Multiple sequence alignment - TraesCS3B01G225300

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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 TraesCS3B01G225300 chr3B 100.000 1992 0 0 1 1992 309416358 309418349 0.000000e+00 3679.0
1 TraesCS3B01G225300 chr3B 100.000 83 0 0 2290 2372 309418647 309418729 1.140000e-33 154.0
2 TraesCS3B01G225300 chr3A 93.602 1735 75 17 1 1707 336607048 336605322 0.000000e+00 2556.0
3 TraesCS3B01G225300 chr3A 92.974 427 16 7 1560 1980 336605326 336604908 5.610000e-171 610.0
4 TraesCS3B01G225300 chr3D 95.848 554 14 2 119 663 253523379 253522826 0.000000e+00 887.0
5 TraesCS3B01G225300 chr3D 95.192 208 9 1 1786 1992 253522821 253522614 6.320000e-86 327.0
6 TraesCS3B01G225300 chr3D 88.618 123 5 7 4 120 253525479 253525360 8.840000e-30 141.0
7 TraesCS3B01G225300 chr3D 96.386 83 3 0 2290 2372 253522604 253522522 1.140000e-28 137.0
8 TraesCS3B01G225300 chr7B 83.429 175 24 5 1118 1290 611730831 611730660 8.780000e-35 158.0
9 TraesCS3B01G225300 chr7B 87.640 89 11 0 1202 1290 612007199 612007111 1.160000e-18 104.0
10 TraesCS3B01G225300 chrUn 81.622 185 29 4 1108 1290 20923062 20922881 5.280000e-32 148.0
11 TraesCS3B01G225300 chr6B 81.081 185 32 3 1107 1290 98992358 98992540 6.830000e-31 145.0
12 TraesCS3B01G225300 chr6B 81.034 174 30 3 1118 1290 98992597 98992768 4.110000e-28 135.0
13 TraesCS3B01G225300 chr6B 79.412 170 32 3 1118 1286 139894390 139894223 1.490000e-22 117.0
14 TraesCS3B01G225300 chr6A 79.885 174 32 3 1118 1290 91423857 91424028 8.900000e-25 124.0
15 TraesCS3B01G225300 chr6A 78.947 152 29 3 1118 1268 81258987 81258838 1.500000e-17 100.0
16 TraesCS3B01G225300 chr6D 78.857 175 34 3 1118 1291 75372459 75372631 5.360000e-22 115.0
17 TraesCS3B01G225300 chr2A 81.982 111 17 3 1118 1227 665844149 665844041 9.030000e-15 91.6
18 TraesCS3B01G225300 chr7A 92.857 56 3 1 1834 1889 380163395 380163449 1.950000e-11 80.5


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 TraesCS3B01G225300 chr3B 309416358 309418729 2371 False 1916.5 3679 100.000 1 2372 2 chr3B.!!$F1 2371
1 TraesCS3B01G225300 chr3A 336604908 336607048 2140 True 1583.0 2556 93.288 1 1980 2 chr3A.!!$R1 1979
2 TraesCS3B01G225300 chr3D 253522522 253525479 2957 True 373.0 887 94.011 4 2372 4 chr3D.!!$R1 2368

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
131 2117 0.666913 TCCGCTAGGTGCTAATCGAC 59.333 55.0 0.00 0.0 40.11 4.20 F
1057 3057 0.462581 TGGCATGCAGATCTTCGTCC 60.463 55.0 21.36 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 3168 0.470341 GGGAGGCAGTATGGAAGGAC 59.53 60.000 0.00 0.0 35.86 3.85 R
1908 4070 1.599797 GTGTTGGGGCACTAACGCT 60.60 57.895 20.21 0.0 36.51 5.07 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
29 30 5.701290 CGGTTGTCTTTATCTTGTCTCCTTT 59.299 40.000 0.00 0.00 0.00 3.11
69 70 4.611367 TCCTTCTTTCTCTATCCCTTCGT 58.389 43.478 0.00 0.00 0.00 3.85
77 78 1.672854 CTATCCCTTCGTCACCGCCA 61.673 60.000 0.00 0.00 0.00 5.69
126 2112 0.978151 TTTGGTCCGCTAGGTGCTAA 59.022 50.000 0.00 0.00 40.11 3.09
131 2117 0.666913 TCCGCTAGGTGCTAATCGAC 59.333 55.000 0.00 0.00 40.11 4.20
160 2146 1.206849 TGCTATCCGCATGTGTCTTCA 59.793 47.619 5.38 0.00 45.47 3.02
239 2225 2.622436 CCGGTCTCTTTTCTTGCCTAG 58.378 52.381 0.00 0.00 0.00 3.02
249 2235 0.979665 TCTTGCCTAGCTGTGCTCTT 59.020 50.000 10.19 0.00 40.44 2.85
424 2411 6.016943 CCCTTTGGTTTAGATCACGTTACAAA 60.017 38.462 0.00 0.00 0.00 2.83
531 2527 4.886579 AGGAACACATGAAAAGGAAATGC 58.113 39.130 0.00 0.00 0.00 3.56
548 2544 1.896220 TGCAACTAAGGCAAGTCCAG 58.104 50.000 0.00 0.00 38.54 3.86
720 2716 3.689161 GCACTACATGTTCTATGTTGGCA 59.311 43.478 2.30 0.00 33.76 4.92
741 2737 4.320057 GCATCGAGGCTTCTTATTTGATGG 60.320 45.833 16.00 0.00 34.15 3.51
763 2759 2.579860 AGGAGGAGCATTTTGTCCATCT 59.420 45.455 0.00 0.00 35.02 2.90
773 2769 1.133181 TTGTCCATCTGTGCCCCTCA 61.133 55.000 0.00 0.00 0.00 3.86
792 2789 4.318332 CTCAGTGAGGTTTCATTGCTACA 58.682 43.478 12.67 0.00 39.96 2.74
803 2800 6.208644 GTTTCATTGCTACATGTTTCTGTGT 58.791 36.000 2.30 0.00 0.00 3.72
839 2837 2.223845 GGTTTGTTTGCCATTCATGTGC 59.776 45.455 0.00 0.00 0.00 4.57
859 2858 2.872858 GCGCCTTATACTAAAGCAAGCT 59.127 45.455 0.00 0.00 0.00 3.74
916 2915 4.019231 ACCACTTATGAGGAAGGGAAAGAC 60.019 45.833 0.00 0.00 30.86 3.01
983 2982 1.291132 GCCACGTCTAGAAATGAGGC 58.709 55.000 11.62 11.62 35.27 4.70
1057 3057 0.462581 TGGCATGCAGATCTTCGTCC 60.463 55.000 21.36 0.00 0.00 4.79
1216 3217 2.945668 GGTGGTATGCTGATCTTTGTCC 59.054 50.000 0.00 0.00 0.00 4.02
1228 3229 1.416401 TCTTTGTCCAGACACTCACCC 59.584 52.381 0.00 0.00 41.67 4.61
1236 3237 0.759346 AGACACTCACCCACAAGACC 59.241 55.000 0.00 0.00 0.00 3.85
1241 3242 1.072331 ACTCACCCACAAGACCATCAC 59.928 52.381 0.00 0.00 0.00 3.06
1242 3243 1.072173 CTCACCCACAAGACCATCACA 59.928 52.381 0.00 0.00 0.00 3.58
1269 3270 2.167487 GGAAGAGTCCTCTGACACCATC 59.833 54.545 0.00 0.00 44.33 3.51
1271 3272 1.004862 AGAGTCCTCTGACACCATCGA 59.995 52.381 0.00 0.00 44.33 3.59
1366 3378 2.028484 GTCGACGACCAACCAGCA 59.972 61.111 17.25 0.00 0.00 4.41
1372 3384 2.695359 GACGACCAACCAGCATCTAAA 58.305 47.619 0.00 0.00 0.00 1.85
1373 3385 2.415512 GACGACCAACCAGCATCTAAAC 59.584 50.000 0.00 0.00 0.00 2.01
1415 3427 1.408822 GGCTAAGCATAGGCCTGTTGT 60.409 52.381 17.99 0.00 46.26 3.32
1422 3434 1.064463 CATAGGCCTGTTGTGGTCCAT 60.064 52.381 17.99 0.00 30.64 3.41
1447 3459 2.149803 TGCATGGCAAGCTGTCAAGC 62.150 55.000 16.31 9.88 45.65 4.01
1498 3510 0.038744 CCAAGGTGATTCACTGCCCT 59.961 55.000 16.02 2.40 34.40 5.19
1509 3521 2.250031 TCACTGCCCTCTTTTACCGTA 58.750 47.619 0.00 0.00 0.00 4.02
1515 3527 0.247185 CCTCTTTTACCGTACGGGCA 59.753 55.000 35.86 21.65 40.62 5.36
1594 3606 2.238646 ACAAGACAGGTGTTCAACTCCA 59.761 45.455 11.22 0.00 34.35 3.86
1651 3808 7.946655 TTAATGCGATAAGTATTCCTCTGTG 57.053 36.000 0.00 0.00 36.55 3.66
1652 3809 3.717707 TGCGATAAGTATTCCTCTGTGC 58.282 45.455 0.00 0.00 0.00 4.57
1672 3829 2.679930 GCATCTACTGTACCCACAACCC 60.680 54.545 0.00 0.00 33.22 4.11
1717 3876 0.394488 GACTAAAAGGAGGCCCAGGC 60.394 60.000 0.00 0.00 41.06 4.85
1732 3893 0.745468 CAGGCTACGTAGAGGGGTTC 59.255 60.000 26.53 6.19 0.00 3.62
1766 3927 1.298859 ATGCGCGAGTGAACTTTCCC 61.299 55.000 12.10 0.00 0.00 3.97
1767 3928 1.668151 GCGCGAGTGAACTTTCCCT 60.668 57.895 12.10 0.00 0.00 4.20
1768 3929 1.901650 GCGCGAGTGAACTTTCCCTG 61.902 60.000 12.10 0.00 0.00 4.45
1769 3930 1.869690 GCGAGTGAACTTTCCCTGC 59.130 57.895 0.00 0.00 0.00 4.85
1770 3931 1.578206 GCGAGTGAACTTTCCCTGCC 61.578 60.000 0.00 0.00 0.00 4.85
1771 3932 0.955919 CGAGTGAACTTTCCCTGCCC 60.956 60.000 0.00 0.00 0.00 5.36
1830 3991 6.265196 TCATCACTGCCACTGAATAAAAGTTT 59.735 34.615 0.00 0.00 0.00 2.66
1859 4020 3.817647 CGTAGGGTATTACGCTTCCTAGT 59.182 47.826 17.33 0.00 41.82 2.57
1908 4070 6.268617 CCATGTGGTAGATAGAGGATTTGAGA 59.731 42.308 0.00 0.00 0.00 3.27
1959 4121 2.598787 GGTGTTCCACATCCCCGGA 61.599 63.158 0.73 0.00 35.86 5.14
2315 4477 4.314121 GTTCAGAGAGATACATGGCCATC 58.686 47.826 17.61 5.44 0.00 3.51
2318 4480 4.596212 TCAGAGAGATACATGGCCATCAAT 59.404 41.667 17.61 12.37 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.306987 AGAAGGAGAGGAAAAGCAAATACAA 58.693 36.000 0.00 0.00 0.00 2.41
69 70 0.947180 GAAGCGTAAAGTGGCGGTGA 60.947 55.000 0.00 0.00 38.85 4.02
77 78 1.165270 GGCATGGTGAAGCGTAAAGT 58.835 50.000 0.00 0.00 0.00 2.66
126 2112 3.093057 GGATAGCAGGTATGAGGTCGAT 58.907 50.000 0.00 0.00 0.00 3.59
150 2136 6.392354 CCATAAACAAAGCATGAAGACACAT 58.608 36.000 0.00 0.00 0.00 3.21
160 2146 2.825532 ACGAAGGCCATAAACAAAGCAT 59.174 40.909 5.01 0.00 0.00 3.79
217 2203 0.036306 GGCAAGAAAAGAGACCGGGA 59.964 55.000 6.32 0.00 0.00 5.14
239 2225 1.230324 ACGGAAAGAAAGAGCACAGC 58.770 50.000 0.00 0.00 0.00 4.40
249 2235 5.190677 ACCTGAAAGAAAGAACGGAAAGAA 58.809 37.500 0.00 0.00 34.07 2.52
531 2527 4.918810 AAAACTGGACTTGCCTTAGTTG 57.081 40.909 0.00 0.00 37.63 3.16
548 2544 2.412089 CCTGATCTCGTCCGACAAAAAC 59.588 50.000 0.00 0.00 0.00 2.43
720 2716 5.296151 TCCATCAAATAAGAAGCCTCGAT 57.704 39.130 0.00 0.00 0.00 3.59
741 2737 2.496899 TGGACAAAATGCTCCTCCTC 57.503 50.000 0.00 0.00 0.00 3.71
773 2769 4.655963 ACATGTAGCAATGAAACCTCACT 58.344 39.130 0.00 0.00 33.30 3.41
803 2800 6.036953 GCAAACAAACCAAGAATGTGAAATCA 59.963 34.615 0.00 0.00 0.00 2.57
839 2837 3.871594 ACAGCTTGCTTTAGTATAAGGCG 59.128 43.478 0.00 0.00 0.00 5.52
859 2858 1.203994 GTAAGGCCAAGAGCGTCTACA 59.796 52.381 5.01 0.00 45.17 2.74
1010 3009 4.681978 GGCCTGGACGAGCGTTGT 62.682 66.667 0.00 0.00 0.00 3.32
1057 3057 2.233271 AGGTTTCCTGTGTTGCATCTG 58.767 47.619 0.00 0.00 29.57 2.90
1144 3145 4.421131 AGACTCCTTCTGGATGTTGTAGT 58.579 43.478 0.00 0.00 42.29 2.73
1166 3167 1.204146 GGAGGCAGTATGGAAGGACA 58.796 55.000 0.00 0.00 35.86 4.02
1167 3168 0.470341 GGGAGGCAGTATGGAAGGAC 59.530 60.000 0.00 0.00 35.86 3.85
1193 3194 3.347216 ACAAAGATCAGCATACCACCAC 58.653 45.455 0.00 0.00 0.00 4.16
1216 3217 1.541233 GGTCTTGTGGGTGAGTGTCTG 60.541 57.143 0.00 0.00 0.00 3.51
1228 3229 2.810274 CCTCAAGTGTGATGGTCTTGTG 59.190 50.000 0.00 0.00 39.36 3.33
1236 3237 3.594134 GGACTCTTCCTCAAGTGTGATG 58.406 50.000 0.00 0.00 36.65 3.07
1261 3262 2.352651 CCATGACATTGTCGATGGTGTC 59.647 50.000 24.93 15.72 40.21 3.67
1265 3266 1.381522 TGCCATGACATTGTCGATGG 58.618 50.000 26.92 26.92 40.59 3.51
1269 3270 3.770263 ATCTTTGCCATGACATTGTCG 57.230 42.857 11.97 0.00 34.95 4.35
1349 3361 1.352156 GATGCTGGTTGGTCGTCGAC 61.352 60.000 17.16 17.16 0.00 4.20
1350 3362 1.080093 GATGCTGGTTGGTCGTCGA 60.080 57.895 0.00 0.00 0.00 4.20
1361 3373 2.040213 CTGCGCCGTTTAGATGCTGG 62.040 60.000 4.18 0.00 0.00 4.85
1366 3378 1.682451 TAGCCCTGCGCCGTTTAGAT 61.682 55.000 4.18 0.00 38.78 1.98
1408 3420 2.334946 CGCCATGGACCACAACAGG 61.335 63.158 18.40 0.00 0.00 4.00
1415 3427 4.045781 ATGCACCGCCATGGACCA 62.046 61.111 18.40 0.00 42.00 4.02
1436 3448 1.963338 GTGCTCCGCTTGACAGCTT 60.963 57.895 0.00 0.00 44.85 3.74
1453 3465 0.949105 CTAACACTTTGGAGGCGCGT 60.949 55.000 8.43 0.27 0.00 6.01
1498 3510 1.069823 TGTTGCCCGTACGGTAAAAGA 59.930 47.619 31.24 17.84 38.05 2.52
1509 3521 1.003355 CTGATGAGGTGTTGCCCGT 60.003 57.895 0.00 0.00 38.26 5.28
1515 3527 1.229428 CACGTTGCTGATGAGGTGTT 58.771 50.000 0.00 0.00 0.00 3.32
1594 3606 0.892755 TGTCTTCGTATCCCGTTGCT 59.107 50.000 0.00 0.00 37.94 3.91
1633 3790 5.777802 AGATGCACAGAGGAATACTTATCG 58.222 41.667 0.00 0.00 0.00 2.92
1638 3795 4.959210 ACAGTAGATGCACAGAGGAATACT 59.041 41.667 0.00 0.00 0.00 2.12
1651 3808 2.629051 GGTTGTGGGTACAGTAGATGC 58.371 52.381 0.00 0.00 38.23 3.91
1652 3809 2.838202 AGGGTTGTGGGTACAGTAGATG 59.162 50.000 0.00 0.00 38.23 2.90
1672 3829 3.217242 GTCACCACAGTGGCTACAG 57.783 57.895 20.48 4.97 45.51 2.74
1717 3876 1.939255 GAGTCGAACCCCTCTACGTAG 59.061 57.143 16.73 16.73 0.00 3.51
1732 3893 3.668656 TCGCGCATATCAAAATAGAGTCG 59.331 43.478 8.75 0.00 0.00 4.18
1768 3929 1.979155 GAACCTTCCTTGCTGGGGC 60.979 63.158 0.00 0.00 36.20 5.80
1769 3930 0.895559 GTGAACCTTCCTTGCTGGGG 60.896 60.000 0.00 0.00 36.20 4.96
1770 3931 0.895559 GGTGAACCTTCCTTGCTGGG 60.896 60.000 0.00 0.00 36.20 4.45
1771 3932 1.237285 CGGTGAACCTTCCTTGCTGG 61.237 60.000 0.00 0.00 37.10 4.85
1813 3974 3.989817 CCTGCAAACTTTTATTCAGTGGC 59.010 43.478 0.00 0.00 0.00 5.01
1830 3991 1.677576 CGTAATACCCTACGTCCTGCA 59.322 52.381 0.00 0.00 39.81 4.41
1882 4044 4.899352 AATCCTCTATCTACCACATGGC 57.101 45.455 0.00 0.00 39.32 4.40
1908 4070 1.599797 GTGTTGGGGCACTAACGCT 60.600 57.895 20.21 0.00 36.51 5.07
2315 4477 5.769662 TGGTAGGCCTGAAATATGCTAATTG 59.230 40.000 17.99 0.00 35.27 2.32
2318 4480 5.381184 TTGGTAGGCCTGAAATATGCTAA 57.619 39.130 17.99 0.00 35.27 3.09


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

AutoCloner maintained by Alex Coulton.