Multiple sequence alignment - TraesCS7D01G369800

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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 TraesCS7D01G369800 chr7D 100.000 2645 0 0 1 2645 478413750 478416394 0.000000e+00 4885
1 TraesCS7D01G369800 chr7D 93.526 1313 64 11 1344 2645 79045868 79044566 0.000000e+00 1934
2 TraesCS7D01G369800 chr7D 94.422 1219 59 6 1436 2645 59691540 59690322 0.000000e+00 1866
3 TraesCS7D01G369800 chr7D 90.041 964 94 2 783 1745 223709124 223710086 0.000000e+00 1247
4 TraesCS7D01G369800 chr7D 88.863 431 48 0 783 1213 79047044 79046614 5.010000e-147 531
5 TraesCS7D01G369800 chr2B 94.205 1277 61 6 1382 2645 86848818 86847542 0.000000e+00 1936
6 TraesCS7D01G369800 chr2B 91.964 1120 83 3 1164 2279 401017632 401018748 0.000000e+00 1563
7 TraesCS7D01G369800 chr2B 94.787 211 11 0 783 993 86849969 86849759 1.960000e-86 329
8 TraesCS7D01G369800 chr5B 94.113 1274 65 6 1382 2645 290878565 290879838 0.000000e+00 1929
9 TraesCS7D01G369800 chr5B 93.774 257 16 0 1104 1360 658346496 658346752 1.150000e-103 387
10 TraesCS7D01G369800 chr5B 93.750 256 16 0 1104 1359 290877637 290877892 4.130000e-103 385
11 TraesCS7D01G369800 chr5B 94.787 211 11 0 783 993 17593401 17593611 1.960000e-86 329
12 TraesCS7D01G369800 chr5B 94.787 211 11 0 783 993 658346287 658346497 1.960000e-86 329
13 TraesCS7D01G369800 chr1A 93.798 1290 69 7 1367 2645 365222469 365223758 0.000000e+00 1929
14 TraesCS7D01G369800 chr6B 93.569 1275 71 5 1382 2645 396297307 396298581 0.000000e+00 1890
15 TraesCS7D01G369800 chr6B 91.068 918 67 7 1000 1915 131932124 131931220 0.000000e+00 1227
16 TraesCS7D01G369800 chr6B 93.846 260 16 0 1104 1363 651661653 651661394 2.470000e-105 392
17 TraesCS7D01G369800 chr5D 94.262 1220 60 6 1436 2645 170711802 170713021 0.000000e+00 1857
18 TraesCS7D01G369800 chr5D 94.605 797 39 3 2 795 486973676 486972881 0.000000e+00 1230
19 TraesCS7D01G369800 chr5D 94.571 792 37 6 1 788 490051930 490051141 0.000000e+00 1219
20 TraesCS7D01G369800 chr5D 94.515 784 39 4 2 782 126853039 126853821 0.000000e+00 1206
21 TraesCS7D01G369800 chr5D 94.275 786 41 4 2 784 422647315 422648099 0.000000e+00 1199
22 TraesCS7D01G369800 chr5D 94.787 211 11 0 783 993 170710913 170711123 1.960000e-86 329
23 TraesCS7D01G369800 chr2D 94.267 1221 57 9 1436 2645 621170111 621168893 0.000000e+00 1855
24 TraesCS7D01G369800 chr6A 93.939 1221 61 10 1436 2645 298325209 298326427 0.000000e+00 1832
25 TraesCS7D01G369800 chr6A 90.011 931 67 15 1000 1915 73682552 73681633 0.000000e+00 1181
26 TraesCS7D01G369800 chr7B 91.341 1074 89 2 1164 2233 8676871 8675798 0.000000e+00 1465
27 TraesCS7D01G369800 chr7B 91.200 250 21 1 783 1031 8677129 8676880 3.260000e-89 339
28 TraesCS7D01G369800 chr1D 95.026 784 35 4 2 782 53653844 53654626 0.000000e+00 1229
29 TraesCS7D01G369800 chr1D 94.891 783 39 1 1 782 348874051 348874833 0.000000e+00 1223
30 TraesCS7D01G369800 chr3D 94.770 784 37 4 2 782 192045706 192046488 0.000000e+00 1218
31 TraesCS7D01G369800 chr3D 94.656 786 35 6 2 783 457477286 457476504 0.000000e+00 1212
32 TraesCS7D01G369800 chr3D 94.515 784 39 3 2 782 130357035 130357817 0.000000e+00 1206
33 TraesCS7D01G369800 chr3D 95.261 211 10 0 783 993 482588053 482588263 4.220000e-88 335
34 TraesCS7D01G369800 chr6D 90.183 927 69 10 997 1915 58462008 58461096 0.000000e+00 1188
35 TraesCS7D01G369800 chr1B 95.261 211 10 0 783 993 149122450 149122240 4.220000e-88 335


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 TraesCS7D01G369800 chr7D 478413750 478416394 2644 False 4885.0 4885 100.0000 1 2645 1 chr7D.!!$F2 2644
1 TraesCS7D01G369800 chr7D 59690322 59691540 1218 True 1866.0 1866 94.4220 1436 2645 1 chr7D.!!$R1 1209
2 TraesCS7D01G369800 chr7D 223709124 223710086 962 False 1247.0 1247 90.0410 783 1745 1 chr7D.!!$F1 962
3 TraesCS7D01G369800 chr7D 79044566 79047044 2478 True 1232.5 1934 91.1945 783 2645 2 chr7D.!!$R2 1862
4 TraesCS7D01G369800 chr2B 401017632 401018748 1116 False 1563.0 1563 91.9640 1164 2279 1 chr2B.!!$F1 1115
5 TraesCS7D01G369800 chr2B 86847542 86849969 2427 True 1132.5 1936 94.4960 783 2645 2 chr2B.!!$R1 1862
6 TraesCS7D01G369800 chr5B 290877637 290879838 2201 False 1157.0 1929 93.9315 1104 2645 2 chr5B.!!$F2 1541
7 TraesCS7D01G369800 chr1A 365222469 365223758 1289 False 1929.0 1929 93.7980 1367 2645 1 chr1A.!!$F1 1278
8 TraesCS7D01G369800 chr6B 396297307 396298581 1274 False 1890.0 1890 93.5690 1382 2645 1 chr6B.!!$F1 1263
9 TraesCS7D01G369800 chr6B 131931220 131932124 904 True 1227.0 1227 91.0680 1000 1915 1 chr6B.!!$R1 915
10 TraesCS7D01G369800 chr5D 486972881 486973676 795 True 1230.0 1230 94.6050 2 795 1 chr5D.!!$R1 793
11 TraesCS7D01G369800 chr5D 490051141 490051930 789 True 1219.0 1219 94.5710 1 788 1 chr5D.!!$R2 787
12 TraesCS7D01G369800 chr5D 126853039 126853821 782 False 1206.0 1206 94.5150 2 782 1 chr5D.!!$F1 780
13 TraesCS7D01G369800 chr5D 422647315 422648099 784 False 1199.0 1199 94.2750 2 784 1 chr5D.!!$F2 782
14 TraesCS7D01G369800 chr5D 170710913 170713021 2108 False 1093.0 1857 94.5245 783 2645 2 chr5D.!!$F3 1862
15 TraesCS7D01G369800 chr2D 621168893 621170111 1218 True 1855.0 1855 94.2670 1436 2645 1 chr2D.!!$R1 1209
16 TraesCS7D01G369800 chr6A 298325209 298326427 1218 False 1832.0 1832 93.9390 1436 2645 1 chr6A.!!$F1 1209
17 TraesCS7D01G369800 chr6A 73681633 73682552 919 True 1181.0 1181 90.0110 1000 1915 1 chr6A.!!$R1 915
18 TraesCS7D01G369800 chr7B 8675798 8677129 1331 True 902.0 1465 91.2705 783 2233 2 chr7B.!!$R1 1450
19 TraesCS7D01G369800 chr1D 53653844 53654626 782 False 1229.0 1229 95.0260 2 782 1 chr1D.!!$F1 780
20 TraesCS7D01G369800 chr1D 348874051 348874833 782 False 1223.0 1223 94.8910 1 782 1 chr1D.!!$F2 781
21 TraesCS7D01G369800 chr3D 192045706 192046488 782 False 1218.0 1218 94.7700 2 782 1 chr3D.!!$F2 780
22 TraesCS7D01G369800 chr3D 457476504 457477286 782 True 1212.0 1212 94.6560 2 783 1 chr3D.!!$R1 781
23 TraesCS7D01G369800 chr3D 130357035 130357817 782 False 1206.0 1206 94.5150 2 782 1 chr3D.!!$F1 780
24 TraesCS7D01G369800 chr6D 58461096 58462008 912 True 1188.0 1188 90.1830 997 1915 1 chr6D.!!$R1 918

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
46 48 0.035881 TCTCTGCCTTGGCAAGACAG 59.964 55.0 30.51 30.51 39.98 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2666 0.392863 CATGCGACCATCCTGACCAA 60.393 55.0 0.0 0.0 0.0 3.67 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
46 48 0.035881 TCTCTGCCTTGGCAAGACAG 59.964 55.000 30.51 30.51 39.98 3.51
263 267 2.002586 CAATCCGAAGACAATCTGCGT 58.997 47.619 5.53 0.00 43.94 5.24
379 383 0.036952 ACTGATGGGCTGTGAAGACG 60.037 55.000 0.00 0.00 0.00 4.18
405 409 1.891150 ACCGAAGACCATACTCGTGTT 59.109 47.619 0.00 0.00 0.00 3.32
473 477 7.224362 CAGCTGTGAAGATTCCTTCTTATGTAG 59.776 40.741 5.25 0.00 44.88 2.74
480 484 6.069331 AGATTCCTTCTTATGTAGCCGACTA 58.931 40.000 0.00 0.00 0.00 2.59
584 588 7.233757 CACATAGGCTAGACTTCTAGGGTTTAT 59.766 40.741 1.68 0.00 44.63 1.40
598 602 7.008332 TCTAGGGTTTATCCATTACGATCTCA 58.992 38.462 0.00 0.00 38.11 3.27
881 887 2.484287 CTTTCTCCACCCCACGCCAT 62.484 60.000 0.00 0.00 0.00 4.40
921 927 4.278513 CTGTTCCCCACCGCCCAA 62.279 66.667 0.00 0.00 0.00 4.12
924 930 3.503839 TTCCCCACCGCCCAACTT 61.504 61.111 0.00 0.00 0.00 2.66
1015 1021 0.733150 CGTGATGGAGCTGTCGTCTA 59.267 55.000 0.00 0.00 0.00 2.59
1031 1037 2.202570 TACTTTCGAGGAGCGCGC 60.203 61.111 26.66 26.66 40.61 6.86
1048 1054 2.443394 GCCCGATGGATGGAGGACA 61.443 63.158 0.00 0.00 0.00 4.02
1050 1056 1.337384 CCCGATGGATGGAGGACACA 61.337 60.000 0.00 0.00 0.00 3.72
1060 1066 2.203153 AGGACACACGCAACCACC 60.203 61.111 0.00 0.00 0.00 4.61
1196 1216 3.083349 CATGGACCTCGCCTCCCA 61.083 66.667 0.00 0.00 0.00 4.37
1230 1250 3.371063 ACCGACATCGACGCCACT 61.371 61.111 2.09 0.00 43.02 4.00
1289 1310 2.490217 CAACGGCGAGATCGAGGT 59.510 61.111 16.62 0.00 43.02 3.85
1434 2107 1.506493 CCTCTGTGTCTCAACTGCAC 58.494 55.000 0.00 0.00 0.00 4.57
1707 2396 5.294306 AGCTCATCAATCGCTTCGAATTAAA 59.706 36.000 0.00 0.00 39.99 1.52
1716 2405 6.597262 TCGCTTCGAATTAAAGATGCAATA 57.403 33.333 0.00 0.00 37.38 1.90
1783 2474 7.867752 TGTAGTGTTACTTTTAGGCAAATGTC 58.132 34.615 0.00 0.00 34.74 3.06
1787 2478 5.180492 TGTTACTTTTAGGCAAATGTCGAGG 59.820 40.000 0.00 0.00 34.74 4.63
1850 2544 2.301577 GCCACTTGCACTCCTACTAG 57.698 55.000 0.00 0.00 40.77 2.57
1882 2576 6.223852 ACGAACTTCAAATGTCTCTACATGT 58.776 36.000 2.69 2.69 45.79 3.21
1985 2684 0.107508 CTTGGTCAGGATGGTCGCAT 60.108 55.000 0.00 0.00 36.16 4.73
1998 2697 1.474077 GGTCGCATGCCTTCAAGATTT 59.526 47.619 13.15 0.00 0.00 2.17
2063 2765 1.214589 CGACGGGTACAGGTTCAGG 59.785 63.158 0.00 0.00 0.00 3.86
2087 2792 7.721399 AGGTCATCCATGAATTGGTAGTTATTC 59.279 37.037 0.00 0.00 46.52 1.75
2365 3074 4.170062 CATCCACAAGCAGCGCCG 62.170 66.667 2.29 0.00 0.00 6.46
2398 3107 1.200020 CTGCTTCAAACCCAATCCGTC 59.800 52.381 0.00 0.00 0.00 4.79
2399 3108 1.243902 GCTTCAAACCCAATCCGTCA 58.756 50.000 0.00 0.00 0.00 4.35
2570 3284 7.275888 TGTATGTGAAGGAATTGGATAATGC 57.724 36.000 0.00 0.00 0.00 3.56
2578 3296 4.646492 AGGAATTGGATAATGCGCTCTTTT 59.354 37.500 9.73 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 48 2.683859 GGACGCGGTTTTACTGGCC 61.684 63.158 12.47 0.00 0.00 5.36
164 166 4.539726 TCCGGACCTGTATACATAGTTGT 58.460 43.478 5.91 0.00 39.98 3.32
172 174 9.487790 GTAGTAGATATATCCGGACCTGTATAC 57.512 40.741 6.12 7.39 0.00 1.47
214 216 1.823169 TTCCCTCCTTCCGAACACCG 61.823 60.000 0.00 0.00 38.18 4.94
217 219 1.486145 GGGTTCCCTCCTTCCGAACA 61.486 60.000 0.00 0.00 38.08 3.18
297 301 1.388065 CCAGGACTCCCTCAGTAGCG 61.388 65.000 0.00 0.00 42.02 4.26
332 336 3.917760 GATAGCAGGCCGGACGCT 61.918 66.667 25.91 25.91 39.80 5.07
379 383 3.731264 CGAGTATGGTCTTCGGTCTTCAC 60.731 52.174 0.00 0.00 0.00 3.18
405 409 1.613255 GCCAAGGAAAGTCCAATCCGA 60.613 52.381 0.00 0.00 39.61 4.55
473 477 2.954318 TCTAGGGTTACATGTAGTCGGC 59.046 50.000 5.56 0.00 0.00 5.54
480 484 4.145807 CGGAGAGATCTAGGGTTACATGT 58.854 47.826 2.69 2.69 0.00 3.21
584 588 6.516739 GATCTACCATGAGATCGTAATGGA 57.483 41.667 23.19 11.18 43.00 3.41
598 602 7.039011 TGAGTGTTACAAGAGTTGATCTACCAT 60.039 37.037 3.54 0.00 37.23 3.55
818 823 1.674322 GGATCCAACGTGGGTGTGG 60.674 63.158 9.33 2.38 38.32 4.17
995 1001 1.213013 GACGACAGCTCCATCACGT 59.787 57.895 0.00 0.00 36.71 4.49
1031 1037 1.337384 TGTGTCCTCCATCCATCGGG 61.337 60.000 0.00 0.00 0.00 5.14
1035 1041 1.221840 GCGTGTGTCCTCCATCCAT 59.778 57.895 0.00 0.00 0.00 3.41
1036 1042 1.763546 TTGCGTGTGTCCTCCATCCA 61.764 55.000 0.00 0.00 0.00 3.41
1048 1054 3.659092 CATGCGGTGGTTGCGTGT 61.659 61.111 0.00 0.00 42.88 4.49
1050 1056 3.353836 GACATGCGGTGGTTGCGT 61.354 61.111 0.00 0.00 34.24 5.24
1060 1066 1.811266 CTTGGAGACGGGACATGCG 60.811 63.158 0.00 0.00 0.00 4.73
1213 1233 3.338126 GAGTGGCGTCGATGTCGGT 62.338 63.158 4.52 0.00 40.29 4.69
1707 2396 1.739466 CGCCACACTTGTATTGCATCT 59.261 47.619 0.00 0.00 0.00 2.90
1716 2405 2.347490 CTAGCCCGCCACACTTGT 59.653 61.111 0.00 0.00 0.00 3.16
1783 2474 7.761409 TCATCCATTAGTTCAAAATTTCCTCG 58.239 34.615 0.00 0.00 0.00 4.63
1850 2544 6.430451 AGACATTTGAAGTTCGTTTCATCAC 58.570 36.000 0.00 0.00 36.97 3.06
1967 2666 0.392863 CATGCGACCATCCTGACCAA 60.393 55.000 0.00 0.00 0.00 3.67
1985 2684 2.288152 GCCGTTGAAAATCTTGAAGGCA 60.288 45.455 0.00 0.00 41.46 4.75
1998 2697 2.355363 CGAGACACCGCCGTTGAA 60.355 61.111 0.00 0.00 0.00 2.69
2047 2746 0.470456 TGACCTGAACCTGTACCCGT 60.470 55.000 0.00 0.00 0.00 5.28
2087 2792 7.860613 TGACCAAATTGCAACTATATATGACG 58.139 34.615 0.00 0.00 0.00 4.35
2095 2800 3.440173 CGGACTGACCAAATTGCAACTAT 59.560 43.478 0.00 0.00 38.90 2.12
2104 2809 1.604604 CACAACCGGACTGACCAAAT 58.395 50.000 9.46 0.00 38.90 2.32
2145 2850 6.098838 TCCTACATGACAGATCTAGCACATTT 59.901 38.462 0.00 0.00 0.00 2.32
2146 2851 5.600069 TCCTACATGACAGATCTAGCACATT 59.400 40.000 0.00 0.00 0.00 2.71
2353 3062 2.796483 TTACATCCGGCGCTGCTTGT 62.796 55.000 21.19 21.19 0.00 3.16
2365 3074 5.452777 GTTTGAAGCAGTCAACTTACATCC 58.547 41.667 2.57 0.00 46.09 3.51
2398 3107 8.674263 AATCTAGTTGATTAAGAGGAGCAATG 57.326 34.615 0.00 0.00 43.04 2.82
2436 3149 8.475639 GGTAACATATCCAAGAAGTTCAGTAGA 58.524 37.037 5.50 0.00 0.00 2.59
2578 3296 3.122297 CAGCGTCCTTCATTTTGCAAAA 58.878 40.909 25.76 25.76 0.00 2.44


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

AutoCloner maintained by Alex Coulton.