Multiple sequence alignment - TraesCS7A01G255200

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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 TraesCS7A01G255200 chr7A 100.000 2978 0 0 1 2978 242949453 242946476 0.000000e+00 5500.0
1 TraesCS7A01G255200 chr7D 94.600 2315 81 14 1 2308 230380939 230378662 0.000000e+00 3542.0
2 TraesCS7A01G255200 chr7D 93.093 666 28 4 2309 2970 230378598 230377947 0.000000e+00 959.0
3 TraesCS7A01G255200 chr7B 94.965 1569 63 3 745 2308 201261495 201259938 0.000000e+00 2446.0
4 TraesCS7A01G255200 chr7B 91.395 674 32 4 2309 2978 201259873 201259222 0.000000e+00 900.0
5 TraesCS7A01G255200 chr3D 76.970 165 32 6 1415 1573 579621760 579621924 4.090000e-14 89.8
6 TraesCS7A01G255200 chr5B 91.667 48 4 0 1526 1573 40459062 40459109 1.920000e-07 67.6
7 TraesCS7A01G255200 chr5B 91.667 48 4 0 1526 1573 40776166 40776213 1.920000e-07 67.6
8 TraesCS7A01G255200 chr5A 91.667 48 4 0 1526 1573 32993189 32993236 1.920000e-07 67.6
9 TraesCS7A01G255200 chr3B 74.850 167 33 6 1415 1573 735076405 735076240 1.920000e-07 67.6
10 TraesCS7A01G255200 chr1A 97.297 37 1 0 262 298 7175596 7175632 2.480000e-06 63.9
11 TraesCS7A01G255200 chr5D 89.583 48 5 0 1526 1573 43100950 43100997 8.910000e-06 62.1
12 TraesCS7A01G255200 chr3A 80.769 78 11 4 1498 1573 634666993 634666918 1.150000e-04 58.4


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 TraesCS7A01G255200 chr7A 242946476 242949453 2977 True 5500.0 5500 100.0000 1 2978 1 chr7A.!!$R1 2977
1 TraesCS7A01G255200 chr7D 230377947 230380939 2992 True 2250.5 3542 93.8465 1 2970 2 chr7D.!!$R1 2969
2 TraesCS7A01G255200 chr7B 201259222 201261495 2273 True 1673.0 2446 93.1800 745 2978 2 chr7B.!!$R1 2233

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
496 500 1.636148 AGCAATGGCATTGTTGTCCT 58.364 45.0 33.64 22.03 44.61 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 2283 0.882042 AAGCTTCAGGACAGTGTGCG 60.882 55.0 9.3 4.83 0.0 5.34 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
18 19 3.248043 TCCCAAAAGATGCGACCAG 57.752 52.632 0.00 0.00 0.00 4.00
198 199 2.050077 GCAAAGTGCGGGCTTCAC 60.050 61.111 2.29 2.29 31.71 3.18
282 283 4.499188 CCGAGTTATAATCGAGAGGCACAA 60.499 45.833 14.77 0.00 42.76 3.33
316 317 2.993937 TGGGGAACTAATTAAGCCACG 58.006 47.619 0.00 0.00 0.00 4.94
341 342 5.743398 CCGCAAAACAATAATACATGACTGG 59.257 40.000 0.00 0.00 0.00 4.00
495 499 3.591196 TTAGCAATGGCATTGTTGTCC 57.409 42.857 33.64 20.41 44.61 4.02
496 500 1.636148 AGCAATGGCATTGTTGTCCT 58.364 45.000 33.64 22.03 44.61 3.85
547 551 3.708631 TGGTGTTTTCAATGTGGGTGAAT 59.291 39.130 0.00 0.00 35.03 2.57
617 623 3.861263 GACGCGGGTGGAATTCGC 61.861 66.667 10.96 0.00 45.15 4.70
645 651 2.257371 CGTTCAGAAGTCGGCGGA 59.743 61.111 7.21 0.00 0.00 5.54
835 841 5.660864 CCCTACCTCTTCTGATCTCTTTTCT 59.339 44.000 0.00 0.00 0.00 2.52
875 885 9.737427 ATATATACGGTCGATTCAGATTGATTC 57.263 33.333 0.00 0.00 0.00 2.52
911 921 7.384660 GGAGTCAGATTGATATAGAGTTTGCTG 59.615 40.741 0.00 0.00 0.00 4.41
1048 1058 7.230712 AGTTCGAACTGGAATATTCAAAAACCT 59.769 33.333 29.24 0.00 37.98 3.50
1129 1139 6.726490 TCTGGAAGATATACTGTTACCCAC 57.274 41.667 0.00 0.00 38.67 4.61
1263 1273 0.314935 CTGGGCGTGCAAAAAGATGT 59.685 50.000 0.00 0.00 0.00 3.06
1374 1384 2.422127 CCGGAAAGGATGCGTTACATTT 59.578 45.455 0.00 0.00 45.00 2.32
1420 1430 1.677966 AGCTCCATTGCTGTGCCAG 60.678 57.895 0.00 0.00 42.33 4.85
1515 1525 1.709760 CGAGACGTTTCATGCGCAT 59.290 52.632 19.28 19.28 0.00 4.73
1617 1627 1.067635 ACGCTGCATGAAATTGAACCC 60.068 47.619 0.00 0.00 0.00 4.11
1618 1628 1.632422 GCTGCATGAAATTGAACCCG 58.368 50.000 0.00 0.00 0.00 5.28
1641 1651 2.619646 GGTGTTTAAAACCCTGCTTCGA 59.380 45.455 0.00 0.00 0.00 3.71
2010 2020 4.234550 AGTGGGATGCATCTCCACTTATA 58.765 43.478 37.99 16.85 46.72 0.98
2017 2027 6.128063 GGATGCATCTCCACTTATATTTCAGC 60.128 42.308 25.28 0.00 35.24 4.26
2088 2098 6.432190 TGGGGACTACTATATCATATGGGT 57.568 41.667 2.13 0.00 0.00 4.51
2127 2137 2.819608 TCCTTTTGCAGCACTGGATTAC 59.180 45.455 0.00 0.00 0.00 1.89
2181 2192 2.576648 AGTAAGGGGACATGGAGGAAAC 59.423 50.000 0.00 0.00 0.00 2.78
2190 2201 1.278127 CATGGAGGAAACCGTGGTACT 59.722 52.381 0.00 0.00 41.64 2.73
2191 2202 2.307496 TGGAGGAAACCGTGGTACTA 57.693 50.000 0.00 0.00 0.00 1.82
2217 2228 2.800881 TACAGAGCTATGGATGTGCG 57.199 50.000 13.85 0.00 0.00 5.34
2226 2237 2.821366 GGATGTGCGCTGTCCTGG 60.821 66.667 9.73 0.00 0.00 4.45
2251 2262 3.323751 TTGTAGGCTACTTTCGGTTCC 57.676 47.619 24.07 0.00 0.00 3.62
2272 2283 1.404583 GCACCATTTTGTCCTGGATGC 60.405 52.381 0.00 0.00 36.35 3.91
2296 2309 3.129287 CACACTGTCCTGAAGCTTGTTTT 59.871 43.478 2.10 0.00 0.00 2.43
2297 2310 3.763897 ACACTGTCCTGAAGCTTGTTTTT 59.236 39.130 2.10 0.00 0.00 1.94
2324 2401 6.195600 TGTCCATATGGTCCCTTATAAACC 57.804 41.667 21.28 0.00 36.34 3.27
2364 2441 6.193514 AGTTTGGTTTTGCAATGAAAAAGG 57.806 33.333 0.00 0.00 0.00 3.11
2365 2442 5.709631 AGTTTGGTTTTGCAATGAAAAAGGT 59.290 32.000 0.00 0.00 0.00 3.50
2372 2449 1.799544 CAATGAAAAAGGTGCTGGGC 58.200 50.000 0.00 0.00 0.00 5.36
2411 2488 7.448161 TCTTCAGTTAAAATGAGAGAATTGCCA 59.552 33.333 0.00 0.00 0.00 4.92
2475 2561 9.055248 CATGATTTTCTAACAATCGTTTCACTC 57.945 33.333 0.00 0.00 36.52 3.51
2476 2562 8.378172 TGATTTTCTAACAATCGTTTCACTCT 57.622 30.769 0.00 0.00 36.52 3.24
2477 2563 8.495949 TGATTTTCTAACAATCGTTTCACTCTC 58.504 33.333 0.00 0.00 36.52 3.20
2478 2564 8.608844 ATTTTCTAACAATCGTTTCACTCTCT 57.391 30.769 0.00 0.00 36.52 3.10
2479 2565 8.433421 TTTTCTAACAATCGTTTCACTCTCTT 57.567 30.769 0.00 0.00 36.52 2.85
2480 2566 9.537192 TTTTCTAACAATCGTTTCACTCTCTTA 57.463 29.630 0.00 0.00 36.52 2.10
2481 2567 9.537192 TTTCTAACAATCGTTTCACTCTCTTAA 57.463 29.630 0.00 0.00 36.52 1.85
2482 2568 8.516811 TCTAACAATCGTTTCACTCTCTTAAC 57.483 34.615 0.00 0.00 36.52 2.01
2483 2569 8.358148 TCTAACAATCGTTTCACTCTCTTAACT 58.642 33.333 0.00 0.00 36.52 2.24
2535 2621 9.865321 TTATCGAAAACCATATATAGCTACCAC 57.135 33.333 0.00 0.00 0.00 4.16
2536 2622 7.534723 TCGAAAACCATATATAGCTACCACT 57.465 36.000 0.00 0.00 0.00 4.00
2537 2623 7.600065 TCGAAAACCATATATAGCTACCACTC 58.400 38.462 0.00 0.00 0.00 3.51
2538 2624 6.812160 CGAAAACCATATATAGCTACCACTCC 59.188 42.308 0.00 0.00 0.00 3.85
2539 2625 7.524863 CGAAAACCATATATAGCTACCACTCCA 60.525 40.741 0.00 0.00 0.00 3.86
2540 2626 7.814693 AAACCATATATAGCTACCACTCCAT 57.185 36.000 0.00 0.00 0.00 3.41
2541 2627 7.425224 AACCATATATAGCTACCACTCCATC 57.575 40.000 0.00 0.00 0.00 3.51
2542 2628 6.746894 ACCATATATAGCTACCACTCCATCT 58.253 40.000 0.00 0.00 0.00 2.90
2543 2629 6.836527 ACCATATATAGCTACCACTCCATCTC 59.163 42.308 0.00 0.00 0.00 2.75
2544 2630 6.266558 CCATATATAGCTACCACTCCATCTCC 59.733 46.154 0.00 0.00 0.00 3.71
2582 2668 0.319900 AGCCAACACTAGCACGTCTG 60.320 55.000 0.00 0.00 0.00 3.51
2633 2719 2.929301 TCCTTACTTCATTCCCCTGGT 58.071 47.619 0.00 0.00 0.00 4.00
2635 2721 4.641868 TCCTTACTTCATTCCCCTGGTAT 58.358 43.478 0.00 0.00 0.00 2.73
2636 2722 5.043762 TCCTTACTTCATTCCCCTGGTATT 58.956 41.667 0.00 0.00 0.00 1.89
2646 2732 3.747852 TCCCCTGGTATTTCATCCTTCT 58.252 45.455 0.00 0.00 0.00 2.85
2675 2761 3.710209 AGACCCTTTCCTCTCATGTTG 57.290 47.619 0.00 0.00 0.00 3.33
2748 2837 3.377172 GCTATTCACCTTACGTTTGCCAT 59.623 43.478 0.00 0.00 0.00 4.40
2796 2885 3.157881 CCTTTCCTTTCCCCTTGTTCTC 58.842 50.000 0.00 0.00 0.00 2.87
2807 2896 1.143305 CTTGTTCTCCAGTGTCGCAG 58.857 55.000 0.00 0.00 0.00 5.18
2882 2971 2.158579 GGGAAGGTGGTGGTTGTTCTAA 60.159 50.000 0.00 0.00 0.00 2.10
2897 2986 7.505585 TGGTTGTTCTAAGATTTTGGAGACATT 59.494 33.333 0.00 0.00 42.32 2.71
2898 2987 8.023706 GGTTGTTCTAAGATTTTGGAGACATTC 58.976 37.037 0.00 0.00 42.32 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 5.047377 TCCAGGACAAATAAGGCAAATTGAC 60.047 40.000 0.00 0.00 0.00 3.18
178 179 1.234615 TGAAGCCCGCACTTTGCTAC 61.235 55.000 0.00 0.00 42.25 3.58
210 211 4.156008 ACCTCGCAAAAATAGGTTCATCAC 59.844 41.667 0.00 0.00 40.82 3.06
260 261 4.224715 TGTGCCTCTCGATTATAACTCG 57.775 45.455 9.60 9.60 37.47 4.18
316 317 5.229887 CAGTCATGTATTATTGTTTTGCGGC 59.770 40.000 0.00 0.00 0.00 6.53
446 450 6.990939 AGTATTCCCTAAATTACTCCTTTCGC 59.009 38.462 0.00 0.00 0.00 4.70
447 451 8.422566 AGAGTATTCCCTAAATTACTCCTTTCG 58.577 37.037 5.56 0.00 33.28 3.46
529 533 8.303876 ACTATGTAATTCACCCACATTGAAAAC 58.696 33.333 6.70 0.00 36.57 2.43
547 551 4.529897 TGGGCTAGTTCTCGACTATGTAA 58.470 43.478 0.00 0.00 40.01 2.41
727 733 3.003173 CACTCCTCCCGCCTTCCA 61.003 66.667 0.00 0.00 0.00 3.53
835 841 8.071967 CGACCGTATATATAGAACTGAACAACA 58.928 37.037 0.00 0.00 0.00 3.33
854 860 5.515797 AGAATCAATCTGAATCGACCGTA 57.484 39.130 0.00 0.00 36.88 4.02
855 861 4.392921 AGAATCAATCTGAATCGACCGT 57.607 40.909 0.00 0.00 36.88 4.83
856 862 5.725110 AAAGAATCAATCTGAATCGACCG 57.275 39.130 0.00 0.00 38.79 4.79
946 956 3.842007 TCCTCCAACTACGTTTCCAAA 57.158 42.857 0.00 0.00 0.00 3.28
1048 1058 1.301401 CGCCGACTGAAAGGTTCCA 60.301 57.895 0.00 0.00 39.30 3.53
1122 1132 0.774276 TCTTGGTGCCATGTGGGTAA 59.226 50.000 0.54 0.00 39.65 2.85
1129 1139 3.291611 GGCCTTCTTGGTGCCATG 58.708 61.111 0.00 0.00 44.70 3.66
1148 1158 0.818296 GGAGACGTATCTGCCTGTGT 59.182 55.000 10.44 0.00 37.33 3.72
1242 1252 1.535204 ATCTTTTTGCACGCCCAGGG 61.535 55.000 0.00 0.00 0.00 4.45
1374 1384 3.008594 ACAGAACCGTGATCCCACATAAA 59.991 43.478 0.00 0.00 43.34 1.40
1509 1519 2.438254 AGAATTGCCCGATGCGCA 60.438 55.556 14.96 14.96 45.60 6.09
1605 1615 2.060050 ACACCACGGGTTCAATTTCA 57.940 45.000 0.00 0.00 31.02 2.69
1617 1627 1.679153 AGCAGGGTTTTAAACACCACG 59.321 47.619 6.45 4.09 34.56 4.94
1618 1628 3.713288 GAAGCAGGGTTTTAAACACCAC 58.287 45.455 6.45 0.00 34.56 4.16
1641 1651 3.861840 CAGGGAATCAGTGTACACGAAT 58.138 45.455 19.93 14.19 36.20 3.34
1920 1930 7.416213 CGAATAGAGGGGAATTTATGCAACAAA 60.416 37.037 0.00 0.00 0.00 2.83
2010 2020 1.474077 GCAATCCTTGACGGCTGAAAT 59.526 47.619 0.00 0.00 0.00 2.17
2017 2027 3.306166 CGTACTAAAGCAATCCTTGACGG 59.694 47.826 0.00 0.00 33.01 4.79
2066 2076 5.602978 CCACCCATATGATATAGTAGTCCCC 59.397 48.000 3.65 0.00 0.00 4.81
2088 2098 5.930837 AAGGAACAGTTTGAAATCAACCA 57.069 34.783 0.00 0.00 35.28 3.67
2139 2150 2.751143 TTGCCAGTATCACTTGGCAACA 60.751 45.455 22.81 6.34 46.82 3.33
2181 2192 5.563085 GCTCTGTATCTGAATAGTACCACGG 60.563 48.000 0.00 0.00 0.00 4.94
2190 2201 7.578380 GCACATCCATAGCTCTGTATCTGAATA 60.578 40.741 0.00 0.00 0.00 1.75
2191 2202 6.699366 CACATCCATAGCTCTGTATCTGAAT 58.301 40.000 0.00 0.00 0.00 2.57
2217 2228 1.677217 CCTACAAAGCTCCAGGACAGC 60.677 57.143 0.00 0.00 37.12 4.40
2226 2237 2.930682 CCGAAAGTAGCCTACAAAGCTC 59.069 50.000 4.41 0.00 41.83 4.09
2251 2262 1.135315 CATCCAGGACAAAATGGTGCG 60.135 52.381 0.00 0.00 37.84 5.34
2272 2283 0.882042 AAGCTTCAGGACAGTGTGCG 60.882 55.000 9.30 4.83 0.00 5.34
2457 2534 8.358148 AGTTAAGAGAGTGAAACGATTGTTAGA 58.642 33.333 0.00 0.00 45.86 2.10
2532 2618 2.959030 TCTTATCGTGGAGATGGAGTGG 59.041 50.000 0.00 0.00 40.40 4.00
2533 2619 3.634448 ACTCTTATCGTGGAGATGGAGTG 59.366 47.826 13.40 6.11 44.21 3.51
2534 2620 3.904717 ACTCTTATCGTGGAGATGGAGT 58.095 45.455 10.42 10.42 42.77 3.85
2535 2621 4.927978 AACTCTTATCGTGGAGATGGAG 57.072 45.455 0.00 9.56 41.64 3.86
2536 2622 4.709886 TGAAACTCTTATCGTGGAGATGGA 59.290 41.667 0.00 0.00 40.40 3.41
2537 2623 4.806247 GTGAAACTCTTATCGTGGAGATGG 59.194 45.833 0.00 0.00 40.40 3.51
2538 2624 5.410924 TGTGAAACTCTTATCGTGGAGATG 58.589 41.667 0.00 0.00 37.76 2.90
2539 2625 5.661056 TGTGAAACTCTTATCGTGGAGAT 57.339 39.130 0.00 0.00 39.75 2.75
2540 2626 5.661056 ATGTGAAACTCTTATCGTGGAGA 57.339 39.130 0.00 0.00 38.04 3.71
2541 2627 5.460419 GCTATGTGAAACTCTTATCGTGGAG 59.540 44.000 0.00 0.00 38.04 3.86
2542 2628 5.348986 GCTATGTGAAACTCTTATCGTGGA 58.651 41.667 0.00 0.00 38.04 4.02
2543 2629 4.508124 GGCTATGTGAAACTCTTATCGTGG 59.492 45.833 0.00 0.00 38.04 4.94
2544 2630 5.109210 TGGCTATGTGAAACTCTTATCGTG 58.891 41.667 0.00 0.00 38.04 4.35
2582 2668 1.566018 GACTACGTGTGCCCAGCAAC 61.566 60.000 0.00 0.00 41.47 4.17
2633 2719 6.319658 GTCTTGAATGCCAGAAGGATGAAATA 59.680 38.462 0.00 0.00 36.89 1.40
2635 2721 4.460382 GTCTTGAATGCCAGAAGGATGAAA 59.540 41.667 0.00 0.00 36.89 2.69
2636 2722 4.012374 GTCTTGAATGCCAGAAGGATGAA 58.988 43.478 0.00 0.00 36.89 2.57
2646 2732 1.428912 AGGAAAGGGTCTTGAATGCCA 59.571 47.619 0.00 0.00 0.00 4.92
2675 2761 4.314440 TGTGGGCAGCGTGAGGAC 62.314 66.667 0.00 0.00 0.00 3.85
2748 2837 1.378911 CACTAGCTGGCCATGGCAA 60.379 57.895 36.56 26.87 44.11 4.52
2796 2885 0.671472 TGCTTCATCTGCGACACTGG 60.671 55.000 0.00 0.00 0.00 4.00
2807 2896 2.109126 GGAGGGCACGTGCTTCATC 61.109 63.158 36.84 27.20 41.70 2.92
2852 2941 1.383799 CCACCTTCCCAATCTGGCA 59.616 57.895 0.00 0.00 35.79 4.92
2853 2942 0.967380 CACCACCTTCCCAATCTGGC 60.967 60.000 0.00 0.00 35.79 4.85
2882 2971 8.655935 AAACCATAAGAATGTCTCCAAAATCT 57.344 30.769 0.00 0.00 0.00 2.40
2897 2986 9.239002 CAAAACACATTCGTAAAAACCATAAGA 57.761 29.630 0.00 0.00 0.00 2.10
2898 2987 9.026074 ACAAAACACATTCGTAAAAACCATAAG 57.974 29.630 0.00 0.00 0.00 1.73
2937 3027 5.446860 TCTTCCAACATATCGACTAGGAGT 58.553 41.667 0.00 0.00 0.00 3.85
2947 3037 8.843262 TGAATGAATCACATCTTCCAACATATC 58.157 33.333 0.00 0.00 38.38 1.63


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

AutoCloner maintained by Alex Coulton.