Multiple sequence alignment - TraesCS6B01G196800

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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 TraesCS6B01G196800 chr6B 100.000 4013 0 0 1 4013 233089984 233085972 0.000000e+00 7411.0
1 TraesCS6B01G196800 chr6B 89.750 1961 176 16 1072 3015 233674004 233672052 0.000000e+00 2484.0
2 TraesCS6B01G196800 chr6B 96.855 636 20 0 3378 4013 22931537 22932172 0.000000e+00 1064.0
3 TraesCS6B01G196800 chr6B 94.137 307 16 2 3074 3380 22929277 22929581 2.180000e-127 466.0
4 TraesCS6B01G196800 chr6D 95.607 2299 89 3 775 3073 134742725 134740439 0.000000e+00 3675.0
5 TraesCS6B01G196800 chr6D 95.488 2305 93 4 775 3073 134337790 134335491 0.000000e+00 3670.0
6 TraesCS6B01G196800 chr6D 90.367 1962 162 18 1072 3015 134588309 134586357 0.000000e+00 2551.0
7 TraesCS6B01G196800 chr6D 90.260 1961 166 16 1072 3015 135041759 135039807 0.000000e+00 2540.0
8 TraesCS6B01G196800 chr6D 85.915 213 26 3 567 777 186979320 186979110 1.450000e-54 224.0
9 TraesCS6B01G196800 chr6D 76.159 453 59 26 13 422 186979912 186979466 4.090000e-45 193.0
10 TraesCS6B01G196800 chr6D 91.791 134 9 2 1 133 186979835 186979703 6.850000e-43 185.0
11 TraesCS6B01G196800 chr6D 91.026 78 7 0 1689 1766 33243212 33243135 5.490000e-19 106.0
12 TraesCS6B01G196800 chr6A 96.601 1618 53 1 1456 3073 175997191 175995576 0.000000e+00 2682.0
13 TraesCS6B01G196800 chr6A 90.311 1961 165 16 1072 3015 176293959 176292007 0.000000e+00 2545.0
14 TraesCS6B01G196800 chr6A 96.460 452 12 1 775 1226 176003248 176002801 0.000000e+00 743.0
15 TraesCS6B01G196800 chr6A 95.676 185 8 0 1221 1405 175997372 175997188 8.430000e-77 298.0
16 TraesCS6B01G196800 chr6A 91.525 59 4 1 202 260 133794252 133794195 3.320000e-11 80.5
17 TraesCS6B01G196800 chr7B 98.452 775 11 1 1 774 583152852 583152078 0.000000e+00 1363.0
18 TraesCS6B01G196800 chr7B 84.762 210 29 2 567 774 616532589 616532797 1.460000e-49 207.0
19 TraesCS6B01G196800 chr7B 90.370 135 11 2 1 134 616524153 616524286 4.120000e-40 176.0
20 TraesCS6B01G196800 chrUn 91.438 946 45 9 3072 4013 77507365 77508278 0.000000e+00 1266.0
21 TraesCS6B01G196800 chrUn 90.370 135 11 2 1 134 292093460 292093327 4.120000e-40 176.0
22 TraesCS6B01G196800 chrUn 78.333 240 29 9 202 419 38127673 38127911 2.520000e-27 134.0
23 TraesCS6B01G196800 chrUn 77.778 243 31 9 202 422 425561131 425560890 1.170000e-25 128.0
24 TraesCS6B01G196800 chr5B 90.880 943 54 10 3073 4013 369019500 369020412 0.000000e+00 1236.0
25 TraesCS6B01G196800 chr5B 77.887 814 124 28 13 775 592804662 592805470 4.730000e-124 455.0
26 TraesCS6B01G196800 chr5B 76.614 821 130 27 13 774 664505571 664504754 2.910000e-106 396.0
27 TraesCS6B01G196800 chr5B 91.111 135 10 2 1 134 592804739 592804872 8.860000e-42 182.0
28 TraesCS6B01G196800 chr5B 88.435 147 12 5 12 155 664505484 664505340 5.330000e-39 172.0
29 TraesCS6B01G196800 chr2B 92.601 865 36 6 3150 4013 58670925 58671762 0.000000e+00 1218.0
30 TraesCS6B01G196800 chr2B 86.014 143 13 4 2377 2512 138547272 138547130 3.230000e-31 147.0
31 TraesCS6B01G196800 chr2A 89.776 802 56 7 1 777 113588848 113589648 0.000000e+00 1003.0
32 TraesCS6B01G196800 chr2A 76.248 661 130 18 2068 2707 705532001 705532655 3.870000e-85 326.0
33 TraesCS6B01G196800 chr3A 87.594 798 74 12 1 775 707173505 707172710 0.000000e+00 902.0
34 TraesCS6B01G196800 chr2D 93.466 352 22 1 3554 3905 80216249 80215899 4.600000e-144 521.0
35 TraesCS6B01G196800 chr2D 87.443 438 33 8 3074 3503 80216872 80216449 6.030000e-133 484.0
36 TraesCS6B01G196800 chr2D 76.212 660 129 22 2068 2707 565090943 565091594 1.390000e-84 324.0
37 TraesCS6B01G196800 chr2D 94.118 102 6 0 3870 3971 80215907 80215806 5.370000e-34 156.0
38 TraesCS6B01G196800 chr7D 75.208 601 125 23 1085 1673 30264407 30264995 3.080000e-66 263.0
39 TraesCS6B01G196800 chr4A 75.000 600 128 21 1085 1673 698171046 698170458 1.430000e-64 257.0
40 TraesCS6B01G196800 chr4B 86.755 151 15 4 13 159 622955437 622955288 3.210000e-36 163.0
41 TraesCS6B01G196800 chr1A 79.681 251 27 9 191 419 20943794 20944042 4.150000e-35 159.0
42 TraesCS6B01G196800 chr3D 84.106 151 21 3 628 777 153943406 153943258 4.180000e-30 143.0
43 TraesCS6B01G196800 chr4D 83.007 153 22 4 631 779 126767377 126767529 7.000000e-28 135.0
44 TraesCS6B01G196800 chr5A 100.000 30 0 0 3956 3985 555102823 555102852 5.600000e-04 56.5


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 TraesCS6B01G196800 chr6B 233085972 233089984 4012 True 7411.000000 7411 100.000000 1 4013 1 chr6B.!!$R1 4012
1 TraesCS6B01G196800 chr6B 233672052 233674004 1952 True 2484.000000 2484 89.750000 1072 3015 1 chr6B.!!$R2 1943
2 TraesCS6B01G196800 chr6B 22929277 22932172 2895 False 765.000000 1064 95.496000 3074 4013 2 chr6B.!!$F1 939
3 TraesCS6B01G196800 chr6D 134740439 134742725 2286 True 3675.000000 3675 95.607000 775 3073 1 chr6D.!!$R4 2298
4 TraesCS6B01G196800 chr6D 134335491 134337790 2299 True 3670.000000 3670 95.488000 775 3073 1 chr6D.!!$R2 2298
5 TraesCS6B01G196800 chr6D 134586357 134588309 1952 True 2551.000000 2551 90.367000 1072 3015 1 chr6D.!!$R3 1943
6 TraesCS6B01G196800 chr6D 135039807 135041759 1952 True 2540.000000 2540 90.260000 1072 3015 1 chr6D.!!$R5 1943
7 TraesCS6B01G196800 chr6D 186979110 186979912 802 True 200.666667 224 84.621667 1 777 3 chr6D.!!$R6 776
8 TraesCS6B01G196800 chr6A 176292007 176293959 1952 True 2545.000000 2545 90.311000 1072 3015 1 chr6A.!!$R3 1943
9 TraesCS6B01G196800 chr6A 175995576 175997372 1796 True 1490.000000 2682 96.138500 1221 3073 2 chr6A.!!$R4 1852
10 TraesCS6B01G196800 chr7B 583152078 583152852 774 True 1363.000000 1363 98.452000 1 774 1 chr7B.!!$R1 773
11 TraesCS6B01G196800 chrUn 77507365 77508278 913 False 1266.000000 1266 91.438000 3072 4013 1 chrUn.!!$F2 941
12 TraesCS6B01G196800 chr5B 369019500 369020412 912 False 1236.000000 1236 90.880000 3073 4013 1 chr5B.!!$F1 940
13 TraesCS6B01G196800 chr5B 592804662 592805470 808 False 318.500000 455 84.499000 1 775 2 chr5B.!!$F2 774
14 TraesCS6B01G196800 chr5B 664504754 664505571 817 True 284.000000 396 82.524500 12 774 2 chr5B.!!$R1 762
15 TraesCS6B01G196800 chr2B 58670925 58671762 837 False 1218.000000 1218 92.601000 3150 4013 1 chr2B.!!$F1 863
16 TraesCS6B01G196800 chr2A 113588848 113589648 800 False 1003.000000 1003 89.776000 1 777 1 chr2A.!!$F1 776
17 TraesCS6B01G196800 chr2A 705532001 705532655 654 False 326.000000 326 76.248000 2068 2707 1 chr2A.!!$F2 639
18 TraesCS6B01G196800 chr3A 707172710 707173505 795 True 902.000000 902 87.594000 1 775 1 chr3A.!!$R1 774
19 TraesCS6B01G196800 chr2D 80215806 80216872 1066 True 387.000000 521 91.675667 3074 3971 3 chr2D.!!$R1 897
20 TraesCS6B01G196800 chr2D 565090943 565091594 651 False 324.000000 324 76.212000 2068 2707 1 chr2D.!!$F1 639
21 TraesCS6B01G196800 chr7D 30264407 30264995 588 False 263.000000 263 75.208000 1085 1673 1 chr7D.!!$F1 588
22 TraesCS6B01G196800 chr4A 698170458 698171046 588 True 257.000000 257 75.000000 1085 1673 1 chr4A.!!$R1 588

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
848 992 1.292242 TGACCCATCTTCTAGCTCCCT 59.708 52.381 0.00 0.00 0.00 4.20 F
2121 2289 0.894184 ACTCCGAACTCGAGAAGGCA 60.894 55.000 21.68 8.12 43.02 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2718 2901 1.125093 TCTCCCCTCTTTTGTCGCCA 61.125 55.0 0.0 0.0 0.0 5.69 R
3086 3269 0.324943 CCATTCCACTCCGTTCCTGT 59.675 55.0 0.0 0.0 0.0 4.00 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
459 563 2.873133 ATCGGTCGATGAGGAAGTTC 57.127 50.000 4.97 0.00 32.98 3.01
592 732 1.743855 GCAAGATTCGCCGTCTCGTC 61.744 60.000 0.00 0.00 0.00 4.20
817 961 3.246619 AGACGAGCGAAAAGATTGACTC 58.753 45.455 0.00 0.00 0.00 3.36
847 991 1.794714 TGACCCATCTTCTAGCTCCC 58.205 55.000 0.00 0.00 0.00 4.30
848 992 1.292242 TGACCCATCTTCTAGCTCCCT 59.708 52.381 0.00 0.00 0.00 4.20
849 993 1.967779 GACCCATCTTCTAGCTCCCTC 59.032 57.143 0.00 0.00 0.00 4.30
850 994 1.347062 CCCATCTTCTAGCTCCCTCC 58.653 60.000 0.00 0.00 0.00 4.30
859 1003 4.042251 GCTCCCTCCAGCTGTAGT 57.958 61.111 13.81 0.00 36.38 2.73
863 1007 2.303175 CTCCCTCCAGCTGTAGTCTAC 58.697 57.143 13.81 2.81 0.00 2.59
883 1027 1.529010 CTCTGCAGCAACCACCCAA 60.529 57.895 9.47 0.00 0.00 4.12
903 1047 4.522022 CCAATGGAAAGAAGAAAGCAGAGT 59.478 41.667 0.00 0.00 0.00 3.24
942 1086 2.050714 ATCGTACCGCCGCATACG 60.051 61.111 14.96 14.96 44.34 3.06
973 1117 2.203252 CAGCCACAGTGCCACACT 60.203 61.111 0.00 0.00 46.51 3.55
1419 1572 2.181021 CGCGGCGAGACCTACTTT 59.819 61.111 19.16 0.00 35.61 2.66
1716 1872 2.024176 TTCCCTTCACCACTCTGCTA 57.976 50.000 0.00 0.00 0.00 3.49
1857 2022 2.107546 GTCGGTGTTGGTGTCGGT 59.892 61.111 0.00 0.00 0.00 4.69
1869 2034 0.942410 GTGTCGGTGTTCTTGCGCTA 60.942 55.000 9.73 0.00 0.00 4.26
1906 2071 3.436704 CCTGATGTTGTTATGTGTTCGCT 59.563 43.478 0.00 0.00 0.00 4.93
2036 2204 1.413077 GGCAGCTACGATAACCTCCTT 59.587 52.381 0.00 0.00 0.00 3.36
2121 2289 0.894184 ACTCCGAACTCGAGAAGGCA 60.894 55.000 21.68 8.12 43.02 4.75
2226 2394 4.760047 GTGGCCGGCGATGTGAGT 62.760 66.667 22.54 0.00 0.00 3.41
2394 2577 4.077188 GTGTGGAAGCAGCGCGTC 62.077 66.667 8.43 0.00 36.39 5.19
2816 2999 3.585990 GCGGGCATTCATGGACCG 61.586 66.667 10.12 10.12 46.78 4.79
3047 3230 4.542662 AATCACTTGATGCGTAATCTGC 57.457 40.909 0.00 0.00 36.15 4.26
3063 3246 4.485554 GCTGGTGTAGCGAGAGTG 57.514 61.111 0.00 0.00 43.63 3.51
3118 3301 5.221185 GGAGTGGAATGGAATGTCATGATTG 60.221 44.000 0.00 0.00 0.00 2.67
3133 3316 7.281841 TGTCATGATTGCATTCCACTAGAATA 58.718 34.615 0.00 0.00 43.63 1.75
3134 3317 7.940688 TGTCATGATTGCATTCCACTAGAATAT 59.059 33.333 0.00 0.00 43.63 1.28
3143 3326 4.563337 TCCACTAGAATATGTCGGTTCG 57.437 45.455 0.00 0.00 0.00 3.95
3291 3475 3.102972 TCTTCCCTGAGAATGGTGAGAG 58.897 50.000 0.00 0.00 32.82 3.20
3306 3498 6.262056 TGGTGAGAGTACCTCTGACATATA 57.738 41.667 11.92 0.00 44.39 0.86
3347 3539 5.343307 ACATATTGCCCAAAATCTGAACC 57.657 39.130 0.00 0.00 0.00 3.62
3484 5637 2.924757 ATGATGCATCTGTGGACGAT 57.075 45.000 26.32 7.13 0.00 3.73
3817 6158 0.250234 TGTGCTTCGGAGGAGGAATG 59.750 55.000 0.00 0.00 0.00 2.67
3830 6171 0.644937 AGGAATGGAGGAGGTAGCCT 59.355 55.000 0.00 0.00 42.17 4.58
3996 6366 0.395311 TGGAGGTATCGCTCGGTTCT 60.395 55.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
451 555 0.841289 TTGACCGGTTGGAACTTCCT 59.159 50.000 9.42 0.00 37.46 3.36
459 563 2.038269 CCCATCGTTGACCGGTTGG 61.038 63.158 9.42 11.61 38.91 3.77
598 738 0.251033 TCGGGAGAGAAACGTCCAGA 60.251 55.000 0.00 0.00 35.03 3.86
817 961 1.078708 ATGGGTCAACGGCGTAAGG 60.079 57.895 15.20 6.44 38.28 2.69
847 991 1.332375 GAGCGTAGACTACAGCTGGAG 59.668 57.143 25.03 25.03 38.17 3.86
848 992 1.065345 AGAGCGTAGACTACAGCTGGA 60.065 52.381 25.95 9.06 38.17 3.86
849 993 1.064803 CAGAGCGTAGACTACAGCTGG 59.935 57.143 25.95 17.66 38.17 4.85
850 994 1.532921 GCAGAGCGTAGACTACAGCTG 60.533 57.143 25.95 21.04 38.17 4.24
883 1027 4.759183 GTGACTCTGCTTTCTTCTTTCCAT 59.241 41.667 0.00 0.00 0.00 3.41
903 1047 2.624838 GGACGGACGGAATTATAGGTGA 59.375 50.000 0.00 0.00 0.00 4.02
948 1092 2.031163 ACTGTGGCTGGCGTTCTC 59.969 61.111 0.00 0.00 0.00 2.87
994 1138 3.880846 CGGAGCGGCCATTGCTTC 61.881 66.667 2.24 0.55 44.18 3.86
1083 1227 2.262915 GCCTCGTACTGCTGCTGT 59.737 61.111 16.37 16.37 0.00 4.40
1419 1572 2.779755 AGGTGTTGTTGGCGATGATA 57.220 45.000 0.00 0.00 0.00 2.15
1507 1663 2.874664 CGGTGAGGTTGTTCCCGGA 61.875 63.158 0.73 0.00 36.75 5.14
1575 1731 0.976073 GGTAGGTGAGCAGGTGCCTA 60.976 60.000 0.00 0.00 43.38 3.93
1819 1984 2.452813 CGACGGCAATCCACTTCCG 61.453 63.158 0.00 0.00 46.61 4.30
1857 2022 2.434185 CCCGCTAGCGCAAGAACA 60.434 61.111 31.35 0.00 43.02 3.18
2028 2196 2.224066 CGCCGATGAAGATAAGGAGGTT 60.224 50.000 0.00 0.00 0.00 3.50
2036 2204 1.206132 ACACCAACGCCGATGAAGATA 59.794 47.619 0.00 0.00 0.00 1.98
2121 2289 1.517832 CTCCGAGAATCCTGCCGTT 59.482 57.895 0.00 0.00 0.00 4.44
2718 2901 1.125093 TCTCCCCTCTTTTGTCGCCA 61.125 55.000 0.00 0.00 0.00 5.69
3047 3230 1.813178 TCTTCACTCTCGCTACACCAG 59.187 52.381 0.00 0.00 0.00 4.00
3063 3246 2.100749 CCAAACACACCCTTGGTTCTTC 59.899 50.000 0.00 0.00 37.83 2.87
3086 3269 0.324943 CCATTCCACTCCGTTCCTGT 59.675 55.000 0.00 0.00 0.00 4.00
3118 3301 4.632153 ACCGACATATTCTAGTGGAATGC 58.368 43.478 11.70 0.00 43.68 3.56
3133 3316 1.375523 GCAGGAACCGAACCGACAT 60.376 57.895 0.00 0.00 0.00 3.06
3134 3317 2.029964 GCAGGAACCGAACCGACA 59.970 61.111 0.00 0.00 0.00 4.35
3143 3326 3.071479 TCACTTATCAAACGCAGGAACC 58.929 45.455 0.00 0.00 0.00 3.62
3179 3362 4.202070 CCAAACACTGAAATGGTACCGTTT 60.202 41.667 28.37 28.37 37.80 3.60
3347 3539 7.212274 AGTTTGATTTTCAGAAATGGTTGGAG 58.788 34.615 0.00 0.00 35.65 3.86
3387 5537 4.167268 GTGGTTTTTACTTGTTGCGTGAA 58.833 39.130 0.00 0.00 0.00 3.18
3484 5637 5.070313 TGTGTTCTAGATGGTGCTATGCATA 59.930 40.000 6.20 6.20 41.91 3.14
3817 6158 3.445888 GCGTAGGCTACCTCCTCC 58.554 66.667 18.58 0.00 37.66 4.30
3830 6171 2.686405 TCTTCCTTCGATTAGCAGCGTA 59.314 45.455 0.00 0.00 0.00 4.42


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

AutoCloner maintained by Alex Coulton.