Multiple sequence alignment - TraesCS7D01G140300

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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 TraesCS7D01G140300 chr7D 100.000 3029 0 0 1 3029 89721639 89724667 0.000000e+00 5594
1 TraesCS7D01G140300 chr7A 94.424 2708 102 23 1 2691 90650856 90653531 0.000000e+00 4119
2 TraesCS7D01G140300 chr7A 95.968 124 5 0 2682 2805 90654981 90655104 5.120000e-48 202
3 TraesCS7D01G140300 chr7A 92.969 128 7 2 2901 3026 90658049 90658176 5.160000e-43 185
4 TraesCS7D01G140300 chr7B 95.631 2083 62 10 1 2082 40399228 40401282 0.000000e+00 3315
5 TraesCS7D01G140300 chr7B 86.809 705 34 15 2067 2758 40401304 40401962 0.000000e+00 732
6 TraesCS7D01G140300 chr7B 96.273 161 5 1 2857 3016 40402157 40402317 2.320000e-66 263


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 TraesCS7D01G140300 chr7D 89721639 89724667 3028 False 5594.000000 5594 100.000000 1 3029 1 chr7D.!!$F1 3028
1 TraesCS7D01G140300 chr7A 90650856 90658176 7320 False 1502.000000 4119 94.453667 1 3026 3 chr7A.!!$F1 3025
2 TraesCS7D01G140300 chr7B 40399228 40402317 3089 False 1436.666667 3315 92.904333 1 3016 3 chr7B.!!$F1 3015

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
119 121 1.222115 GCGGTCGTGCAAACTCTCTT 61.222 55.0 0.0 0.0 34.15 2.85 F
1101 1104 1.237285 ACGCCATCACCAAGTTCAGC 61.237 55.0 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1452 1455 0.391661 CAACTGCCCACGAGTATGCT 60.392 55.0 0.0 0.0 0.0 3.79 R
2146 2186 0.606130 TGATGTGAGTGCGTGCCATT 60.606 50.0 0.0 0.0 0.0 3.16 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
45 47 2.302733 TGTCTGTCCTCTATGCAGCAAA 59.697 45.455 0.00 0.00 0.00 3.68
119 121 1.222115 GCGGTCGTGCAAACTCTCTT 61.222 55.000 0.00 0.00 34.15 2.85
120 122 1.933500 GCGGTCGTGCAAACTCTCTTA 60.934 52.381 0.00 0.00 34.15 2.10
121 123 2.607187 CGGTCGTGCAAACTCTCTTAT 58.393 47.619 0.00 0.00 0.00 1.73
122 124 2.599082 CGGTCGTGCAAACTCTCTTATC 59.401 50.000 0.00 0.00 0.00 1.75
123 125 3.585862 GGTCGTGCAAACTCTCTTATCA 58.414 45.455 0.00 0.00 0.00 2.15
124 126 3.368236 GGTCGTGCAAACTCTCTTATCAC 59.632 47.826 0.00 0.00 0.00 3.06
125 127 3.987868 GTCGTGCAAACTCTCTTATCACA 59.012 43.478 0.00 0.00 0.00 3.58
126 128 4.627467 GTCGTGCAAACTCTCTTATCACAT 59.373 41.667 0.00 0.00 0.00 3.21
127 129 5.120830 GTCGTGCAAACTCTCTTATCACATT 59.879 40.000 0.00 0.00 0.00 2.71
128 130 5.700832 TCGTGCAAACTCTCTTATCACATTT 59.299 36.000 0.00 0.00 0.00 2.32
129 131 5.791974 CGTGCAAACTCTCTTATCACATTTG 59.208 40.000 0.00 0.00 0.00 2.32
130 132 6.347644 CGTGCAAACTCTCTTATCACATTTGA 60.348 38.462 0.00 0.00 35.73 2.69
131 133 7.533426 GTGCAAACTCTCTTATCACATTTGAT 58.467 34.615 0.00 0.00 45.04 2.57
132 134 8.025445 GTGCAAACTCTCTTATCACATTTGATT 58.975 33.333 0.00 0.00 39.66 2.57
259 261 9.099454 GAGTGTATTTTTAGAAGATCCGTCAAT 57.901 33.333 0.00 0.00 0.00 2.57
353 355 9.218440 CATTTTTAAATTAACACCCTTCATGCT 57.782 29.630 0.00 0.00 0.00 3.79
397 399 8.131731 ACTCATTAGCTTTTGACTTCTCAAAAC 58.868 33.333 0.00 3.62 46.79 2.43
517 519 1.723288 TGGTCACCATGTGTCACCTA 58.277 50.000 0.00 0.00 33.38 3.08
575 577 7.673180 TGGCTTAAACTACTACAAGTACATGT 58.327 34.615 8.98 8.98 37.32 3.21
651 654 6.127897 CCCTGTTTACCTTCATTGAGATGTTC 60.128 42.308 0.00 0.00 34.77 3.18
838 841 4.326826 AGTCACACGAATCATGAATGGTT 58.673 39.130 0.00 0.00 32.92 3.67
854 857 3.029320 TGGTTTCATTTCTGCACATGC 57.971 42.857 0.00 0.00 42.50 4.06
869 872 5.496133 GCACATGCATTCAGATAGTCTTT 57.504 39.130 0.00 0.00 41.59 2.52
1056 1059 6.989759 TCGTTTTAGGATATGCTTTATGCTCA 59.010 34.615 0.65 0.00 43.37 4.26
1101 1104 1.237285 ACGCCATCACCAAGTTCAGC 61.237 55.000 0.00 0.00 0.00 4.26
1333 1336 2.045536 CCCCTCTGCTGGTTGCTC 60.046 66.667 0.00 0.00 43.37 4.26
1689 1692 1.998257 CGCGTTTGTTGCTGTGTCG 60.998 57.895 0.00 0.00 0.00 4.35
1758 1761 1.301716 GAAAGCGGTCTCTGCCACA 60.302 57.895 0.00 0.00 0.00 4.17
2065 2068 4.023963 GCAGGTACTCAGTTTTGTCCTTTC 60.024 45.833 0.00 0.00 34.60 2.62
2076 2116 6.036735 CAGTTTTGTCCTTTCGTCTAGAACAA 59.963 38.462 0.00 0.00 38.83 2.83
2106 2146 8.009974 CCGAGTCTTCAAAACTTGTTATAACTG 58.990 37.037 16.33 11.32 0.00 3.16
2146 2186 7.815840 TCAGGATGTATTTTGTTGTTGAAGA 57.184 32.000 0.00 0.00 37.40 2.87
2185 2225 7.063426 CACATCACAAGTTACATGTACACTAGG 59.937 40.741 4.68 10.33 0.00 3.02
2187 2227 6.920817 TCACAAGTTACATGTACACTAGGAG 58.079 40.000 4.68 7.59 0.00 3.69
2262 2302 4.216411 TGTTTACTAGAATCACCTGCCC 57.784 45.455 0.00 0.00 0.00 5.36
2297 2338 7.473366 ACATGTAGTCGTTTAGTGATGTCTAG 58.527 38.462 0.00 0.00 0.00 2.43
2308 2349 2.017782 TGATGTCTAGTGTCGCTCCTC 58.982 52.381 0.00 0.00 0.00 3.71
2309 2350 2.017782 GATGTCTAGTGTCGCTCCTCA 58.982 52.381 0.00 0.00 0.00 3.86
2355 2398 1.264288 GCAGCAACAACTCTGTACACC 59.736 52.381 0.00 0.00 33.45 4.16
2372 2415 6.999950 TGTACACCGCATATTATTGGTAGAT 58.000 36.000 0.00 0.00 32.29 1.98
2420 2463 1.191096 CGGTTAATCATTTGCAGCGC 58.809 50.000 0.00 0.00 0.00 5.92
2430 2475 3.198236 TTGCAGCGCAAACCTCAGC 62.198 57.895 11.47 0.51 45.96 4.26
2439 2484 1.067565 GCAAACCTCAGCCTTAAAGCC 60.068 52.381 0.00 0.00 0.00 4.35
2440 2485 1.546029 CAAACCTCAGCCTTAAAGCCC 59.454 52.381 0.00 0.00 0.00 5.19
2444 2489 0.462759 CTCAGCCTTAAAGCCCGAGG 60.463 60.000 5.54 0.00 32.04 4.63
2470 2515 1.295792 TTCCGGCGATGTAGAATTGC 58.704 50.000 9.30 0.00 0.00 3.56
2492 2548 6.166279 TGCTGAGTACTCTCTTTTACAATGG 58.834 40.000 23.01 0.00 40.98 3.16
2494 2550 7.039293 TGCTGAGTACTCTCTTTTACAATGGTA 60.039 37.037 23.01 0.00 40.98 3.25
2538 2606 5.355071 TCAGCTTCATGCATTGGTACTTTAG 59.645 40.000 0.00 0.00 45.94 1.85
2541 2609 5.727791 GCTTCATGCATTGGTACTTTAGTCG 60.728 44.000 0.00 0.00 42.31 4.18
2549 2617 6.074463 GCATTGGTACTTTAGTCGCATAGTAC 60.074 42.308 0.00 0.00 41.25 2.73
2550 2618 5.160699 TGGTACTTTAGTCGCATAGTACG 57.839 43.478 0.00 0.00 42.32 3.67
2656 2724 7.295340 TGGCTCTTAATACTATCTGGACAGTA 58.705 38.462 0.00 0.00 0.00 2.74
2693 4220 7.525688 ACATCATGACGACTAAGTTTACATG 57.474 36.000 0.00 0.00 36.17 3.21
2758 4285 5.819379 TGTAATCTCAGGCTCACAAATGATC 59.181 40.000 0.00 0.00 33.22 2.92
2782 4309 5.416947 GTGTGTCGATGGTTAGGATAGTTT 58.583 41.667 0.00 0.00 0.00 2.66
2814 4341 5.599999 CTAGCCCGCTAGGATTATACATT 57.400 43.478 14.75 0.00 41.58 2.71
2815 4342 4.473477 AGCCCGCTAGGATTATACATTC 57.527 45.455 0.00 0.00 41.02 2.67
2816 4343 3.838317 AGCCCGCTAGGATTATACATTCA 59.162 43.478 0.00 0.00 41.02 2.57
2817 4344 4.081420 AGCCCGCTAGGATTATACATTCAG 60.081 45.833 0.00 0.00 41.02 3.02
2818 4345 4.184629 CCCGCTAGGATTATACATTCAGC 58.815 47.826 0.00 0.00 41.02 4.26
2819 4346 4.322725 CCCGCTAGGATTATACATTCAGCA 60.323 45.833 0.00 0.00 41.02 4.41
2820 4347 4.867047 CCGCTAGGATTATACATTCAGCAG 59.133 45.833 0.00 0.00 41.02 4.24
2821 4348 5.336770 CCGCTAGGATTATACATTCAGCAGA 60.337 44.000 0.00 0.00 41.02 4.26
2822 4349 5.804473 CGCTAGGATTATACATTCAGCAGAG 59.196 44.000 0.00 0.00 0.00 3.35
2823 4350 6.349694 CGCTAGGATTATACATTCAGCAGAGA 60.350 42.308 0.00 0.00 0.00 3.10
2824 4351 7.555087 GCTAGGATTATACATTCAGCAGAGAT 58.445 38.462 0.00 0.00 0.00 2.75
2825 4352 7.492020 GCTAGGATTATACATTCAGCAGAGATG 59.508 40.741 0.00 0.00 0.00 2.90
2826 4353 7.550597 AGGATTATACATTCAGCAGAGATGA 57.449 36.000 7.79 0.00 0.00 2.92
2833 4360 3.599730 TTCAGCAGAGATGATTGACGT 57.400 42.857 0.00 0.00 0.00 4.34
3009 7408 6.358030 GTGTTTCTCAAAAAGATGATCGTGTG 59.642 38.462 0.00 0.00 32.82 3.82
3021 7420 0.034896 ATCGTGTGCTTCTTCGGGTT 59.965 50.000 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 3.500343 CTTCTTGACCTGGAAAATGGGT 58.500 45.455 0.00 0.00 35.89 4.51
126 128 9.056005 CGGAACCAATATGATAAGAGAATCAAA 57.944 33.333 0.00 0.00 39.25 2.69
127 129 8.210946 ACGGAACCAATATGATAAGAGAATCAA 58.789 33.333 0.00 0.00 39.25 2.57
128 130 7.735917 ACGGAACCAATATGATAAGAGAATCA 58.264 34.615 0.00 0.00 40.07 2.57
129 131 7.872993 TGACGGAACCAATATGATAAGAGAATC 59.127 37.037 0.00 0.00 0.00 2.52
130 132 7.657761 GTGACGGAACCAATATGATAAGAGAAT 59.342 37.037 0.00 0.00 0.00 2.40
131 133 6.984474 GTGACGGAACCAATATGATAAGAGAA 59.016 38.462 0.00 0.00 0.00 2.87
132 134 6.323996 AGTGACGGAACCAATATGATAAGAGA 59.676 38.462 0.00 0.00 0.00 3.10
165 167 3.252458 AGCAACAGGTTGTTCGGTAATTC 59.748 43.478 13.19 0.00 38.77 2.17
231 233 7.759886 TGACGGATCTTCTAAAAATACACTCAG 59.240 37.037 0.00 0.00 0.00 3.35
259 261 4.515191 GCTTTGACCGGCATGAAAGATATA 59.485 41.667 15.54 0.00 0.00 0.86
384 386 5.129634 TGCCAATACAGTTTTGAGAAGTCA 58.870 37.500 5.37 0.00 0.00 3.41
421 423 7.232118 TGATAATCGATTGCCTATCTCTGAA 57.768 36.000 20.87 0.00 0.00 3.02
500 502 3.525537 CAGATAGGTGACACATGGTGAC 58.474 50.000 8.08 0.00 36.96 3.67
517 519 4.098894 ACATCAATTTCCTTTGCCCAGAT 58.901 39.130 0.00 0.00 0.00 2.90
651 654 4.392921 CACCTCCTACAATCTACAGGTG 57.607 50.000 1.66 1.66 43.69 4.00
854 857 6.492007 ACAAGTGCAAAGACTATCTGAATG 57.508 37.500 0.00 0.00 0.00 2.67
869 872 1.677576 CTGCTCTGGAAAACAAGTGCA 59.322 47.619 0.00 0.00 0.00 4.57
1056 1059 3.191162 TGTTAATGATCGCAAGCAAGCTT 59.809 39.130 0.59 0.59 36.60 3.74
1101 1104 1.002274 AGTGAGGAGGCCAGGGTAG 59.998 63.158 5.01 0.00 0.00 3.18
1333 1336 1.374758 GGAAGGTGGTGTCAGCGAG 60.375 63.158 0.00 0.00 45.29 5.03
1452 1455 0.391661 CAACTGCCCACGAGTATGCT 60.392 55.000 0.00 0.00 0.00 3.79
1689 1692 3.414700 CCGAACACGCAGGACAGC 61.415 66.667 0.00 0.00 0.00 4.40
1758 1761 1.005394 CCCCGTCACTGTAAACGCT 60.005 57.895 8.81 0.00 37.56 5.07
2065 2068 2.978489 GACTCGGTGTTTGTTCTAGACG 59.022 50.000 0.00 0.00 0.00 4.18
2076 2116 4.007659 ACAAGTTTTGAAGACTCGGTGTT 58.992 39.130 0.00 0.00 0.00 3.32
2106 2146 5.124457 ACATCCTGAATTGTCTGTATTGCAC 59.876 40.000 0.00 0.00 0.00 4.57
2146 2186 0.606130 TGATGTGAGTGCGTGCCATT 60.606 50.000 0.00 0.00 0.00 3.16
2262 2302 8.495949 ACTAAACGACTACATGTTCATGAAAAG 58.504 33.333 17.96 13.51 0.00 2.27
2320 2361 1.575576 GCTGCTGCAGACAACAGAGG 61.576 60.000 32.30 3.79 41.62 3.69
2355 2398 9.383519 AGGTGATTTATCTACCAATAATATGCG 57.616 33.333 11.36 0.00 36.94 4.73
2372 2415 6.058833 TGCTGTAAACTGTTGAGGTGATTTA 58.941 36.000 0.00 0.00 0.00 1.40
2420 2463 1.546029 GGGCTTTAAGGCTGAGGTTTG 59.454 52.381 17.78 0.00 41.09 2.93
2430 2475 2.420058 AATCACCTCGGGCTTTAAGG 57.580 50.000 0.00 0.00 36.21 2.69
2439 2484 1.800681 GCCGGAAAAATCACCTCGG 59.199 57.895 5.05 0.00 40.33 4.63
2440 2485 1.017177 TCGCCGGAAAAATCACCTCG 61.017 55.000 5.05 0.00 0.00 4.63
2444 2489 2.933906 TCTACATCGCCGGAAAAATCAC 59.066 45.455 5.05 0.00 0.00 3.06
2513 2581 3.012518 AGTACCAATGCATGAAGCTGAC 58.987 45.455 0.00 0.00 45.94 3.51
2538 2606 4.012319 TCAAAGAGACGTACTATGCGAC 57.988 45.455 0.00 0.00 0.00 5.19
2541 2609 4.933330 TCCATCAAAGAGACGTACTATGC 58.067 43.478 0.00 0.00 0.00 3.14
2549 2617 2.254459 CGTCACTCCATCAAAGAGACG 58.746 52.381 8.30 8.30 46.07 4.18
2550 2618 2.028930 ACCGTCACTCCATCAAAGAGAC 60.029 50.000 0.00 0.00 35.27 3.36
2656 2724 6.258727 GTCGTCATGATGTATTCATTTGGACT 59.741 38.462 14.52 0.00 42.62 3.85
2670 2738 7.394099 CACATGTAAACTTAGTCGTCATGATG 58.606 38.462 20.82 8.74 36.23 3.07
2758 4285 2.579207 ATCCTAACCATCGACACACG 57.421 50.000 0.00 0.00 44.09 4.49
2782 4309 4.041762 CGGGCTAGGGGGCACAAA 62.042 66.667 0.00 0.00 42.84 2.83
2801 4328 8.655935 TCATCTCTGCTGAATGTATAATCCTA 57.344 34.615 12.15 0.00 0.00 2.94
2805 4332 9.217278 GTCAATCATCTCTGCTGAATGTATAAT 57.783 33.333 12.15 1.73 0.00 1.28
2806 4333 7.383300 CGTCAATCATCTCTGCTGAATGTATAA 59.617 37.037 12.15 0.09 0.00 0.98
2807 4334 6.865205 CGTCAATCATCTCTGCTGAATGTATA 59.135 38.462 12.15 0.33 0.00 1.47
2808 4335 5.695363 CGTCAATCATCTCTGCTGAATGTAT 59.305 40.000 12.15 5.84 0.00 2.29
2809 4336 5.045872 CGTCAATCATCTCTGCTGAATGTA 58.954 41.667 12.15 4.47 0.00 2.29
2810 4337 3.869832 CGTCAATCATCTCTGCTGAATGT 59.130 43.478 12.15 2.82 0.00 2.71
2811 4338 3.869832 ACGTCAATCATCTCTGCTGAATG 59.130 43.478 0.00 2.73 0.00 2.67
2812 4339 4.134379 ACGTCAATCATCTCTGCTGAAT 57.866 40.909 0.00 0.00 0.00 2.57
2813 4340 3.599730 ACGTCAATCATCTCTGCTGAA 57.400 42.857 0.00 0.00 0.00 3.02
2814 4341 3.599730 AACGTCAATCATCTCTGCTGA 57.400 42.857 0.00 0.00 0.00 4.26
2815 4342 3.241900 CGAAACGTCAATCATCTCTGCTG 60.242 47.826 0.00 0.00 0.00 4.41
2816 4343 2.926200 CGAAACGTCAATCATCTCTGCT 59.074 45.455 0.00 0.00 0.00 4.24
2817 4344 2.029728 CCGAAACGTCAATCATCTCTGC 59.970 50.000 0.00 0.00 0.00 4.26
2818 4345 3.061295 CACCGAAACGTCAATCATCTCTG 59.939 47.826 0.00 0.00 0.00 3.35
2819 4346 3.254060 CACCGAAACGTCAATCATCTCT 58.746 45.455 0.00 0.00 0.00 3.10
2820 4347 2.993899 ACACCGAAACGTCAATCATCTC 59.006 45.455 0.00 0.00 0.00 2.75
2821 4348 2.736721 CACACCGAAACGTCAATCATCT 59.263 45.455 0.00 0.00 0.00 2.90
2822 4349 2.478894 ACACACCGAAACGTCAATCATC 59.521 45.455 0.00 0.00 0.00 2.92
2823 4350 2.489971 ACACACCGAAACGTCAATCAT 58.510 42.857 0.00 0.00 0.00 2.45
2824 4351 1.942677 ACACACCGAAACGTCAATCA 58.057 45.000 0.00 0.00 0.00 2.57
2825 4352 4.657075 ATAACACACCGAAACGTCAATC 57.343 40.909 0.00 0.00 0.00 2.67
2826 4353 6.542574 TTAATAACACACCGAAACGTCAAT 57.457 33.333 0.00 0.00 0.00 2.57
2833 4360 7.455641 AATCCACATTAATAACACACCGAAA 57.544 32.000 0.00 0.00 0.00 3.46
2970 7368 1.203523 GAAACACCAAGGCACAACACA 59.796 47.619 0.00 0.00 0.00 3.72
2971 7369 1.476488 AGAAACACCAAGGCACAACAC 59.524 47.619 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.