Multiple sequence alignment - TraesCS6D01G200300

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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 TraesCS6D01G200300 chr6D 100.000 2393 0 0 1 2393 278996510 278998902 0.000000e+00 4420.0
1 TraesCS6D01G200300 chr2B 93.224 1653 82 8 766 2393 171700964 171699317 0.000000e+00 2405.0
2 TraesCS6D01G200300 chr7A 86.172 1374 102 33 766 2096 221434544 221433216 0.000000e+00 1404.0
3 TraesCS6D01G200300 chr3D 96.005 776 21 4 1 768 415376204 415376977 0.000000e+00 1253.0
4 TraesCS6D01G200300 chr3D 95.736 774 24 3 1 766 415370818 415371590 0.000000e+00 1238.0
5 TraesCS6D01G200300 chr3D 90.698 43 4 0 1552 1594 424015850 424015808 9.240000e-05 58.4
6 TraesCS6D01G200300 chr5D 95.507 779 20 5 1 766 18331388 18330612 0.000000e+00 1230.0
7 TraesCS6D01G200300 chr5D 95.065 770 31 6 1 765 66496829 66497596 0.000000e+00 1205.0
8 TraesCS6D01G200300 chr7D 95.189 769 31 4 1 766 167021320 167022085 0.000000e+00 1210.0
9 TraesCS6D01G200300 chr2D 95.071 771 32 4 1 767 541501137 541501905 0.000000e+00 1208.0
10 TraesCS6D01G200300 chr4D 94.981 777 25 7 1 766 295583992 295584765 0.000000e+00 1206.0
11 TraesCS6D01G200300 chr4D 88.516 923 81 5 766 1666 152331653 152332572 0.000000e+00 1094.0
12 TraesCS6D01G200300 chr4D 93.890 491 20 3 1663 2152 152357838 152358319 0.000000e+00 732.0
13 TraesCS6D01G200300 chr4D 93.137 102 7 0 2292 2393 152369574 152369675 1.480000e-32 150.0
14 TraesCS6D01G200300 chr1D 95.276 762 32 4 9 766 461983679 461982918 0.000000e+00 1205.0
15 TraesCS6D01G200300 chr1D 94.852 777 28 9 1 766 488175539 488176314 0.000000e+00 1203.0
16 TraesCS6D01G200300 chr3B 90.773 802 64 6 1595 2393 324213141 324213935 0.000000e+00 1062.0
17 TraesCS6D01G200300 chr3B 87.500 344 36 3 1257 1594 324212666 324213008 8.020000e-105 390.0
18 TraesCS6D01G200300 chr3B 92.000 50 2 2 1545 1594 552226028 552226075 4.270000e-08 69.4
19 TraesCS6D01G200300 chr2A 89.924 794 35 17 1311 2096 701366969 701366213 0.000000e+00 981.0
20 TraesCS6D01G200300 chr2A 87.025 316 31 4 947 1252 701367792 701367477 4.900000e-92 348.0
21 TraesCS6D01G200300 chr2A 87.919 298 30 4 2095 2391 701366160 701365868 1.760000e-91 346.0
22 TraesCS6D01G200300 chr2A 91.852 135 9 2 766 899 701368301 701368168 1.130000e-43 187.0


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 TraesCS6D01G200300 chr6D 278996510 278998902 2392 False 4420.0 4420 100.0000 1 2393 1 chr6D.!!$F1 2392
1 TraesCS6D01G200300 chr2B 171699317 171700964 1647 True 2405.0 2405 93.2240 766 2393 1 chr2B.!!$R1 1627
2 TraesCS6D01G200300 chr7A 221433216 221434544 1328 True 1404.0 1404 86.1720 766 2096 1 chr7A.!!$R1 1330
3 TraesCS6D01G200300 chr3D 415376204 415376977 773 False 1253.0 1253 96.0050 1 768 1 chr3D.!!$F2 767
4 TraesCS6D01G200300 chr3D 415370818 415371590 772 False 1238.0 1238 95.7360 1 766 1 chr3D.!!$F1 765
5 TraesCS6D01G200300 chr5D 18330612 18331388 776 True 1230.0 1230 95.5070 1 766 1 chr5D.!!$R1 765
6 TraesCS6D01G200300 chr5D 66496829 66497596 767 False 1205.0 1205 95.0650 1 765 1 chr5D.!!$F1 764
7 TraesCS6D01G200300 chr7D 167021320 167022085 765 False 1210.0 1210 95.1890 1 766 1 chr7D.!!$F1 765
8 TraesCS6D01G200300 chr2D 541501137 541501905 768 False 1208.0 1208 95.0710 1 767 1 chr2D.!!$F1 766
9 TraesCS6D01G200300 chr4D 295583992 295584765 773 False 1206.0 1206 94.9810 1 766 1 chr4D.!!$F4 765
10 TraesCS6D01G200300 chr4D 152331653 152332572 919 False 1094.0 1094 88.5160 766 1666 1 chr4D.!!$F1 900
11 TraesCS6D01G200300 chr1D 461982918 461983679 761 True 1205.0 1205 95.2760 9 766 1 chr1D.!!$R1 757
12 TraesCS6D01G200300 chr1D 488175539 488176314 775 False 1203.0 1203 94.8520 1 766 1 chr1D.!!$F1 765
13 TraesCS6D01G200300 chr3B 324212666 324213935 1269 False 726.0 1062 89.1365 1257 2393 2 chr3B.!!$F2 1136
14 TraesCS6D01G200300 chr2A 701365868 701368301 2433 True 465.5 981 89.1800 766 2391 4 chr2A.!!$R1 1625

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
285 286 0.25064 AAGCCCTCCATGATCGATGC 60.251 55.0 0.54 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 2991 0.106708 GACATGGCCTTATCCAGCGA 59.893 55.0 3.32 0.0 39.89 4.93 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
85 86 6.194796 ACTTGATCATAAACCCACAATTCG 57.805 37.500 0.00 0.00 0.00 3.34
93 94 1.259609 ACCCACAATTCGTCGGTCTA 58.740 50.000 0.00 0.00 33.07 2.59
275 276 2.027192 GTGTTGATGTAGAAGCCCTCCA 60.027 50.000 0.00 0.00 0.00 3.86
285 286 0.250640 AAGCCCTCCATGATCGATGC 60.251 55.000 0.54 0.00 0.00 3.91
504 533 1.559682 GCCCTCCTGGTTGATGTCTTA 59.440 52.381 0.00 0.00 36.04 2.10
515 544 3.770263 TGATGTCTTAACGTAGGGTCG 57.230 47.619 0.00 0.00 0.00 4.79
532 561 1.819288 GTCGAAGTCCTCTGGATCACA 59.181 52.381 0.00 0.00 32.73 3.58
792 823 1.805539 CGGCGATGCTCTTCAACGA 60.806 57.895 0.00 0.00 42.63 3.85
865 896 1.141657 GCAGCCCATGTATTGAGAGGA 59.858 52.381 0.00 0.00 0.00 3.71
867 898 3.409570 CAGCCCATGTATTGAGAGGATG 58.590 50.000 0.00 0.00 0.00 3.51
933 995 1.443407 CTATCTCACCCTGGCCACG 59.557 63.158 0.00 0.00 0.00 4.94
1005 1375 1.518352 CGTCGATTCGGTCATGCCA 60.518 57.895 6.18 0.00 36.97 4.92
1010 1380 2.040213 GATTCGGTCATGCCACTGCG 62.040 60.000 6.92 0.00 41.78 5.18
1109 1489 1.070445 CCCATCGTCAGCTCATCCC 59.930 63.158 0.00 0.00 0.00 3.85
1201 1582 3.574074 GAAGCTCTTGCCCAGCCCA 62.574 63.158 0.00 0.00 40.80 5.36
1269 1650 4.617520 TGCGCCGTTGCTTCTCCA 62.618 61.111 4.18 0.00 35.36 3.86
1283 1664 0.320374 TCTCCAACTGCCGTTAGTGG 59.680 55.000 0.00 0.00 0.00 4.00
1305 2138 1.244019 CCCAAAGCTTCCTTCCACCG 61.244 60.000 0.00 0.00 0.00 4.94
1457 2292 2.093658 CCGTTGCATCCTGTAGGTAAGT 60.094 50.000 0.00 0.00 36.34 2.24
1555 2395 8.427276 TGAACTGAATAATATCATCTCTGCAGT 58.573 33.333 14.67 0.00 34.68 4.40
1623 2595 0.465460 TGAAGCTTGGTCAACGCCTT 60.465 50.000 2.10 0.00 0.00 4.35
1653 2625 9.717942 GAGGTCAGAATAGTATTCATTAAGCAT 57.282 33.333 22.00 6.31 0.00 3.79
1824 2799 7.443259 TTGTTTACCATTAGCTTGTAGTTCC 57.557 36.000 0.00 0.00 0.00 3.62
1825 2800 6.535540 TGTTTACCATTAGCTTGTAGTTCCA 58.464 36.000 0.00 0.00 0.00 3.53
1826 2801 6.999272 TGTTTACCATTAGCTTGTAGTTCCAA 59.001 34.615 0.00 0.00 0.00 3.53
1827 2802 7.502895 TGTTTACCATTAGCTTGTAGTTCCAAA 59.497 33.333 0.00 0.00 0.00 3.28
2015 2991 5.163478 GGACCAACCTATAACTCGTATGTGT 60.163 44.000 0.00 0.00 35.41 3.72
2144 3174 9.883142 CCTCTCTAATTTTCTATGAAGACAACT 57.117 33.333 0.00 0.00 0.00 3.16
2191 3221 2.746904 TCACCATGTGGCAACGATTTAG 59.253 45.455 0.00 0.00 39.32 1.85
2293 3323 2.755876 TCGCCGTCTCCATGCTCT 60.756 61.111 0.00 0.00 0.00 4.09
2304 3334 2.971330 CTCCATGCTCTACTCCTCCAAT 59.029 50.000 0.00 0.00 0.00 3.16
2348 3378 4.220693 TCTGTTGCTAATGTGGCTATGT 57.779 40.909 0.00 0.00 0.00 2.29
2349 3379 4.588899 TCTGTTGCTAATGTGGCTATGTT 58.411 39.130 0.00 0.00 0.00 2.71
2364 3395 3.118445 GCTATGTTGAGCTCCTTTCCTCT 60.118 47.826 12.15 0.00 39.50 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 3.597377 GGTGTGTTTGTTTAGACCGAC 57.403 47.619 0.00 0.00 0.00 4.79
93 94 3.305398 TCTTTTGCGGTGTGTTTGTTT 57.695 38.095 0.00 0.00 0.00 2.83
226 227 3.381590 CCTCTCCGATGATGTGTGAGTAA 59.618 47.826 0.00 0.00 0.00 2.24
275 276 2.587247 CGGAGGGGGCATCGATCAT 61.587 63.158 0.00 0.00 0.00 2.45
331 333 1.003718 GCCGCAACCTTCTGTACCT 60.004 57.895 0.00 0.00 0.00 3.08
504 533 1.172175 GAGGACTTCGACCCTACGTT 58.828 55.000 0.00 0.00 31.84 3.99
515 544 3.118956 ACGAATGTGATCCAGAGGACTTC 60.119 47.826 0.00 0.00 32.98 3.01
625 655 2.037847 GGCCCAGCCCAGAATTGT 59.962 61.111 0.00 0.00 44.06 2.71
758 789 4.048241 TCGCCGACACATAATTGATACA 57.952 40.909 0.00 0.00 0.00 2.29
810 841 1.377725 CTGGTGGGCTGGATGTGAC 60.378 63.158 0.00 0.00 0.00 3.67
847 878 2.224719 GCATCCTCTCAATACATGGGCT 60.225 50.000 0.00 0.00 0.00 5.19
848 879 2.157738 GCATCCTCTCAATACATGGGC 58.842 52.381 0.00 0.00 0.00 5.36
853 884 1.202568 CGGCTGCATCCTCTCAATACA 60.203 52.381 4.84 0.00 0.00 2.29
933 995 7.025365 CGATTTAGGTTTAGGTTTAGGTTTGC 58.975 38.462 0.00 0.00 0.00 3.68
1071 1451 2.745492 GTCACCTCAGGCTGCTGC 60.745 66.667 10.34 7.10 38.76 5.25
1109 1489 3.630148 GATGCGGCATCGGTCGTG 61.630 66.667 25.47 0.00 45.79 4.35
1182 1563 2.753446 GGCTGGGCAAGAGCTTCC 60.753 66.667 0.00 0.00 41.70 3.46
1201 1582 2.125147 CACGTCGGGATGCACCAT 60.125 61.111 0.00 0.00 41.20 3.55
1283 1664 1.984570 GGAAGGAAGCTTTGGGGGC 60.985 63.158 0.00 0.00 0.00 5.80
1396 2231 3.438131 TGACAAGGGGGAATAGGAGAT 57.562 47.619 0.00 0.00 0.00 2.75
1399 2234 1.494721 GCATGACAAGGGGGAATAGGA 59.505 52.381 0.00 0.00 0.00 2.94
1555 2395 9.591792 CTCTGTACATAGATTCAATTGAAGACA 57.408 33.333 24.17 16.39 37.48 3.41
1666 2638 9.801714 CTGCAATGAAAACATGATAAGAAAAAC 57.198 29.630 0.00 0.00 0.00 2.43
1834 2810 4.098914 TGAGCAAGGGTTCAAGTGTATT 57.901 40.909 0.00 0.00 30.76 1.89
1835 2811 3.788227 TGAGCAAGGGTTCAAGTGTAT 57.212 42.857 0.00 0.00 30.76 2.29
2015 2991 0.106708 GACATGGCCTTATCCAGCGA 59.893 55.000 3.32 0.00 39.89 4.93
2165 3195 1.337728 CGTTGCCACATGGTGACTAGA 60.338 52.381 0.00 0.00 35.23 2.43
2191 3221 0.676151 CACCTTGCCAGAGAAGAGCC 60.676 60.000 0.00 0.00 0.00 4.70
2246 3276 4.163427 GGAGGAGTGGATGAGGATGAATA 58.837 47.826 0.00 0.00 0.00 1.75
2304 3334 0.396695 GGTGACCCTACTGGATCCGA 60.397 60.000 7.39 0.00 38.00 4.55


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

AutoCloner maintained by Alex Coulton.