59.134 41.667 0.00 0.00 0.00 3.51
3831 3948 3.511540 GGCAACCATAAAGGAAAAGCTCT 59.488 43.478 0.00 0.00 41.22 4.09
3861 3978 0.034756 CACCCACCAACGATGAGACA 59.965 55.000 0.00 0.00 0.00 3.41
3894 4011 6.238374 GGAGTAATTCAACATCAATGGTACCG 60.238 42.308 7.57 0.00 0.00 4.02
3903 4020 4.649267 TGGTGGGAGTAATTCAACATCA 57.351 40.909 0.00 0.00 0.00 3.07
3911 4031 4.927267 TCAAGTGATGGTGGGAGTAATT 57.073 40.909 0.00 0.00 0.00 1.40
3941 4061 6.490040 CAGGTTTTCTGGGAAAGAACTGATAA 59.510 38.462 11.20 0.00 44.77 1.75
4044 4164 0.324943 AAGCCGTACAGGAATGCAGT 59.675 50.000 7.77 0.00 45.00 4.40
4235 4355 7.216494 TGTGATCTCAAGTTTATCAAGTGACA 58.784 34.615 0.00 0.00 31.77 3.58
4905 5040 7.281774 CCACATAATCAATTGTGACTCTTAGCT 59.718 37.037 5.13 0.00 44.74 3.32
5088 5236 1.757574 CACAAAATGTGCTGGTGACG 58.242 50.000 0.00 0.00 41.89 4.35
5318 5515 1.812235 TTGCATGTCTACAGCACTGG 58.188 50.000 2.21 0.00 38.11 4.00
5608 5878 3.369147 CCTCATGCTGAAAGTCAACTACG 59.631 47.826 0.00 0.00 35.30 3.51


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

AutoCloner maintained by Alex Coulton.