Multiple sequence alignment - TraesCS7D01G163700

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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 TraesCS7D01G163700 chr7D 100.000 4187 0 0 1 4187 113273584 113277770 0.000000e+00 7733
1 TraesCS7D01G163700 chr7D 93.472 2635 126 20 1583 4187 442603660 442606278 0.000000e+00 3871
2 TraesCS7D01G163700 chr7D 93.199 1588 100 8 1 1583 442600975 442602559 0.000000e+00 2327
3 TraesCS7D01G163700 chr5A 95.439 4210 151 14 1 4187 627513102 627517293 0.000000e+00 6673
4 TraesCS7D01G163700 chr2A 94.828 4060 163 12 1 4032 536422427 536418387 0.000000e+00 6290
5 TraesCS7D01G163700 chr2A 94.224 1333 72 2 1 1329 473131418 473130087 0.000000e+00 2030
6 TraesCS7D01G163700 chr2A 88.336 1226 110 16 2201 3398 454474787 454473567 0.000000e+00 1441
7 TraesCS7D01G163700 chr2A 89.200 963 92 6 1 962 447637887 447638838 0.000000e+00 1192
8 TraesCS7D01G163700 chr2A 89.108 964 92 7 1 962 454476415 454475463 0.000000e+00 1186
9 TraesCS7D01G163700 chr2A 89.691 679 59 7 3516 4186 454473269 454472594 0.000000e+00 856
10 TraesCS7D01G163700 chr2A 84.204 861 103 27 1053 1905 454475982 454475147 0.000000e+00 806
11 TraesCS7D01G163700 chr2A 87.658 632 75 3 1053 1683 447638320 447638949 0.000000e+00 732
12 TraesCS7D01G163700 chr2A 91.924 421 30 2 1780 2197 447639026 447639445 1.680000e-163 586
13 TraesCS7D01G163700 chr2A 88.020 409 42 5 3785 4186 447640436 447640844 1.050000e-130 477
14 TraesCS7D01G163700 chr2A 91.756 279 19 4 1923 2200 454475100 454474825 6.570000e-103 385
15 TraesCS7D01G163700 chr2A 93.434 198 12 1 2201 2397 447639486 447639683 4.090000e-75 292
16 TraesCS7D01G163700 chr2A 98.198 111 2 0 4077 4187 536418386 536418276 1.190000e-45 195
17 TraesCS7D01G163700 chr2A 90.833 120 11 0 3397 3516 447639800 447639919 1.200000e-35 161
18 TraesCS7D01G163700 chr3B 93.205 3635 204 20 252 3856 583350937 583354558 0.000000e+00 5304
19 TraesCS7D01G163700 chr3B 96.121 232 9 0 1 232 583350660 583350891 3.060000e-101 379
20 TraesCS7D01G163700 chr3B 90.987 233 20 1 3853 4084 583354756 583354988 3.140000e-81 313
21 TraesCS7D01G163700 chr6A 94.402 2358 92 18 1846 4184 507399421 507397085 0.000000e+00 3587
22 TraesCS7D01G163700 chr6A 92.803 1848 89 23 2362 4187 507440356 507438531 0.000000e+00 2636
23 TraesCS7D01G163700 chr6A 95.270 1205 57 0 3 1207 507400638 507399434 0.000000e+00 1910
24 TraesCS7D01G163700 chr2D 89.461 1224 92 10 1005 2197 330084054 330085271 0.000000e+00 1511
25 TraesCS7D01G163700 chr2D 89.141 1234 98 13 2197 3396 330085308 330086539 0.000000e+00 1504
26 TraesCS7D01G163700 chr2D 92.747 455 25 7 3516 3966 330086837 330087287 0.000000e+00 651
27 TraesCS7D01G163700 chr2D 90.833 120 11 0 3397 3516 330086589 330086708 1.200000e-35 161
28 TraesCS7D01G163700 chr7B 88.934 1229 101 14 2197 3398 383712579 383713799 0.000000e+00 1483
29 TraesCS7D01G163700 chr7B 88.589 964 81 13 1 962 383710952 383711888 0.000000e+00 1144
30 TraesCS7D01G163700 chr7B 88.326 651 70 6 1053 1700 383711369 383712016 0.000000e+00 776
31 TraesCS7D01G163700 chr7B 92.308 507 32 4 1697 2197 383712038 383712543 0.000000e+00 713
32 TraesCS7D01G163700 chr7B 90.875 526 40 8 3518 4039 383714101 383714622 0.000000e+00 699
33 TraesCS7D01G163700 chr7B 85.897 156 12 2 4036 4187 383714734 383714883 1.560000e-34 158
34 TraesCS7D01G163700 chr7B 90.000 120 12 0 3397 3516 383713851 383713970 5.600000e-34 156
35 TraesCS7D01G163700 chr5B 75.974 462 67 27 1380 1800 686754753 686754295 9.180000e-47 198
36 TraesCS7D01G163700 chr5D 90.826 109 8 2 1697 1804 55808088 55807981 1.210000e-30 145


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 TraesCS7D01G163700 chr7D 113273584 113277770 4186 False 7733.000000 7733 100.000000 1 4187 1 chr7D.!!$F1 4186
1 TraesCS7D01G163700 chr7D 442600975 442606278 5303 False 3099.000000 3871 93.335500 1 4187 2 chr7D.!!$F2 4186
2 TraesCS7D01G163700 chr5A 627513102 627517293 4191 False 6673.000000 6673 95.439000 1 4187 1 chr5A.!!$F1 4186
3 TraesCS7D01G163700 chr2A 536418276 536422427 4151 True 3242.500000 6290 96.513000 1 4187 2 chr2A.!!$R3 4186
4 TraesCS7D01G163700 chr2A 473130087 473131418 1331 True 2030.000000 2030 94.224000 1 1329 1 chr2A.!!$R1 1328
5 TraesCS7D01G163700 chr2A 454472594 454476415 3821 True 934.800000 1441 88.619000 1 4186 5 chr2A.!!$R2 4185
6 TraesCS7D01G163700 chr2A 447637887 447640844 2957 False 573.333333 1192 90.178167 1 4186 6 chr2A.!!$F1 4185
7 TraesCS7D01G163700 chr3B 583350660 583354988 4328 False 1998.666667 5304 93.437667 1 4084 3 chr3B.!!$F1 4083
8 TraesCS7D01G163700 chr6A 507397085 507400638 3553 True 2748.500000 3587 94.836000 3 4184 2 chr6A.!!$R2 4181
9 TraesCS7D01G163700 chr6A 507438531 507440356 1825 True 2636.000000 2636 92.803000 2362 4187 1 chr6A.!!$R1 1825
10 TraesCS7D01G163700 chr2D 330084054 330087287 3233 False 956.750000 1511 90.545500 1005 3966 4 chr2D.!!$F1 2961
11 TraesCS7D01G163700 chr7B 383710952 383714883 3931 False 732.714286 1483 89.275571 1 4187 7 chr7B.!!$F1 4186

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
970 1005 0.036388 TACTGGAAAAGCTGCTCCCG 60.036 55.0 1.0 7.78 0.0 5.14 F
1034 1679 0.247460 CTGAACACCCATGAGAGCGA 59.753 55.0 0.0 0.00 0.0 4.93 F
1278 1924 1.111116 ACTTCGACGGAACAGGACCA 61.111 55.0 0.0 0.00 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 3766 5.616270 TGCACTACCAATCTGAAACTAACA 58.384 37.500 0.0 0.0 0.00 2.41 R
3003 4874 6.157211 CGTATATCAACGCTATCCTTTCCTT 58.843 40.000 0.0 0.0 35.87 3.36 R
3219 5110 2.266055 CCAAGTCCTCCCAGCGAC 59.734 66.667 0.0 0.0 0.00 5.19 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
361 388 0.830444 ACCACAGGTACTCGCTCCAA 60.830 55.000 0.00 0.00 34.60 3.53
364 391 0.542232 ACAGGTACTCGCTCCAACCT 60.542 55.000 0.00 0.00 43.15 3.50
648 681 8.873830 CATTTTCTCTAGAACAACGATGTACAT 58.126 33.333 8.43 8.43 39.40 2.29
691 724 2.497675 CAGTGCTACACCTGAGGTACAT 59.502 50.000 2.59 0.00 34.49 2.29
893 928 7.781056 ACAAACAAGAGTGAAACCAATAATGT 58.219 30.769 0.00 0.00 37.80 2.71
894 929 8.257306 ACAAACAAGAGTGAAACCAATAATGTT 58.743 29.630 0.00 0.00 37.80 2.71
895 930 8.542132 CAAACAAGAGTGAAACCAATAATGTTG 58.458 33.333 0.00 0.00 37.80 3.33
896 931 7.581213 ACAAGAGTGAAACCAATAATGTTGA 57.419 32.000 0.00 0.00 37.80 3.18
898 933 7.285401 ACAAGAGTGAAACCAATAATGTTGAGT 59.715 33.333 0.00 0.00 37.80 3.41
899 934 7.206981 AGAGTGAAACCAATAATGTTGAGTG 57.793 36.000 0.00 0.00 37.80 3.51
900 935 6.998074 AGAGTGAAACCAATAATGTTGAGTGA 59.002 34.615 0.00 0.00 37.80 3.41
901 936 7.667219 AGAGTGAAACCAATAATGTTGAGTGAT 59.333 33.333 0.00 0.00 37.80 3.06
919 954 7.455891 TGAGTGATGATTATGGTATGATTGCT 58.544 34.615 0.00 0.00 0.00 3.91
920 955 7.389607 TGAGTGATGATTATGGTATGATTGCTG 59.610 37.037 0.00 0.00 0.00 4.41
937 972 8.985315 TGATTGCTGGATTAATAATTCAGAGT 57.015 30.769 22.08 8.76 45.68 3.24
957 992 8.812972 TCAGAGTAAGAAAGCTATTTTACTGGA 58.187 33.333 16.72 12.47 27.21 3.86
958 993 9.436957 CAGAGTAAGAAAGCTATTTTACTGGAA 57.563 33.333 16.72 0.00 27.21 3.53
962 997 9.343103 GTAAGAAAGCTATTTTACTGGAAAAGC 57.657 33.333 3.90 2.65 40.34 3.51
963 998 7.767250 AGAAAGCTATTTTACTGGAAAAGCT 57.233 32.000 5.86 5.86 40.34 3.74
964 999 7.597386 AGAAAGCTATTTTACTGGAAAAGCTG 58.403 34.615 11.32 2.44 40.34 4.24
966 1001 5.012893 AGCTATTTTACTGGAAAAGCTGCT 58.987 37.500 10.08 11.76 40.34 4.24
968 1003 4.790765 ATTTTACTGGAAAAGCTGCTCC 57.209 40.909 1.00 7.30 40.34 4.70
970 1005 0.036388 TACTGGAAAAGCTGCTCCCG 60.036 55.000 1.00 7.78 0.00 5.14
972 1007 3.804193 GGAAAAGCTGCTCCCGCG 61.804 66.667 1.00 0.00 39.65 6.46
973 1008 4.467062 GAAAAGCTGCTCCCGCGC 62.467 66.667 1.00 0.00 39.65 6.86
979 1014 4.441695 CTGCTCCCGCGCTCTTCA 62.442 66.667 5.56 0.00 39.65 3.02
980 1015 4.742201 TGCTCCCGCGCTCTTCAC 62.742 66.667 5.56 0.00 39.65 3.18
987 1022 3.112709 GCGCTCTTCACCGTGGTC 61.113 66.667 0.00 0.00 0.00 4.02
988 1023 2.338620 CGCTCTTCACCGTGGTCA 59.661 61.111 0.00 0.00 0.00 4.02
990 1025 1.069090 GCTCTTCACCGTGGTCACA 59.931 57.895 0.00 0.00 0.00 3.58
992 1027 0.600255 CTCTTCACCGTGGTCACACC 60.600 60.000 0.00 0.00 44.86 4.16
993 1028 1.597027 CTTCACCGTGGTCACACCC 60.597 63.158 0.00 0.00 44.86 4.61
998 1033 2.046314 CGTGGTCACACCCCCATC 60.046 66.667 1.90 0.00 44.86 3.51
1000 1035 2.121735 TGGTCACACCCCCATCCA 60.122 61.111 0.00 0.00 37.50 3.41
1001 1036 1.543642 TGGTCACACCCCCATCCAT 60.544 57.895 0.00 0.00 37.50 3.41
1002 1037 1.076777 GGTCACACCCCCATCCATG 60.077 63.158 0.00 0.00 30.04 3.66
1003 1038 1.754234 GTCACACCCCCATCCATGC 60.754 63.158 0.00 0.00 0.00 4.06
1005 1040 4.127744 ACACCCCCATCCATGCCG 62.128 66.667 0.00 0.00 0.00 5.69
1008 1043 4.962836 CCCCCATCCATGCCGCTC 62.963 72.222 0.00 0.00 0.00 5.03
1034 1679 0.247460 CTGAACACCCATGAGAGCGA 59.753 55.000 0.00 0.00 0.00 4.93
1215 1860 6.017192 CCTCAAGCCCCTATACAGAAGTATA 58.983 44.000 0.00 0.00 41.15 1.47
1278 1924 1.111116 ACTTCGACGGAACAGGACCA 61.111 55.000 0.00 0.00 0.00 4.02
1419 2065 7.285401 ACTTCACCATGATCTTTTACTTTGTGT 59.715 33.333 0.00 0.00 0.00 3.72
1946 3766 5.349061 TGATGCTCTGAATGTCATACAGT 57.651 39.130 0.00 0.00 33.93 3.55
2117 3937 4.219288 AGTGCCACTTCCAAGAATCAAATC 59.781 41.667 0.00 0.00 0.00 2.17
2385 4245 5.811399 TTCGCTTCCAGTATGTAATTTGG 57.189 39.130 0.00 0.00 32.84 3.28
2391 4251 6.509418 TTCCAGTATGTAATTTGGACAAGC 57.491 37.500 0.00 0.00 38.21 4.01
2511 4371 4.000988 GTGGATAAAGGTGTGTACTGTGG 58.999 47.826 0.00 0.00 0.00 4.17
2739 4610 4.632153 AGTCTGATACAACACAGAACACC 58.368 43.478 0.00 0.00 43.29 4.16
3003 4874 4.121317 CTGCAACCATTTTGAGAAAAGCA 58.879 39.130 0.00 0.00 33.22 3.91
3255 5146 1.133598 GGTGGTAATTTACAAGGCCGC 59.866 52.381 8.73 0.00 0.00 6.53
3316 5211 9.337396 TCACATGTTATTAGAATGGATGTTACC 57.663 33.333 0.00 0.00 0.00 2.85
3332 5227 5.614923 TGTTACCACAACATTTCCGTATG 57.385 39.130 0.00 0.00 0.00 2.39
3966 6509 5.976534 CCTCAATTTCAATCAACGTCAAACA 59.023 36.000 0.00 0.00 0.00 2.83
4029 6572 8.649973 AGTATAGCTCTTATTTCTTTCCGTTG 57.350 34.615 0.00 0.00 0.00 4.10
4030 6573 8.258708 AGTATAGCTCTTATTTCTTTCCGTTGT 58.741 33.333 0.00 0.00 0.00 3.32
4031 6574 9.525409 GTATAGCTCTTATTTCTTTCCGTTGTA 57.475 33.333 0.00 0.00 0.00 2.41
4032 6575 6.723131 AGCTCTTATTTCTTTCCGTTGTAC 57.277 37.500 0.00 0.00 0.00 2.90
4033 6576 6.228258 AGCTCTTATTTCTTTCCGTTGTACA 58.772 36.000 0.00 0.00 0.00 2.90
4034 6577 6.879458 AGCTCTTATTTCTTTCCGTTGTACAT 59.121 34.615 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
361 388 8.598041 ACAGAGATAAAACAGTTCATCTAAGGT 58.402 33.333 9.37 6.55 0.00 3.50
364 391 9.587772 GCTACAGAGATAAAACAGTTCATCTAA 57.412 33.333 9.37 0.00 0.00 2.10
493 522 2.693069 CTCGAGCAGGACACAAAATCT 58.307 47.619 0.00 0.00 0.00 2.40
579 612 0.044092 TCCACATAGGGGCTTGAGGA 59.956 55.000 0.00 0.00 38.24 3.71
648 681 1.537348 CGGTCAGTGTTCCGTCAAAGA 60.537 52.381 16.84 0.00 41.58 2.52
691 724 6.183360 GGTTTGGCATGTGGATTATACAATGA 60.183 38.462 0.00 0.00 0.00 2.57
893 928 7.940688 AGCAATCATACCATAATCATCACTCAA 59.059 33.333 0.00 0.00 0.00 3.02
894 929 7.389607 CAGCAATCATACCATAATCATCACTCA 59.610 37.037 0.00 0.00 0.00 3.41
895 930 7.148289 CCAGCAATCATACCATAATCATCACTC 60.148 40.741 0.00 0.00 0.00 3.51
896 931 6.657966 CCAGCAATCATACCATAATCATCACT 59.342 38.462 0.00 0.00 0.00 3.41
898 933 6.781943 TCCAGCAATCATACCATAATCATCA 58.218 36.000 0.00 0.00 0.00 3.07
899 934 7.876936 ATCCAGCAATCATACCATAATCATC 57.123 36.000 0.00 0.00 0.00 2.92
900 935 9.758021 TTAATCCAGCAATCATACCATAATCAT 57.242 29.630 0.00 0.00 0.00 2.45
901 936 9.758021 ATTAATCCAGCAATCATACCATAATCA 57.242 29.630 0.00 0.00 0.00 2.57
912 947 8.985315 ACTCTGAATTATTAATCCAGCAATCA 57.015 30.769 0.00 0.00 0.00 2.57
930 965 9.436957 CCAGTAAAATAGCTTTCTTACTCTGAA 57.563 33.333 0.45 0.00 0.00 3.02
937 972 9.297037 AGCTTTTCCAGTAAAATAGCTTTCTTA 57.703 29.630 0.00 0.00 36.49 2.10
972 1007 1.069090 TGTGACCACGGTGAAGAGC 59.931 57.895 10.28 0.00 0.00 4.09
973 1008 0.600255 GGTGTGACCACGGTGAAGAG 60.600 60.000 10.28 0.00 42.80 2.85
974 1009 1.444250 GGTGTGACCACGGTGAAGA 59.556 57.895 10.28 0.00 42.80 2.87
975 1010 1.597027 GGGTGTGACCACGGTGAAG 60.597 63.158 10.28 0.00 42.80 3.02
976 1011 2.506962 GGGTGTGACCACGGTGAA 59.493 61.111 10.28 0.00 42.80 3.18
977 1012 3.552384 GGGGTGTGACCACGGTGA 61.552 66.667 10.28 0.00 42.80 4.02
978 1013 4.636435 GGGGGTGTGACCACGGTG 62.636 72.222 0.00 0.00 44.60 4.94
980 1015 3.622060 GATGGGGGTGTGACCACGG 62.622 68.421 0.00 0.00 44.60 4.94
981 1016 2.046314 GATGGGGGTGTGACCACG 60.046 66.667 0.00 0.00 44.60 4.94
982 1017 1.863155 ATGGATGGGGGTGTGACCAC 61.863 60.000 0.00 0.00 42.31 4.16
983 1018 1.543642 ATGGATGGGGGTGTGACCA 60.544 57.895 0.00 0.00 41.02 4.02
984 1019 1.076777 CATGGATGGGGGTGTGACC 60.077 63.158 0.00 0.00 37.60 4.02
985 1020 1.754234 GCATGGATGGGGGTGTGAC 60.754 63.158 0.00 0.00 0.00 3.67
986 1021 2.682846 GCATGGATGGGGGTGTGA 59.317 61.111 0.00 0.00 0.00 3.58
987 1022 2.442643 GGCATGGATGGGGGTGTG 60.443 66.667 0.00 0.00 0.00 3.82
988 1023 4.127744 CGGCATGGATGGGGGTGT 62.128 66.667 0.00 0.00 0.00 4.16
992 1027 2.916527 AAAGAGCGGCATGGATGGGG 62.917 60.000 1.45 0.00 0.00 4.96
993 1028 1.039233 AAAAGAGCGGCATGGATGGG 61.039 55.000 1.45 0.00 0.00 4.00
998 1033 1.379044 AGGGAAAAGAGCGGCATGG 60.379 57.895 1.45 0.00 0.00 3.66
1000 1035 0.038166 TTCAGGGAAAAGAGCGGCAT 59.962 50.000 1.45 0.00 0.00 4.40
1001 1036 0.889186 GTTCAGGGAAAAGAGCGGCA 60.889 55.000 1.45 0.00 0.00 5.69
1002 1037 0.889186 TGTTCAGGGAAAAGAGCGGC 60.889 55.000 0.00 0.00 0.00 6.53
1003 1038 0.875059 GTGTTCAGGGAAAAGAGCGG 59.125 55.000 0.00 0.00 0.00 5.52
1005 1040 1.248486 GGGTGTTCAGGGAAAAGAGC 58.752 55.000 0.00 0.00 0.00 4.09
1006 1041 2.656947 TGGGTGTTCAGGGAAAAGAG 57.343 50.000 0.00 0.00 0.00 2.85
1008 1043 2.821969 CTCATGGGTGTTCAGGGAAAAG 59.178 50.000 0.00 0.00 0.00 2.27
1215 1860 5.705609 AAATTGTAGAACGGCAAGATTGT 57.294 34.783 0.00 0.00 0.00 2.71
1278 1924 2.219875 CCTCAGGTGGAGCACTGGT 61.220 63.158 0.00 0.00 42.62 4.00
1419 2065 2.884012 CAACATAAGGTGTGGTTGCAGA 59.116 45.455 0.00 0.00 41.14 4.26
1851 3641 5.733676 TGTGCGCTGATCCATAACATATAT 58.266 37.500 9.73 0.00 0.00 0.86
1946 3766 5.616270 TGCACTACCAATCTGAAACTAACA 58.384 37.500 0.00 0.00 0.00 2.41
3003 4874 6.157211 CGTATATCAACGCTATCCTTTCCTT 58.843 40.000 0.00 0.00 35.87 3.36
3219 5110 2.266055 CCAAGTCCTCCCAGCGAC 59.734 66.667 0.00 0.00 0.00 5.19
3255 5146 5.460646 ACCAGTTACATGAAAAATGCTTCG 58.539 37.500 0.00 0.00 0.00 3.79
3332 5227 3.485877 GCAAAGATCTGTGGCATACGTTC 60.486 47.826 14.88 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.