Multiple sequence alignment - TraesCS6D01G152700

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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 TraesCS6D01G152700 chr6D 100.000 2991 0 0 1 2991 126869793 126872783 0.000000e+00 5524.0
1 TraesCS6D01G152700 chr6A 94.352 1930 68 17 523 2414 152062298 152060372 0.000000e+00 2922.0
2 TraesCS6D01G152700 chr6A 93.600 500 30 2 2493 2991 152060327 152059829 0.000000e+00 745.0
3 TraesCS6D01G152700 chr6A 98.566 279 4 0 202 480 152063033 152062755 7.450000e-136 494.0
4 TraesCS6D01G152700 chr6A 95.098 204 9 1 1 204 152063317 152063115 1.340000e-83 320.0
5 TraesCS6D01G152700 chr6B 97.281 1177 26 4 1 1171 225866200 225867376 0.000000e+00 1991.0
6 TraesCS6D01G152700 chr6B 95.648 1080 32 7 1173 2237 225867483 225868562 0.000000e+00 1720.0
7 TraesCS6D01G152700 chr6B 95.845 361 15 0 2631 2991 225869115 225869475 4.300000e-163 584.0
8 TraesCS6D01G152700 chr6B 94.798 173 5 2 2257 2426 225868656 225868827 1.770000e-67 267.0
9 TraesCS6D01G152700 chr6B 91.515 165 11 3 2480 2643 225868833 225868995 1.080000e-54 224.0
10 TraesCS6D01G152700 chr1D 84.892 139 21 0 1826 1964 472561544 472561682 1.120000e-29 141.0
11 TraesCS6D01G152700 chr5B 84.173 139 22 0 1826 1964 532877282 532877420 5.200000e-28 135.0
12 TraesCS6D01G152700 chr5B 79.699 133 27 0 1838 1970 381715364 381715232 2.450000e-16 97.1
13 TraesCS6D01G152700 chr5A 84.173 139 22 0 1826 1964 553421511 553421649 5.200000e-28 135.0
14 TraesCS6D01G152700 chr1B 84.286 140 20 2 1826 1964 657272693 657272831 5.200000e-28 135.0
15 TraesCS6D01G152700 chr1A 84.173 139 22 0 1826 1964 566564801 566564939 5.200000e-28 135.0
16 TraesCS6D01G152700 chr5D 82.734 139 24 0 1826 1964 438360600 438360738 1.130000e-24 124.0


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 TraesCS6D01G152700 chr6D 126869793 126872783 2990 False 5524.00 5524 100.0000 1 2991 1 chr6D.!!$F1 2990
1 TraesCS6D01G152700 chr6A 152059829 152063317 3488 True 1120.25 2922 95.4040 1 2991 4 chr6A.!!$R1 2990
2 TraesCS6D01G152700 chr6B 225866200 225869475 3275 False 957.20 1991 95.0174 1 2991 5 chr6B.!!$F1 2990

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
59 60 0.033781 TTTTGGAGGCATTGCACTGC 59.966 50.0 19.95 19.95 41.53 4.40 F
1744 2367 0.460459 GCCTTGAGAAGTACCTCGGC 60.460 60.0 0.00 0.00 35.99 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2568 0.253610 TGTTGTTGTTGACGGGGTCT 59.746 50.000 0.0 0.0 33.15 3.85 R
2629 3477 1.001248 AAGCATCTGGGCAAGGCAT 59.999 52.632 0.0 0.0 35.83 4.40 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
59 60 0.033781 TTTTGGAGGCATTGCACTGC 59.966 50.000 19.95 19.95 41.53 4.40
100 101 9.178758 GGAATTTCTTGTATTAGTGGTCTTCAT 57.821 33.333 0.00 0.00 0.00 2.57
121 122 8.565896 TTCATATCTGATTAAACAACAGTGCT 57.434 30.769 0.00 0.00 33.93 4.40
468 552 9.108284 CCAATTGTCTTTACCTTGTGAAAATTT 57.892 29.630 4.43 0.00 27.53 1.82
482 566 6.491394 TGTGAAAATTTACTTTGGTCTCGTG 58.509 36.000 0.00 0.00 0.00 4.35
484 568 6.970613 GTGAAAATTTACTTTGGTCTCGTGTT 59.029 34.615 0.00 0.00 0.00 3.32
498 582 2.330286 TCGTGTTACCGCACACAATAG 58.670 47.619 5.95 0.00 46.45 1.73
771 1271 2.746375 CCCTTATCCCAGCGCACCT 61.746 63.158 11.47 0.00 0.00 4.00
854 1354 4.166144 ACATCGGAATAAGATTTCCCTGGT 59.834 41.667 0.00 0.00 41.87 4.00
923 1423 1.064017 AGTGGGTGAGTTTTGGAGCAA 60.064 47.619 0.00 0.00 0.00 3.91
1005 1508 0.828762 AGCTTGCAGGAACAATGGCA 60.829 50.000 0.00 0.00 0.00 4.92
1056 1559 3.791586 GGGAGGCCTCTGCAGTCC 61.792 72.222 31.36 19.18 40.03 3.85
1137 1640 1.455849 CCCTGCCAAGGTCAGTTCA 59.544 57.895 8.86 0.00 42.74 3.18
1143 1646 1.876156 GCCAAGGTCAGTTCAACTCTG 59.124 52.381 0.00 0.00 0.00 3.35
1150 1653 1.699083 TCAGTTCAACTCTGGCCATGA 59.301 47.619 5.51 3.73 34.15 3.07
1151 1654 1.808945 CAGTTCAACTCTGGCCATGAC 59.191 52.381 5.51 2.35 0.00 3.06
1190 1798 2.694628 CTGATGAGAGCTAGCTGGAGTT 59.305 50.000 24.99 2.45 0.00 3.01
1194 1802 2.028658 TGAGAGCTAGCTGGAGTTGTTG 60.029 50.000 24.99 0.00 0.00 3.33
1336 1959 1.251251 GGCAGTGTGGCAAAGAGAAT 58.749 50.000 0.00 0.00 43.14 2.40
1390 2013 2.113139 CTGCCCGGTGACTTTGGT 59.887 61.111 0.00 0.00 0.00 3.67
1729 2352 0.842467 AGCAGTACTTCCTGGGCCTT 60.842 55.000 4.53 0.00 32.92 4.35
1744 2367 0.460459 GCCTTGAGAAGTACCTCGGC 60.460 60.000 0.00 0.00 35.99 5.54
1945 2568 1.000771 CCTCCTCGACCACCTCTCA 60.001 63.158 0.00 0.00 0.00 3.27
2175 2798 4.808077 AATTAGTGCATTGCATCTCTCG 57.192 40.909 15.49 0.00 41.91 4.04
2185 2808 4.397481 TTGCATCTCTCGTCATCTTCAT 57.603 40.909 0.00 0.00 0.00 2.57
2190 2817 5.346522 CATCTCTCGTCATCTTCATCAACA 58.653 41.667 0.00 0.00 0.00 3.33
2240 2869 4.996344 TCTGGTTATCGTACGTGCAATTA 58.004 39.130 16.05 0.00 0.00 1.40
2250 2879 1.498865 CGTGCAATTAGGCGGCTAGG 61.499 60.000 18.86 13.32 36.28 3.02
2253 2882 1.340600 TGCAATTAGGCGGCTAGGTTT 60.341 47.619 18.86 11.22 36.28 3.27
2371 3083 9.979578 TCAAAATAAAGTGAATTGTTGCTGTAT 57.020 25.926 0.00 0.00 0.00 2.29
2378 3090 8.574196 AAGTGAATTGTTGCTGTATAAAACAC 57.426 30.769 0.00 0.00 33.73 3.32
2379 3091 7.711846 AGTGAATTGTTGCTGTATAAAACACA 58.288 30.769 0.00 0.00 33.73 3.72
2414 3130 5.391312 AAGGTTTATCACAGGATGCAAAC 57.609 39.130 0.00 0.00 42.53 2.93
2415 3131 4.406456 AGGTTTATCACAGGATGCAAACA 58.594 39.130 0.00 0.00 42.53 2.83
2416 3132 4.832266 AGGTTTATCACAGGATGCAAACAA 59.168 37.500 0.00 0.00 42.53 2.83
2417 3133 5.304101 AGGTTTATCACAGGATGCAAACAAA 59.696 36.000 0.00 0.00 42.53 2.83
2419 3135 6.311200 GGTTTATCACAGGATGCAAACAAATC 59.689 38.462 0.00 0.00 42.53 2.17
2422 3138 4.143543 TCACAGGATGCAAACAAATCTGA 58.856 39.130 0.00 0.00 42.53 3.27
2423 3139 4.216902 TCACAGGATGCAAACAAATCTGAG 59.783 41.667 0.00 0.00 42.53 3.35
2425 3141 4.022589 ACAGGATGCAAACAAATCTGAGTG 60.023 41.667 0.00 0.00 42.53 3.51
2428 3144 5.069516 AGGATGCAAACAAATCTGAGTGTTT 59.930 36.000 13.53 13.53 46.27 2.83
2429 3145 5.754890 GGATGCAAACAAATCTGAGTGTTTT 59.245 36.000 15.64 6.05 43.64 2.43
2430 3146 6.258507 GGATGCAAACAAATCTGAGTGTTTTT 59.741 34.615 15.64 7.46 43.64 1.94
2458 3174 1.242076 GCAAATCTGAGTGGCTGTGT 58.758 50.000 0.00 0.00 0.00 3.72
2459 3175 1.610522 GCAAATCTGAGTGGCTGTGTT 59.389 47.619 0.00 0.00 0.00 3.32
2460 3176 2.035066 GCAAATCTGAGTGGCTGTGTTT 59.965 45.455 0.00 0.00 0.00 2.83
2461 3177 3.491447 GCAAATCTGAGTGGCTGTGTTTT 60.491 43.478 0.00 0.00 0.00 2.43
2462 3178 4.685924 CAAATCTGAGTGGCTGTGTTTTT 58.314 39.130 0.00 0.00 0.00 1.94
2505 3221 3.242446 GCGGTTTCTTCTATGCTTACAGC 60.242 47.826 0.00 0.00 42.82 4.40
2553 3269 1.084289 AGAAACGCGTTGGAATAGGC 58.916 50.000 27.34 7.63 0.00 3.93
2584 3300 2.195389 CGGTCCACGGTTAGATCCA 58.805 57.895 0.00 0.00 39.42 3.41
2585 3301 0.750850 CGGTCCACGGTTAGATCCAT 59.249 55.000 0.00 0.00 39.42 3.41
2587 3303 1.070289 GGTCCACGGTTAGATCCATCC 59.930 57.143 0.00 0.00 0.00 3.51
2588 3304 1.037493 TCCACGGTTAGATCCATCCG 58.963 55.000 15.29 15.29 46.98 4.18
2589 3305 0.600255 CCACGGTTAGATCCATCCGC 60.600 60.000 16.34 0.00 45.76 5.54
2590 3306 0.939577 CACGGTTAGATCCATCCGCG 60.940 60.000 16.34 0.00 45.76 6.46
2591 3307 1.372997 CGGTTAGATCCATCCGCGG 60.373 63.158 22.12 22.12 36.68 6.46
2592 3308 1.668151 GGTTAGATCCATCCGCGGC 60.668 63.158 23.51 4.91 0.00 6.53
2593 3309 2.022129 GTTAGATCCATCCGCGGCG 61.022 63.158 23.51 16.78 0.00 6.46
2595 3311 2.416244 TTAGATCCATCCGCGGCGAC 62.416 60.000 25.92 8.33 0.00 5.19
2634 3482 0.394488 TCTCTCTTCGACGGATGCCT 60.394 55.000 0.00 0.00 0.00 4.75
2660 3508 4.722535 TGCTTCCCCTCCTCCGCT 62.723 66.667 0.00 0.00 0.00 5.52
2662 3510 3.157949 CTTCCCCTCCTCCGCTCC 61.158 72.222 0.00 0.00 0.00 4.70
2884 3732 0.966370 GACACTACCACTCCCTCGCT 60.966 60.000 0.00 0.00 0.00 4.93
2982 3830 0.105658 TGATCTAACCCTCCTCCCCG 60.106 60.000 0.00 0.00 0.00 5.73
2984 3832 0.342313 ATCTAACCCTCCTCCCCGTT 59.658 55.000 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.015098 AGAGATATCAGAACTTGGTATGGAGTG 59.985 40.741 5.32 0.00 33.17 3.51
59 60 8.096414 ACAAGAAATTCCCATGAAAAACTATGG 58.904 33.333 0.00 0.00 42.77 2.74
100 101 7.552330 TGCATAGCACTGTTGTTTAATCAGATA 59.448 33.333 0.00 0.00 31.71 1.98
121 122 7.814587 CGAACCAGATTCTGATACTTATGCATA 59.185 37.037 15.36 1.16 34.88 3.14
165 166 8.575649 AAAGGTTATGGTTAGTTAAGGTGATG 57.424 34.615 0.00 0.00 0.00 3.07
468 552 2.607771 GCGGTAACACGAGACCAAAGTA 60.608 50.000 0.00 0.00 35.26 2.24
482 566 3.061161 CGGTTACTATTGTGTGCGGTAAC 59.939 47.826 0.00 0.00 40.49 2.50
484 568 2.878580 CGGTTACTATTGTGTGCGGTA 58.121 47.619 0.00 0.00 0.00 4.02
923 1423 5.070446 TGGTACAGACTGAGATGAAAGTGTT 59.930 40.000 10.08 0.00 0.00 3.32
1005 1508 0.617249 CAGAGAGAAGACCCTGGGCT 60.617 60.000 14.08 8.32 0.00 5.19
1056 1559 1.407258 GAAGACGACCTGGAGATGGAG 59.593 57.143 0.00 0.00 0.00 3.86
1137 1640 1.028330 CATGCGTCATGGCCAGAGTT 61.028 55.000 13.05 0.00 38.11 3.01
1143 1646 0.527565 AGAAAACATGCGTCATGGCC 59.472 50.000 19.30 0.00 45.16 5.36
1150 1653 4.318332 TCAGATCAGAAGAAAACATGCGT 58.682 39.130 0.00 0.00 0.00 5.24
1151 1654 4.934075 TCAGATCAGAAGAAAACATGCG 57.066 40.909 0.00 0.00 0.00 4.73
1190 1798 8.739972 AGAAGAAGAAAAAGAAAGTTAGCAACA 58.260 29.630 0.00 0.00 0.00 3.33
1295 1907 2.288666 CCAGGTGTAATATGTTGCGCT 58.711 47.619 9.73 0.00 32.04 5.92
1336 1959 3.256704 ACCCAACACCTCCTAAATCAGA 58.743 45.455 0.00 0.00 0.00 3.27
1729 2352 2.707849 GCCGCCGAGGTACTTCTCA 61.708 63.158 3.27 0.00 41.55 3.27
1801 2424 1.178276 TCTCCTTCTCGCTCTTGGTC 58.822 55.000 0.00 0.00 0.00 4.02
1945 2568 0.253610 TGTTGTTGTTGACGGGGTCT 59.746 50.000 0.00 0.00 33.15 3.85
2150 2773 5.575957 AGAGATGCAATGCACTAATTTTCG 58.424 37.500 11.23 0.00 43.04 3.46
2175 2798 5.873712 AGACACAGATGTTGATGAAGATGAC 59.126 40.000 0.00 0.00 39.95 3.06
2185 2808 4.821805 GGGAAAGAAAGACACAGATGTTGA 59.178 41.667 0.00 0.00 39.95 3.18
2190 2817 2.876079 GCGGGGAAAGAAAGACACAGAT 60.876 50.000 0.00 0.00 0.00 2.90
2240 2869 1.375523 CGTCAAAACCTAGCCGCCT 60.376 57.895 0.00 0.00 0.00 5.52
2250 2879 1.435577 ACGGCCACTATCGTCAAAAC 58.564 50.000 2.24 0.00 34.20 2.43
2253 2882 2.304092 AGATACGGCCACTATCGTCAA 58.696 47.619 2.24 0.00 40.31 3.18
2371 3083 7.625469 ACCTTTTCCCAAAATTCTGTGTTTTA 58.375 30.769 0.00 0.00 0.00 1.52
2376 3088 7.930865 TGATAAACCTTTTCCCAAAATTCTGTG 59.069 33.333 0.00 0.00 0.00 3.66
2377 3089 7.931407 GTGATAAACCTTTTCCCAAAATTCTGT 59.069 33.333 0.00 0.00 0.00 3.41
2378 3090 7.930865 TGTGATAAACCTTTTCCCAAAATTCTG 59.069 33.333 0.00 0.00 0.00 3.02
2379 3091 8.028652 TGTGATAAACCTTTTCCCAAAATTCT 57.971 30.769 0.00 0.00 0.00 2.40
2428 3144 6.735694 GCCACTCAGATTTGCAGTTCTAAAAA 60.736 38.462 0.66 0.00 0.00 1.94
2429 3145 5.278463 GCCACTCAGATTTGCAGTTCTAAAA 60.278 40.000 0.66 0.00 0.00 1.52
2430 3146 4.216257 GCCACTCAGATTTGCAGTTCTAAA 59.784 41.667 0.66 0.00 0.00 1.85
2431 3147 3.753272 GCCACTCAGATTTGCAGTTCTAA 59.247 43.478 0.66 0.00 0.00 2.10
2432 3148 3.008375 AGCCACTCAGATTTGCAGTTCTA 59.992 43.478 0.66 0.00 0.00 2.10
2437 3153 1.199327 CACAGCCACTCAGATTTGCAG 59.801 52.381 0.00 0.00 0.00 4.41
2438 3154 1.241165 CACAGCCACTCAGATTTGCA 58.759 50.000 0.00 0.00 0.00 4.08
2466 3182 0.521291 CGCAGCCGGATTCTCAAAAA 59.479 50.000 5.05 0.00 0.00 1.94
2467 3183 2.170738 CGCAGCCGGATTCTCAAAA 58.829 52.632 5.05 0.00 0.00 2.44
2468 3184 3.889227 CGCAGCCGGATTCTCAAA 58.111 55.556 5.05 0.00 0.00 2.69
2478 3194 0.652592 CATAGAAGAAACCGCAGCCG 59.347 55.000 0.00 0.00 0.00 5.52
2479 3195 0.378610 GCATAGAAGAAACCGCAGCC 59.621 55.000 0.00 0.00 0.00 4.85
2505 3221 2.028883 GCCCGATTTAAGAACTTCGTCG 59.971 50.000 0.00 0.00 0.00 5.12
2553 3269 1.971695 GGACCGGTGAAAAGCTGGG 60.972 63.158 14.63 0.00 36.71 4.45
2629 3477 1.001248 AAGCATCTGGGCAAGGCAT 59.999 52.632 0.00 0.00 35.83 4.40
2634 3482 2.215451 GAGGGGAAGCATCTGGGCAA 62.215 60.000 0.00 0.00 35.83 4.52
2737 3585 2.779033 CCCGTACACTAGGCCGGAC 61.779 68.421 5.05 0.00 43.01 4.79
2744 3592 1.135575 GTCACCGAACCCGTACACTAG 60.136 57.143 0.00 0.00 0.00 2.57
2754 3602 1.525077 TGGCTGTTGTCACCGAACC 60.525 57.895 0.00 0.00 0.00 3.62
2884 3732 1.457643 CTCCCCGGCAGAGGATACA 60.458 63.158 11.02 0.00 41.41 2.29


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

AutoCloner maintained by Alex Coulton.