Multiple sequence alignment - TraesCS6B01G226300

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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 TraesCS6B01G226300 chr6B 100.000 3347 0 0 1 3347 348621620 348624966 0.000000e+00 6181
1 TraesCS6B01G226300 chr6B 86.384 2666 337 20 1 2648 538509515 538506858 0.000000e+00 2889
2 TraesCS6B01G226300 chr6B 86.560 2634 329 17 1 2623 484243021 484240402 0.000000e+00 2880
3 TraesCS6B01G226300 chr6B 85.548 2664 355 17 1 2648 567208891 567211540 0.000000e+00 2760
4 TraesCS6B01G226300 chr6B 85.420 2668 355 26 1 2648 494566935 494564282 0.000000e+00 2741
5 TraesCS6B01G226300 chr6B 96.148 701 25 2 2648 3347 392493997 392494696 0.000000e+00 1144
6 TraesCS6B01G226300 chr6B 85.526 228 25 5 1 220 395398288 395398061 7.220000e-57 231
7 TraesCS6B01G226300 chr4B 86.988 2659 320 17 1 2641 222895125 222897775 0.000000e+00 2970
8 TraesCS6B01G226300 chr4B 85.543 2663 362 18 1 2648 274188629 274191283 0.000000e+00 2763
9 TraesCS6B01G226300 chr1B 86.567 2665 334 15 1 2648 549976740 549974083 0.000000e+00 2916
10 TraesCS6B01G226300 chr1B 96.286 700 25 1 2649 3347 304403038 304403737 0.000000e+00 1147
11 TraesCS6B01G226300 chr1B 96.143 700 26 1 2649 3347 145584847 145585546 0.000000e+00 1142
12 TraesCS6B01G226300 chr1B 96.137 699 25 2 2651 3347 145570092 145570790 0.000000e+00 1140
13 TraesCS6B01G226300 chr1B 84.648 469 56 7 1 461 248094700 248094240 1.420000e-123 453
14 TraesCS6B01G226300 chr1B 90.395 177 11 3 1 176 481167267 481167438 9.340000e-56 228
15 TraesCS6B01G226300 chr7B 86.519 2663 336 18 1 2648 627199575 627196921 0.000000e+00 2907
16 TraesCS6B01G226300 chr7B 88.760 258 20 7 1 250 163951570 163951826 1.170000e-79 307
17 TraesCS6B01G226300 chr7B 89.450 218 15 5 1 216 357147815 357148026 5.500000e-68 268
18 TraesCS6B01G226300 chr7B 90.640 203 15 3 1 202 101554712 101554911 1.980000e-67 267
19 TraesCS6B01G226300 chr7B 89.706 204 13 7 1 198 446300124 446300325 1.540000e-63 254
20 TraesCS6B01G226300 chr1D 86.219 2663 341 17 1 2648 211045626 211048277 0.000000e+00 2861
21 TraesCS6B01G226300 chr5B 88.316 2174 213 17 2 2148 223645764 223643605 0.000000e+00 2569
22 TraesCS6B01G226300 chr5B 96.000 700 27 1 2649 3347 66404752 66404053 0.000000e+00 1136
23 TraesCS6B01G226300 chr5B 90.237 717 54 8 1 708 318260729 318261438 0.000000e+00 922
24 TraesCS6B01G226300 chr5B 88.102 706 69 8 1 698 217898742 217899440 0.000000e+00 824
25 TraesCS6B01G226300 chr5B 81.891 751 87 20 1 710 288618197 288618939 3.720000e-164 588
26 TraesCS6B01G226300 chr5B 87.264 212 20 6 1 206 165657991 165658201 5.580000e-58 235
27 TraesCS6B01G226300 chr5B 86.385 213 21 7 1 206 166040894 166041105 3.360000e-55 226
28 TraesCS6B01G226300 chr2B 96.429 700 23 2 2649 3347 411588198 411587500 0.000000e+00 1153
29 TraesCS6B01G226300 chr2B 96.000 700 27 1 2649 3347 275443967 275443268 0.000000e+00 1136
30 TraesCS6B01G226300 chr2B 84.449 881 107 12 1 867 218830571 218829707 0.000000e+00 841
31 TraesCS6B01G226300 chr2B 88.129 278 22 7 3 271 283836163 283835888 1.500000e-83 320
32 TraesCS6B01G226300 chr2B 85.385 260 27 7 1 251 430003249 430002992 3.310000e-65 259
33 TraesCS6B01G226300 chr4D 96.000 700 27 1 2649 3347 331100311 331099612 0.000000e+00 1136
34 TraesCS6B01G226300 chr3B 96.000 700 27 1 2649 3347 438348362 438347663 0.000000e+00 1136
35 TraesCS6B01G226300 chr3B 85.878 871 81 17 1 856 444380752 444379909 0.000000e+00 889
36 TraesCS6B01G226300 chr4A 79.452 876 132 32 1 867 516075571 516074735 8.050000e-161 577


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 TraesCS6B01G226300 chr6B 348621620 348624966 3346 False 6181 6181 100.000 1 3347 1 chr6B.!!$F1 3346
1 TraesCS6B01G226300 chr6B 538506858 538509515 2657 True 2889 2889 86.384 1 2648 1 chr6B.!!$R4 2647
2 TraesCS6B01G226300 chr6B 484240402 484243021 2619 True 2880 2880 86.560 1 2623 1 chr6B.!!$R2 2622
3 TraesCS6B01G226300 chr6B 567208891 567211540 2649 False 2760 2760 85.548 1 2648 1 chr6B.!!$F3 2647
4 TraesCS6B01G226300 chr6B 494564282 494566935 2653 True 2741 2741 85.420 1 2648 1 chr6B.!!$R3 2647
5 TraesCS6B01G226300 chr6B 392493997 392494696 699 False 1144 1144 96.148 2648 3347 1 chr6B.!!$F2 699
6 TraesCS6B01G226300 chr4B 222895125 222897775 2650 False 2970 2970 86.988 1 2641 1 chr4B.!!$F1 2640
7 TraesCS6B01G226300 chr4B 274188629 274191283 2654 False 2763 2763 85.543 1 2648 1 chr4B.!!$F2 2647
8 TraesCS6B01G226300 chr1B 549974083 549976740 2657 True 2916 2916 86.567 1 2648 1 chr1B.!!$R2 2647
9 TraesCS6B01G226300 chr1B 304403038 304403737 699 False 1147 1147 96.286 2649 3347 1 chr1B.!!$F3 698
10 TraesCS6B01G226300 chr1B 145584847 145585546 699 False 1142 1142 96.143 2649 3347 1 chr1B.!!$F2 698
11 TraesCS6B01G226300 chr1B 145570092 145570790 698 False 1140 1140 96.137 2651 3347 1 chr1B.!!$F1 696
12 TraesCS6B01G226300 chr7B 627196921 627199575 2654 True 2907 2907 86.519 1 2648 1 chr7B.!!$R1 2647
13 TraesCS6B01G226300 chr1D 211045626 211048277 2651 False 2861 2861 86.219 1 2648 1 chr1D.!!$F1 2647
14 TraesCS6B01G226300 chr5B 223643605 223645764 2159 True 2569 2569 88.316 2 2148 1 chr5B.!!$R2 2146
15 TraesCS6B01G226300 chr5B 66404053 66404752 699 True 1136 1136 96.000 2649 3347 1 chr5B.!!$R1 698
16 TraesCS6B01G226300 chr5B 318260729 318261438 709 False 922 922 90.237 1 708 1 chr5B.!!$F5 707
17 TraesCS6B01G226300 chr5B 217898742 217899440 698 False 824 824 88.102 1 698 1 chr5B.!!$F3 697
18 TraesCS6B01G226300 chr5B 288618197 288618939 742 False 588 588 81.891 1 710 1 chr5B.!!$F4 709
19 TraesCS6B01G226300 chr2B 411587500 411588198 698 True 1153 1153 96.429 2649 3347 1 chr2B.!!$R4 698
20 TraesCS6B01G226300 chr2B 275443268 275443967 699 True 1136 1136 96.000 2649 3347 1 chr2B.!!$R2 698
21 TraesCS6B01G226300 chr2B 218829707 218830571 864 True 841 841 84.449 1 867 1 chr2B.!!$R1 866
22 TraesCS6B01G226300 chr4D 331099612 331100311 699 True 1136 1136 96.000 2649 3347 1 chr4D.!!$R1 698
23 TraesCS6B01G226300 chr3B 438347663 438348362 699 True 1136 1136 96.000 2649 3347 1 chr3B.!!$R1 698
24 TraesCS6B01G226300 chr3B 444379909 444380752 843 True 889 889 85.878 1 856 1 chr3B.!!$R2 855
25 TraesCS6B01G226300 chr4A 516074735 516075571 836 True 577 577 79.452 1 867 1 chr4A.!!$R1 866

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
820 907 0.734309 TGATGATGTGTGGCGATTGC 59.266 50.0 0.0 0.0 41.71 3.56 F
1195 1283 0.169009 GCCAGCGAACATCACTTTCC 59.831 55.0 0.0 0.0 0.00 3.13 F
1748 1837 0.250901 CTATGGAATCTTGGGGGCGG 60.251 60.0 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 1837 1.060698 GTAGGCGAATCTTGTCGTTGC 59.939 52.381 0.0 0.0 43.06 4.17 R
2185 2280 1.153349 GAGGAATCAGCACGGTCCC 60.153 63.158 0.0 0.0 0.00 4.46 R
2928 3026 3.632145 CACAACTCCTACCAGCACTTTTT 59.368 43.478 0.0 0.0 0.00 1.94 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
176 205 3.644966 TTTATAGTGGCCTTGGTCCTG 57.355 47.619 3.32 0.00 0.00 3.86
437 505 3.297134 AAGAGGAAACCTGCACTTTGA 57.703 42.857 0.00 0.00 31.76 2.69
446 515 1.002430 CCTGCACTTTGAGCCTGTCTA 59.998 52.381 0.00 0.00 0.00 2.59
571 640 2.352805 CCTCAGGGGTCTTGGTGC 59.647 66.667 0.00 0.00 0.00 5.01
820 907 0.734309 TGATGATGTGTGGCGATTGC 59.266 50.000 0.00 0.00 41.71 3.56
833 920 3.918253 GATTGCTGGGACGTGGGCA 62.918 63.158 0.00 0.00 0.00 5.36
870 957 1.600916 GCCTCGGCAACTGTTTCCT 60.601 57.895 7.59 0.00 41.49 3.36
874 961 2.289444 CCTCGGCAACTGTTTCCTTCTA 60.289 50.000 7.59 0.00 0.00 2.10
956 1044 1.003355 CTTCTCCCAGCAGCGGAAA 60.003 57.895 4.99 0.00 0.00 3.13
963 1051 0.883833 CCAGCAGCGGAAAAACTCAT 59.116 50.000 0.00 0.00 0.00 2.90
995 1083 3.624707 CGATTTTCCCCTCCAATCCTTCA 60.625 47.826 0.00 0.00 0.00 3.02
1065 1153 2.361483 TGGTACGAGCCGGCACTA 60.361 61.111 31.54 13.42 0.00 2.74
1148 1236 4.546674 GATAACAAATGGAAGGGGATGGT 58.453 43.478 0.00 0.00 0.00 3.55
1166 1254 4.329545 GCTCTGGGTTGCCACCGA 62.330 66.667 0.03 0.00 45.39 4.69
1195 1283 0.169009 GCCAGCGAACATCACTTTCC 59.831 55.000 0.00 0.00 0.00 3.13
1209 1297 3.722101 TCACTTTCCTCCCTTTCTTCCTT 59.278 43.478 0.00 0.00 0.00 3.36
1218 1306 1.532868 CCTTTCTTCCTTCACAGCGTG 59.467 52.381 2.79 2.79 34.45 5.34
1265 1353 1.257539 CGCTTCTTCTACGTCGTTCC 58.742 55.000 1.78 0.00 0.00 3.62
1365 1453 2.120909 GTTCATGGGGGTGATGCCG 61.121 63.158 0.00 0.00 38.44 5.69
1432 1520 1.378382 CATCCCGTTGGGTGCATCA 60.378 57.895 0.00 0.00 44.74 3.07
1447 1535 1.153489 ATCAGCTTCGTCGCAGCAT 60.153 52.632 18.89 1.87 39.99 3.79
1593 1682 2.950990 AGGGGTGGTACTCTGAGAAT 57.049 50.000 12.44 0.00 0.00 2.40
1617 1706 0.256177 CTAACCCTTCCCTGAAGCCC 59.744 60.000 0.00 0.00 38.24 5.19
1725 1814 3.382832 CTCCAAGGTCGCTCCCGT 61.383 66.667 0.00 0.00 36.75 5.28
1748 1837 0.250901 CTATGGAATCTTGGGGGCGG 60.251 60.000 0.00 0.00 0.00 6.13
1767 1856 1.355971 GCAACGACAAGATTCGCCTA 58.644 50.000 0.00 0.00 43.06 3.93
1772 1861 1.480219 GACAAGATTCGCCTACGCCG 61.480 60.000 0.00 0.00 39.84 6.46
1888 1977 2.579738 GAGTCAACGGGGAGGAGC 59.420 66.667 0.00 0.00 0.00 4.70
1894 1983 2.529744 AACGGGGAGGAGCTTGCTT 61.530 57.895 0.00 0.00 0.00 3.91
2087 2182 6.825721 CCTGATGATGATGATGATGATGATGT 59.174 38.462 0.00 0.00 0.00 3.06
2097 2192 3.040477 TGATGATGATGTGCCTCTGGTA 58.960 45.455 0.00 0.00 0.00 3.25
2151 2246 2.873557 GATCCGGGGTGTCCTCCTCA 62.874 65.000 0.00 0.00 0.00 3.86
2185 2280 2.742372 CGGCCACGAAGAAGGGTG 60.742 66.667 2.24 0.00 44.60 4.61
2270 2365 1.515020 CGAGTTCTCCTGCTCCCAG 59.485 63.158 0.00 0.00 38.85 4.45
2292 2387 2.454832 CTTCAGCTCCGGTTGCCTCA 62.455 60.000 16.16 1.22 0.00 3.86
2298 2393 1.667154 CTCCGGTTGCCTCATCTCGA 61.667 60.000 0.00 0.00 0.00 4.04
2332 2427 3.190874 GGCTTGAAGAGGAACTATGTCG 58.809 50.000 0.00 0.00 41.55 4.35
2368 2463 2.959030 GTCTTCTCCTTGGCCTTGTTTT 59.041 45.455 3.32 0.00 0.00 2.43
2415 2510 2.826128 TCTTCGTCTGTCATTAGGCAGT 59.174 45.455 0.00 0.00 34.57 4.40
2437 2532 1.801178 GTCGTCAAAGAAGCAGAAGGG 59.199 52.381 0.00 0.00 0.00 3.95
2528 2625 4.320456 CTGCAGCTCCGGTGGTGT 62.320 66.667 29.93 3.62 37.70 4.16
2577 2674 3.669036 CTCAGGAGGTGTCGACGCG 62.669 68.421 21.89 3.53 0.00 6.01
2900 2998 4.914983 AGTAGGGGTTGTTTAGGTAAAGC 58.085 43.478 0.00 0.00 0.00 3.51
2902 3000 4.187506 AGGGGTTGTTTAGGTAAAGCAA 57.812 40.909 0.00 0.00 0.00 3.91
2910 3008 9.483916 GGTTGTTTAGGTAAAGCAACAATAAAT 57.516 29.630 15.92 0.00 40.33 1.40
2936 3034 3.813529 ATAGCGAGTGTGAAAAAGTGC 57.186 42.857 0.00 0.00 0.00 4.40
3190 3288 4.518970 GGGTTTATGCTTCTGTCACTCAAA 59.481 41.667 0.00 0.00 0.00 2.69
3310 3409 7.770897 ACATAACCACAAGCAAATTAAACCAAA 59.229 29.630 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 40 3.945921 TCCACTGTACTAGTTCATCCTCG 59.054 47.826 0.00 0.00 37.60 4.63
369 415 1.617947 GGTGTCCCGAGGAATCAGCT 61.618 60.000 0.00 0.00 31.38 4.24
460 529 0.948623 CGTGAGCCATGACGACCAAA 60.949 55.000 0.00 0.00 37.81 3.28
639 717 1.100510 CACCATGTGGCTTCATCAGG 58.899 55.000 0.00 0.00 39.32 3.86
668 754 2.386935 GGGTATCCAGCCCTGCCTT 61.387 63.158 0.00 0.00 42.81 4.35
820 907 2.358737 GAGTTGCCCACGTCCCAG 60.359 66.667 0.00 0.00 0.00 4.45
833 920 1.612726 GCAGCATGGAGAAGTGGAGTT 60.613 52.381 0.00 0.00 35.86 3.01
870 957 2.757894 TGGCACCCCTTTTGTTAGAA 57.242 45.000 0.00 0.00 0.00 2.10
874 961 1.341080 CAGATGGCACCCCTTTTGTT 58.659 50.000 0.00 0.00 0.00 2.83
919 1007 1.144936 GGGATCTGGAGCAAGACGG 59.855 63.158 0.00 0.00 0.00 4.79
956 1044 3.834489 ATCGGCAGATCTGATGAGTTT 57.166 42.857 27.04 5.30 39.29 2.66
963 1051 1.134098 GGGGAAAATCGGCAGATCTGA 60.134 52.381 27.04 5.94 35.74 3.27
995 1083 1.895798 TCTTCTCAGCGACCATTGAGT 59.104 47.619 0.00 0.00 41.21 3.41
1040 1128 1.380112 GGCTCGTACCAGGAGGAGT 60.380 63.158 0.00 0.00 38.69 3.85
1114 1202 0.531974 TTGTTATCCTGGATCGCCGC 60.532 55.000 13.54 1.16 36.79 6.53
1121 1209 3.052944 CCCCTTCCATTTGTTATCCTGGA 60.053 47.826 0.00 0.00 36.02 3.86
1123 1211 4.249638 TCCCCTTCCATTTGTTATCCTG 57.750 45.455 0.00 0.00 0.00 3.86
1148 1236 4.641645 CGGTGGCAACCCAGAGCA 62.642 66.667 4.14 0.00 44.42 4.26
1179 1267 1.339151 GGGAGGAAAGTGATGTTCGCT 60.339 52.381 0.00 0.00 39.20 4.93
1195 1283 2.431454 GCTGTGAAGGAAGAAAGGGAG 58.569 52.381 0.00 0.00 0.00 4.30
1209 1297 2.632544 CCCCGAGTACACGCTGTGA 61.633 63.158 14.18 0.00 36.96 3.58
1265 1353 1.811558 CGTGGAGGCCATAATGGTGAG 60.812 57.143 5.01 0.00 40.46 3.51
1365 1453 3.554692 CGGAGCATGGCGACGAAC 61.555 66.667 0.00 0.00 35.40 3.95
1432 1520 2.816958 CCATGCTGCGACGAAGCT 60.817 61.111 27.49 11.27 41.42 3.74
1460 1548 1.612146 TTCCCGGCACAGGAGATCA 60.612 57.895 0.00 0.00 34.08 2.92
1593 1682 3.454812 GCTTCAGGGAAGGGTTAGTGATA 59.545 47.826 7.97 0.00 39.76 2.15
1617 1706 3.370315 CCTCCTCCATCTTCTTCACCAAG 60.370 52.174 0.00 0.00 0.00 3.61
1748 1837 1.060698 GTAGGCGAATCTTGTCGTTGC 59.939 52.381 0.00 0.00 43.06 4.17
1772 1861 3.787001 CCTCCAGAAGGGCGTCCC 61.787 72.222 0.08 4.26 45.90 4.46
1784 1873 1.229304 TTGCTCAGCTCCTCCTCCA 60.229 57.895 0.00 0.00 0.00 3.86
1785 1874 1.521616 CTTGCTCAGCTCCTCCTCC 59.478 63.158 0.00 0.00 0.00 4.30
1860 1949 1.393539 CCGTTGACTCGGCAATACAAG 59.606 52.381 0.00 0.00 43.96 3.16
1888 1977 2.488355 CGGCATGGCAGAAGCAAG 59.512 61.111 20.37 0.00 44.61 4.01
1894 1983 1.675310 CAAAGACCGGCATGGCAGA 60.675 57.895 20.37 0.00 43.94 4.26
1956 2045 1.826096 GAGGACAGGTCTACCAAGGAC 59.174 57.143 1.26 0.00 38.89 3.85
2087 2182 4.461119 CCTCCACTACCAGAGGCA 57.539 61.111 0.00 0.00 43.11 4.75
2151 2246 2.985847 GTCCGCTTGGGCTGCTTT 60.986 61.111 0.00 0.00 33.30 3.51
2185 2280 1.153349 GAGGAATCAGCACGGTCCC 60.153 63.158 0.00 0.00 0.00 4.46
2270 2365 2.035442 GCAACCGGAGCTGAAGTCC 61.035 63.158 9.46 0.00 0.00 3.85
2273 2368 1.743252 GAGGCAACCGGAGCTGAAG 60.743 63.158 9.46 0.00 37.17 3.02
2314 2409 4.321750 GGTGACGACATAGTTCCTCTTCAA 60.322 45.833 0.00 0.00 0.00 2.69
2332 2427 2.557490 AGAAGACTTACTGGTCGGTGAC 59.443 50.000 0.00 0.00 40.76 3.67
2368 2463 5.235186 GCTAAGCATCGCTTCTAGAATCAAA 59.765 40.000 5.44 0.00 46.77 2.69
2415 2510 3.306088 CCCTTCTGCTTCTTTGACGACTA 60.306 47.826 0.00 0.00 0.00 2.59
2482 2579 3.721706 CTCTCCTTTGCCCGGGCT 61.722 66.667 43.34 0.00 42.51 5.19
2487 2584 2.035442 GCGACACTCTCCTTTGCCC 61.035 63.158 0.00 0.00 0.00 5.36
2528 2625 1.284111 ATGCTCTGGGGAGATGGCAA 61.284 55.000 0.00 0.00 41.86 4.52
2910 3008 7.960738 GCACTTTTTCACACTCGCTATATTTAA 59.039 33.333 0.00 0.00 0.00 1.52
2928 3026 3.632145 CACAACTCCTACCAGCACTTTTT 59.368 43.478 0.00 0.00 0.00 1.94
2936 3034 4.455877 GGACAATTTCACAACTCCTACCAG 59.544 45.833 0.00 0.00 0.00 4.00
3190 3288 6.957631 TCATGATTCACTTATAGTGGGTTGT 58.042 36.000 6.96 0.00 45.94 3.32
3310 3409 5.376625 ACCGGTATTGATGAATTGCTATGT 58.623 37.500 4.49 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.