Multiple sequence alignment - TraesCS2B01G432400

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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 TraesCS2B01G432400 chr2B 100.000 4028 0 0 1 4028 621624860 621620833 0.000000e+00 7439
1 TraesCS2B01G432400 chr2B 92.487 1930 101 18 2112 4028 503642671 503644569 0.000000e+00 2721
2 TraesCS2B01G432400 chr2B 94.127 1243 67 6 2790 4028 665892097 665890857 0.000000e+00 1886
3 TraesCS2B01G432400 chr5B 95.858 4032 139 6 1 4028 638652957 638656964 0.000000e+00 6495
4 TraesCS2B01G432400 chr5B 94.051 2219 117 13 1 2213 400996157 400993948 0.000000e+00 3352
5 TraesCS2B01G432400 chr5B 94.151 1966 91 13 2083 4028 400994122 400992161 0.000000e+00 2972
6 TraesCS2B01G432400 chr5B 88.336 2229 217 29 511 2713 680706247 680704036 0.000000e+00 2636
7 TraesCS2B01G432400 chr5B 87.500 536 57 8 9 544 671838329 671838854 9.570000e-171 610
8 TraesCS2B01G432400 chr7B 94.732 4062 173 12 1 4028 26278537 26274483 0.000000e+00 6277
9 TraesCS2B01G432400 chr7B 86.329 2209 246 42 14 2198 630453906 630451730 0.000000e+00 2355
10 TraesCS2B01G432400 chr4A 92.000 4050 248 43 1 4028 744462667 744458672 0.000000e+00 5614
11 TraesCS2B01G432400 chr6B 90.662 4080 282 61 1 4028 571758160 571754128 0.000000e+00 5332
12 TraesCS2B01G432400 chr6B 93.585 1933 101 12 2112 4028 439012553 439010628 0.000000e+00 2861
13 TraesCS2B01G432400 chr6B 86.252 611 60 22 1982 2584 169033929 169034523 3.390000e-180 641
14 TraesCS2B01G432400 chr1B 90.203 4083 293 57 1 4028 631058778 631054748 0.000000e+00 5225
15 TraesCS2B01G432400 chr1B 86.120 2255 233 55 2 2223 667349136 667346929 0.000000e+00 2357
16 TraesCS2B01G432400 chr3B 95.121 2152 98 5 1 2149 675587427 675589574 0.000000e+00 3386
17 TraesCS2B01G432400 chr3B 94.674 1915 83 10 2125 4028 675589481 675591387 0.000000e+00 2953
18 TraesCS2B01G432400 chr3B 94.682 1241 61 4 2789 4028 698404392 698403156 0.000000e+00 1921
19 TraesCS2B01G432400 chr3B 86.654 547 53 15 1 544 17277509 17276980 4.480000e-164 588
20 TraesCS2B01G432400 chr5A 84.844 2758 332 63 1 2713 555572429 555575145 0.000000e+00 2699
21 TraesCS2B01G432400 chr4B 86.721 2229 238 44 1 2202 335936742 335934545 0.000000e+00 2423
22 TraesCS2B01G432400 chr2A 88.205 1543 157 18 1190 2713 651447730 651449266 0.000000e+00 1818
23 TraesCS2B01G432400 chr2A 87.532 1540 158 23 1190 2713 701047378 701045857 0.000000e+00 1749
24 TraesCS2B01G432400 chr7A 86.483 873 100 14 1851 2713 678425014 678424150 0.000000e+00 942


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 TraesCS2B01G432400 chr2B 621620833 621624860 4027 True 7439.0 7439 100.0000 1 4028 1 chr2B.!!$R1 4027
1 TraesCS2B01G432400 chr2B 503642671 503644569 1898 False 2721.0 2721 92.4870 2112 4028 1 chr2B.!!$F1 1916
2 TraesCS2B01G432400 chr2B 665890857 665892097 1240 True 1886.0 1886 94.1270 2790 4028 1 chr2B.!!$R2 1238
3 TraesCS2B01G432400 chr5B 638652957 638656964 4007 False 6495.0 6495 95.8580 1 4028 1 chr5B.!!$F1 4027
4 TraesCS2B01G432400 chr5B 400992161 400996157 3996 True 3162.0 3352 94.1010 1 4028 2 chr5B.!!$R2 4027
5 TraesCS2B01G432400 chr5B 680704036 680706247 2211 True 2636.0 2636 88.3360 511 2713 1 chr5B.!!$R1 2202
6 TraesCS2B01G432400 chr5B 671838329 671838854 525 False 610.0 610 87.5000 9 544 1 chr5B.!!$F2 535
7 TraesCS2B01G432400 chr7B 26274483 26278537 4054 True 6277.0 6277 94.7320 1 4028 1 chr7B.!!$R1 4027
8 TraesCS2B01G432400 chr7B 630451730 630453906 2176 True 2355.0 2355 86.3290 14 2198 1 chr7B.!!$R2 2184
9 TraesCS2B01G432400 chr4A 744458672 744462667 3995 True 5614.0 5614 92.0000 1 4028 1 chr4A.!!$R1 4027
10 TraesCS2B01G432400 chr6B 571754128 571758160 4032 True 5332.0 5332 90.6620 1 4028 1 chr6B.!!$R2 4027
11 TraesCS2B01G432400 chr6B 439010628 439012553 1925 True 2861.0 2861 93.5850 2112 4028 1 chr6B.!!$R1 1916
12 TraesCS2B01G432400 chr6B 169033929 169034523 594 False 641.0 641 86.2520 1982 2584 1 chr6B.!!$F1 602
13 TraesCS2B01G432400 chr1B 631054748 631058778 4030 True 5225.0 5225 90.2030 1 4028 1 chr1B.!!$R1 4027
14 TraesCS2B01G432400 chr1B 667346929 667349136 2207 True 2357.0 2357 86.1200 2 2223 1 chr1B.!!$R2 2221
15 TraesCS2B01G432400 chr3B 675587427 675591387 3960 False 3169.5 3386 94.8975 1 4028 2 chr3B.!!$F1 4027
16 TraesCS2B01G432400 chr3B 698403156 698404392 1236 True 1921.0 1921 94.6820 2789 4028 1 chr3B.!!$R2 1239
17 TraesCS2B01G432400 chr3B 17276980 17277509 529 True 588.0 588 86.6540 1 544 1 chr3B.!!$R1 543
18 TraesCS2B01G432400 chr5A 555572429 555575145 2716 False 2699.0 2699 84.8440 1 2713 1 chr5A.!!$F1 2712
19 TraesCS2B01G432400 chr4B 335934545 335936742 2197 True 2423.0 2423 86.7210 1 2202 1 chr4B.!!$R1 2201
20 TraesCS2B01G432400 chr2A 651447730 651449266 1536 False 1818.0 1818 88.2050 1190 2713 1 chr2A.!!$F1 1523
21 TraesCS2B01G432400 chr2A 701045857 701047378 1521 True 1749.0 1749 87.5320 1190 2713 1 chr2A.!!$R1 1523
22 TraesCS2B01G432400 chr7A 678424150 678425014 864 True 942.0 942 86.4830 1851 2713 1 chr7A.!!$R1 862

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
698 723 1.302752 GGACATGGTGTGAGCTGCA 60.303 57.895 1.02 0.0 0.00 4.41 F
1586 1706 0.322098 TTGGAATCCACGCCGAACAT 60.322 50.000 0.00 0.0 30.78 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 1799 0.468226 AAAGAGAAGTGGTCGGTGCA 59.532 50.0 0.00 0.0 0.0 4.57 R
3270 3605 1.009389 GTGTCCTCTTCCGCGTTCTG 61.009 60.0 4.92 0.0 0.0 3.02 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
45 47 5.109210 TCCTGAAATACTGTGATAGTTGCG 58.891 41.667 0.00 0.00 40.89 4.85
71 73 4.789012 ACATACTTTTCCATGTGGCAAG 57.211 40.909 0.00 8.47 34.15 4.01
175 187 6.434028 AGTTGCCACACTGTATGAATTGTAAT 59.566 34.615 0.00 0.00 0.00 1.89
248 261 3.419915 GCAACTAATCTGCACATCAACG 58.580 45.455 0.00 0.00 39.69 4.10
455 470 3.702330 CAGCATGTCTGTTGCCATATTG 58.298 45.455 8.46 0.00 41.06 1.90
515 533 1.447938 GCAGACGCAATTTTCGTGTTG 59.552 47.619 7.18 6.89 40.59 3.33
685 710 5.385198 ACTCATTTGGTGTGTTTAGGACAT 58.615 37.500 0.00 0.00 41.10 3.06
698 723 1.302752 GGACATGGTGTGAGCTGCA 60.303 57.895 1.02 0.00 0.00 4.41
797 826 8.295288 TCAACATTTTGTTTTCAAGTGCATTTT 58.705 25.926 0.00 0.00 38.77 1.82
970 1075 6.873076 GCATTCTGTTTTCATTTTCCACCATA 59.127 34.615 0.00 0.00 0.00 2.74
1041 1146 8.302965 GTCAGAACGATGATGATGATTTCATA 57.697 34.615 0.00 0.00 45.29 2.15
1111 1224 0.601841 GGTAACTGTCCACACACCCG 60.602 60.000 0.00 0.00 0.00 5.28
1289 1408 3.577649 ACGACTGACTACATTGACTGG 57.422 47.619 0.00 0.00 0.00 4.00
1290 1409 2.891580 ACGACTGACTACATTGACTGGT 59.108 45.455 0.00 0.00 0.00 4.00
1577 1697 1.893137 GTTTCCTGGGTTGGAATCCAC 59.107 52.381 0.00 0.00 44.55 4.02
1586 1706 0.322098 TTGGAATCCACGCCGAACAT 60.322 50.000 0.00 0.00 30.78 2.71
1588 1708 0.742990 GGAATCCACGCCGAACATGA 60.743 55.000 0.00 0.00 0.00 3.07
1616 1737 2.124819 AGATTCGCTGCAGGCCAG 60.125 61.111 17.12 0.00 44.67 4.85
1629 1750 2.362889 GCCAGGACAACCCATGGG 60.363 66.667 30.23 30.23 42.03 4.00
1677 1799 4.973168 TGTACCTCATCTCAGCTGTTTTT 58.027 39.130 14.67 0.00 0.00 1.94
1965 2096 7.599998 GCATTCTCAAACAAGATGTACCAAAAT 59.400 33.333 0.00 0.00 0.00 1.82
2135 2364 5.833406 TGGCAACTACCATCATTACAATG 57.167 39.130 0.00 0.00 33.75 2.82
2162 2437 3.966979 ACTGCCATCATTACAATGTGGA 58.033 40.909 19.20 0.00 38.62 4.02
2638 2939 9.467796 TCAGAAGAGATGACTATCTTTGTTAGA 57.532 33.333 0.00 0.00 43.63 2.10
2719 3021 3.120649 GCTGAAACTTACATTCGCGTCTT 60.121 43.478 5.77 0.00 0.00 3.01
2877 3208 0.602638 GTGGATGGACGTGCACTCAA 60.603 55.000 13.47 5.58 37.45 3.02
3002 3336 2.750166 TCCTTCTTTGTTTCGTGCACAA 59.250 40.909 18.64 7.62 32.16 3.33
3004 3338 3.181501 CCTTCTTTGTTTCGTGCACAAGA 60.182 43.478 18.64 13.77 35.57 3.02
3144 3479 3.068024 GCAGTTCACTTCATTTGTCCCAA 59.932 43.478 0.00 0.00 0.00 4.12
3270 3605 0.855349 GGATGACGACGATGACATGC 59.145 55.000 0.00 3.62 0.00 4.06
3443 3779 1.274703 GGGCTCCAGAGGATGTTGGA 61.275 60.000 0.00 0.00 41.06 3.53
3494 3830 2.880629 ATCCCGTAGCTGCCAGGAGT 62.881 60.000 12.72 1.26 0.00 3.85
3515 3853 8.039538 AGGAGTAGGTTCGACTTTAATTTTAGG 58.960 37.037 0.00 0.00 0.00 2.69
3613 3954 1.474077 GATGTCTGACAATTGCCACCC 59.526 52.381 15.31 0.00 0.00 4.61
3646 3988 1.118965 TCTTTCACGTGCAGGGAGGA 61.119 55.000 11.67 2.61 31.37 3.71
3648 3990 2.111999 TTTCACGTGCAGGGAGGAGG 62.112 60.000 11.67 0.00 31.37 4.30
3685 4027 3.131396 CAGTTACGAAGAAACAGGCACT 58.869 45.455 0.00 0.00 43.88 4.40
3793 4136 2.656069 CGTCCAACACCGGGGATCT 61.656 63.158 12.96 0.00 35.25 2.75
3925 4269 1.288188 TGGGCTTCTGTCATCATCCA 58.712 50.000 0.00 0.00 0.00 3.41
3938 4282 5.163216 TGTCATCATCCACATATGGCAACTA 60.163 40.000 7.80 0.00 46.80 2.24
4005 4351 5.701290 GCAACTCCTACTTGTCTTTACATGT 59.299 40.000 2.69 2.69 43.94 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 4.923281 GCCACATGGAAAAGTATGTTTGTC 59.077 41.667 0.87 0.00 35.46 3.18
175 187 5.929992 GCAGTGACTACCAATTAACTACACA 59.070 40.000 0.00 0.00 0.00 3.72
455 470 6.398918 CCACATTATACCCTATACTGACTGC 58.601 44.000 0.00 0.00 0.00 4.40
515 533 1.019673 ATCGCAAGTCATCATGGCAC 58.980 50.000 0.00 0.00 39.48 5.01
685 710 0.109153 AGATGTTGCAGCTCACACCA 59.891 50.000 1.17 0.00 0.00 4.17
698 723 3.254166 CACTGCACAAAGCCTAAGATGTT 59.746 43.478 0.00 0.00 44.83 2.71
797 826 7.490962 ACATTTGAAAAAGTGTACAGATCGA 57.509 32.000 0.00 0.00 0.00 3.59
970 1075 5.061721 AGGTAGGAACAGACCAAATTGTT 57.938 39.130 0.00 0.00 38.83 2.83
1041 1146 2.224378 CCGATTATGCTGTGGTGGATCT 60.224 50.000 0.00 0.00 0.00 2.75
1111 1224 4.899352 ATAACATATGCAGGAGGAGGAC 57.101 45.455 1.58 0.00 0.00 3.85
1289 1408 5.213675 CCTTCTGATCGTCGGTAAATCTAC 58.786 45.833 0.00 0.00 0.00 2.59
1290 1409 4.277672 CCCTTCTGATCGTCGGTAAATCTA 59.722 45.833 0.00 0.00 0.00 1.98
1369 1488 2.356125 GCCAGTCACATACAGGGTTGAT 60.356 50.000 0.00 0.00 35.33 2.57
1451 1570 1.076332 CACGGATTCCTCGTTCAACC 58.924 55.000 0.30 0.00 38.94 3.77
1577 1697 0.992072 CAGTACAGTCATGTTCGGCG 59.008 55.000 0.00 0.00 41.01 6.46
1586 1706 1.404181 GCGAATCTGCCAGTACAGTCA 60.404 52.381 0.00 0.00 38.84 3.41
1588 1708 0.898320 AGCGAATCTGCCAGTACAGT 59.102 50.000 0.00 0.00 38.84 3.55
1616 1737 4.684623 CATCCCCATGGGTTGTCC 57.315 61.111 29.33 0.00 44.74 4.02
1629 1750 8.268850 TGAGTAGCTTCATCTTAAAAACATCC 57.731 34.615 0.00 0.00 0.00 3.51
1677 1799 0.468226 AAAGAGAAGTGGTCGGTGCA 59.532 50.000 0.00 0.00 0.00 4.57
1965 2096 3.190327 CCATTAAATGCAGTCGACAACCA 59.810 43.478 19.50 11.55 0.00 3.67
2040 2177 1.108776 ATGATCAGGTTGCCATGCAC 58.891 50.000 0.09 0.00 38.71 4.57
2162 2437 7.643569 TGCCATATTGTAATGATGACAGTTT 57.356 32.000 0.00 0.00 0.00 2.66
2638 2939 2.045634 ATGCGCAGACAGCCATGT 60.046 55.556 18.32 0.00 44.31 3.21
3002 3336 1.127343 GCTCAATAGGTGCCCTCTCT 58.873 55.000 0.00 0.00 34.61 3.10
3004 3338 1.419387 GATGCTCAATAGGTGCCCTCT 59.581 52.381 0.00 0.00 34.61 3.69
3144 3479 1.228003 TTGGCCGATGTGTCCGTTT 60.228 52.632 0.00 0.00 0.00 3.60
3270 3605 1.009389 GTGTCCTCTTCCGCGTTCTG 61.009 60.000 4.92 0.00 0.00 3.02
3594 3934 1.076024 AGGGTGGCAATTGTCAGACAT 59.924 47.619 14.22 4.40 0.00 3.06
3620 3961 0.684535 TGCACGTGAAAGATGGAGGA 59.315 50.000 22.23 0.00 0.00 3.71
3646 3988 3.699894 CTCGTCCACCAGCTGCCT 61.700 66.667 8.66 0.00 0.00 4.75
3648 3990 4.687215 TGCTCGTCCACCAGCTGC 62.687 66.667 8.66 0.00 36.53 5.25
3685 4027 1.962306 GAAGCACGGGTTGGCGTTA 60.962 57.895 0.00 0.00 34.54 3.18
3789 4132 1.461127 GTCTGGCAACACGACAAGATC 59.539 52.381 0.00 0.00 46.17 2.75
3793 4136 0.813610 CAGGTCTGGCAACACGACAA 60.814 55.000 6.89 0.00 46.17 3.18
3890 4234 1.608055 CCCATGTGACAAGCTGAACA 58.392 50.000 0.00 0.00 0.00 3.18
3938 4282 7.227314 GGAAGGAAAATCATTTTGAAAAGCAGT 59.773 33.333 0.00 0.00 31.94 4.40
4005 4351 4.454678 CATTTGGCCTAGATAGCAGTTGA 58.545 43.478 3.32 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.