Multiple sequence alignment - TraesCS7A01G544200

Loading Multiple Alignment...

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 TraesCS7A01G544200 chr7A 100.000 4079 0 0 1 4079 720884208 720888286 0.000000e+00 7533
1 TraesCS7A01G544200 chr7A 83.795 2240 340 13 825 3060 720864168 720861948 0.000000e+00 2104
2 TraesCS7A01G544200 chr7B 93.286 3262 197 13 825 4073 723929356 723932608 0.000000e+00 4791
3 TraesCS7A01G544200 chr7B 88.791 2052 210 9 825 2866 723907865 723909906 0.000000e+00 2497
4 TraesCS7A01G544200 chr7B 85.298 2299 287 29 825 3093 724955757 724953480 0.000000e+00 2326
5 TraesCS7A01G544200 chr7B 83.829 2288 342 16 825 3106 723902772 723900507 0.000000e+00 2150
6 TraesCS7A01G544200 chr7B 83.311 2283 331 31 826 3091 466669073 466671322 0.000000e+00 2060
7 TraesCS7A01G544200 chr7B 99.034 828 7 1 1 828 924255 923429 0.000000e+00 1483
8 TraesCS7A01G544200 chr7B 88.276 1160 93 17 2900 4049 723909906 723911032 0.000000e+00 1349
9 TraesCS7A01G544200 chr7B 79.474 190 37 2 3884 4073 570399898 570399711 2.560000e-27 134
10 TraesCS7A01G544200 chr7D 94.049 3075 170 5 825 3895 625227522 625224457 0.000000e+00 4652
11 TraesCS7A01G544200 chr7D 85.127 2286 295 23 825 3084 625355223 625352957 0.000000e+00 2296
12 TraesCS7A01G544200 chr7D 84.464 2240 324 17 825 3057 625250710 625252932 0.000000e+00 2187
13 TraesCS7A01G544200 chr7D 82.778 2282 344 27 825 3091 448855599 448857846 0.000000e+00 1991
14 TraesCS7A01G544200 chr7D 79.000 200 36 4 3881 4075 220986924 220987122 9.200000e-27 132
15 TraesCS7A01G544200 chr6A 89.941 2873 269 11 827 3692 608493610 608490751 0.000000e+00 3687
16 TraesCS7A01G544200 chr6A 85.405 370 49 5 3709 4075 608490407 608490040 2.980000e-101 379
17 TraesCS7A01G544200 chr1D 81.778 2250 367 27 826 3057 453113523 453115747 0.000000e+00 1844
18 TraesCS7A01G544200 chr1D 83.117 154 23 3 3915 4068 11975922 11975772 1.980000e-28 137
19 TraesCS7A01G544200 chr2A 99.150 824 6 1 1 824 38773144 38773966 0.000000e+00 1482
20 TraesCS7A01G544200 chr2A 98.912 827 7 1 1 825 161811733 161812559 0.000000e+00 1476
21 TraesCS7A01G544200 chr2B 99.029 824 8 0 1 824 543583530 543584353 0.000000e+00 1478
22 TraesCS7A01G544200 chr3B 99.029 824 6 1 1 824 623458100 623457279 0.000000e+00 1476
23 TraesCS7A01G544200 chr3B 80.628 191 34 3 3884 4073 776547992 776548180 1.180000e-30 145
24 TraesCS7A01G544200 chr5B 98.910 826 8 1 1 825 649840773 649839948 0.000000e+00 1474
25 TraesCS7A01G544200 chr5B 98.786 824 8 1 1 824 691233526 691234347 0.000000e+00 1465
26 TraesCS7A01G544200 chr4A 98.909 825 8 1 1 824 712925446 712924622 0.000000e+00 1472
27 TraesCS7A01G544200 chr1A 98.558 832 8 2 1 832 58399585 58400412 0.000000e+00 1467
28 TraesCS7A01G544200 chr1A 79.275 193 32 8 3884 4073 519418763 519418950 1.190000e-25 128
29 TraesCS7A01G544200 chr3D 81.481 189 31 4 3888 4075 495232304 495232119 7.060000e-33 152
30 TraesCS7A01G544200 chr4B 81.122 196 28 6 3880 4073 559843141 559843329 9.130000e-32 148


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 TraesCS7A01G544200 chr7A 720884208 720888286 4078 False 7533 7533 100.0000 1 4079 1 chr7A.!!$F1 4078
1 TraesCS7A01G544200 chr7A 720861948 720864168 2220 True 2104 2104 83.7950 825 3060 1 chr7A.!!$R1 2235
2 TraesCS7A01G544200 chr7B 723929356 723932608 3252 False 4791 4791 93.2860 825 4073 1 chr7B.!!$F2 3248
3 TraesCS7A01G544200 chr7B 724953480 724955757 2277 True 2326 2326 85.2980 825 3093 1 chr7B.!!$R4 2268
4 TraesCS7A01G544200 chr7B 723900507 723902772 2265 True 2150 2150 83.8290 825 3106 1 chr7B.!!$R3 2281
5 TraesCS7A01G544200 chr7B 466669073 466671322 2249 False 2060 2060 83.3110 826 3091 1 chr7B.!!$F1 2265
6 TraesCS7A01G544200 chr7B 723907865 723911032 3167 False 1923 2497 88.5335 825 4049 2 chr7B.!!$F3 3224
7 TraesCS7A01G544200 chr7B 923429 924255 826 True 1483 1483 99.0340 1 828 1 chr7B.!!$R1 827
8 TraesCS7A01G544200 chr7D 625224457 625227522 3065 True 4652 4652 94.0490 825 3895 1 chr7D.!!$R1 3070
9 TraesCS7A01G544200 chr7D 625352957 625355223 2266 True 2296 2296 85.1270 825 3084 1 chr7D.!!$R2 2259
10 TraesCS7A01G544200 chr7D 625250710 625252932 2222 False 2187 2187 84.4640 825 3057 1 chr7D.!!$F3 2232
11 TraesCS7A01G544200 chr7D 448855599 448857846 2247 False 1991 1991 82.7780 825 3091 1 chr7D.!!$F2 2266
12 TraesCS7A01G544200 chr6A 608490040 608493610 3570 True 2033 3687 87.6730 827 4075 2 chr6A.!!$R1 3248
13 TraesCS7A01G544200 chr1D 453113523 453115747 2224 False 1844 1844 81.7780 826 3057 1 chr1D.!!$F1 2231
14 TraesCS7A01G544200 chr2A 38773144 38773966 822 False 1482 1482 99.1500 1 824 1 chr2A.!!$F1 823
15 TraesCS7A01G544200 chr2A 161811733 161812559 826 False 1476 1476 98.9120 1 825 1 chr2A.!!$F2 824
16 TraesCS7A01G544200 chr2B 543583530 543584353 823 False 1478 1478 99.0290 1 824 1 chr2B.!!$F1 823
17 TraesCS7A01G544200 chr3B 623457279 623458100 821 True 1476 1476 99.0290 1 824 1 chr3B.!!$R1 823
18 TraesCS7A01G544200 chr5B 649839948 649840773 825 True 1474 1474 98.9100 1 825 1 chr5B.!!$R1 824
19 TraesCS7A01G544200 chr5B 691233526 691234347 821 False 1465 1465 98.7860 1 824 1 chr5B.!!$F1 823
20 TraesCS7A01G544200 chr4A 712924622 712925446 824 True 1472 1472 98.9090 1 824 1 chr4A.!!$R1 823
21 TraesCS7A01G544200 chr1A 58399585 58400412 827 False 1467 1467 98.5580 1 832 1 chr1A.!!$F1 831

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
272 273 0.105224 TCGCTTCCGACCACTTCAAA 59.895 50.000 0.00 0.0 38.82 2.69 F
954 963 1.139095 CGACTGGCCGTAGAAGACC 59.861 63.158 0.00 0.0 0.00 3.85 F
2086 2119 1.057275 TGTGGCACTAGGGTGTTGGA 61.057 55.000 19.83 0.0 44.65 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1287 1303 0.797542 TGGTGGTATTAAACGCACGC 59.202 50.0 0.0 0.0 32.90 5.34 R
2790 2832 0.249868 CCCAGTCTGAAACACGAGCA 60.250 55.0 0.0 0.0 0.00 4.26 R
3782 4179 0.702902 TACTCCAGAGGGGTCGTTCT 59.297 55.0 0.0 0.0 38.11 3.01 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
272 273 0.105224 TCGCTTCCGACCACTTCAAA 59.895 50.000 0.00 0.00 38.82 2.69
632 638 1.375523 CCTTTAGTCGCGGTTGGCT 60.376 57.895 6.13 0.00 40.44 4.75
954 963 1.139095 CGACTGGCCGTAGAAGACC 59.861 63.158 0.00 0.00 0.00 3.85
1004 1013 3.202097 TGTGACGTCTTCTTCAAATGCA 58.798 40.909 17.92 0.00 0.00 3.96
1055 1071 2.747686 GTCGTCAAGGGCCAAGGA 59.252 61.111 6.18 0.00 0.00 3.36
1056 1072 1.671379 GTCGTCAAGGGCCAAGGAC 60.671 63.158 6.18 9.26 0.00 3.85
1057 1073 2.359975 CGTCAAGGGCCAAGGACC 60.360 66.667 6.18 1.57 45.79 4.46
1114 1130 2.813226 TACCGACACATTGCTGCCCC 62.813 60.000 0.00 0.00 0.00 5.80
1287 1303 9.784531 AGTAATGATATATGGACAAAGAACAGG 57.215 33.333 0.00 0.00 0.00 4.00
1353 1376 6.040391 CAGGGTATTTTCTTGGAAGTGACAAA 59.960 38.462 0.00 0.00 0.00 2.83
1381 1404 1.145571 TAAGGCTGTTGACTGGGGTT 58.854 50.000 0.00 0.00 0.00 4.11
1390 1413 1.462426 TGACTGGGGTTATGGGGTTT 58.538 50.000 0.00 0.00 0.00 3.27
1419 1442 7.148188 CGGAGATTAACATTGGATTATGATGGG 60.148 40.741 0.00 0.00 0.00 4.00
2082 2115 4.316025 AATATTTGTGGCACTAGGGTGT 57.684 40.909 19.83 0.81 44.65 4.16
2086 2119 1.057275 TGTGGCACTAGGGTGTTGGA 61.057 55.000 19.83 0.00 44.65 3.53
2457 2490 7.475299 AGAATGGTTCTTTGGATAAAACCCTA 58.525 34.615 0.00 0.00 36.36 3.53
2790 2832 4.883021 TCTCCTAGAACTACTCATGGGT 57.117 45.455 2.45 2.45 0.00 4.51
3007 3058 3.892284 TGCCTAGAGGAAGACAGTAGAG 58.108 50.000 0.00 0.00 37.39 2.43
3137 3196 8.243426 ACACAACATGTCATGTATGGTTATTTC 58.757 33.333 23.91 0.00 44.07 2.17
3157 3216 6.737254 TTTCTGGATCGAAAACAAGATACC 57.263 37.500 0.00 0.00 30.49 2.73
3203 3262 4.163552 TCGTTGTCATTGTCATCGTAGTC 58.836 43.478 11.98 0.00 32.27 2.59
3222 3282 6.138236 CGTAGTCGTATACTTAGCAAGTTTCG 59.862 42.308 0.56 9.06 42.81 3.46
3234 3294 4.743493 AGCAAGTTTCGCTTTTCTTTTGA 58.257 34.783 0.00 0.00 35.82 2.69
3242 3302 4.278858 TCGCTTTTCTTTTGATTCGTGTG 58.721 39.130 0.00 0.00 0.00 3.82
3255 3315 9.790389 TTTTGATTCGTGTGTAAACTTGTTTAT 57.210 25.926 8.87 0.00 0.00 1.40
3300 3362 3.259123 GGTGTGCCTTGGAATTCTTGAAT 59.741 43.478 5.23 0.00 0.00 2.57
3319 3381 5.056480 TGAATGAATTGAACACTGAGTCGT 58.944 37.500 0.00 0.00 0.00 4.34
3331 3393 5.180271 ACACTGAGTCGTTTTGTAAGGAAA 58.820 37.500 0.00 0.00 30.64 3.13
3429 3492 4.142665 CCATTTGTTGCAGAGAGAGATGTG 60.143 45.833 0.00 0.00 0.00 3.21
3431 3494 3.758755 TGTTGCAGAGAGAGATGTGTT 57.241 42.857 0.00 0.00 0.00 3.32
3454 3517 1.864711 TCGGTTGCAGAAAAAGAGACG 59.135 47.619 0.00 0.00 0.00 4.18
3506 3569 4.322574 GCTCCTCTGCAATGAGCTATATGA 60.323 45.833 19.20 2.27 46.19 2.15
3532 3595 8.017373 ACAGTACTGAATTTCGATTTCACATTG 58.983 33.333 29.30 7.72 0.00 2.82
3544 3607 0.179234 TCACATTGTGACCACACCGT 59.821 50.000 15.41 0.49 45.40 4.83
3664 3731 7.500141 TCAATTAGCACTACTGATAGCAATCA 58.500 34.615 0.00 0.00 39.87 2.57
3670 3737 5.371526 CACTACTGATAGCAATCAACCCAT 58.628 41.667 0.00 0.00 41.57 4.00
3681 3748 4.620567 GCAATCAACCCATTACCAAACTCC 60.621 45.833 0.00 0.00 0.00 3.85
3724 4121 9.015577 TCTTGTGTATTCGTTGTTTCAAATTTC 57.984 29.630 0.00 0.00 0.00 2.17
3810 4207 2.040012 CCCCTCTGGAGTACTATCGCTA 59.960 54.545 0.00 0.00 35.39 4.26
3848 4245 1.550327 TATTTGGTGGGCATTTCGCA 58.450 45.000 0.00 0.00 45.17 5.10
3850 4247 1.112315 TTTGGTGGGCATTTCGCAGT 61.112 50.000 0.00 0.00 45.17 4.40
3920 4321 1.539388 CACATGGTGGCGCTTCTTTTA 59.461 47.619 7.64 0.00 0.00 1.52
3941 4342 1.985159 TCTAAGTGATGGTTGGGTGCT 59.015 47.619 0.00 0.00 0.00 4.40
3942 4343 2.086869 CTAAGTGATGGTTGGGTGCTG 58.913 52.381 0.00 0.00 0.00 4.41
3959 4362 4.464597 GGTGCTGGGGTTTGATATGTTTTA 59.535 41.667 0.00 0.00 0.00 1.52
3960 4363 5.128663 GGTGCTGGGGTTTGATATGTTTTAT 59.871 40.000 0.00 0.00 0.00 1.40
3966 4369 6.325286 TGGGGTTTGATATGTTTTATTAGGCC 59.675 38.462 0.00 0.00 0.00 5.19
3974 4377 8.212312 TGATATGTTTTATTAGGCCGGTTTCTA 58.788 33.333 1.90 0.00 0.00 2.10
4010 4414 5.766150 AAATCATTCGCCCGATCAAAATA 57.234 34.783 0.00 0.00 0.00 1.40
4012 4416 5.766150 ATCATTCGCCCGATCAAAATAAA 57.234 34.783 0.00 0.00 0.00 1.40
4049 4453 9.695526 TCAAAGTTGAATACCTCAATTGAATTG 57.304 29.630 11.54 11.54 45.74 2.32
4075 4479 7.631717 AGAGCTTCAAAATTAGGGAACATAC 57.368 36.000 0.00 0.00 0.00 2.39
4076 4480 6.603599 AGAGCTTCAAAATTAGGGAACATACC 59.396 38.462 0.00 0.00 0.00 2.73
4077 4481 5.357032 AGCTTCAAAATTAGGGAACATACCG 59.643 40.000 0.00 0.00 0.00 4.02
4078 4482 5.355910 GCTTCAAAATTAGGGAACATACCGA 59.644 40.000 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 273 2.912956 TGAACCATCCAGCTAGTTCCTT 59.087 45.455 9.08 0.00 38.24 3.36
632 638 2.821969 ACCTTTAGTCGCGGTTCTTCTA 59.178 45.455 6.13 0.00 0.00 2.10
692 698 3.582780 CTTAAGAACCGCGACTAAAGGT 58.417 45.455 8.23 0.00 40.50 3.50
976 985 4.438148 TGAAGAAGACGTCACATTGTTCA 58.562 39.130 19.50 18.94 34.85 3.18
1004 1013 2.099756 GTCCAACAACTGAGCTTGCTTT 59.900 45.455 0.00 0.00 0.00 3.51
1055 1071 4.646492 GCCAAAGAATGATATCACCTTGGT 59.354 41.667 24.06 10.84 0.00 3.67
1056 1072 4.646040 TGCCAAAGAATGATATCACCTTGG 59.354 41.667 21.59 21.59 0.00 3.61
1057 1073 5.840243 TGCCAAAGAATGATATCACCTTG 57.160 39.130 17.82 13.48 0.00 3.61
1058 1074 6.628844 GCTTTGCCAAAGAATGATATCACCTT 60.629 38.462 21.00 11.43 41.02 3.50
1059 1075 5.163478 GCTTTGCCAAAGAATGATATCACCT 60.163 40.000 21.00 5.61 41.02 4.00
1060 1076 5.045872 GCTTTGCCAAAGAATGATATCACC 58.954 41.667 21.00 3.18 41.02 4.02
1061 1077 5.899299 AGCTTTGCCAAAGAATGATATCAC 58.101 37.500 21.00 0.00 41.02 3.06
1114 1130 4.872124 TGCAGCACTAGTAATGTTCTGATG 59.128 41.667 0.00 0.00 32.00 3.07
1287 1303 0.797542 TGGTGGTATTAAACGCACGC 59.202 50.000 0.00 0.00 32.90 5.34
1353 1376 7.386059 CCCAGTCAACAGCCTTAAAATTTAAT 58.614 34.615 0.00 0.00 0.00 1.40
1381 1404 0.834612 AATCTCCGCGAAACCCCATA 59.165 50.000 8.23 0.00 0.00 2.74
1390 1413 2.971660 TCCAATGTTAATCTCCGCGA 57.028 45.000 8.23 0.00 0.00 5.87
1979 2012 4.997395 GTGATCCACTTTGACTGCTCTTAA 59.003 41.667 0.00 0.00 0.00 1.85
2082 2115 3.509575 CCTCCATTCCGAACAAAATCCAA 59.490 43.478 0.00 0.00 0.00 3.53
2086 2119 1.824852 GCCCTCCATTCCGAACAAAAT 59.175 47.619 0.00 0.00 0.00 1.82
2457 2490 7.664318 CACCCAAGTAACCTTTCACTACTAAAT 59.336 37.037 0.00 0.00 0.00 1.40
2751 2793 4.857509 GAGAACCACTCCGAAGCTATAT 57.142 45.455 0.00 0.00 39.53 0.86
2790 2832 0.249868 CCCAGTCTGAAACACGAGCA 60.250 55.000 0.00 0.00 0.00 4.26
3007 3058 1.347062 TTTTCCATGGTGGGCCTTTC 58.653 50.000 12.58 0.00 38.32 2.62
3106 3165 6.714810 ACCATACATGACATGTTGTGTAAAGT 59.285 34.615 25.34 18.18 41.63 2.66
3137 3196 3.555956 CCGGTATCTTGTTTTCGATCCAG 59.444 47.826 0.00 0.00 0.00 3.86
3157 3216 5.885230 AATAATGCATGATACACATCCCG 57.115 39.130 0.00 0.00 37.07 5.14
3203 3262 5.697848 AAGCGAAACTTGCTAAGTATACG 57.302 39.130 0.00 8.85 43.14 3.06
3222 3282 7.220108 AGTTTACACACGAATCAAAAGAAAAGC 59.780 33.333 0.00 0.00 0.00 3.51
3242 3302 6.372981 CACCCGGTGTAATAAACAAGTTTAC 58.627 40.000 9.64 0.00 40.63 2.01
3255 3315 1.531365 ACGACTCCACCCGGTGTAA 60.531 57.895 16.55 3.44 39.13 2.41
3300 3362 5.123186 ACAAAACGACTCAGTGTTCAATTCA 59.877 36.000 0.00 0.00 0.00 2.57
3354 3416 3.057946 CCAACTCCACAGCTTTTTCTAGC 60.058 47.826 0.00 0.00 41.53 3.42
3429 3492 4.024048 TCTCTTTTTCTGCAACCGATCAAC 60.024 41.667 0.00 0.00 0.00 3.18
3431 3494 3.498397 GTCTCTTTTTCTGCAACCGATCA 59.502 43.478 0.00 0.00 0.00 2.92
3454 3517 1.918609 GGACTCGCGTATGTGAAGTTC 59.081 52.381 5.77 0.00 33.42 3.01
3506 3569 7.672983 ATGTGAAATCGAAATTCAGTACTGT 57.327 32.000 21.99 2.89 37.46 3.55
3532 3595 2.094182 ACATATCTGACGGTGTGGTCAC 60.094 50.000 0.00 0.00 41.76 3.67
3626 3693 5.869888 AGTGCTAATTGAAGACCTTAACTCG 59.130 40.000 0.00 0.00 0.00 4.18
3634 3701 6.422400 GCTATCAGTAGTGCTAATTGAAGACC 59.578 42.308 0.00 0.00 0.00 3.85
3664 3731 1.074889 AGCGGAGTTTGGTAATGGGTT 59.925 47.619 0.00 0.00 0.00 4.11
3700 3767 8.587950 GTGAAATTTGAAACAACGAATACACAA 58.412 29.630 0.00 0.00 34.83 3.33
3724 4121 5.989477 TGTATGGATCCAAAGGACTTAGTG 58.011 41.667 20.67 0.00 32.98 2.74
3782 4179 0.702902 TACTCCAGAGGGGTCGTTCT 59.297 55.000 0.00 0.00 38.11 3.01
3810 4207 6.302269 CAAATATCTAATGGGAAGGAGCAGT 58.698 40.000 0.00 0.00 0.00 4.40
3920 4321 2.578021 AGCACCCAACCATCACTTAGAT 59.422 45.455 0.00 0.00 37.48 1.98
3941 4342 6.325286 GGCCTAATAAAACATATCAAACCCCA 59.675 38.462 0.00 0.00 0.00 4.96
3942 4343 6.516028 CGGCCTAATAAAACATATCAAACCCC 60.516 42.308 0.00 0.00 0.00 4.95
3959 4362 2.193993 ACCAGTAGAAACCGGCCTAAT 58.806 47.619 0.00 0.00 0.00 1.73
3960 4363 1.648116 ACCAGTAGAAACCGGCCTAA 58.352 50.000 0.00 0.00 0.00 2.69
3966 4369 3.670625 TGGAATCAACCAGTAGAAACCG 58.329 45.455 0.00 0.00 34.77 4.44
3985 4388 1.675483 TGATCGGGCGAATGATTTTGG 59.325 47.619 0.00 0.00 0.00 3.28
4049 4453 6.575162 TGTTCCCTAATTTTGAAGCTCTTC 57.425 37.500 2.80 2.80 39.91 2.87


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

AutoCloner maintained by Alex Coulton.