Multiple sequence alignment - TraesCS7A01G461600

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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 TraesCS7A01G461600 chr7A 100.000 3197 0 0 1 3197 657521142 657517946 0.000000e+00 5904
1 TraesCS7A01G461600 chr7A 88.949 371 40 1 1109 1479 474143520 474143151 1.050000e-124 457
2 TraesCS7A01G461600 chr7A 96.825 63 2 0 1109 1171 631782311 631782373 4.360000e-19 106
3 TraesCS7A01G461600 chr7D 92.643 3262 145 43 1 3197 568757206 568753975 0.000000e+00 4606
4 TraesCS7A01G461600 chr7B 91.615 3220 147 56 37 3197 624948250 624945095 0.000000e+00 4337
5 TraesCS7A01G461600 chr7B 84.877 324 33 10 1156 1479 604278042 604278349 2.390000e-81 313
6 TraesCS7A01G461600 chr7B 91.855 221 18 0 1153 1373 532456383 532456163 3.100000e-80 309
7 TraesCS7A01G461600 chr4B 90.135 223 21 1 1151 1373 235738423 235738644 4.040000e-74 289
8 TraesCS7A01G461600 chr5A 98.246 57 1 0 1109 1165 102507872 102507816 2.030000e-17 100
9 TraesCS7A01G461600 chrUn 95.161 62 3 0 1109 1170 312658405 312658344 7.300000e-17 99
10 TraesCS7A01G461600 chrUn 95.161 62 3 0 1109 1170 312666039 312665978 7.300000e-17 99
11 TraesCS7A01G461600 chrUn 95.161 62 3 0 1109 1170 478091031 478090970 7.300000e-17 99
12 TraesCS7A01G461600 chr2B 95.161 62 3 0 1109 1170 760342690 760342751 7.300000e-17 99


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 TraesCS7A01G461600 chr7A 657517946 657521142 3196 True 5904 5904 100.000 1 3197 1 chr7A.!!$R2 3196
1 TraesCS7A01G461600 chr7D 568753975 568757206 3231 True 4606 4606 92.643 1 3197 1 chr7D.!!$R1 3196
2 TraesCS7A01G461600 chr7B 624945095 624948250 3155 True 4337 4337 91.615 37 3197 1 chr7B.!!$R2 3160

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
717 758 0.389025 TCAGCGAGTTCTTCACTGCA 59.611 50.0 0.0 0.0 36.2 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2594 2702 0.378257 ATCACGATTGGCGATTGCAC 59.622 50.0 7.38 0.0 45.35 4.57 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
29 30 8.193250 TCTTTGAACTGGATAGTTATTTACGC 57.807 34.615 0.00 0.00 46.79 4.42
35 36 6.827727 ACTGGATAGTTATTTACGCCTCAAT 58.172 36.000 0.00 0.00 31.66 2.57
151 156 1.610522 CAGGTCAAGTGGAAAAGGCAG 59.389 52.381 0.00 0.00 0.00 4.85
165 170 3.820595 GGCAGTGGAATTTTCTGGC 57.179 52.632 13.05 13.05 44.66 4.85
194 199 3.191078 AGCTCGAGGAGATTGGATTTG 57.809 47.619 15.58 0.00 0.00 2.32
239 244 2.672996 CCGTGTCTGCAAAGGGGG 60.673 66.667 0.00 0.00 0.00 5.40
535 549 6.644592 CGTTGGACCATTTTAACATGTGATTT 59.355 34.615 0.00 0.00 0.00 2.17
553 567 1.561643 TTTGACCACCCACAAGCAAA 58.438 45.000 0.00 0.00 0.00 3.68
556 570 1.411977 TGACCACCCACAAGCAAAATG 59.588 47.619 0.00 0.00 0.00 2.32
703 744 7.489435 TCTTAGAACTGTAATTGATCTTCAGCG 59.511 37.037 0.00 0.00 0.00 5.18
717 758 0.389025 TCAGCGAGTTCTTCACTGCA 59.611 50.000 0.00 0.00 36.20 4.41
720 761 1.869767 AGCGAGTTCTTCACTGCAAAG 59.130 47.619 0.00 0.00 35.01 2.77
998 1053 2.813908 GTGTGATCGGTCGGTGGC 60.814 66.667 0.00 0.00 0.00 5.01
1209 1264 1.409381 GGCCAGTACCCGTACTACTCT 60.409 57.143 7.19 0.00 43.98 3.24
1332 1396 4.778415 CAGGTGCGGTCGAGGTCG 62.778 72.222 0.00 0.00 41.45 4.79
1353 1417 3.212450 GTCCAAGTCGACCAAGTCC 57.788 57.895 13.01 0.00 0.00 3.85
1471 1535 1.739562 GCGTCCAAGCTCAGGTGAG 60.740 63.158 2.37 2.37 44.75 3.51
1570 1635 2.623416 TCATTCTGACGATCATAGCCGT 59.377 45.455 0.00 0.00 42.17 5.68
1736 1801 3.414700 CTGGACGAACCACAGCGC 61.415 66.667 0.00 0.00 44.64 5.92
1971 2039 4.203076 GCCGCCGACGACTATGGT 62.203 66.667 0.00 0.00 43.93 3.55
2234 2305 3.321111 GCAGAAGCATGATGGGATTTGAT 59.679 43.478 0.00 0.00 41.58 2.57
2235 2306 4.558898 GCAGAAGCATGATGGGATTTGATC 60.559 45.833 0.00 0.00 41.58 2.92
2236 2307 4.583073 CAGAAGCATGATGGGATTTGATCA 59.417 41.667 0.00 0.00 33.20 2.92
2237 2308 5.243954 CAGAAGCATGATGGGATTTGATCAT 59.756 40.000 0.00 0.00 39.43 2.45
2238 2309 5.839063 AGAAGCATGATGGGATTTGATCATT 59.161 36.000 0.00 0.00 37.23 2.57
2239 2310 6.326583 AGAAGCATGATGGGATTTGATCATTT 59.673 34.615 0.00 0.00 37.23 2.32
2240 2311 5.853936 AGCATGATGGGATTTGATCATTTG 58.146 37.500 0.00 0.00 37.23 2.32
2241 2312 5.600898 AGCATGATGGGATTTGATCATTTGA 59.399 36.000 0.00 0.00 37.23 2.69
2268 2339 4.382470 CCCACATTAGGTCTCAACTCTCAG 60.382 50.000 0.00 0.00 0.00 3.35
2272 2343 2.685106 AGGTCTCAACTCTCAGGTCA 57.315 50.000 0.00 0.00 0.00 4.02
2297 2368 6.653989 TCCACTCAAAAGAAGAGAAAGAAGT 58.346 36.000 0.00 0.00 36.91 3.01
2299 2370 8.265055 TCCACTCAAAAGAAGAGAAAGAAGTTA 58.735 33.333 0.00 0.00 36.91 2.24
2342 2441 9.850198 TTGATGATATGTCCAGATCAACATTTA 57.150 29.630 13.33 0.28 41.64 1.40
2421 2520 2.426842 ACAAAGCTCCTAGAATGCCC 57.573 50.000 0.00 0.00 0.00 5.36
2441 2541 3.243569 CCCCAAGATGAGACGATGTAGTC 60.244 52.174 0.00 0.00 41.23 2.59
2505 2608 5.195940 AGGTCAACATATGGAAGAACATGG 58.804 41.667 7.80 0.00 32.39 3.66
2527 2633 4.097286 GGTTTTCTCAACACAAGCAGGTTA 59.903 41.667 0.00 0.00 0.00 2.85
2533 2640 5.417580 TCTCAACACAAGCAGGTTACTTTTT 59.582 36.000 0.00 0.00 0.00 1.94
2545 2652 8.142551 AGCAGGTTACTTTTTCCTCGTATATAG 58.857 37.037 0.00 0.00 0.00 1.31
2590 2698 6.472686 AGGTTACAGTCTTATGATCAGGTC 57.527 41.667 0.09 0.00 0.00 3.85
2594 2702 5.193663 ACAGTCTTATGATCAGGTCATCG 57.806 43.478 0.00 0.00 44.23 3.84
2615 2724 2.224079 GTGCAATCGCCAATCGTGATAT 59.776 45.455 0.00 0.00 40.94 1.63
2723 2832 7.425606 AGTCTCATCAAATGTTACACAAAACC 58.574 34.615 0.00 0.00 0.00 3.27
2756 2865 0.810648 GAATGCAATGACCAAGGCGA 59.189 50.000 0.00 0.00 0.00 5.54
2763 2872 1.698506 ATGACCAAGGCGACCAAAAA 58.301 45.000 0.00 0.00 0.00 1.94
2772 2881 1.798223 GGCGACCAAAAATTTCCAAGC 59.202 47.619 0.00 0.00 0.00 4.01
2786 2895 0.034896 CCAAGCGGAACACTACACCT 59.965 55.000 0.00 0.00 0.00 4.00
2796 2905 0.865769 CACTACACCTGTGGCGAAAC 59.134 55.000 1.91 0.00 34.19 2.78
2817 2926 0.106894 CCGCCTTATCTTCTCCACCC 59.893 60.000 0.00 0.00 0.00 4.61
2829 2938 5.277250 TCTTCTCCACCCTGTGTATAATCA 58.723 41.667 0.00 0.00 0.00 2.57
2831 2940 5.551305 TCTCCACCCTGTGTATAATCATG 57.449 43.478 0.00 0.00 0.00 3.07
2844 2953 9.407380 TGTGTATAATCATGCTATTTTGTCCTT 57.593 29.630 0.00 0.00 0.00 3.36
2907 3016 6.165577 TGAAATCAGAACATCTTCATCGTCA 58.834 36.000 0.00 0.00 0.00 4.35
2913 3022 4.219507 AGAACATCTTCATCGTCACTGTCT 59.780 41.667 0.00 0.00 0.00 3.41
2921 3030 0.400594 TCGTCACTGTCTGGGAGAGA 59.599 55.000 0.00 0.00 0.00 3.10
3048 3157 4.719026 ATGGATTGCTATGTCAGGTCAT 57.281 40.909 0.00 0.00 0.00 3.06
3084 3193 9.294030 CAAGACAGCATCCATTCTTTTATTTAC 57.706 33.333 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.823045 AGGGAGTAGAAAATTAATTGAGGCG 59.177 40.000 0.39 0.00 0.00 5.52
28 29 6.603599 ACAGGGAGTAGAAAATTAATTGAGGC 59.396 38.462 0.39 0.00 0.00 4.70
29 30 9.681062 TTACAGGGAGTAGAAAATTAATTGAGG 57.319 33.333 0.39 0.00 33.43 3.86
86 87 6.930731 TCTTGTTAATGGTTTCCCTTTATGC 58.069 36.000 0.00 0.00 32.21 3.14
89 90 7.899648 TGTTCTTGTTAATGGTTTCCCTTTA 57.100 32.000 0.00 0.00 31.10 1.85
239 244 1.536709 GGGATGATCATGTTTTGCCGC 60.537 52.381 14.30 1.21 0.00 6.53
319 324 0.107654 GCGTGCAAGAGGGGAGTAAT 60.108 55.000 2.99 0.00 0.00 1.89
368 373 7.465513 GCCTAGCTGTTGTGTTGTTGTATATAC 60.466 40.741 5.89 5.89 0.00 1.47
535 549 1.561643 TTTTGCTTGTGGGTGGTCAA 58.438 45.000 0.00 0.00 0.00 3.18
597 612 5.821516 TGTAATGTTTTTGACAGGACGTT 57.178 34.783 0.00 0.00 42.62 3.99
599 614 8.789881 TTTATTGTAATGTTTTTGACAGGACG 57.210 30.769 0.00 0.00 42.62 4.79
703 744 5.057149 TCCTAACTTTGCAGTGAAGAACTC 58.943 41.667 3.66 0.00 36.83 3.01
717 758 2.423538 GTCGCCATTGCATCCTAACTTT 59.576 45.455 0.00 0.00 37.32 2.66
720 761 0.304705 CGTCGCCATTGCATCCTAAC 59.695 55.000 0.00 0.00 37.32 2.34
732 777 0.101759 GGTACTAATCAGCGTCGCCA 59.898 55.000 14.86 0.39 0.00 5.69
961 1016 0.951040 GCACCAGAGCACACCACTAC 60.951 60.000 0.00 0.00 0.00 2.73
998 1053 1.208052 ACCTCCATGACTCGTCCATTG 59.792 52.381 0.00 0.00 0.00 2.82
1187 1242 1.453745 TAGTACGGGTACTGGCCGG 60.454 63.158 19.10 11.02 45.25 6.13
1353 1417 1.064946 GGAGCTGATCACCGACGAG 59.935 63.158 0.00 0.00 0.00 4.18
1471 1535 4.210304 GCGCACGAATCGTCTGGC 62.210 66.667 4.88 5.88 38.32 4.85
1570 1635 1.664873 CAATGGGCCTGCAAAACGA 59.335 52.632 4.53 0.00 0.00 3.85
1639 1704 2.329678 CTGCTCTGGTACTCGGCTCG 62.330 65.000 0.00 0.00 0.00 5.03
1641 1706 2.716017 GCTGCTCTGGTACTCGGCT 61.716 63.158 0.00 0.00 0.00 5.52
1644 1709 0.528017 TGAAGCTGCTCTGGTACTCG 59.472 55.000 1.00 0.00 0.00 4.18
1755 1820 4.368808 CCGTTGTTGCTGACCGCG 62.369 66.667 0.00 0.00 43.27 6.46
1782 1847 3.500642 CGCGACGAGGAGCTCTCA 61.501 66.667 14.64 0.00 42.55 3.27
1968 2036 2.009774 GACGGCGAGTAGTAGTAACCA 58.990 52.381 16.62 0.00 0.00 3.67
1971 2039 2.555199 GAGGACGGCGAGTAGTAGTAA 58.445 52.381 16.62 0.00 0.00 2.24
2055 2123 2.107750 ATCGCCTCCTGCATCACG 59.892 61.111 0.00 0.00 41.33 4.35
2234 2305 3.245586 ACCTAATGTGGGCCTTCAAATGA 60.246 43.478 4.53 0.00 0.00 2.57
2235 2306 3.099141 ACCTAATGTGGGCCTTCAAATG 58.901 45.455 4.53 0.00 0.00 2.32
2236 2307 3.011708 AGACCTAATGTGGGCCTTCAAAT 59.988 43.478 4.53 0.00 35.12 2.32
2237 2308 2.378547 AGACCTAATGTGGGCCTTCAAA 59.621 45.455 4.53 0.00 35.12 2.69
2238 2309 1.992557 AGACCTAATGTGGGCCTTCAA 59.007 47.619 4.53 0.00 35.12 2.69
2239 2310 1.559682 GAGACCTAATGTGGGCCTTCA 59.440 52.381 4.53 4.62 35.12 3.02
2240 2311 1.559682 TGAGACCTAATGTGGGCCTTC 59.440 52.381 4.53 0.00 35.12 3.46
2241 2312 1.668826 TGAGACCTAATGTGGGCCTT 58.331 50.000 4.53 0.00 35.12 4.35
2268 2339 4.899502 TCTCTTCTTTTGAGTGGATGACC 58.100 43.478 0.00 0.00 33.59 4.02
2272 2343 7.286313 ACTTCTTTCTCTTCTTTTGAGTGGAT 58.714 34.615 0.00 0.00 33.59 3.41
2297 2368 6.436847 TCATCAATGGGCAACTTCAAATCTAA 59.563 34.615 0.00 0.00 0.00 2.10
2299 2370 4.773674 TCATCAATGGGCAACTTCAAATCT 59.226 37.500 0.00 0.00 0.00 2.40
2342 2441 7.015098 TCCATGACAAAACATTACAGTGGAAAT 59.985 33.333 0.00 0.00 0.00 2.17
2361 2460 5.404946 CAAATGTGTTCAATCCTCCATGAC 58.595 41.667 0.00 0.00 0.00 3.06
2421 2520 3.381590 TGGACTACATCGTCTCATCTTGG 59.618 47.826 0.00 0.00 34.38 3.61
2441 2541 7.450323 TCTTTACCCTTAATTTTCCTGAACTGG 59.550 37.037 0.00 0.00 0.00 4.00
2493 2596 4.952957 TGTTGAGAAAACCATGTTCTTCCA 59.047 37.500 0.00 0.00 35.46 3.53
2505 2608 3.782889 ACCTGCTTGTGTTGAGAAAAC 57.217 42.857 0.00 0.00 0.00 2.43
2533 2640 8.929746 CGAAGTATGTAACACTATATACGAGGA 58.070 37.037 0.00 0.00 37.25 3.71
2590 2698 0.655337 CGATTGGCGATTGCACGATG 60.655 55.000 7.38 0.00 45.35 3.84
2592 2700 1.739929 ACGATTGGCGATTGCACGA 60.740 52.632 7.38 0.00 45.35 4.35
2594 2702 0.378257 ATCACGATTGGCGATTGCAC 59.622 50.000 7.38 0.00 45.35 4.57
2615 2724 4.635765 GTGGCAGCAGAATCTGTGTATTAA 59.364 41.667 12.29 0.00 36.49 1.40
2723 2832 0.179103 GCATTCTTTCCATTGCCCGG 60.179 55.000 0.00 0.00 0.00 5.73
2772 2881 0.949105 GCCACAGGTGTAGTGTTCCG 60.949 60.000 0.00 0.00 35.24 4.30
2796 2905 1.069358 GGTGGAGAAGATAAGGCGGAG 59.931 57.143 0.00 0.00 0.00 4.63
2817 2926 9.060347 AGGACAAAATAGCATGATTATACACAG 57.940 33.333 0.00 0.00 0.00 3.66
2829 2938 5.948162 AGTCATCACAAGGACAAAATAGCAT 59.052 36.000 0.00 0.00 38.66 3.79
2831 2940 5.645497 AGAGTCATCACAAGGACAAAATAGC 59.355 40.000 0.00 0.00 38.66 2.97
2844 2953 5.653769 TGATATCACACAGAGAGTCATCACA 59.346 40.000 0.00 0.00 0.00 3.58
2907 3016 2.516227 TCGAATCTCTCCCAGACAGT 57.484 50.000 0.00 0.00 32.26 3.55
2913 3022 1.500474 AAGCCATCGAATCTCTCCCA 58.500 50.000 0.00 0.00 0.00 4.37
2921 3030 0.676466 TGCGGTCAAAGCCATCGAAT 60.676 50.000 0.00 0.00 0.00 3.34
3035 3144 7.290110 TGACCTGTATTATGACCTGACATAG 57.710 40.000 0.00 0.00 34.80 2.23
3048 3157 4.469586 TGGATGCTGTCTTGACCTGTATTA 59.530 41.667 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.